Sodium and Magnesium Ion Location at the Backbone and at the Nucleobase of RNA: Ab Initio Molecular Dynamics in Water Solution.

ABSTRACT: The interactions between Na⁺ or Mg²⁺ ions with different parts of single-stranded RNA molecules, namely, the oxygen atoms from the phosphate groups or the guanine base, in water solution have been studied using first-principles molecular dynamics. Sodium ions were found to be much more mobile than Mg²⁺ ions and readily underwent transitions between a state directly bonded to RNA oxygen atoms and a completely solvated state. The inner solvation shell of Na⁺ ions fluctuated stochastically at a femtosecond timescale coordinating on average 5 oxygen atoms for bonded Na⁺ ions and 5.5 oxygen atoms for solvated Na⁺ ions. In contrast, the inner solvation shell of Mg²⁺ ions was stable in both RNA-bonded and completely solv

SUBMITTER: Kolev SK 

PROVIDER: S-EPMC9280761 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature