1
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Moni D, Sasmal M, Katarkar A, Islam ASM, Habibullah M, Basu A, Ali M. Selective Sensing of Human Serum Albumin by a D···π···A-Based Self-Assembled Nanoprobe via a Disassembly Mechanism: Quantification and Live Cell Imaging Applications. ACS APPLIED BIO MATERIALS 2025. [PMID: 40448677 DOI: 10.1021/acsabm.5c00650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2025]
Abstract
Human serum albumin (HSA) serves as a vital biomarker for diagnosing kidney and liver diseases. Herein, we describe the detailed synthetic procedure of a D···π···A-based fluorescent probe HPQM [(E)-2-(2-(8-(3-hydroxypropoxy)-2,3,6,7-tetrahydro-1H,5H-pyrido[3,2,1-ij]quinolin-9-yl)vinyl)-1,1,3-trimethyl-1H-benzo[e]indol-3-ium], which forms weakly fluorescent nanoaggregates in aqueous environments due to the aggregation-caused quenching phenomenon. Nevertheless, in the presence of HSA, it becomes highly fluorescent (∼25-fold enhancement), facilitating the disassembly of nanoaggregates into its monomer. The study reveals that noncovalent interactions between HPQM and HSA promote the disassembly of the nanoaggregates and trapping of the HPQM monomer in the HSA cavity, resulting in red fluorescence by prohibiting the free rotation of the probe molecules owing to the substantial steric hindrance and low polarity environment present inside the HSA cavity. Multiple circular dichroism spectral analyses of HSA in the absence and presence of the probe revealed HPQM-induced conformational changes in the secondary and tertiary structures of HSA. The 3σ/slope technique yielded a limit of detection value of 29.8 nM (1.98 mg/L) in aqueous solutions, highlighting its high sensitivity toward HSA. Also, HPQM offers some practical utility including live cell imaging of HSA and the detection and estimation of HSA content in human blood and urine.
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Affiliation(s)
- Dolan Moni
- Department of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Mihir Sasmal
- Department of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Atul Katarkar
- Waste & Chemical Toxicity Assessment CSIR-National Environmental Engineering Research Institute, Nagpur 440020, India
| | - Abu Saleh Musha Islam
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Kolkata 700032, India
| | | | - Anamika Basu
- Department of Biochemistry, Gurudas College, Kolkata 700054, India
| | - Mahammad Ali
- Department of Chemistry, Jadavpur University, Kolkata 700032, India
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2
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Huang Y, Zhang P, Wang H, Chen Y, Liu T, Luo X. Genetic Code Expansion: Recent Developments and Emerging Applications. Chem Rev 2025; 125:523-598. [PMID: 39737807 PMCID: PMC11758808 DOI: 10.1021/acs.chemrev.4c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 12/02/2024] [Accepted: 12/09/2024] [Indexed: 01/01/2025]
Abstract
The concept of genetic code expansion (GCE) has revolutionized the field of chemical and synthetic biology, enabling the site-specific incorporation of noncanonical amino acids (ncAAs) into proteins, thus opening new avenues in research and applications across biology and medicine. In this review, we cover the principles of GCE, including the optimization of the aminoacyl-tRNA synthetase (aaRS)/tRNA system and the advancements in translation system engineering. Notable developments include the refinement of aaRS/tRNA pairs, enhancements in screening methods, and the biosynthesis of noncanonical amino acids. The applications of GCE technology span from synthetic biology, where it facilitates gene expression regulation and protein engineering, to medicine, with promising approaches in drug development, vaccine production, and gene editing. The review concludes with a perspective on the future of GCE, underscoring its potential to further expand the toolkit of biology and medicine. Through this comprehensive review, we aim to provide a detailed overview of the current state of GCE technology, its challenges, opportunities, and the frontier it represents in the expansion of the genetic code for novel biological research and therapeutic applications.
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Affiliation(s)
- Yujia Huang
- State
Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular
and Cellular Pharmacology, School of Pharmaceutical Sciences, Chemical
Biology Center, Peking University, Beijing 100191, China
| | - Pan Zhang
- Shenzhen
Key Laboratory for the Intelligent Microbial Manufacturing of Medicines,
Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic
Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese
Academy of Sciences, Shenzhen 518055, P.R. China
| | - Haoyu Wang
- State
Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular
and Cellular Pharmacology, School of Pharmaceutical Sciences, Chemical
Biology Center, Peking University, Beijing 100191, China
| | - Yan Chen
- Shenzhen
Key Laboratory for the Intelligent Microbial Manufacturing of Medicines,
Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic
Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese
Academy of Sciences, Shenzhen 518055, P.R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Tao Liu
- State
Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular
and Cellular Pharmacology, School of Pharmaceutical Sciences, Chemical
Biology Center, Peking University, Beijing 100191, China
| | - Xiaozhou Luo
- Shenzhen
Key Laboratory for the Intelligent Microbial Manufacturing of Medicines,
Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic
Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese
Academy of Sciences, Shenzhen 518055, P.R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
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3
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Kulinich AV, Ishchenko AA. Merocyanines: Electronic Structure and Spectroscopy in Solutions, Solid State, and Gas Phase. Chem Rev 2024; 124:12086-12144. [PMID: 39423353 DOI: 10.1021/acs.chemrev.4c00317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2024]
Abstract
Merocyanines, owing to their readily tunable electronic structure, are arguably the most versatile functional dyes, with ample opportunities for tailored design via variations of both the donor/acceptor (D/A) end groups and π-conjugated polymethine chain. A plethora of spectral properties, such as strong solvatochromism, high polarizability and hyperpolarizabilities, and sensitizing capacity, motivates extensive studies for their applications in light-converting materials for optoelectronics, nonlinear optics, optical storage, fluorescent probes, etc. Evidently, an understanding of the intrinsic structure-property relationships is a prerequisite for the successful design of functional dyes. For merocyanines, these regularities have been explored for over 70 years, but only in the past three decades have these studies expanded beyond the theory of their color and solvatochromism toward their electronic structure in the ground and excited states. This Review outlines the fundamental principles, essential for comprehension of the variable nature of merocyanines, with the main emphasis on understanding the impact of internal (chemical structure) and external (intermolecular interactions) factors on the electronic symmetry of the D-π-A chromophore. The research on the structure and properties of merocyanines in different media is reviewed in the context of interplay of the three virtual states: nonpolar polyene, ideal polymethine, and zwitterionic polyene.
