-
1
-
-
15944429355
-
DNA-protein crosslinks: Their induction, repair, and biological consequences
-
Barker, S., Weinfeld, M., and Murray, D. (2005) DNA-protein crosslinks: Their induction, repair, and biological consequences Mutat. Res. 589, 111-135
-
(2005)
Mutat. Res.
, vol.589
, pp. 111-135
-
-
Barker, S.1
Weinfeld, M.2
Murray, D.3
-
2
-
-
0033852536
-
Loss of DNA-protein crosslinks from formaldehyde-exposed cells occurs through spontaneous hydrolysis and an active repair process linked to proteosome function
-
Quievryn, G. and Zhitkovich, A. (2000) Loss of DNA-protein crosslinks from formaldehyde-exposed cells occurs through spontaneous hydrolysis and an active repair process linked to proteosome function Carcinogenesis 21, 1573-1580
-
(2000)
Carcinogenesis
, vol.21
, pp. 1573-1580
-
-
Quievryn, G.1
Zhitkovich, A.2
-
3
-
-
0034652143
-
Subcellular localization of proteasomes and their regulatory complexes in mammalian cells
-
Brooks, P., Fuertes, G., Murray, R. Z., Bose, S., Knecht, E., Rechsteiner, M. C., Hendil, K. B., Tanaka, K., Dyson, J., and Rivett, J. (2000) Subcellular localization of proteasomes and their regulatory complexes in mammalian cells Biochem. J. 346, 155-161
-
(2000)
Biochem. J.
, vol.346
, pp. 155-161
-
-
Brooks, P.1
Fuertes, G.2
Murray, R.Z.3
Bose, S.4
Knecht, E.5
Rechsteiner, M.C.6
Hendil, K.B.7
Tanaka, K.8
Dyson, J.9
Rivett, J.10
-
4
-
-
0036678202
-
Clastosome: A subtype of nuclear body enriched in 19S and 20S proteasomes, ubiquitin, and protein substrates of proteasome
-
Lafarga, M., Berciano, M. T., Pena, E., Mayo, I., Castano, J. G., Bohmann, D., Rodrigues, J. P., Tavanez, J. P., and Carmo-Fonseca, M. (2002) Clastosome: A subtype of nuclear body enriched in 19S and 20S proteasomes, ubiquitin, and protein substrates of proteasome Mol. Biol. Cell 13, 2771-2782
-
(2002)
Mol. Biol. Cell
, vol.13
, pp. 2771-2782
-
-
Lafarga, M.1
Berciano, M.T.2
Pena, E.3
Mayo, I.4
Castano, J.G.5
Bohmann, D.6
Rodrigues, J.P.7
Tavanez, J.P.8
Carmo-Fonseca, M.9
-
5
-
-
0030854371
-
Ubiquitin-dependent destruction of topoisomerase i is stimulated by the antitumor drug camptothecin
-
Desai, S. D., Liu, L. F., Vazquez-Abad, D., and DArpa, P. (1997) Ubiquitin-dependent destruction of topoisomerase I is stimulated by the antitumor drug camptothecin J. Biol. Chem. 272, 24159-24164
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 24159-24164
-
-
Desai, S.D.1
Liu, L.F.2
Vazquez-Abad, D.3
Darpa, P.4
-
6
-
-
14344255692
-
Initiation of repair of DNA-polypeptide cross-links by the UvrABC nuclease
-
Minko, I. G., Kurtz, A. J., Croteau, D. L., Van Houten, B., Harris, T. M., and Lloyd, R. S. (2005) Initiation of repair of DNA-polypeptide cross-links by the UvrABC nuclease Biochemistry 44, 3000-3009
-
(2005)
Biochemistry
, vol.44
, pp. 3000-3009
-
-
Minko, I.G.1
Kurtz, A.J.2
Croteau, D.L.3
Van Houten, B.4
Harris, T.M.5
Lloyd, R.S.6
-
7
-
-
3343008808
-
Interactions between UvrA and UvrB: The role of UvrBs domain 2 in nucleotide excision repair
-
Truglio, J. J., Croteau, D. L., Skorvaga, M., DellaVecchia, M. J., Theis, K., Mandavilli, B. S., Van Houten, B., and Kisker, C. (2004) Interactions between UvrA and UvrB: The role of UvrBs domain 2 in nucleotide excision repair EMBO J. 23, 2498-2509
-
(2004)
EMBO J.
