We have developed a synchronously switched cyclic capillary electrophoresis (CE) separator that is fabricated on a silicon substrate and glass containing reservoirs, Au electrode, and isolated channels. The advantage of a cyclic separator is the high resolution and ability to separate each sample to the designated reservoir from mixed samples. This approach makes it possible to reduce the supplied voltage and the total size. Another goal of this work is to introduce the methodolgy of electroosmosis flow(EOF) to silicon substrate and to separate DNA samples using a modified double-T injector.