1
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Pezzotti G, Adachi T, Imamura H, Bristol DR, Adachi K, Yamamoto T, Kanamura N, Marin E, Zhu W, Kawai T, Mazda O, Kariu T, Waku T, Nichols FC, Riello P, Rizzolio F, Limongi T, Okuma K. In Situ Raman Study of Neurodegenerated Human Neuroblastoma Cells Exposed to Outer-Membrane Vesicles Isolated from Porphyromonas gingivalis. Int J Mol Sci 2023; 24:13351. [PMID: 37686157 PMCID: PMC10488263 DOI: 10.3390/ijms241713351] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
The aim of this study was to elucidate the chemistry of cellular degeneration in human neuroblastoma cells upon exposure to outer-membrane vesicles (OMVs) produced by Porphyromonas gingivalis (Pg) oral bacteria by monitoring their metabolomic evolution using in situ Raman spectroscopy. Pg-OMVs are a key factor in Alzheimer's disease (AD) pathogenesis, as they act as efficient vectors for the delivery of toxins promoting neuronal damage. However, the chemical mechanisms underlying the direct impact of Pg-OMVs on cell metabolites at the molecular scale still remain conspicuously unclear. A widely used in vitro model employing neuroblastoma SH-SY5Y cells (a sub-line of the SK-N-SH cell line) was spectroscopically analyzed in situ before and 6 h after Pg-OMV contamination. Concurrently, Raman characterizations were also performed on isolated Pg-OMVs, which included phosphorylated dihydroceramide (PDHC) lipids and lipopolysaccharide (LPS), the latter in turn being contaminated with a highly pathogenic class of cysteine proteases, a key factor in neuronal cell degradation. Raman characterizations located lipopolysaccharide fingerprints in the vesicle structure and unveiled so far unproved aspects of the chemistry behind protein degradation induced by Pg-OMV contamination of SH-SY5Y cells. The observed alterations of cells' Raman profiles were then discussed in view of key factors including the formation of amyloid β (Aβ) plaques and hyperphosphorylated Tau neurofibrillary tangles, and the formation of cholesterol agglomerates that exacerbate AD pathologies.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160-0023, Japan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy;
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Tetsuya Adachi
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan
| | - Hayata Imamura
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Davide Redolfi Bristol
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Keiji Adachi
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
| | - Toshihisa Kawai
- Department of Oral Science and Translational Research, College of Dental Medicine, Nova Southeastern University, 3301 College Avenue, Fort Lauderdale, FL 33314, USA;
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
| | - Toru Kariu
- Department of Life Science, Shokei University, Chuo-ku, Kuhonji, Kumamoto 862-8678, Japan;
| | - Tomonori Waku
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan;
| | - Frank C. Nichols
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, University of Connecticut, 263 Farmington Avenue, Storrs, CT 06030, USA;
| | - Pietro Riello
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Flavio Rizzolio
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Tania Limongi
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy;
| | - Kazu Okuma
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan
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2
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Junjuri R, Saghi A, Lensu L, Vartiainen EM. Effect of non-resonant background on the extraction of Raman signals from CARS spectra using deep neural networks. RSC Adv 2022; 12:28755-28766. [PMID: 36320545 PMCID: PMC9549484 DOI: 10.1039/d2ra03983d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/29/2022] [Indexed: 01/25/2023] Open
Abstract
We report the retrieval of the Raman signal from coherent anti-Stokes Raman scattering (CARS) spectra using a convolutional neural network (CNN) model. Three different types of non-resonant backgrounds (NRBs) were explored to simulate the CARS spectra viz (1) product of two sigmoids following the original SpecNet model, (2) Single Sigmoid, and (3) fourth-order polynomial function. Later, 50 000 CARS spectra were separately synthesized using each NRB type to train the CNN model and, after training, we tested its performance on 300 simulated test spectra. The results have shown that imaginary part extraction capability is superior for the model trained with Polynomial NRB, and the extracted line shapes are in good agreement with the ground truth. Moreover, correlation analysis was carried out to compare the retrieved Raman signals to real ones, and a higher correlation coefficient was obtained for the model trained with the Polynomial NRB (on average, ∼0.95 for 300 test spectra), whereas it was ∼0.89 for the other NRBs. Finally, the predictive capability is evaluated on three complex experimental CARS spectra (DMPC, ADP, and yeast), where the Polynomial NRB model performance is found to stand out from the rest. This approach has a strong potential to simplify the analysis of complex CARS spectroscopy and can be helpful in real-time microscopy imaging applications.
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Affiliation(s)
- Rajendhar Junjuri
- LUT School of Engineering Science, LUT University Lappeenranta 53851 Finland
| | - Ali Saghi
- LUT School of Engineering Science, LUT University Lappeenranta 53851 Finland
| | - Lasse Lensu
- LUT School of Engineering Science, LUT University Lappeenranta 53851 Finland
| | - Erik M Vartiainen
- LUT School of Engineering Science, LUT University Lappeenranta 53851 Finland
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3
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Moeller C, Schmidt C, Guyot F, Wilke M. Hydrolysis rate constants of ATP determined in situ at elevated temperatures. Biophys Chem 2022; 290:106878. [DOI: 10.1016/j.bpc.2022.106878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/04/2022] [Accepted: 08/12/2022] [Indexed: 11/30/2022]
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4
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Bebesi T, Kitka D, Gaál A, Szigyártó IC, Deák R, Beke-Somfai T, Koprivanacz K, Juhász T, Bóta A, Varga Z, Mihály J. Storage conditions determine the characteristics of red blood cell derived extracellular vesicles. Sci Rep 2022; 12:977. [PMID: 35046483 PMCID: PMC8770621 DOI: 10.1038/s41598-022-04915-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/21/2021] [Indexed: 12/18/2022] Open
Abstract
Extracellular vesicles (EVs) are released during the storage of red blood cell (RBC) concentrates and might play adverse or beneficial roles throughout the utilization of blood products (transfusion). Knowledge of EV release associated factors and mechanism amends blood product management. In the present work the impact of storage time and medium (blood preserving additive vs isotonic phosphate buffer) on the composition, size, and concentration of EVs was studied using attenuated total reflection infrared (ATR-IR) spectroscopy, microfluidic resistive pulse sensing (MRPS) and freeze-fraction combined transmission electron micrography (FF-TEM). The spectroscopic protein-to-lipid ratio based on amide and the C-H stretching band intensity ratio indicated the formation of various vesicle subpopulations depending on storage conditions. After short storage, nanoparticles with high relative protein content were detected. Spectral analysis also suggested differences in lipid and protein composition, too. The fingerprint region (from 1300 to 1000 cm-1) of the IR spectra furnishes additional information about the biomolecular composition of RBC-derived EVs (REVs) such as adenosine triphosphate (ATP), lactose, glucose, and oxidized hemoglobin. The difference between the vesicle subpopulations reveals the complexity of the REV formation mechanism. IR spectroscopy, as a quick, cost-effective, and label-free technique provides valuable novel biochemical insight and might be used complementary to traditional omics approaches on EVs.
