Journal of molecular biology

(J Mol Biol) ISSNs: , 1089-8638

References in Journal of molecular biology:

Title Authors Year
Structure and function of a mycobacterial NHEJ DNA repair polymerase. Pitcher RS, Brissett NC, Picher AJ, Andrade P, Juarez R, Thompson D, Fox GC, Blanco L, Doherty AJ 2007
How E. coli DNA polymerase I (Klenow fragment) distinguishes between deoxy- and dideoxynucleotides. Astatke M, Grindley ND, Joyce CM 1998
A novel mechanism of sugar selection utilized by a human X-family DNA polymerase. Brown JA, Fiala KA, Fowler JD, Sherrer SM, Newmister SA, Duym WW, Suo Z 2010
Effect of single DNA lesions on in vitro replication with DNA polymerase III holoenzyme. Comparison with other polymerases. Belguise-Valladier P, Maki H, Sekiguchi M, Fuchs RP 1994
A highly conserved lysine residue in phi29 DNA polymerase is important for correct binding of the templating nucleotide during initiation of phi29 DNA replication. Truniger V, Lázaro JM, Blanco L, Salas M 2002
Crystallization and 7 A resolution electron density map of the large fragment of Escherichia coli DNA polymerase I. Brick P, Ollis D, Steitz TA 1983
The Rate of Polymerase Release upon Filling the Gap between Okazaki Fragments Is Inadequate to Support Cycling during Lagging Strand Synthesis. Dohrmann PR, Manhart CM, Downey CD, McHenry CS 2011
Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase. Wang L, Broyde S, Zhang Y 2009
Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution. Ding J, Das K, Hsiou Y, Sarafianos SG, Clark AD, Jacobo-Molina A, Tantillo C, Hughes SH, Arnold E 1998
De novo DNA synthesis by human DNA polymerase lambda, DNA polymerase mu and terminal deoxyribonucleotidyl transferase. Ramadan K, Shevelev IV, Maga G, Hübscher U 2004
Polymerase-specific differences in the DNA intermediates of frameshift mutagenesis. In vitro synthesis errors of Escherichia coli DNA polymerase I and its large fragment derivative. Papanicolaou C, Ripley LS 1989
DNA polymerase X of African swine fever virus: insertion fidelity on gapped DNA substrates and AP lyase activity support a role in base excision repair of viral DNA. García-Escudero R, García-Díaz M, Salas ML, Blanco L, Salas J 2003
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 polymerases. Bessman MJ, Muzyczka N, Goodman MF, Schnaar RL 1974
Spectrum of spontaneous frameshift mutations. Sequences of bacteriophage T4 rII gene frameshifts. Ripley LS, Clark A, deBoer JG 1986
Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. Yang L, Beard WA, Wilson SH, Broyde S, Schlick T 2002
A DNA polymerase III holoenzyme-like subassembly from an extreme thermophilic eubacterium. McHenry CS, Seville M, Cull MG 1997
Characterization of the tryptophan fluorescence and hydrodynamic properties of rat DNA polymerase beta. Kim SJ, Lewis MS, Knutson JR, Porter DK, Kumar A, Wilson SH 1994
Studies on the biochemical basis of spontaneous mutation. III. Rate model for DNA polymerase-effected nucleotide misincorporation. Goodman MF, Gore WC, Muzyczka N, Bessman MJ 1974
Functional characterization of the genes coding for the terminal protein and DNA polymerase from bacteriophage GA-1. Evidence for a sliding-back mechanism during protein-primed GA-1 DNA replication. Illana B, Blanco L, Salas M 1996
Probing conformational changes of human DNA polymerase lambda using mass spectrometry-based protein footprinting. Fowler JD, Brown JA, Kvaratskhelia M, Suo Z 2009
Induction of DNA polymerase in mouse L cells. Chang LM, Brown M, Bollum FJ 1973
DNA polymerase switching on homotrimeric PCNA at the replication fork of the euryarchaea Pyrococcus abyssi. Rouillon C, Henneke G, Flament D, Querellou J, Raffin JP 2007
Lesion bypass activity of DNA polymerase theta (POLQ) is an intrinsic property of the pol domain and depends on unique sequence inserts. Hogg M, Seki M, Wood RD, Doublié S, Wallace SS 2011
Crystal structures of clinically relevant Lys103Asn/Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside inhibitor HBY 097. Das K, Sarafianos SG, Clark AD, Boyer PL, Hughes SH, Arnold E 2007
Interaction between DNA and an Escherichia coli protein omega. Wang JC 1971
Mutational patterns associated with the 69 insertion complex in multi-drug-resistant HIV-1 reverse transcriptase that confer increased excision activity and high-level resistance to zidovudine. Cases-González CE, Franco S, Martínez MA, Menéndez-Arias L 2007
Characterization of a Bacillus subtilis 64-kDa DNA polymerase X potentially involved in DNA repair. Baños B, Lázaro JM, Villar L, Salas M, de Vega M 2008
General antimutators are improbable. Drake JW 1993
Snapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4. Wong JH, Fiala KA, Suo Z, Ling H 2008
Crystal structures of an N-terminal fragment from Moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain. Najmudin S, Coté ML, Sun D, Yohannan S, Montano SP, Gu J, Georgiadis MM 2000
Phage phi 29 DNA polymerase residues involved in the proper stabilisation of the primer-terminus at the 3'-5' exonuclease active site. de Vega M, Lázaro JM, Salas M 2000
phi29 DNA polymerase-terminal protein interaction. Involvement of residues specifically conserved among protein-primed DNA polymerases. Rodríguez I, Lázaro JM, Salas M, de Vega M 2004
An in vitro transversion by a mutationally altered T4-induced DNA polymerase. Hall ZW, Lehman IR 1968
The nucleoside analogs 4'C-methyl thymidine and 4'C-ethyl thymidine block DNA synthesis by wild-type HIV-1 RT and excision proficient NRTI resistant RT variants. Boyer PL, Julias JG, Ambrose Z, Siddiqui MA, Marquez VE, Hughes SH 2007
Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase. Fiala KA, Brown JA, Ling H, Kshetry AK, Zhang J, Taylor JS, Yang WW, Suo Z 2007
Structural mechanisms of drug resistance for mutations at codons 181 and 188 in HIV-1 reverse transcriptase and the improved resilience of second generation non-nucleoside inhibitors. Ren J, Nichols C, Bird L, Chamberlain P, Weaver KL, Short S, Stuart DI, Stammers DK 2001
Thermodynamic dissection of the polymerizing and editing modes of a DNA polymerase. Bailey MF, Van der Schans EJ, Millar DP 2004
Amino acid architecture that influences dNTP insertion efficiency in Y-family DNA polymerase V of E. coli. Seo KY, Yin J, Donthamsetti P, Chandani S, Lee CH, Loechler EL 2009
The glycine-rich motif of Pyrococcus abyssi DNA polymerase D is critical for protein stability. Castrec B, Laurent S, Henneke G, Flament D, Raffin JP 2010
Analysis of amino insertion mutations in the fingers subdomain of HIV-1 reverse transcriptase. Boyer PL, Lisziewicz J, Lori F, Hughes SH 1999
The solution structure of functionally active human proliferating cell nuclear antigen determined by small-angle neutron scattering. Schurtenberger P, Egelhaaf SU, Hindges R, Maga G, Jónsson ZO, May RP, Glatter O, Hübscher U 1998
T4 DNA polymerase. Rates and processivity on single-stranded DNA templates. Mace DC, Alberts BM 1984
Increased error frequency of DNA polymerases from senescent human fibroblasts. Murray V, Holliday R 1981
Dual mode of interaction of DNA polymerase epsilon with proliferating cell nuclear antigen in primer binding and DNA synthesis. Maga G, Jónsson ZO, Stucki M, Spadari S, Hübscher U 1999
Stimulation of T4 bacteriophage DNA polymerase by the protein product of T4 gene 32. Huberman JA, Kornberg A, Alberts BM 1971
In vitro selection of sequence contexts which enhance bypass of abasic sites and tetrahydrofuran by T4 DNA polymerase holoenzyme. Hatahet Z, Zhou M, Reha-Krantz LJ, Ide H, Morrical SW, Wallace SS 1999
A role for DNA polymerase in the specificity of nucleotide incorporation opposite N-acetyl-2-aminofluorene adducts. Rabkin SD, Strauss BS 1984
Enzymatic determinants of DNA polymerase accuracy. Theory of coliphage T4 polymerase mechanisms. Galas DJ, Branscomb EW 1978
Recognition of template-primer and gapped DNA substrates by the human DNA polymerase beta. Rajendran S, Jezewska MJ, Bujalowski W 2001
A conserved insertion in protein-primed DNA polymerases is involved in primer terminus stabilisation. Dufour E, Rodríguez I, Lázaro JM, de Vega M, Salas M 2003
Isolation of bacteriophage T4 DNA polymerase mutator mutants. Reha-Krantz LJ, Liesner EM, Parmaksizoglu S, Stocki S 1986
Adduct size limits efficient and error-free bypass across bulky N2-guanine DNA lesions by human DNA polymerase eta. Choi JY, Guengerich FP 2005
Analysis of O29 DNA polymerase by partial proteolysis: binding of terminal protein in the double-stranded DNA channel. Truniger V, Blanco L, Salas M 2000
Amino acid changes coded by bacteriophage T4 DNA polymerase mutator mutants. Relating structure to function. Reha-Krantz LJ 1988
Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance. Hsiou Y, Das K, Ding J, Clark AD, Kleim JP, Rösner M, Winkler I, Riess G, Hughes SH, Arnold E 1998
o29 DNA polymerase residue Lys383, invariant at motif B of DNA-dependent polymerases, is involved in dNTP binding. Saturno J, Lázaro JM, Esteban FJ, Blanco L, Salas M 1997
phi29 DNA polymerase active site: role of residue Val250 as metal-dNTP complex ligand and in protein-primed initiation. Pérez-Arnaiz P, Lázaro JM, Salas M, de Vega M 2010
Characterization of a protein covalently linked to the 5' termini of the DNA of Bacillus subtilis phage phi29. Salas M, Mellado RP, Viñuela E 1978
