Protocols for Nucleic Acid Analysis by Nonradioactive Probes

263 Pages·1994·23.176 MB·English

by  Peter G. Isaac (auth.), Peter G. Isaac (eds.)

Protocols for Nucleic Acid Analysis
by Nonradioactive Probes
Methods in Molecular Biology
John M. Walker,
SERIES EDITOR
28. Protocols for Nucleic Acid Analysis by Nonradioactive Probes,
edited by Peter G. Isaac, 1994
27. Biomembrane Protocols: II. Architecture and Function, ec~ted by
John M. Graham and Joan A. Higgins, 1994
26. Protocols for OHgonucleotide Conjugates, edited by Sudhir Agrawal, 1994
25. Computer Analysis of Sequence Data: Part II, edited by Annette M. Griffin
and Hugh G. Griffin, 1994
24. Computer Analysis of Sequence Data: Part I, ecfited byAnnette M. Griffin
and Hugh G. Griffin, 1994
23. DNA Sequencing Protocols, edited by Hugh G. Griffin
and Annette M. Griffin, 1993
22. Optical Spectroscopy, Microscopy, and Macroscopic Technlque~
edited by Christopher Jones, Barbara Mulloy,
and Adrian H. Thomas, 1994
21. Protocols in Molecular Parasitology, edited byJohnK Hyde, 1993
20. Protocols for OHgonucleotides and Analogs, ~lited bySudhirAgrawal,
1993
19. Biomembrane Protocols: I. Isolation and Analysis, edited by
John M. Graham and Joan A. Higgins, 1993
18. Transgenesis Techniques, edited by David Murphy
and David A. Carter, 1993
17. Spectroscopic Methods and Analyses, edited by Christopher Jones,
Barbara MuUoy, and Adrian H. Thomas, 1993
16. Enzymes of Molecular Biology, edited by Michael M. Burrell, 1993
15. PCR Protocols, edited by Brace A. White, 1993
14. Glycoprotein Analysis in Biomedicine, edited by Elizabeth F. Hounsell, 1993
13. Protocols in Molecular Neurobiology, edited by ALlaonn gstaff
and Patricia Revest, 1992
12. Pulsed-Field Gel Electrophoresis, edited by MargitBurmeister
and Levy Ulanovsky, 1992
11. Practical Protein Chromatography, edited by Andrew Kenney
and Susan Fowell, 1992
10. Immunochemical Protocols, edited by Margaret M. Manson, 1992
9. Protocols in Human Molecular Genetics, edited by
Christopher G. Mathew, 1991
8. Practical Molecular Virology, edited by Mary K. I~ Collins, 1991
7. Gene Transfer and Expression Protocols, edited by
Edward J. Murray, 1991
6. Plant Cell and Tissue Culture, edited by Jeffrey W. Pollard
and John M. Walker, 1990
5. ~,nlmal Cell Culture, edited by Jeffrey W. Pollard and John M. Walker, 1990
4. New Nucleic Acid Techniques, edited by John M. Walker, 1988
3. New Protein Techniques, edited by John M. Walker, 1988
2. Nucleic Acids, edited by John M. Walker, 1984
1. Proteins, edited by John M. Walker, 1984
Protocols
for Nucleic Acid Analysis
by Nonradioactive
Probes
Edited by
P e t e r G. I s a a c
Nickerson BIOCEM Ltd., Cambridge, UK
Humana Press ~
Totowa, New Jersey
© 1994 Humana Press Inc.
999 Riverview Drive, Suite 208
Totowa, New Jersey 07512
All rights reserved.
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Printed intheUnitedStatesofAmerica. 9 8 7 6 5 4 3 2
Library of Congress Cataloging in Publication Data
Main entry under title:
Methods in molecular biology.
Protocols for nucleic acid analysis by nonradioactive probes / edited
by Peter G. Isaac.
p. cm. -- (Methods in molecular biology ; 28)
Includes index.
ISBN 0-89603-254-X
1. Nucleic acid probes. 2. Nucleic acids--Analysis. I. Isaac,
Peter G. II. Title: Nonradioactive probes. III. Series: Methods in
molecular biology (Totowa, NJ) ; 28.
QP620.P765 1993
574.19'249---dc20 93-29390
CIP
Preface
In assembling this book, Protocols for Nucleic Acid Analysis by
Nonradioactive Probes, I have endeavored to select protocols that
have wide applicability. My aim in doing so is to allow nucleic acid
analysis to move from the confines of specialized research laborato-
ries and into general purpose and teaching laboratories. In particular,
disciplines such as population biology and clinical diagnostics (where
the application of the technology is important, not the technology
itself) will find the newer techniques easier to perform with the quan-
tity of samples that are normally required in these fields. Die-hard
molecular biologists with hot fingers will find, by trying some of the
protocols in this book, that nonradioactive protocols are normally
faster than their radioactive brethren, and give more reliable results.
