title: Role of structural and energetic factors in regulating repair of a bulky DNA lesion with different opposite partner bases.
abstract: Extensive molecular modeling with molecular dynamics simulations and van der Waals energy analyses were used to elucidate the striking finding that a mutagenic benzo[a]pyrene-derived DNA lesion, the base-displaced intercalated 10R-(+)-cis-anti-B[a]P-N(2)-dG (G*), manifests large differences in nucleotide excision repair (NER) efficiencies in DNA duplexes, which depend on the identities of the partner base opposite G*. The nature of the partner base causes marked differences in the extent of its major groove extrusion and dynamics, as well as energetic stability of the intercalation pocket that parallels the relative NER efficiencies.
authors.affiliation: Department of Biology, New York University, New York, NY 10003, USA.
authors.forename: Hong
authors.initials: H
authors.lastname: Mu
authors.forename: Konstantin
authors.initials: K
authors.lastname: Kropachev
authors.forename: Ying
authors.initials: Y
authors.lastname: Chen
authors.forename: Hong
authors.initials: H
authors.lastname: Zhang
authors.forename: Yuqin
authors.initials: Y
authors.lastname: Cai
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Geacintov
authors.forename: Suse
authors.initials: S
authors.lastname: Broyde
mesh_terms: D001580:Benzopyrenes / Q000737:chemistry* / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018736:DNA Adducts / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004260:DNA Repair; D006860:Hydrogen Bonding; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry / Q000378:metabolism; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics
chemical_list: D001580:Benzopyrenes; D018736:DNA Adducts; D009711:Nucleotides; D004247:DNA
references.citation: EMBO J. 2009 Aug 19;28(16):2387-99
references.pmid: 19609301
references.citation: Mol Cell. 2007 Oct 26;28(2):184-6
references.pmid: 17964258
references.citation: Chem Res Toxicol. 2002 Feb;15(2):118-26
references.pmid: 11849037
references.citation: Chem Res Toxicol. 2013 Jul 15;26(7):1115-25
references.pmid: 23758590
references.citation: Chem Res Toxicol. 2013 May 20;26(5):783-93
references.pmid: 23570232
references.citation: Biochemistry. 2002 May 14;41(19):6100-6
references.pmid: 11994005
references.citation: Nature. 2007 Oct 4;449(7162):570-5
references.pmid: 17882165
references.citation: EMBO J. 2009 Feb 18;28(4):383-93
references.pmid: 19153606
references.citation: Biochemistry. 1993 Apr 27;32(16):4145-55
references.pmid: 8476845
references.citation: Chem Res Toxicol. 1989 Sep-Oct;2(5):334-40
references.pmid: 2519824
references.citation: J Biol Chem. 1996 Oct 11;271(41):25089-98
references.pmid: 8810263
references.citation: Biopolymers. 2002 Nov 5;65(3):202-10
references.pmid: 12228925
references.citation: Biochemistry. 1997 Oct 28;36(43):13263-9
references.pmid: 9341216
references.citation: J Biol Chem. 2004 Dec 17;279(51):53298-305
references.pmid: 15475561
references.citation: Nat Rev Cancer. 2005 Feb;5(2):113-25
references.pmid: 15660110
references.citation: J Am Chem Soc. 1972 Nov 15;94(23):8205-12
references.pmid: 5079964
references.citation: Cancer Res. 1982 Dec;42(12):4875-917
references.pmid: 6814745
references.citation: Mol Cell Biol. 1997 Dec;17(12):7069-76
references.pmid: 9372938
references.citation: DNA Repair (Amst). 2002 Jan 22;1(1):95-107
references.pmid: 12509299
references.citation: Biochemistry. 2012 Feb 21;51(7):1486-99
references.pmid: 22242833
references.citation: Nucleic Acids Res. 2011 Nov 1;39(20):8752-64
references.pmid: 21764772
references.citation: Biochemistry. 1998 Jul 14;37(28):10164-72
references.pmid: 9665722
references.citation: Nucleic Acids Res. 2012 Oct;40(19):9675-90
references.pmid: 22904073
references.citation: DNA Repair (Amst). 2006 Apr 8;5(4):515-22
references.pmid: 16483853
references.citation: Biochemistry. 1993 Jul 27;32(29):7531-41
references.pmid: 8338850
references.citation: J Mol Biol. 2000 Jul 7;300(2):275-90
references.pmid: 10873465
references.citation: DNA Repair (Amst). 2011 Jul 15;10(7):684-96
references.pmid: 21741328
references.citation: J Cell Biol. 2010 May 3;189(3):445-63
references.pmid: 20439997
references.citation: J Nucleic Acids. 2010 Aug 23;2010:
references.pmid: 20871811