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

TL;DR

This study uses DNA-PAINT to map and quantify electromagnetic field enhancement inside 3D plasmonic nanopores, revealing optimal fluorophore-metal distances and coupling effects in hybrid structures.

Contribution

It introduces DNA-PAINT as a novel method for nanoscale optical field mapping within plasmonic nanopores, enabling quantitative analysis of field enhancement and quenching effects.

Findings

Optimal fluorophore-metal distance around 6 nm identified.

DNA-PAINT successfully maps active binding sites with nanometric precision.

Lateral coupling observed in Au/Si hybrid nanopores.

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.