Physics of single-molecule electrokinetically driven confinement

Existing nanofluidic systems can perform parallel manipulation of single biopolymers via geometric confinement in nanoscale structures such as nanoslits, nanochannels and nanocavities. Such technology is powerful but the need to introduce molecules intact from bulk solution into nanoconfined environments introduces certain challenges and limitations (such as fragmentation of large molecules). Here we present a device that can perform molecular confinement electrically and allows direct loading of dsDNA from bulk solution. In our approach, we locally sculpt an electric field applied between two parallel electrodes via coating the lower electrode with a dielectric layer that contains arrays of etched holes. The field lines are concentrated at the position of the etched holes, leading to a locally enhanced field at the holes that acts electrokinetically to capture dsDNA; the holes thus act as attractive potential wells for the DNA. We find periodic driving of the device using signals with frequencies in the 1kHz to 1MHz range leads to long-range capture and reversible confinement of the molecules in the field wells while avoiding electrochemical degradation of the device and analytes. We find that the degree of confinement is frequency-dependent, allowing fine sub nanometer control of the molecules; different tunable confinement regimes can be described by the dynamics of resetting. Trapping of larger dsDNA leads to multi-well states where a molecule spans multiple wells with a resulting frequency dependent well occupancy.