RNA-protein interaction protocols.

Format:

Book

Contributor:

Lin, Ren-Jang.

Series:

Methods in molecular biology (Clifton, N.J.) ; v. 488.

Methods in molecular biology ; v. 488

Language:

English

Subjects (All):

RNA-protein interactions--Laboratory manuals.

RNA-protein interactions.

RNA-Binding Proteins--analysis.

RNA--chemistry.

Ribonucleoproteins--analysis.

Medical Subjects:

RNA-Binding Proteins--analysis.

RNA--chemistry.

Ribonucleoproteins--analysis.

Genre:

Laboratory manuals.

Physical Description:

xv, 416 pages : illustrations (some color) ; 24 cm.

Edition:

Second edition / edited by Ren-Jang Lin.

Place of Publication:

Totowa, N.J. : Humana ; London : Springer [distributor], 2008.

Summary:

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.

Contents:

1 Isolation of a Sequence-Specific RNA Binding Protein, Polypyrimidine Tract Binding Protein, Using RNA Affinity Chromatography / Shalini Sharma 1

2 An Affinity Oligonucleotide Displacement Strategy to Purify Ribonucleoprotein Complexes Applied to Human Telomerase / Isabel Kurth, Gael Cristofari, Joachim Lingner 9

3 RNA Affinity Tags for the Rapid Purification and Investigation of RNAs and RNA-Protein Complexes / Scott C. Walker, Felicia H. Scott, Chatchawan Srisawat, David R. Engelke 23

4 Assembly and Glycerol Gradient Isolation of Yeast Spliceosomes Containing Transcribed or Synthetic U6 snRNA / Kenneth J. Dery, Shyue-Lee Yean, Ren-Jang Lin 41

5 Purification of Ribonucleoproteins Using Peptide-Elutable Antibodies and Other Affinity Techniques / Scott W. Stevens 65

6 CLIP: Crosslinking and ImmunoPrecipitation of In Vivo RNA Targets of RNA-Binding Proteins / Kirk B. Jensen, Robert B. Darnell 85

7 Quantitative Analysis of Protein-RNA Interactions by Gel Mobility Shift / Sean P. Ryder, Michael I. Recht, James R. Williamson 99

8 Monitoring Assembly of Ribonucleoprotein Complexes by Isothermal Titration Calorimetry / Michael I. Recht, Sean P. Ryder, James R. Williamson 117

9 Characterization of RNA-Protein Interactions by Phosphorothioate Footprinting and Its Applications to the Ribosome / A. Ozlem Tastan Bishop, Ulrich Stelzl, Markus Pech, Knud H. Nierhaus 129

10 In Vivo Analysis of Ribonucleoprotein Complexes Using Nucleotide Analog Interference Mapping / Lara B. Weinstein Szewczak 153

11 T7 RNA Polymerase-Mediated Incorporation of 8-N[subscript 3]AMP Into RNA for Studying Protein-RNA Interactions / Rajesh K. Gaur 167

12 A Simple Crosslinking Method, CLAMP, to Map the Sites of RNA-Contacting Domains Within a Protein / Hiren Banerjee, Ravinder Singh 181

13 Proteins Specifically Modified With a Chemical Nuclease as Probes of RNA-Protein Interaction / Oliver A. Kent, Andrew M. MacMillan 191

14 RNA-Protein Crosslink Mapping Using TEV Protease / Ian A. Turner, Chris M. Norman, Mark J. Churcher, Andrew J. Newman 201

15 Structural Analysis of Protein-RNA Interactions With Mass Spectrometry / Mamuka Kvaratskhelia, Stuart F.J. Le Grice 213

16 Analyzing RNA-Protein Crosslinking Sites in Unlabeled Ribonucleoprotein Complexes by Mass Spectrometry / Henning Urlaub, Eva Kuhn-Holsken, Reinhard Luhrmann 221

17 In Vitro Selection of Random RNA Fragments to Identify Protein-Binding Sites Within Large RNAs / Ulrich Stelzl, Knud H. Nierhaus 247

18 Immunoprecipitation Analysis to Study RNA-Protein Interactions in Xenopus Oocytes / Naoto Mabuchi, Kaoru Masuyama, Mutsuhito Ohno 257

19 Mapping the Regions of RNase P Catalytic RNA That Are Potentially in Close Contact With Its Protein Cofactor / Phong Trang, Fenyong Liu 267

20 Quantification of MicroRNAs, Splicing Isoforms, and Homologous mRNAs With the Invader Assay / Peggy S. Eis, Mariano A. Garcia-Blanco 279

21 Analysis of RNA Structure and RNA-Protein Interactions in Mammalian Cells by Use of Terminal Transferase-Dependent PCR / Hsiu-Hua Chen, Jeanne LeBon, Arthur D. Riggs 319

22 Duplex Unwinding and RNP Remodeling With RNA Helicases / Eckhard Jankowsky, Margaret E. Fairman 343

23 Preparation of Efficient Splicing Extracts From Whole Cells, Nuclei, and Cytoplasmic Fractions / Naoyuki Kataoka, Gideon Dreyfuss 357

24 Designing and Utilization of siRNAs Targeting RNA Binding Proteins / Dong-Ho Kim, Mark Behlke, John J. Rossi 367

25 The Use of Saccharomyces cerevisiae Proteomic Libraries to Identify RNA-Modifying Proteins / Jane E. Jackman, Elizabeth J. Grayhack, Eric M. Phizicky 383.

Notes:

Previous ed.: 1999.

Includes bibliographical references and index.

ISBN:

9781588294197

1588294196

OCLC:

166378576