We present a formal language for specifying via constraints a "design space" of DNA constructs composed of genetic parts, and an algorithm for automatically and correctly creating a novel representation of the space of satisfying designs. The language is simple, captures a large class of design spaces, and possesses algorithms for common operations on design spaces. The flexibility of this approach is demonstrated using a 16-gene nitrogen fixation pathway and genetic logic circuits.
Bibliographical noteFunding Information:
S.P.B, M.J.S., C.A.V, and D.M.D were supported by the Defense Advanced Research Projects Agency (DARPA) Living Foundries grant HR0011-12-C-0067 during the creation of this research. This work was also supported by the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 from the U.S. Army Research Office. S.P.B and D.M.D were also supported by the NSF’s Living Computing Project (Award #1522074). The content of the information does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred. We thank Dr. Nicholas Roehner for helping elucidate the application of the proposed design language to genetic circuits.
© 2017 American Chemical Society.