Handbook of RNA Biochemistry. Edition No. 2

Table of Contents

VOLUME 1

RNA SYNTHESIS AND DETECTION
Enzymatic RNA Synthesis Using Bacteriophage T7 RNA Polymerase
Production of RNAs with Homogeneous 5'- and3' -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

STRUCTURE DETERMINATION
Direct Determination of RNA Sequence and Modification by Radiolabeling Methods
Probing RNA Structure In Vitro with Enzymes and Chemicals
Probing RNA Solution Structure by Photocrosslinking: Incorporation of Photoreactive Groups at RNA Termini and Determination of Crosslinked Sites by Primer Extension
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): A Combinatorial Approach to Study RNA Structure, Folding, and Interaction with Proteins
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 Gel Electrophoresis of RNA
UV Melting Studies with RNA
RNA Crystallization
Studying RNA Using Single Molecule Fluorescence Resonance Energy Transfer
Atomic Force Microscopy Imaging and Force Spectroscopy of RNA

VOLUME 2

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 Non-Coding RNAs
Predict RNA 2D and 3D Structure over the Internet using MC-Tools
S2S-Assemble2: A Semi-Automatic Bioinformatics Framework to Study and Model RNA 3D Architectures
Molecular Dynamics Simulations 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-Enhanced Crosslinking and Immunoprecipitation)
Global Analysis of Protein-RNA Interactions with Single-Nucleotide Resolution Using iCLIP

RNA FUNCTION, RNP ANALYSIS, SELEX, RANi
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 (RNPs)
Immunopurification of Endogenous RNAs Associated with RNA Binding Proteins In vivo
Protein-RNA Crosslinking in Native Ribonucleoprotein Particles
Sedimentation Analysis of Ribonucleoprotein Complexes
Identification and Characterization of RNA Binding Proteins through Three-Hybrid Analysis
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

Appendix: UV Spectroscopy for the Quantitation of RNA
Index

Authors

Roland K. Hartmann University of Marburg, Germany. Albrecht Bindereif University of Marburg, Germany. Astrid Sch¿n University of Marburg, Germany. Eric Westhof University of Marburg, Germany.