title: PELDOR spectroscopy reveals preorganization of the neomycin-responsive riboswitch tertiary structure.
abstract: Pulsed electron double resonance (PELDOR) spectroscopy reveals a prearranged tertiary structure of the 27 nucleotides long engineered neomycin-responsive riboswitch. Measured distances between spin labels at positions U4-U14, U4-U15, U14-U26, and U15-U26 were unchanged upon neomycin binding which implies that the global stem-loop architecture is preserved in the absence and presence of the ligand. On the basis of our results, we infer that low-temperature PELDOR data unambiguously demonstrate the existence of an enthalpically favorable set of RNA conformations ready to bind the ligand without major global rearrangement.
authors.affiliation: Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany.
authors.forename: Ivan
authors.initials: I
authors.lastname: Krstić
authors.forename: Olga
authors.initials: O
authors.lastname: Frolow
authors.forename: Deniz
authors.initials: D
authors.lastname: Sezer
authors.forename: Burkhard
authors.initials: B
authors.lastname: Endeward
authors.forename: Julia E
authors.initials: JE
authors.lastname: Weigand
authors.forename: Beatrix
authors.initials: B
authors.lastname: Suess
authors.forename: Joachim W
authors.initials: JW
authors.lastname: Engels
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Prisner
mesh_terms: D000900:Anti-Bacterial Agents / Q000378:metabolism*; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D009355:Neomycin / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012313:RNA / Q000032:analysis* / Q000378:metabolism; D013113:Spin Labels; D014529:Uridine / Q000032:analysis
chemical_list: D000900:Anti-Bacterial Agents; D013113:Spin Labels; D012313:RNA; D009355:Neomycin; D014529:Uridine