1
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Jain N, Sonawane PM, Roychaudhury A, Park SJ, An J, Kim CH, Nimse SB, Churchill DG. An indole-based near-infrared fluorescent "Turn-On" probe for H 2O 2: Selective detection and ultrasensitive imaging of zebrafish gallbladder. Talanta 2024; 269:125459. [PMID: 38011812 DOI: 10.1016/j.talanta.2023.125459] [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: 07/06/2023] [Revised: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023]
Abstract
Fluorescent probes play essential roles in medical imaging, where the researchers can select one of many molecules to use to help monitor the status of living systems under investigation. To date, a few scaffolds that allow the in vivo detection of H2O2 are available only. Herein, we provide a highly sensitive and selective near-infrared fluorescent probe that detects H2O2 based on the ICT sensing mechanism. We report the first indole-incorporated fluorescent probe Indo-H2O2 that allows H2O2 detection with a LOD of 25.2 nM featuring a boronate group conjugated to an indole scaffold; the boronate cleaves upon reaction with H2O2. A 5-membered malononitrile derivative was incorporated; Indo-H2O2 has near-infrared (NIR) properties and the reaction time is low (∼25 min) compared to other related probes. Indo-H2O2 was successfully employed in both endogenous and exogenous imaging trials of H2O2 in living cells. Indo-H2O2 also allows the real-time monitoring of H2O2in vivo. It preferentially accesses the gallbladder of zebrafish. Our findings support Indo-H2O2 as a highly sensitive fluorescent NIR probe for detecting H2O2, and an idea to incorporate a central indole unit in future fluorescent probe designs.
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Affiliation(s)
- Neha Jain
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Prasad M Sonawane
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | | | - Su Jeong Park
- Institute of Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Jongkeol An
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Satish Balasaheb Nimse
- Institute of Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon, 24252, Republic of Korea.
| | - David G Churchill
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; KAIST Institute for Health Science and Technology (KIHST) (Therapeutic Bioengineering Section), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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2
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Meng T, Ma W, Fan M, Tang W, Duan X. Enhancing the Contrast of Tumor Imaging for Image-Guided Surgery Using a Tumor-Targeting Probiotic with the Continuous Expression of a Biomarker. Anal Chem 2022; 94:10109-10117. [PMID: 35802615 DOI: 10.1021/acs.analchem.2c01200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tumor recurrence commonly results from tumor-positive resection margins and metastatic lesions. The complete removal of tumor-positive margins is particularly essential in clinics. Thus, we designed a strategy based on Escherichia coli Nissle 1917 (EcN) nitroreductase (NTR) with a polyethylene glycol (PEG) polymer coating (PC-EcN-NTR) to specifically target and colonize in tumors for high-contrast tumor imaging by providing a large amount of NTR as biomarkers in situ. NTR is a favorable biomarker for tumor detection and imaging. The nfsB-encoding plasmid with a 16S promoter was transfected into EcN for the continuous and stable expression of NTR (E. coli. NfsB). PC-EcN-NTR can accumulate and proliferate for a long time in tumors to substantially express NTR. When the NTR-activated fluorescence (FL) probe was sprayed on the tumor, the tumor region showed fluorescence signals within 5 min. Compared to the tumor without colonization with bacteria, the PC-EcN-NTR-colonized tumors displayed 3.15× enhanced fluorescence signals. Furthermore, the fluorescence signals of the whole tumor can last at least 3 h, which is suitable for a long and meticulous surgical operation. More importantly, in the PC-EcN-NTR-harboring tumor, obvious FL appeared even at the very edge (approximately 200 μm away from the edge) of the tumor tissue. A TCF-Based near-infrared-II fluorescent probe (probe 2) was designed and synthesized. Results similar to those of probe 1 were observed when probe 2 was used for in vivo tumor imaging, which further proved the generality of the enhancing ability of the tumor-targeting probiotic. This strategy will hopefully guide the surgical resection of tumors via monitoring intense NTR activity. It may spur the use of tumor-targeting probiotic and enzyme-activated fluorescent probes for the processes of tumor diagnosis and image-guided surgery.
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Affiliation(s)
- Tianjiao Meng
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang'an Street, Xi'an, Shaanxi 710119, People's Republic of China
| | - Wenbo Ma
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang'an Street, Xi'an, Shaanxi 710119, People's Republic of China
| | - Mengyue Fan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang'an Street, Xi'an, Shaanxi 710119, People's Republic of China
| | - Wei Tang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang'an Street, Xi'an, Shaanxi 710119, People's Republic of China
| | - Xinrui Duan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang'an Street, Xi'an, Shaanxi 710119, People's Republic of China
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3
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Wu Y, Deng X, Ye L, Zhang W, Xu H, Zhang B. A TCF-Based Carbon Monoxide NIR-Probe without the Interference of BSA and Its Application in Living Cells. Molecules 2022; 27:4155. [PMID: 35807401 PMCID: PMC9268636 DOI: 10.3390/molecules27134155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
As toxic gaseous pollution, carbon monoxide (CO) plays an essential role in many pathological and physiological processes, well-known as the third gasotransmitter. Owning to the reducibility of CO, the Pd0-mediated Tsuji-Trost reaction has drawn much attention in CO detection in vitro and in vivo, using allyl ester and allyl ether caged fluorophores as probes and PdCl2 as co-probes. Because of its higher decaging reactivity than allyl ether in the Pd0-mediated Tsuji-Trost reaction, the allyl ester group is more popular in CO probe design. However, during the application of allyl ester caged probes, it was found that bovine serum albumin (BSA) in the fetal bovine serum (FBS), an irreplaceable nutrient in cell culture media, could hydrolyze the allyl ester bond, and thus give erroneous imaging results. In this work, dicyanomethylenedihydrofuran (TCF) and dicyanoisophorone (DCI) were selected as electron acceptors for constructing near-infrared-emission fluorophores with electron donor phenolic OH. An allyl ester and allyl ether group were installed onto TCF-OH and DCI-OH, constructing four potential CO fluorescent probes, TCF-ester, TCF-ether, DCI-ester, and DCI-ether. Our data revealed that ester bonds of TCF-ester and DCI-ester could completely hydrolyze in 20 min, but ether bonds in TCF-ether and DCI-ether tolerate the hydrolysis of BSA and no released fluorescence was observed even up to 2 h. Moreover, passing through the screen, it was concluded that TCF-ether is superior to DCI-ether due to its higher reactivity in a Pd0-mediated Tsuji-Trost reaction. Also, the large stokes shift of TCF-OH, absorption and emission at 408 nm and 618 nm respectively, make TCF-ether desirable for fluorescent imaging because of differentiating signals from the excitation light source. Lastly, TCF-ether has been successfully applied to the detection of CO in H9C2 cells.
