1
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Wu L, Tanwar S, Kaur G, Date S, Goel L, Chatterjee A, McGuiggan P, Barman I. DNA Origami-Engineered Plasmonic Nanoprobes for Targeted Cancer Imaging. ADVANCED FUNCTIONAL MATERIALS 2024; 34:2309929. [PMID: 39131199 PMCID: PMC11309351 DOI: 10.1002/adfm.202309929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Indexed: 08/13/2024]
Abstract
Plasmonic nanomaterials bearing targeting ligands are of great interest for surface-enhanced Raman scattering (SERS)-based bioimaging applications. However, the practical utility of SERS-based imaging strategies has been hindered by the lack of a straightforward method to synthesize highly sensitive SERS-active nanostructures with high yield and efficiency. In this work, leveraging DNA origami principles, we report the first-in-class design of a SERS-based plasmonically coupled nanoprobe for targeted cancer imaging (SPECTRA). The nanoprobe harnesses a cancer cell targeting DNA aptamer sequence and vibrational tag with stretching frequency in the cell-silent Raman window. Through the integration of aptamer sequence specific for DU145 cells, we show the unique capabilities of SPECTRA for targeted imaging of DU145 cells. Our results demonstrate that the scalability, cost-effectiveness, and reproducibility of this method of fabrication of SERS nanoprobes can serve as a versatile platform for creating nanoprobes with broad applications in the fields of cancer biology and biomedical imaging.
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Affiliation(s)
- Lintong Wu
- Department of Mechanical Engineering, Johns Hopkins University, Maryland 21218, USA
| | - Swati Tanwar
- Department of Mechanical Engineering, Johns Hopkins University, Maryland 21218, USA
| | - Gagandeep Kaur
- Department of Mechanical Engineering, Johns Hopkins University, Maryland 21218, USA
| | - Siddhi Date
- Department of Biomedical Engineering, Johns Hopkins University, Maryland 21218, USA
| | - Linika Goel
- Department of Biomedical Engineering, Johns Hopkins University, Maryland 21218, USA
| | - Arnab Chatterjee
- Department of Mechanical Engineering, Johns Hopkins University, Maryland 21218, USA
| | - Patty McGuiggan
- Department of Material Science and Engineering, Johns Hopkins University, Maryland 21218, USA
- Department of Chemistry, Johns Hopkins University, Maryland 21218, USA
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Maryland 21218, USA
- The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Maryland 21205, USA
- Department of Oncology, Johns Hopkins University, Maryland 21231, USA
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2
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Li Y, Sun Y, Shi L. Viewing 3D spatial biology with highly-multiplexed Raman imaging: from spectroscopy to biotechnology. Chem Commun (Camb) 2024. [PMID: 39041798 DOI: 10.1039/d4cc02319f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Understansding complex biological systems requires the simultaneous characterization of a large number of interacting components in their native 3D environment with high spatial resolution. Highly-multiplexed Raman imaging is an emerging general strategy for detecting biomarkers with scalable multiplexity and ultra-sensitivity based on a series of stimulated Raman scattering (SRS) techniques. Here we review recent advances in highly-multiplexed Raman imaging and how they contribute to the technological revolution in 3D spatial biology, focusing on the developmental pathway from spectroscopy study to biotechnology invention. We envision highly-multiplexed Raman imaging is taking off, which will greatly facilitate our understanding in biological and medical research fields.
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Affiliation(s)
- Yingying Li
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Yuchen Sun
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Lixue Shi
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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3
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Fujioka H, Murao Y, Okinaka M, John Spratt S, Shou J, Kawatani M, Kojima R, Tachibana R, Urano Y, Ozeki Y, Kamiya M. Cyano-Hydrol green derivatives: Expanding the 9-cyanopyronin-based resonance Raman vibrational palette. Bioorg Med Chem Lett 2024; 106:129757. [PMID: 38636718 DOI: 10.1016/j.bmcl.2024.129757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
9-cyanopyronin is a promising scaffold that exploits resonance Raman enhancement to enable sensitive, highly multiplexed biological imaging. Here, we developed cyano-Hydrol Green (CN-HG) derivatives as resonance Raman scaffolds to expand the color palette of 9-cyanopyronins. CN-HG derivatives exhibit sufficiently long wavelength absorption to produce strong resonance Raman enhancement for near-infrared (NIR) excitation, and their nitrile peaks are shifted to a lower frequency than those of 9-cyanopyronins. The fluorescence of CN-HG derivatives is strongly quenched due to the lack of the 10th atom, unlike pyronin derivatives, and this enabled us to detect spontaneous Raman spectra with high signal-to-noise ratios. CN-HG derivatives are powerful candidates for high performance vibrational imaging.
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Affiliation(s)
- Hiroyoshi Fujioka
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho. Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Yuta Murao
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho. Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Momoko Okinaka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Spencer John Spratt
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Jingwen Shou
- Department of Electrical Engineering and Information Systems, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Minoru Kawatani
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho. Midori-ku, Yokohama, Kanagawa 226-8501, Japan; Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryosuke Kojima
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryo Tachibana
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasuyuki Ozeki
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan; Department of Electrical Engineering and Information Systems, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Mako Kamiya
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho. Midori-ku, Yokohama, Kanagawa 226-8501, Japan; Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Autonomous Systems Meterialogy (ASMat), Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho. Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
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4
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Huang X, Xue Z, Zhang D, Lee HJ. Pinpointing Fat Molecules: Advances in Coherent Raman Scattering Microscopy for Lipid Metabolism. Anal Chem 2024; 96:7945-7958. [PMID: 38700460 DOI: 10.1021/acs.analchem.4c01398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Affiliation(s)
- Xiangjie Huang
- College of Biomedical Engineering & Instrument Science, and Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China
| | - Zexin Xue
- College of Biomedical Engineering & Instrument Science, and Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China
| | - Delong Zhang
- MOE Frontier Science Center for Brain Science & Brain-Machine Integration, Zhejiang University, Hangzhou 310027, China
- Zhejiang Key Laboratory of Micro-nano Quantum Chips and Quantum Control, and School of Physics, Zhejiang University, Hangzhou 310027, China
| | - Hyeon Jeong Lee
- College of Biomedical Engineering & Instrument Science, and Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China
- MOE Frontier Science Center for Brain Science & Brain-Machine Integration, Zhejiang University, Hangzhou 310027, China
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5
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Chadha RS, Guerrero JA, Wei L, Sanchez LM. Seeing is Believing: Developing Multimodal Metabolic Insights at the Molecular Level. ACS CENTRAL SCIENCE 2024; 10:758-774. [PMID: 38680555 PMCID: PMC11046475 DOI: 10.1021/acscentsci.3c01438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 05/01/2024]
Abstract
This outlook explores how two different molecular imaging approaches might be combined to gain insight into dynamic, subcellular metabolic processes. Specifically, we discuss how matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and stimulated Raman scattering (SRS) microscopy, which have significantly pushed the boundaries of imaging metabolic and metabolomic analyses in their own right, could be combined to create comprehensive molecular images. We first briefly summarize the recent advances for each technique. We then explore how one might overcome the inherent limitations of each individual method, by envisioning orthogonal and interchangeable workflows. Additionally, we delve into the potential benefits of adopting a complementary approach that combines both MSI and SRS spectro-microscopy for informing on specific chemical structures through functional-group-specific targets. Ultimately, by integrating the strengths of both imaging modalities, researchers can achieve a more comprehensive understanding of biological and chemical systems, enabling precise metabolic investigations. This synergistic approach holds substantial promise to expand our toolkit for studying metabolites in complex environments.
