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Traditional Chemical Mapping of RNA Structure In Vitro and In Vivo

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RNA Structure Determination

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1490))

Abstract

Chemical probing is often used to gain knowledge on the secondary and tertiary structures of RNA molecules either free or engaged in complexes with ligands. The method monitors the reactivity of each nucleotide towards chemicals of various specificities reflecting the hydrogen bonding environment of each nucleotide within the RNA molecule. In addition, information can be obtained on the binding site of a ligand (noncoding RNAs, protein, metabolites), and on RNA conformational changes that accompanied ligand binding or perturbation of the environmental cues. The detection of the modifications can be obtained either by using end-labeled RNA molecules or by primer extension using reverse transcriptase. The goal of this chapter is to provide the reader with an experimental guide to probe the structure of RNA in vitro and in vivo with the most suitable chemical probes.

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Acknowledgments

We thank all members of the team for helpful discussions, and we are grateful to E. Westhof for his constant support. This work was supported by the Centre National de Recherche (CNRS), the Agence Nationale de la Recherche (ANR-09-BLAN-0024-01; ANR-PATHOGENOMICS-ARMSA). D.P. receives support from the CNRS and the Délégation Générale de l’Armement.

Author information

Authors and Affiliations

  1. Architecture et Réactivité de l’ARN, CNRS, IBMC, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France

    Delphine Parmentier, Olivier Fuchsbauer, Pascale Romby & Stefano Marzi

  2. College of Veterinary Medicine, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China

    ZongFu Wu

  3. Biotechnologie et Signalisation Cellulaire, CNRS-INSERM, ESBS, Université de Strasbourg, 300 boulevard Sebastien Brant, Illkirch, 67412, France

    Pierre Fechter

Authors
  1. Pierre Fechter
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  2. Delphine Parmentier
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  3. ZongFu Wu
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  4. Olivier Fuchsbauer
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  5. Pascale Romby
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  6. Stefano Marzi
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Corresponding author

Correspondence to Pascale Romby .

Editor information

Editors and Affiliations

  1. Department of Chemistry and Center for RNA Biology, University of Rochester College of Arts and Sciences, Rochester, New York, USA

    Douglas H. Turner

  2. Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, USA

    David H. Mathews

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Fechter, P., Parmentier, D., Wu, Z., Fuchsbauer, O., Romby, P., Marzi, S. (2016). Traditional Chemical Mapping of RNA Structure In Vitro and In Vivo. In: Turner, D., Mathews, D. (eds) RNA Structure Determination. Methods in Molecular Biology, vol 1490. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6433-8_7

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  • DOI: https://doi.org/10.1007/978-1-4939-6433-8_7

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6431-4

  • Online ISBN: 978-1-4939-6433-8

  • eBook Packages: Springer Protocols

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