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Affiliation(s)
- Andrii V Kulinich
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Akademika Kukharya St., Kyiv 02094, Ukraine
| | - Alexander A Ishchenko
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Akademika Kukharya St., Kyiv 02094, Ukraine
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4
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Dunkelmann DL, Chin JW. Engineering Pyrrolysine Systems for Genetic Code Expansion and Reprogramming. Chem Rev 2024; 124:11008-11062. [PMID: 39235427 PMCID: PMC11467909 DOI: 10.1021/acs.chemrev.4c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
Over the past 16 years, genetic code expansion and reprogramming in living organisms has been transformed by advances that leverage the unique properties of pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs. Here we summarize the discovery of the pyrrolysine system and describe the unique properties of PylRS/tRNAPyl pairs that provide a foundation for their transformational role in genetic code expansion and reprogramming. We describe the development of genetic code expansion, from E. coli to all domains of life, using PylRS/tRNAPyl pairs, and the development of systems that biosynthesize and incorporate ncAAs using pyl systems. We review applications that have been uniquely enabled by the development of PylRS/tRNAPyl pairs for incorporating new noncanonical amino acids (ncAAs), and strategies for engineering PylRS/tRNAPyl pairs to add noncanonical monomers, beyond α-L-amino acids, to the genetic code of living organisms. We review rapid progress in the discovery and scalable generation of mutually orthogonal PylRS/tRNAPyl pairs that can be directed to incorporate diverse ncAAs in response to diverse codons, and we review strategies for incorporating multiple distinct ncAAs into proteins using mutually orthogonal PylRS/tRNAPyl pairs. Finally, we review recent advances in the encoded cellular synthesis of noncanonical polymers and macrocycles and discuss future developments for PylRS/tRNAPyl pairs.
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Affiliation(s)
- Daniel L. Dunkelmann
- Medical
Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
- Max
Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jason W. Chin
- Medical
Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
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5
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Choi JH, Kim S, Kang OY, Choi SY, Hyun JY, Lee HS, Shin I. Selective fluorescent labeling of cellular proteins and its biological applications. Chem Soc Rev 2024; 53:9446-9489. [PMID: 39109465 DOI: 10.1039/d4cs00094c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Proteins, which are ubiquitous in cells and critical to almost all cellular functions, are indispensable for life. Fluorescence imaging of proteins is key to understanding their functions within their native milieu, as it provides insights into protein localization, dynamics, and trafficking in living systems. Consequently, the selective labeling of target proteins with fluorophores has emerged as a highly active research area, encompassing bioorganic chemistry, chemical biology, and cell biology. Various methods for selectively labeling proteins with fluorophores in cells and tissues have been established and are continually being developed to visualize and characterize proteins. This review highlights research findings reported since 2018, with a focus on the selective labeling of cellular proteins with small organic fluorophores and their biological applications in studying protein-associated biological events. We also discuss the strengths and weaknesses of each labeling approach for their utility in living systems.
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Affiliation(s)
- Joo Hee Choi
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Sooin Kim
- Department of Chemistry, Sogang University, 04107 Seoul, Republic of Korea.
| | - On-Yu Kang
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Seong Yun Choi
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
- Pharmaceutical Chemistry, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Ji Young Hyun
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
- Pharmaceutical Chemistry, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 04107 Seoul, Republic of Korea.
| | - Injae Shin
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
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6
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Wang BL, Zeng P, Jiang C, Chen Y, Qu J, Song J. Aromatic Alcohol-Based pH-Sensitive Chromophore with a Unique Near-Infrared Dual-Band Solvatochromic Property and Its Application as a Ratiometric Fluorescent Sensor for G-Quadruplexes. Anal Chem 2024; 96:6186-6194. [PMID: 38594223 DOI: 10.1021/acs.analchem.3c05104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Solvatochromes have gained great attention because of their unique roles in monitoring biomolecular location, interaction, and dynamics. Particularly, solvatochromes presenting both red-shifting excitation and dual-band switchable emission are in great demand yet significantly difficult to come true. In this article, we disclose an aromatic alcohol-based pH-sensitive chromophore NIR-HBT that not only presents red-shifting excitation and solvent-dependent dual-band emission but also shows high photostability and excellent brightness. To the best of our knowledge, this is the first solvatochrome to simultaneously display these optical properties. Especially, in contrast to the reported dual-band solvatochromes whose solvatochromism is achieved by affecting their excited state behaviors, the solvatochromism of NIR-HBT is realized by modulating its ground state proton dissociation, which is a new solvatochromic mechanism that has not been reported. Furthermore, based on the dual-band solvatochromism of NIR-HBT and its intrinsic binding ability to GQs, near-infrared ratiometric detection of GQs is achieved. These results indicate that NIR-HBT is an attractive solvatochrome that can be used to develop near-infrared ratiometric biosensors for biological research. More broadly, the discovered solvatochromic mechanism can also open new horizons for exploring the solvatochrome.
