RNA-Protein Interaction Protocols

by Ren-Jang Lin (Editor)

Overview

Due to the vital biological importance of RNA and proteins functioning together within a cell, a prool volume describing experimental procedures to study their interactions should find a home in many laboratories. RNA-Protein Interaction Prools, 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 prools, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls.

Comprehensive and up-to-date, RNA-Protein Interaction Prools, Second Edition is an ideal guide for researchers continuing the study of this all-important biological partnership.

Product Details

ISBN-13:	9781617375552
Publisher:	Springer-Verlag New York, LLC
Publication date:	11/19/2010
Series:	Methods in Molecular Biology , #488
Edition description:	Softcover reprint of hardcover 2nd ed. 2008
Pages:	416
Product dimensions:	6.10(w) x 9.25(h) x 0.04(d)

Table of Contents

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 inClose 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.

Editorial Reviews

From the reviews of the second edition:

"Detailed prools for analysis of specific examples of RNA protein interactions are described. … Anyone studying RNA protein interactions should seriously consider reading this book, not only as a technical reference, but also as a source of ideas. … It’s a book for the lab bench and the PIs office. Highly recommended." (Laurence Tiley, Microbiology Today, February, 2009)

"The second edition of RNA-protein interaction prools is part of the Methods in Molecular Biology series and includes detailed methods covering a wide range of approaches to characterise RNA-protein interactions. … This book … is well written, well indexed and well referenced. Each prool is described in enough detail to be followed by an experienced user. For an RNA-based laboratory this book provides an excellent description of the latest techniques with particular attention given to manipulation of RNPs from in vivo sources." (Matthew Bentham, British Toxicology Society Newsletter, June-August, 2009)

From the Publisher