Mutational analysis of phi29 DNA polymerase residues acting as ssDNA ligands for 3'-5' exonucleolysis. de Vega M, Lázaro JM, Salas M, Blanco L 1998
Kinetic analysis of base-pairing preference for nucleotide incorporation opposite template pyrimidines by human DNA polymerase iota. Choi JY, Lim S, Eoff RL, Guengerich FP 2009
Molecular analyses of an unusual translesion DNA polymerase from Methanosarcina acetivorans C2A. Lin LJ, Yoshinaga A, Lin Y, Guzman C, Chen YH, Mei S, Lagunas AM, Koike S, Iwai S, Spies MA, Nair SK, Mackie RI, Ishino Y, Cann IK 2010
Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects. Oelschlaeger P, Klahn M, Beard WA, Wilson SH, Warshel A 2007
Binding to PCNA in Euryarchaeal DNA Replication requires two PIP motifs for DNA polymerase D and one PIP motif for DNA polymerase B. Castrec B, Rouillon C, Henneke G, Flament D, Querellou J, Raffin JP 2009
Oligonucleotide inhibitors of Taq DNA polymerase facilitate detection of low copy number targets by PCR. Dang C, Jayasena SD 1996
Role of genes 46 and 47 in bacteriophage T4 reproduction. II. Formation of gaps on parental DNA of polynucleotide ligase defective mutants. Prashad N, Hosoda J 1972
In vitro replication slippage by DNA polymerases from thermophilic organisms. Viguera E, Canceill D, Ehrlich SD 2001
Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures. Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian TD, Wang J, Konigsberg WH 2011
Multidrug-resistant HIV-1 reverse transcriptase: involvement of ribonucleotide-dependent phosphorolysis in cross-resistance to nucleoside analogue inhibitors. Mas A, Vázquez-Alvarez BM, Domingo E, Menéndez-Arias L 2002
Structural determinants in human DNA polymerase gamma account for mitochondrial toxicity from nucleoside analogs. Lim SE, Ponamarev MV, Longley MJ, Copeland WC 2003
The roles of Tyr391 and Tyr619 in RB69 DNA polymerase replication fidelity. Jacewicz A, Makiela K, Kierzek A, Drake JW, Bebenek A 2007
Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition. Sarafianos SG, Marchand B, Das K, Himmel DM, Parniak MA, Hughes SH, Arnold E 2009
An invariant lysine residue is involved in catalysis at the 3'-5' exonuclease active site of eukaryotic-type DNA polymerases. de Vega M, Ilyina T, Lázaro JM, Salas M, Blanco L 1997
Error rate and specificity of human and murine DNA polymerase eta. Matsuda T, Bebenek K, Masutani C, Rogozin IB, Hanaoka F, Kunkel TA 2001
phi29 DNA polymerase residue Phe128 of the highly conserved (S/T)Lx(2)h motif is required for a stable and functional interaction with the terminal protein. Rodríguez I, Lázaro JM, Salas M, de Vega M 2003
A new class of mutants in DNA polymerase I that affects gene transposition. Syvanen M, Hopkins JD, Clements M 1982
Structural homology between DNA binding sites of DNA polymerase beta and DNA topoisomerase II. Mizushina Y, Sugawara F, Iida A, Sakaguchi K 2000
DNA polymerase lambda (Pol lambda), a novel eukaryotic DNA polymerase with a potential role in meiosis. García-Díaz M, Domínguez O, López-Fernández LA, de Lera LT, Saníger ML, Ruiz JF, Párraga M, García-Ortiz MJ, Kirchhoff T, del Mazo J, Bernad A, Blanco L 2000
Role of the first aspartate residue of the "YxDTDS" motif of phi29 DNA polymerase as a metal ligand during both TP-primed and DNA-primed DNA synthesis. Saturno J, Lázaro JM, Blanco L, Salas M 1998
Structure-function studies of the bacteriophage T4 DNA polymerase. Isolation of a novel suppressor mutant. Reha-Krantz LJ, Lambert JK 1985
Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus. Yang L, Beard WA, Wilson SH, Roux B, Broyde S, Schlick T 2002
Oligomeric structures of the phage phi29 histone-like protein p6. Abril AM, Marco S, Carrascosa JL, Salas M, Hermoso JM 1999
Phi 29 DNA polymerase requires the N-terminal domain to bind terminal protein and DNA primer substrates. Truniger V, Lázaro JM, Salas M, Blanco L 1998
Contribution of 3' leads to 5' exonuclease activity of DNA polymerase III holoenzyme from Escherichia coli to specificity. Fersht AR, Knill-Jones JW 1983
Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates. Brautigam CA, Steitz TA 1998
Effect of N2-guanyl modifications on early steps in catalysis of polymerization by Sulfolobus solfataricus P2 DNA polymerase Dpo4 T239W. Zhang H, Guengerich FP 2010
Prokaryotic DNA polymerase I: evolution, structure, and "base flipping" mechanism for nucleotide selection. Patel PH, Suzuki M, Adman E, Shinkai A, Loeb LA 2001
Backbone dynamics and refined solution structure of the N-terminal domain of DNA polymerase beta. Correlation with DNA binding and dRP lyase activity. Maciejewski MW, Liu D, Prasad R, Wilson SH, Mullen GP 2000
