A pore-Cavity-Pore Device to Trap and Investigate Single Nano-Scale Objects in Femto-Liter Compartments: Confined Diffusion and Narrow Escape

Abstract

Spatial confinement from the nano- to the micro-scale is ubiquitous in nature. Striving to emulate biological compartmentalization and to understand the fundamental physical behavior of molecules in confined domains, micro- and nano-structuring techniques have been used extensively to create artificial devices comprising liquid-filled compartments and channels. In addition, the development of robust solid-state structures, which allow for the observation and manipulation of single nano-scale objects is key for the realization of future lab-on-chip devices with improved functionality. Here we introduce an electrically addressable nano-fluidic silicon device that consists of two stacked nanopores forming the in/outlets to a pyramidal cavity of micrometer dimensions, i.e. femto-liter volume. The electrical properties of the PCP structure are investigated by impedance spectroscopy. Furthermore, we present a FEM simulation of the electric field inside the device. We then demonstrate how individual fluorescent nano-particles and DNA can be actively (by electrical means) and passively (entropically driven) loaded into, trapped inside, and unloaded from the ‘pore-cavity-pore’ (PCP) device. A fundamentally important problem in biology is the escape of nano-objects from a micro-domain through a small opening (narrow escape problem). Using the PCP device it is possible for the first time to obtain data on the narrow escape time under well-defined geometrical and experimental conditions. Single particle tracking and residence time data are presented and quantitatively compared to random walk simulations and analytical theories on confined diffusion and the narrow escape problem. Furthermore, we extend the escape studies towards polymeric analytes like DNA.