title: Conformation-specific recognition of carcinogen-DNA adduct in escherichia coli nucleotide excision repair.
abstract: We report a systematic and quantitative structure-function relationship study of the major N-[deoxyguanosin-8-yl]-2-aminofluorene adduct (AF) derived from the prototype carcinogen 2-aminofluorene and its derivatives. The AF adduct is known to exist in two distinct conformational motifs, depending upon the location of the hydrophobic fluorine moiety: major groove binding "B type" (B) conformation (AF-dGanti) and base-displaced "stacked" (S) conformation (AF-dGsyn). The AF-induced S/B conformational heterogeneity is sequence-dependent and follows a typical two-site dynamic chemical exchange. The population of S conformation decreases in the order of 3'-G > A > C > T, indicating the importance of the purine flanking bases in promoting the stacking structure. Line-shape analysis showed that the S/B interconversion energy barriers (DeltaG) are in the narrow 14-16 kcal/mol range. The energy differences of the two conformers are relatively small (<0.5 kcal/mol), suggesting a possibility for a facile adduct conformation switch in the active site of a polymerase. The S/B equilibrium modulates the efficiency of Escherichia coli UvrABC-based nucleotide excision repair (NER) in a conformation-specific manner. The 19F NMR/NER results indicate greater repair susceptibility for the base-displaced S conformer, which lacks a Watson-Crick base pair at the lesion site. These findings represent the first of its kind quantitative structure-function work relating NER activity to a specific adduct conformer and will lead to a better understanding of how bulky DNA adducts are accommodated by the repair protein.
authors.affiliation: Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 41 Lower College Road, Kingston, Rhode Island 02881, USA.
authors.forename: Srinivasarao
authors.initials: S
authors.lastname: Meneni
authors.forename: Steven M
authors.initials: SM
authors.lastname: Shell
authors.forename: Yue
authors.initials: Y
authors.lastname: Zou
authors.forename: Bongsup P
authors.initials: BP
authors.lastname: Cho
mesh_terms: D001483:Base Sequence; D002273:Carcinogens / Q000737:chemistry*; D018736:DNA Adducts / Q000737:chemistry*; D004260:DNA Repair; D004926:Escherichia coli / Q000235:genetics*; D009682:Magnetic Resonance Spectroscopy; D008968:Molecular Conformation; D013816:Thermodynamics
chemical_list: D002273:Carcinogens; D018736:DNA Adducts