Biochemistry

ISSNs: , 1520-4995

References in Biochemistry:

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
Novikoff hepatoma deoxyribonucleic acid polymerase. Purification and properties of a homogeneous beta polymerase. Stalker DM, Mosbaugh DW, Meyer RR 1976
Catalytic center of DNA polymerase beta for excision of deoxyribose phosphate groups. Matsumoto Y, Kim K, Katz DS, Feng JA 1998
Attenuation of DNA replication by HIV-1 reverse transcriptase near the central termination sequence. Ignatov ME, Berdis AJ, Le Grice SF, Barkley MD 2005
Role of glutamine-151 of human immunodeficiency virus type-1 reverse transcriptase in RNA-directed DNA synthesis. Kaushik N, Harris D, Rege N, Modak MJ, Yadav PN, Pandey VN 1997
Biochemical analysis of catalytically crucial aspartate mutants of human immunodeficiency virus type 1 reverse transcriptase. Kaushik N, Rege N, Yadav PN, Sarafianos SG, Modak MJ, Pandey VN 1996
Misalignment-mediated DNA polymerase beta mutations: comparison of microsatellite and frame-shift error rates using a forward mutation assay. Eckert KA, Mowery A, Hile SE 2002
dNTP binding site in rat DNA polymerase beta revealed by controlled proteolysis and azido photoprobe cross-linking. Srivastava DK, Evans RK, Kumar A, Beard WA, Wilson SH 1996
A conformational change in E. coli DNA polymerase I (Klenow fragment) is induced in the presence of a dNTP complementary to the template base in the active site. Dzantiev L, Romano LJ 2000
Inhibition of Klenow fragment DNA polymerase on double-helical templates by oligonucleotide-directed triple-helix formation. Hacia JG, Dervan PB, Wold BJ 1994
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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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