1
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Vardaki MZ, Gregoriou VG, Chochos CL. Biomedical applications, perspectives and tag design concepts in the cell - silent Raman window. RSC Chem Biol 2024; 5:273-292. [PMID: 38576725 PMCID: PMC10989507 DOI: 10.1039/d3cb00217a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/12/2024] [Indexed: 04/06/2024] Open
Abstract
Spectroscopic studies increasingly employ Raman tags exhibiting a signal in the cell - silent region of the Raman spectrum (1800-2800 cm-1), where bands arising from biological molecules are inherently absent. Raman tags bearing functional groups which contain a triple bond, such as alkyne and nitrile or a carbon-deuterium bond, have a distinct vibrational frequency in this region. Due to the lack of spectral background and cell-associated bands in the specific area, the implementation of those tags can help overcome the inherently poor signal-to-noise ratio and presence of overlapping Raman bands in measurements of biological samples. The cell - silent Raman tags allow for bioorthogonal imaging of biomolecules with improved chemical contrast and they have found application in analyte detection and monitoring, biomarker profiling and live cell imaging. This review focuses on the potential of the cell - silent Raman region, reporting on the tags employed for biomedical applications using variants of Raman spectroscopy.
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Affiliation(s)
- Martha Z Vardaki
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue Athens 11635 Greece
| | - Vasilis G Gregoriou
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue Athens 11635 Greece
- Advent Technologies SA, Stadiou Street, Platani Rio Patras 26504 Greece
| | - Christos L Chochos
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue Athens 11635 Greece
- Advent Technologies SA, Stadiou Street, Platani Rio Patras 26504 Greece
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2
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Streu K, Hunsberger S, Patel J, Wan X, Daly CA. Development of a universal method for vibrational analysis of the terminal alkyne C≡C stretch. J Chem Phys 2024; 160:074106. [PMID: 38364010 DOI: 10.1063/5.0185580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/07/2024] [Indexed: 02/18/2024] Open
Abstract
The terminal alkyne C≡C stretch has a large Raman scattering cross section in the "silent" region for biomolecules. This has led to many Raman tag and probe studies using this moiety to study biomolecular systems. A computational investigation of these systems is vital to aid in the interpretation of these results. In this work, we develop a method for computing terminal alkyne vibrational frequencies and isotropic transition polarizabilities that can easily and accurately be applied to any terminal alkyne molecule. We apply the discrete variable representation method to a localized version of the C≡C stretch normal mode. The errors of (1) vibrational localization to the terminal alkyne moiety, (2) anharmonic normal mode isolation, and (3) discretization of the Born-Oppenheimer potential energy surface are quantified and found to be generally small and cancel each other. This results in a method with low error compared to other anharmonic vibrational methods like second-order vibrational perturbation theory and to experiments. Several density functionals are tested using the method, and TPSS-D3, an inexpensive nonempirical density functional with dispersion corrections, is found to perform surprisingly well. Diffuse basis functions are found to be important for the accuracy of computed frequencies. Finally, the computation of vibrational properties like isotropic transition polarizabilities and the universality of the localized normal mode for terminal alkynes are demonstrated.
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Affiliation(s)
- Kristina Streu
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Sara Hunsberger
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Jeanette Patel
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Xiang Wan
- Department of Mathematics and Statistics, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, Illinois 60660, USA
| | - Clyde A Daly
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
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3
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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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4
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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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5
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Abstract
Lipids are essential cellular components forming membranes, serving as energy reserves, and acting as chemical messengers. Dysfunction in lipid metabolism and signaling is associated with a wide range of diseases including cancer and autoimmunity. Heterogeneity in cell behavior including lipid signaling is increasingly recognized as a driver of disease and drug resistance. This diversity in cellular responses as well as the roles of lipids in health and disease drive the need to quantify lipids within single cells. Single-cell lipid assays are challenging due to the small size of cells (∼1 pL) and the large numbers of lipid species present at concentrations spanning orders of magnitude. A growing number of methodologies enable assay of large numbers of lipid analytes, perform high-resolution spatial measurements, or permit highly sensitive lipid assays in single cells. Covered in this review are mass spectrometry, Raman imaging, and fluorescence-based assays including microscopy and microseparations.
