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Munan S, Chang YT, Samanta A. Chronological development of functional fluorophores for bio-imaging. Chem Commun (Camb) 2024; 60:501-521. [PMID: 38095135 DOI: 10.1039/d3cc04895k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Functional fluorophores represent an emerging research field, distinguished by their diverse applications, especially in sensing and cellular imaging. After the discovery of quinine sulfate and subsequent elucidation of the fluorescence mechanism by Sir George Stokes, research in the field of fluorescence gained momentum. Over the past few decades, advancements in sophisticated instruments, including super-resolution microscopy, have further promoted cellular imaging using traditional fluorophores. These advancements include deciphering sensing mechanisms via photochemical reactions and scrutinizing the applications of fluorescent probes that specifically target organelles. This approach elucidates molecular interactions with biomolecules. Despite the abundance of literature illustrating different classes of probe development, a concise summary of newly developed fluorophores remains inadequate. In this review, we systematically summarize the chronological discovery of traditional fluorophores along with new fluorophores. We briefly discuss traditional fluorophores ranging from visible to near-infrared (NIR) in the context of cellular imaging and in vivo imaging. Furthermore, we explore ten new core fluorophores developed between 2007 and 2022, which exhibit advanced optical properties, providing new insights into bioimaging. We illustrate the utilization of new fluorophores in cellular imaging of biomolecules, such as reactive oxygen species (ROS), reactive nitrogen species (RNS), and proteins and microenvironments, especially pH and viscosity. Few of the fluorescent probes provided new insights into disease progression. Furthermore, we speculate on the potential prospects and significant challenges of existing fluorophores and their potential biomedical research applications. By addressing these aspects, we intend to illuminate the compelling advancements in fluorescent probe development and their potential influence across various fields.
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Affiliation(s)
- Subrata Munan
- Molecular Sensors and Therapeutics (MST) Research Laboratory, Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi NCR, NH 91, Tehsil Dadri 201314, Uttar Pradesh, India.
| | - Young-Tae Chang
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
| | - Animesh Samanta
- Molecular Sensors and Therapeutics (MST) Research Laboratory, Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi NCR, NH 91, Tehsil Dadri 201314, Uttar Pradesh, India.
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2
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Xu ST, Yang C, Yan XP. Organic Mass Cytometry Discriminating Cycle Stages of Single Cells with Small Molecular Indicators. Anal Chem 2023; 95:2312-2320. [PMID: 36651064 DOI: 10.1021/acs.analchem.2c04165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cell cycle is a significant factor toward cellular heterogeneity, so cell cycle discrimination is a precise measurement on the top of single-cell analysis. Single-cell analysis based on organic mass spectrometry has received great attention for its unique ability to profile single-cell metabolome, but the influence of cell cycle on cellular metabolome heterogeneity has been overlooked until now due to the lack of a compatible cell cycle discrimination method. Here, we report a robust protocol based on the combination of three small molecular indicators, consisting of two small molecular labels (Hoechst and docetaxel) and one cellular endogenous compound [phosphocholine (34:1)], to discriminate single cells at different cycle stages in real time by organic mass cytometry. More than 6000 HeLa cells were acquired by an improved organic mass cytometry system to build a cell cycle differentiation model. The model successfully discriminated single HeLa cells, SCC7, and Hep G2 cells, at G0/G1, S, and G2/M stages with larger than 85% sensitivity and larger than 89% specificity. Along with cell cycle discrimination, obvious heterogeneity of amino acids, nucleotides, energy metabolic intermediates, and phospholipids was observed among single cells at different cycle stages by this protocol, further demonstrating the necessity of cell cycle discrimination for cellular metabolome heterogeneity research and the potential of more endogenous small molecular compounds for cell cycle discrimination.
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Affiliation(s)
- Shu-Ting Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Cheng Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiu-Ping Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China
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Wang T, Shah I, Yang Z, Yin W, Zhang S, Yang Y, Yin P, Ma H. Incorporating Thiourea into Fluorescent Probes: A Reliable Strategy for Mitochondrion-Targeted Imaging and Superoxide Anion Tracking in Living Cells. Anal Chem 2020; 92:2824-2829. [PMID: 31957439 DOI: 10.1021/acs.analchem.9b05320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Three aggregation-induced emission active fluorescent compounds, TPA-Pyr-Octane, TPA-Pyr-Br, and TPA-Pyr-Thiourea (TPA = triphenylamine pyridinium), are synthesized; their tiny differences in chemical structures result in a huge difference in cell-imaging applications. Especially, incorporating thiourea into fluorescent probes is found as a reliable strategy for mitochondrion-targeted imaging and superoxide anion tracking in living cells, which is possibly due to the presence of hydrogen bonding between thiourea and mitochondrion proteins. This finding is very useful for the design of biosensors and delivery carriers in disease treatment.
