Capillary Electrophoresis of Nucleic Acids Vol 2 - Practical Applications of Capillary Electrophoresis; Volume 163 of Methods in Molecular Biology - Humana

396 Pages·2016·2.92 MB·English

by  Mitchelson K.R.

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Capillary Electrophoresis of Nucleic Acids
Volume II
M E T H O D S I N M O L E C U L A R B I O L O G YTM
John M. Walker, SERIES EDITOR
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M E T H O D S I N M O L E C U L A R B I O L O G YTM
Capillary
Electrophoresis
of Nucleic Acids
Volume II: Practical Applications
of Capillary Electrophoresis
Edited by
Keith R. Mitchelson
Australian Genome Research Facility, University of Queensland,
Brisbane; and Walter & Eliza Hall Institute,
Parkville, Australia
and
Jing Cheng
Biochip Research and Development Center
State Key Laboratory for Biomembrane and Membrane Biotechnology,
Tsinghua University, Beijing, China; and Aviva Biosciences Corporation,
San Diego, CA
Humana Press Totowa, New Jersey
Dedication
To Nanne and Moon
Each is unique.
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Methods in molecular biology™.
Capillary electrophoresis of nucleic acids/edited by Keith R. Mitchelson and Jing Cheng.
p. cm. -- (Methods in molecular biology; 162-163)
Includes bibliographical references and index.
Contents: v. 1. Introduction to the capillary electrophoresis of nucleic acids-- v.2.
Practical applications of capillary electrophoresis
ISBN 0-89603-765-7 (v. 1: alk. paper) -- ISBN 0-89603-765-7 (v.2: alk. paper)
1. Nucleic acids--Separation. 2. Capillary electrophoresis. I. Mitchelson, Keith R. II.
Cheng, Jing. III. Series.
QP620.C36 2000 00-038911
572.8--dc21 CIP
Preface
The development of PCR, which enables extremely small amounts of
DNA to be amplified, led to the rapid development of a multiplicity of ana-
lytical procedures to utilize this new resource for analysis of genetic variation
and for the detection of disease causing mutations. The advent of capillary
electrophoresis (CE), with its power to separate and analyze very small amounts
of DNA, has also stimulated researchers to develop analytical procedures for
the CE format. The advantages of CE in terms of speed and reproducibility of
analysis are manifold. Further, the high sensitivity of detection, and the abil-
ity to increase sample throughput with parallel analysis, has led to the creation
of a full range of analysis of DNA molecules, from modified DNA-adducts
and single–strand oligonucleotides through to PCR-amplified DNA fragments
and whole chromosomes. Capillary Electrophoresis of Nucleic Acidsfocuses
on such analytical protocols, which can be used for detection and analysis of
mutations and modification, from precise DNA loci through to entire genomes
of organisms. Important practical considerations for CE, such as the choice of
separation media, electrophoresis conditions, and the influence of buffer
additives and dyes on DNA mobility, are discussed in several key chapters
and within particular applications. The use of CE for the analysis of drug–
DNA interactions and for examination of the metabolism of therapeutic oligo-
nucleotides and modified nucleosides illustrate the burgeoning applications
of CE for the analysis of a wide range of medical and molecular diagnostic
problems. The study of interactions between nucleic acids and diverse ligands
by CE is also a new and rapidly developing area. Microanalytical devices, which
include capillary electrophoretic separations, have resulted from the fusion of semi-
conductor devices and microdiagnostic analysis. Several seminal papers on
the application of microchip-based capillary electrophoresis for genotyping
and DNA sequence determination signal the revolution that is occurring in
both capillary electrophoresis and laboratory analysis.
Capillary Electrophoresis of Nucleic Acidscomprises two volumes divided
into twelve parts, each part containing chapters that address particular general
goals, or experimental approaches. Broadly, Volume I addresses instrumenta-
tion, signal detection, and the capillary environment, as well as the integration
of mass spectrometry and CE for the analysis of small oligonucleotides and
v
vi Preface
modified nucleotides. Volume II broadly addresses techniques for high-
throughput analysis of DNA fragments of less than 1 kb, employing SNP de-
tection, mutation detection, DNA sequencing methods, and DNA-ligand
interactions.
Volume I
Volume I, Part I presents basic CE instrumentation and the theoretical
background to the separation of DNA by CE. The choice of different modes of
CE and detection systems, the characteristics of sieving matrices, sample prepa-
ration, and quantitation of measurement are emphasized. DNA sequencing by
CE is discussed. Methods for the manufacture of microchip devices are
illustrated.
Volume I, Part II presents important factors, such as choice of
capillary coatings and separation media, which offer new possibilities for sepa-
rations. The theoretical background for the selection and composition of sieving
polymers for optimal separation is illustrated.
Volume I, Part III presents choices of separation media and the CE
environment for size-based (fragment length) separations of DNAs. Emphasis
