title: Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping.
abstract: The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg(2+) that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.
authors.affiliation: Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.
authors.forename: Paul S
authors.initials: PS
authors.lastname: Henke
authors.affiliation: Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.
authors.forename: Chi H
authors.initials: CH
authors.lastname: Mak
mesh_terms: D001665:Binding Sites; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012313:RNA