-
1
-
-
0030839865
-
Oxidative decay of DNA
-
Beckman KB, Ames BN (1997) Oxidative decay of DNA. J Biol Chem 272: 19633-19636
-
(1997)
J Biol Chem
, vol.272
, pp. 19633-19636
-
-
Beckman, K.B.1
Ames, B.N.2
-
2
-
-
3543028588
-
Investigating the role of the little finger domain of Y-family DNA polymerases in low-fidelity synthesis and translesion replication
-
in press
-
Boudsocq F, Kokoska RJ, Plosky BS, Vaisman A, Ling H, Kunkel TA, Yang W, Woodgate R (2004) Investigating the role of the little finger domain of Y-family DNA polymerases in low-fidelity synthesis and translesion replication. J Biol Chem, (in press)
-
(2004)
J Biol Chem
-
-
Boudsocq, F.1
Kokoska, R.J.2
Plosky, B.S.3
Vaisman, A.4
Ling, H.5
Kunkel, T.A.6
Yang, W.7
Woodgate, R.8
-
3
-
-
0027217643
-
Compilation, alignment, and phylogenetic relationships of DNA polymerases
-
Braithwaite DK, Ito J (1993) Compilation, alignment, and phylogenetic 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
-
4
-
-
0032005866
-
Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes
-
Brautigam CA, Steitz TA (1998) Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr Opin Struct Biol 8: 54-63
-
(1998)
Curr Opin Struct Biol
, vol.8
, pp. 54-63
-
-
Brautigam, C.A.1
Steitz, T.A.2
-
5
-
-
3543012707
-
Crystallography & NMR system: A new software suite for macromolecular structure determination
-
Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D 54: 905-921
-
(1998)
Acta Crystallogr D
, 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
-
6
-
-
0030824517
-
Ribbons
-
Carson M (1997) Ribbons. Methods Enzymol 277: 493-505
-
(1997)
Methods Enzymol
, vol.277
, pp. 493-505
-
-
Carson, M.1
-
7
-
-
0025191508
-
15N nuclear magnetic resonance studies on the tautomerism of 8-hydroxy-2′-deoxyguanosine, 8-hydroxyguanosine, and other C8-substituted guanine nucleosides
-
Cho BP, Kadlubar FF, Culp SJ, Evans FE (1990) 15N nuclear magnetic resonance studies on the tautomerism of 8-hydroxy-2′-deoxyguanosine, 8-hydroxyguanosine, and other C8-substituted guanine nucleosides. Chem Res Toxicol 3: 445-452
-
(1990)
Chem Res Toxicol
, vol.3
, pp. 445-452
-
-
Cho, B.P.1
Kadlubar, F.F.2
Culp, S.J.3
Evans, F.E.4
-
8
-
-
0038799736
-
Oxidative DNA damage: Mechanisms, mutation, and disease
-
Cooke MS, Evans MD, Dizdaroglu M, Lunec J (2003) Oxidative DNA damage: mechanisms, mutation, and disease. FASEB J 17: 1195-1214
-
(2003)
FASEB J
, vol.17
, pp. 1195-1214
-
-
Cooke, M.S.1
Evans, M.D.2
Dizdaroglu, M.3
Lunec, J.4
-
10
-
-
0032425080
-
The mechanism of action of T7 DNA polymerase
-
Doublie S, Ellenberger T (1998) The mechanism of action of T7 DNA polymerase. Curr Opin Struct Biol 8: 704-712
-
(1998)
Curr Opin Struct Biol
, vol.8
, pp. 704-712
-
-
Doublie, S.1
Ellenberger, T.2
-
12
-
-
0032518398
-
Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
-
Doublie S, Tabor S, Long AM, Richardson CC, Ellenberger T (1998) Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature 391: 251-258
-
(1998)
Nature
, vol.391
, pp. 251-258
-
-
Doublie, S.1
Tabor, S.2
Long, A.M.3
Richardson, C.C.4
Ellenberger, T.5
-
13
-
-
0025783442
-
Fidelity mechanisms in DNA replication
-
Echols H, Goodman MF (1991) Fidelity mechanisms in DNA replication. Annu Rev Biochem 60: 477-511
-
(1991)
Annu Rev Biochem
, vol.60
, pp. 477-511
-
-
Echols, H.1
Goodman, M.F.2
-
14
-
-
0035830851
-
Fidelity of nucleotide insertion at 8-oxo-7,8-dihydroguanine by mammalian DNA polymerase delta. Steady-state and pre-steady-state kinetic analysis
-
Einolf HJ, Guengerich FP (2001) Fidelity of nucleotide insertion at 8-oxo-7,8-dihydroguanine by mammalian DNA polymerase delta. Steady-state and pre-steady-state kinetic analysis. J Biol Chem 276: 3764-3771
-
(2001)
J Biol Chem
, vol.276
, pp. 3764-3771
-
-
Einolf, H.J.1
Guengerich, F.P.2
-
15
-
-
0032558424
-
