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De Paepe L, Madder A, Cadoni E. Exploiting G-Quadruplex-DNA Damage as a Tool to Quantify Singlet Oxygen Production. SMALL METHODS 2024:e2301570. [PMID: 38623961 DOI: 10.1002/smtd.202301570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/18/2024] [Indexed: 04/17/2024]
Abstract
G-Quadruplexes (G4s) are highly dynamic and polymorphic nucleic acid structures that can adopt a variety of conformations. When exposed to oxidative conditions, more specifically singlet oxygen, the guanosine nucleobases can be oxidized, which in turn can affect the conformation and folding of the G4. Based on this peculiar phenomenon, it is rationalized that G4s can serve as quantification sensors for the production of singlet oxygen. Here, a method for determining the quantum yield of singlet oxygen generation for visible as well as UV-light excited photosensitizers, using a short G4 DNA sequence, readily available from common DNA companies, as a biological and water-soluble probe, is presented.
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Affiliation(s)
- Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, Ghent, B-9000, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, Ghent, B-9000, Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, Ghent, B-9000, Belgium
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2
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Kodadek T. Catalytic Protein Inhibitors. Angew Chem Int Ed Engl 2024; 63:e202316726. [PMID: 38064411 DOI: 10.1002/anie.202316726] [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: 11/03/2023] [Indexed: 01/13/2024]
Abstract
Many of the highest priority targets in a wide range of disease states are difficult-to-drug proteins. The development of reversible small molecule inhibitors for the active sites of these proteins with sufficient affinity and residence time on-target is an enormous challenge. This has engendered interest in strategies to increase the potency of a given protein inhibitor by routes other than further improvement in gross affinity. Amongst these, the development of catalytic protein inhibitors has garnered the most attention and investment, particularly with respect to protein degraders, which catalyze the destruction of the target protein. This article discusses the genesis of the burgeoning field of catalytic inhibitors, the current state of the art, and exciting future directions.
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Affiliation(s)
- Thomas Kodadek
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 120 Scripps Way, Jupiter, FL 33458, USA
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3
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Liang J, Han J, Gao X, Jia H, Li R, Tse ECM, Li Y. Clickable APEX2 Probes for Enhanced RNA Proximity Labeling in Live Cells. Anal Chem 2024; 96:685-693. [PMID: 38099807 DOI: 10.1021/acs.analchem.3c03614] [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: 12/30/2023]
Abstract
Although APEX2-mediated proximity labeling has been extensively implemented for studying RNA subcellular localization in live cells, the biotin-phenoxyl radical used for labeling RNAs has a relatively low efficiency, which can limit its compatibility with other profiling methods. Herein, a set of phenol derivatives were designed as APEX2 probes through balancing reactivity, hydrophilicity, and lipophilicity. Among these derivatives, Ph_N3 exhibited reliable labeling ability and enabled two biotinylation routes for downstream analysis. As a proof of concept, we used APEX2/Ph_N3 labeling with high-throughput sequencing analysis to examine the transcriptomes in the mitochondrial matrix, demonstrating high sensitivity and specificity. To further expand the utility of Ph_N3, we employed mechanistically orthogonal APEX2 and singlet oxygen (1O2)-mediated strategies for dual location labeling in live cells. Specifically, DRAQ5, a DNA-intercalating photosensitizer, was applied for nucleus-restricted 1O2 labeling. We validated the orthogonality of APEX2/Ph_N3 and DRAQ5-1O2 at the imaging level, providing an attractive and feasible approach for future studies of RNA translocation in live cells.
