Influence of Na(+) and Mg(2+) ions on RNA structures studied with molecular dynamics simulations

The structure of ribonucleic acid (RNA) polymers is strongly dependent on the presence of, in particular Mg(2+) cations to stabilize structural features. Only in high-resolution X-ray crystallography structures can ions be identified reliably. Here, we perform molecular dynamics simulations of 24 RNA structures with varying ion concentrations. Twelve of the structures were helical and the others complex folded. The aim of the study is to predict ion positions but also to evaluate the impact of different types of ions (Na(+) or Mg(2+)) and the ionic strength on structural stability and variations of RNA. As a general conclusion Mg(2+) is found to conserve the experimental structure better than Na(+) and, where experimental ion positions are available, they can be reproduced with reasonable accuracy. If a large surplus of ions is present the added electrostatic screening makes prediction of binding-sites less reproducible. Distinct differences in ion-binding between helical and complex folded structures are found. The strength of binding (ΔG(‡) for breaking RNA atom-ion interactions) is found to differ between roughly 10 and 26 kJ/mol for the different RNA atoms. Differences in stability between helical and complex folded structures and of the influence of metal ions on either are discussed.