Handbook of RNA biochemistry

Content: V. 1: --
Part I. RNA SYNTHESIS --
I.1. Enzymatic RNA synthesis using bacteriophage T7 RNA polymerase: / Heike Gruegelsiepe [and others] --
Production of RNAs with homogeneous 5' and 3' ends / Mario Mörl [and others] --
RNA ligation using T4 DNA ligase / Mikko J. Frilander, Janne J. Turunen --
T4 RNA ligase / Tina Persson [and others] --
Co- and post-transcriptional incorporation of specific modifications including photoreactive groups into RNA molecules / Nathan H. Zahler, Michael E. Harris --
3'-terminal attachment of fluorescent dyes and biotin / Dagmar K. Willkomm, Roland K. Hartmann --
I.2. Chemical RNA synthesis: --
Chemical RNA synthesis, purification and analysis / Brian S. Sproat --
Modified RNAs as tools in RNA biochemistry / Thomas E. Edwards, Snorri Th. Sigurdsson --
Part II. STRUCTURE DETERMINATION --
II. 1. Molecular biology methods: --
Direct determination of RNA sequence and modification by radiolabeling methods / Olaf Gimple, Astrid Schön --
Probing RNA structures with enzymes and chemcials In Vitro and In Vivo / Eric Huntzinger [and others] --
Study of RNA-protein interactions and RNA structure in ribonucleoprotein particles / Virginie Marchand [and others] --
Terbium(III) footprinting as a probe of RNA structure and metal-binding sites / Dinari A. Harris, Nils G. Walter --
Pb²-induced cleavage of RNA / Leif A. Kirsebom, Jerzy Ciesiolka --
In Vivo determination of RNA structure by dimethylsulfate / Christina Waldsich, Renée Schroeder --
Probing structure and binding sties on RNA by Fenton Cleavage / Gesine Bauer, Christian Berens --
Measuring the stoichiometry of magnesium ions bound to RNA / A.J. Andrews, Carol Fierke --
Nucleotide analog interference mapping and suppression: specific applications in studies of RNA tertiary structure, dynamic helicase mechanism and RNA-protein interactions / Olga Fedorova [and others] --
Nucleotide analog interference mapping: application to the RNase P system / Simona Cuzic, Roland K. Hartmann --
Identification and characterization of metal ion binding by thiophilic metal ion rescue / Eric L. Christian --
Identification of divalent metal ion binding sites in RNA/DNA-metabolizing enzymes by Fe(II)-mediated hydroxyl radical cleavage / Yan-Guo Ren [and others] --
Protein-RNA crosslinking in native ribonucleoprotein particles / Henning Urlaub [and others] --
Probing RNA structure by photoaffinity crosslinking with 4-thiouridine and 6-thioguanosine / Michael E. Harris, Eric L. Christian --
II. 2. Biophysical methods: --
Structural analysis of RNA and RNA-protein complexes by small-angle x-ray scattering / Tao Pan, Tobin R. Sosnick --
Temperature-gradient gel electrophoresis of RNA / Detlev Riesner, Gerhard Steger --
UV melting, native gels and RNA conformation / Andreas Werner --
Sedimentation analysis of ribonucleoprotein complexes / Jan Medenbach [and others] --
Preparation and handling of RNA crystals / Boris François [and others] --
II. 3. Fluorescence and single molecule studies: --
Fluorescence labeling of RNA for single molecule studies / Filipp Oesterhelt [and others] --
Scanning force microscopy and scanning force spectroscopy of RNA / Wolfgang Nellen --
v. 2. --
Comparative analysis of RNA secondary structure: 6S RNA / James W. Brown, J. Christopher Ellis --
Secondary structure prediction / Gerhard Steger --
Modeling the architecture of structures RNAs within a modular and hierarchical framework / Benoît Masquida, Eric Westhof --
Modeling large RNA assemblies using a reduced representation / Jason A. Mears [and others] --
Molecular dynamics simulations of RNA systems / Pascal Auffinger, Andrea C. Vaiana --
Seeking RNA motifs in genomic sequences / Matthieu Legendre, Daniel Gautheret --
Approaches to identify novel non-messenger RNAs in bacteria and to investigate their biological functions: RNA mining / Jörg Vogel, E. Gerhart H. Wagner --
Approaches to identify novel non-messenger RNAs in bacteria and to investigate their biological functions: functional analysis of identified non-mRNAs / E. Gerhart H. Wagner, Jörg Vogel --
Experimental RNomics: a global approach to identify non-coding RNAs in model organisms / Alexander Hüttenhofer --
Large-scale analysis of mRNA splice variants by microarray / Young-Soo Kwon [and others] --
PART IV. ANALYSIS OF RNA FUNCTION --
IV. 1 RNA-protein interactions in vitro --
Use of RNA affinity matrices for the isolation of RNA-binding proteins / Steffen Schiffer [and others] --
Biotin-based affinity purification of RNA-protein complexes / Zsofia Palfi [and others] --
Immunoaffinity purification of spliceosomal and small nuclear ribonucleoprotein complexes / Cindy L. Will [and others] --
Northwestern techniques for the identification of RNA-binding proteins from cDNA expression libraries and the analysis of RNA-protein interactions / Ángel Emilio Martínez de Alba [and others] --
IV. 2. RNA-protein interations in vivo: --
Fluorescent detection of nascent transcripts and RNA-binding proteins in cell nuclei / Jennifer A. Geiger, Karla M. Neugebauer --
Identification and characterization of RNA-binding proteins through three-hybrid analysis / Felicia Scott, David R. Engelke --
Analysis of alternative splicing in vivo using using minigenes / Yesheng Tang [and others] --
IV. 3 SELEX: --
Artificial selection: finding function amongst randomized sequences / Ico de Zwart [and others] --
Aptamer selection against biological macromolecules: proteins and carbohydrates / C. Stefan Vörtler, Maria Milovinkova --
In vivo SELEX strategies / Thomas A. Cooper --
In vitro selection against small targets / Dirk Eulberg [and others] --
SELEX strategies to identify antisense and protein target sites in RNA or heterogeneous nuclear ribonucleoprotein complexes / Martin Lützelberger [and others] --
PART V. RNAi --
Gene silencing methods for mammalian cells: application of synthetic short interfering RNAs / Matthias John [and others].