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Affiliation(s)
- Jiying Liang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jinghua Han
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xutao Gao
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Han Jia
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ran Li
- Academy for Advanced Interdisciplinary Studies, PKU-Tsinghua Center for Life Science, Peking University, Beijing 100871, China
| | - Edmund C M Tse
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, New Territories, Hong Kong, China
| | - Ying Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, New Territories, Hong Kong, China
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4
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Andrés CMC, de la Lastra JMP, Juan CA, Plou FJ, Pérez-Lebeña E. Chemical Insights into Oxidative and Nitrative Modifications of DNA. Int J Mol Sci 2023; 24:15240. [PMID: 37894920 PMCID: PMC10607741 DOI: 10.3390/ijms242015240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
This review focuses on DNA damage caused by a variety of oxidizing, alkylating, and nitrating species, and it may play an important role in the pathophysiology of inflammation, cancer, and degenerative diseases. Infection and chronic inflammation have been recognized as important factors in carcinogenesis. Under inflammatory conditions, reactive oxygen species (ROS) and reactive nitrogen species (RNS) are generated from inflammatory and epithelial cells, and result in the formation of oxidative and nitrative DNA lesions, such as 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8-nitroguanine. Cellular DNA is continuously exposed to a very high level of genotoxic stress caused by physical, chemical, and biological agents, with an estimated 10,000 modifications occurring every hour in the genetic material of each of our cells. This review highlights recent developments in the chemical biology and toxicology of 2'-deoxyribose oxidation products in DNA.
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Affiliation(s)
| | - José Manuel Pérez de la Lastra
- Institute of Natural Products and Agrobiology, CSIC-Spanish Research Council, Avda. AstrofísicoFco. Sánchez, 3, 38206 La Laguna, Spain
| | - Celia Andrés Juan
- Cinquima Institute and Department of Organic Chemistry, Faculty of Sciences, Valladolid University, Paseo de Belén, 7, 47011 Valladolid, Spain;
| | - Francisco J. Plou
- Institute of Catalysis and Petrochemistry, CSIC-Spanish Research Council, 28049 Madrid, Spain;
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Tang Z, Ma D, Yang J, Chen J, Lin Z, Liang Q, Jiao Y, Qu W, Xia D. Solar-driven strongly coupled plasmonic Au nanoarrays on mesoporous silica nanodisks enable selective fungal and bacterial inactivation in well water. WATER RESEARCH 2023; 245:120612. [PMID: 37729695 DOI: 10.1016/j.watres.2023.120612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/13/2023] [Accepted: 09/09/2023] [Indexed: 09/22/2023]
Abstract
Well water is an important water source in isolated rural areas but easily suffers from microbial contamination. Herein, we anchored periodic Au nanoarrays on mesoporous silica nanodisks (Au-MSN) to fabricate a solar-driven nano-stove for well water disinfection. The solar/Au-MSN process completely inactivated 3.98, 6.55, 7.11 log10 cfu/mL, and 3.37 log10 pfu/mL of Aspergillus niger spores, Escherichia coli, chlorine-resistant Spingopyxis sp. BM1-1, and bacteriophage MS2 within 5 min, respectively. Moreover, the complete inactivation of various microorganisms (even at a viable but nonculturable state) was achieved in the flow-through reactor under natural solar light in real well water matrixes. Thorough characterizations and theoretical simulations verified that the densely anchoring strategy of Au-MSN's nanoarray worked on broadband absorption via the photon confinement effect, and trace amounts of Au can induce strong electromagnetic fields and collective localized heating. The resulting surge of 1O2 and heat synergically destroyed membranes, dysfunction cellular self-defense and metabolic system, induced intracellular oxidative stress, and ultimately inactivated microorganisms. Additionally, the 1O2-dominated oxidation and cell adhesion facilitated the selective disinfection in real well water matrixes. This study provides a cost-effective and practical solution for efficient well water disinfection, which assists isolated rural areas in getting safe drinking water.
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Affiliation(s)
- Zhuoyun Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Dingren Ma
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Jingling Yang
- School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinjuan Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhuohang Lin
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Qiwen Liang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Yimu Jiao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Wei Qu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Dehua Xia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China.
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Barr J, Colpaert G, Cadoni E, Madder A. Furan-based (photo)oxidation reactions and their application in nucleic acid and protein targeting. Methods 2023; 218:189-197. [PMID: 37597698 DOI: 10.1016/j.ymeth.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
Oligonucleotides (ODNs) find applications as diagnostic and therapeutic tools due to their unique ability to interact, thanks to Watson-Crick base pairing, with a specific DNA or RNA target strand. Although most of the tools available today rely on mere hydrogen bond formation, chemical modifications to enable covalent interstrand-crosslinking (ICL) have been reported, and are gaining a place under the spotlight as they potentially offer a series of advantages over the state of the art, including a higher potency and selectivity. This methodological paper focuses on the use of a pro-reactive furan moiety and its subsequent oxidation for applications in ODN targeting. The design of effective capture and targeting probes to ensure high ICL yields is discussed and the mechanisms underlying the (photo)chemical oxidation of furan are explained. Furthermore, examples of furan-containing DNAs designed for different applications, including DNA-DNA or DNA-RNA ICL and DNA-peptide/protein targeting, are provided. The paper highlights the advantages of using different oxidative chemical triggers, such as N-bromosuccinimide or singlet oxygen, to offer additional selectivity control over the ICL reaction.
