Abstract
Solid-state nanopores promise a scalable platform for single-molecule DNA analysis. Direct, real-time identification of nucleobases in DNA strands is still limited by the sensitivity and the spatial resolution of established ionic sensing strategies. Here, we study a different but promising strategy based on optical spectroscopy. We use an optically engineered elongated nanopore structure, a plasmonic nanoslit, to locally enable single-molecule surface enhanced Raman spectroscopy (SERS). Combining SERS with nanopore fluidics facilitates both the electrokinetic capture of DNA analytes and their local identification through direct Raman spectroscopic fingerprinting of four nucleobases. By studying the stochastic fluctuation process of DNA analytes that are temporarily adsorbed inside the pores, we have observed asynchronous spectroscopic behavior of different nucleobases, both individual and incorporated in DNA strands. These results provide evidences for the single-molecule sensitivity and the sub-nanometer spatial resolution of plasmonic nanoslit SERS.
Highlights
Solid-state nanopores promise a scalable platform for single-molecule DNA analysis
We experimentally study the feasibility of combining SERS with nanopore fluidics for addressing the three fundamental challenges related to DNA sensing and even sequencing
In this work, we have studied the feasibility of spectroscopic nanopore sensing based on plasmonic nanoslit SERS
Summary
Real-time identification of nucleobases in DNA strands is still limited by the sensitivity and the spatial resolution of established ionic sensing strategies. By studying the stochastic fluctuation process of DNA analytes that are temporarily adsorbed inside the pores, we have observed asynchronous spectroscopic behavior of different nucleobases, both individual and incorporated in DNA strands. These results provide evidences for the single-molecule sensitivity and the sub-nanometer spatial resolution of plasmonic nanoslit SERS. By studying the fluctuations of adsorbed DNA oligonucleotides, we can identify adjacent bases incorporated in DNA strands, indicating the sub-nanometer spatial resolution of the nanoslit SERS. We cannot study these fast translocation events of DNA molecules yet, the discussed features of nanoslit SERS can still be interesting for singlemolecule DNA sensing in a label-free and real-time way
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