# Chemically Tuned Silicon Nitride Nanopores for Nucleic Acid Sequencing

> **NIH NIH R21** · UNIVERSITY OF RHODE ISLAND · 2021 · $251,851

## Abstract

PROJECT SUMMARY
This project aims to improve DNA and RNA sequencing technology by at least an order of
magnitude by dramatically improving the ability to control silicon nitride nanopore surface
chemistry and to modify silicon nitride nanopore size. While silicon nitride is a conventional
material for nanopore sequencing applications, its complex charged native surface chemistry
can present a challenging and complicated environment for a charged nucleic acid biopolymer
passing through a nanopore not much larger than itself. Highly desirable long read lengths
heighten the need for chemical control over the nanopore surface. Coating the nanopore
surface with even a single molecular layer will change the nanopore diameter, which thus also
provides for molecular-scale tuning of nanopore dimensions. Broadly, chemically tuned
nanopore surface chemistry affords control over motion of (native or labelled) nucleic acid
polymers through the pore through electrostatics, specific chemical interactions, and
electrokinetics (e.g. electroosmosis). It offers the potential for passivation against fouling in
complex matrices, thereby supporting more minimal sample processing. It also affords control
over interfacial phenomena that can affect nanopore current noise.
Thin-film silicon nitride is a widely used nanofabrication material with widespread commercial
utility, so that its continued use in a host of nanopore sequencing implementations is warranted
in spite of its often challenging surface chemistry. But efforts to control and improve its surface
chemistry using silane chemistry have not gained traction in the field, in significant part because
the chemistry is inherently challenging to implement, the more so given the variability of the
silicon nitride oxide coating. We thus propose to develop a radically different type of surface
chemical modification strategy that is simple to implement, produces highly reliable results, and
that can be used to install surface coatings with a wide variety of chemical properties and sizes.
We propose to test the surface coatings through their effect on the nanopore conductance and
current noise, and on the sequence-specific signal characteristics when sensing well-defined
sequences of DNA.
The project will be implemented by an interdisciplinary team that combines more than 20 years
of Principal and Co-Investigator experience in physical organic chemistry and chemical
synthesis (MK); materials science (MK&JRD); and nanofabrication (JRD), with a decade of
experience in nanopore science begun in nanopore genotyping (JRD), including a specialization
in nanopore surface chemistry modification and characterization.

## Key facts

- **NIH application ID:** 10162635
- **Project number:** 5R21HG011096-02
- **Recipient organization:** UNIVERSITY OF RHODE ISLAND
- **Principal Investigator:** Jason Rodger Dwyer
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $251,851
- **Award type:** 5
- **Project period:** 2020-05-11 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10162635

## Citation

> US National Institutes of Health, RePORTER application 10162635, Chemically Tuned Silicon Nitride Nanopores for Nucleic Acid Sequencing (5R21HG011096-02). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10162635. Licensed CC0.

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