1
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Paez‐Perez M, Kuimova MK. Molecular Rotors: Fluorescent Sensors for Microviscosity and Conformation of Biomolecules. Angew Chem Int Ed Engl 2024; 63:e202311233. [PMID: 37856157 PMCID: PMC10952837 DOI: 10.1002/anie.202311233] [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: 08/03/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023]
Abstract
The viscosity and crowding of biological environment are considered vital for the correct cellular function, and alterations in these parameters are known to underly a number of pathologies including diabetes, malaria, cancer and neurodegenerative diseases, to name a few. Over the last decades, fluorescent molecular probes termed molecular rotors proved extremely useful for exploring viscosity, crowding, and underlying molecular interactions in biologically relevant settings. In this review, we will discuss the basic principles underpinning the functionality of these probes and will review advances in their use as sensors for lipid order, protein crowding and conformation, temperature and non-canonical nucleic acid structures in live cells and other relevant biological settings.
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Affiliation(s)
- Miguel Paez‐Perez
- Department of Chemistry, Imperial College London, MSRHImperial College LondonWood LaneLondonW12 0BZUK
| | - Marina K. Kuimova
- Department of Chemistry, Imperial College London, MSRHImperial College LondonWood LaneLondonW12 0BZUK
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2
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Kumagai T, Kinoshita B, Hirashima S, Sugiyama H, Park S. Thiophene-Extended Fluorescent Nucleosides as Molecular Rotor-Type Fluorogenic Sensors for Biomolecular Interactions. ACS Sens 2023; 8:923-932. [PMID: 36740828 DOI: 10.1021/acssensors.2c02617] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescent molecular rotors are versatile tools for the investigation of biomolecular interactions and the monitoring of microenvironmental changes in biological systems. They can transform invisible information into a fluorescence signal as a straightforward response. Their utility is synergistically amplified when they are merged with biomolecules. Despite the tremendous significance and superior programmability of nucleic acids, there are very few reports on the development of molecular rotor-type isomorphic nucleosides. Here, we report the synthesis and characterization of a highly emissive molecular rotor-containing thymine nucleoside (ThexT) and its 2'-O-methyluridine analogue (2'-OMe-ThexU) as fluorogenic microenvironment-sensitive sensors that emit vivid fluorescence via an interaction with the target proteins. ThexT and 2'-OMe-ThexU may potentially serve as robust probes for a broad range of applications, such as fluorescence mapping, to monitor viscosity changes and specific protein-binding interactions in biological systems.
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Affiliation(s)
- Tomotaka Kumagai
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ban Kinoshita
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shingo Hirashima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Soyoung Park
- Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan
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3
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Kuznetsova VE, Shershov VE, Guseinov TO, Miftakhov RA, Solyev PN, Novikov RA, Levashova AI, Zasedatelev AS, Lapa SA, Chudinov AV. Synthesis of Cy5-Labelled C5-Alkynyl-modified cytidine triphosphates via Sonogashira coupling for DNA labelling. Bioorg Chem 2023; 131:106315. [PMID: 36528924 DOI: 10.1016/j.bioorg.2022.106315] [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: 10/04/2022] [Revised: 11/15/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
New applications of palladium-catalyzed Sonogashira-type cross-coupling reaction between C5-halogenated 2'-deoxycytidine-5'-monophosphate and novel cyanine dyes with a terminal alkyne group have been developed. The present methodology allows to synthesize of fluorescently labeled C5-nucleoside triphosphates with different acetylene linkers between the fluorophore and pyrimidine base in good to excellent yields under mild reaction conditions. Modified 2'-deoxycytidine-5'-triphosphates were shown to be good substrates for DNA polymerases and were incorporated into the DNA by polymerase chain reaction.
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Affiliation(s)
- Viktoriya E Kuznetsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Valeriy E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Teimur O Guseinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Rinat A Miftakhov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Pavel N Solyev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Roman A Novikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna I Levashova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergey A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
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4
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Kuba M, Pohl R, Kraus T, Hocek M. Nucleotides Bearing Red Viscosity-Sensitive Dimethoxy-Bodipy Fluorophore for Enzymatic Incorporation and DNA Labeling. Bioconjug Chem 2023; 34:133-139. [PMID: 36519639 DOI: 10.1021/acs.bioconjchem.2c00547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleosides and 2'-deoxyribonucleoside triphosphates (dNTPs) bearing 3,3'-dimethoxy-2,2'-diphenyl-6-(4-hydroxyphenyl)-bodipy fluorophore attached through a propargyl or propargyl-triethylene glycol linker to position 5 of 2'-deoxycytidine were designed and synthesized. They exerted bright red fluorescence and good sensitivity to viscosity changing their lifetime from 1.6 to 4.5 ns. The modifed dNTPs were substrates for DNA polymerases and were used in enzymatic synthesis of labeled DNA through primer extension. The modified DNA probes served as viscosity sensors responding to protein binding by changes of lifetime. The nucleotide with longer linker (dCpegMOBTP) was transported to live cells and incorporated into the genomic DNA, which can be useful for staining of DNA and imaging of DNA synthesis.
