Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop.

ABSTRACT: A kissing loop is a highly stable complex formed by loop-loop base-pairing between two RNA hairpins. This common structural motif is utilized in a wide variety of RNA-mediated processes, including antisense recognition, substrate recognition in riboswitches, and viral replication. Recent work has shown that the Tar-Tar(*) complex, an archetypal kissing loop, can form without Mg(2+), so long as high concentrations of alkali chloride salts are present. Interestingly, the stability of the complex is found to decrease with increasing cation size. In this work, we used molecular simulations to develop a molecular-level understanding of the origins of the observed counterion specificity. The ionic atmosphere of the Tar-Tar(*) complex was examined in the presence of 800 mm (where m denotes molali

SUBMITTER: Chen AA 

PROVIDER: S-EPMC3057057 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature