Identification of the metal ion binding site on an RNA motif from hammerhead ribozymes using (15)N NMR spectroscopy

J Am Chem Soc. 2002 May 1;124(17):4595-601. doi: 10.1021/ja011520c.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Cadmium / chemistry*
  • Cadmium / metabolism
  • Cations, Divalent
  • Molecular Mimicry
  • Nitrogen Isotopes
  • Nuclear Magnetic Resonance, Biomolecular / methods
  • Nucleic Acid Conformation
  • RNA / chemistry*
  • RNA / metabolism
  • RNA, Catalytic / chemistry*
  • RNA, Catalytic / metabolism

Substances

  • Cations, Divalent
  • Nitrogen Isotopes
  • RNA, Catalytic
  • hammerhead ribozyme
  • Cadmium
  • RNA