-
1
-
-
14244272868
-
PHENIX: Building new software for automated crystallographic structure determination
-
Adams PD, Grosse-Kunstleve RW, Hung L-W, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D 58: 1948-1954
-
(2002)
Acta Crystallogr D
, vol.58
, pp. 1948-1954
-
-
Adams, P.D.1
Grosse-Kunstleve, R.W.2
Hung, L.-W.3
Ioerger, T.R.4
McCoy, A.J.5
Moriarty, N.W.6
Read, R.J.7
Sacchettini, J.C.8
Sauter, N.K.9
Terwilliger, T.C.10
-
2
-
-
0037133706
-
Quantitative measurement of translesion replication in human cells: Evidence for bypass of abasic sites by a replicative DNA polymerase
-
Avkin S, Adar S, Blander G, Livneh Z (2002) Quantitative measurement of translesion replication in human cells: evidence for bypass of abasic sites by a replicative DNA polymerase. Proc Natl Acad Sci USA 99: 3764-3769
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 3764-3769
-
-
Avkin, S.1
Adar, S.2
Blander, G.3
Livneh, Z.4
-
3
-
-
70450257567
-
DNA polymerase b substrate specificity: Side chain modulation of the 'A-rule'
-
Beard WA, Shock DD, Batra VK, Pedersen LC, Wilson SH (2009) DNA polymerase b substrate specificity: side chain modulation of the 'A-rule'. J Biol Chem 284: 31680-31689
-
(2009)
J Biol Chem
, vol.284
, pp. 31680-31689
-
-
Beard, W.A.1
Shock, D.D.2
Batra, V.K.3
Pedersen, L.C.4
Wilson, S.H.5
-
4
-
-
33846300306
-
Human DNA polymerase alpha uses a combination of positive and negative selectivity to polymerize purine dNTPs with high fidelity
-
Beckman J, Kincaid K, Hocek M, Spratt T, Engels J, Cosstick R, Kuchta RD (2007) Human DNA polymerase alpha uses a combination of positive and negative selectivity to polymerize purine dNTPs with high fidelity. Biochemistry 46: 448-460
-
(2007)
Biochemistry
, vol.46
, pp. 448-460
-
-
Beckman, J.1
Kincaid, K.2
Hocek, M.3
Spratt, T.4
Engels, J.5
Cosstick, R.6
Kuchta, R.D.7
-
5
-
-
0030906056
-
Base miscoding and strand misalignment errors by mutator Klenow polymerases with amino acid substitutions at tyrosine 766 in the O helix of the fingers subdomain
-
Bell JB, Eckert KA, Joyce CM, Kunkel TA (1997) Base miscoding and strand misalignment errors by mutator Klenow polymerases with amino acid substitutions at tyrosine 766 in the O helix of the fingers subdomain. J Biol Chem 272: 7345-7351
-
(1997)
J Biol Chem
, vol.272
, pp. 7345-7351
-
-
Bell, J.B.1
Eckert, K.A.2
Joyce, C.M.3
Kunkel, T.A.4
-
6
-
-
0027217643
-
Compilation, alignment, and phyloge-netic relationships of DNA polymerases
-
Braithwaite DK, Ito J (1993) Compilation, alignment, and phyloge-netic relationships of DNA polymerases. Nucleic Acids Res 21: 787-802
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 787-802
-
-
Braithwaite, D.K.1
Ito, J.2
-
7
-
-
4644259458
-
Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase
-
Brieba LG, Eichman BF, Kokoska RJ, Doublié S, Kunkel TA, Ellenberger T (2004) Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase. EMBO J 23: 3452-3461
-
(2004)
EMBO J
, vol.23
, pp. 3452-3461
-
-
Brieba, L.G.1
Eichman, B.F.2
Kokoska, R.J.3
Doublié, S.4
Kunkel, T.A.5
Ellenberger, T.6
-
8
-
-
59649110607
-
Nucleic acid polymerases use a general acid for nucleotidyl transfer
-
Castro C, Smidansky ED, Arnold JJ, Maksimchuk KR, Moustafa I, Uchida A, Götte M, Konigsberg W, Cameron CE (2009) Nucleic acid polymerases use a general acid for nucleotidyl transfer. Nat Struct Mol Biol 16: 212-218
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 212-218
-
-
Castro, C.1
Smidansky, E.D.2
Arnold, J.J.3
Maksimchuk, K.R.4
Moustafa, I.5
Uchida, A.6
Götte, M.7
Konigsberg, W.8
Cameron, C.E.9
-
9
-
-
65249142734
-
