Part I: Computational Tools for Design and Assembly of Synthetic DNA
1. A Guide to Using STITCHER for Overlapping Assembly PCR Applications
Damien M. O'Halloran
2. Synthetic Gene Design Using Codon Optimization On-Line (COOL)
Kai Yu, Kok Siong Ang, and Dong-Yup Lee
3. Shuffle Optimizer: A Program to Optimize DNA Shuffling for Protein Engineering
John N. Milligan and Daniel J. Garry
Part II: DNA Synthesis, Assembly, and Cloning
4. Simple Cloning by Prolonged Overlap Extension PCR with Application to the Preparation of Large-Size Random Gene Mutagenesis Library in Escherichia coli
Chao Zhong, Chun You, Ping Wei, and Yi-Heng Percival Zhang
5. SpeedyGenes: Exploiting an Improved Gene Synthesis Method for the Efficient Production of Error-corrected, Synthetic Protein Libraries for Directed Evolution
Andrew Currin, Neil Swainston, Philip J. Day, and Douglas Kell
6. BASIC - A Simple and Accurate Modular DNA Assembly Method
Marko Storch, Arturo Casini, Ben Mackrow, Tom Ellis, and Geoff Baldwin
7. Enzymatic Synthesis of Single Stranded Clonal Pure Oligonucleotides
Cosimo Ducani and Bjorn Hogberg
8. Rapid Assembly of DNA via Ligase Cycling Reaction (LCR)
Sunil Chandran
9. PaperClip: A Simple Method for Flexible Multi-part DNA Assembly
Maryia Trubitsyna, Chao-Kuo Liu, Alejandro Salinas, Alistair Elfick, and Christopher French
10. The Polymerase Step Reaction (PSR) Method for Gene and Library Synthesis
Brian DeDecker
11. Clonetegration Using OSIP Plasmids - One Step DNA Assembly and Site Specific Genomic Integration in Bacteria
Lun Cui and Keith Sherwin
12. Generation of DNA Constructs Using the Golden GATEway Cloning Method
Stephan Kirchmaier, Katharin Lust, and Jochen Wittbrodt
13. Gene Deletion by Synthesis in Yeast
Jinsil Kim, Dong-uk Kim, and Kawang-Lae Hoe
14. Efficient Assembly of DNA Using Yeast Homologous Recombination (YHR)
Sunil Chandran and Elaine Shapland
15. Simultaneous Removal of Multiple DNA Segments by Polymerase Chain Reactions
Vishnu Krishnamurthy and Kai Zhang
16. Rapid Construction of Recombinant Plasmids by QuickStep-Cloning
Pawel Jajesniak and Tuck Seng Wong
Part III: Reducing Error in Synthetic DNA
17. Immobilized MutS-mediated Error Removal of Microchip-synthesized DNA
Wen Wan, Dongmei Wang, Xiaolian Gao, and Jiong Hong
18. Selection of Error-less Synthetic Genes in Yeast
Hisashi Hoshida, Tohru Yarimizu, and Rinji Akada