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Affiliation(s)
- Ming Yao
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; , ,
| | | | - Nancy L Allbritton
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; , ,
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6
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Romei M, von Krusenstiern EV, Ridings ST, King RN, Fortier JC, McKeon CA, Nichols KM, Charkoudian LK, Londergan CH. Frequency Changes in Terminal Alkynes Provide Strong, Sensitive, and Solvatochromic Raman Probes of Biochemical Environments. J Phys Chem B 2023; 127:85-94. [PMID: 36538691 PMCID: PMC9841980 DOI: 10.1021/acs.jpcb.2c06176] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/19/2022] [Indexed: 12/24/2022]
Abstract
The C≡C stretching frequencies of terminal alkynes appear in the "clear" window of vibrational spectra, so they are attractive and increasingly popular as site-specific probes in complicated biological systems like proteins, cells, and tissues. In this work, we collected infrared (IR) absorption and Raman scattering spectra of model compounds, artificial amino acids, and model proteins that contain terminal alkyne groups, and we used our results to draw conclusions about the signal strength and sensitivity to the local environment of both aliphatic and aromatic terminal alkyne C≡C stretching bands. While the IR bands of alkynyl model compounds displayed surprisingly broad solvatochromism, their absorptions were weak enough that alkynes can be ruled out as effective IR probes. The same solvatochromism was observed in model compounds' Raman spectra, and comparisons to published empirical solvent scales (including a linear regression against four meta-aggregated solvent parameters) suggested that the alkyne C≡C stretching frequency mainly reports on local electronic interactions (i.e., short-range electron donor-acceptor interactions) with solvent molecules and neighboring functional groups. The strong solvatochromism observed here for alkyne stretching bands introduces an important consideration for Raman imaging studies based on these signals. Raman signals for alkynes (especially those that are π-conjugated) can be exceptionally strong and should permit alkynyl Raman signals to function as probes at very low concentrations, as compared to other widely used vibrational probe groups like azides and nitriles. We incorporated homopropargyl glycine into a transmembrane helical peptide via peptide synthesis, and we installed p-ethynylphenylalanine into the interior of the Escherichia coli fatty acid acyl carrier protein using a genetic code expansion technique. The Raman spectra from each of these test systems indicate that alkynyl C≡C bands can act as effective and unique probes of their local biomolecular environments. We provide guidance for the best possible future uses of alkynes as solvatochromic Raman probes, and while empirical explanations of the alkyne solvatochromism are offered, open questions about its physical basis are enunciated.
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Affiliation(s)
- Matthew
G. Romei
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Eliana V. von Krusenstiern
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Stephen T. Ridings
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Renee N. King
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Julia C. Fortier
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Caroline A. McKeon
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Krysta M. Nichols
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Louise K. Charkoudian
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
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7
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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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8
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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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9
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Itoga M, Yamanishi M, Udagawa T, Kobayashi A, Maekawa K, Takemoto Y, Naka H. Iridium-catalyzed α-selective deuteration of alcohols. Chem Sci 2022; 13:8744-8751. [PMID: 35975159 PMCID: PMC9350590 DOI: 10.1039/d2sc01805e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/29/2022] [Indexed: 11/23/2022] Open
Abstract
The development of chemoselective C(sp3)-H deuteration is of particular interest in synthetic chemistry. We herein report the α-selective, iridium(iii)-bipyridonate-catalyzed hydrogen(H)/deuterium(D) isotope exchange of alcohols using deuterium oxide (D2O) as the primary deuterium source. This method enables the direct, chemoselective deuteration of primary and secondary alcohols under basic or neutral conditions without being affected by coordinative functional groups such as imidazole and tetrazole. Successful substrates for deuterium labelling include the pharmaceuticals losartan potassium, rapidosept, guaifenesin, and diprophylline. The deuterated losartan potassium shows higher stability towards the metabolism by CYP2C9 than the protiated analogue. Kinetic and DFT studies indicate that the direct deuteration proceeds through dehydrogenation of alcohol to the carbonyl intermediate, conversion of [IrIII-H] to [IrIII-D] with D2O, and deuteration of the carbonyl intermediate to give the α-deuterated product.
