Biochemistry

ISSNs: , 1520-4995

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Title	Authors	Year
Contribution of polar residues of the J-helix in the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I (Klenow fragment): Q677 regulates the removal of terminal mismatch.	Singh K, Modak MJ	2005
Pre-steady-state kinetic studies of the fidelity of Sulfolobus solfataricus P2 DNA polymerase IV.	Fiala KA, Suo Z	2004
Determinants of DNA mismatch recognition within the polymerase domain of the Klenow fragment.	Thompson EH, Bailey MF, Van der Schans EJ, Joyce CM, Millar DP	2002
Comparison of DNA polymerase alpha and delta from bone marrow.	Byrnes JJ, Black VL	1978
Aspartic acid residues at positions 190 and 192 of rat DNA polymerase beta are involved in primer binding.	Date T, Yamamoto S, Tanihara K, Nishimoto Y, Matsukage A	1991
Human DNA polymerases lambda and beta show different efficiencies of translesion DNA synthesis past abasic sites and alternative mechanisms for frameshift generation.	Blanca G, Villani G, Shevelev IV, Ramadan K, Spadari S, Hübscher U, Maga G	2004
Properties of tyrosine 766-->serine mutant of Escherichia coli DNA polymerase I: template-specific effects.	Desai SD, Pandey VN, Modak MJ	1994
Comparative enzymatic study of HIV-1 reverse transcriptase resistant to 2',3'-dideoxynucleotide analogs using the single-nucleotide incorporation assay.	Ueno T, Mitsuya H	1997
Pre-steady-state kinetics of nucleotide insertion following 8-oxo-7,8-dihydroguanine base pair mismatches by bacteriophage T7 DNA polymerase exo-.	Furge LL, Guengerich FP	1998
Assignments of 1H, 15N, and 13C resonances for the backbone and side chains of the N-terminal domain of DNA polymerase beta. Determination of the secondary structure and tertiary contacts.	Liu D, DeRose EF, Prasad R, Wilson SH, Mullen GP	1994
Structure-function analysis of DNA polymerase-beta using monoclonal antibodies: identification of a putative nucleotide binding domain.	Recupero AJ, Rein DC, Meyer RR	1992
Structure-function analysis of the mammalian DNA polymerase beta active site: role of aspartic acid 256, arginine 254, and arginine 258 in nucleotidyl transfer.	Menge KL, Hostomsky Z, Nodes BR, Hudson GO, Rahmati S, Moomaw EW, Almassy RJ, Hostomska Z	1995
DNA polymerase fidelity: kinetics, structure, and checkpoints.	Joyce CM, Benkovic SJ	2004
Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant.	Patel SS, Wong I, Johnson KA	1991
Incorporation of nucleosides into the nucleotide pools of human erythrocytes. Adenosine and its analogs.	Parks RE, Brown PR	1973
Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity.	Arora K, Beard WA, Wilson SH, Schlick T	2005
Molecular mechanisms of chemical mutagenesis: 9-aminoacridine inhibits DNA replication in vitro by destabilizing the DNA growing point and interacting with the DNA polymerase.	Topal MD	1984
Human placental DNA polymerase delta: identification of a 170-kilodalton polypeptide by activity staining and immunoblotting.	Lee MY, Toomey NL	1987
Regulation of catalytic activity and processivity of human telomerase.	Sun D, Lopez-Guajardo CC, Quada J, Hurley LH, Von Hoff DD	1999
Loss of polymerase activity due to Tyr to Phe substitution in the YMDD motif of human immunodeficiency virus type-1 reverse transcriptase is compensated by Met to Val substitution within the same motif.	Harris D, Yadav PN, Pandey VN	1998
Human immunodeficiency virus reverse transcriptase: steady-state and pre-steady-state kinetics of nucleotide incorporation.	Reardon JE	1992
High molecular weight deoxyribonucleic acid polymerase from crown gall tumor cells of periwinkle (Vinca rosea).	Gardner JM, Kado CI	1976
Mechanisms of selective inhibition of 3' to 5' exonuclease activity of Escherichia coli DNA polymerase I by nucleoside 5'-monophosphates.	Que BG, Downey KM, So AG	1978
DNA polymerase epsilon interacts with proliferating cell nuclear antigen in primer recognition and elongation.	Maga G, Hübscher U	1995
Effects of accessory proteins on the bypass of a cis-syn thymine-thymine dimer by Saccharomyces cerevisiae DNA polymerase eta.	McCulloch SD, Wood A, Garg P, Burgers PM, Kunkel TA	2007
Deoxyribonucleic acid polymerase with rat liver ribosomes and smooth membranes. Purification and properties of the enzymes.	Baril EF, Brown OE, Jenkins MD, Laszlo J	1971
Fidelity of HIV-1 reverse transcriptase copying RNA in vitro.	Ji JP, Loeb LA	1992
DNA polymerase beta: multiple conformational changes in the mechanism of catalysis.	Zhong X, Patel SS, Werneburg BG, Tsai MD	1997
Translesion synthesis by human DNA polymerase kappa on a DNA template containing a single stereoisomer of dG-(+)- or dG-(-)-anti-N(2)-BPDE (7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene).	Suzuki N, Ohashi E, Kolbanovskiy A, Geacintov NE, Grollman AP, Ohmori H, Shibutani S	2002
