Handbook of RNA Biochemistry.pdf
Roland K. Hartmann is Professor of Pharmaceutical Chemistry at the Philipps-Universitat Marburg (Germany). He studied Biochemistry at the Freie Universitat 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 Tubingen 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 Schon received her PhD from the Institute of Biochemistry at the University of Wurzburg, and was a graduate fellow and postdoctoral associate with Dieter Soll 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 Universite 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.
VOLUME 1 PART I: RNA Synthesis and Detection Enzymatic RNA Synthesis Using Bacteriophage T7 RNA polymerase 2 Production of RNAs with Homogeneous 5?- and 3?-Ends RNA Ligation Northern Blot Detection of Small RNAs Rapid, Non-denaturing, Large-scale Purification of in vitro Transcribed RNA Using Weak Anion-exchange Chromatography 3?-Terminal Attachment of Fluorescent Dyes and Biotin Chemical RNA Synthesis, Purification and Analysis Modified RNAs as Tools in RNA Biochemistry PART II: Structure Determination Direct Determination of RNA Sequence and Modification by Radiolabelling Probing RNA Structure in vitro with Enzymes and Chemicals Probing RNA Solution Structure by Photocrosslinking Terbium(III) Footprinting as a Probe of RNA Structure and Metal-Binding Sites Pb2+-induced Cleavage of RNA Identification and Characterization of Metal Ion Coordination Interactions with RNA by Quantitative Analysis of Thiophilic Metal Ion Rescue of Site-specific Phosphorothioate Modifications Probing RNA Structure and Ligand Binding Sites on RNA by Fenton Cleavage Measuring the Stoichiometry of Magnesium Ions Bound to RNA Nucleotide Analog Interference Mapping and Suppression (NAIM/NAIS) Nucleotide Analog Interference Mapping (NAIM): Application to the RNase P System Identification of Divalent Metal Ion Binding Sites in RNA/DNA-metabolizing Enzymes by Fe(II)-mediated Hydroxyl Radical Cleavage RNA Structure and Folding Analyzed Using Small-angle X-ray Scattering Temperature-Gradient Gelectrophoresis of RNA UV-melting Studies with RNA RNA Crystallisation Atomic Force Microscopy Imaging and Force Spectroscopy of RNA VOLUME 2 PART III: RNA Genomics & Bioinformatics, Global Approaches Secondary Structure Prediction RNA Secondary Structure Analysis Using Abstract Shapes Screening Genome Sequences for Known RNA Genes or Motifs Homology Search for Small Structured ncRNAs Molecular Dynamics of RNA Systems Identification and Characterization of Small Non-coding RNAs in Bacteria The Identification of Bacterial non-coding RNAs through Complementary Approaches Experimental RNomics, A Global Approach to Identify Non-coding RNAs in Model Organisms, and RNPomics to Analyze the Non-coding RNP Transcriptome Computational Methods for Gene Expression Profiling Using Next-generation Sequencing (RNA-Seq) Characterization and Prediction of miRNA Targets Barcoded cDNA Libraries for miRNA Profiling by Next-generation Sequencing Transcriptome-wide Identification of Protein-binding Sites on RNA by PAR-CLIP (Photoactivatable Ribonucleoside Analog Enhanced Crosslinking and Immunoprecipitation) PART IV: RNA Function, RNP Analysis, SELEX, RNAi Global Analysis of Protein-RNA Interactions with Single-nucleotide Resolution Using iCLIP Use of RNA Affinity Matrices for the Isolation of RNA-binding Proteins Biotin-based Affinity Purification of RNA-protein Complexes Affinity Purification of Spliceosomal and Small Nuclear Ribonucleoprotein Complexes Study of RNA-protein Interactions and RNA Structure in Ribonucleoprotein Particles Immunopurification of Endogenous RNAs Associated with RNA-binding Proteins in vivo Protein?RNA Crosslinking in Native Ribonucleoprotein Particles Sedimentation Analysis of Ribonucleoprotein Complexes Experimental Identification of microRNA Targets Aptamer Selection against Biological Macromolecules: Proteins and Carbohydrates In vitro Selection against Small Targets SELEX Strategies to Identify Antisense and Protein Target Sites in RNA or hnRNP Complexes Genomic SELEX In Vivo SELEX Strategies Gene Silencing Methods Using Vector-encoded siRNAs or miRNAs Using Chemical Modification to Enhance siRNA Performance
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.