Fast and sensitive DNA hybridization through micro-fluidics

The research target for DNA hybridization through microfluidics is to achieve a fast hybridization reaction by investigating the effect of different pertinent parameters using computational and experimental methods. The mathematical model that we developed couples mass transport of DNA from the bulk of the solution with the surface reaction kinetics for the DNA hybridization reaction in a micro fluidic channel. A 2-D analysis of the classical mass transport equation under laminar flow conditions combined with an overall second order rate constant for the surface hybridization reaction elucidates the effect of changing the fluid flow rates, bulk concentration, channel heights and the utilization of bluff bodies, on the DNA hybridization efficiency.; As the channel height decreases or the fluid flow rate increases (for continuous fluid flow), the mean velocity through the channel increases for a fixed volume flow rate and the model shows that the latter enhances the transport of target DNA molecules by convection. Thus, the time taken to reach the equilibrium condition is shorter. Performing the hybridization experiment with a large bulk concentration, also leads to faster equilibrium condition. The channel with the bluff body set-up showed a yet better performance over the regular channel.; In the experimental work, flow through hybridization, as well as, passive hybridization experiments were carried out. Two channels were utilized: a regular and one with a grooved surface---to provide chaotic mixing in the fluid stream. A master mold was first prepared using lithography. The flow cells are then replicated from the master mold using Polydimethylsiloxane (PDMS). The PDMS structure was then set on a gold spotted glass slide, with DNA reaction sites immobilized on the gold, to seal it, and together they form the microfluidic channel.; It was verified that an increase in target DNA concentration provides a dramatic increase in the hybridization rate, which confirms our theoretical modeling result. For a fixed sample volume, the slower flow provides a higher hybridization rate. The hybridization rate using the grooved surface, versus the plain channel is doubled and quintiled with respect to the passive experiment.