Strategies for understanding RNA recognition by X-ray crystallography and NMR methods.

One class of non-coding RNA molecules, termed riboswitches, are the regulatory elements with ability to control gene expression by sensing different cellular metabolites. Specific recognition of the corresponding ligand induced the conformation rearrangement of riboswitch, and thus turned on/off the down-stream gene expression. In this chapter, we will focus on two principal methods that are currently used to investigate the recognition mechanism of riboswitches, including X-ray crystallography and NMR spectroscopy. First, we present that how to get the diffraction-quality crystals of riboswitches in specific functional states. Then we focus on how to use NMR spectroscopy as a tool to learn the dynamics of riboswitches. Detailed protocols are listed below.