Electrokinetic Flow Dynamics of Weakly Aggregated λDNA Confined in Nanochannels

Abstract

Flow dynamics in nano-scaled structures such as nanochannels and nanopores have recently become important in developing next-generation high-speed DNA sequencers. In the present paper, we report the electrokinetic flow dynamics of λDNA confined in nanochannels having heights that are smaller than the molecular radius of gyration. Nanochannels of varying heights of from 330 to 650 nm were used in the experiments in order to systematically investigate the effect of confinement. Weakly aggregated λDNA flowed in a direction opposite to an applied electric field as a result of the competition of electrophoresis and electroosmotic flows. The terminal velocity of λDNA was proportional to the strength of the electric field, and the mobility was found to decrease with the channel height. A simple theoretical model explaining the decrease in the mobility was developed taking into account the shear stress due to small clearances between λDNA and the walls of nanochannels. The validity of the model was confirmed by reasonable agreement between the theoretical and experimental results. The theoretical model and the transport properties under confinement provide basic design data for the development of next-generation DNA sequencers.