Fabrication of Sub-50 nm Three-Dimensional Rhombic Zero-Depth PDMS Nanopores with Enhanced Conductance via Silicon Micro-Blade Molding

Zero-depth nanopores present a promising solution to the challenges associated with ultrathin membranes used in solid-state resistive pulse sensors for DNA sequencing. Most existing fabrication methods are either complex or lack the nanoscale precision required. In this study, we introduce a cost-effective approach that combines PDMS molding at the intersection of silicon micro-blades with an innovative high-resolution nano-positioning technique. These blades are created through photolithography and a two-step KOH wet etching process, allowing for the formation of sub-50 nm 3D rhombic zero-depth nanopores featuring large vertex angles. To address the limitations of SEM imaging—such as dielectric charging and deformation of PDMS membranes under electron beam exposure—we devised a finite element model (FEM) that correlates electrical conductance with pore size and electrolyte concentration. This model aligns closely with experimental data, yielding a mean absolute percentage error of 3.69%, thereby enabling real-time indirect sizing of the nanopores based on the measured conductance. Additionally, we identified a critical channel length beyond which pore resistance becomes negligible, facilitating a linear relationship between conductance and pore diameter. The nanopores produced using this method exhibited a 2.4-fold increase in conductance compared to earlier designs, highlighting their potential for high-precision DNA sequencing applications.