Fluorescent oligonucleotides and deoxynucleotide triphosphates: preparation and their interaction with the large (Klenow) fragment of Escherichia coli DNA polymerase I.	Allen DJ, Darke PL, Benkovic SJ	1989
Interactions between DNA polymerase beta and the major covalent adduct of the carcinogen (+)-anti-benzo[a]pyrene diol epoxide with DNA at a primer-template junction.	Singh SB, Beard WA, Hingerty BE, Wilson SH, Broyde S	1998
Efficient and erroneous incorporation of oxidized DNA precursors by human DNA polymerase eta.	Shimizu M, Grúz P, Kamiya H, Masutani C, Xu Y, Usui Y, Sugiyama H, Harashima H, Hanaoka F, Nohmi T	2007
Depurination-induced infidelity of deoxyribonucleic acid synthesis with purified deoxyribonucleic acid replication proteins in vitro.	Kunkel TA, Schaaper RM, Loeb LA	1983
Oligothymidylate analogues having stereoregular, alternating methylphosphonate/phosphodiester backbones as primers for DNA polymerase.	Miller PS, Annan ND, McParland KB, Pulford SM	1982
Dimerization of the Klenow fragment of Escherichia coli DNA polymerase I is linked to its mode of DNA binding.	Bailey MF, Van der Schans EJ, Millar DP	2007
Clamp subunit dissociation dictates bacteriophage T4 DNA polymerase holoenzyme disassembly.	Soumillion P, Sexton DJ, Benkovic SJ	1998
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 complex.	Dosanjh MK, Essigmann JM, Goodman MF, Singer B	1990
Residues at the carboxy terminus of T4 DNA polymerase are important determinants for interaction with the polymerase accessory proteins.	Goodrich LD, Lin TC, Spicer EK, Jones C, Konigsberg WH	1997
cis-syn thymine dimers are not absolute blocks to replication by DNA polymerase I of Escherichia coli in vitro.	Taylor JS, O'Day CL	1990
Isolation of temperature-sensitive DNA polymerase III from Saccharomyces cerevisiae cdc2-2.	Blank A, Loeb LA	1991
Base selectivity is impaired by mutants that perturb hydrogen bonding networks in the RB69 DNA polymerase active site.	Yang G, Wang J, Konigsberg WH	2005
The dimer of the beta subunit of Escherichia coli DNA polymerase III holoenzyme is dissociated into monomers upon binding magnesium(II).	Griep MA, McHenry CS	1988
Facile polymerization of dNTPs bearing unnatural base analogues by DNA polymerase alpha and Klenow fragment (DNA polymerase I).	Chiaramonte M, Moore CL, Kincaid K, Kuchta RD	2003
Interaction of DNA polymerase I (Klenow fragment) with the single-stranded template beyond the site of synthesis.	Turner RM, Grindley ND, Joyce CM	2003
A mutant of DNA polymerase I (Klenow fragment) with reduced fidelity.	Carroll SS, Cowart M, Benkovic SJ	1991
An importin alpha/beta-recognized bipartite nuclear localization signal mediates targeting of the human herpes simplex virus type 1 DNA polymerase catalytic subunit pUL30 to the nucleus.	Alvisi G, Musiani D, Jans DA, Ripalti A	2007
Calcium is a cofactor of polymerization but inhibits pyrophosphorolysis by the Sulfolobus solfataricus DNA polymerase Dpo4.	Irimia A, Zang H, Loukachevitch LV, Eoff RL, Guengerich FP, Egli M	2006
Base sequence dependence of in vitro translesional DNA replication past a bulky lesion catalyzed by the exo- Klenow fragment of Pol I.	Zhuang P, Kolbanovskiy A, Amin S, Geacintov NE	2001
Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase.	Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao C, Beckman J, Christian TD, Konigsberg WH	2011
Probing DNA polymerase-DNA interactions: examining the template strand in exonuclease complexes using 2-aminopurine fluorescence and acrylamide quenching.	Tleugabulova D, Reha-Krantz LJ	2007
Characterization of the DNA-dependent ATPase and a DNA unwinding activity associated with the yeast DNA polymerase alpha complex.	Biswas EE, Ewing CM, Biswas SB	1993
DNA polymerase catalysis in the absence of Watson-Crick hydrogen bonds: analysis by single-turnover kinetics.	Potapova O, Chan C, DeLucia AM, Helquist SA, Kool ET, Grindley ND, Joyce CM	2006
Interactions of conformationally biased north and south 2'-fluoro-2', 3'-dideoxynucleoside 5'-triphosphates with the active site of HIV-1 reverse transcriptase.	Mu L, Sarafianos SG, Nicklaus MC, Russ P, Siddiqui MA, Ford H, Mitsuya H, Le R, Kodama EN, Meier C, Knispel T, Anderson L, Barchi JJ, Marquez VE	2000
Induction of DNA polymerase activities in the regenerating rat liver.	Yang CL, Zhang SJ, Toomey NL, Palmer TN, Lee MY	1991
Dynamics of translesion DNA synthesis catalyzed by the bacteriophage T4 exonuclease-deficient DNA polymerase.	Berdis AJ	2001
The activity of selected RB69 DNA polymerase mutants can be restored by manganese ions: the existence of alternative metal ion ligands used during the polymerization cycle.	Zakharova E, Wang J, Konigsberg WH	2004
