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

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 la...

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Bibliographic Details
Published in:	Journal of biomolecular NMR 1998-10, Vol.12 (3), p.423-433
Main Authors:	Kolk, M.H, Wijmenga, S.S, Heus, H.A, Hilbers, C.W
Format:	Article
Language:	eng
Subjects:	genomics Magnetic resonance spectroscopy N.M.R nuclear magnetic resonance spectroscopy Ribonucleic acid RNA RNA viruses Sugar Turnip yellow mosaic virus
Online Access:	Get full text
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Summary:	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 ^sup 13^C/^sup 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.[PUBLICATION ABSTRACT]
ISSN:	0925-2738 1573-5001