Identifying the features of purine dNTPs that allow accurate and efficient DNA replication by herpes simplex virus i DNA poly-merase
-
Cavanaugh NA, Urban M, Beckman J, Spratt TE, Kuchta RD (2009) Identifying the features of purine dNTPs that allow accurate and efficient DNA replication by herpes simplex virus I DNA poly-merase. Biochemistry 48: 3554-3564
-
(2009)
Biochemistry
, vol.48
, pp. 3554-3564
-
-
Cavanaugh, N.A.1
Urban, M.2
Beckman, J.3
Spratt, T.E.4
Kuchta, R.D.5
-
10
-
-
38349188454
-
DNA oligonucleotides with A, T, G or C opposite an abasic site: Structure and dynamics
-
Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J (2008) DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics. Nucleic Acids Res 36: 253-262
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 253-262
-
-
Chen, J.1
Dupradeau, F.Y.2
Case, D.A.3
Turner, C.J.4
Stubbe, J.5
-
11
-
-
0023734473
-
Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases
-
Clark JM (1988) Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases. Nucleic Acids Res 16: 9677-9686
-
(1988)
Nucleic Acids Res
, vol.16
, pp. 9677-9686
-
-
Clark, J.M.1
-
12
-
-
0023645858
-
Novel blunt-end addition reactions catalyzed by DNA polymerase i of Escherichia coli
-
Clark JM, Joyce CM, Beardsley GP (1987) Novel blunt-end addition reactions catalyzed by DNA polymerase I of Escherichia coli. J Mol Biol 198: 123-127
-
(1987)
J Mol Biol
, vol.198
, pp. 123-127
-
-
Clark, J.M.1
Joyce, C.M.2
Beardsley, G.P.3
-
14
-
-
0025040632
-
An attempt to unify the structure of polymerases
-
Delarue M, Poch O, Tordo N, Moras D, Argos P (1990) An attempt to unify the structure of polymerases. Protein Eng 3: 461-467
-
(1990)
Protein Eng
, vol.3
, pp. 461-467
-
-
Delarue, M.1
Poch, O.2
Tordo, N.3
Moras, D.4
Argos, P.5
-
15
-
-
49449109718
-
Opposed steric constraints in human DNA polymerase beta and E. coli DNA polymerase I
-
Di Pasquale F, Fischer D, Grohmann D, Restle T, Geyer A, Marx A (2008) Opposed steric constraints in human DNA polymerase beta and E. coli DNA polymerase I. J Am Chem Soc 130: 10748-10757
-
(2008)
J Am Chem Soc
, vol.130
, pp. 10748-10757
-
-
Di Pasquale, F.1
Fischer, D.2
Grohmann, D.3
Restle, T.4
Geyer, A.5
Marx, A.6
-
16
-
-
0031038053
-
Abasic translesion synthesis by DNA polymerase beta violates the 'A-rule'. Novel types of nucleotide incorporation by human DNA polymerase beta at an abasic lesion in different sequence contexts
-
Efrati E, Tocco G, Eritja R, Wilson SH, Goodman MF (1997) Abasic translesion synthesis by DNA polymerase beta violates the 'A-rule'. Novel types of nucleotide incorporation by human DNA polymerase beta at an abasic lesion in different sequence contexts. J Biol Chem 272: 2559-2569
-
(1997)
J Biol Chem
, vol.272
, pp. 2559-2569
-
-
Efrati, E.1
Tocco, G.2
Eritja, R.3
Wilson, S.H.4
Goodman, M.F.5
-
17
-
-
13244281317
-
Coot: Model-building tools for molecular graphics
-
Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D60: 2126-2132
-
(2004)
Acta Crystallogr D
, vol.60
, pp. 2126-2132
-
-
Emsley, P.1
Cowtan, K.2
-
18
-
-
33845638804
-
Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase
-
Fiala KA, Brown JA, Ling H, Kshetry AK, Zhang J, Taylor J-S, Yang W, Suo Z (2007b) Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase. J Mol Biol 365: 590-602
-
(2007)
J Mol Biol
, vol.365
, pp. 590-602
-
-
Fiala, K.A.1
Brown, J.A.2
Ling, H.3
Kshetry, A.K.4
Zhang, J.5
Taylor, J.-S.6
Yang, W.7
Suo, Z.8
-
19
-
-
34247181139
-
Mechanism of abasic lesion bypass catalyzed by a Y-family DNA polymerase
-
DOI 10.1074/jbc.M610718200
-
