A thermodynamic framework for the magnesium-dependent folding of RNA

Abstract

The goal of this review is to present a unified picture of the relationship between ion binding and RNA folding based on recent theoretical and computational advances. In particular, we present a model describing how the association of magnesium ions is coupled to the tertiary structure folding of several well-characterized RNA molecules. This model is developed in terms of the nonlinear Poisson–Boltzmann (NLPB) equation, which provides a rigorous electrostatic description of the interaction between Mg 2+ and specific RNA structures. In our description, most of the ions surrounding an RNA behave as a thermally fluctuating ensemble distributed according to a Boltzmann weighted average of the mean electrostatic potential around the RNA. In some cases, however, individual ions near the RNA may shed some of their surrounding waters to optimize their Coulombic interactions with the negatively charged ligands on the RNA. These chelated ions are energetically distinct from the surrounding ensemble and must be treated explicitly. This model is used to explore several different RNA systems that interact differently with Mg 2+ . In each case, the NLPB equation accurately describes the stoichiometric and energetic linkage between Mg 2+ binding and RNA folding without requiring any fitted parameters in the calculation. Based on this model, we present a physical description of how Mg 2+ binds and stabilizes specific RNA structures to promote the folding reaction. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 118–136, 2003