1
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Miao Y, Yu ZQ, Xu S, Yan M. Quinone Methide Based Self-Immobilizing Molecular Fluorescent Probes for In Situ Imaging of Enzymes. Chem Asian J 2024; 19:e202400189. [PMID: 38514393 DOI: 10.1002/asia.202400189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 03/23/2024]
Abstract
Enzymes play important roles not only in normal physiological processes but in the development of many diseases. In situ imaging of enzymes with high-resolution in living systems would helpful for clinical diagnosis and treatment. However, many molecular fluorescent probes suffer from the drawback of diffusing away from the reaction site of enzymes even out of the cells, losing the in situ information and resulting in poor imaging resolution. Quinone methide (QM) based self-immobilizing probes allow the fluorescent signal to be immobilized near the target for an extended period without deactivating the target enzymes, ensuring that it will provide amplified signals and in situ information of the target with high resolution. In this review, we summarized the recent progress of QM-based self-immobilizing probes including their design strategies, working mechanisms, classifications and applications in in situ enzyme imaging. This review calls for the development of more activatable QM-based probe with the advantages of high stability in the absence of the target but very high labeling efficiency after activation.
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Affiliation(s)
- Yeru Miao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Zhen-Qing Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Shuai Xu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Mei Yan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
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2
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Aktalay A, Khan TA, Bossi ML, Belov VN, Hell SW. Photoactivatable Carbo- and Silicon-Rhodamines and Their Application in MINFLUX Nanoscopy. Angew Chem Int Ed Engl 2023; 62:e202302781. [PMID: 37555720 DOI: 10.1002/anie.202302781] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 08/05/2023] [Accepted: 08/08/2023] [Indexed: 08/10/2023]
Abstract
New photoactivatable fluorescent dyes (rhodamine, carbo- and silicon-rhodamines [SiR]) with emission ranging from green to far red have been prepared, and their photophysical properties studied. The photocleavable 2-nitrobenzyloxycarbonyl unit with an alpha-carboxyl group as a branching point and additional functionality was attached to a polycyclic and lipophilic fluorescent dye. The photoactivatable probes having the HaloTagTM amine (O2) ligand bound with a dye core were obtained and applied for live-cell staining in stable cell lines incorporating Vimentin (VIM) or Nuclear Pore Complex Protein NUP96 fused with the HaloTag. The probes were applied in 2D (VIM, NUP96) and 3D (VIM) MINFLUX nanoscopy, as well as in superresolution fluorescence microscopy with single fluorophore activation (VIM, live-cell labeling). Images of VIM and NUPs labeled with different dyes were acquired and their apparent dimensions and shapes assessed on a lower single-digit nanometer scale. Applicability and performance of the photoactivatable dye derivatives were evaluated in terms of photoactivation rate, labeling and detection efficiency, number of detected photons per molecule and other parameters related to MINFLUX nanoscopy.
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Affiliation(s)
- Ayse Aktalay
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research (MPI-MR), Jahnstraße 29, 69120, Heidelberg, Germany
| | - Taukeer A Khan
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), Am Fassberg 11, 37077, Göttingen, Germany
| | - Mariano L Bossi
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research (MPI-MR), Jahnstraße 29, 69120, Heidelberg, Germany
| | - Vladimir N Belov
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), Am Fassberg 11, 37077, Göttingen, Germany
| | - Stefan W Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research (MPI-MR), Jahnstraße 29, 69120, Heidelberg, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), Am Fassberg 11, 37077, Göttingen, Germany
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3
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Jung YL, Sarkar S, Ha J, Park SB, Ahn KH. Fluorophore Labeling of Proteins: a Versatile Trigger-Release-Conjugation Platform Based on the Quinone Methide Chemistry. Bioconjug Chem 2022; 33:1543-1551. [PMID: 35900309 DOI: 10.1021/acs.bioconjchem.2c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In situ conjugation of fluorescent molecules to biomolecules such as proteins under spatiotemporal control offers a powerful means for studying biological systems. For that purpose, the o-quinone methide chemistry involving a sequence of the trigger-release-conjugation (TRC) process provides a versatile conjugation method. We have developed a new TRC platform bearing a quaternary ammonium salt for the release process, which can be structurally modified and readily synthesized from commonly used aryl alcohol-type organic fluorophores under environmentally benign conditions. We show that different aryl alcohol fluorophores containing the o-(morpholinium)methyl group for the release process allow efficient fluorophore labeling of proteins under both light- and chemical-triggering conditions. The bioconjugation in cells as well as in tissues was further demonstrated with an o-(morpholinium)methyl analogue containing a triggering group sensitive to reactive oxygen species. The new TRC system thus provides a versatile and unique platform for in situ fluorophore labeling of proteins in biological systems under spatiotemporal control.
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Affiliation(s)
- Yun Lim Jung
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Cheongam-ro 77, Nam-gu, Pohang 37673, Republic of Korea
| | - Sourav Sarkar
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Cheongam-ro 77, Nam-gu, Pohang 37673, Republic of Korea
| | - Jaeyoung Ha
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Seung Bum Park
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Kyo Han Ahn
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Cheongam-ro 77, Nam-gu, Pohang 37673, Republic of Korea
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4
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Jemas A, Xie Y, Pigga JE, Caplan JL, am Ende CW, Fox JM. Catalytic Activation of Bioorthogonal Chemistry with Light (CABL) Enables Rapid, Spatiotemporally Controlled Labeling and No-Wash, Subcellular 3D-Patterning in Live Cells Using Long Wavelength Light. J Am Chem Soc 2022; 144:1647-1662. [PMID: 35072462 PMCID: PMC9364228 DOI: 10.1021/jacs.1c10390] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Described is the spatiotemporally controlled labeling and patterning of biomolecules in live cells through the catalytic activation of bioorthogonal chemistry with light, referred to as "CABL". Here, an unreactive dihydrotetrazine (DHTz) is photocatalytically oxidized in the intracellular environment by ambient O2 to produce a tetrazine that immediately reacts with a trans-cyclooctene (TCO) dienophile. 6-(2-Pyridyl)dihydrotetrazine-3-carboxamides were developed as stable, cell permeable DHTz reagents that upon oxidation produce the most reactive tetrazines ever used in live cells with Diels-Alder kinetics exceeding k2 of 106 M-1 s-1. CABL photocatalysts are based on fluorescein or silarhodamine dyes with activation at 470 or 660 nm. Strategies for limiting extracellular production of singlet oxygen are described that increase the cytocompatibility of photocatalysis. The HaloTag self-labeling platform was used to introduce DHTz tags to proteins localized in the nucleus, mitochondria, actin, or cytoplasm, and high-yielding subcellular activation and labeling with a TCO-fluorophore were demonstrated. CABL is light-dose dependent, and two-photon excitation promotes CABL at the suborganelle level to selectively pattern live cells under no-wash conditions. CABL was also applied to spatially resolved live-cell labeling of an endogenous protein target by using TIRF microscopy to selectively activate intracellular monoacylglycerol lipase tagged with DHTz-labeled small molecule covalent inhibitor. Beyond spatiotemporally controlled labeling, CABL also improves the efficiency of "ordinary" tetrazine ligations by rescuing the reactivity of commonly used 3-aryl-6-methyltetrazine reporters that become partially reduced to DHTzs inside cells. The spatiotemporal control and fast rates of photoactivation and labeling of CABL should enable a range of biomolecular labeling applications in living systems.
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Affiliation(s)
- Andrew Jemas
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Yixin Xie
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Jessica E. Pigga
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Jeffrey L. Caplan
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
| | - Christopher W. am Ende
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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5
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Tang Q, Liu L, Guo Y, Zhang X, Zhang S, Jia Y, Du Y, Cheng B, Yang L, Huang Y, Chen X. Optical Cell Tagging for Spatially Resolved Single‐Cell RNA Sequencing. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202113929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Qi Tang
- College of Chemistry and Molecular Engineering Peking-Tsinghua Center for Life Sciences Beijing National Laboratory for Molecular Sciences Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Lu Liu
- Biomedical Pioneering Innovation Center (BIOPIC) School of Life Sciences College of Chemistry and Molecular Engineering Beijing Advanced Innovation Center for Genomics (ICG) Peking-Tsinghua Center for Life Science and Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Yilan Guo
- College of Chemistry and Molecular Engineering Peking-Tsinghua Center for Life Sciences Beijing National Laboratory for Molecular Sciences Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Xu Zhang
- College of Chemistry and Molecular Engineering Peking-Tsinghua Center for Life Sciences Beijing National Laboratory for Molecular Sciences Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Shaoran Zhang
- College of Chemistry and Molecular Engineering Peking-Tsinghua Center for Life Sciences Beijing National Laboratory for Molecular Sciences Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Yan Jia
- Renal Division Peking University First Hospital Beijing 100034 China
- Institute of Nephrology Key Laboratory of CKD Prevention and Treatment of Ministry of Education of China Peking University Beijing 100871 China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases Chinese Academy of Medical Sciences Beijing 100730 China
| | - Yifei Du
- College of Chemistry and Molecular Engineering Peking-Tsinghua Center for Life Sciences Beijing National Laboratory for Molecular Sciences Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Bo Cheng
- College of Chemistry and Molecular Engineering Peking-Tsinghua Center for Life Sciences Beijing National Laboratory for Molecular Sciences Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Li Yang
- Renal Division Peking University First Hospital Beijing 100034 China
- Institute of Nephrology Key Laboratory of CKD Prevention and Treatment of Ministry of Education of China Peking University Beijing 100871 China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases Chinese Academy of Medical Sciences Beijing 100730 China
| | - Yanyi Huang
