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RNA Processing Part A

Many methods have been developed or adapted for the study of RNA processing, which plays a key role in the expression of genetic information. Volumes 180 and 181 of Methods in Enzymology, RNA Processing, Parts A and B, represent the first comprehensive collation of protocols used for the preparation of substrates, for the preparation of extracts and enzymes, and for the analysis of products in RNA processing. At least half of the chapters present techniques that are directly applicable to other areas of nucleic acid biochemistry and cell biology.
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Table of Contents

Preparation of Substrates: Purification of RNA Molecules: S.L. Berger and J.M. Chirgwin, Isolation of RNA. T. Ikemura, Purification of RNA Molecules by Gel Techniques. N.K. Tanner, Purifying RNA by Column Chromatography. In Vitro Synthesis of RNA: J.K. Yisraeli and D.A. Melton, Synthesis of Long, Capped Transcripts in Vitro by SP6 and T7 RNA Polymerases. J.F. Milligan and O.C. Uhlenbeck, Synthesis of Small RNAs Using T7 RNA Polymerase. V.M. Reyes and J.N. Abelson, In Vitro Synthesis of End-Mature, Intron-Containing Transfer RNAs. In Vivo Preparation of Substrates: S. Chen-Kiang and D.J. Lavery, Preparation of Precursors to mRNA from Mammalian Cell Nuclei. S. Chen-Kiang and D.J. Lavery, Pulse Labeling of Heterogeneous Nuclear RNA in Isolated Nuclei. J. Klootwijk and R.J. Planta, Isolation and Characterization of Yeast Ribosomal RNA Precursors and Preribosomes. G. Knapp, Preparation of Yeast Transfer RNA Precursors in Vivo. Characterization of RNAs: Primary Structure: C.S. Hahn, E.G. Strauss, and J.H. Strauss, Dideoxy Sequencing of RNA Using Reverse Transcriptase. A.D. Branch, B.J. Benenfeld, and H.D. Robertson, RNA Fingerprinting. Y. Kuchino and S. Nishimura, Enzymatic RNA Sequencing. Y. Furuichi and A.J. Shatkin, Characterization of Cap Structures. J.D. Reilly, J.C. Wallace, R.F. Melhem, D.W. Kopp, and M. Edmonds, Isolation and Characterization of Branched Oligonucleotides from RNA. Secondary Structure: G. Knapp, Enzymatic Approaches to Probing of RNAL Secondary and Tertiary Structure: A. Krol and P. Carbon, A Guide for Probing Native Small Nuclear RNA and Ribonucleoprotein Structures. B.D. James, G.J. Olsen, and N.R. Pace, Phylogenetic Comparative Analysis of RNA Secondary Structure. L.T. Chow and T.R. Broker, Mapping the Genetic Organization of RNA by Electron Microscopy. M. Zuker, Computer Prediction of RNA Structure. C.W.A. Pleij and L. Bosch, RNA Pseudoknots: Structure, Detection, and Prediction. J.D. Puglisi and I. Tinoco, Jr. , Absorbance Melting Curves of RNA. RNA Functions: S.L. Berger, Nuclease Digestion: A Method for Mapping Introns. A.J. Berk, Characterization of RNA Molecules by S1 Nuclease Analysis. W.R. Boorstein and E.A. Craig, Primer Extension Analysis of RNA. L. Conway and M. Wickens, Modification Interference Analysis of Reactions Using RNA Substrates. RNA Interactions: Cross-Linking: M.M. Hanna, Photoaffinity Cross-Linking Methods for Studying RNA-Protein Interactions. S. Pi~ahnol-Roma, S.A. Adam, Y.D. Choi, and G. Dreyfuss, Ultraviolet-Induced Cross-Linking of RNA to Proteins in Vivo. A.D. Branch, B.J. Benenfeld, C.P. Paul, and H.D. Robertson, Analysis of Ultraviolet-Induced RNA-RNA Cross-Links: A Means for Probing RNA Structure-Function Relationships. Other Methods: M.M. Konarska, Analysis of Splicing Complexes and Small Nuclear Ribonucleoprotein Particles by Native Gel Electrophoresis. K.A. Parker and J.A. Steitz, Determination of RNA-Protein and RNA-Ribonucleoprotein Interactions by Nuclease Probing. J.A. Steitz, Immunoprecipitation of Ribonucleoproteins Using Autoantibodies. Y.N. Osheim and A.L. Beyer, Electron Microscopy of Ribonucleoprotein Complexes on Nascent RNA Using Miller Chromatin Spreading Method. R. Parker, Genetic Methods for Identification and Characterization of RNA-RNA and RNA-Protein Interactions. Appendix: R. Reddy, Compilation of Small Nuclear RNA Sequences. J.M. Burke, Sequences and Classification of Group I and Group II Introns. G. Bruening, Compilation of Self-Cleaving Sequences from Plant Virus Satellite RNAs and Other Sources. Each chapter includes references. Author Index. Subject Index.


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