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Affiliation(s)
- Rahuljeet S Chadha
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125 United States
| | - Jason A Guerrero
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064 United States
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125 United States
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064 United States
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6
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Kirsh J, Weaver JB, Boxer SG, Kozuch J. Critical Evaluation of Polarizable and Nonpolarizable Force Fields for Proteins Using Experimentally Derived Nitrile Electric Fields. J Am Chem Soc 2024; 146:6983-6991. [PMID: 38415598 PMCID: PMC10941190 DOI: 10.1021/jacs.3c14775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
Molecular dynamics (MD) simulations are frequently carried out for proteins to investigate the role of electrostatics in their biological function. The choice of force field (FF) can significantly alter the MD results, as the simulated local electrostatic interactions lack benchmarking in the absence of appropriate experimental methods. We recently reported that the transition dipole moment (TDM) of the popular nitrile vibrational probe varies linearly with the environmental electric field, overcoming well-known hydrogen bonding (H-bonding) issues for the nitrile frequency and, thus, enabling the unambiguous measurement of electric fields in proteins (J. Am. Chem. Soc. 2022, 144 (17), 7562-7567). Herein, we utilize this new strategy to enable comparisons of experimental and simulated electric fields in protein environments. Specifically, previously determined TDM electric fields exerted onto nitrile-containing o-cyanophenylalanine residues in photoactive yellow protein are compared with MD electric fields from the fixed-charge AMBER FF and the polarizable AMOEBA FF. We observe that the electric field distributions for H-bonding nitriles are substantially affected by the choice of FF. As such, AMBER underestimates electric fields for nitriles experiencing moderate field strengths; in contrast, AMOEBA robustly recapitulates the TDM electric fields. The FF dependence of the electric fields can be partly explained by the presence of additional negative charge density along the nitrile bond axis in AMOEBA, which is due to the inclusion of higher-order multipole parameters; this, in turn, begets more head-on nitrile H-bonds. We conclude by discussing the implications of the FF dependence for the simulation of nitriles and proteins in general.
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Affiliation(s)
- Jacob
M. Kirsh
- Department
of Chemistry, Stanford University, Stanford, California 94305-5012, United
States
| | - Jared Bryce Weaver
- Department
of Chemistry, Stanford University, Stanford, California 94305-5012, United
States
| | - Steven G. Boxer
- Department
of Chemistry, Stanford University, Stanford, California 94305-5012, United
States
| | - Jacek Kozuch
- Experimental
Molecular Biophysics, Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
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7
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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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8
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Zhou L, Feng RR, Zhang W, Gai F. Triple-Bond Vibrations: Emerging Applications in Energy and Biological Sciences. J Phys Chem Lett 2024; 15:187-200. [PMID: 38156972 DOI: 10.1021/acs.jpclett.3c02619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Triple bonds, such as that formed between two carbon atoms (i.e., C≡C) or that formed between one carbon atom and one nitrogen atom (i.e., C≡N), afford unique chemical bonding and hence vibrational characteristics. As such, they are not only frequently used to construct molecules with tailored chemical and/or physical properties but also employed as vibrational probes to provide site-specific chemical and/or physical information at the molecular level. Herein, we offer our perspective on the emerging applications of various triple-bond vibrations in energy and biological sciences with a focus on C≡C and C≡N triple bonds.
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Affiliation(s)
- Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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9
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Bai Y, Camargo CM, Glasauer SMK, Gifford R, Tian X, Longhini AP, Kosik KS. Single-cell mapping of lipid metabolites using an infrared probe in human-derived model systems. Nat Commun 2024; 15:350. [PMID: 38191490 PMCID: PMC10774263 DOI: 10.1038/s41467-023-44675-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024] Open
Abstract
Understanding metabolic heterogeneity is the key to uncovering the underlying mechanisms of metabolic-related diseases. Current metabolic imaging studies suffer from limitations including low resolution and specificity, and the model systems utilized often lack human relevance. Here, we present a single-cell metabolic imaging platform to enable direct imaging of lipid metabolism with high specificity in various human-derived 2D and 3D culture systems. Through the incorporation of an azide-tagged infrared probe, selective detection of newly synthesized lipids in cells and tissue became possible, while simultaneous fluorescence imaging enabled cell-type identification in complex tissues. In proof-of-concept experiments, newly synthesized lipids were directly visualized in human-relevant model systems among different cell types, mutation status, differentiation stages, and over time. We identified upregulated lipid metabolism in progranulin-knockdown human induced pluripotent stem cells and in their differentiated microglia cells. Furthermore, we observed that neurons in brain organoids exhibited a significantly lower lipid metabolism compared to astrocytes.
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Affiliation(s)
- Yeran Bai
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.
- Photothermal Spectroscopy Corp., Santa Barbara, CA, USA.
| | - Carolina M Camargo
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Stella M K Glasauer
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Raymond Gifford
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Xinran Tian
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Andrew P Longhini
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Kenneth S Kosik
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.
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10
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Yamakoshi H, Shibata D, Bando K, Kajimoto S, Kohyama A, Egoshi S, Dodo K, Iwabuchi Y, Sodeoka M, Fujita K, Nakabayashi T. Ratiometric analysis of reversible thia-Michael reactions using nitrile-tagged molecules by Raman microscopy. Chem Commun (Camb) 2023; 59:14563-14566. [PMID: 37986604 DOI: 10.1039/d3cc05015g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Ratiometric Raman analysis of reversible thia-Michael reactions was achieved using α-cyanoacrylic acid (αCNA) derivatives. Among αCNAs, the smallest derivative, ThioRas (molecular weight: 167 g mol-1), and its glutathione adduct were simultaneously detected in various subcellular locations using Raman microscopy.
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Affiliation(s)
- Hiroyuki Yamakoshi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
| | - Daiki Shibata
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
| | - Kazuki Bando
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- National Institute of Advanced Industrial Science and Technology (AIST), 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shinji Kajimoto
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
- JST PREST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Aki Kohyama
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
| | - Syusuke Egoshi
- 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
| | - 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
| | - Yoshiharu Iwabuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, 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
| | - Katsumasa Fujita
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- National Institute of Advanced Industrial Science and Technology (AIST), 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takakazu Nakabayashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
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11
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Tanwar S, Ghaemi B, Raj P, Singh A, Wu L, Yuan Y, Arifin DR, McMahon MT, Bulte JWM, Barman I. A Smart Intracellular Self-Assembling Bioorthogonal Raman Active Nanoprobe for Targeted Tumor Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304164. [PMID: 37715297 PMCID: PMC10700673 DOI: 10.1002/advs.202304164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/21/2023] [Indexed: 09/17/2023]
Abstract
Inspired by the principle of in situ self-assembly, the development of enzyme-activated molecular nanoprobes can have a profound impact on targeted tumor detection. However, despite their intrinsic promise, obtaining an optical readout of enzyme activity with high specificity in native milieu has proven to be challenging. Here, a fundamentally new class of Raman-active self-assembling bioorthogonal enzyme recognition (nanoSABER) probes for targeted tumor imaging is reported. This class of Raman probes presents narrow spectral bands reflecting their vibrational fingerprints and offers an attractive solution for optical imaging at different bio-organization levels. The optical beacon harnesses an enzyme-responsive peptide sequence, unique tumor-penetrating properties, and vibrational tags with stretching frequencies in the cell-silent Raman window. The design of nanoSABER is tailored and engineered to transform into a supramolecular structure exhibiting distinct vibrational signatures in presence of target enzyme, creating a direct causality between enzyme activity and Raman signal. Through the integration of substrate-specific for tumor-associated enzyme legumain, unique capabilities of nanoSABER for imaging enzyme activity at molecular, cellular, and tissue levels in combination with machine learning models are shown. These results demonstrate that the nanoSABER probe may serve as a versatile platform for Raman-based recognition of tumor aggressiveness, drug accumulation, and therapeutic response.
