Rationally Designed DNA Origami Carriers for Quantitative Single Molecule Detection with Nanopipettes

The ability to detect small concentrations of biomarkers in patient samples is one of the cornerstones of modern healthcare. In general, biosensing approaches employed to
address this need are based on measuring signals resulting from the interaction of a large ensemble of molecules with the sensor. Here, a biosensor platform using DNA origami, featuring a central cavity with a target–specific DNA aptamer, as carriers for translocation through nanopores which enables individual biomarkers to be identified and counted to compile a sensing signal is reported.
It is shown that the modulation of the ion current through the nanopore upon the DNA origami translocation strongly depends on the presence and in fact the size of a central cavity. While DNA origami without a central cavity cause a single peak in the ion current, DNA origami of the same dimensions but featuring a central cavity lead to double peaks
in the ion current. This is also true for DNA origami (with and without central cavities) made of similar sized DNA but of different dimensions. It is also observed that the peak characteristics, peak amplitude and the dwell time, are different depending on the presence or absence of a central cavity.
This work exploits these parameters to generate a biosensing platform capable of detecting human C–reactive protein (CRP) in clinically relevant fluids. DNA origami frames with cavities large enough to lead to clear ion current double peaks were designed and a CRP–specific DNA aptamer was introduced into the cavity. Also, upon binding of CRP, the ion current peak changes to a single peak and the peak characteristics change. Using this three–parameter classification, CRP–occupied and unoccupied carriers can be
distinguished when they translocate through the nanopore. Thus CRP biosensing by computing the ratio of occupied vs total number of frames with a limit of detection of 3 nM is successfully demonstrated.