Molecular modeling of the major adduct of (+)-anti-B[a]PDE(N-2-dG) in the eight conformations and the five DNA sequences most relevant to base substitution mutagenesis

The potent mutagen/carcinogen 7R,8S-dihydroxy-9S, 10R-epoxy-7,8,9,10-tetrah ydrobenzo[n]pyrene [(+)-anti-B[a]PDE], which is the activated form of benzo [a]pyrene (B[a]P), is able to induce different kinds of mutations (G-->T, G -->A, etc.). One hypothesis for this is that different mutations are induce d depending upon the conformation of its major adduct ([+ta]-B[a]P-N-2-dG) when bypassed during DNA replication, Based on molecular modeling, there ap pear to be at least 16 potential conformations that the major adduct [+ta]- B[a]P-N-2-dG can adopt in dsDNA. Regarding base substitution mutagenesis, e ight conformations are most likely to be relevant, In two conformations the dG moiety of the adduct is base paired with its complementary dC and the B [a]P moiety is in the minor groove, In two others the dG moiety of the addu ct is in the Hoogsteen orientation and the B[a]P moiety is in the major gro ove. There are four base displaced structures in which the B[a]P moiety of the adduct is stacked with the surrounding base pairs, two with dG in the m ajor groove and two,vith dG in the minor groove. Using a simulated annealin g protocol, these eight conformations were evaluated in five different DNA sequence contexts (5'-<G(G)under bar>G-3', 5'-C (G) under bar T-3', 5'-A (G ) under bar A-3', 5'-C (G) under bar G-3' and 5'-G (G) under bar G-3'); the latter were chosen because they may be particularly revealing about mutage nic mechanism based on studies with [+ta]-B[a]P-N-2-dG and (+)-anti-B[a]PDE . For each conformation and each sequence context, 25 simulated annealing r uns were conducted by systematically varying several parameters (such as th e initial annealing temperature) based on a protocol established recently. The goal of this work was to exclude conformations that are clearly inferio r. Three conformations are virtually always high in energy, including the t wo Hoogsteen oriented species and one of the base displaced species with dG in the major groove. Remarkably, the remaining five conformations are ofte n quite close in energy and are deemed most likely to be relevant to mutage nesis (see accompanying paper).