RNA Folding, Softcover reprint of the original 1st ed. 2014
Methods and Protocols
Methods in Molecular Biology Series, Vol. 1086

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.

Predicting RNA Structure: Advances and Limitations.- Cis-Acting 5' Hammerhead Optimization for In Vitro Transcription of Highly Structured RNAs.- RNA Structural Analysis by Enzymatic Digestion.- A Mutate-and-Map Protocol for Inferring Base Pairs in Structured RNA.- Mapping RNA StructureIn Vitro Using Nucleobase-Specific Probes.- Massively Parallel RNA Chemical Mapping with a Reduced Bias MAP-Seq Protocol.- Probing RNA Folding by Hydroxyl Radical Footprinting.- Monitoring Global Structural Changes and Specific Metal Binding Sites in RNA by In-Line Probing and Tb(III) Cleavage.- Chemical Probing of RNA in Living Cells.- A Chemogenetic Approach to Study the Structural Basis of Protein-Facilitated RNA Folding.- Applying UV Crosslinking to Study RNA-Protein Interactions in Multicomponent Ribonucleoprotein Complexes.- The Kinetics of Ribozyme Cleavage: A Tool to Analyze RNA Folding as a Function of Catalysis.- RNA Catalytic Activity as a Probe of Chaperone-Mediated RNA Folding.- Evaluation of RNA Chaperone Activity In Vivo and In Vitro Using Misfolded Group I Ribozymes.- RNA Conformational Changes Analyzed by Comparative Gel Electrophoresis.- Detecting RNA Tertiary Folding by Sedimentation Velocity Analytical Ultracentrifugation.- RNA Folding Dynamics Using Laser Assisted Single-Molecule Refolding.- RNA Refolding Studied by Light-Coupled NMR Spectroscopy.- Exploring RNA Oligomerization and Ligand Binding by Fluorescence Correlation Spectroscopy and Small Angle X-Ray Scattering.