RNA remodeling proteins : methods and protocols
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Bibliographic Information
RNA remodeling proteins : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2209）（Springer protocols）
Humana Press, c2021 [i.e. 2020]
2nd ed
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"Springer Science+Business Media, LLC, part of Springer Nature 2015"--T.p. verso
Includes bibliographical references and index
Description and Table of Contents
Description
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.
Table of Contents
1. Key Points to Consider when Studying RNA Remodeling by Proteins
W. Luke Ward and Rick Russell
2. Happy Birthday : 30 Years of RNA Helicases
Martina Valentini and Patrick Linder
3. Known Inhibitors of RNA Helicases and their Therapeutic Potential
Yosser Zina Abdelkrim, Josette Banroque, and N. Kyle Tanner
4. Identifying RNA Helicase Inhibitors Using Duplex Unwinding Assays
John C. Marecki, Alicia K. Byrd, and Kevin D. Raney
5. Thermal Shift Assay for Characterizing the Stability of RNA Helicases and their Interaction with Ligands
Emmanuel Saridakis and Franck Coste
6. SRCD and FTIR Spectroscopies to Monitor Protein-induced Nucleic Acid Remodeling
Frank Wien, Frederic Geinguenaud, Wilfried Grange, and Veronique Arluison
7. High throughput Protein-Nucleic Acid Interaction Assay Based on Protein Induced Fluorescence Enhancement
Jaroslav Fulnecek and Karel Riha
8. Probing RNA Helicase Conformational Changes by Single-molecule FRET Microscopy
Linda Krause and Dagmar Klostermeier
9. A Fluorescent Assay to Monitor Ligand-Dependent Closure of the Hexameric Rho Helicase Ring
Michael R. Lawson and James M. Berger
10. A Simple Fluorescence Microplate Assay to Monitor RNA-DNA Hybrid Unwinding by the Bacterial Transcription Termination Factor Rho
Isabelle Simon and Marc Boudvillain
11. Monitoring Enzymatic RNA G-quadruplex Unwinding Activities by Nuclease Sensitivity and Reverse Transcription Stop Assays
Ewan K.S. McRae, Steven J. Dupas, Negar Atefi, and Sean A. McKenna
12. Using Magnetic Tweezers to Unravel the Mechanism of the G-quadruplex Binding and Unwinding Activities of DHX36 Helicase
Huijuan You, Yu Zhou, and Jie Yan
13. 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 and Markus C. Wahl
14. Monitoring Acetylation of the RNA-helicase DDX3X, a Protein Critical for Formation of Stress Granules
Makoto Saito, Vytautas Iestamantavicius, Daniel Hess, and Patrick Matthias
15. In vivo cross-linking Followed by polyA Enrichment to Identify Yeast mRNA Binding Proteins
Sarah F. Mitchell
16. Deciphering the Dynamic Landscape of Transcription-associated mRNP quality Control Components over the Whole Yeast Genome
Kevin Moreau, Aurelia Le Dantec, and A. Rachid Rahmouni
17. Probing the Conformational State of mRNPs using smFISH and SIM
Srivathsan Adivarahan and Daniel Zenklusen
18. Probing Transcriptome-wide RNA Structural Changes Dependent on the DEAD-box Helicase Dbp2
Yu-Hsuan Lai and Elizabeth J. Tran
19. 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, and Fernando Valiente-Echeverria
20. RNAi Screening to Identify Factors that Control Circular RNA Localization
Deirdre C. Tatomer, Dongming Liang, and Jeremy E. Wilusz
21. A Cell-Free System for Investigating Human MARF1 Endonuclease Activity
Hana Fakim and Marc R. Fabian
22. Monitoring eIF4E-dependent Nuclear 3' end mRNA Cleavage
Mildred Delaleau
23. An In Vitro Approach To Study RNase III Activities Of Plant RTL Proteins Cyril Charbonnel, Anne de Bures, and Julio Saez-Vasquez
24. Analysis of Bacillus subtilis Ribonuclease Activity In Vivo
Laetitia Gilet, Olivier Pellegrini, Aude Trinquier, Anastasia Tolcan, Delphine Allouche, Frederique Braun, Sylvain Durand, and Ciaran Condon
25. Assay of Bacillus subtilis Ribonuclease Activity in vitro
Olivier Pellegrini, Laetitia Gilet, Aude Trinquier, Anastasia Tolcan, Delphine Allouche, Sylvain Durand, Frederique Braun, and Ciaran Condon
26. Protein Pulldown Assays to Monitor the Composition of the Bacterial RNA Degradosome
Steven W. Hardwick, Ben F. Luisi, and Marilis V. Marques
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