Visualization of DNA Translocation and Clogging Using Photoluminescent-Free Silicon Nanopore Arrays

Solid-state nanopore arrays hold promises for high-throughput optical analysis of single molecules. However, the high photoluminescence (PL) background emanating from the commonly used silicon nitride (SiNx) membrane for nanopore fabrication and the nonspecific adsorption of analyte on the pore sidewalls have plagued the high sensing sensitivity and efficiency offered by optical sensing. Here, the present work demonstrates an optical monitoring system using a truncated pyramidal nanopore array on a silicon membrane coated with a lipid bilayer for visualization of DNA translocation events. The silicon membrane produces essentially no PL under blue-green laser illumination, which enables more clear identification of DNA translocation and clogging events than using SiNx-based devices. The lipid bilayer coating based on small unilamellar vesicles (SUVs) minimizes the nonspecific adsorption of DNA. With confocal microscopy, the fluorescent labeled DNA translocation motion is visualized in three dimensions. The statistical results show that the percentage of DNA clogged pores is significantly reduced for the lipid bilayer coated nanopores as compared to the uncoated nanopores.