1. Encapsulation of Fluorescently Labelled RNAs into Surface-Tethered Vesicles for Single-Molecule FRET Studies in TIRF Microscopy
Susann Zelger-Paulus, Mélodie C.A.S. Hadzic, Roland K.O. Sigel, and Richard Börner
2. Preparation of SNAPf-Beads for Colocalization Single-Molecule Spectroscopy (CoSMoS) of RNA-Protein Complexes
Reka A. Haraszti and Joerg E. Braun
3. Comparative Colocalization Single-Molecule Spectroscopy (CoSMoS) with Multiple RNA Species
Reka A. Haraszti and Joerg E. Braun
4. Dynamic Light Scattering Analysis on RNA Associated to Proteins
Serena Bernacchi
5. Bioinformatic Application of Fluorescence-Based In Vivo RNA Regional Accessibility Data to Identify Novel sRNA Targets
Emily K. Bowman, Mia K. Mihailovic, Bridget Li, and Lydia M. Contreras
6. Surface Plasmon Resonance for Investigating Molecular Interactions with RNA
Carmelo Di Primo
7. RNA folding and Unfolding Under Force: Single-Molecule Experiments and their Analysis
Laurent Geffroy, Thierry Bizebard, and Ulrich Bockelmann
8. Mapping of Post-Transcriptional tRNA Modifications by Two-Dimensional Gel Electrophoresis Mass Spectrometry
Laura Antoine and Philippe Wolff
9. Native Electrospray Ionization Mass Spectrometry of RNA-Ligand Complexes
Philippe Wolff and Eric Ennifar
10. Application of FTIR Spectroscopy to Analyse RNA Structure
Fredéric Geinguenaud, Valeria Militello, and Véronique Arluison
11. Application of Synchrotron Radiation Circular Dichroism for RNA Structural Analysis
Etienne Le Brun, Véronique Arluison, and Frank Wien
12. Application of NIR Raman Spectroscopy to Probe the Flexibility of RNA Structure
Hui Bon Hoa Gaston
13. Small Angle Neutron Scattering of RNA-Protein Complexes
Audrone Lapinaite, Teresa Carlomagno, and Frank Gabel
14. Structural Analysis of RNA by Small-Angle X-Ray Scattering
Anne Théobald-Dietrich, Raphaël de Wijn, Kévin Rollet, Alexandra Bluhm, Joëlle Rudinger-Thirion, Caroline Paulus, Bernard Lorber, Aurélien Thureau, Magali Frugier, and Claude Sauter
15. Site-Specific Spin-Labeling of RNA for NMR and EPR Structural Studies
Bertrand Vileno and Isabelle Lebars
16. Analysis of the HIV-1 Genomic RNA Dimerization Initiation Site Binding to Aminoglycoside Antibiotics using Isothermal Titration
Serena Bernacchi and Eric Ennifar
17. Use of Fluorescent Nucleotides to Map RNA-Binding Sites on Protein Surface
V. Balobanov, N. Lekontseva, A. Mikhaylina, and A. Nikulin
18. Fluorescent Oligonucleotide Probes for the Quantification of RNA by Real-Time qPCR
Florent Busi
19. Probing RNA-Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical Ultracentrifugation
Somdeb Mitra and Borries Demeler
20. RNA Nanostructures Molecular Imaging
Olivier Pietrement, Véronique Arluison, and Christophe Lavelle
21. Grad-CryoEM: Tool to Isolate Translation Initiation Complexes from Rabbit Reticulocyte Lysate Suitable for Structural Studies
Javier Rol-Moreno, Lauriane Kuhn, Stefano Marzi, and Angelita Simonetti
22. Application of NMR Spectroscopy to Determine Small RNA Structure
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.