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Michałowska A, Kudelski A. Plasmonic substrates for biochemical applications of surface-enhanced Raman spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123786. [PMID: 38128327 DOI: 10.1016/j.saa.2023.123786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Due to its great practical importance, the detection and determination of many biomolecules in body fluids and other samples is carried out in a large number of laboratories around the world. One of the most promising analytical techniques now being widely introduced into medical analysis is surface-enhanced Raman scattering (SERS) spectroscopy. SERS is one of the most sensitive analytical methods, and in some cases, a good quality SERS spectrum dominated by the contribution of even a single molecule can be obtained. Highly sensitive SERS measurements can only be carried out on substrates generating a very high SERS enhancement factor and a low Raman spectral background, and so using of right nanomaterials is a key element in the success of SERS biochemical analysis. In this review article, we present progress that has been made in the preparation of nanomaterials used in SERS spectroscopy for detecting various kinds of biomolecules. We describe four groups of nanomaterials used in such measurements: nanoparticles of plasmonic metals and deposits of plasmonic nanoparticles on macroscopic substrates, nanocomposites containing plasmonic and non-plasmonic parts, nanostructured macroscopic plasmonic metals, and nanostructured macroscopic non-plasmonic materials covered by plasmonic films. We also describe selected SERS biochemical analyses that utilize the nanomaterials presented. We hope that this review will be useful for researchers starting work in this fascinating field of science and technology.
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Affiliation(s)
| | - Andrzej Kudelski
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Str., PL 02-093 Warsaw, Poland.
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2
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Pezzotti G, Ohgitani E, Fujita Y, Imamura H, Pappone F, Grillo A, Nakashio M, Shin-Ya M, Adachi T, Yamamoto T, Kanamura N, Marin E, Zhu W, Inaba T, Tanino Y, Nukui Y, Higasa K, Yasukochi Y, Okuma K, Mazda O. Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions. ACS Infect Dis 2023; 9:2226-2251. [PMID: 37850869 PMCID: PMC10644350 DOI: 10.1021/acsinfecdis.3c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 10/19/2023]
Abstract
The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream of highly contagious and antibody-resistant strains, which in turn led to classifying Omicron as a variant of concern. We systematically collected Raman spectra from six Omicron subvariants available in Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, and BA.2.75) and applied machine-learning algorithms to decrypt their structural characteristics at the molecular scale. Unique Raman fingerprints of sulfur-containing amino acid rotamers, RNA purines and pyrimidines, tyrosine phenol ring configurations, and secondary protein structures clearly differentiated the six Omicron subvariants. These spectral characteristics, which were linked to infectiousness, transmissibility, and propensity for immune evasion, revealed evolutionary motifs to be compared with the outputs of genomic studies. The availability of a Raman "metabolomic snapshot", which was then translated into a barcode to enable a prompt subvariant identification, opened the way to rationalize in real-time SARS-CoV-2 activity and variability. As a proof of concept, we applied the Raman barcode procedure to a nasal swab sample retrieved from a SARS-CoV-2 patient and identified its Omicron subvariant by coupling a commercially available magnetic bead technology with our newly developed Raman analyses.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department
of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shinmachi, Hirakata, Osaka 573-1010, Japan
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
- Department
of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, 160-0023 Tokyo, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Department
of Molecular Science and Nanosystems, Ca’
Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Eriko Ohgitani
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yuki Fujita
