Beyond Crystallography: Investigating the Conformational Dynamics of the Purine Riboswitch

Riboswitches are structured elements located in the 5'-untranslated regions of numerous bacterial mRNAs that serve to regulate gene expression via their ability to specifically bind metabolites. The purine riboswitch ligand-binding domain has emerged as an important model system for investigating the relationship between RNA structure and function. Directed by NMR and crystallographically generated structures of this RNA, a variety of biophysical and biochemical techniques have been utilized to understand its dynamic nature. In this review, we describe these various approaches and what they reveal about the purine riboswitch. Abbreviations 2AP 2-aminopurine; FRET fluorescence resonance energy transfer; J joining region; L loop; NMIA N-methylisatoic anhydride; SHAPE selective 2'-hydroxyl acylation analyzed by primer extension; smFRET single molecule fluorescence reso- nance energy transfer; TPP thiamine pyrophosphate; UTR untranslated region