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Affiliation(s)
- Bo-Lin Wang
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University); College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, P. R. China
| | - Pengju Zeng
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University); College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, P. R. China
| | - Chuang Jiang
- College of Chemistry, Sichuan University, No. 29 Wangjiang Road, Chengdu 610064, China
| | - Yu Chen
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University); College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, P. R. China
- Medical Engineering and Technology College, Xinjiang Medical University, Urumqi 830011, P. R. China
| | - Junle Qu
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University); College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, P. R. China
- Medical Engineering and Technology College, Xinjiang Medical University, Urumqi 830011, P. R. China
| | - Jun Song
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University); College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, P. R. China
- Medical Engineering and Technology College, Xinjiang Medical University, Urumqi 830011, P. R. China
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7
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Mehl BP, Vairaprakash P, Li L, Hinde E, MacNevin CJ, Hsu CW, Gratton E, Liu B, Hahn KM. Live-cell biosensors based on the fluorescence lifetime of environment-sensing dyes. CELL REPORTS METHODS 2024; 4:100734. [PMID: 38503289 PMCID: PMC10985238 DOI: 10.1016/j.crmeth.2024.100734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/13/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024]
Abstract
In this work, we examine the use of environment-sensitive fluorescent dyes in fluorescence lifetime imaging microscopy (FLIM) biosensors. We screened merocyanine dyes to find an optimal combination of environment-induced lifetime changes, photostability, and brightness at wavelengths suitable for live-cell imaging. FLIM was used to monitor a biosensor reporting conformational changes of endogenous Cdc42 in living cells. The ability to quantify activity using phasor analysis of a single fluorophore (e.g., rather than ratio imaging) eliminated potential artifacts. We leveraged these properties to determine specific concentrations of activated Cdc42 across the cell.
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Affiliation(s)
- Brian P Mehl
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pothiappan Vairaprakash
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Li Li
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Elizabeth Hinde
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California at Irvine, Irvine, CA 92617, USA
| | - Christopher J MacNevin
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chia-Wen Hsu
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California at Irvine, Irvine, CA 92617, USA
| | - Bei Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Klaus M Hahn
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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8
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Zhang F, Chen F, Zhong M, Shen R, Zhao Z, Wei H, Zhang B, Fang J. Imaging of Carbonic Anhydrase Level in Epilepsy with an Environment-Sensitive Fluorescent Probe. Anal Chem 2023; 95:14833-14841. [PMID: 37747928 DOI: 10.1021/acs.analchem.3c01368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Carbonic anhydrases (CAs) participate in various physiological and pathological activities by catalyzing the interconversion between carbon dioxide and bicarbonate ions. Under normal circumstances, they guarantee that the relevant biological reactions in our body occur within an appropriate time scale. Abnormal expression or activity alteration of CAs is closely related to the pathogenesis of diverse diseases. This work reports an inhibitor-directed fluorescent probe FMRs-CA for the detection of CAs. Excellent selectivity, favorable biocompatibility, and desirable blood-brain barrier (BBB) penetration endow the probe with the ability to image the fluctuation of CAs in cells and mice. We achieved in situ visualization of the increased CAs in hypoxic cells with this probe. Additionally, probe FMRs-CA was mainly enriched within the liver and gradually metabolized by the liver. With the help of FMRs-CA, the increase of CAs in epileptic mouse brains was revealed first from the perspective of imaging, providing the mechanism connection between abnormal CA expressions and epilepsy.
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Affiliation(s)
- Fang Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Fan Chen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Miao Zhong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Ruipeng Shen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Zhengjia Zhao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Haopai Wei
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Baoxin Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Jianguo Fang
- School of Chemistry and Chemical Engineering, Nanjing University of Science & Technology, Nanjing, Jiangsu 210094, China
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9
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Islam J, Conroy P, Fercher C, Kim M, Yaari Z, Jones M, Bell TDM, Caradoc-Davies T, Law R, Whisstock J, Heller D, Mahler S, Corrie S. Design of Polarity-Dependent Immunosensors Based on the Structural Analysis of Engineered Antibodies. ACS Chem Biol 2023; 18:1863-1871. [PMID: 37440171 DOI: 10.1021/acschembio.3c00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
"Reagentless" immunosensors are emerging to address the challenge of practical and sensitive detection of important biomarkers in real biological samples without the need for multistep assays and user intervention, with applications ranging from research tools to point-of-care diagnostics. Selective target binding to an affinity reagent is detected and reported in one step without the need for washing or additional reporters. In this study, we used a structure-guided approach to identify a mutation site in an antibody fragment for the polarity-dependent fluorophore, Anap, such that upon binding of the protein target cardiac troponin I, the Anap-labeled antibody would produce a detectable and dose-dependent shift in emission wavelength. We observed a significant emission wavelength shift of the Anap-labeled anti-cTnI mutant, with a blue shift of up to 37 nm, upon binding to the cTnI protein. Key differences in the resulting emission spectra between target peptides in comparison to whole proteins were also found; however, the affinity and binding characteristics remained unaffected when compared to the wild-type antibody. We also highlighted the potential flexibility of the approach by incorporating a near-infrared dye, IRDye800CW, into the same mutation site, which also resulted in a dose-dependent wavelength shift upon target incubation. These reagents can be used in experiments and devices to create simpler and more efficient biosensors across a range of research, medical laboratory, and point-of-care platforms.
