1. Christina D. Smolke
Department of Bioengineering
Stanford University
July 16, 2011
12th Annual eDay

2. Natural chemicals and materials
Taxus brevifolia (pacific yew) spider
taxol silk
Hevea brasiliensis (rubber tree)
rubber
Clostridium acetobutylicum
butanol
Papaver somniferum (opium poppy)
codeine, morphine

3. Microbial biofactories
Taxus brevifolia (pacific yew) spider
taxol silk
Hevea brasiliensis (rubber tree)
rubber
genetic materials,
manipulation & control
Clostridium acetobutylicum
butanol raw materials microbial fermentation New chemicals
Papaver somniferum (opium poppy) materials
codeine, morphine products

4. Intelligent therapeutics
www.neurooncologia.com

5. Apps
Tools c/o D. Endy (Stanford University)

6. 7. Control & dyn. systems
6. Reverse engineering
5. Fab, CAD & EDA
4. Standards & abstraction
3. Languages & grammars
2. Device design
1. Info. theory & signal proc.
c/o D. Endy (Stanford University)

7. Engineering systems
Circuitry
signal processing remote control
automated response memory
Sensors (Inputs) dynamic control communication
chemicals
biomolecules
temperature
light
Actuators (Outputs)
reporting phenotype
delivery self-organization
motility synthesis

8. Synthetic biology
Circuitry
signal processing remote control
automated response memory
Sensors (Inputs) dynamic control communication
chemicals
biomolecules
temperature
light
Actuators (Outputs)
reporting phenotype
delivery self-organization
motility synthesis

9. Ongoing tools revolution
Recombinant DNA Polymerase Chain Reaction DNA Sequencing
First
Gen.
Biotech
=
Basic “Cut” & “Paste” Amplify & Make Simple Changes Read Out the Genetic Code
Next
Gen.
Biotech
Adds = ...
New
Tools
c/o D. Endy (Stanford University)

10. Transformative advances in fabrication platforms
Carr PA, Church GM. 2009. Nat Biotech. 27: 1151-1162
Cellular assembly
engineered
natural
genome
transplantation Gibson DG, et al. 2010. Science. 329: 52-6

11. Now that we can
write in DNA, what
do we say?
Challenge: Design Gap

12. Molecular computers enable programming of function
input
sensor1 / transmitter1 / actuator
output
input A
sensor1 / transmitter2 / actuator
output
input A
sensor2 / transmitter1 / actuator
output
input B
output
input output
Win MN, Smolke CD. 2007. PNAS. 104: 14283-8

13. Molecular computers enable programming of function
input
sensor1 / transmitter1 / actuator
output
input A
sensor1 / transmitter2 / actuator
output
input A
sensor2 / transmitter1 / actuator
output
input B
output
n sensors / n transmitters / actuator
A B output
0 0 1
0 1 1
1 0 1
1 1 0
Win MN, Smolke CD. 2008. Science. 322: 456-60

14. Decoupling & abstraction lead to powerful technology
platforms
harvesting and rational computer- evolving new
refining from nature aided design (CAD) functions
Win MN, Liang JC, Smolke CD. 2009. Chem Biol. 16: 298-310

15. Building scalable bio-manufacturing platforms
Harvesting natural diversity
hair growth
analgesics
Integrating into a
microbial host
antimicrobial anti-HIV
anti-malarial
anticancer
Hawkins KM, Smolke CD. 2008. Nat Chem Biol. 4: 564-73

16. Building a microbial drug factory
Enzymes catalyze reactions:

17. Building a microbial drug factory
Bis-BIAs Sanguinarine / Morphinan
Berberine Alkaloids Alkaloids

18. Building a microbial drug factory
DNA
protein
metabolite
Bis-BIAs Sanguinarine / Morphinan
Berberine Alkaloids Alkaloids

19. Building a microbial drug factory
Bis-BIAs Sanguinarine / Morphinan
Berberine Alkaloids Alkaloids

20. Building a microbial drug factory
Bis-BIAs Sanguinarine / Morphinan
Berberine Alkaloids Alkaloids

21. Building a microbial drug factory
Bis-BIAs Sanguinarine / Morphinan
Berberine Alkaloids Alkaloids

22. Integrated systems design of microbial factories
Targeting biosynthesis to specialized
pH 7-8 compartments
degradation
Mitochondrion
pH 4-5
SalAT-mCherry
SalR-GFP
Vacuole
pH 8-9
Noninvasive detection of chemical
output
Synthesome
synthesis
input A
Nucleus Golgi
ER

23. Building autonomous control systems
Culler SJ, Hoff KG, Smolke CD. 2010. Science. 330: 1251-5

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27. Advancing cell-
based therapies
Chen YY, Jensen MC, Smolke CD. 2010. PNAS. 107: 8531-6

28. Cellular therapies: engineering the immune system
transfer engineered
cells into patient
harvest lymphocytes
recover and engineer from patient
desired cell type
http://www.discoverymedicine.com/Leslie-E-Huye/files/2010/03/

29. T-cell proliferation pathway
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30. A molecular computer controlling immune response
proliferation
apoptosis /
death
Chen YY, Jensen MC, Smolke CD. 2010. PNAS. 107: 8531-6

31. A molecular computer controlling immune response
1.2E+09
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Chen YY, Jensen MC, Smolke CD. 2010. PNAS. 107: 8531-6

32. Apps
Standardization Abstraction Synthesis Device Design Languages & Grammar
AGGTACAGTTATCA
CCCATTGCATGGTA
TTCAAAGAAGTCGT
output
GGCCCAGATTCGAC
AAATCGTGTAGTAA
TGGTCCAGCTGATT input
Tools GGTTCAAATAACGG

33. The Smolke Laboratory
Alumni Funding Sources
Andrew Babiskin Alfred P. Sloan Foundation
Travis Bayer Arnold and Mabel Beckman Foundation
Chase Beisel Bill and Melinda Gates Foundation
Yvonne Chen Defense Advanced Research Projects
Stephanie Culler Agency
Kristy Hawkins National Institutes of Health (NIGMS, NCI)
Kevin Hoff National Science Foundation (CBET, CCF,
Maung Nyan Win CAREER)

34. Let’s design
with DNA…