Tailoring spatio-temporal dynamics with DNA circuits
type: Dataset
description: 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 t…
identifier: NNT: 2012LYO10244
issued: 2026-05-05T11:03:27.044364
language: en
modified: 2026-05-05T11:03:27.044368
contact point: Organization
  fn: CCSD
keyword: adn
keyword: dna
keyword: dynamic-reaction-networks
keyword: enzymes
keyword: infoeu-reposemanticsdoctoralthesis
keyword: molecular-programming
keyword: programmation-moleculaire
keyword: reaction-diffusion
keyword: reseaux-de-reaction-dynamiques
keyword: sdvsalife-sciences-q-bioagricultural-sciences
keyword: theses
landing page: https://theses.hal.science/tel-00992096

Tailoring spatio-temporal dynamics with DNA circuits
type: Distribution
format: HTML
issued: 2026-05-05T11:03:27.046733
modified: 2026-05-05T11:03:27.025051
access URL: https://theses.hal.science/tel-00992096

test_moissonnage_selune
type: Agent