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Affiliation(s)
- Jiaul Islam
- Department of Chemical and Biological Engineering, Monash University, Melbourne 3800, Australia
| | - Paul Conroy
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Christian Fercher
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Mijin Kim
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Centre, New York 10065, United States
| | - Zvi Yaari
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Centre, New York 10065, United States
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Martina Jones
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Toby D M Bell
- School of Chemistry, Monash University, Melbourne 3800, Australia
| | - Tom Caradoc-Davies
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
- Australian Synchrotron - ANSTO, Melbourne 3168, Australia
| | - Ruby Law
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - James Whisstock
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Daniel Heller
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Centre, New York 10065, United States
| | - Stephen Mahler
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Simon Corrie
- Department of Chemical and Biological Engineering, Monash University, Melbourne 3800, Australia
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10
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Mohamed M, Klenke AK, Anokhin MV, Amadou H, Bothwell PJ, Conroy B, Nesterov EE, Nesterova IV. Zero-Background Small-Molecule Sensors for Near-IR Fluorescent Imaging of Biomacromolecular Targets in Cells. ACS Sens 2023; 8:1109-1118. [PMID: 36866808 PMCID: PMC10515643 DOI: 10.1021/acssensors.2c02342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
In this study, we report a general approach to the design of a new generation of small-molecule sensors that produce a zero background but are brightly fluorescent in the near-IR spectral range upon selective interaction with a biomolecular target. We developed a fluorescence turn-on/-off mechanism based on the aggregation/deaggregation of phthalocyanine chromophores. As a proof of concept, we designed, prepared, and characterized sensors for in-cell visualization of epidermal growth factor receptor (EGFR) tyrosine kinase. We established a structure/bioavailability correlation, determined conditions for the optimal sensor uptake and imaging, and demonstrated binding specificity and applications over a wide range of treatment options involving live and fixed cells. The new approach enables high-contrast imaging and requires no in-cell chemical assembly or postexposure manipulations (i.e., washes). The general design principles demonstrated in this work can be extended toward sensors and imaging agents for other biomolecular targets.
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Affiliation(s)
- Myar Mohamed
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Anastasia K. Klenke
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Maksim V. Anokhin
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Harouna Amadou
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Paige J. Bothwell
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Brigid Conroy
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Evgueni E. Nesterov
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Irina V. Nesterova
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
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11
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Xia Q, Wan W, Jin W, Huang Y, Sun R, Wang M, Jing B, Peng C, Dong X, Zhang R, Gao Z, Liu Y. Solvatochromic Cellular Stress Sensors Reveal the Compactness Heterogeneity and Dynamics of Aggregated Proteome. ACS Sens 2022; 7:1919-1925. [PMID: 35776067 DOI: 10.1021/acssensors.2c00566] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deterioration of protein homeostasis (proteostasis) often induces aberrant proteome aggregation. Visualization and dissection of the stressed proteome are of particular interest given their association with numerous degenerative diseases. Recent progress in chemical cellular stress sensors allows for direct visualization of aggregated proteome. Beyond its localization and morphology, the physicochemical nature and the dynamics of the aggregated proteome have been challenging to explore. Herein, we developed a series of solvatochromic fluorene-based D-π-A probes that can selectively and noncovalently bind to a misfolded and aggregated proteome and report on their compactness heterogeneity upon cellular stresses. We achieved this goal by variation of the heterocyclic acceptors to modulate their solvatochromism and binding affinity to amorphous aggregated proteins. The optimized sensor P6 was capable of sensing the polarity differences among different aggregated proteins via its fluorescence emission wavelength. In live cells, P6 revealed the cellular compactness heterogeneity in the aggregated proteome upon cellular stresses. Given the combinative solvatochromic and noncovalent properties, our probe can reversibly monitor the dynamic changes in the aggregated proteome compactness upon stress and after stress recovery, suggesting its potential applications in search of therapeutics to counteract disease-causing proteome stresses.
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Affiliation(s)
- Qiuxuan Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Rui Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Biao Jing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Congcong Peng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Rixin Zhang
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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12
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Al Kelabi D, Dey A, Alimi LO, Piwoński H, Habuchi S, Khashab NM. Photostable polymorphic organic cages for targeted live cell imaging. Chem Sci 2022; 13:7341-7346. [PMID: 35799823 PMCID: PMC9214840 DOI: 10.1039/d2sc00836j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/01/2022] [Indexed: 11/21/2022] Open
Abstract
Fluorescent microscopy is a powerful tool for studying the cellular dynamics of biological systems. Small-molecule organic fluorophores are the most commonly used for live cell imaging; however, they often suffer from low solubility, limited photostability and variable targetability. Herein, we demonstrate that a tautomeric organic cage, OC1, has high cell permeability, photostability and selectivity towards the mitochondria. We further performed a structure–activity study to investigate the role of the keto–enol tautomerization, which affords strong and consistent fluorescence in dilute solutions through supramolecular self-assembly. Significantly, OC1 can passively diffuse through the cell membrane directly targeting the mitochondria without going through the endosomes or the lysosomes. We envisage that designing highly stable and biocompatible self-assembled fluorophores that can passively diffuse through the cell membrane while selectively targeting specific organelles will push the boundaries of fluorescent microscopy to visualize intricate cellular processes at the single molecule level in live samples. In this article, we demonstrate the relatively unexplored potential of organic cages for use in targeted live cell imaging and highlight the importance of inter- and intramolecular interactions to stabilize and improve the performance of fluorophores.![]()
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Affiliation(s)
- Dana Al Kelabi
- Smart Hybrid Materials (SHMs) Laboratory, Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Avishek Dey
- Smart Hybrid Materials (SHMs) Laboratory, Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Lukman O Alimi
- Smart Hybrid Materials (SHMs) Laboratory, Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Hubert Piwoński
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division Thuwal 23955-6900 Saudi Arabia
| | - Satoshi Habuchi
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division Thuwal 23955-6900 Saudi Arabia
| | - Niveen M Khashab
- Smart Hybrid Materials (SHMs) Laboratory, Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Kingdom of Saudi Arabia
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13
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Schultz M, Müller R, Ermakova Y, Hoffmann J, Schultz C. Membrane-Permeant, Bioactivatable Coumarin Derivatives for In-Cell Labelling. Chembiochem 2022; 23:e202100699. [PMID: 35199435 PMCID: PMC9305936 DOI: 10.1002/cbic.202100699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/21/2022] [Indexed: 11/29/2022]
Abstract
The delivery of small molecule fluorophores with minimal compartmentalization is currently one of the most critical technical problems in intracellular labelling. Here we introduce sulfonated and phosphonated coumarin dyes, demonstrate rapid cell entry via a prodrug approach, and show a lack of interaction with membranes, organelles, or other compartments. The dyes show no specific localization and are evenly distributed in the cells. Our fluorogenic, clickable phosphonate derivatives successfully tagged model targets in intact cells and the increase in brightness upon click reaction was around 60-fold.
