1
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Merrild A, Johnsen NK, Zhang M, Bogojevic O, Ouyang Y, Guo Z. De Novo Synthesis of Perdeuterated Phosphoinositide by Installing a Non-native Phospholipid Biopathway in E. coli. ACS Synth Biol 2024. [PMID: 39292964 DOI: 10.1021/acssynbio.4c00413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
Phosphatidylinositol (PI) and its phosphorylated derivatives are of paramount importance in cellular functions and diseases. Understanding their diverse roles is, however, challenged by difficulties in synthesis and labeling techniques. In this proof-of-concept study, we demonstrate that PI can be straightforwardly de novo-synthesized and deuterium (2H)-labeled in Escherichia coli by genomic insertion of PI synthase from Trypanosoma brucei under constitutive synthetic promoter proD. Insertion into loci atpi-gidB and ybb revealed PI accumulation of 41% and 34% (mol/mol), respectively, when cultivated with glycerol as the sole carbon source. Growth of the atpi-gidB-PIS strain in deuterium-labeled (2H) substrates D2O, D8-glycerol, and D6-myo-inositol achieved PI deuteration of 90%, PE deuteration of 95%, and total fatty acids|fatty acid (FA) deuteration of 97%. This study offers an alternative convenient route to chemical and enzymatic labeling synthesis of PI; more excitingly, this work also, in principle, opens a door for tailoring the FA profile of deuterated PI/PE for task-specific application by repurposing FA biosynthesis pathways.
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Affiliation(s)
- Aske Merrild
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Niels Krabbe Johnsen
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Mingliang Zhang
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
- Engineering Research Center of Industrial Microbiology of Ministry of Education, Fujian Normal University, Visiting Researcher at Aarhus University 2022-2024, Fuzhou 350007, China
| | - Oliver Bogojevic
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Yi Ouyang
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Zheng Guo
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
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2
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Greig JC, Tipping WJ, Graham D, Faulds K, Gould GW. New insights into lipid and fatty acid metabolism from Raman spectroscopy. Analyst 2024. [PMID: 39258960 DOI: 10.1039/d4an00846d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
One of the challenges facing biology is to understand metabolic events at a single cellular level. While approaches to examine dynamics of protein distribution or report on spatiotemporal location of signalling molecules are well-established, tools for the dissection of metabolism in single living cells are less common. Advances in Raman spectroscopy, such as stimulated Raman scattering (SRS), are beginning to offer new insights into metabolic events in a range of experimental systems, including model organisms and clinical samples, and across a range of disciplines. Despite the power of Raman imaging, it remains a relatively under-used technique to approach biological problems, in part because of the specialised nature of the analysis. To raise the profile of this method, here we consider some key studies which illustrate how Raman spectroscopy has revealed new insights into fatty acid and lipid metabolism across a range of cellular systems. The powerful and non-invasive nature of this approach offers a new suite of tools for biomolecular scientists to address how metabolic events within cells informs on or underpins biological function. We illustrate potential biological applications, discuss some recent advances, and offer a direction of travel for metabolic research in this area.
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Affiliation(s)
- Justin C Greig
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, UK.
| | | | - Duncan Graham
- Pure and Applied Chemistry, University of Strathclyde, UK
| | - Karen Faulds
- Pure and Applied Chemistry, University of Strathclyde, UK
| | - Gwyn W Gould
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, UK.
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3
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Taniguchi T, Agbo DO, Yang Q, Kapitán J, Wu T, Oyama S, Akai S, Sawama Y, Bouř P. Raman optical activity study of deuterated sugars: deuterium labelling as a tool for structural analysis. Phys Chem Chem Phys 2024; 26:21568-21574. [PMID: 39082369 DOI: 10.1039/d4cp02406k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Structural analyses using Raman optical activity (ROA) spectroscopy conventionally rely on vibrational signals in the fingerprint region ranging from 100 to 1800 cm-1. Use of deuterium labelling to observe ROA signals in the C-D stretching region provides additional information about a local structure of large molecular systems. So far, the potential of C-D stretching ROA signals for structural analysis has rarely been explored. In the present work, we synthesized model deuterated glucose monosaccharides and studied their ROA properties by employing molecular dynamics and density functional theory to interpret the spectra. A good agreement between the simulated and experimental spectra is achieved when the proper conformer ratios are considered. This shows the usefulness of ROA spectroscopy assisted by deuterium labelling for stereochemical and conformational analysis.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Davidson Obinna Agbo
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Tao Wu
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Shuki Oyama
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shuji Akai
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshinari Sawama
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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4
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Zhang HH, Chen MZ, Yu X, Bonnesen PV, Wu Z, Chen HL, O'Neill H. Synthesis of Perdeuterated Alkyl Amines/Amides with Pt/C as Catalyst under Mild Conditions. J Org Chem 2024. [PMID: 38741072 DOI: 10.1021/acs.joc.4c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
A convenient method for the synthesis of perdeuterated alkyl amides/amines is disclosed. Perdeuterated acetyl amides can be achieved by a hydrogen-deuterium (H/D) exchange protocol with Pt/C as a catalyst and D2O as a deuterium source under mild conditions. After removal or reduction of the acetyl group, this protocol can provide perdeuterated primary, secondary, and tertiary amines, which are difficult to achieve via other methods.
