DNA Amplification: Current Technologies and Applications
Publisher: Horizon Bioscience
Editors: Vadim V. Demidov and Natalia E. Broude Boston University, USA
Publication date: July 2004
Pages: xii + 336
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DNA amplification is the cornerstone of modern biotechnology and it is also a key procedure in numerous basic studies involving DNA and other biomolecules. Polymerase chain reaction (PCR) is still the most popular amplification method, however alternatives to PCR have successfully invaded the area. The emergence of such methodologies has significantly widened the range of approaches for DNA amplification and dramatically improved the technological abilities of basic and applied researchers in various fields of life sciences. Whereas most books on DNA amplification focus on PCR-based technologies, this volume presents a wider range of methods to amplify DNA with an emphasis on their diverse applications. The book covers both well-established and newly-developed protocols including ligation-based thermocycling approaches, real-time PCR and other new PCR developments, plus several powerful non-PCR isothermal DNA amplification techniques, for example: real-time strand displacement amplification (SDA), rolling-circle amplification (RCA) and multiple-displacement amplification (MDA). An entire section is devoted to a group of enzymes, both natural and engineered, which are employed for DNA amplification and related purposes. In addition, the use of DNA amplification in the detection of non-DNA analytes is presented. Written and edited by leading experts in the field, this book serves as a practical tool and an invaluable reference source for a broad audience of academic researchers and industry biotechnologists who use DNA amplification techniques.
• Covers theory, practice and applications
• Contains well-established and newly-developed protocols
• Comprehensive and up-to-date
• Includes the latest technology
• A practical laboratory manual
• Aimed at a broad audience
• Fully illustrated throughout
• Useful index
"I ... find it extremely fascinating. I will certainly use it in one of my biophysics/biochemistry courses." from Bengt Nolting, Prussian Private Institute of Technology, Berlin.
"Must be a great book! I will buy it as soon as it becomes available. Good book is worth any money..." from Igor Kutyavin, Research Fellow, Epoch Pharmaceuticals Inc.
"Nice book. I want to have it!" from Juan Aymami, University of Catalunya, Spain.
"Recommended." by Microbiology Today (2004) 31: 201.
"... the book should be an essential tool and reference source to researchers in both academia and industry." from Joshua Marcy in Drug Discovery and Development (2004) 7: 92.
DNA Amplification is a compendium of articles edited by Vadim Demidov and Natalia Broude, including two articles by the editors. The book stands out from the field of similar offerings by virtue of including chapters covering novel and cutting-edge PCR-based methods along with up and coming non-PCR amplification techniques. Readers looking for ideas on how to address research questions where more 'traditional' approaches have not proven quite satisfactory will find this an excellent and informative survey of new thinking. Moreover, explicit methods sections are provided by most authors so readers can readily implement ideas generated by the book. Overall, the book is an engaging and worthwhile read." from David J. Lane Ph.D., Vice President R and D, Hamilton Thorne Biosciences.
"An essential book for all people in this field." from Sajjad Sarikhan, Zanjan University, Iran.
"... a practical tool and invaluable reference source of latest DNA amplification technologies for academic and industrial scientists ..." from Expert Rev. Mol. Diagn. (2005) 5: 127-129.
"This book ... is directed at those with a solid background in molecular biology who desire knowledge of cutting-edge applications ... a good addition to the library of researchers in molecular biology." from Emerg. Infect. Dis. (2005) 11: (2).
"comprehensive and didactical content" Monica Ramirez Concepto Azul, ECUADOR.