An expanded description of the subject areas covered by this
book is given in Chapter 1. The technology herein has very broad
application; for instance, in conventional molecular biology research,
population biology, plant and animal breeding, genetic mapping,
paternity testing, forensics, prenatal diagnosis, and clinical and food
microbiology. I have tried to include comprehensive protocols for
both basic and more complex analyses. There are chapters dealing
with the fundamentals of nucleic acid extraction from plants and ani-
mals, and with the procedures necessary to immobilize nucleic acids
on solid supports. A range of labeling procedures is included, fol-
lowed by a selection of hybridization procedures. These are followed
by articles on hybridization to chromosomes and to gene transcripts
in situ. The final chapters of this book give details of novel, high-
throughput, nucleic acid screening systems.
I would encourage the reader to browse through Protocols for
Nucleic Acid Analysis by Nonradioactive Probes, particularly the
introduction to each chapter, since information relevant to one prob-
ing system will probably be found useful elsewhere. Also, to avoid
13
vi Preface
unnecessary duplication throughout the text, extensive use is made
of cross-references. For instance, the synthesis of RNA probes is
described in Chapter 12 specifically for minisatellite probes. How-
ever, the same technique is used to produce the probes for in situ
analysis in Chapters 29 and 30. There is a range of nonradioactive
systems available, and indications are given in each chapter of the
suitability of a protocol for a particular application.
It would have been impossible to produce this book without the
constant sage advice from the Methods in Molecular Biology series
editor, and so I would like to taker this opportunity to express my
thanks to Prof. John Walker at University of Hertfordshire. In addi-
tion, I would like to thank my colleagues at Nickerson BIOCEM Ltd.,
Justin Stacey, Liz Davies, and Chris Clee, for coping with my fre-
quent periods of gritted teeth during the production of this book. My
colleague Iain Cubitt is also owed an especial debt of thanks for the
encouragement he has given me in this project. Finally, I thank the
contributors, whose labor made this book possible.
Peter G. Isaac
Contents
Preface ....................................................................................................................... v
Contributors ............................................................................................................. xi
CH. 1. About Nonradioactive Nucleic Acid Detection,
Peter G. Isaac .................................................................................... 1
CH. 2. Isolation of DNA from Plants,
Justin Stacey and Peter G. Isaac ..................................................... 9
CH. 3. Isolation of High-Molecular-Weight DNA from Animal Cells,
fan Garner ....................................................................................... 17
CH. 4. Restriction Enzyme Digestion, Gel Electrophoresis, and Vacuum
Blotting of DNA to Nylon Membranes,
Jusan Stacey and Peter G. Isaac ................................................... 25
CH. 5. Isolation of Plant RNA,
Rachel l-lodge .................................................................................. 3 7
CH. 6. Isolation of Total and PolyA÷ RNA from Animal Cells,
fan Garner ....................................................................................... 41
CH. 7. Preparation of RNA Gel Blots,
Rachel ltodge .................................................................................. 49
CH. 8. Preparation of RNA Dot Blots,
Rachel Hodge .................................................................................. 55
CH. 9. Isolation of Plasmids for the Preparation of Probes,
Peter G. Isaac and Justin Staeey ................................................... 59
CH. 10. Production of Hybridization Probes by the PCR Utilizing
Digoxigenin-Modified Nucleotides,
Tom McCreery and Tim Helentjaris ............................................. 67
CH. 11. Production of DNA Hybridization Probes with Digoxigenin-
Modified Nucleotides by Random Hexanucleotide Priming,
Tom McCreery and Tim Helentjaris ............................................. 73
CH. 12. Digoxigenin Labeling of RNA Transcripts from Multi-
and Single-Locus DNA Minisatellite Probes,
Esther N. Signer .............................................................................. 77
CH. 13. Labeling of Double-Stranded DNA Probes with Biotin,
Angela Karp ..................................................................................... 83
vii
viii Contents
CH. 14. Preparation of Horseradish Peroxidase-Labeled Probes,
Ian Durrant and Timothy Stone .................................................... 89
CH. 15. Random Prime Labeling of DNA Probes with Fluorescein- 11-dUTP,
Bronwen M. Harvey, Claire B. Wheeler,
and Martin W. Cunningham ................................................ 93
CH. 16. Labeling of Oligonucleotides with Fluorescein,
Patricia M. E. Chadwick and fan Darrant ................................. 101