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Affiliation(s)
- Hong-Hai Zhang
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Meng-Zhe Chen
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Xinbin Yu
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Peter V Bonnesen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Zili Wu
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hsin-Lung Chen
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Hugh O'Neill
- Neutron Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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5
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Uchiyama H, Ban K, Nozaki S, Ikeda Y, Ishimoto T, Fujioka H, Kamiya M, Amari R, Tsujino H, Arai M, Yamazoe S, Maekawa K, Kato T, Doi M, Kadota K, Tozuka Y, Tomita N, Sajiki H, Akai S, Sawama Y. Impact of multiple H/D replacements on the physicochemical properties of flurbiprofen. RSC Med Chem 2023; 14:2583-2592. [PMID: 38107175 PMCID: PMC10718516 DOI: 10.1039/d3md00357d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/06/2023] [Indexed: 12/19/2023] Open
Abstract
Although deuterium incorporation into pharmaceutical drugs is an attractive way to expand drug modalities, their physicochemical properties have not been sufficiently examined. This study focuses on examining the changes in physicochemical properties between flurbiprofen (FP) and flurbiprofen-d8 (FP-d8), which was successfully prepared by direct and multiple H/D exchange reactions at the eight aromatic C-H bonds of FP. Although the effect of deuterium incorporation was not observed between the crystal structures of FP and FP-d8, the melting point and heat of fusion of FP-d8 were lower than those of FP. Additionally, the solubility of FP-d8 increased by 2-fold compared to that of FP. Calculation of the interaction energy between FP/FP-d8 and water molecules using the multi-component density functional theory method resulted in increased solubility of FP-d8. These novel and valuable findings regarding the changes in physicochemical properties triggered by deuterium incorporation can contribute to the further development of deuterated drugs.
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Affiliation(s)
- Hiromasa Uchiyama
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara Takatsuki Osaka 569-1094 Japan
| | - Kazuho Ban
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6, Yamada-oka Suita Osaka 565-0871 Japan
| | - Shiho Nozaki
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6, Yamada-oka Suita Osaka 565-0871 Japan
| | - Yui Ikeda
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara Takatsuki Osaka 569-1094 Japan
| | - Takayoshi Ishimoto
- Graduate School of Advanced Science and Engineering, Hiroshima University 1-4-1 Kagamiyama Higashi-Hiroshima Hiroshima 739-8527 Japan
| | - Hiroyoshi Fujioka
- Department of Life Science and Technology, Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama Kanagawa 226-8501 Japan
| | - Mako Kamiya
- Department of Life Science and Technology, Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama Kanagawa 226-8501 Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama Kanagawa 226-8501 Japan
| | - Ryugo Amari
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6, Yamada-oka Suita Osaka 565-0871 Japan
| | - Hirofumi Tsujino
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6, Yamada-oka Suita Osaka 565-0871 Japan
| | - Masayoshi Arai
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6, Yamada-oka Suita Osaka 565-0871 Japan
| | - Sachi Yamazoe
- Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts 97-1 Minamihokodate Koudo Kyotanabe, Kyoto 610-0395 Japan
| | - Keiko Maekawa
- Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts 97-1 Minamihokodate Koudo Kyotanabe, Kyoto 610-0395 Japan
| | - Takuma Kato
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara Takatsuki Osaka 569-1094 Japan
| | - Mitsunobu Doi
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara Takatsuki Osaka 569-1094 Japan
| | - Kazunori Kadota
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara Takatsuki Osaka 569-1094 Japan
| | - Yuichi Tozuka
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara Takatsuki Osaka 569-1094 Japan
| | - Naohito Tomita
- Gifu Pharmaceutical University 1-25-4-Daigaku-nishi Gifu 501-1196 Japan
| | - Hironao Sajiki
- Gifu Pharmaceutical University 1-25-4-Daigaku-nishi Gifu 501-1196 Japan
| | - Shuji Akai
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6, Yamada-oka Suita Osaka 565-0871 Japan
| | - Yoshinari Sawama
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6, Yamada-oka Suita Osaka 565-0871 Japan
- Deuterium Science Research Unit, Center for the Promotion of Interdisciplinary Education and Research, Kyoto University Yoshida, Sakyo-ku Kyoto 606-8501 Japan
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6
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Moriyama S, Mae M, Shibata D, Yamakoshi H, Kajimoto S, Nakabayashi T, Ishimoto T, Mogi K, Sajiki H, Akai S, Sawama Y. Multiple deuteration of triphenylphosphine and live-cell Raman imaging of deuterium-incorporated Mito-Q. Chem Commun (Camb) 2023; 59:12100-12103. [PMID: 37721453 DOI: 10.1039/d3cc04410f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
