The Formal Language and Design Principles of Autonomous DNA Walker Circuits.
Lucas, Alexandra E
Turberfield, Andrew J
ACS Synth Biol
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Boemo, M., Lucas, A. E., Turberfield, A. J., & Cardelli, L. (2016). The Formal Language and Design Principles of Autonomous DNA Walker Circuits.. ACS Synth Biol, 5 (8)https://doi.org/10.1021/acssynbio.5b00275
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.
External DOI: https://doi.org/10.1021/acssynbio.5b00275
This record's URL: https://www.repository.cam.ac.uk/handle/1810/301587
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