, vol.23
, pp. 2498-2509
-
-
Truglio, J.J.1
Croteau, D.L.2
Skorvaga, M.3
Dellavecchia, M.J.4
Theis, K.5
Mandavilli, B.S.6
Van Houten, B.7
Kisker, C.8
-
8
-
-
0037133210
-
Incision of DNA-protein crosslinks by UvrABC nuclease suggests a potential repair pathway involving nucleotide excision repair
-
Minko, I. G., Zou, Y., and Lloyd, R. S. (2002) Incision of DNA-protein crosslinks by UvrABC nuclease suggests a potential repair pathway involving nucleotide excision repair Proc. Natl. Acad. Sci. U.S.A. 99, 1905-1909
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 1905-1909
-
-
Minko, I.G.1
Zou, Y.2
Lloyd, R.S.3
-
9
-
-
0019888472
-
Specific nicking of DNA at apurinic sites by peptides containing aromatic residues
-
Pierre, J. and Laval, J. (1981) Specific nicking of DNA at apurinic sites by peptides containing aromatic residues J. Biol. Chem. 256, 10217-10220
-
(1981)
J. Biol. Chem.
, vol.256
, pp. 10217-10220
-
-
Pierre, J.1
Laval, J.2
-
10
-
-
0019416108
-
A tryptophan-containing peptide recognizes and cleaves DNA at apurinic sites
-
DOI 10.1038/292858a0
-
Behmoaras, T., Toulme, J. J., and Helene, C. (1981) A tryptophan-containing peptide recognizes and cleaves DNA at apurinic sites Nature 292, 858-859 (Pubitemid 11015505)
-
(1981)
Nature
, vol.292
, Issue.5826
, pp. 858-859
-
-
Behmoaras, T.1
Toulme, J.J.2
Helene, C.3
-
11
-
-
0026101901
-
Stereochemical studies of the β-elimination reactions at aldehydic abasic sites in DNA: Endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys
-
Mazumder, A., Gerlt, J. A., Absalon, M. J., Stubbe, J., Cunningham, R. P., Withka, J., and Bolton, P. H. (1991) Stereochemical studies of the β-elimination reactions at aldehydic abasic sites in DNA: Endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys Biochemistry 30, 1119-1126
-
(1991)
Biochemistry
, vol.30
, pp. 1119-1126
-
-
Mazumder, A.1
Gerlt, J.A.2
Absalon, M.J.3
Stubbe, J.4
Cunningham, R.P.5
Withka, J.6
Bolton, P.H.7
-
12
-
-
0027301692
-
Evidence for an imino intermediate in the T4 endonuclease v reaction
-
Dodson, M. L., Schrock, R. D., III, and Lloyd, R. S. (1993) Evidence for an imino intermediate in the T4 endonuclease V reaction Biochemistry 32, 8284-8290
-
(1993)
Biochemistry
, vol.32
, pp. 8284-8290
-
-
Dodson, M.L.1
Schrock III, R.D.2
Lloyd, R.S.3
-
13
-
-
0037018939
-
Evidence for multiple imino intermediates and identification of reactive nucleophiles in peptide-catalyzed β-elimination at abasic sites
-
Kurtz, A. J., Dodson, M. L., and Lloyd, R. S. (2002) Evidence for multiple imino intermediates and identification of reactive nucleophiles in peptide-catalyzed β-elimination at abasic sites Biochemistry 41, 7054-7064
-
(2002)
Biochemistry
, vol.41
, pp. 7054-7064
-
-
Kurtz, A.J.1
Dodson, M.L.2
Lloyd, R.S.3
-
14
-
-
0026075807
-
Reductive methylation of the amino terminus of endonuclease v eradicates catalytic activities. Evidence for an essential role of the amino terminus in the chemical mechanisms of catalysis
-
Schrock, R. D., III and Lloyd, R. S. (1991) Reductive methylation of the amino terminus of endonuclease V eradicates catalytic activities. Evidence for an essential role of the amino terminus in the chemical mechanisms of catalysis J. Biol. Chem. 266, 17631-17639
-
(1991)
J. Biol. Chem.
, vol.266
, pp. 17631-17639
-
-
Schrock III, R.D.1
Lloyd, R.S.2
-
15
-
-
0035895359
-
The reaction mechanism of DNA glycosylase/AP lyases at abasic sites
-
McCullough, A. K., Sanchez, A., Dodson, M. L., Marapaka, P., Taylor, J. S., and Lloyd, R. S. (2001) The reaction mechanism of DNA glycosylase/AP lyases at abasic sites Biochemistry 40, 561-568
-
(2001)
Biochemistry
, vol.40
, pp. 561-568
-
-
McCullough, A.K.1
Sanchez, A.2
Dodson, M.L.3
Marapaka, P.4
Taylor, J.S.5
Lloyd, R.S.6
-
16
-
-
0037458649
-
2-deoxyguanosine adducts of acrolein, crotonaldehyde, and trans -4-hydroxynonenal cross-link to peptides via Schiff base linkage
-
2-deoxyguanosine adducts of acrolein, crotonaldehyde, and trans -4-hydroxynonenal cross-link to peptides via Schiff base linkage J. Biol. Chem. 278, 5970-5976
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 5970-5976
-
-
Kurtz, A.J.1
Lloyd, R.S.2
-
17
-
-
0021319465
-
2-propanodeoxyguanosine adducts in DNA upon reaction with acrolein or crotonaldehyde
-
2-propanodeoxyguanosine adducts in DNA upon reaction with acrolein or crotonaldehyde Cancer Res. 44, 990-995
-
(1984)
Cancer Res.