Identification of hydrogen bonds between Escherichia coli DNA polymerase I (Klenow fragment) and the minor groove of DNA by amino acid substitution of the polymerase and atomic substitution of the DNA.	Spratt TE	2001
Probing the protein-DNA contacts of a yeast RNA polymerase III transcription complex in a crude extract: solid phase synthesis of DNA photoaffinity probes containing a novel photoreactive deoxycytidine analog.	Lannutti BJ, Persinger J, Bartholomew B	1996
Single-stranded-DNA-dependent ATPase from HeLa cells that stimulates DNA polymerase alpha-primase activity: purification and characterization of the ATPase.	Vishwanatha JK, Baril EF	1990
Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to be inserted opposite 7,8-dihydro-8-oxoguanine .	Beckman JW, Wang M, Blaha G, Wang J, Konigsberg WH	2010
Mechanism of bacteriophage T4 DNA holoenzyme assembly: the 44/62 protein acts as a molecular motor.	Berdis AJ, Benkovic SJ	1997
Kinetic mechanism of the 3'-->5' proofreading exonuclease of DNA polymerase III. Analysis by steady state and pre-steady state methods.	Miller H, Perrino FW	1996
DNA replication machinery: functional characterization of a complex containing DNA polymerase alpha, DNA polymerase delta, and replication factor C suggests an asymmetric DNA polymerase dimer.	Maga G, Hübscher U	1996
Mismatched and matched dNTP incorporation by DNA polymerase beta proceed via analogous kinetic pathways.	Roettger MP, Bakhtina M, Tsai MD	2008
Pre-steady-state kinetic analysis of sequence-dependent nucleotide excision by the 3'-exonuclease activity of bacteriophage T4 DNA polymerase.	Bloom LB, Otto MR, Eritja R, Reha-Krantz LJ, Goodman MF, Beechem JM	1994
DNA polymerase beta: structure-fidelity relationship from Pre-steady-state kinetic analyses of all possible correct and incorrect base pairs for wild type and R283A mutant.	Ahn J, Werneburg BG, Tsai MD	1997
In vitro replication of primer-templates containing benzo[a]pyrene adducts by exonuclease-deficient Escherichia coli DNA polymerase I (Klenow fragment): effect of sequence context on lesion bypass.	Alekseyev YO, Romano LJ	2000
Three-dimensional solution structure of the N-terminal domain of DNA polymerase beta and mapping of the ssDNA interaction interface.	Liu D, Prasad R, Wilson SH, DeRose EF, Mullen GP	1996
RB69 DNA polymerase mutants with expanded nascent base-pair-binding pockets are highly efficient but have reduced base selectivity.	Zhang H, Beckman JW, Wang J, Konigsberg WH	2009
Elementary steps in the DNA polymerase I reaction pathway.	Bryant FR, Johnson KA, Benkovic SJ	1983
Mechanisms of mutation by oxidative DNA damage: reduced fidelity of mammalian DNA polymerase beta.	Feig DI, Loeb LA	1993
DNA polymerase photoprobe 2-[(4-azidophenacyl)thio]-2'-deoxyadenosine 5'-triphosphate labels an Escherichia coli DNA polymerase I Klenow fragment substrate binding site.	Moore BM, Jalluri RK, Doughty MB	1996
Interaction of DNA polymerase I (Klenow fragment) with DNA substrates containing extrahelical bases: implications for proofreading of frameshift errors during DNA synthesis.	Lam WC, Van der Schans EJ, Sowers LC, Millar DP	1999
Metal activation of synthetic and degradative activities of phi 29 DNA polymerase, a model enzyme for protein-primed DNA replication.	Esteban JA, Bernad A, Salas M, Blanco L	1992
Kinetic analysis of the unique error signature of human DNA polymerase ν	Arana ME, Potapova O, Kunkel TA, Joyce CM	2011
Kinetic Mechanism of Active Site Assembly and Chemical Catalysis of DNA Polymerase β	Balbo PB, Wang EC, Tsai MD	2011
Purification and characterization of a gamma-like DNA polymerase from Chlamydomonas reinhardtii.	Wang ZF, Yang J, Nie ZQ, Wu M	1991
Isolation of multiple forms of DNA polymerase delta: evidence of proteolytic modification during isolation.	Lee MY	1988
Properties of the 3' to 5' exonuclease associated with calf DNA polymerase delta.	Sabatino RD, Bambara RA	1988
A thymine isostere in the templating position disrupts assembly of the closed DNA polymerase beta ternary complex.	Kirby TW, DeRose EF, Beard WA, Wilson SH, London RE	2005
Detection and characterization of a novel factor that stimulates DNA polymerase alpha.	Kawasaki K, Enomoto T, Suzuki M, Seki M, Hanaoka F, Yamada M	1986
Inhibition of DNA replication and DNA polymerase alpha activity by monoclonal anti-(DNA polymerase alpha) immunoglobulin G and F(ab) fragments.	Miller MR, Seighman C, Ulrich RG	1985
Polymerization fidelity of a replicative DNA polymerase from the hyperthermophilic archaeon Sulfolobus solfataricus P2.	Zhang L, Brown JA, Newmister SA, Suo Z	2009
Dynamic domains of DNA polymerase alpha in regenerating rat liver.	Smith HC, Berezney R	1983
Properties of the primer-binding site and the role of magnesium ion in primer-template recognition by KB cell DNA polymerase alpha.	Fisher PA, Korn D	1981