All aromatic C-H bonds of triphenylphosphine (PPh3) were efficiently replaced by C-D bonds using Ru/C and Ir/C co-catalysts in 2-PrOH and D2O, an inexpensive deuterium source. Furthermore, non-radioactive and safe deuterium-incorporated Mito-Q (drug candidate) was prepared from deuterated PPh3 and used for the live-cell Raman imaging to evaluate the mitochondrial uptake.
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Affiliation(s)
- Shogo Moriyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Miyu Mae
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Daiki Shibata
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Hiroyuki Yamakoshi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Shinji Kajimoto
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
- JST PRESTO, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
| | - Takakazu Nakabayashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Takayoshi Ishimoto
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Kaiki Mogi
- Gifu Pharmaceutical University, 1-25-4-Daigaku-nishi, Gifu 501-1196, Japan
| | - Hironao Sajiki
- Gifu Pharmaceutical University, 1-25-4-Daigaku-nishi, Gifu 501-1196, Japan
| | - Shuji Akai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Yoshinari Sawama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka 565-0871, Japan.
- Deuterium Science Research Unit, Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
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7
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Law SY, Asanuma M, Shou J, Ozeki Y, Kodama Y, Numata K. Deuterium- and Alkyne-Based Bioorthogonal Raman Probes for In Situ Quantitative Metabolic Imaging of Lipids within Plants. JACS AU 2023; 3:1604-1614. [PMID: 37388682 PMCID: PMC10302745 DOI: 10.1021/jacsau.3c00041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 07/01/2023]
Abstract
Plants can rapidly respond to different stresses by activating multiple signaling and defense pathways. The ability to directly visualize and quantify these pathways in real time using bioorthogonal probes would have practical applications, including characterizing plant responses to both abiotic and biotic stress. Fluorescence-based labels are widely used for tagging of small biomolecules but are relatively bulky and with potential effects on their endogenous localization and metabolism. This work describes the use of deuterium- and alkyne-derived fatty acid Raman probes to visualize and track the real-time response of plants to abiotic stress within the roots. Relative quantification of the respective signals could be used to track their localization and overall real-time responses in their fatty acid pools due to drought and heat stress without labor-intensive isolation procedures. Their overall usability and low toxicity suggest that Raman probes have great untapped potential in the field of plant bioengineering.
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Affiliation(s)
- Simon
Sau Yin Law
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, Wako, Saitama 351-0198, Japan
| | - Masato Asanuma
- Graduate
School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jingwen Shou
- Graduate
School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yasuyuki Ozeki
- Graduate
School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yutaka Kodama
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, Wako, Saitama 351-0198, Japan
- Center
for Bioscience Research and Education, Utsunomiya
University, Utsunomiya, Tochigi 321-8505, Japan
| | - Keiji Numata
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, Wako, Saitama 351-0198, Japan
- Department
of Material Chemistry, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
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8
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Terrones O, Olazar-Intxausti J, Anso I, Lorizate M, Nieto-Garai JA, Contreras FX. Raman Spectroscopy as a Tool to Study the Pathophysiology of Brain Diseases. Int J Mol Sci 2023; 24:2384. [PMID: 36768712 PMCID: PMC9917237 DOI: 10.3390/ijms24032384] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
The Raman phenomenon is based on the spontaneous inelastic scattering of light, which depends on the molecular characteristics of the dispersant. Therefore, Raman spectroscopy and imaging allow us to obtain direct information, in a label-free manner, from the chemical composition of the sample. Since it is well established that the development of many brain diseases is associated with biochemical alterations of the affected tissue, Raman spectroscopy and imaging have emerged as promising tools for the diagnosis of ailments. A combination of Raman spectroscopy and/or imaging with tagged molecules could also help in drug delivery and tracing for treatment of brain diseases. In this review, we first describe the basics of the Raman phenomenon and spectroscopy. Then, we delve into the Raman spectroscopy and imaging modes and the Raman-compatible tags. Finally, we center on the application of Raman in the study, diagnosis, and treatment of brain diseases, by focusing on traumatic brain injury and ischemia, neurodegenerative disorders, and brain cancer.