, vol.44
, pp. 990-995
-
-
Chung, F.L.1
Young, R.2
Hecht, S.S.3
-
18
-
-
0024389936
-
2-propanodeoxyguanosine adducts in DNA of rats treated with N-nitrosopyrrolidine and mice treated with crotonaldehyde
-
2-propanodeoxyguanosine adducts in DNA of rats treated with N-nitrosopyrrolidine and mice treated with crotonaldehyde Carcinogenesis 10, 1291-1297
-
(1989)
Carcinogenesis
, vol.10
, pp. 1291-1297
-
-
Chung, F.L.1
Young, R.2
Hecht, S.S.3
-
19
-
-
0029824077
-
Lipid peroxidation as a potential endogenous source for the formation of exocyclic DNA adducts
-
Chung, F. L., Chen, H. J., and Nath, R. G. (1996) Lipid peroxidation as a potential endogenous source for the formation of exocyclic DNA adducts Carcinogenesis 17, 2105-2111
-
(1996)
Carcinogenesis
, vol.17
, pp. 2105-2111
-
-
Chung, F.L.1
Chen, H.J.2
Nath, R.G.3
-
20
-
-
0034654638
-
Deoxyguanosine adducts of t-4-hydroxy-2-nonenal are endogenous DNA lesions in rodents and humans: Detection and potential sources
-
Chung, F. L., Nath, R. G., Ocando, J., Nishikawa, A., and Zhang, L. (2000) Deoxyguanosine adducts of t-4-hydroxy-2-nonenal are endogenous DNA lesions in rodents and humans: Detection and potential sources Cancer Res. 60, 1507-1511
-
(2000)
Cancer Res.
, vol.60
, pp. 1507-1511
-
-
Chung, F.L.1
Nath, R.G.2
Ocando, J.3
Nishikawa, A.4
Zhang, L.5
-
22
-
-
29344440479
-
2-propano-2′-deoxyguanosine DNA adduct
-
2-propano-2′-deoxyguanosine DNA adduct J. Am. Chem. Soc. 127, 17686-17696
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 17686-17696
-
-
Cho, Y.J.1
Kim, H.Y.2
Huang, H.3
Slutsky, A.4
Minko, I.G.5
Wang, H.6
Nechev, L.V.7
Kozekov, I.D.8
Kozekova, A.9
Tamura, P.10
Jacob, J.11
Voehler, M.12
Harris, T.M.13
Lloyd, R.S.14
Rizzo, C.J.15
Stone, M.P.16
-
23
-
-
33748646770
-
2-[3-oxo-1(S)- methyl-propyl]-dG DNA adduct hinders interstrand cross-link formation in the 5′-CpG-3′ sequence
-
2-[3-oxo-1(S)-methyl-propyl]-dG DNA adduct hinders interstrand cross-link formation in the 5′-CpG-3′ sequence Chem. Res. Toxicol. 19, 1019-1029
-
(2006)
Chem. Res. Toxicol.
, vol.19
, pp. 1019-1029
-
-
Cho, Y.J.1
Wang, H.2
Kozekov, I.D.3
Kozekova, A.4
Kurtz, A.J.5
Jacob, J.6
Voehler, M.7
Smith, J.8
Harris, T.M.9
Rizzo, C.J.10
Lloyd, R.S.11
Stone, M.P.12
-
24
-
-
55949136881
-
Replication bypass of the acrolein-mediated deoxyguanine DNA-peptide cross-links by DNA polymerases of the DinB family
-
Minko, I. G., Yamanaka, K., Kozekov, I. D., Kozekova, A., Indiani, C., ODonnell, M. E., Jiang, Q., Goodman, M. F., Rizzo, C. J., and Lloyd, R. S. (2008) Replication bypass of the acrolein-mediated deoxyguanine DNA-peptide cross-links by DNA polymerases of the DinB family Chem. Res. Toxicol. 21, 1983-1990
-
(2008)
Chem. Res. Toxicol.
, vol.21
, pp. 1983-1990
-
-
Minko, I.G.1
Yamanaka, K.2
Kozekov, I.D.3
Kozekova, A.4
Indiani, C.5
Odonnell, M.E.6
Jiang, Q.7
Goodman, M.F.8
Rizzo, C.J.9
Lloyd, R.S.10
-
25
-
-
67649933847
-
2-deoxyguanosine adducts of the α,β-unsaturated aldehydes acrolein, crotonaldehyde, and 4-hydroxynonenal
-
2-deoxyguanosine adducts of the α,β-unsaturated aldehydes acrolein, crotonaldehyde, and 4-hydroxynonenal Chem. Res. Toxicol. 22, 759-778
-
(2009)
Chem. Res. Toxicol.
