Abstract
Surface-enhanced Raman spectroscopy (SERS) sensing of DNA bases by plasmonic nanopores could pave a way to novel methods for DNA analyses and 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. In fact, DNA molecules flow through the nanopores so rapidly that the SERS signals collected are not sufficient for single-molecule analysis. Here, we report an approach to control the residence time of molecules in the hot spot by an electro-plasmonic trapping effect. By directly adsorbing molecules onto a gold nanoparticle and then trapping the single nanoparticle in a plasmonic nanohole up to several minutes, we demonstrate single-molecule SERS detection of all four 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.
Highlights
Surface-enhanced Raman spectroscopy (SERS) sensing of DNA bases by plasmonic nanopores could pave a way to novel methods for DNA analyses and new generation singlemolecule sequencing platforms
The sharp tips of the AuNU will couple with the sidewall of the nanohole creating plasmonic hot spots, which exhibit a greatly enhanced electromagnetic field for SERS detection of the nucleotides already adsorbed on the tips
Plasmonic hot spots are formed by coupling the AuNU tip and the nanohole for reproducible SERS detection of nucleotides that are adsorbed on the AuNU before the trapping
Summary
Surface-enhanced Raman spectroscopy (SERS) sensing of DNA bases by plasmonic nanopores could pave a way to novel methods for DNA analyses and new generation singlemolecule sequencing platforms. DNA strands flow through solid-state nanopores so fast (a few microseconds) that SERS signals collected are not sufficient for single-molecule analysis[3] Another recent work reported that SERS detection of nucleobases by plasmonic nanoslits could not achieve single-molecule resolution until a collection time of 100 ms was used[2]. Reports that combine these effects to demonstrate single-molecule SERS in the flow-through scheme are still missing By overcoming this challenge, it may create a revolution of diagnostic devices in, for example, DNA sequencing that reached market level years ago by utilizing solid-state nanopores[12]. It may create a revolution of diagnostic devices in, for example, DNA sequencing that reached market level years ago by utilizing solid-state nanopores[12] In comparison with those pioneering nanopore technologies, Raman-based sensors offer even more advantages, thanks to much higher discrimination power provided by Raman spectroscopy. As we show thereafter in detail, by applying electric potentials, we can keep the AuNUs trapped for minutes such that DNA bases can stay in the hot spots long enough to achieve single-molecule analysis
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