Structural and functional analysis of Sulfolobus solfataricus Y-family DNA polymerase Dpo4-catalyzed bypass of the malondialdehyde-deoxyguanosine adduct.	Eoff RL, Stafford JB, Szekely J, Rizzo CJ, Egli M, Guengerich FP, Marnett LJ	2009
Selective inhibition of the polymerase activity of DNA polymerase. I. Further evidence for separate active sites for polymerase and 3' to 5' exonuclease activities.	Que BG, Downey KM, So AG	1979
Dynamics of nucleotide incorporation: snapshots revealed by 2-aminopurine fluorescence studies.	Hariharan C, Bloom LB, Helquist SA, Kool ET, Reha-Krantz LJ	2006
A conserved Tyr residue is required for sugar selectivity in a Pol alpha DNA polymerase.	Yang G, Franklin M, Li J, Lin TC, Konigsberg WH	2002
Purification and characterization of DNA polymerase alpha-associated replication protein A-dependent yeast DNA helicase A.	Biswas SB, Chen PH, Biswas EE	1997
Domain organization and DNA-induced conformational changes of an archaeal family B DNA polymerase.	Pisani FM, Manco G, Carratore V, Rossi M	1996
Large complexes of beta-poly(L-malate) with DNA polymerase alpha, histones, and other proteins in nuclei of growing plasmodia of Physarum polycephalum.	Angerer B, Holler E	1995
Phosphorylation of the p68 Subunit of Pol δ Acts as a Molecular Switch to Regulate Its Interaction with PCNA.	Rahmeh AA, Zhou Y, Xie B, Li H, Lee EY, Lee MY	2011
Site-directed mutagenesis of recombinant rat DNA polymerase beta: involvement of arginine-183 in primer recognition.	Date T, Yamamoto S, Tanihara K, Nishimoto Y, Liu N, Matsukage A	1990
Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity.	Kuchta RD, Benkovic P, Benkovic SJ	1988
Discrimination between right and wrong purine dNTPs by DNA polymerase I from Bacillus stearothermophilus.	Trostler M, Delier A, Beckman JW, Urban M, Patro JN, Spratt TE, Beese LS, Kuchta RD	2009
Effects of coordination of diammineplatinum(II) with DNA on the activities of Escherichia coli DNA polymerase I.	Bernges F, Holler E	1988
Binding of captan to DNA polymerase I from Escherichia coli and the concomitant effect on 5'----3' exonuclease activity.	Freeman-Wittig MJ, Welch W, Lewis RA	1989
Pyridoxal 5'-phosphate mediated inactivation of Escherichia coli DNA polymerase I: identification of lysine-635 as an essential residue for the processive mode of DNA synthesis.	Basu S, Basu A, Modak MJ	1988
2',3'-Dideoxythymidine 5'-triphosphate inhibition of DNA replication and ultraviolet-induced DNA repair synthesis in human cells: evidence for involvement of DNA polymerase delta.	Dresler SL, Kimbro KS	1987
ABC excinuclease incises both 5' and 3' to the CC-1065-DNA adduct and its incision activity is stimulated by DNA helicase II and DNA polymerase I.	Selby CP, Sancar A	1988
Inhibition of klenow fragment (exo-) catalyzed DNA polymerization by (5R)-5,6-dihydro-5-hydroxythymidine and structural analogue 5,6-dihydro-5-methylthymidine.	Greenberg MM, Matray TJ	1997
Use of viscogens, dNTPalphaS, and rhodium(III) as probes in stopped-flow experiments to obtain new evidence for the mechanism of catalysis by DNA polymerase beta.	Bakhtina M, Lee S, Wang Y, Dunlap C, Lamarche BJ, Tsai MD	2005
Inhibition of short patch and long patch base excision repair by an oxidized abasic site.	Guan L, Bebenek K, Kunkel TA, Greenberg MM	2010
Ordered sequential mechanism of substrate recognition and binding by KB cell DNA polymerase alpha.	Fisher PA, Korn D	1981
Nonrandom substitution of 2-aminopurine for adenine during deoxyribonucleic acid synthesis in vitro.	Pless RC, Levitt LM, Bessman MJ	1981
Translesion synthesis past platinum DNA adducts by human DNA polymerase mu.	Havener JM, Nick McElhinny SA, Bassett E, Gauger M, Ramsden DA, Chaney SG	2003
Expression of human DNA polymerase beta in Escherichia coli and characterization of the recombinant enzyme.	Abbotts J, SenGupta DN, Zmudzka BZ, Widen SG, Notario V, Wilson SH	1988
Petasiphenol: a DNA polymerase lambda inhibitor.	Mizushina Y, Kamisuki S, Kasai N, Ishidoh T, Shimazaki N, Takemura M, Asahara H, Linn S, Yoshida S, Koiwai O, Sugawara F, Yoshida H, Sakaguchi K	2002
The Asp285 variant of DNA polymerase beta extends mispaired primer termini via increased nucleotide binding.	Murphy DL, Kosa JL, Jaeger J, Sweasy JB	2008
Use of 2-aminopurine fluorescence to examine conformational changes during nucleotide incorporation by DNA polymerase I (Klenow fragment).	Purohit V, Grindley ND, Joyce CM	2003
Two functional domains of the epsilon subunit of DNA polymerase III.	Perrino FW, Harvey S, McNeill SM	1999
Insights into Base Selectivity from the 1.8 A Resolution Structure of an RB69 DNA Polymerase Ternary Complex.	Wang M, Xia S, Blaha G, Steitz TA, Konigsberg WH, Wang J	2011
Altering DNA polymerase incorporation fidelity by distorting the dNTP binding pocket with a bulky carcinogen-damaged template.	Yan SF, Wu M, Geacintov NE, Broyde S	2004
Effect of A and B metal ion site occupancy on conformational changes in an RB69 DNA polymerase ternary complex.	Wang M, Lee HR, Konigsberg WH	2009
Prostate-cancer-associated I260M variant of DNA polymerase beta is a sequence-specific mutator.	Dalal S, Hile SE, Eckert KA, Sun KW, Starcevic D, Sweasy JB	2005
O4-Methyl-, O4-ethyl-, and O4-isopropylthymidine 5'-triphosphates as analogues of thymidine 5'-triphosphate: kinetics of incorporation by Escherichia coli DNA polymerase I.	Singer B, Chavez F, Spengler SJ	1986
DNA binding domain of Escherichia coli DNA polymerase I: identification of arginine-841 as an essential residue.	Mohan PM, Basu A, Basu S, Abraham KI, Modak MJ	1988
Using 2-aminopurine fluorescence to detect bacteriophage T4 DNA polymerase-DNA complexes that are important for primer extension and proofreading reactions.	Hariharan C, Reha-Krantz LJ	2005
Stoichiometry and mechanism of assembly of SV40 T antigen complexes with the viral origin of DNA replication and DNA polymerase alpha-primase.	Huang SG, Weisshart K, Gilbert I, Fanning E	1998
Dissociation of bacteriophage T4 DNA polymerase and its processivity clamp after completion of Okazaki fragment synthesis.	Carver TE, Sexton DJ, Benkovic SJ	1997
Fidelity of DNA polymerase delta holoenzyme from Saccharomyces cerevisiae: the sliding clamp proliferating cell nuclear antigen decreases its fidelity.	Hashimoto K, Shimizu K, Nakashima N, Sugino A	2003
Conformational changes during normal and error-prone incorporation of nucleotides by a Y-family DNA polymerase detected by 2-aminopurine fluorescence.	DeLucia AM, Grindley ND, Joyce CM	2007
Evidence that DNA polymerase delta isolated by immunoaffinity chromatography exhibits high-molecular weight characteristics and is associated with the KIAA0039 protein and RPA.	Mo J, Liu L, Leon A, Mazloum N, Lee MY	2000
Steric and electrostatic effects in DNA synthesis by the SOS-induced DNA polymerases II and IV of Escherichia coli.	Silverman AP, Jiang Q, Goodman MF, Kool ET	2007
Effects of the anticancer drug cis-diamminedichloroplatinum(II) on the activities of calf thymus DNA polymerase epsilon.	Huang L, Turchi JJ, Wahl AF, Bambara RA	1993
Interaction of DNA polymerase I of Escherichia coli with nucleotides. Antagonistic effects of single-stranded polynucleotide homopolymers.	Muise O, Holler E	1985
Fidelity of mispair formation and mispair extension is dependent on the interaction between the minor groove of the primer terminus and Arg668 of DNA polymerase I of Escherichia coli.	McCain MD, Meyer AS, Schultz SS, Glekas A, Spratt TE	2005
Analysis of non-template-directed nucleotide addition and template switching by DNA polymerase.	García PB, Robledo NL, Islas AL	2004
Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes.	Arndt JW, Gong W, Zhong X, Showalter AK, Liu J, Dunlap CA, Lin Z, Paxson C, Tsai MD, Chan MK	2001
Translesional synthesis past acetylaminofluorene-derived DNA adducts catalyzed by human DNA polymerase kappa and Escherichia coli DNA polymerase IV.	Suzuki N, Ohashi E, Hayashi K, Ohmori H, Grollman AP, Shibutani S	2001
Specificity of the catalytic interaction of human DNA polymerase beta with nucleic acid substrates.	Wang TS, Korn D	1982
Fidelity of mammalian DNA replication and replicative DNA polymerases.	Thomas DC, Roberts JD, Sabatino RD, Myers TW, Tan CK, Downey KM, So AG, Bambara RA, Kunkel TA	1991
The thiocarboxanilide nonnucleoside UC781 is a tight-binding inhibitor of HIV-1 reverse transcriptase.	Barnard J, Borkow G, Parniak MA	1997
Pre-steady-state kinetics of RB69 DNA polymerase and its exo domain mutants: effect of pH and thiophosphoryl linkages on 3'-5' exonuclease activity.	Wang CX, Zakharova E, Li J, Joyce CM, Wang J, Konigsberg WH	2004
Inhibition of HIV-1 reverse transcriptase-catalyzed DNA strand transfer reactions by 4-chlorophenylhydrazone of mesoxalic acid.	Davis WR, Tomsho J, Nikam S, Cook EM, Somand D, Peliska JA	2000
An RNA polymerase mutant with reduced accuracy of chain elongation.	Blank A, Gallant JA, Burgess RR, Loeb LA	1986
Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate.	Beese LS, Friedman JM, Steitz TA	1993
3'-5' Exonucleolytic activity of DNA polymerases: structural features that allow kinetic discrimination between ribo- and deoxyribonucleotide residues.	Lin TC, Wang CX, Joyce CM, Konigsberg WH	2001
Ribonucleic acid dependent deoxyribonucleic acid synthesis by Escherichia coli deoxyribonucleic acid polymerase. I. Characterization of the polymerization reaction.	Travaglini EC, Loeb LA	1974
Comparison of polymerase insertion and extension kinetics of a series of O2-alkyldeoxythymidine triphosphates and O4-methyldeoxythymidine triphosphate.	Singer B, Chavez F, Spengler SJ, Kuśmierek JT, Mendelman L, Goodman MF	1989