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Affiliation(s)
- Yingxu Wu
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China; (Y.W.); (X.D.)
| | - Xiaojing Deng
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China; (Y.W.); (X.D.)
| | - Lan Ye
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian 116044, China;
| | - Wei Zhang
- Department of Spine Surgery, The Second Hospital of Dalian Medical University, Dalian 116023, China;
| | - Hu Xu
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian 116044, China;
| | - Boyu Zhang
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China; (Y.W.); (X.D.)
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4
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Wang Z, Xing B. Small-molecule fluorescent probes: big future for specific bacterial labeling and infection detection. Chem Commun (Camb) 2021; 58:155-170. [PMID: 34882159 DOI: 10.1039/d1cc05531c] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial infections remain a global healthcare problem that is particularly attributed to the spread of antibiotic resistance and the evolving pathogenicity. Accurate and swift approaches for infection diagnosis are urgently needed to facilitate antibiotic stewardship and effective medical treatment. Direct optical imaging for specific bacterial labeling and infection detection offers an attractive prospect of precisely monitoring the infectious disease status and therapeutic response in real time. This feature article focuses on the recent advances of small-molecule probes developed for fluorescent imaging of bacteria and infection, which covers the probe design, responsive mechanisms and representative applications. In addition, the perspective and challenges to advance small-molecule fluorescent probes in the field of rapid drug-resistant bacterial detection and clinical diagnosis of bacterial infections are discussed. We envision that the continuous advancement and clinical translations of such a technique will have a strong impact on future anti-infective medicine.
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Affiliation(s)
- Zhimin Wang
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Bengang Xing
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, 637371, Singapore. .,School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore, 637459, Singapore
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5
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Liu T, Wang Y, Feng L, Tian X, Cui J, Yu Z, Wang C, Zhang B, James TD, Ma X. 2D Strategy for the Construction of an Enzyme-Activated NIR Fluorophore Suitable for the Visual Sensing and Profiling of Homologous Nitroreductases from Various Bacterial Species. ACS Sens 2021; 6:3348-3356. [PMID: 34469146 PMCID: PMC8477384 DOI: 10.1021/acssensors.1c01216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022]
Abstract
Nitroreductases (NTRs) mediate the reduction of nitroaromatic compounds to the corresponding nitrite, hydroxylamine, or amino derivatives. The activity of NTRs in bacteria facilitates the metabolic activation and antibacterial activity of 5-nitroimidazoles. Therefore, NTR activity correlates with the drug susceptibility and resistance of pathogenic bacteria. As such, it is important to develop a rapid and visual assay for the real-time sensing of bacterial NTRs for the evaluation and development of antibiotics. Herein, an activatable near-infrared fluorescent probe (HC-NO2) derived from a hemicyanine fluorophore was designed and developed based on two evaluation factors, including the calculated partition coefficient (Clog P) and fluorescence wavelength. Using HC-NO2 as the special substrate of NTRs, NTR activity can be assayed efficiently, and then, bacteria can be imaged based on the detection of NTRs. More importantly, a sensitive in-gel assay using HC-NO2 has been developed to selectively identify NTRs and sensitively determine NTR activity. Using the in-gel assay, NTRs from various bacterial species have been profiled visually from the "fluorescence fingerprints", which facilitates the rapid identification of NTRs from bacterial lysates. Thus, various homologous NTRs were identified from three metronidazole-susceptible bacterial species as well as seven unsusceptible species, which were confirmed by the whole-genome sequence. As such, the evaluation of NTRs from different bacterial species should help improve the rational usage of 5-nitroimidazole drugs as antibiotics.
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Affiliation(s)
- Tao Liu
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
- State
Key Laboratory of Fine Chemicals, Dalian
University of Technology, Dalian 116024, China
| | - Yifei Wang
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Lei Feng
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Xiangge Tian
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Jingnan Cui
- State
Key Laboratory of Fine Chemicals, Dalian
University of Technology, Dalian 116024, China
| | - Zhenlong Yu
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Chao Wang
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Baojing Zhang
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Tony D. James
- Department
of Chemistry, University of Bath, Bath BA2 7AY, U.K.
- School
of Chemistry and Chemical Engineering, Henan
Normal University, Xinxiang 453007, China
| | - Xiaochi Ma
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
- Jiangsu
Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
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6
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Huang Y, Chen W, Chung J, Yin J, Yoon J. Recent progress in fluorescent probes for bacteria. Chem Soc Rev 2021; 50:7725-7744. [PMID: 34013918 DOI: 10.1039/d0cs01340d] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Food fermentation, antibiotics, and pollutant degradation are closely related to bacteria. Bacteria play an irreplaceable role in life. However, some bacteria seriously threaten human health and cause large-scale infectious diseases. Therefore, there is a pressing need to develop strategies to accurately monitor bacteria. Technology based on molecular probes and fluorescence imaging is noninvasive, results in little damage, and has high specificity and sensitivity, so it has been widely applied in the detection of bacteria. In this review, we summarize the recent progress in bacterial detection using fluorescence. In particular, we generalize the mechanisms commonly used to design organic fluorescent probes for detecting and imaging bacteria. Moreover, a perspective regarding fluorescent probes for bacterial detection is discussed.
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Affiliation(s)
- Yurou Huang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of education, Hubei International Scientific and technological cooperation Base of Pesticide and Green Synthesis, International Joint research center for Intelligent Biosensing Technology and Health, College of chemistry, Central China Normal University, Wuhan 430079, P. R. China and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan 430062, P. R. China
| | - Weijie Chen
- Key Laboratory of Pesticide and Chemical Biology, Ministry of education, Hubei International Scientific and technological cooperation Base of Pesticide and Green Synthesis, International Joint research center for Intelligent Biosensing Technology and Health, College of chemistry, Central China Normal University, Wuhan 430079, P. R. China and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan 430062, P. R. China
| | - Jeewon Chung
- Department of Chemistry and Nano Science, Ewha Womans University, 11-1 Daehyon-Dong, Sodaemun-Ku, Seoul 120-750, Korea.
| | - Jun Yin
- Key Laboratory of Pesticide and Chemical Biology, Ministry of education, Hubei International Scientific and technological cooperation Base of Pesticide and Green Synthesis, International Joint research center for Intelligent Biosensing Technology and Health, College of chemistry, Central China Normal University, Wuhan 430079, P. R. China and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan 430062, P. R. China
| | - Juyoung Yoon
- Department of Chemistry and Nano Science, Ewha Womans University, 11-1 Daehyon-Dong, Sodaemun-Ku, Seoul 120-750, Korea.
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7
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Hira J, Uddin MJ, Haugland MM, Lentz CS. From Differential Stains to Next Generation Physiology: Chemical Probes to Visualize Bacterial Cell Structure and Physiology. Molecules 2020; 25:E4949. [PMID: 33114655 PMCID: PMC7663024 DOI: 10.3390/molecules25214949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022] Open
Abstract
Chemical probes have been instrumental in microbiology since its birth as a discipline in the 19th century when chemical dyes were used to visualize structural features of bacterial cells for the first time. In this review article we will illustrate the evolving design of chemical probes in modern chemical biology and their diverse applications in bacterial imaging and phenotypic analysis. We will introduce and discuss a variety of different probe types including fluorogenic substrates and activity-based probes that visualize metabolic and specific enzyme activities, metabolic labeling strategies to visualize structural features of bacterial cells, antibiotic-based probes as well as fluorescent conjugates to probe biomolecular uptake pathways.
