-
1
-
-
0025858529
-
Mechanisms of spontaneous mutation in DNA repair-proficient Escherichia coli
-
Halliday, J.A. and Glickman, B.W. (1991) Mechanisms of spontaneous mutation in DNA repair-proficient Escherichia coli. Mutat. Res., 250, 55-71.
-
(1991)
Mutat. Res.
, vol.250
, pp. 55-71
-
-
Halliday, J.A.1
Glickman, B.W.2
-
2
-
-
84895784747
-
Mechanisms of base substitution mutagenesis in cancer genomes
-
Bacolla, A., Cooper, D.N. and Vasquez, K.M. (2014) Mechanisms of base substitution mutagenesis in cancer genomes. Genes, 5, 108-146.
-
(2014)
Genes
, vol.5
, pp. 108-146
-
-
Bacolla, A.1
Cooper, D.N.2
Vasquez, K.M.3
-
3
-
-
0024368667
-
Fidelity of DNA polymerases in DNA amplification
-
Keohavong, P and Thilly, W.G (1989) Fidelity of DNA polymerases in DNA amplification. Proc. Natl Acad. Sci. U.S.A., 86, 9253-9257.
-
(1989)
Proc. Natl Acad. Sci. U.S.A
, vol.86
, pp. 9253-9257
-
-
Keohavong, P.1
Thilly, W.G.2
-
4
-
-
0025160871
-
The fidelity of DNA synthesis catalyzed by derivatives of Escherichia coli DNA polymerase I
-
Bebenek, K., Joyce, C.M., Fitzgerald, M.P. and Kunkel, T.A. (1990) The fidelity of DNA synthesis catalyzed by derivatives of Escherichia coli DNA polymerase I. J. Biol. Chem., 265, 13878-13887.
-
(1990)
J. Biol. Chem.
, vol.265
, pp. 13878-13887
-
-
Bebenek, K.1
Joyce, C.M.2
Fitzgerald, M.P.3
Kunkel, T.A.4
-
5
-
-
33846026386
-
Fidelity of the human mitochondrial DNA polymerase
-
Lee, H.R. and Johnson, K.A. (2006) Fidelity of the human mitochondrial DNA polymerase. J. Biol. Chem., 281, 36236-36240.
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 36236-36240
-
-
Lee, H.R.1
Johnson, K.A.2
-
6
-
-
0344527720
-
The fidelity of DNA polymerase β during distributive and processive DNA synthesis
-
Osheroff, W.P., Jung, H.K., Beard, W.A., Wilson, S.H. and Kunkel, T.A. (1999) The Fidelity of DNA Polymerase β during Distributive and Processive DNA Synthesis. J. Biol. Chem. 274, 3642-3650.
-
(1999)
J. Biol. Chem
, vol.274
, pp. 3642-3650
-
-
Osheroff, W.P.1
Jung, H.K.2
Beard, W.A.3
Wilson, S.H.4
Kunkel, T.A.5
-
7
-
-
80055079975
-
Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis
-
Wang, W., Hellinga, H.W. and Beese, L.S. (2011) Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Proc. Natl Acad. Sci. U.S.A., 108, 17644-17648.
-
(2011)
Proc. Natl Acad. Sci. U.S.A
, vol.108
, pp. 17644-17648
-
-
Wang, W.1
Hellinga, H.W.2
Beese, L.S.3
-
8
-
-
84872113855
-
DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase
-
Xia, S., Wang, J. and Konigsberg, W.H. (2013) DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase. J. Am. Chem. Soc, 135, 193-202.
-
(2013)
J. Am. Chem. Soc
, vol.135
, pp. 193-202
-
-
Xia, S.1
Wang, J.2
Konigsberg, W.H.3
-
9
-
-
27144542782
-
Fidelity of dpo4: Effect of metal ions, nucleotide selection and pyrophosphorolysis
-
Vaisman, A., Ling, H., Woodgate, R. and Yang, W. (2005) Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. EMBO J., 24, 2957-2967.