Mechanism of DNA replication fidelity for three mutants of DNA polymerase I: Klenow fragment KF(exo+), KF(polA5), and KF(exo-).	Eger BT, Kuchta RD, Carroll SS, Benkovic PA, Dahlberg ME, Joyce CM, Benkovic SJ	1991
Interaction of DNA with the Klenow fragment of DNA polymerase I studied by time-resolved fluorescence spectroscopy.	Guest CR, Hochstrasser RA, Dupuy CG, Allen DJ, Benkovic SJ, Millar DP	1991
Resonance energy transfer measurements between substrate binding sites within the large (Klenow) fragment of Escherichia coli DNA polymerase I.	Allen DJ, Benkovic SJ	1989
Exonucleolytic proofreading by a mammalian DNA polymerase.	Kunkel TA, Mosbaugh DW	1989
Low molecular weight deoxyribonucleic acid polymerase from rabbit bone marrow.	Chang LM, Bollum FJ	1972
Translesion DNA synthesis by human DNA polymerase eta on templates containing a pyrimidopurinone deoxyguanosine adduct, 3-(2'-deoxy-beta-d-erythro-pentofuranosyl)pyrimido-[1,2-a]purin-10(3H)-one .	Stafford JB, Eoff RL, Kozekova A, Rizzo CJ, Guengerich FP, Marnett LJ	2009
Site-specific pausing of deoxyribonucleic acid synthesis catalyzed by four forms of Escherichia coli DNA polymerase III.	LaDuca RJ, Fay PJ, Chuang C, McHenry CS, Bambara RA	1983
Synthesis by DNA polymerase I on bleomycin-treated deoxyribonucleic acid: a requirement for exonuclease III.	Niwa O, Moses RE	1981
Protection of oligonucleotide primers against degradation by DNA polymerase I.	Ott J, Eckstein F	1987
Temperature-sensitive DNA polymerase induced by a bacteriophage T5 mutant: relationship between polymerase and exonuclease activities.	Fujimura RK, Roop BC	1976
Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69.	Hogg M, Rudnicki J, Midkiff J, Reha-Krantz LJ, Doublié S, Wallace SS	2010
Structural basis of ubiquitin recognition by translesion synthesis DNA polymerase iota.	Cui G, Benirschke RC, Tuan HF, Juranić N, Macura S, Botuyan MV, Mer G	2010
Drug binding to a DNA BZ molecule: analysis by chemical footprinting.	Guo Q, Lu M, Shahrestanifar M, Sheardy RD, Kallenbach NR	1991
Carbonyldiphosphonate, a selective inhibitor of mammalian DNA polymerase delta.	Talanian RV, Brown NC, McKenna CE, Ye TG, Levy JN, Wright GE	1989
Analysis of the stimulation of DNA polymerase V of Escherichia coli by processivity proteins.	Maor-Shoshani A, Livneh Z	2002
Effect of N-2-acetylaminofluorene and 2-aminofluorene adducts on DNA binding and synthesis by yeast DNA polymerase eta.	Vooradi V, Romano LJ	2009
Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.	Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H	1997
Immunoaffinity-purified DNA polymerase alpha displays novel properties.	Nasheuer HP, Grosse F	1987
Interactions of the 8-kDa domain of rat DNA polymerase beta with DNA.	Jezewska MJ, Rajendran S, Bujalowski W	2001
Enzymatic synthesis of deoxyribonucleic acid. XXXIV. Termination of chain growth by a 2',3'-dideoxyribonucleotide.	Atkinson MR, Deutscher MP, Kornberg A, Russell AF, Moffatt JG	1969
Pyrene nucleotide as a mechanistic probe: evidence for a transient abasic site-like intermediate in the bypass of dipyrimidine photoproducts by T7 DNA polymerase.	Sun L, Wang M, Kool ET, Taylor JS	2000
Identification and amino acid sequence of the deoxynucleoside triphosphate binding site in Escherichia coli DNA polymerase I.	Basu A, Modak MJ	1987
Pre-steady-state kinetic studies of the fidelity and mechanism of polymerization catalyzed by truncated human DNA polymerase lambda.	Fiala KA, Abdel-Gawad W, Suo Z	2004
DNA polymerase delta holoenzyme: action on single-stranded DNA and on double-stranded DNA in the presence of replicative DNA helicases.	Podust VN, Podust LM, Müller F, Hübscher U	1995
Use of damaged DNA and dNTP substrates by the error-prone DNA polymerase X from African swine fever virus.	Kumar S, Lamarche BJ, Tsai MD	2007
Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase.	Tindall KR, Kunkel TA	1988
Molecular architecture of the mutagenic active site of human immunodeficiency virus type 1 reverse transcriptase: roles of the beta 8-alpha E loop in fidelity, processivity, and substrate interactions.	Weiss KK, Isaacs SJ, Tran NH, Adman ET, Kim B	2000
Properties of two forms of DNA polymerase delta from calf thymus.	Wahl AF, Crute JJ, Sabatino RD, Bodner JB, Marraccino RL, Harwell LW, Lord EM, Bambara RA	1986
Rational attempts to optimize non-natural nucleotides for selective incorporation opposite an abasic site.	Zhang X, Donnelly A, Lee I, Berdis AJ	2006
Glutamine 151 participates in the substrate dNTP binding function of HIV-1 reverse transcriptase.	Sarafianos SG, Pandey VN, Kaushik N, Modak MJ	1995
Implication of the tRNA initiation step for human immunodeficiency virus type 1 reverse transcriptase in the mechanism of 3'-azido-3'-deoxythymidine (AZT) resistance.	Vaccaro JA, Anderson KS	1998
