Bookedited by Roland K. Hartmann ... [et al.].
Contents:
Part I. RNA Synthesis - Enzymatic RNA Synthesis, Ligation and Modification
Chapter 1. Enzymatic RNA Synthesis using Bacteriophage T7 RNA Polymerase / Heike Gruegelsiepe, Astrid Schön, Leif A. Kirsebom and Roland K. Hartmann, p. 3-21
Chapter 2. Production of RNAs with Homogeneous 5' and 3' Ends / Mario Mörl, Esther Lizano, Dagmar K. Willkomm and Roland K. Hartmann, p. 22-35
Chapter 3. RNA Ligation using T4 DNA Ligase / Mikko J. Frilander and Janne J. Turunen, p. 36-52
Chapter 4. T4 RNA Ligase / Tina Persson, Dagmar K. Willkomm and Roland K. Hartmann, p. 53-74
Chapter 5. Co- and Post-Transcriptional Incorporation of Specific Modifications Including Photoreactive Groups into RNA Molecules / Nathan H. Zahler and Michael E. Harris, p. 75-85
Chapter 6. 3'-Terminal Attachment of Fluorescent Dyes and Biotin / Dagmar K. Willkomm and Roland K. Hartmann, p. 86-94
Part I. RNA Synthesis - Chemical RNA Synthesis
Chapter 7. Chemical RNA Synthesis, Purification and Analysis / Brian S. Sproat, p. 95-111
Chapter 8. Modified RNAs as Tools in RNA Biochemistry / Thomas E. Edwards and Snorri T. H. Sigurdsson, p. 112-129
Part II. Structure Determination - Molecular Biology Methods
Chapter 9. Direct Determination of RNA Sequence and Modification by Radiolabeling Methods / Olaf Gimple and Astrid Schön, p. 132-150
Chapter 10. Probing RNA Structures with Enzymes and Chemicals In Vitro and In Vivo / Eric Huntzinger, Maria Possedko, Flore Winter, Hervé Moine, Chantal Ehresmann and Pascale Romby, p. 151-171
Chapter 11. Study of RNA-Protein Interactions and RNA Structure in Ribonucleoprotein Particles / Virginie Marchand, Annie Mougin, Agnès Méreau and Christiane Branlant, p. 172-204
Chapter 12. Terbium(III) Footprinting as a Probe of RNA Structure and Metal-binding Sites / Dinari A. Harris and Nils G. Walter, p. 205-213
Chapter 13. Pb²⁺-induced Cleavage of RNA / Leif A. Kirsebom and Jerzy Ciesiolka, p. 214-228
Chapter 14. In Vivo Determination of RNA Structure by Dimethylsulfate / Christina Waldsich and Renée Schroeder, p. 229-237
Chapter 15. Probing Structure and Binding Sites on RNA by Fenton Cleavage / Gesine Bauer and Christian Berens, p. 238-249
Chapter 16. Measuring the Stoichiometry of Magnesium Ions Bound to RNA / A. J. Andrews and Carol Fierke, p. 250-258
Chapter 17. Nucleotide Analog Interference Mapping and Suppression: Specific Applications in Studies of RNA Tertiary Structure, Dynamic Helicase Mechanism and RNA-Protein Interactions, p. 259-293 / Olga Fedorova, Marc Boudvillain, Jane Kawaoka and Anna Marie Pyle
Chapter 18. Nucleotide Analog Interference Mapping: Application to the RNase P System / Simona Cuzic and Roland K. Hartmann, p. 294-318
Chapter 19. Identification and Characterization of Metal Ion Binding by Thiophilic Metal Ion Rescue / Eric L. Christian, p. 319-344
Chapter 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, p. 345-353
Chapter 21. Protein-RNA Crosslinking in Native Ribonucleoprotein Particles / Henning Urlaub, Klaus Hartmuth and Reinhard Lührmann, p. 354-373
Chapter 22. Probing RNA Structure by Photoaffinity Crosslinking with 4-Thiouridine and 6-Thioguanosine / Michael E. Harris and Eric L. Christian, p. 374-384
Part II. Structure Determination - Biophysical Methods
Chapter 23. Structural Analysis of RNA and RNA-Protein Complexes by Small-angle X-ray Scattering / Tao Pan and Tobin R. Sosnick, p. 385-397
Chapter 24. Temperature-Gradient Gel Electrophoresis of RNA / Detlev Riesner and Gerhard Steger, p. 398-414
Chapter 25. UV Melting, Native Gels and RNA Conformation / Andreas Werner, p. 415-427
Chapter 26. Sedimentation Analysis of Ribonucleoprotein Complexes / Jan Medenbach, Andrey Damianov, Silke Schreiner and Albrecht Bindereif, p. 428-437
Chapter 27. Preparation and Handling of RNA Crystals / Boris François, Aurélie Lescoute-Phillips, Andreas Werner and Benoît Masquida, p. 438-452
Part II. Structure Determination - Fluorescence and Single Molecule Studies