-
(2005)
EMBO J
, vol.24
, pp. 2957-2967
-
-
Vaisman, A.1
Ling, H.2
Woodgate, R.3
Yang, W.4
-
10
-
-
84877867629
-
Mechanism of somatic hypermutation at the WA motif by human DNA polymerase η
-
Zhao, Y, Gregory, M.T, Biertümpfel, C, Hua, Y.-J., Hanaoka, F and Yang, W. (2013) Mechanism of somatic hypermutation at the WA motif by human DNA polymerase η. Proc. Natl Acad. Sci. U.S.A., 110, 8146-8151.
-
(2013)
Proc. Natl Acad. Sci. U.S.A
, vol.110
, pp. 8146-8151
-
-
Zhao, Y.1
Gregory, M.T.2
Biertümpfel, C.3
Hua, Y.-J.4
Hanaoka, F.5
Yang, W.6
-
11
-
-
79952143760
-
Replication infidelity via a mismatch with watson-crick geometry
-
Bebenek, K., Pedersen, L.C. and Kunkel, T.A. (2011) Replication infidelity via a mismatch with Watson-Crick geometry. Proc. Natl Acad. Sci. U.S.A., 108, 1862-1867.
-
(2011)
Proc. Natl Acad. Sci. U.S.A
, vol.108
, pp. 1862-1867
-
-
Bebenek, K.1
Pedersen, L.C.2
Kunkel, T.A.3
-
12
-
-
17544370107
-
Enzyme-DNA interactions required for efficient nucleotide incorporation and discrimination in human DNA polymerase beta
-
Osheroff, W.P (1996) Enzyme-DNA interactions required for efficient nucleotide incorporation and discrimination in human DNA polymerase beta. J. Biol. Chem., 271, 12141-12144.
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 12141-12144
-
-
Osheroff, W.P.1
-
13
-
-
0036300448
-
Involvement of DNA polymerase beta in DNA replication and mutagenic consequences
-
Servant, L., Bieth, A., Hayakawa, H., Cazaux, C. and Hoffmann, J.-S. (2002) Involvement of DNA polymerase beta in DNA replication and mutagenic consequences. J. Mol. Biol, 315, 1039-1047.
-
(2002)
J. Mol. Biol
, vol.315
, pp. 1039-1047
-
-
Servant, L.1
Bieth, A.2
Hayakawa, H.3
Cazaux, C.4
Hoffmann, J.-S.5
-
14
-
-
0345620782
-
Overexpression of DNA polymerase beta: A genomic instability enhancer process
-
Canitrot Y., Frechet, M., Servant, L., Cazaux, C. and Hoffmann, J.S. (1999) Overexpression of DNA polymerase beta: a genomic instability enhancer process. FASEB J., 13, 1107-1111.
-
(1999)
FASEB J
, vol.13
, pp. 1107-1111
-
-
Canitrot, Y.1
Frechet, M.2
Servant, L.3
Cazaux, C.4
Hoffmann, J.S.5
-
15
-
-
42949164023
-
Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation
-
Batra, V.K., Beard, W.A., Shock, DD., Pedersen, L.C. and Wilson, S.H. (2008) Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation. Mol. Cell, 30, 315-324.
-
(2008)
Mol. Cell
, vol.30
, pp. 315-324
-
-
Batra, V.K.1
Beard, W.A.2
Shock, D.D.3
Pedersen, L.C.4
Wilson, S.H.5
-
16
-
-
0030930760
-
Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: Evidence for an induced fit mechanism
-
Sawaya, M.R., Prasad, R., Wilson, S.H., Kraut, J. and Pelletier, H. (1997) Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism. Biochemistry, 36, 11205-11215.
-
(1997)
Biochemistry
, vol.36
, pp. 11205-11215
-
-
Sawaya, M.R.1
Prasad, R.2
Wilson, S.H.3
Kraut, J.4
Pelletier, H.5
-
17
-
-
33645984577
-
Magnesium-induced assembly of a complete DNA polymerase catalytic complex
-
Batra, V.K., Beard, W.A., Shock, DD., Krahh, J., Pedersen, L.C and Wilson, S.H. (2006) Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Structure, 14, 757-766.
-
(2006)
Structure
, vol.14
, pp. 757-766
-
-
Batra, V.K.1
Beard, W.A.2
Shock, D.D.3
Krahh, J.4
Pedersen, L.C.5
Wilson, S.H.6
-
19
-
-
0029817866
-
Crystal structures of human DNA polymerase beta complexed with DNA: Implications for catalytic mechanism, processivity, and fidelity
-
Pelletier, H., Sawaya, M.R., Wolfe, W., Wilson, S.H. and Kraut, J. (1996) Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity. Biochemistry, 35, 12742-12761.
-
(1996)
Biochemistry
, vol.35
, pp. 12742-12761
-
-
Pelletier, H.1
Sawaya, M.R.2
Wolfe, W.3
Wilson, S.H.4
Kraut, J.5
-
21
-
-
79953737180
-
Overview of the CCP4 suite and current developments
-
Winn, M.D., Ballard, CC, Cowtan, K.D., Dodson, E.J., Emsley, P, Evans, PR., Keegan, R.M., Krissinel, E.B., Leslie, A.G.W., McCoy, A. et al. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr, 67, 235-242.
-
(2011)
Acta Crystallogr. D Biol. Crystallogr
, vol.67
, pp. 235-242
-
-
Winn, M.D.1
Ballard, C.C.2
Cowtan, K.D.3
Dodson, E.J.4
Emsley, P.5
Evans, P.R.6
Keegan, R.M.7
Krissinel, E.B.8
Leslie, A.G.W.9
McCoy, A.10
-
22
-
-
34547592557
-
MolProbity: All-atom contacts and structure validation for proteins and nucleic acids
-
Davis, I.W., Leaver-Fay, A., Chen, V.B., Block, J.N, Kapral, GJ, Wang, X., Murray, L.W., Arendall, W.B., Snoeyink, J., Richardson, J.S. et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res., 35, W375-W383.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. W375-W383
-
-
Davis, I.W.1
Leaver-Fay, A.2
Chen, V.B.3
Block, J.N.4
Kapral, G.J.5
Wang, X.6
Murray, L.W.7
Arendall, W.B.8
Snoeyink, J.9
Richardson, J.S.10
-
23
-
-
0348244547
-
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe, N and MacKerell, A.D. Jr (2000) All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 21, 86-104.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerell, A.D.2
-
24
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamic studies of proteins
-
MacKerell, A.D., Bashford, D., Bellott, M., Dunbrack, R.L., Evanseck, J.D, Field, M.J., Fischer, S., Gao, J., Guo, H, Ha, S. et al (1998) All-atom empirical potential for molecular modeling and dynamic studies of proteins. J. Phys. Chem. B 102, 3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
-
25
-
-
1642576012
-
Improved treatment of the protein backbone in empirical force fields
-
MacKerell, A.D., Feig, M. and Brooks, CL. (2004) Improved treatment of the protein backbone in empirical force fields. J. Am. Chem. Soc. 126, 698-699.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 698-699
-
-
MacKerell, A.D.1
Feig, M.2
Brooks, C.L.3
-
26
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W.L., Chandrasekhar, J., Madura, J.D, Impey, R.W. and Klein, M.L. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
27
-
-
36449007976
-
The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the ewald and truncated list methods
-
York, D.M., Darden, T.A. and Pedersen, L.G (1993) The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods. J. Chem. Phys. 99, 8345-8348.
-
(1993)
J. Chem. Phys
, vol.99
, pp. 8345-8348
-
-
York, D.M.1
Darden, T.A.2
Pedersen, L.G.3
-
28
-
-
84878377737
-
Amino acid substitution in the active site of DNA polymerase β explains the energy Barrier of the nucleotidyl transfer reaction
-
Batra, V.K., Perera, L., Lin, P, Shock, DD., Beard, W.A., Pedersen, L.C, Pedersen, L.G and Wilson, S.H. (2013) Amino acid substitution in the active site of DNA polymerase β explains the energy barrier of the nucleotidyl transfer reaction. J. Am. Chem. Soc., 135, 8078-8088.
