2.7.7.7: DNA-directed DNA polymerase
This is an abbreviated version!
For detailed information about DNA-directed DNA polymerase, go to the full flat file.
Word Map on EC 2.7.7.7
-
2.7.7.7
-
strand
-
single-stranded
-
fidelity
-
holoenzyme
-
mismatch
-
bacteriophage
-
pcna
-
fork
-
polymerization
-
aphidicolin
-
duplex
-
proofreading
-
calf
-
endonuclease
-
thymus
-
clamp
-
misincorporation
-
helicase
-
abasic
-
template-primer
-
5'-triphosphate
-
dntps
-
stall
-
thymine
-
error-free
-
mispairs
-
anneal
-
sliding
-
uv-induced
-
incoming
-
exonucleolytic
-
replisome
-
transversions
-
deoxyribonucleoside
-
xeroderma
-
pigmentosum
-
ssdna
-
deoxynucleotide
-
hypermutation
-
undamaged
-
okazaki
-
dtmp
-
slippage
-
cyclobutane
-
transcriptases
-
dnab
-
watson-crick
-
high-fidelity
-
myeloblastosis
-
aquaticus
-
synthesis
-
analysis
-
drug development
-
diagnostics
-
biotechnology
-
medicine
-
molecular biology
- 2.7.7.7
- strand
-
single-stranded
-
fidelity
-
holoenzyme
- mismatch
- bacteriophage
- pcna
- fork
- polymerization
- aphidicolin
- duplex
-
proofreading
-
calf
- endonuclease
- thymus
-
clamp
-
misincorporation
- helicase
-
abasic
-
template-primer
- 5'-triphosphate
- dntps
-
stall
- thymine
-
error-free
- mispairs
-
anneal
-
sliding
-
uv-induced
-
incoming
-
exonucleolytic
- replisome
-
transversions
- deoxyribonucleoside
- xeroderma
- pigmentosum
- ssdna
-
deoxynucleotide
-
hypermutation
-
undamaged
-
okazaki
- dtmp
-
slippage
-
cyclobutane
- transcriptases
- dnab
-
watson-crick
-
high-fidelity
-
myeloblastosis
- aquaticus
- synthesis
- analysis
- drug development
- diagnostics
- biotechnology
- medicine
- molecular biology
Reaction
Synonyms
3'–5'-exonuclease, ABO4/POL2a/TIL1, Afu polymerase, ASFV DNA polymerase, ASFV Pol X, B-family replicative DNA polymerase, beta type DNA polymerase, Bst DNA polymerase, CpDNApolI, DBH, Dbh DNA polymerase, Dbh polymerase, ddNTP-sensitive DNA polymerase, Deep Vent DNA polymerase, DeepVent DNA polymerase, deoxynucleate polymerase, deoxyribonucleate nucleotidyltransferase, deoxyribonucleic acid duplicase, deoxyribonucleic acid polymerase, deoxyribonucleic duplicase, deoxyribonucleic polymerase, deoxyribonucleic polymerase I, DinB DNA polymerase, DinB homologue, Dmpol zeta, DNA deoxynucleotidyltransferase, DNA duplicase, DNA nucleotidyltransferase, DNA nucleotidyltransferase (DNA-directed), DNA pol, DNA pol B1, DNA Pol eta, DNA Pol lambda, DNA pol NI, DNA pol Y1, DNA polmerase beta, DNA polymerase, DNA polymerase 1, DNA polymerase 2, DNA polymerase 4, DNA polymerase A, DNA polymerase alpha, DNA polymerase B, DNA polymerase B1, DNA polymerase B2, DNA polymerase B3, DNA polymerase beta, DNA polymerase D, DNA polymerase Dbh, DNA polymerase delta, DNA polymerase Dpo4, DNA polymerase epsilon, DNA polymerase eta, DNA polymerase gamma, DNA polymerase I, DNA polymerase II, DNA polymerase III, DNA polymerase III epsilon