Fiala KA, Hypes CD, Suo Z (2007) Mechanism of abasic lesion bypass catalyzed by a Y-family DNA polymerase. J Biol Chem 282: 8188-8198 (Pubitemid 47093544)
-
(2007)
Journal of Biological Chemistry
, vol.282
, Issue.11
, pp. 8188-8198
-
-
Fiala, K.A.1
Hypes, C.D.2
Suo, Z.3
-
20
-
-
0029410817
-
Structure-energy analysis of the role of metal ions in phosphodiester bond hydrolysis by DNA polymerase i
-
Fothergill M, Goodman MF, Petruska J, Warshel A (1995) Structure-energy analysis of the role of metal ions in phosphodiester bond hydrolysis by DNA polymerase I. J Am Chem Soc 117: 11619-11627
-
(1995)
J Am Chem Soc
, vol.117
, pp. 11619-11627
-
-
Fothergill, M.1
Goodman, M.F.2
Petruska, J.3
Warshel, A.4
-
21
-
-
2342484512
-
Lesion (in)-tolerance reveals insights into DNA replication fidelity
-
Freisinger E, Grollman AP, Miller H, Kisker C (2004) Lesion (in)-tolerance reveals insights into DNA replication fidelity. EMBO J 23: 1494-1505
-
(2004)
EMBO J
, vol.23
, pp. 1494-1505
-
-
Freisinger, E.1
Grollman, A.P.2
Miller, H.3
Kisker, C.4
-
22
-
-
0030924437
-
Hydrogen bonding revisited: Geometric selection as a principal determinant of DNA replication fidelity
-
Goodman MF (1997) Hydrogen bonding revisited: geometric selection as a principal determinant of DNA replication fidelity. Proc Natl Acad Sci USA 94: 10493-10495
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 10493-10495
-
-
Goodman, M.F.1
-
23
-
-
0035997344
-
Error-prone repair DNA polymerases in prokaryotes and eukaryotes
-
Goodman MF (2002) Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu Rev Biochem 71: 17-50
-
(2002)
Annu Rev Biochem
, vol.71
, pp. 17-50
-
-
Goodman, M.F.1
-
24
-
-
0028027428
-
Nucleotide insertion and primer extension at abasic template sites in different sequence contexts
-
Goodman MF, Cai H, Bloom LB, Eritja R (1994) Nucleotide insertion and primer extension at abasic template sites in different sequence contexts. Ann N YAcad Sci 726: 132-142
-
(1994)
Ann N YAcad Sci
, vol.726
, pp. 132-142
-
-
Goodman, M.F.1
Cai, H.2
Bloom, L.B.3
Eritja, R.4
-
25
-
-
0035902108
-
Genome maintenance mechanisms for preventing cancer
-
Hoeijmakers JH (2001) Genome maintenance mechanisms for preventing cancer. Nature 411: 366-374
-
(2001)
Nature
, vol.411
, pp. 366-374
-
-
Hoeijmakers, J.H.1
-
26
-
-
2342537864
-
Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site
-
Hogg M, Wallace SS, Doublié S (2004) Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site. EMBO J 23: 1483-1493
-
(2004)
EMBO J
, vol.23
, pp. 1483-1493
-
-
Hogg, M.1
Wallace, S.S.2
Doublié, S.3
-
27
-
-
4544273926
-
Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase
-
Hsu GW, Ober M, Carell T, Beese LS (2004) Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Nature 431: 217-221
-
(2004)
Nature
, vol.431
, pp. 217-221
-
-
Hsu, G.W.1
Ober, M.2
Carell, T.3
Beese, L.S.4
-
29
-
-
8744305009
-
Role of base stacking and sequence context in the inhibition of yeast DNA polymerase eta by pyrene nucleotide
-
Hwang H, Taylor JS (2004) Role of base stacking and sequence context in the inhibition of yeast DNA polymerase eta by pyrene nucleotide. Biochemistry 43: 14612-14623
-
(2004)
Biochemistry
, vol.43
, pp. 14612-14623
-
-
Hwang, H.1
Taylor, J.S.2
-
30
-
-
0025766848
-
Compilation and alignment of DNA polymerase sequences
-
Ito J, Braithwaite DK (1991) Compilation and alignment of DNA polymerase sequences. Nucleic Acids Res 19: 4045-4057
-
(1991)
Nucleic Acids Res
, vol.19
, pp. 4045-4057
-
-
Ito, J.1
Braithwaite, D.K.2
-
31
-
-
0027879008
-
Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants
-
