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RNA Secondary Structure Modeling Following the IPANEMAP Workflow

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RNA Folding

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2726))

Abstract

The structure of RNA molecules and their complexes are crucial for understanding biology at the molecular level. Resolving these structures holds the key to understanding their manifold structure-mediated functions ranging from regulating gene expression to catalyzing biochemical processes. Predicting RNA secondary structure is a prerequisite and a key step to accurately model their three dimensional structure. Although dedicated modelling software are making fast and significant progresses, predicting an accurate secondary structure from the sequence remains a challenge. Their performance can be significantly improved by the incorporation of experimental RNA structure probing data. Many different chemical and enzymatic probes have been developed; however, only one set of quantitative data can be incorporated as constraints for computer-assisted modelling. IPANEMAP is a recent workflow based on RNAfold that can take into account several quantitative or qualitative data sets to model RNA secondary structure. This chapter details the methods for popular chemical probing (DMS, CMCT, SHAPE-CE, and SHAPE-Map) and the subsequent analysis and structure prediction using IPANEMAP.

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Acknowledgments

Research in B.S laboratory is funded by the CNRS, the Université Paris Cité, a grant from “la Fondation pour la Recherche Médicale” (FRM DBI20141423337), ANR INSANNE (ANR 21-CE45-0034-03), ANR PARNASSUS (ANR 19-CE45-0023-02), and ANR DECRYPTED (ANR 19-CE30-0021-03), awarded to BS and YP laboratories. AS and DA were recipient of a PhD fellowship from FRM (FRM DBI20141423337); GdB was recipient of a fellowship from the French Ministry for Education and Research (MESR); PH was recipient of a fellowship from ANR PRE-RIBO60S (ANR 20-CE12-0026-02).

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Authors and Affiliations

  1. CiTCOM, Cibles Thérapeutiques et conception de médicaments, UMR8038 CNRS, Université de PARIS, Paris, France

    Delphine Allouche, Grégoire De Bisschop, Pierre Hardouin, Francois-Xavier Lyonnet du Moutier & Sargueil Bruno

  2. Sanofi mRNA center of excellence 1541, Marcy-l’Etoile, France

    Delphine Allouche

  3. Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada

    Grégoire De Bisschop

  4. Georgia Institute of Technology, School of Mathematics, Atlanta, GA, USA

    Afaf Saaidi

  5. CNRS UMR 7161, LIX, Ecole Polytechnique, Palaiseau, France

    Yann Ponty

Authors
  1. Delphine Allouche
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  2. Grégoire De Bisschop
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  3. Afaf Saaidi
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  4. Pierre Hardouin
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  5. Francois-Xavier Lyonnet du Moutier
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  6. Yann Ponty
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  7. Sargueil Bruno
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Corresponding authors

Correspondence to Yann Ponty or Sargueil Bruno .

Editor information

Editors and Affiliations

  1. Institute for Theoretical Chemistry, University of Vienna, Wien, Wien, Austria

    Ronny Lorenz

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© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Allouche, D. et al. (2024). RNA Secondary Structure Modeling Following the IPANEMAP Workflow. In: Lorenz, R. (eds) RNA Folding. Methods in Molecular Biology, vol 2726. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3519-3_4

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  • DOI: https://doi.org/10.1007/978-1-0716-3519-3_4

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3518-6

  • Online ISBN: 978-1-0716-3519-3

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