RNA-protein interaction protocols

Title:

Series:

Methods in molecular biology ; v. 488

Edition:

2nd ed.

Publication Information:

Totowa, NJ : Humana Press, 2008

Physical Description:

xv, 416 p. : ill. ; 24 cm.

ISBN:

9781588294197

Subject Term:

RNA-protein interactions -- Laboratory manuals

Added Author:

Lin, Ren-Jang

Available:*

Library	Item Barcode	Call Number	Material Type	Item Category 1	Status
Searching... PSZ JB	30000010193461	QP623.8.P75 R63 2008	Open Access Book	Book	Searching... Unknown

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.

Shalini SharmaIsabel Kurth and Gael Cristofari and Joachim LingnerScott C. Walker and Felicia H. Scott and Chatchawan Srisawat and David R. EngelkeKenneth J. Dery and Shyue-Lee Yean and Ren-Jang LinScott W. StevensKirk B. Jensen and Robert B. DarnellSean P. Ryder and Michael I. Recht and James R. WilliamsonMichael I. Recht and Sean P. Ryder and James R. WilliamsonA. Ozlem Tastan Bishop and Ulrich Stelzl and Markus Pech and Knud H. NierhausLara B. Weinstein SzewczakRajesh K. GaurHiren Banerjee and Ravinder SinghOliver A. Kent and Andrew M. MacMillanIan A. Turner and Chris M. Norman and Mark J. Churcher and Andrew J. NewmanMamuka Kvaratskhelia and Stuart F.J. Le GriceHenning Urlaub and Eva Kuhn-Holsken and Reinhard LuhrmannUlrich Stelzl and Knud H. NierhausNaoto Mabuchi and Kaoru Masuyama and Mutsuhito OhnoPhong Trang and Fenyong LiuPeggy S. Eis and Mariano A. Garcia-BlancoHsiu-Hua Chen and Jeanne LeBon and Arthur D. RiggsEckhard Jankowsky and Margaret E. FairmanNaoyuki Kataoka and Gideon DreyfussDong-Ho Kim and Mark Behlke and John J. RossiJane E. Jackman and Elizabeth J. Grayhack and Eric M. Phizicky

Preface	p. v
Contributors	p. xiii
1 Isolation of a Sequence-Specific RNA Binding Protein, Polypyrimidine Tract Binding Protein, Using RNA Affinity Chromatography	p. 1
2 An Affinity Oligonucleotide Displacement Strategy to Purify Ribonucleoprotein Complexes Applied to Human Telomerase	p. 9
3 RNA Affinity Tags for the Rapid Purification and Investigation of RNAs and RNA-Protein Complexes	p. 23
4 Assembly and Glycerol Gradient Isolation of Yeast Spliceosomes Containing Transcribed or Synthetic U6 snRNA	p. 41
5 Purification of Ribonucleoproteins Using Peptide-Elutable Antibodies and Other Affinity Techniques	p. 65
6 CLIP: Crosslinking and ImmunoPrecipitation of In Vivo RNA Targets of RNA-Binding Proteins	p. 85
7 Quantitative Analysis of Protein-RNA Interactions by Gel Mobility Shift	p. 99
8 Monitoring Assembly of Ribonucleoprotein Complexes by Isothermal Titration Calorimetry	p. 117
9 Characterization of RNA-Protein Interactions by Phosphorothioate Footprinting and Its Applications to the Ribosome	p. 129
10 In Vivo Analysis of Ribonucleoprotein Complexes Using Nucleotide Analog Interference Mapping	p. 153
11 T7 RNA Polymerase-Mediated Incorporation of 8-N[subscript 3]AMP Into RNA for Studying Protein-RNA Interactions	p. 167
12 A Simple Crosslinking Method, CLAMP, to Map the Sites of RNA-Contacting Domains Within a Protein	p. 181
13 Proteins Specifically Modified With a Chemical Nuclease as Probes of RNA-Protein Interaction	p. 191
14 RNA-Protein Crosslink Mapping Using TEV Protease	p. 201
15 Structural Analysis of Protein-RNA Interactions With Mass Spectrometry	p. 213
16 Analyzing RNA-Protein Crosslinking Sites in Unlabeled Ribonucleoprotein Complexes by Mass Spectrometry	p. 221
17 In Vitro Selection of Random RNA Fragments to Identify Protein-Binding Sites Within Large RNAs	p. 247
18 Immunoprecipitation Analysis to Study RNA-Protein Interactions in Xenopus Oocytes	p. 257
19 Mapping the Regions of RNase P Catalytic RNA That Are Potentially in Close Contact With Its Protein Cofactor	p. 267
20 Quantification of MicroRNAs, Splicing Isoforms, and Homologous mRNAs With the Invader Assay	p. 279
21 Analysis of RNA Structure and RNA-Protein Interactions in Mammalian Cells by Use of Terminal Transferase-Dependent PCR	p. 319
22 Duplex Unwinding and RNP Remodeling With RNA Helicases	p. 343
23 Preparation of Efficient Splicing Extracts From Whole Cells, Nuclei, and Cytoplasmic Fractions	p. 357
24 Designing and Utilization of siRNAs Targeting RNA Binding Proteins	p. 367
25 The Use of Saccharomyces cerevisiae Proteomic Libraries to Identify RNA-Modifying Proteins	p. 383
Index	p. 395

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