About this book

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their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints.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.

Contents:

Part I : RNA Synthesis and Detection

CHAPTER 1

Enzymatic RNA Synthesis Using Bacteriophage T7 RNA Polymerase (Pages: 1-28)

Markus Gößringer,  Dominik Helmecke,  Karen Köhler,  Dr. Astrid Schön,  Leif A. Kirsebom,  Prof. Dr. Albrecht Bindereif,  Prof. Dr. Roland K. Hartmann

CHAPTER 2

Production of RNAs with Homogeneous 5′- and 3′-Ends (Pages: 29-44)

Mario Mörl,  Prof. Dr. Roland K. Hartmann

HAPTER 3

RNA Ligation (Pages: 45-88)

Janne J. Turunen,  Liudmila V. Pavlova,  Martin Hengesbach,  Mark Helm,  Sabine Müller,  Prof. Dr. Roland K. Hartmann,  Mikko J. Frilander

HAPTER 4

Northern Blot Detection of Small RNAs (Pages: 89-104)

Benedikt M. Beckmann,  Arnold Grünweller,  Prof. Dr. Roland K. Hartmann

CHAPTER 5

Rapid, Non-Denaturing, Large-Scale Purification of In Vitro Transcribed RNA Using Weak Anion-Exchange Chromatography (Pages: 105-116)

Laura E. Easton,  Yoko Shibata,  Peter J. Lukavsky

CHAPTER 6

3′-Terminal Attachment of Fluorescent Dyes and Biotin (Pages: 117-128)

Dagmar K. Willkomm,  Prof. Dr. Roland K. Hartmann

CHAPTER 7

Chemical RNA Synthesis, Purification, and Analysis (Pages: 129-150)

Brian S. Sproat

HAPTER 8

Modified RNAs as Tools in RNA Biochemistry (Pages: 151-172)

Thomas E. Edwards,  Snorri Th. Sigurdsson

Part II : Structure Determination

CHAPTER 9

Direct Determination of RNA Sequence and Modification by Radiolabeling Methods (Pages: 173-204)

Olaf Gimple,  Dr. Astrid Schön

CHAPTER 10

Probing RNA Structure In Vitro with Enzymes and Chemicals (Pages: 205-230)

Anne-Catherine Helfer,  Cédric Romilly,  Clément Chevalier,  Efthimia Lioliou,  Stefano Marzi,  Pascale Romby

CHAPTER 11

Probing RNA Solution Structure by Photocrosslinking: Incorporation of Photoreactive Groups at RNA Termini and Determination of Crosslinked Sites by Primer Extension (Pages: 231-254)

Michael E. Harris

CHAPTER 12

Terbium(III) Footprinting as a Probe of RNA Structure and Metal Binding Sites (Pages: 255-268)

Dinari A. Harris,  Gabrielle C. Todd,  Nils G. Walter

CHAPTER 13

Pb²⁺-Induced Cleavage of RNA (Pages: 269-284)

Leif A. Kirsebom,  Jerzy Ciesiolka

CHAPTER 14

Identification and Characterization of Metal Ion Coordination Interactions with RNA by Quantitative Analysis of Thiophilic Metal Ion Rescue of Site-Specific Phosphorothioate Modifications (Pages: 285-300)

Michael E. Harris

CHAPTER 15

Probing RNA Structure and Ligand Binding Sites on RNA by Fenton Cleavage (Pages: 301-318)

Corina G. Heidrich,  Christian Berens

CHAPTER 16

Measuring the Stoichiometry of Magnesium Ions Bound to RNA (Pages: 319-328)

Andrew J. Andrews,  Carol A. Fierke

CHAPTER 17

Nucleotide Analog Interference Mapping and Suppression (NAIM/NAIS): a Combinatorial Approach to Study RNA Structure, Folding, and Interaction with Proteins (Pages: 329-368)

Olga Fedorova,  Marc Boudvillain,  Christina Waldsich

CHAPTER 18

Nucleotide Analog Interference Mapping (NAIM): Application to the RNase P System (Pages: 369-396)

Simona Cuzic-Feltens,  Prof. Dr. Roland K. Hartmann

CHAPTER 19

Identification of Divalent Metal Ion Binding Sites in RNA/DNA-Metabolizing Enzymes by Fe(II)-Mediated Hydroxyl Radical Cleavage (Pages: 397-406)

Yan-Guo Ren,  Niklas Henriksson,  Anders Virtanen

CHAPTER 20

RNA Structure and Folding Analyzed Using Small-Angle X-Ray Scattering (Pages: 407-426)

Nathan J. Baird,  Jeremey West,  Tobin R. Sosnick

CHAPTER 21

Temperature-Gradient Gel Electrophoresis of RNA (Pages: 427-444)

Detlev Riesner,  Gerhard Steger

CHAPTER 22

UV Melting Studies with RNA (Pages: 445-480)

Philippe Dumas,  Eric Ennifar,  François Disdier,  Philippe Walter

CHAPTER 23

RNA Crystallization (Pages: 481-498)

Jiro Kondo,  Claude Sauter,  Benoît Masquida

CHAPTER 24

Studying RNA Using Single Molecule Fluorescence Resonance Energy Transfer (Pages: 499-526)

Felix Spenkuch,  Olwen Domingo,  Gerald Hinze,  Thomas Basché,  Mark Helm

CHAPTER 25

Atomic Force Microscopy Imaging and Force Spectroscopyof RNA (Pages: 527-546)

Malte Bussiek,  Antonie Schöne,  Wolfgang Nellen

Part III : RNA Genomics & Bioinformatics, Global Approaches

CHAPTER 26

Secondary Structure Prediction (Pages: 547-578)

Gerhard Steger

CHAPTER 27

RNA Secondary Structure Analysis Using Abstract Shapes (Pages: 579-594)

Robert Giegerich,  Björn Voß

CHAPTER 28

Screening Genome Sequences for known RNA Genes or Motifs (Pages: 595-618)

Daniel Gautheret

CHAPTER 29

Homology Search for Small Structured Non-coding RNAs (Pages: 619-632)

Manja Marz,  Stefanie Wehner,  Peter F. Stadler

CHAPTER 30

Predict RNA 2D and 3D Structure over the Internet Using MC-Tools (Pages: 633-666)

Stephen Leong Koan,  Jonathan Roy,  Marc Parisien,  François Major

CHAPTER 31

S2S-Assemble2: a Semi-Automatic Bioinformatics Framework to Study and Model RNA 3D Architectures (Pages: 667-686)

Fabrice Jossinet,  Prof. Dr. Eric Westhof

CHAPTER 32

Molecular Dynamics Simulations of RNA Systems (Pages: 687-718)

Pascal Auffinger

CHAPTER 33

Identification and Characterization of Small Non-coding RNAs in Bacteria (Pages: 719-786)

Dimitri Podkaminski,  Marie Bouvier,  Jörg Vogel

CHAPTER 34

The Identification of Bacterial Non-coding RNAs through Complementary Approaches (Pages: 787-800)

Björn Voß,  Wolfgang R. Hess

CHAPTER 35

Experimental RNomics, a Global Approach to Identify Non-coding RNAs in Model Organisms, and RNPomics to Analyze the Non-coding RNP Transcriptome (Pages: 801-820)

Mathieu Rederstorff,  Alexander Hüttenhofer

CHAPTER 36

Computational Methods for Gene Expression Profiling Using Next-Generation Sequencing (RNA-Seq) (Pages: 821-832)

John C. Castle

CHAPTER 37

Characterization and Prediction of miRNA Targets (Pages: 833-860)

Jean Hausser,  Mihaela Zavolan

CHAPTER 38

Barcoded cDNA Libraries for miRNA Profiling by Next-Generation Sequencing (Pages: 861-876)

Markus Hafner,  Neil Renwick,  John Pena,  Aleksandra Mihailovic,  Thomas Tuschl

CHAPTER 39

Transcriptome-Wide Identification of Protein Binding Sites on RNA by PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) (Pages: 877-898)

Jessica I. Hoell,  Markus Hafner,  Markus Landthaler,  Manuel Ascano,  Thalia A. Farazi,  Greg Wardle,  Jeff Nusbaum,  Pavol Cekan,  Mohsen Khorshid,  Lukas Burger,  Mihaela Zavolan,  Thomas Tuschl

CHAPTER 40

Global Analysis of Protein–RNA Interactions with Single-Nucleotide Resolution Using iCLIP (Pages: 899-918)

Julian König,  Nicholas J. McGlincy,  Jernej Ule

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

CHAPTER 41

Use of RNA Affinity Matrices for the Isolation of RNA Binding Proteins (Pages: 919-934)

Markus Englert,  Bettina Späth,  Steffen Schiffer,  Sylvia Rösch,  Hildburg Beier,  Anita Marchfelder

CHAPTER 42

Biotin-Based Affinity Purification of RNA–Protein Complexes (Pages: 935-956)

Marco Preußner,  Silke Schreiner,  Inna Grishina,  Zsofia Palfi,  Jingyi Hui,  Prof. Dr. Albrecht Bindereif

CHAPTER 43

Affinity Purification of Spliceosomal and Small Nuclear Ribonucleoprotein Complexes (Pages: 957-974)

Julia Dannenberg,  Patrizia Fabrizio,  Cindy L. Will,  Reinhard Lührmann

CHAPTER 44

Study of RNA–Protein Interactions and RNA Structure in Ribonucleoprotein Particles (RNPs) (Pages: 975-1016)

Virginie Marchand,  Annie Mougin,  Agnès Méreau,  Isabelle Behm-Ansmant,  Yuri Motorin,  Christiane Branlant

CHAPTER 45

Immunopurification of Endogenous RNAs Associated with RNA Binding Proteins In vivo (Pages: 1017-1028)

Minna-Liisa Änkö,  Karla M. Neugebauer

CHAPTER 46

Protein–RNA Crosslinking in Native Ribonucleoprotein Particles (Pages: 1029-1054)

Olexandr Dybkov,  Henning Urlaub,  Reinhard Lührmann

CHAPTER 47

Sedimentation Analysis of Ribonucleoprotein Complexes (Pages: 1055-1066)

Tanja Rösel,  Jan Medenbach,  Andrey Damianov,  Silke Schreiner,  Prof. Dr. Albrecht Bindereif

CHAPTER 48

Identification and Characterization of RNA Binding Proteins through Three-Hybrid Analysis (Pages: 1067-1086)

Felicia Scott,  David R. Engelke

CHAPTER 49

Experimental Identification of MicroRNA Targets (Pages: 1087-1096)

Michaela Beitzinger,  Gunter Meister

CHAPTER 50

Aptamer Selection against Biological Macromolecules: Proteins and Carbohydrates (Pages: 1097-1138)

Franziska Peter,  C. Stefan Voertler

CHAPTER 51

In Vitro Selection against Small Targets (Pages: 1139-1164)

Dirk Eulberg,  Christian Maasch,  Werner G. Purschke,  Sven Klussmann

CHAPTER 52

SELEX Strategies to Identify Antisense and Protein Target Sites in RNA or hnRNP Complexes (Pages: 1165-1184)

Martin Lützelberger,  Martin R. Jakobsen,  Jørgen Kjems

CHAPTER 53

Genomic SELEX (Pages: 1185-1206)

Jennifer L. Boots,  Katarzyna Matylla-Kulinska,  Marek Zywicki,  Bob Zimmermann,  Renée Schroeder

CHAPTER 54

In vivo SELEX Strategies (Pages: 1207-1220)

Thomas A. Cooper

CHAPTER 55

Gene Silencing Methods Using Vector-Encoded siRNAs or miRNAs (Pages: 1221-1242)

Ying Poi Liu,  Ben Berkhout

CHAPTER 56

Using Chemical Modification to Enhance siRNA Performance (Pages: 1243-1278)

Jesper B. Bramsen,  Arnold Grünweller,  Prof. Dr. Roland K. Hartmann,  Jørgen Kjems