subunit, DNA polymerase iota, DNA polymerase IV, DNA polymerase kappa, DNA polymerase lambda, DNA polymerase mu, DNA polymerase ny, DNA polymerase pyrococcus kodakaraensis, DNA polymerase theta, DNA polymerase V, DNA polymerase X, DNA polymerase zeta, DNA polymerases B, DNA polymerases D, DNA polymmerase I, DNA primase-polymerase, DNA replicase, DNA replication polymerase, DNA-dependent DNA polymerase, DNAP, DP1Pho, DP2Pho, Dpo1, Dpo2, Dpo3, Dpo4, Dpo4 polymerase, Dpo4-like enzyme, duplicase, error-prone DNA polymerase, error-prone DNA polymerase X, family B-type DNA polymerase, hoPolD, HSV 1 POL, Igni_0062, K4 polymerase, K4pol, K4PolI, kDNA replication protein, KDO XL DNA polymerase, KF(exo-), KF-, Klenow fragment, Klenow-like DNA polymerase I, KOD DNA polymerases, lesion-bypass DNA polymerase, M1 DNA polymerase, M1pol, MacDinB-1, MA_4027, Miranda pol beta protein, mitochondrial DNA polymerase, Mka polB, More, MsDpo4, mtDNA polymerase NI, mtDNA replicase, Neq DNA polymerase, non-replicative DNA polymerase III, nucleotidyltransferase, deoxyribonucleate, OsPOLP1, PabPol D, PabpolB, PabpolD, Pfu, Pfu DNA polymerase, Pfu Pol, Pfu-POl, PH0121, PH0123, phi29 DNA polymerase, phi29 DNApol, PhoPolD, phPol D, Pol, pol alpha, Pol B, Pol B1, pol beta, Pol BI, pol delta, pol E, POl epsilon, Pol eta, Pol gamma, Pol I, Pol II, pol III, pol iota, Pol IV, pol kappa, pol kappaDELTAC, Pol lambda, Pol mu, pol NI, Pol ny, Pol theta, Pol V, pol Vent (exo-), Pol X, Pol zeta, Pol-beta, POL1, Pol2, POL2a, Pol3, Pol31, PolB, POlB1, polbeta, polD, POLD4, Poldelta, POLdelta1, PolDPho, Polepsilon, Poleta, POLG, PolH, polI, POLIB, POLIC, POLID, poliota, Polkappa, PolX, PolY, poly iota, polymerase alpha catalytic subunit A, polymerase III, pORF30, Pwo DNA polymerase, R2 polymerase, R2 reverse transcriptase, R2-RT, RAD30, RB69 DdDp, RB69 DNA Polymerase, RB69pol, Rec1, repair polymerase, replicative DNA polymerase, reverse transcriptase, RKOD DNA polymerase, Rv1537, Rv3056, Saci_0554, sequenase, Sso, Sso DNA pol B1, Sso DNA pol Y1, Sso DNA polymerase Y1, Sso DNApol, Sso pol B1, SSO0552, SSO2448, SsoDpo1, SsoPolB1, SsoPolY, Szi DNA polymerase, T4 DNA polymerase, T7 DNA polymerase, Taq DNA polymerase, Taq Pol I, Taq polymerase, Tba5 DNA polymerase, Tca DNA polymerase, Tga PolB, TGAM_RS07365, Tkod-Pol, translesion DNA polymerase, translesion DNA synthesis polymerase, translesion polymerase Dpo4, UL30/UL42, UmuD'2C, UmuD'2C-RecA-ATP, Vent polymerase, X family DANN polymerase, Y-family DNA polymerase eta
ECTree
2.7.7.7 DNA-directed DNA polymeraseAdvanced search results
results (
results (Substrates Products
Substrates Products on EC 2.7.7.7 - DNA-directed DNA polymerase
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SUBSTRATE 
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
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-[(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
?
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-2Â’-deoxyribofuranosid-5Â’-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
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
-
-
?
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 + primed M13n
diphosphate + primed M13n+1
-
-
-
?
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
-
-
?
poly(dA)/oligo(dT)x + n dTTP
poly(dA)/oligo(dT)x+n + n diphosphate
preferred substrate
-
-
?
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
-
-
?
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-2Â’-deoxyribofuranosid-5Â’-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-2Â’-deoxyribofuranosid-5Â’-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-2Â’-deoxyribofuranosid-5Â’-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-2Â’-deoxyribofuranosid-5Â’-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-2Â’-deoxyribofuranosid-5Â’-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-2Â’-deoxyribofuranosid-5Â’-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
?
-
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 + 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
-
dNTP insertion opposite a benzo[a]pyrene-N2-dG-adduct
-
-
?
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-2Â’-deoxyribofuranosid-5Â’-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-2Â’-deoxyribofuranosid-5Â’-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
-
dNTP insertion opposite a benzo[a]pyrene-N2-dG-adduct
-
-
?
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 Watson–Crick 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 Watson–Crick hydrogen-bonded with dCTP with modest polymerase perturbation, but other nucleotides are more distorting
-
-
?
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
-
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
-
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
-
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
-
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
-
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
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
-
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
-
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
-
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
Deinococcus radiodurans R1 / ATCC 13939 / DSM 20539
-
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
-
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
-
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
-
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 10–15fold 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
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
-
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
-
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
-
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
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
-
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
-
-
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
-
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
-
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
-
-
?
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
-
template specificity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
standard substrate PTJ1 and substrate PTJ2
-
-
?
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
-
-
?
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
-
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
-
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
-
-
?
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
-
-
?
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
-
-
?
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
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
replicative DNA polymerase
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-
?
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
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the enzyme plays an essential role in DNA replication, repair, and recombination
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
the carboxyl-terminal (1255–1332) of the large subunit (DP2Pho) and two regions, the 201–260 and 599–622, of the small subunit (DP1Pho) are critical for the complex formation, and probable subunit interaction of PolDPho. The amino-terminal (1–300) of DP2Pho is essential for the folding of PolDPho and is likely the oligomerization domain of PolDPho
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-
?
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
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-
?
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
-
-
-
?
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
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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
-
-
-
?
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 3–4 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)
-
-
?
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
-
-
?
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
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-
?
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
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
bypass of apurinic/apyrimidinic sites lacking A or G is nearly 100% mutagenic. The majority (70–80%) 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
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-
?
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
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-
?
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
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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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
exclusively incorporates 8-OH-GTP opposite adenine
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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
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-
?
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)
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-
?
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
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-
?
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
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-
?
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
-
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
-
exonuclease 5'--3' activity, pol I
-
-
?
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
-
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
-
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
-
-
-
?
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
-
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
-
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
-
exonuclease 5'--3' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
no exonuclease 3'--5' activity
-
?
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
-
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
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
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
-
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
-
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
?
-
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
-
dNTP insertion opposite a benzo[a]pyrene-N2-dG-adduct
-
-
?
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
-
-
?
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-2Â’-deoxyribofuranosid-5Â’-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-2Â’-deoxyribofuranosid-5Â’-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
-
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
-
activity assay with plus-strand m13 DNA annealed to 5'-32P end-labeled primer 5'-GCTGTTGGGAAGGGCGATCG-3'
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
-
dNTP insertion opposite a benzo[a]pyrene-N2-dG-adduct
-
-
?
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
incorporation of dTTP into poly(rA)-p(dT)45
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
incorporation of dTTP into poly(rA)-p(dT)45
-
-
?
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
?
-
Pyrococcus abyssi GE5 / CNCM I-1302 / DSM 25543
-
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 1.5–4.5-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
?
-
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 Dpo4Â’s 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 Dpo4Â’s 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
?
-
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
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
-
-
?
