Main description:

This book provides a wide spectrum of methods to study RNA chaperones in vitro, at the single molecule level, and protocols useful for cell-based assays. Beginning with a section on a number of bacterial proteins for study, the volume also explores proteins from eukaryotic cells and how to delve into the complex interactions between RNA chaperones and the folding and unfolding of proteins. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, RNA Chaperones: Methods and Protocols serves as an ideal guide for scientists and students interested in RNA biology and RNA chaperones.

Chapter 3 is available Open Access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Contents:

1. Biochemical Methods for the Study of the FinO Family of Bacterial RNA Chaperones

Hyeong Jin Kim, Steven Chaulk, David Arthur, Ross A. Edwards, and J.N. Mark Glover

2. Quantitative Analysis of RNA Chaperone Activity by Native Gel Electrophoresis and Fluorescence Spectroscopy

Subrata Panja, Ewelina M. Malecka, Andrew Santiago-Frangos, and Sarah A. Woodson

3. Fluorescent Molecular Beacons Mimicking RNA Secondary Structures to Study RNA Chaperone Activity

Pilar Menendez-Gil, Carlos J. Caballero, Cristina Solano, and Alejandro Toledo-Arana

4. Specific Nucleic Acid Chaperone Activity of HIV-1 Nucleocapsid Protein Deduced from Hairpin Unfolding

Micah J. McCauley, Ioulia Rouzina, and Mark C. Williams

5. Real-Time Fluorescence-Based Approaches to Disentangle Mechanisms of a Protein's RNA Chaperone Activity

Tobias Schmidt, Susann Friedrich, Ralph P. Golbik, and Sven-Erik Behrens

6. Use of tRNA-Mediated Suppression to Assess RNA Chaperone Function

Jennifer Porat and Mark A. Bayfield

7. Salt-Dependent Modulation of the RNA Chaperone Activity of RNA-Binding Protein La

Gunhild Sommer, Christina Sendlmeier, and Tilman Heise

8. Kinetic and Thermodynamic Analyses of RNA-Protein Interactions

Ryo Amano and Taiichi Sakamoto

9. Detection of MicroRNAs Released from Argonautes

Kyung-Won Min, J. Grayson Evans, Erick C. Won, and Je-Hyun Yoon

10. Mapping the RNA Chaperone Activity of the T. brucei Editosome Using SHAPE-Chemical Probing

W.-Matthias Leeder and H. Ulrich Goeringer

11. RNA Remodeling by RNA Chaperones Monitored by RNA Structure Probing

Susann Friedrich, Tobias Schmidt, and Sven-Erik Behrens

12. In Vivo RNA Chemical Footprinting Analysis in Archaea

Robert Knuppel, Martin Fenk, Michael Juttner, and Sebastien Ferreira-Cerca

13. RNA Structure Analysis by Chemical Probing with DMS and CMCT

Jose M. Andrade, Ricardo F. dos Santos, and Cecilia M. Arraiano

14. Disordered RNA Binding Region Prediction with DisoRDPbind

Christopher J. Oldfield, Zhenling Peng, and Lukasz Kurgan

15. Delivering Molecular Beacons via an Electroporation-Based Approach Enables Live-Cell Imaging of Single RNA Transcripts and Genomic Loci

Shiqi Mao, Yachen Ying, Xiaotian Wu, and Antony K. Chen

16. Site-Specific Dual-Color Labeling of Long RNAs

Meng Zhao, Richard Boerner, Roland K.O. Sigel, and Eva Freisinger

17. Single-Molecule FRET Assay for Studying Cotranscriptional RNA Folding

Heesoo Uhm and Sungchul Hohng

18. Characterizing Complex Nucleic Acid Interactions of LINE1 ORF1p by Single Molecule Force Spectroscopy

M. Nabuan Naufer and Mark C. Williams

19. Isolation and Analysis of Bacterial Ribosomes through Sucrose Gradient Ultracentrifugation

Ricardo F. dos Santos, Cecilia M. Arraiano, and Jose M. Andrade