Genetic circuit design automation

Computation can be performed in living cells by DNA-encoded circuits that process sensory information and control biological functions. Their construction is time-intensive, requiring manual part assembly and balancing of regulator expression. We describe a design environment, Cello, in which a user writes Verilog code that is automatically transformed into a DNA sequence. Algorithms build a circuit diagram, assign and connect gates, and simulate performance. Reliable circuit design requires the insulation of gates from genetic context, so that they function identically when used in different circuits. We used Cello to design 60 circuits forEscherichia coli(880,000 base pairs of DNA), for which each DNA…

• NS
  National Science Foundation

  Award: 1147158
• BA
  Bill and Melinda Gates Foundation
• NR
  National Research Council Sri Lanka
• MU
  Multidisciplinary University Research Initiative

  Award: N00014-13-1-0074
• OO
  Office of Naval Research
• NI
  National Institute of General Medical Sciences

  Award: P50 GMO98792
• AF
  Air Force Office of Scientific Research