Stability and Ion Distributions Around Left- and Right-Handed DNA and RNA Duplexes: A Comparative Study

Abstract

The determination of the relative stability of nucleic acids structures is often critical for the understanding of their molecular functions. Theoretically, the relative stability of polynucleotides is determined via free energy or thermal melting simulations. These quantities may, however, be computationally quite intensive and therefore challenging. As an interesting alternative, we explore the use of a non-equilibrium laser melting approach combined with molecular dynamics simulations in order to determine the relative stability of B-DNA and Z-DNA duplexes. Specifically, a fast laser pulse is applied to the d(5’-CGCGCGCGCGCG-3’)2 dodecamer in either form. A laser pulse, whose frequency is tuned to disrupt the Watson-Crick hydrogen bonds, is applied and induces a partial melting of the DNA duplexes. The subsequent structural relaxations and partial refolding is indicative of the greater stability of B-DNA in different aqueous environments. In addition, we have also carried out a detailed investigation of the ion atmosphere around both the B- and Z-DNA/RNA duplexes. This ion atmosphere is an intrinsic part of the structure of the solvated nucleic acids, but is difficult to probe experimentally. The ions investigated include Na+, K+, Mg2+, and Cl- in various concentrations. The simulations results quantitatively describe the characteristics of the ion distributions around the different nucleic acid structures. These, in turn, reflect the effect of the different ion types and the atomistic and structural elements of the nucleic acids, which are described and contrasted.