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Nucleic Acids Res. 1983 July 11; 11(13): 4483–4499.
PMCID: PMC326060

Nuclear magnetic resonance studies on yeast tRNAPhe. II. Assignment of the iminoproton resonances of the anticodon and T stem by means of nuclear Overhauser effect experiments at 500 MHz.


Resonances of the water exchangeable iminoprotons of the T and anticodon stem of yeast tRNAPhe were assigned by means of Nuclear Overhauser Effects (NOE's). Together with our previous assignments of iminoproton resonances from the acceptor and D stem (A. Heerschap, C.A.G. Haasnoot and C.W. Hilbers (1982) Nucleic Acids Res. 10, 6981-7000) the present results constitute a complete assignment of all resonances of iminoprotons involved in the secondary structure of yeast tRNAPhe with a reliability and spectral resolution not reached heretofore. Separate identification of the methylprotons in m5C40 and m5C49 was also possible due to specific NOE patterns in the lowfield part of the spectrum. Our experiments indicate that in solution the psi 39 residue in the anticodon stem is orientated in a syn conformation in contrast to the normally observed anti orientation of the uracil base in AU basepairs. Evidence is presented that in solution the acceptor stem is stacked upon the T stem. Furthermore, it turns out that in a similar way the anticodon stem forms a continuous stack with the D stem, but here the m2(2)G26 residue is located between the latter two stems (as is found in the X-ray crystal structure). The stacking of these stems is not strictly dependent on the presence of magnesium ions. NOE experiments show that these structural features are preserved when proceeding from a buffer with magnesium ions to a buffer without magnesium ions although differences in chemical shifts and NOE intensities indicate changes in the conformation of the tRNA.

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Selected References

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  • Kearns DR, Patel DJ, Shulman RG. High resolution nuclear magnetic resonance studies of hydrogen bonded protons of tRNA in water. Nature. 1971 Jan 29;229(5283):338–339. [PubMed]
  • Johnston PD, Redfield AG. Pulsed FT-NMR double resonance studies of yeast tRNAPhe: specific nuclear Overhauser effects and reinterpretation of low temperature relaxation data. Nucleic Acids Res. 1978 Oct;5(10):3913–3927. [PMC free article] [PubMed]
  • Roy S, Redfield AG. Nuclear Overhauser effect study and assignment of D stem and reverse-Hoogsteen base pair proton resonances in yeast tRNAAsp. Nucleic Acids Res. 1981 Dec 21;9(24):7073–7083. [PMC free article] [PubMed]
  • Hare DR, Reid BR. Direct assignment of the dihydrouridine-helix imino proton resonances in transfer ribonucleic acid nuclear magnetic resonance spectra by means of the nuclear Overhauser effect. Biochemistry. 1982 Apr 13;21(8):1835–1842. [PubMed]
  • Heerschap A, Haasnoot CA, Hilbers CW. Nuclear magnetic resonance studies on yeast tRNAPhe I. Assignment of the iminoproton resonances of the acceptor and D stem by means of Nuclear Overhauser Effect experiments at 500 MHz. Nucleic Acids Res. 1982 Nov 11;10(21):6981–7000. [PMC free article] [PubMed]
  • Hingerty B, Brown RS, Jack A. Further refinement of the structure of yeast tRNAPhe. J Mol Biol. 1978 Sep 25;124(3):523–534. [PubMed]
  • Sussman JL, Holbrook SR, Warrant RW, Church GM, Kim SH. Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. J Mol Biol. 1978 Aug 25;123(4):607–630. [PubMed]
  • Kan LS, Ts'o PO, Sprinzl M, vd Harr F, Cramer F. 1H nuclear magnetic resonance studies of transfer RNA: the methyl and methylene resonances of baker's yeast phenylalanine transfer RNA and its fragments. Biochemistry. 1977 Jul 12;16(14):3143–3154. [PubMed]
  • Davanloo P, Sprinzl M, Cramer F. Proton nuclear magnetic resonance of minor nucleosides in yeast phenylalanine transfer ribonucleic acid. Conformational changes as a consequence of aminoacylation, removal of the Y base, and codon--anticodon interaction. Biochemistry. 1979 Jul 24;18(15):3189–3199. [PubMed]
  • Cornelis AG, Haasnoot JH, den Hartog JF, de Rooij M, van Boom JH, Cornelis A. Local destabilisation of a DNA double helix by a T--T wobble pair. Nature. 1979 Sep 20;281(5728):235–236. [PubMed]
  • Haasnoot CA, den Hartog JH, de Rooij JF, van Boom JH, Altona C. Loopstructures in synthetic oligodeoxynucleotides. Nucleic Acids Res. 1980 Jan 11;8(1):169–181. [PMC free article] [PubMed]
  • Johnston PD, Redfield AG. Nuclear magnetic resonance and nuclear Overhauser effect study of yeast phenylalanine transfer ribonucleic acid imino protons. Biochemistry. 1981 Mar 3;20(5):1147–1156. [PubMed]
  • Hare DR, Reid BR. Nuclear Overhauser assignment of the imino protons of the acceptor helix and the ribothymidine helix in the nuclear magnetic resonance spectrum of Escherichia coli isoleucine transfer ribonucleic acid: evidence for costacked helices in solution. Biochemistry. 1982 Oct 12;21(21):5129–5135. [PubMed]
  • Roy S, Papastavros MZ, Redfield AG. Procedure for C2 deuteration of nucleic acids and determination of A psi 31 pseudouridine conformation by nuclear Overhauser effect in yeast tRNAPhe. Nucleic Acids Res. 1982 Dec 20;10(24):8341–8349. [PMC free article] [PubMed]
  • Hurd RE, Reid BR. NMR spectroscopy of the ring nitrogen protons of uracil and substituted uracils; relevance to A psi base pairing in the solution structure of transfer RNA. Nucleic Acids Res. 1977 Aug;4(8):2747–2755. [PMC free article] [PubMed]
  • Cortese R, Landsberg R, Haar RA, Umbarger HE, Ames BN. Pleiotropy of hisT mutants blocked in pseudouridine synthesis in tRNA: leucine and isoleucine-valine operons. Proc Natl Acad Sci U S A. 1974 May;71(5):1857–1861. [PubMed]
  • Lewis JA, Ames BN. Histidine regulation in Salmonella typhimurium. XI. The percentage of transfer RNA His charged in vivo and its relation to the repression of the histidine operon. J Mol Biol. 1972 Apr 28;66(1):131–142. [PubMed]

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