Nucleotide selectivity opposite a benzo[a]pyrene-derived N²-dG adduct in a Y-family DNA polymerase: A 5′-slippage mechanism

The Y-family DNA polymerase Dpo4, from the archaeon bacterium Sulfolobus solfataricus, is a member of the DinB family, which also contains human Pol κ. It has a spacious active site that can accommodate two templating bases simultaneously, with one of them skipped by the incoming dNTP. Assays of single dNTP insertion opposite a benzo[a]pyrene-derived N²-dG adduct, 10S(+)-trans-anti-[BP]-N²-dG ([BP]G*), reveal that an incoming dATP is significantly preferred over the other three dNTPs in the TG₁ *G₂ sequence context. Molecular modeling and dynamics simulations were carried out to interpret this experimental observation on a molecular level. Modeling studies suggest that the significant preference for dATP insertion observed experimentally can result from two possible dATP incorporation modes. The dATP can be inserted opposite the T on the 5′ side of the adduct G₁*, using an unusual 5′-slippage pattern, in which the unadducted G₂, rather than G ₁*, is skipped, to produce a -1 deletion. In addition, the dATP can be misincorporated opposite the adduct. The 5′-slippage pattern may be generally facilitated in cases where the base 3′ to the lesion is the same as the adducted base.