NMR solution structures have been described for 3 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 (BPDE). These are two nonanucleotide duplexes with deoxyguanosine (dG) mismatches opposite dA adducts derived from the enantiomers (+)-BPDE-2 and (-)-BPDE-2 [diastereomer with the benzylic hydroxyl group and epoxide oxygen trans], and an undecanucleotide duplex with the same internal sequence and a T residue opposite a dA adduct derived from (-) -BPDE-1 [diastereomer with the benzylic hydroxyl group and epoxide oxygen cis]. Major findings are; i) The aromatic portion of the hydrocarbon is intercalated into the DNA helix, and lies toward the 5'-end of the modified DNA strand when the absolute configuration at C-10 is R, and toward the 3--end when the configuration at C-10 is S; ii) In the oligomer derived from (-)-BPDE-2, the glycosidic bond of the modified dA has a normal, anti conformation, and the mismatched G is rotated out of the DNA helix, whereas the glycosidic bond of the (+)-BPDE-2 dA adduct has an unusual syn conformation, and the A is hydrogen bonded to the mismatched G; iii) The BPDE-1 dA adduct in the modified undercamer maintains normal hydrogen bonding with a complementary T; iv) Both duplexes with a mismatched G opposite a modified A exhibit a major and a minor conformation by NMR, in contrast to oligonucleotides containing trans BPDE-2 adducts at the exocyclic N-2 of dG, which were observed to be conformationally homogeneous. Fluorescence decay profiles of the two nonanucleotide duplexes containing dA adducts, as well as two undecanucleotides containing trans dG adducts from (=)-and (-)-BPDE-2, are similar, and exhibit two short-lived components (more than 95% of total intensity) and one minor, long-lived component. Since the dG modified oligonucleotides show only one conformation by NMR, their two fluorescence lifetimes may result from conformations that interconvert rapidly on the NMR time scale. In 18mer templates, trans dA adducts from BPDEs block primer extension by DNA polymerases to an extent that depends both on the specific enzyme and the absolute configuration of the adduct.
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