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Affiliation(s)
- Oihana Terrones
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - June Olazar-Intxausti
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Itxaso Anso
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, 48903 Barakaldo, Spain
| | - Maier Lorizate
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Jon Ander Nieto-Garai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Francesc-Xabier Contreras
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, 48940 Leioa, Spain
- Ikerbasque, Basque Foundation of Science, 48011 Bilbao, Spain
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9
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Thabet NM, Abdel-Rafei MK, Askar MA, Abdelmohsen SA, Ahmed OM, Elbakry MM. Nanocomposite zinc oxide@ γ-linolenic acid-canagliflozin-fucoxanthin and/or γ-radiation perturbs key metabolic effectors and suppresses the proliferation of breast cancer cells in vitro. J Drug Deliv Sci Technol 2023. [DOI: 10.1016/j.jddst.2023.104161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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10
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Dodo K, Fujita K, Sodeoka M. Raman Spectroscopy for Chemical Biology Research. J Am Chem Soc 2022; 144:19651-19667. [PMID: 36216344 PMCID: PMC9635364 DOI: 10.1021/jacs.2c05359] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Indexed: 11/29/2022]
Abstract
In chemical biology research, various fluorescent probes have been developed and used to visualize target proteins or molecules in living cells and tissues, yet there are limitations to this technology, such as the limited number of colors that can be detected simultaneously. Recently, Raman spectroscopy has been applied in chemical biology to overcome such limitations. Raman spectroscopy detects the molecular vibrations reflecting the structures and chemical conditions of molecules in a sample and was originally used to directly visualize the chemical responses of endogenous molecules. However, our initial research to develop "Raman tags" opens a new avenue for the application of Raman spectroscopy in chemical biology. In this Perspective, we first introduce the label-free Raman imaging of biomolecules, illustrating the biological applications of Raman spectroscopy. Next, we highlight the application of Raman imaging of small molecules using Raman tags for chemical biology research. Finally, we discuss the development and potential of Raman probes, which represent the next-generation probes in chemical biology.
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Affiliation(s)
- Kosuke Dodo
- Synthetic
Organic Chemistry Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Catalysis
and Integrated Research Group, RIKEN Center
for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Katsumasa Fujita
- Department
of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Institute
for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan
- AIST-Osaka
University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science
and Technology (AIST), Suita, Osaka 565-0871, Japan
| | - Mikiko Sodeoka
- Synthetic
Organic Chemistry Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Catalysis
and Integrated Research Group, RIKEN Center
for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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11
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Andrew R, Stimson RH. Mapping endocrine networks by stable isotope tracing. CURRENT OPINION IN ENDOCRINE AND METABOLIC RESEARCH 2022; 26:100381. [PMID: 39185272 PMCID: PMC11344083 DOI: 10.1016/j.coemr.2022.100381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Hormones regulate metabolic homeostasis through interlinked dynamic networks of proteins and small molecular weight metabolites, and state-of-the-art chemical technologies have been developed to decipher these complex pathways. Stable-isotope tracers have largely replaced radiotracers to measure flux in humans, building on advances in nuclear magnetic resonance spectroscopy and mass spectrometry. These technologies are now being applied to localise molecules within tissues. Radiotracers are still highly valuable both preclinically and in 3D imaging by positron emission tomography. The coming of age of vibrational spectroscopy in conjunction with stable-isotope tracing offers detailed cellular insights to map complex biological processes. Together with computational modelling, these approaches are poised to coalesce into multi-modal platforms to provide hitherto inaccessible dynamic and spatial insights into endocrine signalling.