The interrelation between DNA synthesis and various DNA polymerase activities in synchronized HeLa cells. Spadari S, Weissbach A 1974
Letter: Cytoplasmic DNA polymerase: polymeric forms and their conversion into an active monomer resembling nuclear DNA polymerase. Lazarus LH, Kitron N 1973
Kinetics of base misinsertion by DNA polymerase I of Escherichia coli. Fersht AR, Shi JP, Tsui WC 1983
Influence of diverse gene 43 DNA polymerases on the incorporation and replication in vivo of 2-aminopurine at A X T base-pairs in bacteriophage T4. Ripley LS 1981
HIV-1 reverse transcriptase can simultaneously engage its DNA/RNA substrate at both DNA polymerase and RNase H active sites: implications for RNase H inhibition. Beilhartz GL, Wendeler M, Baichoo NS, Rausch JW, Le Grice SF, Götte M 2009
Identification of a new motif in family B DNA polymerases by mutational analyses of the bacteriophage t4 DNA polymerase. Li V, Hogg M, Reha-Krantz LJ 2010
Crystallization of 31 kDa C-terminal fragment of rat DNA polymerase beta. Shirakihara Y, Matsukage A, Nishimoto Y, Date T 1994
The herpes simplex virus processivity factor, UL42, binds DNA as a monomer. Randell JC, Coen DM 2004
Efficient and high fidelity incorporation of dye-terminators by a novel archaeal DNA polymerase mutant. Arezi B, Hansen CJ, Hogrefe HH 2002
Functional importance of bacteriophage phi29 DNA polymerase residue Tyr148 in primer-terminus stabilisation at the 3'-5' exonuclease active site. Pérez-Arnaiz P, Lázaro JM, Salas M, de Vega M 2009
Interactions of the DNA polymerase X of African swine fever virus with double-stranded DNA. Functional structure of the complex. Jezewska MJ, Bujalowski PJ, Bujalowski W 2007
Novel blunt-end addition reactions catalyzed by DNA polymerase I of Escherichia coli. Clark JM, Joyce CM, Beardsley GP 1987
A single tyrosine prevents insertion of ribonucleotides in the eukaryotic-type phi29 DNA polymerase. Bonnin A, Lázaro JM, Blanco L, Salas M 1999
Structural insights into yeast DNA polymerase delta by small angle X-ray scattering. Jain R, Hammel M, Johnson RE, Prakash L, Prakash S, Aggarwal AK 2009
Inactivation of the 3'-5' exonuclease of the replicative T4 DNA polymerase allows translesion DNA synthesis at an abasic site. Tanguy Le Gac N, Delagoutte E, Germain M, Villani G 2004
Staying straight with A-tracts: a DNA analog of the HIV-1 polypurine tract. Coté ML, Pflomm M, Georgiadis MM 2003
Role of the "YxGG/A" motif of Phi29 DNA polymerase in protein-primed replication. Truniger V, Blanco L, Salas M 1999
Characterization of the stimulatory effect of T4 gene 45 protein and the gene 44/62 protein complex on DNA synthesis by T4 DNA polymerase. Mace DC, Alberts BM 1984
Initiation of bacteriophage phi29 DNA replication in vivo: assembly of a membrane-associated multiprotein complex. Bravo A, Salas M 1997
The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance. Hsiou Y, Ding J, Das K, Clark AD, Boyer PL, Lewi P, Janssen PA, Kleim JP, Rösner M, Hughes SH, Arnold E 2001
Interplay between DNA polymerase and proliferating cell nuclear antigen switches off base excision repair of uracil and hypoxanthine during replication in archaea. Emptage K, O'Neill R, Solovyova A, Connolly BA 2008
A role for replication repair in the genesis of templated mutations. Schultz GE, Carver GT, Drake JW 2006
Bacteriophage T7 RNA polymerase and its active-site mutants. Kinetic, spectroscopic and calorimetric characterization. Osumi-Davis PA, Sreerama N, Volkin DB, Middaugh CR, Woody RW, Woody AY 1994
Asp537, Asp812 are essential and Lys631, His811 are catalytically significant in bacteriophage T7 RNA polymerase activity. Osumi-Davis PA, de Aguilera MC, Woody RW, Woody AY 1992
Two positively charged residues of phi29 DNA polymerase, conserved in protein-primed DNA polymerases, are involved in stabilisation of the incoming nucleotide. Truniger V, Lázaro JM, Salas M 2004
Evaluating the effects of enhanced processivity and metal ions on translesion DNA replication catalyzed by the bacteriophage T4 DNA polymerase. Reineks EZ, Berdis AJ 2003
Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant. Das K, Ding J, Hsiou Y, Clark AD, Moereels H, Koymans L, Andries K, Pauwels R, Janssen PA, Boyer PL, Clark PK, Smith RH, Kroeger Smith MB, Michejda CJ, Hughes SH, Arnold E 1996
Studies on the biochemical basis of mutation VI. Selection and characterization of a new bacteriophage T4 mutator DNA polymerase. Reha-Krantz LJ, Bessman MJ 1981
Autogenous translational operator recognized by bacteriophage T4 DNA polymerase. Tuerk C, Eddy S, Parma D, Gold L 1990
