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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