Detection of small-sized DNA fragments in a glassy nanopore by utilization of CRISPR-Cas12a as a converter system

The fabrication of nanopores with a matched pore size, and the existence of multiple interferents make
the reproducible detection of small-sized molecules by means of solid-state nanopores still challenging.
A useful method to solve these problems is based on the detection of large DNA nanostructures related
to the existence of small-sized targets. In particular, a DNA tetrahedron with a well-defined 3D nanostructure
is the ideal candidate for use as a signal transducer. Here, we demonstrate the detection of an
L1-encoding gene of HPV18 as a test DNA target sequence in a reaction buffer solution, where long
single-stranded DNA linking DNA tetrahedra onto the surface of the magnetic beads is cleaved by a target
DNA-activated CRISPR-cas12 system. The DNA tetrahedra are subsequently released and can be detected
by the current pulse in a glassy nanopore. This approach has several advantages: (1) one signal transducer
can be used to detect different targets; (2) a glassy nanopore with a pore size much larger than the target
DNA fragment can boost the tolerance of the contaminants and interferents which often degrade the
performance of a nanopore sensor.