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Affiliation(s)
- Madeleine Schultz
- Cell Biology & Biophysics UnitEuropean Molecular Biology LaboratoryMeyerhofstr. 1HeidelbergGermany
| | - Rainer Müller
- Cell Biology & Biophysics UnitEuropean Molecular Biology LaboratoryMeyerhofstr. 1HeidelbergGermany
| | - Yulia Ermakova
- Cell Biology & Biophysics UnitEuropean Molecular Biology LaboratoryMeyerhofstr. 1HeidelbergGermany
| | - Jan‐Erik Hoffmann
- Cell Biology & Biophysics UnitEuropean Molecular Biology LaboratoryMeyerhofstr. 1HeidelbergGermany
| | - Carsten Schultz
- Cell Biology & Biophysics UnitEuropean Molecular Biology LaboratoryMeyerhofstr. 1HeidelbergGermany
- Dept. of Chemical Physiology and BiochemistryOregon Health & Science UniversityPortland, ORUSA
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14
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Li C, Wang T, Fan M, Wang N, Lin X, Sun Y, Cui X. Hydrogen Bond-Enhanced Nanoaggregation and Antisolvatochromic Fluorescence for Protein-Recognition by Si-Coumarins. NANO LETTERS 2022; 22:1954-1962. [PMID: 35138866 DOI: 10.1021/acs.nanolett.1c04551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Silicon-substituted coumarin (SiC) was established as a substantial family of both intramolecular and intermolecular hydrogen bond (H-bond) enhanced fluorescent probes for sensitively tracking proteins in vivo through the assemble and disassemble of its nanoaggregates. The intramolecular H-bond in SiC has led to significant aggregation, antisolvatochromism, and strong fluorescence with bathochromically shifted spectra into far-red or near-infrared (NIR) regions in polar, protic environments. Without further furnishing with organic linkers, the compact skeleton of SiC bearing H-bond has ensured sensitively and selectively sensing the targeting proteins with the protic reaction pockets through efficient disassemble of the aggregates. In the existence of strong intermolecular H-bonds with the target protein pocket, SiC resolved as high as >250-fold fluorescence enhancement. Selectively tracking proteins, including human serum albumin, human carbonic anhydrase (hCAII), avidin, SNAP-tag protein, and translocator protein, has confirmed SiC a versatile skeleton for sensitively monitoring proteins in complicated biological systems.
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Affiliation(s)
- Chen Li
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P.R. China
| | - Ting Wang
- Department of Organic Chemistry, College of Pharmacy, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, P.R. China
| | - Mengting Fan
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P.R. China
| | - Ning Wang
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P.R. China
| | - Xiaofeng Lin
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P.R. China
| | - Yan Sun
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P.R. China
| | - Xiaoyan Cui
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P.R. China
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15
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Dong X, Wan W, Zeng L, Jin W, Huang Y, Shen D, Bai Y, Zhao Q, Zhang L, Liu Y, Gao Z. Regulation of Fluorescence Solvatochromism To Resolve Cellular Polarity upon Protein Aggregation. Anal Chem 2021; 93:16447-16455. [PMID: 34859995 DOI: 10.1021/acs.analchem.1c03401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Common solvatochromic fluorophores exhibit a bathochromic fluorescence emission wavelength shift accompanied by intensity attenuation due to the presence of nonradiative decay pathways at the excited state. Such intrinsic but inevitable fluorescence quenching of solvatochromism impedes its applications to faithfully quantify local polarity, especially in a polar environment. Herein, we report a new donor-π-acceptor (D-π-A) type solvatochromic fluorophore scaffold containing a perfluorophenyl group that exhibits both a solvatochromic emission wavelength shift and a controllable emission intensity upon polarity fluctuation. The regulation of fluorescence solvatochromism and colors was achieved by tuning the aryl donors. We exploited such desired solvatochromism of these probes to monitor protein misfolding and aggregation via wavelength shift. Finally, the polarity of pathogenic aggregated proteins was quantified by HaloTag bioorthogonal labeling technology in live cells. While much effort has been devoted to resolving the morphology of pathogenic aggregated proteins, this work provides quantitative hints regarding the chemical information at this disease-related protein interphase.
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Affiliation(s)
- Xuepeng Dong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, P. R. China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Lianggang Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,University of the Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, P. R. China
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16
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Bai Y, Wan W, Huang Y, Jin W, Lyu H, Xia Q, Dong X, Gao Z, Liu Y. Quantitative interrogation of protein co-aggregation using multi-color fluorogenic protein aggregation sensors. Chem Sci 2021; 12:8468-8476. [PMID: 34221329 PMCID: PMC8221170 DOI: 10.1039/d1sc01122g] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/19/2021] [Indexed: 12/27/2022] Open
Abstract
Co-aggregation of multiple pathogenic proteins is common in neurodegenerative diseases but deconvolution of such biochemical process is challenging. Herein, we developed a dual-color fluorogenic thermal shift assay to simultaneously report on the aggregation of two different proteins and quantitatively study their thermodynamic stability during co-aggregation. Expansion of spectral coverage was first achieved by developing multi-color fluorogenic protein aggregation sensors. Orthogonal detection was enabled by conjugating sensors of minimal fluorescence crosstalk to two different proteins via sortase-tag technology. Using this assay, we quantified shifts in melting temperatures in a heterozygous model protein system, revealing that the thermodynamic stability of wild-type proteins was significantly compromised by the mutant ones but not vice versa. We also examined how small molecule ligands selectively and differentially interfere with such interplay. Finally, we demonstrated these sensors are suited to visualize how different proteins exert influence on each other upon their co-aggregation in live cells.
