title: Pseudoknot preorganization of the preQ1 class I riboswitch.
abstract: To explore folding and ligand recognition of metabolite-responsive RNAs is of major importance to comprehend gene regulation by riboswitches. Here, we demonstrate, using NMR spectroscopy, that the free aptamer of a preQ(1) class I riboswitch preorganizes into a pseudoknot fold in a temperature- and Mg(2+)-dependent manner. The preformed pseudoknot represents a structure that is close to the ligand-bound state and that likely represents the conformation selected by the ligand. Importantly, a defined base pair mutation within the pseudoknot interaction stipulates whether, in the absence of ligand, dimer formation of the aptamer competes with intramolecular pseudoknot formation. This study pinpoints how RNA preorganization is a crucial determinant for the adaptive recognition process of RNA and ligand.
authors: Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Austria.
authors: Tobias
authors: T
authors: Santner
authors: Ulrike
authors: U
authors: Rieder
authors: Christoph
authors: C
authors: Kreutz
authors: Ronald
authors: R
authors: Micura
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020029:Base Pairing; D001483:Base Sequence; D016967:Fusobacterium nucleatum / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008024:Ligands; D008274:Magnesium / Q000378:metabolism*; D009154:Mutation; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D058928:Riboswitch; D013696:Temperature
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D012329:RNA, Bacterial; D058928:Riboswitch; D008274:Magnesium