title: Conformational Rearrangements of Individual Nucleotides during RNA-Ligand Binding Are Rate-Differentiated.
abstract: A pronounced rate differentiation has been found for conformational rearrangements of individual nucleobases that occur during ligand recognition of the preQ1 class-I riboswitch aptamer from Thermoanaerobacter tengcongensis. Rate measurements rely on the 2ApFold approach by analyzing the fluorescence response of riboswitch variants, each with a single, strategically positioned 2-aminopurine nucleobase substitution. Observed rate discrimination between the fastest and the slowest conformational adaption is 22-fold, with the largest rate observed for the rearrangement of a nucleoside directly at the binding site and the smallest rate observed for the 3'-unpaired nucleoside that stacks onto the pseudo-knot-closing Watson-Crick base pair. Our findings provide novel insights into how compact, prefolded RNAs that follow the induced-fit recognition mechanism adapt local structural elements in response to ligand binding on a rather broad time scale and how this process culminates in a structural signal that is responsible for efficient downregulation of ribosomal translation.
authors.affiliation: Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck , 6020 Innsbruck, Austria.
authors.forename: Marina
authors.initials: M
authors.lastname: Frener
authors.affiliation: Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck , 6020 Innsbruck, Austria.
authors.forename: Ronald
authors.initials: R
authors.lastname: Micura
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D058928:Riboswitch; D013050:Spectrometry, Fluorescence / Q000379:methods; D046968:Thermoanaerobacter / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D058928:Riboswitch; D012313:RNA