-
3
-
-
77954759002
-
Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[ a ]pyrene-derived DNA lesion
-
Cai, Y., Kropachev, K., Xu, R., Tang, Y., Kolbanovskii, M., Kolbanovskii, A., Amin, S., Patel, D. J., Broyde, S., and Geacintov, N. E. (2010) Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[ a ]pyrene-derived DNA lesion J. Mol. Biol. 399, 397-409
-
(2010)
J. Mol. Biol.
, vol.399
, pp. 397-409
-
-
Cai, Y.1
Kropachev, K.2
Xu, R.3
Tang, Y.4
Kolbanovskii, M.5
Kolbanovskii, A.6
Amin, S.7
Patel, D.J.8
Broyde, S.9
Geacintov, N.E.10
-
4
-
-
80455149268
-
Base sequence context effects on nucleotide excision repair
-
DOI: 10.4061/2010/174252
-
Cai, Y., Patel, D. J., Broyde, S., and Geacintov, N. E. (2010) Base sequence context effects on nucleotide excision repair. J. Nucleic Acids 2010, DOI: 10.4061/2010/174252
-
(2010)
J. Nucleic Acids
, vol.2010
-
-
Cai, Y.1
Patel, D.J.2
Broyde, S.3
Geacintov, N.E.4
-
5
-
-
57749188239
-
Differential nucleotide excision repair susceptibility of bulky DNA adducts in different sequence contexts: Hierarchies of recognition signals
-
Cai, Y., Patel, D. J., Geacintov, N. E., and Broyde, S. (2009) Differential nucleotide excision repair susceptibility of bulky DNA adducts in different sequence contexts: hierarchies of recognition signals J. Mol. Biol. 385, 30-44
-
(2009)
J. Mol. Biol.
, vol.385
, pp. 30-44
-
-
Cai, Y.1
Patel, D.J.2
Geacintov, N.E.3
Broyde, S.4
-
6
-
-
0037027367
-
Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery
-
Geacintov, N. E., Broyde, S., Buterin, T., Naegeli, H., Wu, M., Yan, S., and Patel, D. J. (2002) Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery Biopolymers 65, 202-210
-
(2002)
Biopolymers
, vol.65
, pp. 202-210
-
-
Geacintov, N.E.1
Broyde, S.2
Buterin, T.3
Naegeli, H.4
Wu, M.5
Yan, S.6
Patel, D.J.7
-
7
-
-
60849122212
-
The sequence dependence of human nucleotide excision repair efficiencies of benzo[ a ]pyrene-derived DNA lesions: Insights into the structural factors that favor dual incisions
-
Kropachev, K., Kolbanovskii, M., Cai, Y., Rodriguez, F., Kolbanovskii, A., Liu, Y., Zhang, L., Amin, S., Patel, D., Broyde, S., and Geacintov, N. E. (2009) The sequence dependence of human nucleotide excision repair efficiencies of benzo[ a ]pyrene-derived DNA lesions: insights into the structural factors that favor dual incisions J. Mol. Biol. 386, 1193-1203
-
(2009)
J. Mol. Biol.
, vol.386
, pp. 1193-1203
-
-
Kropachev, K.1
Kolbanovskii, M.2
Cai, Y.3
Rodriguez, F.4
Kolbanovskii, A.5
Liu, Y.6
Zhang, L.7
Amin, S.8
Patel, D.9
Broyde, S.10
Geacintov, N.E.11
-
8
-
-
32644450616
-
Molecular mechanisms of mammalian global genome nucleotide excision repair
-
Gillet, L. C. and Scharer, O. D. (2006) Molecular mechanisms of mammalian global genome nucleotide excision repair Chem. Rev. 106, 253-276
-
(2006)
Chem. Rev.
, vol.106
, pp. 253-276
-
-
Gillet, L.C.1
Scharer, O.D.2
-
9
-
-
84870656872
-
Nucleotide Excision Repair from Bacteria to Humans: Structure-Function Studies
-
(Penning, T. M. Ed.), Springer Science+Business Media, LLC, Dordrecht, The Netherlands
-
Peng, Y., Wang, H., Santana dos Santos, L., Kisker, C., and Van Houten, B. (2011) Nucleotide Excision Repair from Bacteria to Humans: Structure-Function Studies, in Chemical Carcinogenesis, Current Cancer Research (Penning, T. M., Ed.) pp 267-296, Springer Science+Business Media, LLC, Dordrecht, The Netherlands.
-
(2011)
Chemical Carcinogenesis, Current Cancer Research
, pp. 267-296
-
-
Peng, Y.1
Wang, H.2
Santana Dos Santos, L.3
Kisker, C.4
Van Houten, B.5
-
10
-
-
80455159027
-
Mechanisms of Base Excision Repair and Nucleotide Excision Repair
-
(Geacintov, N. E. and Broyde, S. Eds.), Wiley-VCH, Weinheim, Germany
-
Schärer, O. D. and Campbell, A. J. (2010) Mechanisms of Base Excision Repair and Nucleotide Excision Repair, in The Chemical Biology of DNA Damage (Geacintov, N. E. and Broyde, S., Eds.) pp 239-260, Wiley-VCH, Weinheim, Germany.
