1. Synthetic Biology: A Brief Survey
Isaac Larkin 01/11/2016

2. What is Synthetic Biology?
Synthetic biology is programming biological matter.
Schwille, P. Science 333, 1252–4 (2011).

3. The Synthetic Biology Stack
Biomolecular Circuit/“Device” Characterization and Design
Biomolecule “Part” Characterization and Design
DNA Insertion/
Genome Manipulation
Level of
Abstraction
DNA Assembly
DNA Sequencing and Synthesis

4. Falling Cost of DNA Sequencing and Synthesis Facilitates Synthetic Biology
IDT oligo synthesis (iBuy):
15-60 bp for
$0.01-$0.03 /base/nmole
synthesis.cc/2014/02/time-for-new-cost-
curves-2014.html

5. Falling Cost of DNA Sequencing and Synthesis Facilitates Synthetic Biology
Twist’s Price: 10¢ / base
Elizabeth Segran, Fast Company, 2015 (goo.gl/l4JGnP)

6. Advances in DNA Assembly Enable Whole Genome Synthesis
Assembly strategy for synthetic genomes
Holt, R. A.Nat. Biotechnol. 26, 296–7 (2008).

7. Advances in DNA Assembly Enable Whole Genome Synthesis
Gibson Assembly
Up to 10
fragments
at once
One pot,
50ºC,
15-60 min
neb.com/products/
synbio.tsl.ac.uk/gibson-assembly/

8. Advances in DNA Assembly Enable Whole Genome Synthesis
Goal here is to make a bacterium that can be programmed easily, predictably and reliably
Mycoplasma laboratorium
jcvi.org, 2010

9. Advances in DNA Assembly Enable Whole Genome Synthesis
Synthetic Yeast Project
syntheticyeast.org

10. Advances in DNA Assembly Enable Whole Genome Synthesis
Synthetic Yeast Project
Science 344, 55–8 (2014).

11. Genome Manipulation Leads to Rewriting the Genetic Code
MAGE:
Multiplex Automated
Genome Engineering
in E. coli
MAGE enables rapid, introduction of ~10 simultaneous mutations in E. coli
Wang, H. H. et al. Nature 460, 894–8 (2009).

12. Genome Manipulation Leads to Rewriting the Genetic Code
Only 314 UAG
in the whole
E. coli genome!
Ma, N. J., Moonan, D. W. & Isaacs, F. J.
Nat. Protoc. 9, 2285–300 (2014)

13. Genome Manipulation Leads to Rewriting the Genetic Code
CAGE enables genome-wide UAGUAA codon reassignment
(Science 2013)
Ma, N. J., Moonan, D. W. & Isaacs, F. J.
Nat. Protoc. 9, 2285–300 (2014)

14. Genome Manipulation Leads to Rewriting the Genetic Code
Genomically Recoded Organisms (GROs) enable efficient NSAA incorporation
Lajoie, M. J. et al. Science 342, 357–60 (2013)

15. Genome Manipulation Leads to Rewriting the Genetic Code
Azides
Photo-Crosslinker
Alkynes
Fluorophores
Quast, R. B. et al. FEBS Lett. 589, 1703–12 (2015)

16. Prediction and Programming of Biomolecule Structure is Improving
Predicted Structure
Crystal Structure
Marks, D. S., Hopf, T. A. & Sander, C.
Nat. Biotechnol. 30, 1072–80 (2012)

17. Prediction and Programming of Biomolecule Structure is Improving
Baker Lab designs 2-component, tetrahedral protein nanoparticles
King, N. P. et al. Nature 510, 103–8 (2014)

18. Prediction and Programming of Protein Structure is Improving
Baker Lab designs 2-component, tetrahedral protein nanoparticles
King, N. P. et al. Nature 510, 103–8 (2014)

19. Design of Biomolecule Function Produces Novel “Parts” for Synthetic Biologists
DNA promoter libraries enable tuning of maximum expression
Project_improving_araBAD

20. Design of Biomolecule Function Produces Novel “Parts” for Synthetic Biologists
Spinach:
An RNA mimic of GFP
Paige, J. S., Wu, K. Y. & Jaffrey, S. R.
Science 333, 642–6 (2011).

21. Design of Biomolecule Function Produces Novel “Parts” for Synthetic Biologists
Paige, J. S., Wu, K. Y. & Jaffrey, S. R.
Science 333, 642–6 (2011).

22. Design of Biomolecule Function Produces Novel “Parts” for Synthetic Biologists
Enzyme engineering: still really hard, but not impossible
Engineered formolase (FLS):
-Incorporates formaldehyde into central metabolism
-Potentially, a new CO2 fixation route
Siegel, J. B. et al. Proc. Natl. Acad. Sci.
112, 3704–9 (2015).

23. From Parts to Complex Devices: Design of Genetic Circuits
Origin of the field!
1. Cameron, D. E., Bashor, C. J. & Collins, J. J.
Nat. Rev. Microbiol. 12, 381–90 (2014).

24. From Parts to Complex Devices: Design of Genetic Circuits
Origin of the field!
1. Cameron, D. E., Bashor, C. J. & Collins, J. J.
Nat. Rev. Microbiol. 12, 381–90 (2014).

25. From Parts to Complex Devices: Design of Genetic Circuits
Circuit fidelity has improved
1. Elowitz, M. B. & Leibler, S.
Nature 403, 335–8 (2000).

26. From Parts to Complex Devices: Design of Genetic Circuits
Circuit fidelity has improved
1. Danino, T. et al. Nature 463, 326–30 (2010).

27. Therapeutic Genetic Circuits
Cellular system to sense and repress psoriasis in mice
1. Schukur, L. et al. Sci. Transl. Med. 7,
318ra201–318ra201 (2015).

28. Programming Metabolic Circuits to Make Useful Small Molecules
1st triumph:
Artemisinic Acid
Production
Paddon, C. J. et al. Nature 496,
528–32 (2013).

29. Programming Metabolic Circuits to Make Useful Small Molecules
~700-fold better
than first strain’s yield!
1st triumph:
Artemisinic Acid
Production
At an economically viable scale! (After 7 years of optimizing).
Paddon, C. J. et al. Nature 496,
528–32 (2013).

30. Programming Metabolic Circuits to Make Useful Small Molecules
Complete Opiate
Biosynthesis in Yeast
(Currently tiny
yields)
1. Galanie, S. et al. Science (80-. ).
349, 1095–1100 (2015).

31. The Synthetic Biology Stack
Biomolecular Circuit/“Device” Characterization and Design
Biomolecule “Part” Characterization and Design
DNA Insertion/
Genome Manipulation
Level of
Abstraction
DNA Assembly
DNA Sequencing and Synthesis

32. Thanks! Sarah Joe Weston Mike Jewett The NU Synthetic Biology Center1.