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Handbook of RNA Biochemistry, 2nd, Completely Revised and Enlarged Edition



Handbook of RNA Biochemistry, 2nd, Completely Revised and Enlarged Edition

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The second edition of a highly acclaimed handbook and ready reference.
Unmatched in its breadth and quality, around 100 specialists from all over the world share their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints.
They cover all modern techniques for the handling, analysis and modification of RNAs and their complexes with proteins. Throughout, they bear the practising bench scientist in mind, providing quick and reliable access to a plethora of solutions for practical questions of RNA research, ranging from simple to highly complex.
This broad scope allows the treatment of specialized methods side by side with basic biochemical techniques, making the book a real treasure trove for every researcher experimenting with RNA.

Preface XXXV

List of Contributors XXXVII

Part I RNA Synthesis and Detection 1

1 Enzymatic RNA Synthesis Using Bacteriophage T7 RNA Polymerase 3
Markus Gößringer, Dominik Helmecke, Karen Köhler, Astrid Schön, Leif A. Kirsebom, Albrecht Bindereif, and Roland K. Hartmann

2 Production of RNAs with Homogeneous 5'- and 3'-Ends 29
Mario Mörl and Roland K. Hartmann

3 RNA Ligation 45
Janne J. Turunen, Liudmila V. Pavlova, Martin Hengesbach, Mark Helm, Sabine Müller, Roland K. Hartmann, and Mikko J. Frilander

4 Northern Blot Detection of Small RNAs 89
Benedikt M. Beckmann, Arnold Grünweller, and Roland K. Hartmann

5 Rapid, Non-Denaturing, Large-Scale Purification of In Vitro Transcribed RNA Using Weak Anion-Exchange Chromatography 105
Laura E. Easton, Yoko Shibata, and Peter J. Lukavsky

6 3'-Terminal Attachment of Fluorescent Dyes and Biotin 117
Dagmar K. Willkomm and Roland K. Hartmann

7 Chemical RNA Synthesis, Purification, and Analysis 129
Brian S. Sproat

8 Modified RNAs as Tools in RNA Biochemistry 151
Thomas E. Edwards and Snorri Th. Sigurdsson

Part II Structure Determination 173

9 Direct Determination of RNA Sequence and Modification by Radiolabeling Methods 175
Olaf Gimple and Astrid Schön

10 Probing RNA Structure In Vitro with Enzymes and Chemicals 205
Anne-Catherine Helfer, Cédric Romilly, Clément Chevalier, Efthimia Lioliou, Stefano Marzi, and Pascale Romby

11 Probing RNA Solution Structure by Photocrosslinking: Incorporation of Photoreactive Groups at RNA Termini and Determination of Crosslinked Sites by Primer Extension 231
Michael E. Harris

12 Terbium(III) Footprinting as a Probe of RNA Structure and Metal Binding Sites 255
Dinari A. Harris, Gabrielle C. Todd, and Nils G. Walter

13 Pb2+-Induced Cleavage of RNA 269
Leif A. Kirsebom and Jerzy Ciesiolka

14 Identification and Characterization of Metal Ion Coordination Interactions with RNA by Quantitative Analysis of Thiophilic Metal Ion Rescue of Site-Specific Phosphorothioate Modifications 285
Michael E. Harris

15 Probing RNA Structure and Ligand Binding Sites on RNA by Fenton Cleavage 301
Corina G. Heidrich and Christian Berens

16 Measuring the Stoichiometry of Magnesium Ions Bound to RNA 319
Andrew J. Andrews and Carol A. Fierke

17 Nucleotide Analog Interference Mapping and Suppression (NAIM/NAIS): a Combinatorial Approach to Study RNA Structure, Folding, and Interaction with Proteins 329
Olga Fedorova, Marc Boudvillain, and Christina Waldsich

18 Nucleotide Analog Interference Mapping (NAIM): Application to the RNase P System 369
Simona Cuzic-Feltens and Roland K. Hartmann

19 Identification of Divalent Metal Ion Binding Sites in RNA/DNA-Metabolizing Enzymes by Fe(II)-Mediated Hydroxyl Radical Cleavage 397
Yan-Guo Ren, Niklas Henriksson, and Anders Virtanen

20 RNA Structure and Folding Analyzed Using Small-Angle X-Ray Scattering 407
Nathan J. Baird, Jeremey West, and Tobin R. Sosnick

21 Temperature-Gradient Gel Electrophoresis of RNA 427
Detlev Riesner and Gerhard Steger

22 UV Melting Studies with RNA 445
Philippe Dumas, Eric Ennifar, Francois Disdier, and Philippe Walter

23 RNA Crystallization 481
Jiro Kondo, Claude Sauter, and Benôýt Masquida

24 Studying RNA Using Single Molecule Fluorescence Resonance Energy Transfer 499
Felix Spenkuch, Olwen Domingo, Gerald Hinze, Thomas Basché, and Mark Helm

