Biological organisms process information through the use of complex reaction networks. These can bea 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 ofspatio-temporal dynamics from the bottom-up.First, we design a monitoring technique of DNA hybridization by harnessing a usually neglectedinteraction between the nucleobases and an attached fluorophore. This fluorescence technique -calledN-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 rulesat the sequence level. With this experience behind us, we tackle the construction of reaction circuitsdisplaying bistability. We link the bistable behavior to a topology of circuit, which asks for specificDNA sequence parameters. This leads to a robust bistable circuit that we further use to explore themodularity of the DNA-toolbox. By wiring additional modules to the bistable function, we make twolarger circuits that can be flipped between states: a two-input switchable memory, and a single-inputpush-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 thismodular approach, it should be possible to construct even larger, more complex reaction circuits: eachsuccess along this line will prove our good understanding of the underlying design rules, and eachfailure may hide some still unknown rules to unveil.Finally, we propose a simple method to bring DNA-toolbox made reaction circuits from zerodimensional,well-mixed conditions, to a two-dimensional environment allowing both reaction anddiffusion. We run an oscillating reaction circuit in two-dimensions and, by locally perturbing it, areable to provoke the emergence of traveling and spiral waves. This opens up the way to the building ofcomplex, tailor-made spatiotemporal patterns.
| Identifer | oai:union.ndltd.org:CCSD/oai:tel.archives-ouvertes.fr:tel-00992096 |
| Date | 29 November 2012 |
| Creators | Padirac, Adrien |
| Publisher | Université Claude Bernard - Lyon I |
| Source Sets | CCSD theses-EN-ligne, France |
| Language | English |
| Detected Language | English |
| Type | PhD thesis |
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