Handbook of Nucleic Acid Purification

570 Pages·2009·8.2 MB·English

by  Dongyou Liu (ed.)

HANDBOOK OF
NUCLEIC ACID
PURIFICATION
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HANDBOOK OF
NUCLEIC ACID
PURIFICATION
Edited by
Dongyou Liu

Boca Raton London New York
CRC Press is an imprint of the
Taylor & Francis Group, an informa business
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Library of Congress Cataloging-in-Publication Data
Handbook of nucleic acid purification / editor, Dongyou Liu.
p. ; cm.
Includes bibliographical references and index.
ISBN 978-1-4200-7096-5 (hardcover : alk. paper)
1. Nucleic acids--Purification--Handbooks, manuals, etc. I. Liu, Dongyou.
[DNLM: 1. Nucleic Acids--isolation & purification. QU 58 H236 2009]
QP620.H35 2009
572’.33--dc22 2008029325
Visit the Taylor & Francis Web site at
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Contents
Preface
Editor
Contributors
Chapter 1 Nucleic Acids: Structures, Functions, and Applications
Valentin V. Vlassov, Dmitrii V. Pyshnyi, and Pavel E. Vorobjev
PART I Purifi cation of Nucleic Acids from Viruses
Chapter 2 Isolation of Viral DNA from Cultures
Larry A. Hanson
Chapter 3 Isolation of Viral RNA from Cultures
Ling Zhao and Zhen F. Fu
Chapter 4 Preparation of Viral Samples for Direct Molecular Applications
Grant S. Hansman
PART II Purifi cation of Nucleic Acids from Bacteria
Chapter 5 Isolation of Bacterial DNA from Cultures
Dongyou Liu
Chapter 6 Isolation of Bacterial RNA from Cultures
Som Subhra Chatterjee and Trinad Chakraborty
Chapter 7 Isolation of Plasmids
Armelle Bigot and Alain Charbit
Chapter 8 Preparation of Bacterial Samples for Direct Molecular Applications
Knut Rudi, Robert C. Wilson, Kjetill S. Jakobsen, and Dongyou Liu
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PART III Purifi cation of Nucleic Acids from Fungi
Chapter 9 Isolation of Nucleic Acids from Yeasts
Lakshman P. Samaranayake, Nipuna B. Parahitiyawa,
and C. Jayampath Seneviratne
Chapter 10 Isolation of Nucleic Acids from Filamentous Fungi
Margaret E. Katz and Brian F. Cheetham
Chapter 11 Preparation of Fungal Specimens for Direct Molecular Applications
Françoise Irlinger, Nicolas Berthet, Tatiana Vallaeys, Valérie Vasseur,
Renaud Ioos, Marc Buée, and Jérôme Mounier
PART IV Purifi cation of Nucleic Acids from Parasites
and Insects
Chapter 12 Isolation of Nucleic Acids from Protozoa
Vitaliano A. Cama and Lihua Xiao
Chapter 13 Isolation of Nucleic Acids from Helminthes
Munehiro Okamoto and Akira Ito
Chapter 14 Isolation of Nucleic Acids from Insects
Kun Yan Zhu
Chapter 15 Preparation of Parasitic Specimens for Direct Molecular Applications
Huw Vaughan Smith and Rosely Angela Bergamin Nichols

PART V Purifi cation of Nucleic Acids from Mammals
Chapter 16 Isolation of Nucleic Acids from Body Fluids
Karen Page and Jacqueline Amanda Shaw
Chapter 17 Isolation of Nucleic Acids from Soft Tissues
Sergey Kovalenko
Chapter 18 Isolation of Nucleic Acids from Hard Tissues
Judith Weidenhofer and Jennifer A. Byrne
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Chapter 19 Isolation of DNA from Ancient Samples
Paula F. Campos, Eske Willerslev, and M. Thomas P. Gilbert
Chapter 20 Preparation of Forensic Samples for Direct Molecular Applications
Erin K. Hanson and Jack Ballantyne
PART VI Purifi cation of Nucleic Acids from Plants
Chapter 21 Isolation of Nucleic Acids from Plants
Song Weining and Dongyou Liu
Chapter 22 Isolation of Megabase-Sized DNA Fragments from Plants
Meiping Zhang, Yaning Li, and Hong-Bin Zhang
PART VII P urifi cation of Nucleic Acids from Miscellaneous
Sources
Chapter 23 Purifi cation of Nucleic Acids from Gels
Chunfang Zhang and Theo Papakonstantinou

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Preface
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are m acromolecules composed of single
or double strands of nucleotides, with each nucleotide consisting of a nitrogenous base (a derivative
of purine [adenine and guanine] or pyrimidine [thymine, uracil, and cytosine]) and a sugar (a pen-
tose deoxyribose or ribose, together referred to as a nucleoside) as well as a phosphate group.
Although the fi rst isolation of DNA was reported by Friedrich Miescher in 1869, it was only in 1953
that the molecular structure of the DNA duplex was elucidated by James Watson and F rancis Crick.
This landmark discovery uncovered the role of DNA as the chemical bearer and t ransmitter of
hereditary features, and expedited the development of contemporary molecular biology and biotech-
nology, with its full impact yet to be felt in the years to come.
Because of the structural and functional complexities within prokaryotic and eukaryotic cells,
purifi cation of nucleic acids often forms a vital fi rst step in the study of molecular biology of living
organisms as well as in the evolutionary/phylogenetic analysis of ancient specimens. To this end,
many innovative nucleic acid isolation methods have been designed, which are treated in a variety
of professional journals and books. This book aims to be all encompassing on nucleic acid purifi ca-
tion strategies for viruses, bacteria, fungi, parasites, insects, mammals, and plants as well as ancient
samples, with an additional emphasis on sample preparation methods for direct molecular
applications.
Each chapter begins with informative coverage of the biological background followed by an
expert review of basic principles and current techniques for isolation of nucleic acids from specifi c
sample types along with an insightful discussion of future development trends. Besides providing a
comprehensive, reliable reference on nucleic acid purifi cation for anyone with an interest in molecu-
lar biology, this book is a practical guide for clinical, forensic, and research scientists involved in
molecular analysis of biological specimens; a convenient textbook for prospective undergraduate
and graduate students intending to pursue a career in molecular biology, microbiology, and forensic
science; and an indispensable roadmap for upcoming and experienced researchers wishing to acquire
or sharpen their skills in nucleic acid preparation.
The scope and depth of the topics covered in this book would clearly have been impossible
without a concerted team effort. I am fortunate and honored to have a panel of international scien-
tists as contributors with expertise in their respective fi elds of molecular biology, whose knowledge
and technical insights have enriched this book tremendously. In addition, the professionalism and
dedication of editorial staff at CRC Press have further enhanced presentation. I hope the readers
through the perusal of this book will fi nd it rewarding as it develops an understanding of the theory
and practice of nucleic acid purifi cation from virtually all sample types in a few weeks that may
otherwise take many years.
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