-
(2010)
The Chemical Biology of DNA Damage
, pp. 239-260
-
-
Schärer, O.D.1
Campbell, A.J.2
-
11
-
-
0032134423
-
Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair
-
Sugasawa, K., Ng, J. M., Masutani, C., Iwai, S., van der Spek, P. J., Eker, A. P., Hanaoka, F., Bootsma, D., and Hoeijmakers, J. H. (1998) Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair Mol. Cell 2, 223-232
-
(1998)
Mol. Cell
, vol.2
, pp. 223-232
-
-
Sugasawa, K.1
Ng, J.M.2
Masutani, C.3
Iwai, S.4
Van Der Spek, P.J.5
Eker, A.P.6
Hanaoka, F.7
Bootsma, D.8
Hoeijmakers, J.H.9
-
12
-
-
77951819090
-
Stochastic and reversible assembly of a multiprotein DNA repair complex ensures accurate target site recognition and efficient repair
-
Luijsterburg, M. S., von Bornstaedt, G., Gourdin, A. M., Politi, A. Z., Mone, M. J., Warmerdam, D. O., Goedhart, J., Vermeulen, W., van Driel, R., and Hofer, T. (2010) Stochastic and reversible assembly of a multiprotein DNA repair complex ensures accurate target site recognition and efficient repair J. Cell. Biol. 189, 445-463
-
(2010)
J. Cell. Biol.
, vol.189
, pp. 445-463
-
-
Luijsterburg, M.S.1
Von Bornstaedt, G.2
Gourdin, A.M.3
Politi, A.Z.4
Mone, M.J.5
Warmerdam, D.O.6
Goedhart, J.7
Vermeulen, W.8
Van Driel, R.9
Hofer, T.10
-
13
-
-
34948892722
-
Recognition of DNA damage by the Rad4 nucleotide excision repair protein
-
Min, J. H. and Pavletich, N. P. (2007) Recognition of DNA damage by the Rad4 nucleotide excision repair protein Nature 449, 570-575
-
(2007)
Nature
, vol.449
, pp. 570-575
-
-
Min, J.H.1
Pavletich, N.P.2
-
14
-
-
35348954826
-
Achieving broad substrate specificity in damage recognition by binding accessible nondamaged DNA
-
Schärer, O. D. (2007) Achieving broad substrate specificity in damage recognition by binding accessible nondamaged DNA Mol. Cell 28, 184-186
-
(2007)
Mol. Cell
, vol.28
, pp. 184-186
-
-
Schärer, O.D.1
-
15
-
-
37549068196
-
Hot topics in DNA repair: The molecular basis for different disease states caused by mutations in TFIIH and XPG
-
Schärer, O. D. (2008) Hot topics in DNA repair: the molecular basis for different disease states caused by mutations in TFIIH and XPG DNA Repair 7, 339-344
-
(2008)
DNA Repair
, vol.7
, pp. 339-344
-
-
Schärer, O.D.1
-
16
-
-
0029840823
-
Recognition of DNA adducts by human nucleotide excision repair. Evidence for a thermodynamic probing mechanism
-
Gunz, D., Hess, M. T., and Naegeli, H. (1996) Recognition of DNA adducts by human nucleotide excision repair. Evidence for a thermodynamic probing mechanism J. Biol. Chem. 271, 25089-25098
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 25089-25098
-
-
Gunz, D.1
Hess, M.T.2
Naegeli, H.3
-
17
-
-
0026002897
-
Comparative dose-response tumorigenicity studies of dibenzo[ alpha,l ]pyrene versus 7,12-dimethylbenz[ alpha ]anthracene, benzo[ alpha ]pyrene and two dibenzo[ alpha,l ]pyrene dihydrodiols in mouse skin and rat mammary gland
-
Cavalieri, E. L., Higginbotham, S., RamaKrishna, N. V., Devanesan, P. D., Todorovic, R., Rogan, E. G., and Salmasi, S. (1991) Comparative dose-response tumorigenicity studies of dibenzo[ alpha,l ]pyrene versus 7,12-dimethylbenz[ alpha ]anthracene, benzo[ alpha ]pyrene and two dibenzo[ alpha,l ]pyrene dihydrodiols in mouse skin and rat mammary gland Carcinogenesis 12, 1939-1944
-
(1991)
Carcinogenesis
, vol.12
, pp. 1939-1944
-
-
Cavalieri, E.L.1
Higginbotham, S.2
Ramakrishna, N.V.3
Devanesan, P.D.4
Todorovic, R.5
Rogan, E.G.6
Salmasi, S.7
-
18
-
-
0000402517
-
Dibenzo[ a,l ]pyrene:The most potent carcinogenic aromatic hydrocarbon
-
Cavalieri, E. L., Higginbotham, S., and Rogan, E. G. (1994) Dibenzo[ a,l ]pyrene:The most potent carcinogenic aromatic hydrocarbon Polycyclic Aromat. Compd. 6, 177-183
-
(1994)
Polycyclic Aromat. Compd.
