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Nucleic Acids Research, 1983, Vol. 11, No. 13 4483-4499
© 1983

CHEMISTRY

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

A. Heerschap, C.A.G. Haasnoot and C.W. Hilbers

Department of Biophysical Chemistry, University of Nijmegen Toernooiveld, 6525 ED Nijmegen, The Netherlands

Received May 4, 1983. Accepted June 1, 1983.

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 Formula 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 dependant 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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 Proc. Natl. Acad. Sci. USAHome page
M. W. Friederich, E. Vacano, and P. J. Hagerman
Global flexibility of tertiary structure in RNA: Yeast tRNAPhe as a model system
PNAS, March 31, 1998; 95(7): 3572 - 3577.
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