Boemo M A, Lucas A E, Turberfield A J, Cardelli L

ACS Synth. Biol., 2016, April 25

• Department of Physics, University of Oxford, Oxford OX1 2JD, U.K.
• Department of Computer Science, University of Oxford, Oxford OX1 2JD, U.K.
• Microsoft Research Cambridge, Cambridge CB1 2FB, U.K.

Simple computation can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be described as a stochastic Petri net. The system can be verified by mapping the Petri net onto a continuous-time Markov chain, which can also be used to find an optimal design for the circuit. This theoretical machinery can be applied to create software that automatically designs a DNA circuit, linking an abstract propositional formula to a physical DNA computation system that is capable of evaluating it. We conclude by introducing example mechanisms that can implement such circuits experimentally and discuss their individual strengths and weaknesses.