Kabsch W (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl Crystallogr 26: 795-800
-
(1993)
J Appl Crystallogr
, vol.26
, pp. 795-800
-
-
Kabsch, W.1
-
32
-
-
0035997351
-
Active site tightness and substrate fit in DNA replication
-
Kool ET (2002) Active site tightness and substrate fit in DNA replication. Annu Rev Biochem 71: 191-219
-
(2002)
Annu Rev Biochem
, vol.71
, pp. 191-219
-
-
Kool, E.T.1
-
33
-
-
0029056926
-
Crystal structure of the large fragment of Thermus aquaticus DNA polymerase i at 2.5-A resolution: Structural basis for thermo-stability
-
Korolev S, Nayal M, Barnes WM, Di Cera E, Waksman G (1995) Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermo-stability. Proc Natl Acad Sci USA 92: 9264-9268
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 9264-9268
-
-
Korolev, S.1
Nayal, M.2
Barnes, W.M.3
Di Cera, E.4
Waksman, G.5
-
34
-
-
0025375829
-
Mutation frequency and spectrum resulting from a single abasic site in a single-stranded vector
-
Lawrence CW, Borden A, Banerjee S K, LeClerc JE (1990) Mutation frequency and spectrum resulting from a single abasic site in a single-stranded vector. Nucleic Acids Res 18: 2153-2157
-
(1990)
Nucleic Acids Res
, vol.18
, pp. 2153-2157
-
-
Lawrence, C.W.1
Borden, A.2
Banerjee, S.K.3
Leclerc, J.E.4
-
35
-
-
0032535528
-
Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation
-
Li Y, Korolev S, Waksman G (1998) Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. EMBO J 17: 7514-7525
-
(1998)
EMBO J
, vol.17
, pp. 7514-7525
-
-
Li, Y.1
Korolev, S.2
Waksman, G.3
-
36
-
-
0035019856
-
Crystal structures of a ddATP-, ddTTP-, ddCTP, and ddGTP-trapped ternary complex of Klentaq1: Insights into nucleotide incorporation and selectivity
-
Li Y, Waksman G (2001) Crystal structures of a ddATP-, ddTTP-, ddCTP, and ddGTP-trapped ternary complex of Klentaq1: insights into nucleotide incorporation and selectivity. Protein Sci 10: 1225-1233
-
(2001)
Protein Sci
, vol.10
, pp. 1225-1233
-
-
Li, Y.1
Waksman, G.2
-
37
-
-
0027278557
-
Instability and decay of the primary structure of DNA
-
Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362: 709-715
-
(1993)
Nature
, vol.362
, pp. 709-715
-
-
Lindahl, T.1
-
38
-
-
0015504248
-
Rate of depurination of native deoxyr-ibonucleic acid
-
Lindahl T, Nyberg B (1972) Rate of depurination of native deoxyr-ibonucleic acid. Biochemistry 11: 3610-3618
-
(1972)
Biochemistry
, vol.11
, pp. 3610-3618
-
-
Lindahl, T.1
Nyberg, B.2
-
39
-
-
0041864009
-
Replication of a cis-syn thymine dimer at atomic resolution
-
Ling H, Boudsocq F, Plosky BS, Woodgate R, Yang W (2003) Replication of a cis-syn thymine dimer at atomic resolution. Nature 424: 1083-1087
-
(2003)
Nature
, vol.424
, pp. 1083-1087
-
-
Ling, H.1
Boudsocq, F.2
Plosky, B.S.3
Woodgate, R.4
Yang, W.5
-
40
-
-
1642382214
-
Snapshots of replication through an abasic lesion: Structural basis for base substitutions and frameshifts
-
Ling H, Boudsocq F, Woodgate R, Yang W (2004a) Snapshots of replication through an abasic lesion: structural basis for base substitutions and frameshifts. Mol Cell 13: 751-762
-
(2004)
Mol Cell
, vol.13
, pp. 751-762
-
-
Ling, H.1
Boudsocq, F.2
Woodgate, R.3
Yang, W.4
-
41
-
-
1442355023
-
Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase
-
Ling H, Sayer JM, Plosky BS, Yagi H, Boudsocq F, Woodgate R, Jerina DM, Yang W (2004b) Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase. Proc Natl Acad Sci USA 101: 2265-2269
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 2265-2269
-
-
Ling, H.1
Sayer, J.M.2
Plosky, B.S.3
Yagi, H.4
Boudsocq, F.5
Woodgate, R.6
Jerina, D.M.7