, vol.6
, pp. 177-183
-
-
Cavalieri, E.L.1
Higginbotham, S.2
Rogan, E.G.3
-
19
-
-
0033591845
-
Tobacco smoke carcinogens and lung cancer
-
Hecht, S. S. (1999) Tobacco smoke carcinogens and lung cancer J. Natl. Cancer Inst. 91, 1194-1210
-
(1999)
J. Natl. Cancer Inst.
, vol.91
, pp. 1194-1210
-
-
Hecht, S.S.1
-
20
-
-
63249099610
-
On the impact of the molecule structure in chemical carcinogenesis
-
Luch, A. (2009) On the impact of the molecule structure in chemical carcinogenesis EXS 99, 151-179
-
(2009)
EXS
, vol.99
, pp. 151-179
-
-
Luch, A.1
-
21
-
-
0036949669
-
Smoking-related DNA and protein adducts in human tissues
-
Phillips, D. H. (2002) Smoking-related DNA and protein adducts in human tissues Carcinogenesis 23, 1979-2004
-
(2002)
Carcinogenesis
, vol.23
, pp. 1979-2004
-
-
Phillips, D.H.1
-
22
-
-
79952111402
-
Some Non-Heterocyclic Polycyclic Aromatic Hydrocarbons and Some Related Exposures
-
IARC, International Agency for Research on Cancer, Lyon, France
-
IARC (2010) Some Non-Heterocyclic Polycyclic Aromatic Hydrocarbons and Some Related Exposures, in IARC Monographs Evaluating Carcinogenic Risks in Humans, pp 1-853, International Agency for Research on Cancer, Lyon, France.
-
(2010)
IARC Monographs Evaluating Carcinogenic Risks in Humans
, pp. 1-853
-
-
-
23
-
-
55549138434
-
The structure of overcrowded aromatic compounds. Part VII. Out-of-plane deformation in benzo[ c ]-phenanthrene and 1,12-dimethyl-benzo[ c ]phenanthrene
-
Hirshfeld, F. L. (1963) The structure of overcrowded aromatic compounds. Part VII. Out-of-plane deformation in benzo[ c ]-phenanthrene and 1,12-dimethyl-benzo[ c ]phenanthrene J. Chem. Soc. 2108-2125
-
(1963)
J. Chem. Soc.
, pp. 2108-2125
-
-
Hirshfeld, F.L.1
-
24
-
-
0031687879
-
Dibenzo[ a,l ]pyrene (dibenzo[ def,p ]chrysene): Fjord-region distortions
-
Katz, A. K., Carrell, H. L., and Glusker, J. P. (1998) Dibenzo[ a,l ]pyrene (dibenzo[ def,p ]chrysene): fjord-region distortions Carcinogenesis 19, 1641-1648
-
(1998)
Carcinogenesis
, vol.19
, pp. 1641-1648
-
-
Katz, A.K.1
Carrell, H.L.2
Glusker, J.P.3
-
25
-
-
0020431144
-
Induction of microsomal enzymes by foreign chemicals and carcinogenesis by polycyclic aromatic hydrocarbons: G. H. A. Clowes Memorial Lecture
-
Conney, A. H. (1982) Induction of microsomal enzymes by foreign chemicals and carcinogenesis by polycyclic aromatic hydrocarbons: G. H. A. Clowes Memorial Lecture Cancer Res. 42, 4875-4917
-
(1982)
Cancer Res.
, vol.42
, pp. 4875-4917
-
-
Conney, A.H.1
-
26
-
-
20444412643
-
Metabolic activation of polycyclic and heterocyclic aromatic hydrocarbons and DNA damage: A review
-
Xue, W. and Warshawsky, D. (2005) Metabolic activation of polycyclic and heterocyclic aromatic hydrocarbons and DNA damage: a review Toxicol. Appl. Pharmacol. 206, 73-93
-
(2005)
Toxicol. Appl. Pharmacol.
, vol.206
, pp. 73-93
-
-
Xue, W.1
Warshawsky, D.2
-
27
-
-
84867965856
-
Polycyclic Aromatic Hydrocarbons: Multiple Metabolic Pathways and the DNA Lesions Formed
-
(Geacintov, N. E. and Broyde, S. Eds.) Chapter 6, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany
-
Penning, T. M. (2010) Polycyclic Aromatic Hydrocarbons: Multiple Metabolic Pathways and the DNA Lesions Formed, in The Chemical Biology of DNA Damage (Geacintov, N. E. and Broyde, S., Eds.) Chapter 6, pp 131-155, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany.
-
(2010)
The Chemical Biology of DNA Damage
, pp. 131-155
-
-
Penning, T.M.1
-
28
-
-
84872721856
-
Exposure to polycyclic aromatic hydrocarbons: Bulky DNA adducts and cellular responses
-
Henkler, F., Stolpmann, K., and Luch, A. (2012) Exposure to polycyclic aromatic hydrocarbons: bulky DNA adducts and cellular responses EXS. 101, 107-131
-
(2012)
EXS.
, vol.101
, pp. 107-131
-
-
Henkler, F.1
Stolpmann, K.2
Luch, A.3
-
29
-
-
0030911969
-
Sequence specific mutagenesis of the major (+)- anti -benzo[ a ]pyrene diol epoxide-DNA adduct at a mutational hot spot in vitro and in Escherichia coli cells
-
Hanrahan, C. J., Bacolod, M. D., Vyas, R. R., Liu, T., Geacintov, N. E., Loechler, E. L., and Basu, A. K. (1997) Sequence specific mutagenesis of the major (+)- anti -benzo[ a ]pyrene diol epoxide-DNA adduct at a mutational hot spot in vitro and in Escherichia coli cells Chem. Res. Toxicol. 10, 369-377
-
(1997)
Chem. Res. Toxicol.