Effects of depurination on the fidelity of DNA synthesis. Shearman CW, Loeb LA 1979
Sliding clamp-DNA interactions are required for viability and contribute to DNA polymerase management in Escherichia coli. Heltzel JM, Scouten Ponticelli SK, Sanders LH, Duzen JM, Cody V, Pace J, Snell EH, Sutton MD 2009
An aspartic acid residue in TPR-1, a specific region of protein-priming DNA polymerases, is required for the functional interaction with primer terminal protein. Dufour E, Méndez J, Lázaro JM, de Vega M, Blanco L, Salas M 2000
DNA polymerase X from African swine fever virus: quantitative analysis of the enzyme-ssDNA interactions and the functional structure of the complex. Jezewska MJ, Marcinowicz A, Lucius AL, Bujalowski W 2006
Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit. Wing RA, Bailey S, Steitz TA 2008
Fluorescence measurements on the E.coli DNA polymerase clamp loader: implications for conformational changes during ATP and clamp binding. Goedken ER, Levitus M, Johnson A, Bustamante C, O'Donnell ME, Kuriyan J 2004
NTP concentration effects on initial transcription by T7 RNAP indicate that translocation occurs through passive sliding and reveal that divergent promoters have distinct NTP concentration requirements for productive initiation. Guajardo R, Lopez P, Dreyfus M, Sousa R 1998
Identification of amino acid residues in the human immunodeficiency virus type-1 reverse transcriptase tryptophan-repeat motif that are required for subunit interaction using infectious virions. Mulky A, Sarafianos SG, Jia Y, Arnold E, Kappes JC 2005
Determination of mutation rates in bacteriophage T4 by unneighborly base pairs: genetic analysis. Conkling MA, Koch RE, Drake JW 1980
DNA polymerase switching: I. Replication factor C displaces DNA polymerase alpha prior to PCNA loading. Maga G, Stucki M, Spadari S, Hübscher U 2000
The biochemical requirements of DNA polymerase V-mediated translesion synthesis revisited. Fujii S, Gasser V, Fuchs RP 2004
Structural mechanism for coordination of proofreading and polymerase activities in archaeal DNA polymerases. Kuroita T, Matsumura H, Yokota N, Kitabayashi M, Hashimoto H, Inoue T, Imanaka T, Kai Y 2005
DNA structure and polymerase fidelity. Timsit Y 1999
Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography. Firbank SJ, Wardle J, Heslop P, Lewis RJ, Connolly BA 2008
DNA polymerase from Sulfolobus acidocaldarius. Replication at high temperature of long stretches of single-stranded DNA. Salhi S, Elie C, Forterre P, de Recondo AM, Rossignol JM 1989
Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1. Hashimoto H, Nishioka M, Fujiwara S, Takagi M, Imanaka T, Inoue T, Kai Y 2001
Effects of mutations in the polymerase domain on the polymerase, RNase H and strand transfer activities of human immunodeficiency virus type 1 reverse transcriptase. Gao HQ, Boyer PL, Arnold E, Hughes SH 1998
The role of steric hindrance in 3TC resistance of human immunodeficiency virus type-1 reverse transcriptase. Gao HQ, Boyer PL, Sarafianos SG, Arnold E, Hughes SH 2000
Plasticity of the gene functions for DNA replication in the T4-like phages. Petrov VM, Nolan JM, Bertrand C, Levy D, Desplats C, Krisch HM, Karam JD 2006
DNA sequencing by partial ribosubstitution. Barnes WM 1978
Similarities and differences in the RNase H activities of human immunodeficiency virus type 1 reverse transcriptase and Moloney murine leukemia virus reverse transcriptase. Gao HQ, Sarafianos SG, Arnold E, Hughes SH 1999
Crystallization of DNA polymerase II from Escherichia coli. Anderson WF, Prince DB, Yu H, McEntee K, Goodman MF 1994
DNA polymerase theta purified from human cells is a high-fidelity enzyme. Maga G, Shevelev IV, Ramadan K, Spadari S, Hübscher U 2002
Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7. Rodriguez AC, Park HW, Mao C, Beese LS 2000
A new approach to DNA polymerase kinetics. Bernardi F, Saghi M, Dorizzi M, Ninio J 1979
Kinetics of deoxy-CTP incorporation opposite a dG-C8-N-2-aminofluorene adduct by a high-fidelity DNA polymerase. Burnouf DY, Wagner JE 2009
Replication of bacteriophage M13. X. M13 replication in a mutant of Escherichia coli defective in the 5' leads to 3' exonuclease associated with DNA polymerase I. Chen TC, Ray DS 1976
Human DNA polymerase lambda possesses terminal deoxyribonucleotidyl transferase activity and can elongate RNA primers: implications for novel functions. Ramadan K, Maga G, Shevelev IV, Villani G, Blanco L, Hübscher U 2003
A bipartite polymerase-processivity factor interaction: only the internal beta binding site of the alpha subunit is required for processive replication by the DNA polymerase III holoenzyme. Dohrmann PR, McHenry CS 2005