, vol.22
, pp. 759-778
-
-
Minko, I.G.1
Kozekov, I.D.2
Harris, T.M.3
Rizzo, C.J.4
Lloyd, R.S.5
Stone, M.P.6
-
26
-
-
37249015575
-
Mutagenic potential of DNA-peptide crosslinks mediated by acrolein-derived DNA adducts
-
Minko, I. G., Kozekov, I. D., Kozekova, A., Harris, T. M., Rizzo, C. J., and Lloyd, R. S. (2008) Mutagenic potential of DNA-peptide crosslinks mediated by acrolein-derived DNA adducts Mutat. Res. 637, 161-172
-
(2008)
Mutat. Res.
, vol.637
, pp. 161-172
-
-
Minko, I.G.1
Kozekov, I.D.2
Kozekova, A.3
Harris, T.M.4
Rizzo, C.J.5
Lloyd, R.S.6
-
27
-
-
55549141867
-
Replication bypass of interstrand cross-link intermediates by Escherichia coli DNA polymerase IV
-
Kumari, A., Minko, I. G., Harbut, M. B., Finkel, S. E., Goodman, M. F., and Lloyd, R. S. (2008) Replication bypass of interstrand cross-link intermediates by Escherichia coli DNA polymerase IV J. Biol. Chem. 283, 27433-27437
-
(2008)
J. Biol. Chem.
, vol.283
, pp. 27433-27437
-
-
Kumari, A.1
Minko, I.G.2
Harbut, M.B.3
Finkel, S.E.4
Goodman, M.F.5
Lloyd, R.S.6
-
28
-
-
0026951903
-
Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions
-
Piotto, M., Saudek, V., and Sklenar, V. (1992) Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions J. Biomol. NMR 2, 661-665
-
(1992)
J. Biomol. NMR
, vol.2
, pp. 661-665
-
-
Piotto, M.1
Saudek, V.2
Sklenar, V.3
-
29
-
-
0000425457
-
MARDIGRAS - A procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure
-
Borgias, B. A. and James, T. L. (1990) MARDIGRAS - A procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure J. Magn. Reson. 87, 475-487
-
(1990)
J. Magn. Reson.
, vol.87
, pp. 475-487
-
-
Borgias, B.A.1
James, T.L.2
-
30
-
-
0030117290
-
Correcting NOESY cross-peak intensities for partial relaxation effects enabling accurate distance information
-
Liu, H., Tonelli, M., and James, T. L. (1996) Correcting NOESY cross-peak intensities for partial relaxation effects enabling accurate distance information J. Magn. Reson. B 111, 85-89
-
(1996)
J. Magn. Reson. B
, vol.111
, pp. 85-89
-
-
Liu, H.1
Tonelli, M.2
James, T.L.3
-
31
-
-
0029450044
-
Interproton distance bounds from 2D NOE intensities: Effect of experimental noise and peak integration errors
-
Liu, H., Spielmann, H. P., Ulyanov, N. B., Wemmer, D. E., and James, T. L. (1995) Interproton distance bounds from 2D NOE intensities: Effect of experimental noise and peak integration errors J. Biomol. NMR 6, 390-402
-
(1995)
J. Biomol. NMR
, vol.6
, pp. 390-402
-
-
Liu, H.1
Spielmann, H.P.2
Ulyanov, N.B.3
Wemmer, D.E.4
James, T.L.5
-
32
-
-
0024381278
-
2-propanodeoxyguanosine adducts (X) opposite purines in DNA duplexes: Protonated X(syn):A(anti) pairing (acidic pH) and X(syn):G(anti) pairing (neutral pH) at the lesion site
-
2- propanodeoxyguanosine adducts (X) opposite purines in DNA duplexes: Protonated X(syn):A(anti) pairing (acidic pH) and X(syn):G(anti) pairing (neutral pH) at the lesion site Biochemistry 28, 5647-5657
-
(1989)
Biochemistry
, vol.28
, pp. 5647-5657
-
-
Kouchakdjian, M.1
Marinelli, E.2
Gao, X.3
Johnson, F.4
Grollman, A.5
Patel, D.6
-
33
-
-
0023111788
-
Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: A graphical method
-
Rinkel, L. J. and Altona, C. (1987) Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: A graphical method J. Biomol. Struct. Dyn. 4, 621-649
-
(1987)
J. Biomol. Struct. Dyn.
, vol.4
, pp. 621-649
-
-
Rinkel, L.J.1
Altona, C.2
-
35
-
-
77954829347
-
-
GAUSSIAN 98, 1998 ed., Gaussian, Inc., Pittsburgh, PA
-
Frisch, M. J., (1998) GAUSSIAN 98, 1998 ed., Gaussian, Inc., Pittsburgh, PA.