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Affiliation(s)
- Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Qiuxuan Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University 467 Zhongshan Road Dalian 116044 China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University 467 Zhongshan Road Dalian 116044 China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
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17
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Raja SO, Sivaraman G, Biswas S, Singh G, Kalim F, Kandaswamy P, Gulyani A. A Tunable Palette of Molecular Rotors Allows Multicolor, Ratiometric Fluorescence Imaging and Direct Mapping of Mitochondrial Heterogeneity. ACS APPLIED BIO MATERIALS 2021; 4:4361-4372. [PMID: 35006848 DOI: 10.1021/acsabm.1c00135] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Environment-sensitive molecular probes offer the potential for a comprehensive mapping of the complex cellular milieu. We present here a radically new strategy of multiplexing highly sensitive, spectrally tuned fluorescent dyes for sensing cellular microenvironment. To achieve this multicolor, ratiometric cellular imaging, we first developed a series of highly sensitive, tunable molecular rotors for mitochondrial imaging, with emission wavelengths spanning the visible spectrum. These fluorogenic merocyanine dyes are all sensitive to solvent viscosity despite distinctive photophysical features. Our results show that merocyanine dyes can show a rotor-like behavior despite significant changes to the conventional donor-acceptor or push-pull scaffolds, thereby revealing conserved features of rotor dye chemistry. Developing closely related but spectrally separated dyes that have distinct response functions allows us to do ″two-color, two-dye″ imaging of the mitochondrial microenvironment. Our results with multidye, combinatorial imaging provide a direct visualization of the intrinsic heterogeneity of the mitochondrial microenvironment. The overall mitochondrial microenvironment (including contributions from local membrane order) as reported through two-color fluorescence ″ratio″ changes of multiplexed rotor dyes shows dynamic heterogeneity with distinct spatiotemporal signatures that evolve over time and respond to chemical perturbations. Our results offer a powerful illustration of how multiplexed dye imaging allows the quantitative imaging of mitochondrial membrane order and cellular microenvironment.
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Affiliation(s)
- Sufi O Raja
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bengaluru 560065, India.,Department of Physics, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Gandhi Sivaraman
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bengaluru 560065, India.,Gandhigram Rural Institute, Gandhigram, Tamil Nadu 624302, India
| | - Sayan Biswas
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bengaluru 560065, India
| | - Gaurav Singh
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bengaluru 560065, India
| | - Fouzia Kalim
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bengaluru 560065, India.,National Centre for Biological Sciences, GKVK Post, Bellary Road, Bengaluru 560065, India
| | - Ponnuvel Kandaswamy
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bengaluru 560065, India
| | - Akash Gulyani
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bengaluru 560065, India.,Department of Biochemistry, School of Life Sciences, University of Hyderabad, Central University Post, Prof. C.R. Rao, Gachibowli, Hyderabad, Telengana 500046, India
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18
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Zuo WF, Zhou J, Wu YL, Fang HY, Lang XJ, Li Y, Zhan G, Han B. Synthesis of spiro(indoline-2,3′-hydropyridazine) via an “on-water” [4 + 2] annulation reaction. Org Chem Front 2021. [DOI: 10.1039/d0qo01422b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An on-water [4 + 2] annulation reaction between 2-methyl-3H-indolium salt and α-bromo N-acyl hydrazone has been developed. The environmentally friendly strategy provides the first facile access to spiro(indoline-2,3'-hydropyridazine) scaffolds.
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Affiliation(s)
- Wei-Fang Zuo
- State Key Laboratory of Southwestern Chinese Medicine Resources
- School of Pharmacy
- Chengdu University of Traditional Chinese Medicine
- Chengdu 611137
- P.R. China
| | - Jin Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources
- School of Pharmacy
- Chengdu University of Traditional Chinese Medicine
- Chengdu 611137
- P.R. China
| | - Yu-Ling Wu
- State Key Laboratory of Southwestern Chinese Medicine Resources
- School of Pharmacy
- Chengdu University of Traditional Chinese Medicine
- Chengdu 611137
- P.R. China
| | - Hua-Ying Fang
- State Key Laboratory of Southwestern Chinese Medicine Resources
- School of Pharmacy
- Chengdu University of Traditional Chinese Medicine
- Chengdu 611137
- P.R. China
| | - Xing-Jiang Lang
- State Key Laboratory of Southwestern Chinese Medicine Resources
- School of Pharmacy
- Chengdu University of Traditional Chinese Medicine
- Chengdu 611137
- P.R. China
| | - Ya Li
- State Key Laboratory of Southwestern Chinese Medicine Resources
- School of Pharmacy
- Chengdu University of Traditional Chinese Medicine
- Chengdu 611137
- P.R. China
| | - Gu Zhan
- State Key Laboratory of Southwestern Chinese Medicine Resources
- School of Pharmacy
- Chengdu University of Traditional Chinese Medicine
- Chengdu 611137
- P.R. China
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources
- School of Pharmacy
- Chengdu University of Traditional Chinese Medicine
- Chengdu 611137
- P.R. China
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19
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Matikonda SS, Ivanic J, Gomez M, Hammersley G, Schnermann MJ. Core remodeling leads to long wavelength fluoro-coumarins. Chem Sci 2020; 11:7302-7307. [PMID: 34123014 PMCID: PMC8159424 DOI: 10.1039/d0sc02566f] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Low molecular weight, uncharged far-red and NIR dyes would be enabling for a range of imaging applications. Rational redesign of the coumarin scaffold leads to Fluoro-Coumarins (FCs), the lowest molecular weight dyes with emission maxima beyond 700, 800, and 900 nm. FCs display large Stokes shifts and high environmental sensitivity, with a 40-fold increase in emission intensity in hydrophobic solvents. Untargeted variants exhibit selective lipid droplet and nuclear staining in live cells. Furthermore, sulfo-lipid derivatization enables active targeting to the plasma membrane. Overall, these studies report a promising platform for the development of biocompatible, context-responsive imaging agents. Fluoro-Coumarins are a novel class of far-red and near-infrared solvent sensitive dyes of exceptionally low molecular weight.![]()
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Affiliation(s)
- Siddharth S Matikonda
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick Maryland 21702 USA
| | - Joseph Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research Frederick Maryland 21702 USA
| | - Miguel Gomez
