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RNA Spectroscopy

Methods and Protocols

  • Book
  • © 2020

Overview

Editors:
  1. Véronique Arluison

    1. Université de Paris, Paris, France, Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, Gif-sur-Yvette, France

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    You can also search for this editor in PubMed   Google Scholar

  2. Frank Wien

    1. Synchrotron SOLEIL L’Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2113)

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Encapsulation of Fluorescently Labeled 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, Richard Börner
    Pages 1-16

  3. Preparation of SNAPf-Beads for Colocalization Single-Molecule Spectroscopy (CoSMoS) of RNA-Protein Complexes

    • Reka A. Haraszti, Joerg E. Braun
    Pages 17-22

  4. Comparative Colocalization Single-Molecule Spectroscopy (CoSMoS) with Multiple RNA Species

    • Reka A. Haraszti, Joerg E. Braun
    Pages 23-29

  5. Dynamic Light Scattering Analysis on RNA Associated to Proteins

    • Serena Bernacchi
    Pages 31-39

  6. Bioinformatic Application of Fluorescence-Based In Vivo RNA Regional Accessibility Data to Identify Novel sRNA Targets

    • Emily K. Bowman, Mia K. Mihailovic, Bridget Li, Lydia M. Contreras
    Pages 41-71

  7. Surface Plasmon Resonance for Investigating Molecular Interactions with RNA

    • Carmelo Di Primo
    Pages 73-88

  8. RNA Folding and Unfolding Under Force: Single-Molecule Experiments and Their Analysis

    • Laurent Geffroy, Thierry Bizebard, Ulrich Bockelmann
    Pages 89-100

  9. Mapping of Posttranscriptional tRNA Modifications by Two-Dimensional Gel Electrophoresis Mass Spectrometry

    • Laura Antoine, Philippe Wolff
    Pages 101-110

  10. Native Electrospray Ionization Mass Spectrometry of RNA-Ligand Complexes

    • Philippe Wolff, Eric Ennifar
    Pages 111-118

  11. Application of FTIR Spectroscopy to Analyze RNA Structure

    • Frédéric Geinguenaud, Valeria Militello, Véronique Arluison
    Pages 119-133

  12. Application of Synchrotron Radiation Circular Dichroism for RNA Structural Analysis

    • Etienne Le Brun, Véronique Arluison, Frank Wien
    Pages 135-148

  13. Application of NIR Raman Spectroscopy to Probe the Flexibility of RNA Structure

    • Hui Bon Hoa Gaston
    Pages 149-164

  14. Small-Angle Neutron Scattering of RNA–Protein Complexes

    • Audrone Lapinaite, Teresa Carlomagno, Frank Gabel
    Pages 165-188

  15. 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 et al.
    Pages 189-215

  16. Site-Specific Spin Labeling of RNA for NMR and EPR Structural Studies

    • Bertrand Vileno, Isabelle Lebars
    Pages 217-235

  17. Analysis of the HIV-1 Genomic RNA Dimerization Initiation Site Binding to Aminoglycoside Antibiotics Using Isothermal Titration Calorimetry

    • Serena Bernacchi, Eric Ennifar
    Pages 237-250

  18. Use of Fluorescent Nucleotides to Map RNA-Binding Sites on Protein Surface

    • V. Balobanov, N. Lekontseva, A. Mikhaylina, A. Nikulin
    Pages 251-262

  19. Fluorescent Oligonucleotide Probes for the Quantification of RNA by Real-Time qPCR

    • Florent Busi
    Pages 263-280

  20. Probing RNA–Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical Ultracentrifugation

    • Somdeb Mitra, Borries Demeler
    Pages 281-317
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Keywords

About this book

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.



Editors and Affiliations

  • Université de Paris, Paris, France, Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, Gif-sur-Yvette, France

    Véronique Arluison

  • Synchrotron SOLEIL L’Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France

    Frank Wien

Bibliographic Information

  • Book Title: RNA Spectroscopy

  • Book Subtitle: Methods and Protocols

  • Editors: Véronique Arluison, Frank Wien

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0278-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2020

  • Hardcover ISBN: 978-1-0716-0277-5Published: 01 February 2020

  • Softcover ISBN: 978-1-0716-0280-5Published: 01 February 2021

  • eBook ISBN: 978-1-0716-0278-2Published: 31 January 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 356

  • Number of Illustrations: 16 b/w illustrations, 80 illustrations in colour

  • Topics: Human Genetics, Spectroscopy/Spectrometry

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