Identification of the metal ion binding site on an RNA motif from hammerhead ribozymes using ¹⁵N 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 ¹⁵N-labeled guanosine at each of the four guanosine residues. The ¹⁵N-chemical shift perturbation with Cd(II) ions by one-dimensional (1 D) ¹⁵N 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.