-
1
-
-
0028071555
-
Mutations in the p53 tumor suppressor gene: Clues to cancer etiology and molecular pathogenesis
-
Greenbaltt, M.S., Bennett, W.P., Hollstein, M.H. and Harris, C.C. (1994) Mutations in the p53 tumor suppressor gene: clues to cancer etiology and molecular pathogenesis. Cancer Res., 54, 4855-4878. (Pubitemid 24289415)
-
(1994)
Cancer Research
, vol.54
, Issue.18
, pp. 4855-4878
-
-
Greenblatt, M.S.1
Bennett, W.P.2
Hollstein, M.3
Harris, C.C.4
-
2
-
-
0004228157
-
-
(2nd edn). ASM Press, Washington
-
Friedberg, E.C., Walker, G.C., Siede, W., Wood, R.D., Schultz, R.A., Ellenberger, T. (eds) (2006) DNA Repair and Mutagenesis (2nd edn). ASM Press, Washington.
-
(2006)
DNA Repair and Mutagenesis
-
-
Friedberg, E.C.1
Walker, G.C.2
Siede, W.3
Wood, R.D.4
Schultz, R.A.5
Ellenberger, T.6
-
3
-
-
13444273224
-
Nature and nurture-lessons from chemical carcinogenesis
-
Luch, A. (2005) Nature and nurture-lessons from chemical carcinogenesis. Nat. Rev. Cancer, 5, 113-125.
-
(2005)
Nat. Rev. Cancer
, vol.5
, pp. 113-125
-
-
Luch, A.1
-
5
-
-
78649295926
-
Structure-function characteristics of aromatic amine-DNA adducts
-
Geacintov, N.E. and Broyde, S. (eds) Wiley-VCH, Weinheim, Germany
-
Cho, B. (2010) Structure-function characteristics of aromatic amine-DNA adducts. In: Geacintov, N.E. and Broyde, S. (eds), The Chemical Biology of DNA Damage. Wiley-VCH, Weinheim, Germany, pp. 217-233.
-
(2010)
The Chemical Biology of DNA Damage
, pp. 217-233
-
-
Cho, B.1
-
6
-
-
35048822835
-
Spectroscopic and theoretical insights into sequence effects of aminofluorene-induced conformational heterogeneity and nucleotide excision repair
-
DOI 10.1021/bi700858s
-
Meneni, S.R., Shell, S.M., Gao, L., Jurecka, P., Lee, W., Sponer, J., Zou, Y., Chiarelli, M.P. and Cho, B.P. (2007) Spectroscopic and theoretical insights into sequence effects of aminofluorene-induced conformational heterogeneity and nucleotide excision repair. Biochemistry, 46, 11263-11278. (Pubitemid 47556754)
-
(2007)
Biochemistry
, vol.46
, Issue.40
, pp. 11263-11278
-
-
Meneni, S.R.1
Shell, S.M.2
Gao, L.3
Jurecka, P.4
Lee, W.5
Sponer, J.6
Zou, Y.7
Chiarelli, M.P.8
Cho, B.P.9
-
7
-
-
84861394741
-
Conformational and thermodynamic properties modulate the nucleotide excision repair of 2-aminofluorene and 2-acetylaminofluorene dG adducts in the NarI sequence
-
Jain, V., Hilton, B., Patnaik, S., Zou, Y., Chiarelli, M.P. and Cho, B.P. (2012) Conformational and thermodynamic properties modulate the nucleotide excision repair of 2-aminofluorene and 2-acetylaminofluorene dG adducts in the NarI sequence. Nucleic Acids Res., 40, 3939-3951.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 3939-3951
-
-
Jain, V.1
Hilton, B.2
Patnaik, S.3
Zou, Y.4
Chiarelli, M.P.5
Cho, B.P.6
-
8
-
-
78649236407
-
Structures of 2-acetylaminofluorene modified DNA revisited: Insight into conformational heterogeneity
-
Patnaik, S. and Cho, B.P. (2010) Structures of 2-acetylaminofluorene modified DNA revisited: insight into conformational heterogeneity. Chem. Res. Toxicol., 23, 1650-1652.
-
(2010)
Chem. Res. Toxicol
, vol.23
, pp. 1650-1652
-
-
Patnaik, S.1
Cho, B.P.2
-
9
-
-
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. (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.7
-
10
-
-
79551624662
-
Structure of UvrA nucleotide excision repair protein in complex with modified DNA
-
Jaciuk, M., Nowak, E., Skowronek, K., Tanska, A. and Nowotny, M. (2011) Structure of UvrA nucleotide excision repair protein in complex with modified DNA. Nat. Struct. Mol. Biol., 18, 191-197.
