RNA remodeling proteins : methods and protocols

著者

書誌事項

RNA remodeling proteins : methods and protocols

edited by Marc Boudvillain

（Methods in molecular biology / John M. Walker, series editor, 2209）（Springer protocols）

Humana Press, c2021 [i.e. 2020]

2nd ed

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注記

"Springer Science+Business Media, LLC, part of Springer Nature 2015"--T.p. verso

Includes bibliographical references and index

内容説明・目次

内容説明

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.

目次

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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