The Formal Language and Design Principles of Autonomous DNA Walker Circuits

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 ho...

Full description

Saved in:
Bibliographic Details
Published in:ACS synthetic biology 2016-08, Vol.5 (8), p.878-884
Main Authors: Boemo, Michael A, Lucas, Alexandra E, Turberfield, Andrew J, Cardelli, Luca
Format: Article
Language:English
Subjects:
Computers, Molecular
DNA - genetics
Software
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:2161-5063
2161-5063
DOI:10.1021/acssynbio.5b00275