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Affiliation(s)
- Miroslav Kuba
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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5
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Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
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6
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Schreier VN, Loehr MO, Lattmann E, Luedtke NW. Active Uptake and Trafficking of Nucleoside Triphosphates In Vivo. ACS Chem Biol 2022; 17:1799-1810. [PMID: 35700414 DOI: 10.1021/acschembio.2c00153] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Modified nucleoside triphosphates (NTPs) are powerful probes and medicines, but their anionic character impedes membrane permeability. As such, invasive delivery techniques, transport carriers, or prodrug strategies are required for their in vivo use. Here, we present a fluorescent 2'-deoxyribonucleoside triphosphate "TAMRA-dATP" that exhibits surprisingly high bioavailability in vivo. TAMRA-dATP spontaneously forms nanoparticles in Mg+2-containing buffers that are taken into the vesicles of living cells and animals by energy-dependent processes. In cell cultures, photochemical activation with yellow laser light (561 nm) facilitated endosomal escape of TAMRA-dATP, resulting in its metabolic incorporation into DNA in vitro. In contrast, in vivo studies revealed that TAMRA-dATP is extensively trafficked by active pathways into cellular DNA of zebrafish (Danio rerio) and Caenorhabditis elegans where DNA labeling was observed in live animals, even without photochemical release. Metabolic labeling of DNA in whole, living animals can therefore be achieved by simply soaking animals in a buffer containing TAMRA-dATP or a structurally related compound, Cy3-dATP.
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Affiliation(s)
- Verena N Schreier
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland.,Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Morten O Loehr
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland.,Department of Chemistry, McGill University, Montréal, Quebec H3A 0B8, Canada
| | - Evelyn Lattmann
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Nathan W Luedtke
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland.,Department of Chemistry, McGill University, Montréal, Quebec H3A 0B8, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montréal, Quebec H3G 1Y6, Canada
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7
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Choi H, Kim H, Kim KT. Fluorescent nucleobase analogs constructed by
aldol‐type
condensation: Design, properties, and synthetic optimization for fluorogenic labeling of
5‐formyluracil. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12534] [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)
- Hayeon Choi
- Department of Chemistry Chungbuk National University Cheongju Republic of Korea
| | - Hokyung Kim
- Department of Chemistry Chungbuk National University Cheongju Republic of Korea
| | - Ki Tae Kim
- Department of Chemistry Chungbuk National University Cheongju Republic of Korea
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8
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Abstract
Two sets of bioorthogonally applicable, double fluorogenic probes, capable of sensing DNA–protein interactions, were prepared by installing an azide or tetrazine motif onto structurally fluorogenic, DNA sensitive frames. Installation of these bioorthogonal functions onto DNA intercalating dyes furnished these scaffolds with reactivity based fluorogenicity, rendering these probes double-fluorogenic, AND-type logic switches that require the simultaneous occurrence of a bioorthogonal reaction and interaction with DNA to trigger high intensity fluorescence. The probes were evaluated for double fluorogenic behavior in the presence/absence of DNA and a complementary bioorthogonal function. Our studies revealed that azide and tetrazine appending thiazole orange frames show remarkable double fluorogenic features. One of these probes, a membrane permeable tetrazine modified thiazole orange derivative was further tested in live cell labeling studies. Cells expressing bioorthogonalized DNA-binding proteins showed intensive fluorescence characteristics of the localization of the proteins upon treatment with our double fluorogenic probe. On the contrary, labeling similarly bioorthogonalized cytosolic proteins did not result in the appearance of the fluorescence signal. These studies suggest that such double-fluorogenic probes are indeed capable of sensing DNA–protein interactions in cells.
