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Handbook of RNA biochemistry

Author: Roland K Hartmann; Andrew J Andrews
Publisher: Weinheim, Germany : Wiley-VCH, 2015. ©2015
Edition/Format:   eBook : Document : German : Second, completely revised and enlarged editionView all editions and formats
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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  Read more...

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Genre/Form: Electronic books
Additional Physical Format: Print version:
Handbook of RNA biochemistry.
Weinheim, Germany : Wiley-VCH, ©2015
liv, 1314 pages
Material Type: Document, Internet resource
Document Type: Internet Resource, Computer File
All Authors / Contributors: Roland K Hartmann; Andrew J Andrews
ISBN: 9783527650552 3527650555
OCLC Number: 908071114
Description: 1 online resource (1,371 pages) : illustrations, tables
Contents: Preface XXXV List of Contributors XXXVII Part I RNA Synthesis and Detection 1 1 Enzymatic RNA Synthesis Using Bacteriophage T7 RNA Polymerase 3Markus Goessringer, Dominik Helmecke, Karen Koehler, Astrid Schoen, Leif A. Kirsebom, Albrecht Bindereif, and Roland K. Hartmann 2 Production of RNAs with Homogeneous 5'- and 3'-Ends 29Mario Moerl and Roland K. Hartmann 3 RNA Ligation 45Janne J. Turunen, Liudmila V. Pavlova, Martin Hengesbach, Mark Helm, Sabine Muller, Roland K. Hartmann, and Mikko J. Frilander 4 Northern Blot Detection of Small RNAs 89Benedikt M. Beckmann, Arnold Grunweller, and Roland K. Hartmann 5 Rapid, Non-Denaturing, Large-Scale Purification of In Vitro Transcribed RNA Using Weak Anion-Exchange Chromatography 105Laura E. Easton, Yoko Shibata, and Peter J. Lukavsky 6 3'-Terminal Attachment of Fluorescent Dyes and Biotin 117Dagmar K. Willkomm and Roland K. Hartmann 7 Chemical RNA Synthesis, Purification, and Analysis 129Brian S. Sproat 8 Modified RNAs as Tools in RNA Biochemistry 151Thomas E. Edwards and Snorri Th. Sigurdsson Part II Structure Determination 173 9 Direct Determination of RNA Sequence and Modification by Radiolabeling Methods 175Olaf Gimple and Astrid Schoen 10 Probing RNA Structure In Vitro with Enzymes and Chemicals 205Anne-Catherine Helfer, Cedric Romilly, Clement 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 231Michael E. Harris 12 Terbium(III) Footprinting as a Probe of RNA Structure and Metal Binding Sites 255Dinari A. Harris, Gabrielle C. Todd, and Nils G. Walter 13 Pb2+-Induced Cleavage of RNA 269Leif 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 285Michael E. Harris 15 Probing RNA Structure and Ligand Binding Sites on RNA by Fenton Cleavage 301Corina G. Heidrich and Christian Berens 16 Measuring the Stoichiometry of Magnesium Ions Bound to RNA 319Andrew 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 329Olga Fedorova, Marc Boudvillain, and Christina Waldsich 18 Nucleotide Analog Interference Mapping (NAIM): Application to the RNase P System 369Simona 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 397Yan-Guo Ren, Niklas Henriksson, and Anders Virtanen 20 RNA Structure and Folding Analyzed Using Small-Angle X-Ray Scattering 407Nathan J. Baird, Jeremey West, and Tobin R. Sosnick 21 Temperature-Gradient Gel Electrophoresis of RNA 427Detlev Riesner and Gerhard Steger 22 UV Melting Studies with RNA 445Philippe Dumas, Eric Ennifar, Francois Disdier, and Philippe Walter 23 RNA Crystallization 481Jiro Kondo, Claude Sauter, and Benoyt Masquida 24 Studying RNA Using Single Molecule Fluorescence Resonance Energy Transfer 499Felix Spenkuch, Olwen Domingo, Gerald Hinze, Thomas Basche, and Mark Helm 25 Atomic Force Microscopy Imaging and Force Spectroscopy of RNA 527Malte Bussiek, Antonie Schoene, and Wolfgang Nellen Part III RNA Genomics & Bioinformatics, Global Approaches 547 26 Secondary Structure Prediction 549Gerhard Steger 27 