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ACS Synth Biol. 2016 Aug 19;5(8):878-84. doi: 10.1021/acssynbio.5b00275. Epub 2016 May 11.

The Formal Language and Design Principles of Autonomous DNA Walker Circuits.

Author information

1
Department of Physics, University of Oxford , Oxford OX1 2JD, U.K.
2
Department of Computer Science, University of Oxford , Oxford OX1 2JD, U.K.
3
Microsoft Research Cambridge , Cambridge CB1 2FB, 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.

KEYWORDS:

DNA computation; DNA walkers; Petri nets; distributed systems; logic gates

PMID:
27114350
DOI:
10.1021/acssynbio.5b00275
[Indexed for MEDLINE]

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