Nanopipette-DNA-Nanopore Hybrid System for Small Molecule Detection

Hybrid nanopores composed of a solid-state nanopore and a DNA origami nanopore are excellent candidates for highly molecular-selective nanopore sensors owing to the high designability and functionalization potential of DNA origami structures. Although the detection of macromolecules, including ssDNAs and proteins, has been demonstrated using hybrid nanopores, their applicability for small-molecule detection has not yet been revealed. The critical issue hindering the application of the hybrid nanopore is the limited understanding of the behavior of DNA origami nanoplates trapped on a solid-state nanopore under high applied potentials. Here, we developed a hybrid nanopore constructed by electrophoretically trapping an adenosine triphosphate (ATP) aptamer-modified DNA origami nanopore onto a nanopipette. This hybrid nanopore generates open/close signals through the binding and dissociation of ATP to the aptamer modified on the central aperture of the DNA origami nanopore. Ion current measurements revealed four distinct kinds of ion current signals in the presence and absence of ATP. Moreover, the ratio of open/close signals in the presence of ATP increased threefold compared with the ATP-free condition or ATP analogs, including cytidine triphosphate, demonstrating specific ATP detection using the hybrid nanopore. We believe that these results provide fundamental insight into the development of versatile hybrid nanopore sensors.