-
(1998)
-
-
Frisch, M.J.1
-
36
-
-
0004023353
-
-
7.0 ed., University of California, San Francisco, CA
-
Case, D. A., Pearlman, D. A., Caldwell, J. W., Cheatham, T. E., III, Wang, J., Ross, W. S., Simmerling, C. L., Darden, T. A., Merz, K. M., Stanton, R. V., Cheng, A. L., Vincent, J. J., Crowley, M., Tsui, V., Gohlke, H., Radmer, R. J., Duan, Y., Pitera, J., Massova, I., Seibel, G. L., Singh, U. C., Weiner, P. K., and Kollman, P. A. (2002) AMBER, 7.0 ed., University of California, San Francisco, CA.
-
(2002)
AMBER
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham III, T.E.4
Wang, J.5
Ross, W.S.6
Simmerling, C.L.7
Darden, T.A.8
Merz, K.M.9
Stanton, R.V.10
Cheng, A.L.11
Vincent, J.J.12
Crowley, M.13
Tsui, V.14
Gohlke, H.15
Radmer, R.J.16
Duan, Y.17
Pitera, J.18
Massova, I.19
Seibel, G.L.20
Singh, U.C.21
Weiner, P.K.22
Kollman, P.A.23
more..
-
37
-
-
0002636134
-
Pairwise solute descreening of solute charges from a dielectric medium
-
Hawkins, G. D., Cramer, C. J., and Truhlar, D. G. (1995) Pairwise solute descreening of solute charges from a dielectric medium Chem. Phys. Lett. 246, 122-129
-
(1995)
Chem. Phys. Lett.
, vol.246
, pp. 122-129
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
38
-
-
33748390341
-
Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium
-
Hawkins, G. D., Cramer, C. J., and Truhlar, D. G. (1996) Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium J. Phys. Chem. 100, 19824-19839
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 19824-19839
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
39
-
-
14244273182
-
Theory and applications of the Generalized Born solvation model in macromolecular simulations
-
DOI 10.1002/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E
-
Tsui, V. and Case, D. A. (2000) Theory and applications of the generalized Born solvation model in macromolecular simulations Biopolymers 56, 275-291 (Pubitemid 34105875)
-
(2000)
Biopolymers
, vol.56
, Issue.4
, pp. 275-291
-
-
Tsui, V.1
Case, D.A.2
-
40
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J.-P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes J. Comput. Phys. 23, 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
41
-
-
0001053688
-
A theoretical study of distance determination from NMR. Two-dimensional nuclear Overhauser effect spectra
-
Keepers, J. W. and James, T. L. (1984) A theoretical study of distance determination from NMR. Two-dimensional nuclear Overhauser effect spectra J. Magn. Reson. 57, 404-426
-
(1984)
J. Magn. Reson.
, vol.57
, pp. 404-426
-
-
Keepers, J.W.1
James, T.L.2
-
42
-
-
0026890432
-
A systematic comparison of three structure determination methods from NMR data: Dependence upon quality and quantity of data
-
Liu, Y., Zhao, D., Altman, R., and Jardetzky, O. (1992) A systematic comparison of three structure determination methods from NMR data: Dependence upon quality and quantity of data J. Biomol. NMR 2, 373-388
-
(1992)
J. Biomol. NMR
, vol.2
, pp. 373-388
-
-
Liu, Y.1
Zhao, D.2
Altman, R.3
Jardetzky, O.4
-
43
-
-
0026061575
-
Protein solution structure determination using distances from two-dimensional nuclear Overhauser effect experiments: Effect of approximations on the accuracy of derived structures
-
Thomas, P. D., Basus, V. J., and James, T. L. (1991) Protein solution structure determination using distances from two-dimensional nuclear Overhauser effect experiments: Effect of approximations on the accuracy of derived structures Proc. Natl. Acad. Sci. U.S.A. 88, 1237-1241
-
(1991)
Proc. Natl. Acad. Sci. U.S.A.
, vol.88
, pp. 1237-1241
-
-
Thomas, P.D.1
Basus, V.J.2
James, T.L.3
-
44
-
-
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
-
45
-
-
0023395002
-
Sequence-specific assignments and their use in NMR studies of DNA structure
-
Reid, B. R. (1987) Sequence-specific assignments and their use in NMR studies of DNA structure Q. Rev. Biophys. 20, 2-28
-
(1987)
Q. Rev. Biophys.
, vol.20
, pp. 2-28
-
-
Reid, B.R.1
-
46
-
-
0023386995
-
DNA and RNA: NMR studies of conformations and dynamics in solution
-
Patel, D. J., Shapiro, L., and Hare, D. (1987) DNA and RNA: NMR studies of conformations and dynamics in solution Q. Rev. Biophys. 20, 35-112
-
(1987)