, vol.10
, pp. 369-377
-
-
Hanrahan, C.J.1
Bacolod, M.D.2
Vyas, R.R.3
Liu, T.4
Geacintov, N.E.5
Loechler, E.L.6
Basu, A.K.7
-
30
-
-
0031041812
-
NMR solution structures of stereoisometric covalent polycyclic aromatic carcinogen-DNA adduct: Principles, patterns, and diversity
-
Geacintov, N. E., Cosman, M., Hingerty, B. E., Amin, S., Broyde, S., and Patel, D. J. (1997) NMR solution structures of stereoisometric covalent polycyclic aromatic carcinogen-DNA adduct: principles, patterns, and diversity Chem. Res. Toxicol. 10, 111-146
-
(1997)
Chem. Res. Toxicol.
, vol.10
, pp. 111-146
-
-
Geacintov, N.E.1
Cosman, M.2
Hingerty, B.E.3
Amin, S.4
Broyde, S.5
Patel, D.J.6
-
31
-
-
33644626078
-
NMR structures of damaged DNA
-
Lukin, M. and de Los Santos, C. (2006) NMR structures of damaged DNA Chem. Rev. 106, 607-686
-
(2006)
Chem. Rev.
, vol.106
, pp. 607-686
-
-
Lukin, M.1
De Los Santos, C.2
-
32
-
-
9644265249
-
Dynamic conformational heterogeneities of carcinogen-DNA adducts and their mutagenic relevance
-
Cho, B. P. (2004) Dynamic conformational heterogeneities of carcinogen-DNA adducts and their mutagenic relevance J. Environ. Sci. Health, Part C C22, 57-90
-
(2004)
J. Environ. Sci. Health, Part C
, vol.22
, pp. 57-90
-
-
Cho, B.P.1
-
33
-
-
80052905361
-
Chemistry and structural biology of DNA damage and biological consequences
-
Stone, M. P., Huang, H., Brown, K. L., and Shanmugam, G. (2011) Chemistry and structural biology of DNA damage and biological consequences Chem. Biodiversity 8, 1571-1615
-
(2011)
Chem. Biodiversity
, vol.8
, pp. 1571-1615
-
-
Stone, M.P.1
Huang, H.2
Brown, K.L.3
Shanmugam, G.4
-
34
-
-
84857382560
-
Nucleotide excision repair efficiencies of bulky carcinogen-DNA adducts are governed by a balance between stabilizing and destabilizing interactions
-
Cai, Y., Geacintov, N. E., and Broyde, S. (2012) Nucleotide excision repair efficiencies of bulky carcinogen-DNA adducts are governed by a balance between stabilizing and destabilizing interactions Biochemistry 51, 1486-1499
-
(2012)
Biochemistry
, vol.51
, pp. 1486-1499
-
-
Cai, Y.1
Geacintov, N.E.2
Broyde, S.3
-
35
-
-
0037418535
-
Role of base sequence context in conformational equilibria and nucleotide excision repair of benzo[ a ]pyrene diol epoxide-adenine adducts
-
Yan, S., Wu, M., Buterin, T., Naegeli, H., Geacintov, N. E., and Broyde, S. (2003) Role of base sequence context in conformational equilibria and nucleotide excision repair of benzo[ a ]pyrene diol epoxide-adenine adducts Biochemistry 42, 2339-2354
-
(2003)
Biochemistry
, vol.42
, pp. 2339-2354
-
-
Yan, S.1
Wu, M.2
Buterin, T.3
Naegeli, H.4
Geacintov, N.E.5
Broyde, S.6
-
37
-
-
0027525482
-
Solution conformation of the (+)- trans - Anti -[BPh]dA adduct opposite dT in a DNA duplex: Intercalation of the covalently attached benzo[ c ]phenanthrene to the 5′-side of the adduct site without disruption of the modified base pair
-
Cosman, M., Fiala, R., Hingerty, B. E., Laryea, A., Lee, H., Harvey, R. G., Amin, S., Geacintov, N. E., Broyde, S., and Patel, D. (1993) Solution conformation of the (+)- trans-anti -[BPh]dA adduct opposite dT in a DNA duplex: intercalation of the covalently attached benzo[ c ]phenanthrene to the 5′-side of the adduct site without disruption of the modified base pair Biochemistry 32, 12488-12497
-
(1993)
Biochemistry
, vol.32
, pp. 12488-12497
-
-
Cosman, M.1
Fiala, R.2
Hingerty, B.E.3
Laryea, A.4
Lee, H.5
Harvey, R.G.6
Amin, S.7
Geacintov, N.E.8
Broyde, S.9
Patel, D.10
-
38
-
-
0032564393
-
6-[10-(7,8,9,10-tetrahydrobenzo[ a ]pyrenyl)]-2′-deoxyadenosyl adduct in the N-ras codon 61 sequence
-
6-[10-(7, 8,9,10-tetrahydrobenzo[ a ]pyrenyl)]-2′-deoxyadenosyl adduct in the N-ras codon 61 sequence Biochemistry 37, 16516-16528
-
(1998)
Biochemistry
, vol.37
, pp. 16516-16528
-
-
Zegar, I.S.1
Chary, P.2
Jabil, R.J.3
Tamura, P.J.4
Johansen, T.N.5
Lloyd, R.S.6
Harris, C.M.7
Harris, T.M.8
Stone, M.P.9
-
39
-
-
0029989672
-
1H NMR
-
1H NMR Biochemistry 35, 6212-6224
-
(1996)
Biochemistry
, vol.35
, pp. 6212-6224
-
-
Zegar, I.S.1
Kim, S.J.2
Johansen, T.N.3
Horton, P.J.4
Harris, C.M.5
Harris, T.M.6
Stone, M.P.7
-
40
-
-
84877997319
-
Adenine-DNA adducts derived from the highly tumorigenic dibenzo[ a,l ]pyrene are resistant to nucleotide excision repair while guanine adducts are not
-
Kropachev, K., Kolbanovskiy, M., Liu, Z., Cai, Y., Zhang, L., Schwaid, A. G., Kolbanovskiy, A., Ding, S., Amin, S., Broyde, S., and Geacintov, N. E. (2013) Adenine-DNA adducts derived from the highly tumorigenic dibenzo[ a,l ]pyrene are resistant to nucleotide excision repair while guanine adducts are not Chem. Res. Toxicol. 26, 783-793
-
(2013)
Chem. Res. Toxicol.
