Handbook of RNA biochemistry
著者
書誌事項
Handbook of RNA biochemistry
Wiley-VCH, 2009
Student ed
- : pbk
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注記
Originally published: 2005
Includes bibliographical references and index
内容説明・目次
内容説明
This all-in-one compendium of current laboratory techniques for the study of RNA brings together numerous novel methods that were hitherto only available through the primary literature. The editors - themselves experienced RNA researchers - have gathered expert authors from the US and Europe for the ultimate in everyday working knowledge. In more than 300 detailed protocols, all the techniques covered are treated with the user in mind, including practical advice and an invaluable 'troubleshooting' section. The broad scope of the book allows the side-by-side treatment of specialized methods with basic biochemical techniques for the isolation, characterization and functional analysis of RNA. All pertinent laboratory methods are presented in detail, including, RNA synthesis, modification and ligation; Sequence and structure determination of RNA; Isolation and purification of ribonucleoproteins; RNA crystallization + Single molecule studies on RNA; Analysis of splice variants; RNA imaging in vivo; Modeling and prediction of RNA structure; RNA microarrays; Aptamer libraries and SELEX technology; and, RNA interference.
In short, a guide to successful experimentation for molecular biologists, biochemists and biotechnologists and of interest to every researcher experimenting with RNA.
目次
- Preface. List of Contributors. Part I: RNA Synthesis. I.1 Enzymatic RNA Synthesis using Bacteriophage T7 Polymerase (Heike Gruegelsiepe, Astrid Schon, Leif A. Kirsebom and Roland K. Hartmann). 2. Production to RNAs with Homogenous 5' and 3' Ends (Mario Morl, Esther Lizano, Dagmar K. Willkomm and Roland K, Hartmann). 3. RNA Ligation using T4 DNA Ligase (Mikko J. Frilander and Janne J. Turunen). 4. T4 RNA Ligase (Tina Persson, Dagmar K. Willkomm and Roland K. Hartmann). 5. Co- and Post-Transcriptional Incorporation of Specific Modifications Including Photoreactive Groups into RNA Molecules (Nathabn H. Zahler and Michael E. Harris). 6. 3'-Terminal Attachment of Fluorescent Dyes and Biotin (Dagmar K. Willkomm and Roland K. Hartmann). I.2. Chemical RNA Synthesis, Purification and Analysis (Brian S. Sproat). 8. Modified RNAs as Tools in RNA Biochemistry (Thomas E. Edwards and Snorri Th. Sigurdsson). Part II: Structure Determination. II.1. Molecular Biology Methods. 9. Direct Determination of RNA Sequence and Modification by Radiolabeling methods (Olaf Gimple and Astrid Schon). 10. Probing RNA Structures with Enzymes and Chemicals In Vitro and In Vivo (Eric Huntzinger, Maria Possedko, Flore Winter, Herve Moine, Chantal Ehresmann and Pascale Romby). 11. Study of RNA-Protein Interactions and RNA Structure in Ribonucleoprotein Particles (Virginie Marchand< Annie Mougin, Agnes Mereau and Christiane Branlant). 12. Terbium (III) Footprinting as a Probe of RNA Structure and Metal-binding Sites (Dinari A. Harris and Nils G. Walter). 13. Pb2+ - induced Cleavage of RNA (Leif A. Kirsebom and Jerzy Ciesiolka). 14. In Vivo Determination of RNA Structure by Dimethylsulfate (Christina Waldsich and Renee Schroeder). 15. Probing Structure and binding Sites on RNA by Fenton Cleavage (Gesine Bauer and Christian Berens). 16. Measure the Stoichiometry of Magnesium Ions Bound to RNA (A. J. Andrews and Carol Fierke). 17. Nucleotide Analog Interference Mapping and Suppression: Specific Applications in Studies of RNA Tertiary Structure, Dynamic Helicase Mechanism and RNA-Protein Interactions (Olga Fedorova, Marc Boudvillain, Jane Kawaoka and Anna Marie Pyle). 18. Nucleotide Analog Interference Mapping: Application to the RNase P System (Simina Cuzic and Roland K. Hartmann). 19. Identification and Characterization of Metal Ion Binding by Thiophilic Metal Ion Rescue (Eric L. Christian). 20. Identification of Divalent Metal Ion Binding Sites in RNA/DNA-metabolizing Enzymes by Fe(II)-Mediated Hydroxyl Radical Cleavage (Yan-Guo Ren, Niklas Henriksson and Anders Virtanen). 21. Protein-RNA Crosslinking in Native Ribonucleoprotein Particles (Henning Urlaub, Klaus Hartmuth and Reinhard Luhrmann). 22. Probing RNA Structure by Photoaffinity Crosslinking with 4-Thiouridine and 6-Thioguanosine (Michael E. Harris and Eric L.
