Characterization and optimization of an entropic trap for DNA separation

Abstract

Recently, a microfabricated entropic trap array was demonstrated to be useful in separating large (5-200 kbp) DNA molecules efficiently (within approximately 30 min), by dc electrophoresis, on a microchip platform without a sieving matrix. This paper reports further development of the technique, with emphasis on optimizing separation selectivity and resolution. The interaction of DNA molecules with regularly spaced entropic barriers was modeled in order to predict the effect of changing various structural parameters. The selectivity (differential mobility) was shown to be dependent on the depth of deep and shallow channel regions, applied electric field, and number of entropic barriers. Experimental data were compared with the prediction of the model. It was expected from the model that, in the low-field (severe trapping) limit, separation resolution should depend only on the number of entropic traps. However, in reality, resolution did depend on the applied field because the relaxation of DNA is not achieved at high fields. The requirement and feasibility of megabase pair DNA separation with the entropic trap array device was discussed.