Assignment of imino proton signals of G-C base pairs and magnesium ion binding: An NMR study of bovine mitochondrial tRNA(Ser)(GCU) lacking the entire D arm

Ikuko Hayashi, Takashi Yokogawa, Gota Kawai, Takuya Ueda, Kazuya Nishikawa, Kimitsuna Watanabe

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

The mammalian mitochondrial tRNA(Ser)(GCU) (mt tRNA(Ser)(GCU)) has a unique structure in that it lacks the whole D arm. To elucidate its higher-order structure, we synthesized unmodified bovine mt tRNA(Ser)(GCU) using T7 RNA polymerase and measured its 1H-NMR spectrum in the imino proton region. Although the imino proton signals heavily overlapped, we succeeded in assigning all the seven imino proton signals of the G-C base pairs by a combination of base replacement and 15N-labeling of the G residues of a whole tRNA molecule or of the 3'-half fragment. The results indicate that the tRNA possesses the secondary structure that has been supposed on the basis of biochemical studies. Analysis of the effect of the magnesium concentration on the G-C pairs suggests that the acceptor and T stems do not form a co-axial helix, and that the core region of the tRNA does not interact with magnesium ions. These features are significantly different from those of canonical tRNAs. Despite this, it is very likely that the tRNA as a whole takes a nearly L-shape tertiary structure.

Original languageEnglish
Pages (from-to)1115-1122
Number of pages8
JournalJournal of biochemistry
Volume121
Issue number6
DOIs
Publication statusPublished - 1997 Jan 1
Externally publishedYes

Fingerprint

Transfer RNA
Base Pairing
Magnesium
Protons
Nuclear magnetic resonance
Ions
RNA, Transfer, Ser
Labeling
seryl-tRNA(GCU)
Molecules

Keywords

  • N-labeling
  • H-NMR
  • Assignment of imino proton signals
  • Magnesium effect
  • Mitochondrial tRNA

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Assignment of imino proton signals of G-C base pairs and magnesium ion binding : An NMR study of bovine mitochondrial tRNA(Ser)(GCU) lacking the entire D arm. / Hayashi, Ikuko; Yokogawa, Takashi; Kawai, Gota; Ueda, Takuya; Nishikawa, Kazuya; Watanabe, Kimitsuna.

In: Journal of biochemistry, Vol. 121, No. 6, 01.01.1997, p. 1115-1122.

Research output: Contribution to journalArticle

Hayashi, Ikuko ; Yokogawa, Takashi ; Kawai, Gota ; Ueda, Takuya ; Nishikawa, Kazuya ; Watanabe, Kimitsuna. / Assignment of imino proton signals of G-C base pairs and magnesium ion binding : An NMR study of bovine mitochondrial tRNA(Ser)(GCU) lacking the entire D arm. In: Journal of biochemistry. 1997 ; Vol. 121, No. 6. pp. 1115-1122.
@article{f2591e6f87854d60a64d2827c315f607,
title = "Assignment of imino proton signals of G-C base pairs and magnesium ion binding: An NMR study of bovine mitochondrial tRNA(Ser)(GCU) lacking the entire D arm",
abstract = "The mammalian mitochondrial tRNA(Ser)(GCU) (mt tRNA(Ser)(GCU)) has a unique structure in that it lacks the whole D arm. To elucidate its higher-order structure, we synthesized unmodified bovine mt tRNA(Ser)(GCU) using T7 RNA polymerase and measured its 1H-NMR spectrum in the imino proton region. Although the imino proton signals heavily overlapped, we succeeded in assigning all the seven imino proton signals of the G-C base pairs by a combination of base replacement and 15N-labeling of the G residues of a whole tRNA molecule or of the 3'-half fragment. The results indicate that the tRNA possesses the secondary structure that has been supposed on the basis of biochemical studies. Analysis of the effect of the magnesium concentration on the G-C pairs suggests that the acceptor and T stems do not form a co-axial helix, and that the core region of the tRNA does not interact with magnesium ions. These features are significantly different from those of canonical tRNAs. Despite this, it is very likely that the tRNA as a whole takes a nearly L-shape tertiary structure.",
keywords = "N-labeling, H-NMR, Assignment of imino proton signals, Magnesium effect, Mitochondrial tRNA",
author = "Ikuko Hayashi and Takashi Yokogawa and Gota Kawai and Takuya Ueda and Kazuya Nishikawa and Kimitsuna Watanabe",
year = "1997",
month = "1",
day = "1",
doi = "10.1093/oxfordjournals.jbchem.a021703",
language = "English",
volume = "121",
pages = "1115--1122",
journal = "Journal of Biochemistry",
issn = "0021-924X",
publisher = "Oxford University Press",
number = "6",

