RNA does the folding dance of twist, turn, stack

Abstract

RNA molecules have long been known to adopt unusual conformations. The first crystal structure of an RNA was that of yeast tRNAphe (1, 2), which provided a portent of what was to come. With more structures available now from X-ray crystallography and NMR, that promise has been met beyond expectations. The RNAs that are folded in molecular dynamics simulations by Chen and Garcia (3) are tetraloops (RNA hairpin loops of only four nucleotides) that are among the most unusual small structures known today. Although or because they are unusual with atypical thermal stability, these loops are also ubiquitous in longer RNA strands [rUUCG (4); rGNRA and rCUUG (5)]; they were first identified as the most abundant hairpins in prokaryotic rRNA. The function of these loops varies: the GNRA tetraloops (where N is any base and R is a purine) is often found in RNA:RNA tertiary interactions to anchor a global fold. The UUCG tetraloop is solitary, with no known interactions with RNA or proteins: it is thought to nucleate folding and so direct in vivo RNA folding patterns. These little hairpins have been the objects of considerable in vitro experimental structural characterization by NMR and X-ray crystallography, and are found to consistently form a single unique structure. The rUUCG tetraloop in particular has been subjected to many thermodynamic investigations to measure the sources of its unusual stability (6). The rCUUG hairpin is structurally the most flexible, because it tucks its first U into the minor groove but its second U is relatively unconstrained. Among the three tetraloops, CUUG has a propensity for significant conformational exchange (7). Although the three tetraloops used in the Chen and Garcia (3) computational folding experiments are all unusually stable, they achieve their stability by very different means. Their structural diversity makes them excellent candidates for folding studies, because no one mechanism dominates their ability to adopt their unique structures.