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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [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: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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2
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Polanco EA, Opdam LV, Passerini L, Huber M, Bonnet S, Pandit A. An artificial metalloenzyme that can oxidize water photocatalytically: design, synthesis, and characterization. Chem Sci 2024; 15:3596-3609. [PMID: 38455019 PMCID: PMC10915814 DOI: 10.1039/d3sc05870k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/29/2024] [Indexed: 03/09/2024] Open
Abstract
In nature, light-driven water oxidation (WO) catalysis is performed by photosystem II via the delicate interplay of different cofactors positioned in its protein scaffold. Artificial systems for homogeneous photocatalytic WO are based on small molecules that often have limited solubility in aqueous solutions. In this work, we alleviated this issue and present a cobalt-based WO-catalyst containing artificial metalloenzyme (ArM) that is active in light-driven, homogeneous WO catalysis in neutral-pH aqueous solutions. A haem-containing electron transfer protein, cytochrome B5 (CB5), served to host a first-row transition-metal-based WO catalyst, CoSalen (CoIISalen, where H2Salen = N,N'-bis(salicylidene)ethylenediamine), thus producing an ArM capable of driving photocatalytic WO. The CoSalen ArM formed a water-soluble pre-catalyst in the presence of [Ru(bpy)3](ClO4)2 as photosensitizer and Na2S2O8 as the sacrificial electron acceptor, with photocatalytic activity similar to that of free CoSalen. During photocatalysis, the CoSalen-protein interactions were destabilized, and the protein partially unfolded. Rather than forming tens of nanometer sized CoOx nanoparticles as free CoSalen does under photocatalytic WO conditions, the CB5 : CoSalen ArM showed limited protein cross-linking and remained soluble. We conclude that a weak, dynamic interaction between a soluble cobalt species and apoCB5 was formed, which generated a catalytically active adduct during photocatalysis. A detailed analysis was performed on protein stability and decomposition processes during the harsh oxidizing reaction conditions of WO, which will serve for the future design of WO ArMs with improved activity and stability.
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Affiliation(s)
- Ehider A Polanco
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Laura V Opdam
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Leonardo Passerini
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Sylvestre Bonnet
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anjali Pandit
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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3
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Gallio A, Fung SSP, Cammack-Najera A, Hudson AJ, Raven EL. Understanding the Logistics for the Distribution of Heme in Cells. JACS AU 2021; 1:1541-1555. [PMID: 34723258 PMCID: PMC8549057 DOI: 10.1021/jacsau.1c00288] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Indexed: 05/03/2023]
Abstract
Heme is essential for the survival of virtually all living systems-from bacteria, fungi, and yeast, through plants to animals. No eukaryote has been identified that can survive without heme. There are thousands of different proteins that require heme in order to function properly, and these are responsible for processes such as oxygen transport, electron transfer, oxidative stress response, respiration, and catalysis. Further to this, in the past few years, heme has been shown to have an important regulatory role in cells, in processes such as transcription, regulation of the circadian clock, and the gating of ion channels. To act in a regulatory capacity, heme needs to move from its place of synthesis (in mitochondria) to other locations in cells. But while there is detailed information on how the heme lifecycle begins (heme synthesis), and how it ends (heme degradation), what happens in between is largely a mystery. Here we summarize recent information on the quantification of heme in cells, and we present a discussion of a mechanistic framework that could meet the logistical challenge of heme distribution.
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Affiliation(s)
- Andrea
E. Gallio
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Simon S.-P. Fung
- Department
of Chemistry and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Ana Cammack-Najera
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Andrew J. Hudson
- Department
of Chemistry and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Emma L. Raven
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
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4
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Zou Y, Takeda R, Han J, Konno H, Moriwaki H, Abe H, Izawa K, Soloshonok VA. Asymmetric Synthesis of
N
‐Fmoc‐(
S
)‐7‐aza‐tryptophan via Alkylation of Chiral Nucleophilic Glycine Equivalent. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yupiao Zou
- Jiangsu Co – Innovation Center of Efficient Processing and Utilization of Forest Resources International Innovation Center for Forest Chemicals and Materials College of Chemical Engineering Nanjing Forestry University 159 Longpan Road 210037 Nanjing China
| | - Ryosuke Takeda
- Hamari Chemicals Ltd. 1-4-29 Kunijima, Higashi-Yodogawa-ku 533-0024 Osaka Japan
| | - Jianlin Han
- Jiangsu Co – Innovation Center of Efficient Processing and Utilization of Forest Resources International Innovation Center for Forest Chemicals and Materials College of Chemical Engineering Nanjing Forestry University 159 Longpan Road 210037 Nanjing China
| | - Hiroyuki Konno
- Department of Biological Engineering Graduate School of Science and Engineering Yamagata University Yonezawa 992-8510 Yamagata Japan
| | - Hiroki Moriwaki
- Hamari Chemicals Ltd. 1-4-29 Kunijima, Higashi-Yodogawa-ku 533-0024 Osaka Japan
| | - Hidenori Abe
- Hamari Chemicals Ltd. 1-4-29 Kunijima, Higashi-Yodogawa-ku 533-0024 Osaka Japan
| | - Kunisuke Izawa
- Hamari Chemicals Ltd. 1-4-29 Kunijima, Higashi-Yodogawa-ku 533-0024 Osaka Japan
| | - Vadim A. Soloshonok
- Department of Organic Chemistry I Faculty of Chemistry University of the Basque Country UPV/EHU Paseo Manuel Lardizábal 3 20018 San Sebastián Spain
- IKERBASQUE, Basque Foundation for Science Alameda Urquijo 36–5, Plaza Bizkaia 48011 Bilbao Spain
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5
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Zhao CX, Liu T, Xu M, Lin H, Zhang CJ. A fundamental study on the fluorescence-quenching effect of nitro groups in tetraphenylethene AIE dyes with electron-withdrawing groups. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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6
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Walter EH, Ge Y, Mason JC, Boyle JJ, Long NJ. A Coumarin-Porphyrin FRET Break-Apart Probe for Heme Oxygenase-1. J Am Chem Soc 2021; 143:6460-6469. [PMID: 33845576 PMCID: PMC8154531 DOI: 10.1021/jacs.0c12864] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Indexed: 12/15/2022]
Abstract
Heme oxygenase-1 (HO-1) is a vital enzyme in humans that primarily regulates free heme concentrations. The overexpression of HO-1 is commonly associated with cardiovascular and neurodegenerative diseases including atherosclerosis and ischemic stroke. Currently, there are no known chemical probes to detect HO-1 activity, limiting its potential as an early diagnostic/prognostic marker in these serious diseases. Reported here are the design, synthesis, and photophysical and biological characterization of a coumarin-porphyrin FRET break-apart probe to detect HO-1 activity, Fe-L1. We designed Fe-L1 to "break-apart" upon HO-1-catalyzed porphyrin degradation, perturbing the efficient FRET mechanism from a coumarin donor to a porphyrin acceptor fluorophore. Analysis of HO-1 activity using Escherichia coli lysates overexpressing hHO-1 found that a 6-fold increase in emission intensity at 383 nm was observed following incubation with NADPH. The identities of the degradation products following catabolism were confirmed by MALDI-MS and LC-MS, showing that porphyrin catabolism was regioselective at the α-position. Finally, through the analysis of Fe-L2, we have shown that close structural analogues of heme are required to maintain HO-1 activity. It is anticipated that this work will act as a foundation to design and develop new probes for HO-1 activity in the future, moving toward applications of live fluorescent imaging.
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Affiliation(s)
- Edward
R. H. Walter
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K.
- National
Lung and Heart Institute, Imperial College London, Du Cane Road, London W12 0NN, U.K.
| | - Ying Ge
- National
Lung and Heart Institute, Imperial College London, Du Cane Road, London W12 0NN, U.K.
| | - Justin C. Mason
- National
Lung and Heart Institute, Imperial College London, Du Cane Road, London W12 0NN, U.K.
| | - Joseph J. Boyle
- National
Lung and Heart Institute, Imperial College London, Du Cane Road, London W12 0NN, U.K.
| | - Nicholas J. Long
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K.
