Strategies for RNA folding

Abstract

RNAs are surprisingly adept at folding into specific shapes capable of ligand recognition and catalysis. Thermodynamic analysis of the unfolding of several different RNAs suggests that there are at least three strategies an RNA might use to achieve a very stable and compactly folded structure: hydrogen bonding between irregular complementary surfaces (as in transfer RNA tertiary structure); monovalent and divalent lons bound to specific sites (as found in a ribosomal RNA fragment) and pseudoknot folds (exemplified by a messenger RNA fragment with extensive non-canonical structure).