Thirty-Cycle Temperature Optimization of a Closed-Cycle Capillary PCR Machine

The performance of a novel thermal cycler has been characterized in a 30-cycle PCR. The device consists of a microcapillary equipped with bidirectional pressure-driven flow and in situ optical position sensors. A 1-μL droplet of reaction mixture moves between three heat zones in a 1-mm i.d., oilfilled capillary using a multi-element scattered light detector and active feedback. The design permits time and number of cycles to be changed without hardware modification, unlike other flow-in-capillary PCR systems. Temperature optimization has been performed on the three PCR heat steps. The optimal denaturation temperature is 94°C-96°C, which is identical to commercial machines. The optimal extension temperature of 62°C-66°C is lower than reported for DNA polymerase (70°C-80°C) because of the high enzyme concentration and/or the absence of detergent in the PCR mixture. The optimal annealing temperature seems to be the same as the optimal extension temperature. This is because extension occurs when the sample is inside of the annealing heat zone. Annealing takes place as the sample travels between heat zones. Device speed (23 min for 30 cycles without time optimization) is competitive with other rapid PCR designs for efficiencies comparable to a commercial machine.