SPAD-Based Detection System for Nanopore Sequencing Through Surface-Enhanced Raman Spectroscopy

Surface-Enhanced Raman Spectroscopy (SERS) is a powerful technique for molecular identification, based on the correspondence between Raman spectral peaks and the characteristic vibrational modes of the analyte. To intensify the Raman response, SERS relies on nanostructured metallic surfaces, like plasmonic nanopores, that can amplify the electromagnetic field in a highly confined space. When applied to sequencing applications, this approach overcomes the limitations of traditional electrical sensing in biological and solid-state nanopores, offering higher molecular discrimination and enabling fast optical readout. In this work, we propose an experimental setup for protein and DNA sequencing exploiting a Single-Photon Avalanche Diode (SPAD)-based detection system coupled with a custom software application. Our current setup includes plasmonic nanopores, a continuous-wave laser for excitation, gratings to resolve spectral components and a microscope equipped with a SPAD camera for detection. We provide a detailed description of the camera and custom software, followed by preliminary results demonstrating a 10-μs translocation time per nucleotide and highlighting the potential for biomolecules sequencing applications, while outlining the remaining steps needed for single-residue resolution. Future steps include fluorescence background suppression exploiting the SPAD array time-gating feature, and also nanopore and SPAD arrays performance improvement to better control the molecule position and translocation, thus leading to full sequencing capabilities.