25 Atomic Force Microscopy Imaging and Force Spectroscopy of RNA 527
Malte Bussiek, Antonie Schöne, and Wolfgang Nellen

Part III RNA Genomics & Bioinformatics, Global Approaches 547

26 Secondary Structure Prediction 549
Gerhard Steger

27 RNA Secondary Structure Analysis Using Abstract Shapes 579
Robert Giegerich and Björn Voß

28 Screening Genome Sequences for known RNA Genes or Motifs 595
Daniel Gautheret

29 Homology Search for Small Structured Non-coding RNAs 619
Manja Marz, Stefanie Wehner, and Peter F. Stadler

30 Predict RNA 2D and 3D Structure over the Internet Using MC-Tools 633
Stephen Leong Koan, Jonathan Roy, Marc Parisien, and Francois Major

31 S2S-Assemble2: a Semi-Automatic Bioinformatics Framework to Study and Model RNA 3D Architectures 667
Fabrice Jossinet and Eric Westhof

32 Molecular Dynamics Simulations of RNA Systems 687
Pascal Auffinger

33 Identification and Characterization of Small Non-coding RNAs in Bacteria 719
Dimitri Podkaminski, Marie Bouvier, and Jörg Vogel

34 The Identification of Bacterial Non-coding RNAs through Complementary Approaches 787
Björn Voß and Wolfgang R. Hess

35 Experimental RNomics, a Global Approach to Identify Non-coding RNAs in Model Organisms, and RNPomics to Analyze the Non-coding RNP Transcriptome 801
Mathieu Rederstorff and Alexander Hüttenhofer

36 Computational Methods for Gene Expression Profiling Using Next-Generation Sequencing (RNA-Seq) 821
John C. Castle

37 Characterization and Prediction of miRNA Targets 833
Jean Hausser and Mihaela Zavolan

38 Barcoded cDNA Libraries for miRNA Profiling by Next-Generation Sequencing 861
Markus Hafner, Neil Renwick, John Pena, Aleksandra Mihailovic, and Thomas Tuschl

39 Transcriptome-Wide Identification of Protein Binding Sites on RNA by PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) 877
Jessica I. Hoell, Markus Hafner, Markus Landthaler, Manuel Ascano, Thalia A. Farazi, Greg Wardle, Jeff Nusbaum, Pavol Cekan, Mohsen Khorshid, Lukas Burger, Mihaela Zavolan, and Thomas Tuschl

40 Global Analysis of Protein–RNA Interactions with Single-Nucleotide Resolution Using iCLIP 899
Julian König, Nicholas J. Mc Glincy, and Jernej Ule

Part IV RNA Function, RNP Analysis, SELEX, RNAi 919

41 Use of RNA Affinity Matrices for the Isolation of RNA Binding Proteins 921
Markus Englert, Bettina Späth, Steffen Schiffer, Sylvia Rösch, Hildburg Beier, and Anita Marchfelder

42 Biotin-Based Affinity Purification of RNA–Protein Complexes 935
Marco Preußner, Silke Schreiner, Inna Grishina, Zsofia Palfi, Jingyi Hui, and Albrecht Bindereif

43 Affinity Purification of Spliceosomal and Small Nuclear Ribonucleoprotein Complexes 957
Julia Dannenberg, Patrizia Fabrizio, Cindy L. Will, and Reinhard Lührmann

44 Study of RNA–Protein Interactions and RNA Structure in Ribonucleoprotein Particles (RNPs) 975
Virginie Marchand, Annie Mougin, Agn´es Méreau, Isabelle Behm-Ansmant, Yuri Motorin, and Christiane Branlant

45 Immunopurification of Endogenous RNAs Associated with RNA Binding Proteins In vivo 1017
Minna-Liisa Änkö and Karla M. Neugebauer

46 Protein–RNA Crosslinking in Native Ribonucleoprotein Particles 1029
Olexandr Dybkov, Henning Urlaub, and Reinhard Lührmann

47 Sedimentation Analysis of Ribonucleoprotein Complexes 1055
Tanja Rösel, Jan Medenbach, Andrey Damianov, Silke Schreiner, and Albrecht Bindereif

48 Identification and Characterization of RNA Binding Proteins through Three-Hybrid Analysis 1067
Felicia Scott and David R. Engelke

49 Experimental Identification of MicroRNA Targets 1087
Michaela Beitzinger and Gunter Meister

50 Aptamer Selection against Biological Macromolecules: Proteins and Carbohydrates 1097
Franziska Peter and C. Stefan Voertler

51 In Vitro Selection against Small Targets 1139
Dirk Eulberg, Christian Maasch, Werner G. Purschke, and Sven Klussmann

52 SELEX Strategies to Identify Antisense and Protein Target Sites in RNA or hnRNP Complexes 1165
Martin Lützelberger, Martin R. Jakobsen, and Jørgen Kjems

53 Genomic SELEX 1185
Jennifer L. Boots, Katarzyna Matylla-Kulinska, Marek Zywicki, Bob Zimmermann, and Renée Schroeder

54 In vivo SELEX Strategies 1207
Thomas A. Cooper

55 Gene Silencing Methods Using Vector-Encoded siRNAs or miRNAs 1221
Ying Poi Liu and Ben Berkhout

56 Using Chemical Modification to Enhance siRNA Performance 1243
Jesper B. Bramsen, Arnold Grünweller, Roland K. Hartmann, and Jørgen Kjems

Appendix: UV Spectroscopy for the Quantitation of RNA 1279

Index 1283