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Hayata Imamura
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Francesco Pappone
- Department
of Mathematical Science, Politecnico di
Torino, Corso Duca degli
Abruzzi 24, 10129 Torino, Italy
| | - Alfio Grillo
- Department
of Mathematical Science, Politecnico di
Torino, Corso Duca degli
Abruzzi 24, 10129 Torino, Italy
| | - Maiko Nakashio
- Department
of Infection Control & Laboratory Medicine, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Masaharu Shin-Ya
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Tetsuya Adachi
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Department
of Microbiology, Kansai Medical University,
School of Medicine, 2-5-1
Shinmachi, Hirakata 573-1010, Osaka Prefecture, Japan
| | - Toshiro Yamamoto
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Narisato Kanamura
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Elia Marin
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Wenliang Zhu
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Tohru Inaba
- Department
of Infection Control & Laboratory Medicine, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yoko Tanino
- Department of Clinical Laboratory, University
Hospital, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yoko Nukui
- Department of Clinical Laboratory, University
Hospital, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Koichiro Higasa
- Genome Analysis, Institute of Biomedical
Science, Kansai Medical University, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan
| | - Yoshiki Yasukochi
- Genome Analysis, Institute of Biomedical
Science, Kansai Medical University, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan
| | - Kazu Okuma
- Department
of Microbiology, Kansai Medical University,
School of Medicine, 2-5-1
Shinmachi, Hirakata 573-1010, Osaka Prefecture, Japan
| | - Osam Mazda
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
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Sharma A, Mondal S, Ahuja T, Karmakar T, Siddhanta S. Ion-Mediated Protein Stabilization on Nanoscopic Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1227-1237. [PMID: 36622301 DOI: 10.1021/acs.langmuir.2c03010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The emergence of nanoparticles in biomedical applications has made their interactions with proteins inevitable. Nanoparticles conjugated with proteins and peptide-based constructs form an integral part of nanotherapeutics and have recently shown promise in treating a myriad of diseases. The proper functioning of proteins is critical to achieve their biological functions. However, interface issues result in the denaturation of proteins, and the loss of orientation and steric hindrance can adversely affect the function of the conjugate. Furthermore, surface-induced denaturation also triggers protein aggregation, resulting in amyloid-like species. Understanding the mechanistic underpinnings of protein-nanoparticle interactions and controlling their interfacial characteristics are critical and challenging due to the complex nature of the conjugates. In this milieu, we demonstrate that ionic liquids can be suitable candidates for stabilizing protein-nanoparticle interactions by virtue of their excellent protein-preserving properties. We also probe the previously unexplored mechanism of ion-mediated stabilization of the protein molecules on the nanoparticle surface. The protein-nanoparticle conjugates consist of lysozyme and choline-based ionic liquids characterized by optical and electron microscopy techniques combined with surface-sensitive plasmon-enhanced Raman spectroscopy. Furthermore, atomistic molecular dynamics simulations of the conjugates delineate interfacial interactions of the protein molecules and the modulation by the ions, particularly the conformational changes and the dynamic correlation when the protein and specific ionic liquid molecules are adsorbed on the nanoparticle surface. The combined experimental and computational studies showed the synergistic behavior of the ions of the ionic liquids, specifically the orientation and coverage of the anions aided by the cations to control the surface interactions and hence the overall protein stability. These studies pave the way for using ionic liquids, particularly their biocompatible counterparts in nanoparticle-based complexes, as stabilizing agents for biomedical applications.
