• Nanopore & NanoFluidic Device Fabrication

TEM image of nanopore in a thin SiN membrane

We invented nanopore fabrication by controlled breakdown (CBD), a simple, rapid, and cost-effective method for creating individual solid-state nanopores directly in a neutral KCl solution. Conventional transmission electron and focused ion beam pore drilling methods were slow, cumbersome, suffered from low yield, and required millions of dollars of clean room equipment. In contrast, our CBD method consists simply of applying to a solid-state membrane an electric field whose strength is at or near the dielectric breakdown strength of the membrane.  A tunneling current is monitored until a sharp increase indicates the spontaneous formation of a nanopore and the onset of ionic current. The pore size can be precisely enlarged by applying time-varying voltage waveforms. Compared to the millions of dollars of cleanroom equipment require for beam-based fabrication, CBD requires a simple voltage source and current monitor and the method can even be implemented with a 9V battery and a few bucks of op-amps, capacitors and resistors. Our revolutionary fabrication method possesses the following distinguishing attributes over other state-of-the-art fabrication techniques:
Ultra-low cost: Price of equipment almost nil, a >10^6-fold reduction over beam-based methods.
Precise pore sizing: Diameter of pore from 0.5-nm to 100-nm achieved with sub-nm precision.
Fast and Efficient: Pore fabrication directly in salt solution in seconds to minutes, and ready for biosensing, eliminating lengthy post-processing steps of beam-fabricated nanopores.
Versatility: Applicable to various materials (e.g. SiN, graphene), multilayered membranes (incl. metal-coated dielectrics) and diverse device architectures (e.g. microfluidics).
Amenable to integration: pores can be fabricated in-situ, within embedded structures with no need for direct line-of-sight access, using similar electronics and electrodes to those employed in sensing applications.
So far, we have published 4 articles describing the principles of our CBD technology (#1, #2, #3, #4) and filed 4 patent applications (2 of which are now issued).

We own an Atomic Layer Deposition system (Savannah S100 from Cambridge Nanotech) to coat our nanopores with various oxides and metals (in a conformal fashion, and one atomic layer at a time). We are also using this tool to design unique membranes.

Our group is continuing to explore alternative fabrication strategies for making individual nanopores, fine tuning a pore size, and creating large nanopore arrays.


  • Solid-State Nanopore Force Spectroscopy (NFS)

The electric field inside the pore is used to pull on charged molecules. For fields spanning from 10^4 – 10^8 V/m, the force on nucleic acids ranges from 0.1 pN to 1nN

Single-molecule force spectroscopy (SMFS) methods, such as AFM or optical traps, can, in principle,  be used for highly specific molecular recognition assays, by not only reporting binding but the strength of bonds between probe and target molecules. Complexity and low throughput of conventional SMFS techniques render such applications impractical.

As recently demonstrated [ACS 2009], solid-state nanopores can be used to rapidly probe the strength of biological bonds. Nanopore-based force spectroscopy (NFS) can typically acquire hundreds to thousands of single-molecule (SM) events in minutes, and with the prospect of parallelized measurements, molecular complexes could be probed in seconds, opening the door to the development of new high-throughput, SM assays for the life sciences or for biomedical applications.

We are currently employing NFS to study aptamer-protein, and aptamer-virus interactions. The goal is to develop NFS so that it can be used in the selection of apatmers (i.e. synthetic anti-bodies) against specific proteins and map the energy lanscape of nucleic acid-protein complexes.  This work is in collaboration with Prof. Maxim Berezovski (Chemistry, uOttawa).

Scheme employed to study aptamer-protein interactions. (i) aptamer-protein complex diffuses to the pore; (ii) The unstructured tail of the aptamer is captured; (iii) Force is applied to the aptamer, the protein larger than the pore, prevents full translocation; (iv) eventually (stochastic process) the bond ruptures and the aptamer translocates, while the protein diffuses away.
  • NanoFluidic Transistors

Schematic of a gated nanopore.

We are fabricating nanofluidic transistor devices using field-effect gated nanopore devices. A gated nanopore is a nanometer-scale hole in a thin membrane equipped with an embedded metal electrode – which is coated with a thin gate oxide via ALD. When immersed in a liquid electrolyte the applied bias at the gate can be used to modulate the ionic current or control the capture and passage of biological molecules (DNA, proteins) – hence the transistor analogy. This project is in collaboration with the Stanford Genome Technology Center.




  • Multiplexed Protein Detection from Complex Biological Samples

Proteins bound to DNA translocating a nanopore array.

We are developing a multiplexing scheme to detect proteins using solid-state nanopores. The strategy relies on binding proteins to DNA molecules and counting the proteins as complexes transverse the pore. The nanopore sensor will be integrated onto a microfluidic chip for processing of complex biological samples (e.g. blood, tissue biopsies), and extraction of specific proteins. This work is in collaboration with Prof. Michel Godin (Physics, uOttawa).




Visit the Equipment page for a list of our instrumentation.



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