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Affiliation(s)
- Jack Barr
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Gertjan Colpaert
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium.
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium.
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7
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Luo H, Gao S. Recent advances in fluorescence imaging-guided photothermal therapy and photodynamic therapy for cancer: From near-infrared-I to near-infrared-II. J Control Release 2023; 362:425-445. [PMID: 37660989 DOI: 10.1016/j.jconrel.2023.08.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/20/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
Phototherapy (including photothermal therapy, PTT; and photodynamic therapy, PDT) has been widely used for cancer treatment, but conventional PTT/PDT show limited therapeutic effects due to the lack of disease recognition ability. The integration of fluorescence imaging with PTT/PDT can reveal tumor locations in a real-time manner, holding great potential in early diagnosis and precision treatment of cancers. However, the traditional fluorescence imaging in the visible and near-infrared-I regions (VIS/NIR-I, 400-900 nm) might be interfered by the scattering and autofluorescence from tissues, leading to a low imaging resolution and high false positive rate. The deeper near-infrared-II (NIR-II, 1000-1700 nm) fluorescence imaging can address these interferences. Combining NIR-II fluorescence imaging with PTT/PDT can significantly improve the accuracy of tumor theranostics and minimize damages to normal tissues. This review summarized recent advances in tumor PTT/PDT and NIR-II fluorophores, especially discussed achievements, challenges and prospects around NIR-II fluorescence imaging-guided PTT/PDT for cancers.
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Affiliation(s)
- Hangqi Luo
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06511, USA
| | - Shuai Gao
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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8
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Khan ZU, Khan LU, Brito HF, Gidlund M, Malta OL, Di Mascio P. Colloidal Quantum Dots as an Emerging Vast Platform and Versatile Sensitizer for Singlet Molecular Oxygen Generation. ACS OMEGA 2023; 8:34328-34353. [PMID: 37779941 PMCID: PMC10536110 DOI: 10.1021/acsomega.3c03962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/15/2023] [Indexed: 10/03/2023]
Abstract
Singlet molecular oxygen (1O2) has been reported in wide arrays of applications ranging from optoelectronic to photooxygenation reactions and therapy in biomedical proposals. It is also considered a major determinant of photodynamic therapy (PDT) efficacy. Since the direct excitation from the triplet ground state (3O2) of oxygen to the singlet excited state 1O2 is spin forbidden; therefore, a rational design and development of heterogeneous sensitizers is remarkably important for the efficient production of 1O2. For this purpose, quantum dots (QDs) have emerged as versatile candidates either by acting individually as sensitizers for 1O2 generation or by working in conjunction with other inorganic materials or organic sensitizers by providing them a vast platform. Thus, conjoining the photophysical properties of QDs with other materials, e.g., coupling/combining with other inorganic materials, doping with the transition metal ions or lanthanide ions, and conjugation with a molecular sensitizer provide the opportunity to achieve high-efficiency quantum yields of 1O2 which is not possible with either component separately. Hence, the current review has been focused on the recent advances made in the semiconductor QDs, perovskite QDs, and transition metal dichalcogenide QD-sensitized 1O2 generation in the context of ongoing and previously published research work (over the past eight years, from 2015 to 2023).