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Affiliation(s)
- Arti Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi110016, India
| | - Soumya Mondal
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi110016, India
| | - Tripti Ahuja
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi110016, India
| | - Tarak Karmakar
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi110016, India
| | - Soumik Siddhanta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi110016, India
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Morganti D, Faro MJL, Leonardi AA, Fazio B, Conoci S, Irrera A. Luminescent Silicon Nanowires as Novel Sensor for Environmental Air Quality Control. SENSORS (BASEL, SWITZERLAND) 2022; 22:8755. [PMID: 36433351 PMCID: PMC9698341 DOI: 10.3390/s22228755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/28/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Air quality monitoring is an increasingly debated topic nowadays. The increasing spillage of waste products released into the environment has contributed to the increase in air pollution. Consequently, the production of increasingly performing devices in air monitoring is increasingly in demand. In this scenario, the attention dedicated to workplace safety monitoring has led to the developing and improving of new sensors. Despite technological advancements, sensors based on nanostructured materials are difficult to introduce into the manufacturing flow due to the high costs of the processes and the approaches that are incompatible with the microelectronics industry. The synthesis of a low-cost ultra-thin silicon nanowires (Si NWs)-based sensor is here reported, which allows us the detection of various dangerous gases such as acetone, ethanol, and the ammonia test as a proof of concept in a nitrogen-based mixture. A modified metal-assisted chemical etching (MACE) approach enables to obtain ultra-thin Si NWs by a cost-effective, rapid and industrially compatible process that exhibit an intense light emission at room temperature. All these gases are common substances that we find not only in research or industrial laboratories, but also in our daily life and can pose a serious danger to health, even at small concentrations of a few ppm. The exploitation of the Si NWs optical and electrical properties for the detection of low concentrations of these gases through their photoluminescence and resistance changes will be shown in a nitrogen-based gas mixture. These sensing platforms give fast and reversible responses with both optical and electrical transductions. These high performances and the scalable synthesis of Si NWs could pave the way for market-competitive sensors for ambient air quality monitoring.
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Affiliation(s)
- Dario Morganti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy
| | - Maria José Lo Faro
- Department of Physics and Astronomy, University of Catania, Via Santa Sofia 64, 95123 Catania, Italy
- CNR-IMM UoS Catania, Via Santa Sofia 64, 95123 Catania, Italy
| | - Antonio Alessio Leonardi
- Department of Physics and Astronomy, University of Catania, Via Santa Sofia 64, 95123 Catania, Italy
- CNR-IMM UoS Catania, Via Santa Sofia 64, 95123 Catania, Italy
| | - Barbara Fazio
- URT LAB SENS, Beyond Nano—CNR, c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy
| | - Sabrina Conoci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy
- URT LAB SENS, Beyond Nano—CNR, c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy
- CNR-IMM Istituto per la Microelettronica e Microsistemi, Zona Industriale, VIII Strada 5, 95121 Catania, Italy
| | - Alessia Irrera
- URT LAB SENS, Beyond Nano—CNR, c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 5, 98166 Messina, Italy
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5
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Estrela PFN, dos Santos CA, Resende PC, Lima PM, da Silva TDSC, Saboia-Vahia L, Siqueira MM, Silveira-Lacerda EDP, Duarte GRM. Fast, low-cost and highly specific colorimetric RT-LAMP assays for inference of SARS-CoV-2 Omicron BA.1 and BA.2 lineages. Analyst 2022; 147:5613-5622. [DOI: 10.1039/d2an01625g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The RT-LAMP assays can quickly and cheaply infer and distinguish colorimetrically two lineages (BA.1 and BA.2) of the Omicron variant, enabling the rationalization of genetic sequencing.
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Affiliation(s)
- Paulo Felipe Neves Estrela
- Laboratório de Biomicrofluídica – Instituto de Química – Universidade Federal de Goiás, 74690-900, Goiânia, GO, Brazil
| | - Carlos Abelardo dos Santos
- Laboratório de Genética Molecular e Citogenética – Instituto de Ciências Biológicas – Universidade Federal de Goiás, 74001-970, Goiânia, GO, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Reference Laboratory for COVID-19 (WHO), 21040-360, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Patricia Mayer Lima
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Reference Laboratory for COVID-19 (WHO), 21040-360, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Thauane dos Santos Correia da Silva
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Reference Laboratory for COVID-19 (WHO), 21040-360, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Leonardo Saboia-Vahia
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Reference Laboratory for COVID-19 (WHO), 21040-360, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Reference Laboratory for COVID-19 (WHO), 21040-360, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Elisângela de Paula Silveira-Lacerda
- Laboratório de Genética Molecular e Citogenética – Instituto de Ciências Biológicas – Universidade Federal de Goiás, 74001-970, Goiânia, GO, Brazil
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