Q. Rev. Biophys.
, vol.20
, pp. 35-112
-
-
Patel, D.J.1
Shapiro, L.2
Hare, D.3
-
47
-
-
0000146208
-
1H NMR spectra of oligonucleotides by two-dimensional NMR spectroscopy. Application to a lac operator fragment
-
1H NMR spectra of oligonucleotides by two-dimensional NMR spectroscopy. Application to a lac operator fragment J. Magn. Reson. 62, 378-386
-
(1985)
J. Magn. Reson.
, vol.62
, pp. 378-386
-
-
Boelens, R.1
Scheek, R.M.2
Dijkstra, K.3
Kaptein, R.4
-
48
-
-
0035961532
-
Structural studies of an oligodeoxynucleotide containing a trimethylene interstrand cross-link in a 5′-(CpG) motif: Model of a malondialdehyde cross-link
-
Dooley, P. A., Tsarouhtsis, D., Korbel, G. A., Nechev, L. V., Shearer, J., Zegar, I. S., Harris, C. M., Stone, M. P., and Harris, T. M. (2001) Structural studies of an oligodeoxynucleotide containing a trimethylene interstrand cross-link in a 5′-(CpG) motif: Model of a malondialdehyde cross-link J. Am. Chem. Soc. 123, 1730-1739
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 1730-1739
-
-
Dooley, P.A.1
Tsarouhtsis, D.2
Korbel, G.A.3
Nechev, L.V.4
Shearer, J.5
Zegar, I.S.6
Harris, C.M.7
Stone, M.P.8
Harris, T.M.9
-
49
-
-
0037425566
-
NMR determination of the conformation of a trimethylene interstrand cross-link in an oligodeoxynucleotide duplex containing a 5′-d(GpC) motif
-
Dooley, P. A., Zhang, M., Korbel, G. A., Nechev, L. V., Harris, C. M., Stone, M. P., and Harris, T. M. (2003) NMR determination of the conformation of a trimethylene interstrand cross-link in an oligodeoxynucleotide duplex containing a 5′-d(GpC) motif J. Am. Chem. Soc. 125, 62-72
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 62-72
-
-
Dooley, P.A.1
Zhang, M.2
Korbel, G.A.3
Nechev, L.V.4
Harris, C.M.5
Stone, M.P.6
Harris, T.M.7
-
50
-
-
70350686719
-
The role of DNA shape in protein-DNA recognition
-
Rohs, R., West, S. M., Sosinsky, A., Liu, P., Mann, R. S., and Honig, B. (2009) The role of DNA shape in protein-DNA recognition Nature 461, 1248-1253
-
(2009)
Nature
, vol.461
, pp. 1248-1253
-
-
Rohs, R.1
West, S.M.2
Sosinsky, A.3
Liu, P.4
Mann, R.S.5
Honig, B.6
-
51
-
-
0024580271
-
The electrostatic potential of B-DNA
-
Jayaram, B., Sharp, K. A., and Honig, B. (1989) The electrostatic potential of B-DNA Biopolymers 28, 975-993
-
(1989)
Biopolymers
, vol.28
, pp. 975-993
-
-
Jayaram, B.1
Sharp, K.A.2
Honig, B.3
-
52
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig, B. and Nicholls, A. (1995) Classical electrostatics in biology and chemistry Science 268, 1144-1149
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
53
-
-
0033605083
-
Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending
-
Hud, N. V., Sklenar, V., and Feigon, J. (1999) Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending J. Mol. Biol. 286, 651-660
-
(1999)
J. Mol. Biol.
, vol.286
, pp. 651-660
-
-
Hud, N.V.1
Sklenar, V.2
Feigon, J.3
-
54
-
-
0035964383
-
Locating monovalent cations in the grooves of B-DNA
-
Howerton, S. B., Sines, C. C., VanDerveer, D., and Williams, L. D. (2001) Locating monovalent cations in the grooves of B-DNA Biochemistry 40, 10023-10031
-
(2001)
Biochemistry
, vol.40
, pp. 10023-10031
-
-
Howerton, S.B.1
Sines, C.C.2
Vanderveer, D.3
Williams, L.D.4
-
55
-
-
0034802485
-
Influence of the dynamic positions of cations on the structure of the DNA minor groove: Sequence-dependent effects
-
Hamelberg, D., Williams, L. D., and Wilson, W. D. (2001) Influence of the dynamic positions of cations on the structure of the DNA minor groove: Sequence-dependent effects J. Am. Chem. Soc. 123, 7745-7755
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 7745-7755
-
-
Hamelberg, D.1
Williams, L.D.2
Wilson, W.D.3
-
56
-
-
0035367927
-
DNA-cation interactions: The major and minor grooves are flexible ionophores
-
Hud, N. V. and Polak, M. (2001) DNA-cation interactions: The major and minor grooves are flexible ionophores Curr. Opin. Struct. Biol. 11, 293-301
