Synthetic Biology

Part I: Introduction

1. What is Synthetic Biology?

Karen M Polizzi

Part II: DNA Assembly

2. Gene Synthesis Method Based on Overlap Extension PCR and DNAWorks Program

Gang Li, Bing-Xue Dong, Yu-Huan Liu, Chang-Jie Li, and Li-Ping Zhang

3. BioBrick^(TM) Assembly Using the In-Fusion PCR Cloning Kit

Sean C. Sleight and Herbert M. Sauro

4. Overlap Extension PCR Cloning

Anton Bryksin and Ichiro Matsumura

5. One-Step Isothermal Assembly of DNA Fragments

Rui TL Rodrigues and Travis S Bayer

PartIII: Part, Pathway, and Genome Engineering

6. Creation and Characterization of Component Libraries for Synthetic Biology

Tim Weenink and Tom Ellis

7. In vivo and in vitro Characterisation of s⁷⁰ Constitutive Promoter BioParts by Real-time PCR and Fluorescent Measurements

James Chappell and Paul Freemont

8. In Vivo Screening of Artificial Small RNAs for Silencing Endogenous Genes in Escherichia coli

Vandana Sharma and Yohei Yokobayashi

9. Construction and Engineering of Large Biochemical Pathways via DNA Assembler

Zengyi Shao and Huimin Zhao

10. Assembly of Multi-gene Pathways and Combinatorial Pathway Libraries through ePathBrick Vectors

Peng Xu and Mattheos A.G. Koffas

11. Tandem Recombineering by SLIC Cloning and Cre-LoxP Fusion to Generate Multigene Expression Constructs for Protein Complex Research

Matthias Haffke, Cristina Viola, Yan Nie, and Imre Berger

12. Combinatorial DNA Assembly using Golden Gate Cloning

Carola Engler and Sylvestre Marillonnet

13. Construction of Synthetic Gene Circuits in the Escherichia coli Genome

Bei-Wen Ying, Yuya Akeno, and Tetsuya Yomo

David Bikard and Didier Mazel

Part IV: Computational Tools for Modelling Biological Systems

15. Systematic Methodology for the Development of Mathematical Models for Biological Processes

Cleo Kontoravdi

16. SOBOLHDMR: A General Purpose Modelling Software

Dr Sergei Kucherenko