Yang, W.8
-
42
-
-
0023015325
-
Mutagenesis by apurinic/apyrimidinic sites
-
Loeb LA, Preston BD (1986) Mutagenesis by apurinic/apyrimidinic sites. Annu Rev Genet 20: 201-230
-
(1986)
Annu Rev Genet
, vol.20
, pp. 201-230
-
-
Loeb, L.A.1
Preston, B.D.2
-
43
-
-
34249660610
-
Highly tolerated amino acid substitutions increase the fidelity of Escherichia coli DNA poly-merase i
-
Loh E, Choe J, Loeb LA (2007) Highly tolerated amino acid substitutions increase the fidelity of Escherichia coli DNA poly-merase I. J Biol Chem 282: 12201-12209
-
(2007)
J Biol Chem
, vol.282
, pp. 12201-12209
-
-
Loh, E.1
Choe, J.2
Loeb, L.A.3
-
44
-
-
27844554439
-
Mutability of DNA polymerase I: Implications for the creation of mutant DNA polymerases
-
Loh E, Loeb LA (2005) Mutability of DNA polymerase I: implications for the creation of mutant DNA polymerases. DNA Repair 4: 1390-1398
-
(2005)
DNA Repair
, vol.4
, pp. 1390-1398
-
-
Loh, E.1
Loeb, L.A.2
-
45
-
-
34547114028
-
DNA polymerases eta and theta function in the same genetic pathway to generate mutations at A/T during somatic hypermutation of Ig genes
-
Masuda K, Ouchida R, Hikida M, Kurosaki T, Yokoi M, Masutani C, Seki M, Wood RD, Hanaoka F, O-Wang J (2007) DNA polymerases eta and theta function in the same genetic pathway to generate mutations at A/T during somatic hypermutation of Ig genes. J Biol Chem 282: 17387-17394
-
(2007)
J Biol Chem
, vol.282
, pp. 17387-17394
-
-
Masuda, K.1
Ouchida, R.2
Hikida, M.3
Kurosaki, T.4
Yokoi, M.5
Masutani, C.6
Seki, M.7
Wood, R.D.8
Hanaoka, F.9
O-Wang, J.10
-
46
-
-
0033578081
-
A specific partner for abasic damage in DNA
-
Matray TJ, Kool ET (1999) A specific partner for abasic damage in DNA. Nature 399: 704-708
-
(1999)
Nature
, vol.399
, pp. 704-708
-
-
Matray, T.J.1
Kool, E.T.2
-
47
-
-
17144371499
-
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) 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. Biochemistry 44: 5647-5659
-
(2005)
Biochemistry
, vol.44
, pp. 5647-5659
-
-
McCain, M.D.1
Meyer, A.S.2
Schultz, S.S.3
Glekas, A.4
Spratt, T.E.5
-
48
-
-
4043150758
-
Escherichia coli DNA polymerase i (Klenow fragment) uses a hydrogen-bonding fork from Arg668 to the primer terminus and incoming deoxynucleo-tide triphosphate to catalyze DNA replication
-
Meyer AS, Blandino M, Spratt TE (2004) Escherichia coli DNA polymerase I (Klenow fragment) uses a hydrogen-bonding fork from Arg668 to the primer terminus and incoming deoxynucleo-tide triphosphate to catalyze DNA replication. J Biol Chem 279: 33043-33046
-
(2004)
J Biol Chem
, vol.279
, pp. 33043-33046
-
-
Meyer, A.S.1
Blandino, M.2
Spratt, T.E.3
-
49
-
-
0033613841
-
Side chains that influence fidelity at the polymerase active site of Escherichia coli DNA polymerase i (Klenow fragment)
-
Minnick DT, Bebenek K, Osheroff WP, Turner Jr RM, Astatke M, Liu L, Kunkel TA, Joyce CM (1999) Side chains that influence fidelity at the polymerase active site of Escherichia coli DNA polymerase I (Klenow fragment). J Biol Chem 274: 3067-3075
-
(1999)
J Biol Chem
, vol.274
, pp. 3067-3075
-
-
Minnick, D.T.1
Bebenek, K.2
Osheroff, W.P.3
Turner Jr, R.M.4
Astatke, M.5
Liu, L.6
Kunkel, T.A.7
Joyce, C.M.8
-
50
-
-
4644289452
-
Human DNA primase uses Watson-Crick hydrogen bonds to distinguish between correct and incorrect nucleoside triphosphates
-
Moore CL, Zivkovic A, Engels JW, Kuchta RD (2004) Human DNA primase uses Watson-Crick hydrogen bonds to distinguish between correct and incorrect nucleoside triphosphates. Biochemistry 43: 12367-12374
-
(2004)
Biochemistry
, vol.43
, pp. 12367-12374
-
-
Moore, C.L.1