, vol.26
, pp. 783-793
-
-
Kropachev, K.1
Kolbanovskiy, M.2
Liu, Z.3
Cai, Y.4
Zhang, L.5
Schwaid, A.G.6
Kolbanovskiy, A.7
Ding, S.8
Amin, S.9
Broyde, S.10
Geacintov, N.E.11
-
41
-
-
85133747116
-
Structural Aspects of Polycyclic Aromatic Carcinogen-Damaged DNA and Its Recognition by NER Proteins
-
(Siede, W. Kow, Y. and Doetsch, P. Eds.), Taylor and Francis, New York
-
Geacintov, N., Naegeli, H., Patel, D. J., and Broyde, S. (2005) Structural Aspects of Polycyclic Aromatic Carcinogen-Damaged DNA and Its Recognition by NER Proteins. in DNA Damage Recognition (Siede, W., Kow, Y., and Doetsch, P., Eds.), pp 263-296, Taylor and Francis, New York.
-
(2005)
DNA Damage Recognition
, pp. 263-296
-
-
Geacintov, N.1
Naegeli, H.2
Patel, D.J.3
Broyde, S.4
-
42
-
-
0034029834
-
Unrepaired fjord region polycyclic aromatic hydrocarbon-DNA adducts in ras codon 61 mutational hot spots
-
Buterin, T., Hess, M. T., Luneva, N., Geacintov, N. E., Amin, S., Kroth, H., Seidel, A., and Naegeli, H. (2000) Unrepaired fjord region polycyclic aromatic hydrocarbon-DNA adducts in ras codon 61 mutational hot spots Cancer Res. 60, 1849-1856
-
(2000)
Cancer Res.
, vol.60
, pp. 1849-1856
-
-
Buterin, T.1
Hess, M.T.2
Luneva, N.3
Geacintov, N.E.4
Amin, S.5
Kroth, H.6
Seidel, A.7
Naegeli, H.8
-
43
-
-
78650497367
-
Base flipping free energy profiles for damaged and undamaged DNA
-
Zheng, H., Cai, Y., Ding, S., Tang, Y., Kropachev, K., Zhou, Y., Wang, L., Wang, S., Geacintov, N. E., Zhang, Y., and Broyde, S. (2010) Base flipping free energy profiles for damaged and undamaged DNA Chem. Res. Toxicol. 23, 1868-1870
-
(2010)
Chem. Res. Toxicol.
, vol.23
, pp. 1868-1870
-
-
Zheng, H.1
Cai, Y.2
Ding, S.3
Tang, Y.4
Kropachev, K.5
Zhou, Y.6
Wang, L.7
Wang, S.8
Geacintov, N.E.9
Zhang, Y.10
Broyde, S.11
-
44
-
-
84870522870
-
2-guanine: Intercalation from the B-DNA minor groove with ruptured Watson-Crick pairing at the lesion site
-
2-guanine: intercalation from the B-DNA minor groove with ruptured Watson-Crick pairing at the lesion site Biochemistry 51, 9751-9762
-
(2012)
Biochemistry
, vol.51
, pp. 9751-9762
-
-
Tang, Y.1
Liu, Z.2
Ding, S.3
Rodriguez, F.A.4
Sayer, J.M.5
Jerina, D.M.6
Cai, Y.7
Amin, S.8
Broyde, S.9
Geacintov, N.E.10
-
45
-
-
78649282711
-
A bulky DNA lesion derived from a highly potent polycyclic aromatic tumorigen stabilizes nucleosome core particle structure
-
Cai, Y., Wang, L., Ding, S., Schwaid, A., Geacintov, N. E., and Broyde, S. (2010) A bulky DNA lesion derived from a highly potent polycyclic aromatic tumorigen stabilizes nucleosome core particle structure Biochemistry 49, 9943-9945
-
(2010)
Biochemistry
, vol.49
, pp. 9943-9945
-
-
Cai, Y.1
Wang, L.2
Ding, S.3
Schwaid, A.4
Geacintov, N.E.5
Broyde, S.6
-
46
-
-
84880300016
-
Correlations between the characteristics of fjord region dibenzo[ a,l ]pyrene diol epoxide-guanine and -adenine adducts in double-stranded DNA and nucleotide excision repair
-
Schwaid, A., Liu, Z., Tang, Y., Rodriguez, F., Kolbanovskii, A., Cai, Y., Ding, S., Amin, S., Broyde, S., and Geacintov, N. E. (2010) Correlations between the characteristics of fjord region dibenzo[ a,l ]pyrene diol epoxide-guanine and -adenine adducts in double-stranded DNA and nucleotide excision repair Chem. Res. Toxicol. 23, 281-282
-
(2010)
Chem. Res. Toxicol.
, vol.23
, pp. 281-282
-
-
Schwaid, A.1
Liu, Z.2
Tang, Y.3
Rodriguez, F.4
Kolbanovskii, A.5
Cai, Y.6
Ding, S.7
Amin, S.8
Broyde, S.9
Geacintov, N.E.10
-
47
-
-
0033578345
-
Solution structure of the (+)- cis-anti -benzo[ a ]pyrene-dA ([BP]dA) adduct opposite dT in a DNA duplex
-
Mao, B., Gu, Z., Gorin, A., Chen, J., Hingerty, B. E., Amin, S., Broyde, S., Geacintov, N. E., and Patel, D. J. (1999) Solution structure of the (+)- cis-anti -benzo[ a ]pyrene-dA ([BP]dA) adduct opposite dT in a DNA duplex Biochemistry 38, 10831-10842
-
(1999)
Biochemistry
, vol.38
, pp. 10831-10842
-
-
Mao, B.1
Gu, Z.2
Gorin, A.3
Chen, J.4
Hingerty, B.E.5
Amin, S.6
Broyde, S.7
Geacintov, N.E.8
Patel, D.J.9
-
48
-
-
0024556774
-
Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows
-
Ravishanker, G., Swaminathan, S., Beveridge, D. L., Lavery, R., and Sklenar, H. (1989) Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows J. Biomol. Struct. Dyn. 6, 669-699
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 669-699
-
-
Ravishanker, G.1
Swaminathan, S.2
Beveridge, D.L.3
Lavery, R.4
Sklenar, H.5
-
49
-
-
0343870829
-
-
Wesleyan University, Middletown, CT
-
Ravishanker, G., Wang, W., and Beveridge, D. L. (1993) MD Toolchest, Wesleyan University, Middletown, CT.
-
(1993)
MD Toolchest
-
-
Ravishanker, G.1
Wang, W.2
Beveridge, D.L.3
-
50
-
-
30344440627
-
-
11 th ed. University of California, San Francisco, San Francisco, CA
-
Case, D. A., Darden, T. A., Cheatham, T. E., III, Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Walker, R. C., Zhang, W., Merz, K. M., Roberts, B., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Kolossváry, I., Wong, K. F., Paesani, F., Vanicek, J., Liu, J., Wu, X., Brozell, S. R., Steinbrecher, T., Gohlke, H., Cai, Q., Ye, X., Wang, J., Hsieh, M. J., Cui, G., Roe, D. R., Mathews, D. H., Seetin, M. G., Sagui, C., Babin, V., Gusarov, S., Kovalenko, A., and Kollman, P. A. (2010) AMBER, 11 th ed., University of California, San Francisco, San Francisco, CA.
-
(2010)
AMBER
-
-
Case, D.A.1
Darden, T.A.2
Cheatham Iii, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Walker, R.C.8
Zhang, W.9
Merz, K.M.10
Roberts, B.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossváry, I.16
Wong, K.F.17
Paesani, F.18
Vanicek, J.19
Liu, J.20
Wu, X.21
Brozell, S.R.22
Steinbrecher, T.23
Gohlke, H.24
Cai, Q.25
Ye, X.26
Wang, J.27
Hsieh, M.J.28
Cui, G.29
Roe, D.R.30
Mathews, D.H.31
Seetin, M.G.32
Sagui, C.33
Babin, V.34
Gusarov, S.35
Kovalenko, A.36
Kollman, P.A.37
more..
-
51
-
-
0345577694
-
-
Kluwer, The Netherlands
-
Simmerling, C., Elber, R., and Zhang, J. (1995), Modelling of Biomolecular Structure and Mechanisms, pp 241-265, Kluwer, The Netherlands.
-
(1995)
Modelling of Biomolecular Structure and Mechanisms
, pp. 241-265
-
-
Simmerling, C.1
Elber, R.2
Zhang, J.3
-
52
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank Nucleic Acids Res. 28, 235-242
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
53
-
-
30344440627
-
-
10 th ed. University of California, San Francisco, San Francisco, CA
-
Case, D. A., Darden, T. A., Cheatham, T. E., III, Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Crowley, M., Walker, R. C., Zhang, W., Merz, K. M., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Kolossváry, I., Wong, K. F., Paesani, F., Vanicek, J., Wu, X., Brozell, S. R., Steinbrecher, T., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Mathews, D. H., Seetin, M. G., Sagui, C., Babin, V., and Kollman, P. A. (2008) AMBER 10 th ed., University of California, San Francisco, San Francisco, CA.
-
(2008)
AMBER
-
-
Case, D.A.1
Darden, T.A.2
Cheatham Iii, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
Merz, K.M.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossváry, I.16
Wong, K.F.17
Paesani, F.18
Vanicek, J.19
Wu, X.20
Brozell, S.R.21
Steinbrecher, T.22
Gohlke, H.23
Yang, L.24
Tan, C.25
Mongan, J.26
Hornak, V.27
Cui, G.28
Mathews, D.H.29
Seetin, M.G.30
Sagui, C.31
Babin, V.32
Kollman, P.A.33
more..