Chapter 28. Fluorescence Labeling of RNA for Single Molecule Studies / Filipp Oesterhelt, Enno Schweinberger and Claus Seidel, p. 453-474
Chapter 29. Scanning Force Microscopy and Scanning Force Spectroscopy of RNA / Wolfgang Nellen, p. 475-487
Part III. RNA Genomics and Bioinformatics - Fluorescence and Single Molecule Studies
Chapter 30. Comparative Analysis of RNA Secondary Structure: 6S RNA / James W. Brow and J. Christopher Ellis, p. 490-512
Chapter 31. Secondary Structure Prediction / Gerhard Steger, p. 513-535
Chapter 32. Modeling the Architecture of Structured RNAs within a Modular and Hierarchical Framework, p. 536-545 / Benoît Masquida and Eric Westhof
Chapter 33. Modeling Large RNA Assemblies using a Reduced Representation, p. 546-559 / Jason A. Mears, Scott M. Stagg and Stephen C. Harvey
Chapter 34. Molecular Dynamics Simulations of RNA Systems / Pascal Auffinger and Andrea C. Vaiana, p. 560-576
Chapter 35. Seeking RNA Motifs in Genomic Sequences / Matthieu Legendre and Daniel Gautheret, p. 577-594
Chapter 36. Approaches to Identify Novel Non-messenger RNAs in Bacteria and to Investigate their Biological Functions: RNA Mining / Jörg Vogel, E. Gerhart and H. Wagner, p. 595-613
Chapter 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 Jörg Vogel, p. 614-642
Chapter 38. Experimental RNomics: A Global Approach to Identify Non-coding RNAs in Model Organisms / Alexander Hüttenhofer, p. 643-654
Chapter 39. Large-scale Analysis of mRNA Splice Variants by Microarray / Young-Soo Kwon, Hai-Ri Li and Xiang-Dong Fu, p. 655-663
Part IV. Analysis of RNA Function 665 - RNA-Protein Interactions in vitro
Chapter 40. RNA-Protein Interactions in vitro / Steffen Schiffer, Sylvia Rösch, Bettina Späth, Markus Englert, Hildburg Beier and Anita Marchfelder, p. 666-675
Chapter 41. Biotin-based Affinity Purification of RNA-Protein Complexes / Zsofia Palfi, Jingyi Hui and Albrecht Bindereif, p. 676-693
Chapter 42. Immunoaffinity Purification of Spliceosomal and Small Nuclear Ribonucleoprotein Complexes / Cindy L. Will, Evgeny M. Makarov, Olga V. Makarova and Reinhard Lührmann, p. 694-709
Chapter 43. Northwestern Techniques for the Identification of RNA-binding Proteins from cDNA Expression Libraries and the Analysis of RNA-Protein Interactions / Ángel Emilio Martínez De Alba, Michela Alessandra Denti and Martin Tabler, p. 710-728
Part IV. Analysis of RNA Function 665 - RNA-Protein Interactions in vivo
Chapter 44. Fluorescent Detection of Nascent Transcripts and RNA-binding Proteins in Cell Nuclei, p. 729-736 / Jennifer A. Geiger and Karla M. Neugebauer
Chapter 45. Identification and Characterization of RNA-binding Proteins through Three-hybrid Analysis / Felicia Scott and David R. Engelke, p. 737-754
Chapter 46. Analysis of Alternative Splicing In Vivo using Minigenes / Yesheng Tang, Tatyana Novoyatleva, Natalya Benderska, Shivendra Kishore, Alphonse Thanaraj and Stefan Stamm, p. 755-782
Part IV. Analysis of RNA Function 665 - SELEX
Chapter 47. Artificial Selection: Finding Function amongst Randomized Sequences / Ico de Zwart, Catherine Lozupone, Rob Knight, Amanda Birmingham, Mali Illangasekare, Vasant Jadhav, Michal Legiewicz, Irene Majerfeld, Jeremy Widmann and Michael Yarus, p. 783-806
Chapter 48. Aptamer Selection against Biological Macromolecules: Proteins and Carbohydrates / C. Stefan Vörtler and Maria Milovnikova, p. 807-839
Chapter 49. In Vivo SELEX Strategies / Thomas A. Cooper, p. 840-852
Chapter 50. In Vitro Selection against Small Targets / Dirk Eulberg, Christian Maasch, Werner G. Purschke and Sven Klussmann, p. 853-877
Chapter 51. SELEX Strategies to Identify Antisense and Protein Target Sites in RNA or Heterogeneous Nuclear Ribonucleoprotein Complexes / Martin Lützelberger, Martin R. Jakobsen and Jørgen Kjems, p. 878-894
Chapter 52. Gene Silencing Methods for Mammalian Cells: Application of Synthetic Short Interfering RNAs / Matthias John, Anke Geick, Philipp Hadwiger, Hans-Peter Vomlocher and Olaf Heidenreich, p. 896-909
Appendix. UV Spectroscopy for the Quantitation of RNA, p. 910-913.