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An innovative micro polymerase chain reaction (PCR) chip, micro oscillating flow-through PCR chip, was designed and fabricated by using silicon microfabrication technique with double-sided lithography. Three different temperature zones, which are stable at 93°C, 72°C and 50°C and isolated from each other by deep groove, are integrated with a straight microchannel in the chip to form the basic functional structure. It is indicated numerically that the time needed for the temperature varying to the target value is less than 1 second, and the temperature difference in the reaction zone is less than 0.2°C at the same time. A quasi multi-systems lumped heat capacity method has been advanced to analyze the chip's transient thermal performance, which was validated by numerical simulation. A microliter-sized droplet of reagent with HPV-DNA inside was injected into the chip and forced to flow through the three temperature zones in an oscillating manner to realize DNA amplification. The amplification results of the chip are analyzed by slab gel electrophoresis with separation of DNA markers in parallel.