Energetics of superhelicity and of B-Z transitions in superhelical DNA

The linking difference, alpha, imposed upon a superhelically constrained DNA molecule must be partitioned between twisting and bending deformations. Transitions to alternative secondary structures can occur at susceptible sites, altering the local molecular twist by an amount delta Twtrans. That part of the linking difference not accommodated in this way, the residual linking difference alpha res, must be manifested as smooth torsional and flexural deformations of secondary structure. The competition among the alternative ways of accommodating the imposed linking difference alpha determines a stressed equilibrium state. The superhelical free energy, G(alpha), is the excess free energy of the equilibrium state at linking difference alpha above that of the relaxed state under identical conditions. In this paper a method is described by which the free energies associated both to linking, G(alpha), and to residual linking differences can be determined from data on superhelical conformational transitions. The application of this approach to previously published experimental data on the B-Z transition suggests that the free energy associated with alpha res is about 30% larger at substantial superhelicities than it is near the relaxed state. At the onset of transition the functional form of G(alpha) is shown to change in a manner dependent upon the length of the Z-susceptible site.