RNA-Protein Interaction Protocols

Labeling and Purification of RNA Synthesized by In Vitro Transcription, Paul A. Clarke. Joining RNA Molecules with T4 DNA Ligase, Melissa J. Moore. RNA-Protein Crosslinking with Photoreactive Nucleotide Analogs, Michelle M. Hanna, Lori Bentsen, Michael Lucido, and Archana Sapre. The Methylene Blue Mediated Photocrosslinking Method for Dectection of Proteins that Interact with Double-Stranded RNA. Zhi-Ren Liu and Christopher W. J. Smith. Probing RNA-Protein Interactions by Psoralen Photocrosslinking, Zhuying Wang and Tariq M. Rana. Identification and Sequence Analysis of RNA-Protein Contact Sites by N-Terminal Sequencing and MALDI-MS, Bernd Thiede, Henning Urlaub, Helga Neubauer, and Brigitte Wittmann-Liebold. RNA Footprinting and Modification Interference Analysis, Paul A. Clarke. Oligonucleotide-Targeted RNase H Protection Analysis of RNA-Protein Complexes, Arthur Gunzl and Albrecht Bindereif. Nitrocellulose Filter Binding for Determination of Dissociation Constants, Kathleen B. Hall and James K. Kranz. Measuring Equilibrium and Kinetic Constants Using Gel Retardation Assays, David R. Setzer. PACE Analysis of RNA-Peptide Interactions, Christopher D. Cilley and James R. Williamson. Detection of Nucleic Acid Interactions Using Surface Plasmon Resonance, Robert J. Crouch, Makoto Wakasa, and Mitsuru Haruki. An Escherichia coli-Based Genetic Strategy for Characterizing RNA Binding Proteins, Chaitanya Jain. Screening RNA-Binding Libraries Using a Bacterial Transcription Antitermination Assay, Kazuo Harada and Alan D. Frankel. In Vitro Genetic Analysis of RNA-Binding Proteins Using Phage Display, Ite A. Laird-Offringa. In Vitro Selection of Aptamers from RNA Libraries, Daniel J. Kenan and Jack D. Keene. Identification of Specific Protein-RNA Target Sites Using Libraries of Natural Sequences, Lucy G. Andrews and Jack D. Keene. Northwestern Screening of Expression Libraries, Paramjeet S. Bagga and Jeffrey Wilusz. Screening Expression Libraries with Solution-Based Assay, Philippa J. Webster and Paul M. Macdonald. An Immunoprecipitation-RNA: rPCR Method for the In Vivo Isolation of Ribonucleoprotein Complexes, Edward Chu, John C. Schmitz, Jingfang Ju, and Sitki M. Copur. Purification and Depletion of RNP Particles by Antisense Affinity Chromatography, Benjamin J. Blencowe and Angus I. Lamond. Purification of U Small Nuclear Ribonucleoprotein Particles, Berthold Kastner and Reinhard Luhrmann. Preparation of Heterogeneous Nuclear Ribonucleoprotein Complexes, Maurice S. Swanson and Gideon Dreyfuss. Preparation of Hela Cell Nuclear and Cytosolic S100 Extracts for In Vitro Splicing, Akila Mayeda and Adrian R. Krainer. Mammalian In Vitro Splicing Assays, Akila Mayeda and Adrian R. Krainer. Yeast Pre-mRNA Splicing Extracts, Stephanie W. Ruby. Prespliceosome and Spliceosome Isolation and Analysis, Laura A. Lindsey and Mariano A. Garcia-Blanco. A Yeast Spliceosome Assay, Stephanie W. Ruby. Defining Pre-mRNA cis Elements that Regulate Cell-Specific Splicing, Thomas A. Cooper. In Vivo SELEX in Vertebrate Cells, Thomas A. Cooper. Purification of SR Protein Splicing Factors, Alan M. Zahler. Processing mRNA 3' Ends In Vitro, Michael J. Imperiale. Analysis of Poly(A) Tail Lengths by PCR: The PAT Assay, Fernando J. Salles and Sidney Strickland. In Vitro Translation Extracts from Tissue Culture Cells, Kazuko Shiroki and Akio Nomoto. Messenger RNA Turnover in Cell-Free Extracts from Higher Eukaryotes, Jeff Ross