Pressure-driven DNA transport across an artificial nanotopography

Abstract

The pressure-driven transport of DNA was studied in slit-like nanochannels with an embedded nanotopography consisting of linear arrays of nanopits. We imaged individual DNA molecules moving single-file down the nanopit array, undergoing sequential pit-to-pit hops using fluorescence video microscopy. Distinct transport dynamics were observed depending on whether a molecule could occupy a single pit, or was forced to subtend multiple pits. We interpret these results in terms of a scaling theory of the free energy of polymer chains in a linear array of pits. Molecules contained within a single pit are predicted to face an entropic free energy barrier, and to hop between pits by thermally activated transport. Molecules that subtend multiple pits, on the other hand, can transfer DNA contour from upstream to downstream pits in response to an applied fluid flow, which lowers the energy barrier. When the trailing pit completely empties, or when the leading pit reaches its capacity, the energy barrier is predicted to vanish, and the low-pressure, thermally activated transport regime gives way to a high-pressure, dissipative transport regime. These results contribute to our understanding of polymers in nanoconfined environments, and may guide the development of nanoscale lab-on-a-chip applications.