Molecular Dynamics Study of Cobalt(III) Hexammine Counter-Ion Distributions around B-DNA and A-RNA Duplexes

Abstract

Multivalent ions are known to induce strong attractive forces between DNA strands resulting in DNA condensation. At the same time, short double-stranded (ds) RNA helices resist condensation by trivalent Cobalt hexammine (Cohex) in the DNA condensing ionic conditions. To explore the factors that could lead to this difference in condensation, we have carried out a set of explicit solvent molecular dynamics simulations of 25 base pairs canonical B-DNA and A-RNA duplexes under different salt conditions. Several mixtures of monovalent (Na, Cl) and trivalent (Cohex) ions are considered. The results of simulation show that Co-hex ions effectively displace monovalent Na ions from the major groove of dsRNA binding to the RNA phosphate oxygens. The ions are buried within the major groove with a distribution peak at 7.3 Angstrom from the helix axis. their density rapidly decreases and becomes negligible at 11 A from the axis. In contrast to that, the distribution of Cohex around B-DNA is shifted outside the helix with a peak at 13.3 A from the helix axis. The ions prefer to bind to the phosphate groups on the outer surface of B-DNA. The observed difference in Cohex distributions around B-DNA and A-RNA is in agreement with the proposed explanation of the resistance of RNA to condensation due to a difference in Cohex binding to DNA and RNA (L.Li et al., PRL 106, 108101 (2011)).