title: Formation of a ligand-assisted complex of two RNA hairpin loops.
abstract: The hairpin structure is one of the most common secondary structures in RNA and holds a central position in the stream of RNA folding from a non-structured RNA to structurally complex and functional ribonucleoproteins. Since the RNA secondary structure is strongly correlated to the function and can be modulated by the binding of small molecules, we have investigated the modulation of RNA folding by a ligand-assisted formation of loop-loop complexes of two RNA hairpin loops. With a ligand (NCT6), designed based on the ligand binding to the G-G mismatches in double-stranded DNA, we successfully demonstrated the formation of both inter- and intra-molecular NCT6-assisted complex of two RNA hairpin loops. NCT6 selectively bound to the two hairpin loops containing (CGG)3 in the loop region. Native polyacrylamide gel electrophoresis analysis of two doubly-labeled RNA hairpin loops clearly showed the formation of intermolecular NCT6-assisted loop-loop complex. Förster resonance energy-transfer studies of RNA constructs containing two hairpin loops, in which each hairpin was labeled with Alexa488 and Cy3 fluorophores, showed the conformational change of the RNA constructs upon binding of NCT6. These experimental data showed that NCT6 simultaneously bound to two hairpin RNAs at the loop region, and can induce the conformational change of the RNA molecule. These data strongly support that NCT6 functions as molecular glue for two hairpin RNAs.
authors.affiliation: Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047 (Japan), Fax: (+81) 6-6879-8459.
authors.forename: Changfeng
authors.initials: C
authors.lastname: Hong
authors.forename: Takahiro
authors.initials: T
authors.lastname: Otabe
authors.forename: Saki
authors.initials: S
authors.lastname: Matsumoto
authors.forename: Chikara
authors.initials: C
authors.lastname: Dohno
authors.forename: Asako
authors.initials: A
authors.lastname: Murata
authors.forename: Masaki
authors.initials: M
authors.lastname: Hagihara
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Nakatani
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D031541:Fluorescence Resonance Energy Transfer; D008024:Ligands; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D012313:RNA / Q000737:chemistry*; D054852:Small Molecule Libraries / Q000737:chemistry* / Q000494:pharmacology*
chemical_list: D008024:Ligands; D054852:Small Molecule Libraries; D012313:RNA
keywords: FRET; RNA; ligands; small molecules