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Affiliation(s)
- Jonathan Hira
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Md. Jalal Uddin
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Marius M. Haugland
- Department of Chemistry and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway;
| | - Christian S. Lentz
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
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8
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Yang X, Zhou J, Li Y, Yan M, Cui Y, Sun G. A reaction-based sensing scheme for volatile organic amine reagents with the chromophoric-fluorogenic dual mode. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 240:118539. [PMID: 32590310 DOI: 10.1016/j.saa.2020.118539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/20/2020] [Accepted: 05/24/2020] [Indexed: 05/24/2023]
Abstract
In this study, we present the classical Michael's addition reaction-based sensing scheme for volatile organic amine reagents such as ethylenediamine, N, N-dimethylethylenediamine and diethylenetriamine using a near-infrared fluorescent dye TCF1. Obvious spectral changes in the UV-vis absorption and fluorescence spectra of TCF1 were observed upon addition of these amine reagents with an effective catalyst DBU, resulting in significant and fast color changes detectable by the naked-eye. TCF1 showed an efficient response to these amine reagents with a low detection limit, especially for diethylenetriamine. NMR and MS spectral analysis proved that the mechanism of the detection was based on the classical Michael addition, which was also verified by the theoretical calculations. In addition, a portable test paper incorporated with TCF1 had also successfully realized the detection of a low concentration of these amine reagents.
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Affiliation(s)
- Xiaofeng Yang
- School of Chemistry and Chemical Engineering, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, China.
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, China
| | - Yexin Li
- School of Chemistry and Chemical Engineering, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, China
| | - Mei Yan
- School of Chemistry and Chemical Engineering, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, China
| | - Yu Cui
- School of Chemistry and Chemical Engineering, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, China
| | - Guoxin Sun
- School of Chemistry and Chemical Engineering, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, China
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9
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Recent progress in the design principles, sensing mechanisms, and applications of small-molecule probes for nitroreductases. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213460] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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10
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Xu L, Sun L, Zeng F, Wu S. Activatable fluorescent probe based on aggregation-induced emission for detecting hypoxia-related pathological conditions. Anal Chim Acta 2020; 1125:152-161. [DOI: 10.1016/j.aca.2020.05.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/11/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022]
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11
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Yang Q, Wen Y, Zhong A, Xu J, Shao S. An HBT-based fluorescent probe for nitroreductase determination and its application in Escherichia coli cell imaging. NEW J CHEM 2020. [DOI: 10.1039/d0nj03286g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
HBTPN exhibited excellent performance such as rapid response time, large Stokes shift, good selectivity and sensitivity, and long-wavelength emission.
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Affiliation(s)
- Quanzhi Yang
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
| | - Yujie Wen
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
| | - Aiguo Zhong
- Department of Chemistry
- Taizhou College
- Taizhou 318000
- P. R. China
| | - Jian Xu
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
| | - Shijun Shao
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
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12
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Jradi FM, Lavis LD. Chemistry of Photosensitive Fluorophores for Single-Molecule Localization Microscopy. ACS Chem Biol 2019; 14:1077-1090. [PMID: 30997987 DOI: 10.1021/acschembio.9b00197] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Development of single-molecule localization microscopy (SMLM) has sparked a revolution in biological imaging, allowing "super-resolution" fluorescence microscopy below the diffraction limit of light. The past decade has seen an explosion in not only optical hardware for SMLM but also the development or repurposing of fluorescent proteins and small-molecule fluorescent probes for this technique. In this review, written by chemists for chemists, we detail the history of single-molecule localization microscopy and collate the collection of probes with demonstrated utility in SMLM. We hope it will serve as a primer for probe choice in localization microscopy as well as an inspiration for the development of new fluorophores that enable imaging of biological samples with exquisite detail.
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Affiliation(s)
- Fadi M. Jradi
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
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13
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Pardeshi KA, Kumar TA, Ravikumar G, Shukla M, Kaul G, Chopra S, Chakrapani H. Targeted Antibacterial Activity Guided by Bacteria-Specific Nitroreductase Catalytic Activation to Produce Ciprofloxacin. Bioconjug Chem 2019; 30:751-759. [DOI: 10.1021/acs.bioconjchem.8b00887] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kundansingh A. Pardeshi
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
| | - T. Anand Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
| | - Govindan Ravikumar
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
| | - Manjulika Shukla
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
| | - Grace Kaul
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
| | - Sidharth Chopra
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
| | - Harinath Chakrapani
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
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14
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Abstract
Fluorogenic probes efficiently reduce non-specific background signals, which often results in highly improved signal-to-noise ratios.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group
- Institute of Organic Chemistry
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1117 Budapest
| | - Péter Kele
- Chemical Biology Research Group
- Institute of Organic Chemistry
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1117 Budapest
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15
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Qi Y, Lu X, Feng Q, Fan W, Liu C, Li Z. An Enzyme-Free MicroRNA Assay Based On Fluorescence Counting of Click Chemical Ligation-Illuminated Magnetic Nanoparticles with Total Internal Reflection Fluorescence Microscopy. ACS Sens 2018; 3:2667-2674. [PMID: 30456947 DOI: 10.1021/acssensors.8b01169] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) have been considered as promising cancer biomarkers. However, the simple but sensitive detection of low levels of miRNAs in biological samples still remains challenging. Herein, we wish to report an entirely enzyme-free, simple, and highly sensitive miRNA assay based on the counting of cycling click chemical ligation (3CL)-illuminated fluorescent magnetic nanoparticles (MNPs) with a total internal reflection fluorescence microscopy (TIRFM). In this strategy, each miRNA molecule can trigger many cycles of click chemical ligation reactions to produce plentiful ligated oligonucleotides (ODNs) with both 5'-biotin and 3'-fluorophore, resulting in efficient signal amplification. It is worth noting that only the ligated ODNs can bring fluorophores onto streptavidin-functionalized MNPs (STV-MNPs). Notably, merely 10 fluorescent molecules on each 50 nm MNP can make it bright enough to be clearly visualized by the TIRFM, which can significantly improve the detection sensitivity for miRNA. Through fluorescence counting of individual MNPs and integrating their fluorescence intensities, the amount of target miRNA can be quantitatively determined. This miRNA assay can be accomplished in a mix-and-read manner just by simply mixing the enzyme-free 3CL reaction system with the MNPs before TIRFM imaging, which avoids tedious immobilization, washing, and purification steps. Despite the extremely simple operation, this strategy exhibits high sensitivity with a quite low detection limit of 50 fM target miRNA as well as high specificity to well discriminate miRNA sequences with a single-base variation. Furthermore, the applicability of this method in real biological samples is also verified through the accurate detection of the miRNA target in cancer cells.
