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Tailoring spatiotemporal dynamics with DNA circuits

Abstract : Biological organisms process information through the use of complex reaction networks. These can be a great source of inspiration for the tailoring of dynamic chemical systems. Using basic DNA biochemistry -the DNA-toolbox- modeled after the cell regulatory processes, we explore the construction of spatio-temporal dynamics from the bottom-up. First, we design a monitoring technique of DNA hybridization by harnessing a usually neglected interaction between the nucleobases and an attached fluorophore. This fluorescence technique -called N-quenching- proves to be an essential tool to monitor and troubleshoot our dynamic reaction circuits. We then go on a journey to the roots of the DNA-toolbox, aiming at defining the best design rules at the sequence level. With this experience behind us, we tackle the construction of reaction circuits displaying bistability. We link the bistable behavior to a topology of circuit, which asks for specific DNA sequence parameters. This leads to a robust bistable circuit that we further use to explore the modularity of the DNA-toolbox. By wiring additional modules to the bistable function, we make two larger circuits that can be flipped between states: a two-input switchable memory, and a single-input push-push memory. Because all the chemical parameters of the DNA-toolbox are easily accessible, these circuits can be very well described by quantitative mathematical modeling. By iterating this modular approach, it should be possible to construct even larger, more complex reaction circuits: each success along this line will prove our good understanding of the underlying design rules, and each failure may hide some still unknown rules to unveil. Finally, we propose a simple method to bring DNA-toolbox made reaction circuits from zero-dimensional, well-mixed conditions, to a two-dimensional environment allowing both reaction and diffusion. We run an oscillating reaction circuit in two-dimensions and, by locally perturbing it, are able to provoke the emergence of traveling and spiral waves. This opens up the way to the building of complex, tailor-made spatiotemporal patterns.
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https://tel.archives-ouvertes.fr/tel-00856610
Contributor : Adrien Padirac <>
Submitted on : Monday, September 2, 2013 - 8:09:19 AM
Last modification on : Monday, October 19, 2020 - 11:09:41 AM
Long-term archiving on: : Tuesday, December 3, 2013 - 5:17:24 AM

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  • HAL Id : tel-00856610, version 1

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Adrien Padirac. Tailoring spatiotemporal dynamics with DNA circuits. Molecular Networks [q-bio.MN]. Université Claude Bernard - Lyon I, 2012. English. ⟨tel-00856610⟩

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