Zivkovic, A.2
Engels, J.W.3
Kuchta, R.D.4
-
51
-
-
25844440534
-
Rev1 employs a novel mechanism of DNA synthesis using a protein template
-
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2005) Rev1 employs a novel mechanism of DNA synthesis using a protein template. Science 309: 2219-2222
-
(2005)
Science
, vol.309
, pp. 2219-2222
-
-
Nair, D.T.1
Johnson, R.E.2
Prakash, L.3
Prakash, S.4
Aggarwal, A.K.5
-
52
-
-
33745808012
-
Hoogsteen base pair formation promotes synthesis opposite the 1,N6-ethenodeoxyadenosine lesion by human DNA polymerase iota
-
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2006) Hoogsteen base pair formation promotes synthesis opposite the 1,N6-ethenodeoxyadenosine lesion by human DNA polymerase iota. Nat Struct Mol Biol 13: 619-625
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 619-625
-
-
Nair, D.T.1
Johnson, R.E.2
Prakash, L.3
Prakash, S.4
Aggarwal, A.K.5
-
53
-
-
64049116254
-
DNA synthesis across an abasic lesion by human DNA polymer-ase iota
-
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2009) DNA synthesis across an abasic lesion by human DNA polymer-ase iota. Structure 17: 530-537
-
(2009)
Structure
, vol.17
, pp. 530-537
-
-
Nair, D.T.1
Johnson, R.E.2
Prakash, L.3
Prakash, S.4
Aggarwal, A.K.5
-
54
-
-
17944380943
-
The Y-family of DNA polymerases
-
Ohmori H, Friedberg EC, Fuchs RP, Goodman MF, Hanaoka F, Hinkle D, Kunkel TA, Lawrence CW, Livneh Z, Nohmi T, Prakash L, Prakash S, Todo T, Walker GC, Wang Z, Woodgate R (2001) The Y-family of DNA polymerases. Mol Cell 8: 486-487
-
(2001)
Mol Cell
, vol.8
, pp. 486-487
-
-
Ohmori, H.1
Friedberg, E.C.2
Fuchs, R.P.3
Goodman, M.F.4
Hanaoka, F.5
Hinkle, D.6
Kunkel, T.A.7
Lawrence, C.W.8
Livneh, Z.9
Nohmi, T.10
Prakash, L.11
Prakash, S.12
Todo, T.13
Walker, G.C.14
Wang, Z.15
Woodgate, R.16
-
55
-
-
39549097102
-
Mutational specificity and genetic control of replicative bypass of an abasic site in yeast
-
Pagès V, Johnson RE, Prakash L, Prakash S (2008) Mutational specificity and genetic control of replicative bypass of an abasic site in yeast. Proc Natl Acad Sci USA 105: 1170-1175
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 1170-1175
-
-
Pagès, V.1
Johnson, R.E.2
Prakash, L.3
Prakash, S.4
-
56
-
-
0035906661
-
Prokaryotic DNA polymerase I: Evolution, structure, and 'base flipping' mechanism for nucleotide selection
-
Patel PH, Suzuki M, Adman E, Shinkai A, Loeb LA (2001) Prokaryotic DNA polymerase I: evolution, structure, and 'base flipping' mechanism for nucleotide selection. J Mol Biol 308: 823-837
-
(2001)
J Mol Biol
, vol.308
, pp. 823-837
-
-
Patel, P.H.1
Suzuki, M.2
Adman, E.3
Shinkai, A.4
Loeb, L.A.5
-
57
-
-
0026486193
-
Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase
-
Peliska JA, Benkovic SJ (1992) Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase. Science 258: 1112-1118
-
(1992)
Science
, vol.258
, pp. 1112-1118
-
-
Peliska, J.A.1
Benkovic, S.J.2
-
58
-
-
0023654801
-
Nucleotide insertion kinetics opposite abasic lesions in DNA
-
Randall SK, Eritja R, Kaplan BE, Petruska J, Goodman MF (1987) Nucleotide insertion kinetics opposite abasic lesions in DNA. J Biol Chem 262: 6864-6870
-
(1987)
J Biol Chem
, vol.262
, pp. 6864-6870
-
-
Randall, S.K.1
Eritja, R.2
Kaplan, B.E.3
Petruska, J.4
Goodman, M.F.5
-
59
-
-
31144460784
-
Stepwise translocation of Dpo4 polymerase during error-free bypass of oxoG lesion
-
Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov N, Patel DJ (2006) Stepwise translocation of Dpo4 polymerase during error-free bypass of oxoG lesion. PLoS Biol 4: 25-42
-
(2006)
PLoS Biol
, vol.4
