A guide to ions and RNA structure
Abstract
RNA folding into stable tertiary structures is remarkably sensitive to the concentrations and types of cations present; an understanding of the physical basis of ion-RNA interactions is therefore a prerequisite for a quantitative accounting of RNA stability. This article summarizes the energetic factors that must be considered when ions interact with two different RNA environments. “Diffuse ions” accumulate near the RNA because of the RNA electrostatic field and remain largely hydrated. A “chelated” ion directly contacts a specific location on the RNA surface and is held in place by electrostatic forces. Energetic costs of ion chelation include displacement of some of the waters of hydration by the RNA surface and repulsion of diffuse ions. Methods are discussed for computing both the free energy of the set of diffuse ions associated with an RNA and the binding free energies of individual chelated ions. Such calculations quantitatively account for the effects of Mg2+ on RNA stability where experimental data are available. An important conclusion is that diffuse ions are a major factor in the stabilization of RNA tertiary structures.
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Footnotes
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↵1 Wyman and Gill (1990), on page 64 of their classic book, cautioned against the use of a binding polynomial approach to treat salt- or solvent-dependent phenomena. A general discussion of Wyman’s linkage relations and charged molecules is in section II.A of M.T. Record’s comprehensive review of salt effects on biopolymers (Record et al. 1998).
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↵2 The conclusion that tRNA interactions with ions are dominated by the polyelectrolyte character of RNA, rather than by a small number of special binding sites, was clearly stated by M. Guéron and J.L. Leroy more than 20 years ago (Leroy and Guéron 1977; Guéron and Leroy 1982).
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Article and publication are at http://www.rnajournal.org/cgi/doi/10.1261/rna.5205404.
- Copyright 2004 by RNA Society
