ENERGETICS OF BASE-PAIR OPENING IN A DNA DODECAMER CONTAINING AN A(3)T(3) TRACT

Nuclear magnetic resonance spectroscopy has been used to characterize the kinetics and energetics of opening of base pairs in the DNA dodeca mer [d(CGCAAATTTGCG)](2). The dodecamer contains an A(3)T(3) tract tha t induces intrinsic curvature of the helix axis. previous studies from this and other laboratories have shown that the kinetics of base pair opening in A(3)T(3) tracts is unique: the opening rates of the A . T base pairs in the interior of the tract are much lower than that of th e A . T base pair at the 5'-end of the tract. In the present work, we have investigated the energetics of the pathways for opening of the A . T base pairs in the A(3)T(3) tract. The energetic parameters of the activated state(s) are obtained from the temperature dependence of the opening rate constants. The lower opening rates for the A . T base pa irs situated in the interior of the tract are shown to originate from higher activation enthalpies which are compensated, in part, by increa ses in the activation entropies. We have also obtained an energetic ch aracterization of the open state(s) of the A . T base pairs in the dod ecamer by measuring the equilibrium constants for base pair opening an d their temperature dependence. The results suggest that the transitio ns from closed to open state(s) in the A . T base pairs of the A(3)T(3 ) tract are energetically similar.