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7
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Hisamatsu Y, Otani K, Takase H, Umezawa N, Higuchi T. Fluorescence Response and Self-Assembly of a Tweezer-Type Synthetic Receptor Triggered by Complexation with Heme and Its Catabolites. Chemistry 2021; 27:6489-6499. [PMID: 33026121 DOI: 10.1002/chem.202003872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/28/2020] [Indexed: 11/11/2022]
Abstract
There is increasing interest in the development and applications of synthetic receptors that recognize target biomolecules in aqueous media. We have developed a new tweezer-type synthetic receptor that gives a significant fluorescence response upon complexation with heme in aqueous solution at pH 7.4. The synthetic receptor consists of a tweezer-type heme recognition site and sulfo-Cy5 as a hydrophilic fluorophore. The receptor-heme complex exhibits a supramolecular amphiphilic character that facilitates the formation of self-assembled aggregates, and both the tweezer moiety and the sulfo-Cy5 moiety are important for this property. The synthetic receptor also exhibits significant fluorescence responses to biliverdin and bilirubin, but shows very weak fluorescence responses to flavin mononucleotide, folic acid, and nicotinamide adenine dinucleotide, which contain smaller π-scaffolds.
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Affiliation(s)
- Yosuke Hisamatsu
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Koki Otani
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Hiroshi Takase
- Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
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8
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9
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Gbotosho OT, Kapetanaki MG, Kato GJ. The Worst Things in Life are Free: The Role of Free Heme in Sickle Cell Disease. Front Immunol 2021; 11:561917. [PMID: 33584641 PMCID: PMC7873693 DOI: 10.3389/fimmu.2020.561917] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
Hemolysis is a pathological feature of several diseases of diverse etiology such as hereditary anemias, malaria, and sepsis. A major complication of hemolysis involves the release of large quantities of hemoglobin into the blood circulation and the subsequent generation of harmful metabolites like labile heme. Protective mechanisms like haptoglobin-hemoglobin and hemopexin-heme binding, and heme oxygenase-1 enzymatic degradation of heme limit the toxicity of the hemolysis-related molecules. The capacity of these protective systems is exceeded in hemolytic diseases, resulting in high residual levels of hemolysis products in the circulation, which pose a great oxidative and proinflammatory risk. Sickle cell disease (SCD) features a prominent hemolytic anemia which impacts the phenotypic variability and disease severity. Not only is circulating heme a potent oxidative molecule, but it can act as an erythrocytic danger-associated molecular pattern (eDAMP) molecule which contributes to a proinflammatory state, promoting sickle complications such as vaso-occlusion and acute lung injury. Exposure to extracellular heme in SCD can also augment the expression of placental growth factor (PlGF) and interleukin-6 (IL-6), with important consequences to enthothelin-1 (ET-1) secretion and pulmonary hypertension, and potentially the development of renal and cardiac dysfunction. This review focuses on heme-induced mechanisms that are implicated in disease pathways, mainly in SCD. A special emphasis is given to heme-induced PlGF and IL-6 related mechanisms and their role in SCD disease progression.
