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Measurement of imino 1H–1H residual dipolar couplings in RNA

Journal of Biomolecular NMR volume 43, pages 121–129 (2009)Cite this article

Abstract

Imino 1H–15N residual dipolar couplings (RDCs) provide additional structural information that complements standard 1H–1H NOEs leading to improvements in both the local and global structure of RNAs. Here, we report measurement of imino 1H–1H RDCs for the Iron Responsive Element (IRE) RNA and native E. coli tRNAVal using a BEST-Jcomp-HMQC2 experiment. 1H–1H RDCs are observed between the imino protons in G–U wobble base pairs and between imino protons on neighboring base pairs in both RNAs. These imino 1H–1H RDCs complement standard 1H–15N RDCs because the 1H–1H vectors generally point along the helical axis, roughly perpendicular to 1H–15N RDCs. The use of longitudinal relaxation enhancement increased the signal-to-noise of the spectra by ~3.5-fold over the standard experiment. The ability to measure imino 1H–1H RDCs offers a new restraint, which can be used in NMR domain orientation and structural studies of RNAs.

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Acknowledgements

We thank Dr. J. Boisbouvier for providing the original pulse sequence and Dr. A. Bax for valuable discussions. This work was supported in part by NIH grant AI33098, and MPL was supported in part by a NIH training grant T32 GM65103. The NMR instrumentation was purchased with partial support from NIH grant RR11969 and NSF grants 9602941 and 0230966.

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  1. Michael P. Latham

    Present address: Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada

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  1. Department of Chemistry and Biochemistry, 215 UCB, University of Colorado, Boulder, CO, 80309-0215, USA

    Michael P. Latham & Arthur Pardi

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  1. Michael P. Latham
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  2. Arthur Pardi
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Correspondence to Arthur Pardi.

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Latham, M.P., Pardi, A. Measurement of imino 1H–1H residual dipolar couplings in RNA. J Biomol NMR 43, 121–129 (2009). https://doi.org/10.1007/s10858-008-9293-8

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  • DOI: https://doi.org/10.1007/s10858-008-9293-8

Keywords

  • Residual dipolar couplings
  • RNA structure
  • Partial alignment
  • tRNA
  • Iron responsive element RNA