Nucleic Acid Electrophoresis

340 Pages·1998·7.68 MB·English

by  Nancy C. Stellwagen (auth.)

SPRINGER
LAB MANUAL
Springer-Verlag Berlin Heidelberg GmbH
Dietmar Tietz (Ed.)
Nucleci Acdi
Electrophoressi
With 62 Figures and 10 Tables
DIETMAR TIETZ
8167 Shoal Creek Drive
Laurel, MD 20724-2950
USA
ISBN 978-3-642-47763-8
Library of Congress Cataloging-in-Publication Data
Nucleic acid electrophoressi / Dietmar Tietz (ed.). - Berlin ;
Heidelberg ; New York : Springer, 1998
(Springer lab manua)l
ISBN 978-3-642-47763-8 ISBN 978-3-642-58924-9 (eBook)
DOI 10.1007/978-3-642-58924-9
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© Springer-Verlag Berlin Heidelberg 1998
Originally published by Springer-Verlag Berlin Heidelberg New York in 1998
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Dedicated to the memory ofJohn S. Fawcett (t February 2, 1998),
an outstanding human being, a highly creative scientist,
a good friend and a very helpful colleague
Preface
Modern publications are generally written in a very concise fashion with
the main focus on results rather than experimental procedures. There
fore, when Springer-Verlag approached me to edit a book on nucleic acid
electrophoresis for their lab manual series, I welcomed this as an oppor
tunity to publish all those usually hidden technical details so important
for the success of many projects in molecular biology, medicine, analyt
ical biochemistry, agriculture, forensic sciences and other important dis
ciplines.
The book's concept is to focus on laboratory electrophoretic proce
dures and to assist a wide readership by describing experimental techni
ques. It addresses the experienced scientist and technician in search of a
new electrophoretic method, as well as the student who wants to become
familiar with this originally "blue fingers" discipline that is rapidly
changing into a high-tech enterprise.
This lab manual does not follow the path of a traditional textbook and
makes no attempt to provide an exhaustive coverage of as many aspects
as possible. Instead, we took the approach of inviting experts in the most
important electrophoretic techniques and asked them to write a meth
odological chapter of their own choice. The rationale was to obtain the
best contributions by letting authors write about their favorite subject.
We also seek to encourage use of the new electronic media by providing
e-mail addresses and data about helpful Internet newsgroups and Web
sites. In addition, a Web site will be created to accompany this book and
provide more information and comments from our readers:
http://www.his.com/~ djtllabmanual.html.
At this point we wish to thank all the contributors for providing their
articles preformatted for electronic publication and for giving their time
and effort without payment in order to produce a more accessible book.
This lab manual project was started in the Department of Biometry and
Population Genetics at Justus-Liebig University in GieBen, Germany, and
was continued using the scientific resources of the National Institutes of
VIn Preface
Health (NIH) in Bethesda, Maryland, USA. I wish to gratefully acknowl
edge the support of these two institutions and their staff. In particular, I
would like to mention Prof. Dr. Wolfgang Kohler (GieBen), Dr. Andreas
Chrambach (NIH) and Dianeth Dorris (NIH). Special thanks are also
due to Dr. Jutta Lindenborn and other members of Springer-Verlag for
their very helpful support of this venture and for their patience. We hope
that the contributions will benefit a number of scientific projects.
Bethesda, December 1997 Dietmar Tietz
Corresponding address:
DR. DIETMAR TIETZ
8167 Shoal Creek Drive
Laurel, Maryland 2072-4-2950
USA
e-mail: [email protected]
Table of Contents
1 DNA Gel Electrophoresis ................................... 1
NANCY C. STELLWAGEN
2 Denaturating Electrophoresis in DNA Sequencing:
A Brief History and Current Protocols. . . . . . . . . . . . . . . . . . . . .. 54
ALEXANDER KRAEV
3 An Introduction to DNA Fingerprinting Using RFLP
and RAPD Techniques. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 99
R.J. SNOWDON AND A. LANGSDORF
4 Pulsed-Field Gel Electrophoresis for Genomic Fingerprinting
of Pathogenic Bacteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 129
MICHAEL B. COULTHART, WENDY M. JOHNSON,
FRASER E. ASHTON
5 Ultrasensitive Silver Based Stains
for Nucleic Acid Detection ............................... 152
CARL R. MERRIL, KAREN M. WASHART, ROBERT C. ALLEN
6 The Analysis of Microsatellites by Silver Staining
of Nondenaturing Polyacrylamide Gels .................... 162
SHIRIN S. JOSEPH
7 Capillary Electrophoretic Separation of DNA Fragments . . . .. 170
JOHN M. BUTLER and DENNIS J. REEDER
8 Rapid Detection of Hepatitis C Virus in Plasma
and Liver Biopsies by Capillary Electrophoresis ............. 193
SAMEER A. SAKALLAH, ROBERT W. LANNING, DAVID 1. COOPER
X Table of Contents
9 Electrophoresis in the Field of Forensic Science ............. 202
HILDEGARD HAAS-RoCHHOLZ
10 The Electrophoretic Mobility Shift Assay (EMSA)
for Detection and Analysis of Protein-DNA Interactions ..... 239
MICHAEL G. FRIED and MARK M. GARNER
11 Mobility Shift Analysis of Protein-DNA Complexes
by Capillary Electrophoresis ............................. 272
JUN XIAN and MICHAEL G. HARRINGTON
12 Polyacrylamide Gel Electrophoresis
of DNA/Protein Complexes ............................... 292
ANDREAS KYAS, WINFRIED MXUELER, JOERG T. EpPLEN
13 Detection of DNA Curvature Using Transverse Pore Gradient
Polyacrylamide Gel Electrophoresis ....................... 311
DAVID WHEELER
Subject Index .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 325
Authors' Addresses
NANCY C. STELLWAGEN (Chapter 1)
Nancy C. Stellwagen, Department of Biochemistry, University of Iowa,
4403 Bowen Science Building, Iowa City, Iowa 52242, USA
(phone + 1-319-335-7932; fax + 1-319-335-9570;
e-mail [email protected])
ALEXANDER KRAEV (Chapter 2)
Alexander Kraev, Laboratory of Biochemistry III, Swiss Federal Institute
of Technology (ETH), Universitatsstrasse 16, 8092 Ziirich, Switzerland
(phone [phone]; fax [phone];
e-mail [email protected]; web site http://www.bc.biol.ethz.ch/Bio
chemistryIII/Sasha/kraev.html)
R. J. SNOWDON and A. LANGSDORF (Chapter 3)
R.J. Snowdon, A. Langsdorf, Department of Biometry and Population
Genetics, Justus-Liebig Universitat, Ludwigstrasse 37, 35390 Giessen,
Germany)
Correspondence to R.J. Snowdon: phone [phone]; fax +49-641-
9937549; e-mail [email protected])
MICHAEL B. COULTHART, WENDY M. JOHNSON, FRASER E. ASHTON
(Chapter 4)
Correspondence to Michael B. Coulthart, Laboratory Centre for Disease
Control, Room 240, HPB Building #7, PL 0700F, Ottawa, Ontario,
Canada KIA OL2
(phone + 1-613-952-7312; fax + 1-613-941-2408;
e-mail [email protected])