The formal language and design principles of autonomous DNA walker circuits

Journal article

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.

Authors: Boemo, M; Lucas, A; Turberfield, A; Cardelli, L

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: American Chemical Society
• Journal: ACS Synthetic Biology
• Volume: 5
• Issue: 8
• Pages: 878–884
• Publication date: 2016-04-25
• DOI: 10.1021/acssynbio.5b00275
• EISSN: 2161-5063
• ISSN: 2161-5063
• Language: English
• Keywords: logic gates; DNA walker; distributed systems; DNA computation; Petri nets