Study of a chaotic mixing system for DNA chip hybridization chambers

Florence Raynal (1) , Frédéric Plaza (1) , Aurélien Beuf (1) , Philippe Carrière (1) , Éliane Souteyrand (2) , Jean-René Martin (2) , Jean-Pierre Cloarec (2) , Michel Cabrera (3)

1 LMFA - Laboratoire de Mecanique des Fluides et d'Acoustique
2 INL - C&N - INL - Chimie et Nanobiotechnologies
3 INL - LOCI - INL - Lab-On-Chip et Instrumentation

Numerical simulations of a micromixing system based on chaotic advection for improved deoxyribonucleic acid (DNA) chip hybridization are presented. To attain best chip performance, homogeneous dispersion of DNA molecules throughout the chamber in which the chip is placed is of primary importance. Poincaré sections of a simple time-periodic flow, based on numerical simulations of the flow, are compared with visualizations in a scaled-up experiment, with good agreement. The influence on mixing efficiency of varying the period of the flow at fixed volume flow rate is studied and a trade off is found between the absence of regular islands and a small enough total sample volume. The results illustrate the potential for optimization of such devices based on numerical flow simulations. The DNA chip has become one of the core technologies in genetics research. A DNA chip is composed of an array of biological probes, such as arrays of oligonucleotides with predetermined sequences, fixed to a solid surface. With improvements of miniaturization techniques, it is possible to have hundreds of thousands of probes on a chip of 1 cm width or less. There are many different methods for making and reading such a chip, but this lies outside the scope of the paper (see Ref. 1 for an overview). In the process of genetic analysis, the array is exposed to labeled DNA samples (with fluorescent markers, for instance). When complementary sequences combine together, the chip is said to be hybridized. That is to say (in theory): the labeled DNA samples are hy-bridized specifically to their complementary biological probes, and are not hybridized to noncomplementary probes. Thus, using a fluorescence technique, some spots on the array fluoresce and others do not, leading to the determination of the chemical composition (the genetic sequence) of the DNA samples. Hybridization requires that complementary molecules encounter each other at some point in time. This may be achieved by pure molecular diffusion of DNA in the solution. In that case it is possible to estimate the typical diffusion

Domaines: Mécanique des fluides [physics.class-ph]; Milieux fluides et réactifs

Florence Raynal, Frédéric Plaza, Aurélien Beuf, Philippe Carrière, Éliane Souteyrand, et al.. Study of a chaotic mixing system for DNA chip hybridization chambers. Physics of Fluids, 2004, 16, pp.L63. ⟨10.1063/1.1775807⟩. ⟨hal-01346926⟩