CH. 17. Hybridization of Digoxigenin-Labeled Probes to Southern Blots
and Detection by Chemiluminescence,
Tom MeCreery and Tim Helentjaris ........................................... 107
CH. 18. Southern Blot Hybridization of Digoxigenin-Labeled RNA
Minisatellite Probes and Color Detection,
Esther N. Signer ............................................................................ 113
CH. 19. Hybridization and Detection of Digoxigenin Probes
on RNA Blots,
Elizabeth Davies, Rachel Hodge, and Peter G. Isaac ................ 121
CH. 20. Hybridization of Horeradish Peroxidase-Labeled Probes
and Detection by Enhanced Chemiluminescence,
Timothy Stone and fan Durrant .................................................. 127
CH. 21. Hybridization and Detection of Fluorescein-Labeled
DNA Probes Using Enhanced Chemiluminescence,
Bronwen M. Harvey and Claire B. Wheeler ............................... 135
CH. 22. Hybridization of Fluorescein-Labeled Oligonucleotide Probes
and Enhanced Chemiluminescence Detection,
lan Durrant and Patricia M. E. Chadwick ................................. 141
CH. 23. Preparation of Chromosome Spreads by Root-Tip
Meristem Dissection for In Situ Hybridization
with Biotin-Labeled Probes,
Angela Karp ................................................................................... 149
CH. 24. Enzymatic Treatment of Plant Material to Spread Chromosomes
for In Situ Hybridization,
Trude Schwarzacher and Andrew R. Leitch ............................... 153
Ca. 25. Use of Biotin-Labeled Probes on Plant Chromosomes,
Angela Karp ................................................................................... 161
Ca. 26. Direct Fluorochrome-Labeled DNA Probes for Direct Fluorescent
In Situ Hybridization to Chromosomes,
Trude Sehwa~acher and J. S. (Pat) Heslop-Harrison .............. 167
CH. 27. Detection of Dioxigenin-Labeled DNA Probes Hybridized
to Plant Chromosomes In Situ,
Ilia J. Leitch and J. S. (Pat) Hesiop-Harrison ........................... 177
CH. 28. Preparation of Tissue Sections and Slides for mRNA
Hybridization,
Giorgio Terenghi and Julia M. Polak ......................................... 187
Con~n~
CH. 29. Detecting mRNA in Tissue Sections with Digoxigenin-Labeled
Probes,
Giorgio Terenghi and J1ut4li. a Polak ......................................... 193
CH. 30. Detection of mRNA in Whole Mounts of Mouse Embryos
Using Digoxigenin Riboprobes,
Barry Rosen and Rosa Beddington ............................................. 201
CH. 31. PACE (Probe Assay--Chemiluminescence Enhanced): A Magnetic
Bead Assay for Noncultural Diagnosis of Gonorrhea,
Paul A. Granato ............................................................................ 209
CH. 32. Detection of Foodborne Pathogens Using DNA Probes
and a Dipstick Format,
E. Patrick Groody .......................................................................... 217
Ca. 33. Analysis of Gene Sequences by Hybridization of PCR-Amplified
DNA to Covalently Bound Oligonucleotide Probes:
The Reverse Dot Blot Method,
Ernest S. Kawasaki and Farid F. Chehab .................................. 225
CH. 34. RAPD Assay: A Novel Technique for Genetic Diagnostics,
Joseph P. del Tufa and Scott 1I. Tingey ...................................... 237
CH. 35. Nonradioactive Oligonucleotide Probes for Detecting Products
of the Ligase Chain Reaction,
Jon Kratochvil aTnhdo mas G. Laffler ....................................... 243
CH. 36. Nucleic Acid Sequence-Based Amplification (NASBA~"),
Larry Malek, Roy Sooknanan, and Jean Compton .................... 253
Index ...................................................................................................................... 261
Contributors
ROSA BEDDINGTON * Centre for Genome Research, University of
Edinburgh, Scotland, UK
PATRICIA M. E. CHADWICK • Life Sciences Research and Development,
Amersham International plc, Amersham, UK
FARID F. CHEHAB "Department of Laboratory Medicine, University of
California, San Francisco, CA
JEAN COMPTON • Cangene Corporation, Mississauga, Ontario, Canada
MARTIN W. CUNNINGHAM • Research and Development Division,
Amersham International plc, Amersham, UK
ELIZABETH DAVIES "Nickerson BIOCEM Ltd., Cambridge, UK
JOSEPH P. DEE TUFO • Ou Pont Agricultural Products, E. I. du Pont de
Nemours and Company, Wilmington, DE
IAN DURRANT • Life Sciences Research and Development, Amersham
International plc, Amersham, UK
IAN GARNER • Pharmaceutical Proteins Ltd., Edinburgh, Scotland, UK
PAUL A. GRANATO • Crouse Irving Memorial Hospital, Syracuse, NY
E. PATRICK GROODY ° Vernon Hills, 1L
BRONWEN M. HARVEY ° Research and Development Division,
Amersham International plc, Amersham, UK
TIM HELENTJARIS ° Department of Plant Sciences, University of
Arizona, Tucson, AZ
J. S. (PAT) HESLOP-HARRISON • Karyobiology Group, Department of
Cell Biology, John Innes Centre, Norwich, UK
RACHEL HODGE • Department of Botany, University of Leicester, UK
PETER G. ISAAC ° Nickerson BIOCEM Ltd., Cambridge, UK
ANOELA KARP • Department of Agricultural Sciences, University of
Bristol, AFRC Institute of Arable Crops Research, Long Ashton
Research Station, Bristol, UK
ERNEST S. KAWASAKI " Procept Inc., Cambridge, MA
xi