-
54
-
-
0037422594
-
Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase
-
Huang, N., Banavali, N. K., and MacKerell, A. D., Jr. (2003) Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase Proc. Natl. Acad. Sci. U.S.A. 100, 68-73
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 68-73
-
-
Huang, N.1
Banavali, N.K.2
Mackerell Jr., A.D.3
-
55
-
-
33644622321
-
Computational approaches for investigating base flipping in oligonucleotides
-
Priyakumar, U. D. and MacKerell, A. D., Jr. (2006) Computational approaches for investigating base flipping in oligonucleotides Chem. Rev. 106, 489-505
-
(2006)
Chem. Rev.
, vol.106
, pp. 489-505
-
-
Priyakumar, U.D.1
Mackerell Jr., A.D.2
-
56
-
-
33745469232
-
Base flipping in a GCGC containing DNA dodecamer: A comparative study of the performance of the nucleic acid force fields, CHARMM, AMBER, and BMS
-
Priyakumar, U. D. and MacKerell, A. D. (2006) Base flipping in a GCGC containing DNA dodecamer: A comparative study of the performance of the nucleic acid force fields, CHARMM, AMBER, and BMS J. Chem. Theory Comput. 2, 187-200
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 187-200
-
-
Priyakumar, U.D.1
Mackerell, A.D.2
-
57
-
-
0029633155
-
The calculation of the potential of mean force using computer-simulations
-
Roux, B. (1995) The calculation of the potential of mean force using computer-simulations Comput. Phys. Commun. 91, 275-282
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 275-282
-
-
Roux, B.1
-
58
-
-
84858705206
-
Crystal structures of putative phosphoglycerate kinases from B. anthracis and C. jejuni
-
Zheng, H., Filippova, E. V., Tkaczuk, K. L., Dworzynski, P., Chruszcz, M., Porebski, P. J., Wawrzak, Z., Onopriyenko, O., Kudritska, M., Grimshaw, S., Savchenko, A., Anderson, W. F., and Minor, W. (2012) Crystal structures of putative phosphoglycerate kinases from B. anthracis and C. jejuni J. Struct. Funct. Genomics 13, 15-26
-
(2012)
J. Struct. Funct. Genomics
, vol.13
, pp. 15-26
-
-
Zheng, H.1
Filippova, E.V.2
Tkaczuk, K.L.3
Dworzynski, P.4
Chruszcz, M.5
Porebski, P.J.6
Wawrzak, Z.7
Onopriyenko, O.8
Kudritska, M.9
Grimshaw, S.10
Savchenko, A.11
Anderson, W.F.12
Minor, W.13
-
59
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules J. Am. Chem. Soc. 117, 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
60
-
-
0032922174
-
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
-
Cheatham, T. E., Cieplak, P., and Kollman, P. A. (1999) A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat J. Biomol. Struct. Dyn. 16, 845-862
-
(1999)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 845-862
-
-
Cheatham, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
61
-
-
34250318638
-
Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers
-
Pérez, A., Marchán, I., Svozil, D., Sponer, J., Cheatham, T. E., III, Laughton, C. A., and Orozco, M. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers Biophys. J. 92, 3817-3829
-
(2007)
Biophys. J.
, vol.92
, pp. 3817-3829
-
-
Pérez, A.1
Marchán, I.2
Svozil, D.3
Sponer, J.4
Cheatham Iii, T.E.5
Laughton, C.A.6
Orozco, M.7
-
62
-
-
0034822656
-
Stereochemical, structural, and thermodynamic origins of stability differences between stereoisomeric benzo[ a ]pyrene diol epoxide deoxyadenosine adducts in a DNA mutational hot spot sequence
-
Yan, S., Shapiro, R., Geacintov, N. E., and Broyde, S. (2001) Stereochemical, structural, and thermodynamic origins of stability differences between stereoisomeric benzo[ a ]pyrene diol epoxide deoxyadenosine adducts in a DNA mutational hot spot sequence J. Am. Chem. Soc. 123, 7054-7066
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 7054-7066
-
-
Yan, S.1
Shapiro, R.2
Geacintov, N.E.3
Broyde, S.4
-
63
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., Chandreskhar, J., Madura, J. D., Imprey, 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
Chandreskhar, J.2
Madura, J.D.3
Imprey, R.W.4
Klein, M.L.5
-
64
-
-
33846823909
-
Particle mesh Ewald: An N log(N) method for Ewald sums in large systems
-
Darden, T., York, D., and Pedersen, L. (1993) Particle mesh Ewald: an N log(N) method for Ewald sums in large systems J. Chem. Phys. 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
65
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pederson, L. G. (1995) A smooth particle mesh Ewald method J. Chem. Phys. 103, 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pederson, L.G.6
-
66
-
-
33646940952
-
Numerical integration of 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 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
-
67
-
-
84859340826
-
Structure and stability of DNA containing an aristolactam II-dA lesion: Implications for the NER recognition of bulky adducts
