The linkage between magnesium binding and RNA folding

Understanding the linkage between Mg2+ binding and RNA folding requires a proper theoretical model describing the energetics of Mg2+ binding to the folded and unfolded states of RNA. Our current understanding of Mg2+ binding to these different RNA states derives from empirical thermodynamic models that depend on a number of unjustified assumptions. We present a rigorous theoretical model describing the linkage between RNA folding and magnesium ion binding. In this model, based on the non-linear Poisson-Boltzmann (NLPB) equation, the stabilization of RNA by Mg2+ arises from two distinct binding modes, diffuse binding and site binding. Diffusely bound Mg2+ are described as an ensemble of hydrated ions that are attracted to the negative charge of the RNA. Site-bound Mg2+ are partially desolvated ions that are attracted to electronegative pockets on the RNA surface. We explore two systems, yeast tRNA(Phe) and a 58-nucleotide rRNA fragment, with different Mg2+ binding properties. The NLPB equation accurately describes both the stoichiometric and energetic linkage between imaging for both of these systems without requiring any fitted parameters in the calculation. Moreover, the NLPB model presents a well-defined physical description of how Mg2+ binding helps fold an RNA. For both of the molecules studied here, the relevant unfolded state is a disordered intermediate state (1) that contains stable helical secondary structure without any tertiary contacts. Diffusely bound Mg2+ interact with these secondary structure elements to stabilize the I state. The secondary structural elements of the I state fold into a compact, native tertiary structure (the N state). Diffuse binding plays a dominant role in stabilizing the N state for both RNAs studied. However, for the rRNA fragment, site-binding to a location with extraordinarily high electrostatic potential is also coupled to folding. Our results suggest that much experimental data measuring the linkage between Mg2+ binding and RNA folding must be reinterpreted. (C) 2002 Elsevier Science Ltd.