Biochemical basis of DNA replication fidelity

scientific article

Biochemical basis of DNA replication fidelity is …
instance of (P31):
review articleQ7318358
scholarly articleQ13442814

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P356DOI10.3109/10409239309086792
P698PubMed publication ID8485987

P2093author name stringGoodman MF
Creighton S
Bloom LB
Petruska J
P2860cites workGenetical Implications of the Structure of Deoxyribonucleic AcidQ22122440
Base pairing and mutagenesis: observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMRQ24630526
Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS)Q24635921
Primer-directed enzymatic amplification of DNA with a thermostable DNA polymeraseQ26778389
Crystal structure and stability of a DNA duplex containing A(anti).G(syn) base-pairsQ27727725
Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutationsQ27728602
Refined crystal structure of an octanucleotide duplex with G . T mismatched base-pairsQ27728951
Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMPQ27728960
Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemiaQ27861076
SOS Repair Hypothesis: Phenomenology of an Inducible DNA Repair Which is Accompanied by MutagenesisQ28141658
The structure of DNAQ28210412
Regulation and expression of the adaptive response to alkylating agentsQ28289093
Mutagenesis by apurinic/apyrimidinic sitesQ28300337
MutT protein specifically hydrolyses a potent mutagenic substrate for DNA synthesisQ28343030
Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodGQ29616532
The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8-oxoguanine)Q29619959
Genetic and crystallographic studies of the 3',5'-exonucleolytic site of DNA polymerase I.Q30400206
Ionized and wobble base-pairing for bromouracil-guanine in equilibrium under physiological conditions. A nuclear magnetic resonance study on an oligonucleotide containing a bromouracil-guanine base-pair as a function of pH.Q30868730
Analysis of the RNA- and DNA-dependent DNA polymerase activities of point mutants of HIV-1 reverse transcriptase lacking ribonuclease H activityQ42616916
O6-methylguanine and A.C and G.T mismatches cause asymmetric structural defects in DNA that are affected by DNA sequenceQ43620668
A general structure for DNA-dependent DNA polymerases.Q43654996
Polymerase-specific differences in the DNA intermediates of frameshift mutagenesis. In vitro synthesis errors of Escherichia coli DNA polymerase I and its large fragment derivativeQ43974674
Antimutagenic DNA polymerases of bacteriophage T4.Q44086575
Comparative efficiency of forming m4T.G versus m4T.A base pairs at a unique site by use of Escherichia coli DNA polymerase I (Klenow fragment) and Drosophila melanogaster polymerase alpha-primase complexQ44210738
Effect of pH on the base-mispairing properties of 5-bromouracil during DNA synthesisQ44527969
Detection of ras point mutations by polymerase chain reaction using mutation-specific, inosine-containing oligonucleotide primersQ44701782
Studies on the biochemical basis of spontaneous mutation. II. The incorporation of a base and its analogue into DNA by wild-type, mutator and antimutator DNA polymerasesQ44705872
Studies on the biochemical basis of spontaneous mutation. III. Rate model for DNA polymerase-effected nucleotide misincorporationQ44741297
RecA protein and SOS. Correlation of mutagenesis phenotype with binding of mutant RecA proteins to duplex DNA and LexA cleavageQ44834679
Fidelity of the RNA-dependent DNA synthesis exhibited by the reverse transcriptases of human immunodeficiency virus types 1 and 2 and of murine leukemia virus: mispair extension frequenciesQ45872557
Fidelity of human immunodeficiency virus type I reverse transcriptase in copying natural RNAQ45873683
Kinetics of extension of O6-methylguanine paired with cytosine or thymine in defined oligonucleotide sequencesQ46254218
DNA replication fidelity: kinetics and thermodynamicsQ46859027
Characterization of the high pH wobble structure of the 2-aminopurine.cytosine mismatch by N-15 NMR spectroscopyQ47580781
The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutantsQ50192890
Bacterial mutator genes and the control of spontaneous mutationQ50228161
