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2'-deoxyguanosine triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate + DNAn
diphosphate + ?
2-hydroxy-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase eta incorporates 2-hydroxy-2'-deoxyadenosine 5'-triphosphate opposite template G during DNA synthesis
-
-
?
5-ethynyl-dCTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
5-ethynyl-dUTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
5-phenyl-dCTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
5-phenyl-dUTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
5-vinyl-dCTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
5-vinyl-dUTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
5-[(1E)-3-[(4-[[(5-azido-2-nitrophenyl)carbonyl]amino]butanoyl)amino]prop-1-en-1-yl]uridine 5'-triphosphate + DNAn
?
5-[(1E)-3-{[(5-azido-2-nitrophenyl)carbonyl]amino}prop-1-en-1-yl]-2'-deoxyuridine 5'-triphosphate + DNAn
?
5-[N-(2-nitro-5-azidobenzoyl)ami-nomethyl]-2'-deoxyuridine 5'-triphosphate + DNAn
?
7-deaza-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + ?
7-deaza-dGTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
7-ethynyl-7-deaza-dATP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
7-ethynyl-7-deaza-dGTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
7-methyl-7-deaza-dATP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
7-methyl-7-deaza-dGTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
7-phenyl-7-deaza-dATP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
7-phenyl-7-deaza-dGTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
7-vinyl-7-deaza-dATP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
7-vinyl-7-deaza-dGTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
8-hydroxy-2'-deoxyguanosine 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase eta incorporates 8-hydroxy-2'-deoxyguanosine 5'-triphosphate opposite template A and slightly opposite template C during DNA synthesis
-
-
?
8-oxo-dATP + DNAn
?
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
8-oxodGTP + DNAn
diphosphate + DNAn+1
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
ATP + primed M13
?
-
-
-
-
?
Cy3-dATP + DNAn
diphosphate + DNAn+1
-
systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
-
-
?
Cy3-dCTP + DNAn
diphosphate + DNAn+1
-
systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
-
-
?
Cy3-dGTP + DNAn
diphosphate + DNAn+1
-
systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
-
-
?
Cy3-dUTP + DNAn
diphosphate + DNAn+1
-
systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
-
-
?
dADP + DNAn
phosphate + DNAn+1
activation energy analysis of the forward (DNA synthesis) and reverse (phosphorolysis of DNA) reactions catalyzed by the Taq DNA polymerase shows that DNA synthesis is strongly favored, allowing robust replication from low-energy substrates
-
-
?
dATP + DNAn
diphosphate + ?
dATP + DNAn
diphosphate + DNAn+1
dCTP + DNAn
diphosphate + DNAn+1
deoxxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the phosphoryl transfer step may be rate limiting for the non-cognate nucleotide incorporation by the enzyme
-
-
?
deoxynucleoside triphosphate + DNAn
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
deoxynucleoside triphosphate + primed M13n
diphosphate + primed M13n+1
-
-
-
?
dGTP + DNAn
diphosphate + DNAn+1
DNA 21/41-mer + dTTP
? + diphosphate
dNTP + dAMP:dA
?
-
-
-
-
?
dNTP + dAMP:dG
?
-
-
-
-
?
dNTP + dCMP:dA
?
-
-
-
-
?
dNTP + dCMP:dG
?
-
-
-
-
?
dNTP + dGMP:dA
?
-
-
-
-
?
dNTP + dGMP:dG
?
-
-
-
-
?
dNTP + DNAn
diphosphate + DNAn+1
dNTP + dTMP:dA
?
-
-
-
-
?
dNTP + dTMP:dG
?
-
-
-
-
?
dPTP + DNAn
?
i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-beta-D-2'-deoxyribofuranosid 5'-triphosphate. dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
N1-methyl-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + ?
North-methanocarba-dATP + DNAn
?
nucleotide + DNAn
?
-
-
-
-
?
poly(dA)/oligo(dT)x + n dTTP
poly(dA)/oligo(dT)x+n + n diphosphate
preferred substrate
-
-
?
poly(rA)/(dT)12 + dTTP
poly(rA)/(dT)13 + diphosphate
-
-
-
-
?
r8-oxo-GTP + DNAn
diphosphate + DNAn+1
relative to correct dGTP insertion, r8-oxo-GTP insertion efficiency opposite dC and dA is reduced more than 250000fold and 4000fold, respectively. Insertion of r8-oxo-GTP is less efficient than 8-oxodGTP by 700- and 4300fold opposite dA and dC, respectively
-
-
?
rGTP + DNAn
diphosphate + DNAn+1
-
-
-
?
South-methanocarba-dATP + DNAn
?
TTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
additional information
?
-
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate + DNAn
diphosphate + ?
-
-
-
?
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate + DNAn
diphosphate + ?
-
-
-
?
2-thio-dCTP + DNAn
?
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
2-thio-dCTP + DNAn
?
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
5-methyl-dCTP + DNAn
?
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
5-methyl-dCTP + DNAn
?
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
5-[(1E)-3-[(4-[[(5-azido-2-nitrophenyl)carbonyl]amino]butanoyl)amino]prop-1-en-1-yl]uridine 5'-triphosphate + DNAn
?
-
-
-
-
?
5-[(1E)-3-[(4-[[(5-azido-2-nitrophenyl)carbonyl]amino]butanoyl)amino]prop-1-en-1-yl]uridine 5'-triphosphate + DNAn
?
-
-
-
-
?
5-[(1E)-3-{[(5-azido-2-nitrophenyl)carbonyl]amino}prop-1-en-1-yl]-2'-deoxyuridine 5'-triphosphate + DNAn
?
-
-
-
-
?
5-[(1E)-3-{[(5-azido-2-nitrophenyl)carbonyl]amino}prop-1-en-1-yl]-2'-deoxyuridine 5'-triphosphate + DNAn
?
-
-
-
-
?
5-[N-(2-nitro-5-azidobenzoyl)ami-nomethyl]-2'-deoxyuridine 5'-triphosphate + DNAn
?
-
-
-
-
?
5-[N-(2-nitro-5-azidobenzoyl)ami-nomethyl]-2'-deoxyuridine 5'-triphosphate + DNAn
?
-
-
-
-
?
7-deaza-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + ?
-
-
-
?
7-deaza-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + ?
-
-
-
?
8-bromo-dATP + DNAn
?
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
8-bromo-dATP + DNAn
?
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
the enzyme features poor filling activity of DNA gaps consisting of 15 bases, and exerts a more efficient action at the expense of DNA substrates containing a recessed end of equal length. Shortening the recessed end of DNA substrates decreases the rate of DNA elongation catalysed by ASFV Pol X. DNA binding is a step responsible for restraining the efficiency of ASFV Pol X catalytic action
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
African swine fever virus Badajoz 1971 Vero-adapted
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
African swine fever virus Badajoz 1971 Vero-adapted
the enzyme features poor filling activity of DNA gaps consisting of 15 bases, and exerts a more efficient action at the expense of DNA substrates containing a recessed end of equal length. Shortening the recessed end of DNA substrates decreases the rate of DNA elongation catalysed by ASFV Pol X. DNA binding is a step responsible for restraining the efficiency of ASFV Pol X catalytic action
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
DnaG primase and DNA polymerase III holoenzyme are able to bind concurrently to a primed template during DNA replication
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTP's (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
the template-dependent polymerase that can repair non-complementary DNA double strand breaks with unpaired 3' primer termini by nonhomologous end joining. Its role is to fill short gaps arising as intermediates in the process of V(D)J recombination and during processing of accidental double strand breaks
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Pol1 has flap endonuclease activity on the flap RNA strand of an RNA:DNA hybrid duplex as well as reverse transcriptase activity on a DNA-primed RNA template
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
Pol1 has flap endonuclease activity on the flap RNA strand of an RNA:DNA hybrid duplex as well as reverse transcriptase activity on a DNA-primed RNA template
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
the yeast two-hybrid system is employed to define regions of intermolecular interaction between small subunit DP1, large subunit DP2, and proliferating cell nuclear antigen PCNA. Intra- and intermolecular interactions between these domains are verified by using surface plasmon resonance
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
the yeast two-hybrid system is employed to define regions of intermolecular interaction between small subunit DP1, large subunit DP2, and proliferating cell nuclear antigen PCNA. Intra- and intermolecular interactions between these domains are verified by using surface plasmon resonance
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTPs (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
the complex DNA binding mechanism of a Y-family DNA polymerase involves aspects of both induced-fit and conformational selection mechanisms. Intradomain protein motions are observed throughout nucleotide binding and incorporation, some of which may kinetically limit the rate of correct nucleotide incorporation
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
the complex DNA binding mechanism of a Y-family DNA polymerase involves aspects of both induced-fit and conformational selection mechanisms. Intradomain protein motions are observed throughout nucleotide binding and incorporation, some of which may kinetically limit the rate of correct nucleotide incorporation
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
the catalytic core of yeast DNA polymerase eta prefers to incorporate dCTP opposite 7,8-dihydro-8-oxo-2'-deoxyguanosine (damage produced by reactive oxygen species in DNA). dCTP incorporation is slower than the dissociation of the polymerase from DNA. 57% of the extension products beyond the 7,8-dihydro-8-oxo-2'-deoxyguanosine are the products corresponding to the correct incorporation (C) and 43% corresponding to dATP misincorporation
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
the catalytic core of yeast DNA polymerase eta prefers to incorporate dCTP opposite 7,8-dihydro-8-oxo-2'-deoxyguanosine (damage produced by reactive oxygen species in DNA). dCTP incorporation is slower than the dissociation of the polymerase from DNA. 57% of the extension products beyond the 7,8-dihydro-8-oxo-2'-deoxyguanosine are the products corresponding to the correct incorporation (C) and 43% corresponding to dATP misincorporation
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
the enzyme is able to efficiently bypass uracil in DNA. The enzyme is halted by an AP site in DNA. Tga PolB extends the mismatched ends with reduced efficiencies. It possesses 3'-5' exonuclease activity. The enzyme can efficiently bind to ssDNA and primed DNA, and has a marked preference for primed DNA
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
the enzyme is able to efficiently bypass uracil in DNA. The enzyme is halted by an AP site in DNA. Tga PolB extends the mismatched ends with reduced efficiencies. It possesses 3'-5' exonuclease activity. The enzyme can efficiently bind to ssDNA and primed DNA, and has a marked preference for primed DNA
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTPs (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTPs (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
DNA replication can be accomplished using dNDPs as substrates. In thermophiles, genome replication may be less sensitive to the energy charge of the cell than in mesophiles because thermostable polymerases can accept the diphosphorylated as well as the triphosphorylated substrates. DNA replication is thus less affected by the intracellular ATP/ADP ratio, and the relatively high efficiency with which DNA is synthesized at elevated temperatures suggests that thermophiles may be able to dispense with the triphosphorylated substrates entirely
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
activation energy analysis of the forward (DNA synthesis) and reverse (phosphorolysis of DNA) reactions catalyzed by the Taq DNA polymerase shows that DNA synthesis is strongly favored, allowing robust replication from low-energy substrates
-
-
?
dATP + DNAn
?
-
-
-
-
?
dATP + DNAn
?
-
Dbh is a distributive enzyme showing a low DNA and nucleotide binding affinity along with a slow polymerization rate. DNA binding occurs in a single step, diffusion-controlled manner. The rate-limiting step of nucleotide incorporation (correct and incorrect) is the chemical step (phosphoryl transfer) and not a conformational change of the enzyme. An induced fit mechanism to select and incorporate nucleotides during DNA polymerization can not be detected for the enzyme
-
-
?
dATP + DNAn
?
in addition to the correct insertion of dATP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dATP + DNAn
?
in addition to the correct insertion of dATP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dATP + DNAn
?
-
activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16-fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
-
-
?
dATP + DNAn
?
-
activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16-fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
-
-
?
dATP + DNAn
diphosphate + ?
-
-
-
?
dATP + DNAn
diphosphate + ?
-
-
-
?
dATP + DNAn
diphosphate + DNAn+1
-
systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
-
-
?
dATP + DNAn
diphosphate + DNAn+1
-
with labeled 20/33-mer primer-template duplex DNA
-
-
?
dATP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dATP + DNAn
diphosphate + DNAn+1
-
with activated calf thymus DNA
-
-
?
dATP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dATP + DNAn
diphosphate + DNAn+1
-
dNTP insertion opposite a benzo[a]pyrene-N2-dG-adduct
-
-
?
dATP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dATP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dCTP + DNAn
?
-
-
-
-
?
dCTP + DNAn
?
-
Dbh is a distributive enzyme showing a low DNA and nucleotide binding affinity along with a slow polymerization rate. DNA binding occurs in a single step, diffusion-controlled manner. The rate-limiting step of nucleotide incorporation (correct and incorrect) is the chemical step (phosphoryl transfer) and not a conformational change of the enzyme. An induced fit mechanism to select and incorporate nucleotides during DNA polymerization can not be detected for the enzyme
-
-
?
dCTP + DNAn
?
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-methyl-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
dCTP + DNAn
?
dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
-
-
?
dCTP + DNAn
?
in addition to the correct insertion of dCTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dCTP + DNAn
?
in addition to the correct insertion of dCTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dCTP + DNAn
?
dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
-
-
?
dCTP + DNAn
?
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-methyl-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
dCTP + DNAn
diphosphate + DNAn+1
-
systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
-
-
?
dCTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dCTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dCTP + DNAn
diphosphate + DNAn+1
-
with activated calf thymus DNA
-
-
?
dCTP + DNAn
diphosphate + DNAn+1
-
dNTP insertion opposite a benzo[a]pyrene-N2-dG-adduct
-
-
?
dCTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dCTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
?
the enzyme can preferentially insert C opposite N-(deoxyguanosin-8-yl)-2-acetylaminofluorene. An anti glycosidic torsion with C1'-exo deoxyribose conformation allows N-(deoxyguanosin-8-yl)-2-acetylaminofluorene to be WatsonCrick hydrogen-bonded with dCTP with modest polymerase perturbation, but other nucleotides are more distorting
-
-
?
deoxynucleoside triphosphate + DNAn
?
the enzyme can preferentially insert C opposite N-(deoxyguanosin-8-yl)-2-acetylaminofluorene. An anti glycosidic torsion with C1'-exo deoxyribose conformation allows N-(deoxyguanosin-8-yl)-2-acetylaminofluorene to be WatsonCrick hydrogen-bonded with dCTP with modest polymerase perturbation, but other nucleotides are more distorting
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
specific preference for five base pairs, relatively low catalytic activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
natural substrate is gapped DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
a fast fluorescence transition corresponding to conformational closing, and a slow fluorescence transition matching the rate of single-nucleotide incorporation. This transition represents a conformational event after chemistry, likely subdomain reopening
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
use of damaged DNA and dNTP substrates by the enzyme
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the enzyme contains a double strand-dependent 3'-5' proofreading exonuclease activity, but lacks any 5'-3' exonuclease activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
no exonuclease 5'--3' activity: pol II
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
can initiate polymer synthesis de novo, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
nicked duplex is no substrate of polymerase I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
nicked duplex, as poly d(A-T), pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
template specificity polymerase I, II and III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
polymerase I plays a role in repair of chromosomal damage
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
physiological role of pol I and pol III
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
polymerase III is necessary for DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
no exonuclease 5'--3' activity: pol II
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
nicked duplex, as poly d(A-T), pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Betapolyomavirus macacae
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity, pol epsilon
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
template specificity of DNA polymerase epsilon
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
R2-RT is capable of efficiently utilizing single-stranded DNA (ssDNA) as a template. The processivity of the enzyme on ssDNA templates is higher than its processivity on RNA templates. This finding suggests that R2-RT is also capable of synthesizing the second DNA strand during retrotransposition
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
incorporates alpha-D-dNTPs and beta-D-dNTPs, L-dNTPs are no substrate
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
polymerase alpha: role in DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
overview: physiological roles in replication and in DNA repair synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme exhibits its highest specific activity with gapped-duplex (activated) calf thymus DNA as the substrate, less activity with double-stranded salmon sperm DNA or heat-denatured double-stranded salmon sperm DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
no detectable 3' exonuclease activity. CpDNApolI-dependent DNA synthesis is performed using DNA templates carrying different lesions. DNAs containing 2'-deoxyuridine (dU), 2'-deoxyinosine (dI) or 2'-deoxy-8-oxo-guanosine (8-oxo-dG) serve as templates as effectively as unmodified DNAs for CpDNApolI. Furthermore, the CpDNApolI can bypass natural apurinic/apyrimidinic sites (AP sites), deoxyribose (dR), and synthetic AP site tetrahydrofuran (THF). CpDNApolI can incorporate any dNMPs opposite both of deoxyribose and tetrahydrofuran with the preference to dAMP-residue. CpDNApolI preferentially extends primer with 3'-dAMP opposite deoxyribose during DNA synthesis, however all four primers with various 3'-end nucleosides (dA, dT, dC, and dG) opposite THF can be extended by CpDNApolI. Efficiently bypassing of AP sites by CpDNApolI is hypothetically attributed to lack of 3' exonuclease activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
no detectable 3' exonuclease activity. CpDNApolI-dependent DNA synthesis is performed using DNA templates carrying different lesions. DNAs containing 2'-deoxyuridine (dU), 2'-deoxyinosine (dI) or 2'-deoxy-8-oxo-guanosine (8-oxo-dG) serve as templates as effectively as unmodified DNAs for CpDNApolI. Furthermore, the CpDNApolI can bypass natural apurinic/apyrimidinic sites (AP sites), deoxyribose (dR), and synthetic AP site tetrahydrofuran (THF). CpDNApolI can incorporate any dNMPs opposite both of deoxyribose and tetrahydrofuran with the preference to dAMP-residue. CpDNApolI preferentially extends primer with 3'-dAMP opposite deoxyribose during DNA synthesis, however all four primers with various 3'-end nucleosides (dA, dT, dC, and dG) opposite THF can be extended by CpDNApolI. Efficiently bypassing of AP sites by CpDNApolI is hypothetically attributed to lack of 3' exonuclease activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
enzyme is active only in cells at meiotic prophase, in somatic cells it is in an inactive state
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the enzyme shows deoxynucleotide transferase activity, short patch DNA synthesis activity on heteropolymeric DNA substrate, 5'-deoxyribose phosphate lyase activity and base excision repair function in vitro
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the enzyme shows deoxynucleotide transferase activity, short patch DNA synthesis activity on heteropolymeric DNA substrate, 5'-deoxyribose phosphate lyase activity and base excision repair function in vitro
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
interaction of polymerases with template-primers containing chemically modified or damaged bases
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
fidelity of DNA replication
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase delta: with its auxiliary factor i.e. proliferating cell nuclear antigen, largely responsible for leading-strand synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
overview: physiological roles in replication and in DNA repair synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase alpha: with its associated primase largely responsible for lagging-strand synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
preference for poly(dA)/oligo(dT)10:1 as a template primer and has high processivity for DNA synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
template specificity, enzyme overexpressed in E. coli
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
643657, 643658, 691213, 691785, 692423, 692685, 693797, 703192, 704160, 704278, 705887, 722100 -
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 5'--3' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity, pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity, pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
no exonuclease 5'--3' activity: pol II
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity, pol II
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
can initiate polymer synthesis de novo, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
single strands, pol I, but not pol II and III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
single-stranded 5'-ends greater than 100 nucleotides, pol I, but not pol II and pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease activity associated with the replicative polymerase is contained within the epsilon subunit
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity, pol I
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease activity utilizes both, ssDNA and melted dsDNA templates, mismatched basepair is preferred over a correct basepair, removes an incorrect base incorporated opposite a template lesion
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
template specificity of polymerase II
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
nicked duplex is no substrate of pol II and III of E. coli
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
nicked duplex, as poly d(A-T), pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
can not initiate polymer synthesis de novo: pol II and III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 5'--3' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 5'--3' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 5'--3' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
physiological role of pol I
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
physiological role of pol I, II and pol III
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
pol III can repair short gaps created by nuclease in duplex DNA, for efficient replication of the long, single-stranded templates pol III requires auxiliary subunits
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
polymerase III: role in replication of chromosomal DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
polymerase II: role in DNA repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase V is involved in translesion synthesis and mutagenesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
beta sliding clamp plays an essential role in pol V-dependent translesion DNA synthesis in vivo
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase V is involved in translesion synthesis and mutagenesis. Two factors are essential for efficient Pol V-mediated lesion bypass: 1. a DNA substrate onto which the beta-clamp is stably loaded and 2. an extended single-stranded RecA/ATP filament assembled downstream from the lesion site. For efficient bypass, Pol V needs to interact simultaneously with the beta-clamp and the 3' tip of the RecA filament
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
a fast fluorescence transition corresponding to conformational closing, and a slow fluorescence transition matching the rate of single-nucleotide incorporation. This transition represents a conformational event after chemistry, likely subdomain reopening
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
wild-type DinB inserts deoxycytidine opposite N2-furfuryl-dG with 1015fold greater catalytic proficiency than opposite undamaged dG
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the Klenow fragment of DNA polymerase I is able to dimerize on a DNA primer/template. Dimerization is favored when the first molecule is bound in the polymerizing mode, but disfavored when it is bound in the editing mode. Self-association of the polymerase may play an important role in coordinating high-fidelity DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
bacteriohage T4 and bacteriophage RB69 replicative DNA polymerases exhibit differing abilities to form various base pairs. Formation of Watson-Crick base pairs occurs at similar rates between the two proteins but the incoming nucleotides are bound less tightly by RB69 DNA polymerase. Incorporation of an A opposite furan by T4 DNA polymerase is more rapid than for RB69 DNA polymerase with the two proteins having similar binding constants for the incoming dATP. An A:C mismatch is formed almost equally well by both proteins, while a significant difference exists when a T:T mismatch is formed
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
two proton transfers occur in the transition state for nucleotidyl-transfer reactions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity and 5'--3' activity, phage T7-induced DNA polymerase
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
nicked duplex is no substrate of phage T4-induced DNA polymerase
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
mechanical tension on DNA controls speed and direction of DNA polymerase motor
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the effects of varied DNA substrate size on the synthesis of DNA by the high fidelity T7 DNA polymerase: the T7 enzyme is highly sensitive in kinetic efficiency to size changes across this analog series. The T7 enzyme shows a strong dependence on substrate size and shows a preference for smaller substrates
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
gamma-phosphates of the incoming dNTP, contributing to charge neutralization and alignment of the alpha-phosphate for reaction
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
overview: physiological roles in replication and in DNA repair synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
standard substrate PTJ1 and substrate PTJ2
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
standard substrate PTJ1 and substrate PTJ2
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
RNase H domain degrades RNA component of RNA-DNA hybrids
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Herpes simplex virus
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Herpes simplex virus
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Herpes simplex virus
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Herpes simplex virus
-
beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
643649, 643650, 643668, 671388, 691213, 691631, 692423, 692685, 693396, 693630, 701733, 702026, 702071, 702087, 702630, 703192, 703443, 704160, 704422, 704480, 705693, 705867, 705979, 721129, 721707, 722686, 723570, 723694 -
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
highly stereospecific, polymerase alpha, beta and epsilon incorporate only natural beta-D-dNTPs, L-dNTPs are no substrate
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
polymerase gamma also has proofreading activity with an RNA template, reverse transcriptase activity and incorporates ribonucleotide triphosphates into a DNA primer
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
interaction of polymerases with template-primers containing chemically modified or damaged bases
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
fidelity of DNA replication
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
overview: functional role of mammalian DNA polymerases
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
polymerase alpha: role in DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
polymerase beta: role in DNA repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase delta: with its auxiliary factor i.e. proliferating cell nuclear antigen, largely responsible for leading-strand synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
overview: physiological roles in replication and in DNA repair synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase alpha: with its associated primase largely responsible for lagging-strand synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Pol lambda plays a role in the short-patch base excision repair rather than contributes to the long-patch base excision repair pathway
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase lambda possesses the ability to synthesise in vitro short fragments of DNA in the absence of a primer-template or even a primer or a template. Amino acid Phe506 of poly lambda is essential for the de novo synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase mu possesses the ability to synthesize in vitro short fragments of DNA in the absence of a primer-template or even a primer or a template. Amino acid Phe506 of poly lambda is essential for the de novo synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
in addition to a slow and distributive DNA polymerase activity, Pol mu possesses a weak strand-displacement activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Pol eta effectively bypasses N2-methylguanine, N2-ethylguanine, N2-isobutylguanine, N2-benzylguanine, and N2-CH2(2-naphthyl)guanine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Pol lambda is unable to catalyze strand displacement synthesis using nicked DNA, although this enzyme efficiently incorporates a dNMP into a one-nucleotide gap
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase iota may play a limited and error-prone role in translesion synthesis across the N2-guanine adducts (possibly medium sized adducts up to N2-benzylguanine) due to the low polymerization rates and high error rates
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase mu could be involved in the repair of a DSB subset when resolution of junctions requires some gap filling
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
downstream strand and its 5'-phosphate moiety are critical to the polymerase efficiency of the enzyme. Nucleotide-gapped DNA substrates containing a 1,2-dideoxyribose-5-phosphate moiety (a 2-deoxyribose-5-phosphate mimic) moderately decrease the polymerase efficiency by 3.4fold
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
inefficient and error-prone bypass across bulky N2-guanine DNA adducts. Effectively bypasses N2-methylguanine and N2-ethylguanine, partially bypasses N2-isobutylguanine and N2-benzylguanine, and is blocked at N2-CH2(2-naphthyl)guanine, N2-CH2(9-anthracenyl)guanine, and N2-CH2(6-benzo[a]pyrenyl)guanine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
poly(dA)/oligo(dT)10:1. 2-thiomethyl-6-phenyl-4-(4'-hydroxybutyl)-1,2,4,-triazole (5,1-C)(1,2,4)triazine-7-one triphosphate can be incorporated on both templates but only by the Y505A mutant enzyme. N-(Benzyloxycarbonyl)-4-aminobutyl triphosphate can be incorporated by DNA pol lambda either wild type or the Y505A mutant, opposite to an abasic site only. Incorporation efficiency of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymmerase lambda wild type is 22fold higher opposite an abasic site than on the intact template. DNA polymerase lambda wild type incorporates (biphenylcarbonyl)-4-oxobutyl triphosphate 2.2fold more frequently than dCTP opposite the lesion. The DNA polymerase lambda Y505A mutant shows a 5.3fold preference for dCTP versus (biphenylcarbonyl)-4-oxobutyl triphosphate incorporation opposite the lesion
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
poly(dA)/oligo(dT)10:1. In the presence of Mn2+, DNA polymerase beta incorporates (biphenylcarbonyl)-4-oxobutyl triphosphate both on an intact template and opposite to an abasic site. DNA polymerase beta incorporates dCTP on the undamaged template, whereas it exclusively incorporates dATP opposite the abasic site. The incorporation efficiency of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta is 2fold higher in the presence of the undamaged template, with respect to the one carrying an abasic site. When Mn2+ is replaced by Mg2+, this difference becomes even more striking, so that (biphenylcarbonyl)-4-oxobutyl triphosphate can be exclusively incorporated on the undamaged in the presence of Mg2+, the incorporation of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta becomes strictly dependent on the presence of a templating base. Replacement of Mn2+ with Mg2+, however, greatly enhances the preference for incorporation of dCTP versus (biphenylcarbonyl)-4-oxobutyl triphosphate opposite a template G by DNA polymerase beta, which increases from 23fold to 239fold
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
polymerase gamma is required for replication of mitochondrial DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
DNA polymerase iota preferentially misincorporates nucleotides opposite thymines and halts replication at T bases
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
naturally occurring DNA structures are physiological substrates of both pol eta and pol kappa
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
with undamaged templating purines DNA polymerase iota normally favors Hoogsteen base pairing, DNA polymerase iota can incorporate nucleotides opposite a benzo[a]pyrene-derived adenine lesion
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
assays of Pol delta complexes on poly(dA)/oligo(dT) template/primers
DNA products synthesized by Pol delta and its subassemblies on primed M13 DNA, overview
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
reversibility of the polymerase reaction at the level of the template with diphosphate as leaving group, not with the alternative leaving groups, overview
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
herpes polymerase only elongates primase-synthesized primers at least 8 nucleotides long
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
role in DNA gap repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
two proton transfers in the transition state for nucleotidyl transfer
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
overview: functional role of mammalian DNA polymerases
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
overview: physiological roles in replication and in DNA repair synthesis
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
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deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
template specificity
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
standard substrate PTJ1 and substrate PTJ2
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
MacDinB-1 synthesizes long products (approximately 7.2 kb) in the presence of its cognate proliferating cell nuclear antigen (PCNA). MacDinB-1 works in an error-free mode to repair cyclobutane pyrimidine dimers
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?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 5'--3' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
no exonuclease 5'--3' activity: pol II
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
can initiate polymer synthesis de novo, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
single strands, pol I, but not pol II and III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
single-stranded 5'-ends greater than 100 nucleotides, pol I, but not pol II and pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
nicked duplex is no substrate of polymerase I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
nicked duplex, as poly d(A-T), pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 5'--3' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the enzyme utilizes deaminated bases and is also able to amplify lambda DNA fragments using dUTP and dITP
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
OsPOLP1 might be involved in a repair pathway similar to long-patch base excision repair. Possible role of POLPs in plastidial DNA replication and repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
OsPOLP1 efficiently catalyzed strand displacement on nicked DNA with a 5'-deoxyribose phosphate
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
polB and polD preferentially insert dAMP opposite an apurinic/apyrimidinic site, albeit inefficiently
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
PabPolD might play an important role in DNA replication likely together with PabpolB, suggesting that archaea require two DNA polymerases at the replication fork
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
both DNA polymerase D and DNA polymerases B are DNA polymerizing enzymes exclusively. DNA polymerase D has a preference for a primed template. DNA polymerase D is a primer-directed DNA polymerase independently of the primer composition whereas DNA polymerase B behaves as an exclusively DNA primer-directed DNA polymerase. Proliferating cell nuclear antigen is required for DNA polymerases D to perform efficient DNA synthesis but not DNA polymerases B. DNA polymerase D, but not DNA polymerase B, contains strand displacement activity. In the presence of PabPCNA, however, both DNA polymerases D and B show strand displacement activity. Direct interaction between DNA polymerase D and proliferating cell nuclear antigen is DNA-dependent
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
PCR performance and fidelity parameters are highest in the presence of 20 mM Tris-HCl, pH 9.0, 1.5 mM MgSO4, 25 mM KCl, 10 mM (NH4)2SO4 and 40 microM of each dNTP. Under these conditions, the error rate is 0.66.10(-6) mutations/nucleotide/duplication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
PCR performance and fidelity parameters are highest in the presence of 20 mM Tris-HCl, pH 9.0, 1.5 mM MgSO4, 25 mM KCl, 10 mM (NH4)2SO4 and 40 microM of each dNTP. Under these conditions, the error rate is 0.66.10(-6) mutations/nucleotide/duplication
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
wild-type Pfu-Pol makes about one mistake for every 1000000 bases incorporated, wild-type variant Pfu-Pol(exo-)(D473F)is 60fold less accurate
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme has a template-primer preference which is characteristic of a replicative DNA polymerase
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
measurement of the incorporation of methyl-TTP into acid insoluble material. The single-stranded DNA substrate is more sensitive than the double stranded substrate. The polymerase and exonuclease domains in the family B DNA polymerases are functionally interdependent
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
replicative DNA polymerase
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the DNA polymerase from Pyrococcus furiosus has the lowest error rate of any known polymerase in polymerase chain reaction amplification
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme utilizes activated DNA as a template-primer, artificial substrate (activated poly(dA-dT)) is preferred by the enzyme. M13 single-stranded DNA primed with 17 base oligonucleotide is not a good substrate. DNA elongation ability of Pol II using a natural DNA template is much lower than that of Pol I from this organism and DNA synthesis of Pol II seems to be non-processive
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the enzyme plays an essential role in DNA replication, repair, and recombination
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the carboxyl-terminal (12551332) of the large subunit (DP2Pho) and two regions, the 201260 and 599622, of the small subunit (DP1Pho) are critical for the complex formation, and probable subunit interaction of PolDPho. The amino-terminal (1300) of DP2Pho is essential for the folding of PolDPho and is likely the oligomerization domain of PolDPho
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the functional motif, K253xRxxxD259 (outside known motifs Exo I, II, and III), that is important not only for exonuclease activity but also for polymerizing activity, confirms functional interdependence between the polymerase and exonuclease domains. The short loop region, K253G254R255, probably contributes to binding to DNA substrates
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
polymerase alpha: role in DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
a fast fluorescence transition corresponding to conformational closing, and a slow fluorescence transition matching the rate of single-nucleotide incorporation. This transition represents a conformational event after chemistry, likely subdomain reopening. Rotation of the Arg258 side chain is not rate-limiting in the overall kinetic pathway of Pol beta, yet is kinetically significant in subdomain reopening
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Ruellia sp.