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Affiliation(s)
- Tímea Bebesi
- grid.425578.90000 0004 0512 3755Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences (RCNS), Magyar tudósok körútja 2, 1117 Budapest, Hungary ,grid.5591.80000 0001 2294 6276Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Diána Kitka
- grid.425578.90000 0004 0512 3755Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences (RCNS), Magyar tudósok körútja 2, 1117 Budapest, Hungary ,grid.5591.80000 0001 2294 6276Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Anikó Gaál
- grid.425578.90000 0004 0512 3755Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences (RCNS), Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Imola Csilla Szigyártó
- grid.425578.90000 0004 0512 3755Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences (RCNS), Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Róbert Deák
- grid.425578.90000 0004 0512 3755Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences (RCNS), Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Tamás Beke-Somfai
- grid.425578.90000 0004 0512 3755Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences (RCNS), Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Kitti Koprivanacz
- grid.425578.90000 0004 0512 3755Institute of Enzymology, Research Centre for Natural Sciences (RCNS), Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Tünde Juhász
- grid.425578.90000 0004 0512 3755Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences (RCNS), Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Attila Bóta
- grid.425578.90000 0004 0512 3755Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences (RCNS), Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Zoltán Varga
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences (RCNS), Magyar tudósok körútja 2, 1117, Budapest, Hungary.
| | - Judith Mihály
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences (RCNS), Magyar tudósok körútja 2, 1117, Budapest, Hungary.
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Gomes MC, Chen J, Cunha A, Trindade T, Zheng G, Tomé JPC. Complex cellular environments imaged by SERS nanoprobes using sugars as an all-in-one vector. J Mater Chem B 2021; 9:9285-9294. [PMID: 34709285 DOI: 10.1039/d1tb01360b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman spectroscopy coupled with confocal microscopy offers an alternative bioimaging technique overcoming limitations associated with sensitivity, tissue penetration and image resolution. Allied to the surface-enhanced Raman scattering (SERS) properties of gold nanoparticles (AuNP), we designed SERS nanoprobes with enhanced properties and straightforward application as bio-labelling agents for gliomas. The ensuing nanoprobes coated with simple sugar units (galactose or glucose) allowed assessing information about their intracellular localization (vesicular structures), with impressive sensitivity towards complex environments and proved the ability to overcome biological auto-fluorescence and high penetration in tissues. We validate the use of sugars as an all-in-one vector (Raman reporter, conferring high stability, biocompatibility and affinity to glioma cells) as imaging agents using an impressive technique.
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Affiliation(s)
- Maria C Gomes
- LAQV-REQUINTE and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.,Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.
| | - Juan Chen
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.
| | - Angela Cunha
- CESAM and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Tito Trindade
- CICECO-Aveiro Institute of Materials and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Gang Zheng
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - João P C Tomé
- LAQV-REQUINTE and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.,CQE and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal.
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6
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Pezzotti G, Boschetto F, Ohgitani E, Fujita Y, Zhu W, Marin E, McEntire BJ, Bal BS, Mazda O. Silicon nitride: a potent solid-state bioceramic inactivator of ssRNA viruses. Sci Rep 2021; 11:2977. [PMID: 33536558 PMCID: PMC7858580 DOI: 10.1038/s41598-021-82608-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 01/19/2021] [Indexed: 01/30/2023] Open
Abstract
Surface inactivation of human microbial pathogens has a long history. The Smith Papyrus (2600 ~ 2200 B.C.) described the use of copper surfaces to sterilize chest wounds and drinking water. Brass and bronze on doorknobs can discourage microbial spread in hospitals, and metal-base surface coatings are used in hygiene-sensitive environments, both as inactivators and modulators of cellular immunity. A limitation of these approaches is that the reactive oxygen radicals (ROS) generated at metal surfaces also damage human cells by oxidizing their proteins and lipids. Silicon nitride (Si3N4) is a non-oxide ceramic compound with known surface bacterial resistance. We show here that off-stoichiometric reactions at Si3N4 surfaces are also capable of inactivating different types of single-stranded RNA (ssRNA) viruses independent of whether their structure presents an envelop or not. The antiviral property of Si3N4 derives from a hydrolysis reaction at its surface and the subsequent formation of reactive nitrogen species (RNS) in doses that could be metabolized by mammalian cells but are lethal to pathogens. Real-time reverse transcription (RT)-polymerase chain reaction (PCR) tests of viral RNA and in situ Raman spectroscopy suggested that the products of Si3N4 hydrolysis directly react with viral proteins and RNA. Si3N4 may have a role in controlling human epidemics related to ssRNA mutant viruses.
