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RNA remodeling proteins : methods and protocols / edited by Marc Boudvillain -- Second edition -- New York : Humana Press, 2021. – (58.17/M592/v.2209) |
Contents
Preface
Contributors
1 Key Points to Consider When Studying RNA Remodeling by Proteins
2 Happy Birthday: 30 Years of RNA Helicases
3 Known Inhibitors of RNA Helicases and Their Therapeutic Potential
4 Identifying RNA Helicase Inhibitors Using Duplex Unwinding Assays
5 Thermal Shift Assay for Characterizing the Stability of RNA Helicases and Their Interaction with Ligands
6 SRCD and FTIR Spectroscopies to Monitor Protein-Induced Nucleic Acid Remodeling
7 High-Throughput Protein-Nucleic Acid Interaction Assay Based on Protein-Induced Fluorescence Enhancement
8 Probing RNA Helicase Conformational Changes by Single-Molecule FRET Microscopy
9 A Fluorescent Assay to Monitor Ligand-Dependent Closure of the Hexameric Rho Helicase Ring
10 A Simple Fluorescence Microplate Assay to Monitor RNA-DNA Hybrid Unwinding by the Bacterial Transcription Termination Factor Rho
11 Monitoring Enzymatic RNA G-Quadruplex Unwinding Activities by Nuclease Sensitivity and Reverse Transcription Stop Assays
12 Using Magnetic Tweezers to Unravel the Mechanism of the G-quadruplex Binding and Unwinding Activities of DHX36 Helicase
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
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
16 Deciphering the Dynamic Landscape of Transcription-Associated mRNP Quality Control Components Over the Whole Yeast Genome
17 Probing the Conformational State of mRNPs Using smFISH and SIM
18 Probing Transcriptome-Wide RNA Structural Changes Dependent on the DEAD-box Helicase Dbp2
19 In Situ Hybridization-Proximity Ligation Assay (ISH-PLA) to Study the Interaction of HIV-1 RNA and Remodeling Proteins
20 RNAi Screening to Identify Factors That Control Circular RNA Localization
21 A Cell-Free System for Investigating Human MARF1 Endonuclease Activity
22 Monitoring eIF4E-Dependent Nuclear 3' End mRNA Cleavage
23 An In Vitro Approach To Study RNase III Activities of Plant RTL Proteins
24 Analysis of Bacillus subtilis Ribonuclease Activity In Vivo
25 Assay of Bacillus subtilis Ribonuclease Activity In Vitro
26 Protein Pulldown Assays to Monitor the Composition of the Bacterial RNA Degradosome
Index
