An apparatus based on an atomic force microscope for implementing tip-controlled local breakdown.

Solid-state nanopores are powerful tools for sensing of single biomolecules in solution. Fabrication of solid-state nanopores is still challenging, however; in particular, new methods are needed to facilitate the integration of pores with larger nanofluidic and electronic device architectures. We have developed the tip-controlled local breakdown (TCLB) approach, in which an atomic force microscope (AFM) tip is brought into contact with a silicon nitride membrane that is placed onto an electrolyte reservoir. The application of a voltage bias at the AFM tip induces a dielectric breakdown that leads to the formation of a nanopore at the tip position. In this work, we report on the details of the apparatus used to fabricate nanopores using the TCLB method, and we demonstrate the formation of nanopores with smaller, more controlled diameters using a current limiting circuit that zeroes the voltage upon pore formation. Additionally, we demonstrate the capability of TCLB to fabricate pores aligned to embedded topographical features on the membranes.

Single-molecule studies of repressor-DNA interactions show long-range interactions.

We have performed single-molecule studies of GFP-LacI repressor proteins bound to bacteriophage lambda DNA containing a 256 tandem lac operator insertion confined in nanochannels. An integrated photon molecular counting method was developed to determine the number of proteins bound to DNA. By using this method, we determined the saturated mean occupancy of the 256 tandem lac operators to be 13, which constitutes only 2.5% of the available sites. This low occupancy level suggests that the repressors influence each other even when they are widely separated, at distances on the order of 200 nm, or several DNA persistence lengths.

Dynamics of capillary spreading along hydrophilic microstripes.

We have studied the capillary spreading of a Newtonian liquid along hydrophilic microstripes that are chemically defined on a hydrophobic substrate. The front of the spreading film advances in time according to a power law x=Bt(1/2). This exponent of 1/2 is much larger than the value 1/10 observed in the axisymmetric spreading of a wetting droplet. It is identical to the exponent found for wicking in open or closed microchannels. Even though no wicking occurs in our system, the influence of surface curvature induced by the lateral confinement of the liquid stripe also leads to an exponent of 1/2 but with a strongly modified prefactor B. We obtain excellent experimental agreement with the predicted time dependence of the front location and the dependence of the front speed on the stripe width. Additional experiments and simulations reveal the influence of the reservoir volume, liquid material parameters, edge roughness, and nonwetting defects. These results are relevant to liquid dosing applications or microfluidic delivery systems based on free-surface flow.