期刊
ACS SYNTHETIC BIOLOGY
卷 5, 期 8, 页码 878-884出版社
AMER CHEMICAL SOC
DOI: 10.1021/acssynbio.5b00275
关键词
DNA computation; DNA walkers; distributed systems; Petri nets; logic gates
资金
- Engineering and Physical Sciences Research Council [EP/G037930/1, EP/J500495/1]
- Biotechnology and Biological Sciences Research Council [BB/J00054X/1]
- Marie Curie Initial Training Network EScoDNA (FP7) [317110]
- Royal Society-Wolfson Research Merit Award
- BBSRC [BB/J00054X/1] Funding Source: UKRI
- EPSRC [EP/G037930/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/J00054X/1] Funding Source: researchfish
- Engineering and Physical Sciences Research Council [GR/A10274/01, 1075621, EP/G037930/1] Funding Source: researchfish
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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