INFLUENCE OF ALPHA-DEOXYADENOSINE ON THE STABILITY AND STRUCTURE OF DNA - THERMODYNAMIC AND MOLECULAR MECHANICS STUDIES

The a anomer of deoxyadenosine (a) and an abasic site (tetrahydrofuran , F), which are DNA lesions produced by free radicals, were site-speci fically incorporated in 9-mer duplexes d(TGAGXGTAC). d-(GTACNCTCA), wh ere X = alpha or F and N = A, G, C, or T. Their influence on thermodyn amic stability and structure of DNA was assessed by UV-melting measure ments and molecular mechanics calculations. UV-melting studies reveale d that a duplex containing an alpha T pair was as stable as the parent al duplex containing an alpha T pair at the same site. Furthermore, th e stability of duplexes containing alpha varied depending on the base opposite this lesion, with the T-m decreasing in the following order: alpha T > alpha C approximate to alpha A > alpha G. On the contrary, a n abasic site introduced in the same site showed a significantly great er destabilizing effect than alpha, but variation of T-m with the base s opposite F was less evident. To delineate the molecular mechanism of the thermodynamic effects of an alpha lesion, molecular mechanics cal culations were performed for the same duplexes as used for UV-melting measurements. The results suggest that the structural perturbation int roduced into DNA by an alpha N pair is alpha G > alpha A > alpha C > a lpha T, showing a parallel correlation with the destabilizing effects of alpha N pairs. On the basis of these results, it is discussed how t he perturbations introduced by these DNA lesions may influence the sel ection of nucleotides opposite the lesions by DNA polymerases and the interaction with DNA repair enzymes such as Escherichia coli endonucle ase IV and exonuclease III.