Quad-Nanopore Array Enables High-Resolution Identification of Four Single-Stranded DNA Homopolymers

The solid-state nanopore technique holds the potential to develop mechanically stable and miniaturized DNA sequencing devices. However, the limited temporal resolution due to the high electric field inside the nanopore and the lack of an effective speed control strategy have hindered the realization of sequencing. Here, we reported a quad-array (four nanopores milled with ∼30 nm interpore spacing as a detection unit) that induced a redistribution of the electric field inside and outside the nanopore array and offered high-resolution discrimination of four ssDNA homopolymer types. We demonstrated that the quad-nanopore array well resolved the translocation events of polyA₂₅ and had a length resolution of 20 nt. The molecular dynamic simulation confirmed the slowed-down translocations and superior performance of a quad-nanopore array. We found that the nanopore array configuration induced a direct reduction of the electric field inside the nanopore as well as an increase in the electrical field outside the nanopore due to electric field crosstalk. This dual benefit not only reduced the large driving force on DNA but also facilitated molecule capture through nanopores, therefore decreasing the voltage thresholds. Finally, the successful discrimination of four ssDNA homopolymer types (polyA₂₅, polyT₂₅, polyC₂₅, and polyG₁₀) was achieved using a voltage as low as 30 mV with a translocation speed of 8 μs/nt. These findings provide insights into nanopore arrays for discriminating short single-stranded nucleotides with high resolution and demonstrate promising potential for developing DNA sequencers that utilize nanopore arrays as sensing units.