Revisiting the Salt-Induced Conformational Change of DNA with 3D-RISM Theory

Abstract

The salt-induced conformational transition of DNA is revisited on the basis of the 3D-RISM theory with the purpose of clarifying its physical origin. To take all the contributions to the stability of the molecule into consideration, we performed the optimization of the free energy of B- and Z-DNA in aqueous solutions. Our results exhibited the transition from the B to Z forms with increasing salt concentrations, which is in qualitative accord with the experiments. The results indicate that the transition is caused by an interplay of essentially two contributions, which determine the stability of the molecules, the electrostatic repulsion among charged phosphate groups, and the negative free energy due to counterion binding to those groups. The result is consistent with one of the two models proposed earlier concerning the physical origin of the salt-induced transition of DNA, which attributes the phenomena to the screening of the electrostatic repulsion among phosphate groups, not to the "economy" of hydration, which has been proposed by Saenger et al.