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Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping.

Authors :
Henke, Paul S.
Mak, Chi H.
Source :
Journal of Chemical Physics; 8/14/2014, Vol. 141 Issue 6, p1-11, 11p, 1 Color Photograph, 4 Diagrams, 7 Graphs
Publication Year :
2014

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<superscript>2+</superscript> 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 counterionmediated free energy conclusively directs folding into a compact structure. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
00219606
Volume :
141
Issue :
6
Database :
Complementary Index
Journal :
Journal of Chemical Physics
Publication Type :
Academic Journal
Accession number :
97525156
Full Text :
https://doi.org/10.1063/1.4892059