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Sso DNA pol B1 recognizes the presence of uracil and hypoxanthine in the template strand and stalls synthesis 34 bases upstream of this lesion (read-ahead function). Sso DNA pol Y1 is able to synthesize across these and other lesions on the template strand. Sso DNA pol B1 physically interacts with DNA pol Y1. The region of DNA pol B1 responsible for this interaction has been mapped in the central portion of the polypeptide chain (from the amino acid residue 482 to 617)
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
with template guanine and Watson-Crick paired dCTP as the nascent base pair. Water-mediated and substrate-assisted mechanism: the initial proton transfer to the R-phosphate of the substrate via a bridging crystal water molecule is the rate-limiting step, the nucleotidyl-transfer step is associative with a metastable pentacovalent phosphorane intermediate, and the diphosphate leaving is facilitated by a highly coordinated proton relay mechanism through mediation of water which neutralizes the evolving negative charge. The conserved carboxylates, which retain their liganding to the two Mg2+ ions during the reaction process, are found to be essential in stabilizing transition states. This water-mediated and substrate-assisted mechanism takes specific advantage of the unique structural features of this low-fidelity lesion-bypass Y-family polymerase, which has a more spacious and solvent-exposed active site than replicative and repair polymerases
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
two representative types of lesions: (i) 7,8-dihydro-8-oxoguanine, a small, highly prevalent lesion caused by oxidative damage; and (ii) bulky lesions derived from the environmental pre-carcinogen benzo[a]pyrene. The diol epoxide (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[ a]pyrene reacts largely, but not exclusively, with the exocyclic amino group of guanine to produce the major 10S (+) trans-anti-BP-N2-dG adduct, that is bypassed by Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
mechanism of purine-purine mispair formation, substrate specificity and binding structure, the kpol/Kd dNTP values for the insertion of dATP and dGTP opposite 7-deazaadenine and 7-deazaguanine are decreased over 10fold with respect to those of the unmodified nucleotides during formation of purine-purine mispairs. In addition, the rate of incorporation of 1-deaza-dATP opposite guanine is decreased 5fold. Dpo4 holds the incoming dNTP in the normal anti conformation while allowing the template nucleotide to change conformations to allow reaction to occur. This result may be functionally relevant in the replication of damaged DNA in that the polymerase may allow the template to adopt multiple configurations, overview
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in DNA polymerase IV, 5'-slippage mechanism: the dATP can be inserted opposite the T on the 5' side of the adduct G1*, in which the unadducted G2, rather than G1*, is skipped, to produce a -1 deletion, molecular modeling and dynamics simulations, overview
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
substrate is a 44-mer DNA template containing a site-specific cisplatin-d(GpG) adduct, Dpo4 is able to bypass a single, site-specifically placed cisplatin-d(GpG) adduct, although, the incorporation efficiency of dCTP opposite the first and second cross-linked guanine bases is decreased by 72 and 860fold, respectively, enzyme fidelity, overview
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the nucleotidyl-transfer reaction coupled with the conformational transitions in DNA polymerases is critical for maintaining the fidelity and efficiency of DNA synthesis, correct insertion of dCTP opposite 8-oxoguanine and quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization, overview
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
two representative types of lesions: (i) 7,8-dihydro-8-oxoguanine, a small, highly prevalent lesion caused by oxidative damage; and (ii) bulky lesions derived from the environmental pre-carcinogen benzo[a]pyrene, Dpo4 bypasses 8-oxoG accurately
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
approximately 2/3 of the errors made by the enzyme are single-base substitutions, of which 58% are C->T transition. Frameshift mutations, mostly resulting from single-base deletions, account for 19% of the total errors. An exonuclease-deficient mutant of Sso pol B1 is three times as mutagenic as the wild-type enzyme, suggesting that the intrinsic proofreading function contributed only modestly to the fidelity of the enzyme
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
bypass of apurinic/apyrimidinic sites lacking A or G is nearly 100% mutagenic. The majority (7080%) of bypass events are insertion of dAMP opposite the apurinic/apyrimidinic site
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
in the absence of additional cofactor the enzyme is an essentially distributive enzyme that only extends primers by 1-2 nt per binding event. At high enzyme to primer/template ratios, dissociation and rebinding of the enzyme to the primer/template is robust and can lead to the synthesis of polynucleotide chains of several hundred nucleotides in length
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
modeling and molecular dynamics simulations for 2'-deoxy-8-[(1-methyl-6-phenyl-1H-imidazo[4,5-b]pyridin-2-yl)amino]guanosine suggest that the adduct would increase the infidelity of Dpo4 and hinder translocation by the enzyme
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
products of replication of polycyclic aromatic hydrocarbon-modified DNA by the translesion DNA polymerase Dpo4 are complex
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
propenal and malondialdehyde react with DNA to form adducts, including 3-(2'-deoxy-beta-D-erythro-pentofuranosyl) pyrimido[1,2-alpha]purin-10(3H)-one (M1dG). When paired opposite cytosine in duplex DNA at physiological pH, M1dG undergoes ring opening to form N2-(3-oxo-1-propenyl)-dG. To improve the understanding of the basis for M1dG-induced mutagenesis, the mechanism of translesion DNA synthesis opposite M1dG by the model Y-family polymerase Dpo4 is studied at a molecular level using kinetic and structural approaches. The enzyme can bypass the exocyclic M1dG adduct in largely an error-prone fashion
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
replication bypass studies in vitro reveal that the polymerase inserts dNTPs opposite the (6S,8R,11S)-trans-4-hydroxynonenal-1,N2-dGuo adduct in a sequence-specific manner. If the template 5'-neighbor base is dCyt, the polymerase inserts primarily dGTP. If the template 5'-neighbor base is dThy, the polymerase inserts primarily dATP
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
ribonucleotide discrimination by the DinB homolog (Dbh) DNA polymerase is as stringent as in other polymerases. When making a deletion error, ribonucleotide discrimination by wild-type and F12A Dbh is the same as in normal DNA synthesis
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme bypasses aflatoxin B1-N7-dG in an error-free manner but conducts error-prone replication past the aflatoxin B1-formamidopyrimidine adduct, including misinsertion of dATP
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme is nonprocessive and can bypass an abasic site
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme shows a limited decrease in catalytic efficiency (kcat/Km) for insertion of dCTP opposite a series of N2-alkylguanine templates of increasing size from (methyl (Me) to (9-anthracenyl)-Me (Anth)). Fidelity is maintained with increasing size up to (2-naphthyl)-Me (Naph). The catalytic efficiency increases slightly going from the N2-NaphG to the N2-AnthG substrate, at the cost of fidelity. A set of oligonucleotides differing only in their N2-substitution at a single G site is used in this study with Dpo4
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the pre-steady-state kinetic methods is used to determine the base substitution fidelity and mismatch extension fidelity of PolB1
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the rate-constant defining Dpo4-catalyzed incorporation of dCTP is about 6-fold slower for incorporation opposite O6-MeG relative to G. The basis for the decreased rate is revealed by the crystal structure to be formation of a wobble base pairing between O6-MeG and C
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
translesion synthesis of the 7-(2-oxoheptyl)-1,N2-etheno-2'-deoxyguanosine lesion by the enzyme in 5'-TXG-3' and 5'-CXG-3' local sequence contexts is examined and compared to 1,N2-etheno-2'-deoxyguanosine lesions
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme can efficiently incorporate nucleotides opposite 8-oxoG and extend from an 8-oxoG:C base pair with a mechanism similar to that observed for the replication of undamaged DNA
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
deamination of cytosine to uracil is a hydrolytic reaction that is greatly accelerated at high temperatures. The resulting uracil pairs with adenine during DNA replication, thereby inducing G:C to A:T transitions in the progeny. B-family DNA polymerases from hyperthermophilic archaea recognize the presence of uracil in DNA and stall DNA synthesis. Although PolB1 per se specifically binds to uracil-containing single-stranded DNA, the binding efficiency is substantially enhanced by the initiation of DNA synthesis. The generation of ds DNA is significantly inhibited, however, by the presence of template uracil. Pol B1 more efficiently recognizes uracil in DNA during DNA synthesis rather than during random diffusion in solution. Single molecules of Pol B1 bind to template uracil and stall DNA synthesis
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the enzyme bypasses DNA adducts pyrrolo-deoxycytosine, dP, N6-furfuryl-deoxyadenosine, and 1,N6-ethenodeoxyadenosine in a process known as translesion synthesis
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
an abasic lesion causes Dpo4 to switch from a normal to a very mutagenic mode of replication. Incorporation upstream of the abasic lesion is replicated error-free. Once Dpo4 encounters the lesion, synthesis became sloppy, with bypass products containing a myriad of mutagenic events. Incorporation of dAMP (29%) and dCMP (53%) opposite the abasic lesion at 37°C correlates exceptionally well with our kinetic results and demonstrates two dominant bypass pathways via the A-rule and the lesion loop-out mechanism. The percentage of overall frameshift mutations increases from 71% (37°C) to 87% (75°C)
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
an abasic lesion causes the enzyme to switch from a normal to a very mutagenic mode of replication
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
ATP binding to replication factor C is sufficient for loading the heterotrimeric PCNA123 [proliferating cell nuclear antigen (PCNA)] clamp onto DNA that includes a rate-limiting conformational rearrangement of the complex. ATP hydrolysis is required for favorable recruitment and interactions with the replication polymerase (PolB1) that most likely include clamp closing and dissociation of replication factor C. Surprisingly, the assembled holoenzyme complex synthesizes DNA distributively and with low processivity, unlike most other well-characterized DNA polymerase holoenzyme complexes. PolB1 repeatedly disengages from the DNA template, leaving PCNA123 behind. Interactions with a C-terminal PCNA-interacting peptide (PIP) motif on PolB1 specifically with PCNA2 are required for holoenzyme formation and continuous re-recruitment during synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
bifunctional enzyme EC 2.7.7.7/EC 3.1.11.2. The polymerization and the 3'-5' exonuclease activity of a family B DNA polymerase can be ascribed to physically distinct modules of the enzyme molecule
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Dbh polymerase is much less accurate than the classical polymerases, but it shows a remarkable tendency to skip over a template pyrimidine positioned immediately 3' to a G residue, generating a single-base deletion. The rate of incorporation of dCTP opposite a template G is about 10fold faster than for the other three dNTPs opposite their complementary partners
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
distributive enzyme but a substantial increase in the processivity was observed on poly(dA)-oligo(dT) in the presence of proliferating cell nuclear antigen (039p or 048p) and replication factor CRFC. The length of the synthesized DNA product reaches at least 200 nucleotides
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
DNA polymerase Dpo4 can replicate past a variety of DNA lesions. When replicating undamaged DNA, the enzyme is prone to make base pair substitutions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase pol Y1 exclusively incorporates 8-OH-GTP opposite adenine. DNA polymerase pol Y1 incorporates 2-OH-dATP predominantly opposite guanine and thymine. DNA polymerase pol B1 incorporates 8-OH-GTP opposite adenine and cytosine. DNA polymerase pol B1 incorporates 2-OH-dATP opposite thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
Dpo4 in most cases selects the correctly paired partner for each benzo-expanded DNA base, but with efficiency lowered by the enlarged pair size
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Dpo4 predominantly uses a template slippage deletion mechanism when replicating repetitive DNA sequences. Dpo4 stabilizes the skipped template base in an extrahelical conformation between the polymerase and the little-finger domains of the enzyme
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
even at 60°C, excessive amounts of Dpo4 are needed to carry out minimal bypass of the cyclobutane pyrimidine dimers
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exclusively incorporates 8-OH-GTP opposite adenine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
GTP incorporation by the wild-type enzyme is about 1000fold slower than dGTP incorporation. The rate of GTP incorporation by the mutant enzyme F12A Dbh is 2-3fold slower than incorporation of dGTP. The enzyme makes single-base deletion errors at high frequency in particular sequence contexts
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
in addition to the correct insertion of dCTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
incorporated of 2-amino-3-methylimidazo[4,5-f]quinoline C8- and N2-dGuo adducts into the G1- and G3-positions of the NarI recognition sequence (5'-G1G2CG3CC-3'), which is a hotspot for arylamine modification. Replication of the C8-adduct at the G3-position results in two-base deletion, whereas error-free bypass and extension is observed at the G1-position. The N2-adduct is bypassed and extended when positioned at the G1-position, and the error-free product is observed. The N2-adduct at the G3-position is more blocking and is bypassed and extended only by Dpo4 to produce an errorfree product. The replication of the 2-amino-3-methylimidazo[4,5-f]quinoline-adducts of dGuo is strongly influenced by the local sequence and the regioisomer of the adduct
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
low fidelity. When copying undamaged DNA, Dpo4 is highly inaccurate for essentially all types of single base substitutions and deletions in a large number of different sequence contexts
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
mechanism of template-independent nucleotide incorporation. Based on the efficiency ratios, Dpo4 selects nucleotides for blunt-end addition in the order of decreasing efficiency: dATP, dTTP, dCTP, dGTP, with dATP favored by five to 50fold over the other nucleotides. The first bluntend dATP incorporation is 80fold more efficient than the second, and among natural deoxynucleotides, dATP is the preferred substrate due to its stronger intrahelical base-stacking ability
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
proliferating cell nuclear antigen facilitates DNA synthesis with Dpo3, as with Dpo1 and Dpo4, but very weakly with Dpo2. DNA synthesis in the presence of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein is most processive with DNA polymerase Dpo1 in comparison to DNA polymerase Dpo3 and Dpo4. DNA lesion bypass DNA synthesis in the presence of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein is most effective with DNA polymerase Dpo4 in comparison to DNA polymerase Dpo1 and Dpo3. Both Dpo2 and Dpo3, but not Dpo1, bypass hypoxanthine and 8-oxoguanine. Dpo2 and Dpo3 bypass uracil and cis-syn cyclobutane thymine dimer, respectively. DNA polymerase Dpo2 and Dpo3 possess very low DNA polymerase and 3' to 5' exonuclease activities in vitro compared with Dpo1 and Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
relative to undamaged DNA the enzyme generates far more mutations (base deletions, insertions, and substitutions) with a DNA template containing a site-specifically placed N-(deoxyguanosin-8-yl)-1-aminopyrene. Opposite N-(deoxyguanosin-8-yl)-1-aminopyrened and at an immediate downstream template position, the most frequent base substitutions are dA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
removal of the 2-amino group from the template dG (i.e. deoxyinosine) has little impact on the catalytic efficiency of either polymerase, although the misincorporation frequency is increased by an order of magnitude. Deoxyxanthosine is highly miscoding with both polymerases, and incorporation of several bases is observed. The addition of bromine or oxygen at C2 lowers the Tm further, strongly inhibits and increases the frequency of misincorporation
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
ring-opening of the 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-8-hydroxypyrimido[1,2-a] purin-10(3H)-one adduct promotes error-free bypass by the Sulfolobus solfataricus DNA polymerase Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the binding of a correct nucleotide induces a fast and surprising DNA translocation event. All four domains of the polymerase rapidly move in a synchronized manner before and after the polymerization reaction. Repositioning of active site residues is the rate-limiting step during correct nucleotide incorporation. The motions of the polymerase and the polymerase bound DNA substrate are tightly coupled to catalysis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the conformational dynamics of the Y-family DNA polymerase Dpo4 on DNA is characterized in real time using single-molecule Förster resonance energy transfers (mFRET). Two different binary complexes consistent with DNA translocation in the polymerase active site
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the enzyme binds to DNA in at least three distinct conformations. The relative frequency of each conformation can be modulated by both the identity of the primer 3' terminus and the presence of an incoming dNTP
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme bypasses Pt-GG DNA (1,2-intrastrand covalent linkage, cis-Pt-1,2-d(GpG)). This is a dynamic process, in which the lesion is converted from an open and angular conformation at the first insertion to a depressed and nearly parallel conformation at the subsequent reaction stages to fit into the active site of Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the enzyme catalyze DNA synthesis using either activated calf thymus DNA or oligonucleotide-primed single-stranded DNA as a template
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme does not efficiently insert nucleotides opposite to the (6S,8R,11S)-1,N2-deoxyguanosine adduct, consistent with the low levels of Gua->Thy mutations. However it extends past the (6S,8R,11S)-1,N2-deoxyguanosine:dCyd pair. A series of ternary (Dpo4-DNA-dNTP) structures with (6S,8R,11S)-1,N2-deoxyguanosine-adducted templates suggest that during replication, the ring-closed (6S,8R,11S)-1,N2-deoxyguanosine lesion at the active site hinders incorporation of dNTPs opposite the lesion, whereas the ring-opened form of the lesion in the (6S,8R,11S)-1,N2-deoxyguanosine:dCyd pair allows for extension to full-length product
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the enzyme incorporates dTTP in a 61 mer template containing pyrrolo-deoxycytosine, dP, N6-furfuryl-deoxyadenosine, and 1,N6-ethenodeoxyadenosine (translesion synthesis)
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme is able to bypass N-(deoxyguanosin-8-yl)-1-aminopyrene, but pauses strongly at two sites: opposite the lesion and immediately downstream from the lesion. Both nucleotide incorporation efficiency and fidelity decrease significantly at the pause sites, especially during extension of the bypass product. Interestingly, a 4-fold tighter inding affinity of damaged DNA to Dpo4 DNA polymerase promotes catalysis through putative interactions between the active site residues of Dpo4 and 1-aminopyrene moiety at the first pause site
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme is inefficient at extending mispairs opposite a template G or T, which include, a G*T mispair expected to conform closely to Watson-Crick geometry. It is hindered in extending a G*T mismatch by a reverse wobble
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the enzyme possess a remarkable DNA stabilizing ability for maintaining weak base pairing interactions to facilitate primer extension. This thermal stabilization by Dpo1 allows for template-directed synthesis at temperatures more than 30°C above the melting temperature of naked DNA. Dpo1 elongates single stranded DNA in template-dependent and template-independent manners. Initial deoxyribonucleotide incorporation is complementary to the template. Rate-limiting steps that include looping back and annealing to the template allow for a unique template-dependent terminal transferase activity. Dpo1 also displays a competing terminal deoxynucleotide transferase activity unlike any other B-family DNA polymerase
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme shows little decreases opposite N2-MeG, 13fold decrease opposite N2-BzG but 260-370fold decreases opposite O6-MeG, O6-BzG, and the abasic site site as compared to G. Dpo4 favored correct C insertion opposite opposite N2-MeG, opposite O6-MeG, opposite an abasic site site and oppositeN2-BzG. DNA polymerase Vent (exo-) from Thermococcus litoralis is as or more efficient as polymerase Dpo4 from Sulfolobus solfataricus in synthesis opposite O6-MeG and AP lesions, whereas DNA polymerase Dpo4 from Sulfolobus solfataricus is much or more efficient opposite N2-alkylGs than DNA polymerase Vent (exo-) from Thermococcus litoralis, irrespective of DNA-binding affinity. DNA polymerase Dpo4 strongly favors minor-groove N2-alkylG lesions over major-groove or noninstructive lesions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the fidelity of Dpo4 is in the range of 0.001-0.0001. The ground-state binding affinity of correct nucleotides is 10-50-fold weaker than those of replicative DNA polymerases. The affinity of incorrect nucleotides for Dpo4 is about 2-10-fold weaker than that of correct nucleotides. The mismatched dCTP has an affinity similar to that of the matched nucleotides when it is incorporated against a pyrimidine template base flanked by a 5'-template guanine. The mismatch incorporation rates, regardless of the 5'-template base, are about 2-3 orders of magnitude slower than the incorporation rates for matched nucleotides, which is the predominant contribution to the fidelity of Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by the enzyme, with hydrogen bonding capacity being a major influence. Modifications at the C2-position of dCTP increases the selectivity for incorporation opposite O6-methylguanine without a significant loss of efficiency
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the initial enzyme/DNA/dNTP complex undergoes a rapid (18/s), reversible (21/s) conformational change, followed by relatively rapid phosphodiester bond formation (11/s) and then fast release of pyrophosphate, followed by a rate-limiting relaxation of the active conformation (2/s) and then rapid DNA release, yielding an overall steady-state kcat of less than 1/s
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the molecular dynamics simulations suggest that mismatched nucleotide insertion opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG is increased at 55°C compared with 37°C because the higher temperature shifts the preference of the damaged base from the anti to the syn conformation, with the carcinogen on the more open major groove side. The mismatched dNTP structures are less distorted when the damaged base is syn than when it is anti, at the higher temperature. With the normal partner dCTP, the anti conformation with close to Watson-Crick alignment remains more favorable. The molecular dynamics simulations are consistent with the kcat values for nucleotide incorporation opposite the lesion studied, providing structural interpretation of the experimental observations. The observed temperature effect suggests that conformational flexibility plays a role in nucleotide incorporation and bypass fidelity opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG by Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the rate of insertion of dNTPs opposite and extension past both O2-[4-(3-pyridyl)-4-oxobut-1-yl]-thymidine and O2-methylthymidine is measured. The size of the alkyl chain only marginally affects the reactivity and the specificity of adduct bypass is very low. Dpo4 catalyzes the incorporation opposite and extension past the adducts approximately 1000fold more slowly than undamaged DNA. dA is the preferred base pair partner for O2-[4-(3-pyridyl)-4-oxobut-1-yl]-thymidine and dT is the preferred base pair partner for O2-methylthymidine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the rate of mismatched nucleotide incorporation is greater than the rate of correct dC insertion at 55 °C, whereas at 37 °C there is little selectivity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
when insertion is opposite an unmodified G, insertion of dATP or dGTP is 1000 less efficient than dCTP. For insertion opposite 8-oxoG, the order of decreasing efficiency is dCTP, dATP, dGTP, with an order of magnitude or more difference in catalytic efficiency (kcat/Km) in each pair of comparisons. The insertion of dCTP opposite G and 8-oxoG shows similar catalytic efficiency, even with differences in the trends for kcat and Km. 90fold higher incorporation efficiency of dCTP compared to dATP opposite 8-oxoG and 4fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. The 8-oxoG:C pair shows classic Watson-Crick geometry; the 8-oxoG:A pair is in the syn:anti configuration, with the A hybridized in a Hoogsteen pair with 8-oxoG. With dGTP placed opposite 8-oxoG, pairing was not to the 8-oxoG but to the 5'C (and in classic Watson-Crick geometry), consistent with the low frequency of this frameshiftevent observed in the catalytic assays
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
while showing efficient bypass, the enzyme pauses when incorporating nucleotides directly opposite and one position downstream from an abasic lesion because of a drop of several orders of magnitude in catalytic efficiency. Biphasic kinetics for incorporation indicating that Dpo4 primarily forms a nonproductive complex with DNA that converts slowly to a productive complex. These strong pause sites are mutational hot spots with the embedded lesion even affecting the efficiency of five to six downstream incorporations
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme inefficiently bypasses (5'S)-8,5'-cyclo-2'-deoxyguanosine with dCTP preferably incorporated and dATP misincorporated. (5'S)-8,5'-cyclo-2'-Deoxyguanosine attenuates K(d,dNTP,app) and k(pol)
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme inefficiently bypasses (5'S)-8,5'-cyclo-2'-deoxyguanosine with dCTP preferably incorporated and dTTP misincorporated. The (5'S)-8,5'-cyclo-2'-Deoxyguanosine-adduct-duplex complex causes 6fold decrease in Dpo4:DNA binding affinity, and significantly reduces the concentration of the productive Dpo4:DNA:dCTP complex
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase pol Y1 exclusively incorporates 8-OH-GTP opposite adenine. DNA polymerase pol Y1 incorporates 2-OH-dATP predominantly opposite guanine and thymine. DNA polymerase pol B1 incorporates 8-OH-GTP opposite adenine and cytosine. DNA polymerase pol B1 incorporates 2-OH-dATP opposite thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exclusively incorporates 8-OH-GTP opposite adenine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the pre-steady-state kinetic methods is used to determine the base substitution fidelity and mismatch extension fidelity of PolB1
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
translesion synthesis of the 7-(2-oxoheptyl)-1,N2-etheno-2'-deoxyguanosine lesion by the enzyme in 5'-TXG-3' and 5'-CXG-3' local sequence contexts is examined and compared to 1,N2-etheno-2'-deoxyguanosine lesions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase pol Y1 exclusively incorporates 8-OH-GTP opposite adenine. DNA polymerase pol Y1 incorporates 2-OH-dATP predominantly opposite guanine and thymine. DNA polymerase pol B1 incorporates 8-OH-GTP opposite adenine and cytosine. DNA polymerase pol B1 incorporates 2-OH-dATP opposite thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exclusively incorporates 8-OH-GTP opposite adenine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the molecular dynamics simulations suggest that mismatched nucleotide insertion opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG is increased at 55°C compared with 37°C because the higher temperature shifts the preference of the damaged base from the anti to the syn conformation, with the carcinogen on the more open major groove side. The mismatched dNTP structures are less distorted when the damaged base is syn than when it is anti, at the higher temperature. With the normal partner dCTP, the anti conformation with close to Watson-Crick alignment remains more favorable. The molecular dynamics simulations are consistent with the kcat values for nucleotide incorporation opposite the lesion studied, providing structural interpretation of the experimental observations. The observed temperature effect suggests that conformational flexibility plays a role in nucleotide incorporation and bypass fidelity opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG by Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
removal of the 2-amino group from the template dG (i.e. deoxyinosine) has little impact on the catalytic efficiency of either polymerase, although the misincorporation frequency is increased by an order of magnitude. Deoxyxanthosine is highly miscoding with both polymerases, and incorporation of several bases is observed. The addition of bromine or oxygen at C2 lowers the Tm further, strongly inhibits and increases the frequency of misincorporation
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
ATP binding to replication factor C is sufficient for loading the heterotrimeric PCNA123 [proliferating cell nuclear antigen (PCNA)] clamp onto DNA that includes a rate-limiting conformational rearrangement of the complex. ATP hydrolysis is required for favorable recruitment and interactions with the replication polymerase (PolB1) that most likely include clamp closing and dissociation of replication factor C. Surprisingly, the assembled holoenzyme complex synthesizes DNA distributively and with low processivity, unlike most other well-characterized DNA polymerase holoenzyme complexes. PolB1 repeatedly disengages from the DNA template, leaving PCNA123 behind. Interactions with a C-terminal PCNA-interacting peptide (PIP) motif on PolB1 specifically with PCNA2 are required for holoenzyme formation and continuous re-recruitment during synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
proliferating cell nuclear antigen facilitates DNA synthesis with Dpo3, as with Dpo1 and Dpo4, but very weakly with Dpo2. DNA synthesis in the presence of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein is most processive with DNA polymerase Dpo1 in comparison to DNA polymerase Dpo3 and Dpo4. DNA lesion bypass DNA synthesis in the presence of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein is most effective with DNA polymerase Dpo4 in comparison to DNA polymerase Dpo1 and Dpo3. Both Dpo2 and Dpo3, but not Dpo1, bypass hypoxanthine and 8-oxoguanine. Dpo2 and Dpo3 bypass uracil and cis-syn cyclobutane thymine dimer, respectively. DNA polymerase Dpo2 and Dpo3 possess very low DNA polymerase and 3' to 5' exonuclease activities in vitro compared with Dpo1 and Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme inefficiently bypasses (5'S)-8,5'-cyclo-2'-deoxyguanosine with dCTP preferably incorporated and dATP misincorporated. (5'S)-8,5'-cyclo-2'-Deoxyguanosine attenuates K(d,dNTP,app) and k(pol)
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
in the absence of additional cofactor the enzyme is an essentially distributive enzyme that only extends primers by 1-2 nt per binding event. At high enzyme to primer/template ratios, dissociation and rebinding of the enzyme to the primer/template is robust and can lead to the synthesis of polynucleotide chains of several hundred nucleotides in length
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
products of replication of polycyclic aromatic hydrocarbon-modified DNA by the translesion DNA polymerase Dpo4 are complex
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
replication bypass studies in vitro reveal that the polymerase inserts dNTPs opposite the (6S,8R,11S)-trans-4-hydroxynonenal-1,N2-dGuo adduct in a sequence-specific manner. If the template 5'-neighbor base is dCyt, the polymerase inserts primarily dGTP. If the template 5'-neighbor base is dThy, the polymerase inserts primarily dATP