-
(2011)
Nat. Struct. Mol. Biol
, vol.18
, pp. 191-197
-
-
Jaciuk, M.1
Nowak, E.2
Skowronek, K.3
Tanska, A.4
Nowotny, M.5
-
11
-
-
34948892722
-
Recognition of DNA damage by the Rad4 nucleotide excision repair protein
-
DOI 10.1038/nature06155, PII NATURE06155
-
Min, J.H. and Pavletich, N.P. (2007) Recognition of DNA damage by the Rad4 nucleotide excision repair protein. Nature, 449, 570-575. (Pubitemid 47525148)
-
(2007)
Nature
, vol.449
, Issue.7162
, pp. 570-575
-
-
Min, J.-H.1
Pavletich, N.P.2
-
12
-
-
80455149268
-
Base sequence context effects on nucleotide excision repair
-
Article ID 174252 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 Article ID 174252, doi:10.4061/2010/174252.
-
(2010)
J. Nucleic Acids 2010
-
-
Cai, Y.1
Patel, D.J.2
Broyde, S.3
Geacintov, N.E.4
-
13
-
-
0033597348
-
Sequence-dependent modulation of frameshift mutagenesis at NarI-derived mutation hot spots
-
DOI 10.1006/jmbi.1999.2667
-
Broschard, T.H., Koffel-Schwartz, N. and Fuchs, R.P. (1999) Sequence-dependent modulation of frameshift mutagenesis at NarI-derived mutation hot spots. J. Mol. Biol., 288, 191-199. (Pubitemid 29201514)
-
(1999)
Journal of Molecular Biology
, vol.288
, Issue.1
, pp. 191-199
-
-
Broschard, T.H.1
Koffel-Schwartz, N.2
Fuchs, R.P.P.3
-
14
-
-
0039547559
-
Single adduct mutagenesis: Strong effect of the position of a single acetylaminofluorene adduct within a mutation hot spot
-
DOI 10.1073/pnas.86.11.4147
-
Burnouf, D., Koehl, P. and Fuchs, R.P. (1989) Single adduct mutagenesis: strong effect of the position of a single acetylaminofluorene adduct within a mutation hot spot. Proc. Natl Acad. Sci. USA, 86, 4147-4151. (Pubitemid 19154752)
-
(1989)
Proceedings of the National Academy of Sciences of the United States of America
, vol.86
, Issue.11
, pp. 4147-4151
-
-
Burnouf, D.1
Koehl, P.2
Fuchs, R.P.P.3
-
15
-
-
0029960774
-
Binding and incision activities of UvrABC excinuclease on slipped DNA intermediates that generate frameshift mutations
-
DOI 10.1006/jmbi.1996.0216
-
Delagoutte, E., Bertrand-Burggraf, E., Lambert, I.B. and Fuchs, R.P. (1996) Binding and incision activities of UvrABC excinuclease on slipped DNA intermediates that generate frameshift mutations. J. Mol. Biol., 257, 970-976. (Pubitemid 26117083)
-
(1996)
Journal of Molecular Biology
, vol.257
, Issue.5
, pp. 970-976
-
-
Delagoutte, E.1
Bertrand-Burggraf, E.2
Lambert, I.B.3
Fuchs, R.P.P.4
-
16
-
-
0021417277
-
PBR322 plasmid DNA modified with 2-acetylaminofluorene derivatives: Transforming activity and in vitro strand cleavage by the Escherichia coli uvrABC endonuclease
-
Fuchs, R.P. and Seeberg, E. (1984) pBR322 plasmid DNA modified with 2-acetylaminofluorene derivatives: transforming activity and in vitro strand cleavage by the Escherichia coli uvrABC endonuclease. EMBO J., 3, 757-760.
-
(1984)
EMBO J
, vol.3
, pp. 757-760
-
-
Fuchs, R.P.1
Seeberg, E.2
-
17
-
-
0028595954
-
Human and E. coli excinucleases are affected differently by the sequence context of acetylaminofluorene-guanine adduct
-
Mu, D., Bertrand-Burggraf, E., Huang, J.C., Fuchs, R.P., Sancar, A. and Fuchs, B.P. (1994) Human and E. coli excinucleases are affected differently by the sequence context of acetylaminofluorene-guanine adduct. Nucleic Acids Res., 22, 4869-4871.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4869-4871
-
-
Mu, D.1
Bertrand-Burggraf, E.2
Huang, J.C.3
Fuchs, R.P.4
Sancar, A.5
Fuchs, B.P.6
-
18
-
-
0025105173
-
Acetylaminofluorene bound to different guanines of the sequence-GGCGCC-is excised with different efficiencies by the UvrABC excision nuclease in a pattern not correlated to the potency of mutation induction
-
Seeberg, E. and Fuchs, R.P. (1990) Acetylaminofluorene bound to different guanines of the sequence-GGCGCC-is excised with different efficiencies by the UvrABC excision nuclease in a pattern not correlated to the potency of mutation induction. Proc. Natl Acad. Sci. USA, 87, 191-194.
