Conformation-Specific Recognition of Carcinogen−DNA Adduct in Escherichia coliNucleotide Excision Repair.

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 (G) 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 coliUvrABC-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. [ABSTRACT FROM AUTHOR]