Identifying RNA Recombination Events and Non-covalent RNA-RNA Interactions with the Molecular Colony Technique -- RNA-directed Recombination of RNA in Vitro -- RNA-RNA Selex -- Identification of Antisense RNA S0tem-loops that Inhibit RNA-protein Interactions using a Bacterial Reporter System -- Trans-activation of Large Ribozymes -- Native Purification and Labeling of RNA for Single Molecule Fluorescence Studies -- Single Molecule Studies of RNA-RNA Interactions -- Modification Interference Analysis of the Ribosome -- Assessing Intermolecular RNA:RNA Interactions Within a Ribonucleoprotein Complex Using Heavy Metal Cleavage Mapping -- Monitoring RNA-RNA Interactions With Electrophoretic Mobility Shift Assays: Analysis Of Trna Binding To The T Box Riboswitch Antiterminator RNA -- Electrophoretic Mobility Shift Assay of RNA-RNA Complexes -- Structural Studies of a Double-stranded RNA from Trypanosome RNA Editing by Small Angle X-ray Scattering -- Fusion RNAs in Crystallographic Studies of Double-stranded RNA from Trypanosome RNA Editing.

 In this volume expert researchers in the field detail many of the methods which are now commonly used to study RNA. These methods are presented as a guidebook to scientists who are experienced with RNA research and want to brush up on a new technique. 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 key tips on troubleshooting and avoiding known pitfalls. Thorough and intuitive, RNA-RNA Interactions: Methods and Protocols guides scientists investigating biological systems and studying RNA.