Thermodynamic Studies of the Hybridization Properties of Photolesions in DNA

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Abstract
In order to gain insight into the mechanism of mutations induced by photolesions in DNA, the thermal melting curves of oligonucleotide duplexes containing the (6-4) photoproducts of TT and TC and the Dewar isomer were measured at varying concentrations, and the thermodynamic parameters were determined. The duplexes were designed to be used as models for template-primer systems. In the case of d(CAXYAGCACGAC)·d(GTCGTGCTN), in which XY = T(6-4)T, T(6-4)C, or T(Dewar)T and N = A, G, C, or T, the −ΔG° values were the largest when N = G, and the difference between N = G and N = C or T was 1.1, 0.8, and 0.5 kcal/mol at 25 °C for XY = T(6-4)T, T(6-4)C, and T(Dewar)T, respectively. These results provide evidence of base pair formation between the 3‘-pyrimidone and the opposite guanine, which was proposed previously to explain the T → C transition induced at the 3‘ side of the T(6-4)T photoproduct. This interaction was weakened by isomerization to the Dewar photoproduct, which would explain the lower mutation specificity. For d(CAXYAGCACGAC)·d(GTCGTGCTGN), no obvious differences were observed regarding the base opposite the 5‘-pyrimidine of the photoproducts. In contrast to the tertiary structure, determined by NMR, of a duplex containing T(6-4)T in its center [Kim, J.-K., & Choi, B.-S. (1995) Eur. J. Biochem. 228, 849−854], base pair formation at the 5‘-pyrimidine was not detected for any photoproduct used in this study, even when the base opposite the 3‘-pyrimidone of T(6-4)T was changed to adenine.