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Affiliation(s)
- Giuseppe Pezzotti
- grid.419025.b0000 0001 0723 4764Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto, 606–8585 Japan ,grid.410793.80000 0001 0663 3325Department of Orthopedic Surgery, Tokyo Medical University, 6–7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160–0023 Japan ,grid.136593.b0000 0004 0373 3971The Center for Advanced Medical Engineering and Informatics, Osaka University, 2–2 Yamadaoka, Suita, Osaka 565–0854 Japan ,grid.272458.e0000 0001 0667 4960Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto, 602–8566 Japan ,grid.272458.e0000 0001 0667 4960Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto, 602–8566 Japan
| | - Francesco Boschetto
- grid.419025.b0000 0001 0723 4764Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto, 606–8585 Japan ,grid.272458.e0000 0001 0667 4960Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto, 602–8566 Japan
| | - Eriko Ohgitani
- grid.272458.e0000 0001 0667 4960Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto, 602–8566 Japan
| | - Yuki Fujita
- grid.419025.b0000 0001 0723 4764Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto, 606–8585 Japan
| | - Wenliang Zhu
- grid.419025.b0000 0001 0723 4764Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto, 606–8585 Japan
| | - Elia Marin
- grid.419025.b0000 0001 0723 4764Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto, 606–8585 Japan ,grid.272458.e0000 0001 0667 4960Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto, 602–8566 Japan
| | - Bryan J. McEntire
- grid.422391.f0000 0004 6010 3714SINTX Technologies Corporation, 1885 West 2100 South, Salt Lake City, UT 84119 USA
| | - B. Sonny Bal
- grid.422391.f0000 0004 6010 3714SINTX Technologies Corporation, 1885 West 2100 South, Salt Lake City, UT 84119 USA
| | - Osam Mazda
- grid.272458.e0000 0001 0667 4960Department 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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7
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Andrei CC, Moraillon A, Larquet E, Potara M, Astilean S, Jakab E, Bouckaert J, Rosselle L, Skandrani N, Boukherroub R, Ozanam F, Szunerits S, Gouget-Laemmel AC. SERS characterization of aggregated and isolated bacteria deposited on silver-based substrates. Anal Bioanal Chem 2021; 413:1417-1428. [PMID: 33388848 DOI: 10.1007/s00216-020-03106-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 12/11/2022]
Abstract
Surface-enhanced Raman scattering (SERS), based on the enhancement of the Raman signal of molecules positioned within a few nanometres from a structured metal surface, is ideally suited to provide bacterial-specific molecular fingerprints which can be used for analytical purposes. However, for some complex structures such as bacteria, the generation of reproducible SERS spectra is still a challenging task. Among the various factors influencing the SERS variability (such as the nature of SERS-active substrate, Raman parameters and bacterial specificity), we demonstrate in this study that the environment of Gram-positive and Gram-negative bacteria deposited on ultra-thin silver films also impacts the origin of the SERS spectra. In the case of densely packed bacteria, the obtained SERS signatures were either characteristic of the secretion of adenosine triphosphate for Staphylococcus aureus (S. aureus) or the cell wall and the pili/flagella for Escherichia coli (E. coli), allowing for an easy discrimination between the various strains. In the case of isolated bacteria, SERS mapping together with principal component analysis revealed some variabilities of the spectra as a function of the bacteria environment and the bactericidal effect of the silver. However, the variability does not preclude the SERS signatures of various E. coli strains to be discriminated.
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Affiliation(s)
- Cristina-Cassiana Andrei
- Laboratoire de Physique de la Matière Condensée, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Anne Moraillon
- Laboratoire de Physique de la Matière Condensée, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Eric Larquet
- Laboratoire de Physique de la Matière Condensée, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Monica Potara
- Nanobiophotonics and Laser Microspectroscopy Center, Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, T. Laurian Str. 42, 400271, Cluj-Napoca, Romania
| | - Simion Astilean
- Nanobiophotonics and Laser Microspectroscopy Center, Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, T. Laurian Str. 42, 400271, Cluj-Napoca, Romania.,Department of Biomolecular Physics, Faculty of Physics, Babes-Bolyai University, M Kogalniceanu Str. 1, 400084, Cluj-Napoca, Romania
| | - Endre Jakab
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babes-Bolyai University, Clinicilor 5-7, 400006, Cluj-Napoca, Romania.,Molecular Biology Center, Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, T. Laurian Str. 42, 400271, Cluj-Napoca, Romania
| | - Julie Bouckaert
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), UMR 8576 of the CNRS, University of Lille, 50 avenue de Halley, 59658, Villeneuve-d'Ascq, France
| | - Léa Rosselle
- TissueAegis SAS, 14E rue Pierre de Coubertin, 21000, Dijon, France.,University of Lille, CNRS, Centrale Lille, University of Polytechnique Hauts-de-France, UMR 8520 - IEMN, F-59000, Lille, France
| | - Nadia Skandrani
- TissueAegis SAS, 14E rue Pierre de Coubertin, 21000, Dijon, France
| | - Rabah Boukherroub
- University of Lille, CNRS, Centrale Lille, University of Polytechnique Hauts-de-France, UMR 8520 - IEMN, F-59000, Lille, France
| | - François Ozanam
- Laboratoire de Physique de la Matière Condensée, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Sabine Szunerits
- University of Lille, CNRS, Centrale Lille, University of Polytechnique Hauts-de-France, UMR 8520 - IEMN, F-59000, Lille, France.
| | - Anne Chantal Gouget-Laemmel
- Laboratoire de Physique de la Matière Condensée, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France.
