RNA Processing Part A: General Methods

✍ Scribed by James E. Dahlberg, John N. Abelson (Eds.)

• Publisher: Academic Press
• Year: 1989
• Tongue: English
• Leaves: 625
• Series: Methods in Enzymology 180
• Edition: 1
• Category: Library

✦ Synopsis

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

✦ Table of Contents

Content:
Contributors to volume 180
Pages ix-xi

Preface
Page xiii
James E. Dahlberg, John N. Abelson

Volumes in series
Pages xv-xxix

[1] Isolation of RNA Original Research Article
Pages 3-13
Shelby L. Berger, John M. Chirgwin

[2] Purification of RNA molecules gel techniques Original Research Article
Pages 14-25
Toshimichi Ikemura

[3] Purifying RNA by column chromatography Original Research Article
Pages 25-41
N.Kyle Tanner

[4] Synthesis of long, capped transcripts in Vitro by SP6 and T7 RNA polymerases Original Research Article
Pages 42-50
Joel K. Yisraeli, Doug A. Melton

[5] Synthesis of small RNAs using T7 RNA polymerase Original Research Article
Pages 51-62
John F. Milligan, Olke C. Uhlenbeck

[6] In vitro synthesis of end-mature, intron-containing transfer RNAs Original Research Article
Pages 63-69
Vicente M. Reyes, John N. Abelson

[7] Preparation of precursors to mRNA from mammalian cell nuclei Original Research Article
Pages 69-82
Selina Chen-Kiang, Daniel J. Lavery

[8] Pulse labeling of heterogeneous nuclear RNA in isolated nuclei Original Research Article
Pages 82-96
Selina Chen-Kiang, Daniel J. Lavery

[9] Isolation and characterization of yeast ribosomal RNA precursors and preribosomes Original Research Article
Pages 96-109
Jacobus Klootwuk, Rudi J. Planta

[10] Preparation of yeast transfer RNA precursors in Vivo Original Research Article
Pages 110-117
Gayle Knapp

[11] Dideoxy sequencing of RNA using reverse transcriptase Original Research Article
Pages 121-130
Chang Shahn, Ellen G. Strauss, James H. Strauss

[12] RNA fingerprinting Original Research Article
Pages 130-154
Andrea D. Branch, Bonnie J. Benenfeld, Hugh D. Robertson

[13] Enzymatic RNA sequencing Original Research Article
Pages 154-163
Y. Kuchino, S. Nishimura

[14] Characterization of cap structures Original Research Article
Pages 164-176
Yasuhiro Furuichi, Aaron J. Shatkin

[15] Isolation and characterization of branched oligonucleotides from RNA Original Research Article
Pages 177-191
J. David Reilly, John C. Wallace, Randa F. Melhem, David W. Kopp, Mary Edmonds

[16] Enzymatic approaches to probing of RNA secondary and tertiary structure Original Research Article
Pages 192-212
Gayle Knapp

[17] A guide for probing native small nuclear RNA and ribonucleoprotein structures Original Research Article
Pages 212-227
Alain Krol, Philippe Carbon

[18] Phylogenetic comparative analysis of RNA secondary structure Original Research Article
Pages 227-239
Bryan D. James, Gary J. Olsen, Norman R. Pace

[19] Mapping the genetic organization of RNA by electron microscopy Original Research Article
Pages 239-261
Louise T. Chow, Thomas R. Broker

[20] Computer prediction of RNA structure Original Research Article
Pages 262-288
Michael Zuker

[21] RNA pseudoknot: Structure, detection, and prediction Original Research Article
Pages 289-303
C.W.A. Pleij, L. Bosch

[22] absorbance melting curves of RNA Original Research Article
Pages 304-325
Joseph D. Puglisi, Ignacio Tinoco Jr.

[23] Nuclease digestion: A method for mapping introns Original Research Article
Pages 325-334
Shelby L. Berger

[24] Characterization of RNA molecules by S1 nuclease analysis Original Research Article
Pages 334-347
Arnold J. Berk

[25] Primer extension analysis of RNA Original Research Article
Pages 347-369
William R. Boorstein, Elizabeth A. Craig

[26] Modification interference analysis of reactions using RNA substrates Original Research Article
Pages 369-379
Laura Conway, Marvin Wickens

[27] Photoaffinity cross-linking methods for studying RNA-protein interactions Original Research Article
Pages 383-409
Michelle M. Hanna

[28] Ultraviolet-induced cross-linking of rna to proteins in vivo Original Research Article
Pages 410-418
SerafГ­n PiЕ„ol-Roma, Stephen A. Adam, Yang Do Choi, Gideon Dreyfuss

[29] Analysis of ultraviolet-induced RNA-RNA cross-links: A means for probing RNA structure-function relationships Original Research Article
Pages 418-442
Andrea D. Branch, Bonnie J. Benenfeld, Cynthia P. Paul, Hugh D. Robertson

[30] analysis of splicing complexes and small nuclear ribonucleoprotein particles by native gel electrophoresis Original Research Article
Pages 442-453
Maria M. Konarska

[31] Determination of RNA-protein and RNA-ribonucleoprotein interactions by nuclease probing Original Research Article
Pages 454-468
Katherine A. Parker, Joan A. Steitz

[32] Immunoprecipitation of ribonucleoproteins using autoantibodies Original Research Article
Pages 468-481
Joan A. Steitz

[33] Electron microscopy of ribonucleoprotein complexes on nascent RNA using miller chromatin spreading method Original Research Article
Pages 481-509
Yvonne N. Osheim, Ann L. Beyer

[34] Genetic Methods for identification and characterization of RNA-RNA and RNA-protein interactions Original Research Article
Pages 510-517
Roy Parker

[35] Compilation of small nuclear RNA sequences Original Research Article
Pages 521-532
Ram Reddy

[36] Sequences and classification of group I and group II introns Original Research Article
Pages 533-545
John M. Burke

[37] Compilation of self-cleaving sequences from plant virus satellite RNAs and other sources Original Research Article
Pages 546-558
George Bruening

Author index
Pages 559-578

Subject index
Pages 579-600