-
1
-
-
0031027125
-
How easily oxidizable is DNA? One-electron reduction potentials of adenosine and guanosine radicals in aqueous solution
-
Steenken, S., and Jovanovic, S. V. (1997) How easily oxidizable is DNA? One-electron reduction potentials of adenosine and guanosine radicals in aqueous solution. J. Am. Chem. Soc. 119, 617-618.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 617-618
-
-
Steenken, S.1
Jovanovic, S.V.2
-
2
-
-
0035817980
-
The pH-dependent role of superoxide in riboflavin-catalyzed photooxidation of 8-oxo7,8-dihydroguanosine
-
Luo, W., Muller, J. G., and Burrows, C. J. (2001) The pH-dependent role of superoxide in riboflavin-catalyzed photooxidation of 8-oxo7,8- dihydroguanosine. Org. Lett. 3, 2801-2804.
-
(2001)
Org. Lett.
, vol.3
, pp. 2801-2804
-
-
Luo, W.1
Muller, J.G.2
Burrows, C.J.3
-
3
-
-
0034624588
-
Characterization of spiroiminodihydantoin as a product of one-electron oxidation of 8-oxo-7,8-dihydroguanosine
-
Luo, W., Muller, J. G., Rachlin, E. M., and Burrows, C. J. (2000) Characterization of spiroiminodihydantoin as a product of one-electron oxidation of 8-oxo-7,8-dihydroguanosine. Org, Lett. 2, 613-616.
-
(2000)
Org, Lett.
, vol.2
, pp. 613-616
-
-
Luo, W.1
Muller, J.G.2
Rachlin, E.M.3
Burrows, C.J.4
-
4
-
-
0034932109
-
Characterization of hydantoin products from one-electron oxidation of 8-oxo-7,8-dihydroguanosine in a nucleoside model
-
Luo, W., Muller, J. G., Rachlin, E. M., and Burrows, C. J. (2001) Characterization of hydantoin products from one-electron oxidation of 8-oxo-7,8-dihydroguanosine in a nucleoside model. Chem. Res. Toxicol. 14, 927-938.
-
(2001)
Chem. Res. Toxicol.
, vol.14
, pp. 927-938
-
-
Luo, W.1
Muller, J.G.2
Rachlin, E.M.3
Burrows, C.J.4
-
5
-
-
0036802909
-
Structure and potential mutagenicity of new hydantoin products from guanosine and 8-oxo7,8-dihydroguanine oxidation by transition metals
-
Burrows, C. J., Muller, J. G., Kornyushyna, O., Luo, W., Duarte, V., Leipold, M. D., and David, S. S. (2002) Structure and potential mutagenicity of new hydantoin products from guanosine and 8-oxo7,8-dihydroguanine oxidation by transition metals. Environ Health Perspect. 110 (Suppl. 5), 713-717.
-
(2002)
Environ Health Perspect.
, vol.110
, Issue.SUPPL. 5
, pp. 713-717
-
-
Burrows, C.J.1
Muller, J.G.2
Kornyushyna, O.3
Luo, W.4
Duarte, V.5
Leipold, M.D.6
David, S.S.7
-
6
-
-
25444521980
-
Nei deficient Escherichia coli are sensitive to chromate and accumulate the oxidized guanine lesion spiroiminodihydantoin
-
Hailer, M. K., Slade, P. G., Martin, B. D., and Sugden, K. D. (2005) Nei deficient Escherichia coli are sensitive to chromate and accumulate the oxidized guanine lesion spiroiminodihydantoin. Chem. Res. Toxicol. 18, 1378-1383.
-
(2005)
Chem. Res. Toxicol.