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Affiliation(s)
- Zahid U. Khan
- Institute
of Chemistry, University of Sao Paulo (USP), 05508-000 São
Paulo-SP, Brazil
| | - Latif U. Khan
- Institute
of Chemistry, University of Sao Paulo (USP), 05508-000 São
Paulo-SP, Brazil
- Synchrotron-light
for Experimental Science and Applications in the Middle East (SESAME), P.O. Box 7, Allan 19252, Jordan
| | - Hermi F. Brito
- Institute
of Chemistry, University of Sao Paulo (USP), 05508-000 São
Paulo-SP, Brazil
| | - Magnus Gidlund
- Institute
of Biomedical Sciences-IV, University of
Sao Paulo (USP), 05508-000 São Paulo-SP, Brazil
| | - Oscar L. Malta
- Departamento
de Química Fundamental, Universidade
Federal de Pernambuco, Recife, PE 50740-560, Brazil
| | - Paolo Di Mascio
- Institute
of Chemistry, University of Sao Paulo (USP), 05508-000 São
Paulo-SP, Brazil
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Rontani JF, Bonin P. Cellular Damage of Bacteria Attached to Senescent Phytoplankton Cells as a Result of the Transfer of Photochemically Produced Singlet Oxygen: A Review. Microorganisms 2023; 11:1565. [PMID: 37375067 DOI: 10.3390/microorganisms11061565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Several studies set out to explain the presence of high proportions of photooxidation products of cis-vaccenic acid (generally considered to be of bacterial origin) in marine environments. These studies show that these oxidation products result from the transfer of singlet oxygen from senescent phytoplankton cells to the bacteria attached to them in response to irradiation by sunlight. This paper summarizes and reviews the key findings of these studies, i.e., the demonstration of the process at work and the effect of different parameters (intensity of solar irradiance, presence of bacterial carotenoids, and presence of polar matrices such as silica, carbonate, and exopolymeric substances around phytoplankton cells) on this transfer. A large part of this review looks at how this type of alteration of bacteria can affect the preservation of algal material in the marine environment, especially in polar regions where conditions drive increased transfer of singlet oxygen from sympagic algae to bacteria.
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Affiliation(s)
- Jean-François Rontani
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Patricia Bonin
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
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Para-N-Methylpyridinium Pyrenes: Impact of Positive Charge on ds-DNA/RNA and Protein Recognition, Photo-Induced Bioactivity, and Intracellular Localisation. Pharmaceutics 2022; 14:pharmaceutics14112499. [PMID: 36432689 PMCID: PMC9696974 DOI: 10.3390/pharmaceutics14112499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022] Open
Abstract
The 2- and 2,7- substituted para-N-methylpyridinium pyrene cations show high-affinity intercalation into ds-DNAs, whereas their non-methylated analogues interacted with ds-DNA/RNA only in the protonated form (at pH 5), but not at physiological conditions (pH 7). The fluorescence from non-methylated analogues was strongly dependent on the protonation of the pyridines; consequently, they act as fluorescence ratiometric probes for simultaneous detection of both ds-DNA and BSA at pH 5, relying on the ratio between intensities at 420 nm (BSA specific) and 520 nm (DNA specific), whereby exclusively ds-DNA sensing could be switched-off by adjustment to pH 7. Only methylated, permanently charged pyrenes show photoinduced cleavage of circular DNA, attributed to pyrene-mediated irradiation-induced production of singlet oxygen. Consequently, the moderate toxicity of these cations against human cell lines is strongly increased upon irradiation. Detailed studies revealed increased total ROS production in cells treated by the compounds studied, accompanied by cell swelling and augmentation of cellular complexity. The most photo-active 2-para-N-methylpyridinium pyrene showed significant localization at mitochondria, its photo-bioactivity likely due to mitochondrial DNA damage. Other derivatives were mostly non-selectively distributed between various cytoplasmic organelles, thus being less photoactive.
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The Journey of 1-Keto-1,2,3,4-Tetrahydrocarbazole Based Fluorophores: From Inception to Implementation. J Fluoresc 2022; 32:2023-2052. [PMID: 35829843 DOI: 10.1007/s10895-022-03004-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/01/2022] [Indexed: 10/17/2022]
Abstract
Carbazole is a unique template associated with several biological activities. It is due to the diverse and versatile biological properties of carbazole derivatives that they are of immense interest to the research community. 1-keto-1,2,3,4-tetrahydrocarbazoles are important synthetic intermediates to obtain carbazole derivatives. Several members of this family emit fluorescence on photoexcitation. In the context of biochemical and biophysical research, designing and characterising small molecule environment sensitive fluorophores is extremely significant. This article aims to be a state of the art review with synthetic and photophysical details of a variety of fluorophores based on 1-keto-1,2,3,4-tetrahydrocarbazole skeleton.
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