Single-molecule DNA Bases Discrimination in Oligonucleotides by Controllable Trapping in Plasmonic Nanoholes

Surface-enhanced Raman spectroscopy (SERS) sensing of DNA sequences by plasmonic nanopores could pave a way to new generation single-molecule sequencing platforms. The SERS discrimination of single DNA bases depends critically on the time that a DNA strand resides within the plasmonic hot spot. However, DNA molecules flow through the nanopores so rapidly that the SERS signals collected are not sufficient for single-molecule analysis. In this work, we report an approach to control the time that molecules reside in the hot spot by physically adsorbing them onto a gold nanoparticle and then trapping the single nanoparticle in a plasmonic nanohole. By trapping the nanoparticle for up to minutes, we demonstrate single-molecule SERS detection of all 4 DNA bases as well as discrimination of single nucleobases in a single oligonucleotide. Our method can be extended easily to label-free sensing of single-molecule amino acids and proteins.