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Updated: Mar 22, 2026

Designing a Bio-responsive Robot from DNA Origami
Published on: July 8, 2013
The Formal Language and Design Principles of Autonomous DNA Walker Circuits
Michael A Boemo1, Alexandra E Lucas1, Andrew J Turberfield1
1Department of Physics, University of Oxford , Oxford OX1 2JD, U.K.
Abstract:
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.
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