Main description:

The de novo fabrication of custom DNA molecules is a transformative technology that significantly affects the biotechnology industry. Basic genetic engineering techniques for manipulating DNA in vitro opened an incredible field of opportunity in the life sciences. In, Gene Synthesis: Methods and Protocols expert researchers in the field detail many of the methods which are now commonly used to fabricate DNA . These include methods and techniques for the assembly of oligonucleotide, cloning of synthons into larger fragments, protocols and software applications, and educational and biosecurity impacts of gene synthesis. Written in the highly successful Methods in Molecular Biology (TM) series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory.

Thorough and intuitive, Gene Synthese: Methods and Protocols aids scientists in understanding all the different stages of a complex gene synthesis process, while refining their understanding of gene synthesis and determine what part of the process they can or should do in their laboratory and what parts should be contracted to a specialized service provider.

Contents:

Section I: Assembly of Oligonucleotides in Synthons

1. Building Block Synthesis using the Polymerase Chain Assembly (PCA) 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, Mo-Huang Li

4. De novo DNA Synthesis using Single-molecule PCR

Tuval Ben Yehezkel, Gregory Linshiz, and Ehud Shapiro

Section 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, Heloise 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 & 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

Heloise Muller, Narayana Annaluru, Joy Wu Schwerzmann ,Sarah M. Richardson, Jessica S. Dymond, Eric M. Cooper, Joel S. Bader, Jef D. Boeke, 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

Section III: Software for gene synthesis

15. In Silico Design of Functional DNA Constructs

Alan Villalobos, Mark Welch, and Jeremy Minshull

16. Using DNAWorks 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, Li Shi Lim

18. Design-A-Gene with GeneDesign

Sarah M. Richardson, Steffi Liu, Jef D. Boeke, and Joel S. Bader

Section IV: Education and Security

19. Leading a Successful iGEM Team

Wayne Materi

20. The Build-a-Genome Course

Eric M. Cooper, Heloeise Muller, Srinivasan Chandrasegaran, Joel Bader, and Jef D. Boeke

21. DNA Synthesis Security

Ali Nouri and Christopher F. Chyba