Synthetic Biology, Part B: Computer Aided Design and DNA Assembly

Synthetic biology encompasses a variety of different approaches, methodologies and disciplines, and many different definitions exist. This Volume of Methods in Enzymology has been split into 2 Parts and covers topics such as Measuring and Engineering Central Dogma Processes, Mathematical and Computational Methods and Next-Generation DNA Assembly and Manipulation.

Encompasses a variety of different approaches, methodologies and disciplinesSplit into 2 parts and covers topics such as measuring and engineering central dogma processes, mathematical and computational methods and next-generation DNA assembly and manipulation

Voigt / MIE Vol

Table of Contents

Synthetic biology, Part B

Subtitle: Computer Aided Design and DNA Assembly

Section I. Mathematical and Computational Methods

1. DNA-binding specificity prediction with FoldX

Alejandro D. Nadra, Luis Serrano, Andreu Alibés

2. The Ribosome Binding Site Calculator

Howard M. Salis

3. Designing Genes for Successful Protein Expression

Mark Welch, Alan Villalobos, Claes Gustafsson and Jeremy Minshull

4. Application of Metabolic Flux Analysis in Metabolic Engineering

Sang Yup Lee, Jong Myoung Park and Tae Yong Kim

Section II. Grammars, Languages, and Computer-Aided Design

5. Clotho: A Software Platform for the Creation of Synthetic Biological Systems

Swapnil Bhatia, Bing Xia, Ben Bubenheim, Maisam Dadgar, Douglas Densmore and J. Christopher Anderson

6. SynBioSS-Aided Design of Synthetic Biological Constructs

Yiannis N. Kaznessis

7. The Eugene Language for Synthetic Biology

Lesia Bilitchenko, Adam Liu, Douglas Densmore

8. A step by step introduction to rule-based design of synthetic genetic constructs using GenoCAD

Mandy L. Wilson, Russell Hertzberg, Laura Adam, Jean Peccoud

9. Methods for open innovation on a genome-design platform associating scientific, commercial, and educational communities in synthetic biology

Tetsuro Toyoda

Section III. Next-Generation DNA Assembly and Manipulation

10. Recursive construction and error correction of DNA molecules and libraries from synthetic and natural DNA

Tuval Ben Yehezkel and Ehud Shapiro

11. Industrial scale gene synthesis

Frank Notka, Michael Liss & Ralf Wagner

12. Chemical DNA Synthesis: Methods and Applications

Randall A. Hughes, Aleksandr E. Miklos, and Andrew D. Ellington

13. Assembly of BioBrick standard biological parts using three antibiotic assembly

Reshma Shetty, Meagan Lizarazo, Randy Rettberg, and Thomas F. Knight, Jr

14. Genetic Assembly Tools for Synthetic Biology

Billyana Tsvetanova, Lansha Peng, Xiquan Liang, Ke Li, Jian-Ping Yang, Tony Ho, Josh Shirley, Liewei Xu, Jason Potter, Wieslaw Kudlicki, Todd Peterson, and Federico Katzen

15. Enzymatic assembly of overlapping DNA fragments

Daniel G. Gibson

16. Automated assembly of standard biological parts

Mariana Leguia, Jennifer Brophy, Douglas Densmore and J. Christopher Anderson

17. MEGAWHOP Cloning: A method of creating random mutagenesis libraries via megaprimer PCR of whole plasmids

Kentaro Miyazaki

Section III. Genome-scale Engineering

18. Rapid and Multiplexed Genome Engineering and Genotyping Methods: Applications for Synthetic Biology and Protein and Pathway Engineering

Harris H. Wang and George M. Church

19. Construction and manipulation of giant DNA by a genome vector

Mitsuhiro ITAYA and Kenji TSUGE

20. Mapping E. coli RNA Polymerase and associated transcription factors and identifying promoters genome-wide

Sarah E. Davis, Rachel A. Mooney, Elenita I. Kanin, Jeff Grass, Robert Landick and Aseem Z. Ansari