, pp. 25-42
-
-
Rechkoblit, O.1
Malinina, L.2
Cheng, Y.3
Kuryavyi, V.4
Broyde, S.5
Geacintov, N.6
Patel, D.J.7
-
60
-
-
0346463162
-
Evaluating the contribution of base stacking during translesion DNA replication
-
Reineks EZ, Berdis AJ (2004) Evaluating the contribution of base stacking during translesion DNA replication. Biochemistry 43: 393-404
-
(2004)
Biochemistry
, vol.43
, pp. 393-404
-
-
Reineks, E.Z.1
Berdis, A.J.2
-
61
-
-
23044492225
-
Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: Implications for the molecular basis of fidelity in DNA polymerases
-
Rothwell PJ, Mitaksov V, Waksman G (2005) Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: implications for the molecular basis of fidelity in DNA polymerases. Mol Cell 19: 345-355
-
(2005)
Mol Cell
, vol.19
, pp. 345-355
-
-
Rothwell, P.J.1
Mitaksov, V.2
Waksman, G.3
-
62
-
-
0021102422
-
Insertion of nucleotides opposite apuri-nic/apyrimidinic sites in deoxyribonucleic acid during in vitro synthesis: Uniqueness of adenine nucleotides
-
Sagher D, Strauss B (1983) Insertion of nucleotides opposite apuri-nic/apyrimidinic sites in deoxyribonucleic acid during in vitro synthesis: uniqueness of adenine nucleotides. Biochemistry 22: 4518-4526
-
(1983)
Biochemistry
, vol.22
, pp. 4518-4526
-
-
Sagher, D.1
Strauss, B.2
-
63
-
-
0020650113
-
Infidelity of DNA synthesis associated with bypass of apurinic sites
-
Schaaper RM, Kunkel TA, Loeb LA (1983) Infidelity of DNA synthesis associated with bypass of apurinic sites. Proc Natl Acad Sci USA 80: 487-491
-
(1983)
Proc Natl Acad Sci USA
, vol.80
, pp. 487-491
-
-
Schaaper, R.M.1
Kunkel, T.A.2
Loeb, L.A.3
-
64
-
-
10044288293
-
High-efficiency bypass of DNA damage by human DNA polymerase Q
-
Seki M, Masutani C, Yang LW, Schuffert A, Iwai S, Bahar I, Wood RD (2004) High-efficiency bypass of DNA damage by human DNA polymerase Q. EMBO J 23: 4484-4494
-
(2004)
EMBO J
, vol.23
, pp. 4484-4494
-
-
Seki, M.1
Masutani, C.2
Yang, L.W.3
Schuffert, A.4
Iwai, S.5
Bahar, I.6
Wood, R.D.7
-
65
-
-
0030971099
-
Translesional synthesis on DNA templates containing a single abasic site. A mechanistic study of the A rule
-
Shibutani S, Takeshita M, Grollman AP (1997) Translesional synthesis on DNA templates containing a single abasic site. A mechanistic study of the A rule. J Biol Chem 272: 13916-13922
-
(1997)
J Biol Chem
, vol.272
, pp. 13916-13922
-
-
Shibutani, S.1
Takeshita, M.2
Grollman, A.P.3
-
66
-
-
0035814929
-
Identification of hydrogen bonds between Escherichia coli DNA polymerase i (Klenow fragment) and the minor groove of DNA by amino acid substitution of the poly-merase and atomic substitution of the DNA
-
Spratt TE (2001) Identification of hydrogen bonds between Escherichia coli DNA polymerase I (Klenow fragment) and the minor groove of DNA by amino acid substitution of the poly-merase and atomic substitution of the DNA. Biochemistry 40: 2647-2652
-
(2001)
Biochemistry
, vol.40
, pp. 2647-2652
-
-
Spratt, T.E.1
-
67
-
-
0032518374
-
A mechanism for all polymerases
-
Steitz TA (1998) A mechanism for all polymerases. Nature 391: 231-232
-
(1998)
Nature
, vol.391
, pp. 231-232
-
-
Steitz, T.A.1
-
68
-
-
0036012782
-
The A rule revisited: Polymerases as determinants of mutational specificity
-
Strauss BS (2002) The A rule revisited: polymerases as determinants of mutational specificity. DNA Repair (Amst) 1: 125-135
-
(2002)
DNA Repair (Amst)
, vol.1
, pp. 125-135
-
-
Strauss, B.S.1
-
69
-
-
0029845979
-
Random mutagenesis of Thermus aquaticus DNA polymerase I: Concordance of immutable sites in vivo with the crystal structure
-
