Raman identification of single nucleotides flowing through permeable plasmonic films

Kirill Khabarov, Maria Blanco Formoso, Ilaria Micol Baldi, Foroogh Khozeymeh Sarbishe, Riccardo Marongiu, Giulia Bruno, Bikash Bhandari, Veronica Storari, Henri Haka, Michele Dipalo, Paolo Canepa, Francesco Gentile, Nick Goldman, Federica Villa, Francesco Tantussi () and Francesco De Angelis ()
Additional contact information
Kirill Khabarov: Istituto Italiano di Tecnologia
Maria Blanco Formoso: Istituto Italiano di Tecnologia
Ilaria Micol Baldi: Istituto Italiano di Tecnologia
Foroogh Khozeymeh Sarbishe: Istituto Italiano di Tecnologia
Riccardo Marongiu: Istituto Italiano di Tecnologia
Giulia Bruno: Istituto Italiano di Tecnologia
Bikash Bhandari: Wellcome Genome Campus
Veronica Storari: Politecnico di Milano
Henri Haka: Politecnico di Milano
Michele Dipalo: Istituto Italiano di Tecnologia
Paolo Canepa: University of Genova
Francesco Gentile: University of “Magna Graecia” of Catanzaro
Nick Goldman: Wellcome Genome Campus
Federica Villa: Politecnico di Milano
Francesco Tantussi: Istituto Italiano di Tecnologia
Francesco De Angelis: Istituto Italiano di Tecnologia

Nature Communications, 2025, vol. 16, issue 1, 1-8

Abstract: Abstract Surface-Enhanced Raman Scattering has been studied for decades as a recognition technique due to its high sensitivity and discriminative power, particularly in biological applications. Inspired by nanopore sequencing technology, we developed a plasmonic device capable of operating in a flow-through configuration to detect individual molecules passing through plasmonic hotspots. This device is a permeable plasmonic film, through which single molecules are sequentially delivered via electrophoresis, while Raman spectra are recorded in real-time. A very effective light-matter coupling, combined with the ultrasmall size of plasmonic spots, enabled access to angstrom spatial and microsecond temporal scales compatible with polymer sequencing. We successfully slowed the translocation process and captured Raman spectra of the four nucleotides at a time resolution down to 20 μs under our experimental conditions. We achieved a discrimination accuracy of 89% at the single-molecule level. Also, we demonstrated a spatial resolution on the order of a few nucleotides, suggesting the potential for sequencing applications.

Date: 2025
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DOI: 10.1038/s41467-025-64165-9

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