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 293-301
-
-
Hud, N.V.1
Polak, M.2
-
57
-
-
0038036707
-
Surprising roles of electrostatic interactions in DNA-ligand complexes
-
Howerton, S. B., Nagpal, A., and Williams, L. D. (2003) Surprising roles of electrostatic interactions in DNA-ligand complexes Biopolymers 69, 87-99
-
(2003)
Biopolymers
, vol.69
, pp. 87-99
-
-
Howerton, S.B.1
Nagpal, A.2
Williams, L.D.3
-
58
-
-
0024502258
-
Isolation and characterization of proteins cross-linked to DNA by the antitumor agent methylene dimethanesulfonate and its hydrolytic product formaldehyde
-
OConnor, P. M. and Fox, B. W. (1989) Isolation and characterization of proteins cross-linked to DNA by the antitumor agent methylene dimethanesulfonate and its hydrolytic product formaldehyde J. Biol. Chem. 264, 6391-6397
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 6391-6397
-
-
Oconnor, P.M.1
Fox, B.W.2
-
59
-
-
0034764032
-
Isolation of SDS-stable complexes of the intermediate filament protein vimentin with repetitive, mobile, nuclear matrix attachment region, and mitochondrial DNA sequence elements from cultured mouse and human fibroblasts
-
Tolstonog, G. V., Mothes, E., Shoeman, R. L., and Traub, P. (2001) Isolation of SDS-stable complexes of the intermediate filament protein vimentin with repetitive, mobile, nuclear matrix attachment region, and mitochondrial DNA sequence elements from cultured mouse and human fibroblasts DNA Cell Biol. 20, 531-554
-
(2001)
DNA Cell Biol.
, vol.20
, pp. 531-554
-
-
Tolstonog, G.V.1
Mothes, E.2
Shoeman, R.L.3
Traub, P.4
-
60
-
-
0023697096
-
The detection of DNA-protein cross-links in rat tracheal implants exposed in vivo to benzo[ a ]pyrene and formaldehyde
-
Cosma, G. N., Wilhite, A. S., and Marchok, A. C. (1988) The detection of DNA-protein cross-links in rat tracheal implants exposed in vivo to benzo[ a ]pyrene and formaldehyde Cancer Lett. 42, 13-21
-
(1988)
Cancer Lett.
, vol.42
, pp. 13-21
-
-
Cosma, G.N.1
Wilhite, A.S.2
Marchok, A.C.3
-
61
-
-
0023881799
-
Review of the genotoxicity of formaldehyde
-
Ma, T. H. and Harris, M. M. (1988) Review of the genotoxicity of formaldehyde Mutat. Res. 196, 37-59
-
(1988)
Mutat. Res.
, vol.196
, pp. 37-59
-
-
Ma, T.H.1
Harris, M.M.2
-
62
-
-
0025288510
-
Formaldehyde toxicity - New understanding
-
Heck, H. D., Casanova, M., and Starr, T. B. (1990) Formaldehyde toxicity - New understanding Crit. Rev. Toxicol. 20, 397-426
-
(1990)
Crit. Rev. Toxicol.
, vol.20
, pp. 397-426
-
-
Heck, H.D.1
Casanova, M.2
Starr, T.B.3
-
63
-
-
0031106285
-
Comparison of inhaled formaldehyde dosimetry predictions with DNA-protein cross-link measurements in the rat nasal passages
-
Hubal, E. A., Schlosser, P. M., Conolly, R. B., and Kimbell, J. S. (1997) Comparison of inhaled formaldehyde dosimetry predictions with DNA-protein cross-link measurements in the rat nasal passages Toxicol. Appl. Pharmacol. 143, 47-55
-
(1997)
Toxicol. Appl. Pharmacol.
, vol.143
, pp. 47-55
-
-
Hubal, E.A.1
Schlosser, P.M.2
Conolly, R.B.3
Kimbell, J.S.4
-
64
-
-
0038309688
-
DNA-protein crosslinks and p53 protein expression in relation to occupational exposure to formaldehyde
-
Shaham, J., Bomstein, Y., Gurvich, R., Rashkovsky, M., and Kaufman, Z. (2003) DNA-protein crosslinks and p53 protein expression in relation to occupational exposure to formaldehyde Occup. Environ. Med. 60, 403-409
-
(2003)
Occup. Environ. Med.
, vol.60
, pp. 403-409
-
-
Shaham, J.1
Bomstein, Y.2
Gurvich, R.3
Rashkovsky, M.4
Kaufman, Z.5
-
65
-
-
32844474337
-
Studies on formation and repair of formaldehyde-damaged DNA by detection of DNA-protein crosslinks and DNA breaks
-
Liu, Y., Li, C. M., Lu, Z., Ding, S., Yang, X., and Mo, J. (2006) Studies on formation and repair of formaldehyde-damaged DNA by detection of DNA-protein crosslinks and DNA breaks Front. Biosci. 11, 991-997
-
(2006)
Front. Biosci.