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Affiliation(s)
- Moeko Itoga
- Graduate School of Pharmaceutical Sciences, Kyoto University Kyoto 606-8501 Japan
| | - Masako Yamanishi
- Graduate School of Pharmaceutical Sciences, Kyoto University Kyoto 606-8501 Japan
| | - Taro Udagawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University Yanagido 1-1 Gifu 501-1193 Japan
| | - Ayane Kobayashi
- Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts Kodo, Kyotanabe Kyoto 610-0395 Japan
| | - Keiko Maekawa
- Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts Kodo, Kyotanabe Kyoto 610-0395 Japan
| | - Yoshiji Takemoto
- Graduate School of Pharmaceutical Sciences, Kyoto University Kyoto 606-8501 Japan
| | - Hiroshi Naka
- Graduate School of Pharmaceutical Sciences, Kyoto University Kyoto 606-8501 Japan
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10
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Abstract
As an emerging optical imaging modality, stimulated Raman scattering (SRS) microscopy provides invaluable opportunities for chemical biology studies using its rich chemical information. Through rapid progress over the past decade, the development of Raman probes harnessing the chemical biology toolbox has proven to play a key role in advancing SRS microscopy and expanding biological applications. In this perspective, we first discuss the development of biorthogonal SRS imaging using small tagging of triple bonds or isotopes and highlight their unique advantages for metabolic pathway analysis and microbiology investigations. Potential opportunities for chemical biology studies integrating small tagging with SRS imaging are also proposed. We next summarize the current designs of highly sensitive and super-multiplexed SRS probes, as well as provide future directions and considerations for next-generation functional probe design. These rationally designed SRS probes are envisioned to bridge the gap between SRS microscopy and chemical biology research and should benefit their mutual development.
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Affiliation(s)
- Jiajun Du
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Haomin Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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11
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Bi X, Miao K, Wei L. Alkyne-Tagged Raman Probes for Local Environmental Sensing by Hydrogen-Deuterium Exchange. J Am Chem Soc 2022; 144:8504-8514. [PMID: 35508077 DOI: 10.1021/jacs.2c01991] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alkyne-tagged Raman probes have shown high promise for noninvasive and sensitive visualization of small biomolecules to understand their functional roles in live cells. However, the potential for alkynes to sense cellular environments that goes beyond imaging remains to be further explored. Here, we report a general strategy for Raman imaging-based local environment sensing by hydrogen-deuterium exchange (HDX) of terminal alkynes (termed alkyne-HDX). We first demonstrate, in multiple Raman probes, that deuterations of the alkynyl hydrogens lead to remarkable shifts of alkyne Raman peaks for about 130 cm-1, providing resolvable signals suited for imaging-based analysis with high specificity. Both our analytical derivation and experimental characterizations subsequently establish that HDX kinetics are linearly proportional to both alkyne pKas and environmental pDs. After validating the quantitative nature of this strategy, we apply alkyne-HDX to sensing local chemical and cellular environments. We establish that alkyne-HDX exhibits high sensitivity to various DNA structures and demonstrates the capacity to detect DNA structural changes in situ from UV-induced damage. We further show that this strategy is also applicable to resolve subtle pD variations in live cells. Altogether, our work lays the foundation for utilizing alkyne-HDX strategy to quantitatively sense the local environments for a broad spectrum of applications in complex biological systems.
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Affiliation(s)
- Xiaotian Bi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Kun Miao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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12
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Chan MYT, Anwar A, Lockley WJS. Practical approaches to labelling terminal alkynes with deuterium. J Labelled Comp Radiopharm 2022; 65:101-111. [PMID: 35067956 PMCID: PMC9303397 DOI: 10.1002/jlcr.3963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 11/12/2022]
Abstract
Base catalysed exchange with sodium hydroxide, calcium oxide or N,N,N,N‐tetramethylguanidine in deuterium oxide is a viable procedure for the preparation of terminally deuterated alkynes for those alkynes stable to strong base. The use of silver perchlorate as a catalyst is an alternative practical option when labelling alkynes which are sensitive to base or contain functionalities which would lead to labelling elsewhere in the molecule. Labelling with this catalyst takes place smoothly at ambient temperature in a mixture of N,N‐dimethylformamide and deuterium oxide.
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Affiliation(s)
- Melanie Y. T. Chan
- Department of Chemistry, Faculty of Engineering and Physical Sciences University of Surrey Guildford UK
| | - Arbab Anwar
- Department of Chemistry, Faculty of Engineering and Physical Sciences University of Surrey Guildford UK
| | - William J. S. Lockley
- Department of Chemistry, Faculty of Engineering and Physical Sciences University of Surrey Guildford UK
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