• Nanopore & NanoFluidic Device Fabrication

TEM images of nanopores drilled in a 30nm thick SiNx membrane

We are fabricating 1-10 nm pores in thin silicon nitride membranes with a transmission electron microscope (TEM – JEOL JEM-2100F FETEM), located in the Material Characterization Facility in the Centre for Catalysis Research and Innovation at uOttawa. These pores are mainly used for nucleic acid or protein analysis. We are also drilling >100nm pores via focused ion beam (FIB) for other applications (such as virus detection or nanofluidic transistor measurements).

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 exploring 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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