Technologies and Tools For Programming Genetic Systems

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1 Technologies and Tools For Programming Genetic Systems Christina D. Smolke Department of Bioengineering Stanford University July 9, 29 Opportunities and Challenges in Synthetic Biology Tools and Techniques Enabling Innovation

2 Synthetic Engineering biology systems Sensors (Inputs) chemicals biomolecules temperature light Circuitry signal processing automated response dynamic control remote control memory communication Foundational Technologies synthesis Engineering Frameworks standardization composition Actuators (Outputs) Outputs) reporting delivery motility c/o C. Voigt (UCSF) phenotype self-organization synthesis Engineered Biological Systems environment health and medicine

3 Fabrication tools Itaya M, et al. 25. PNAS. 2: Gibson DG. 28. Science. 39: 25-2

4 Model circuits Biosynthesis applications Why the gap between tools and applications? Levskaya A, et al. 25. Nature. 438: 44-2 Basu S, et al. 25. Nature. 434: 3-4 Martin VJ, et al. 23. Nat Biotech. 2:

5 . Refinement and optimization of tools for applications represents a significant challenge 2. The culture of biological research traditionally rewards novelty and does not equally celebrate engineering contributions 3. Changing models and perspectives for how biological applications should be approached 4. Applications are generally narrowly directed to the end product and not toward developing a technology-base to broadly support many different products 5. Technology and tool development requires an upfront investment of time and effort

6 Information processing, computation, and control Small molecules Proteins RNA DNA Metal ions Temperature ph Sensor receive information SD CD Computation Actuator effect response AD define & control action Transcription Translation Degradation Splicing Enzyme activity Complex formation Key Engineering Properties scalability portability utility composability reliability

7 Plan for developing a programmable I/O tool Win MN, Liang JC, Smolke CD. 29. Chem Biol. 6: 298-3

8 A platform for programming device function sensor transmitter actuator device Transmitter # Buffer gate Device response OFF state ON state gene AAAAA AAAAA Transmitter #2 Inverter gate gene AAAAA AAAAA Device response ON state OFF state Win MN, Smolke CD. 27. PNAS. 4: Theophylline concentration (mm)

9 A platform for programming device inputs sensor transmitter actuator device Sensor # Buffer gate Sensor #2 Buffer gate gene AAAAA AAAAA Device signal t h e o p h y l l i n e tetracycline gene AAAAA AAAAA Win MN, Smolke CD. 27. PNAS. 4:

10 A B A B Higher-order computation - logic gate devices AND gate A theo AB B tc output output GFP NOR gate A theo A+B B tc output output GFP input A input B output protein (high when AB) input A input B output protein (high when A+B) Win MN, Smolke CD. 28. Science. 322: AAAAA AAAAA Device response in unit expression Device response in unit expression GFP low low low high theo + + tc GFP high low low low theo + + tc + +

11 Applications: Cellular therapeutics cytokines Engineered T-cell function activated cytolytic T cell cytolytic proteins CD28 B7 engineered cytolytic T cell infected dendritic cell Natural T-cell function tumor cell

12 Challenges to I/O tool development

13 Design challenge: CAD tools that predict device function from sequence Zuker, M. 23. Nuc Acids Res. 3: Beisel CL, et al. 28. Mol Sys Biol. 4: 224 Beisel CL, Smolke CD. 29. PLoS Comp Biol. 5: e363

14 Scalability challenge: libraries of nucleic acid sensors refined sensor libraries device platforms applications metabolites noninvasive diagnostics disease biomarkers bioprocessing / biosynthesis agricultural biotechnology exogenous chemicals intelligent therapeutics Engineering optimization and development needed on selection and characterization strategies

15 Summary The gap between technology/tool development and applications must be bridged Invention and implementation of engineering design principles is critical to effective tool development Strategies and mindsets supporting the implementation of foundational technologies and tools must be fostered Funding and support for new technology and tool development at scales and time frames appropriate for the challenges that must be addressed is critical