Conformational sampling by riboswitch aptamers

Riboswitches are structured elements found in the 5’-untranslated regions of mRNAs that directly bind a small molecule to regulate gene expression in a cis-fashion. These riboregulatory elements typically consist of two domains: an aptamer domain that binds a cellular metabolite and an expression platform that directs expression of the mRNA. Our laboratory is primarily focused upon understanding the three-dimensional structures of these mRNA elements in complex with their effector ligand and how this binding event leads to regulatory control. We have solved the X-ray crystal structures of the aptamer domains of a number of riboswitches in complex with their cognate ligands, each revealing a complex tertiary architecture that scaffolds the ligand-binding pocket. In each case, the RNA directly or indirectly senses almost all of the functional groups of the ligand, resulting in high binding specificity. Complementing these structures, we have used biochemical methods to probe the nature of the unliganded form of the aptamer domains, illuminating aspects of their ligand-dependent folding. These studies reveal that regulation is achieved through a series of ligand-induced tertiary structural changes in the RNA that serve to stabilize a helix that forms part of a secondary structural switch with the expression platform.