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Solid-state nanopore membranes for DNA detection and sequencing

A technology portfolio comprising fabrication and detection methods for improved DNA sequencing using nanoporous membranes.


Biomolecule detection and sequencing lay a foundation for personalized medicine and drug discovery. DNA sequencing has emerged as a primary tool for understanding the whole genome. Such measurements can be made by passing a biomolecule through a nanopore and measuring resulting changes in ion current values. Primary barriers to efficient DNA sequencing include high signal to noise ratios allowing for discrimination between DNA bases and detection of short nucleotide sequences through nanoporous membranes.


This technology portfolio allows for the detection of short DNA sequences using ultra-thin membranes with small diameter nanopores, resulting in higher ionic conductance and increased bias current. Additionally, it allows for insulated electrode gaps, resulting in improved signal to noise ratios.

Technology Overview: 

This technology portfolio consists of fabrication methods for generating ultra-thin Silicon Nitride (SiN) membranes and ultra- low capacity, glass supported dielectric membranes for DNA sequencing. Ultra-thin SiN membranes are generated using local thinning via ion etching on a defined region onto which nanopores are generating using electron beans. Ultra-thin SiN membranes allow for the detection of short nucleic acid molecules. Glass-only supported SiN membranes reduce silicon-supported nanopore device capacitance, and are generated by selectively etching small pores in a aSi/SiN/Glass/SiN/aSi substrate.

Additionally, fabrication methods for generating 1-2nm diameter nanopores in membranes and generating insulated nanoscale electrode gaps have been developed. The small nanopore diameter is comparable with the width of single stranded DNA. A silicone chip is first coated with silicon dioxide with silicon nitride subsequently deposited. The chips are then etched, and the resulting window is locally thinned and nanopores are drilled. The insulated nanoscale electrode gaps are fabricated using beam lithography to create coarse gaps. A dielectric material is then added to provide insulation to focus the current density between electrodes.

Lastly, methods for generating and using graphene nanopore membranes to measure DNA translocation have been developed. The use of graphene-based nanopore devices improves the overall signal-to-noise ratio. A Chemical Vapor Deposition technique is used to fabricate a multi-layer graphene membrane. Transmission electron beam ablation lithography and UV/ozone treatments are then applied to create nanopores within the membrane.


  • Optimized detection of short nucleic acid molecules and single stranded DNA
  • Increased bias current and higher ionic conductance
  • Focused current density between nanoelectrodes due to electrode insulation
  • Improved signal to noise values during DNA sequencing
  • Reduced device capacitance from other Si-supported designs from ~50pF to ~0.1 pF, the capacity for sequencing free-running DNA

Details of solid-state nanopore fabrication. Stacked silicon chips covered with silicon dioxide and SiN (A). The chips are etched to create a window from which nanopores are drilled (B).  The nanopore has a diameter of approximately 1.4 nm(C). The thickness of the thinned region (D), and the experimental design of SNA passing through the nanopore (E).

Stage of Development: 

  • Proof of Concept
  • Prototype developed

Intellectual Property: 

  • US8039368: Nanogaps: methods and devices containing same
  • US8173335: Beam ablation lithography
  • US9121823 and corresponding foreign issued patents: High-resolution analysis devices and related methods
  • US10017813: Differentiation of macromolecules and analysis of their internal content in solid-state nanopore devices
  • US10274478: Ultra low capacitance glass supported dielectric membranes for macromolecular analysis
  • US application pending: Insulated nanoelectrode-nanopore devices and related methods
  • US application pending: Graphene-Based Nanopore and Nanostructure Devices and Methods for Macromolecular Analysis

Reference Media: 

Desired Partnerships: 

  • License
  • Co-development

Patent Information:


Marija Drndic

Docket # Z6635

For Information, Contact:

Qishui Chen
Licensing Officer, SEAS/SAS Licensing Group
University of Pennsylvania