RNA Chaperones: Methods and Protocols

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. Front Matter ....Pages i-xi Biochemical Methods for the Study of the FinO Family of Bacterial RNA Chaperones (Hyeong Jin Kim, Steven Chaulk, David Arthur, Ross A. Edwards, J. N. Mark Glover)....Pages 1-18 Quantitative Analysis of RNA Chaperone Activity by Native Gel Electrophoresis and Fluorescence Spectroscopy (Subrata Panja, Ewelina M. Małecka, Andrew Santiago-Frangos, Sarah A. Woodson)....Pages 19-39 Fluorescent Molecular Beacons Mimicking RNA Secondary Structures to Study RNA Chaperone Activity (Pilar Menendez-Gil, Carlos J. Caballero, Cristina Solano, Alejandro Toledo-Arana)....Pages 41-58 Specific Nucleic Acid Chaperone Activity of HIV-1 Nucleocapsid Protein Deduced from Hairpin Unfolding (Micah J. McCauley, Ioulia Rouzina, Mark C. Williams)....Pages 59-88 Real-Time Fluorescence-Based Approaches to Disentangle Mechanisms of a Protein’s RNA Chaperone Activity (Tobias Schmidt, Susann Friedrich, Ralph P. Golbik, Sven-Erik Behrens)....Pages 89-106 Use of tRNA-Mediated Suppression to Assess RNA Chaperone Function (Jennifer Porat, Mark A. Bayfield)....Pages 107-120 Salt-Dependent Modulation of the RNA Chaperone Activity of RNA-Binding Protein La (Gunhild Sommer, Christina Sendlmeier, Tilman Heise)....Pages 121-136 Kinetic and Thermodynamic Analyses of RNA–Protein Interactions (Ryo Amano, Taiichi Sakamoto)....Pages 137-150 Detection of MicroRNAs Released from Argonautes (Kyung-Won Min, J. Grayson Evans, Erick C. Won, Je-Hyun Yoon)....Pages 151-159 Mapping the RNA Chaperone Activity of the T. brucei Editosome Using SHAPE Chemical Probing (W.-Matthias Leeder, H. Ulrich Göringer)....Pages 161-178 RNA Remodeling by RNA Chaperones Monitored by RNA Structure Probing (Susann Friedrich, Tobias Schmidt, Sven-Erik Behrens)....Pages 179-192 In Vivo RNA Chemical Footprinting Analysis in Archaea (Robert Knüppel, Martin Fenk, Michael Jüttner, Sébastien Ferreira-Cerca)....Pages 193-208 RNA Structure Analysis by Chemical Probing with DMS and CMCT (José M. Andrade, Ricardo F. dos Santos, Cecília M. Arraiano)....Pages 209-223 Disordered RNA-Binding Region Prediction with DisoRDPbind (Christopher J. Oldfield, Zhenling Peng, Lukasz Kurgan)....Pages 225-239 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, Antony K. Chen)....Pages 241-252 Site-Specific Dual-Color Labeling of Long RNAs (Meng Zhao, Richard Börner, Roland K. O. Sigel, Eva Freisinger)....Pages 253-270 Single-Molecule FRET Assay for Studying Cotranscriptional RNA Folding (Heesoo Uhm, Sungchul Hohng)....Pages 271-282 Characterizing Complex Nucleic Acid Interactions of LINE1 ORF1p by Single Molecule Force Spectroscopy (M. Nabuan Naufer, Mark C. Williams)....Pages 283-297 Isolation and Analysis of Bacterial Ribosomes Through Sucrose Gradient Ultracentrifugation (Ricardo F. dos Santos, Cecília M. Arraiano, José M. Andrade)....Pages 299-310 Back Matter ....Pages 311-314