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme does not efficiently insert nucleotides opposite to the (6S,8R,11S)-1,N2-deoxyguanosine adduct, consistent with the low levels of Gua->Thy mutations. However it extends past the (6S,8R,11S)-1,N2-deoxyguanosine:dCyd pair. A series of ternary (Dpo4-DNA-dNTP) structures with (6S,8R,11S)-1,N2-deoxyguanosine-adducted templates suggest that during replication, the ring-closed (6S,8R,11S)-1,N2-deoxyguanosine lesion at the active site hinders incorporation of dNTPs opposite the lesion, whereas the ring-opened form of the lesion in the (6S,8R,11S)-1,N2-deoxyguanosine:dCyd pair allows for extension to full-length product
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme bypasses aflatoxin B1-N7-dG in an error-free manner but conducts error-prone replication past the aflatoxin B1-formamidopyrimidine adduct, including misinsertion of dATP
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
when insertion is opposite an unmodified G, insertion of dATP or dGTP is 1000 less efficient than dCTP. For insertion opposite 8-oxoG, the order of decreasing efficiency is dCTP, dATP, dGTP, with an order of magnitude or more difference in catalytic efficiency (kcat/Km) in each pair of comparisons. The insertion of dCTP opposite G and 8-oxoG shows similar catalytic efficiency, even with differences in the trends for kcat and Km. 90fold higher incorporation efficiency of dCTP compared to dATP opposite 8-oxoG and 4fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. The 8-oxoG:C pair shows classic Watson-Crick geometry; the 8-oxoG:A pair is in the syn:anti configuration, with the A hybridized in a Hoogsteen pair with 8-oxoG. With dGTP placed opposite 8-oxoG, pairing was not to the 8-oxoG but to the 5'C (and in classic Watson-Crick geometry), consistent with the low frequency of this frameshiftevent observed in the catalytic assays
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the rate-constant defining Dpo4-catalyzed incorporation of dCTP is about 6-fold slower for incorporation opposite O6-MeG relative to G. The basis for the decreased rate is revealed by the crystal structure to be formation of a wobble base pairing between O6-MeG and C
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme shows a limited decrease in catalytic efficiency (kcat/Km) for insertion of dCTP opposite a series of N2-alkylguanine templates of increasing size from (methyl (Me) to (9-anthracenyl)-Me (Anth)). Fidelity is maintained with increasing size up to (2-naphthyl)-Me (Naph). The catalytic efficiency increases slightly going from the N2-NaphG to the N2-AnthG substrate, at the cost of fidelity. A set of oligonucleotides differing only in their N2-substitution at a single G site is used in this study with Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
modeling and molecular dynamics simulations for 2'-deoxy-8-[(1-methyl-6-phenyl-1H-imidazo[4,5-b]pyridin-2-yl)amino]guanosine suggest that the adduct would increase the infidelity of Dpo4 and hinder translocation by the enzyme
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme can efficiently incorporate nucleotides opposite 8-oxoG and extend from an 8-oxoG:C base pair with a mechanism similar to that observed for the replication of undamaged DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the fidelity of Dpo4 is in the range of 0.001-0.0001. The ground-state binding affinity of correct nucleotides is 10-50-fold weaker than those of replicative DNA polymerases. The affinity of incorrect nucleotides for Dpo4 is about 2-10-fold weaker than that of correct nucleotides. The mismatched dCTP has an affinity similar to that of the matched nucleotides when it is incorporated against a pyrimidine template base flanked by a 5'-template guanine. The mismatch incorporation rates, regardless of the 5'-template base, are about 2-3 orders of magnitude slower than the incorporation rates for matched nucleotides, which is the predominant contribution to the fidelity of Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
incorporated of 2-amino-3-methylimidazo[4,5-f]quinoline C8- and N2-dGuo adducts into the G1- and G3-positions of the NarI recognition sequence (5'-G1G2CG3CC-3'), which is a hotspot for arylamine modification. Replication of the C8-adduct at the G3-position results in two-base deletion, whereas error-free bypass and extension is observed at the G1-position. The N2-adduct is bypassed and extended when positioned at the G1-position, and the error-free product is observed. The N2-adduct at the G3-position is more blocking and is bypassed and extended only by Dpo4 to produce an errorfree product. The replication of the 2-amino-3-methylimidazo[4,5-f]quinoline-adducts of dGuo is strongly influenced by the local sequence and the regioisomer of the adduct
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
in addition to the correct insertion of dCTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme shows little decreases opposite N2-MeG, 13fold decrease opposite N2-BzG but 260-370fold decreases opposite O6-MeG, O6-BzG, and the abasic site site as compared to G. Dpo4 favored correct C insertion opposite opposite N2-MeG, opposite O6-MeG, opposite an abasic site site and oppositeN2-BzG. DNA polymerase Vent (exo-) from Thermococcus litoralis is as or more efficient as polymerase Dpo4 from Sulfolobus solfataricus in synthesis opposite O6-MeG and AP lesions, whereas DNA polymerase Dpo4 from Sulfolobus solfataricus is much or more efficient opposite N2-alkylGs than DNA polymerase Vent (exo-) from Thermococcus litoralis, irrespective of DNA-binding affinity. DNA polymerase Dpo4 strongly favors minor-groove N2-alkylG lesions over major-groove or noninstructive lesions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
ring-opening of the 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-8-hydroxypyrimido[1,2-a] purin-10(3H)-one adduct promotes error-free bypass by the Sulfolobus solfataricus DNA polymerase Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme bypasses Pt-GG DNA (1,2-intrastrand covalent linkage, cis-Pt-1,2-d(GpG)). This is a dynamic process, in which the lesion is converted from an open and angular conformation at the first insertion to a depressed and nearly parallel conformation at the subsequent reaction stages to fit into the active site of Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Dpo4 predominantly uses a template slippage deletion mechanism when replicating repetitive DNA sequences. Dpo4 stabilizes the skipped template base in an extrahelical conformation between the polymerase and the little-finger domains of the enzyme
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
low fidelity. When copying undamaged DNA, Dpo4 is highly inaccurate for essentially all types of single base substitutions and deletions in a large number of different sequence contexts
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
DNA polymerase Dpo4 can replicate past a variety of DNA lesions. When replicating undamaged DNA, the enzyme is prone to make base pair substitutions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the rate of mismatched nucleotide incorporation is greater than the rate of correct dC insertion at 55 °C, whereas at 37 °C there is little selectivity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
while showing efficient bypass, the enzyme pauses when incorporating nucleotides directly opposite and one position downstream from an abasic lesion because of a drop of several orders of magnitude in catalytic efficiency. Biphasic kinetics for incorporation indicating that Dpo4 primarily forms a nonproductive complex with DNA that converts slowly to a productive complex. These strong pause sites are mutational hot spots with the embedded lesion even affecting the efficiency of five to six downstream incorporations
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the initial enzyme/DNA/dNTP complex undergoes a rapid (18/s), reversible (21/s) conformational change, followed by relatively rapid phosphodiester bond formation (11/s) and then fast release of pyrophosphate, followed by a rate-limiting relaxation of the active conformation (2/s) and then rapid DNA release, yielding an overall steady-state kcat of less than 1/s
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme is able to bypass N-(deoxyguanosin-8-yl)-1-aminopyrene, but pauses strongly at two sites: opposite the lesion and immediately downstream from the lesion. Both nucleotide incorporation efficiency and fidelity decrease significantly at the pause sites, especially during extension of the bypass product. Interestingly, a 4-fold tighter inding affinity of damaged DNA to Dpo4 DNA polymerase promotes catalysis through putative interactions between the active site residues of Dpo4 and 1-aminopyrene moiety at the first pause site
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
mechanism of template-independent nucleotide incorporation. Based on the efficiency ratios, Dpo4 selects nucleotides for blunt-end addition in the order of decreasing efficiency: dATP, dTTP, dCTP, dGTP, with dATP favored by five to 50fold over the other nucleotides. The first bluntend dATP incorporation is 80fold more efficient than the second, and among natural deoxynucleotides, dATP is the preferred substrate due to its stronger intrahelical base-stacking ability
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme is inefficient at extending mispairs opposite a template G or T, which include, a G*T mispair expected to conform closely to Watson-Crick geometry. It is hindered in extending a G*T mismatch by a reverse wobble
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the conformational dynamics of the Y-family DNA polymerase Dpo4 on DNA is characterized in real time using single-molecule Förster resonance energy transfers (mFRET). Two different binary complexes consistent with DNA translocation in the polymerase active site
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
even at 60°C, excessive amounts of Dpo4 are needed to carry out minimal bypass of the cyclobutane pyrimidine dimers
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme inefficiently bypasses (5'S)-8,5'-cyclo-2'-deoxyguanosine with dCTP preferably incorporated and dTTP misincorporated. The (5'S)-8,5'-cyclo-2'-Deoxyguanosine-adduct-duplex complex causes 6fold decrease in Dpo4:DNA binding affinity, and significantly reduces the concentration of the productive Dpo4:DNA:dCTP complex
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity, identical to RTHI nuclease
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
template specificity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
role in non-homologous end joining of double strand breaks, perhaps including those with damaged ends, possible role for pol IV in base excision repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the enzyme has intrinsic 5'-2-deoxyribose-5-phosphate lyase activity. Pol IV has low processivity and can fill short gaps in DNA. The gap-filling activity of pol IV is not enhanced by a 5'-phosphate on the downstream primer but is stimulated by a 5'-terminal synthetic abasic site. Pol IV incorporates rNTPs into DNA with high efficiency relative to dNTPs. Pol IV is highly inaccurate, with an unusual error specificity indicating the ability to extend primer termini with limited homology
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
double-stranded DNA property of DNA polymerase epsilon is required for epigenetic silencing at telomeres
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Salasvirus phi29
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Salasvirus phi29
-
enzyme has two exonuclease 3'--5' degradative activities: an exonuclease activity and an inorganic diphosphate-dependent degradative activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Salasvirus phi29
-
44kDa C-terminal fragment has no exonuclease activity, reduced efficiency with Mn2+ and reduced capacity to initiate terminal protein-primed DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Salasvirus phi29
-
Phi29 DNA polymerase belongs to the family B DNA polymerases able to start replication by protein-priming
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Salasvirus phi29
-
phi29 DNA polymerase accomplishes sequential template-directed addition of dNMP units onto the 3'-OH group of a growing DNA chain, in addition phi29 DNApol catalyses 3'-5' exonucleolysis, that is, the release of dNMP units from the 3' end of a DNA strand
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 5'--3' activity, pol I
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the flexibility on the template side of the Dbh active site allows for a consistent location of the incoming dNTP regardless of whether or not it is correctly paired with its templating partner. Contact of the dNTP sugar with the Phe12 steric gate side chain is maintained in all circumstances with the result that Dbh shows stringent discrimination against ribonucleotides but does not use the steric gate side chain as a discriminator against nascent mispairs
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
at optimal temperature (70-75°C) a singly primed, single-stranded recombinant phage M13 DNA is efficiently replicated in ten min using a ratio of enzyme molecule to primed-template of 0.8
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the activated herring sperm DNA is an optimal template and gives 3times higher activity than that obtained with poly(dA)/oligo(dT). The DNA polymerase can not use templates without primer (poly(dA) and poly(dT)), even when appropriate priming ribonucleotides (UTP or ATP, respectively) are supplied. It does not accept a polyribonucleotide template (poly(rA):oligo(dT))
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
DNA polymerase Dpo4 can replicate past a variety of DNA lesions. When replicating undamaged DNA, the enzyme is prone to make base pair substitutions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
most of the dNTP analogs with modified sugar moiety tested are shown to be specific terminating substrates for the synthesis irreversibly blocking further elongation of a nascent chain. The most powerful inhibitors are the 3'-amino derivatives of deoxy and arabino nucleoside triphosphates, while specific reverse transcriptase inhibitors, 3'-azido and 3'-methoxy derivatives of dNTP, were found to be inactive
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the activated herring sperm DNA is an optimal template and gives 3times higher activity than that obtained with poly(dA)/oligo(dT). The DNA polymerase can not use templates without primer (poly(dA) and poly(dT)), even when appropriate priming ribonucleotides (UTP or ATP, respectively) are supplied. It does not accept a polyribonucleotide template (poly(rA):oligo(dT))
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
DNA polymerase Dpo4 can replicate past a variety of DNA lesions. When replicating undamaged DNA, the enzyme is prone to make base pair substitutions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
calf thymus DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
nicked duplex is no substrate of phage T4-induced DNA polymerase
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
template specificity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
preferentially removes purines opposite an abasic site
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
exonuclease 3'--5' activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
exonuclease activity utilizes both, ssDNA and melted dsDNA templates, mismatched basepair is preferred over a correct basepair, removes an incorrect base incorporated opposite a template lesion
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
exonuclease 3'--5', phage T4-induced DNA polymerase
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
exonuclease 3'--5', phage T4-induced DNA polymerase
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
primed single strands
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
exonuclease activity contributes to the avoidance of alkylation mutations
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
phage T4 DNA polymerase is essential for initiation and maintenance of viral DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
bacteriohage T4 and bacteriophage RB69 replicative DNA polymerases exhibit differing abilities to form various base pairs. Formation of Watson-Crick base pairs occurs at similar rates between the two proteins but the incoming nucleotides are bound less tightly by RB69 DNA polymerase. Incorporation of an A opposite furan by T4 DNA polymerase is more rapid than for RB69 DNA polymerase with the two proteins having similar binding constants for the incoming dATP. An A:C mismatch is formed almost equally well by both proteins, while a significant difference exists when a T:T mismatch is formed
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequatrovirus T4
-
T4 DNA polymerase can remove two incorrect nucleotides under single turnover conditions, which includes presumed exonuclease-to-polymerase and polymerase-to-exonuclease active site switching steps and proofreading reactions that initiate in the polymerase active center are not intrinsically processive
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequintavirus T5
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequintavirus T5
-
exonuclease 3'--5' and 5'--3' activity activity, phage T5-induced DNA polymerase
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequintavirus T5
-
phage T5-induced DNA polymerase
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Tequintavirus T5
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
Testudines agrionemys
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
PI-TfuI recognizes a minimal sequence of 16 base pairs, PI-TfuII requires a sequence of 21 base pairs, both enzymes have endonuclease activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
the DNA polymerase also shows 3'-5' exonuclease activity. The 3'5' exonuclease activity of the DNA polymerase is important for DNA elongation with high fidelity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the enzyme readily bypasses N2-methyl(Me)G and O6-MeG, but is strongly blocked at O6-benzyl(Bz)G and N2-BzG. the enzyme shows 110-, 180-, and 300fold decreases in catalytic efficiency (kcat/Km) for nucleotide insertion opposite an abasicP site, N2-MeG, and O6-MeG but 1800- and 5000fold decreases opposite O6-BzG and N2-BzG, respectively, as compared to G. DNA polymerase Vent (exo-) from Thermococcus litoralis is as or more efficient as polymerase Dpo4 from Sulfolobus solfataricus in synthesis opposite O6-MeG and AP lesions, whereas DNA polymerase Dpo4 from Sulfolobus solfataricus is much or more efficient opposite N2-alkylGs than DNA polymerase Vent (exo-) from Thermococcus litoralis, irrespective of DNA-binding affinity. DNA polymerase Vent (exo-) accepts nonbulky DNA lesions (e.g., N2- or O6-MeG and an AP site) as manageable substrates despite causing errorprone synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
wild-type enzyme, but not the truncated form has exonuclease 5'--3' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 5'--3' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
no exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exonuclease 5'--3' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
no exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
enzyme also has RNAse H/exonuclease 5'--3' activity, enzyme prefers RNA/DNA substrate over DNA/DNA duplex
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
several dTTP analoges bearing a photoreactive 2-nitro-5-azidobenzoyl group attached at position 5 of uracil through linkers of various lengths, are substrates in the elongation reaction of the 5'-32P-labeled primer-template complex. The incorporation of the analogs into the 3' primer end did not impede further elongation of the chain in the presence of natural dNTP
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
in the presence of Mg2+ or Mn2+, the POLX catalytic domain inserts dIMP, IMP and 8-oxo-dGMP opposite deoxycytosine as well as dGMP and GMP, PolX likely prefers deoxyguanine to deoxythymidine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
DNA-dependent DNA polymerase activity to incorporate dNTP into gapped M13mp2 DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
several dTTP analoges bearing a photoreactive 2-nitro-5-azidobenzoyl group attached at position 5 of uracil through linkers of various lengths, are substrates in the elongation reaction of the 5'-32P-labeled primer-template complex. The incorporation of the analogs into the 3' primer end did not impede further elongation of the chain in the presence of natural dNTP
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
in the presence of Mg2+ or Mn2+, the POLX catalytic domain inserts dIMP, IMP and 8-oxo-dGMP opposite deoxycytosine as well as dGMP and GMP, PolX likely prefers deoxyguanine to deoxythymidine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
DNA-dependent DNA polymerase activity to incorporate dNTP into gapped M13mp2 DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
overview: physiological roles in replication and in DNA repair synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
template specificity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
dGTP + DNAn
?
-
-
-
-
?
dGTP + DNAn
?
-
Dbh is a distributive enzyme showing a low DNA and nucleotide binding affinity along with a slow polymerization rate. DNA binding occurs in a single step, diffusion-controlled manner. The rate-limiting step of nucleotide incorporation (correct and incorrect) is the chemical step (phosphoryl transfer) and not a conformational change of the enzyme. An induced fit mechanism to select and incorporate nucleotides during DNA polymerization can not be detected for the enzyme
-
-
?
dGTP + DNAn
?
in addition to the correct insertion of dGTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dGTP + DNAn
?
in addition to the correct insertion of dGTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dGTP + DNAn
diphosphate + DNAn+1
-
systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
-
-
?
dGTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dGTP + DNAn
diphosphate + DNAn+1
-
-
-
?
dGTP + DNAn
diphosphate + DNAn+1
-
with activated calf thymus DNA
-
-
?
dGTP + DNAn
diphosphate + DNAn+1
-
dNTP insertion opposite a benzo[a]pyrene-N2-dG-adduct
-
-
?
dGTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
DNA 21/41-mer + dTTP
? + diphosphate
kinetic mechanism for DNA polymerization is proposed, the enzyme utilizes an induced-fit mechanism to select correct incoming nucleotides
-
-
?
DNA 21/41-mer + dTTP
? + diphosphate
kinetic mechanism for DNA polymerization is proposed, the enzyme utilizes an induced-fit mechanism to select correct incoming nucleotides
-
-
?
dNTP + DNAn
diphosphate + DNAn+1
-
-
-
?
dNTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dTTP + DNAn
?
-
-
-
-
?
dTTP + DNAn
?
-
Dbh is a distributive enzyme showing a low DNA and nucleotide binding affinity along with a slow polymerization rate. DNA binding occurs in a single step, diffusion-controlled manner. The rate-limiting step of nucleotide incorporation (correct and incorrect) is the chemical step (phosphoryl transfer) and not a conformational change of the enzyme. An induced fit mechanism to select and incorporate nucleotides during DNA polymerization can not be detected for the enzyme
-
-
?
dTTP + DNAn
?
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
dTTP + DNAn
?
dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
-
-
?
dTTP + DNAn
?
in addition to the correct insertion of dTTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dTTP + DNAn
?
in addition to the correct insertion of dTTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dTTP + DNAn
?
dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
-
-
?
dTTP + DNAn
?
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2-deoxyribofuranosid-5-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
dTTP + DNAn
?
-
activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16-fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
-
-
?
dTTP + DNAn
?
-
activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16-fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
systematic determination of the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
with labeled 20/33-mer primer-template duplex DNA
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
activity assay with plus-strand m13 DNA annealed to 5'-32P end-labeled primer 5'-GCTGTTGGGAAGGGCGATCG-3'
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
with activated calf thymus DNA
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
dNTP insertion opposite a benzo[a]pyrene-N2-dG-adduct
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
incorporation of dTTP into poly(rA)-p(dT)45
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
incorporation of dTTP into poly(rA)-p(dT)45
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
incorporation of dTTP into poly(rA)-p(dT)45
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
incorporation of dTTP into poly(rA)-p(dT)45
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
-
-
-
?
N1-methyl-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + ?
-
-
-
?
N1-methyl-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + ?
-
-
-
?
North-methanocarba-dATP + DNAn
?
the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme preferentially inserts North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker compared to a South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
-
-
?
North-methanocarba-dATP + DNAn
?
the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme relatively tolerant to the substrate conformation: North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker or South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
-
-
?
North-methanocarba-dATP + DNAn
?
the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme relatively tolerant to the substrate conformation: North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker or South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
-
-
?
North-methanocarba-dATP + DNAn
?
the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme preferentially inserts North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker compared to a South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
-
-
?
South-methanocarba-dATP + DNAn
?
the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme relatively tolerant to the substrate conformation: North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker or South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
-
-
?
South-methanocarba-dATP + DNAn
?
the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme relatively tolerant to the substrate conformation: North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker or South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
-
-
?
additional information
?
-
the enzyme also displays 3'5'-exonuclease activity
-
-
?
additional information
?
-
-
the R2 polymerase can utilize both RNA and DNA templates, but the processivity of the enzyme on single stranded DNA templates is higher than its processivity on RNA templates, R2-RT is also capable of synthesizing the second DNA strand during retrotransposition
-
-
?
additional information
?
-
single-strand-dependent and double-strand-dependent 3'-5' exonuclease activity and marginal 5'-3' exonuclease activity
-
-
?
additional information
?
-
-
Pol beta does incorporate size augmented thymidine analogues besides the unmodified TTP
-
-
?
additional information
?
-
-
small 4'-methyl and -ethyl modifications of the nucleoside triphosphate do not perturb Klenow fragment catalysis
-
-
?
additional information
?
-
-
PolH can be up-regulated by DNA breaks induced by ionizing radiation or chemotherapeutic agents, and knockdown of PolH gives cells resistance to apoptosis induced by DNA breaks in multiple cell lines and cell types in a p53-dependent manner. PolH has a role in the DNA damage checkpoint. POlH is target of p53
-
-
?
additional information
?
-
modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase
-
-
?
additional information
?
-
-
all pols exclusively promote misincorporation of dCMP opposite a 2'-deoxyinosine lesion during translesion synthesis, isozymes pol alpha, pol eta, and pol kappaDELTAC promote preferential incorporation of 2'-deoxycytidine monophosphate , the wrong base, opposite a 2'-deoxyinosine lesion, no incorporation of 2'-deoxythymidine monophosphate, the correct base, is observed opposite the lesion
-
-
?
additional information
?
-
-
(2R,4R)-4-(2-amino-6-oxo-9H-purin-9-yl)-1,3-dioxolan-2-yl-methanol triphosphate and 2',3'-dideoxy-2',3'-didehydroguanoside triphosphate, and carbovir triphosphate are much less efficiently incorporated than the natural deoxynucleoside triphosphate dGTP
-
-
?
additional information
?
-
-
Pol beta does not incorporate size augmented thymidine analogues, while the unmodified TTP is processed
-
-
?
additional information
?
-
-
the excision of the matched 3'-monophosphorylated form of 2'-deoxy-2',2'-difluorocytidine moiety by the wild type pol gamma is 55fold slower than the excision of matched 3'-dCMP
-
-
?
additional information
?
-
-
while small 4'-methyl and -ethyl modifications of the nucleoside triphosphate perturb Pol beta catalysis, extension of modified primer strands is only marginally affected
-
-
?
additional information
?
-
-
comparing RNA primer-templates and DNA primer templates of identical sequence show that herpes polymerase greatly prefers to elongate the DNA primer by 650-26000fold, thus accounting for the extremely low efficiency with which herpes polymerase elongates primase-synthesized primers
-
-
?
additional information
?
-
-
Neq L and Neq S are needed to form the active DNA polymerase that possesses higher proofreading activity. The genetically protein splicing-processed Neq P shows the same properties as the protein trans-spliced Neq C
-
-
?
additional information
?
-
-
the enzyme is responsible for mutagenesis, e.g. UV-induced, in human host cells of lungs of cystic fibrosis patients contributing to morbidity and mortality of these people, with a striking correlation between mutagenesis and the persistence of Pseudomonas aeruginosa, mechanisms of mutagenesis, enzyme regulation, overview, the enzyme is responsible for resistance to to nitrofurazone and 4-nitroquinoline-1-oxide toxification
-
-
?
additional information
?
-
-
DNA synthesis on M13Gori single-stranded phage DNA as template DNA
-
-
?
additional information
?
-
-
the enzyme causes 1-bp deletions and different base substitutions in plasmids pKTpheA56+A and pKTpheA22TAG, pKTpheA22TAA, and pKTpheA22TGA, respectively, in stationary cells, overview, Pol IV-dependent mutagenesis causes an approximately 10fold increase in the frequency of accumulation of 1-bp deletion mutations on selective plates in wild-type populations starved for more than 1 week, development of a mutant detection assay system allowing to separately detect the mutants, no effect of Pol IV on the frequency of accumulation of base substitution mutations in starving cells is observed, overview, RecA independence of Pol IV-associated mutagenesis mechanisms different from the classical RecA-dependent SOS response can elevate Pol IV-dependent mutagenesis in starving cells, overview
-
-
?
additional information
?
-
-
DNA polymerase switching mechanism by which PabPol B displaces PabPol D from proliferating cell nuclear antigen on the DNA duplex
-
-
?
additional information
?
-
primer ssM13 DNA is the preferred substrate
-
-
?
additional information
?
-
primer ssM13 DNA is the preferred substrate
-
-
?
additional information
?
-
-
DNA polymerases PolB and PolD slip in vitro on a template that consists of single-stranded DNA (ssDNA) with a hairpin structure flanked by short direct repeats. Pyrococcus abyssi proliferating cell nuclear antigen increases replication fidelity of this template
-
-
?
additional information
?
-
-
DNA polymerase switching mechanism by which PabPol B displaces PabPol D from proliferating cell nuclear antigen on the DNA duplex
-
-
?
additional information
?
-
-
polymerase binds DNA containing uracil 1.54.5-fold more strongly than hypoxanthine
-
-
?
additional information
?
-
the enzyme has strong 3'->5' exonucleolytic activity and has a template-primer preference which is characteristic of a replicative DNA polymerase
-
-
?
additional information
?
-
-
the enzyme has strong 3'->5' exonucleolytic activity and has a template-primer preference which is characteristic of a replicative DNA polymerase
-
-
?
additional information
?
-
FEN-1 has both 5'-flap endonuclease and 5'3' exonuclease activities, FEN-1 activity is elevated by the presence of a 1 nucleotide expansion at the 3' end in the upstream primer of substrates called: structures with a 1 nt 3'-flap, which appear to be the most preferable substrates for FEN-1. Serial intermediates with a 1 nt 3'-flap and 5' variable-length flaps are formed by cooperative functioning of Pyrococcus horikoshii FEN-1 with either B or D DNA polymerases
-
-
?
additional information
?
-
-
FEN-1 has both 5'-flap endonuclease and 5'3' exonuclease activities, FEN-1 activity is elevated by the presence of a 1 nucleotide expansion at the 3' end in the upstream primer of substrates called: structures with a 1 nt 3'-flap, which appear to be the most preferable substrates for FEN-1. Serial intermediates with a 1 nt 3'-flap and 5' variable-length flaps are formed by cooperative functioning of Pyrococcus horikoshii FEN-1 with either B or D DNA polymerases
-
-
?
additional information
?
-
FEN-1 has both 5'-flap endonuclease and 5'3' exonuclease activities, FEN-1 activity is elevated by the presence of a 1 nucleotide expansion at the 3' end in the upstream primer of substrates called: structures with a 1 nt 3'-flap, which appear to be the most preferable substrates for FEN-1. Serial intermediates with a 1 nt 3'-flap and 5' variable-length flaps are formed by cooperative functioning of Pyrococcus horikoshii FEN-1 with either B or D DNA polymerases
-
-
?
additional information
?
-
-
at low pH the chemical step is rate limiting for catalysis, but at high pH, a postchemistry conformational step is rate limiting due to a pH-dependent increase in the rate of nucleotidyl transfer
-
-
?
additional information
?
-
-
lesion-bypass DNA polymerase
-
-
?
additional information
?
-
replication cycle of Dpo4, and induced fit and translocation mechanisms, overview
-
-
?
additional information
?
-
-
replication cycle of Dpo4, and induced fit and translocation mechanisms, overview
-
-
?
additional information
?
-
-
the widely used anticancer drug, cis-diamminedichloroplatinum(II), i.e. cisplatin, reacts with adjacent purine bases in DNA to form predominantly cis-[Pt(NH3)2(d(GpG)-N7(1),-N7(2))] intrastrand cross-links, DNA polymerase IV is able to perform translesion synthesis in the presence of DNA-distorting damage such as cisplatin-DNA adducts, overview
-
-
?
additional information
?
-
Dpo4 produces mismatch and frameshift mutations at benzo[a]pyrene-derived lesions, overview
-
-
?
additional information
?
-
-
Dpo4 produces mismatch and frameshift mutations at benzo[a]pyrene-derived lesions, overview
-
-
?
additional information
?
-
-
Dpo4 utilizes an induced-fit mechanism to select correct incoming nucleotides at 37°C, overview
-
-
?
additional information
?
-
-
potential structures of purine-purine base pairs, overview
-
-
?
additional information
?
-
significant preferential dATP insertion, dATP can be misincorporated opposite the benzo[a]pyrene-derived N2-dG adduct, standing-start single-nucleotide insertion assays, overview
-
-
?
additional information
?
-
-
significant preferential dATP insertion, dATP can be misincorporated opposite the benzo[a]pyrene-derived N2-dG adduct, standing-start single-nucleotide insertion assays, overview
-
-
?
additional information
?
-
-
simulation model of the solvated Dpo4/DNA/8-oxoG:dCTP complex, catalytic site structure, overview
-
-
?
additional information
?
-
Dpo3 has an active exonuclease proofreading domain, it shows intrinsic exonuclease activity
-
-
?
additional information
?
-
-
Dpo3 has an active exonuclease proofreading domain, it shows intrinsic exonuclease activity
-
-
?
additional information
?
-
-
simulations, based on crystal complexes of Dpo4 are performed, exploring possible transitions and mechanisms associated with Dpo4s catalytic cycle. Dynamics simulations before the nucleotidyl-transfer reaction and simulations after the reaction are performed. Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV may accommodate lesion bypass
-
-
?
additional information
?
-
-
the DNA lesion bypass polymerase can bind up to eight base pairs of double-stranded DNA which is entirely in B-type. Thus, the DNA binding cleft of Dpo4 is flexible and can accommodate both A- and B-type oligodeoxyribonucleotide duplexes as well as damaged DNA
-
-
?
additional information
?
-
-
the DNA lesion bypass polymerase can bind up to eight base pairs of double-stranded DNA which is entirely in B-type. Thus, the DNA binding cleft of Dpo4 is flexible and can accommodate both A- and B-type oligodeoxyribonucleotide duplexes as well as damaged DNA
-
-
?
additional information
?
-
-
simulations, based on crystal complexes of Dpo4 are performed, exploring possible transitions and mechanisms associated with Dpo4s catalytic cycle. Dynamics simulations before the nucleotidyl-transfer reaction and simulations after the reaction are performed. Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV may accommodate lesion bypass
-
-
?
additional information
?
-
Dpo3 has an active exonuclease proofreading domain, it shows intrinsic exonuclease activity
-
-
?
additional information
?
-
Szi DNA polymerase possesses associated 3'-5' and 5'-3' exonuclease activities
-
-
?
additional information
?
-
the E664 residue (located in thumb domain) acts as a steric gate, which is involved in recognition of the DNA substrate by the enzyme
-
-
?
additional information
?
-
the DNA polymerase gene of Thermococcus marinus contains an intein inserted at the pol-b site
-
-
?
additional information
?
-
-
the DNA polymerase possesses a 3'->5' exonuclease activity
-
-
?
additional information
?
-
-
the DNA polymerase possesses a 3'->5' exonuclease activity
-
-
?
additional information
?
-
the enzyme also posseses 3'->5' exonuclease activity
-
-
?
additional information
?
-
the enzyme also posseses 3'->5' exonuclease activity
-
-
?
additional information
?
-
-
a 3'->5' exonuclease activity is associated with the purified DNA polymerase
-
-
?
additional information
?
-
DNA-dependent DNA polymerase commonly accepts DNA and dNTP and excludes RNA and rNTP, but some enzyme mutants also show RNA-dependent DNA polymerase activity as reverse transcriptases, overview. Reverse transcriptase is the enzyme that catalyzes DNA polymerization using RNA as a template, i.e. RNA-dependent DNA polymerase, see for EC 2.7.7.49
-
-
?
additional information
?
-
-
only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, EC 2.7..7.49
-
-
?
additional information
?
-
-
only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, no activity with the wild-type enzyme
-
-
?
additional information
?
-
-
only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, EC 2.7..7.49
-
-
?
additional information
?
-
-
only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, no activity with the wild-type enzyme
-
-
?
additional information
?
-
DNA-dependent DNA polymerase commonly accepts DNA and dNTP and excludes RNA and rNTP, but some enzyme mutants also show RNA-dependent DNA polymerase activity as reverse transcriptases, overview. Reverse transcriptase is the enzyme that catalyzes DNA polymerization using RNA as a template, i.e. RNA-dependent DNA polymerase, see for EC 2.7.7.49
-
-
?
additional information
?
-
-
DNA-dependent DNA polymerase commonly accepts DNA and dNTP and excludes RNA and rNTP, but some enzyme mutants also show RNA-dependent DNA polymerase activity as reverse transcriptases, overview. Reverse transcriptase is the enzyme that catalyzes DNA polymerization using RNA as a template, i.e. RNA-dependent DNA polymerase, see for EC 2.7.7.49
-
-
?
additional information
?
-
-
the mutant enzyme shows single deoxynucleotide additions with dCTP, dATP and dTTP, but not with dGTP as it results in addition of two successive base incorporations on the chosen template 2 hybridised to the DNA primer 1, thereby invalidating the single-turnover kinetic model, Michaelis-Menten mechanism, overview
-
-
?
additional information
?
-
-
the catalytic efficiency of PolX is almost the same with and without dNTPs, whereas that of the domain mixture increases on the addition of dNTPs
-
-
?
additional information
?
-
-
the catalytic efficiency of PolX is almost the same with and without dNTPs, whereas that of the domain mixture increases on the addition of dNTPs
-
-
?
additional information
?
-
-
the enzyme is unable to use single stranded DNA or double stranded blunt end DNA
-
-
?
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(2E)-2-(3-nitro-4-[[6-(trifluoromethyl)pyridin-3-yl]sulfanyl]benzylidene)-5-thioxo-1,3-thiazolidin-4-one
-
-
(2E)-2-(4-chloro-3-ethylbenzylidene)-5-thioxo-1,3-thiazolidin-4-one
-
-
(2E)-2-(pentafluorobenzylidene)-5-thioxodihydrothiophen-3(2H)-one
-
-
(2E)-2-[4-(2-hydroxyethyl)-3-nitrobenzylidene]-5-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-(4-chloro-3-nitrobenzylidene)-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[3-bromo-4-[(4-fluorobenzyl)oxy]benzylidene]-1,3-thiazolidine-2,4-dione
-
-
(5Z)-5-[3-bromo-4-[(4-fluorophenyl)sulfanyl]benzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[3-nitro-4-(pyridin-3-ylsulfanyl)benzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-(4-methylphenoxy)-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-(cyclohexylsulfanyl)-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-bromophenyl)sulfanyl]-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-chlorophenyl)sulfanyl]-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-fluorobenzyl)oxy]-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-fluorobenzyl)oxy]benzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-methylphenyl)sulfanyl]-3-nitrobenzylidene]-3-(prop-2-en-1-yl)-2-thioxo-1,3-thiazolidin-4-one
-
-
(9-adenylmethylcarbonyl)-4-aminobutyl triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A
(biphenylcarbonyl)-4-oxobutyl triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A; inhibits wild-type enzyme and mutant enzyme Y505A
(NH4)2SO4
-
optimal concentration of 20 mM, inhibition below and above 20 mM
1,2,3,4-tetrahydro-5-methoxynaphthalene-1,4-diol
-
i.e. nodulisporol. Strong inhibition of pol lambda, but does not influence the activities of mammalian pols alpha to kappa, and shows no effect on the activities of plant pols alpha and beta, prokaryotic pols, and other DNA metabolic enzymes such as calf terminal deoxynucleotidyl transferase, human immunodeficiency virus type-1 (HIV-1) reverse transcriptase, human telomerase, T7 RNA polymerase, and bovine deoxyribonuclease I
1,3-bis[2-chloroethyl]-2-nitrosourea
-
-
16-oxoaphidicholin
Tequatrovirus T4
-
-
2',3'-dideoxy-ATP
-
poor inhibitor
2',3'-dideoxyribosylthymine triphosphate
2',3'-dideoxythymidine 5'-triphosphate
2-(4-azidophenacyl)thio-2'-deoxyadenosine 5'-triphosphate
-
template-competitive DNA polymerase inhibitor
-
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
2-butylanilino-dATP
-
potent and highly selective inhibitor
2-methoxy-4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl 2,4-dichlorobenzoate
-
-
2-methoxy-4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl 3-bromobenzoate
-
-
2-thiomethyl-6-phenyl-4-(4'-hydroxybutyl)-1,2,4,-triazole (5,1-C)(1,2,4)triazine-7-one triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP; fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A
3'-azido-2',3'-dideoxythymidine 5'-phosphate
-
50% inhibition at 0.22 mM
3'-azido-2',3'-dideoxythymidine triphosphate
-
-
3,4-dihydro-4-hydroxy-8-methoxynaphthalen-1(2H)-one
-
i.e. nodulisporone. Strong inhibition of pol lambda, but does not influence the activities of mammalian pols alpha to kappa, and shows no effect on the activities of plant pols alpha and beta, prokaryotic pols, and other DNA metabolic enzymes such as calf terminal deoxynucleotidyl transferase, human immunodeficiency virus type-1 (HIV-1) reverse transcriptase, human telomerase, T7 RNA polymerase, and bovine deoxyribonuclease I
3,5-dimethyl-8-methoxy-3,4-dihydroisocoumarin
-
-
3-(2'-deoxy-beta-D-erythro-pentofuranosyl) pyrimido[1,2-alpha]purin-10(3H)-one
-
i.e. M1dG. When paired opposite cytosine in duplex DNA at physiological pH,M1dG undergoes ring opening to form N2-(3-oxo-1-propenyl)-dG. To improve the understanding of the basis for M1dG-induced mutagenesis, the mechanism of translesion DNA synthesis opposite M1dG by the model Y-family polymerase Dpo4 is studied at a molecular level using kinetic and structural approaches. Steady-state and transient-state kinetic results both indicate that Dpo4 catalysis is inhibited by M1dG (260-2900-fold), with dATP being the favored insertion event for both sequences tested
3-epiaphidicholine
Tequatrovirus T4
-
-
35dd(G) DNA
-
competitive inhibition
-
4-chloromercuribenzoic acid
4-chlorophenyl 2,4-dinitrophenyl sulfide
-
-
4-hydroxy-5-methyl-3-tetradecyl-dihydrofuran-2(3H)-one
-
-
4-hydroxymercuribenzoate
Tequatrovirus T4
-
95% inhibition at 0.4 mM
4-oxo-dihydroquinoline
-
binds at the polymerase active site interacting non-covalently with both the polymerase and the DNA duplex
4-[(4-methylphenyl)sulfanyl]-3-nitrobenzaldehyde
-
-
4-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]-2-methoxyphenyl 3-bromobenzoate
-
-
4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl 2-chlorobenzoate
-
-
5-(5-nitro-2-[[6-(trifluoromethyl)pyridin-3-yl]sulfanyl]benzylidene)-2-thioxo-1,3-thiazolidin-4-one
-
-
5-[2-(cyclohexylsulfanyl)-5-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
5-[2-[(4-chlorophenyl)sulfanyl]-5-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
5-[2-[(4-methylphenyl)sulfanyl]-5-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
6-chloro-1,4-dihydro-4-oxo-1-(beta-D-ribofuranosyl) quinoline-3-carboxylic acid
-
noncompetitive inhibitor
6-chloro-1,4-dihydro-4-oxo-1H-quinoline-3-carboxylic acid
-
-
acrolein
-
irreversible inhibition
acyclovir triphosphate
-
-
alpha-(4-azidophenyl)-1,N6-etheno-dATP
-
template-competitive DNA polymerase inhibitor
alpha-Amanitin
Ruellia sp.
-
88% inhibition at 0.2 mg/ml
ammonium-21-tungsto-9-antimoniate
-
HPA-23, antiviral drug, noncompetitive to TTP, activated DNA, poly(rA)-oligo(dT), wheat germ DNA polymerase A, a gamma-like DNA polymerase
-
aptamer
-
nucleotide ligands of small size and unique three-dimensional structure, TQ21 family, presence of loop is necessary for inhibition
-
Arabinofuranosylnucleoside triphosphates
-
and related compounds
aurintricarboxylic acid
-
potent nanomolar inhibitor of pol beta, pol iota, and pol zeta
Benzyloxycarbonyl-Leu-Leu-al
cerebroside sulfate ester
-
inhibition of polymerase alpha and gamma
cholesterol hemisuccinate
cis-syn thymine dimer
Dpo4 is severely blocked by the presence of a cis-syn thymine dimer in the template
cloretazine
-
i.e. 1,2-bis[methylsulfonyl]-1-[2-chloroethyl]-2-[(methylamino)carbonyl]hydrazine
corylifolin
Betapolyomavirus macacae
-
isolated from Psoralea corylifolia
coumermycin A
-
50% inhibition at 0.05 mM
daidzein
Betapolyomavirus macacae
-
isolated from Psoralea corylifolia, slight inhibition
dATP
-
using dATP as an inhibitor and dCTP as a varied substrate, the pattern of inhibition is competitive
deoxynucleoside triphosphate
-
work as competitive inhibitors depending on their incorporation sites, A-incorporation is strongly inhibited by dTTP and dGTP, T-incorporation is inhibited by dATP, G-and C-incorporation sites are less sensitive to competitive inhibition
Dideoxyadenosine triphosphate
-
weak inhibitor
dideoxyguanosine triphosphate
-
-
Dideoxynucleoside 5'-triphosphate
Dideoxythymidine triphosphate
ellagic acid
-
potent nanomolar inhibitor of pol beta, pol iota, and pol zeta
epigallocatechin gallate
-
-
flavonoids
Ruellia sp.
-
substitution of hydroxyl groups with glycosides
gemcitabine
-
i.e. 2'-deoxy-2',2'-difluorocytidine, when gemcitabine is encountered as a template base DNA polymerase gamma pauses at the lesion and one downstream position but eventually elongates the primer to full-length product, these pauses are because of a 1000fold decrease in nucleotide incorporation efficiency
glycolipids
-
sulfate- and sialic acid-containing
-
hydroxyphenylazouracil
-
inhibits only polymerase III
hymenoic acid
-
specific inhibitor of human DNA polymerase lambda, non-competitive inhibition with respect to both the DNA template-primer and the dNTP, i.e trans-4-[(1'E,5'S)-5'-carboxy-1'-methyl-1'-hexenyl]cyclohexanecarboxylic acid, does not influence the activities of the other mammalian pols alpha, gamma, delta, epsilon, eta, iota, and kappa, and also shows no effect even on the activity of pol beta
hypoxanthine
-
traces of uracil and hypoxanthine in DNA can lead to inhibition of the polymerase chain reaction by archaeal DNA polymerases
iodoacetate
-
DNA polymerase beta
N-(2,4-dinitro-5-fluorophenyl)-2-aminoethyl triphosphate
-
inhibition of mutant enzyme Y505A, inactive against wild-type enzyme
N-(2,4-dinitro-5-fluorophenyl)-4-aminobutyl triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A
N-(2,4-dinitro-5-imidazolylphenyl)-2-aminoethyl triphosphate
-
inhibition of mutant enzyme Y505A, inactive against wild-type enzyme
N-(2,4-dinitro-5-imidazolylphenyl)-4-aminobutyl triphosphate
-
inhibition of mutant enzyme Y505A, inactive against wild-type enzyme
N-(2,4-dinitrophenyl)-4-aminobutyl triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A
N-(benzyloxycarbonyl)-4-aminobutyl triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A; inhibits wild-type enzyme and mutant enzyme Y505A
N-[6-N-(2,4-dinitrophenyl)aminohexanoyl]-2-aminoethyl triphosphate
-
inhibition of mutant enzyme Y505A, inactive against wild-type enzyme
N2,N2-dimethyl guanine
the presence of N2,N2-dimethyl guanine lowers the catalytic efficiency for incorporation of dCTP of DNA polymerase Dpo4 16000fold
N2,N2-dimethylguanine
the presence of N2,N2-dimethylguanine lowers the catalytic efficiency of the DNA polymerase Dpo4 16000fold. Dpo4 inserts dNTPs almost at random during bypass of N2,N2-dimethylguanine, and much of the enzyme is kinetically trapped by an inactive ternary complex when N2,N2-dimethylguanine is present
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
N2-CH2(6-benzo[a]pyrenyl)guanine
-
severely blocks activity
N2-CH2(9-anthracenyl)guanine
-
severely blocks activity, frequencies of dATP misinsertion and extension beyond mispairs are proportionally increased, great decrease in pre-steady-state kinetic burst rate. 2.6fold decrease in dCTP binding affinity and increased DNA substrate binding affinity
neobavaisoflavone
Betapolyomavirus macacae
-
isolated from Psoralea corylifolia, inhibition at moderate to high concentrations
NSC-666715
potent, small molecular weight inhibitor of DNA polymerase beta, blocks Pol-beta-directed single-nucleotide- and long-patch-base excisison repair
pamoic acid
-
pol beta inhibitor
Phosphoformate
Herpes simplex virus
-
-
pyridoxal 5'-phosphate
-
50% inhibition at 0.48 mM
RecA
-
exonuclease activity of pol II can be inhibited by the presence of RecA protein and single-strand binding protein
-
Replication factor C
DNA polymerization by Dpo2 and Dpo3 is strongly inhibited; DNA polymerization by Dpo2 and Dpo3 is strongly inhibited
-
resveratrol
Betapolyomavirus macacae
-
isolated from Psoralea corylifolia
rhodanines
-
most potent inhibitors for DNA Pol lambda, they are up to 10times less active against the highly similar DNA polymerase beta, structure-activity relationships, overview. 5-Arylidene-2,4-thiazolidinediones are class I rhodanines, rhodanine class II has members of carbohydrazides, and class III contains a common 2,4-pentadione substructure element
-
single-stranded binding protein
DNA polymerization by Dpo2 and Dpo3 is strongly inhibited; DNA polymerization by Dpo2 and Dpo3 is strongly inhibited; DNA synthesis by DNA polymerase Dpo2 and Dpo3 is remarkably decreased by single-stranded binding protein; DNA synthesis by DNA polymerase Dpo2 and Dpo3 is remarkably decreased by single-stranded binding protein
-
Sodium dodecyl sulfate
-
-
sphingosine
-
polymerase alpha and beta
SsoCdc6-2 protein
-
inhibits both the DNA-binding activity and DNA polymerization activity of SsoPolY on the DNA substrates containing mismatched bases, while it forms a large complex with SsoPolY and stimulates DNA-binding activity on paired primer-template DNA substrates
-
stavudine triphosphate
-
-
sucrose
-
50% inhibition with 4% sucrose
sulfoglycolipid beta-sulfoquinovosyldiacylglycerol
-
inhibits the DNA polymerase activity of pol lambda by binding to the Met1-Arg95 region and inhibiting its nuclear transit
-
sulfoquinovosyl diacylglycerol
-
significant inhibition of activity at 0.1 mg/ml in strain JM109, but not in strains TOP10, TOP10F, or DH5alpha
Uracil
-
traces of uracil and hypoxanthine in DNA can lead to inhibition of the polymerase chain reaction by archaeal DNA polymerases
vitamin K3
-
more than 80% inhibition of pol gamma at 0.03 mM, does not affect other human DNA polymerase isozymes
zalcitabine triphosphate
-
-
Zn2+
Herpes simplex virus
-
-
[3-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenoxy]acetic acid
-
-
1,10-phenanthroline
-
-
1-deoxyrubralactone
-
potent inhibitor of isozymes pol kappa, pol lambda, pol iota, and pol eta, but does not inhibit DNA polymerase isozymes pol delta, pol epsilon, and pol gamma
1-deoxyrubralactone
-
potent inhibitor
10-epi-pyragonicin
-
-
19-epi-jimenezin
-
-
2',3'-dideoxyribosylthymine triphosphate
-
17% and 33% inhibition are observed with ddTTP/dTTP ratios of 1:1 and 5:1, respectively
2',3'-dideoxyribosylthymine triphosphate
-
the enzyme is slightly sensitive to. 25% inhibition is observed with a ddTTP/dTTP ratio of 50
2',3'-dideoxythymidine 5'-triphosphate
-
-
2',3'-dideoxythymidine 5'-triphosphate
-
-
2',3'-dideoxythymidine 5'-triphosphate
Ruellia sp.
-
-
2',3'-dideoxythymidine 5'-triphosphate
-
-
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
-
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
DNA polymerase alpha
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold lower concentration than DNA polymerase delta
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
polymerase delta and epsilon
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
DNA polymerase alpha
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
DNA polymerase alpha
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
DNA polymerase alpha
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold lower concentration than DNA polymerase delta
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
DNA polymerase alpha
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold lower concentration than DNA polymerase delta
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold lower concentration than DNA polymerase delta
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold lower concentration than DNA polymerase delta
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
Tequatrovirus T4
-
phage T4 enzyme inhibited with lower sensitivity than other members of the B family DNA polymerases
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
DNA polymerase alpha
4-chloromercuribenzoic acid
-
-
4-chloromercuribenzoic acid
-
-
4-chloromercuribenzoic acid
-
-
adefovir diphosphate
-
-
Allicin
-
-
alliin
-
-
aphidicolin
-
10% inhibition at 0.05 mM
aphidicolin
-
DNA polymerase epsilon, 80% inhibition at 0.002 mg/ml
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
polymerase alpha and delta
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
DNA polymerase alpha; polymerase alpha, delta and epsilon
aphidicolin
-
relatively insensitive
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
inhibition at 0.01 and 0.1 mg/ml
aphidicolin
-
IC50: 0.01 mM
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
Herpes simplex virus
-
-
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
DNA polymerase alpha
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
inhibition is competitive for dCTP, noncompetitive for dATP, dGTP and dTTP and uncompetitive for activated DNA
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
alpha-like enzyme
aphidicolin
Ruellia sp.
-
-
aphidicolin
-
50% inhibition at 0.0006 mM
aphidicolin
Tequatrovirus T4
-
phage T4 enzyme inhibited with lower sensitivity than other members of the B family DNA polymerases
aphidicolin
-
DNA polymerase alpha; DNA polymerase delta; DNA polymerase epsilon
aphidicolin
-
50% inhibition at 0.05 mM
ara-ATP
Herpes simplex virus
-
-
Ara-CTP
-
no inhibition of pol I and III
Ara-CTP
-
polymerase II and III
Ara-CTP
-
50% inhibition at 0.05 mM
bakuchiol
Betapolyomavirus macacae
-
isolated from Psoralea corylifolia
bakuchiol
-
inhibition of polymerase epsilon
Benzyloxycarbonyl-Leu-Leu-al
-
-
Benzyloxycarbonyl-Leu-Leu-al
-
-
Carbonyldiphosphonate
-
DNA polymerase delta; no inhibition of polymerase alpha
Carbonyldiphosphonate
-
polymerase delta and epsilon
Carbonyldiphosphonate
-
polymerase alpha, delta and epsilon
Carbonyldiphosphonate
-
DNA polymerase delta; no inhibition of polymerase alpha
Carbonyldiphosphonate
-
DNA polymerase delta; no inhibition of polymerase alpha
Carbonyldiphosphonate
-
DNA polymerase delta; no inhibition of polymerase alpha
Carbonyldiphosphonate
-
-
Carbonyldiphosphonate
-
50% inhibition at 0.15 mM
Carbonyldiphosphonate
-
DNA polymerase delta; no inhibition of polymerase alpha
Carbonyldiphosphonate
-
-
Carbonyldiphosphonate
-
-
Carbonyldiphosphonate
-
-
Carbonyldiphosphonate
Tequatrovirus T4
-
-
Carbonyldiphosphonate
-
DNA polymerase delta; no inhibition of polymerase alpha
cholesterol hemisuccinate
-
pol beta
cholesterol hemisuccinate
-
pol beta; pol iota; pol kappa; pol lambda
cholesterol hemisuccinate
-
pol beta
Dansyl-Leu-Leu-Leu-CH2Cl
-
inhibition of pol I
Dansyl-Leu-Leu-Leu-CH2Cl
-
inhibition of polymerase alpha, beta and gamma
ddTTP
0.4 mM, about 80% loss of activity
ddTTP
-
processivity is strongly inhibited in the presence of 0.01 and 0.02 mM ddTTP
diallyl pentasulfide
-
-
diallyl tetrasulfide
-
-
diallyl trisulfide
-
-
Dideoxynucleoside 5'-triphosphate
-
-
Dideoxynucleoside 5'-triphosphate
-
DNA polymerase beta
Dideoxynucleoside 5'-triphosphate
-
-
Dideoxynucleoside 5'-triphosphate
-
polymerase epsilon, slightly sensitive
Dideoxynucleoside 5'-triphosphate
-
DNA polymerase beta
Dideoxynucleoside 5'-triphosphate
-
DNA polymerase beta
Dideoxynucleoside 5'-triphosphate
-
-
Dideoxynucleoside 5'-triphosphate
-
-
Dideoxynucleoside 5'-triphosphate
Herpes simplex virus
-
-
Dideoxynucleoside 5'-triphosphate
-
DNA polymerase beta
Dideoxynucleoside 5'-triphosphate
-
-
Dideoxynucleoside 5'-triphosphate
-
polymerase epsilon, slightly sensitive
Dideoxynucleoside 5'-triphosphate
-
DNA polymerase beta
Dideoxynucleoside 5'-triphosphate
-
-
Dideoxynucleoside 5'-triphosphate
-
polymerase epsilon, slightly sensitive
Dideoxynucleoside 5'-triphosphate
-
-
Dideoxynucleoside 5'-triphosphate
-
polymerase epsilon, slightly sensitive
Dideoxynucleoside 5'-triphosphate
-
polymerase epsilon, slightly sensitive
Dideoxynucleoside 5'-triphosphate
-
-
Dideoxynucleoside 5'-triphosphate
-
-
Dideoxynucleoside 5'-triphosphate
-
DNA polymerase beta
Dideoxynucleoside 5'-triphosphate
-
-
Dideoxynucleoside 5'-triphosphate
-
-
Dideoxythymidine triphosphate
-
inhibition at 0.05 mM
Dideoxythymidine triphosphate
-
-
Dideoxythymidine triphosphate
-
75% inhibition at 0.000001 mM
Dideoxythymidine triphosphate
Ruellia sp.
-
-
Dideoxythymidine triphosphate
-
-
Dideoxythymidine triphosphate
-
50% inhibition at 0.25 mM
dimethyl sulfoxide
-
inhibition of DNA polymerase epsilon, stimulation of DNA polymerase delta
dimethyl sulfoxide
-
stimulates DNA polymerase alpha and delta, inhibits human DNA polymerase epsilon
dimethyl sulfoxide
-
67% inhibition of RNAse H activity at 10%
diphosphate
-
DNA polymerase beta
diphosphate
Tequatrovirus T4
-
analogs, phage T4 enzyme inhibited with lower sensitivity than other members of the B family DNA polymerases
EDTA
-
-
EDTA
-
complete inhibition
EDTA
-
complete inhibition
EDTA
2 mM, complete inhibition
EDTA
Mg2+ and Mn2+, can restore activity
ethanol
-
3%, 50% inhibition
ethanol
Ruellia sp.
-
21% inhibition at 10%
glycerol
-
50% inhibition with 15% glycerol
glycerol
-
33% inhibition of RNAse H activity at 10%
Halenaquinol sulfate
-
potential inhibitor of DNA polymerase alpha and epsilon, less effective against Escherichia coli DNA polymerase
Halenaquinol sulfate
-
potential inhibitor of DNA polymerase alpha and epsilon, less effective against Escherichia coli DNA polymerase
jimenezin
-
-
K+
-
optimum concentration 125 mM, inhibition at higher concentration
K+
-
50% inhibition at 270 mM
K+
-
optimum concentration 50 mM, inhibition at higher concentration
KCl
at 100 mM KCl, 98%b loss of activity
KCl
150 mM, 90% inhibition
KCl
-
inhibition at 0.2 mM
KCl
inhibition above 20 mM
KCl
100 mM, 80% inhibition
lamivudine triphosphate
-
-
lamivudine triphosphate
-
-
lysophosphatidic acid
-
isolated from myxamoebae of Physarum polycephalum, 90% inhibition of polymerase alpha, weak inhibitor of polymerase beta
lysophosphatidic acid
-
weak inhibitor
Mg2+
-
DNA polymerase alpha: free Mg2+ competes with primer for enzyme binding, dramatic inhibition at Mg2+ concentration above the optimum
Mg2+
-
DNA polymerase alpha: free Mg2+ competes with primer for enzyme binding, dramatic inhibition at Mg2+ concentration above the optimum
Mg2+
-
required, substrate-like inhibition by Mg2+ occur, the inhibition is not due to enzyme inactivation, but instead due to the decrease in rate of a step after chemistry
Mg2+
-
Mg2+ concentrations beyond 6 mM are inhibitory in activity assay
Mn2+
-
inhibits 3'-5'-proofreading activity, thereby decreasing the fidelity of DNA replication by 50%
mucocin
-
-
muconin
-
-
N-ethylmaleimide
-
polymerase I and II; polymerase III
N-ethylmaleimide
-
DNA polymerase alpha, gamma, delta
N-ethylmaleimide
-
polymerase alpha and delta
N-ethylmaleimide
-
inhibition at 1 mM
N-ethylmaleimide
-
relatively insensitive
N-ethylmaleimide
-
DNA polymerase alpha, gamma, delta
N-ethylmaleimide
-
abolishes polymerase III activity at 10 mM
N-ethylmaleimide
-
great sensitivity of phage-induced enzyme, relative insensitivity of pol I
N-ethylmaleimide
-
DNA polymerase alpha, gamma, delta
N-ethylmaleimide
-
polymerase gamma
N-ethylmaleimide
Herpes simplex virus
-
-
N-ethylmaleimide
-
DNA polymerase alpha, gamma, delta
N-ethylmaleimide
-
DNA polymerase
N-ethylmaleimide
-
60% inhibition at 0.2 mM
N-ethylmaleimide
-
69-96% inhibition at 0.0007 mM, 46-54% inhibition at 0.007 mM
N-ethylmaleimide
-
50% inhibition at less than 1 mM
N-ethylmaleimide
-
DNA polymerase alpha, gamma, delta
N-ethylmaleimide
1 mM, about 80% loss of activity
N-ethylmaleimide
Ruellia sp.
