Electrokinetic transport of DNA in nanoslits

Abstract

This thesis presents the results of fundamental investigations of the electrokinetic transport of -DNA and Litmus DNA (XbaI digested) in nanoslits of 20, 60 and 120 nm in height. In order to understand the DNA separation using nanostructures, we start with the main theories developed in gel electrophoresis. The transport of the -DNA molecules was first investigated in 20 nm heigh nanoslits when electric DC fields were applied. The -DNA molecules showed a field dependent mobility and followed preferential pathways through the nanoslits. The increasing mobility up to a DC field strength of 30 kV/m and the observation of preferential pathways can both be explained by the biased reptation model. At electrical DC fields strengths of 30 kV/m and below the molecules moved in a fluent way, however above field strengths of 30 kV/m this fluent movement changed in an intermittent movement and trapping of -DNA molecules. For the intermittent movement and the trapping we suggested a mechanical and/or a dielectrophoretic mechanism. Also Litmus DNA showed a field dependent mobility which was lower when comparing to the -DNA molecules and was only transported in an intermittent way. The hypothesis of a possible dielectrophoretic trapping mechanism was first investigated. For this purpose the electrokinetic transport of the -DNA molecules was analyzed when AC electrical fields (10 – 200 kV/m; 100 Hz and 1 kHz) were superimposed onto DC electrical fields (10 – 200 kV/m). For a larger part of the data, no significant influence of the superimposed AC field was found which indicates that dielectrophoretic phenomena are not important. In this investigation we found both fluent and intermittent movements of the -DNA molecules at different AC and DC field strengths. Apart from this, we also found preferential pathways. Again the increase in mobility we found with increasing AC field strength at low DC fields can be explained by the biased reptation model, assuming the AC fields cause an increased orientation of the DNA molecules in the field direction. We also investigated the transport of -DNA molecules in 60 and 120 high nanoslits. Only in the 60 nm high nanoslits some intermittent movement was seen, but merely for a small percentage of the -DNA molecules whereas most of the molecules moved fluently through the nanoslit. The mobility of -DNA was furthermore independent of the field strength and no preferential pathways were observed. Interestingly, the mobility at a DC field of 30 kV/m decreased in the order 20 nm > 60 nm > 120 nm. We currently have no explanation for this observation. The Litmus DNA was also investigated, however we were not able to track these molecules in these higher slits. For future investigations of the separation possibilities using nanoslits, we also manufactured a charged patterned nanoslit device, as described in the last chapter.