Molecular modeling of the major adduct of (+)-anti-B[a]PDE(N2-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-tetrahydrobenzo[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 induced 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 appear 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, eight 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 adduct is in the Hoogsteen orientation and the B[a]P moiety is in the major groove. 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 major groove and two,vith dG in the minor groove. Using a simulated annealing 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 mutagenic 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 runs were conducted by systematically varying several parameters (such as the initial annealing temperature) based on a protocol established recently. The goal of this work was to exclude conformations that are clearly inferior. Three conformations are virtually always high in energy, including the two Hoogsteen oriented species and one of the base displaced species with dG in the major groove. Remarkably, the remaining five conformations are often quite close in energy and are deemed most likely to be relevant to mutagenesis (see accompanying paper).