Steady-state and pre-steady-state kinetic analysis of 8-oxo-7,8-dihydroguanosine triphosphate incorporation and extension by replicative and repair DNA polymerases
-
Einolf HJ, Schnetz-Boutaud N, Guengerich FP (1998) Steady-state and pre-steady-state kinetic analysis of 8-oxo-7,8-dihydroguanosine triphosphate incorporation and extension by replicative and repair DNA polymerases. Biochemistry 37: 13300-13312
-
(1998)
Biochemistry
, vol.37
, pp. 13300-13312
-
-
Einolf, H.J.1
Schnetz-Boutaud, N.2
Guengerich, F.P.3
-
16
-
-
0025373259
-
Oxidative damage to DNA during aging: 8-Hydroxy-2′-deoxyguanosine in rat organ DNA and urine
-
Fraga CG, Shigenaga MK, Park JW, Degan P, Ames BN (1990) Oxidative damage to DNA during aging: 8-hydroxy-2′-deoxyguanosine in rat organ DNA and urine. Proc Natl Acad Sci USA 87: 4533-4537
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 4533-4537
-
-
Fraga, C.G.1
Shigenaga, M.K.2
Park, J.W.3
Degan, P.4
Ames, B.N.5
-
17
-
-
0035369086
-
Structure of the replicating complex of a pol alpha family DNA polymerase
-
Franklin MC, Wang J, Steitz TA (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
-
-
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
-
19
-
-
0030918969
-
Analysis of nucleotide insertion and extension at 8-oxo-7,8- dihydroguanine by replicative T7 polymerase exo- and human immunodeficiency virus-1 reverse transcriptase using steady-state and pre- steady-state kinetics
-
Furge LL, Guengerich FP (1997) Analysis of nucleotide insertion and extension at 8-oxo-7,8-dihydroguanine by replicative T7 polymerase exo- and human immunodeficiency virus-1 reverse transcriptase using steady-state and pre- steady-state kinetics. Biochemistry 36: 6475-6487
-
(1997)
Biochemistry
, vol.36
, pp. 6475-6487
-
-
Furge, L.L.1
Guengerich, F.P.2
-
20
-
-
0344588773
-
Pre-steady-state kinetics of nucleotide insertion following 8-oxo-7,8-dihydroguanine base pair mismatches by bacteriophage T7 DNA polymerase exo
-
Furge LL, Guengerich FP (1998) Pre-steady-state kinetics of nucleotide insertion following 8-oxo-7,8-dihydroguanine base pair mismatches by bacteriophage T7 DNA polymerase exo. Biochemistry 37: 3567-3574
-
(1998)
Biochemistry
, vol.37
, pp. 3567-3574
-
-
Furge, L.L.1
Guengerich, F.P.2
-
21
-
-
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
-
22
-
-
0034425754
-
Efficient and accurate replication in the presence of 7,8-dihydro-8-oxoguanine by DNA polymerase eta
-
Haracska L, Yu SL, Johnson RE, Prakash L, Prakash S (2000) Efficient and accurate replication in the presence of 7,8-dihydro-8-oxoguanine by DNA polymerase eta. Nat Genet 25: 458-461
-
(2000)
Nat Genet
, vol.25
, pp. 458-461
-
-
Haracska, L.1
Yu, S.L.2
Johnson, R.E.3
Prakash, L.4
Prakash, S.5
-
23
-
-
0037388383
-
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations
-
Johnson SJ, Taylor JS, Beese LS (2003) Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc Natl Acad Sci USA 100: 3895-3900
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 3895-3900
-
-
Johnson, S.J.1
Taylor, J.S.2
Beese, L.S.3
-
24
-
-
84889120137
-
Improved methods for building protein models in electron density maps and the location of errors in these models
-
Jones TA, Zou JY, Cowan SW, Kjeldgaard M (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 47: 110-119
-
(1991)
Acta Crystallogr A
, vol.47
, pp. 110-119
-
-
Jones, T.A.1
Zou, J.Y.2
Cowan, S.W.3
Kjeldgaard, M.4
-
26
-
-
0347379857
-
The efficiency and specificity of apurinic/apyrimidinic site bypass by human DNA polymerase eta and Sulfolobus solfataricus Dpo4
-
Kokoska RJ, McCulloch SD, Kunkel TA (2003) The efficiency and specificity of apurinic/apyrimidinic site bypass by human DNA polymerase eta and Sulfolobus solfataricus Dpo4. J Biol Chem 278: 50537-50545
-
(2003)
J Biol Chem
, vol.278
, pp. 50537-50545
-
-
Kokoska, R.J.1
McCulloch, S.D.2
Kunkel, T.A.3
-
27
-
-
