This volume provides protocols and procedures for determining and modeling RNA structure. Chapters guide the reader through protocols for RNA secondary structure prediction, single sequence modeling, Crumple, RNAstructure to model conserved secondary structures with multiple homologs, the prediction of bimolecular secondary structures with RNAstructure, STarMir, protocols for structure mapping, mapping data to constrain or restrain RNA secondary structure prediction with RNAstructure, unassigned NMR resonances, modeling protocols for Rosetta FARFAR, RNAComposer , ModeRNA, and MC-Fold. 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.
Authoritative and Practical, RNA Structure Determination: Methods and Protocols aims to ensure successful results in the further study of this vital field.
Table of Contents
Crumple: An Efficient Tool to Explore thoroughly the RNA Folding Landscape.- Secondary Structure Prediction of Single Sequences using RNAstructure.- Prediction of Secondary Structures Conserved in Multiple RNA Sequences.- Predicting RNA-RNA Interactions Using RNAstructure.- A Method to Predict the Structure and Stability of RNA/RNA Complexes.- STarMir Tools for Prediction of microRNA Binding Sites.- Traditional Chemical Mapping of RNA Structure in vitro and in vivo.- High-throughput Nuclease Probing of RNA Structures using FragSeq.- Mapping RNA Structure in vitro with SHAPE Chemistry and Next Generation Sequencing (SHAPE-Seq).- Experiment-assisted Secondary Structure Prediction with RNAstructure.- RNA Secondary Structure Determination by NMR.- Modeling Small Non-canonical RNA Motifs with the Rosetta FARFAR Server.- Automated RNA 3D Structure Prediction with RNAComposer.- RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS.- Exploring Alternative RNA Structure Sets using MC-FLashfold and db2cm.- NMR Methods for Characterization of RNA Secondary Structure.- The Quick and the Dead: A Guide to Fast Phasing of Small Ribozyme and Riboswitch Crystal Structures.