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8
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Anti-fouling SERS-based immunosensor for point-of-care detection of the B7–H6 tumor biomarker in cervical cancer patient serum. Anal Chim Acta 2020; 1138:110-122. [DOI: 10.1016/j.aca.2020.09.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 12/13/2022]
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9
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Pezzotti G, Zhu W, Adachi T, Horiguchi S, Marin E, Boschetto F, Ogitani E, Mazda O. Metabolic machinery encrypted in the Raman spectrum of influenza A virus-inoculated mammalian cells. J Cell Physiol 2019; 235:5146-5170. [PMID: 31710091 DOI: 10.1002/jcp.29392] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 10/15/2019] [Indexed: 12/22/2022]
Abstract
Raman spectroscopy was applied with a high spectral resolution to a structural study of Influenza (type A) virus before and after its inoculation into Madin-Darby canine kidney cells. This study exploits the fact that the major virus and cell constituents, namely DNA/RNA, lipid, and protein molecules, exhibit peculiar fingerprints in the Raman spectrum, which clearly differed between cells and viruses, as well as before and after virus inoculation into cells. These vibrational features, which allowed us to discuss viral assembly, membrane lipid evolution, and nucleoprotein interactions of the virus with the host cells, reflected the ability of the virus to alter host cells' pathways to enhance its replication efficiency. Upon comparing Raman signals from the host cells before and after virus inoculation, we were also able to discuss in detail cell metabolic reactions against the presence of the virus in terms of compositional variations of lipid species, the formation of fatty acids, dephosphorylation of high-energy adenosine triphosphate molecules, and enzymatic hydrolysis of the hemagglutinin glycoprotein.
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Affiliation(s)
- Giuseppe Pezzotti
- Faculty of Materials Science and Engineering, Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan.,Department of Orthopedic Surgery, Tokyo Medical University, Tokyo, Japan.,The Center for Advanced Medical Engineering and Informatics, Osaka University, Osaka, Japan.,Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Wenliang Zhu
- Faculty of Materials Science and Engineering, Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan
| | - Tetsuya Adachi
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoshi Horiguchi
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Elia Marin
- Faculty of Materials Science and Engineering, Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan.,Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Francesco Boschetto
- Faculty of Materials Science and Engineering, Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan.,Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Eriko Ogitani
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
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10
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Pezzotti G, Adachi T, Boschetto F, Zhu W, Zanocco M, Marin E, Bal BS, McEntire BJ. Off-Stoichiometric Reactions at the Cell-Substrate Biomolecular Interface of Biomaterials: In Situ and Ex Situ Monitoring of Cell Proliferation, Differentiation, and Bone Tissue Formation. Int J Mol Sci 2019; 20:E4080. [PMID: 31438530 PMCID: PMC6751500 DOI: 10.3390/ijms20174080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/15/2019] [Accepted: 08/17/2019] [Indexed: 11/18/2022] Open
Abstract
The availability of osteoinductive biomaterials has encouraged new therapies in bone regeneration and has potentially triggered paradigmatic shifts in the development of new implants in orthopedics and dentistry. Among several available synthetic biomaterials, bioceramics have gained attention for their ability to induce mesenchymal cell differentiation and successive bone formation when implanted in the human body. However, there is currently a lack of understanding regarding the fundamental biochemical mechanisms by which these materials can induce bone formation. Phenomenological studies of retrievals have clarified the final effect of bone formation, but have left the chemical interactions at the cell-material interface uncharted. Accordingly, the knowledge of the intrinsic material properties relevant for osteoblastogenesis and osteoinduction remains incomplete. Here, we systematically monitored in vitro the chemistry of mesenchymal cell metabolism and the ionic exchanges during osteoblastogenesis on selected substrates through conventional biological assays as well as via in situ and ex situ spectroscopic techniques. Accordingly, the chemical behavior of different bioceramic substrates during their interactions with mesenchymal cells could be unfolded and compared with that of biomedical titanium alloy. Our goal was to clarify the cascade of chemical equations behind the biological processes that govern osteoblastogenic effects on different biomaterial substrates.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan.
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160-0023, Japan.
- The Center for Advanced Medical Engineering and Informatics, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0854, Japan.
- 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 Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Francesco Boschetto
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Matteo Zanocco
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, 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
| | - B Sonny Bal
- SINTX Technologies Corporation, 1885 West 2100 South, Salt Lake City, UT 84119, USA
| | - Bryan J McEntire
- SINTX Technologies Corporation, 1885 West 2100 South, Salt Lake City, UT 84119, USA
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Pezzotti G. Silicon Nitride: A Bioceramic with a Gift. ACS APPLIED MATERIALS & INTERFACES 2019; 11:26619-26636. [PMID: 31251018 DOI: 10.1021/acsami.9b07997] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the closing decades of the 20th century, silicon nitride (Si3N4) was extensively developed for high-temperature gas turbine applications. Technologists attempted to take advantage of its superior thermal and mechanical properties to improve engine reliability and fuel economy. Yet, this promise was never realized in spite of the worldwide research, which was conducted at that time. Notwithstanding this disappointment, its use in medical applications in the early 21st century has been an unexpected gift. While retaining all of its engineered mechanical properties, it is now recognized for its peculiar surface chemistry. When immersed in an aqueous environment, the slow elution of silicon and nitrogen from its surface enhances healing of soft and osseous tissue, inhibits bacterial proliferation, and eradicates viruses. These benefits permit it to be used in a wide array of different disciplines inside and outside of the human body including orthopedics, dentistry, virology, agronomy, and environmental remediation. Given the global public health threat posed by mutating viruses and bacteria, silicon nitride offers a valid and straightforward alternative approach to fighting these pathogens. However, there is a conundrum behind these recent discoveries: How can this unique bioceramic be both friendly to mammalian cells while concurrently lysing invasive pathogens? This unparalleled characteristic can be explained by the pH-dependent kinetics of two ammonia species-NH4+ and NH3-both of which are leached from the wet Si3N4 surface.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory , Kyoto Institute of Technology , Sakyo-ku, Matsugasaki , Kyoto 606-8585 , Japan