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Affiliation(s)
- Yan Qi
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi Province 710119, P. R. China
| | - Xiaohui Lu
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi Province 710119, P. R. China
| | - Qinya Feng
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi Province 710119, P. R. China
| | - Wenjiao Fan
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi Province 710119, P. R. China
| | - Chenghui Liu
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi Province 710119, P. R. China
| | - Zhengping Li
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi Province 710119, P. R. China
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16
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Sun J, Hu Z, Wang R, Zhang S, Zhang X. A Highly Sensitive Chemiluminescent Probe for Detecting Nitroreductase and Imaging in Living Animals. Anal Chem 2018; 91:1384-1390. [DOI: 10.1021/acs.analchem.8b03955] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jinyu Sun
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Zhian Hu
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Ruihua Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Sichun Zhang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Xinrong Zhang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
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17
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Gruber TD, Krishnamurthy C, Grimm JB, Tadross MR, Wysocki LM, Gartner ZJ, Lavis LD. Cell-Specific Chemical Delivery Using a Selective Nitroreductase-Nitroaryl Pair. ACS Chem Biol 2018; 13:2888-2896. [PMID: 30111097 DOI: 10.1021/acschembio.8b00524] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The utility of small molecules to probe or perturb biological systems is limited by the lack of cell-specificity. "Masking" the activity of small molecules using a general chemical modification and "unmasking" it only within target cells overcomes this limitation. To this end, we have developed a selective enzyme-substrate pair consisting of engineered variants of E. coli nitroreductase (NTR) and a 2-nitro- N-methylimidazolyl (NM) masking group. To discover and optimize this NTR-NM system, we synthesized a series of fluorogenic substrates containing different nitroaromatic masking groups, confirmed their stability in cells, and identified the best substrate for NTR. We then engineered the enzyme for improved activity in mammalian cells, ultimately yielding an enzyme variant (enhanced NTR, or eNTR) that possesses up to 100-fold increased activity over wild-type NTR. These improved NTR enzymes combined with the optimal NM masking group enable rapid, selective unmasking of dyes, indicators, and drugs to genetically defined populations of cells.
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Affiliation(s)
- Todd D Gruber
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
| | - Chithra Krishnamurthy
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - Jonathan B Grimm
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
| | - Michael R Tadross
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
| | - Laura M Wysocki
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - Luke D Lavis
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
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18
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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19
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Meng YL, Xin ZH, Jia YJ, Kang YF, Ge LP, Zhang CH, Dai MY. A near-infrared fluorescent probe for direct and selective detection of cysteine over homocysteine and glutathione. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 202:301-304. [PMID: 29800893 DOI: 10.1016/j.saa.2018.05.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 05/13/2018] [Accepted: 05/15/2018] [Indexed: 06/08/2023]
Abstract
In this work, we have designed and synthesized the fluorescent probe 1, which showed a highly selective and sensitive response to Cys over Hcy/GSH in the test. Moreover, the color of probe solution has changed dramatically from colorless to pink with the addition of Cys within 10 min. Meanwhile, the fluorescence intensity exhibited perfectly positive correlation with concentration of Cys from 0 to 200 μM, which offered the important condition for quantitative analysis. Finally, the bioimaging and fluorescence response of probe 1 for fetal calf serum are a powerful safeguard for practical detection of Cys. Therefore, this near-infrared probe will be of great benefit for detecting Cys in the biological systems.
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Affiliation(s)
- Ya-Li Meng
- College of Laboratory Medicine, Hebei North University, 11 Diamond Street South, Zhangjiakou 075000, Hebei Province, China
| | - Zhen-Hui Xin
- College of Laboratory Medicine, Hebei North University, 11 Diamond Street South, Zhangjiakou 075000, Hebei Province, China
| | - Yu-Jie Jia
- College of Economics and Management, Hebei North University, 11 Diamond Street South, Zhangjiakou 075000, Hebei Province, China
| | - Yan-Fei Kang
- College of Laboratory Medicine, Hebei North University, 11 Diamond Street South, Zhangjiakou 075000, Hebei Province, China.
| | - Li-Ping Ge
- College of Laboratory Medicine, Hebei North University, 11 Diamond Street South, Zhangjiakou 075000, Hebei Province, China
| | - Cun-Hui Zhang
- College of Laboratory Medicine, Hebei North University, 11 Diamond Street South, Zhangjiakou 075000, Hebei Province, China
| | - Ming-Yan Dai
- College of Laboratory Medicine, Hebei North University, 11 Diamond Street South, Zhangjiakou 075000, Hebei Province, China
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20
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Herten DP, Haderspeck A, Braun F, Wadepohl H. Copper(II)-induced Fluorescence Quenching of a BODIPY Fluorophore. Z Anorg Allg Chem 2018. [DOI: 10.1002/zaac.201800154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Dirk-Peter Herten
- Institute of Physical Chemistry; Heidelberg University; Im Neuenheimer Feld 229 69120 Heidelberg Germany
| | - Andreas Haderspeck
- Institute of Physical Chemistry; Heidelberg University; Im Neuenheimer Feld 229 69120 Heidelberg Germany
| | - Felix Braun
- Institute of Physical Chemistry; Heidelberg University; Im Neuenheimer Feld 229 69120 Heidelberg Germany
| | - Hubert Wadepohl
- Institute of Inorganic Chemistry; Heidelberg University; Im Neuenheimer Feld 270 69120 Heidelberg Germany
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21
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Teng X, Tian M, Zhang J, Tang L, Xin J. A TCF-based colorimetric and fluorescent probe for palladium detection in an aqueous solution. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.06.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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22
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Gutiérrez-Arzaluz L, López-Arteaga R, Cortés-Guzmán F, Peon J. Nitrated Fluorophore Formation upon Two-Photon Excitation of an Azide with Extended Conjugation. J Phys Chem B 2017; 121:9910-9919. [PMID: 28981286 DOI: 10.1021/acs.jpcb.7b09446] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The transformation of an aromatic azide into a highly fluorescent species through a nonlinear optical process was studied. The azide system was designed to undergo N2 release and nitrene to nitro conversion upon two-photon electronic excitation. The formation of the nitro form of the compound through reactions with O2 and its high radiative quantum yield implies that the azide can be used as a biphotonic activatable fluorogen. The electronic state in which the azide to nitrene transformation takes place can be accessed nonlinearly with near-infrared light which allows for photoactivation with commonly available lasers. Furthermore, the system was built with a sulfonate functionality which allows for the molecule to be adsorbed at surfaces like that of cadmium sulfide nanocrystals which further improves the nonlinear optical absorption properties in the composite, through an energy transfer mechanism. The yield of the process as a function of the excitation photon energy together with computational studies indicate that the N2 release in this azide is due to a reactive channel in the second singlet excited state of the molecule. This feature implies that the system is intrinsically photostable for excitation below and above a certain wavelength and that the system can be phototriggered selectively by the nonlinear optical process.
