<p>An separation method comprising a temperature control process useful for microchip electrophoresis such as microchip DGGE is provided along with a device therefor. The present invention relates to a microchip electrophoresis method for separating double-stranded nucleic acids by means of differences in nucleotide sequence while maintaining a preset temperature, wherein the temperature during separation of double-stranded nucleic acids in an separation region comprising an separation microchannel is controlled to within ±2.5 °C of the preset temperature.</p>