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Affiliation(s)
- Ruth Andrew
- University/ British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, 47, Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Roland H Stimson
- University/ British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, 47, Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
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12
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Deuterium Raman imaging for lipid analysis. Curr Opin Chem Biol 2022; 70:102181. [DOI: 10.1016/j.cbpa.2022.102181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/18/2022]
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13
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Wang DH, Vidovic D, McKay AI, Darwish T, Park HG, Garza SM, Shields SW, Brodbelt JS, Wang Z, Lacombe RJS, Shmanai VV, Lysenko IL, Bekish AV, Schmidt K, Redfield C, Brenna JT, Shchepinov MS. Quantitative High-Field NMR- and Mass Spectrometry-Based Fatty Acid Sequencing Reveals Internal Structure in Ru-Catalyzed Deuteration of Docosahexaenoic Acid. Anal Chem 2022; 94:12971-12980. [PMID: 36098546 DOI: 10.1021/acs.analchem.2c00923] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ru-based catalysis results in highly unsaturated fatty acid (HUFA) ethyl esters (EE) deuterated to various extents. The products carry 2H (D) mainly at their bis-allylic positions, where they are resistant to autoxidation compared to natural HUFA and are promising as neurological and retinal drugs. We characterized the extent of deuteration at each allylic position of docosa-4,7,10,13,16,19-hexaenoic acid deuterated to completion at bis-allylic and allylic positions (D-DHA) by two-dimensional (2D) and high-field (600 and 950 MHz) NMR. In separate experiments, the kinetics of docosahexaenoic acid (DHA) EE deuteration was evaluated using Paternò-Büchi (PB) reaction tandem mass spectrometry (MS/MS) analysis, enabling deuteration to be quantitatively characterized for isotopologues (D0-D14 DHA) at each internal allylic position. NMR analysis shows that the net deuteration of the isotopologue mixture is about 94% at the bis-allylic positions, and less than 1% remained as the protiated -CH2-. MS analysis shows that deuteration kinetics follow an increasing curve at bis-allylic positions with higher rate for internal bis-allylic positions. Percent D of bis-allylic positions increases linearly from D1 to D9 in which all internal bis-allylic positions (C9, C12, C15) deuterate uniformly and more rapidly than external bis-allylic positions (C6, C18). The mono-allylic positions near the methyl end (C21) show a steep increase of D only after the D10 isotopologue has been deuterated to >90%, while the mono-allylic position near the carboxyl position, C3, deuterates last and least. These data establish detailed methods for the characterization of Ru-catalyzed deuteration of HUFA as well as the phenomenological reaction kinetics as net product is formed.
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Affiliation(s)
- Dong Hao Wang
- Dell Pediatric Research Institute, Departments of Pediatrics, of Chemistry, and of Nutrition, University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, Texas 78723, United States
- Division of Nutritional Sciences and Department of Food Science, Cornell University, Ithaca, New York 14850, United States
| | - Dragoslav Vidovic
- School of Chemistry, Monash University, Clayton, Victoria 3800 Australia
| | - Alasdair I McKay
- School of Chemistry, Monash University, Clayton, Victoria 3800 Australia
| | - Tamim Darwish
- National Deuteration Facility-ANSTO, Sydney, New Illawarra Rd, Lucas Heights, NSW 2234, Australia
| | - Hui Gyu Park
- Dell Pediatric Research Institute, Departments of Pediatrics, of Chemistry, and of Nutrition, University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, Texas 78723, United States
- Division of Nutritional Sciences and Department of Food Science, Cornell University, Ithaca, New York 14850, United States
| | - Secilia Martinez Garza
- Dell Pediatric Research Institute, Departments of Pediatrics, of Chemistry, and of Nutrition, University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, Texas 78723, United States
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712 United States
| | - Samuel W Shields
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712 United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712 United States
| | - Zhen Wang
- Dell Pediatric Research Institute, Departments of Pediatrics, of Chemistry, and of Nutrition, University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, Texas 78723, United States
- Division of Nutritional Sciences and Department of Food Science, Cornell University, Ithaca, New York 14850, United States
| | - R J Scott Lacombe
- Dell Pediatric Research Institute, Departments of Pediatrics, of Chemistry, and of Nutrition, University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, Texas 78723, United States
| | - Vadim V Shmanai
- Institute of Physical Organic Chemistry, National Academy of Science of Belarus, 13 Surganova Street, Minsk 220072, Belarus
| | - Ivan L Lysenko
- Institute of Physical Organic Chemistry, National Academy of Science of Belarus, 13 Surganova Street, Minsk 220072, Belarus
| | - Andrei V Bekish
- Institute of Physical Organic Chemistry, National Academy of Science of Belarus, 13 Surganova Street, Minsk 220072, Belarus
| | | | - Christina Redfield
