RNA spectroscopy : methods and protocols
Author(s)
Bibliographic Information
RNA spectroscopy : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2113）（Springer protocols）
Humana Press, c2020
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Includes bibliographical references and index
Description and Table of Contents
Description
This volume looks at the different spectroscopic and biophysical methods used by researchers to study the structure and folding of RNA, and to follow their interactions with proteins. The chapters in this book cover topics such as single-molecule spectroscopy of multiple RNA species; surface plasmon resonance, MS or microcalorimetry for investigating molecular interactions with RNA; FTIR, SAXS, SANS and SRCD spectroscopies to analyze RNA structure; use of fluorescent nucleotides to map RNA-binding sites on proteins surfaces or CryoEM; and much more. Written in the highly successful Methods in Molecular Biology series format, 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.
Cutting-edge and comprehensive, RNA Spectroscopy: Methods and Protocols is a valuable resource for anyone interested in learning more about this developing field.
Table of Contents
Preface...Table of Contents...Contributing Authors...
1. Encapsulation of Fluorescently Labelled RNAs into Surface-Tethered Vesicles for Single-Molecule FRET Studies in TIRF MicroscopySusann Zelger-Paulus, Melodie C.A.S. Hadzic, Roland K.O. Sigel, and Richard Boerner
2. Preparation of SNAPf-Beads for Colocalization Single-Molecule Spectroscopy (CoSMoS) of RNA-Protein ComplexesReka A. Haraszti and Joerg E. Braun
3. Comparative Colocalization Single-Molecule Spectroscopy (CoSMoS) with Multiple RNA SpeciesReka A. Haraszti and Joerg E. Braun
4. Dynamic Light Scattering Analysis on RNA Associated to ProteinsSerena Bernacchi
5. Bioinformatic Application of Fluorescence-Based In Vivo RNA Regional Accessibility Data to Identify Novel sRNA TargetsEmily K. Bowman, Mia K. Mihailovic, Bridget Li, and Lydia M. Contreras
6. Surface Plasmon Resonance for Investigating Molecular Interactions with RNACarmelo Di Primo
7. RNA folding and Unfolding Under Force: Single-Molecule Experiments and their AnalysisLaurent Geffroy, Thierry Bizebard, and Ulrich Bockelmann 8. Mapping of Post-Transcriptional tRNA Modifications by Two-Dimensional Gel Electrophoresis Mass SpectrometryLaura Antoine and Philippe Wolff
9. Native Electrospray Ionization Mass Spectrometry of RNA-Ligand ComplexesPhilippe Wolff and Eric Ennifar
10. Application of FTIR Spectroscopy to Analyse RNA StructureFrederic Geinguenaud, Valeria Militello, and Veronique Arluison
11. Application of Synchrotron Radiation Circular Dichroism for RNA Structural AnalysisEtienne Le Brun, Veronique Arluison, and Frank Wien
12. Application of NIR Raman Spectroscopy to Probe the Flexibility of RNA StructureHui Bon Hoa Gaston
13. Small Angle Neutron Scattering of RNA-Protein ComplexesAudrone Lapinaite, Teresa Carlomagno, and Frank Gabel
14. Structural Analysis of RNA by Small-Angle X-Ray ScatteringAnne Theobald-Dietrich, Raphael de Wijn, Kevin Rollet, Alexandra Bluhm, Joelle Rudinger-Thirion, Caroline Paulus, Bernard Lorber, Aurelien Thureau, Magali Frugier, and Claude Sauter
15. Site-Specific Spin-Labeling of RNA for NMR and EPR Structural StudiesBertrand Vileno and Isabelle Lebars
16. Analysis of the HIV-1 Genomic RNA Dimerization Initiation Site Binding to Aminoglycoside Antibiotics using Isothermal TitrationSerena Bernacchi and Eric Ennifar
17. Use of Fluorescent Nucleotides to Map RNA-Binding Sites on Protein SurfaceV. Balobanov, N. Lekontseva, A. Mikhaylina, and A. Nikulin
18. Fluorescent Oligonucleotide Probes for the Quantification of RNA by Real-Time qPCRFlorent Busi
19. Probing RNA-Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical UltracentrifugationSomdeb Mitra and Borries Demeler
20. RNA Nanostructures Molecular ImagingOlivier Pietrement, Veronique Arluison, and Christophe Lavelle
21. Grad-CryoEM: Tool to Isolate Translation Initiation Complexes from Rabbit Reticulocyte Lysate Suitable for Structural StudiesJavier Rol-Moreno, Lauriane Kuhn, Stefano Marzi, and Angelita Simonetti
22. Application of NMR Spectroscopy to Determine Small RNA StructurePengzhi Wu, Xiaodan Liu, Qingguo Gong, Yunyu Shi, and Jihui Wu
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