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RNA Folding

Methods and Protocols

  • Book
  • © 2014

Overview

Editors:
  1. Christina Waldsich

    1. Dept. of Biochemistry & Cell Biology, University of Vienna Max F. Perutz Laboratories, Vienna, Austria

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  • Includes cutting-edge methods and protocols for the study of RNA folding, which features in vivo techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and vital implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1086)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Predicting RNA Structure: Advances and Limitations

    • Ivo L. Hofacker, Ronny Lorenz
    Pages 1-19

  3. Cis-Acting 5’ Hammerhead Ribozyme Optimization for In Vitro Transcription of Highly Structured RNAs

    • Mélanie Meyer, Benoît Masquida
    Pages 21-40

  4. RNA Structural Analysis by Enzymatic Digestion

    • Elisa Biondi, Donald H. Burke
    Pages 41-52

  5. The Mutate-and-Map Protocol for Inferring Base Pairs in Structured RNA

    • Pablo Cordero, Wipapat Kladwang, Christopher C. VanLang, Rhiju Das
    Pages 53-77

  6. Mapping RNA Structure In Vitro Using Nucleobase-Specific Probes

    • Nora Sachsenmaier, Stefan Handl, Franka Debeljak, Christina Waldsich
    Pages 79-94

  7. Massively Parallel RNA Chemical Mapping with a Reduced Bias MAP-Seq Protocol

    • Matthew G. Seetin, Wipapat Kladwang, John P. Bida, Rhiju Das
    Pages 95-117

  8. Probing RNA Folding by Hydroxyl Radical Footprinting

    • Maria Costa, Dario Monachello
    Pages 119-142

  9. Monitoring Global Structural Changes and Specific Metal-Ion-Binding Sites in RNA by In-line Probing and Tb(III) Cleavage

    • Pallavi K. Choudhary, Sofia Gallo, Roland K. O. Sigel
    Pages 143-158

  10. Chemical Probing of RNA in Living Cells

    • Michael Wildauer, Georgeta Zemora, Andreas Liebeg, Verena Heisig, Christina Waldsich
    Pages 159-176

  11. A Chemogenetic Approach to Study the Structural Basis of Protein-Facilitated RNA Folding

    • Olga Fedorova
    Pages 177-191

  12. Applying UV Crosslinking to Study RNA–Protein Interactions in Multicomponent Ribonucleoprotein Complexes

    • Andrey S. Krasilnikov
    Pages 193-207

  13. The Kinetics of Ribozyme Cleavage: A Tool to Analyze RNA Folding as a Function of Catalysis

    • Nora Zingler
    Pages 209-224

  14. RNA Catalytic Activity as a Probe of Chaperone-Mediated RNA Folding

    • Brant Gracia, Rick Russell
    Pages 225-237

  15. Evaluation of RNA Chaperone Activity In Vivo and In Vitro Using Misfolded Group I Ribozymes

    • Katharina Semrad
    Pages 239-254

  16. RNA Conformational Changes Analyzed by Comparative Gel Electrophoresis

    • Sébastien H. Eschbach, Daniel A. Lafontaine
    Pages 255-264

  17. Detecting RNA Tertiary Folding by Sedimentation Velocity Analytical Ultracentrifugation

    • Somdeb Mitra
    Pages 265-288

  18. RNA Folding Dynamics Using Laser-Assisted Single-Molecule Refolding

    • Bishnu Paudel, David Rueda
    Pages 289-307

  19. RNA Refolding Studied by Light-Coupled NMR Spectroscopy

    • Harald Schwalbe, Boris Fürtig
    Pages 309-319

  20. Exploring RNA Oligomerization and Ligand Binding by Fluorescence Correlation Spectroscopy and Small Angle X-Ray Scattering

    • Eileen Magbanua, Petr V. Konarev, Dmitri I. Svergun, Ulrich Hahn
    Pages 321-334
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Keywords

About this book

Focusing on in vitro and intracellular RNA structure formation, RNA Folding: Methods and Protocols provides a comprehensive collection of experimental protocols which are suitable to dissect RNA folding pathways and to characterize the structure of RNA folding intermediates at nucleotide or even atomic resolution. The presented techniques include powerful tools with a long tradition in RNA research as well as more advanced, novel methods, thus the methods span multiple disciplines, including molecular biology, biochemistry, biophysics, and computational biology.  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.

 

Practical and authoritative, RNA Folding: Methods and Protocols serves as a vital reference for researchers attempting to gain insights into the secrets of this astounding macromolecule.

Editors and Affiliations

  • Dept. of Biochemistry & Cell Biology, University of Vienna Max F. Perutz Laboratories, Vienna, Austria

    Christina Waldsich

Bibliographic Information

  • Book Title: RNA Folding

  • Book Subtitle: Methods and Protocols

  • Editors: Christina Waldsich

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-667-2

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2014

  • Hardcover ISBN: 978-1-62703-666-5Published: 18 October 2013

  • Softcover ISBN: 978-1-4939-6058-3Published: 23 August 2016

  • eBook ISBN: 978-1-62703-667-2Published: 18 October 2013

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 340

  • Number of Illustrations: 18 b/w illustrations, 43 illustrations in colour

  • Topics: Human Genetics, Nucleic Acid Chemistry

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