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick Maryland 21702 USA
| | - Gabrielle Hammersley
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick Maryland 21702 USA
| | - Martin J Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick Maryland 21702 USA
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20
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Gu Y, Zhao Z, Niu G, Zhang H, Wang Y, Kwok RTK, Lam JWY, Tang BZ. Visualizing semipermeability of the cell membrane using a pH-responsive ratiometric AIEgen. Chem Sci 2020; 11:5753-5758. [PMID: 32832051 PMCID: PMC7422962 DOI: 10.1039/d0sc02097d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/14/2020] [Indexed: 12/15/2022] Open
Abstract
In clinical chemotherapy, some basic drugs cannot enter the hydrophobic cell membrane because of ionization in the acidic tumor microenvironment, a phenomenon known as ion trapping. In this study, we developed a method to visualize this ion trapping phenomenon by utilizing a pH-responsive ratiometric AIEgen, dihydro berberine (dhBBR). By observing the intracellular fluorescence of dhBBR, we found that non-ionized dhBBR can enter cells more easily than ionized forms, which is in accordance with the concept of ion trapping. In addition, dhBBR shows superior anti-photobleaching ability to Curcumin thanks to its AIE properties. These results suggest that dhBBR can serve as a bioprobe for ion trapping.
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Affiliation(s)
- Yuan Gu
- Department of Chemical and Biological Engineering , Department of Chemistry , The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction , Institute for Advanced Study , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China .
- HKUST-Shenzhen Research Institute , No. 9 Yuexing 1st RD, South Area Hi-tech Park , Nanshan , Shenzhen 518057 , China
| | - Zheng Zhao
- Department of Chemical and Biological Engineering , Department of Chemistry , The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction , Institute for Advanced Study , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China .
- HKUST-Shenzhen Research Institute , No. 9 Yuexing 1st RD, South Area Hi-tech Park , Nanshan , Shenzhen 518057 , China
| | - Guangle Niu
- Department of Chemical and Biological Engineering , Department of Chemistry , The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction , Institute for Advanced Study , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China .
- HKUST-Shenzhen Research Institute , No. 9 Yuexing 1st RD, South Area Hi-tech Park , Nanshan , Shenzhen 518057 , China
| | - Han Zhang
- Center for Aggregation-Induced Emission , SCUT-HKUST Joint Research Institute , State Key Laboratory of Luminescent Materials and Devices , South China University of Technology , Guangzhou 510640 , China
| | - Yiming Wang
- Department of Chemical and Biological Engineering , Department of Chemistry , The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction , Institute for Advanced Study , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China .
- HKUST-Shenzhen Research Institute , No. 9 Yuexing 1st RD, South Area Hi-tech Park , Nanshan , Shenzhen 518057 , China
| | - Ryan T K Kwok
- Department of Chemical and Biological Engineering , Department of Chemistry , The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction , Institute for Advanced Study , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China .
- HKUST-Shenzhen Research Institute , No. 9 Yuexing 1st RD, South Area Hi-tech Park , Nanshan , Shenzhen 518057 , China
| | - Jacky W Y Lam
- Department of Chemical and Biological Engineering , Department of Chemistry , The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction , Institute for Advanced Study , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China .
- HKUST-Shenzhen Research Institute , No. 9 Yuexing 1st RD, South Area Hi-tech Park , Nanshan , Shenzhen 518057 , China
| | - Ben Zhong Tang
- Department of Chemical and Biological Engineering , Department of Chemistry , The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction , Institute for Advanced Study , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China .
- HKUST-Shenzhen Research Institute , No. 9 Yuexing 1st RD, South Area Hi-tech Park , Nanshan , Shenzhen 518057 , China
- Center for Aggregation-Induced Emission , SCUT-HKUST Joint Research Institute , State Key Laboratory of Luminescent Materials and Devices , South China University of Technology , Guangzhou 510640 , China
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21
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Ducharme GT, LaCasse Z, Sheth T, Nesterova IV, Nesterov EE. Design of Turn‐On Near‐Infrared Fluorescent Probes for Highly Sensitive and Selective Monitoring of Biopolymers. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gerard T. Ducharme
- Department of Chemistry Louisiana State University Baton Rouge LA 70803 USA
| | - Zane LaCasse
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Tanya Sheth
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Irina V. Nesterova
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Evgueni E. Nesterov
- Department of Chemistry Louisiana State University Baton Rouge LA 70803 USA
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
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22
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Ducharme GT, LaCasse Z, Sheth T, Nesterova IV, Nesterov EE. Design of Turn‐On Near‐Infrared Fluorescent Probes for Highly Sensitive and Selective Monitoring of Biopolymers. Angew Chem Int Ed Engl 2020; 59:8440-8444. [DOI: 10.1002/anie.202000108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/03/2020] [Indexed: 11/05/2022]
Affiliation(s)
- Gerard T. Ducharme
- Department of Chemistry Louisiana State University Baton Rouge LA 70803 USA
| | - Zane LaCasse
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Tanya Sheth
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Irina V. Nesterova
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Evgueni E. Nesterov
- Department of Chemistry Louisiana State University Baton Rouge LA 70803 USA
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
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23
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Abstract
The dynamic nature of histone post-translational modifications such as methylation or acetylation makes possible the alteration of disease associated epigenetic states through the manipulation of the associated epigenetic machinery. One approach is through small molecule perturbation. Chemical probes of epigenetic reader domains have been critical in improving our understanding of the biological consequences of modulating their targets, while also enabling the development of novel probe-based reagents. By appending a functional handle to a reader domain probe, a chemical toolbox of reagents can be created to facilitate chemiprecipitation of epigenetic complexes, evaluate probe selectivity, develop in vitro screening assays, visualize cellular target localization, enable target degradation and recruit epigenetic machinery to a site within the genome in a highly controlled fashion.
