An alternative polymerase chain reactor (PCR) driven by electrokinetic flow was developed and tested. A single straight microchannel and a double-T intersection were designed for injection of DNA samples and thermal cycling by shuttling between constant temperature zones. Thermal performance of the device was studied using numerical and analytical models to understand the temperature distribution. Devices were made on a polycarbonate substrate by hot embossing with a micromilled brass mold insert. A PID control system, with a tolerance of ± 0.2°C, was used to maintain the temperatures in each zone during experiments. Power consumption in each zone was predicted using thermal simulations. Molecular diffusion of 500 bp DNA was evaluated using two methods, an empirical equation and an analytical model, and the diffusion length after 20 cycles from both models was 100 μm with a 0.97 μm difference. Electroosmotic flow (EOF) was minimized by using dynamic coating and Joule heating was reduced by decreasing the KCl component in the DNA cocktail. Successful amplification of 500 bp DNA fragments at shuttle velocities of 1mm s-1 (620 seconds), 2mm s-1 (310 seconds), and 3mm s-1 (207 seconds) was demonstrated for 20 thermal cycles. The amplification efficiencies were 31%, 28%, and 18%, respectively. Unintentional flows resulting from siphoning phenomenon due to hydrostatic pressure, and Laplace pressure due to surface tension, may be responsible for the reduced amplification performance.

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