# Nanopore-based multi-target analysis of Zika virus infection

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA SANTA CRUZ · 2021 · $494,127

## Abstract

Principal Investigator/Program Director: Schmidt, Holger
Project Summary
Spurred by the explosive growth in personalized medicine which requires highly sensitive
genomic and proteomic analysis, single molecule detection is rapidly developing from a
fundamental research technique into the foundation for advanced molecular diagnostic
techniques. Whereas optical fluorescence detection used to be the approach of choice,
electrical detection of single molecules as they are drawn through a nanopore has recently
gained great attention, particularly in the context of next generation sequencing. The direct,
label-free detection of a wide range of molecules using nanopores has much broader potential.
However, a major obstacle for fully exploiting the exquisite sensitivity of nanopore detection is
the mismatch between the minute electrostatic capture volume of a nanopore and the low
concentrations encountered in real-world applications, e.g. in molecular diagnostics.
The goal of this project is to overcome this limitation with a novel, innovative approach to high-
throughput molecular diagnostics using single molecule nanopore analysis. The specific
objectives of this application are to increase the capture rate (throughput) of a nanopore by
orders of magnitude and to validate this approach with clinical samples for Zika virus (ZIKV)
infection. Our central hypothesis is that this can be accomplished by delivering target molecules
isolated on microbeads within the capture radius of the pore using a chip-based optical trap on a
waveguide-based optofluidic chip.
The objectives of this application will be accomplished by the following Specific Aims: (1)
Nanopore capture rate enhancement using optical trapping of carrier beads. This Aim will
validate the core of our new approach and demonstrate a 50,000x improvement for both nucleic
acids and proteins; (2) On-chip integration of microfluidic sample processing with high
throughput molecular detection at ultralow (attomolar) concentrations; and (3) Multiplex direct
detection of ZIKV infection starting from complex sample matrices (serum, saliva, urine, semen).
The innovative contributions of the proposed work are: (i) Optical trapping of carrier particles for
molecular target delivery; (ii) Creating an integrated chip-based system for nanopore-based,
label-free detection of diverse molecular biomarkers; and (iii) Clinical validation of nanopore-
based analysis of multiple analyte types. The proposed work is significant because it will
introduce the first integrated system that matches the sensitivity, simplicity, and versatility of
single-molecule nanopore detection with the real-world constraints for molecular diagnostics. As
such, this approach will be applicable to many molecular targets and applications.
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## Key facts

- **NIH application ID:** 10146370
- **Project number:** 5R01EB028608-03
- **Recipient organization:** UNIVERSITY OF CALIFORNIA SANTA CRUZ
- **Principal Investigator:** Holger Schmidt
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $494,127
- **Award type:** 5
- **Project period:** 2019-08-01 → 2023-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10146370

## Citation

> US National Institutes of Health, RePORTER application 10146370, Nanopore-based multi-target analysis of Zika virus infection (5R01EB028608-03). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10146370. Licensed CC0.

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