Discrimination of Short ssDNA Using Nanopore-Fabricated Self-Assembled Metal–Organic Framework Membranes

Two-dimensional nanopores are considered to be a promising and high-resolution single-molecule sensing technique due to their ultrathin thickness. However, it is still challenging to discriminate among short single-stranded DNA (ssDNA) species with distinct sequences due to the fast DNA translocation speed passing though the nanopore. Here, we develop a metal–organic framework (MOF) nanopore sensor that is capable of slowing down and differentiating the translocations of short ssDNA. The nanopore sensor is built through transferring a self-assembly 2D Cu-TCPP MOF (Cu(NO3)2, 4,4,4,4-(porphine-5,10,15,20-tetrayl) tetrakis(benzoic acid)) membrane in the liquid phase onto a SiNx chip with a nanopore, followed by the fabrication of a nanopore in the suspended Cu-TCPP membrane using controlled dielectric breakdown. Since DNA and the organic ligands of the Cu-TCPP membrane interact during DNA translocation due to their high affinity, the interaction results in extending the translocation time. Additionally, the metal node copper can provide hydrophilic regions to limit DNA’s nonspecific adsorption with the membrane. Benefiting from the advantages, two types of ssDNA homopolymers, poly(dA)30 and poly(dC)30, can be successfully discriminated by Cu-TCPP nanopores. The study shows the feasibility of a 2D MOF as a nanopore-based sensing membrane and its ability to slow down DNA translocation.