-
59% inhibition at 1 mM
N-ethylmaleimide
-
5 mM; 66% inhibition
N-ethylmaleimide
Tequatrovirus T4
-
great sensitivity of phage-induced enzyme, relative insensitivity of pol I
N-ethylmaleimide
Tequintavirus T5
-
great sensitivity of phage-induced enzyme, relative insensitivity of pol I
N-ethylmaleimide
-
inhibited when preincubation with this reagent is performed at 65°C
N-ethylmaleimide
-
DNA polymerase alpha, gamma, delta
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
-
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition of DNA polymerase alpha
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold; lower concentration than DNA polymerase delta
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
100-fold, polymerase delta and epsilon
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition at 0.1 mM
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold; lower concentration than DNA polymerase delta
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold; lower concentration than DNA polymerase delta
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold; lower concentration than DNA polymerase delta
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold; lower concentration than DNA polymerase delta
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
alpha-like enzyme relatively resistant
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
-
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
-
50% inhibition at 0.08 mg/ml
N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate
Tequatrovirus T4
-
mechanism depends upon assay conditions, reversible competitive inhibition predominates
NaCl
-
-
NaCl
in absence of NaCl, Tga PolB displays 67% polymerization activity. From 50 to 200 mM NaCl, the activity is higher than 90%, but it is significantly reduced at NaCl concentrations above 400 mM
NaCl
-
enzyme is inhibited 50% by 200 mM
NH4Cl
-
-
NH4Cl
-
150 mM, 50% inhibition
Oosporein
-
50% inhibition at 0.7 mM
Oosporein
Herpes simplex virus
-
50% inhibition at 0.075 mM
Oosporein
-
50% inhibition at 0.61 mM
phosphate
-
strong inhibitor
phosphate
-
DNA polymerase beta
Phosphonoacetate
-
-
Phosphonoacetate
Herpes simplex virus
-
-
poly(rA)-p(dT)45
-
inhibitory effect towards the reverse transcriptase activity of K4polL329A
-
poly(rA)-p(dT)45
inhibitory effect towards the reverse transcriptase activity of M1pol
-
pyragonicin
-
-
pyranicin
-
potent inhibitor
pyranicin
-
potent inhibitor
pyranicin
-
potent inhibitor
pyranicin
-
potent inhibitor
pyranicin
Tequatrovirus T4
-
-
Salt
-
concentrations above 50 mM inhibit: human KB cell polymerase alpha
Salt
-
sensitive to high ionic strength
Salt
Tequatrovirus T4
-
optimal activity in presence of total salt concentration of approximately 0.1 M, 97% inhibition at 0.3 M
Salt
-
sensitive to high ionic strength
SH-blocking agents
-
pol II and III
-
SH-blocking agents
-
pol II and III
-
SH-blocking agents
-
pol II and III
-
SH-blocking agents
-
pol II and III
-
single-stranded DNA
-
-
single-stranded DNA
-
inhibition of polymerase alpha, competitive with respect to activated DNA substrate
single-stranded DNA
-
inhibition of polymerase alpha, competitive with respect to activated DNA substrate
talaroflavone
-
-
tenofovir diphosphate
-
-
tenofovir diphosphate
-
-
zidovudine triphosphate
-
-
zidovudine triphosphate
-
-
additional information
-
Pol X is not inhibited noticeably by up to 1 mM diphosphate, at higher concentrations there is modest inhibition
-
additional information
-
-
-
additional information
-
no inhibition of polymerase I by ara-CTP
-
additional information
-
-
-
additional information
-
no inhibition of DNA polymerase epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
additional information
-
no inhibition by dideoxynucleoside 5'-triphosphate; no inhibition of DNA polymerase beta and gamma by aphidicolin; no inhibition of DNA polymerase beta by N-ethylmaleimide; no inhibition of DNA polymerase beta, gamma, delta, epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate; no inhibition of polymerase alpha and delta by dideoxynucleoside 5'-triphosphate
-
additional information
-
inhibitor analysis of calf thymus DNA polymerase alpha, delta and epsilon
-
additional information
-
-
-
additional information
-
not inhibited by 1-deoxyrubralactone and talaroflavone
-
additional information
-
DNA polymerase alpha is not inhibited by vitamin K1, vitamin K2, and vitamin K3
-
additional information
-
DNA polymerase alpha is not inhibited by allicin, alliin, diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
-
not inhibited by gamma-lactone
-
additional information
-
not inhibited by 1-deoxyrubralactone and talaroflavone
-
additional information
-
DNA polymerase isozymes I and II are not inhibited by diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
-
no inhibition by aphidicolin; no inhibition by ara-CTP
-
additional information
-
no inhibition by dideoxynucleoside 5'-triphosphate; no inhibition of DNA polymerase beta and gamma by aphidicolin; no inhibition of DNA polymerase beta by N-ethylmaleimide; no inhibition of DNA polymerase beta, gamma, delta, epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate; no inhibition of polymerase alpha and delta by dideoxynucleoside 5'-triphosphate
-
additional information
-
enzyme is resistant to NEM and 2',3'-dideoxythymidine 5-triphosphate
-
additional information
-
no inhibition by entecavir
-
additional information
-
DNA polymerase isozymes alpha, delta and epsilon are not inhibited by diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
-
pol II and III not inhibited by pol I antiserum
-
additional information
-
no inhibition of DNA polymerase beta or gamma from various eukaryotic species, DNA polymerase I from E. coli by lysophosphatidic acid
-
additional information
-
not inhibited by 1-deoxyrubralactone and talaroflavone
-
additional information
-
DNA polymerase I is not inhibited by diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
-
monogalactosyl diacylglycerol and digalactosyl diacylglycerol do not have any inhibitory effect on enzymatic activity
-
additional information
-
no inhibition by dideoxynucleoside 5'-triphosphate; no inhibition of DNA polymerase beta and gamma by aphidicolin; no inhibition of DNA polymerase beta by N-ethylmaleimide; no inhibition of DNA polymerase beta, gamma, delta, epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate; no inhibition of polymerase alpha and delta by dideoxynucleoside 5'-triphosphate
-
additional information
polI activity requires the presence of monovalent ions, above 100 mM, monovalent salts become inhibitory for the activity
-
additional information
-
no inhibition by dideoxynucleoside 5'-triphosphate; no inhibition of DNA polymerase beta and gamma by aphidicolin; no inhibition of DNA polymerase beta by N-ethylmaleimide; no inhibition of DNA polymerase beta, gamma, delta, epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate; no inhibition of polymerase alpha and delta by dideoxynucleoside 5'-triphosphate
-
additional information
-
-
-
additional information
-
no inhibition by (9-adenylmethylcarbonyl)-4-aminobutyl, N-(2,4-dinitrophenyl)-4-aminobutyl triphosphate, N-(2,4-dinitro-5-fluorophenyl)-4-aminobutyl triphosphate, N-[6-N-(2,4-dinitrophenyl)aminohexanoyl]-2-aminoethyl triphosphate, N-(2,4-dinitro-5-fluorophenyl)-2-aminoethyl triphosphate, N-(2,4-dinitro-5-imidazolylphenyl)-4-aminobutyl triphosphate and N-(2,4-dinitro-5-imidazolylphenyl)-2-aminoethyl triphosphate
-
additional information
-
DNA polymerase isozymes are not inhibited by vitamin K1 and vitamin K2
-
additional information
-
DNA polymerase lambda is strongly inhibited by an extract from Allium sativum consisting of diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide, competitive inhibitor
-
additional information
-
isozyme DNA polymerase lambda is not inhibited by mucocin
-
additional information
-
no inhibition by 2',3'-dideoxythymidine 5'-triphosphate; no inhibition by aphidicolin; no inhibition by ara-CTP
-
additional information
-
no inhibition by dideoxynucleoside 5'-triphosphate; no inhibition of DNA polymerase beta and gamma by aphidicolin; no inhibition of DNA polymerase beta by N-ethylmaleimide; no inhibition of DNA polymerase beta, gamma, delta, epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate; no inhibition of polymerase alpha and delta by dideoxynucleoside 5'-triphosphate
-
additional information
-
no inhibition of DNA polymerase beta or gamma from various eukaryotic species, DNA polymerase I from E. coli by lysophosphatidic acid
-
additional information
-
-
-
additional information
-
DNA polymerase delta is not inhibited by diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
no inhibition by 0.1 mM aphidicolin
-
additional information
no inhibition by 0.1 mM aphidicolin
-
additional information
no inhibition by aphidicolin (4 mM)
-
additional information
DNA polymerizing activity is not inhibited by aphidicolin at concentrations up to 2 mM that inhibit the activities of Pfu Pol I and other alpha-like DNA polymerases.
-
additional information
-
DNA polymerizing activity is not inhibited by aphidicolin at concentrations up to 2 mM that inhibit the activities of Pfu Pol I and other alpha-like DNA polymerases.
-
additional information
-
DNA polymerase beta is not inhibited by vitamin K1, vitamin K2, and vitamin K3
-
additional information
-
DNA polymerase beta is strongly inhibited by an extract from Allium sativum consisting of diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide, competitive inhibitor
-
additional information
-
not inhibited by gamma-lactone, mucocin, jimenezin, and 19-epi-jimenezin
-
additional information
-
reverse gyrase inhibits DNA polymerase PolB1. Inhibition of PolY activity depends on both ATPase and topoisomerase activities of reverse gyrase, suggesting that the intact positive supercoiling activity is required for PolY inhibition. In vivo, reverse gyrase and PolY are degraded after induction of DNA damage. Inhibition by reverse gyrase and degradation might act as a double mechanism to control DNA polymerase PolY and prevent its potentially mutagenic activity when undesired. Inhibition of a translesion polymerase by topoisomerase-induced modification of DNA structure may represent a mechanism of regulation of these enzymes
-
additional information
-
the enzyme is resistant to 0.02 mg/ml aphidicolin
-
additional information
no inhibition by 0.02 mg/ml aphidicolin. The enzyme is inhibited by dideoxy- and arabinosine-analogs and SH-blocking agents
-
additional information
Tequatrovirus T4
-
inhibitor analysis of bacteriophage T4 DNA polymerase
-
additional information
Tequatrovirus T4
-
not inhibited by 1-deoxyrubralactone and talaroflavone
-
additional information
Tequatrovirus T4
-
DNA polymerase is not inhibited by diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
PI-TfuII is inhibited by one of the cleavage products
-
additional information
-
the enzyme is resistant to aphidicolin
-
additional information
-
high concentrations of DNA-primed RNA template decrease the efficiency of cDNA synthesis with bacterial family A DNA polymerases
-
additional information
-
not inhibited by 1-deoxyrubralactone and talaroflavone
-
additional information
-
DNA polymerase is not inhibited by diallyl trisulfide, diallyl tetrasulfide, and diallyl pentasulfide
-
additional information
high concentrations of DNA-primed RNA template decrease the efficiency of cDNA synthesis with bacterial family A DNA polymerases
-
additional information
-
enzyme is not inhibited by cytosine-beta-D-arabinofuranoside 5'-triphosphate which is an inhibitor of alpha-polymerase, monoclonal antibodies against human DNA polymerase alpha do not bind; no inhibition by aphidicolin
-
additional information
-
no inhibition by dideoxynucleoside 5'-triphosphate; no inhibition of DNA polymerase beta and gamma by aphidicolin; no inhibition of DNA polymerase beta by N-ethylmaleimide; no inhibition of DNA polymerase beta, gamma, delta, epsilon by 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate; no inhibition of polymerase alpha and delta by dideoxynucleoside 5'-triphosphate
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
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0.00012
2'-deoxyguanosine triphosphate
-
in 50 mM Tris-HCl (pH 7.6), 100 mM KCl, 5 mM MgCl2, 10% (v/v) glycerol, 1 mM dithiothreitol, at 30°C
0.006 - 0.0144
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
0.0151
5-ethynyl-dCTP
-
pH and temperature not specified in the publication
-
0.0063
5-ethynyl-dUTP
-
pH and temperature not specified in the publication
-
0.013 - 1.22
5-Methyl-dCTP
0.006
5-phenyl-dCTP
-
pH and temperature not specified in the publication
-
0.0079
5-phenyl-dUTP
-
pH and temperature not specified in the publication
-
0.0141
5-vinyl-dCTP
-
pH and temperature not specified in the publication
-
0.0131
5-vinyl-dUTP
-
pH and temperature not specified in the publication
-
0.0003
5-[(1E)-3-[(4-[[(5-azido-2-nitrophenyl)carbonyl]amino]butanoyl)amino]prop-1-en-1-yl]uridine 5'-triphosphate
-
pH 9.0, 25°C
0.0055
5-[(1E)-3-{[(5-azido-2-nitrophenyl)carbonyl]amino}prop-1-en-1-yl]-2'-deoxyuridine 5'-triphosphate
-
pH 9.0, 25°C
0.04
5-[N-(2-nitro-5-azidobenzoyl)ami-nomethyl]-2'-deoxyuridine 5'-triphosphate
-
pH 9.0, 25°C
0.0011 - 0.344
7-deaza-2'-deoxyadenosine 5'-triphosphate
0.0125
7-deaza-dGTP
-
pH and temperature not specified in the publication
0.0073
7-ethynyl-7-deaza-dATP
-
pH and temperature not specified in the publication
-
0.0075
7-ethynyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
-
0.0061
7-methyl-7-deaza-dATP
-
pH and temperature not specified in the publication
-
0.0111
7-methyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
-
0.0056
7-phenyl-7-deaza-dATP
-
pH and temperature not specified in the publication
-
0.0041
7-phenyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
-
0.0109
7-vinyl-7-deaza-dATP
-
pH and temperature not specified in the publication
-
0.0095
7-vinyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
-
0.00623
Cy3-dATP
-
pH 8.0, 25°C
-
0.003
Cy3-dCTP
-
pH 8.0, 25°C
-
0.0112
Cy3-dGTP
-
pH 8.0, 25°C
-
0.00893
Cy3-dUTP
-
pH 8.0, 25°C
-
0.1056
dAMP:dA
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template A
-
0.551
dCMP:dA
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template A
-
0.00002772 - 0.00002847
dCMP:dG
-
0.00118 - 0.64
deoxynucleoside triphosphate
2.091
dGMP:dA
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template A
-
0.16
dPTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.00003176
dTMP:dA
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template A
-
0.223 - 0.403
N1-methyl-2'-deoxyadenosine 5'-triphosphate
0.0012 - 0.0087
North-methanocarba-dATP
0.0013
South-methanocarba-dATP
pH 7.5, 37°C
0.0032
TTP
-
pH and temperature not specified in the publication
additional information
additional information
-
0.006
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.0144
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.067
2-thio-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.98
2-thio-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.013
5-Methyl-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
1.22
5-Methyl-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.0011
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.0024
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.0028
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.297
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite an abasic site
0.344
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
1.153
dAMP:dG
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template G
-
1.42
dAMP:dG
-
37°C, pH 7.5, mutant enzyme D362A, substitution opposite the template G
-
0.00028
dATP
-
pH 8.0, 25°C
0.0008
dATP
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.002
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409M
0.0025
dATP
-
55°C, pH not specified in the publication, wild-type enzyme
0.0028
dATP
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.0032
dATP
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.007
dATP
pH 7.8, 37°C, dATP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.0087
dATP
-
pH and temperature not specified in the publication
0.0088
dATP
pH 7.8, 37°C, dATP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCGT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-TCAATCCTTACGAGCATCGCCCCC-3'
0.01
dATP
-
55°C, pH not specified in the publication, mutant enzyme A408S
0.011
dATP
-
template base: dT, pH 7.5, 37°C
0.012
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409V
0.014
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409I
0.02
dATP
pH 7.8, 37°C, incorporation of dATP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5'
0.022
dATP
-
pH 9.0, 37°C, recombinant mutant enzyme
0.022
dATP
pH 7.8, 37°C, dATP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.03
dATP
pH 7.8, 37°C, dATP insertion opposite an unmodified deoxyguanosine in 5'-TCGT-G-TCAATCCTTACGAGCATCGCCCCC-3'
0.046
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410V
0.069
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410L
0.13
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410I
0.18
dATP
pH 7.8, 37°C, incorporation of dATP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.2
dATP
-
template base: dI, pH 7.5, 37°C
0.205
dATP
pH 7.5, 60°C, incorporation opposite an abasic site
0.253
dATP
-
pH 8.0, 37°C, recombinant enzyme
0.274
dATP
-
pH 8.0, 50°C, recombinant enzyme
0.325
dATP
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.39
dATP
pH 7.5, 37°C, DNA polymerase Dpo3
0.43
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.49
dATP
-
template base: dG, pH 7.5, 37°C
0.59
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.69
dATP
pH 7.5, 37°C, DNA polymerase Dpo4
0.72
dATP
-
template base: dX, pH 7.5, 37°C
0.74
dATP
-
pH and temperature not specified in the publication
0.77
dATP
-
pH and temperature not specified in the publication
0.79
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.84
dATP
-
template base: dA, pH 7.5, 37°C
0.88
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
1.1
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
1.2
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
1.5
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
1.9
dATP
-
template base: dC, pH 7.5, 37°C
2.1
dATP
pH 7.5, 37°C, DNA polymerase Dpo1
2.2
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
2.3
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
2.5
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
2.8
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
3.2
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.00002772
dCMP:dG
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template G
-
0.00002847
dCMP:dG
-
37°C, pH 7.5, mutant enzyme D362A, substitution opposite the template G
-
0.000077
dCTP
pH 7.8, 37°C, dCTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.000098
dCTP
pH 7.8, 37°C, dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.0002
dCTP
pH 7.8, 37°C, dCTP insertion opposite an unmodified deoxyguanosine in 5'-TCGT-G-TCAATCCTTACGAGCATCGCCCCC-3'
0.00027
dCTP
-
pH 8.0, 25°C
0.00044
dCTP
pH 7.8, 37°C, incorporation of dCTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5'
0.00071
dCTP
pH 7.8, 37°C, dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCGT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-TCAATCCTTACGAGCATCGCCCCC-3'
0.00249
dCTP
-
mutant L606K, pH 7.5, 37°C, misincorporation of dTTP with G at first position
0.0025
dCTP
-
template base: dG, pH 7.5, 37°C
0.0041
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.00464
dCTP
-
wild-type enzyme, pH 7.5, 37°C, misincorporation of dTTP with G at first position
0.0062
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.0067
dCTP
-
pH and temperature not specified in the publication
0.0068
dCTP
-
template base: 2-fluoro-2'-deoxyinosine, pH 7.5, 37°C
0.0077
dCTP
pH 7.8, 37°C, incorporation of dCTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.00792
dCTP
-
mutant L606G, pH 7.5, 37°C, misincorporation of dTTP with G at first position
0.0084
dCTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.0098
dCTP
pH 7.5, 37°C, DNA polymerase Dpo2
0.01
dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.012
dCTP
37°C, pH 7.4, mutant enzyme T239W
0.012
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.014
dCTP
37°C, pH 7.4, mutant enzyme N188W
0.017
dCTP
-
template base: dI, pH 7.5, 37°C
0.018
dCTP
pH 7.5, 37°C, dCTP insertion opposite the N6dA-butanetriol in 5'-TCTC-N6dA-butanetriol-GTTTATGGACCACC-3'
0.02
dCTP
pH 7.5, 37°C, dCTP insertion opposite the N6dA-(OH)2butyl-GSH in 5'-TCTC-N6dA-(OH)2butyl-GSH-GTTTATGGACCACC-3'
0.022
dCTP
pH 7.5, 37°C, dCTP insertion opposite an unmodified deoxyadenosine in 5'-TCTCAGTTTATGGACCACC-3'
0.024
dCTP
-
pH 9.0, 37°C, recombinant mutant enzyme
0.026
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.027
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.039
dCTP
pH 7.5, 37°C, DNA polymerase Dpo4
0.045
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.052
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.075
dCTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.13
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.65
dCTP
-
pH and temperature not specified in the publication
0.73
dCTP
-
template base: dX, pH 7.5, 37°C
0.773
dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.83
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.94
dCTP
-
template base: dT, pH 7.5, 37°C
1
dCTP
-
template base: dA, pH 7.5, 37°C
1.2
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
1.3
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
1.8
dCTP
-
template base: dC, pH 7.5, 37°C
2
dCTP
-
template base: 2-bromo-2'-deoxyinosine, pH 7.5, 37°C
2.4
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
2.5
dCTP
-
pH and temperature not specified in the publication
0.00118
deoxynucleoside triphosphate
-
DNA polymerase lambda, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, and 0.1 mM EDTA, at 37°C
0.0014
deoxynucleoside triphosphate
wild type enzyme, in 50 mM Tris-HCl (pH 7.8), 1 mM dithiothreitol, at 25°C
0.0015
deoxynucleoside triphosphate
mutant enzyme R821A, in 50 mM Tris-HCl (pH 7.8), 1 mM dithiothreitol, at 25°C
0.002
deoxynucleoside triphosphate
mutant enzyme Y824A, in 50 mM Tris-HCl (pH 7.8), 1 mM dithiothreitol, at 25°C
0.0026
deoxynucleoside triphosphate
mutant enzyme R823A, in 50 mM Tris-HCl (pH 7.8), 1 mM dithiothreitol, at 25°C
0.003
deoxynucleoside triphosphate
pH 8.6, 75°C, mM of each nucleotide in an equimolar mixture of the four nucleotides, mutant enzyme H633R
0.003
deoxynucleoside triphosphate
pH 8.6, 75°C, mM of each nucleotide in an equimolar mixture of the four nucleotides, wild-type enzyme
0.00305
deoxynucleoside triphosphate
-
DNA polymerase beta, in 50 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, 50% (v/v) glycerol, and 0.1 mM EDTA, at 37°C
0.0034
deoxynucleoside triphosphate
mutant enzyme R822A/Y824A in 50 mM Tris-HCl (pH 7.8), 1 mM dithiothreitol, at 25°C
0.0037
deoxynucleoside triphosphate
mutant enzyme R822A, in 50 mM Tris-HCl (pH 7.8), 1 mM dithiothreitol, at 25°C
0.17
deoxynucleoside triphosphate
-
pH 7.5, 75°C, KM-value of each nucleotide in an equimolar mixture of the four nucleotides, fusion protein of the Sso7d protein to the C-terminus of Tpa DNA polymerase
0.64
deoxynucleoside triphosphate
-
pH 7.5, 75°C, KM-value of each nucleotide in an equimolar mixture of the four nucleotides, unmodified Tpa DNA polymerase
0.263
dGMP:dG
-
37°C, pH 7.5, mutant enzyme D362A, substitution opposite the template G
-
0.3511
dGMP:dG
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template G
-
0.00022
dGTP
-
pH 8.0, 25°C
0.0053
dGTP
-
pH and temperature not specified in the publication
0.012
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.013
dGTP
pH 7.8, 37°C, dGTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.017
dGTP
-
template base: dC, pH 7.5, 37°C
0.028
dGTP
pH 7.8, 37°C, incorporation of dGTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5'
0.049
dGTP
pH 7.8, 37°C, dGCTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.05
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.077
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.084
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.086
dGTP
pH 7.8, 37°C, incorporation of dGTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.19
dGTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.19
dGTP
-
template base: dG, pH 7.5, 37°C
0.2
dGTP
-
template base: dI, pH 7.5, 37°C
0.25
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.31
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.43
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.47
dGTP
pH 7.5, 37°C, DNA polymerase Dpo4
0.48
dGTP
-
template base: dX, pH 7.5, 37°C
0.58
dGTP
-
template base: dT, pH 7.5, 37°C
0.6
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.77
dGTP
-
template base: dA, pH 7.5, 37°C
1.2
dGTP
-
pH and temperature not specified in the publication
1.2
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
1.4
dGTP
-
pH and temperature not specified in the publication
1.6
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
2.3
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
2.3
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
2.5
dGTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.00000066
DNAn
-
0.0000032
DNAn
-
pH 7.5, 75°C, template in the presence of an excess of annealed primer, fusion protein of the Sso7d protein to the C-terminus of Tpa DNA polymerase
0.0000057
DNAn
-
pH 7.5, 75°C, template in the presence of an excess of annealed primer, unmodified Tpa DNA polymerase
0.0000066
DNAn
pH 8.6, 75°C, mM of template, in the presence of an excess of annealed primer, mutant enzyme H633R
0.0000104
DNAn
pH 8.6, 75°C, mM of template, in the presence of an excess of annealed prime, wild-type enzyme
0.0013
DNAn
-
in the presence of dNTPs
0.0017
DNAn
-
in the absence of dNTPs
1.26
dTMP:dG
-
37°C, pH 7.5, wild-type enzyme, substitution opposite the template G
-
1.43
dTMP:dG
-
37°C, pH 7.5, mutant enzyme D362A, substitution opposite the template G
-
0.00035
dTTP
-
pH 8.0, 25°C
0.00132
dTTP
pH 8.8, 30°C, recombinant enzyme, in presence of Mn2+
0.002
dTTP
-
pH 9.0, 25°C
0.006
dTTP
pH 7.8, 37°C, dTTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.0061
dTTP
-
template base: dA, pH 7.5, 37°C
0.0093
dTTP
pH 7.5, 37°C, dTTP insertion opposite the N6dA-butanetriol in 5'-TCTC-N6dA-butanetriol-GTTTATGGACCACC-3'
0.0103
dTTP
pH 7.5, 37°C, dTTP insertion opposite an unmodified deoxyadenosine in 5'-TCTCAGTTTATGGACCACC-3'
0.013
dTTP
pH 7.5, 37°C, dTTP insertion opposite the N6dA-(OH)2butyl-GSH in 5'-TCTC-N6dA-(OH)2butyl-GSH-GTTTATGGACCACC-3'
0.01469
dTTP
pH 8.8, 30°C, recombinant enzyme, in presence of Mg2+
0.029
dTTP
pH 7.8, 37°C, dTTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.0314
dTTP
-
pH 8.0, 22°C, recombinant enzyme
0.11
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.14
dTTP
-
pH 9.0, 37°C, recombinant mutant enzyme
0.175
dTTP
-
wild-type enzyme, pH 7.5, 37°C, misincorporation of dTTP with G at first position
0.2
dTTP
-
template base: 2-fluoro-2'-deoxyinosine, pH 7.5, 37°C
0.211
dTTP
-
mutant L606G, pH 7.5, 37°C, misincorporation of dTTP with G at first position
0.23
dTTP
pH 8.2, 50°C, recombinant M1pol
0.28
dTTP
-
pH 8.2, 50°C, recombinant enzyme mutant K4polL329A
0.316
dTTP
-
pH 8.0, 22°C, recombinant enzyme
0.38
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.56
dTTP
-
template base: dX, pH 7.5, 37°C
0.75
dTTP
-
template base: dT, pH 7.5, 37°C
0.78
dTTP
-
template base: dG, pH 7.5, 37°C
0.82
dTTP
-
template base: dI, pH 7.5, 37°C
0.87
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.93
dTTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.94
dTTP
-
pH and temperature not specified in the publication
0.94
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.96
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.99
dTTP
-
template base: 2-bromo-2'-deoxyinosine, pH 7.5, 37°C
1
dTTP
-
pH and temperature not specified in the publication
1.1
dTTP
-
template base: dC, pH 7.5, 37°C
1.3
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
1.6
dTTP
pH 7.5, 37°C, DNA polymerase Dpo4
1.8
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
2.1
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
2.3
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
2.7
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
3.1
dTTP
pH 7.5, 37°C, DNA polymerase Dpo1
3.7
dTTP
pH 7.5, 37°C, DNA polymerase Dpo2
3.8
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
8.9
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
38.1
dTTP
-
pH 8.0, 37°C, recombinant enzyme
47.4
dTTP
-
pH 8.0, 50°C, recombinant enzyme
0.223
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite an abasic site
0.232
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.279
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.287
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.403
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.0012
North-methanocarba-dATP
pH 7.5, 37°C
0.0087
North-methanocarba-dATP
pH 7.5, 37°C
additional information
additional information
-
-
-
additional information
additional information
-
-
-
additional information
additional information
Tequatrovirus T4
-
-
-
additional information
additional information
-
-
-
additional information
additional information
Salasvirus phi29
-
-
-
additional information
additional information
-
-
additional information
additional information
-
steady-state kinetics
-
additional information
additional information
-
biphasic kinetic analysis support a universal kinetic mechanism for the bypass of DNA double lesions, binding constants of the Dpo4-DNA binary complex, overview
-
additional information
additional information
-
pre-steady state kinetics, and biphasic kinetics of nucleotide incorporation at 56°C
-
additional information
additional information
-
kinetic parameters for nucleotide incorporation by Sso pol B1 exo(-) at 55°C
-
additional information
additional information
-
kinetic parameters of several elementary steps for the forward polymerization reaction
-
additional information
additional information
-
pre-steady-state kinetic constants for dNTP and rNTP incorporation by wild-type and F12A mutant enzyme
-
additional information
additional information
pre-steady-state kinetic constants for dNTP and rNTP incorporation by wild-type and F12A mutant enzyme
-
additional information
additional information
-
steady-state kinetic parameters for dCTP incorporation by Dpo4 T239W
-
additional information
additional information
-
steady-state kinetic parameters for next-base extension past 3-(2'-deoxy-beta-D-erythro-pentofuranosyl) pyrimido[1,2-alpha]purin-10(3H)-one
-
additional information
additional information
steady-state kinetic parameters for one-base incorporation
-
additional information
additional information
-
steady-state kinetic parameters for one-base incorporation
-
additional information
additional information
steady-state kinetic parameters for one-base incorporation opposite G and N2-alkyl G adducts by Dpo4. Steady-state kinetic parameters for next base extension from G (or N2-alkyl G):C (or T) template primer termini by Dpo4
-
additional information
additional information
-
steady-state kinetic parameters for one-base incorporation opposite G and N2-alkyl G adducts by Dpo4. Steady-state kinetic parameters for next base extension from G (or N2-alkyl G):C (or T) template primer termini by Dpo4
-
additional information
additional information
steady-state kinetic parameters for single-base extension reactions by Dpo4 in the presence of either Ca2+ or Mg2+
-
additional information
additional information
-
steady-state kinetic parameters for single-base extension reactions by Dpo4 in the presence of either Ca2+ or Mg2+
-
additional information
additional information
-
steady-state kinetic parameters for the single dNTP incorporation by Dpo4 T239W
-
additional information
additional information
-
biphasic dissociation kinetics of the polymerase-DNA binary complex
-
additional information
additional information
-
in pre-steady-state kinetic measurements, when temperature is raised from 22°C to 50°C, the rate (kpol) for cognate dTTP and non-cognate dATP nucleotide incorporations increases 6 and 4fold, respectively, whereas the Kd for both nucleotide incorporations changes only slightly. Single turnover kinetics
-
additional information
additional information
-
kinetic constants for DNA-dependent and RNA-dependent DNA polymerization Michaelis-Menten mechanism and kinetic model of the mutant enzyme, overview
-
additional information
additional information
-
kinetics of nucleotide binding and incorporation, detailed overview. Weak binding is followed by a fast conformational change leading to much tighter binding, which is then followed by the chemical reaction, fast release of diphosphate, structure-function modeling
-
additional information
additional information
-
kinetics of nucleotide binding and incorporation, detailed overview. Weak binding is followed by a fast conformational change leading to much tighter binding, which is then followed by the chemical reaction, following the chemistry step, the enzyme shows fast release of diphosphate and then translocates to allow the binding of the next nucleotide, structure-function modeling. single turnover analysis shows that that the rate of the chemical reaction and the rate of diphosphate release are coincident
-
additional information
additional information
-
Michaelis-Menten kinetics and single nucleotide kinetics of wild-type and mutat enzymes, overview
-
additional information
additional information
-
the reaction rate of K4polL329A exhibits a saturated profile of the Michaelis-Menten kinetics for dTTP concentrations but a substrate inhibition profile for poly(rA)-p(dT)45 concentrations
-
additional information
additional information
the reaction rate of M1pol exhibits a saturated profile of the Michaelis-Menten kinetics for dTTP concentrations but a substrate inhibition profile for poly(rA)-p(dT)45 concentrations
-
additional information
additional information
-
transient state kinetic analyses of DNA polymerase beta, stopped flow absorbance assay development and kinetic modeling and simulations, overview. Pre-steady-state kinetic experiments measuring single nucleotide incorporation catalyzed by Pol beta are performed at 37°C, pH 7.1, over a range of both [Mg2+] and [Mg·dATP2?]. Rapid quench kinetics. Kinetics of nucleotide-induced subdomain closing
-
additional information
additional information
kinetic for nucleotide insertion opposite template cytosine
-
additional information
additional information
-
kinetic for nucleotide insertion opposite template cytosine
-
additional information
additional information
kinetic parameters for single dNTP incorporation opposite template 26-mer-N-(deoxyguanosin-8-yl)-1-aminopyrene
-
additional information
additional information
-
kinetic parameters for single dNTP incorporation opposite template 26-mer-N-(deoxyguanosin-8-yl)-1-aminopyrene
-
additional information
additional information
pH 7.5, 24°C, steady-state kinetic parameters for mispair extension by Dpo4
-
additional information
additional information
-
pH 7.5, 50°C, Km is 0.71 mM for incorporation of dTTP in a 61mer template containing N6-furfuryl-deoxyadenosine
-
additional information
additional information
-
steady-state kinetic parameters for next base extension from G:C and AP site:A (or C) template:primer termini
-
additional information
additional information
steady-state kinetic parameters for next base extension from G:C and AP site:A (or C) template:primer termini
-
additional information
additional information
steady-state kinetic parameters for single-nucleotide incorporation opposite the C8- and N2-2-amino-3-methylimidazo[4,5-f]quinoline adducts of dGuo at the G3- and G1-positions of the NarI recognition sequence by Dpo4
-
additional information
additional information
-
steady-state parameters for the enzyme catalyzed insertion opposite and extension past O2-alkyl-dT
-
additional information
additional information
-
kinetic study of dNTP primer-extension opposite a benzo[a]pyrene-N2-dG-adduct with four DNA polymerases, including Sulfolobus solfataricus Dpo4 and Sulfolobus acidocaldarius Dbh. Vmax/Km is similar for correct dCTP insertion with Dpo4 and Dbh. Compared to Dpo4, Dbh misinsertion is slower for dATP (about 20fold), dGTP (about 110fold) and dTTP (about 6fold), due to decreases in Vmax. These findings provide support that Dbh is in the same Y-Family DNA polymerase class as eukaryotic DNA polymerase kappa and bacterial DNA polymerase IV, which accurately bypass N2-dG adducts
-
additional information
additional information
-
kinetic study of dNTP primer-extension opposite a benzo[a]pyrene-N2-dG-adduct with four DNA polymerases, including Sulfolobus solfataricus Dpo4 and Sulfolobus acidocaldarius Dbh. Vmax/Km is similar for correct dCTP insertion with Dpo4 and Dbh. Compared to Dpo4, Dbh misinsertion is slower for dATP (about 20fold), dGTP (about 110fold) and dTTP (about 6fold), due to decreases in Vmax. These findings provide support that Dbh is in the same Y-Family DNA polymerase class as eukaryotic DNA polymerase kappa and bacterial DNA polymerase IV, which accurately bypass N2-dG adducts
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
0.29 - 0.34
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
10.4
5-ethynyl-dCTP
-
pH and temperature not specified in the publication
-
4.6
5-ethynyl-dUTP
-
pH and temperature not specified in the publication
-
0.02 - 0.33
5-Methyl-dCTP
7.5
5-phenyl-dCTP
-
pH and temperature not specified in the publication
-
9.3
5-phenyl-dUTP
-
pH and temperature not specified in the publication
-
15.4
5-vinyl-dCTP
-
pH and temperature not specified in the publication
-
17.7
5-vinyl-dUTP
-
pH and temperature not specified in the publication
-
0.068 - 0.405
7-deaza-2'-deoxyadenosine 5'-triphosphate
12.1
7-deaza-dGTP
-
pH and temperature not specified in the publication
6.3
7-ethynyl-7-deaza-dATP
-
pH and temperature not specified in the publication
-
17.5
7-ethynyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
-
5.5
7-methyl-7-deaza-dATP
-
pH and temperature not specified in the publication
-
12.7
7-methyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
-
13.5
7-phenyl-7-deaza-dATP
-
pH and temperature not specified in the publication
-
13.7
7-phenyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
-
7.1
7-vinyl-7-deaza-dATP
-
pH and temperature not specified in the publication
-
13.8
7-vinyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
-
0.056
ATP
-
polymerase activity, D190A mutant, pH 7.6, 37°C
1.16
Cy3-dATP
-
pH 8.0, 25°C
-
1.75
Cy3-dCTP
-
pH 8.0, 25°C
-
1.64
Cy3-dGTP
-
pH 8.0, 25°C
-
1.57
Cy3-dUTP
-
pH 8.0, 25°C
-
6
dADP
pH and temperature not specified in the publication
0.0667 - 116
deoxynucleoside triphosphate
0.05
dPTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.012 - 0.15
N1-methyl-2'-deoxyadenosine 5'-triphosphate
0.014 - 0.08
North-methanocarba-dATP
0.000042 - 0.011
primed M13
-
0.0088
South-methanocarba-dATP
pH 7.5, 37°C
6.6
TTP
-
pH and temperature not specified in the publication
additional information
additional information
-
0.29
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.34
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.03
2-thio-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.04
2-thio-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.02
5-Methyl-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.33
5-Methyl-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.068
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.085
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite an abasic site
0.2
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.265
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.405
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.000016
dATP
pH 7.5, 37°C, DNA polymerase Dpo3
0.000083
dATP
pH 7.8, 37°C, incorporation of dATP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.0002
dATP
pH 7.8, 37°C, dATP insertion opposite N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.00024
dATP
pH 7.8, 37°C, dATP insertion opposite N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine in 5'-TCGT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-TCAATCCTTACGAGCATCGCCCCC-3'
0.00025
dATP
pH 7.8, 37°C, dATP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-G-GAATCCTTACGAGCATCGCCCCC-3'
0.00029
dATP
pH 7.8, 37°C, dATP insertion opposite an unmodified deoxyguanosine in 5'-TCGT-G-TCAATCCTTACGAGCATCGCCCCC-3'
0.0012
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0016
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0017
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0018
dATP
pH 7.5, 37°C, DNA polymerase Dpo1
0.0025
dATP
pH 7.8, 37°C, incorporation of dATP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8oxoG)CACT-5'
0.0027
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0028
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.0029
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0036
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0053
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0057
dATP
-
template base: dG, pH 7.5, 37°C
0.0068
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0098
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.011
dATP
-
template base: dC, pH 7.5, 37°C
0.012
dATP
-
template base: dI, pH 7.5, 37°C
0.02
dATP
-
template base: dX, pH 7.5, 37°C
0.021
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.022
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409I
0.022
dATP
-
template base: dA, pH 7.5, 37°C
0.028
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409M
0.029
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410V
0.034
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409V
0.037
dATP
-
55°C, pH not specified in the publication, mutant enzyme A408S
0.043
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.045
dATP
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.063
dATP
pH 7.5, 60°C, incorporation opposite an abasic site
0.073
dATP
pH 7.5, 37°C, DNA polymerase Dpo4
0.185
dATP
-
pH 8.0, 37°C, recombinant enzyme
0.22
dATP
-
55°C, pH not specified in the publication, wild-type enzyme
0.23
dATP
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.24
dATP
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.31
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410L
0.32
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410I
0.36
dATP
-
template base: dT, pH 7.5, 37°C
0.38
dATP
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.4
dATP
-
pH 8.0, 50°C, recombinant enzyme
0.96
dATP
-
pH 9.0, 37°C, recombinant mutant enzyme
8
dATP
-
pH and temperature not specified in the publication
0.000053
dCTP
pH 7.5, 37°C, DNA polymerase Dpo2
0.0001
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.00024
dCTP
pH 7.8, 37°C, dCTP insertion opposite an unmodified deoxyguanosine in 5'-TCGT-G-TCAATCCTTACGAGCATCGCCCCC-3'
0.00027
dCTP
pH 7.8, 37°C, dCTP insertion opposite N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.0003
dCTP
pH 7.8, 37°C, dCTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-G-GAATCCTTACGAGCATCGCCCCC-3'
0.00053
dCTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.00053
dCTP
pH 7.8, 37°C, dCTP insertion opposite N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine in 5'-TCGT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-TCAATCCTTACGAGCATCGCCCCC-3'
0.0008
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0021
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.0022
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.005
dCTP
pH 7.8, 37°C, incorporation of dCTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8oxoG)CACT-5'
0.0054
dCTP
-
template base: dA, pH 7.5, 37°C
0.0055
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0057
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0062
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.011
dCTP
-
template base: dC, pH 7.5, 37°C
0.011
dCTP
-
template base: dX, pH 7.5, 37°C
0.013
dCTP
pH 7.8, 37°C, incorporation of dCTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.015
dCTP
-
template base: dT, pH 7.5, 37°C
0.019
dCTP
-
template base: 2-bromo-2'-deoxyinosine, pH 7.5, 37°C
0.02
dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.022
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.027
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.038
dCTP
pH 7.5, 37°C, dCTP insertion opposite the N6dA-(OH)2butyl-GSH in 5'-TCTC-N6dA-(OH)2butyl-GSH-GTTTATGGACCACC-3'
0.042
dCTP
pH 7.5, 37°C, dCTP insertion opposite the N6dA-butanetriol in 5'-TCTC-N6dA-butanetriol-GTTTATGGACCACC-3'
0.044
dCTP
-
template base: 2-fluoro-2'-deoxyinosine, pH 7.5, 37°C
0.056
dCTP
pH 7.5, 37°C, dCTP insertion opposite an unmodified deoxyadenosine in 5'-TCTCAGTTTATGGACCACC-3'
0.065
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.092
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.23
dCTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.28
dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.34
dCTP
37°C, pH 7.4, mutant enzyme T239W
0.38
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.41
dCTP
-
template base: dI, pH 7.5, 37°C
0.47
dCTP
37°C, pH 7.4, mutant enzyme N188W
0.89
dCTP
-
pH 9.0, 37°C, recombinant mutant enzyme
0.93
dCTP
-
template base: dG, pH 7.5, 37°C
6.1
dCTP
-
pH and temperature not specified in the publication
12
dCTP
pH 7.5, 37°C, DNA polymerase Dpo4
0.0667
deoxynucleoside triphosphate
-
wild-type enzyme, pH 7.5, 60°C
0.0667
deoxynucleoside triphosphate
-
wild-type enzyme, pH 7.5, 60°C
0.15
deoxynucleoside triphosphate
-
G418K/E507Q mutant, pH 7.5, 60°C
0.15
deoxynucleoside triphosphate
-
G418K/E507Q mutant, pH 7.5, 60°C
1.05
deoxynucleoside triphosphate
-
equimolar mixture of all nucleotides, pH 7.5, 70°C
2.5 - 4
deoxynucleoside triphosphate
-
pH 7.6, 30°C
3.9
deoxynucleoside triphosphate
pH 8.6, 75°C, mM of each nucleotide in an equimolar mixture of the four nucleotides, wild-type enzyme
4.2
deoxynucleoside triphosphate
pH 8.6, 75°C, mM of each nucleotide in an equimolar mixture of the four nucleotides, mutant enzyme H633R
92
deoxynucleoside triphosphate
-
pH 7.5, 75°C, turnover number of each nucleotide in an equimolar mixture of the four nucleotides, unmodified Tpa DNA polymerase
116
deoxynucleoside triphosphate
-
pH 7.5, 75°C, turnover number of each nucleotide in an equimolar mixture of the four nucleotides, fusion protein of the Sso7d protein to the C-terminus of Tpa DNA polymerase
0.000013
dGTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.0002
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.00032
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.00038
dGTP
pH 7.8, 37°C, incorporation of dGTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8oxoG)CACT-5'
0.00043
dGTP
pH 7.8, 37°C, dGTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-G-GAATCCTTACGAGCATCGCCCCC-3'
0.00055
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0006
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0006
dGTP
pH 7.8, 37°C, dGTP insertion opposite N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.00068
dGTP
pH 7.8, 37°C, incorporation of dGTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.0016
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0016
dGTP
-
template base: dI, pH 7.5, 37°C
0.0033
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.0045
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.0046
dGTP
-
template base: dA, pH 7.5, 37°C
0.0049
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0052
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0063
dGTP
-
template base: dG, pH 7.5, 37°C
0.0067
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0068
dGTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.01
dGTP
-
template base: dX, pH 7.5, 37°C
0.042
dGTP
-
template base: dT, pH 7.5, 37°C
0.043
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.15
dGTP
pH 7.5, 37°C, DNA polymerase Dpo4
0.54
dGTP
-
template base: dC, pH 7.5, 37°C
13.1
dGTP
-
pH and temperature not specified in the publication
2.4
DNAn
pH 8.6, 75°C, mM of template, in the presence of an excess of annealed primer, mutant enzyme H633R
2.6
DNAn
pH 8.6, 75°C, mM of template, in the presence of an excess of annealed primer, wild-type enzyme
12.9
DNAn
-
pH 7.5, 75°C, mol of template, in the presence of an excess of annealed primer, fusion protein of the Sso7d protein to the C-terminus of Tpa DNA polymerase
13.6
DNAn
-
pH 7.5, 75°C, mol of template, in the presence of an excess of annealed primer, unmodified Tpa DNA polymerase
0.0000072
dTTP
pH 7.5, 37°C, DNA polymerase Dpo2
0.00011
dTTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.00013
dTTP
pH 7.8, 37°C, dTTP insertion opposite N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.00019
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.00029
dTTP
pH 7.8, 37°C, dTTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-G-GAATCCTTACGAGCATCGCCCCC-3'
0.0004
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0021
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0023
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.003
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0046
dTTP
-
template base: 2-bromo-2'-deoxyinosine, pH 7.5, 37°C
0.0047
dTTP
-
template base: 2-fluoro-2'-deoxyinosine, pH 7.5, 37°C
0.0096
dTTP
pH 8.8, 30°C, recombinant enzyme, in presence of Mn2+
0.012
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.0123
dTTP
pH 8.8, 30°C, recombinant enzyme, in presence of Mg2+
0.014
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.014
dTTP
-
template base: dI, pH 7.5, 37°C
0.017
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.017
dTTP
-
template base: dC, pH 7.5, 37°C
0.021
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.025
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.025
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.031
dTTP
-
template base: dT, pH 7.5, 37°C
0.034
dTTP
-
template base: dG, pH 7.5, 37°C
0.035
dTTP
-
template base: dX, pH 7.5, 37°C
0.043
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.063
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.096
dTTP
-
pH 8.0, 22°C, recombinant enzyme
0.096
dTTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.16
dTTP
-
template base: dA, pH 7.5, 37°C
0.28
dTTP
pH 7.5, 37°C, dTTP insertion opposite the N6dA-butanetriol in 5'-TCTC-N6dA-butanetriol-GTTTATGGACCACC-3'
0.35
dTTP
pH 7.5, 37°C, dTTP insertion opposite the N6dA-(OH)2butyl-GSH in 5'-TCTC-N6dA-(OH)2butyl-GSH-GTTTATGGACCACC-3'
0.36
dTTP
pH 7.5, 37°C, dTTP insertion opposite an unmodified deoxyadenosine in 5'-TCTCAGTTTATGGACCACC-3'
0.48
dTTP
pH 7.5, 37°C, DNA polymerase Dpo4
1
dTTP
pH 8.2, 50°C, recombinant M1pol
1.4
dTTP
-
pH 9.0, 37°C, recombinant mutant enzyme
1.7
dTTP
-
pH 8.2, 50°C, recombinant enzyme mutant K4polL329A
25.8
dTTP
-
pH 8.0, 22°C, recombinant enzyme
75.6
dTTP
-
pH 8.0, 37°C, recombinant enzyme
175
dTTP
-
pH 8.0, 50°C, recombinant enzyme
0.012
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.028
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite an abasic site
0.063
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.145
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.15
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.014
North-methanocarba-dATP
pH 7.5, 37°C
0.08
North-methanocarba-dATP
pH 7.5, 37°C
4.17
Nucleotide
-
pol II
0.000042
primed M13
-
exonuclease activity, D190A mutant, pH 7.6, 37°C
-
0.011
primed M13
-
exonuclease activity, wild-type, pH 7.6, 37°C
-
additional information
additional information
-
-
-
additional information
additional information
-
-
additional information
additional information
DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine
-
additional information
additional information
-
DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine
-
additional information
additional information
-
pre-steady-state kinetic constants for dNTP and rNTP incorporation by wild-type and F12A mutant enzyme
-
additional information
additional information
pre-steady-state kinetic constants for dNTP and rNTP incorporation by wild-type and F12A mutant enzyme
-
additional information
additional information
-
steady-state kinetic parameters for dCTP incorporation by Dpo4 T239W
-
additional information
additional information
steady-state kinetic parameters for one-base incorporation
-
additional information
additional information
-
steady-state kinetic parameters for one-base incorporation
-
additional information
additional information
steady-state kinetic parameters for one-base incorporation opposite G and N2-alkyl G adducts by Dpo4. Steady-state kinetic parameters for next base extension from G (or N2-alkyl G):C (or T) template primer termini by Dpo4
-
additional information
additional information
-
steady-state kinetic parameters for one-base incorporation opposite G and N2-alkyl G adducts by Dpo4. Steady-state kinetic parameters for next base extension from G (or N2-alkyl G):C (or T) template primer termini by Dpo4
-
additional information
additional information
steady-state kinetic parameters for single-base extension reactions by Dpo4 in the presence of either Ca2+ or Mg2+
-
additional information
additional information
-
steady-state kinetic parameters for single-base extension reactions by Dpo4 in the presence of either Ca2+ or Mg2+
-
additional information
additional information
-
steady-state kinetic parameters for the single dNTP incorporation by Dpo4 T239W
-
additional information
additional information
the fidelity of nucleotide incorporation by Dpo3 from the polymerase active site alone is 1000-10000 at 37°C. The functional exonuclease proofreading active site will increase fidelity by at least 100
-
additional information
additional information
-
the fidelity of nucleotide incorporation by Dpo3 from the polymerase active site alone is 1000-10000 at 37°C. The functional exonuclease proofreading active site will increase fidelity by at least 100
-
additional information
additional information
-
Tpa-S DNA polymerase (the fusion of the Sso7d protein to the C-terminus of Tpa DNA polymerase) has nearly an identical turnover rate for DNA with the unmodified Tpa DNA polymerase. However, Tpa-S DNA polymerase has a somewhat higher (about 1.26fold) turnover rate in nucleotide incorporation than Tpa DNA polymerase
-
additional information
additional information
kinetic for nucleotide insertion opposite template cytosine
-
additional information
additional information
-
kinetic for nucleotide insertion opposite template cytosine
-
additional information
additional information
kinetic parameters for single dNTP incorporation opposite template 26-mer-N-(deoxyguanosin-8-yl)-1-aminopyrene
-
additional information
additional information
-
kinetic parameters for single dNTP incorporation opposite template 26-mer-N-(deoxyguanosin-8-yl)-1-aminopyrene
-
additional information
additional information
pH 7.5, 24°C, steady-state kinetic parameters for mispair extension by Dpo4
-
additional information
additional information
-
pH 7.5, 50°C, kcat is 0.16/s for incorporation of dTTP in a 61mer template containing N6-furfuryl-deoxyadenosine
-
additional information
additional information
-
steady-state kinetic parameters for next base extension from G:C and AP site:A (or C) template:primer termini
-
additional information
additional information
steady-state kinetic parameters for next base extension from G:C and AP site:A (or C) template:primer termini
-
additional information
additional information
steady-state kinetic parameters for single-nucleotide incorporation opposite the C8- and N2-2-amino-3-methylimidazo[4,5-f]quinoline adducts of dGuo at the G3- and G1-positions of the NarI recognition sequence by Dpo4
-
additional information
additional information
-
steady-state parameters for the enzyme catalyzed insertion opposite and extension past O2-alkyl-dT
-
additional information
additional information
the average speed of utilization of dNTPs by the Taq polymerase is kcat: 47/s
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
20.14 - 56.7
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
690
5-ethynyl-dCTP
-
pH and temperature not specified in the publication
-
730
5-ethynyl-dUTP
-
pH and temperature not specified in the publication
-
0.016 - 25.38
5-Methyl-dCTP
1250
5-phenyl-dCTP
-
pH and temperature not specified in the publication
-
1180
5-phenyl-dUTP
-
pH and temperature not specified in the publication
-
1100
5-vinyl-dCTP
-
pH and temperature not specified in the publication
-
1350
5-vinyl-dUTP
-
pH and temperature not specified in the publication
-
0.2 - 240.9
7-deaza-2'-deoxyadenosine 5'-triphosphate
970
7-deaza-dGTP
-
pH and temperature not specified in the publication
880
7-ethynyl-7-deaza-dATP
-
pH and temperature not specified in the publication
-
2330
7-ethynyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
-
900
7-methyl-7-deaza-dATP
-
pH and temperature not specified in the publication
-
1140
7-methyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
-
2410
7-phenyl-7-deaza-dATP
-
pH and temperature not specified in the publication
-
3340
7-phenyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
-
650
7-vinyl-7-deaza-dATP
-
pH and temperature not specified in the publication
-
1450
7-vinyl-7-deaza-dGTP
-
pH and temperature not specified in the publication
-
186
Cy3-dATP
-
pH 8.0, 25°C
-
583
Cy3-dCTP
-
pH 8.0, 25°C
-
146
Cy3-dGTP
-
pH 8.0, 25°C
-
176
Cy3-dUTP
-
pH 8.0, 25°C
-
0.31
dPTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.0000000019 - 18800
dTTP
0.04 - 0.625
N1-methyl-2'-deoxyadenosine 5'-triphosphate
9.2 - 11.7
North-methanocarba-dATP
6.8
South-methanocarba-dATP
pH 7.5, 37°C
2060
TTP
-
pH and temperature not specified in the publication
additional information
additional information
-
20.14
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
56.7
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.03
2-thio-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.6
2-thio-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.016
5-Methyl-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
25.38
5-Methyl-dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
0.2
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.29
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite an abasic site
71.4
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
168.7
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
240.9
7-deaza-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
0.000000041
dATP
pH 7.5, 37°C, DNA polymerase Dpo3
0.00000086
dATP
pH 7.5, 37°C, DNA polymerase Dpo1
0.00011
dATP
pH 7.5, 37°C, DNA polymerase Dpo4
0.00046
dATP
pH 7.8, 37°C, incorporation of dATP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.001
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0011
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0011
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0016
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0021
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0022
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0026
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0032
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.0034
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0043
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.0058
dATP
-
template base: dC, pH 7.5, 37°C
0.01
dATP
pH 7.8, 37°C, dATP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.01
dATP
pH 7.8, 37°C, dATP insertion opposite an unmodified deoxyguanosine in 5'-TCGT-G-TCAATCCTTACGAGCATCGCCCCC-3'
0.012
dATP
-
template base: dG, pH 7.5, 37°C
0.02
dATP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.026
dATP
-
template base: dA, pH 7.5, 37°C
0.028
dATP
-
template base: dX, pH 7.5, 37°C
0.03
dATP
pH 7.8, 37°C, dATP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.03
dATP
pH 7.8, 37°C, dATP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCGT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-TCAATCCTTACGAGCATCGCCCCC-3'
0.06
dATP
-
template base: dI, pH 7.5, 37°C
0.099
dATP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.125
dATP
pH 7.8, 37°C, incorporation of dATP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5'
0.138
dATP
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.31
dATP
pH 7.5, 60°C, incorporation opposite an abasic site
0.731
dATP
-
pH 8.0, 37°C, recombinant enzyme
1
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410V
1.46
dATP
-
pH 8.0, 50°C, recombinant enzyme
2
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409I
2
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410I
3
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409V
4
dATP
-
55°C, pH not specified in the publication, mutant enzyme A408S
4
dATP
-
55°C, pH not specified in the publication, mutant enzyme Y410L
9
dATP
-
55°C, pH not specified in the publication, wild-type enzyme
14
dATP
-
55°C, pH not specified in the publication, mutant enzyme L409M
33
dATP
-
template base: dT, pH 7.5, 37°C
44
dATP
-
pH 9.0, 37°C, recombinant mutant enzyme
75
dATP
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
235.7
dATP
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
287.5
dATP
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
990
dATP
-
pH and temperature not specified in the publication
0.0000054
dCTP
pH 7.5, 37°C, DNA polymerase Dpo2
0.0000071
dCTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.000042
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0025
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.0054
dCTP
-
template base: dA, pH 7.5, 37°C
0.0061
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0061
dCTP
-
template base: dC, pH 7.5, 37°C
0.0095
dCTP
-
template base: 2-bromo-2'-deoxyinosine, pH 7.5, 37°C
0.015
dCTP
-
template base: dX , pH 7.5, 37°C
0.016
dCTP
-
template base: dT, pH 7.5, 37°C
0.019
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.021
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.026
dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with O6-methylguanine as template
0.027
dCTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.083
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.11
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.12
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.31
dCTP
pH 7.5, 37°C, DNA polymerase Dpo4
0.7
dCTP
pH 7.8, 37°C, dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCGT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-TCAATCCTTACGAGCATCGCCCCC-3'
1.2
dCTP
pH 7.8, 37°C, dCTP insertion opposite an unmodified deoxyguanosine in 5'-TCGT-G-TCAATCCTTACGAGCATCGCCCCC-3'
1.7
dCTP
pH 7.8, 37°C, incorporation of dCTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
1.9
dCTP
pH 7.5, 37°C, dCTP insertion opposite the N6dA-(OH)2butyl-GSH in 5'-TCTC-N6dA-(OH)2butyl-GSH-GTTTATGGACCACC-3'
2.3
dCTP
pH 7.5, 37°C, dCTP insertion opposite the N6dA-butanetriol in 5'-TCTC-N6dA-butanetriol-GTTTATGGACCACC-3'
2.4
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
2.5
dCTP
pH 7.5, 37°C, dCTP insertion opposite an unmodified deoxyadenosine in 5'-TCTCAGTTTATGGACCACC-3'
2.8
dCTP
pH 7.8, 37°C, dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
3.9
dCTP
pH 7.8, 37°C, dCTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
6.5
dCTP
-
template base: 2-fluoro-2'-deoxyinosine, pH 7.5, 37°C
11
dCTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
11.36
dCTP
pH 7.8, 37°C, incorporation of dCTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5'
23
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
28
dCTP
37°C, pH 7.4, mutant enzyme T239W
28
dCTP
pH 7.4, 37°C, steady-state kinetics for single nucleotide primer extension with guanine as template
31
dCTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
34
dCTP
37°C, pH 7.4, mutant enzyme N188W
34
dCTP
-
template base: dI, pH 7.5, 37°C
37
dCTP
-
pH 9.0, 37°C, recombinant mutant enzyme
370
dCTP
-
template base: dG, pH 7.5, 37°C
910
dCTP
-
pH and temperature not specified in the publication
0.000000068
dGTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.0000027
dGTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.00032
dGTP
pH 7.5, 37°C, DNA polymerase Dpo4
0.0004
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.00064
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0029
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.0055
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.006
dGTP
-
template base: dA, pH 7.5, 37°C
0.0065
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.008
dGTP
pH 7.8, 37°C, incorporation of dGTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5'
0.008
dGTP
-
template base: dI, pH 7.5, 37°C
0.01
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.01
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.01
dGTP
pH 7.8, 37°C, dGTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.014
dGTP
pH 7.8, 37°C, incorporation of dGTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5'
0.019
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.019
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.021
dGTP
-
template base: dX, pH 7.5, 37°C
0.027
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.03
dGTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.033
dGTP
-
template base: dG, pH 7.5, 37°C
0.05
dGTP
pH 7.8, 37°C, dGTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.062
dGTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.072
dGTP
-
template base: dT, pH 7.5, 37°C
32
dGTP
-
template base: dC, pH 7.5, 37°C
2470
dGTP
-
pH and temperature not specified in the publication
29500
dGTP
-
pH 8.0, 25°C
28
DNAn
-
in the absence of dNTPs
38
DNAn
-
in the presence of dNTPs
0.0000000019
dTTP
pH 7.5, 37°C, DNA polymerase Dpo2
0.00000012
dTTP
pH 7.5, 37°C, DNA polymerase Dpo3
0.000031
dTTP
pH 7.5, 37°C, DNA polymerase Dpo1
0.00017
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0003
dTTP
pH 7.5, 37°C, DNA polymerase Dpo4
0.0012
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.0015
dTTP
-
template base: dC, pH 7.5, 37°C
0.0016
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-BzG
0.0026
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0028
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.0031
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-BzG
0.0046
dTTP
-
template base: 2-bromo-2'-deoxyinosine, pH 7.5, 37°C
0.0081
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template: abasic site
0.01
dTTP
pH 7.8, 37°C, dTTP insertion opposite an unmodified deoxyguanosine in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.016
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.017
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.017
dTTP
-
template base: dI, pH 7.5, 37°C
0.019
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: N2-MeG
0.02
dTTP
pH 7.8, 37°C, dTTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion in 5'-TCAT-(N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine)-GAATCCTTACGAGCATCGCCCCC-3'
0.022
dTTP
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: G
0.024
dTTP
-
template base: 2-fluoro-2'-deoxyinosine, pH 7.5, 37°C
0.037
dTTP
-
pH 7.5, 37°C, dNTP incorporation opposite DNA lesions, template base: O6-MeG
0.041
dTTP
-
template base: dT, pH 7.5, 37°C
0.044
dTTP
-
template base: dG, pH 7.5, 37°C
0.063
dTTP
-
template base: dX, pH 7.5, 37°C
0.304
dTTP
-
pH 8.0, 22°C, recombinant enzyme
0.83
dTTP
pH 8.8, 30°C, recombinant enzyme, in presence of Mg2+
7.16
dTTP
pH 8.8, 30°C, recombinant enzyme, in presence of Mn2+
9.9
dTTP
-
pH 9.0, 37°C, recombinant mutant enzyme
26
dTTP
-
template base: dA, pH 7.5, 37°C
26.9
dTTP
pH 7.5, 37°C, dTTP insertion opposite the N6dA-(OH)2butyl-GSH in 5'-TCTC-N6dA-(OH)2butyl-GSH-GTTTATGGACCACC-3'
30
dTTP
pH 7.5, 37°C, dTTP insertion opposite the N6dA-butanetriol in 5'-TCTC-N6dA-butanetriol-GTTTATGGACCACC-3'
35
dTTP
pH 7.5, 37°C, dTTP insertion opposite an unmodified deoxyadenosine in 5'-TCTCAGTTTATGGACCACC-3'
821.7
dTTP
-
pH 8.0, 22°C, recombinant enzyme
1984
dTTP
-
pH 8.0, 37°C, recombinant enzyme
3692
dTTP
-
pH 8.0, 50°C, recombinant enzyme
18800
dTTP
-
pH 8.0, 25°C
0.04
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of a cis-syn thymine dimer of the template
0.13
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite an abasic site
0.156
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of a cis-syn thymine dimer of the template
0.54
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 3'-thymine of an nondamaged template
0.625
N1-methyl-2'-deoxyadenosine 5'-triphosphate
pH 7.5, 60°C, incorporation opposite the 5'-thymine of an nondamaged template
9.2
North-methanocarba-dATP
pH 7.5, 37°C
11.7
North-methanocarba-dATP
pH 7.5, 37°C
additional information
additional information
DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine
-
additional information
additional information
-
DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine
-
additional information
additional information
-
pre-steady-state kinetic constants for dNTP and rNTP incorporation by wild-type and F12A mutant enzyme
-
additional information
additional information
pre-steady-state kinetic constants for dNTP and rNTP incorporation by wild-type and F12A mutant enzyme
-
additional information
additional information
-
steady-state kinetic parameters for dCTP incorporation by Dpo4 T239W
-
additional information
additional information
steady-state kinetic parameters for one-base incorporation
-
additional information
additional information
-
steady-state kinetic parameters for one-base incorporation
-
additional information
additional information
steady-state kinetic parameters for one-base incorporation opposite G and N2-alkyl G adducts by Dpo4. Steady-state kinetic parameters for next base extension from G (or N2-alkyl G):C (or T) template primer termini by Dpo4
-
additional information
additional information
-
steady-state kinetic parameters for one-base incorporation opposite G and N2-alkyl G adducts by Dpo4. Steady-state kinetic parameters for next base extension from G (or N2-alkyl G):C (or T) template primer termini by Dpo4
-
additional information
additional information
steady-state kinetic parameters for single-base extension reactions by Dpo4 in the presence of either Ca2+ or Mg2+
-
additional information
additional information
-
steady-state kinetic parameters for single-base extension reactions by Dpo4 in the presence of either Ca2+ or Mg2+
-
additional information
additional information
-
steady-state kinetic parameters for the single dNTP incorporation by Dpo4 T239W
-
additional information
additional information
transient-state kinetic analysis of Dpo4 mutants and dATP Incorporation opposite 8-oxoG.Transient-state kinetic analysis of Dpo4 mutants and dCTP incorporation opposite 8-oxoG
-
additional information
additional information
-
transient-state kinetic analysis of Dpo4 mutants and dATP Incorporation opposite 8-oxoG.Transient-state kinetic analysis of Dpo4 mutants and dCTP incorporation opposite 8-oxoG
-
additional information
additional information
kinetic for nucleotide insertion opposite template cytosine
-
additional information
additional information
-
kinetic for nucleotide insertion opposite template cytosine
-
additional information
additional information
kinetic parameters for single dNTP incorporation opposite template 26-mer-N-(deoxyguanosin-8-yl)-1-aminopyrene
-
additional information
additional information
-
kinetic parameters for single dNTP incorporation opposite template 26-mer-N-(deoxyguanosin-8-yl)-1-aminopyrene
-
additional information
additional information
pH 7.5, 24°C, steady-state kinetic parameters for mispair extension by Dpo4
-
additional information
additional information
-
pH 7.5, 50°C, kcat/Km is 0.0225/s * mM for incorporation of dTTP in a 61mer template containing N6-furfuryl-deoxyadenosine
-
additional information
additional information
-
steady-state kinetic parameters for next base extension from G:C and AP site:A (or C) template:primer termini
-
additional information
additional information
steady-state kinetic parameters for next base extension from G:C and AP site:A (or C) template:primer termini
-
additional information
additional information
steady-state kinetic parameters for single-nucleotide incorporation opposite the C8- and N2-2-amino-3-methylimidazo[4,5-f]quinoline adducts of dGuo at the G3- and G1-positions of the NarI recognition sequence by Dpo4
-
additional information
additional information
-
steady-state parameters for the enzyme catalyzed insertion opposite and extension past O2-alkyl-dT
-
additional information
additional information
DNA synthesis from dNDPs is a little over an order of magnitude lower than from dNTPs and that Vmax/KM is about 400 times lower for dNDPs than for dNTPs
-
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G534R
-
abscisic acid overly sensitive mutant, also hypersensitive to methyl methanesulfonate and UV-B light
E170A
complete loss of the 3'-5'exonuclease activity
DELTA413470
-
mutation in the spacer region of the alpha-subunit. Obtained in small amounts due to low solubility, mutant has barely detectable DNA polymerase activity
DELTA483533
-
expressed efficiently and purified as soluble holoenzyme complex associated with wild-type beta-subunit. The DNA polymerase activity of the mutant holoenzyme is reduced greatly as compared to wild type
DELTA536581
-
expressed efficiently and purified as soluble holoenzyme complex associated with wild-type beta-subunit. The DNA polymerase activity of the mutant enzyme is 80% of wild-type holoenzyme
DELTA666742
-
mutation in the spacer region of the alpha-subunit. Obtained in small amounts due to low solubility, mutant has barely detectable DNA polymerase activity
F576A
-
mutation in alpha-subunit, mutant enzyme retains about 50% of wild-type activity
G575A
-
mutation in alpha-subunit, mutant enzyme has nearly normal activity
G575A/W576A/F578A
-
mutation in alpha-subunit completely reduces DNA polymerase activity
K557A
-
mutation in alpha-subunit, mutant enzyme has nearly normal activity
K687A/D688A/F689A
-
mutation in alpha-subunit resulted in DNA polymerase activities that is 6080% of wild-type enzyme
L558A
-
mutation in alpha-subunit, mutant enzyme retains about 50% of wild-type activity
P556A
-
mutation in alpha-subunit, mutant enzyme has nearly normal activity
P556A/K557A/L558A
-
mutation in alpha-subunit completely reduces DNA polymerase activity
S719A/Y720A/W721
-
mutation in alpha-subunit completely reduces DNA polymerase activity
W576A
-
mutation in alpha-subunit, mutant enzyme is nearly inactive
Y419A/E420A/D421A
-
mutation in alpha-subunit resulted in DNA polymerase activities that is 6080% of wild-type enzyme
F12A
-
mutant enzyme shows disproportionately reduced activity on the damaged template
F13V
-
mutant enzyme is almost unable to carry out translesion synthesis over N2-furfuryl-dG, although its activity on undamaged DNA is unaffected. The F13V mutation has a modest effect on the ability of DinB to discriminate against ribonucleotides, increasing the frequency of their misincorporation from less than 0.00001 to 0.001
F771A
the mutation shows 30% decreased polymerase activity compared to the wild type enzyme
L823A
the mutation shows 3% decreased polymerase activity compared to the wild type enzyme
N678A
no change in polymerase activity, increased mismatch-directed exonuclease activity
P680G
reduced kcat, no change in relative DNA binding affinity or Km, nearly complete loss in the processive mode of DNA synthesis
P680Q
reduced kcat, no change in relative DNA binding affinity or Km, nearly complete loss in the processive mode of DNA synthesis
Q667A
polymerase defective, no change in exonuclease activity
R821A
the mutation shows 19% increased polymerase activity compared to the wild type enzyme
R822A
the mutation shows 5% increased polymerase activity compared to the wild type enzyme
R822A/Y824A
the mutation shows 36% increased polymerase activity compared to the wild type enzyme
Y824A
the mutation shows 25% increased polymerase activity compared to the wild type enzyme
L561A
-
the mutant has pre-steadystate Kd,app and kpol values for the incorporation of correct dNMPs that are comparable to or exhibits kpol values that are somewhat greater than wild type DNA polymerase
L561A/Y567A
-
the mutant has pre-steadystate Kd,app and kpol values for the incorporation of correct dNMPs that are comparable to or exhibits kpol values that are somewhat greater than wild type DNA polymerase
L561A/Y567A/S565G
-
the mutant has pre-steadystate Kd,app and kpol values for the incorporation of correct dNMPs that are comparable to or exhibits kpol values that are somewhat greater than wild type RB69 DNA polymerase
Y567A
-
the mutant has pre-steadystate Kd,app and kpol values for the incorporation of correct dNMPs that are comparable to or exhibits kpol values that are somewhat greater than wild type DNA polymerase
D424A
-
a proofreading deficient mutant of the Klenow fragment
D378A
-
site-directed mutagenesis, the mutant is inactive in presence of Mg2+
D378E
-
site-directed mutagenesis, the mutant is inactive in presence of Mg2+, it shows 35% of maximal activity in presenceof Mn2+
D380A
-
site-directed mutagenesis, the mutant is inactive in presence of Mg2+
D380E
-
site-directed mutagenesis, the mutant is inactive in presence of Mg2+ or Mn2+
D531A
-
site-directed mutagenesis, the mutant is inactive in presence of Mg2+
D531E
-
site-directed mutagenesis, the mutant is inactive in presence of Mg2+, it shows 60% of maximal activity in presenceof Mn2+
R113A
Herpes simplex virus
-
mutation reduces viral yield (2fold), alters the kinetics of viral DNA replication, and decreases the fidelity of DNA replication
R182A
Herpes simplex virus
-
mutation reduces viral yield (2fold), alters the kinetics of viral DNA replication, and decreases the fidelity of DNA replication
R279A
Herpes simplex virus
-
mutation reduces viral yield (5fold), alters the kinetics of viral DNA replication, and decreases the fidelity of DNA replication
R280A
Herpes simplex virus
-
mutation reduces viral yield (5fold), alters the kinetics of viral DNA replication, and decreases the fidelity of DNA replication
A329A
not meaningfully associated with breast cancer risk; more likely to respond to Pt-based chemotherapy
A467T
-
naturally occuring mutation, the mutation is the most common POLG mutation and has been found to be associated with all of the disease symptoms analyzed. The A467T pol gamma possesses only 4% of the wild-type DNA polymerase activity and is compromised for its ability to interact with the p55 accessory subunit
A471V
moderate decrease in activity
A957S
-
naturally occuring mutation, involved in autosomal dominant progressive external ophthalmoplegia, the mutation is associated with motiif B in the active site
D115A/E116A
-
catalytically inactive
D189G
impaired for extension step of TLS
D198A/E200A
-
site-directed mutagenesis in the exonuclease domain resulting in loss of exonuclease activity
D275A/E277A/D368A
mutation in the catalytic subunit, exonuclease-deficient variant
E1143G
-
naturally occuring mutation, that is a frequent cause of ataxia-neuropathy syndrome, and found in 4% of European populations
E200A
-
exonuclease-deficient mutant
E29K
decreased insertion opposite abasic site (2-20)
E419G
20fold decrease in kcat/Km on dG and 670fold decrease on N2-CH2-Anth-dG, extension defect
E430G
low activity on AP site
E449K
low activity on AP site, low fidelity
F155S
decreased activity on model abasic site
F506G
-
inactive mutant enzyme
F506R
-
complete loss of de novo DNA synthesis
G154E
decreased activity opposite model abasic site, pathogenic
G848S
-
naturally occuring mutation, involved in Alpers syndrome, the mutant shows compromised DNA binding ability that affects its overall functional efficiency
G923D
-
naturally occuring mutation, involved in autosomal dominant progressive external ophthalmoplegia, the mutation is associated with motiif B in the active site
L442F
low activity on AP site
L606G
-
site-directed mutagenesis, the mutant shows increased polymerase activity and slightly reduced exonuclease activity compared to the wild-type enzyme, mutant pol delta L606G is highly error prone, incorporating single noncomplementary nucleotides at a high frequency during DNA synthesis
L606K
-
site-directed mutagenesis, the mutant shows increased polymerase activity and reduced exonuclease activity compared to the wild-type enzyme, mutant pol delta L606K is extremely accurate, with a higher fidelity of single nucleotide incorporation by the active site than that of wild-type pol delta, it does not catalyze detectable nucleotide mis-insertion even with nucleotide concentrations as high as 4 mM, but pol delta L606K mutant is impaired in the bypass of DNA adducts
R246X
5-10fold less active with 8-oxo-dG-, N2-CH2-Anth-dG-, O6-Me-dG- and abasic-containing templates
R512W
decreased activity on undamaged and damaged DNA
R61A
the mutations decreases the ability of the enzyme to distinguish between a thymine-thymine dimer lesion and undamaged DNA. Mutation does not impact the global structure and equilibrium motions of DNA polymerase eta. Only local conformational changes around the mutation sites are observed
R61K
the mutations decreases the ability of the enzyme to distinguish between a thymine-thymine dimer lesion and undamaged DNA. Mutation does not impact the global structure and equilibrium motions of DNA polymerase eta. Only local conformational changes around the mutation sites are observed
R852C
-
naturally occuring mutation, involved in Alpers syndrome, the mutant shows compromised DNA binding ability that affects its overall functional efficiency
R853Q
-
naturally occuring mutation, involved in Alpers syndrome, the mutant shows compromised DNA binding ability that affects its overall functional efficiency
R943H
-
naturally occuring mutation, involved in autosomal dominant progressive external ophthalmoplegia, the mutation is associated with motiif B in the active site, the mutant retains less than 1% of the wild-type polymerase activity and displays a severe decrease in processivity
S423R
1.6fold more effcient than wild-type, 2fold increased DNA binding affinity, pathogenic
S62A
the mutations decreases the ability of the enzyme to distinguish between a thymine-thymine dimer lesion and undamaged DNA. Mutation does not impact the global structure and equilibrium motions of DNA polymerase eta. Only local conformational changes around the mutation sites are observed
S62L
the mutations decreases the ability of the enzyme to distinguish between a thymine-thymine dimer lesion and undamaged DNA. Mutation does not impact the global structure and equilibrium motions of DNA polymerase eta. Only local conformational changes around the mutation sites are observed
T44M
lesion-specific reduction in activity. Reduced activity with N2-CH2-Anth-dG, O6-Me-dG and abasic sites
T473A
decreased activity on undamaged and damaged DNA
T851A
-
naturally occuring mutation, involved in Alpers syndrome, the mutant shows compromised DNA binding ability that affects its overall functional efficiency
V130I
mutant has relaxed discrimination against the major groove adduct N6-furfuryl-dA
W748S
-
naturally occuring mutation that has intrinsic lower polymerase activity as well as a demonstrated lower affinity for DNA compared to the wild-type enzyme
W748S/E1143G
-
naturally occuring mutation, the E1143G single-nucleotide polymorphism can modulate the deleterious effect of the W748S mutation
Y271G
the mutant is rationally designed to provide flexibility to the steric gate backbone carboxyl of Tyr-271 in pol beta
Y955C
-
naturally occuring mutation, involved in autosomal dominant progressive external ophthalmoplegia, the mutation is associated with motiif B in the active site, the mutant retains less than 1% of the wild-type polymerase activity and displays a severe decrease in processivity, the mutation increases nucleotide misinsertion replication errors 10-100 fold in the absence of exonucleolytic proofreading
D907V
-
mutant is less resistant to acyclovir and cidofovir than the wild type enzyme
L778M
-
mutant is less resistant to acyclovir and cidofovir than the wild type enzyme
H329A
-
mutation has little effect on template-dependent synthesis by Pol l from a paired primer terminus, but it reduces both template-independent and template-dependent synthesis during nonhomologous DNA end joining of intermediates whose 3' ends lack complementary template strand nucleotides
D362A
-
the misincorporation frequency values of the D362A mutant are slightly higher (1.44.9fold) than those of the wild type protein
A408S
-
A408S mutation results in a significant increase in both dNTP binding affinity and fidelity, kcat/Km for dATP is about 45% compared to the wild-type enzyme, D215A mutation results in inactivation of 3'-5'-exonuclease activity
D215A
-
3'-5'-exonuclease inactive mutant enzyme
D405A
-
mutant enzyme loses 99.8% of DNA polymerizing activity and 90% of 3'->5' exonucleolytic activity
D405E
-
mutant enzyme loses 95.8% of DNA polymerizing activity and 90% of 3'->5' exonucleolytic activity
D473G
-
wild-type variant Pfu-Pol(exo-) is is 60fold less accurate than Pfu-Pol(exo+)
DELTAH672-S775
-
mutant enzyme loses 99% of DNA polymerizing activity and 97% of 3'->5' exonucleolytic activity
DELTAL717-S775
-
mutant enzyme loses 97% of DNA polymerizing activity and 97% of 3'->5' exonucleolytic activity
DELTAL746-S775
-
mutant protein has DNA polymerizing activity with 2.3fold higher specific activity than that of the wild-type but retains only 10% of the 3'->5' exonucleolytic activity of the wild-type
L409I
-
kcat/Km for dATP is about 20% compared to the wild-type enzyme
L409M
-
L409 mutation results in drastically reduced affinity for the correct dNTP, a much higher efficiency of both misincorporation and mismatch extension, and substantially lower fidelity as demonstrated by a PCR-based forward mutation assay, kcat/Km for dATP is about 155% compared to the wild-type enzyme, D215A mutation results in inactivation of 3'-5'-exonuclease activity
L409V
-
kcat/Km for dATP is about 35% compared to the wild-type enzyme
T471A
-
less accurate, by factors of 1.6 than the wild-type variant Pfu-Pol(exo-)
T471G
-
less accurate, by factors of 1.2 than the wild-type variant Pfu-Pol(exo-)
Y410I
-
kcat/Km for dATP is about 20% compared to the wild-type enzyme
Y410L
-
kcat/Km for dATP is about 45% compared to the wild-type enzyme
Y410V
-
Y410V mutation results in high fidelity in both misincorporation assays and forward mutation assays, but displays a substantially higher Km than wild-type enzyme, kcat/Km for dATP is about 10% compared to the wild-type enzyme, D215A mutation results in inactivation of 3'-5'-exonuclease activity
D1122A
loss of polymerization activity
D1122E
mutant enzyme with reduced polymerization activity, polymerization activity is 15% compared to wild-type activity, 3'-5' exonuclease activity remains, the mutant has lower Mg2+ affinity than does the wild-type
D1124A
loss of polymerization activity
D1124E
mutant enzyme with reduced polymerization activity, polymerization activity is 43% compared to wild-type activity,
D1124N
mutant enzyme with reduced polymerization activity, 3'-5' exonuclease activity remains, the mutant has lower Mg2+ affinity than does the wild-type
D259E
moderate decrease of the polymerizing activity
D259G
moderate decrease of the polymerizing activity
D259K
the exonuclease activity of the mutant enzyme decreases drastically to 0.58% compared with that of the wild-type DNA polymerase
D259N
moderate decrease of the polymerizing activity
G1123A
mutant enzyme has 13% of the activity of the wild type enzyme
G1123R
mutant enzyme has 0.8% of the activity of the wild type enzyme
K253E
exonuclease activity of mutant increases 2.7fold compared to wild-type activity
K253E/R255E
exonuclease activity of mutant increases 1.8fold compared to wild-type activity
R255D
exonuclease activity of mutant increases 2.9fold compared to wild-type activity
R258A |
-
mutant of Pol beta has a facilitated subdomain-reopening step. Rate of single-nucleotide incorporation catalyzed by R258A is identical to that of wild-type
D424A
mutation in polymerase active site, the polymerase activity is reduced more than 30fold compared to the wild-type activity
D424A/D542A
mutation in polymerase active site, complete inactivation of polymerase activity
D542A
mutation in polymerase active site, the polymerase activity is reduced more than 50fold compared to the wild-type activity
N188W
kcat/Km for dCTP is 2.9fold compared to kcat/Km of wild-type enzyme
N249Y
exhibits increased catalytic activity when compared to the wild-type enzyme, the mutation decreases the affinity for NAD(H) cofactor
R322H
the His332 mutant exhibits faster forward rate constants relative to wild-type Dpo4. The kpol values for the His332 mutant incorporation opposite G and 8-oxoG are 3.6- and 4.6fold faster than for wild-type Dpo4. The nucleotide binding affinity trend is opposite that of wild-type Dpo4, Glu332, and Leu332, with tighter dCTP binding during bypass of G. As in the case of Ala332, the kinetic analysis indicates that His332 inserts dCTP opposite G with slightly greater efficiency than opposite 8-oxoG
R322L
kpol (forward rate of polymerization) values for the Leu332 mutant incorporation opposite G and 8-oxoG are 4.1- and 1.9fold higher than those for wild-type Dpo4. The Leu332 mutant is about 2fold more efficient at incorporation of dCTP opposite 8-oxoG compared with G
R331A/R322A
mutant has lower forward rate constants relative to wild-type enzyme for both G and 8-oxoG. The double mutant-catalyzed insertion of dCTP opposite 8-oxoG is about 4fold higher than dCTP insertion opposite G. The measured binding affinity of dCTP is tighter than that of wild-type Dpo4 for unmodified DNA, but the binding affinity of dCTP opposite 8-oxoG is similar to that observed for wild-type enzyme. The catalytic efficiency for dCTP incorporation increases about 4fold for unmodified DNA and decreases about 2fold for 8-oxoG-modified DNA. The mutant fails to incorporate dATP opposite 8-oxoG in the presteady-state experiments. It inserts dCTP opposite 8-oxoG with an about 200fold greater efficiency than it does dATP and the steady-state efficiency of dATP incorporation is decreased about 27fold relative to the wild-type enzyme
R332A
mutant enzyme displays a higher affinity (lower KD,dCTP) for dCTP when bound to the unmodified DNA compared with the KD,dCTP measured for mutant-catalyzed incorporation of dCTP opposite 8-oxoG. Wild-type enzyme shows a greater affinity for dCTP opposite to 8-oxoG-modified DNA. The catalytic efficiency of the mutant is 23fold higher at incorporation of C opposite G and 1.2fold lower than wild-type enzyme in dCTP incorporation opposite 8-oxoG
R332E
mutant enzyme retains fidelity against bypass of 7,8-dihydro-8-oxodeoxyguanosine (8-oxoG) that is similar to wild enzyme. A crystal structure of the mutant and 8-oxoG:C pair reveals water-mediated hydrogen bonds between Glu332 and the O-8 atom of 8-oxoG. The kpol (forward rate of polymerization) value for dCTP incorporation opposite G is 4.8fold higher than for wild-type enzyme. The kpol (forward rates of polymerization) value for dCTP incorporation opposite 8-oxoG is 3.5fold higher than wild-type enzyme insertion of dCTP opposite 8-oxoG. The catalytic efficiency of the Glu332 mutant is 2.3fold greater than wild-type Dpo4 for dCTP incorporation opposite G but 1.7fold less efficient than wild-type Dpo4 for incorporation opposite 8-oxoG
F12A
-
no detectable incorporation of ribonucleotide triphosphate is observed with the wild-type enzyme, the mutant form F12A efficiently incorporates and extends ribonucleotide triphosphate, even in the absence of Mn2+ ions
-
D424A
-
mutation in polymerase active site, the polymerase activity is reduced more than 30fold compared to the wild-type activity
-
D424A/D542A
-
mutation in polymerase active site, complete inactivation of polymerase activity
-
D542A
-
mutation in polymerase active site, the polymerase activity is reduced more than 50fold compared to the wild-type activity
-
F12A
-
no detectable incorporation of ribonucleotide triphosphate is observed with the wild-type enzyme, the mutant form F12A efficiently incorporates and extends ribonucleotide triphosphate, even in the absence of Mn2+ ions
-
N188W
-
kcat/Km for dCTP is 2.9fold compared to kcat/Km of wild-type enzyme
-
N249Y
-
exhibits increased catalytic activity when compared to the wild-type enzyme, the mutation decreases the affinity for NAD(H) cofactor
-
R322H
-
the His332 mutant exhibits faster forward rate constants relative to wild-type Dpo4. The kpol values for the His332 mutant incorporation opposite G and 8-oxoG are 3.6- and 4.6fold faster than for wild-type Dpo4. The nucleotide binding affinity trend is opposite that of wild-type Dpo4, Glu332, and Leu332, with tighter dCTP binding during bypass of G. As in the case of Ala332, the kinetic analysis indicates that His332 inserts dCTP opposite G with slightly greater efficiency than opposite 8-oxoG
-
R322L
-
kpol (forward rate of polymerization) values for the Leu332 mutant incorporation opposite G and 8-oxoG are 4.1- and 1.9fold higher than those for wild-type Dpo4. The Leu332 mutant is about 2fold more efficient at incorporation of dCTP opposite 8-oxoG compared with G
-
R331A/R322A
-
mutant has lower forward rate constants relative to wild-type enzyme for both G and 8-oxoG. The double mutant-catalyzed insertion of dCTP opposite 8-oxoG is about 4fold higher than dCTP insertion opposite G. The measured binding affinity of dCTP is tighter than that of wild-type Dpo4 for unmodified DNA, but the binding affinity of dCTP opposite 8-oxoG is similar to that observed for wild-type enzyme. The catalytic efficiency for dCTP incorporation increases about 4fold for unmodified DNA and decreases about 2fold for 8-oxoG-modified DNA. The mutant fails to incorporate dATP opposite 8-oxoG in the presteady-state experiments. It inserts dCTP opposite 8-oxoG with an about 200fold greater efficiency than it does dATP and the steady-state efficiency of dATP incorporation is decreased about 27fold relative to the wild-type enzyme
-
R332A
-
mutant enzyme displays a higher affinity (lower KD,dCTP) for dCTP when bound to the unmodified DNA compared with the KD,dCTP measured for mutant-catalyzed incorporation of dCTP opposite 8-oxoG. Wild-type enzyme shows a greater affinity for dCTP opposite to 8-oxoG-modified DNA. The catalytic efficiency of the mutant is 23fold higher at incorporation of C opposite G and 1.2fold lower than wild-type enzyme in dCTP incorporation opposite 8-oxoG
-
R332E
-
mutant enzyme retains fidelity against bypass of 7,8-dihydro-8-oxodeoxyguanosine (8-oxoG) that is similar to wild enzyme. A crystal structure of the mutant and 8-oxoG:C pair reveals water-mediated hydrogen bonds between Glu332 and the O-8 atom of 8-oxoG. The kpol (forward rate of polymerization) value for dCTP incorporation opposite G is 4.8fold higher than for wild-type enzyme. The kpol (forward rates of polymerization) value for dCTP incorporation opposite 8-oxoG is 3.5fold higher than wild-type enzyme insertion of dCTP opposite 8-oxoG. The catalytic efficiency of the Glu332 mutant is 2.3fold greater than wild-type Dpo4 for dCTP incorporation opposite G but 1.7fold less efficient than wild-type Dpo4 for incorporation opposite 8-oxoG
-
M644F
-
mutant enzyme has reduced fidelity resulting from strongly increased misinsertion rates
M644L
-
mutant enzyme synthesizes DNA with high fidelity
M644W
-
mutant enzyme synthesizes DNA with high fidelity
Y708A
-
