Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

Phys Rev Lett. 2015 Jun 26;114(25):258105. doi: 10.1103/PhysRevLett.114.258105. Epub 2015 Jun 26.

Abstract

RNA is highly sensitive to the ionic environment and typically requires Mg(2+) to form compact structures. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. We present a model of RNA electrostatics and apply it within coarse-grained molecular dynamics simulation. The model treats Mg(2+) ions explicitly to account for ion-ion correlations neglected by mean-field theories. Since mean-field theories capture KCl well, it is treated implicitly by a generalized Manning counterion condensation model. The model extends Manning condensation to deal with arbitrary RNA conformations, nonlimiting KCl concentrations, and the ion inaccessible volume of RNA. The model is tested against experimental measurements of the excess Mg(2+) associated with the RNA, Γ(2+), because Γ(2+) is directly related to the Mg(2+)-RNA interaction free energy. The excellent agreement with experiment demonstrates that the model captures the ionic dependence of the RNA free energy landscape.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Cations, Monovalent / chemistry
  • Magnesium / chemistry*
  • Models, Chemical*
  • Nucleic Acid Conformation
  • RNA / chemistry*
  • Static Electricity

Substances

  • Cations, Monovalent
  • RNA
  • Magnesium