An All-Electric Single-Molecule Hybridisation Detector for short DNA Fragments

TL;DR

This paper introduces an all-electric, label-free nanopipette-based sensor capable of detecting short DNA fragments and their hybridisation states, promising rapid, high-throughput, point-of-care DNA analysis.

Contribution

It presents a novel single-molecule hybridisation detection method combining DNA nanotechnology with resistive pulse sensing in nanopipettes, enabling discrimination of subtle DNA structural differences.

Findings

Successfully identified hybridisation states of short DNA probes

Demonstrated detection of disease-related DNA fragments

Showed potential for multiplexed, high-throughput analysis

Abstract

In combining DNA nanotechnology and high-bandwidth single-molecule detection in nanopipettes, we demonstrate an all-electric, label-free hybridisation sensor for short DNA sequences (< 100 nt). Such short fragments are known to occur as circulating cell-free DNA in various bodily fluids, such as blood plasma and saliva, and have been identified as disease markers for cancer and infectious diseases. To this end, we use as a model system a 88-mer target from the RV1910c gene in Mycobacterium tuberculosis that is associated with antibiotic (isoniazid) resistance in TB. Upon binding to short probes attached to long carrier DNA, we show that resistive pulse sensing in nanopipettes is capable of identifying rather subtle structural differences, such as the hybridisation state of the probes, in a statistically robust manner. With significant potential towards multiplexing and high-throughput analysis, our study points towards a new, single-molecule DNA assay technology that is fast, easy to use and compatible with point of care environments.