-
Lukin, M., Zaliznyak, T., Johnson, F., and de Los Santos, C. (2012) Structure and stability of DNA containing an aristolactam II-dA lesion: implications for the NER recognition of bulky adducts Nucleic Acids Res. 40, 2759-2770
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 2759-2770
-
-
Lukin, M.1
Zaliznyak, T.2
Johnson, F.3
De Los Santos, C.4
-
68
-
-
73949110049
-
An improved reaction coordinate for nucleic acid base flipping studies
-
Song, K., Campbell, A. J., Bergonzo, C., de los Santos, C., Grollman, A. P., and Simmerling, C. (2009) An improved reaction coordinate for nucleic acid base flipping studies J. Chem. Theory Comput. 5, 3105-3113
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 3105-3113
-
-
Song, K.1
Campbell, A.J.2
Bergonzo, C.3
De Los Santos, C.4
Grollman, A.P.5
Simmerling, C.6
-
69
-
-
0037178070
-
Base flipping in DNA: Pathways and energetics studied with molecular dynamic simulations
-
Varnai, P. and Lavery, R. (2002) Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations J. Am. Chem. Soc. 124, 7272-7273
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 7272-7273
-
-
Varnai, P.1
Lavery, R.2
-
70
-
-
84875412829
-
Unusual sequence effects on nucleotide excision repair of arylamine lesions: DNA bending/distortion as a primary recognition factor
-
Jain, V., Hilton, B., Lin, B., Patnaik, S., Liang, F., Darian, E., Zou, Y., Mackerell, A. D., Jr., and Cho, B. P. (2013) Unusual sequence effects on nucleotide excision repair of arylamine lesions: DNA bending/distortion as a primary recognition factor Nucleic Acids Res. 41, 869-880
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 869-880
-
-
Jain, V.1
Hilton, B.2
Lin, B.3
Patnaik, S.4
Liang, F.5
Darian, E.6
Zou, Y.7
Mackerell Jr., A.D.8
Cho, B.P.9
-
71
-
-
79960372834
-
Probing for DNA damage with beta-hairpins: Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro
-
Liu, Y., Reeves, D., Kropachev, K., Cai, Y., Ding, S., Kolbanovskiy, M., Kolbanovskiy, A., Bolton, J. L., Broyde, S., Van Houten, B., and Geacintov, N. E. (2011) Probing for DNA damage with beta-hairpins: similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro DNA Repair 10, 684-696
-
(2011)
DNA Repair
, vol.10
, pp. 684-696
-
-
Liu, Y.1
Reeves, D.2
Kropachev, K.3
Cai, Y.4
Ding, S.5
Kolbanovskiy, M.6
Kolbanovskiy, A.7
Bolton, J.L.8
Broyde, S.9
Van Houten, B.10
Geacintov, N.E.11
-
72
-
-
79960380158
-
Resistance of bulky DNA lesions to nucleotide excision repair can result from extensive aromatic lesion-base stacking interactions
-
Reeves, D. A., Mu, H., Kropachev, K., Cai, Y., Ding, S., Kolbanovskiy, A., Kolbanovskiy, M., Chen, Y., Krzeminski, J., Amin, S., Patel, D. J., Broyde, S., and Geacintov, N. E. (2011) Resistance of bulky DNA lesions to nucleotide excision repair can result from extensive aromatic lesion-base stacking interactions Nucleic Acids Res. 39, 8752-8764
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 8752-8764
-
-
Reeves, D.A.1
Mu, H.2
Kropachev, K.3
Cai, Y.4
Ding, S.5
Kolbanovskiy, A.6
Kolbanovskiy, M.7
Chen, Y.8
Krzeminski, J.9
Amin, S.10
Patel, D.J.11
Broyde, S.12
Geacintov, N.E.13
-
73
-
-
80052801205
-
Energetic preference of 8-oxoG eversion pathways in a DNA glycosylase
-
Bergonzo, C., Campbell, A. J., de los Santos, C., Grollman, A. P., and Simmerling, C. (2011) Energetic preference of 8-oxoG eversion pathways in a DNA glycosylase J. Am. Chem. Soc. 133, 14504-14506
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 14504-14506
-
-
Bergonzo, C.1
Campbell, A.J.2
De Los Santos, C.3
Grollman, A.P.4
Simmerling, C.5
-
74
-
-
84857031313
-
Damage recognition in nucleotide excision DNA repair
-
Kuper, J. and Kisker, C. (2012) Damage recognition in nucleotide excision DNA repair Curr. Opin. Struct. Biol. 22, 88-93
-
(2012)
Curr. Opin. Struct. Biol.
, vol.22
, pp. 88-93
-
-
Kuper, J.1
Kisker, C.2
-
75
-
-
79960350167
-
The xeroderma pigmentosum pathway: Decision tree analysis of DNA quality
-
Naegeli, H. and Sugasawa, K. (2011) The xeroderma pigmentosum pathway: decision tree analysis of DNA quality DNA Repair 10, 673-683
-
(2011)
DNA Repair
, vol.10
, pp. 673-683
-
-
Naegeli, H.1
Sugasawa, K.2
-
76
-
-
70449717367
-
Two-step recognition of DNA damage for mammalian nucleotide excision repair: Directional binding of the XPC complex and DNA strand scanning
-
Sugasawa, K., Akagi, J., Nishi, R., Iwai, S., and Hanaoka, F. (2009) Two-step recognition of DNA damage for mammalian nucleotide excision repair: Directional binding of the XPC complex and DNA strand scanning Mol. Cell 36, 642-653
-
(2009)
Mol. Cell
, vol.36
, pp. 642-653
-
-
Sugasawa, K.1
Akagi, J.2
Nishi, R.3
Iwai, S.4
Hanaoka, F.5
|