- Dept of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - J Thomas Brenna
- Dell Pediatric Research Institute, Departments of Pediatrics, of Chemistry, and of Nutrition, University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, Texas 78723, United States
- Division of Nutritional Sciences and Department of Food Science, Cornell University, Ithaca, New York 14850, United States
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712 United States
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14
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Moir M, Yepuri N, Marshall D, Blanksby S, Darwish T. Synthesis of Perdeuterated Linoleic Acid‐d31 and Chain Deuterated 1‐Palmitoyl‐2‐linoleoyl‐sn‐glycero‐3‐phosphocholine‐d62. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michael Moir
- Australian Nuclear Science and Technology Organisation AUSTRALIA
| | - Nageshwar Yepuri
- Australian Nuclear Science and Technology Organisation AUSTRALIA
| | | | | | - Tamim Darwish
- Australian Nuclear Science and Technology Organisation AUSTRALIA
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15
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Krishna R, Colak I. Advances in Biomedical Applications of Raman Microscopy and Data Processing: A Mini Review. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2094391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Ram Krishna
- Department of Mechanical Engineering, Madanapalle Institute of Technology & Science, Madanapalle, Andhra Pradesh, India
- Electrical and Electronics Engineering, Nisantasi University, Istanbul, Turkey
- Ohm Janki Biotech Research Private Limited, India
| | - Ilhami Colak
- Electrical and Electronics Engineering, Nisantasi University, Istanbul, Turkey
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16
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Watanabe A, Hama K, Watanabe K, Fujiwara Y, Yokoyama K, Murata S, Takita R. Controlled Tetradeuteration of Straight‐Chain Fatty Acids: Synthesis, Application, and Insight into the Metabolism of Oxidized Linoleic Acid. Angew Chem Int Ed Engl 2022; 61:e202202779. [PMID: 35411582 PMCID: PMC9324819 DOI: 10.1002/anie.202202779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Ayako Watanabe
- One-stop Sharing Facility Center for Future Drug Discoveries Graduate School of Pharmaceutical Sciences University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Kotaro Hama
- Faculty of Pharma-Sciences Teikyo University 2-11-1 Kaga, Itabashi-ku Tokyo 173-8605 Japan
- Advanced Comprehensive Research Organization (ACRO) Teikyo University Japan
| | - Kohei Watanabe
- One-stop Sharing Facility Center for Future Drug Discoveries Graduate School of Pharmaceutical Sciences University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Yuko Fujiwara
- Faculty of Pharma-Sciences Teikyo University 2-11-1 Kaga, Itabashi-ku Tokyo 173-8605 Japan
| | - Kazuaki Yokoyama
- Faculty of Pharma-Sciences Teikyo University 2-11-1 Kaga, Itabashi-ku Tokyo 173-8605 Japan
| | - Shigeo Murata
- One-stop Sharing Facility Center for Future Drug Discoveries Graduate School of Pharmaceutical Sciences University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Ryo Takita
- One-stop Sharing Facility Center for Future Drug Discoveries Graduate School of Pharmaceutical Sciences University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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17
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Watanabe A, Hama K, Watanabe K, Fujiwara Y, Yokoyama K, Murata S, Takita R. Controlled Tetradeuteration of Straight‐Chain Fatty Acids: Synthesis, Application, and Insight into the Metabolism of Oxidized Linoleic Acid. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ayako Watanabe
- One-stop Sharing Facility Center for Future Drug Discoveries Graduate School of Pharmaceutical Sciences University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Kotaro Hama
- Faculty of Pharma-Sciences Teikyo University 2-11-1 Kaga, Itabashi-ku Tokyo 173-8605 Japan
- Advanced Comprehensive Research Organization (ACRO) Teikyo University Japan
| | - Kohei Watanabe
- One-stop Sharing Facility Center for Future Drug Discoveries Graduate School of Pharmaceutical Sciences University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Yuko Fujiwara
- Faculty of Pharma-Sciences Teikyo University 2-11-1 Kaga, Itabashi-ku Tokyo 173-8605 Japan
| | - Kazuaki Yokoyama
- Faculty of Pharma-Sciences Teikyo University 2-11-1 Kaga, Itabashi-ku Tokyo 173-8605 Japan
| | - Shigeo Murata
- One-stop Sharing Facility Center for Future Drug Discoveries Graduate School of Pharmaceutical Sciences University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Ryo Takita
- One-stop Sharing Facility Center for Future Drug Discoveries Graduate School of Pharmaceutical Sciences University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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18
