Measuring the Dimensions of a Compact Kinetic Intermediate in the Folding Pathway of the GlmS Ribozyme

Abstract

Using complementary time-resolved biochemical and x-ray probes of RNA structure in solution, we investigate the cation-induced folding of the glmS ribozyme, a metabolite-sensing RNA switch that regulates gene expression in bacteria. Hydroxyl radical footprinting experiments have shown a concerted folding transition within the first 10 seconds after adding magnesium. From small angle x-ray scattering (SAXS) experiments performed under similar conditions, we find that native tertiary contact formation is preceded by the collapse of the molecule to a relatively compact intermediate. The subsequent compaction observed by SAXS correlates temporally with changes in hydroxyl radical protection. We propose a structural model for the intermediate and possible implications for the role of secondary structure and electrostatics in the folding process of this ribozyme.