Studies on the biochemical basis of mutation. IV. Effect of amino acid substitution on the enzymatic and biological properties of bacteriophage T4 DNA polymerase. Reha-Krantz LJ, Bessman MJ 1977
DNA polymerase switching: II. Replication factor C abrogates primer synthesis by DNA polymerase alpha at a critical length. Mossi R, Keller RC, Ferrari E, Hübscher U 2000
Different populations of DNA polymerase alpha in HeLa cells. Jackson DA, Cook PR 1986
A cell-cycle-dependent DNA polymerase activity that replicates intact DNA in chromatin. Jackson DA, Cook PR 1986
Recognition of B and Z forms of DNA by Escherichia coli DNA polymerase I. Ramesh N, Shouche YS, Brahmachari SK 1986
Oxygen radical induced mutagenesis is DNA polymerase specific. Feig DI, Loeb LA 1994
Dynamics of bacteriophage T4 DNA polymerase function: identification of amino acid residues that affect switching between polymerase and 3' --> 5' exonuclease activities. Stocki SA, Nonay RL, Reha-Krantz LJ 1995
Involvement of DNA polymerase beta in DNA replication and mutagenic consequences. Servant L, Bieth A, Hayakawa H, Cazaux C, Hoffmann JS 2002
RNA polymerase binding sites and transcription map of the DNA of Bacillus subtilis phage phi29. Sogo JM, Inciarte MR, Corral J, Viñuela E, Salas M 1979
Mnemonic aspects of Escherichia coli DNA polymerase I. Interaction with one template influences the next interaction with another template. Papanicolaou C, Lecomte P, Ninio J 1986
Template recognition and chain elongation in DNA synthesis in vitro. Travaglini EC, Dube DK, Surrey S, Loeb LA 1976
Identification of critical residues for the tight binding of both correct and incorrect nucleotides to human DNA polymerase lambda. Brown JA, Pack LR, Sherrer SM, Kshetry AK, Newmister SA, Fowler JD, Taylor JS, Suo Z 2010
DNA polymerase beta can incorporate ribonucleotides during DNA synthesis of undamaged and CPD-damaged DNA. Bergoglio V, Ferrari E, Hübscher U, Cazaux C, Hoffmann JS 2003
Two DNA polymerase sliding clamps from the thermophilic archaeon Sulfolobus solfataricus. De Felice M, Sensen CW, Charlebois RL, Rossi M, Pisani FM 1999
Transition between different binding modes in rat DNA polymerase beta-ssDNA complexes. Jezewska MJ, Rajendran S, Bujalowski W 1998
Protein trans-splicing and characterization of a split family B-type DNA polymerase from the hyperthermophilic archaeal parasite Nanoarchaeum equitans. Choi JJ, Nam KH, Min B, Kim SJ, Söll D, Kwon ST 2006
Crystal structures of an intein from the split dnaE gene of Synechocystis sp. PCC6803 reveal the catalytic model without the penultimate histidine and the mechanism of zinc ion inhibition of protein splicing. Sun P, Ye S, Ferrandon S, Evans TC, Xu MQ, Rao Z 2005
The complex of DNA gyrase and quinolone drugs on DNA forms a barrier to the T7 DNA polymerase replication complex. Wentzell LM, Maxwell A 2000
Biochemical and mutational studies of the 5'-3' exonuclease of DNA polymerase I of Escherichia coli. Xu Y, Derbyshire V, Ng K, Sun XC, Grindley ND, Joyce CM 1997
Initiation of DNA replication at cloned origins of bacteriophage T7. Rabkin SD, Richardson CC 1988
Molecular modeling of RNA polymerase II mutations onto DNA polymerase I. Kim WJ, Burke LP, Mortin MA 1994
Analysis of amino acids in the beta7-beta8 loop of human immunodeficiency virus type 1 reverse transcriptase for their role in virus replication. Mulky A, Vu BC, Conway JA, Hughes SH, Kappes JC 2007
The ribonuclease H activity of the reverse transcriptases of human immunodeficiency viruses type 1 and type 2 is affected by the thumb subdomain of the small protein subunits. Sevilya Z, Loya S, Hughes SH, Hizi A 2001
Reversal of a mutator activity by a nearby fidelity-neutral substitution in the RB69 DNA polymerase binding pocket. Trzemecka A, Jacewicz A, Carver GT, Drake JW, Bebenek A 2010
Polymerase Chaperoning and Multiple ATPase Sites Enable the E. coli DNA Polymerase III Holoenzyme to Rapidly Form Initiation Complexes. Downey CD, Crooke E, McHenry CS 2011
Interaction of the family-B DNA polymerase from the archaeon Pyrococcus furiosus with deaminated bases. Gill S, O'Neill R, Lewis RJ, Connolly BA 2007
Different behaviors in vivo of mutations in the beta hairpin loop of the DNA polymerases of the closely related phages T4 and RB69. Trzemecka A, Płochocka D, Bebenek A 2009
Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex. Lansdon EB, Samuel D, Lagpacan L, Brendza KM, White KL, Hung M, Liu X, Boojamra CG, Mackman RL, Cihlar T, Ray AS, McGrath ME, Swaminathan S 2010
