Fabrication and characterization of solid-state nanopore arrays for high-throughput DNA sequencing

We report the fabrication and characterization of uniformly sized nanopore arrays, integrated into an optical detection system for high-throughput DNA sequencing applications. Nanopore arrays were fabricated using focused ion beam milling, followed by TiO₂ coating using atomic layer deposition. The TiO₂ layer decreases the initial pore diameter down to the sub-10 nm range, compatible with the requirements for nanopore-based sequencing using optical readout. We find that the TiO₂ layers produce a lower photoluminescence background as compared with the more widely used Al₂O₃ coatings. The functionality of the nanopore array was demonstrated by the simultaneous optical detection of DNA-quantum dot conjugates, which were electro-kinetically driven through the nanopores. Our optical scheme employs total internal reflection fluorescence microscopy to illuminate a wide area of the TiO₂-coated membrane. A highly parallel system for observing DNA capture events in a uniformly sized 6 × 6 nanopore array was experimentally realized.