Comparative theoretical study of hydration of B- and Z-DNA double helix

Abstract

To study the hydration effect in B-DNA and Z-DNA, a theoretical study of hydration of B-DNA and Z-DNA has been carried out using empirical potential energy functions. Interaction energy between water and model compounds has been computed by considering the first hydration shell only. The results of this study showed that the number of binding water molecules, was thirty-six and twenty-five B-DNA, and Z-DNA, respectively. Because of the conformational difference between B-DNA and Z-DNA, the number of binding water molecules is very different. The water molecules in first hydration shell of the B-DNA were very well ordered along the phosphate position of backbone. But, the water molecules in first hydration shell of Z-DNA are more disordered than B-DNA because the phosphate backbone follows a zig-zag course. Also, the water molecules near the first hydration shell of Z-DNA are freer than B-DNA because the number of water molecules in first hydration shell of Z-DNA are less than B-DNA. Generally, the hydration disfavors the Z-DNA relative to B-DNA.