-
(1990)
Proc. Natl Acad. Sci. USA
, vol.87
, pp. 191-194
-
-
Seeberg, E.1
Fuchs, R.P.2
-
19
-
-
84868133144
-
Nucleotide excision repair of 2-acetylaminofluorene-and 2-aminofluorene-(C8)-guanine adducts: Molecular dynamics simulations elucidate how lesion structure and base sequence context impact repair efficiencies
-
Mu, H., Kropachev, K., Wang, L., Zhang, L., Kolbanovskiy, A., Kolbanovskiy, M., Geacintov, N.E. and Broyde, S. (2012) Nucleotide excision repair of 2-acetylaminofluorene-and 2-aminofluorene-(C8)-guanine adducts: molecular dynamics simulations elucidate how lesion structure and base sequence context impact repair efficiencies. Nucleic Acids Res., 40, 9675-9690.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 9675-9690
-
-
Mu, H.1
Kropachev, K.2
Wang, L.3
Zhang, L.4
Kolbanovskiy, A.5
Kolbanovskiy, M.6
Geacintov, N.E.7
Broyde, S.8
-
20
-
-
36248931510
-
19F NMR, UV, and CD spectroscopy
-
DOI 10.1021/bi701386f
-
Jain, N., Li, Y., Zhang, L., Meneni, S.R. and Cho, B.P. (2007) Probing the sequence effects on NarI-induced-2 frameshift mutagenesis by dynamic 19F NMR, UV, and CD spectroscopy. Biochemistry, 46, 13310-13321. (Pubitemid 350136371)
-
(2007)
Biochemistry
, vol.46
, Issue.46
, pp. 13310-13321
-
-
Jain, N.1
Li, Y.2
Zhang, L.3
Meneni, S.R.4
Cho, B.P.5
-
21
-
-
63249108233
-
Influence of flanking sequence context on the conformational flexibility of aminofluorene-modified dG adduct in da mismatch DNA duplexes
-
Jain, N., Meneni, S., Jain, V. and Cho, B.P. (2009) Influence of flanking sequence context on the conformational flexibility of aminofluorene-modified dG adduct in dA mismatch DNA duplexes. Nucleic Acids Res., 37, 1628-1637.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 1628-1637
-
-
Jain, N.1
Meneni, S.2
Jain, V.3
Cho, B.P.4
-
22
-
-
75349112841
-
Enthalpy-entropy contribution to carcinogen-induced DNA conformational heterogeneity
-
Liang, F. and Cho, B.P. (2010) Enthalpy-entropy contribution to carcinogen-induced DNA conformational heterogeneity. Biochemistry, 49, 259-266.
-
(2010)
Biochemistry
, vol.49
, pp. 259-266
-
-
Liang, F.1
Cho, B.P.2
-
23
-
-
32644440758
-
Sequence effects of aminofluorene-modified DNA duplexes: Thermodynamic and circular dichroism properties
-
DOI 10.1093/nar/gkj480
-
Meneni, S.R., D'Mello, R., Norigian, G., Baker, G., Gao, L., Chiarelli, M.P. and Cho, B.P. (2006) Sequence effects of aminofluorene-modified DNA duplexes: thermodynamic and circular dichroism properties. Nucleic Acids Res., 34, 755-763. (Pubitemid 43240261)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.2
, pp. 755-763
-
-
Meneni, S.R.1
D'Mello, R.2
Norigian, G.3
Baker, G.4
Gao, L.5
Chiarelli, M.P.6
Cho, B.P.7
-
24
-
-
48349085387
-
Sequence verification of oligonucleotides containing multiple arylamine modifications by enzymatic digestion and liquid chromatography mass spectrometry (LC/MS)
-
Gao, L., Zhang, L., Cho, B.P. and Chiarelli, M.P. (2008) Sequence verification of oligonucleotides containing multiple arylamine modifications by enzymatic digestion and liquid chromatography mass spectrometry (LC/MS). J. Am. Soc. Mass Spectrom., 19, 1147-1155.
-
(2008)
J. Am. Soc. Mass Spectrom
, vol.19
, pp. 1147-1155
-
-
Gao, L.1
Zhang, L.2
Cho, B.P.3
Chiarelli, M.P.4
-
25
-
-
0033572750
-
Thermal stability of PNA/DNA and DNA/DNA duplexes by differential scanning calorimetry
-
Chakrabarti, M.C. and Schwarz, F.P. (1999) Thermal stability of PNA/DNA and DNA/DNA duplexes by differential scanning calorimetry. Nucleic Acids Res., 27, 4801-4806. (Pubitemid 30006671)
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.24
, pp. 4801-4806
-
-
Chakrabarti, M.C.1
Schwarz, F.P.2
-
26
-
-
33748668675
-
Induced circular dichroism characteristics as conformational probes for carcinogenic aminofluorene-DNA adducts
-
DOI 10.1021/tx0601253
-
Liang, F., Meneni, S. and Cho, B.P. (2006) Induced circular dichroism characteristics as conformational probes for carcinogenic aminofluorene-DNA adducts. Chem. Res. Toxicol., 19, 1040-1043. (Pubitemid 44384833)
-
(2006)
Chemical Research in Toxicology
, vol.19
, Issue.8
, pp. 1040-1043
-
-
Liang, F.1
Meneni, S.2
Cho, B.P.3
-
27
-
-
0033535926
-
Probing the conformational heterogeneity of the acetylaminofluorene- modified 20-deoxyguanosine and DNA by 19F NMR spectroscopy
-
Cho, B.P. and Zhou, L. (1999) Probing the conformational heterogeneity of the acetylaminofluorene-modified 20-deoxyguanosine and DNA by 19F NMR spectroscopy. Biochemistry, 38, 7572-7583.
