Synthetic Biology, Part a

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.

Section I. Measuring and Engineering Central Dogma Processes

1. Sequence-specificity and Energy Landscapes of DNA-binding Molecules

Joshua R. Tietjen, Leslie J. Donato, Devesh Bhimisaria and Aseem Z. Ansari

2. Promoter Reliability in Modular Transcriptional Networks

Rajat Anand, Navneet Rai and Mukund Thattai

3. The Analysis of ChIP-seq Data

Wenxiu Ma and Wing Hung Wong

4. Using DNA Microarrays to Assay Part Function

Virgil A. Rhodius and Carol A. Gross

5. Orthogonal gene expression in Escherichia coli

Wenlin An and Jason Chin

6. Directed evolution of promoters and tandem gene arrays for customizing RNA synthesis rates and regulation

Keith E.J. Tyo, Elke Nevoigt and Gregory Stephanopoulos

Section II. Device and System Design, Optimization, and Debugging

7. Design and Connection of Robust Genetic Circuits

Ron Weiss

8. Engineering RNAi circuits

Yaakov Benenson

9. From SELEX to cell: Dual selections for synthetic riboswitches

Joy Sinha, Shana Topp, and Justin P. Gallivan

10. Using noisy gene expression mediated by engineered adenovirus to probe signaling dynamics in mammalian cells

Jeffrey V. Wong, Guang Yao, Joseph R. Nevins and Lingchong You

11. De novo design and construction of an inducible gene expression system in mammalian cells

Maria Karlsson, Wilfried Weber and Martin Fussenegger

12. BioBuilding: Using banana-scented bacteria to teach synthetic biology

James Dixon and Natalie Kuldell

Section III. Device Measurement, Optimization, and Debugging

13. Use of Fluorescence Microscopy to Analyze Genetic Circuit Dynamics

Gürol Süel

14. Microfluidics for synthetic biology: From design to execution

M. S. Ferry, I. A. Razinkov, J. Hasty

15. Plate-based assays for light-regulated gene expression systems

Jeffrey J. Tabor

16. Spatiotemporal control of small GTPases with light using the LOV domain

Yi I. Wu, Xiaobo Wang, Li He, Denise Montell and Klaus M. Hahn

17. Light Control of Plasma Membrane Recruitment using the Phy-PIF system

Jared E. Toettcher, Delquin Gong, Wendell A. Lim, Orion D. Weiner

18. Synthetic Physiology: Strategies for Adapting Tools from Nature for Genetically-Targeted Control of Fast Biological Processes

Ed Boyden

Section IV. Devices for Metabolic Engineering

19. Metabolic Pathway Flux Enhancement by Synthetic Protein Scaffolding

John E. Dueber and Weston R. Whitaker

20. A Synthetic Iterative Pathway for ketoacid elongation

C. R. Shen, J. C. Liao

Section V. Expanding Chasses

21. Synthetic Biology in Streptomyces bacteria

Marnix Medema, Rainer Breitling and Eriko Takano

22. Methods for Engineering Sulfate Reducing Bacteria of the Genus Desulfovibrio

Kimberly L. Keller, Judy D. Wall and Swapnil Chhabra

23. Modification of the Genome of Rhodobacter sphaeroides and Construction of Synthetic Operons

Paul R. Jaschke, Rafael G. Saer, Stephan Noll and J. Thomas Beatty

24. Synthetic Biology in Cyanobacteria: Engineering and Analyzing Novel Functions

Thorsten Heidorn, Daniel Camsund, Hsin-Ho Huang, Pia Lindberg, Paulo Oliveira, Karin Stensjö, and Peter Lindblad

25. Developing a Synthetic Signal Transduction System in Plants

Kevin J. Morey, Mauricio S. Antunes, Kirk D. Albrecht, Tessa A. Bowen, Jared F. Troupe, Keira L. Havens and June I. Medford

26. Lentiviral Vectors to Study Stochastic Noise in Gene Expression

Kate Franz, Abhyudai Singh, and Leor S. Weinberger