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Affiliation(s)
- Oluwabukola T. Gbotosho
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Maria G. Kapetanaki
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Gregory J. Kato
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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10
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Hopp MT, Schmalohr BF, Kühl T, Detzel MS, Wißbrock A, Imhof D. Heme Determination and Quantification Methods and Their Suitability for Practical Applications and Everyday Use. Anal Chem 2020; 92:9429-9440. [PMID: 32490668 DOI: 10.1021/acs.analchem.0c00415] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many research institutions, clinical diagnostic laboratories, and blood banks are desperately searching for a possibility to identify and quantify heme in different physiological and pathological settings as well as various research applications. The reasons for this are the toxicity of the heme and the fact that it acts as a hemolytic and pro-inflammatory molecule. Heme only exerts these severe and undesired effects when it is not incorporated in hemoproteins. Upon release from the hemoproteins, it enters a biologically available state (labile heme), in which it is loosely associated with proteins, lipids, nucleic acids, or other molecules. While the current methods and procedures for quantitative determination of heme have been used for many years in different settings, their value is limited by the challenging chemical properties of heme. A major cause of inadequate quantification is the separation of labile and permanently bound heme and its high aggregation potential. Thus, none of the current methods are utilized as a generally applicable, standardized approach. The aim of this Feature is to describe and summarize the most common and frequently used chemical, analytical, and biochemical methods for the quantitative determination of heme. Based on this overview, the most promising approaches for future solutions to heme quantification are highlighted.
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Affiliation(s)
- Marie-T Hopp
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, D-53121 Bonn, Germany
| | - Benjamin F Schmalohr
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, D-53121 Bonn, Germany
| | - Toni Kühl
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, D-53121 Bonn, Germany
| | - Milena S Detzel
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, D-53121 Bonn, Germany
| | - Amelie Wißbrock
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, D-53121 Bonn, Germany
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, D-53121 Bonn, Germany
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11
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Fluorescent amino acids as versatile building blocks for chemical biology. Nat Rev Chem 2020; 4:275-290. [PMID: 37127957 DOI: 10.1038/s41570-020-0186-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2020] [Indexed: 12/13/2022]
Abstract
Fluorophores have transformed the way we study biological systems, enabling non-invasive studies in cells and intact organisms, which increase our understanding of complex processes at the molecular level. Fluorescent amino acids have become an essential chemical tool because they can be used to construct fluorescent macromolecules, such as peptides and proteins, without disrupting their native biomolecular properties. Fluorescent and fluorogenic amino acids with unique photophysical properties have been designed for tracking protein-protein interactions in situ or imaging nanoscopic events in real time with high spatial resolution. In this Review, we discuss advances in the design and synthesis of fluorescent amino acids and how they have contributed to the field of chemical biology in the past 10 years. Important areas of research that we review include novel methodologies to synthesize building blocks with tunable spectral properties, their integration into peptide and protein scaffolds using site-specific genetic encoding and bioorthogonal approaches, and their application to design novel artificial proteins, as well as to investigate biological processes in cells by means of optical imaging.
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12
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A TAT peptide-based ratiometric two-photon fluorescent probe for detecting biothiols and sequentially distinguishing GSH in mitochondria. Talanta 2020; 218:121127. [PMID: 32797884 DOI: 10.1016/j.talanta.2020.121127] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 12/19/2022]
Abstract
Although biothiols, including cysteine (Cys), glutathione (GSH), and homocysteine (Hcy) can be used to diagnose many diseases and research physiological metabolism in many physiological processes, in situ real-time detection and differentiation of biothiols is still challenging because their similar chemical properties and molecular structures. Herein, we utilized the native chemical ligation (NCL) reaction mechanism to develop a Förster resonance energy transfer (FRET) strategy for designing a cell penetration peptide TAT-modified ratiometric two-photon biothiols probe (TAT-probe). The TAT-probe can not only rapidly enter into mitochondria assisted by TAT peptide, but also simultaneously detect biothiols and sequentially distinguish GSH. When the TAT-probe was excited with 404/820 nm wavelength light, it showed a change in the ratio of fluorescence after adding biothiols, including a quenched red fluorescence intensity (λem = 585 nm) and an enhanced signal in green fluorescence intensity (λem = 520 nm). Excitingly, the TAT-probe excited at 545 nm could display a red fluorescence (λem = 585 nm) towards GSH and a quenched signal towards Hcy or Cys. This specific fluorescence response indicated the TAT-probe could effectively detect biothiols and differentiate GSH from Cys/Hcy in mitochondria. This work pioneered a new approach to design and synthesize biothiol-probes based on peptides and NCL reaction mechanism.
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