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Affiliation(s)
- Luis Gutiérrez-Arzaluz
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
| | - Rafael López-Arteaga
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
| | - Fernando Cortés-Guzmán
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
| | - Jorge Peon
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
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23
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Hao Y, Zhang Y, Ruan K, Meng F, Li T, Guan J, Du L, Qu P, Xu M. A highly selective long-wavelength fluorescent probe for hydrazine and its application in living cell imaging. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 184:355-360. [PMID: 28531842 DOI: 10.1016/j.saa.2017.04.041] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 03/30/2017] [Accepted: 04/18/2017] [Indexed: 06/07/2023]
Abstract
A highly selective long-wavelength turn-on fluorescent probe has been developed for the detection of N2H4. The probe was prepared by conjugation the tricyanofuran-based D-π-A system with a recognizing moiety of acetyl group. In the presence of N2H4, the probe can be effectively hydrazinolysized and produce a turn-on fluorescent emission at 610nm as well as a large red-shift in the absorption spectrum corresponding to a color change from yellow to blue. The sensing mechanism was confirmed by HPLC, MS, UV-vis, emission spectroscopic and theoretical calculation studies. The probe displayed high selectivity and sensitivity for N2H4 with a LOD (limit of detection) of 0.16μM. Moreover, the probe was successfully utilized for the detection of hydrazine in living cells.
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Affiliation(s)
- Yuanqiang Hao
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu 476000, China
| | - Yintang Zhang
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu 476000, China.
| | - Kehong Ruan
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan410083, China
| | - Fanteng Meng
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu 476000, China
| | - Ting Li
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu 476000, China
| | - Jinsheng Guan
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu 476000, China
| | - Lulu Du
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu 476000, China
| | - Peng Qu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu 476000, China
| | - Maotian Xu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu 476000, China.
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24
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von Diezmann A, Shechtman Y, Moerner WE. Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking. Chem Rev 2017; 117:7244-7275. [PMID: 28151646 PMCID: PMC5471132 DOI: 10.1021/acs.chemrev.6b00629] [Citation(s) in RCA: 260] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single-molecule super-resolution fluorescence microscopy and single-particle tracking are two imaging modalities that illuminate the properties of cells and materials on spatial scales down to tens of nanometers or with dynamical information about nanoscale particle motion in the millisecond range, respectively. These methods generally use wide-field microscopes and two-dimensional camera detectors to localize molecules to much higher precision than the diffraction limit. Given the limited total photons available from each single-molecule label, both modalities require careful mathematical analysis and image processing. Much more information can be obtained about the system under study by extending to three-dimensional (3D) single-molecule localization: without this capability, visualization of structures or motions extending in the axial direction can easily be missed or confused, compromising scientific understanding. A variety of methods for obtaining both 3D super-resolution images and 3D tracking information have been devised, each with their own strengths and weaknesses. These include imaging of multiple focal planes, point-spread-function engineering, and interferometric detection. These methods may be compared based on their ability to provide accurate and precise position information on single-molecule emitters with limited photons. To successfully apply and further develop these methods, it is essential to consider many practical concerns, including the effects of optical aberrations, field dependence in the imaging system, fluorophore labeling density, and registration between different color channels. Selected examples of 3D super-resolution imaging and tracking are described for illustration from a variety of biological contexts and with a variety of methods, demonstrating the power of 3D localization for understanding complex systems.
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Affiliation(s)
| | - Yoav Shechtman
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
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25
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26
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Progress and prospects for small-molecule probes of bacterial imaging. Nat Chem Biol 2017; 12:472-8. [PMID: 27315537 DOI: 10.1038/nchembio.2109] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 05/13/2016] [Indexed: 11/09/2022]
Abstract
Fluorescence microscopy is an essential tool for the exploration of cell growth, division, transcription and translation in eukaryotes and prokaryotes alike. Despite the rapid development of techniques to study bacteria, the size of these organisms (1-10 μm) and their robust and largely impenetrable cell envelope present major challenges in imaging experiments. Fusion-based strategies, such as attachment of the protein of interest to a fluorescent protein or epitope tag, are by far the most common means for examining protein localization and expression in prokaryotes. While valuable, the use of genetically encoded tags can result in mislocalization or altered activity of the desired protein, does not provide a readout of the catalytic state of enzymes and cannot enable visualization of many other important cellular components, such as peptidoglycan, lipids, nucleic acids or glycans. Here, we highlight the use of biomolecule-specific small-molecule probes for imaging in bacteria.
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27
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Yu T, Yin G, Yin P, Zeng Y, Li H, Zhang Y, Yao S. A novel long-wavelength fluorescent probe for discrimination of different palladium species based on Pd-catalyzed reactions. RSC Adv 2017. [DOI: 10.1039/c7ra01731f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have synthesized a novel long-wavelength fluorescent probe MFC for detection of palladium (Pd0).
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Affiliation(s)
- Ting Yu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Hunan Normal University
- Changsha 410081
| | - Guoxing Yin
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Hunan Normal University
- Changsha 410081
| | - Peng Yin
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Hunan Normal University
- Changsha 410081
| | - Ying Zeng
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Hunan Normal University
- Changsha 410081
| | - Haitao Li
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Hunan Normal University
- Changsha 410081
| | - Youyu Zhang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Hunan Normal University
- Changsha 410081
| | - Shouzhuo Yao
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Hunan Normal University
- Changsha 410081
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28
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Tuson HH, Aliaj A, Brandes ER, Simmons LA, Biteen JS. Addressing the Requirements of High-Sensitivity Single-Molecule Imaging of Low-Copy-Number Proteins in Bacteria. Chemphyschem 2016; 17:1435-40. [PMID: 26888309 PMCID: PMC4894654 DOI: 10.1002/cphc.201600035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 11/11/2022]
Abstract
Single-molecule fluorescence super-resolution imaging and tracking provide nanometer-scale information about subcellular protein positions and dynamics. These single-molecule imaging experiments can be very powerful, but they are best suited to high-copy number proteins where many measurements can be made sequentially in each cell. We describe artifacts associated with the challenge of imaging a protein expressed in only a few copies per cell. We image live Bacillus subtilis in a fluorescence microscope, and demonstrate that under standard single-molecule imaging conditions, unlabeled B. subtilis cells display punctate red fluorescent spots indistinguishable from the few PAmCherry fluorescent protein single molecules under investigation. All Bacillus species investigated were strongly affected by this artifact, whereas we did not find a significant number of these background sources in two other species we investigated, Enterococcus faecalis and Escherichia coli. With single-molecule resolution, we characterize the number, spatial distribution, and intensities of these impurity spots.
