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On the NMR structure determination of a 44n RNA pseudoknot: Assignment strategies and derivation of torsion angle restraints

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Abstract

The complete T- and pseudoknotted acceptor arm of the tRNA-like structure of turnip yellow mosaic virus (TYMV) genomic RNA has been studied by NMR spectroscopy. Resonance assignment and the gathering of restraints of the 44-mer are impeded by spectral complexity as well as by line broadening. The latter is caused by local dynamical effects in the pseudoknot domain in the molecule. These specific problems could be solved by using different field strengths and selectively 13C/15 labeled samples. Experiments for assigning the sugar spin systems were adjusted to satisfy the requirements of this system. Furthermore, the quality of the structure could be improved by determining the backbone torsion angles β, γ and ε, using new approaches that were tailored for use in large RNA molecules.

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Author notes

  1. Sybren S. Wijmenga

    Present address: Department of Medical Biochemistry and Biophysics, University of Umeå, S901 87, Sweden

Authors and Affiliations

  1. NSR Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, Toernooiveld, 6525 ED, Nijmegen, The Netherlands

    Michaël H. Kolk, Hans A. Heus & Cornelis W. Hilbers

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  1. Michaël H. Kolk
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  2. Sybren S. Wijmenga
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  3. Hans A. Heus
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  4. Cornelis W. Hilbers
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Kolk, M.H., Wijmenga, S.S., Heus, H.A. et al. On the NMR structure determination of a 44n RNA pseudoknot: Assignment strategies and derivation of torsion angle restraints. J Biomol NMR 12, 423–433 (1998). https://doi.org/10.1023/A:1008339405010

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