Improving DNA microarray hybridization with a pulsed source-sink mixing device

A fundamental study of fluid mixing is used to guide the design of a hybridization chamber for DNA microarray analysis. The focus is on a system consisting of a simple arrangement of flow sources and sinks that efficiently delivers targets across a conventional glass slide array using a series of flow pulses. A quantification of chaotic advection in a reduced-order flow model suggests that optimal results for this system will be obtained when each flow pulse exchanges approximately 35-45% of the chamber fluid volume. Hybridization experiments were conducted for a relative pulse volume of approximately 40% across a microarray printed with a pattern of 102 identical probe spots containing a 65-mer oligonucleotide capture probe. Hybridization of a 725-bp fluorescently labeled target was used to quantify target hybridization levels. Relative to a conventional 24-hour static hybridization, a 1-hour mixing-based analysis was found to produce an increase in signal intensity and a reduction in spot-to-spot signal variation.