title: Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components.
abstract: Biochemical circuits made of rationally designed DNA molecules are proofs of concept for embedding control within complex molecular environments. They hold promise for transforming the current technologies in chemistry, biology, medicine and material science by introducing programmable and responsive behaviour to diverse molecular systems. As the transformative power of a technology depends on its accessibility, two main challenges are an automated design process and simple experimental procedures. Here we demonstrate the use of circuit design software, combined with the use of unpurified strands and simplified experimental procedures, for creating a complex DNA strand displacement circuit that consists of 78 distinct species. We develop a systematic procedure for overcoming the challenges involved in using unpurified DNA strands. We also develop a model that takes synthesis errors into consideration and semi-quantitatively reproduces the experimental data. Our methods now enable even novice researchers to successfully design and construct complex DNA strand displacement circuits.
authors.affiliation: Bioengineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.
authors.forename: Anupama J
authors.initials: AJ
authors.lastname: Thubagere
authors.affiliation: Computer Science, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Thachuk
authors.affiliation: Computer Science, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Berleant
authors.affiliation: Bioengineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.
authors.forename: Robert F
authors.initials: RF
authors.lastname: Johnson
authors.affiliation: Applied and Computational Mathematics, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.
authors.forename: Diana A
authors.initials: DA
authors.lastname: Ardelean
authors.affiliation: Bioengineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Cherry
authors.affiliation: Bioengineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.|Computer Science, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.
authors.forename: Lulu
authors.initials: L
authors.lastname: Qian
mesh_terms: D002138:Calibration; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008128:Logic; D008962:Models, Theoretical; D012984:Software
chemical_list: D004247:DNA