, vol.11
, pp. 991-997
-
-
Liu, Y.1
Li, C.M.2
Lu, Z.3
Ding, S.4
Yang, X.5
Mo, J.6
-
66
-
-
33846070797
-
Genotoxic effects induced by formaldehyde in human blood and implications for the interpretation of biomonitoring studies
-
Schmid, O. and Speit, G. (2007) Genotoxic effects induced by formaldehyde in human blood and implications for the interpretation of biomonitoring studies Mutagenesis 22, 69-74
-
(2007)
Mutagenesis
, vol.22
, pp. 69-74
-
-
Schmid, O.1
Speit, G.2
-
67
-
-
33645210785
-
Repair of DNA-polypeptide crosslinks by human excision nuclease
-
Reardon, J. T. and Sancar, A. (2006) Repair of DNA-polypeptide crosslinks by human excision nuclease Proc. Natl. Acad. Sci. U.S.A. 103, 4056-4061
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 4056-4061
-
-
Reardon, J.T.1
Sancar, A.2
-
68
-
-
0022970758
-
Thermostability of double-stranded deoxyribonucleic acids: Effects of covalent additions of a psoralen
-
Shi, Y. and Hearst, J. E. (1986) Thermostability of double-stranded deoxyribonucleic acids: Effects of covalent additions of a psoralen Biochemistry 25, 5895-5902
-
(1986)
Biochemistry
, vol.25
, pp. 5895-5902
-
-
Shi, Y.1
Hearst, J.E.2
-
69
-
-
1842785956
-
A model for initial DNA lesion recognition by NER and MMR based on local conformational flexibility
-
Isaacs, R. J. and Spielmann, H. P. (2004) A model for initial DNA lesion recognition by NER and MMR based on local conformational flexibility DNA Repair (Amsterdam) 3, 455-464
-
(2004)
DNA Repair (Amsterdam)
, vol.3
, pp. 455-464
-
-
Isaacs, R.J.1
Spielmann, H.P.2
-
70
-
-
0027944087
-
Substrate spectrum of human excinuclease: Repair of abasic sites, methylated bases, mismatches, and bulky adducts
-
Huang, J. C., Hsu, D. S., Kazantsev, A., and Sancar, A. (1994) Substrate spectrum of human excinuclease: Repair of abasic sites, methylated bases, mismatches, and bulky adducts Proc. Natl. Acad. Sci. U.S.A. 91, 12213-12217
-
(1994)
Proc. Natl. Acad. Sci. U.S.A.
, vol.91
, pp. 12213-12217
-
-
Huang, J.C.1
Hsu, D.S.2
Kazantsev, A.3
Sancar, A.4
-
71
-
-
11144237897
-
Quantitative analysis of translesion DNA synthesis across a benzo[ a ]pyrene-guanine adduct in mammalian cells: The role of DNA polymerase ?
-
Avkin, S., Goldsmith, M., Velasco-Miguel, S., Geacintov, N., Friedberg, E. C., and Livneh, Z. (2004) Quantitative analysis of translesion DNA synthesis across a benzo[ a ]pyrene-guanine adduct in mammalian cells: The role of DNA polymerase ? J. Biol. Chem. 279, 53298-53305
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 53298-53305
-
-
Avkin, S.1
Goldsmith, M.2
Velasco-Miguel, S.3
Geacintov, N.4
Friedberg, E.C.5
Livneh, Z.6
-
72
-
-
20444437200
-
DNA polymerase - is specifically required for recovery from the benzo[ a ]pyrene-dihydrodiol epoxide (BPDE)-induced S-phase checkpoint
-
Bi, X., Slater, D. M., Ohmori, H., and Vaziri, C. (2005) DNA polymerase - is specifically required for recovery from the benzo[ a ]pyrene-dihydrodiol epoxide (BPDE)-induced S-phase checkpoint J. Biol. Chem. 280, 22343-22355
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 22343-22355
-
-
Bi, X.1
Slater, D.M.2
Ohmori, H.3
Vaziri, C.4
-
74
-
-
77949350060
-
Novel enzymatic function of DNA polymerase ? in translesion DNA synthesis past major groove DNA-peptide and DNA-DNA cross-links
-
Yamanaka, K., Minko, I. G., Takata, K., Kolbanovskiy, A., Kozekov, I. D., Wood, R. D., Rizzo, C. J., and Lloyd, R. S. (2010) Novel enzymatic function of DNA polymerase ? in translesion DNA synthesis past major groove DNA-peptide and DNA-DNA cross-links Chem. Res. Toxicol. 23, 689-695
-
(2010)
Chem. Res. Toxicol.
, vol.23
, pp. 689-695
-
-
Yamanaka, K.1
Minko, I.G.2
Takata, K.3
Kolbanovskiy, A.4
Kozekov, I.D.5
Wood, R.D.6
Rizzo, C.J.7
Lloyd, R.S.8
|