Comparative rates of spontaneous mutationQ50244165
Kinetic mechanism of DNA polymerase I (Klenow).Q52582535
Fidelity of replication of bacteriophage X174 DNA in vitro and in VivoQ52873405
Influence of local nucleotide sequence on substitution of 2-aminopurine for adenine during deoxyribonucleic acid synthesis in vitroQ52873585
Nonrandom substitution of 2-aminopurine for adenine during deoxyribonucleic acid synthesis in vitro.Q52875047
Thermodynamic comparison of the base pairs formed by the carcinogenic lesion O6-methylguanine with reference both to Watson-Crick pairs and to mismatched pairs.Q53514339
Genetic control of mutation rates in bacteriophageT4.Q53766791
The specific mutagenic effect of base analogues on Phage T4Q54094851
Mutational specificity of a conditional Escherichia coli mutator, mutD5Q54154876
In vitro evidence that UV-induced frameshift and substitution mutations at T tracts are the result of misalignment-mediated replication past a specific thymine dimer.Q54680558
The accuracy of reverse transcriptase from HIV-1.Q54738770
Oxidative damage in DNA. Lack of mutagenicity by thymine glycol lesions.Q54748389
Mechanism of mutagenesis by O6-methylguanineQ59068375
DNA repair enzymesQ39532106
DNA mismatch correctionQ39664959
Inducible DNA repair systemsQ39826678
Fidelity of DNA synthesisQ40113209
2-AminopurineQ40281516
The SOS regulatory system of Escherichia coliQ40335741
Synthesis and biophysical studies of short oligodeoxynucleotides with novel modifications: a possible approach to the problem of mixed base oligodeoxynucleotide synthesis.Q40461899
Synthesis and physicochemical properties of two analogs of poly(dA): poly(2-aminopurine-9-β-D-deoxyribonucleotide) and poly 2-amino-deoxyadenylic acidQ40465040
Fidelity of human immunodeficiency virus type I reverse transcriptase in copying natural DNA.Q40521759
Complementary base pairing and the origin of substitution mutationsQ41060332
Interaction of DNA with the Klenow fragment of DNA polymerase I studied by time-resolved fluorescence spectroscopyQ33376429
Direct electrophoretic detection of the allelic state of single DNA molecules in human sperm by using the polymerase chain reactionQ33635397
Comparison between DNA melting thermodynamics and DNA polymerase fidelityQ33642760
Mechanisms of mutagenesis in the Escherichia coli mutator mutD5: role of DNA mismatch repairQ33663239
Frequency and spectrum of mutations produced by a single cis-syn thymine-thymine cyclobutane dimer in a single-stranded vectorQ33663733
A Factor (or Mutator Gene) Influencing Mutation Rates in Escherichia ColiQ33714309
Allele-specific enzymatic amplification of beta-globin genomic DNA for diagnosis of sickle cell anemiaQ33850554
T5 DNA polymerase: structural--functional relationships to other DNA polymerasesQ33861715
A specific role of MutT protein: to prevent dG.dA mispairing in DNA replicationQ33865033
Fidelity of replication of phage phi X174 DNA by DNA polymerase III holoenzyme: spontaneous mutation by misincorporationQ34035189
8-oxoguanine (8-hydroxyguanine) DNA glycosylase and its substrate specificityQ34119141
Structure of an adenine-cytosine base pair in DNA and its implications for mismatch repairQ34196889
Frameshift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthdayQ34229913
Identification of the epsilon-subunit of Escherichia coli DNA polymerase III holoenzyme as the dnaQ gene product: a fidelity subunit for DNA replicationQ34257072
Effect of 3' flanking neighbors on kinetics of pairing of dCTP or dTTP opposite O6-methylguanine in a defined primed oligonucleotide when Escherichia coli DNA polymerase I is usedQ34314972
Extension of mismatched 3' termini of DNA is a major determinant of the infidelity of human immunodeficiency virus type 1 reverse transcriptase.Q34315598
Escherichia coli mutY gene encodes an adenine glycosylase active on G-A mispairsQ34319463
Bacteriophage PRD1 DNA polymerase: evolution of DNA polymerasesQ34369297
Specificity and efficiency of editing of mismatches involved in the formation of base-substitution mutations by the 3'----5' exonuclease activity of phage T4 DNA polymeraseQ34595206
Enzyme associations in T4 phage DNA precursor synthesisQ35041189
Synthesis and properties of defined DNA oligomers containing base mispairs involving 2-aminopurineQ35047947
2-Aminopurine-induced mutagenesis in T4 bacteriophage: a model relating mutation frequency to 2-aminopurine incorporation in DNAQ35059875
Detection of single DNA base differences by competitive oligonucleotide primingQ35222182
Sites of termination of in vitro DNA synthesis on ultraviolet- and N-acetylaminofluorene-treated phi X174 templates by prokaryotic and eukaryotic DNA polymerasesQ35300157
Structure and function of the bacteriophage T4 DNA polymerase holoenzymeQ35359717
On the molecular basis of transition mutations: frequencies of forming 2-aminopurine.cytosine and adenine.cytosine base mispairs in vitroQ35360018
Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T).Q35556177
Thymine glycols and urea residues in M13 DNA constitute replicative blocks in vitro.Q35564216
Comparison of nucleotide interactions in water, proteins, and vacuum: model for DNA polymerase fidelityQ35594093
MutM, a protein that prevents G C→T A transversions, is formamidopyrimidine-DNA glycosylaseQ35770316
Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studiesQ35829749
Mutation frequency and spectrum resulting from a single abasic site in a single-stranded vectorQ35837992
Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCRQ35927120
On the specificity of DNA polymeraseQ35970247
The fidelity of base selection by the polymerase subunit of DNA polymerase III holoenzymeQ36058122
Mutagenic frequencies of site-specifically located O6-methylguanine in wild-type Escherichia coli and in a strain deficient in ada-methyltransferaseQ36129916
SOS-dependent replication past a single trans-syn T-T cyclobutane dimer gives a different mutation spectrum and increased error rate compared with replication past this lesion in uninduced cellsQ36160219
Kinetic measurement of 2-aminopurine X cytosine and 2-aminopurine X thymine base pairs as a test of DNA polymerase fidelity mechanismsQ36317689
Deoxyribonucleotide pools, base pairing, and sequence configuration affecting bromodeoxyuridine- and 2-aminopurine-induced mutagenesisQ36362460
Enzymatic synthesis of deoxyribonucleic acid. X. Influence of bromouracil substitutions on replicationQ36394308
Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitroQ36765526
Evidence that MutY and MutM combine to prevent mutations by an oxidatively damaged form of guanine in DNAQ37132610
Escherichia coli MutY protein has both N-glycosylase and apurinic/apyrimidinic endonuclease activities on A.C and A.G mispairsQ37209405
Fidelity mechanisms in DNA replicationQ37285267
Eukaryotic DNA polymerasesQ37285272
Activity of the purified mutagenesis proteins UmuC, UmuD', and RecA in replicative bypass of an abasic DNA lesion by DNA polymerase IIIQ37296938
Detection of a guanine X adenine base pair in a decadeoxyribonucleotide by proton magnetic resonance spectroscopyQ37341850
The in vivo mutagenic frequency and specificity of O6-methylguanine in phi X174 replicative form DNA.Q37401468
Mutagenic potential of O4-methylthymine in vivo determined by an enzymatic approach to site-specific mutagenesisQ37407082
DNA polymerization in the absence of exonucleolytic proofreading: in vivo and in vitro studiesQ37442754
uvrA and recA mutations inhibit a site-specific transition produced by a single O6-methylguanine in gene G of bacteriophage phi X174.Q37536056
Demonstration of the production of frameshift and base-substitution mutations by quasipalindromic DNA sequencesQ37566558
In vivo mutagenesis by O6-methylguanine built into a unique site in a viral genomeQ37572277
Infidelity of DNA synthesis associated with bypass of apurinic sitesQ37601868
A fidelity assay using "dideoxy" DNA sequencing: a measurement of sequence dependence and frequency of forming 5-bromouracil X guanine base mispairsQ37678883
Mutagenic repair in Escherichia coli: products of the recA gene and of the umuD and umuC genes act at different steps in UV-induced mutagenesisQ37692184
The 'A rule' of mutagen specificity: a consequence of DNA polymerase bypass of non-instructional lesions?Q37713424