Abasic template lesions are strong chain terminators for DNA primase but not for DNA polymerase alpha during the synthesis of new DNA strands.	Zerbe LK, Goodman MF, Efrati E, Kuchta RD	1999
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Purification and characterization of a DNA polymerase beta promoter initiator element-binding transcription factor from bovine testis.	He F, Narayan S, Wilson SH	1996
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A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases.	Kamerlin SC, McKenna CE, Goodman MF, Goondman MF, Warshel A	2009
Simulating 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.	Xiang Y, Oelschlaeger P, Florián J, Goodman MF, Warshel A	2006
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A novel PCNA-binding motif identified by the panning of a random peptide display library.	Xu H, Zhang P, Liu L, Lee MY	2001
Structure of the 1,N(2)-etheno-2'-deoxyguanosine lesion in the 3'-G(epsilon dG)T-5' sequence opposite a one-base deletion.	Shanmugam G, Kozekov ID, Guengerich FP, Rizzo CJ, Stone MP	2010
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RNA priming coupled with DNA synthesis on natural template by calf thymus DNA polymerase alpha-primase.	Suzuki M, Savoysky E, Izuta S, Tatebe M, Okajima T, Yoshida S	1993
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Explanation of pre-steady-state kinetics and decreased burst amplitude of HIV-1 reverse transcriptase at sites of modified DNA bases with an additional, nonproductive enzyme-DNA-nucleotide complex.	Furge LL, Guengerich FP	1999
Misincorporation of dNTPs opposite 1,N2-ethenoguanine and 5,6,7,9-tetrahydro-7-hydroxy-9-oxoimidazo[1,2-a]purine in oligonucleotides by Escherichia coli polymerases I exo- and II exo-, T7 polymerase exo-, human immunodeficiency virus-1 reverse transcriptase, and rat polymerase beta.	Langouët S, Müller M, Guengerich FP	1997
The p12 subunit of human polymerase delta modulates the rate and fidelity of DNA synthesis.	Meng X, Zhou Y, Lee EY, Lee MY, Frick DN	2010
Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase I.	Graham SE, Syeda F, Cisneros GA	2012
Intramolecular chimeras of the p51 subunit between HIV-1 and FIV reverse transcriptases suggest a stabilizing function for the p66 subunit in the heterodimeric enzyme.	Tasara T, Amacker M, Hübscher U	1999
Kinetics and fidelity of polymerization by DNA polymerase III from Sulfolobus solfataricus.	Bauer RJ, Begley MT, Trakselis MA	2012
Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase.	Xia S, Wang M, Blaha G, Konigsberg WH, Wang J	2011
Using a Fluorescent Cytosine Analogue tC(o) To Probe the Effect of the Y567 to Ala Substitution on the Preinsertion Steps of dNMP Incorporation by RB69 DNA Polymerase.	Xia S, Beckman JW, Wang J, Konigsberg WH	2012
The E288K Colon Tumor Variant of DNA Polymerase Beta Is a Sequence Specific Mutator.	Murphy DL, Donigan KA, Jaeger J, Sweasy JB	2012
Contribution of Partial Charge Interactions and Base-Stacking to the Efficiency of Primer-Extension at and beyond Abasic Sites in DNA.	Xia S, Vashishtha AK, Bulkley D, Eom SH, Wang J, Konigsberg WH	2012
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Catalytic Effects of Mutations of Distant Protein Residues in Human DNA Polymerase β: Theory and Experiment.	Klvana M, Murphy DL, Jerabek P, Goodman MF, Warshel A, Sweasy JB, Florian J	2012
Effect of β,γ-CHF- and β,γ-CHCl-dGTP Halogen Atom Stereochemistry on the Transition State of DNA Polymerase β	Oertell K, Wu Y, Zakharova VM, Kashemirov BA, Shock DD, Beard WA, Wilson SH, McKenna CE, Goodman MF	2012
Differential Furanose Selection in the Active Sites of Archaeal DNA Polymerases Probed by Fixed-Conformation Nucleotide Analogues.	Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL	2012
Long patch base excision repair compensates for DNA polymerase β inactivation by the C4'-oxidized abasic site.	Jacobs AC, Kreller CR, Greenberg MM	2011
NMR structure and dynamics of the C-terminal domain from human Rev1 and its complex with Rev1 interacting region of DNA polymerase η.	Pozhidaeva A, Pustovalova Y, D'Souza S, Bezsonova I, Walker GC, Korzhnev DM	2012
Synergistic inhibition of HIV-1 reverse transcriptase DNA polymerase activity and virus replication in vitro by combinations of carboxanilide nonnucleoside compounds.	Fletcher RS, Arion D, Borkow G, Wainberg MA, Dmitrienko GI, Parniak MA	1995
Translesional synthesis on a DNA template containing a single stereoisomer of dG-(+)- or dG-(-)-anti-BPDE (7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene).	Shibutani S, Margulis LA, Geacintov NE, Grollman AP	1993