- Department of Orthopedic Surgery , Tokyo Medical University , 6-7-1 Nishi-Shinjuku , Shinjuku-ku, Tokyo 160-0023 , Japan
- The Center for Advanced Medical Engineering and Informatics , Osaka University , 2-2 Yamadaoka , Suita 565-0854 , Osaka , Japan
- 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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12
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Barkhade T, Phatangare A, Dahiwale S, Mahapatra SK, Banerjee I. Nano‐bio interface study between Fecontent TiO2nanoparticles and adenosine triphosphate biomolecules. SURF INTERFACE ANAL 2019. [DOI: 10.1002/sia.6663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Tejal Barkhade
- School of NanosciencesCentral University of Gujarat Gandhinagar 382030 Gujarat India
| | - Ambadas Phatangare
- Department of PhysicsSavitribai Phule Pune University Pune 411007 Maharashtra India
| | - Shailendra Dahiwale
- Department of PhysicsSavitribai Phule Pune University Pune 411007 Maharashtra India
| | | | - Indrani Banerjee
- School of NanosciencesCentral University of Gujarat Gandhinagar 382030 Gujarat India
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13
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Andersen PV, Wold JP, Gjerlaug-Enger E, Veiseth-Kent E. Predicting post-mortem meat quality in porcine longissimus lumborum using Raman, near infrared and fluorescence spectroscopy. Meat Sci 2018; 145:94-100. [DOI: 10.1016/j.meatsci.2018.06.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 12/01/2022]
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14
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Kumamoto Y, Harada Y, Takamatsu T, Tanaka H. Label-free Molecular Imaging and Analysis by Raman Spectroscopy. Acta Histochem Cytochem 2018; 51:101-110. [PMID: 30083018 PMCID: PMC6066646 DOI: 10.1267/ahc.18019] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 05/25/2018] [Indexed: 01/06/2023] Open
Abstract
Raman scattering of a cell conveys the intrinsic information inherent to chemical structures of biomolecules. The spectroscopy of Raman scattering, or Raman spectroscopy, allows label-free and quantitative molecular sensing of a biological sample in situ without disruption. For the last five decades Raman spectroscopy has been widely utilized in biological research fields. However, it is just within the latest decade that molecular imaging and discrimination of living cells and tissues have become practically available. Here we overview recent progress in Raman spectroscopy and its application to life sciences. We discuss imaging of functional molecules in living cells and tissues; e.g., cancer cells and ischemic or infarcted hearts, together with a number of studies in the biomedical fields. We further explore comprehensive understandings of a complex spectrum by multivariate analysis for, e.g., accurate peripheral nerve detection, and characterization of the histological differences in the healing process of myocardial infarct. Although limitations still remain, e.g., weakness of the scattering intensity and practical difficulty in comprehensive molecular analysis, continuous progress in related technologies will allow wider use of Raman spectroscopy for biomedical applications.
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Affiliation(s)
- Yasuaki Kumamoto
- Department of Pathology and Cell Regulation, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine
| | - Yoshinori Harada
- Department of Pathology and Cell Regulation, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine
| | - Tetsuro Takamatsu
- Department of Medical Photonics, Kyoto Prefectural University of Medicine
| | - Hideo Tanaka
- Department of Pathology and Cell Regulation, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine
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15
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Ligare MR, Rijs AM, Berden G, Kabeláč M, Nachtigallova D, Oomens J, de Vries MS. Resonant Infrared Multiple Photon Dissociation Spectroscopy of Anionic Nucleotide Monophosphate Clusters. J Phys Chem B 2015; 119:7894-901. [PMID: 26004928 DOI: 10.1021/acs.jpcb.5b02222] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report mid-infrared spectra and potential energy surfaces of four anionic, 2'-deoxynucleotide-5'-monophosphates (dNMPs) and the ionic DNA pairs [dGMP-dCMP-H](1-), [dAMP-dTMP-H](1-) with a total charge of the complex equal to -1. We recorded IR action spectra by resonant IR multiple-photon dissociation (IRMPD) using the FELIX free electron laser. The potential energy surface study employed an on-the-fly molecular dynamics quenching method (MD/Q), using a semiempirical AM1 method, followed by an optimization of the most stable structures using density functional theory. By employing infrared multiple-photon dissociation (IRMPD) spectroscopy in combination with high-level computational methods, we aim at a better understanding of the hydrogen bonding competition between the phosphate moieties and the nucleobases. We find that, unlike in multimer double stranded DNA structures, the hydrogen bonds in these isolated nucleotide pairs are predominantly formed between the phosphate groups. This intermolecular interaction appears to exceed the stabilization energy resulting from base pairing and directs the overall cluster structure and alignment.
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Affiliation(s)
- Marshall R Ligare
- †Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Anouk M Rijs
- ‡FELIX Facility, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Giel Berden
- ‡FELIX Facility, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Martin Kabeláč
- §Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Dana Nachtigallova
- ∥Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic
| | - Jos Oomens
- ‡FELIX Facility, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands.,∥Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic.,⊥van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Mattanjah S de Vries
- †Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
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16
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Label-free sensing of adenosine based on force variations induced by molecular recognition. BIOSENSORS-BASEL 2015; 5:85-97. [PMID: 25808841 PMCID: PMC4384084 DOI: 10.3390/bios5010085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/25/2015] [Accepted: 03/11/2015] [Indexed: 01/03/2023]
Abstract
We demonstrate a simple force-based label-free strategy for the highly sensitive sensing of adenosine. An adenosine ssDNA aptamer was bound onto an atomic force microscopy (AFM) probe by covalent modification, and the molecular-interface adsorption force between the aptamer and a flat graphite surface was measured by single-molecule force spectroscopy (SMFS). In the presence of adenosine, the molecular recognition between adenosine and the aptamer resulted in the formation of a folded, hairpin-like DNA structure and hence caused a variation of the adsorption force at the graphite/water interface. The sensitive force response to molecular recognition provided an adenosine detection limit in the range of 0.1 to 1 nM. The addition of guanosine, cytidine, and uridine had no significant interference with the sensing of adenosine, indicating a strong selectivity of this sensor architecture. In addition, operational parameters that may affect the sensor, such as loading rate and solution ionic strength, were investigated.
