The Formal Language and Design Principles of Autonomous DNA Walker Circuits

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• 作者：Michael A. Boemo ; Alexandra E. Lucas ; Andrew J. Turberfield ; Luca Cardelli
• 刊名：ACS Synthetic Biology
• 出版年：2016
• 出版时间：August 19, 2016
• 年：2016
• 卷：5
• 期：8
• 页码：878-884
• 全文大小：313K
• 年卷期：0
• ISSN：2161-5063

文摘

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.