A pore-cavity-pore device to trap and investigate single nanoparticles and DNA molecules in a femtoliter compartment: confined diffusion and narrow escape.

Abstract

Spatial confinement from the nano- to the microscale is ubiquitous in nature. Striving to understand the behavior of nanoscale objects in confined domains we present a nanofluidic silicon device which consists of two stacked nanopores forming the in/outlets to a pyramidal cavity of micrometer dimensions (10 fL volume). Being electrically addressable, charged objects can be actively loaded into, trapped inside, and unloaded from the "pore-cavity-pore" (PCP) device. When operated passively, confined Brownian motion and the entropy barriers of the nanopores govern the behavior of nano-objects within the PCP device. We present measurements with single fluorescent nanoparticles as well as particle-ensembles and analyze their trajectories and residence times. Experimental data are compared to random walk simulations and analytical theories on confined diffusion and the Brownian escape of nano-objects across entropy barriers. Single particle data corroborate analytical solutions of the narrow escape problem, but ensemble measurements indicate crowding effects even at low particle concentrations. The utilization of the device to trap biomolecules is demonstrated for single λ-DNA molecules.