-
(1999)
Biochemistry
, vol.38
, pp. 7572-7583
-
-
Cho, B.P.1
Zhou, L.2
-
28
-
-
0034307608
-
Recognition and incision of site-specifically modified C8 guanine adducts formed by 2-aminofluorene, N-acetyl-2-aminofluorene and 1-nitropyrene by UvrABC nuclease
-
Luo, C., Krishnasamy, R., Basu, A.K. and Zou, Y. (2000) Recognition and incision of site-specifically modified C8 guanine adducts formed by 2-aminofluorene, N-acetyl-2-aminofluorene and 1-nitropyrene by UvrABC nuclease. Nucleic Acids Res., 28, 3719-3724.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 3719-3724
-
-
Luo, C.1
Krishnasamy, R.2
Basu, A.K.3
Zou, Y.4
-
29
-
-
0028784624
-
Interaction of the UvrABC nuclease system with a DNA duplex containing a single stereoisomer of dG-(+)-or dG-(-)-anti-BPDE
-
Zou, Y., Liu, T.M., Geacintov, N.E. and Van Houten, B. (1995) Interaction of the UvrABC nuclease system with a DNA duplex containing a single stereoisomer of dG-(+)-or dG-(-)-anti-BPDE. Biochemistry, 34, 13582-13593.
-
(1995)
Biochemistry
, vol.34
, pp. 13582-13593
-
-
Zou, Y.1
Liu, T.M.2
Geacintov, N.E.3
Van Houten, B.4
-
30
-
-
0033199492
-
2B complex allows dynamic recognition of DNA damage
-
DOI 10.1093/emboj/18.17.4889
-
Zou, Y. and Van Houten, B. (1999) Strand opening by the UvrA(2)B complex allows dynamic recognition of DNA damage. EMBO J., 18, 4889-4901. (Pubitemid 29415542)
-
(1999)
EMBO Journal
, vol.18
, Issue.17
, pp. 4889-4901
-
-
Zou, Y.1
Van Houten, B.2
-
31
-
-
0036306053
-
Free energy and structural pathways of base flipping in a DNA GCGC containing sequence
-
DOI 10.1016/S0022-2836(02)00194-8
-
Banavali, N.K. and MacKerell, A.D. Jr (2002) Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J. Mol. Biol., 319, 141-160. (Pubitemid 34729492)
-
(2002)
Journal of Molecular Biology
, vol.319
, Issue.1
, pp. 141-160
-
-
Banavali, N.K.1
MacKerell Jr., A.D.2
-
32
-
-
33846818707
-
Examination of the long-range effects of aminofluorene-induced conformational heterogeneity and its relevance to the mechanism of translesional DNA synthesis
-
DOI 10.1016/j.jmb.2006.12.023, PII S0022283606016998
-
Meneni, S., Liang, F. and Cho, B.P. (2007) Examination of the long-range effects of aminofluorene-induced conformational heterogeneity and its relevance to the mechanism of translesional DNA synthesis. J. Mol. Biol., 366, 1387-1400. (Pubitemid 46215607)
-
(2007)
Journal of Molecular Biology
, vol.366
, Issue.5
, pp. 1387-1400
-
-
Meneni, S.1
Liang, F.2
Cho, B.P.3
-
33
-
-
0031041812
-
NMR solution structures of stereoisomeric covalent polycyclic aromatic carcinogen-DNA adducts: Principles, patterns, and diversity
-
DOI 10.1021/tx9601418
-
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. (Pubitemid 27091881)
-
(1997)
Chemical Research in Toxicology
, vol.10
, Issue.2
, pp. 111-146
-
-
Geacintov, N.E.1
Cosman, M.2
Hingerty, B.E.3
Amin, S.4
Broyde, S.5
Patel, D.J.6
-
34
-
-
0030757459
-
19F NMR evidence
-
DOI 10.1021/ja9632771
-
Zhou, L., Rajabzadeh, M., Traficante, D.D. and Cho, B.P. (1997) Conformational heterogeneity of arylamine-modified DNA: 19F NMR evidence. J. Am. Chem. Soc., 119, 5384-5389. (Pubitemid 27310714)
-
(1997)
Journal of the American Chemical Society
, vol.119
, Issue.23
, pp. 5384-5389
-
-
Zhou, L.1
Rajabzadeh, M.2
Traficante, D.D.3
Cho, B.P.4
-
35
-
-
33846858612
-
Conformation-specific recognition of carcinogen-DNA adduct in Escherichia coli nucleotide excision repair
-
DOI 10.1021/tx600273h
-
Meneni, S., Shell, S.M., Zou, Y. and Cho, B.P. (2007) Conformation-specific recognition of carcinogen-DNA adduct in escherichia coli nucleotide excision repair. Chem. Res. Toxicol., 20, 6-10. (Pubitemid 46220149)
-
(2007)
Chemical Research in Toxicology
, vol.20
, Issue.1
, pp. 6-10
-
-
Meneni, S.1
Shell, S.M.2
Zou, Y.3
Cho, B.P.4
-
36
-
-
0023644833
-
Interaction between the cyclic AMP receptor protein and DNA
-
Blazy, B., Culard, F. and Maurizot, J.C. (1987) Interaction between the cyclic AMP receptor protein and DNA. Conformational studies. J. Mol. Biol., 195, 175-183.
-
(1987)
Conformational Studies. J. Mol. Biol
, vol.195
, pp. 175-183
-
-
Blazy, B.1
Culard, F.2
Maurizot, J.C.3
-
37
-
-
0028131494
-
DNA binding and bending properties of the post-meiotically expressed Sry-related protein Sox-5
-
Connor, F., Cary, P.D., Read, C.M., Preston, N.S., Driscoll, P.C., Denny, P., Crane-Robinson, C. and Ashworth, A. (1994) DNA binding and bending properties of the post-meiotically expressed Sry-related protein Sox-5. Nucleic Acids Res., 22, 3339-3346.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 3339-3346
-
-
Connor, F.1
Cary, P.D.2
Read, C.M.3
Preston, N.S.4
Driscoll, P.C.5
Denny, P.6
Crane-Robinson, C.7
Ashworth, A.8
-
38
-
-
0030728598
-
High affinity binding of MEF-2C correlates with DNA bending
-
Meierhans, D., Sieber, M. and Allemann, R.K. (1997) High affinity binding of MEF-2C correlates with DNA bending. Nucleic Acids Res., 25, 4537-4544. (Pubitemid 27500765)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.22
, pp. 4537-4544
-
-
Meierhans, D.1
Sieber, M.2
Allemann, R.K.3
-
39
-
-
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
-
40
-
-
0028790549
-
Conformational studies of the (+)-trans, (-)-trans, (+)-cis, and (-)-cis adducts of anti-benzo[a]pyrene diolepoxide to N2-dG in duplex oligonucleotides using polyacrylamide gel electrophoresis and low-temperature fluorescence spectroscopy
-
Suh, M., Ariese, F., Small, G.J., Jankowiak, R., Liu, T.M. and Geacintov, N.E. (1995) Conformational studies of the (+)-trans, (-)-trans, (+)-cis, and (-)-cis adducts of anti-benzo[a]pyrene diolepoxide to N2-dG in duplex oligonucleotides using polyacrylamide gel electrophoresis and low-temperature fluorescence spectroscopy. Biophys. Chem., 56, 281-296.
-
(1995)
Biophys. Chem
, vol.56
, pp. 281-296
-
-
Suh, M.1
Ariese, F.2
Small, G.J.3
Jankowiak, R.4
Liu, T.M.5
Geacintov, N.E.6
-
41
-
-
0032492642
-
Sequence dependence and characteristics of bends induced by site- specific polynuclear aromatic carcinogen - Deoxyguanosine lesions in oligonucleotides
-
DOI 10.1021/bi980291c
-
Tsao, H., Mao, B., Zhuang, P., Xu, R., Amin, S. and Geacintov, N.E. (1998) Sequence dependence and characteristics of bends induced by site-specific polynuclear aromatic carcinogen-deoxyguanosine lesions in oligonucleotides. Biochemistry, 37, 4993-5000. (Pubitemid 28235691)
-
(1998)
Biochemistry
, vol.37
, Issue.14
, pp. 4993-5000
-
-
Tsao, H.1
Mao, B.2
Zhuang, P.3
Xu, R.4
Amin, S.5
Geacintov, N.E.6
-
42
-
-
0028901297
-
Solution conformation of the N-(deoxyguanosin-8-yl)aminoflu orene adduct opposite deoxyinosine and deoxyguanosine in DNA by NMR and computational characterization
-
Abuaf, P., Hingerty, B.E., Broyde, S. and Grunberger, D. (1995) Solution conformation of the N-(deoxyguanosin-8-yl)aminoflu orene adduct opposite deoxyinosine and deoxyguanosine in DNA by NMR and computational characterization. Chem. Res. Toxicol., 8, 369-378.
