Synthetic Biology, Part B, Computer Aided Design and Dna Assembly (Methods in Enzymology, Vol. 498)

Description

Synthetic biology is a new area of biological research that combines science and engineering. Synthetic biology encompasses a variety of different approaches, methodologies and disciplines, and many different definitions exist. What they all have in common, however, is that they see synthetic biology as the design and construction of new biological functions and systems not found in nature.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.

Table of Contents

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