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Affiliation(s)
- Hannah H Tuson
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alisa Aliaj
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Eileen R Brandes
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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29
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Cao J, Campbell J, Liu L, Mason RP, Lippert AR. In Vivo Chemiluminescent Imaging Agents for Nitroreductase and Tissue Oxygenation. Anal Chem 2016; 88:4995-5002. [PMID: 27054463 PMCID: PMC5033617 DOI: 10.1021/acs.analchem.6b01096] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Tissue oxygenation is a driving parameter of the tumor microenvironment, and hypoxia can be a prognostic indicator of aggressiveness, metastasis, and poor response to therapy. Here, we report a chemiluminescence imaging (CLI) agent based on the oxygen-dependent reduction of a nitroaromatic spiroadamantane 1,2-dioxetane scaffold. Hypoxia ChemiLuminescent Probe 2 (HyCL-2) responds to nitroreductase with ∼170-fold increase in luminescence intensity and high selectivity for enzymatic reductase versus other small molecule reductants. HyCL-2 can image exogenous nitroreductase in vitro and in vivo in living mice, and total luminescent intensity is increased by ∼5-fold under low oxygen conditions. HyCL-2 is demonstrated to report on tumor oxygenation during an oxygen challenge in H1299 lung tumor xenografts grown in a murine model as independently confirmed using multispectral optoacoustic tomography (MSOT) imaging of hemoglobin oxygenation.
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Affiliation(s)
- Jian Cao
- Department of Chemistry, Southern Methodist University, Dallas, TX, 75275-0314
- Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, 75275-0314
| | - James Campbell
- Prognostic Imaging Research Laboratory (PIRL), Pre-clinical Imaging Section, Department of Radiology, UT Southwestern Medical Center, Dallas, TX 75390-9058, USA
| | - Li Liu
- Prognostic Imaging Research Laboratory (PIRL), Pre-clinical Imaging Section, Department of Radiology, UT Southwestern Medical Center, Dallas, TX 75390-9058, USA
| | - Ralph P. Mason
- Prognostic Imaging Research Laboratory (PIRL), Pre-clinical Imaging Section, Department of Radiology, UT Southwestern Medical Center, Dallas, TX 75390-9058, USA
| | - Alexander R. Lippert
- Department of Chemistry, Southern Methodist University, Dallas, TX, 75275-0314
- Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, 75275-0314
- Center for Global Health Impact (CGHI), Southern Methodist University, Dallas, TX, 75275-0314
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30
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Baranczak A, Connelly S, Liu Y, Choi S, Grimster NP, Powers ET, Wilson IA, Kelly JW. Fluorogenic small molecules requiring reaction with a specific protein to create a fluorescent conjugate for biological imaging--what we know and what we need to learn. Biopolymers 2016; 101:484-95. [PMID: 24105107 DOI: 10.1002/bip.22407] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/03/2013] [Indexed: 01/03/2023]
Abstract
We seek fluorogenic small molecules that generate a fluorescent conjugate signal if and only if they react with a given protein-of-interest (i.e., small molecules for which noncovalent binding to the protein-of-interest is insufficient to generate fluorescence). Consequently, it is the new chemical entity afforded by the generally irreversible reaction between the small molecule and the protein-of-interest that enables the energy of an electron occupying the lowest unoccupied molecular orbital (LUMO) of the chromophore to be given off as a photon instead of being dissipated by nonradiative mechanisms in complex biological environments. This category of fluorogenic small molecules is created by starting with environmentally sensitive fluorophores that are modified by an essential functional group that efficiently quenches the fluorescence until a chemoselective reaction between that functional group and the protein-of-interest occurs, yielding the fluorescent conjugate. Fluorogenic small molecules are envisioned to be useful for a wide variety of applications, including live cell imaging without the requirement for washing steps and pulse-chase kinetic analyses of protein synthesis, trafficking, degradation, etc.
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Affiliation(s)
- Aleksandra Baranczak
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, 92037
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31
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Yang Z, Sharma A, Qi J, Peng X, Lee DY, Hu R, Lin D, Qu J, Kim JS. Super-resolution fluorescent materials: an insight into design and bioimaging applications. Chem Soc Rev 2016; 45:4651-67. [DOI: 10.1039/c5cs00875a] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
With the emerging of super-resolution fluorescent imaging microscopy techniques, biological targets below 200 nm in size are successful to be localized clearly and precisely with unprecedented details. In this tutorial review, the fluorescent materials, including organic fluorophores and nanomaterials, utilized in STED, single molecule localized microscopy (PALM/STORM) and SOFI microscopies, together with their working principles are mainly discussed.
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Affiliation(s)
- Zhigang Yang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province
- College of Optoelectronic Engineering
- Shenzhen University
- Shenzhen
- China
| | - Amit Sharma
- Department of Chemistry
- Korea University
- Seoul 136-701
- Korea
| | - Jing Qi
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province
- College of Optoelectronic Engineering
- Shenzhen University
- Shenzhen
- China
| | - Xiao Peng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province
- College of Optoelectronic Engineering
- Shenzhen University
- Shenzhen
- China
| | - Dong Yeop Lee
- Department of Chemistry
- Korea University
- Seoul 136-701
- Korea
| | - Rui Hu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province
- College of Optoelectronic Engineering
- Shenzhen University
- Shenzhen
- China
| | - Danying Lin
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province
- College of Optoelectronic Engineering
- Shenzhen University
- Shenzhen
- China
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province
- College of Optoelectronic Engineering
- Shenzhen University
- Shenzhen
- China
| | - Jong Seung Kim
- Department of Chemistry
- Korea University
- Seoul 136-701
- Korea
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32
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Elmes RBP. Bioreductive fluorescent imaging agents: applications to tumour hypoxia. Chem Commun (Camb) 2016; 52:8935-56. [DOI: 10.1039/c6cc01037g] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The development of new optical chemosensors for various reductases presents an ideal approach to visualise areas of tissue hypoxia.
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Affiliation(s)
- Robert B. P. Elmes
- Department of Chemistry
- Maynooth University
- National University of Ireland
- Maynooth
- Ireland
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33
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Abstract
As of 2015, it has been 26 years since the first optical detection and spectroscopy of single molecules in condensed matter. This area of science has expanded far beyond the early low temperature studies in crystals to include single molecules in cells, polymers, and in solution. The early steps relied upon high-resolution spectroscopy of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral fine structure arising directly from the position-dependent fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 1990s, a variety of fascinating physical effects were observed for individual molecules, including imaging of the light from single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency. In the room temperature regime, researchers showed that bursts of light from single molecules could be detected in solution, leading to imaging and microscopy by a variety of methods. Studies of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. All of these early steps provided important fundamentals underpinning the development of super-resolution microscopy based on single-molecule localization and active control of emitting concentration. Current thrust areas include extensions to three-dimensional imaging with high precision, orientational analysis of single molecules, and direct measurements of photodynamics and transport properties for single molecules trapped in solution by suppression of Brownian motion. Without question, a huge variety of studies of single molecules performed by many talented scientists all over the world have extended our knowledge of the nanoscale and many microscopic mechanisms previously hidden by ensemble averaging.