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9
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Matyašovský J, Tack L, Palágyi A, Kuba M, Pohl R, Kraus T, Güixens-Gallardo P, Hocek M. Nucleotides bearing aminophenyl- or aminonaphthyl-3-methoxychromone solvatochromic fluorophores for the enzymatic construction of DNA probes for the detection of protein-DNA binding. Org Biomol Chem 2021; 19:9966-9974. [PMID: 34747967 DOI: 10.1039/d1ob02098f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We designed and synthesized nucleosides bearing aminophenyl- or aminonaphthyl-3-methoxychromone fluorophores attached at position 5 of cytosine or thymine and converted them to nucleoside triphosphates. The fluorophores showed solvatochromic fluorescence with strong fluorescence at 433-457 nm in non-polar solvents and very weak fluorescence at 567 nm in alcohols. The nucleosides and nucleotides also showed only negligible fluorescence in alcohols or water. The triphosphates were substrates for DNA polymerase in the enzymatic synthesis of modified DNA probes that showed only very weak fluorescence in aqueous buffer but a significant light-up and blue shift were observed when they interacted with proteins (histone H3.1 or p53 for double-stranded DNA probes or single-strand binding protein for single-stranded oligonucleotide probes). Hence, nucleotides have good potential in the construction of DNA sensors for studying protein-DNA interactions. The modified dNTPs were also transported into cells using a cyclodextrin-based transporter but they were not incorporated into the genomic DNA.
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Affiliation(s)
- Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, CZ-16610 Prague 6, Czech Republic. .,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2 12843, Czech Republic
| | - Laure Tack
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, CZ-16610 Prague 6, Czech Republic.
| | - Attila Palágyi
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, CZ-16610 Prague 6, Czech Republic. .,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2 12843, Czech Republic
| | - Miroslav Kuba
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, CZ-16610 Prague 6, Czech Republic. .,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2 12843, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, CZ-16610 Prague 6, Czech Republic.
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, CZ-16610 Prague 6, Czech Republic.
| | - Pedro Güixens-Gallardo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, CZ-16610 Prague 6, Czech Republic. .,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2 12843, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, CZ-16610 Prague 6, Czech Republic. .,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2 12843, Czech Republic
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10
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He X, Kuang S, Gao Q, Xie Y, Ming X. Bright fluorescent purine analogues as promising probes. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2021; 41:45-60. [PMID: 34806926 DOI: 10.1080/15257770.2021.2004418] [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] [Received: 10/06/2021] [Revised: 11/06/2021] [Accepted: 11/06/2021] [Indexed: 10/19/2022]
Abstract
Modified bright fluorescent nucleosides that respond to the microenvironment have great potential as probes. A series of novel 8-(phenylethynyl)phenylated 2-amino-2'-deoxyadenosine and 2'-deoxyisoguanosine derivatives have been synthesized by Sonogashira-type coupling reaction and Suzuki reaction. The maximum emission of the new compounds is in the visible region, with strong solvatochromicity and pH-dependent fluorescent properties. Furthermore, some of them exhibit bright fluorescence emissions in various solvents (ε × Φ = 4000-39,000 cm-1 M-1). These consequences indicate that purine analogues could respond to the microenvironment and serve as promising fluorescent probes.Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2021.2004418 .
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Affiliation(s)
- Xin He
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, China
| | - Shuang Kuang
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, China
| | - Qian Gao
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, China
| | - YuXin Xie
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, China
| | - Xin Ming
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, China
- Study on the Structure-Specific Small Molecular Drug in Sichuan Province College Key Laboratory, Chengdu Medical College, Chengdu, Sichuan, China
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11
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Güixens-Gallardo P, Hocek M. Acetophenyl-thienyl-aniline-Linked Nucleotide for Construction of Solvatochromic Fluorescence Light-Up DNA Probes Sensing Protein-DNA Interactions. Chemistry 2021; 27:7090-7093. [PMID: 33769635 DOI: 10.1002/chem.202100575] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Indexed: 12/20/2022]
Abstract
The synthesis of 2'-deoxycytidine and its 5'-O-triphosphate bearing solvatochromic acetophenyl-thienyl-aniline fluorophore was developed using the Sonogashira cross-coupling reaction as the key step. The triphosphate was used for polymerase synthesis of labelled DNA. The labelled nucleotide or DNA exerted weak red fluorescence when excited at 405 nm, but a significant colour change (to yellow or green) and light-up (up to 20 times) was observed when the DNA probes interacted with proteins or lipids.
