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Understanding the Excitation Wavelength Dependence and Thermal Stability of the SARS-CoV-2 Receptor-Binding Domain Using Surface-Enhanced Raman Scattering and Machine Learning

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    Understanding the Excitation Wavelength Dependence and Thermal Stability of the SARS-CoV-2 Receptor-Binding Domain Using Surface-Enhanced Raman Scattering and Machine Learning
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    • Kunyan Zhang
      Kunyan Zhang
      Department of Electrical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      More by Kunyan Zhang
      Orcidhttps://orcid.org/0000-0002-6830-409X
    • Ziyang Wang
      Ziyang Wang
      Department of Electrical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
      More by Ziyang Wang
      Orcidhttps://orcid.org/0000-0003-1368-4539
    • He Liu
      He Liu
      Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      More by He Liu
    • Néstor Perea-López
      Néstor Perea-López
      Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      Center for 2-Dimensional and Layered Materials, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      More by Néstor Perea-López
    • Jeewan C. Ranasinghe
      Jeewan C. Ranasinghe
      Department of Electrical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
      More by Jeewan C. Ranasinghe
    • George Bepete
      George Bepete
      Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      Center for 2-Dimensional and Layered Materials, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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      Orcidhttps://orcid.org/0000-0002-5562-1125
    • Allen M. Minns
      Allen M. Minns
      Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      More by Allen M. Minns
    • Randall M. Rossi
      Randall M. Rossi
      Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      More by Randall M. Rossi
    • Scott E. Lindner
      Scott E. Lindner
      Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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    • Sharon X. Huang
      Sharon X. Huang
      College of Information Sciences and Technology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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    • Mauricio Terrones*
      Mauricio Terrones
      Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      Center for 2-Dimensional and Layered Materials, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      Research Initiative for Supra Materials, Shinshu University, 4-17-1 Wakasato, Nagano 380-8553, Japan
      *Email: [email protected]
      More by Mauricio Terrones
      Orcidhttps://orcid.org/0000-0003-0010-2851
    • Shengxi Huang*
      Shengxi Huang
      Department of Electrical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
      Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
      *Email: [email protected]; [email protected]
      More by Shengxi Huang
      Orcidhttps://orcid.org/0000-0002-3618-9074
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    ACS Photonics

    Cite this: ACS Photonics 2022, 9, 9, 2963–2972
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    https://doi.org/10.1021/acsphotonics.2c00456
    Published August 25, 2022
    Copyright © 2022 American Chemical Society
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    Abstract

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    COVID-19 has cost millions of lives worldwide. The constant mutation of SARS-CoV-2 calls for thorough research to facilitate the development of variant surveillance. In this work, we studied the fundamental properties related to the optical identification of the receptor-binding domain (RBD) of SARS-CoV-2 spike protein, a key component of viral infection. The Raman modes of the SARS-CoV-2 RBD were captured by surface-enhanced Raman spectroscopy (SERS) using gold nanoparticles (AuNPs). The observed Raman enhancement strongly depends on the excitation wavelength as a result of the aggregation of AuNPs. The characteristic Raman spectra of RBDs from SARS-CoV-2 and MERS-CoV were analyzed by principal component analysis that reveals the role of secondary structures in the SERS process, which is corroborated with the thermal stability under laser heating. We can easily distinguish the Raman spectra of two RBDs using machine learning algorithms with accuracy, precision, recall, and F1 scores all over 95%. Our work provides an in-depth understanding of the SARS-CoV-2 RBD and paves the way toward rapid analysis and discrimination of complex proteins of infectious viruses and other biomolecules.

    Copyright © 2022 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acsphotonics.2c00456.

    • Ultraviolet–visible spectra of RBD, surface-enhanced Raman scattering (SERS) of SARS-CoV-2 RBD on 60 and 200 nm gold nanoparticles, SERS of MERS-CoV S1 mouse monoclonal antibody, Raman spectra of 20 amino acids, PCA of other components, visualization of SARS-CoV-2 RBD and MERS-CoV RBD spectra using PLS, amino acids of SARS-CoV-2 RBD and MERS-CoV RBD by sequencing, and SERS of SARS-CoV-2 RBD using AuNP on CNT arrays (PDF)

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    This article is cited by 21 publications.

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    ACS Photonics

    Cite this: ACS Photonics 2022, 9, 9, 2963–2972
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acsphotonics.2c00456
    Published August 25, 2022
    Copyright © 2022 American Chemical Society
    Request reuse permissions

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