title: Ligand-dependent folding of the three-way junction in the purine riboswitch.
abstract: Riboswitches are highly structured cis-acting elements located in the 5'-untranslated region of messenger RNAs that directly bind small molecule metabolites to regulate gene expression. Structural and biochemical studies have revealed riboswitches experience significant ligand-dependent conformational changes that are coupled to regulation. To monitor the coupling of ligand binding and RNA folding within the aptamer domain of the purine riboswitch, we have chemically probed the RNA with N-methylisatoic anhydride (NMIA) over a broad temperature range. Analysis of the temperature-dependent reactivity of the RNA in the presence and absence of hypoxanthine reveals that a limited set of nucleotides within the binding pocket change their conformation in response to ligand binding. Our data demonstrate that a distal loop-loop interaction serves to restrict the conformational freedom of a significant portion of the three-way junction, thereby promoting ligand binding under physiological conditions.
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, Colorado 80309, USA.
authors.forename: Colby D
authors.initials: CD
authors.lastname: Stoddard
authors.forename: Sunny D
authors.initials: SD
authors.lastname: Gilbert
authors.forename: Robert T
authors.initials: RT
authors.lastname: Batey
mesh_terms: D020121:5' Untranslated Regions; D000812:Anhydrides; D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D005786:Gene Expression Regulation; D008024:Ligands; D008954:Models, Biological; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011687:Purines / Q000737:chemistry; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013696:Temperature; D013816:Thermodynamics; D062367:ortho-Aminobenzoates
chemical_list: D020121:5' Untranslated Regions; D000812:Anhydrides; D052157:Aptamers, Nucleotide; D008024:Ligands; D011687:Purines; D012329:RNA, Bacterial; D012333:RNA, Messenger; D062367:ortho-Aminobenzoates; C077537:N-methylisatoic anhydride