Solution conformation of the (+)-cis-anti-[BP]dG adduct opposite a deletion site in a DNA duplex: intercalation of the covalently attached benzo[a]pyrene into the helix with base displacement of the modified deoxyguanosine into the minor groove

We have applied a combined NMR-molecular mechanics approach to determine the solution structure of the (+)-cis-anti-[BP]dG adduct positioned opposite a deletion site in the sequence d(C5-[BP]G6-C7).d(G16-G17) at the DNA oligomer duplex level. Our structural studies establish that the benzo[a]pyrene ring intercalates into the helix opposite the deletion site while the modified deoxyguanosine is displaced into the minor groove with its plane parallel to the helix axis. The intercalation site is wedge-shaped with the benzo[a]pyrene ring stacked over intact flanking Watson-Crick dG.dC base pairs. The modified deoxyguanosine stacks over the minor groove face of the sugar ring of the 5'-flanking dC5 residue. The structure at the lesion site is consistent with the observed intermolecular NOEs which served as input restraints to guide the molecular mechanics calculations, and, in addition, the various stacking interactions explain the observed large ring current shifts associated with adduct formation. The solution structure of the (+)-cis-anti-[BP]dG adduct positioned opposite a deletion site reported in this study is similar to the corresponding structure of the same adduct positioned opposite dC reported previously [Cosman, M., de los Santos, C., Fiala, R., Hingerty, B. E., Luna, E., Harvey, R. G., Geacintov, N. E., Broyde, S., & Patel, D. J. (1993) Biochemistry 32, 4145-4155]. This is not surprising since the dC opposite the lesion site was looped out of the helix and it can be readily replaced by a deletion site through minor changes associated with buckling of the intercalation site. By contrast, the solution structures of the (+)-trans-anti-[BP]dG and (+)-cis-anti-[BP]dG adducts positioned opposite deletion sites in the same sequence context exhibit distinct surface topologies in the grooves of the DNA helix. Thus, even though the benzo[a]pyrene intercalates into the helix opposite the deletion site in both cases, the modified deoxyguanosine is displaced into the major groove for the (+)-trans-anti-[BP]dG adduct while it is displaced into the minor groove for the (+)-cis-anti-[BP]dG stereoisomer. The orientational differences reflect the chiral characteristics of the two [BP]-dG stereoisomeric adducts with the different alignments of the bulky DNA lesion opposite the deletion site likely to influence interactions with the cellular repair machinery.