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RNA-protein interaction protocols / edited by Ren-Jang Lin. — 2nd ed. — Totowa, N.J. : Humana Press ; London : Springer [distributor], 2008. – (58.17/M592/v.488) |
Contents
Contents
Preface
Contributors
1. Isolation of a Sequence-Specific RNA Binding Protein， Polypyrimidine Tract Binding Protein， Using RNA Affinity Chromatography
2. An Affinity Oligonucleotide Displacement Strategy to Purify Ribonucleoprotein Complexes Applied to Human Telomerase
3. RNA Affinity Tags for the Rapid Purification and Investigation of RNAs and RNA-Protein Complexes
4. Assembly and Glycerol Gradient Isolation of Yeast Spliceosomes Containing Transcribed or Synthetic U6 snRNA
5. Purification of Ribonucleoproteins Using Peptide-Elutable Antibodies and Other Affinity Techniques
6. CLIP: Crosslinking and ImmunoPrecipitation of In Vivo RNA Targets of RNA-Binding Proteins
7. Quantitative Analysis of Protein-RNA Interactions by Gel Mobility Shift
8. Monitoring Assembly of Ribonucleoprotein Complexes by Isothermal Titration Calorimetry
9. Characterization of RNA-Protein Interactions by Phosphorothioate Footprinting and Its Applications to the Ribosome
10. In Vivo Analysis of Ribonucleoprotein Complexes Using Nucleotide Analog Interference Mapping
11. T7 RNA Polymerase-Mediated Incorporation of 8-N3AMP Into RNA for Studying Protein-RNA Interactions
12. A Simple Crosslinking Method， CLAMP， to Map the Sites of RNA-Contacting Domains Within a Protein
13. Proteins Specifically Modified With a Chemical Nuclease as Probes of RNA-Protein Interaction
14. RNA-Protein Crosslink Mapping Using TEV Protease
15. Structural Analysis of Protein-RNA Interactions With Mass Spectrometry
16. Analyzing RNA-Protein Crosslinking Sites in Unlabeled Ribonucleoprotein Complexes by Mass Spectrometry
17. In Vitro Selection of Random RNA Fragments to Identify Protein-Binding Sites Within Large RNAs
18. Immunoprecipitation Analysis to Study RNA-Protein Interactions in Xenopus Oocytes
19. Mapping the Regions of RNase P Catalytic RNA That Are Potentially in Close Contact With Its Protein Cofactor
20. Quantification of MicroRNAs， Splicing Isoforms， and Homologous mRNAs With the Invader Assay
21. Analysis of RNA Structure and RNA-Protein Interactions in Mammalian Cells by Use of Terminal Transferase-Dependent PCR
22. Duplex Unwinding and RNP Remodeling With RNA Helicases
23. Preparation of Efficient Splicing Extracts From Whole Cells， Nuclei， and Cytoplasmic Fractions
24. Designing and Utilization of siRNAs Targeting RNA Binding Proteins
25. The Use of Saccharomyces cerevisiae Proteomic Libraries to Identify RNA-Modifying Proteins
Index 395