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17
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Bhaumik A, Shearin AM, Delong R, Wanekaya A, Ghosh K. Probing the Interaction at the Nano-Bio Interface Using Raman Spectroscopy: ZnO Nanoparticles and Adenosine Triphosphate Biomolecules. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2014; 118:18631-18639. [PMID: 25152799 PMCID: PMC4136666 DOI: 10.1021/jp506200a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 07/17/2014] [Indexed: 06/03/2023]
Abstract
With the advent of nanobiotechnology, there will be an increase in the interaction between engineered nanomaterials and biomolecules. Nanoconjugates with cells, organelles, and intracellular structures containing DNA, RNA, and proteins establish sequences of nano-bio boundaries that depend on several intricate complex biophysicochemical reactions. Given the complexity of these interactions, and their import in governing life at the molecular level, it is extremely important to begin to understand such nanoparticle-biomaterial association. Here we report a unique method of probing the kinematics between an energy biomolecule, adenosine triphosphate (ATP), and hydrothermally synthesized ZnO nanostructures using micro Raman spectroscopy, X-ray diffraction, and electron microscopy experiments. For the first time we have shown by Raman spectroscopy analysis that the ZnO nanostructures interact strongly with the nitrogen (N7) atom in the adenine ring of the ATP biomolecule. Raman spectroscopy also confirms the importance of nucleotide base NH2 group hydrogen bonding with water molecules and phosphate group ionization and their pH dependence. Calculation of molecular bond force constants from Raman spectroscopy reinforces our experimental data. These data present convincing evidence of pH-dependent interactions between ATP and zinc oxide nanomaterials. Significantly, Raman spectroscopy is able to probe such difficult to study and subtle nano-bio interactions and may be applied to elegantly elucidate the nano-bio interface more generally.
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Affiliation(s)
- A. Bhaumik
- Department
of Physics, Astronomy and Materials Science, Department of Biomedical
Science, and Department of Chemistry, Missouri State
University, Springfield, Missouri 65897, United
States
| | - A. M. Shearin
- Department
of Physics, Astronomy and Materials Science, Department of Biomedical
Science, and Department of Chemistry, Missouri State
University, Springfield, Missouri 65897, United
States
| | - R. Delong
- Department
of Physics, Astronomy and Materials Science, Department of Biomedical
Science, and Department of Chemistry, Missouri State
University, Springfield, Missouri 65897, United
States
| | - A. Wanekaya
- Department
of Physics, Astronomy and Materials Science, Department of Biomedical
Science, and Department of Chemistry, Missouri State
University, Springfield, Missouri 65897, United
States
| | - K. Ghosh
- Department
of Physics, Astronomy and Materials Science, Department of Biomedical
Science, and Department of Chemistry, Missouri State
University, Springfield, Missouri 65897, United
States
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18
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Scheier R, Bauer A, Schmidt H. Early Postmortem Prediction of Meat Quality Traits of Porcine Semimembranosus Muscles Using a Portable Raman System. FOOD BIOPROCESS TECH 2014. [DOI: 10.1007/s11947-013-1240-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Tenório T, Silva AM, Ramos JM, Buarque CD, Felcman J. Molecular structure of tetraaqua adenosine 5'-triphosphate aluminium(III) complex: a study involving Raman spectroscopy, theoretical DFT and potentiometry. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 105:88-101. [PMID: 23295215 DOI: 10.1016/j.saa.2012.12.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 12/01/2012] [Accepted: 12/06/2012] [Indexed: 06/01/2023]
Abstract
The Alzheimer's disease is one of the most common neurodegenerative diseases that affect elderly population, due to the formation of β-amyloid protein aggregate and several symptoms, especially progressive cognitive decline. The result is a decrease in capture of glucose by cells leading to obliteration, meddling in the Krebs cycle, the principal biochemical route to the energy production leading to a decline in the levels of adenosine 5'-triphosphate. Aluminium(III) is connected to Alzheimer's and its ion provides raise fluidity of the plasma membrane, decrease cell viability and aggregation of amyloid plaques. Studies reveal that AlATP complex promotes the formation of reactive fibrils of β-amyloid protein and independent amyloidogenic peptides, suggesting the action of the complex as a chaperone in the role pathogenic process. In this research, one of complexes formed by Al(III) and adenosine 5'-triphosphate in aqueous solution is analyzed by potentiometry, Raman spectroscopy and ab initio calculations. The value of the logK(AlATP) found was 9.21±0.01 and adenosine 5'-triphosphate should act as a bidentate ligand in the complex. Raman spectroscopy and potentiometry indicate that donor atoms are the oxygen of the phosphate β and the oxygen of the phosphate γ, the terminal phosphates. Computational calculations using Density Functional Theory, with hybrid functions B3LYP and 6-311++G(d,p) basis set regarding water solvent effects, have confirmed the results. Frontier molecular orbitals, electrostatic potential contour surface, electrostatic potential mapped and Mulliken charges of the title molecule were also investigated.
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Affiliation(s)
- Thaís Tenório
- Department of Chemistry, Pontifícia Universidade Católica do Rio de Janeiro, Rua Marquês de São Vicente, 225, Edifício Cardeal Leme, 6° andar, sala 671L, 22453-900 Rio de Janeiro, RJ, Brazil.
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20
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Ostovarpour S, Blanch EW. Phosphorylation detection and characterization in ribonucleotides using Raman and Raman optical activity (ROA) spectroscopies. APPLIED SPECTROSCOPY 2012; 66:289-293. [PMID: 22449305 DOI: 10.1366/11-06467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Raman and Raman optical activity (ROA) spectra are presented for adenosine and seven of its derivative ribonucleotides. Both of these spectroscopic techniques are shown to be sensitive to the site and degree of phosphorylation, with a considerable number of marker bands being identified for these ribonucleotides. ROA spectra are shown to provide the most sensitive diagnostic tool for phosphorylation characterization and quantification.
