Computational Exploration of Thermodynamics and Kinetics of Mobile Ions Around RNA Duplex

Abstract

Atomically detailed distributions of ions around an A-form RNA are computed. Different mixtures of monovalent and divalent ions are considered explicitly. Studies of tightly bound and of diffusive (but bound) ions around 25 base pairs RNA are conducted in a explicit solvent. Replica exchange simulations provide detailed equilibrium distributions with moderate computing resources (20 nanoseconds of simulation using 64 replicas). Magnesium ion distributions show significant near-RNA binding while sodium ion distributions are more diffusive. Predicted binding sites of at the RNA surface are in accord with structures from crystallography. Electric field relaxation is investigated. The relaxation due to solution rearrangements relaxes in tens of picoseconds, while the contribution of RNA tumbling continues to a few nanoseconds. Negative mobile ions can be found near the RNA but must be assisted by proximate and mobile cations. At distances larger than 16A from the RNA center, a continuum model of RNA charge density and solution becomes accurate. At shorter distances, the structure of RNA (and ions) has significant impact on the pair correlation functions.