Origins of conformational differences between cis and trans DNA adducts derived from enantiomeric anti-benzo[a]pyrene diol epoxides

The two enantiomeric metabolites of the carcinogen precursor benzo[a]pyrene , (+)- and (-)-anti-BPDE [(7R,8S)-dihydroxy-(9S,10R)-epoxy-7,8,9,10-tetrahy drobenzo[a]pyrene and the corresponding 7S,8R,9R,10S enantiomer, respective ly], bind predominantly to the exocyclic amino groups of dG residues in dou ble-stranded DNA by either cis or trans addition to yield four stereoisomer ically distinct [BP]-N-2-dG adducts. Both the 10S (+)-trans and 10R (-)-tra ns adducts assume minor groove conformations in normal, full duplexes, but with opposite 5' or 3' orientations, respectively, relative to the modified strand. In contrast, the 10R (+)-cis and 10S (-)-cis adducts assume opposi tely oriented base-displaced intercalative conformations in normal duplexes , with the inserted pyrenyl residues pointing toward the major groove in th e (+)-cis isomer and toward the minor groove in the (-)-cis isomer. A BPDE- modified nucleoside is a small system which can be studied by computational methods with a very thorough survey of the potential energy surface. To in vestigate conformational differences between cis and trans adducts, and to elucidate origins governing the opposite orientations of these (+)- and (-) -diol epoxide adducts, we have carried out extensive investigations of the (+)- and (-)-trans-anti- and (+)- and (-)-cis-anti-[BP]-N-2-dG deoxynucleos ide adduct pairs. We report results for the (+)- and (-)-cis-anti pair, and compare them with the (+)- and (-)-trans-anti adducts. We created 373 248 different conformers for each adduct, which uniformly sampled at 5 degrees intervals the possible rotamers about three flexible torsion angles governi ng base (chi) and carcinogen (alpha' and beta') orientations, and computed each of their energies. The potential energy surface of the molecule was th en mapped from these results. While four potential energy wells or structur al domains are found for the (Jr)-trans adduct and four for the (-)-trans a dduct, only two of these four domains are favored for each of the two cis a dducts. In both cis and trans adducts, the (+)/(-) pairs of each structural domain are nearly mirror images. The most favored of the domains in both c is and trans adducts is observed experimentally in the duplexes containing each of these [BP]-N-2-dG lesions. The opposite orientations in both cis an d trans adducts stem from steric crowding at the benzylic ring, engendered when a (+) stereoisomer is rotated into the analogous conformation of its ( -) partner, and vice versa. Furthermore, the key role of the difference in absolute configuration between trans and cis adducts at the hydroxyls of C9 and C8 in governing conformational preferences and flexibility is delineat ed. Cis adducts are less conformationally flexible than trans adducts becau se they are inherently more sterically crowded, with C9-OH and C8-OH on the same side of the benzylic ring as guanine and sugar, while they are on the opposite side of the benzylic ring in the trans adducts. Consequently, the cis adducts inherently favor less the minor groove position adopted by tra ns adducts in DNA duplexes because the C9-OH and C8-OH are directed inward into the minor groove in the cis adducts. In the trans adducts, the C9-OH a nd C8-OH are directed outward, away from the interior of the minor groove. Observed differential processing of these four adducts by replication, repa ir, and transcription enzymes may well stem from their differing conformati onal preferences.