Enhancement of DNA Microarray Hybridization using Shear-Driven microfluidics

Hybridization on microarray slides is a very slow process. The transport of target molecules towards the immobilized probe spots occurs solely by molecular diffusion and as a result, microarray analyses require overnight incubation and are highly inefficient in terms of capture rate and detection limit. To overcome this diffusion limitation, several solutions have already been reported: electrokinetic flows, ultra-sound mixing, pump-around systems, etc. The present study demonstrates how DNA microarray analysis is enhanced by miniaturization. Only a small sample volume (<5μL) is applied on the microarray and is continuously convected across the microarray surface using a sheardriven flow system. We performed hybridization experiments in a rotating micro-chamber for different hybridization times and with different chamber depths. We demonstrated the benefits of the shear-driven rotating flow system in a biological assay, with complex RNA mixtures (mouse lung and testis total RNA). The shear-driven system is compared with two commonly used hybridization techniques: overnight coverslip diffusion and a commercial hybridization-station (Automated Slide Processor or ASP). The shear-driven system enhanced the hybridization, both in terms of analysis speed and in final spot intensity. We observed that the shear-driven system leads to a tenfold decrease in analysis time and a sixfold increase in final spot intensity.