Genetic insertions and diversification of the PolB-type DNA polymerase (gp43) of T4-related phages. Petrov VM, Ratnayaka S, Karam JD 2010
A novel processive mechanism for DNA synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial DNA polymerase. Fan L, Kim S, Farr CL, Schaefer KT, Randolph KM, Tainer JA, Kaguni LS 2006
Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases. Burnouf DY, Olieric V, Wagner JE, Fujii S, Reinbolt J, Fuchs RP, Dumas P 2004
Evading the proofreading machinery of a replicative DNA polymerase: induction of a mutation by an environmental carcinogen. Perlow RA, Broyde S 2001
Role of human DNA polymerase κ in extension opposite from a cis-syn thymine dimer. Vasquez-Del Carpio R, Silverstein TD, Lone S, Johnson RE, Prakash L, Prakash S, Aggarwal AK 2011
Structural mechanism of ribonucleotide discrimination by a Y-family DNA polymerase. Kirouac KN, Suo Z, Ling H 2011
Mutational analysis of the fingers and palm subdomains of human immunodeficiency virus type-1 (HIV-1) reverse transcriptase. Boyer PL, Ferris AL, Clark PK, Whitmer J, Frank P, Tantillo C, Arnold E, Hughes SH 1994
Locations of anti-AIDS drug binding sites and resistance mutations in the three-dimensional structure of HIV-1 reverse transcriptase. Implications for mechanisms of drug inhibition and resistance. Tantillo C, Ding J, Jacobo-Molina A, Nanni RG, Boyer PL, Hughes SH, Pauwels R, Andries K, Janssen PA, Arnold E 1994
DNA synthesis in strains of Escherichia coli K12 with temperature-sensitive DNA ligase and DNA polymerase I. Konrad EB, Modrich P, Lehman IR 1974
Electron microscopy of DNA polymerase bound to DNA. Griffith J, Huberman JA, Kornberg A 1971
Enzymic synthesis of DNA. 33. Hydrolysis of a 5'-triphosphate-terminated polynucleotide in the active center of DNA polymerase. Cozzarelli NR, Kelly RB, Kornberg A 1969
Visualization of two binding sites for the Escherichia coli UmuD'(2)C complex (DNA pol V) on RecA-ssDNA filaments. Frank EG, Cheng N, Do CC, Cerritelli ME, Bruck I, Goodman MF, Egelman EH, Woodgate R, Steven AC 2000
Effect of accessory proteins on T4 DNA polymerase replication fidelity. Kroutil LC, Frey MW, Kaboord BF, Kunkel TA, Benkovic SJ 1998
Crystal structures of HIV-1 reverse transcriptases mutated at codons 100, 106 and 108 and mechanisms of resistance to non-nucleoside inhibitors. Ren J, Nichols CE, Chamberlain PP, Weaver KL, Short SA, Stammers DK 2004
A Crystallographic Study of the Role of Sequence Context in Thymine Glycol Bypass by a Replicative DNA Polymerase Serendipitously Sheds Light on the Exonuclease Complex. Aller P, Duclos S, Wallace SS, Doublié S 2011
Processive proofreading and the spatial relationship between polymerase and exonuclease active sites of bacteriophage phi29 DNA polymerase. de Vega M, Blanco L, Salas M 1999
DNA synthesis across an abasic lesion by yeast REV1 DNA polymerase. Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK 2011
Effects of mutations F61A and A62V in the fingers subdomain of HIV-1 reverse transcriptase on the translocational equilibrium. Scarth BJ, McCormick S, Götte M 2011
Excision of incorporated nucleotide analogue chain-terminators can diminish their inhibitory effects on viral RNA-dependent RNA polymerases. D'Abramo CM, Cellai L, Götte M 2004
Electrostatic field of the large fragment of Escherichia coli DNA polymerase I. Warwicker J, Ollis D, Richards FM, Steitz TA 1985
Sliding clamps of DNA polymerases. Kuriyan J, O'Donnell ME 1993
Substrate-Dependent Millisecond Domain Motions in DNA Polymerase β Berlow RB, Swain M, Dalal S, Sweasy JB, Loria JP 2012
Crystal structure of SUMO-modified proliferating cell nuclear antigen. Freudenthal BD, Brogie JE, Gakhar L, Kondratick CM, Washington MT 2011
Resistance to nevirapine of HIV-1 reverse transcriptase mutants: loss of stabilizing interactions and thermodynamic or steric barriers are induced by different single amino acid substitutions. Maga G, Amacker M, Ruel N, Hübscher U, Spadari S 1997
The hyperthermophilic euryarchaeota Pyrococcus abyssi likely requires the two DNA polymerases D and B for DNA replication. Henneke G, Flament D, Hübscher U, Querellou J, Raffin JP 2005
Single-turnover kinetic analysis of the mutagenic potential of 8-oxo-7,8-dihydro-2'-deoxyguanosine during gap-filling synthesis catalyzed by human DNA polymerases lambda and beta. Brown JA, Duym WW, Fowler JD, Suo Z 2007
Lagging strand synthesis in coordinated DNA synthesis by bacteriophage t7 replication proteins. Lee J, Chastain PD, Griffith JD, Richardson CC 2002
Helix-destabilizing activity of phi 29 single-stranded DNA binding protein: effect on the elongation rate during strand displacement DNA replication. Soengas MS, Gutiérrez C, Salas M 1995
