Ion atmosphere of three-way junction nucleic acid

The ion atmosphere of three-armed symmetric Y-shaped and asymmetric y-shaped A - RNA junctions in aqueous solution containing multivalent ions is described within the framework of a polyelectrolyte model. The fraction of "screening counterions" per polyion charge that shield the residual unneutralized charges from interacting with one another and the condensed counterions per polyion charge as a function of sodium and magnesium ion concentrations are determined. The predictions for the slope of log(k _o/k _f) as a function of Na ⁺ and Mg ²⁺ concentration, where k _o and k _f are the opening and folding rates of the three-helix junction molecule, respectively, are compared with experimental data (Kim et al. Proc. Nat. Acad. Sci. U.S.A. 2002, 96, 9077-9082).