, vol.18
, pp. 1378-1383
-
-
Hailer, M.K.1
Slade, P.G.2
Martin, B.D.3
Sugden, K.D.4
-
7
-
-
0033555373
-
Insertion of dGMP and dAMP during in vitro DNA synthesis opposite an oxidized form of 7,8-dihydro-8-oxoguanine
-
Duarte, V., Muller, J. G., and Burrows, C. J. (1999) Insertion of dGMP and dAMP during in vitro DNA synthesis opposite an oxidized form of 7,8-dihydro-8-oxoguanine. Nucleic Acids Res. 27, 496-502.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 496-502
-
-
Duarte, V.1
Muller, J.G.2
Burrows, C.J.3
-
8
-
-
0041571565
-
The hydantoin lesions formed from oxidation of 7,8-dihydro8-oxoguanine are potent sources of replication errors in vivo
-
Henderson, P. T., Delaney, J. C., Muller, J. G., Neeley, W. L., Tannenbaum, S. R., Burrows, C. J., and Essigmann, J. M. (2003) The hydantoin lesions formed from oxidation of 7,8-dihydro8-oxoguanine are potent sources of replication errors in vivo. Biochemistry 42, 9257-9262.
-
(2003)
Biochemistry
, vol.42
, pp. 9257-9262
-
-
Henderson, P.T.1
Delaney, J.C.2
Muller, J.G.3
Neeley, W.L.4
Tannenbaum, S.R.5
Burrows, C.J.6
Essigmann, J.M.7
-
9
-
-
0037168491
-
In vitro nucleotide misinsertion opposite the oxidized guanosine lesions spiroiminodihydantoin and guanidinohydantoin and DNA synthesis past the lesions using Escherichia coli DNA polymerase i (Klenow fragment)
-
Kornyushyna, O., Berges, A. M., Muller, J. G., and Burrows, C. J. (2002) In vitro nucleotide misinsertion opposite the oxidized guanosine lesions spiroiminodihydantoin and guanidinohydantoin and DNA synthesis past the lesions using Escherichia coli DNA polymerase I (Klenow fragment). Biochemistry 41, 15304-15314.
-
(2002)
Biochemistry
, vol.41
, pp. 15304-15314
-
-
Kornyushyna, O.1
Berges, A.M.2
Muller, J.G.3
Burrows, C.J.4
-
10
-
-
0242592066
-
Effect of the oxidized guanosine lesions spiroiminodihydantoin and guanidinohydantoin on proofreading by Escherichia coli DNA polymerase i (Klenow fragment) in different sequence contexts
-
Kornyushyna, O., and Burrows, C. J. (2003) Effect of the oxidized guanosine lesions spiroiminodihydantoin and guanidinohydantoin on proofreading by Escherichia coli DNA polymerase I (Klenow fragment) in different sequence contexts. Biochemistry 42, 1300813018.
-
(2003)
Biochemistry
, vol.42
, pp. 1300813018
-
-
Kornyushyna, O.1
Burrows, C.J.2
-
11
-
-
33846846509
-
The substrate specificity of MutY for hyperoxidized guanine lesions in vivo
-
Delaney, S., Neeley, W. L., Delaney, J. C., and Essigmann, J. M. (2007) The substrate specificity of MutY for hyperoxidized guanine lesions in vivo. Biochemistry 46, 1448-1455.
-
(2007)
Biochemistry
, vol.46
, pp. 1448-1455
-
-
Delaney, S.1
Neeley, W.L.2
Delaney, J.C.3
Essigmann, J.M.4
-
12
-
-
2342537864
-
Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site
-
Hogg, M., Wallace, S. S., and 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
-
13
-
-
33644660504
-
Synthesis and characterization of the oxidized dGTP lesions spiroiminodihydantoin-2'-deoxynucleoside-5'- Triphosphate and guanidinohydantoin2'-deoxynucleoside-5'- triphosphate
-
Ye, Y., Muller, J. G., and Burrows, C. J. (2006) Synthesis and characterization of the oxidized dGTP lesions spiroiminodihydantoin-2'- deoxynucleoside-5'- triphosphate and guanidinohydantoin2'-deoxynucleoside-5'- triphosphate. J. Org. Chem. 71, 2181-2184.
-
(2006)
J. Org. Chem.
, vol.71
, pp. 2181-2184
-
-
Ye, Y.1
Muller, J.G.2
Burrows, C.J.3
-
14
-
-
33846493138
-
A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol
-
Aller, P., Rould, M. A., Hogg, M., Wallace, S. S., and Doublié, S. (2007) A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol. Proc. Natl. Acad. Sci. U.S.A. 104, 814-818.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 814-818
-
-
Aller, P.1
Rould, M.A.2
Hogg, M.3
Wallace, S.S.4
Doublié, S.5
-
15
-
-
34548699886
-
Caught bending the A-rule: Crystal structures of translesion DNA synthesis with a non-natural nucleotide
-
Zahn, K. E., Belrhali, H., Wallace, S. S., and 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
-
16
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzvmol. 276, 307-326.
