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

Yoshiyuki Tanaka; Chojiro Kojima; Eugene H. Morita; Yasuhiro Kasai; Kazuhiko Yamasaki; Akira Ono; Masatsune Kainosho; Kazunari Taira

doi:10.1021/ja011520c

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

Yoshiyuki Tanaka, Chojiro Kojima, Eugene H. Morita, Yasuhiro Kasai, Kazuhiko Yamasaki, Akira Ono, Masatsune Kainosho, Kazunari Taira

PHA - Molecular Pharmaceutical Science

Research output: Contribution to journal › Article › peer-review

50 Citations (Scopus)

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 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.

Original language	English
Pages (from-to)	4595-4601
Number of pages	7
Journal	Journal of the American Chemical Society
Volume	124
Issue number	17
DOIs	https://doi.org/10.1021/ja011520c
Publication status	Published - 2002 May 1

ASJC Scopus subject areas

Catalysis
Chemistry(all)
Biochemistry
Colloid and Surface Chemistry

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Identification of the metal ion binding site on an RNA motif from hammerhead ribozymes using ¹⁵N NMR spectroscopy. / Tanaka, Yoshiyuki; Kojima, Chojiro; Morita, Eugene H.; Kasai, Yasuhiro; Yamasaki, Kazuhiko; Ono, Akira; Kainosho, Masatsune; Taira, Kazunari.

In: Journal of the American Chemical Society, Vol. 124, No. 17, 01.05.2002, p. 4595-4601.

Research output: Contribution to journal › Article › peer-review

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title = "Identification of the metal ion binding site on an RNA motif from hammerhead ribozymes using 15N 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 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.",

author = "Yoshiyuki Tanaka and Chojiro Kojima and Morita, {Eugene H.} and Yasuhiro Kasai and Kazuhiko Yamasaki and Akira Ono and Masatsune Kainosho and Kazunari Taira",

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AU - Tanaka, Yoshiyuki

AU - Kojima, Chojiro

AU - Morita, Eugene H.

AU - Kasai, Yasuhiro

AU - Yamasaki, Kazuhiko

AU - Ono, Akira

AU - Kainosho, Masatsune

AU - Taira, Kazunari

PY - 2002/5/1

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N2 - 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.

AB - 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.

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