Labeling and Purification of RNA Synthesized by In Vitro Transcription -- Joining RNA Molecules with T4 DNA Ligase -- RNA-Protein Crosslinking with Photoreactive Nucleotide Analogs -- The Methylene Blue Mediated Photocrosslinking Method for Dectection of Proteins that Interact with Double-Stranded RNA -- Probing RNA-Protein Interactions by Psoralen Photocrosslinking -- Identification and Sequence Analysis of RNA-Protein Contact Sites by N-Terminal Sequencing and MALDI-MS -- RNA Footprinting and Modification Interference Analysis -- Oligonucleotide-Targeted RNase H Protection Analysis of RNA-Protein Complexes -- Nitrocellulose Filter Binding for Determination of Dissociation Constants -- Measuring Equilibrium and Kinetic Constants Using Gel Retardation Assays -- PACE Analysis of RNA-Peptide Interactions -- Detection of Nucleic Acid Interactions Using Surface Plasmon Resonance -- An Escherichia coli-Based Genetic Strategy for Characterizing RNA Binding Proteins -- Screening RNA-Binding Libraries Using a Bacterial Transcription Antitermination Assay -- In Vitro Genetic Analysis of RNA-Binding Proteins Using Phage Display -- In Vitro Selection of Aptamers from RNA Libraries -- Identification of Specific Protein-RNA Target Sites Using Libraries of Natural Sequences -- Northwestern Screening of Expression Libraries -- Screening Expression Libraries with Solution-Based Assay -- An Immunoprecipitation-RNA:rPCR Method for the In Vivo Isolation of Ribonucleoprotein Complexes -- Purification and Depletion of RNP Particles by Antisense Affinity Chromatography -- Purification of U Small Nuclear Ribonucleoprotein Particles -- Preparation of Heterogeneous Nuclear Ribonucleoprotein Complexes -- Preparation of Hela Cell Nuclear and Cytosolic S100 Extracts for In Vitro Splicing -- Mammalian In Vitro Splicing Assays -- Yeast Pre-mRNA Splicing Extracts -- Prespliceosome and Spliceosome Isolation and Analysis -- A Yeast Spliceosome Assay -- Defining Pre-mRNA cis Elements that Regulate Cell-Specific Splicing -- In Vivo SELEX in Vertebrate Cells -- Purification of SR Protein Splicing Factors -- Processing mRNA 3' Ends In Vitro -- Analysis of Poly(A) Tail Lengths by PCR: The PAT Assay -- In Vitro Translation Extracts from Tissue Culture Cells -- Messenger RNA Turnover in Cell-Free Extracts from Higher Eukaryotes.

In RNA-Protein Interaction Protocols, highly skilled experimentalists provide a comprehensive series of commonly used, as well as specialized, techniques for analyzing how proteins and RNA interact. Richly detailed and readily reproducible, these methods enable researchers to analyze the structural details of an RNA-protein interaction, to determine in detail what parts of the protein and RNA are in close contact, and to isolate RNP complexes from cells. There are also in vitro and in vivo methods and protocols for assaying the effects of proteins and RNP complexes on mRNA metabolism. The methods assume only a knowledge of basic molecular biology, biochemistry, and cell culture, and can be readily adapted to other systems. Providing an excellent standard resource for today's bench scientists studying many types of RNA-protein interactions, RNA-Protein Interaction Protocols offers a wide-ranging collection of up-to-date experimental methods that distill a great deal of wisdom and experience into productive, reproducible, step-by-step techniques for all investigators in the field.