RNA Remodeling Proteins: Methods and Protocols

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, Frédéric Geinguenaud, Wilfried Grange, and Véronique Arluison

7. High throughput Protein-Nucleic Acid Interaction Assay Based on Protein Induced Fluorescence Enhancement

Jaroslav Fulnecek and Karel Ríha

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

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

Kévin Moreau, Aurélia 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

Hana Fakim and Marc R. Fabian

22. Monitoring eIF4E-dependent Nuclear 3' end mRNA Cleavage

Mildred Delaleau

24. Analysis of Bacillus subtilis Ribonuclease Activity In Vivo

Laetitia Gilet, Olivier Pellegrini, Aude Trinquier, Anastasia Tolcan, Delphine Allouche, Frédérique Braun, Sylvain Durand, and Ciarán Condon

25. Assay of Bacillus subtilis Ribonuclease Activity in vitro

Olivier Pellegrini, Laetitia Gilet, Aude Trinquier, Anastasia Tolcan, Delphine Allouche, Sylvain Durand, Frédérique Braun, and Ciarán Condon

26. Protein Pulldown Assays to Monitor the Composition of the Bacterial RNA Degradosome

Steven W. Hardwick, Ben F. Luisi, and Marilis V. Marques