Isolation of a Sequence-Specific RNA Binding Protein, Polypyrimidine Tract Binding Protein, Using RNA Affinity Chromatography -- An Affinity Oligonucleotide Displacement Strategy to Purify Ribonucleoprotein Complexes Applied to Human Telomerase -- RNA Affinity Tags for the Rapid Purification and Investigation of RNAs and RNA-Protein Complexes -- Assembly and Glycerol Gradient Isolation of Yeast Spliceosomes Containing Transcribed or Synthetic U6 snRNA -- Purification of Ribonucleoproteins Using Peptide-Elutable Antibodies and Other Affinity Techniques -- CLIP: Crosslinking and ImmunoPrecipitation of In Vivo RNA Targets of RNA-Binding Proteins -- Quantitative Analysis of Protein-RNA Interactions by Gel Mobility Shift -- Monitoring Assembly of Ribonucleoprotein Complexes by Isothermal Titration Calorimetry -- Characterization of RNA-Protein Interactions by Phosphorothioate Footprinting and Its Applications to the Ribosome -- In Vivo Analysis of Ribonucleoprotein Complexes Using Nucleotide Analog Interference Mapping -- T7 RNA Polymerase-Mediated Incorporation of 8-N3AMP Into RNA for Studying Protein-RNA Interactions -- A Simple Crosslinking Method, CLAMP, to Map the Sites of RNA-Contacting Domains Within a Protein -- Proteins Specifically Modified With a Chemical Nuclease as Probes of RNA-Protein Interaction -- RNA-Protein Crosslink Mapping Using TEV Protease -- Structural Analysis of Protein-RNA Interactions With Mass Spectrometry -- Analyzing RNA-Protein Crosslinking Sites in Unlabeled Ribonucleoprotein Complexes by Mass Spectrometry -- In Vitro Selection of Random RNA Fragments to Identify Protein-Binding Sites Within Large RNAs -- Immunoprecipitation Analysis to Study RNA-Protein Interactions in Xenopus Oocytes -- Mapping the Regions of RNase P Catalytic RNA That Are Potentially in Close Contact With Its Protein Cofactor -- Quantification of MicroRNAs, Splicing Isoforms, and Homologous mRNAs With the Invader Assay -- Analysis of RNA Structure and RNA-Protein Interactions in Mammalian Cells by Use of Terminal Transferase-Dependent PCR -- Duplex Unwinding and RNP Remodeling With RNA Helicases -- Preparation of Efficient Splicing Extracts From Whole Cells, Nuclei, and Cytoplasmic Fractions -- Designing and Utilization of siRNAs Targeting RNA Binding Proteins -- The use of Saccharomyces cerevisiae proteomic libraries to identify RNA-modifying proteins.

Due to the vital biological importance of RNA and proteins functioning together within a cell, a protocol volume describing experimental procedures to study their interactions should find a home in many laboratories. RNA-Protein Interaction Protocols, Second Edition updates, complements, and expands upon the popular first edition by providing a collection of cutting-edge techniques developed or refined in the past few years along with tried-and-true methods. The expert contributors explore the isolation and characterization of RNA-protein complexes, the analysis and measurement of RNA-protein interaction, and related novel techniques and strategies. Written in the highly successful Methods in Molecular Biology™ series format, the chapters include brief introductions to the material, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls. Comprehensive and up-to-date, RNA-Protein Interaction Protocols, Second Edition is an ideal guide for researchers continuing the study of this all-important biological partnership.