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Affiliation(s)
- Tao Wang
- Key Laboratory of Eco-Environment-Related Polymer Materials Ministry of Education, College of Chemistry and Chemical Engineering , Northwest Normal University , Lanzhou 730070 , China
| | - Imran Shah
- Key Laboratory of Eco-Environment-Related Polymer Materials Ministry of Education, College of Chemistry and Chemical Engineering , Northwest Normal University , Lanzhou 730070 , China
| | - Zengming Yang
- Key Laboratory of Eco-Environment-Related Polymer Materials Ministry of Education, College of Chemistry and Chemical Engineering , Northwest Normal University , Lanzhou 730070 , China
| | - Weidong Yin
- Key Laboratory of Eco-Environment-Related Polymer Materials Ministry of Education, College of Chemistry and Chemical Engineering , Northwest Normal University , Lanzhou 730070 , China
| | - Shaoxiong Zhang
- Key Laboratory of Eco-Environment-Related Polymer Materials Ministry of Education, College of Chemistry and Chemical Engineering , Northwest Normal University , Lanzhou 730070 , China
| | - Yuan Yang
- Key Laboratory of Eco-Environment-Related Polymer Materials Ministry of Education, College of Chemistry and Chemical Engineering , Northwest Normal University , Lanzhou 730070 , China
| | - Pei Yin
- Key Laboratory of Eco-Environment-Related Polymer Materials Ministry of Education, College of Chemistry and Chemical Engineering , Northwest Normal University , Lanzhou 730070 , China
| | - Hengchang Ma
- Key Laboratory of Eco-Environment-Related Polymer Materials Ministry of Education, College of Chemistry and Chemical Engineering , Northwest Normal University , Lanzhou 730070 , China
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Choi YK, Kim JJ, Chang YT. Holding-Oriented versus Gating-Oriented Live-Cell Distinction: Highlighting the Role of Transporters in Cell Imaging Probe Development. Acc Chem Res 2019; 52:3097-3107. [PMID: 31265234 DOI: 10.1021/acs.accounts.9b00253] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Small molecule imaging probes are powerful tools to understand complex biological systems. The mainstreams of imaging probe developments have been focused on the target holding of the probes; the holding targets are often cell-type-specific biomarkers. This type of the probe mechanism can be designated as holding-oriented live-cell distinction (HOLD). Our group has worked on the development of cell-type-selective probes using a diversity-oriented fluorescence library approach (DOFLA), where unbiased phenotypic screening is employed using fluorescent library compounds. Through the conventional target identification methods such as an affinity-based analysis, we elucidated that some of the probe mechanisms are HOLD. However, we also realized that sometimes there is no specific holding target for probes or the holding targets are ubiquitous. The observation led us to test an alternative mechanism of cell-type-specific probes as gating-oriented live-cell distinction (GOLD). We started to examine the gating mechanism of probes, which is mainly based on transporters but which does not necessarily require probe holding to cellular targets. Transporters can control the in and out movement of various nutrients and chemicals. Different expression levels of transporters in various cell types could provide the molecular mechanism of differential staining of cells by regulating the intracellular accumulation of a certain specific probe. A number of GOLD probes have been developed by modifying or mimicking endogenous substrates of transporters such as inorganic ions, glucose, amino acids, or neurotransmitters, utilizing broad substrate specificity of transporters. The radiolabeled or fluorophore-conjugated substrate mimetics have been widely used for live cell distinction and various applications such as disease-related cell or tissue imaging. In humans, there are about 400 solute carrier (SLC) transporters and 50 ATP-binding cassette (ABC) transporters. Since some transporters have broad substrate specificity, they can transport not only derivatives of endogenous natural substrates but also totally synthetic diverse imaging probes, such as DOFLA probes. Without preconsidering the structure of endogenous substrates, we recently demonstrated a series of live-cell imaging probes and elucidated their molecular mechanism as a gating one, either by SLC or ABC transporters. Transporter inhibitor panel and CRISPR-based transporter libraries could provide a systematic gating target elucidation platform. Considering the generality of DOFLA and the CRISPR-based genomic tool for transporter systems (>450 in humans), the GOLD approach will offer new insight and promise for unprecedented levels of novel cell imaging probe development.
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Affiliation(s)
- Yun-Kyu Choi
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Jong-Jin Kim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 37673, Republic of Korea
| | - Young-Tae Chang
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 37673, Republic of Korea
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Ghosh A, Seth SK, Purkayastha P. A Pyrene-Benzothiazole Probe that is Ultrasensitive to the Environment Polarity and Its Own Characteristics. ChemistrySelect 2018. [DOI: 10.1002/slct.201801943] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ashutosh Ghosh
- Department of Chemical Sciences; Indian Institute of Science Education and Research (IISER) Kolkata; Mohanpur 741246, WB India
| | - Sourav Kanti Seth
- Department of Chemical Sciences; Indian Institute of Science Education and Research (IISER) Kolkata; Mohanpur 741246, WB India
| | - Pradipta Purkayastha
- Department of Chemical Sciences; Indian Institute of Science Education and Research (IISER) Kolkata; Mohanpur 741246, WB India
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Wang L, Wu B, Li W, Wang S, Li Z, Li M, Pan D, Wu M. Amphiphilic Graphene Quantum Dots as Self-Targeted Fluorescence Probes for Cell Nucleus Imaging. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201700191] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Liang Wang
- Institute of Nanochemistry and Nanobiology; School of Environmental and Chemical Engineering; Shanghai University; Shanghai 200444 P. R. China
| | - Bin Wu
- Research Center for Translational Medicine at East Hospital; School of Life Science and Technology; Tongji University; Shanghai 200092 P. R. China
| | - Weitao Li
- Institute of Nanochemistry and Nanobiology; School of Environmental and Chemical Engineering; Shanghai University; Shanghai 200444 P. R. China
| | - Shilong Wang
- Research Center for Translational Medicine at East Hospital; School of Life Science and Technology; Tongji University; Shanghai 200092 P. R. China
| | - Zhen Li
- Shanghai Institute of Applied Radiation; Shanghai University; Shanghai 200444 P. R. China
| | - Ming Li
- Institute of Nanochemistry and Nanobiology; School of Environmental and Chemical Engineering; Shanghai University; Shanghai 200444 P. R. China
| | - Dengyu Pan
- Department of Chemical Engineering; School of Environmental and Chemical Engineering; Shanghai University; Shanghai 200444 P. R. China
| | - Minghong Wu
- Shanghai Institute of Applied Radiation; Shanghai University; Shanghai 200444 P. R. China
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Alamudi SH, Chang YT. Advances in the design of cell-permeable fluorescent probes for applications in live cell imaging. Chem Commun (Camb) 2018; 54:13641-13653. [DOI: 10.1039/c8cc08107g] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Advances in the design strategy of cell-permeable small fluorescent probes are discussed. Their applications in imaging specific cell types and intracellular bioanalytes, as well as the cellular environment in live conditions, are presented.
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Affiliation(s)
- Samira Husen Alamudi
- Singapore Bioimaging Consortium
- Agency for Science, Technology and Research (A*STAR)
- Singapore
- Singapore
| | - Young-Tae Chang
- Singapore Bioimaging Consortium
- Agency for Science, Technology and Research (A*STAR)
- Singapore
- Singapore
- Department of Chemistry
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Wang KN, Chao XJ, Liu B, Zhou DJ, He L, Zheng XH, Cao Q, Tan CP, Zhang C, Mao ZW. Red fluorescent probes for real-time imaging of the cell cycle by dynamic monitoring of the nucleolus and chromosome. Chem Commun (Camb) 2018; 54:2635-2638. [DOI: 10.1039/c8cc00256h] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Two cationic molecular rotors, 1 and 2, capable of real-time cell-cycle imaging by specifically dynamic monitoring of nucleolus and chromosome changes were developed.
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Laishram R, Maitra U. Rapid Sensing of Specific Drugs at Sub-Ppb Levels by Using a Hybrid Organic-Inorganic Photoluminescent Soft Material. ASIAN J ORG CHEM 2017. [DOI: 10.1002/ajoc.201700156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Raju Laishram
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Uday Maitra
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560012 India
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10
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Development of background-free tame fluorescent probes for intracellular live cell imaging. Nat Commun 2016; 7:11964. [PMID: 27321135 PMCID: PMC4915154 DOI: 10.1038/ncomms11964] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 05/16/2016] [Indexed: 01/11/2023] Open
Abstract
Fluorescence labelling of an intracellular biomolecule in native living cells is a powerful strategy to achieve in-depth understanding of the biomolecule's roles and functions. Besides being nontoxic and specific, desirable labelling probes should be highly cell permeable without nonspecific interactions with other cellular components to warrant high signal-to-noise ratio. While it is critical, rational design for such probes is tricky. Here we report the first predictive model for cell permeable background-free probe development through optimized lipophilicity, water solubility and charged van der Waals surface area. The model was developed by utilizing high-throughput screening in combination with cheminformatics. We demonstrate its reliability by developing CO-1 and AzG-1, a cyclooctyne- and azide-containing BODIPY probe, respectively, which specifically label intracellular target organelles and engineered proteins with minimum background. The results provide an efficient strategy for development of background-free probes, referred to as ‘tame' probes, and novel tools for live cell intracellular imaging. The success of a fluorescent dye as a molecular probe to monitor the intracellular activity of biomolecules depends on its physicochemical characteristics. Here, the authors use a predictive model to identify key features that allow them to design cell permeable, background-free fluorescent probes.
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