This paper presents a study of electrokinetic transport in single nanopores integrated into vertically stacked three-dimensional hybrid microfluidic/nanofluidic structures. In these devices, single nanopores, created by focused ion beam (FIB) milling in thin polymer films, provide fluidic connection between two vertically separated, perpendicular microfluidic channels. Experiments address both systems in which the nanoporous membrane is composed of the same (homojunction) or different (heterojunction) polymer as the microfluidic channels. These devices are then used to study the electrokinetic transport properties of synthetic (i.e., polystyrene sulfonate and polyallylamine) and biological (i.e., DNA) polyelectrolytes across these nanopores using both electrical current measurements and confocal microscopy. Both optical and electrical measurements indicate that electro-osmotic transport is predominant over electrophoresis in single nanopores with d>180nm, consistent with results obtained under similar conditions for nanocapillary array membranes.

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