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.