Section 1. Enzymes Used in DNA Amplification
Thermostable Chimeric DNA Polymerases with High Resistance to Inhibitors
Andrey R. Pavlov, Nadejda V. Pavlova, Sergei A. Kozyavkin and Alexei I. Slesarev
Phi29 DNA Polymerase, a Potent Amplification Enzyme
Margarita Salas, Miguel de Vega, José M. Lázaro and Luis Blanco
High-Fidelity Thermostable DNA Ligases as a Tool for DNA Amplification
Section 2. Thermocycling Methods of DNA Amplification
High Multiplexity PCR Based on PCR Suppression
Natalia E. Broude, Adriaan W. van Heusden and Richard Finkers
On-Chip PCR: DNA Amplification and Analysis on Oligonucleotide Microarrays
Martin Huber, Christian Harwanegg, Manfred W. Mueller and Wolfgang M. Schmidt
Analysis of Somatic Mutations via Long-Distance Single Molecule PCR
Yevgenya Kraytsberg, Ekaterina Nekhaeva, Connie Chang, Konstantin Ebralidse and Konstantin Khrapko
Digital PCR Analysis of Allelic Status in Clinical Specimens
Wei Zhou, Tanisha Williams, Cecile Colpaert, Aki Morikawa and Diansheng Zhong
Application of Real-Time Quantitative PCR in the Analysis of Gene Expression
Manohar R. Furtado, Olga V. Petrauskene and Kenneth J. Livak
Quantitative Genetic Analysis with Multiplex Ligation-Dependent Probe amplification (MLPA)
A.O.H Nygren, A. Errami and J.P. Schouten
Section 3. Isothermal Methods of DNA Amplification
Homogeneous Real-Time Strand Displacement amplification
David M. Wolfe, Sha-Sha Wang, Keith Thornton, Andrew M. Kuhn, James G. Nadeau and Tobin J. Hellyer
Loop-Mediated Isothermal Amplification (LAMP) of DNA Analytes
Tsugunori Notomi, Kentaro Nagamine, Yasuyoshi Mori and Hidetoshi Kanda
Ligation-Mediated Rolling Circle DNA Amplification for Non-Gel Detection of Single Nucleotide Polymorphisms (SNPs)
Rolling-Circle Amplification of Duplex DNA Sequences Assisted by PNA Openers
Heiko Kuhn and Vadim V. Demidov
Phi29 DNA Polymerase Based Rolling Circle Amplification of Templates for DNA Sequencing
John C. Detter, John R. Nelson and Paul M. Richardson
Multiple-Displacement Amplification (MDA) of Whole Human Genomes from Various Samples
Roger S. Lasken, Seiyu Hosono and Michael Egholm
Section 4. DNA Amplification in Detection of Non-DNA Analytes
Enhanced Protein Detection Using Real-Time Immuno-PCR
Michael Adler and Christof M. Niemeyer
Rolling Circle Amplification in Multiplex Immunoassays
Michael C. Mullenix, Richard S. Dondero, Hirock D. Datta, Michael Egholm, Stephen F. Kingsmore and Lorah T. Perlee
DNA amplification is the cornerstone of modern biotechnology and it is also a key procedure in numerous basic studies involving DNA molecules. All methods for DNA amplification have rested on the concept of DNA strand complementarity discovered by James Watson and Francis Crick fifty years ago. To an equal extent, these methods became possible with the discovery of DNA polymerases first identified by Arthur Kornberg soon after the Watson-Crick discovery and DNA ligases discovered in 1967 by Martin Gellert, Charles Richardson, Jerard Hurwitz, Robert Lehman and others. Using these enzymes (and later their thermostable variants), a variety of isothermal and temperature-cycling amplification techniques have been developed starting in late 1980s. Among these techniques, Kari Mullis' polymerase chain reaction (PCR) was the first one and it is still the most popular amplification method. Yet, some alternatives to PCR have also successfully invaded the area. The emergence of such methodologies significantly widened the range of approaches for DNA amplification and dramatically changed the abilities of basic and applied researchers in various fields of life sciences. It will not be an exaggeration to say that now no research related to DNA can be performed without the employment of DNA amplification procedures.
Despite the importance of this topic we found to our surprise that only a few books were published that deal with the subject. Moreover, these books cover mostly PCR-based techniques and/or describe the use of PCR and other DNA amplification approaches for specific goals, such as clinical analysis, environmental microbiology, forensics, etc. This information shortage was a major motivation for us to compile a book on a wider range of methods for DNA amplification with emphasis on their diverse applications. Besides, almost twenty years after PCR was invented, we now are witnessing a new stage in the craft of DNA amplification thanks to the introduction of real-time PCR, several powerful non-PCR DNA amplification techniques and microarray technologies. In an attempt to represent the current state-of-the-art our book covers both well-established and newly-developed protocols with promising potential.
Although the book goes far beyond PCR by presenting a number of isothermal assays along with the ligation-based thermocycling approaches, PCR remains, despite some limitations, the dominant diagnostic technique for target DNA amplification and analysis, and recently this primary method has been systematically improved in many ways. That is why a significant part of our book is devoted to new PCR developments. A separate section is devoted to a group of enzymes, both natural and engineered, which are employed for DNA amplification and related purposes. We also present here the use of DNA amplification in the detection of non-DNA analytes. Note that we do not consider per se the methods for the detection of amplicons obtained by one way or another except for those few that establish a new potent amplification approach, as in the case of real-time PCR or real-time strand displacement amplification (SDA).
We hope that our book will serve as a practical tool and reference source for a broad audience of academic researchers and industry biotechnologists who rely in their work on DNA amplification techniques. We are very grateful to all the contributors and to the publisher who made this book possible.
Vadim V. Demidov and Natalia E. Broude
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