Frameshift mutation: determinants of specificityQ37794682
Mutation induced by DNA damage: a many protein affairQ37892175
Minimal kinetic mechanism for misincorporation by DNA polymerase I (Klenow fragment)Q38325804
Reverse transcriptase from human immunodeficiency virus: a single template-primer binding site serves two physically separable catalytic functionsQ38332456
An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kineticsQ38337035
Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutantQ38337038
cis-syn thymine dimers are not absolute blocks to replication by DNA polymerase I of Escherichia coli in vitro.Q38342006
Fluorescent oligonucleotides and deoxynucleotide triphosphates: preparation and their interaction with the large (Klenow) fragment of Escherichia coli DNA polymerase I.Q38344586
DNA substrate structural requirements for the exonuclease and polymerase activities of procaryotic and phage DNA polymerasesQ38345051
Stepwise mechanism of HIV reverse transcriptase: primer function of phosphorothioate oligodeoxynucleotideQ38345288
Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelityQ38346541
Mismatch repair in Escherichia coliQ39480893
P433issue2
P304page(s)83-126
P577publication date1993-01-01
P1433published inCritical Reviews in Biochemistry and Molecular BiologyQ5186661
P1476titleBiochemical basis of DNA replication fidelity
P478volume28

Reverse relations

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Q38847971Replicative Bypass Studies of α-Anomeric Lesions of 2'-Deoxyribonucleosides in Vitro
Q39407326Replicative Bypass of O(2)-Alkylthymidine Lesions in Vitro
Q34348711Reversal of a mutator activity by a nearby fidelity-neutral substitution in the RB69 DNA polymerase binding pocket
Q27939380Role of DNA polymerase eta in the bypass of a (6-4) TT photoproduct
Q24541478Role of human DNA polymerase kappa as an extender in translesion synthesis
Q28363488Roles of yeast DNA polymerases delta and zeta and of Rev1 in the bypass of abasic sites
Q42687325Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol beta
Q57050038Snapshots of a modified nucleotide moving through the confines of a DNA polymerase
Q50134974Sources of spontaneous mutagenesis in bacteria.
Q37371343Steric and electrostatic effects at the C2 atom substituent influence replication and miscoding of the DNA deamination product deoxyxanthosine and analogs by DNA polymerases
Q24537135Stimulation of DNA synthesis activity of human DNA polymerase kappa by PCNA.
Q27677038Structural Basis for Differential Insertion Kinetics of dNMPs Opposite a Difluorotoluene Nucleotide Residue
Q34315115Structure and replication of yDNA: a novel genetic set widened by benzo-homologation
Q45153419Structure of a high fidelity DNA polymerase bound to a benzo[a]pyrene adduct that blocks replication
Q39720937Structure of the hydrogen bonding complex of O6-methylguanine with cytosine and thymine during DNA replication
Q27656089Structure-Function Relationships in Miscoding by Sulfolobus solfataricus DNA Polymerase Dpo4: GUANINE N2,N2-DIMETHYL SUBSTITUTION PRODUCES INACTIVE AND MISCODING POLYMERASE COMPLEXES
Q27758682Structures of apurinic and apyrimidinic sites in duplex DNAs
Q28251979Structures of mismatch replication errors observed in a DNA polymerase
Q43087758Substitution of a residue contacting the triphosphate moiety of the incoming nucleotide increases the fidelity of yeast DNA polymerase zeta
Q39446100Synthesis and in vitro enzymatic and antiviral evaluation of phosphoramidate d4T derivatives as chain terminators
Q57895656Synthesis of 3-(2-deoxy-β-d-ribofuranosyl)pyridin-2-one and 2-amino-6-(N,N-dimethylamino)-9-(2-deoxy-β-d-ribofuranosyl)purine derivatives for an unnatural base pair
Q39256550Synthesis, and in vitro enzymatic and antiviral evaluation of d4T polyphosphate derivatives as chain terminators
Q41174277Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2',4'-bridged nucleosides
Q39117143Systematic characterization of 2'-deoxynucleoside- 5'-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA
Q44531735TNA synthesis by DNA polymerases
Q30769976Targeting of human DNA polymerase iota to the replication machinery via interaction with PCNA.
