Handbook of RNA Biochemistry

Roland K. Hartmann is Professor of Pharmaceutical Chemistry at the Philipps-Universität Marburg (Germany). He studied Biochemistry at the Freie Universität Berlin where in 1988 he received the Ernst Reuter award for outstanding Ph.D. theses. His research interests include natural ribozymes, particularly ribonuclease P, interactions of RNAs with proteins and small ligands, aptamers, antisense and RNA interference.Albrecht Bindereif is Professor of Biochemistry at the University of Giessen (Germany) since 1999. He studied Biochemistry in Tübingen and at the University of California, Berkeley. His postdoctoral work was done in Michael Green's laboratory at Harvard University. His research interests focus on the mechanism and regulation of mRNA splicing, both in the mammalian system and in trypanosomes.Astrid Schön received her PhD from the Institute of Biochemistry at the University of Würzburg, and was a graduate fellow and postdoctoral associate with Dieter Söll at Yale University. She is currently a lecturer at the Institute of Biochemistry, University of Leipzig (Germany). Her research is focused on RNA metabolism and RNA-protein interactions, and the evolution of complex RNA enzymes.Eric Westhof is Professor of Biophysics at the Université Louis Pasteur in Strasbourg (France) since 1988. He studied in Liege and Regensburg and was a Fulbright-Hays Research Fellow at the University of Wisconsin with M. Sundaralingam. His research is centered on the relationships between sequence, structure, evolution and functions of RNA molecules.

• Preface XXXVList of Contributors XXXVIIPart I RNA Synthesis and Detection 11 Enzymatic RNA Synthesis Using Bacteriophage T7 RNA Polymerase 3Markus Gößringer, Dominik Helmecke, Karen Köhler, Astrid Schön, Leif A. Kirsebom, Albrecht Bindereif, and Roland K. Hartmann2 Production of RNAs with Homogeneous 5'- and 3'-Ends 29Mario Mörl and Roland K. Hartmann3 RNA Ligation 45Janne J. Turunen, Liudmila V. Pavlova, Martin Hengesbach, Mark Helm, Sabine Müller, Roland K. Hartmann, and Mikko J. Frilander4 Northern Blot Detection of Small RNAs 89Benedikt M. Beckmann, Arnold Grünweller, and Roland K. Hartmann5 Rapid, Non-Denaturing, Large-Scale Purification of In Vitro Transcribed RNA Using Weak Anion-Exchange Chromatography 105Laura E. Easton, Yoko Shibata, and Peter J. Lukavsky6 3'-Terminal Attachment of Fluorescent Dyes and Biotin 117Dagmar K. Willkomm and Roland K. Hartmann7 Chemical RNA Synthesis, Purification, and Analysis 129Brian S. Sproat8 Modified RNAs as Tools in RNA Biochemistry 151Thomas E. Edwards and Snorri Th. SigurdssonPart II Structure Determination 1739 Direct Determination of RNA Sequence and Modification by Radiolabeling Methods 175Olaf Gimple and Astrid Schön10 Probing RNA Structure In Vitro with Enzymes and Chemicals 205Anne-Catherine Helfer, Cédric Romilly, Clément Chevalier, Efthimia Lioliou, Stefano Marzi, and Pascale Romby11 Probing RNA Solution Structure by Photocrosslinking: Incorporation of Photoreactive Groups at RNA Termini and Determination of Crosslinked Sites by Primer Extension 231Michael E. Harris12 Terbium(III) Footprinting as a Probe of RNA Structure and Metal Binding Sites 255Dinari A. Harris, Gabrielle C. Todd, and Nils G. Walter13 Pb2+-Induced Cleavage of RNA 269Leif A. Kirsebom and Jerzy Ciesiolka14 Identification and Characterization of Metal Ion Coordination Interactions with RNA by Quantitative Analysis of Thiophilic Metal Ion Rescue of Site-Specific Phosphorothioate Modifications 285Michael E. Harris15 Probing RNA Structure and Ligand Binding Sites on RNA by Fenton Cleavage 301Corina G. Heidrich and Christian Berens16 Measuring the Stoichiometry of Magnesium Ions Bound to RNA 319Andrew J. Andrews and Carol A. Fierke17 Nucleotide Analog Interference Mapping and Suppression (NAIM/NAIS): a Combinatorial Approach to Study RNA Structure, Folding, and Interaction with Proteins 329Olga Fedorova, Marc Boudvillain, and Christina Waldsich18 Nucleotide Analog Interference Mapping (NAIM): Application to the RNase P System 369Simona Cuzic-Feltens and Roland K. Hartmann19 Identification of Divalent Metal Ion Binding Sites in RNA/DNA-Metabolizing Enzymes by Fe(II)-Mediated Hydroxyl Radical Cleavage 397Yan-Guo Ren, Niklas Henriksson, and Anders Virtanen20 RNA Structure and Folding Analyzed Using Small-Angle X-Ray Scattering 407Nathan J. Baird, Jeremey West, and Tobin R. Sosnick21 Temperature-Gradient Gel Electrophoresis of RNA 427Detlev Riesner and Gerhard Steger22 UV Melting Studies with