title: Measurement of chemical exchange between RNA conformers by 19F NMR.
abstract: Many noncoding RNA molecules adopt alternative secondary and tertiary conformations that are critical for their roles in gene expression. Although many of these rearrangements are mediated by other biomolecular components, it is important to evaluate the equilibrium relationship of the conformers. To measure the spontaneous interconversion in a bi-stable RNA stem loop sequence into which a single (19)F-uridine label was incorporated, a (19)F-(19)F EXSY experiment was employed. The kinetic exchange rate measured from EXSY experiments for this system was 37.3±2.8s(-1). The advantage of this approach is that exchange kinetics can be monitored in any RNA sequence into which a single (19)F nucleotide is incorporated by commercial synthesis. This method is therefore suitable for application to biologically significant systems in which dynamic conformational rearrangement is important for function and may therefore facilitate studies of RNA structure-function relationships.
authors.affiliation: Department of Chemistry and Biochemistry, Hunter College of The City University of New York, New York, NY, United States.
authors.forename: Caijie
authors.initials: C
authors.lastname: Zhao
authors.affiliation: Department of Chemistry and Biochemistry, Hunter College of The City University of New York, New York, NY, United States.
authors.forename: Matthew
authors.initials: M
authors.lastname: Devany
authors.affiliation: Department of Chemistry and Biochemistry, Hunter College of The City University of New York, New York, NY, United States. Electronic address: nancy.greenbaum@hunter.cuny.edu.
authors.forename: Nancy L
authors.initials: NL
authors.lastname: Greenbaum
mesh_terms: D001483:Base Sequence; D005461:Fluorine / Q000032:analysis* / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D021281:Quantitative Structure-Activity Relationship; D012313:RNA / Q000032:analysis* / Q000737:chemistry*
chemical_list: D005461:Fluorine; D012313:RNA
keywords: (19)F NMR; Conformational exchange; EXSY; RNA