- Christian). II.2 Biophysical Methods. 23. Structural Analysis of RNA and RNA-Protein Complexes by Small-angle X-ray Scattering (Tao Pan and Tobin r. Sosnick). 24. Temperature-Gradient Gel Electrophoresis of RNA (Detlev Riesner and Gerhard Steger). 25. UV Melting, Native Gels and RNA Conformation (Andreas Werner). 26. Sedimentation Analysis of Ribonucleoprotein Complexes (Jan Medenbach, Andrey Damianov, Silke Schreiner and Albrecht Bindereif). 27. Preparation and Handling of RNA Crystals (Boris Francois, Aurelie Lescoute-Phillips, Andreas Werner and Benoit Masquida). II.3. Fluorescence and Single Molecule Studies. 28. Fluorescence Labeling of RNA for Single Molecule Studies (Filipp Oesterhelt, Enno Schweinberger and Claus Seidel). 29. Scanning Force Microscopy and Scanning Force Spectroscopy of RNA (Wolfgang Nellen). Part III: RNA Genomics and Bioinformatics. 30. Comparative Analysis of RNA Secondary Structure: 6S RNA (James W. Brown and J. Christopher Ellis). 31. Secondary Structure Prediction (Gerhard Steger). 32. Modeling the Architecture of Structured RNAs within a Modular and Hierarchical Framework (Benoit Masquida and Eric Westhof). 33. Modeling Large RNA Assemblies using a Reduced Representation (Jason A. Mears, Scott M. Stagg and Stephen C. Harvey). 34. Molecular Dynamics Simulations of RNA Systems (Pascal Auffinger and Andrea C. Vaiana). 35. Seeking RNA Motifs in genomic Sequences (Matthieu Legendre and Daniel Gautheret). 36. Approaches to Identify Novel Non-messenger RNAs in Bacteria and to Investigate Their biological Functions: RNA Mining (Jorg Vogel and E. Gerhart H. Wagner). 37. Approaches to Identify Novel Non-messenger RNAs in Bacteria and to Investigate their Biological Functions: Functional Analysis of Identified Non-mRNAs (E. Gerhart H. Wagner and Jorg Vogel). 38. Experimental RNomics: A Global Approach to Identify Non-coding RNAs in Model Organisms (Alexander Huttenhofer). 39. Large-scale Analysis of mRNA Splice Variants by Microarray (Young-Soo Kwon, Hai-Ri Li and Xiang-Dong Fu). IV: Analysis of RNA Function IV.1. RNA-Protein Interactions in vitro. 40. Use of RNA Affinity Matrices for the Isolation of RNA-binding Proteins (Steffen Schiffer, Sylvia Rosch, Bettina Spath, Markus Englert, Hildburg Beier and Anita Marchfelder). 41. Biotin-based Affinity Purification of RNA-Protein Complexes (Zsofia Palfi, Jingyi Hui and Albrecht Bindereif). 42. Immunoaffinity Purification of Spliceosomal and Small Nuclear Ribonucleoprotein Complexes (Cindy L. Will Evgeny M. Makarov, Olga V. Makarova and Reinhard Luhrmann). 43. Northwestern Techniques for the Identification of RNA-binding Proteins from cDNA Expression Libraries and the Analysis of RNA-Protein Interactions (Angel Emilio Martinez de Alba, Michela Alessandra Denti and Martin Tabler). IV.2. RNA-Protein Interactions in vivo. 44. Fluorescent Detection of Nascent Transcripts and RNA-binding Proteins in Cell Cuclei (Jennifer A. Geiger and Karla M. Neugebauer). 45. Identification and Characterization of RNA-binding Proteins through Three-hubrid Analysis (Felicia Scott and David R. Engelke). 46. Analysis of Alternative Splicing In Vivo using Minigenes (Yesheng Tang, Tatyana Novoyatleva, Natalya Benderska, Shivendra Kishore, Alphonse Thanaraj and Stefan Stamm). IV.3. SELEX. 47. Artificial Selection: Finding Function amongst Randomized Sequences (Ico de Zwart, Catherine Lozupone, Rob Knnight, Amanda Birmingham, Mali Illangasekare, Vasant Jadhav, Michal Legiewicz, Irene Majerfeld, Jeremy Widmann and Michael Yarus). 48. Aptamer Selection against Biological Macromolecules: Proteins and Carbohydrates (C. Stefan Vortler and Maria Milovnikova). 49. In Vivo SELEX Strategies (Thomas A. Cooper). 50. In Vitro Selection against Small Targets (Dirk Eulberg, Christian Maasch, Werner G. Purschke and Sven Klussmann). 51. SELEX Strategies to Identify Antisense and Protein Target Sites in RNA or Heterogeneous Nuclear Ribonucleoprotein Complexes (Martin Lutzelberger, Martin R. Jakobsen and Jorgen Kjems). V. RNAi. 52. Gene Silencing Methods for Mammalian Cells: Application of Synthetic Short Interfering RNAs (Matthias John, Anke Geick, Philipp Hadwiger, Hans-Peter Vornlocher and Olaf Heidenreich). Appendix: UV Spectroscopy for the Quantitation of RNA. Index.
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