Optimal Design and Operation for a Droplet-Based PCR Chip

A two-temperature continuous-flow PCR polymer chip has been constructed that takes advantage of droplet technology to avoid sample contamination and adsorption at the surface. Samples contained in aqueous droplets are continuously moved by an oil carrier-fluid through various temperature zones, introducing the possibility of real-time quantitative PCR. The use of droplet technology also makes it possible to perform high throughput analyses of single cells allowing the study of populations of cells and facilitating a more comprehensive understanding of biological variance with relation to disease. In the present device, the thermal cycling time is significantly reduced and the PCR samples are exposed to more uniform temperatures. This paper investigates many of the factors affecting droplet-based PCR chip design, including specific heat capacity, density, flow rate, and thermal resistance. The study focuses particularly on the fluid and substrate temperature distribution within the PCR chip and the droplet residence times in critical temperature zones. The results show that, in general, the carrier-fluid should have a low thermal mass to ensure minimal heating and cooling times. It was found that the predicted temperature distribution in the chip arises from a subtle thermal interaction between the substrate and the carrier-fluid. The simulations demonstrate that the flow rate strongly affects the carrier-fluid’s temperature field. Above a critical flow rate, the carrier-fluid fails to achieve the temperatures required for DNA amplification. Moreover, the thermal resistance of the different layers is shown to have a major impact on the temperature profile in the channel.