}

TY - JOUR

T1 - Assignment of imino proton signals of G-C base pairs and magnesium ion binding

T2 - An NMR study of bovine mitochondrial tRNA(Ser)(GCU) lacking the entire D arm

AU - Hayashi, Ikuko

AU - Yokogawa, Takashi

AU - Kawai, Gota

AU - Ueda, Takuya

AU - Nishikawa, Kazuya

AU - Watanabe, Kimitsuna

PY - 1997/1/1

Y1 - 1997/1/1

N2 - The mammalian mitochondrial tRNA(Ser)(GCU) (mt tRNA(Ser)(GCU)) has a unique structure in that it lacks the whole D arm. To elucidate its higher-order structure, we synthesized unmodified bovine mt tRNA(Ser)(GCU) using T7 RNA polymerase and measured its 1H-NMR spectrum in the imino proton region. Although the imino proton signals heavily overlapped, we succeeded in assigning all the seven imino proton signals of the G-C base pairs by a combination of base replacement and 15N-labeling of the G residues of a whole tRNA molecule or of the 3'-half fragment. The results indicate that the tRNA possesses the secondary structure that has been supposed on the basis of biochemical studies. Analysis of the effect of the magnesium concentration on the G-C pairs suggests that the acceptor and T stems do not form a co-axial helix, and that the core region of the tRNA does not interact with magnesium ions. These features are significantly different from those of canonical tRNAs. Despite this, it is very likely that the tRNA as a whole takes a nearly L-shape tertiary structure.

AB - The mammalian mitochondrial tRNA(Ser)(GCU) (mt tRNA(Ser)(GCU)) has a unique structure in that it lacks the whole D arm. To elucidate its higher-order structure, we synthesized unmodified bovine mt tRNA(Ser)(GCU) using T7 RNA polymerase and measured its 1H-NMR spectrum in the imino proton region. Although the imino proton signals heavily overlapped, we succeeded in assigning all the seven imino proton signals of the G-C base pairs by a combination of base replacement and 15N-labeling of the G residues of a whole tRNA molecule or of the 3'-half fragment. The results indicate that the tRNA possesses the secondary structure that has been supposed on the basis of biochemical studies. Analysis of the effect of the magnesium concentration on the G-C pairs suggests that the acceptor and T stems do not form a co-axial helix, and that the core region of the tRNA does not interact with magnesium ions. These features are significantly different from those of canonical tRNAs. Despite this, it is very likely that the tRNA as a whole takes a nearly L-shape tertiary structure.

KW - N-labeling

KW - H-NMR

KW - Assignment of imino proton signals

KW - Magnesium effect

KW - Mitochondrial tRNA

UR - http://www.scopus.com/inward/record.url?scp=0030759652&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0030759652&partnerID=8YFLogxK

U2 - 10.1093/oxfordjournals.jbchem.a021703

DO - 10.1093/oxfordjournals.jbchem.a021703

M3 - Article

C2 - 9354385

AN - SCOPUS:0030759652

VL - 121

SP - 1115

EP - 1122

JO - Journal of Biochemistry

JF - Journal of Biochemistry

SN - 0021-924X

IS - 6

ER -