-
(1997)
Methods Enzvmol.
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
17
-
-
0035369086
-
Structure of the replicating complex of a pol alpha family DNA polymerase
-
Franklin, M. C., Wang, J., and Steitz, T. A. (2001) Structure of the replicating complex of a pol alpha family DNA polymerase. Cell 105, 657-667.
-
(2001)
Cell
, vol.105
, pp. 657-667
-
-
Franklin, M.C.1
Wang, J.2
Steitz, T.A.3
-
18
-
-
34447508216
-
Phaser crystallographic software
-
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., and Read, R. J. (2007) Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674.
-
(2007)
J. Appl. Crystallogr.
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
19
-
-
77949535720
-
Features and development of Coot
-
(in press).
-
Emsley, P., Lohkamp, B., Scott, W., and Cowtan, K. (2010) Features and development of Coot, Acta Crystallogr., Sect. D: Biol. Crystallogr. (in press).
-
(2010)
Acta Crystallogr., Sect. D: Biol. Crystallogr.
-
-
Emsley, P.1
Lohkamp, B.2
Scott, W.3
Cowtan, K.4
-
20
-
-
37049014272
-
Version 1.2 of the crystallography and NMR system
-
Brunger, A. T. (2007) Version 1.2 of the crystallography and NMR system. Nat. Protoc. 2, 2728-2733.
-
(2007)
Nat. Protoc.
, vol.2
, pp. 2728-2733
-
-
Brunger, A.T.1
-
21
-
-
3543012707
-
Crystallography & NMR system: A new software suite for macromolecular structure determination
-
Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. Sect. D: Biol. Crystallogr. 54, 905-921.
-
(1998)
Acta Crystallogr. Sect. D: Biol. Crystallogr.
, vol.54
, pp. 905-921
-
-
Brunger, A.T.1
Adams, P.D.2
Clore, G.M.3
Delano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.S.7
Kuszewski, J.8
Nilges, M.9
Pannu, N.S.10
Read, R.J.11
Rice, L.M.12
Simonson, T.13
Warren, G.L.14
-
23
-
-
33847706180
-
Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family
-
Hogg, M., Aller, P., Konigsberg, W., Wallace, S. S., and Doublié, S. (2007) Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family. J. Biol. Chem, 282, 1432-1444.
-
(2007)
J. Biol. Chem
, vol.282
, pp. 1432-1444
-
-
Hogg, M.1
Aller, P.2
Konigsberg, W.3
Wallace, S.S.4
Doublié, S.5
-
24
-
-
0000243829
-
PROCHECK: A program to check the stereochemical quality of protein structures
-
Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291.
-
(1993)
J. Appl. Crystallogr.
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
26
-
-
0242498440
-
18Olabeled guanidinohydantoin from guanosine oxidation with singlet oxygen. Implications for structure and mechanism
-
18Olabeled guanidinohydantoin from guanosine oxidation with singlet oxygen. Implications for structure and mechanism. J. Am. Chem. Soc. 125, 13926-13927.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 13926-13927
-
-
Ye, Y.1
Muller, J.G.2
Luo, W.3
Mayne, C.L.4
Shallop, A.J.5
Jones, R.A.6
Burrows, C.J.7
-
27
-
-
33745133418
-
Involvement of phi29 DNA. polymerase thumb subdomain in the proper coordination of synthesis and degradation during DNA replication
-
Perez-Arnaiz, P., Lazaro, J. M., Salas, M., and de Vega, M. (2006) Involvement of phi29 DNA. polymerase thumb subdomain in the proper coordination of synthesis and degradation during DNA replication. Nucleic Acids Res. 34, 3107-3115.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 3107-3115
-
-
Perez-Arnaiz, P.1
Lazaro, J.M.2
Salas, M.3
De Vega, M.4
-
28
-
-
2342484512
-
Lesion (in)tolerance reveals insights into DNA replication fidelity
-
Freisinger, E., Grollman, A. P., Miller, H., and 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
-
29
-
-
0242396923
-
3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
Lu, X. J., and Olson, W. K. (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 31, 5108-5121.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 5108-5121
-
-
Lu, X.J.1
Olson, W.K.2
-
30
-
-
0003803285
-
-
University Science Books, Sausalito, CA.
