About this book
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 TM 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.
1. Isolation of a Sequence-Specific RNA Binding Protein, Polypyrimidine Tract Binding Protein using RNA Affinity Chromatography; Shalini Sharma; 2 An Affinity Oligonucleotide Displacement Strategy to Purify Ribonucleoprotein Complexes Applied to Human Telomerase; Isabel Kurth, Gael Cristofari, and Joachim Lingner; 3 RNA Affinity Tags for the Rapid Purification and Investigation of RNAs and RNA-Protein Complexes; Scott C. Walker, Felicia H. Scott, Chatchawan Srisawat, and David R. Engelke; 4 Assembly and Glycerol Gradient Isolation of Yeast Spliceosomes Containing Transcribed or Synthetic U6 SnRNA; Ken Dery, Shyue-Lee Yean, and Ren-Jang Lin; 5 Purification of Ribonucleoproteins Using Peptide-Elutable Antibodies and Other Affinity Techniques; Scott Stevens; 6 CLIP: Cross-Linking and ImmunoPrecipitation of In Vivo RNA Targets of RNA Binding Proteins; Kirk B Jensen and Robert B. Darnell; 7 Quantitative Analysis of Protein-RNA Interactions by Gel Mobility Shift; Sean P. Ryder, Michael I. Recht, and James R. Williamson; 8 Monitoring Assembly of Ribonucleoprotein Complexes by Isothermal Titration Calorimetry; Michael I. Recht, Sean P. Ryder, and James R. Williamson; 9 Characterization of RNA-Protein Interactions by Phosphorothioate Footprinting and Its Applications to the Ribosome; A. Ozlem Tastan Bishop, Ulrich Stelzl, Markus Pech, and Knud H. Nierhaus; 10 In vivo Analysis of Ribonucleoprotein Complexes Using Nucleotide Analog Interference Mapping; Lara Weinstein Szewczak; 11 T7 RNA Polymerase Mediated Incorporation of 8-N3AMP into RNA for Studying Protein-RNA Interactions; Rajesh Gaur; 12 A Simple Crosslinking Method, CLAMP, to Map the Sites of RNA Contacting Domains within A Protein; Hiren Banerjee and Ravinder Singh; 13 Proteins Specifically Modified with a Chemical Nuclease as Probes of RNA-Protein Interaction; Oliver A. Ken and Andrew M. MacMillan; 14 RNA-Protein Crosslink Mapping using TEV Protease; Ian A. Turner, Chris M. Norman, Mark J. Churcher, and Andrew J. Newman; 15 Structural Analysis of Protein-RNA Interactions with Mass Spectrometry; Mamuka Kvaratskhelia and Stuart F.J. Le Grice; 16 Analysing RNA--Protein Cross-Linking Sites in Unlabeled Ribonucleoprotein Complexes by Mass Spectrometry; Henning Urlaub, Eva Kuhn-Holsken, and Reinhard Luhrmann; 17 In Vitro Selection of Random RNA Fragments to Identify Protein Binding Sites within Large RNAs; Ulrich Stelzl and Knud H. Nierhaus; 18 Immunoprecipitation Analysis to Study RNA-Protein Interactions in Xenopus Oocytes; Naoto Mabuchi, Kaoru Masuyama, and Mutsuhito Ohno; 19 Mapping the Regions of Rnase P Catalytic RNA That Are Potentially in Close Contact with Its Protein Cofactor; Phong Trang, and Fenyong Liu; 20 Quantification of MicroRNAs, Splicing Isoforms, and Homologous mRNAs with the Invader Assay; Peggy S. Eis and Mariano Garcia-Blanco; 21 Analysis of RNA Structure and RNA-Protein Interactions in Mammalian Cells by Use of Terminal Transferase-Dependent PCR; Hsiu-Hua Chen, Jeanne LeBon, and Arthur D. Riggs; 22 Duplex Unwinding and RNP Remodeling with RNA Helicases; Eckhard Jankowsky and Margaret E. Fairman; 23 Preparation of Efficient Splicing Extracts from Whole Cells, Nuclei, and Cytoplasmic Fractions; Naoyuki Kataoka and Gideon Dreyfuss; 24 Designing and Utilization of Sirnas Targeting RNA-binding Proteins; Dong-Ho Kim, Mark Behlke, and John J. Rossi; 25 The Use of Saccharomyces cerevisiae Proteomic Libraries to Identify RNA-modifying Proteins; Jane E. Jackman and Eric M. Phizicky