BLACKSBURG, Va., July 9, 2012  - Offered in a single book for the first time, Gene Synthesis: Methods and Protocols provides comprehensive, step-by-step methods and protocols spanning all aspects of de novo synthesis of DNA molecules. Edited by Jean Peccoud, Ph.D., Virginia Bioinformatics Institute at Virginia Tech, the book is an essential guide for life scientists interested in using these emerging recombinant DNA technologies for their research.

For a long time biologists were limited to working with DNA molecules they could find in living organisms. During the 20th century, genetic engineering was limited to recombining natural DNA molecules from different origins. For instance, the cloning and production of human growth hormones in bacteria was one of the early successes of the first generation of recombinant DNA technologies. Recently, a second generation of recombinant DNA technologies has made it possible to assemble chemically synthetized oligonucleotides into new DNA molecules. This is a paradigm shift since it allows researchers to make a new DNA molecule without having to first isolate it from a living cell.

Applications are numerous, from tweaking genes to increasing the production of valuable proteins to engineering the genomes of viruses to use them as vaccines. 

Interestingly, gene synthesis is something that can be practiced with instruments found in virtually any molecular biology laboratory. It does not require multi-million dollar clean rooms or other specialized facilities. Yet most gene synthesis users tend to outsource this step to a few companies who specialize in providing these services. “The goal of this volume is help people better understand the different technologies that make gene synthesis possible” said Jean Peccoud. “It provides the tools to implement gene synthesis in house. It also gives users of commercial services a better understanding of the technology, its possibilities, and limitations.”

“If you want to quickly become efficient and effective at building DNA molecules, then you should consider getting this methods and protocols textbook,” said George McArthur, a doctoral student in synthetic biology at Virginia Commonwealth University.  “Genetic engineering has progressed past recombinant DNA technology and the limitations associated with cut-and-paste cloning techniques. This text provides detailed protocols for the latest and best DNA assembly methods, intelligently contrasting techniques for the assembly of oligos into larger constructs and the assembly of these synthons into even larger constructs - even up to genome-sized molecules. In addition, the text points readers toward invaluable software tools for designing DNA molecules and appropriate assembly strategies.”


The book also includes several chapters that will be of interest to students and teachers concerned with educating the rising generation of biologists to work in the new paradigm.

Table of Contents

Part I: Assembly of Oligonucleotides in Synthons

1 Building Block Synthesis Using the Polymerase Chain Assembly Method
Julie A. Marchand and Jean Peccoud

2 Oligonucleotide Assembly in Yeast to Produce Synthetic DNA Fragments
Daniel G. Gibson

3 TopDown Real-Time Gene Synthesis
Mo Chao Huang, Wai Chye Cheong, Hongye Ye, and Mo-Huang Li

4 De Novo DNA Synthesis Using Single-Molecule PCR
Tuval Ben Yehezkel, Gregory Linshiz, and Ehud Shapiro

Part II: Synthon Assembly

5 SLIC: A Method for Sequence- and Ligation-Independent Cloning
Mamie Z. Li and Stephen J. Elledge

6 Assembly of Standardized DNA Parts Using BioBrick Ends in E. coli
Olivia Ho-Shing, Kin Lau, William Vernon, Todd T. Eckdahl,
and A. Malcolm Campbell

7 Assembling DNA Fragments by USER Fusion
Narayana Annaluru, Héloïse Muller, Sivaprakash Ramalingam,
Karthikeyan Kandavelou, Viktoriya London, Sarah M. Richardson,
Jessica S. Dymond, Eric M. Cooper, Joel S. Bader, Jef D. Boeke,
and Srinivasan Chandrasegaran

8 Fusion PCR via Novel Overlap Sequences
Kamonchai Cha-aim, Hisashi Hoshida, Tomoaki Fukunaga,
and Rinji Akada

9 Using Recombineering to Generate Point Mutations: The Oligonucleotide-Based "Hit and Fix" Method
Suhwan Chang, Stacey Stauffer, and Shyam K. Sharan

10 Using Recombineering to Generate Point Mutations: galK-Based Positive-Negative Selection Method
Kajal Biswas, Stacey Stauffer, and Shyam K. Sharan

11 Assembling Large DNA Segments in Yeast
Héloïse Muller, Narayana Annaluru, Joy Wu Schwerzmann,
Sarah M. Richardson, Jessica S. Dymond, Eric M. Cooper,
Joel S. Bader, Jef D. Boeke, and Srinivasan Chandrasegaran

12 Recursive Construction of Perfect DNA Molecules and Libraries
from Imperfect Oligonucleotides
Gregory Linshiz, Tuval Ben Yehezkel, and Ehud Shapiro

13 Cloning Whole Bacterial Genomes in Yeast
Gwynedd A. Benders

14 Production of Infectious Poliovirus from Synthetic Viral Genomes
Jeronimo Cello and Steffen Mueller

Part III: Software for Gene Synthesis

15 In Silico Design of Functional DNA Constructs
Alan Villalobos, Mark Welch, and Jeremy Minshull

16 Using DNA Works in Designing Oligonucleotides for PCR-Based Gene Synthesis
David Hoover

17 De Novo Gene Synthesis Design Using TmPrime Software
Mo-Huang Li, Marcus Bode, Mo Chao Huang, Wai Chye Cheong,
and Li Shi Lim

18 Design-A-Gene with GeneDesign
Sarah M. Richardson, Steffi Liu, Jef D. Boeke, and Joel S. Bader

Part IV: Education and Security

19 Leading a Successful iGEM Team
Wayne Materi

20 The Build-a-Genome Course
Eric M. Cooper, Helöise Müller, Srinivasan Chandrasegaran,
Joel S. Bader, and Jef D. Boeke

21 DNA Synthesis Security
Ali Nouri and Christopher F. Chyba

Index

About the Author
JEAN PECCOUD, PhD, is an associate professor at the Virginia Bioinformatics Institute at Virginia Tech (VBI), heading the Synthetic Biology Research Group. His current scientific interests include the development of linguistic models of DNA sequences, the optimization of DNA fabrication processes, and the development of new instruments to measure the dynamics of gene networks in live cells. Peccoud's group is leading the development of GenoCAD, an open source web-based application to design synthetic DNA molecules from libraries of standard genetic parts.

Publication Date: February 10, 2012 | ISBN-10: 1617795631 | ISBN-13: 978-1617795633 | Edition: 1st

About the Virginia Bioinformatics Institute
The Virginia Bioinformatics Institute at Virginia Tech marries genetic research and high-performance computing to increase our understanding of the complex life forces and social systems that affect the health and safety of plants, animals, and humans. Our work brings together life scientists, biomedical researchers, and information technologists in an array of fields, including experts in genomics, proteomics, applied, informatics, biology, biochemistry, systems biology, statistics, economics, medicine, and cyberinfostructure. Our advanced methods of analysis, sheer computing power, and enormous data storage capacity enable us to turn oceans of data into the insights required to combat disease and to mitigate the consequences of catastrophic events on society.

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Contact:
Jean Peccoud
540-231-0403
jpeccoud@vbi.vt.edu

July 09, 2012