DNA analyzing technologies are commonly used in prevention and treatment of various infectious diseases. A portable DNA analyzer based on impedance spectroscopy facilitates the testing, while low pow consumption is necessary to minimize the battery size. However, traditional impedance spectroscopy techniques utilize power-hungry sinusoid signal to stimulate the DNA sample. In this work, we demonstrate a DNA analyzer chip with square-wave stimulation and detection. The spectral aliasing induced by the harmonics of square wave is avoided by a half-integer over-sampling technique. In this way, the chip eliminates the requirement of power-hungry filters in conventional works. In addition, the impedance spectroscopy corresponding to the 3rd harmonic is utilized to provide an extra stimulus frequency, enabling simultaneous DNA analysis at two frequencies. Fabricated in 65nm CMOS process, the in-vitro DNA testing data of our chip matches favorably with the results of an electrochemical workstation (CHI760E). The proposed DNA analyzer chip consumes 120μW power, and doubles the analyzing speed by the 3rd harmonic based detection.