  Single-molecule surface-enhanced Raman spectroscopy based on a particle
trapped in a plasmonic nanopores provides a unique method for continued and
controlled detection of peptide and DNA oligonucleotides in liquid medium.
However, the Brownian motion of the particle and the molecule diffusion acting
on the particle hinder single-molecule sequencing. In this study, we developed
a method for trapping a gold nanoparticle in an air-filled gold nanowell
(particle-in-well) to stabilize the particle and provide a powerful platform
for continuous single molecule readout. The unlimited resident time of the
particle-in-well device with single-molecule level sensitivity elevates
nucleobase detection to a new level. We present a technique capable of
detecting and monitoring solid-phase molecule diffusion within the plasmonic
hotspot. Furthermore, the measured spectra were employed as input data for the
validation of the plasmonic hotspot size and, consequently, the distance
between the particle and the well. The obtained results form the statistical
and experimental base for molecular translocation and DNA sequencing
technologies.