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Affiliation(s)
- W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
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34
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Chevalier A, Piao W, Hanaoka K, Nagano T, Renard PY, Romieu A. Azobenzene-caged sulforhodamine dyes: a novel class of 'turn-on' reactive probes for hypoxic tumor cell imaging. Methods Appl Fluoresc 2015; 3:044004. [PMID: 29148517 DOI: 10.1088/2050-6120/3/4/044004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
New sulforhodamine-based fluorescent 'turn-on' probes have been developed for the direct imaging of cellular hypoxia. Rapid access to this novel class of water-soluble 'azobenzene-caged' fluorophores was made possible through an easily-implementable azo-coupling reaction between a fluorescent primary arylamine derived from a sulforhodamine 101 scaffold (named SR101-NaphtNH 2 ) and a tertiary aniline whose N-substituents are neutral, cationic, or zwitterionic. The detection mechanism is based on the bioreductive cleavage of the azo bond that restores strong far-red fluorescence (emission maximum at 625 nm) by regenerating the original sulforhodamine SR101-NaphtNH 2 . This valuable fluorogenic response was obtained for the three 'smart' probes studied in this work, as shown by an in vitro assay using rat liver microsomes placed under aerobic and then under hypoxic conditions. Most importantly, the probe namely SR101-NaphtNH 2 -Hyp-diMe was successfully applied for imaging the hypoxic status of tumor cells (A549 cells).
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Affiliation(s)
- Arnaud Chevalier
- Normandie Université, COBRA UMR 6014 & FR 3038; Univ. Rouen; INSA Rouen; CNRS, IRCOF, 1, Rue Tesnières, 76821 Mont-Saint-Aignan cedex, France
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35
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Moerner WEWE. Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture). Angew Chem Int Ed Engl 2015. [PMID: 26088273 DOI: 10.1103/revmodphys.87.1183] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 90s, many fascinating physical effects were observed for individual molecules, and the imaging of single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency provided important forerunners of the later super-resolution microscopy with single molecules. In the room temperature regime, imaging of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and current developments are summarized.
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Affiliation(s)
- W E William E Moerner
- Departments of Chemistry and (by Courtesy) of Applied Physics, Stanford University, Stanford, California 94305 (USA)
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36
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Porterfield WB, Jones KA, McCutcheon DC, Prescher JA. A “Caged” Luciferin for Imaging Cell–Cell Contacts. J Am Chem Soc 2015; 137:8656-9. [DOI: 10.1021/jacs.5b02774] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- William B. Porterfield
- Departments of Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Krysten A. Jones
- Departments of Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - David C. McCutcheon
- Departments of Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Jennifer A. Prescher
- Departments of Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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37
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Moerner WEWE. Spektroskopie, Visualisierung und Photomanipulation einzelner Moleküle: die Grundlage für superhochauflösende Mikroskopie (Nobel-Aufsatz). Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501949] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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Moerner WEWE. Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture). Angew Chem Int Ed Engl 2015; 54:8067-93. [PMID: 26088273 DOI: 10.1002/anie.201501949] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/10/2022]
Abstract
The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 90s, many fascinating physical effects were observed for individual molecules, and the imaging of single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency provided important forerunners of the later super-resolution microscopy with single molecules. In the room temperature regime, imaging of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and current developments are summarized.
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Affiliation(s)
- W E William E Moerner
- Departments of Chemistry and (by Courtesy) of Applied Physics, Stanford University, Stanford, California 94305 (USA)
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39
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Friedrich F, Klehs K, Fichte MAH, Junek S, Heilemann M, Heckel A. A two-photon activatable amino acid linker for the induction of fluorescence. Chem Commun (Camb) 2015; 51:15382-5. [DOI: 10.1039/c5cc05700k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first photolabile quencher for ATTO565 is presented and the application of the new construct in super-resolution microscopy is demonstrated.
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Affiliation(s)
- Felix Friedrich
- Goethe University Frankfurt
- Institute for Organic Chemistry and Chemical Biology
- 60438 Frankfurt
- Germany
| | - Kathrin Klehs
- Goethe University Frankfurt
- Institute for Physical and Theoretical Chemistry
- 60438 Frankfurt
- Germany
| | - Manuela A. H. Fichte
- Goethe University Frankfurt
- Institute for Organic Chemistry and Chemical Biology
- 60438 Frankfurt
- Germany
| | - Stephan Junek
- Imaging facility
- Max Planck Institute for Brain Research
- 60438 Frankfurt am Main
- Germany
| | - Mike Heilemann
- Goethe University Frankfurt
- Institute for Physical and Theoretical Chemistry
- 60438 Frankfurt
- Germany
| | - Alexander Heckel
- Goethe University Frankfurt
- Institute for Organic Chemistry and Chemical Biology
- 60438 Frankfurt
- Germany
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40
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Lee MK, Rai P, Williams J, Twieg RJ, Moerner WE. Small-molecule labeling of live cell surfaces for three-dimensional super-resolution microscopy. J Am Chem Soc 2014; 136:14003-6. [PMID: 25222297 PMCID: PMC4195381 DOI: 10.1021/ja508028h] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Precise
imaging of the cell surface of fluorescently labeled bacteria
requires super-resolution methods because the size-scale of these
cells is on the order of the diffraction limit. In this work, we present
a photocontrollable small-molecule rhodamine spirolactam
emitter suitable for non-toxic and specific labeling of the outer
surface of cells for three-dimensional (3D) super-resolution (SR)
imaging. Conventional rhodamine spirolactams photoswitch
to the emitting form with UV light; however, these wavelengths can
damage cells. We extended photoswitching to visible wavelengths
>400 nm by iterative synthesis and spectroscopic characterization
to optimize the substitution on the spirolactam. Further, an N-hydroxysuccinimide-functionalized derivative enabled
covalent labeling of amines on the surface of live Caulobacter
crescentus cells. Resulting 3D SR reconstructions of the
labeled cell surface reveal uniform and specific sampling with thousands
of localizations per cell and excellent localization precision in x, y, and z. The distribution
of cell stalk lengths (a sub-diffraction-sized cellular structure)
was quantified for a mixed population of cells. Pulse-chase experiments
identified sites of cell surface growth. Covalent labeling with the
optimized rhodamine spirolactam label provides a general
strategy to study the surfaces of living cells with high specificity
and resolution down to 10–20 nm.
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Affiliation(s)
- Marissa K Lee
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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41
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Habuchi S. Super-resolution molecular and functional imaging of nanoscale architectures in life and materials science. Front Bioeng Biotechnol 2014; 2:20. [PMID: 25152893 PMCID: PMC4126472 DOI: 10.3389/fbioe.2014.00020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/30/2014] [Indexed: 11/13/2022] Open
Abstract
Super-resolution (SR) fluorescence microscopy has been revolutionizing the way in which we investigate the structures, dynamics, and functions of a wide range of nanoscale systems. In this review, I describe the current state of various SR fluorescence microscopy techniques along with the latest developments of fluorophores and labeling for the SR microscopy. I discuss the applications of SR microscopy in the fields of life science and materials science with a special emphasis on quantitative molecular imaging and nanoscale functional imaging. These studies open new opportunities for unraveling the physical, chemical, and optical properties of a wide range of nanoscale architectures together with their nanostructures and will enable the development of new (bio-)nanotechnology.
