Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations.

ABSTRACT: The structure of ribonucleic acid (RNA) polymers is strongly dependent on the presence of, in particular Mg2+ 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 Mg2+) and the ionic strength on structural stability and variations of RNA. As a general conclusion Mg2+ is found to conserve the experimental structure better than Na+ and, where experimental ion positions are available, they can be reproduced with reasonable accuracy.

SUBMITTER: Fischer NM 

PROVIDER: S-EPMC6007214 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature