Handbook of RNA Biochemistry, 2 Volume Set

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 PhD theses. His research interests include comparative mechanistic studies of ribozyme-based versus protein-only RNase P enzymes, inhibitors of bacterial RNase P, regulation of bacterial RNA polymerase by 6S RNAs, viral RNA-protein interactions, RNA interference and cancer.Albrecht Bindereif is Professor of Biochemistry at the University of Giessen (Germany). 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 is a Senior Researcher and Lecturer at the Department of Molecular Cell Therapy, University of Leipzig Medical School (Germany). She 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. Her research is focused on RNA function and metabolism, RNAprotein interactions, and the evolution of complex RNA enzymes in eukaryotic organelles.Eric Westhof is Professor of Structural Biology at the Université de Strasbourg (France). He studied in Liège and Regensburg and was a Fulbright-Hays Research Fellow at the University of Wisconsin with M. Sundaralingam. He is a member of the Deutsche Akademie der Wissenschaften Leopoldina and of the French Académie des Sciences. His research is centered on the relationships between sequence, structure, evolution and function of RNA molecules.

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their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints.They cover all modern techniques for the handling, analysis and modification of RNAs and their complexes with proteins.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.

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.

VOLUME 1RNA SYNTHESIS AND DETECTIONEnzymatic RNA Synthesis Using Bacteriophage T7 RNA PolymeraseProduction of RNAs with Homogeneous 5'- and3' -EndsRNA LigationNorthern Blot Detection of Small RNAsRapid, Non-Denaturing, Large-Scale Purification of In Vitro Transcribed RNA Using Weak Anion-Exchange Chromatography3'-Terminal Attachment of Fluorescent Dyes and BiotinChemical RNA Synthesis, Purification, and AnalysisModified RNAs as Tools in RNA BiochemistrySTRUCTURE DETERMINATIONDirect Determination of RNA Sequence and Modification by Radiolabeling MethodsProbing RNA Structure In Vitro with Enzymes and ChemicalsProbing RNA Solution Structure by Photocrosslinking: Incorporation of Photoreactive Groups at RNA Termini and Determination of Crosslinked Sites by Primer ExtensionTerbium(III) Footprinting as a Probe of RNA Structure and Metal Binding SitesPB2+-Induced Cleavage of RNAIdentification and Characterization of Metal Ion Coordination Interactions with RNA by Quantitative Analysis of Thiophilic Metal Ion Rescue of Site-Specific Phosphorothioate ModificationsProbing RNA Structure and Ligand Binding Sites on RNA by Fenton CleavageMeasuring the Stoichiometry of Magnesium Ions Bound to RNANucleotide Analog Interference Mapping and Suppression (NAIM/NAIS): A Combinatorial Approach to Study RNA Structure, Folding, and Interaction with ProteinsNucleotide Analog Interference Mapping (NAIM): Application to the RNase P SystemIdentification of Divalent Metal Ion Binding Sites in RNA/DNA-Metabolizing Enzymes by Fe(II)-Mediated Hydroxyl Radical CleavageRNA Structure and Folding Analyzed Using Small-Angle X-Ray ScatteringTemperature-Gradient Gel Electrophoresis of RNAUV Melting Studies with RNARNA CrystallizationStudying RNA Using Single Molecule Fluorescence Resonance Energy TransferAtomic Force Microscopy Imaging and Force Spectroscopy of RNAVOLUME 2RNA GENOMICS & BIOINFORMATICS, GLOBAL APPROACHESSecondary Structure PredictionRNA Secondary Structure Analysis Using Abstract ShapesScreening Genome Sequences for known RNA Genes or MotifsHomology Search for Small Structured Non-Coding RNAsPredict RNA 2D and 3D Structure over the Internet using MC-ToolsS2S-Assemble2: A Semi-Automatic Bioinformatics Framework to Study and Model RNA 3D ArchitecturesMolecular Dynamics Simulations of RNA SystemsIdentification and Characterization of Small Non-Coding RNAs in BacteriaThe Identification of Bacterial Non-Coding RNAs through Complementary ApproachesExperimental RNomics, a Global Approach to Identify Non-Coding RNAs in Model Organisms, and RNPomics to Analyze the Non-Coding RNP TranscriptomeComputational Methods for Gene Expression Profiling Using Next-Generation Sequencing (RNA-Seq)Characterization and Prediction of miRNA TargetsBarcoded cDNA Libraries for miRNA Profiling by Next-Generation SequencingTranscriptome-Wide Identification of Protein Binding Sites on RNA by PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation)Global Analysis of Protein-RNA Interactions with Single-Nucleotide Resolution Using iCLIPRNA FUNCTION, RNP ANALYSIS, SELEX, RANiUse of RNA Affinity Matrices for the Isolation of RNA Binding ProteinsBiotin-Based Affinity Purification of RNA-Protein ComplexesAffinity Purification of Spliceosomal and Small Nuclear Ribonucleoprotein ComplexesStudy of RNA-Protein Interactions and RNA Structure in Ribonucleoprotein Particles (RNPs)Immunopurification of Endogenous RNAs Associated with RNA Binding Proteins In vivo Protein-RNA Crosslinking in Native Ribonucleoprotein ParticlesSedimentation Analysis of Ribonucleoprotein ComplexesIdentification and Characterization of RNA Binding Proteins through Three-Hybrid AnalysisExperimental Identification of MicroRNA TargetsAptamer Selection against Biological Macromolecules: Proteins and CarbohydratesIn Vitro Selection against Small TargetsSELEX Strategies to Identify Antisense and Protein Target Sites in RNA or hnRNP ComplexesGenomic SELEXIn vivo SELEX StrategiesGene Silencing Methods Using Vector-Encoded siRNAs or miRNAsUsing Chemical Modification to Enhance siRNA PerformanceAppendix: UV Spectroscopy for the Quantitation of RNAIndex