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Application of NMR Spectroscopy to Determine Small RNA Structure

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RNA Spectroscopy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2113))

Abstract

Nuclear magnetic resonance (NMR) spectroscopy is a key experimental method to investigate the structure and dynamics of RNA. RNA often has only partially ordered structures responsible for its function, which makes it difficult to crystallize. In this chapter, we present the methodologies for RNA structure determination by liquid-state NMR, including the preparation of isotopically labeled RNA by in vitro transcription, NMR resonance assignment strategy, and structure calculation. Selected examples of NMR spectra are given for the first stem-loop of DsrA RNA (23 nt).

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Abbreviations

NMR:

Nuclear magnetic resonance

nt:

Nucleotide

PAGE:

Polyacrylamide gel electrophoresis

SL:

Stem-loop

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Acknowledgments

This work was supported by Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China. We are grateful to Richard A. Lease (The Ohio State University, USA) for critical reading of the manuscript and many fruitful comments.

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Author notes

  1. Pengzhi Wu

    Present address: Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland

Authors and Affiliations

  1. Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, China

    Pengzhi Wu, Xiaodan Liu, Qingguo Gong, Yunyu Shi & Jihui Wu

Authors
  1. Pengzhi Wu
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  2. Xiaodan Liu
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  3. Qingguo Gong
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  4. Yunyu Shi
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  5. Jihui Wu
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Corresponding author

Correspondence to Pengzhi Wu .

Editor information

Editors and Affiliations

  1. Université de Paris, Paris, France, Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, Gif-sur-Yvette, France

    Véronique Arluison

  2. Synchrotron SOLEIL L’Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France

    Frank Wien

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Wu, P., Liu, X., Gong, Q., Shi, Y., Wu, J. (2020). Application of NMR Spectroscopy to Determine Small RNA Structure. In: Arluison, V., Wien, F. (eds) RNA Spectroscopy. Methods in Molecular Biology, vol 2113. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0278-2_22

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  • DOI: https://doi.org/10.1007/978-1-0716-0278-2_22

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0277-5

  • Online ISBN: 978-1-0716-0278-2

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