Main description:

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.

Contents:

1. Predicting RNA Structure: Advances and Limitations

Ivo L. Hofacker and Ronny Lorenz

2. Cis-Acting 5' Hammerhead Optimization for In Vitro Transcription of Highly Structured RNAs

Melanie Meyer and Benoit Masquida

3. RNA Structural Analysis by Enzymatic Digestion

Elisa Biondi and Donald H. Burke

4. A Mutate-and-Map Protocol for Inferring Base Pairs in Structured RNA

Pablo Cordero, Wipapat Kladwang, Christopher C. VanLang, and Rhiju Das

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

Nora Sachsenmaier, Stefan Handl, Franka Debeljak, and Christina Waldsich

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

Matthew Seetin, Wipapat Kladwang, John. P. Bida, and Rhiju Das

7. Probing RNA Folding by Hydroxyl Radical Footprinting

Maria Costa and Dario Monachello

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

Pallavi K. Choudhary, Sofia Gallo, and Roland K.O. Sigel

9. Chemical Probing of RNA in Living Cells

Michael Wildauer, Georgeta Zemora, Andreas Liebeg, Verena Heisig, and Christina Waldsich

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

Olga Fedorova

11. Applying UV Crosslinking to Study RNA-Protein Interactions in Multicomponent Ribonucleoprotein Complexes

Andrey S. Krasilnikov

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

Nora Zingler

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

Brant Gracia and Rick Russell

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

Katharina Semrad

15. RNA Conformational Changes Analyzed by Comparative Gel Electrophoresis

Sebastien H. Eschbach and Daniel A. Lafontaine

16. Detecting RNA Tertiary Folding by Sedimentation Velocity Analytical Ultracentrifugation

Somdeb Mitra

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

Bishnu Paudel and David Rueda

18. RNA Refolding Studied by Light-Coupled NMR Spectroscopy

Harald Schwalbe and Boris Furtig

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

Eileen Magbanua, Petr V. Konarev, Dmitri I. Svergun, and Ulrich Hahn