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Affiliation(s)
- Pedro Güixens-Gallardo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
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12
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Ma C, Sun W, Xu L, Qian Y, Dai J, Zhong G, Hou Y, Liu J, Shen B. A minireview of viscosity-sensitive fluorescent probes: design and biological applications. J Mater Chem B 2021; 8:9642-9651. [PMID: 32986068 DOI: 10.1039/d0tb01146k] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microenvironment-related parameters like viscosity, polarity, and pH play important roles in controlling the physical or chemical behaviors of local molecules, which determine the physical or chemical behaviors of surrounding molecules. In general, changes of the internal microenvironment will usually lead to cellular malfunction or the occurrence of relevant diseases. In the last few decades, the field of chemicobiology has received great attention. Also, remarkable progress has been made in developing viscosity-sensitive fluorescent probes. These probes were particularly efficient for imaging viscosity in biomembranes as well as lighting up specific organelles, such as mitochondria and lysosome. Besides, there are some fluorescent probes that can be used to quantify intracellular viscosity when combined with fluorescence lifetime (FLIM) and ratiometric imaging under water-free conditions. In this review, we summarized the majority of viscosity-sensitive chemosensors that have been reported thus far.
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Affiliation(s)
- Chenggong Ma
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China.
| | - Wen Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China.
| | - Limin Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China.
| | - Ying Qian
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Jianan Dai
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China.
| | - Guoyan Zhong
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China.
| | - Yadan Hou
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China.
| | - Jialong Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China.
| | - Baoxing Shen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China.
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13
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Abstract
Labeling of nucleic acids is required for many studies aiming to elucidate their functions and dynamics in vitro and in cells. Out of the numerous labeling concepts that have been devised, covalent labeling provides the most stable linkage, an unrivaled choice of small and highly fluorescent labels and - thanks to recent advances in click chemistry - an incredible versatility. Depending on the approach, site-, sequence- and cell-specificity can be achieved. DNA and RNA labeling are rapidly developing fields that bring together multiple areas of research: on the one hand, synthetic and biophysical chemists develop new fluorescent labels and isomorphic nucleobases as well as faster and more selective bioorthogonal reactions. On the other hand, the number of enzymes that can be harnessed for post-synthetic and site-specific labeling of nucleic acids has increased significantly. Together with protein engineering and genetic manipulation of cells, intracellular and cell-specific labeling has become possible. In this review, we provide a structured overview of covalent labeling approaches for nucleic acids and highlight notable developments, in particular recent examples. The majority of this review will focus on fluorescent labeling; however, the principles can often be readily applied to other labels. We will start with entirely chemical approaches, followed by chemo-enzymatic strategies and ribozymes, and finish with metabolic labeling of nucleic acids. Each section is subdivided into direct (or one-step) and two-step labeling approaches and will start with DNA before treating RNA.
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Affiliation(s)
- Nils Klöcker
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, D-48149 Münster, Germany.
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14
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Luminescent probes for luminescence lifetime sensing and imaging in live cells: a narrative review. JOURNAL OF BIO-X RESEARCH 2020. [DOI: 10.1097/jbr.0000000000000081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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15
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Schreier VN, Loehr MO, Deng T, Lattmann E, Hajnal A, Neuhauss SC, Luedtke NW. Fluorescent dATP for DNA Synthesis In Vivo. ACS Chem Biol 2020; 15:2996-3003. [PMID: 33108866 DOI: 10.1021/acschembio.0c00654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fluorescent nucleoside triphosphates are powerful probes of DNA synthesis, but their potential use in living animals has been previously underexplored. Here, we report the synthesis and characterization of 7-deaza-(1,2,3-triazole)-2'-deoxyadenosine-5'-triphosphate (dATP) derivatives of tetramethyl rhodamine ("TAMRA-dATP"), cyanine ("Cy3-dATP"), and boron-dipyrromethene ("BODIPY-dATP"). Upon microinjection into live zebrafish embryos, all three compounds were incorporated into the DNA of dividing cells; however, their impact on embryonic toxicity was highly variable, depending on the exact structure of the dye. TAMRA-EdATP exhibited superior characteristics in terms of its high brightness, low toxicity, and rapid incorporation and depletion kinetics in both a vertebrate (zebrafish) and a nematode (Caenorhabditis elegans). TAMRA-EdATP allows for unprecedented, real-time visualization of DNA replication and chromosome segregation in vivo.