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Affiliation(s)
- Saeideh Ostovarpour
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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21
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Rinia HA, Bonn M, Müller M. Quantitative multiplex CARS spectroscopy in congested spectral regions. J Phys Chem B 2007; 110:4472-9. [PMID: 16509751 DOI: 10.1021/jp0564849] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel procedure is developed to describe and reproduce experimental coherent anti-Stokes Raman scattering (CARS) data, with particular emphasis on highly congested spectral regions. The approach, exemplified here with high-quality multiplex CARS data, makes use of spontaneous Raman scattering results. It is shown that the underlying vibrational Raman response can be retrieved from the multiplex CARS spectra, so that the Raman spectrum can be reconstituted, provided an adequate signal-to-noise ratio (SNR) is present in the experimental data and sufficient a priori knowledge of the vibrational resonances involved exists. The conversion of CARS to Raman data permits a quantitative interpretation of CARS spectra. This novel approach is demonstrated for highly congested multiplex CARS spectra of adenosine mono-, di-, and triphosphate (AMP, ADP, and ATP), nicotinamide adenine dinucleotide (NAD+), and small unilamellar vesicles (SUVs) of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Quantitative determination of nucleotide concentrations and composition analysis in mixtures is demonstrated.
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Affiliation(s)
- Hilde A Rinia
- Swammerdam Institute for Life Sciences, University of Amsterdam, P.O. Box 94062, 1090 GB Amsterdam, The Netherlands
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Jenkins RH, Tuma R, Juuti JT, Bamford DH, Thomas GJ. A novel Raman spectrophotometric method for quantitative measurement of nucleoside triphosphate hydrolysis. BIOSPECTROSCOPY 2001; 5:3-8. [PMID: 10219876 DOI: 10.1002/(sici)1520-6343(1999)5:1<3::aid-bspy2>3.0.co;2-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A novel spectrophotometric method, based upon Raman spectroscopy, has been developed for accurate quantitative determination of nucleoside triphosphate phosphohydrolase (NTPase) activity. The method relies upon simultaneous measurement in real time of the intensities of Raman marker bands diagnostic of the triphosphate (1115 cm(-1)) and diphosphate (1085 cm(-1)) moieties of the NTPase substrate and product, respectively. The reliability of the method is demonstrated for the NTPase-active RNA-packaging enzyme (protein P4) of bacteriophage phi6, for which comparative NTPase activities have been estimated independently by radiolabeling assays. The Raman-determined rate for adenosine triphosphate substrate (8.6 +/- 1.3 micromol x mg(-1) x min(-1) at 40 degrees C) is in good agreement with previous estimates. The versatility of the Raman method is demonstrated by its applicability to a variety of nucleotide substrates of P4, including the natural ribonucleoside triphosphates (ATP, GTP) and dideoxynucleoside triphosphates (ddATP, ddGTP). Advantages of the present protocol include conservative sample requirements (approximately 10(-6) g enzyme/protocol) and relative ease of data collection and analysis. The latter conveniences are particularly advantageous for the measurement of activation energies of phosphohydrolase activity.
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Affiliation(s)
- R H Jenkins
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, 64110, USA
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23
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Abstract
ATP-Fe and AMP-Fe complexes in water (H2O and 2H2O) at pH 7.5 were studied using Raman spectroscopy. Parallel and perpendicular polarization spectra were recorded in the spectral range 200-1650 cm-1, and the depolarization ratios for most of the bands were calculated. The changes in the frequencies, intensities and depolarization ratios of the ATP and AMP bands after the addition of FeCl3 showed that the adenine moiety, in addition to the phosphate(s), was involved in the binding of Fe to both ATP and AMP. Direct interactions of Fe(III) with the phosphate chain and the N-7 nitrogen and indirect interaction (via water molecules) with the amide group were proposed for the ATP-Fe complex. In contrast, direct interaction with the phosphate group and indirect interaction with the amide group were observed for the AMP-Fe complex. The different interactions of the two complexes suggest an 'anti' conformation for the ATP-Fe complex and a 'syn' conformation for the AMP-Fe complex. The strong binding of Fe to ATP compared with AMP and the difference in the conformation of the ATP-Fe and the AMP-Fe complexes may be significant in the pathway of Fe release in mitochondria.
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Affiliation(s)
- V Zhelyaskov
- Department of Physics, Emory University, Atlanta, GA 30322
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24
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Tajmir-Riahi HA, Langlais M, Savoie R. A laser Raman spectroscopic study of the interaction of the methylmercury cation with AMP, ADP and ATP. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 956:211-6. [PMID: 3167070 DOI: 10.1016/0167-4838(88)90137-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The interaction of the CH3Hg+ cation with adenosine 5'-monophosphate, adenosine 5'-diphosphate, and adenosine 5'-triphosphate has been studied in aqueous solution at neutral pH by laser Raman spectroscopy. Metal binding is shown to occur preferentially at the N-1 ring position of adenine, with some indication of coordination to the N-7 site and substitution of a proton on the exocyclic NH2 group of the nucleic base. Binding of the cation to phosphate groups also occurs extensively, with both the -PO2-3 and -PO-2 groups. The equilibrium constants for the binding to the phosphate groups and for N-1 coordination are approx. 70 and 600 M-1, respectively.
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25
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Yue KT, Martin CL, Chen D, Nelson P, Sloan DL, Callender R. Raman spectroscopy of oxidized and reduced nicotinamide adenine dinucleotides. Biochemistry 1986; 25:4941-7. [PMID: 3768324 DOI: 10.1021/bi00365a033] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We have measured the Raman spectra of oxidized nicotinamide adenine dinucleotide, NAD+, and its reduced form, NADH, as well as a series of fragments and analogues of NAD+ and NADH. In addition, we have studied the effects of pH as well as deuteration of the exchangeable protons on the Raman spectra of these molecules. In comparing the positions and intensities of the peaks in the fragment and analogue spectra with those of NADH and NAD+, we find that it is useful to consider these large molecules as consisting of component parts, namely, adenine, two ribose groups, two phosphate groups, and nicotinamide, for the purpose of assigning their spectral features. The Raman bands of NADH and NAD+ are found generally to arise from molecular motions in one or another of these molecular moieties, although some peaks are not quite so easily identified in this way. This type of assignment is the first step in a detailed understanding of the Raman spectra of NAD+ and NADH. This is needed to understand the binding properties of NADH and NAD+ acting as coenzymes with the NAD-linked dehydrogenases as deduced recently by using Raman spectroscopy.