-
(2013)
J. Am. Chem. Soc.
, vol.135
, pp. 8078-8088
-
-
Batra, V.K.1
Perera, L.2
Lin, P.3
Shock, D.D.4
Beard, W.A.5
Pedersen, L.C.6
Pedersen, L.G.7
Wilson, S.H.8
-
29
-
-
33644634986
-
Structure and mechanism of DNA polymerase β
-
Beard, W.A. and Wilson, S.H. (2006) Structure and mechanism of DNA polymerase β. Chem. Rev., 106, 361-382.
-
(2006)
Chem. Rev.
, vol.106
, pp. 361-382
-
-
Beard, W.A.1
Wilson, S.H.2
-
30
-
-
44449088925
-
Incorrect nucleotide insertion at the active site of a G: A mismatch catalyzed by DNA polymerase
-
Lin, P, Batra, V.K, Pedersen, L.C, Beard, W.A., Wilson, S.H. and Pedersen, L.G (2008) Incorrect nucleotide insertion at the active site of a G: A mismatch catalyzed by DNA polymerase. Proc. Natl Acad. Sci. U.S.A., 105, 5670-5674.
-
(2008)
Proc. Natl Acad. Sci. U.S.A
, vol.105
, pp. 5670-5674
-
-
Lin, P.1
Batra, V.K.2
Pedersen, L.C.3
Beard, W.A.4
Wilson, S.H.5
Pedersen, L.G.6
-
31
-
-
0006962619
-
Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase and Escherichia coli DNA polymerase I
-
Tabor, S. and Richardson, CC (1989) Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase and Escherichia coli DNA polymerase I. Proc. Natl Acad. Sci. US.A., 86, 4076-4080.
-
(1989)
Proc. Natl Acad. Sci. US.A
, vol.86
, pp. 4076-4080
-
-
Tabor, S.1
Richardson, C.C.2
-
32
-
-
84879897415
-
Observing a DNA polymerase choose right from wrong
-
Freudenthal, B.D., Beard, W.A., Shock, D.D and Wilson, S.H. (2013) Observing a DNA polymerase choose right from wrong. Cell, 154, 157-168.
-
(2013)
Cell
, vol.154
, pp. 157-168
-
-
Freudenthal, B.D.1
Beard, W.A.2
Shock, D.D.3
Wilson, S.H.4
-
33
-
-
84899029281
-
Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase β
-
Koag, M.C. and Lee, S. (2014) Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase β. J. Am. Chem. Soc, 136, 5709-5721.
-
(2014)
J. Am. Chem. Soc
, vol.136
, pp. 5709-5721
-
-
Koag, M.C.1
Lee, S.2
-
34
-
-
0027297046
-
Ionization of bromouracil and fluorouracil stimulates base mispairing frequencies with guanine
-
Yu, H., Eritja, R., Bloom, L.B. and Goodman, M.F. (1993) Ionization of bromouracil and fluorouracil stimulates base mispairing frequencies with guanine. J. Biol. Chem., 268, 15935-15943.
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 15935-15943
-
-
Yu, H.1
Eritja, R.2
Bloom, L.B.3
Goodman, M.F.4
-
35
-
-
33749048664
-
Genetical implications of the structure of deoxyribonucleic acid
-
Watson, J.D. and Crick, F.H. (1953) Genetical implications of the structure of deoxyribonucleic acid. Nature, 171, 964-967.
-
(1953)
Nature
, vol.171
, pp. 964-967
-
-
Watson, J.D.1
Crick, F.H.2
-
36
-
-
78549236130
-
Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis
-
Moser, A., Range, K. and York, D.M. (2010) Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis. J. Phys. Chem. B, 114, 13911-13921.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 13911-13921
-
-
Moser, A.1
Range, K.2
York, D.M.3
|