Suzuki M, Baskin D, Hood L, Loeb LA (1996) Random mutagenesis of Thermus aquaticus DNA polymerase I: concordance of immutable sites in vivo with the crystal structure. Proc Natl Acad Sci USA 93: 9670-9675
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 9670-9675
-
-
Suzuki, M.1
Baskin, D.2
Hood, L.3
Loeb, L.A.4
-
70
-
-
0037196080
-
New structural and mechanistic insight into the A-rule and the instructional and non-instructional behavior of DNA photoproducts and other lesions
-
Taylor JS (2002) New structural and mechanistic insight into the A-rule and the instructional and non-instructional behavior of DNA photoproducts and other lesions. Mutat Res 510: 55-70
-
(2002)
Mutat Res
, vol.510
, pp. 55-70
-
-
Taylor, J.S.1
-
71
-
-
66349091016
-
Discrimination between right and wrong purine dNTPs by DNA polymerase i from Bacillus stear-othermophilus
-
Trostler M, Delier A, Beckman J, Urban M, Patro JN, Spratt TE, Beese LS, Kuchta RD (2009) Discrimination between right and wrong purine dNTPs by DNA polymerase I from Bacillus stear-othermophilus. Biochemistry 48: 4633-4641
-
(2009)
Biochemistry
, vol.48
, pp. 4633-4641
-
-
Trostler, M.1
Delier, A.2
Beckman, J.3
Urban, M.4
Patro, J.N.5
Spratt, T.E.6
Beese, L.S.7
Kuchta, R.D.8
-
72
-
-
0037693883
-
Yeast DNA polymerase eta makes functional contacts with the DNA minor groove only at the incoming nucleoside triphosphate
-
Washington MT, Wolfle WT, Spratt TE, Prakash L, Prakash S (2003) Yeast DNA polymerase eta makes functional contacts with the DNA minor groove only at the incoming nucleoside triphosphate. Proc Natl Acad Sci USA 100: 5113-5118
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 5113-5118
-
-
Washington, M.T.1
Wolfle, W.T.2
Spratt, T.E.3
Prakash, L.4
Prakash, S.5
-
73
-
-
23344450921
-
Evidence for a Watson-Crick hydrogen bonding requirement in DNA synthesis by human DNA polymerase kappa
-
Wolfle WT, Washington MT, Kool ET, Spratt TE, Helquist SA, Prakash L, Prakash S (2005) Evidence for a Watson-Crick hydrogen bonding requirement in DNA synthesis by human DNA polymerase kappa. Mol Cell Biol 25: 7137-7143
-
(2005)
Mol Cell Biol
, vol.25
, pp. 7137-7143
-
-
Wolfle, W.T.1
Washington, M.T.2
Kool, E.T.3
Spratt, T.E.4
Helquist, S.A.5
Prakash, L.6
Prakash, S.7
-
74
-
-
3943089138
-
Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template
-
Xiong Y, Steitz TA (2004) Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template. Nature 430: 640-645
-
(2004)
Nature
, vol.430
, pp. 640-645
-
-
Xiong, Y.1
Steitz, T.A.2
-
75
-
-
33645962475
-
Making and breaking nucleic acids: Two-Mg2+-ion catalysis and substrate specificity
-
Yang W, Lee JY, Nowotny M (2006) Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. Mol Cell 22: 5-13
-
(2006)
Mol Cell
, vol.22
, pp. 5-13
-
-
Yang, W.1
Lee, J.Y.2
Nowotny, M.3
-
76
-
-
35648951199
-
What a difference a decade makes: Insights into translesion DNA synthesis
-
Yang W, Woodgate R (2007) What a difference a decade makes: insights into translesion DNA synthesis. Proc Natl Acad Sci USA 104: 15591-15598
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 15591-15598
-
-
Yang, W.1
Woodgate, R.2
-
77
-
-
34548699886
-
Caught bending the A-rule: Crystal structures of translesion DNA synthesis with a non-natural nucleotide
-
Zahn KE, Belrhali H, Wallace SS, Doublié S (2007) Caught bending the A-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide. Biochemistry 46: 10551-10561
-
(2007)
Biochemistry
, vol.46
, pp. 10551-10561
-
-
Zahn, K.E.1
Belrhali, H.2
Wallace, S.S.3
Doublié, S.4
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