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
-
29
-
-
0025891866
-
NMR structural studies of the ionizing radiation adduct 7-hydro-8-oxodeoxyguanosine (8-oxo-7H-dG) opposite deoxyadenosine in a DNA duplex. 8-Oxo-7H-dG(syn).dA (anti) alignment at lesion site
-
Kouchakdjian M, Bodepudi V, Shibutani S, Eisenberg M, Johnson F, Grollman AP, Patel DJ (1991) NMR structural studies of the ionizing radiation adduct 7-hydro-8-oxodeoxyguanosine (8-oxo-7H-dG) opposite deoxyadenosine in a DNA duplex. 8-Oxo-7H-dG(syn).dA (anti) alignment at lesion site. Biochemistry 30: 1403-1412
-
(1991)
Biochemistry
, vol.30
, pp. 1403-1412
-
-
Kouchakdjian, M.1
Bodepudi, V.2
Shibutani, S.3
Eisenberg, M.4
Johnson, F.5
Grollman, A.P.6
Patel, D.J.7
-
30
-
-
0037227566
-
Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential
-
Krahn JM, Beard WA, Miller H, Grollman AP, Wilson SH (2003) Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. Structure 11: 121-127
-
(2003)
Structure
, vol.11
, pp. 121-127
-
-
Krahn, J.M.1
Beard, W.A.2
Miller, H.3
Grollman, A.P.4
Wilson, S.H.5
-
31
-
-
0023647116
-
Misreading of DNA templates containing 8-hydroxydeoxyguanosine at the modified base and at adjacent residues
-
Kuchino Y, Mori F, Kasai H, Inoue H, Iwai S, Miura K, Ohtsuka E, Nishimura S (1987) Misreading of DNA templates containing 8- hydroxydeoxyguanosine at the modified base and at adjacent residues. Nature 327: 77-79
-
(1987)
Nature
, vol.327
, pp. 77-79
-
-
Kuchino, Y.1
Mori, F.2
Kasai, H.3
Inoue, H.4
Iwai, S.5
Miura, K.6
Ohtsuka, E.7
Nishimura, S.8
-
32
-
-
2342419732
-
DNA replication fidelity
-
Kunkel TA (2004) DNA replication fidelity. J Biol Chem 279: 16895-16898
-
(2004)
J Biol Chem
, vol.279
, pp. 16895-16898
-
-
Kunkel, T.A.1
-
33
-
-
3543002207
-
Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7
-
in press
-
Li Y, Dutta S, Doublie S, Moh'd Bdour H, Taylor JS, Ellenberger T (2004) Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7. Nature Struct Mol Biol, (in press)
-
(2004)
Nature Struct Mol Biol
-
-
Li, Y.1
Dutta, S.2
Doublie, S.3
Moh'd Bdour, H.4
Taylor, J.S.5
Ellenberger, T.6
-
34
-
-
0035812849
-
Crystal structure of a Y-family DNA polymerase in action: A mechanism for errorprone and lesion-bypass replication
-
Ling H, Boudsocq F, Woodgate R, Yang W (2001) Crystal structure of a Y-family DNA polymerase in action: a mechanism for errorprone and lesion-bypass replication. Cell 107: 91-102
-
(2001)
Cell
, vol.107
, pp. 91-102
-
-
Ling, H.1
Boudsocq, F.2
Woodgate, R.3
Yang, W.4
-
35
-
-
0028799524
-
X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine
-
Lipscomb LA, Peek ME, Morningstar ML, Verghis SM, Miller EM, Rich A, Essigmann JM, Williams LD (1995) X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine. Proc Natl Acad Sci USA 92: 719-723
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 719-723
-
-
Lipscomb, L.A.1
Peek, M.E.2
Morningstar, M.L.3
Verghis, S.M.4
Miller, E.M.5
Rich, A.6
Essigmann, J.M.7
Williams, L.D.8
-
36
-
-
0033741876
-
Single 8-oxo-guanine and 8-oxo-adenine lesions induce marked changes in the backbone structure of a 25-base DNA strand
-
Malins DC, Polissar NL, Ostrander GK, Vinson MA (2000) Single 8-oxo-guanine and 8-oxo-adenine lesions induce marked changes in the backbone structure of a 25-base DNA strand. Proc Natl Acad Sci USA 97: 12442-12445
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 12442-12445
-
-
Malins, D.C.1
Polissar, N.L.2
Ostrander, G.K.3
Vinson, M.A.4
-
37
-
-
0034011261
-
Oxyradicals and DNA damage
-
Marnett LJ (2000) Oxyradicals and DNA damage. Carcinogenesis 21: 361-370
-
(2000)
Carcinogenesis
, vol.21
, pp. 361-370
-
-
Marnett, L.J.1
-
38
-
-
0027930608
-
Crystal structure of a DNA duplex containing 8-hydroxydeoxyguanine- adenine base pairs
-
McAuley-Hecht KE, Leonard GA, Gibson NJ, Thomson JB, Watson WP, Hunter WN, Brown T (1994) Crystal structure of a DNA duplex containing 8-hydroxydeoxyguanine-adenine base pairs. Biochemistry 33: 10266-10270