- Biomedical Pioneering Innovation Center (BIOPIC) School of Life Sciences College of Chemistry and Molecular Engineering Beijing Advanced Innovation Center for Genomics (ICG) Peking-Tsinghua Center for Life Science and Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Xing Chen
- College of Chemistry and Molecular Engineering Peking-Tsinghua Center for Life Sciences Beijing National Laboratory for Molecular Sciences Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
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Tang Q, Liu L, Guo Y, Zhang X, Zhang S, Jia Y, Du Y, Cheng B, Yang L, Huang Y, Chen X. Optical Cell Tagging for Spatially Resolved Single-Cell RNA Sequencing. Angew Chem Int Ed Engl 2021; 61:e202113929. [PMID: 34970821 DOI: 10.1002/anie.202113929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Indexed: 01/13/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for profiling gene expression of distinct cell populations at the single-cell level. However, the information of the positions of cells within the multicellular samples is missing in scRNA-seq datasets. To overcome this limitation, we herein develop OpTAG (optical cell tagging) as a new chemical platform for attaching functional tags onto cell surfaces in a spatially resolved manner. With OpTAG, we establish OpTAG-seq, which enables spatially resolved scRNA-seq. We apply OpTAG-seq to investigate the spatially defined transcriptional program in migrating cancer cells and identified a list of genes that are potential regulators for cancer cell migration and invasion. OpTAG-seq provides a convenient method for mapping cellular heterogeneity with spatial information within multicellular biological systems.
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Affiliation(s)
- Qi Tang
- College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Lu Liu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, College of Chemistry and Molecular Engineering, Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Science, and Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Yilan Guo
- College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Xu Zhang
- College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Shaoran Zhang
- College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Yan Jia
- Renal Division, Peking University First Hospital, Beijing, 100034, China.,Institute of Nephrology, Key Laboratory of CKD Prevention and Treatment of Ministry of Education of China, Peking University, Beijing, 100871, China.,Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yifei Du
- College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Bo Cheng
- College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Li Yang
- Renal Division, Peking University First Hospital, Beijing, 100034, China.,Institute of Nephrology, Key Laboratory of CKD Prevention and Treatment of Ministry of Education of China, Peking University, Beijing, 100871, China.,Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yanyi Huang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, College of Chemistry and Molecular Engineering, Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Science, and Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
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7
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Liu H, Liu S, Xiao Y, Song W, Li H, Ho LWC, Shen Z, Choi CHJ. A pH-Reversible Fluorescent Probe for in Situ Imaging of Extracellular Vesicles and Their Secretion from Living Cells. NANO LETTERS 2021; 21:9224-9232. [PMID: 34724785 DOI: 10.1021/acs.nanolett.1c03110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Our knowledge in how extracellular vesicles (EVs) are secreted from cells remains inadequate due to the limited technologies available for visualizing them in situ. We report a pH-reversible boron dipyrromethene (BODIPY) fluorescent probe for confocal imaging of EVs secreted from living cells without inducing severe cytotoxicity. This probe predominantly assumes a non-fluorescent leuco-BODIPY form under basic conditions, but it gradually switches to its fluorescent parent BODIPY form upon acidification; such pH transition empowers the imaging of acidic EVs (such as CD81-enriched exosomes and extracellular multivesicular bodies) in weakly basic culture medium and intracellular acidic precursor EVs in weakly basic cytoplasm, with minimal false positive signals frequently encountered for "always-on" dyes. Joint application of this probe with plasmid transfection reveals the secretion of some EVs from cellular pseudopodia via microtubule trackways. This probe may provide mechanistic insights into the extracellular transport of EVs and support the development of EV-based nanomedicines.
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Affiliation(s)
- Hanzhuang Liu
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | - Shaorui Liu
- Department of Surgery, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | - Yu Xiao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | - Wenting Song
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Huize Li
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | - Lok Wai Cola Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
| | - Zhen Shen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Chung Hang Jonathan Choi
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR
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OOYAMA Y, OHIRA K, KAGAWA Y, IMATO K. Synthesis, Optical and Electrochemical Properties of Benzofuro[2,3- c]carbazoloquinol Fluorescent Dyes. ELECTROCHEMISTRY 2021. [DOI: 10.5796/electrochemistry.21-00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Yousuke OOYAMA
- Applied Chemistry Program, Graduate School of Advanced Science and Engineering, Hiroshima University
| | - Kazuki OHIRA
- Applied Chemistry Program, Graduate School of Advanced Science and Engineering, Hiroshima University
| | - Yusuke KAGAWA
- Applied Chemistry Program, Graduate School of Advanced Science and Engineering, Hiroshima University
| | - Keiichi IMATO
- Applied Chemistry Program, Graduate School of Advanced Science and Engineering, Hiroshima University
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