is made on new co-polymer matrix
materials and liquid agaroses.
Volume I, Part IV discusses the fast separations of large DNA
molecules and chromosomes, using pulsed-field capillary electrophoresis for-
mats. Methods of collection of separated CE fractions for the analysis of
supercoiled DNAs are also presented.
Volume I, Part V presents practical choices for the analysis of small
therapeutic oligonucleotides, nucleosides, ribonucleotides, and DNA metabo-
lism products by CE. Practical applications for the control of quality of
nucleotides and oligonucleotides are illustrated.
Volume I, Part VI presents choices for the sensitive CE analysis of
nucleotides and DNA metabolism products arising from environmental and
cellular damage through disease. Practical applications of mass spectrometry
and capillary zone electrophoresis for the detection of oncogenic change are
also presented.
Volume II
Volume II, Part I presents practical considerations necessary for very
rapid and accurate separations of linear DNAs by CE using short capillaries.
SNuPE, heteroduplex analysis, ARMS analysis of DNA, and SSCP analysis.
Volume II, Part III details various modes of genotyping by CE. Par-
ticular emphasis is given to the use of multiplex separations. The techniques
include parallel analysis of multiple simple repeat loci in human and CE analysis
Preface vii
of gene markers following degenerate oligonucleotide amplification from single
cells. Methods for the application of chemical cleavage of mismatched DNA
for mutation detection are illustrated.
Volume II, Part IV presents techniques for the quantitative estimation
of gene expression using CE. Both quantitative RT-PCR and differential dis-
play analyses are highlighted.
Volume II, Part V presents practical choices of separation media and the
capillary electrophoresis environment for DNA sequencing by CE. Rapid
sequencing at elevated temperature and sequencing on micro- and array-CE
devices are discussed. Methods for sequencing with selective primers are also
illustrated.
Volume II, Part VI presents the analysis of DNA protein and DNA ligand
interactions using CE. Techniques discussed include mobility shift assays and
capillar affinity-gel electrophoresis.
Keith Mitchelson
Jing Cheng
CONTENTS OF THE COMPANION VOLUME
Capillary Electrophoresis of Nucleic Acids
Volume I: Introduction to the Capillary Electrophoresis of Nucleic Acids
PART I.ANALYTICAL CONSIDERATIONS FOR CAPILLARY ELECTROPHORESIS
1 Overview: The Application of Capillary Electrophoresis
for DNA Polymorphism Analysis
Keith R. Mitchelson
2 DNA Separation Mechanisms During Capillary Electrophoresis
Gary W. Slater, Claude Desruisseaux, and Sylvain J. Hubert
3 Purification Methods for Preparing Polymerase Chain Reaction
Products for Capillary Electrophoresis Analysis
Joseph M. Devaney and Michael A. Marino
4 Quantitative Measurements
Bruce McCord
5 Microchip-Based Capillary Electrophoresis Systems
Wenzhang Xie, Rong Yang, Junquan Xu, Liang Zhang,
Wanli Xing, and Jing Cheng
6 DNA Sequencing by Capillary Array Electrophoresis
Norman J. Dovichi and JianZhong Zhang
7 Determining Dye-Induced DNA Mobility Shifts for DNA Sequencing
Fragments by Capillary Electrophoresis
John Bashkin
PART II. CAPILLARY MATRIX:CONSIDERATIONSFOR CAPILLARY ELECTROPHORESIS
8 Influence of Polymer Concentration and Polymer Composition
on Capillary Electrophoresis of DNA
Christoph Heller
9 Capillary Coatings: Choices for Capillary Electrophoresis of DNA
Marcella Chiari and Marina Cretich
10 Replaceable Polymers in DNA Sequencing by Capillary
Electrophoresis
Mark A. Quesada and Steve Menchen
xiii
xiv Contents of Companion Volume
11 Sieving Matrix Selection
Tim Wehr, Mingde Zhu, and David T. Mao
12 Parameters Affecting Capillary Electrophoretic Separation of DNA
Haleem J. Issaq
PART III. ELECTROPHORESIS MATRIX:APPLICATIONSFOR DNA FRAGMENT SIZING
13 DNA Separation by Capillary Electrophoresis in Lyotropic Polymer
Liquid Crystals
Yingjie Liu and Randolph L. Rill
14 Capillary Electrophoresis of DNA Fragments
Using Poly(Ethylene Oxide) as a Sieving Material
Yongseong Kim and Edward S. Yeung
15 DNA Capillary Electrophoresis Using Block Copolymer as a New
Separation Medium
Benjamin Chu, Tianbo Liu, Chunhung Wu, and Dehai Liang
16 DNA Analysis Under Highly Denaturing Conditions
in Bare Fused Silica Capillaries
Karel Klepárník, Zdenvka Malá, and Petr Bocvek
17 Capillary Electrophoresis with Glycerol as an Additive
Keith R. Mitchelson and Jing Cheng
18 Capillary Electrophoresis of DNA Fragments
with Replaceable Low-Gelling Agarose Gels
Anders K. Palm
PART IV. PRACTICAL APPLICATIONS FOR LARGE DNA FRAGMENT SIZING
AND FRAGMENT COLLECTION
19 Robust Field Inversion Capillary Electrophoretic Separation
of Long DNA Fragments
Christoph Heller, Soffia Magnúsdóttir, and Jean-Louis Viovy
20 Pulsed-Field Capillary Electrophoresis Separation of Large DNA
Fragments
Michael D. Morris, Jeffrey J. Schwinefus, and Olivia de Carmejane
21 Collection of Capillary Electrophoresis Fractions
on a Moving Membrane
Soffia Magnúsdóttir, Christoph Heller, Phillipe Sergot,
and Jean-Louis Viovy
22 Separation of Supercoiled DNA Using Capillary Electrophoresis
David T. Mao and Roy M. A. Lautamo