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Zaytseva YV, Zaytseva IV, Surovtsev NV. Conformational state diagram of DOPC/DPPC d62/cholesterol mixtures. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183869. [PMID: 35063400 DOI: 10.1016/j.bbamem.2022.183869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Raman spectra of aqueous suspensions of vesicles composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), deuterated 1,2-dipalmitoyl-d62-sn-glycero-3-phosphocholine (DPPCd62), and cholesterol (Chol) were studied at room temperature to determine the conformational states of the phospholipid hydrocarbon chains. Deuteration of DPPCd62 allowed us to characterize the conformational states of DOPC and DPPCd62 independently. The parameters of Raman peaks, which are sensitive to the conformational order, were studied in a wide range of compositions. It was found that the DOPC molecules are conformationally disordered for all compositions. The conformational state of the DPPCd62 molecules changes with composition. Their conformational state is influenced by cholesterol-induced partial disordering and DOPC solvation, transforming the DPPC molecules into the disordered state. The conformational state diagram from the Raman experiment was compared with outcomes from the differential scanning calorimetry (DSC) experiment. The Raman spectra also revealed that the DPPC molecules coexist in the disordered and all-trans ordered states for the DOPC/DPPCd62/Chol mixtures except for the pure liquid-disordered phase.
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Affiliation(s)
- Yu V Zaytseva
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - I V Zaytseva
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - N V Surovtsev
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia.
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19
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Zaytseva YV, Surovtsev NV. Raman scattering in protonated and deuterated 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC): Indicators of conformational and lateral orders. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120583. [PMID: 34782267 DOI: 10.1016/j.saa.2021.120583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
The use of deuterocarbons is an effective method in the Raman spectroscopy of multicomponent lipid materials and biological samples. Here, Raman spectra of hydrated multilamellar vesicles of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), its deuterated analog 1,2-dipalmitoyl-d62-sn-glycero-3-phosphocholine (DPPCd62), and DPPC-DPPCd62 mixtures were studied in a wide temperature range to specify the Raman indicators of conformational and lateral orders. The temperature dependence of the 985 cm-1 line in the deuterated phospholipid unequivocally indicates that this line corresponds to the CC stretching vibrations of deuterated hydrocarbon chains in the all-trans conformation. It was also concluded that the ratio of Raman intensities at the maximum of the peak of the symmetric CD2 stretching and at a maximum near 2168 cm-1 reflects the conformational order of the hydrocarbon chain and can be used for an evaluation of the fraction of the all-trans sequences. The frequency of the symmetric CD2 stretching peak is sensitive to the phase state (gel or fluid) but has a low sensitivity to the partial conformational disordering within the gel phase. The Raman study of DPPC-DPPCd62 mixtures reveals that the lateral order contributes to the ratio of intensities of the antisymmetric and symmetric CH2 stretching peaks as a prefactor enhancing the effect of conformational ordering.
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Affiliation(s)
- Yu V Zaytseva
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - N V Surovtsev
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia.
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20
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Sawama Y. Exhaustive Syntheses of Deuterium-labelled Compounds. YAKUGAKU ZASSHI 2022; 142:139-144. [DOI: 10.1248/yakushi.21-00173-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Okotrub KA, Okotrub SV, Mokrousova VI, Amstislavsky SY, Surovtsev NV. Lipid phase transitions in cat oocytes supplemented with deuterated fatty acids. Biophys J 2021; 120:5619-5630. [PMID: 34767788 DOI: 10.1016/j.bpj.2021.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/18/2021] [Accepted: 11/03/2021] [Indexed: 01/15/2023] Open
Abstract
Cryopreservation of oocytes has already been used to preserve genetic resources, but this technology faces limitations when applied to the species whose oocytes contain large amounts of cytoplasmic lipid droplets. Although cryoinjuries in such oocytes are usually associated with the lipid phase transition in lipid droplets, this phenomenon is still poorly understood. We applied Raman spectroscopy of deuterium-labeled lipids to investigate the freezing of lipid droplets inside cat oocytes. Lipid phase separation was detected in oocytes cryopreserved by slow-freezing protocol. For oocytes supplemented with stearic acid, we found that saturated lipids form the ordered phase being distributed at the periphery of lipid droplets. When an oocyte is warmed to physiological temperatures after cooling, a fraction of saturated lipids may remain in the ordered conformational state. The fractions of monounsaturated and polyunsaturated lipids redistribute to the core of lipid droplets. Monounsaturated lipids undergo the transition to the ordered conformational state below -10°C. Using deuterated fatty acids with a different number of double bonds, we reveal how different lipid fractions are involved in the lipid phase transition of a cytoplasmic lipid droplet and how they can affect cell survival. Raman spectroscopy of deuterated lipids has proven to be a promising tool for studying the lipid phase transitions and lipid redistributions inside single organelles within living cells.