-
(1994)
Biochemistry
, vol.33
, pp. 10266-10270
-
-
McAuley-Hecht, K.E.1
Leonard, G.A.2
Gibson, N.J.3
Thomson, J.B.4
Watson, W.P.5
Hunter, W.N.6
Brown, T.7
-
39
-
-
0032790081
-
Xtal View/Xfit - A versatile program for manipulating atomic coordinates and electron density
-
McRee DE (1991) Xtal View/Xfit - a versatile program for manipulating atomic coordinates and electron density. J Struct Biol 125: 156-165
-
(1991)
J Struct Biol
, vol.125
, pp. 156-165
-
-
McRee, D.E.1
-
40
-
-
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
-
41
-
-
0025854831
-
NMR studies of a DNA containing 8-hydroxydeoxyguanosine
-
Oda Y, Uesugi S, Ikehara M, Nishimura S, Kawase Y, Ishikawa H, Inoue H, Ohtsuka E (1991) NMR studies of a DNA containing 8-hydroxydeoxyguanosine. Nucleic Acids Res 19: 1407-1412
-
(1991)
Nucleic Acids Res
, vol.19
, pp. 1407-1412
-
-
Oda, Y.1
Uesugi, S.2
Ikehara, M.3
Nishimura, S.4
Kawase, Y.5
Ishikawa, H.6
Inoue, H.7
Ohtsuka, E.8
-
42
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Otwinowski Z, Minor W (1996) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307-326
-
(1996)
Methods Enzymol
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
43
-
-
0030930760
-
Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: Evidence for an induced fit mechanism
-
Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H (1997) 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
-
44
-
-
0000127073
-
Sequence-specific recognition of double helical nucleic acids by proteins
-
Seeman NC, Rosenberg JM, Rich A (1976) Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci USA 73: 804-808
-
(1976)
Proc Natl Acad Sci USA
, vol.73
, pp. 804-808
-
-
Seeman, N.C.1
Rosenberg, J.M.2
Rich, A.3
-
45
-
-
0025981359
-
Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG
-
Shibutani S, Takeshita M, Grollman AP (1991) Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG. Nature 349: 431-434
-
(1991)
Nature
, vol.349
, pp. 431-434
-
-
Shibutani, S.1
Takeshita, M.2
Grollman, A.P.3
-
46
-
-
0033581011
-
DNA polymerases: Structural diversity and common mechanisms
-
Steitz TA (1999) DNA polymerases: structural diversity and common mechanisms. J Biol Chem 274: 17395-17398
-
(1999)
J Biol Chem
, vol.274
, pp. 17395-17398
-
-
Steitz, T.A.1
-
47
-
-
0034847259
-
Structure of the catalytic core of S. cerevisiae DNA polymerase eta: Implications for translesion DNA synthesis
-
Trincao J, Johnson RE, Escalante CR, Prakash S, Prakash L, Aggarwal AK (2001) Structure of the catalytic core of S. cerevisiae DNA polymerase eta: implications for translesion DNA synthesis. Mol Cell 8: 417-426
-
(2001)
Mol Cell
, vol.8
, pp. 417-426
-
-
Trincao, J.1
Johnson, R.E.2
Escalante, C.R.3
Prakash, S.4
Prakash, L.5
Aggarwal, A.K.6
-
48
-
-
0017772412
-
Carbon-13 magnetic resonance spectra of 8-substituted purine nucleosides. Characteristic shifts for the syn conformation
-
Uesugi S, Ikehara M (1977) Carbon-13 magnetic resonance spectra of 8-substituted purine nucleosides. Characteristic shifts for the syn conformation. J Am Chem Soc 99: 3250-3253
-
(1977)
J Am Chem Soc
, vol.99
, pp. 3250-3253
-
-
Uesugi, S.1
Ikehara, M.2
-
49
-
-
0026026192
-
An induced-fit kinetic mechanism for DNA replication fidelity: Direct measurement by single-turnover kinetics
-
Wong I, Patel SS, Johnson KA (1991) An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics. Biochemistry 30: 526-537
-
(1991)
Biochemistry
, vol.30
, pp. 526-537
-
-
Wong, I.1
Patel, S.S.2
Johnson, K.A.3
-
50
-
-
0036295231
-
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) Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. J Mol Biol 317: 651-671
-
(2002)
J Mol Biol
, vol.317
, pp. 651-671
-
-
Yang, L.1
Beard, W.A.2
Wilson, S.H.3
Broyde, S.4
Schlick, T.5
|