Solution structure of photo-damaged DNA related to mutagenesis

Abstract

The pyrimidine(6-4)pyrimidone photoproduct [(6-4) adduct] is one of the major photoproducts induced by ultraviolet (UV) irradiation of DNA and occurs at TpT sites. The (6-4) adduct is highly mutagenic and leads most often to a 3′ T → C transition with 85% replicating error frequency. In order to determine the origin of the specific 3′ T→C transition of the (6-4) adduct, we have used experimental NMR restraints and molecular dynamics to determine the solution structure of a (6-4)-lesion DNA decamer duplex which contains a mismatched base pair between the 3′ T residue and an opposed G residue. Normal Watson-Crick-type hydrogen bonding is retained at the 5′ T of the lesion site. The $O_2$ carbonyl of the 3′ T residue forms hydrogen bonds with the imino and amino protons of the opposed G residue. This potential hydrogen bonding stabilizes the overall helix and restores the highly distorted conformation of the (6-4) adduct to the typical B-form-like DNA structure. This structural feature can explain the marked preference for the insertion of an A residue opposite the 5′ T, and a G residue opposite the 3′ T of the (6-4) lesion during translesion replication. Thus these insertions yield the predominant 3′ T → C transition. In contrast to the highly mutagenic (6-4) adduct, its Dewar valence isomer (Dewar product) has low mutagenic potential and produces a broad range of mutations. In order to determine the origin of the mutagenic property of the Dewar product, we used experimental nuclear magnetic resonance restraints and molecular dynamics to determine the solution structure of a Dewar-lesion DNA decamer duplex. This DNA decamer duplex (DW/GA duplex) contains a mismatched base pair between the 3′T residue of the Dewar lesion (T6) and an opposed G residue (G15). The 3′ T (T6) of the Dewar lesion formed the stable hydrogen bonds with the opposing G15 residue. However, the helical bending and unwinding angles of the DW/GA duplex were much larger than those of a second du...