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RNA Remodeling Proteins

Methods and Protocols

  • Book
  • © 2015

Overview

Editors:
  1. Marc Boudvillain

    1. CNRS Centre de Biophysique Moléculaire, Orléans, France

    View editor publications

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproductible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1259)

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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: 25 Years of DEAD-Box Proteins

    • Patrick Linder, Frances Fuller-Pace
    Pages 17-33

  4. In Vivo Cross-Linking Followed by PolyA Enrichment to Identify Yeast mRNA Binding Proteins

    • Sarah F. Mitchell, Roy Parker
    Pages 35-47

  5. Dynamics of the Spb4 Interactome Monitored by Affinity Purification

    • Juan José García-Gómez, Simon Lebaron, Yves Henry, Jesús de la Cruz
    Pages 49-67

  6. Using EMOTE to Map the Exact 5′-Ends of Processed RNA on a Transcriptome-Wide Scale

    • Peter Redder
    Pages 69-85

  7. Cellular Localization of RNA Degradation and Processing Components in Escherichia coli

    • Véronique Arluison, Aziz Taghbalout
    Pages 87-101

  8. Recombineering Applications for the Mutational Analysis of Bacterial RNA-Binding Proteins and Their Sites of Action

    • Nara Figueroa-Bossi, Lionello Bossi
    Pages 103-116

  9. Determination of RNA Chaperone Activity Using an Escherichia coli Mutant

    • Myung-Hee Kim, Ryozo Imai
    Pages 117-123

  10. Biochemical Characterization of G4 Quadruplex Telomerase RNA Unwinding by the RNA Helicase RHAU

    • Evan P. Booy, Ewan K. S. McRae, Sean A. McKenna
    Pages 125-135

  11. ATPase Site Configuration of the RNA Helicase DbpA Probed by ENDOR Spectroscopy

    • Ilia Kaminker, Daniella Goldfarb
    Pages 137-164

  12. Bioinformatics and Biochemical Methods to Study the Structural and Functional Elements of DEAD-Box RNA Helicases

    • Josette Banroques, N. Kyle Tanner
    Pages 165-181

  13. Measuring Helicase Inhibition of the DEAD-Box Protein Dbp2 by Yra1

    • Wai Kit Ma, Elizabeth J. Tran
    Pages 183-197

  14. A FRET-Based, Continuous Assay for the Helicase Activity of DEAD-Box Proteins

    • Thierry Bizebard, Marc Dreyfus
    Pages 199-209

  15. A Fluorescence-Based Screening Assay for Identification of Hepatitis C Virus NS3 Helicase Inhibitors and Characterization of Their Inhibitory Mechanism

    • Atsushi Furuta, Kazi Abdus Salam, Hidenori Tani, Satoshi Tsuneda, Yuji Sekiguchi, Nobuyoshi Akimitsu et al.
    Pages 211-228

  16. Mechanisms of HCV NS3 Helicase Monitored by Optical Tweezers

    • Wei Cheng
    Pages 229-255

  17. Constructing a Magnetic Tweezers to Monitor RNA Translocation at the Single-Molecule Level

    • Desiree Salas, Veronika Gocheva, Marcelo Nöllmann
    Pages 257-273

  18. Probing RNA Translocases with DNA

    • Kimberly A. Reynolds, Veronica M. Raney, Kevin D. Raney
    Pages 275-291

  19. Monitoring RNA Unwinding by the Transcription Termination Factor Rho from Mycobacterium tuberculosis

    • François D’Heygère, Annie Schwartz, Franck Coste, Bertrand Castaing, Marc Boudvillain
    Pages 293-311

  20. Characterization of the Mechanisms of Transcription Termination by the Helicase Sen1

    • Odil Porrua, Domenico Libri
    Pages 313-331
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Keywords

About this book

This volume provides readers with current methods to study RNA remodeling proteins. The methods, ranging from basic to complex, help the scientific community understand the role and fate of RNA species in cells, and their structures and interactions with other biomolecules. The book begins with two introductory chapters, followed by chapters where readers will find 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 of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, RNA Remodeling Proteins: Methods and Protocols seeks to aid scientists in the further study of this ever evolving field of proteins and mechanisms.

Editors and Affiliations

  • CNRS Centre de Biophysique Moléculaire, Orléans, 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/10.1007/978-1-4939-2214-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2015

  • Hardcover ISBN: 978-1-4939-2213-0Published: 13 January 2015

  • Softcover ISBN: 978-1-4939-4899-4Published: 24 September 2016

  • eBook ISBN: 978-1-4939-2214-7Published: 12 January 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 470

  • Number of Illustrations: 44 b/w illustrations, 40 illustrations in colour

  • Topics: Protein Science, Protein Structure

  • Industry Sectors: Biotechnology, Pharma

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