-
Bloomfield, V. A., Crothers, D. M., and Tinoco, I. (2000) Nucleic Acids: Structures, Properties, and Functions, University Science Books, Sausalito, CA.
-
(2000)
Nucleic Acids: Structures, Properties, and Functions
-
-
Bloomfield, V.A.1
Crothers, D.M.2
Tinoco, I.3
-
31
-
-
4644259458
-
Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase
-
Brieba, L. G., Eichman, B. F., Kokoska, R. J., Doublié, S., Kunkel, T. A., and 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
-
32
-
-
4544273926
-
Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase
-
Hsu, G. W., Ober, M., Carell, T., and Beese, L. S. (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
-
34
-
-
36049005269
-
Translesion synthesis by human DNA polymerase eta across oxidative products of guanine
-
(Oxford).
-
Kino, K., Ito, N., Sugasawa, K., Sugiyama, H., and Hanaoka, F. (2004) Translesion synthesis by human DNA polymerase eta across oxidative products of guanine. Nucleic Acids Symp. Ser. (Oxford). 171-172.
-
(2004)
Nucleic Acids Symp. Ser.
, pp. 171-172
-
-
Kino, K.1
Ito, N.2
Sugasawa, K.3
Sugiyama, H.4
Hanaoka, F.5
-
35
-
-
26444571743
-
Structural and thermodynamic features of spiroiminodihydantoin damaged DNA duplexes
-
Jia, L., Shafirovich, V., Shapiro, R., Geacintov, N. E., and Broyde, S. (2005) Structural and thermodynamic features of spiroiminodihydantoin damaged DNA duplexes. Biochemistry 44, 13342-13353.
-
(2005)
Biochemistry
, vol.44
, pp. 13342-13353
-
-
Jia, L.1
Shafirovich, V.2
Shapiro, R.3
Geacintov, N.E.4
Broyde, S.5
-
37
-
-
46849104669
-
Superior removal of hydantoin lesions relative to other oxidized bases by the human DNA glycosylate hNEIL1
-
Krishnamurthy, N., Zhao, X., Burrows, C. J., and David, S. S. (2008) Superior removal of hydantoin lesions relative to other oxidized bases by the human DNA glycosylate hNEIL1. Biochemistry 47, 7137-7146.
-
(2008)
Biochemistry
, vol.47
, pp. 7137-7146
-
-
Krishnamurthy, N.1
Zhao, X.2
Burrows, C.J.3
David, S.S.4
-
38
-
-
1642524959
-
Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases
-
Steitz, T. A., and Yin, Y. W. (2004) Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases. Philos. Trans. R. Soc. London. Ser. B: Biol. Sci. 359, 17-23.
-
(2004)
Philos. Trans. R. Soc. London. Ser. B: Biol. Sci.
, vol.359
, pp. 17-23
-
-
Steitz, T.A.1
Yin, Y.W.2
-
39
-
-
67349086074
-
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., Plochocka, D., and Bebenek, A. (2009) Different behaviors in vivo of mutations in the beta hairpin loop of the DNA polymerases of the closely related phages T4 and RB69. J. Mol. Biol. 389, 797-807.
-
(2009)
J. Mol. Biol.
, vol.389
, pp. 797-807
-
-
Trzemecka, A.1
Plochocka, D.2
Bebenek, A.3
-
40
-
-
13444307044
-
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
-
Krissinel, E., and Henrick, K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. Sect. D: Biol. Crystallogr. 60, 2256-2268.
-
(2004)
Acta Crystallogr. Sect. D: Biol. Crystallogr.
, vol.60
, pp. 2256-2268
-
-
Krissinel, E.1
Henrick, K.2
|