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Affiliation(s)
- Satoshi Habuchi
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology , Jeddah , Saudi Arabia
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42
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Gahlmann A, Moerner WE. Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging. Nat Rev Microbiol 2014; 12:9-22. [PMID: 24336182 DOI: 10.1038/nrmicro3154] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The ability to detect single molecules in live bacterial cells enables us to probe biological events one molecule at a time and thereby gain knowledge of the activities of intracellular molecules that remain obscure in conventional ensemble-averaged measurements. Single-molecule fluorescence tracking and super-resolution imaging are thus providing a new window into bacterial cells and facilitating the elucidation of cellular processes at an unprecedented level of sensitivity, specificity and spatial resolution. In this Review, we consider what these technologies have taught us about the bacterial cytoskeleton, nucleoid organization and the dynamic processes of transcription and translation, and we also highlight the methodological improvements that are needed to address a number of experimental challenges in the field.
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Affiliation(s)
- Andreas Gahlmann
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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43
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Feng L, Liu ZM, Xu L, Lv X, Ning J, Hou J, Ge GB, Cui JN, Yang L. A highly selective long-wavelength fluorescent probe for the detection of human carboxylesterase 2 and its biomedical applications. Chem Commun (Camb) 2014; 50:14519-22. [DOI: 10.1039/c4cc06642a] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A highly selective long-wavelength fluorescent probe for the detection of human carboxylesterase 2 (hCE2) has been developed and well characterized. The probe can be used for measuring the real activities of hCE2 in complex biological systems.
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Affiliation(s)
- Lei Feng
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian, China
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
| | - Zhao-Ming Liu
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian, China
| | - Liang Xu
- School of Chemistry
- Dalian University of Technology
- Dalian, China
| | - Xia Lv
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian, China
| | - Jing Ning
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian, China
| | - Jie Hou
- Dalian Medical University
- Dalian 116044, China
| | - Guang-Bo Ge
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian, China
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
| | - Jing-Nan Cui
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian, China
| | - Ling Yang
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian, China
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44
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Wu MY, Li K, Li CY, Hou JT, Yu XQ. A water-soluble near-infrared probe for colorimetric and ratiometric sensing of SO2derivatives in living cells. Chem Commun (Camb) 2014; 50:183-5. [DOI: 10.1039/c3cc46468g] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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45
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Yan Q, Schwartz SL, Maji S, Huang F, Szent-Gyorgyi C, Lidke DS, Lidke KA, Bruchez MP. Localization microscopy using noncovalent fluorogen activation by genetically encoded fluorogen-activating proteins. Chemphyschem 2013; 15:687-695. [PMID: 24194371 DOI: 10.1002/cphc.201300757] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 09/02/2013] [Indexed: 11/10/2022]
Abstract
The noncovalent equilibrium activation of a fluorogenic malachite green dye and its cognate fluorogen-activating protein (FAP) can produce a sparse labeling distribution of densely tagged genetically encoded proteins, enabling single molecule detection and super-resolution imaging in fixed and living cells. These sparse labeling conditions are achieved by control of the dye concentration in the milieu, and do not require any photoswitching or photoactivation. The labeling is achieved by using physiological buffers and cellular media, in which additives and switching buffers are not required to obtain super-resolution images. We evaluate the super-resolution properties and images obtained from a selected FAP clone fused to actin, and show that the photon counts per object are between those typically reported for fluorescent proteins and switching-dye pairs, resulting in 10-30 nm localization precision per object. This labeling strategy complements existing approaches, and may simplify multicolor labeling of cellular structures.
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Affiliation(s)
- Qi Yan
- Molecular Biosensor and Imaging Center, Carnegie Mellon Unviersity, Pittsburgh PA 15213.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Samantha L Schwartz
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131
| | - Suvrajit Maji
- Molecular Biosensor and Imaging Center, Carnegie Mellon Unviersity, Pittsburgh PA 15213.,Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Fang Huang
- Department of Physics, University of New Mexico, Albuquerque, NM 87131
| | - Chris Szent-Gyorgyi
- Molecular Biosensor and Imaging Center, Carnegie Mellon Unviersity, Pittsburgh PA 15213
| | - Diane S Lidke
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131
| | - Keith A Lidke
- Department of Physics, University of New Mexico, Albuquerque, NM 87131
| | - Marcel P Bruchez
- Molecular Biosensor and Imaging Center, Carnegie Mellon Unviersity, Pittsburgh PA 15213.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213.,Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
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46
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Sahl SJ, Moerner WE. Super-resolution fluorescence imaging with single molecules. Curr Opin Struct Biol 2013; 23:778-87. [PMID: 23932284 PMCID: PMC3805708 DOI: 10.1016/j.sbi.2013.07.010] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 07/05/2013] [Indexed: 11/16/2022]
Abstract
The ability to detect, image and localize single molecules optically with high spatial precision by their fluorescence enables an emergent class of super-resolution microscopy methods which have overcome the longstanding diffraction barrier for far-field light-focusing optics. Achieving spatial resolutions of 20-40nm or better in both fixed and living cells, these methods are currently being established as powerful tools for minimally-invasive spatiotemporal analysis of structural details in cellular processes which benefit from enhanced resolution. Briefly covering the basic principles, this short review then summarizes key recent developments and application examples of two-dimensional and three-dimensional (3D) multi-color techniques and faster time-lapse schemes. The prospects for quantitative imaging - in terms of improved ability to correct for dipole-emission-induced systematic localization errors and to provide accurate counts of molecular copy numbers within nanoscale cellular domains - are discussed.
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Affiliation(s)
- Steffen J Sahl
- Department of Chemistry, Stanford University, Stanford, CA, USA
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47
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Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms. Nat Methods 2013; 10:653-8. [PMID: 23708387 PMCID: PMC3696415 DOI: 10.1038/nmeth.2488] [Citation(s) in RCA: 330] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 04/22/2013] [Indexed: 12/12/2022]
Abstract
Newly developed scientific complementary metal–oxide–semiconductor (sCMOS) cameras have the potential to dramatically accelerate data acquisition in single-molecule switching nanoscopy (SMSN) while simultaneously increasing the effective quantum efficiency. However, sCMOS-intrinsic pixel-dependent readout noise substantially reduces the localization precision and introduces localization artifacts. Here we present algorithms that overcome these limitations and provide unbiased, precise localization of single molecules at the theoretical limit. In combination with a multi-emitter fitting algorithm, we demonstrate single-molecule localization super-resolution imaging at up to 32 reconstructed images/second (recorded at 1,600–3,200 camera frames/second) in both fixed and living cells.
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48
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49
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Li G, Chen Y, Wang J, Lin Q, Zhao J, Ji L, Chao H. A dinuclear iridium(iii) complex as a visual specific phosphorescent probe for endogenous sulphite and bisulphite in living cells. Chem Sci 2013. [DOI: 10.1039/c3sc52301b] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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