Identification of the acidic residues in the active site of DNA polymerase III. Pritchard AE, McHenry CS 1999
Transcriptional organization of the Escherichia coli dnaX gene. Flower AM, McHenry CS 1991
Genetic mapping and DNA sequence analysis of mutations in the polA gene of Escherichia coli. Joyce CM, Fujii DM, Laks HS, Hughes CM, Grindley ND 1985
Genetic characterization of early amber mutations in the Escherichia coli polA gene and purification of the amber peptides. Kelley WS, Joyce CM 1983
Studies on primer binding of HIV-1 reverse transcriptase using a fluorescent probe. Delahunty MD, Wilson SH, Karpel RL 1994
AKAP149 binds to HIV-1 reverse transcriptase and is involved in the reverse transcription. Lemay J, Maidou-Peindara P, Cancio R, Ennifar E, Coadou G, Maga G, Rain JC, Benarous R, Liu LX 2008
Steric and electrostatic effects at the C2 atom substituent influence replication and miscoding of the DNA deamination product deoxyxanthosine and analogs by DNA polymerases. Zhang H, Bren U, Kozekov ID, Rizzo CJ, Stec DF, Guengerich FP 2009
Replication factor C from the hyperthermophilic archaeon Pyrococcus abyssi does not need ATP hydrolysis for clamp-loading and contains a functionally conserved RFC PCNA-binding domain. Henneke G, Gueguen Y, Flament D, Azam P, Querellou J, Dietrich J, Hübscher U, Raffin JP 2002
Chimeric HIV-1 and feline immunodeficiency virus reverse transcriptases: critical role of the p51 subunit in the structural integrity of heterodimeric lentiviral DNA polymerases. Amacker M, Hübscher U 1998
The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA. Nakane S, Ishikawa H, Nakagawa N, Kuramitsu S, Masui R 2012
Mechanism of Replicative DNA Polymerase Delta Pausing and a Potential Role for DNA Polymerase Kappa in Common Fragile Site Replication. Walsh E, Wang X, Lee MY, Eckert KA 2012
Sequences within Pr160gag-pol affecting the selective packaging of primer tRNA(Lys3) into HIV-1. Khorchid A, Javanbakht H, Wise S, Halwani R, Parniak MA, Wainberg MA, Kleiman L 2000
Characterization of human immunodeficiency virus type-1 (HIV-1) particles that express protease-reverse transcriptase fusion proteins. Cherry E, Liang C, Rong L, Quan Y, Inouye P, Li X, Morin N, Kotler M, Wainberg MA 1998
Endogenous reverse transcriptase assays reveal synergy between combinations of the M184V and other drug resistance-conferring mutations in interactions with nucleoside analog triphosphates. Quan Y, Gu Z, Li X, Liang C, Parniak MA, Wainberg MA 1998
Effects of mutations in Pr160gag-pol upon tRNA(Lys3) and Pr160gag-plo incorporation into HIV-1. Mak J, Khorchid A, Cao Q, Huang Y, Lowy I, Parniak MA, Prasad VR, Wainberg MA, Kleiman L 1997
Site-directed mutagenesis in the fingers subdomain of HIV-1 reverse transcriptase reveals a specific role for the beta3-beta4 hairpin loop in dNTP selection. Garforth SJ, Kim TW, Parniak MA, Kool ET, Prasad VR 2007
An iron-sulfur cluster in the polymerase domain of yeast DNA polymerase ε Jain R, Vanamee ES, Dzikovski BG, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK 2013
Molecular recognition of canonical and deaminated bases by P. abyssi family B DNA polymerase. Gouge J, Ralec C, Henneke G, Delarue M 2012
Human DNA Polymerase η Is Pre-Aligned for dNTP Binding and Catalysis. Ummat A, Silverstein TD, Jain R, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK 2011
Recognition of the pro-mutagenic base uracil by family B DNA polymerases from archaea. Shuttleworth G, Fogg MJ, Kurpiewski MR, Jen-Jacobson L, Connolly BA 2004
The biochemistry and fidelity of synthesis by the apicoplast genome replication DNA polymerase Pfprex from the malaria parasite Plasmodium falciparum. Kennedy SR, Chen CY, Schmitt MW, Bower CN, Loeb LA 2011
Positive and negative regulators for glucitol (gut) operon expression in Escherichia coli. Yamada M, Saier MH 1988
Crystal structure of the DNA polymerase processivity factor of T4 bacteriophage. Moarefi I, Jeruzalmi D, Turner J, O'Donnell ME, Kuriyan J 2000
NMR mapping of PCNA interaction with translesion synthesis DNA polymerase Rev1 mediated by Rev1-BRCT domain. Pustovalova Y, Maciejewski MW, Korzhnev DM 2013
All Journals

Using Polbase tables:


Tables may be sorted by clicking on any of the column titles. A second click reverses the sort order. <Ctrl> + click on the column titles to sort by more than one column (e.g. family then name).


It is also possible to filter the table by typing into the search box above the table. This will instantly hide lines from the table that do not contain your search text.