RNA Secondary Structure Analysis Using Abstract Shapes 579Robert Giegerich and Bjoern Voss 28 Screening Genome Sequences for known RNA Genes or Motifs 595Daniel Gautheret 29 Homology Search for Small Structured Non-coding RNAs 619Manja Marz, Stefanie Wehner, and Peter F. Stadler 30 Predict RNA 2D and 3D Structure over the Internet Using MC-Tools 633Stephen Leong Koan, Jonathan Roy, Marc Parisien, and Francois Major 31 S2S-Assemble2: a Semi-Automatic Bioinformatics Framework to Study and Model RNA 3D Architectures 667Fabrice Jossinet and Eric Westhof 32 Molecular Dynamics Simulations of RNA Systems 687Pascal Auffinger 33 Identification and Characterization of Small Non-coding RNAs in Bacteria 719Dimitri Podkaminski, Marie Bouvier, and Joerg Vogel 34 The Identification of Bacterial Non-coding RNAs through Complementary Approaches 787Bjoern 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 801Mathieu Rederstorff and Alexander Huttenhofer 36 Computational Methods for Gene Expression Profiling Using Next-Generation Sequencing (RNA-Seq) 821John C. Castle 37 Characterization and Prediction of miRNA Targets 833Jean Hausser and Mihaela Zavolan 38 Barcoded cDNA Libraries for miRNA Profiling by Next-Generation Sequencing 861Markus 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) 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 Tuschl 40 Global Analysis of Protein RNA Interactions with Single-Nucleotide Resolution Using iCLIP 899Julian Koenig, 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 921Markus Englert, Bettina Spath, Steffen Schiffer, Sylvia Roesch, Hildburg Beier, and Anita Marchfelder 42 Biotin-Based Affinity Purification of RNA Protein Complexes 935Marco Preussner, Silke Schreiner, Inna Grishina, Zsofia Palfi, Jingyi Hui, and Albrecht Bindereif 43 Affinity Purification of Spliceosomal and Small Nuclear Ribonucleoprotein Complexes 957Julia Dannenberg, Patrizia Fabrizio, Cindy L. Will, and Reinhard Luhrmann 44 Study of RNA Protein Interactions and RNA Structure in Ribonucleoprotein Particles (RNPs) 975Virginie Marchand, Annie Mougin, Agn'es Mereau, Isabelle Behm-Ansmant, Yuri Motorin, and Christiane Branlant 45 Immunopurification of Endogenous RNAs Associated with RNA Binding Proteins In vivo 1017Minna-Liisa AEnkoe and Karla M. Neugebauer 46 Protein RNA Crosslinking in Native Ribonucleoprotein Particles 1029Olexandr Dybkov, Henning Urlaub, and Reinhard Luhrmann 47 Sedimentation Analysis of Ribonucleoprotein Complexes 1055Tanja Roesel, Jan Medenbach, Andrey Damianov, Silke Schreiner, and Albrecht Bindereif 48 Identification and Characterization of RNA Binding Proteins through Three-Hybrid Analysis 1067Felicia Scott and David R. Engelke 49 Experimental Identification of MicroRNA Targets 1087Michaela Beitzinger and Gunter Meister 50 Aptamer Selection against Biological Macromolecules: Proteins and Carbohydrates 1097Franziska Peter and C. Stefan Voertler 51 In Vitro Selection against Small Targets 1139Dirk Eulberg, Christian Maasch, Werner G. Purschke, and Sven Klussmann 52 SELEX Strategies to Identify Antisense and Protein Target Sites in RNA or hnRNP Complexes 1165Martin Lutzelberger, Martin R. Jakobsen, and Jorgen Kjems 53 Genomic SELEX 1185Jennifer L. Boots, Katarzyna Matylla-Kulinska, Marek Zywicki, Bob Zimmermann, and Renee Schroeder 54 In vivo SELEX Strategies 1207Thomas A. Cooper 55 Gene Silencing Methods Using Vector-Encoded siRNAs or miRNAs 1221Ying Poi Liu and Ben Berkhout 56 Using Chemical Modification to Enhance siRNA Performance 1243Jesper B. Bramsen, Arnold Grunweller, Roland K. Hartmann, and Jorgen Kjems Appendix: UV Spectroscopy for the Quantitation of RNA 1279 Index 1283
Responsibility: edited by Roland K. Hartmann [and three others] ; contributors Andrew J. Andrews [and one hundred thirty two others].

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