Three-dimensional plasmonic nanopores for DNA-PAINT and dual-material Au/Si architectures

Abstract Plasmonic nanopores combine nanofluidic confinement with electromagnetic field enhancement, enabling optical interrogation of single molecules in sub-wavelength volumes. Building on our previously developed three-dimensional dielectric nanopore platform, here we introduce 3D plasmonic nanopores as an optically active extension for single-molecule studies. We demonstrate, to our knowledge, the first implementation of DNA-PAINT within a solid-state nanopore, showing that transient hybridization events can be optically resolved within a confined plasmonic geometry. In parallel, DNA spacers of controlled length are used to position fluorophores at defined nominal distances from the metallic surface, revealing a non-monotonic fluorescence response consistent with the interplay between electromagnetic enhancement and metal-induced quenching, with an optimum around 6 nm. Finally, we introduce a novel dual-material Au/Si nanopore geometry as a hybrid plasmonic-semiconducting architecture. Static fluorescence measurements with DNA spacers and Rhodamine 6G reveal an optical response distinct from that of fully metallic Au nanopores, while simulations indicate asymmetric electromagnetic field distributions in the multi-material design. Together, these results establish 3D plasmonic nanopores as a platform for single-molecule optical techniques and show that dual-material nanopores provide an additional design parameter for modifying nanoscale optical response. Graphical Abstract