Q28251730Terminal deoxynucleotidyl transferase: the story of a misguided DNA polymerase
Q38341988The 5'-exonuclease activity of bacteriophage T4 RNase H is stimulated by the T4 gene 32 single-stranded DNA-binding protein, but its flap endonuclease is inhibited
Q38356754The Gly-952 residue of Saccharomyces cerevisiae DNA polymerase alpha is important in discriminating correct deoxyribonucleotides from incorrect ones
Q36026062The L561A substitution in the nascent base-pair binding pocket of RB69 DNA polymerase reduces base discrimination
Q40533640The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase
Q24804691The effect of the 2-amino group of 7,8-dihydro-8-oxo-2'-deoxyguanosine on translesion synthesis and duplex stability
Q34780836The effects of the ring fragmentation product of thymidine C5-hydrate on phosphodiesterases and klenow (exo-) fragment
Q40085607The energetic difference between synthesis of correct and incorrect base pairs accounts for highly accurate DNA replication
Q24630867The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases
Q38158093The high cost of fidelity
Q24683573The human DINB1 gene encodes the DNA polymerase Poltheta
Q77892158The mechanism of action of T7 DNA polymerase
Q38333960The proofreading pathway of bacteriophage T4 DNA polymerase.
Q34570808The relative roles in vivo of Saccharomyces cerevisiae Pol eta, Pol zeta, Rev1 protein and Pol32 in the bypass and mutation induction of an abasic site, T-T (6-4) photoadduct and T-T cis-syn cyclobutane dimer
Q27640849The structural basis for the mutagenicity of O6-methyl-guanine lesions
Q40176435The structural impact of DNA mismatches
Q24817153The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system
Q54477526Thermodynamic and mechanistic insights into translesion DNA synthesis catalyzed by Y-family DNA polymerase across a bulky double-base lesion of an antitumor platinum drug.
Q39724036Thermodynamics of internal C.T mismatches in DNA.
Q74036849Thermus aquaticus DNA polymerase I mutants with altered fidelity. Interacting mutations in the O-helix
Q48032922Transcriptional fidelity and proofreading by RNA polymerase II.
Q43619478Translesion DNA synthesis catalyzed by human pol eta and pol kappa across 1,N6-ethenodeoxyadenosine.
Q38312615Translesion synthesis across bulky N2-alkyl guanine DNA adducts by human DNA polymerase kappa
Q37213767Translesion synthesis of 8,5'-cyclopurine-2'-deoxynucleosides by DNA polymerases η, ι, and ζ.
Q39095399Translesional synthesis on DNA templates containing the 2'-deoxyribonolactone lesion.
Q37412973Two Distinct Pathways Support Gene Correction by Single-Stranded Donors at DNA Nicks
Q33617135Universal bases for hybridization, replication and chain termination
Q36174707Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma
Q62590161Using 2-Aminopurine Fluorescence and Mutational Analysis to Demonstrate an Active Role of Bacteriophage T4 DNA Polymerase in Strand Separation Required for 3′ → 5′-Exonuclease Activity
Q38363604Using 2-aminopurine fluorescence to measure incorporation of incorrect nucleotides by wild type and mutant bacteriophage T4 DNA polymerases
Q41496563Variants of sequence family B Thermococcus kodakaraensis DNA polymerase with increased mismatch extension selectivity
Q34157423Varied Molecular Interactions at the Active Sites of Several DNA Polymerases: Nonpolar Nucleoside Isosteres as Probes
Q27653071Versatility of Y-family Sulfolobus solfataricus DNA Polymerase Dpo4 in Translesion Synthesis Past Bulky N2-Alkylguanine Adducts
Q77520952Vertical-scanning mutagenesis of a critical tryptophan in the minor groove binding track of HIV-1 reverse transcriptase. Molecular nature of polymerase-nucleic acid interactions
Q38073986Why nature really chose phosphate
Q34473133Yeast DNA polymerase zeta is an efficient extender of primer ends opposite from 7,8-dihydro-8-Oxoguanine and O6-methylguanine
Q41652726Yeast DNA polymerase ϵ catalytic core and holoenzyme have comparable catalytic rates
Q38291977Yeast Rev1 protein is a G template-specific DNA polymerase

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