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27
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Lanir A, Yu NT. A Raman spectroscopic study of the interaction of divalent metal ions with adenine moiety of adenosine 5'-triphosphate. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)50496-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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28
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Eichler J, Lenz H. Laser applications in medicine and biology: a bibliography. APPLIED OPTICS 1977; 16:27. [PMID: 20168425 DOI: 10.1364/ao.16.000027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This bibliography covers the period from 1963 through 1974; 916 references are classified under 23 subject headings. The references are arranged chronologically.
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Thomas GJ, Livramento J. Kinetics of hydrogen-deuterium exchange in adenosine 5'-monophosphate, adenosine 3':5'-monophosphate, and poly(riboadenylic acid) determined by laser-Raman spectroscopy. Biochemistry 1975; 14:5210-7. [PMID: 172119 DOI: 10.1021/bi00694a030] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pseudo-first-order rate constants governing the deuterium exchange of 8-CH groups in adenosine 5'-monophosphate, adenosine 3':5'-monophosphate, and poly(riboadenylic acid) (poly(rA)) were determined as a function of temperature in the range 20-90 degrees C by means of laser-Raman spectroscopy. For 5'-rAMP, the logarithm of the rate constant exhibits a strictly linear dependence on reciprocal temperature, i.e., kpsi = Ae-Ea/RT, with A = 2.3 X 10(14) hr-1 and Ea = 24.2 +/- 0.6 kcal/mol. For cAMP, above 50 degrees C, kpsi is nearly identical in magnitude and temperature dependence to that of 5'-rAMP. However, below 50 degrees C, isotope exchange in cAMP is much more rapid than in 5'-rAMP, characterized by a lower activation energy (17.7 kcal/mol) and frequency factor (9.6 X 10(9) hr-1). Exchange in poly(rA) is considerably slower than in 5'-rAMP at all temperatures, but like cAMP the in k vs. 1/T plot may be divided into high temperature and low temperature domains, each characterized by different Arrhenius parameters. Above 60 degrees C, poly(rA) gives Ea = 22.0 kcal/mol and A = 3.2 X 10(12) hr-1, while below 60 degrees C, Ea = 27.7 kcal/mol and A = 1.8 X 10(16) hr-1. Thus, increasing the temperature above 60 degrees C does not diminish the retardation of exchange in poly(rA) vis a vis 5'-rAMP. These results indicate that the distribution of electrons in the adenine ring of cAMP is altered by lowering the temperature below 50 degrees C, although no similar perturbation occurs for 5'-rAMP. Retardation of exchange in poly(rA) is most probably due to base stacking at lower temperatures and to steric hindrance from the ribopolymer backbone at higher temperatures. We also report the spectral effects of deuterium exchange on the vibrational Raman frequencies of 5'-rAMP, cAMP, and poly(rA) and suggest a number of new assignments for the 5' and cyclic ribosyl phosphate groups.
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Lewis A, Nelson N, Racker E. Laser Raman spectroscopy as a mechanistic probe of the phosphate transfer from adenosine triphosphate in a model system. Biochemistry 1975; 14:1532-5. [PMID: 1125186 DOI: 10.1021/bi00678a029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Laser Raman spectroscopy has been used to study a phosphate transfer reaction from ATP to Pi or arsenate in dimethyl sulfoxide. The spectra support a mechanism involving Mg-2+ binding to the alpha or beta phosphates of ATP leaving the third phosphate free for the transfer reaction. The data also indicate the formation of a relatively stable intermediate which is facilitated by the presence of dimethyl sulfoxide and a dicarboxylic acid (maleate). The intermediate has a Raman spectrum with a band at 1090.5 cm- minus 1 similar to the end product ADP, but is formed much more rapidly. Since the model reaction has many features in common (e.g., activation by maleate) with the transfer reactions catalyzed by coupling factors from spinach chloroplast, Raman spectroscopy may also prove to be a useful tool in the elucidation of biological energy transfer reactions.
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Rimai L, Maher VM, Gill D, Salmeen I, McCormick J. The temperature dependence of Raman intensities of DNA. ACTA ACUST UNITED AC 1974. [DOI: 10.1016/0005-2787(74)90343-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Thomas GJ, Hartman KA. Raman studies of nucleic acids. 8. Estimation of RNA secondary structure from Raman scattering by phosphate-group vibrations. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 312:311-32. [PMID: 4579230 DOI: 10.1016/0005-2787(73)90376-6] [Citation(s) in RCA: 81] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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INFRARED AND RAMAN SPECTROSCOPY. Biopolymers 1973. [DOI: 10.1016/b978-0-12-734350-1.50009-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Arie G, Da Silva E, Dumas G, Rozansza H, Sebenne C. [Study of biological molecules by Raman spectrometry. Example of application: guanine, uracil and cytosine]. Biochimie 1971; 53:1041-3. [PMID: 5150961 DOI: 10.1016/s0300-9084(71)80072-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Rimai L, Heyde ME. An investigation by Raman spectroscopy of the base-proton dissociation of ATP in aqueous solution and the interactions of ATP with Zn++ and Mn++. Biochem Biophys Res Commun 1970; 41:313-20. [PMID: 5518163 DOI: 10.1016/0006-291x(70)90505-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Thomas GJ. Raman spectral studies of nucleic acids. 3. Laser-excited spectra of ribosomal RNA. BIOCHIMICA ET BIOPHYSICA ACTA 1970; 213:417-23. [PMID: 4927491 DOI: 10.1016/0005-2787(70)90049-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Rimai L, Heyde ME, Carew EB. Effect of divalent metal ion binding on the Raman spectrum of ATP in aqueous solution. Biochem Biophys Res Commun 1970; 38:231-7. [PMID: 5418701 DOI: 10.1016/0006-291x(70)90701-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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