University of Oulu

ACS Photonics 2022, 9, 3, 730–742,

Label-free optical analysis of biomolecules in solid-state nanopores : toward single-molecule protein sequencing

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Author: Zhao, Yingqi1; Iarossi, Marzia1; De Fazio, Angela Federica1;
Organizations: 1Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
2Faculty of Medicine, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 5 A, 90220 Oulu, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 5.7 MB)
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Language: English
Published: American Chemical Society, 2022
Publish Date: 2022-04-26


Sequence identification of peptides and proteins is central to proteomics. Protein sequencing is mainly conducted by insensitive mass spectroscopy because proteins cannot be amplified, which hampers applications such as single-cell proteomics and precision medicine. The commercial success of portable nanopore sequencers for single DNA molecules has inspired extensive research and development of single-molecule techniques for protein sequencing. Among them, three challenges remain: (1) discrimination of the 20 amino acids as building blocks of proteins; (2) unfolding proteins; and (3) controlling the motion of proteins with nonuniformly charged sequences. In this context, the emergence of label-free optical analysis techniques for single amino acids and peptides by solid-state nanopores shows promise for addressing the first challenge. In this Perspective, we first discuss the current challenges of single-molecule fluorescence detection and nanopore resistive pulse sensing in a protein sequencing. Then, label-free optical methods are described to show how they address the single-amino-acid identification within single peptides. They include localized surface plasmon resonance detection and surface-enhanced Raman spectroscopy on plasmonic nanopores. Notably, we report new data to show the ability of plasmon-enhanced Raman scattering to record and discriminate the 20 amino acids at a single-molecule level. In addition, we discuss briefly the manipulation of molecule translocation and liquid flow in plasmonic nanopores for controlling molecule movement to allow high-resolution reading of protein sequences. We envision that a combination of Raman spectroscopy with plasmonic nanopores can succeed in single-molecule protein sequencing in a label-free way.

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Series: ACS photonics
ISSN: 2330-4022
ISSN-E: 2330-4022
ISSN-L: 2330-4022
Volume: 9
Issue: 3
Pages: 730 - 742
DOI: 10.1021/acsphotonics.1c01825
Type of Publication: A2 Review article in a scientific journal
Field of Science: 221 Nanotechnology
Funding: This work has received funding from the European Union’s Horizon 2020 research and innovation program through the project PROID under Grant Agreement No. 964363. This work is also connected to the DigiHealth Project, a strategic profiling project at the University of Oulu that is supported by the Academy of Finland (Project Number 326291) and the University of Oulu.
Copyright information: © 2022 The Authors. Published by American Chemical Society. Published under CC-BY.