Solution structures have been determined by 2D NMR spectroscopy for oligonucleotide duplexes modified at N-6 of the central deoxyadenosine (dA) residue in the sequence 5'-GGTCA*CGAG-3' by trans addition to C- 10 of isomeric 7,8-diol 9,10-epoxide metabolites of benzo(a)pyrene (BPDEs). All dA adducts studied to date have the hydrocarbon intercalated into the DNA helix from the major groove, in contrast to trans dG adducts, in which the hydrocarbon lies outside in the minor groove. We previously described the structures of two nonanucleotide duplexes containing a mismatched deoxyguanosine (dG) opposite dA adducts derived from the enantiomers (+)- and (-)-BPDE2 (diastereomer with the benzylic hydroxyl group and epoxide oxygen trans). In these duplexes, the hydrocarbon moiety intercalates at the 5'-side of the modified dA when the absolute configuration at C-10 of the hydrocarbon is R (trans adduct derived from (-)-(7S,8R,9R,10S)-BPDE2) and at the 3'-side of the modified dA when this absolute configuration is S (trans adduct derived from (+)-(7R,8S,9S,10R)-BPDE2). Duplexes (5'- CGGTCA*CGAGG-3') with a complementary T opposite dA adducts with R configuration at C-10, derived from (-)-BPDE2 (benzylic hydroxyl group and epoxide oxygen trans) and (-)-BPDE1 (benzylic hydroxyl group and epoxide oxygen cis), also exhibit the same relationship between the absolute configuration at C-10 and the orientation of intercalation. In these 10R adduct duplexes, normal Watson-Crick base pairs are formed between T and the modified dA, and only one conformation was detected by NMR. Our observations to date indicate that duplexes containing 10S adducts of BPDEs with T opposite the modified dA are conformationally heterogeneous by NMR, and exhibit decreased thermal stability relative to the corresponding 10R adducts. Minor conformers (approximately 20%) were also observed for both nonamers with a mismatched dG. The structure of the minor conformer with dG opposite the 10S adduct from (+)-BPDE2 has now been deter- mined. Although the hydrocarbon is intercalated at the 3'-side of the modified dA in both conformers, the modified dA in the major conformer has an unusual syn glycosidic torsion angle, whereas this angle in the minor conformer is anti.
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