RNA 445Philippe Dumas, Eric Ennifar, Francois Disdier, and Philippe Walter23 RNA Crystallization 481Jiro Kondo, Claude Sauter, and Benôýt Masquida24 Studying RNA Using Single Molecule Fluorescence Resonance Energy Transfer 499Felix Spenkuch, Olwen Domingo, Gerald Hinze, Thomas Basché, and Mark Helm25 Atomic Force Microscopy Imaging and Force Spectroscopy of RNA 527Malte Bussiek, Antonie Schöne, and Wolfgang NellenPart III RNA Genomics & Bioinformatics, Global Approaches 54726 Secondary Structure Prediction 549Gerhard Steger27 RNA Secondary Structure Analysis Using Abstract Shapes 579Robert Giegerich and Björn Voß28 Screening Genome Sequences for known RNA Genes or Motifs 595Daniel Gautheret29 Homology Search for Small Structured Non-coding RNAs 619Manja Marz, Stefanie Wehner, and Peter F. Stadler30 Predict RNA 2D and 3D Structure over the Internet Using MC-Tools 633Stephen Leong Koan, Jonathan Roy, Marc Parisien, and Francois Major31 S2S-Assemble2: a Semi-Automatic Bioinformatics Framework to Study and Model RNA 3D Architectures 667Fabrice Jossinet and Eric Westhof32 Molecular Dynamics Simulations of RNA Systems 687Pascal Auffinger33 Identification and Characterization of Small Non-coding RNAs in Bacteria 719Dimitri Podkaminski, Marie Bouvier, and Jörg Vogel34 The Identification of Bacterial Non-coding RNAs through Complementary Approaches 787Björn Voß and Wolfgang R. Hess35 Experimental RNomics, a Global Approach to Identify Non-coding RNAs in Model Organisms, and RNPomics to Analyze the Non-coding RNP Transcriptome 801Mathieu Rederstorff and Alexander Hüttenhofer36 Computational Methods for Gene Expression Profiling Using Next-Generation Sequencing (RNA-Seq) 821John C. Castle37 Characterization and Prediction of miRNA Targets 833Jean Hausser and Mihaela Zavolan38 Barcoded cDNA Libraries for miRNA Profiling by Next-Generation Sequencing 861Markus Hafner, Neil Renwick, John Pena, Aleksandra Mihailovic, and Thomas Tuschl39 Transcriptome-Wide Identification of Protein Binding Sites on RNA by PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) 877Jessica 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 Tuschl40 Global Analysis of Protein–RNA Interactions with Single-Nucleotide Resolution Using iCLIP 899Julian König, Nicholas J. Mc Glincy, and Jernej UlePart IV RNA Function, RNP Analysis, SELEX, RNAi 91941 Use of RNA Affinity Matrices for the Isolation of RNA Binding Proteins 921Markus Englert, Bettina Späth, Steffen Schiffer, Sylvia Rösch, Hildburg Beier, and Anita Marchfelder42 Biotin-Based Affinity Purification of RNA–Protein Complexes 935Marco Preußner, Silke Schreiner, Inna Grishina, Zsofia Palfi, Jingyi Hui, and Albrecht Bindereif43 Affinity Purification of Spliceosomal and Small Nuclear Ribonucleoprotein Complexes 957Julia Dannenberg, Patrizia Fabrizio, Cindy L. Will, and Reinhard Lührmann44 Study of RNA–Protein Interactions and RNA Structure in Ribonucleoprotein Particles (RNPs) 975Virginie Marchand, Annie Mougin, Agn´es Méreau, Isabelle Behm-Ansmant, Yuri Motorin, and Christiane Branlant45 Immunopurification of Endogenous RNAs Associated with RNA Binding Proteins In vivo 1017Minna-Liisa Änkö and Karla M. Neugebauer46 Protein–RNA Crosslinking in Native Ribonucleoprotein Particles 1029Olexandr Dybkov, Henning Urlaub, and Reinhard Lührmann47 Sedimentation Analysis of Ribonucleoprotein Complexes 1055Tanja Rösel, Jan Medenbach, Andrey Damianov, Silke Schreiner, and Albrecht Bindereif48 Identification and Characterization of RNA Binding Proteins through Three-Hybrid Analysis 1067Felicia Scott and David R. Engelke49 Experimental Identification of MicroRNA Targets 1087Michaela Beitzinger and Gunter Meister50 Aptamer Selection against Biological Macromolecules: Proteins and Carbohydrates 1097Franziska Peter and C. Stefan Voertler51 In Vitro Selection against Small Targets 1139Dirk Eulberg, Christian Maasch, Werner G. Purschke, and Sven Klussmann52 SELEX Strategies to Identify Antisense and Protein Target Sites in RNA or hnRNP Complexes 1165Martin Lützelberger, Martin R. Jakobsen, and Jørgen Kjems53 Genomic SELEX 1185Jennifer L. Boots, Katarzyna Matylla-Kulinska, Marek Zywicki, Bob Zimmermann, and Renée Schroeder54 In vivo SELEX Strategies 1207Thomas A. Cooper55 Gene Silencing Methods Using Vector-Encoded siRNAs or miRNAs 1221Ying Poi Liu and Ben Berkhout56 Using Chemical Modification to Enhance siRNA Performance 1243Jesper B. Bramsen, Arnold Grünweller, Roland K. Hartmann, and Jørgen KjemsAppendix: UV Spectroscopy for the Quantitation of RNA 1279Index 1283