Pillar size effect on DNA electrophoresis in microchips with sub-micron pillar arrays

This paper presents a systematic study of DNA electrophoresis in microchannels integrated with sub-micron pillar arrays. Electrophoretic mobility of different DNA fragments in channels having pillars of various dimensions is measured. In addition to confirming a previously observed nonlinear relationship with applied electric field following the Biased Reptation with Fluctuations Model, the mobility dependence on DNA size and pillar spacing is characterized and discussed. Similar to conventional slab-gel electrophoresis, short DNA molecules have higher migration mobility. However, a “band inversion”-like phenomenon is observed for larger DNA molecules. The pillar array significantly affects the electric field distribution in the separation channel and, consequently, the resulting mobility. Although this leads to a higher mobility in more closely packed pillars, excessive reduction of the pillar spacing generates a large retarding force. This counteracts the effect of electric field on the overall DNA mobility.