NSTI Nanotech 2009

Optimal Design of Convective Thermocyclers for Rapid Microscale PCR

R. Muddu, Y.A. Hassan, V.M. Ugaz
Texas A&M University, US

Keywords: microfluidics, PCR, convection


Natural convection has recently been explored as a novel way to perform PCR by providing a passive approach to circulate reactants through the correct temperature zones, thus eliminating the need for repeated heating and cooling of the reaction chamber. But optimal reactor design requires the spatial velocity and temperature distributions to be precisely controlled to ensure that the reactants sequentially occupy the correct temperature zones for a sufficient period of time. Here we describe a new effort to perform 3-D numerical simulations of the velocity and temperature distributions in cylindrical reactors of different aspect ratio (height (h) / diameter (d)), and highlight two geometries that exhibit very different flow characteristics. Fluid trajectories range from relatively closed circulatory loops extending between the temperature extremes to more complex paths that continually evolve over time and provide increased exposure to intermediate temperatures. We find that conditions generating these complex flow paths can be more favorable for PCR due to a synergistic combination of continuous exchange across neighboring trajectories that ensure reagents sample the full range of optimal temperature profiles, coupled with increased time spent within the extension temperature zone—the rate limiting step of PCR. This is supported by PCR experiments that show a nearly order or magnitude reduction in the timescales required for DNA amplification in reactors designed to produce these flow conditions.
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