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RNA Remodeling Proteins

Methods and Protocols

  • Book
  • © 2021
  • Latest edition

Overview

Editors:
  1. Marc Boudvillain

    1. Centre de Biophysique Moléculaire, CNRS UPR4301, Orleans Cedex 2, France

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2209)

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About this book

This volume provides the most current methods to study RNA remodeling proteins. Chapters detail methods, ranging from basic to complex, procedures to identify RNA remodeling proteins and their cofactors, physiological RNA targets and biological functions, and complex molecular mechanisms of action using purified components. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and cutting-edge, RNA Remodeling Proteins: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

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Table of contents (26 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Key Points to Consider When Studying RNA Remodeling by Proteins

    • W. Luke Ward, Rick Russell
    Pages 1-16

  3. Happy Birthday: 30 Years of RNA Helicases

    • Martina Valentini, Patrick Linder
    Pages 17-34

  4. Known Inhibitors of RNA Helicases and Their Therapeutic Potential

    • Yosser Zina Abdelkrim, Josette Banroques, N. Kyle Tanner
    Pages 35-52

  5. Identifying RNA Helicase Inhibitors Using Duplex Unwinding Assays

    • John C. Marecki, Alicia K. Byrd, Kevin D. Raney
    Pages 53-72

  6. Thermal Shift Assay for Characterizing the Stability of RNA Helicases and Their Interaction with Ligands

    • Emmanuel Saridakis, Franck Coste
    Pages 73-85

  7. SRCD and FTIR Spectroscopies to Monitor Protein-Induced Nucleic Acid Remodeling

    • Frank Wien, Frédéric Geinguenaud, Wilfried Grange, Véronique Arluison
    Pages 87-108

  8. High-Throughput Protein–Nucleic Acid Interaction Assay Based on Protein-Induced Fluorescence Enhancement

    • Jaroslav Fulneček, Karel Říha
    Pages 109-117

  9. Probing RNA Helicase Conformational Changes by Single-Molecule FRET Microscopy

    • Linda Krause, Dagmar Klostermeier
    Pages 119-132

  10. A Fluorescent Assay to Monitor Ligand-Dependent Closure of the Hexameric Rho Helicase Ring

    • Michael R. Lawson, James M. Berger
    Pages 133-142

  11. A Simple Fluorescence Microplate Assay to Monitor RNA-DNA Hybrid Unwinding by the Bacterial Transcription Termination Factor Rho

    • Isabelle Simon, Marc Boudvillain
    Pages 143-161

  12. Monitoring Enzymatic RNA G-Quadruplex Unwinding Activities by Nuclease Sensitivity and Reverse Transcription Stop Assays

    • Ewan K. S. McRae, Steven J. Dupas, Negar Atefi, Sean A. McKenna
    Pages 163-173

  13. Using Magnetic Tweezers to Unravel the Mechanism of the G-quadruplex Binding and Unwinding Activities of DHX36 Helicase

    • Huijuan You, Yu Zhou, Jie Yan
    Pages 175-191

  14. Characterization of the Brr2 RNA Helicase and Its Regulation by Other Spliceosomal Proteins Using Gel-Based U4/U6 Di-snRNA Binding and Unwinding Assays

    • Eva Absmeier, Markus C. Wahl
    Pages 193-215

  15. Monitoring Acetylation of the RNA Helicase DDX3X, a Protein Critical for Formation of Stress Granules

    • Makoto Saito, Vytautas Iestamantavicius, Daniel Hess, Patrick Matthias
    Pages 217-234

  16. In Vivo Cross-Linking Followed by polyA Enrichment to Identify Yeast mRNA Binding Proteins

    • Sarah F. Mitchell
    Pages 235-249

  17. Deciphering the Dynamic Landscape of Transcription-Associated mRNP Quality Control Components Over the Whole Yeast Genome

    • Kévin Moreau, Aurélia Le Dantec, A. Rachid Rahmouni
    Pages 251-265

  18. Probing the Conformational State of mRNPs Using smFISH and SIM

    • Srivathsan Adivarahan, Daniel Zenklusen
    Pages 267-286

  19. Probing Transcriptome-Wide RNA Structural Changes Dependent on the DEAD-box Helicase Dbp2

    • Yu-Hsuan Lai, Elizabeth J. Tran
    Pages 287-305

  20. In Situ Hybridization-Proximity Ligation Assay (ISH-PLA) to Study the Interaction of HIV-1 RNA and Remodeling Proteins

    • Daniela Toro-Ascuy, Aracelly Gaete-Argel, Victoria Rojas-Celis, Fernando Valiente-Echeverria
    Pages 307-319
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Editors and Affiliations

  • Centre de Biophysique Moléculaire, CNRS UPR4301, Orleans Cedex 2, France

    Marc Boudvillain

Bibliographic Information

  • Book Title: RNA Remodeling Proteins

  • Book Subtitle: Methods and Protocols

  • Editors: Marc Boudvillain

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0935-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-0934-7Published: 18 November 2020

  • Softcover ISBN: 978-1-0716-0937-8Published: 18 November 2021

  • eBook ISBN: 978-1-0716-0935-4Published: 17 November 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XIV, 437

  • Number of Illustrations: 20 b/w illustrations, 57 illustrations in colour

  • Topics: Protein Science

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