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RNA Helix Stability in Mixed Na⁺/Mg²⁺ Solution

Department of Physics and Astronomy and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211

Correspondence: Address reprint requests to Shi-Jie Chen, Tel.: 573-882-6626; E-mail: chenshi{at}missouri.edu.

A recently developed tightly bound ion model can account for the correlation and fluctuation (i.e., different binding modes) of bound ions. However, the model cannot treat mixed ion solutions, which are physiologically relevant and biologically significant, and the model was based on B-DNA helices and thus cannot directly treat RNA helices. In the present study, we investigate the effects of ion correlation and fluctuation on the thermodynamic stability of finite length RNA helices immersed in a mixed solution of monovalent and divalent ions. Experimental comparisons demonstrate that the model gives improved predictions over the Poisson-Boltzmann theory, which has been found to underestimate the roles of multivalent ions such as Mg²⁺ in stabilizing DNA and RNA helices. The tightly bound ion model makes quantitative predictions on how the Na⁺-Mg²⁺ competition determines helix stability and its helix length-dependence. In addition, the model gives empirical formulas for the thermodynamic parameters as functions of Na⁺/Mg²⁺ concentrations and helix length. Such formulas can be quite useful for practical applications.

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