title: Role of base sequence context in conformational equilibria and nucleotide excision repair of benzo[a]pyrene diol epoxide-adenine adducts.
abstract: We investigate the influence of base sequence context on the conformations of the 10S (+)- and 10R (-)-trans-anti-[BP]-N(6)-dA adducts through molecular dynamics (MD) simulations with free energy calculations, and relate the structural findings to results of nucleotide excision repair (NER) assays in human cell extracts. In previous studies, these adducts were studied in the CA*A sequence context, and here we report results for the CA*C sequence. Our simulations indicate that the base sequence context affects the syn-anti conformational equilibrium in the 10S (+) adduct by modulating the barrier heights between these states on the energy surface, with a higher barrier in the CA*C case. Our nucleotide excision repair assay finds greater NER susceptibilities in the 10S (+) adduct for the CA*C sequence context. A structural rationale ties together these results. A sequence specific hydrogen bond, accompanied by a significantly increased roll and consequent bending in the 10S (+) adduct, has been found in our simulations for the CA*C sequence, which could account for the enhanced nucleotide excision repair as well as the syn-anti equilibrium difference we observe in this isomer and sequence. Such sequence specific differential repair could contribute to the existence of mutational hotspots and thereby contribute to the complexity of cancer initiation.
authors.affiliation: Department of Chemistry, New York University, New York, New York 10003, USA.
authors.forename: Shixiang
authors.initials: S
authors.lastname: Yan
authors.forename: Min
authors.initials: M
authors.lastname: Wu
authors.forename: Tonko
authors.initials: T
authors.lastname: Buterin
authors.forename: Hanspeter
authors.initials: H
authors.lastname: Naegeli
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Geacintov
authors.forename: Suse
authors.initials: S
authors.lastname: Broyde
mesh_terms: D015123:7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide / Q000737:chemistry* / Q000378:metabolism; D001483:Base Sequence; D018736:DNA Adducts / Q000737:chemistry* / Q000378:metabolism; D004260:DNA Repair; D003839:Deoxyadenosines / Q000737:chemistry* / Q000378:metabolism; D011905:Genes, ras; D006027:Glycosides / Q000737:chemistry; D006367:HeLa Cells; D006801:Humans; D006860:Hydrogen Bonding; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000378:metabolism; D013237:Stereoisomerism; D013816:Thermodynamics
chemical_list: D018736:DNA Adducts; D003839:Deoxyadenosines; D006027:Glycosides; D009692:Nucleic Acid Heteroduplexes; D015123:7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide