Identification of the metal ion binding site on an RNA motif from hammerhead ribozymes using (15)N NMR spectroscopy.
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.
Tanaka
Yoshiyuki
Y
Gene Discovery Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan.
Kojima
Chojiro
C
Morita
Eugene H
EH
Kasai
Yasuhiro
Y
Yamasaki
Kazuhiko
K
Ono
Akira
A
Kainosho
Masatsune
M
Taira
Kazunari
K
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
D002413:Cations, Divalent; D009587:Nitrogen Isotopes; D016337:RNA, Catalytic; C427204:hammerhead ribozyme; D002104:Cadmium; D012313:RNA