Dissecting the effects of DNA polymerase and ribonuclease H inhibitor combinations on HIV-1 reverse-transcriptase activities.	Shaw-Reid CA, Feuston B, Munshi V, Getty K, Krueger J, Hazuda DJ, Parniak MA, Miller MD, Lewis D	2005
Human immunodeficiency virus type 1 reverse transcriptase dimer destabilization by 1-[Spiro[4"-amino-2",2" -dioxo-1",2" -oxathiole-5",3'-[2', 5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]]]-3-ethylthy mine.	Sluis-Cremer N, Dmitrienko GI, Balzarini J, Camarasa MJ, Parniak MA	2000
Carboxanilide derivative non-nucleoside inhibitors of HIV-1 reverse transcriptase interact with different mechanistic forms of the enzyme.	Fletcher RS, Syed K, Mithani S, Dmitrienko GI, Parniak MA	1995
Physicochemical and biochemical properties of 2',5'-linked RNA and 2',5'-RNA:3',5'-RNA "hybrid" duplexes.	Wasner M, Arion D, Borkow G, Noronha A, Uddin AH, Parniak MA, Damha MJ	1998
Model of elongation of short DNA sequence by thermophilic DNA polymerase under isothermal conditions.	Kato T, Liang X, Asanuma H	2012
DNA Polymerase λ Inactivation by Oxidized Abasic Sites.	Stevens AJ, Guan L, Bebenek K, Kunkel TA, Greenberg MM	2013
Structure and functional analysis of the BRCT domain of translesion synthesis DNA polymerase Rev1.	Pryor JM, Gakhar L, Washington MT	2013
Structural changes in the hydrophobic hinge region adversely affect the activity and fidelity of the I260Q mutator of DNA polymerase ß	Gridley CL, Rangarajan S, Firbank SJ, Dalal S, Sweasy JB, Jaeger J	2013
Misincorporation of 2'-deoxyoxanosine 5'-triphosphate by DNA polymerases and its implication for mutagenesis.	Suzuki T, Yoshida M, Yamada M, Ide H, Kobayashi M, Kanaori K, Tajima K, Makino K	1998
Tyrosine 222, a member of the YXDD motif of MuLV RT, is catalytically essential and is a major component of the fidelity center.	Kaushik N, Singh K, Alluru I, Modak MJ	1999
Polyamide nucleic acid-DNA chimera lacking the phosphate backbone are novel primers for polymerase reaction catalyzed by DNA polymerases.	Misra HS, Pandey PK, Modak MJ, Vinayak R, Pandey VN	1998
Elucidation of the role of Arg 110 of murine leukemia virus reverse transcriptase in the catalytic mechanism: biochemical characterization of its mutant enzymes.	Chowdhury K, Kaushik N, Pandey VN, Modak MJ	1996
Lysine 152 of MuLV reverse transcriptase is required for the integrity of the active site.	Shi Q, Singh K, Srivastava A, Kaushik N, Modak MJ	2002
Valine of the YVDD motif of moloney murine leukemia virus reverse transcriptase: role in the fidelity of DNA synthesis.	Kaushik N, Chowdhury K, Pandey VN, Modak MJ	2000
Identification of the primer binding domain in human immunodeficiency virus reverse transcriptase.	Basu A, Ahluwalia KK, Basu S, Modak MJ	1992
Ferrate oxidation of murine leukemia virus reverse transcriptase: identification of the template-primer binding domain.	Reddy G, Nanduri VB, Basu A, Modak MJ	1991
Photoaffinity labeling of the primer binding domain in murine leukemia virus reverse transcriptase.	Tirumalai RS, Modak MJ	1991
Lysine-329 of murine leukemia virus reverse transcriptase: possible involvement in the template-primer binding function.	Nanduri VB, Modak MJ	1990
Rose Bengal mediated inhibition of DNA polymerases: mechanism of inhibition of avian myeloblastosis virus reverse transcriptase under photooxidative conditions.	Srivastava SK, Modak MJ	1983
Rose Bengal mediated inhibition of DNA polymerases: mechanism of inhibition of avian myeloblastosis virus reverse transcriptase under nonoxidative conditions.	Srivastava SK, Modak MJ	1982
Distinctive effects of domain deletions on the manganese-dependent DNA polymerase and DNA phosphorylase activities of Mycobacterium smegmatis polynucleotide phosphorylase.	Unciuleac MC, Shuman S	2013
Following DNA Chain Extension and Protein Conformational Changes in Crystals of a Y-Family DNA Polymerase via Raman Crystallography.	Espinoza-Herrera SJ, Gaur V, Suo Z, Carey PR	2013
Discrete interactions between bacteriophage T7 primase-helicase and DNA polymerase drive the formation of a priming complex containing two copies of DNA polymerase.	Wallen JR, Majka J, Ellenberger T	2013
Kinetic Mechanism of DNA Polymerization Catalyzed by Human DNA Polymerase ε	Zahurancik WJ, Klein SJ, Suo Z	2013
Replication, Repair and Translesion Polymerase Bypass of N6-Oxopropenyl-2'-deoxyadenosine.	Maddukuri L, Shuck SC, Eoff RL, Zhao L, Rizzo CJ, Guengerich FP, Marnett LJ	2013
DNA polymerase V kinetics support the instructive nature of an oxidized abasic lesion in Escherichia coli.	Bajacan JE, Greenberg MM	2013
Fidelity, mismatch extension, and proofreading activity of the Plasmodium falciparum apicoplast DNA polymerase.	Wingert BM, Parrott EE, Nelson SW	2013
Kinetic partitioning between the exonuclease and polymerase sites in DNA error correction.	Donlin MJ, Patel SS, Johnson KA	1991

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