Thermodynamic and base-pairing studies of matched and mismatched DNA dodecamer duplexes containing cis-syn, (6-4) and Dewar photoproducts of TT

Cis-syn dimers, (6-4) products and their Dewar valence isomers are the major photoproducts of DNA and have different mutagenic properties and rates of repair. To begin to understand the physical basis for these differences, the thermal stability and base pairing properties of the corresponding photoproducts of the TT site in d(GAGTATTATGAG) were investigated. The (6-4) and Dewar products destabilize the duplex form by ∼6 kcal/mol of free energy at 37°C relative to the parent, whereas a cis-syn dimer only destabilizes the duplex form by 1.5 kcal/mol. Duplexes with G opposite the 3′-T of the (6-4) and Dewar products are more stable than those with A by ∼0.4 kcal/mol, whereas the cis-syn dimer prefers A over G by 0.7 kcal/mol. Proton NMR suggests that wobble base pairing takes place between the 3′-T of the cis-syn dimer and an opposed G, whereas there is no evidence of significant H-bonding between these two bases in the (6-4) product. The thermodynamic and H-bonding data for the (6-4) product are consistent with a 4 nt interior loop structure which may facilitate flipping of the photoproduct in and out of the helix.