-
(1995)
Chem. Res. Toxicol
, vol.8
, pp. 369-378
-
-
Abuaf, P.1
Hingerty, B.E.2
Broyde, S.3
Grunberger, D.4
-
43
-
-
0032488634
-
8-dG adduct opposite dC in a DNA duplex
-
DOI 10.1021/bi972257o
-
Mao, B., Hingerty, B.E., Broyde, S. and Patel, D.J. (1998) Solution structure of the aminofluorene [AF]-intercalated conformer of the syn-[AF]-C8-dG adduct opposite dC in a DNA duplex. Biochemistry, 37, 81-94. (Pubitemid 28049110)
-
(1998)
Biochemistry
, vol.37
, Issue.1
, pp. 81-94
-
-
Mao, B.1
Hingerty, B.E.2
Broyde, S.3
Patel, D.J.4
-
44
-
-
0027457947
-
Structural characterization of an N-acetyl-2-aminofluorene (AAF) modified DNA oligomer by NMR, energy minimization, and molecular dynamics
-
O'Handley, S.F., Sanford, D.G., Xu, R., Lester, C.C., Hingerty, B.E., Broyde, S. and Krugh, T.R. (1993) Structural characterization of an N-acetyl-2-aminofluorene (AAF) modified DNA oligomer by NMR, energy minimization, and molecular dynamics. Biochemistry, 32, 2481-2497. (Pubitemid 23090634)
-
(1993)
Biochemistry
, vol.32
, Issue.10
, pp. 2481-2497
-
-
O'Handley, S.F.1
Sanford, D.G.2
Xu, R.3
Lester, C.C.4
Hingerty, B.E.5
Broyde, S.6
Krugh, T.R.7
-
45
-
-
0028033727
-
Structural characterization of two interchangeable conformations of a 2- aminofluorene-modified DNA oligomer by NMR and energy minimization
-
DOI 10.1021/bi00250a012
-
Eckel, L.M. and Krugh, T.R. (1994) Structural characterization of two interchangeable conformations of a 2-aminofluorene-modified DNA oligomer by NMR and energy minimization. Biochemistry, 33, 13611-13624. (Pubitemid 24381922)
-
(1994)
Biochemistry
, vol.33
, Issue.46
, pp. 13611-13624
-
-
Eckel, L.M.1
Krugh, T.R.2
-
46
-
-
25444460601
-
Recognition and incision of γ-radiation-induced cross-linked guanine-thymine tandem lesion G[8,5-Me]T by UvrABC nuclease
-
DOI 10.1021/tx050147+
-
Yang, Z., Colis, L.C., Basu, A.K. and Zou, Y. (2005) Recognition and incision of gamma-radiation-induced cross-linked guanine-thymine tandem lesion G[8, 5-Me]T by UvrABC nuclease. Chem. Res. Toxicol., 18, 1339-1346. (Pubitemid 41361707)
-
(2005)
Chemical Research in Toxicology
, vol.18
, Issue.9
, pp. 1339-1346
-
-
Yang, Z.1
Colis, L.C.2
Basu, A.K.3
Zou, Y.4
-
47
-
-
0242318377
-
Effects of DNA adduct structure and sequence context on strand opening of repair intermediates and incision by UvrABC nuclease
-
DOI 10.1021/bi034446e
-
Zou, Y., Shell, S.M., Utzat, C.D., Luo, C., Yang, Z., Geacintov, N.E. and Basu, A.K. (2003) Effects of DNA adduct structure and sequence context on strand opening of repair intermediates and incision by UvrABC nuclease. Biochemistry, 42, 12654-12661. (Pubitemid 37337556)
-
(2003)
Biochemistry
, vol.42
, Issue.43
, pp. 12654-12661
-
-
Zou, Y.1
Shell, S.M.2
Utzat, C.D.3
Luo, C.4
Yang, Z.5
Geacintov, N.E.6
Basu, A.K.7
-
48
-
-
34250177258
-
Sequence context- and temperature-dependent nucleotide excision repair of a benzo[a]pyrene diol epoxide-guanine DNA adduct catalyzed by thermophilic UvrABC proteins
-
DOI 10.1021/bi700294k
-
Ruan, Q., Liu, T., Kolbanovskiy, A., Liu, Y., Ren, J., Skorvaga, M., Zou, Y., Lader, J., Malkani, B., Amin, S. et al. (2007) Sequence context-and temperature-dependent nucleotide excision repair of a benzo[a]pyrene diol epoxide-guanine DNA adduct catalyzed by thermophilic UvrABC proteins. Biochemistry, 46, 7006-7015. (Pubitemid 46906429)
-
(2007)
Biochemistry
, vol.46
, Issue.23
, pp. 7006-7015
-
-
Ruan, Q.1
Liu, T.2
Kolbanovskiy, A.3
Liu, Y.4
Ren, J.5
Skorvaga, M.6
Zou, Y.7
Lader, J.8
Malkani, B.9
Amin, S.10
Van Houten, B.11
Geacintov, N.E.12
-
49
-
-
0024828173
-
Strong structural effect of the position of a single acetylaminofluorene adduct within a mutation hot spot
-
Koehl, P., Valladier, P., Lefevre, J.F. and Fuchs, R.P. (1989) Strong structural effect of the position of a single acetylaminofluorene adduct within a mutation hot spot. Nucleic Acids Res., 17, 9531-9541. (Pubitemid 20010765)
-
(1989)
Nucleic Acids Research
, vol.17
, Issue.23
, pp. 9531-9541
-
-
Koehl, P.1
Valladier, P.2
Lefevre, J.-F.3
Fuchs, R.P.P.4
-
50
-
-
0242290881
-
DNA basepair step deformability inferred from molecular dynamics simulations
-
Lankas, F., Sponer, J., Langowski, J. and Cheatham, T.E. III (2003) DNA basepair step deformability inferred from molecular dynamics simulations. Biophys. J., 85, 2872-2883. (Pubitemid 37345781)
-
(2003)
Biophysical Journal
, vol.85
, Issue.5
, pp. 2872-2883
-
-
Lankas, F.1
Sponer, J.2
Langowski, J.3
Cheatham III, T.E.4
-
51
-
-
0035900536
-
Molecular dynamics simulations of B'-DNA: Sequence effects on A-tract-induced bending and flexibility
-
DOI 10.1006/jmbi.2001.4926
-
McConnell, K.J. and Beveridge, D.L. (2001) Molecular dynamics simulations of B '-DNA: sequence effects on A-tract-induced bending and flexibility. J. Mol. Biol., 314, 23-40. (Pubitemid 33097288)
-
(2001)
Journal of Molecular Biology
, vol.314
, Issue.1
, pp. 23-40
-
-
McConnell, K.J.1
Beveridge, D.L.2
-
52
-
-
0027159020
-
CA runs increase DNA flexibility in the complex of Cro protein with the O(R)3 site
-
Lyubchenko, Y.L., Shlyakhtenko, L.S., Appella, E. and Harrington, R.E. (1993) CA runs increase DNA flexibility in the complex of lambda Cro protein with the OR3 site. Biochemistry, 32, 4121-4127. (Pubitemid 23127007)
-
(1993)
Biochemistry
, vol.32
, Issue.15
, pp. 4121-4127
-
-
Lyubchenko, Y.L.1
Shlyakhtenko, L.S.2
Appella, E.3
Harrington, R.E.4
-
53
-
-
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. et al. (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 (Amst), 10, 684-696.
-
(2011)
DNA Repair (Amst
, 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
-
54
-
-
0035814936
-
Hierarchy of DNA damage recognition in Escherichia coli nucleotide excision repair
-
DOI 10.1021/bi001504c
-
Zou, Y., Luo, C. and Geacintov, N.E. (2001) Hierarchy of DNA damage recognition in Escherichia coli nucleotide excision repair. Biochemistry, 40, 2923-2931. (Pubitemid 32198295)
-
(2001)
Biochemistry
, vol.40
, Issue.9
, pp. 2923-2931
-
-
Zou, Y.1
Luo, C.2
Geacintov, N.E.3
-
55
-
-
33644619706
-
Prokaryotic nucleotide excision repair: The UvrABC system
-
Truglio, J.J., Croteau, D.L., Van Houten, B. and Kisker, C. (2006) Prokaryotic nucleotide excision repair: the UvrABC system. Chem. Rev., 106, 233-252.
-
(2006)
Chem. Rev
, vol.106
, pp. 233-252
-
-
Truglio, J.J.1
Croteau, D.L.2
Van Houten, B.3
Kisker, C.4
-
56
-
-
24044438506
-
'Close-fitting sleeves': DNA damage recognition by the UvrABC nuclease system
-
DOI 10.1016/j.mrfmmm.2005.03.013, PII S0027510705001739
-
Van Houten, B., Croteau, D.L., DellaVecchia, M.J., Wang, H. and Kisker, C. (2005) 'Close-fitting sleeves': DNA damage recognition by the UvrABC nuclease system. Mutat. Res., 577, 92-117. (Pubitemid 41225491)
-
(2005)
Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis
, vol.577
, Issue.1-2 SPEC. ISS.
, pp. 92-117
-
-
Van Houten, B.1
Croteau, D.L.2
DellaVecchia, M.J.3
Wang, H.4
Kisker, C.5
-
57
-
-
0027350849
-
Mechanism of action of the Escherichia coli UvrABC nuclease: Clues to the damage recognition problem
-
Van Houten, B. and Snowden, A. (1993) Mechanism of action of the Escherichia coli UvrABC nuclease: clues to the damage recognition problem. Bioessays, 15, 51-59.
-
(1993)
Bioessays
, vol.15
, pp. 51-59
-
-
Van Houten, B.1
Snowden, A.2
-
58
-
-
52049089211
-
Functions of base flipping in E. coli nucleotide excision repair
-
Malta, E., Verhagen, C.P., Moolenaar, G.F., Filippov, D.V., van der Marel, G.A. and Goosen, N. (2008) Functions of base flipping in E. coli nucleotide excision repair. DNA Repair (Amst), 7, 1647-1658.
-
(2008)
DNA Repair (Amst
, vol.7
, pp. 1647-1658
-
-
Malta, E.1
Verhagen, C.P.2
Moolenaar, G.F.3
Filippov, D.V.4
Van Der Marel, G.A.5
Goosen, N.6
-
59
-
-
67650500988
-
CHARMM: The biomolecular simulation program
-
Brooks, B.R., Brooks, C.L. III, MacKerell, A.D. Jr, Nilsson, L., Petrella, R.J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S. et al. (2009) CHARMM: the biomolecular simulation program. J. Comp. Chem., 30, 1545-1614.
-
(2009)
J. Comp. Chem
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks III, C.L.2
MacKerell Jr., A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
-
60
-
-
0000214231
-
All-atom empirical force field for nucleic acids 2 Application to solution MD simulations of DNA
-
MacKerell, A.D. Jr and Banavali, N.K. (2000) All-atom empirical force field for nucleic acids: 2) Application to solution MD simulations of DNA. J. Comp. Chem., 21, 105-120.
-
(2000)
J. Comp. Chem
, vol.21
, pp. 105-120
-
-
MacKerell Jr., A.D.1
Banavali, N.K.2
-
61
-
-
0348244547
-
All-atom empirical force field for nucleic acids 1 Parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe, N. and MacKerell, A.D. Jr (2000) All-atom empirical force field for nucleic acids: 1) Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comp. Chem., 21, 86-104.
-
(2000)
J. Comp. Chem
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerell Jr., A.D.2
-
62
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
DOI 10.1002/jcc.20289
-
Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L. and Schulten, K. (2005) Scalable molecular dynamics with NAMD. J. Comp. Chem., 26, 1781-1802. (Pubitemid 43078511)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
63
-
-
76249087938
-
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
-
Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I. et al. (2010) CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comp. Chem., 31, 671-690.
-
(2010)
J. Comp. Chem
, vol.31
, pp. 671-690
-
-
Vanommeslaeghe, K.1
Hatcher, E.2
Acharya, C.3
Kundu, S.4
Zhong, S.5
Shim, J.6
Darian, E.7
Guvench, O.8
Lopes, P.9
Vorobyov, I.10
-
64
-
-
0014675222
-
Refinement of protein conformations using a macromolecular energy minimization procedure
-
Levitt, M. and Lifson, S. (1969) Refinement of protein conformations using a macromolecular energy minimization procedure. J. Mol. Biol., 46, 269-279.
-
(1969)
J. Mol. Biol
, vol.46
, pp. 269-279
-
-
Levitt, M.1
Lifson, S.2
-
65
-
-
0000615669
-
Function minimization by conjugate gradients
-
Fletcher, R. and Reeves, C.M. (1964) Function minimization by conjugate gradients. Comput. J., 7, 149-154.
-
(1964)
Comput. J
, vol.7
, pp. 149-154
-
-
Fletcher, R.1
Reeves, C.M.2
-
66
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W. and Klein, M.L. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79, 926-935.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
68
-
-
33846823909
-
Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems
-
Darden, T.A., York, D. and Pedersen, L.G. (1993) Particle mesh Ewald: an Nlog(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.A.1
York, D.2
Pedersen, L.G.3
-
69
-
-
84986534166
-
New spherical-cutoff methods of long-range forces in macromolecular simulations
-
Steinbach, P.J. and Brooks, B.R. (1994) New spherical-cutoff methods of long-range forces in macromolecular simulations. J. Comp. Chem., 15, 667-683.
-
(1994)
J. Comp. Chem
, vol.15
, pp. 667-683
-
-
Steinbach, P.J.1
Brooks, B.R.2
-
70
-
-
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. Comp. Phys., 23, 327-341.
-
(1977)
J. Comp. Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
71
-
-
84926811618
-
Constant pressure molecular dynamics for molecular systems
-
Nose, S. and Klein, M.L. (1983) Constant pressure molecular dynamics for molecular systems. Mol. Phys., 50, 1055-1076.
-
(1983)
Mol. Phys
, vol.50
, pp. 1055-1076
-
-
Nose, S.1
Klein, M.L.2
-
72
-
-
0001538909
-
Canonical dynamics-equilibrium phase-space distributions
-
Hoover, W.G. (1985) Canonical dynamics-equilibrium phase-space distributions. Phys. Rev. A, 31, 1695-1697.
-
(1985)
Phys. Rev. A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
73
-
-
36449007836
-
Constant pressure molecular dynamics simulation: The Langevin Piston method
-
Feller, S.E., Zhang, Y., Pastor, R.W. and Brooks, R.W. (1995) Constant pressure molecular dynamics simulation: the Langevin Piston method. J. Chem. Phys., 103, 4613-4621.
-
(1995)
J. Chem. Phys
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.2
Pastor, R.W.3
Brooks, R.W.4
-
74
-
-
58149512801
-
Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
-
Zheng, L., Chen, M. and Yang, W. (2008) Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems. Proc. Natl Acad. Sci. USA, 105, 20227-20232.
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 20227-20232
-
-
Zheng, L.1
Chen, M.2
Yang, W.3
-
75
-
-
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
-
76
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules I. The method
-
Kumar, S., Bouzida, D., Swendsen, R.H., Kollman, P.A. and Rosenberg, J.M. (1992) The Weighted Histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comp. Chem., 13, 1011.
-
(1992)
J. Comp. Chem
, vol.13
, pp. 1011
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
78
-
-
0023155210
-
Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
-
DOI 10.1016/0022-2836(87)90358-5
-
Ponder, J.W. and Richards, F.M. (1987) Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol., 193, 775-791. (Pubitemid 17020078)
-
(1987)
Journal of Molecular Biology
, vol.193
, Issue.4
, pp. 775-791
-
-
Ponder, J.W.1
Richards, F.M.2
-
79
-
-
70450261721
-
Conformational analysis of nucleic acids revisited: Curves+
-
Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D. and Zakrzewska, K. (2009) Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res., 37, 5917-5929.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 5917-5929
-
-
Lavery, R.1
Moakher, M.2
Maddocks, J.H.3
Petkeviciute, D.4
Zakrzewska, K.5
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