Probing Electro-Magnetic Field Enhancement in 3D Plasmonic Nanopores Using DNA-PAINT and Nanorulers

Abstract

Plasmonic nanopores combine nanofluidic confinement with electromagnetic field enhancement, enabling optical interrogation of single molecules in sub-wavelength volumes. Yet, direct optical readout within these metallic geometries has remained challenging due to fluorescence quenching near the surface. Here, we implement DNA-PAINT as a molecular reporter of local optical fields inside plasmonic nanopores. Transient hybridization of fluorescent imager strands at the nanopore tips yields stochastic emission bursts that map active binding sites with nanometric precision. By varying the fluorophore-metal distance using DNA spacers of controlled length, we observe a non-monotonic intensity response consistent with near-field quenching and plasmonic enhancement, identifying an optimal separation of around 6 nm. Finally, we extend the concept to dual-material Au/Si nanopores, demonstrating lateral coupling between plasmonic and semiconducting regions. These results establish DNA-PAINT as a quantitative probe of nanoscale optical environments in hybrid nanopores.