This project is aimed at the structural and functional characterization of the aptamer domain of metabolite-sensing mRNAs (riboswitches) that modulate levels of gene expression and are also critical determinants of metabolic homeostasis. The aptamer domains exhibit junctional RNA architectures of sufficient complexity to permit formation of allosteric domains capable of ligand-induced structural and functional modulation. These mRNA riboswitches bind their target metabolites with high affinity and can discriminate against closely related analogs. The project has enormous depth to it since the structures have to be determined of the free and bound states and there is no explanation yet of the molecular basis for the superb selectivity associated with the recognition process. Indeed, structural principles related to recognition of the aptamer scaffolds of metabolite-sensing mRNAs could underlie new approaches to drug design and to development of molecular sensors. I propose to use X-ray and NMR to solve the bound and unbound structures of guanine and adenine sensing riboswitches, identify structural features associated with their metabolite-binding pocket and the nature of the conformational transitions on complex formation.