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Affiliation(s)
- Swati Tanwar
- Department of Mechanical EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
| | - Behnaz Ghaemi
- The Russell H. Morgan Department of Radiology and Radiological ScienceThe Johns Hopkins University School of MedicineBaltimoreMD21205USA
- Cellular Imaging Section and Vascular Biology ProgramInstitute for Cell EngineeringThe Johns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Piyush Raj
- Department of Mechanical EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
| | - Aruna Singh
- The Russell H. Morgan Department of Radiology and Radiological ScienceThe Johns Hopkins University School of MedicineBaltimoreMD21205USA
- F.M. Kirby Research Center for Functional Brain ImagingKennedy Krieger Inc.BaltimoreMD21205USA
| | - Lintong Wu
- Department of Mechanical EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
| | - Yue Yuan
- Department of ChemistryUniversity of Science and Technology of China96 Jinzhai RoadHefeiAnhui230026China
| | - Dian R. Arifin
- The Russell H. Morgan Department of Radiology and Radiological ScienceThe Johns Hopkins University School of MedicineBaltimoreMD21205USA
- Cellular Imaging Section and Vascular Biology ProgramInstitute for Cell EngineeringThe Johns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Michael T. McMahon
- The Russell H. Morgan Department of Radiology and Radiological ScienceThe Johns Hopkins University School of MedicineBaltimoreMD21205USA
- F.M. Kirby Research Center for Functional Brain ImagingKennedy Krieger Inc.BaltimoreMD21205USA
| | - Jeff W. M. Bulte
- The Russell H. Morgan Department of Radiology and Radiological ScienceThe Johns Hopkins University School of MedicineBaltimoreMD21205USA
- Cellular Imaging Section and Vascular Biology ProgramInstitute for Cell EngineeringThe Johns Hopkins University School of MedicineBaltimoreMD21205USA
- F.M. Kirby Research Center for Functional Brain ImagingKennedy Krieger Inc.BaltimoreMD21205USA
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
- Department of Chemical & Biomolecular EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
- Department of OncologyJohns Hopkins UniversityBaltimoreMD21231USA
| | - Ishan Barman
- Department of Mechanical EngineeringJohns Hopkins UniversityBaltimoreMD21218USA
- The Russell H. Morgan Department of Radiology and Radiological ScienceThe Johns Hopkins University School of MedicineBaltimoreMD21205USA
- Department of OncologyJohns Hopkins UniversityBaltimoreMD21231USA
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12
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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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13
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Wang H, Lee D, Cao Y, Bi X, Du J, Miao K, Wei L. Bond-selective fluorescence imaging with single-molecule sensitivity. NATURE PHOTONICS 2023; 17:846-855. [PMID: 38162388 PMCID: PMC10756635 DOI: 10.1038/s41566-023-01243-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/25/2023] [Indexed: 01/03/2024]
Abstract
Bioimaging harnessing optical contrasts and chemical specificity is of vital importance in probing complex biology. Vibrational spectroscopy based on mid-infrared (mid-IR) excitation can reveal rich chemical information about molecular distributions. However, its full potential for bioimaging is hindered by the achievable sensitivity. Here, we report bond selective fluorescence-detected infrared-excited (BonFIRE) spectral microscopy. BonFIRE employs two-photon excitation in the mid-IR and near-IR to upconvert vibrational excitations to electronic states for fluorescence detection, thus encoding vibrational information into fluorescence. The system utilizes tuneable narrowband picosecond pulses to ensure high sensitivity, biocompatibility, and robustness for bond-selective biological interrogations over a wide spectrum of reporter molecules. We demonstrate BonFIRE spectral imaging in both fingerprint and cell-silent spectroscopic windows with single-molecule sensitivity for common fluorescent dyes. We then demonstrate BonFIRE imaging on various intracellular targets in fixed and live cells, neurons, and tissues, with promises for further vibrational multiplexing. For dynamic bioanalysis in living systems, we implement a high-frequency modulation scheme and demonstrate time-lapse BonFIRE microscopy of live HeLa cells. We expect BonFIRE to expand the bioimaging toolbox by providing a new level of bond-specific vibrational information and facilitate functional imaging and sensing for biological investigations.
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Affiliation(s)
- Haomin Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Dongkwan Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Yulu Cao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Xiaotian Bi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Jiajun Du
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Kun Miao
- 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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14
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Du J, Tao X, Begušić T, Wei L. Computational Design of Molecular Probes for Electronic Preresonance Raman Scattering Microscopy. J Phys Chem B 2023; 127:4979-4988. [PMID: 37226966 PMCID: PMC10676804 DOI: 10.1021/acs.jpcb.3c00699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Recently developed electronic preresonance stimulated Raman scattering (epr-SRS) microscopy, in which the Raman signal of a dye is significantly boosted by setting the incident laser frequency near the electronic excitation energy, has pushed the sensitivity of SRS microscopy close to that offered by confocal fluorescence microscopy. Prominently, the maintained narrow line-width of epr-SRS also offers high multiplexity that breaks the "color barrier" in optical microscopy. However, detailed understanding of the fundamental mechanism in these epr-SRS dyes still remains elusive. Here, we combine experiments with theoretical modeling to investigate the structure-function relationship, aiming to facilitate the design of new probes and expanding epr-SRS palettes. Our ab initio approach employing the displaced harmonic oscillator (DHO) model provides a consistent agreement between simulated and experimental SRS intensities of various triple-bond bearing epr-SRS probes with distinct scaffolds. We further review two popular approximate expressions for epr-SRS, namely the short-time and Albrecht A-term equations, and compare them to the DHO model. Overall, the theory allows us to illustrate how the observed intensity differences between molecular scaffolds stem from the coupling strength between the electronic excitation and the targeted vibrational mode, leading to a general design strategy for highly sensitive next-generation vibrational imaging probes.
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Affiliation(s)
- Jiajun Du
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Xuecheng Tao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Tomislav Begušić
- 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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15
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Zhang Y, Zhou Y, Fang W, Zhu H, Ye C, Zhang D, Lee HJ. Spatial sterol metabolism unveiled by stimulated Raman imaging. Front Chem 2023; 11:1166313. [PMID: 37065823 PMCID: PMC10090450 DOI: 10.3389/fchem.2023.1166313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Graphical AbstractHigh-resolution stimulated Raman scattering (SRS) imaging of a genetically engineered model (GEM) enables metabolite imaging in a yeast model and uncovers an unexpected regulatory mechanism of sterol metabolism, providing new insights underpinning the distributional and functional importance of sterol in cells. SRS-GEM demonstrates a promising platform to explore unknown metabolic mechanisms beyond the reach of conventional approaches.
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Affiliation(s)
- Yongqing Zhang
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Interdisciplinary Centre for Quantum Information, Zhejiang University, Hangzhou, China
| | - Yihui Zhou
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Wen Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Hanlin Zhu
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Interdisciplinary Centre for Quantum Information, Zhejiang University, Hangzhou, China
| | - Cunqi Ye
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- *Correspondence: Cunqi Ye, ; Delong Zhang, ; Hyeon Jeong Lee,
| | - Delong Zhang
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Interdisciplinary Centre for Quantum Information, Zhejiang University, Hangzhou, China
- *Correspondence: Cunqi Ye, ; Delong Zhang, ; Hyeon Jeong Lee,
| | - Hyeon Jeong Lee
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
- *Correspondence: Cunqi Ye, ; Delong Zhang, ; Hyeon Jeong Lee,
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