Time-Resolved SAXS Reconstructions Reveal a Kinetic Intermediate in RNA Folding

Abstract

Using complementary time-resolved biochemical and x-ray probes of RNA structure in solution, we study the cation-induced folding of the glmS ribozyme, a metabolite-sensing RNA switch that regulates gene expression in bacteria. Hydroxyl radical footprinting has shown that tertiary contacts form during a concerted folding step. From small angle x-ray scattering experiments performed at CHESS, we find that tertiary contact formation is preceded by the collapse of the molecule to a relatively compact intermediate state. The transition to a final state consistent with the crystal structure correlates temporally with changes in hydroxyl radical protection. We discuss a method for using ab initio reconstructions to obtain average geometrical parameters for the intermediate state and quantify the spatial extent of the molecule as it folds.