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Affiliation(s)
- Konstantin A Okotrub
- Institute of Automation and Electrometry, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
| | - Svetlana V Okotrub
- Institute of Automation and Electrometry, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentina I Mokrousova
- Institute of Automation and Electrometry, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergei Y Amstislavsky
- Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikolay V Surovtsev
- Institute of Automation and Electrometry, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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22
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Bakthavatsalam S, Dodo K, Sodeoka M. A decade of alkyne-tag Raman imaging (ATRI): applications in biological systems. RSC Chem Biol 2021; 2:1415-1429. [PMID: 34704046 PMCID: PMC8496067 DOI: 10.1039/d1cb00116g] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/07/2021] [Indexed: 12/14/2022] Open
Abstract
Alkyne functional groups have Raman signatures in a region (1800 cm-1 to 2800 cm-1) that is free from interference from cell components, known as the "silent region", and alkyne signals in this region were first utilized a decade ago to visualize the nuclear localization of a thymidine analogue EdU. Since then, the strategy of Raman imaging of biological samples by using alkyne functional groups, called alkyne-tag Raman imaging (ATRI), has become widely used. This article reviews the applications of ATRI in biological samples ranging from organelles to whole animal models, and briefly discusses the prospects for this technique.
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Affiliation(s)
- Subha Bakthavatsalam
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research Wako Saitama 351-0198 Japan
| | - Kosuke Dodo
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
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23
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Egoshi S, Dodo K, Ohgane K, Sodeoka M. Deuteration of terminal alkynes realizes simultaneous live cell Raman imaging of similar alkyne-tagged biomolecules. Org Biomol Chem 2021; 19:8232-8236. [PMID: 34528645 DOI: 10.1039/d1ob01479j] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Alkynes were employed as tags to observe small molecules in cells by Raman microscopy. Herein, simple deuteration was found to shift the vibrational frequency of the alkyne by 135 cm-1. Two-color Raman imaging of D-alkynes and H-alkynes made it possible to distinguish between and observe similar small molecules in live cells.
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Affiliation(s)
- Syusuke Egoshi
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Kosuke Dodo
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kenji Ohgane
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
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24
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Xu J, Yu T, Zois CE, Cheng JX, Tang Y, Harris AL, Huang WE. Unveiling Cancer Metabolism through Spontaneous and Coherent Raman Spectroscopy and Stable Isotope Probing. Cancers (Basel) 2021; 13:1718. [PMID: 33916413 PMCID: PMC8038603 DOI: 10.3390/cancers13071718] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 11/25/2022] Open
Abstract
Metabolic reprogramming is a common hallmark in cancer. The high complexity and heterogeneity in cancer render it challenging for scientists to study cancer metabolism. Despite the recent advances in single-cell metabolomics based on mass spectrometry, the analysis of metabolites is still a destructive process, thus limiting in vivo investigations. Being label-free and nonperturbative, Raman spectroscopy offers intrinsic information for elucidating active biochemical processes at subcellular level. This review summarizes recent applications of Raman-based techniques, including spontaneous Raman spectroscopy and imaging, coherent Raman imaging, and Raman-stable isotope probing, in contribution to the molecular understanding of the complex biological processes in the disease. In addition, this review discusses possible future directions of Raman-based technologies in cancer research.
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Affiliation(s)
- Jiabao Xu
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK;
| | - Tong Yu
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK;
| | - Christos E. Zois
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford University, Oxford OX3 9DS, UK;
- Department of Radiotherapy and Oncology, School of Health, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, MS 02215, USA;
| | - Yuguo Tang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China;
| | - Adrian L. Harris
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford University, Oxford OX3 9DS, UK;
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK;
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