title: Identification of the metal ion binding site on an RNA motif from hammerhead ribozymes using (15)N NMR spectroscopy.
abstract: An RNA oligomer, r(GGACGAGUCC), which mimics the metal ion-binding motif of hammerhead ribozymes, was shown to fold by itself into a conformation possessing a metal ion binding property which is similar to that of the intact ribozyme (Tanaka, et al. J. Am. Chem. Soc. 2000, 122, 11303-11310). To determine the metal ion-binding site of this motif at an atomic level, we synthesized a series of RNA oligomers which were selectively labeled with a (15)N-labeled guanosine at each of the four guanosine residues. The (15)N-chemical shift perturbation with Cd(II) ions by one-dimensional (1D) (15)N NMR spectra showed that the chemical shift of the N7 of the G7 residue, N7/G7, in the metal ion-binding motif was specifically perturbed. This is the first experimental evidence to prove that the N7/G7 binds with a Cd(II) ion.
authors.affiliation: Gene Discovery Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan.
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Tanaka
authors.forename: Chojiro
authors.initials: C
authors.lastname: Kojima
authors.forename: Eugene H
authors.initials: EH
authors.lastname: Morita
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Kasai
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Yamasaki
authors.forename: Akira
authors.initials: A
authors.lastname: Ono
authors.forename: Masatsune
authors.initials: M
authors.lastname: Kainosho
authors.forename: Kazunari
authors.initials: K
authors.lastname: Taira
mesh_terms: D001665:Binding Sites; D002104:Cadmium / Q000737:chemistry* / Q000378:metabolism; D002413:Cations, Divalent; D018716:Molecular Mimicry; D009587:Nitrogen Isotopes; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism
chemical_list: D002413:Cations, Divalent; D009587:Nitrogen Isotopes; D016337:RNA, Catalytic; C427204:hammerhead ribozyme; D002104:Cadmium; D012313:RNA