Optimisation du protocole de mélange et de la géométrie d’une chambre d’hybridation de puces à ADN

Optimization of both mixing protocol and geometry of a DNA chip hybridization chamber

Laboratoire de Mécanique des Fluides et d’Acoustique CNRS / Université de Lyon ; École Centrale de Lyon / Université Lyon 1 / INSA Lyon 36, av. Guy de Collongue, 69134, Ecully Cédex, France

Auteur de correspondance : aurelien.beuf@ec-lyon.fr

Abstract

Optimization of both mixing protocol and geometry of a DNA chip hybridization chamber. DNA chip technology requires a rapid and homogeneous dispersion of the DNA molecules over the whole surface of the chip. We present here a numerical study that compares two periodic mixing protocols, based on chaotic advection ; the first protocol uses syringes, the other one pumps. We also compare two different geometries (square and rectangle) of the hybridization chamber in which the chip is placed. To achieve this, the Hele-Shaw flow is modelled by a two-dimensional flow, which allows us to find easily the analytical velocity field in these different shapes. The results are analyzed in terms of Poincaré sections (appearance, filling rate) ; the Lyapunov exponents are also computed. These Poincaré sections are then compared to visualizations in a 10 :1 scaled-up experiment, with good agreement. We show that the protocol that operates with pumps, coupled with the rectangular geometry, is more likely to achieve best chip performance : we get global chaos whatever the period chosen.