This paper presents the effect of temperature distributions in different heaters and channels on DNA amplification for polymerase chain reaction biochip. We utilized the Micro-Electro-Mechanical System to complete biochip accuracy. The TPX (Poly-4-methyl-pentene-1) was used as the polymer material. The microchip composed of two parts. One is the heater and temperature sensor on a top cover, the other is the microchannel and reaction chamber on a bottom substrate. Then we designed two kinds of chip materials: 1. a glass cover and a TPX substrate, 2. a TPX cover and a TPX substrate. Temperature is the most important in PCR, so the more uniform one is better. And we designed two kinds of heater. According to heat conduction simulation, we can find the best heater pattern. The simulation result is that the design of long inside distance and short outside distance between heater columns was the best one. The reagent of 10 μL was repeated twenty-five cycles to complete PCR process. The temperature controller could reach the speed of heating 20° C /sec and the speed of cooling 5°C /sec. Thus the PCR process could be achieved for twenty-five cycles within 35 minutes. Finally we used the instruments to check DNA amplification result qualitatively and quantitatively. The DNA amplification length was 108 bps. The DNA amplification of long inside distance and short outside distance between heater columns was 90.17 ng/μL, and was larger 12 ng/μL than that of equally distances. Excellent correlation between simulation analysis and experimental result was obtained in this study.

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