Mg~(2+)-RNA interaction free energies and their relationship to the folding of RNA tertiary structures

摘要

Mg~(2+) ions are very effective at stabilizing tertiary structures in RNAs. In most cases, folding of an RNA is so strongly coupled to its interactions with Mg~(2+) that it is difficult to separate free energies of Mg~(2+)- RNA interactions from the intrinsic free energy of RNA folding. To devise quantitative models accounting for this phenomenon of Mg~(2+)-induced RNA folding, it is necessary to independently determine Mg~(2+)-RNA interaction free energies for folded and unfolded RNA forms. In this work, the energetics of Mg~(2+)-RNA interactions are derived from an assay that measures the effective concentration of Mg~(2+) in the presence of RNA. These measurements are used with other measures of RNA stability to develop an overall picture of the energetics of Mg~(2+)-induced RNA folding. Two different RNAs are discussed, a pseudoknot and an rRNA fragment. Both RNAs interact strongly with Mg~(2+) when partially unfolded, but the two folded RNAs differ dramatically in their inherent stability in the absence of Mg~(2+) and in the free energy of their interactions with Mg~(2+). From these results, it appears that any comprehensive framework for understanding Mg~(2+)-induced stabilization of RNA will have to (ⅰ) take into account the interactions of ions with the partially unfolded RNAs and (ⅱ) identify factors responsible for the widely different strengths with which folded tertiary structures interact with Mg~(2+).