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Single-wavelength Excited Ratiometric Fluorescence pH Probe to Image Intracellular Trafficking of Tobacco Mosaic Virus. CHINESE JOURNAL OF POLYMER SCIENCE 2019. [DOI: 10.1007/s10118-020-2365-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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25
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Cromwell B, Dubnicka M, Dubrawski S, Levine M. Identification of 15 Phthalate Esters in Commercial Cheese Powder via Cyclodextrin-Promoted Fluorescence Detection. ACS OMEGA 2019; 4:17009-17015. [PMID: 31646248 PMCID: PMC6796234 DOI: 10.1021/acsomega.9b02585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
A challenge for detecting phthalates in commercial products such as cheese powders is that the composition of the products is highly complex, and current methods for detection rely on gas chromatography-mass spectrometry, which is not portable and cannot be used by individual consumers at a time and place of their choosing. Herein, we report the development of a new method for phthalate detection in cheese powder using cyclodextrin-promoted fluorescence detection, in which the presence of the phthalate analytes leads to highly analyte-specific changes in the fluorescence emission signal of a fluorophore bound in a cyclodextrin cavity. This method relies on subtle changes in the analyte affinity for the fluorophore and the cyclodextrin cavity and provides for markedly more straightforward sample preparation procedures and an extremely rapid read-out signal, with potential for the development of portable fluorescence sensors. Using this method, we were able to detect 15 phthalate esters with highly analyte-specific responses and at concentrations as low as 0.12 μM, which is well below regulatory levels of concern. Computational investigations strongly support the observed experimental trends.
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Affiliation(s)
- Benjamin Cromwell
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Mara Dubnicka
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Sage Dubrawski
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
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26
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Zheng Q, Ayala AX, Chung I, Weigel AV, Ranjan A, Falco N, Grimm JB, Tkachuk AN, Wu C, Lippincott-Schwartz J, Singer RH, Lavis LD. Rational Design of Fluorogenic and Spontaneously Blinking Labels for Super-Resolution Imaging. ACS CENTRAL SCIENCE 2019; 5:1602-1613. [PMID: 31572787 PMCID: PMC6764213 DOI: 10.1021/acscentsci.9b00676] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Indexed: 05/24/2023]
Abstract
Rhodamine dyes exist in equilibrium between a fluorescent zwitterion and a nonfluorescent lactone. Tuning this equilibrium toward the nonfluorescent lactone form can improve cell-permeability and allow creation of "fluorogenic" compounds-ligands that shift to the fluorescent zwitterion upon binding a biomolecular target. An archetype fluorogenic dye is the far-red tetramethyl-Si-rhodamine (SiR), which has been used to create exceptionally useful labels for advanced microscopy. Here, we develop a quantitative framework for the development of new fluorogenic dyes, determining that the lactone-zwitterion equilibrium constant (K L-Z) is sufficient to predict fluorogenicity. This rubric emerged from our analysis of known fluorophores and yielded new fluorescent and fluorogenic labels with improved performance in cellular imaging experiments. We then designed a novel fluorophore-Janelia Fluor 526 (JF526)-with SiR-like properties but shorter fluorescence excitation and emission wavelengths. JF526 is a versatile scaffold for fluorogenic probes including ligands for self-labeling tags, stains for endogenous structures, and spontaneously blinking labels for super-resolution immunofluorescence. JF526 constitutes a new label for advanced microscopy experiments, and our quantitative framework will enable the rational design of other fluorogenic probes for bioimaging.
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Affiliation(s)
- Qinsi Zheng
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Anthony X. Ayala
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Inhee Chung
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Aubrey V. Weigel
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Anand Ranjan
- Department of Biology and Department of Molecular
Biology and Genetics, Johns Hopkins University, Baltimore,
Maryland 21218, United States
| | - Natalie Falco
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Ariana N. Tkachuk
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Carl Wu
- Department of Biology and Department of Molecular
Biology and Genetics, Johns Hopkins University, Baltimore,
Maryland 21218, United States
| | | | - Robert H. Singer
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
- Department of Anatomy and Structural Biology,
Albert Einstein College of Medicine, Bronx, New York 10461,
United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
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27
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Du H, Zhang X, Liu Z, Qu F. A supersensitive biosensor based on MoS2 nanosheet arrays for the real-time detection of H2O2 secreted from living cells. Chem Commun (Camb) 2019; 55:9653-9656. [DOI: 10.1039/c9cc03502h] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A self-supported MoS2 nanosheet biosensor for highly sensitive detection of H2O2 secreted from live cells.
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Affiliation(s)
- Huitong Du
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- China
| | - Xinyue Zhang
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- China
| | - Zhe Liu
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- China
| | - Fengli Qu
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- China
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