λ-DNA Through porous materials – Surface Enhanced Raman Scattering in a simple plasmonic nanopore

Engineered electromagnetic fields in plasmonic nanopores enable enhanced optical detection for single molecule sensing and sequencing. Here, a plasmonic nanopore prepared in a thick nanoporous film is used to investigate, by means of surface enhanced Raman spectroscopy, the interaction between the metallic surface of the pore and a long-chain double strand DNA molecule free to diffuse through the pore. We discuss how the matrix of the porous material can interact with the molecule thanks to: i) transient aspecific interactions between the porous surface and DNA; ii) diffusion; iii) thermal and optical forces exerted by the localized field in a metallic nanostructure on the DNA molecule. An interaction time up to tens of milliseconds enables to collect high signal-to-noise Raman signatures, allowing an easy label-free reading of information from the DNA molecule. Moreover, to increase the rate of detection, we tested a polymeric porous hydrogel placed beneath the solid-state membrane. The hydrogel enables a slowdown of the molecule diffusion time, thus increasing the number of detected interaction events by a factor 20. The analysis of the observed Raman peaks and their relative intensities, combined with theoretical simulations, allow to get further information on the process of translocation and on the folding state and orientation of the translocating molecule. Our results demonstrate temporary adsorption of the DNA molecule on the porous material during the translocation due to the diffusion force. Finally, we provide a qualitative evaluation of the nucleotides’ contents in the different groups of collected signal. The proposed approach can find interesting applications not only in DNA sensing and sequencing, but also on generic nanopore spectroscopy.