Computer simulation of the thermodynamics of the B → Z-DNA transition: effect of the ionic size and charge

Abstract

The B- to Z-DNA transition free energy as a function of the size and charge of added ions is investigated by Monte Carlo simulation for simple grooved B- and Z-DNA models. It is shown that the electrostatic contribution to the free energy depends almost linearly on the logarithm of the salt concentration for all the systems. The effect of increasing the size of the ions is to make the curves steeper, although its influence on the transition midpoint is more complex. Divalent cations markedly reduce both the slope and the transition midpoint with respect to monovalent ions. These conclusions are in agreement with the experimental findings. The effect of increasing the charge of the anions—not yet experimentally studied—is less pronounced.