DNA separation chips using temporally asymmetric ratchet effect in nonuniform electric fields

Abstract

We present DNA separation chips using temporally asymmetric ratchet effect in nonuniform electric fields. The present chip redistributes DNA within a specific area in asymmetrically-switched nonuniform electric fields based on the size- and field-dependent nonlinearity of DNA drift velocity. Compared to the conventional electrophoresis chips, the present separation chip is easy to be integrated into the automated DNA analysis systems because of simple structure and starting-point independent DNA separation. Based on the drift velocity of the first three group of different DNA molecules (11.1kbp, 15.6kbp, and 48.5kbp), we extract the asymmetric alternating electric field conditions ($E_1$=4$E_2$ and 23$T_1$=3$T_2$), where Phagemid DNA (15.6kbp) shows zero net velocity while EM3 DNA(11.1kbp) and λ DNA (48.5kbp) migrate -x and +x direction, respectively. In addition, we extract the asymmetric alternating electric field conditions ($E_1$=4$E_2$ and 23$T_1$=5$T_2$), where DNAII’ (496bp) shows zero net velocity while DNA I’(166bp) and DNAIII’ (933bp) migrate -x and +x direction, respectively, based on the measured drift velocity of the second group of DNA molecules (166bp, 496bp, and 933bp). The present chip is composed of a tapered-channel to generate nonuniform electric fields, a DNA loading slit and a pair of electrodes to apply electric field. We focus on the design of DNA separation chips with identifying the nonlinearity of DNA drift velocity using three different DNA molecules in the chips. It is demonstrated that different size of DNA shows different net migration velocity under the nonuniformly-distributed asymmetric alternating electric fields with first group of DNA molecules. Phagemid DNA moved to its own specific location, -1.5mm from the starting point (+2mm from the loading slit), then showed the zero net migration velocity. Other sample DNA molecules, EM3 and λ DNA have migrated 2.2mm in -x direction and 1mm in +x direction, respectively, under the a...