mutation of pol delta, exhibits slow growth, sensitivity to hydroxyurea and strong mutator phenotype for frameshifts and base substitutions
Y831A
-
mutation of pol epsilon, slight sensitivity to hydroxyurea, semidominant mutator phenotype for frameshifts and base substitutions
Y869A
-
mutation of pol alpha, strain is viable, exhibits slow growth, sensitivity to hydroxyurea and spontaneous mutator phenotype for frameshifts and base substitutions
I364Q
Salasvirus phi29
-
binds the substrate with less efficiency than wild-type enzyme
I364R
Salasvirus phi29
-
unable binding of the substrate to the enzyme
K366T
Salasvirus phi29
-
mutant enzyme shows a wild-type like phenotype in DNA-primed polymerisation in the presence of DNA as template, in terminal protein-primed reactions as initiation and transition it is impaired, especially in the presence of the Phi29 DNA-binding protein, protein p6
K371T
Salasvirus phi29
-
binds the substrate with the same efficiency as wild-type enzyme
D10A
-
retains polymerase activity, reduced exonuclease activity, changes in dependency on metal activation of exonuclease activity
D190A
-
retains polymerase activity, reduced exonuclease activity, changes in dependency on metal activation of exonuclease activity
D111A
94% loss of DNA polymerase activity
D171A
96% loss of DNA polymerase activity
E113A
92% loss of DNA polymerase activity
E128A
23% loss of DNA polymerase activity
H145A
98% loss of DNA polymerase activity
H190A
31% loss of DNA polymerase activity
K65A
98% loss of DNA polymerase activity
K66A
70% loss of DNA polymerase activity
K70A
19% loss of DNA polymerase activity
N176A
2% increase of DNA polymerase activity
S184A
46% loss of DNA polymerase activity
T134A
23% loss of DNA polymerase activity
T139A
83% loss of DNA polymerase activity
Y147A
19% loss of DNA polymerase activity
Y178A
40% loss of DNA polymerase activity
Y46A
2% loss of DNA polymerase activity
D112A/E114A
Tequatrovirus T4
-
the mutant T4 DNA polymerases is defective in 3'-5' exonuclease activity and has a 1000fold increase in the development of spontaneous mutations compared to wild type polymerase
D219A
Tequatrovirus T4
-
the mutant T4 DNA polymerases is defective in 3'-5' exonuclease activity and has a 1000fold increase in the development of spontaneous mutations compared to wild type polymerase
D324A
Tequatrovirus T4
-
the mutant T4 DNA polymerases is defective in 3'-5' exonuclease activity and has a 1000fold increase in the development of spontaneous mutations compared to wild type polymerase, the exonuclease activity of the D324A mutant is 100000-fold lower than wild type polymerase
N210D
the mutant enzyme shows very weak 3'-5'-exonuclease activity compared to the wild-type enzyme (0.1%). No significant difference in DNA polymerase activity as compared with that of the wild-type enzyme. Mutation frequency in PCR becomes higher as 3'5' exonuclease activity decreases
Y311F
the mutant enzyme shows very weak 3'-5'-exonuclease activity compared to the wild-type enzyme (0.01%). No significant difference in DNA polymerase activity as compared with that of the wild-type enzyme
H633D
DNA polymerase activity of the mutant enzyme is higher than the polymerase activity of the wild-type enzyme. PCR efficiency of the H633D mutant is higher than that of the N565K mutant enzyme
H633R
significantly improved polymerase function compared to wild-type enzyme in terms of processivity (2-fold), extension rate (1.5fold) and PCR efficiency. The kcat value of the Twa H633R mutant is similar to that of wild-type, but the Km of the Twa H633R mutant is about 1.6fold lower than that of the wild-type
N565K
DNA polymerase activity of the mutant enzyme is higher than the polymerase activity of the wild-type enzyme. PCR efficiency of the H633D mutant is higher than that of the N565K mutant enzyme
F388A
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
L329A/Q384A
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
L329A/Y438A
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
M408A
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
Q384A
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
Q384A/Y438A
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
T326A
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
Y438A
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
F388A
-
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
-
Q384A
-
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
-
T326A
-
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
-
Y438A
-
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
-
E602V/A608V/I614M/E615G
the mutant enzyme is able to incorporate both NTPs and dNTPs with the same catalytic efficiency as the wild-type enzyme incorporates dNTPs. The mutant enzyme allowed the generation of mixed RNADNA amplification products in PCR demonstrating DNA polymerase, RNA polymerase as well as reverse transcriptase activity within the same polypeptide. The mutant displays an expanded substrate spectrum towards other 2'-substituted nucleotides and is able to synthesize nucleic acid polymers in which each base bear a different 2'-substituent
G418K
-
increased exonuclease activity
L831N/A814R
truncated enzyme delta413-L813N/A814R has reduced temperature stability
N483Q/S486Q/T539N/Y545Q/D547T/P548Q/A570Q/D578Q/A597T/W604R /S612N/V730L/R736Q/S739N/M747R
-
selection of a polymerase with 15 mutations, mostly located at the template binding interface, by directed evolution of Thermus aquaticus DNA polymerase I, the mutant enzyme is a single variant of the Stoffel fragment of Taq DNA polymerase I, the enzyme shows broad template specificity and is a thermostable DNA-dependent and RNA-dependent DNA-polymerase, see also EC 2.7.7.49
Q507E
-
increased exonuclease activity
D349A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
D529A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
E413A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
H344A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
H374A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
H440A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
H468A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
H531A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
Q342A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
D349A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
-
D529A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
-
H344A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
-
H374A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
-
Q342A
-
the Mg2+-dependent DNA polymerase activity of the mutant is almost the same as that of wild type enzyme
-
L391F
-
defective in the in vitro replication initiation and DNA polymerase elongation assays and fails to recognize the viral replication origin if the protein is expressed at 37°C, expression at 32°C results in activities similar to wild-type enzyme
E292K
more active than wild-type enzyme
E292K
similar activity as wild-type enzyme
F192C
more active than wild-type enzyme
F192C
slight increase in activity with N2-furfuryl-dG-containing templates
I39T
more active than wild-type enzyme
I39T
similar activity to WT with several types of DNA damage
L21F
30fold decrease in incorporation opposite N2-CH2-(9-anthracenyl)-dG (N2-CH2-Anth-dG)
L21F
more active than wild-type enzyme
P169T
more active than wild-type enzyme
P169T
slight decrease in activity on undamaged DNA
R219I
less active than wild-type enzyme
R219I
slight decrease in activity
R298H
less active than wild-type enzyme, markedly reduced thermal stability
R298H
less active than wild-type on several different lesions
R964C
-
mutation identified in a patient with lactic acidosis. Recombinant R964C Pol gamma shows only 14% activity of wild-type enzyme. The mutation could be associated with the severe lactic acidosis induced by long-term use of nucleoside reverse-transcriptase inhibitors
R964C
-
naturally occuring mutation
R964C
-
the mutation demonstrates a 33% decrease in dTTP incorporation efficiency and a 3fold lower d4TTP discrimination relative to that of the wild type enzyme
Y432S
less active on undamaged and damaged DNA, extension defect, decreased DNA binding affinity
Y432S
less active than wild-type enzyme, markedly reduced thermal stability
Y505A
-
slightly less active in de novo DNA synthesis when compared with wild-type enzyme
Y505A
-
N-[6-N-(2,4-dinitrophenyl)aminohexanoyl]-2-aminoethyl triphosphate, N-(2,4-dinitro-5-fluorophenyl)-2-aminoethyl triphosphate, N-(2,4-dinitro-5-imidazolylphenyl)-4-aminobutyl triphosphate and N-(2,4-dinitro-5-imidazolylphenyl)-2-aminoethyl triphosphate inhibit mutant enzyme Y505A and are inactive against wild-type enzyme. DNA polymerase lambda and its mutant Y505A show different abilities of incorporating NNTPs in the presence of an abasic site on the template strand
F12A
mutant ribonucleoside triphosphates almost as efficiently as deoxyribonucleoside triphosphates, and, unlike analogous mutants in other polymerase families, shows no barrier to adding multiple ribonucleotides, suggesting that Dbh can readily accommodate a DNA/RNA duplex product
F12A
GTP incorporation by the wild-type enzyme is about 1000fold slower than dGTP incorporation. The rate of GTP incorporation by the mutant enzyme F12A Dbh is 2-3fold slower than incorporation of dGTP. When making a deletion error, ribonucleotide discrimination by wild-type and F12A Dbh is the same as in normal DNA synthesis
F12A
-
no detectable incorporation of ribonucleotide triphosphate is observed with the wild-type enzyme, the mutant form F12A efficiently incorporates and extends ribonucleotide triphosphate, even in the absence of Mn2+ ions
T239W
-
the frameshift deletion is selective for purines and involves normal conformational change followed by slow phosphodiester bond formation
T239W
-
the mutant enzyme is used to analyze conformational changes associated with the addition of dCTP opposite N2-alkylG adducts
T239W
kcat/Km for dCTP is 3.6fold compared to kcat/Km of wild-type enzyme
Y12A
-
mutation causes an average increase of 220fold in matched ribonucleotide incorporation efficiency and an average decrease of 9fold in correct deoxyribonucleotide incorporation efficiency, leading to an average reduction of 2000fold in sugar selectivity. The mutant incorporates more than 20 consecutive ribonucleotides into primer/template (DNA/DNA) duplexes, suggesting that this mutant protein possesses both aDNA-dependent DNA polymerase activity and a DNA-dependent RNA polymerase activity
Y12A
active-site mutation Y12A in Dpo4, causes both a dramatic loss of ribonucleotide discrimination and a decrease in nucleotide incorporation efficiency
T239W
-
the frameshift deletion is selective for purines and involves normal conformational change followed by slow phosphodiester bond formation
-
T239W
-
the mutant enzyme is used to analyze conformational changes associated with the addition of dCTP opposite N2-alkylG adducts
-
T239W
-
kcat/Km for dCTP is 3.6fold compared to kcat/Km of wild-type enzyme
-
Y12A
-
mutation causes an average increase of 220fold in matched ribonucleotide incorporation efficiency and an average decrease of 9fold in correct deoxyribonucleotide incorporation efficiency, leading to an average reduction of 2000fold in sugar selectivity. The mutant incorporates more than 20 consecutive ribonucleotides into primer/template (DNA/DNA) duplexes, suggesting that this mutant protein possesses both aDNA-dependent DNA polymerase activity and a DNA-dependent RNA polymerase activity
-
Y12A
-
active-site mutation Y12A in Dpo4, causes both a dramatic loss of ribonucleotide discrimination and a decrease in nucleotide incorporation efficiency
-
K242R/I243K/P244S
mutation of three linker amino acids, polymerase Dbh adopts the standard conformation of polymerase Dpo4. The interdomain linker also affects the single-base deletion frequency and the mispair extension efficiency of these polymerase
K242R/I243K/P244S
-
mutation of three linker amino acids, polymerase Dbh adopts the standard conformation of polymerase Dpo4. The interdomain linker also affects the single-base deletion frequency and the mispair extension efficiency of these polymerase
-
molecular biology
-
the high fidelty of the enzyme is suitable fo polymerase chain reaction (PCR), which requires accurate DNA amplification for gene cloning and diagnostic assay
molecular biology
-
the high fidelty of the enzyme is suitable fo polymerase chain reaction (PCR), which requires accurate DNA amplification for gene cloning and diagnostic assay
-
L329A
-
site-directed mutagenesis
L329A
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
L329A
-
site-directed mutagenesis
-
L329A
-
site-directed mutagenesis, the mutant exhibits DNA-dependent and RNA-dependent DNA polymerase activities, while the wild-type enzyme is a DNA-depedent DNA polymerase
-
additional information
-
null mutations in Arabidopsis POL2a are embryonic lethal
additional information
-
a polX disruption mutant expressing 5'-deoxyribose phosphate lyase and a truncated polymerase domain is comparatively less sensitive to gamma-radiation at 10 kGy than a polX deletion mutant, both mutants show higher sensitivity to hydrogen peroxide
additional information
-
a polX disruption mutant expressing 5'-deoxyribose phosphate lyase and a truncated polymerase domain is comparatively less sensitive to gamma-radiation at 10 kGy than a polX deletion mutant, both mutants show higher sensitivity to hydrogen peroxide
-
additional information
-
insertions in the DNA polymerase III epsilon subunit gene (dnaQ) cause a specific defect in SOS induction by nalidixic acid but not by mitomycin C
additional information
-
generations of deletion umuDC operon mutants, pol V Mut shows altered requirements of accessory factors compared to the wild-type enzyme, overview
additional information
-
insertions in the DNA polymerase III epsilon subunit gene (dnaQ) cause a specific defect in SOS induction by nalidixic acid but not by mitomycin C
-
additional information
-
fusion of RB69 DNA polymerase with its cognate single-stranded DNA binding protein via a short six amino acid linker increases affinity for primer-template DNA by 6fold and subsequently increases processivity by 7fold while maintaining fidelity
additional information
-
DNA binding, dNTP binding and catalytic activity of mutant enzyme in the presence of two metal ions, Mg2+ and Mn2+, overview
additional information
-
engineered DNA polymerases are obtained by the flexible attachment of helix-hairpin-helix DNA binding domains of topoisomerase V of Methanopyrus kandleri to catalytic domains of DNA polymerases, domain fusion using the Taq and Pfu DNA polymerases or the phi29 DNA polymerase. The chimeric polymerases retain high processivity at high concentrations of salts and other inhibitors of DNA synthesis, such as phenol, blood, and DNA intercalating dyes, domain attachment has a potential to greatly increase the thermostability of chimeric DNA polymerases
additional information
-
POLPs have two extra sequences in the polymerase domain that are absent in prokaryotic PolIs. Deletion of either insert from OsPOLP1 causes a decrease in DNA synthetic activity, processivity, and DNA binding activity
additional information
-
deletion of the dinB gene sensitized Pseudomonas aeruginosa to nitrofurazone and 4-nitroquinoline-1-oxide, consistent with a role for DinB in translesion DNA synthesis over N2-dG adducts, while the UV-inducible mutator phenotype is independent of dinB function
additional information
-
reconstitution of replicase activity by co-expression of essential components of DNA polymerase holoenzyme from Pseudomonas aeruginosa: expression of processivity factor, i.e. beta-subunit, single-stranded DNA-binding protein, a complex containing the polymerase, i.e. alpha-subunit, and exonuclease, i.e. epsilon-subunit, and the essential components of the DnaX complex tau3deltadelta', Pseudomonas aeruginosa alphaepsilon can substitute completely for Escherichia coli polymerase III in Escherichia coli holoenzyme reconstitution assays, addition of purified Escherichia coli chi and psi, components of the DnaX complex, increases the apparent specific activity of the Pseudomonas tau3deltadelta' complex about 10-fold and enables the reconstituted enzyme to function better under physiological salt conditions, overview
additional information
-
construction of Pol IV-defective dinB knockout mutants
additional information
-
the (G)-PYF box is located in a hydrophobic region close to the active site. The (G)-PYF box mutants exhibit altered DNA binding properties. In addition, the thermal stability of all mutants is reduced compared to that of wild type, and this effect could be attributed to increased exposure of the hydrophobic region
additional information
-
deletion of the COOH-terminal zinc finger region (12891308) does not abolish the subunit interaction. Instead, while the polymerization of the deletion mutants remains, the 3'-5' exonuclease is completely inactivated. Deletion of DP1Pho(1200) increases the exonuclease and DNA binding activities of PolDPho. Adding DP1Pho(1200) to the truncated protein suppresses the elevated exonuclease activity
additional information
generaion of chimeras of Sulfolobus solfataricus DNA polymerase Dpo4 and Sulfolobus acidocaldarius DNA polymerase Dbh in which their little finger domains have been interchanged. Interestingly, by replacing the little finger domain of Dbh with that of Dpo4, the enzymatic properties of the chimeric enzyme are more Dpo4-like in that the enzyme is more processive, can bypass an abasic site and a thymine-thymine cyclobutane pyrimidine dimer, and predominantly makes base pair substitutions when replicating undamaged DNA. The converse is true for the Dpo4-LF-Dbh chimera, which is more Dbh-like in its processivity and ability to bypass DNA adducts and generate single-base deletion errors. The unique but variable little finger domain of Y-family polymerases plays a major role in determining the enzymatic and biological properties of each individual Y-family member
additional information
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generaion of chimeras of Sulfolobus solfataricus DNA polymerase Dpo4 and Sulfolobus acidocaldarius DNA polymerase Dbh in which their little finger domains have been interchanged. Interestingly, by replacing the little finger domain of Dbh with that of Dpo4, the enzymatic properties of the chimeric enzyme are more Dpo4-like in that the enzyme is more processive, can bypass an abasic site and a thymine-thymine cyclobutane pyrimidine dimer, and predominantly makes base pair substitutions when replicating undamaged DNA. The converse is true for the Dpo4-LF-Dbh chimera, which is more Dbh-like in its processivity and ability to bypass DNA adducts and generate single-base deletion errors. The unique but variable little finger domain of Y-family polymerases plays a major role in determining the enzymatic and biological properties of each individual Y-family member
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generaion of chimeras of Sulfolobus solfataricus DNA polymerase Dpo4 and Sulfolobus acidocaldarius DNA polymerase Dbh in which their little finger domains have been interchanged. Interestingly, by replacing the little finger domain of Dbh with that of Dpo4, the enzymatic properties of the chimeric enzyme are more Dpo4-like in that the enzyme is more processive, can bypass an abasic site and a thymine-thymine cyclobutane pyrimidine dimer, and predominantly makes base pair substitutions when replicating undamaged DNA. The converse is true for the Dpo4-LF-Dbh chimera, which is more Dbh-like in its processivity and ability to bypass DNA adducts and generate single-base deletion errors. The unique but variable little finger domain of Y-family polymerases plays a major role in determining the enzymatic and biological properties of each individual Y-family member
additional information
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generaion of chimeras of Sulfolobus solfataricus DNA polymerase Dpo4 and Sulfolobus acidocaldarius DNA polymerase Dbh in which their little finger domains have been interchanged. Interestingly, by replacing the little finger domain of Dbh with that of Dpo4, the enzymatic properties of the chimeric enzyme are more Dpo4-like in that the enzyme is more processive, can bypass an abasic site and a thymine-thymine cyclobutane pyrimidine dimer, and predominantly makes base pair substitutions when replicating undamaged DNA. The converse is true for the Dpo4-LF-Dbh chimera, which is more Dbh-like in its processivity and ability to bypass DNA adducts and generate single-base deletion errors. The unique but variable little finger domain of Y-family polymerases plays a major role in determining the enzymatic and biological properties of each individual Y-family member
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the DNA coding sequence of KOD from Pyrococcus sp. KOD1 is optimized based on the codon usage bias of Pichia pastoris and synthesized by overlapping PCR, and the nonspecific DNA-binding protein Sso7d from Sulfolobus solfataricus is fused to the C-terminus of KOD. The resulting novel gene is cloned into a pHBM905A vector and introduced into Pichia pastoris GS115 for secretory expression. The yield of the target protein reaches approximately 250 mg/l after a 6 day induction with 1% (v/v) methanol in shake flasks. This yield is much higher than those of other DNA polymerases expressed heterologously in Escherichia coli. The recombinant enzyme expressed in Pichia pastoris exhibits excellent thermostability, extension rate and fidelity. When Sso7d is fused to the enzyme, a significant enhancement of processivity is achieved regardless of the starting processivity of the enzyme
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the DNA coding sequence of KOD from Pyrococcus sp. KOD1 is optimized based on the codon usage bias of Pichia pastoris and synthesized by overlapping PCR, and the nonspecific DNA-binding protein Sso7d from Sulfolobus solfataricus is fused to the C-terminus of KOD. The resulting novel gene is cloned into a pHBM905A vector and introduced into Pichia pastoris GS115 for secretory expression. The yield of the target protein reaches approximately 250 mg/l after a 6 day induction with 1% (v/v) methanol in shake flasks. This yield is much higher than those of other DNA polymerases expressed heterologously in Escherichia coli. The recombinant enzyme expressed in Pichia pastoris exhibits excellent thermostability, extension rate and fidelity. When Sso7d is fused to the enzyme, a significant enhancement of processivity is achieved regardless of the starting processivity of the enzyme
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Tpa-S DNA polymerase (the fusion of the Sso7d protein to the C-terminus of Tpa DNA polymerase) improves the performance of the Tpa DNA polymerase to make it suitable for long and rapid polymerase chain reaction
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Tpa-S DNA polymerase (the fusion of the Sso7d protein to the C-terminus of Tpa DNA polymerase) improves the performance of the Tpa DNA polymerase to make it suitable for long and rapid polymerase chain reaction
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construction of a chimeric DNA polymerase derived from Thermus species Z05 and Thermotoga maritima DNA polymerases. These chimeric DNA polymerases are fashioned using structure-based tools to identify amino acid residues involved in the substrate-binding site of the exonuclease domain of a thermostable DNA polymerase. Mutation of some of these residues results in proteins in which DNA polymerase activity is unaffected, while proofreading activity ranges from 60% of the wild-type level to undetectable levels. Kinetic characterization of the exonuclease activity indicates that the mutations affects catalysis much more than binding. On the basis of their specificity constants (kcat/KM), the mutant enzymes have a 5-15-fold stronger preference for a double-stranded mismatched substrate over a single-stranded substrate than the wild-type DNA polymerase, a desirable attribute for RT/PCR
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generation of a mutated thermostable DNA polymerase, Taq M1, from Thermus aquaticus that exhibits an increased reverse transcriptase activity. The Taq polymerase mutant Taq M1 has similar PCR sensitivity and nuclease activity as the respective Taq wild-type DNA polymerase, but Taq M1 exhibits a significantly increased reverse transcriptase activity especially at high temperatures compared to the wild-type
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the intervening domain of the thermostable Thermus aquaticus DNA polymerase (TAQ: polymerase), which has no catalytic activity, is exchanged for the 3'-5' exonuclease domain of the homologous mesophile Escherichia coli DNA polymerase I (Escherichia coli pol I) and the homologous thermostable Thermotoga neapolitana DNA polymerase (TNE: polymerase). Three chimeric DNA polymerases are constructed using the three-dimensional (3D) structure of the Klenow fragment of the Escherichia coli pol I and 3D models of the intervening and polymerase domains of the TAQ: polymerase and the TNE: polymerase: chimera TaqEc1 (exchange of residues 292-423 from TAQ: polymerase for residues 327-519 of Escherichia coli pol I), chimera TaqTne1 (exchange of residues 292-423 of TAQ: polymerase for residues 295-485 of TNE: polymerase) and chimera TaqTne2 (exchange of residues 292-448 of TAQ: polymerase for residues 295-510 of TNE: polymerase). The chimera TaqEc1 shows characteristics from both parental polymerases at an intermediate temperature of 50°C: high polymerase activity, processivity, 3'-5' exonuclease activity and proof-reading function The chimeras TaqTne1 and TaqTne2 show no significant 3'-5' exonuclease activity and no proof-reading function. The chimera TaqTne1 shows an optimum temperature at 60°C, decreased polymerase activity compared with the TAQ: polymerase and reduced processivity. The chimera TaqTne2 shows high polymerase activity at 72°C, processivity and less reduced thermostability compared with the chimera TaqTne1
additional information
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the intervening domain of the thermostable Thermus aquaticus DNA polymerase (TAQ: polymerase), which has no catalytic activity, is exchanged for the 3'-5' exonuclease domain of the homologous mesophile Escherichia coli DNA polymerase I (Escherichia coli pol I) and the homologous thermostable Thermotoga neapolitana DNA polymerase (TNE: polymerase). Three chimeric DNA polymerases are constructed using the three-dimensional (3D) structure of the Klenow fragment of the Escherichia coli pol I and 3D models of the intervening and polymerase domains of the TAQ: polymerase and the TNE: polymerase: chimera TaqEc1 (exchange of residues 292-423 from TAQ: polymerase for residues 327-519 of Escherichia coli pol I), chimera TaqTne1 (exchange of residues 292-423 of TAQ: polymerase for residues 295-485 of TNE: polymerase) and chimera TaqTne2 (exchange of residues 292-448 of TAQ: polymerase for residues 295-510 of TNE: polymerase). The chimera TaqEc1 shows characteristics from both parental polymerases at an intermediate temperature of 50°C: high polymerase activity, processivity, 3'-5' exonuclease activity and proof-reading function The chimeras TaqTne1 and TaqTne2 show no significant 3'-5' exonuclease activity and no proof-reading function. The chimera TaqTne1 shows an optimum temperature at 60°C, decreased polymerase activity compared with the TAQ: polymerase and reduced processivity. The chimera TaqTne2 shows high polymerase activity at 72°C, processivity and less reduced thermostability compared with the chimera TaqTne1
additional information
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construction of a chimeric DNA polymerase derived from Thermus species Z05 and Thermotoga maritima DNA polymerases. These chimeric DNA polymerases are fashioned using structure-based tools to identify amino acid residues involved in the substrate-binding site of the exonuclease domain of a thermostable DNA polymerase. Mutation of some of these residues results in proteins in which DNA polymerase activity is unaffected, while proofreading activity ranges from 60% of the wild-type level to undetectable levels. Kinetic characterization of the exonuclease activity indicates that the mutations affects catalysis much more than binding. On the basis of their specificity constants (kcat/KM), the mutant enzymes have a 5-15-fold stronger preference for a double-stranded mismatched substrate over a single-stranded substrate than the wild-type DNA polymerase, a desirable attribute for RT/PCR
additional information
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construction of a chimeric DNA polymerase derived from Thermus species Z05 and Thermotoga maritima DNA polymerases. These chimeric DNA polymerases are fashioned using structure-based tools to identify amino acid residues involved in the substrate-binding site of the exonuclease domain of a thermostable DNA polymerase. Mutation of some of these residues results in proteins in which DNA polymerase activity is unaffected, while proofreading activity ranges from 60% of the wild-type level to undetectable levels. Kinetic characterization of the exonuclease activity indicates that the mutations affects catalysis much more than binding. On the basis of their specificity constants (kcat/KM), the mutant enzymes have a 5-15-fold stronger preference for a double-stranded mismatched substrate over a single-stranded substrate than the wild-type DNA polymerase, a desirable attribute for RT/PCR
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additional information
the wild-type enzyme is modified by deletion of the N-terminal 5' to 3' exonuclease domain, by fusion with the DNA-binding protein Sso7d and by introduction of four known effective point mutations from other DNA polymerase mutants, and codon optimization to reduce the GC content. A mutant is obtained that provides higher product yields than the conventional Taq pol without decreased fidelity. Next, four rounds of compartmentalized self-replication (CSR) selection are performed with a randomly mutated library of this modified Tth pol and mutants are obtainwed that provide higher product yields in fewer cycles of emulsion PCR than the parent Tth pol as well as the conventional Taq pol
additional information
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the wild-type enzyme is modified by deletion of the N-terminal 5' to 3' exonuclease domain, by fusion with the DNA-binding protein Sso7d and by introduction of four known effective point mutations from other DNA polymerase mutants, and codon optimization to reduce the GC content. A mutant is obtained that provides higher product yields than the conventional Taq pol without decreased fidelity. Next, four rounds of compartmentalized self-replication (CSR) selection are performed with a randomly mutated library of this modified Tth pol and mutants are obtainwed that provide higher product yields in fewer cycles of emulsion PCR than the parent Tth pol as well as the conventional Taq pol
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dyskinetoplastid bloodstream form parasites produced during RNAi are not viable, disruption of network-free minicircle replication precedes parasite death
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parasites overexpressing Tcpolbeta shows reduced levels of 7,8-dihydro-8-oxoguanine in kDNA and an increased survival after treatment with hydrogen peroxide when compared to control cells. The resistance is lost after treating Tcpolbeta overexpressors with methoxiamine, a potent base-excision repair inhibitor
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