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Affiliation(s)
- Verena N. Schreier
- Department of Chemistry, University of Zurich, Zurich CH-8006, Switzerland
| | - Morten O. Loehr
- Department of Chemistry, University of Zurich, Zurich CH-8006, Switzerland
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Ting Deng
- Department of Molecular Life Sciences, University of Zurich, Zurich CH-8006, Switzerland
| | - Evelyn Lattmann
- Department of Molecular Life Sciences, University of Zurich, Zurich CH-8006, Switzerland
| | - Alex Hajnal
- Department of Molecular Life Sciences, University of Zurich, Zurich CH-8006, Switzerland
| | - Stephan C.F. Neuhauss
- Department of Molecular Life Sciences, University of Zurich, Zurich CH-8006, Switzerland
| | - Nathan W. Luedtke
- Department of Chemistry, University of Zurich, Zurich CH-8006, Switzerland
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3A 0G4, Canada
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16
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Pandey V, Raza MK, Sonowal M, Gupta I. BODIPY based red emitters: Synthesis, computational and biological studies. Bioorg Chem 2020; 106:104467. [PMID: 33223201 DOI: 10.1016/j.bioorg.2020.104467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/20/2022]
Abstract
Donor-Acceptor type BODIPYs with strong absorption and fluorescence in the red region (550-800 nm) are reported. The aromatic groups like N-butylcarbazole/ N-butylphenothiazine/ benzothiadiazole were attached to the C-8 position of the BODIPY core with furan or thiophene spacers. TD-DFT studies indicated significant charge distribution between C-8 aromatic heterocycles and BODIPY core in all the molecules. The in-vitro studies of the N-butylcarbazole substituted BODIPYs indicated significant localization in the endoplasmic reticulum and lysosomes of the cancer cells. The BODIPYs showed decent cytotoxicity after 48 h incubation period (14.9 to 31.8 μM) in HeLa and A549 cancer cells, indicating their potential application as theranostic agents.
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Affiliation(s)
- Vijayalakshmi Pandey
- Indian Institute of Technology Gandhinagar, Palaj Campus, Gandhinagar, Gujarat 382355, India
| | - Md Kausar Raza
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Mridupavan Sonowal
- Indian Institute of Technology Gandhinagar, Palaj Campus, Gandhinagar, Gujarat 382355, India
| | - Iti Gupta
- Indian Institute of Technology Gandhinagar, Palaj Campus, Gandhinagar, Gujarat 382355, India.
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17
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Kužmová E, Zawada Z, Navrátil M, Günterová J, Kraus T. Flow cytometric determination of cell cycle progression via direct labeling of replicated DNA. Anal Biochem 2020; 614:114002. [PMID: 33159846 DOI: 10.1016/j.ab.2020.114002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/19/2020] [Accepted: 10/25/2020] [Indexed: 01/14/2023]
Abstract
The reported method allows for a simple and rapid monitoring of DNA replication and cell cycle progression in eukaryotic cells in vitro. The DNA of replicating cells is labeled by incorporation of a metabolically-active fluorescent (Cy3) deoxyuridine triphosphate derivative, which is delivered into the cells by a synthetic transporter (SNTT1). The cells are then fixed, stained with DAPI and analyzed by flow cytometry. Thus, this protocol obviates post-labeling steps, which are indispensable in currently used incorporation assays (BrdU, EdU). The applicability of the protocol is demonstrated in analyses of cell cycles of adherent (U-2 OS, HeLa S3, RAW 264.7, J774 A.1, Chem-1, U-87 MG) and suspension (CCRF-CEM, MOLT-4, THP-1, HL-60, JURKAT) cell cultures, including those affected by a DNA polymerase inhibitor (aphidicolin). Owing to a short incorporation time (5-60 min) and reduced number of steps, the protocol can be completed within 1-2 h with a minimal cell loss and with excellent reproducibility.
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Affiliation(s)
- Erika Kužmová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic
| | - Zbigniew Zawada
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic; University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Michal Navrátil
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic
| | - Jana Günterová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2, CZ-16610, Prague 6, Czech Republic.
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18
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Karimi A, Börner R, Mata G, Luedtke NW. A Highly Fluorescent Nucleobase Molecular Rotor. J Am Chem Soc 2020; 142:14422-14426. [PMID: 32786749 DOI: 10.1021/jacs.0c05180] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescent base analogs (FBAs) are powerful probes of nucleic acids' structures and dynamics. However, previously reported FBAs exhibit relatively low brightness and therefore limited sensitivity of detection. Here we report the hitherto brightest FBA that has ideal molecular rotor properties for detecting local dynamic motions associated with base pair mismatches. The new trans-stilbene annulated uracil derivative "tsT" exhibits bright fluorescence emissions in various solvents (ε × Φ = 3400-29 700 cm-1 M-1) and is highly sensitive to mechanical motions in duplex DNA (ε × Φ = 150-4250 cm-1 M-1). tsT is thereby a "smart" thymidine analog, exhibiting a 28-fold brighter fluorescence intensity when base paired with A as compared to T or C. Time-correlated single photon counting revealed that the fluorescence lifetime of tsT (τ = 4-11 ns) was shorter than its anisotropy decay in well-matched duplex DNA (θ = 20 ns), yet longer than the dynamic motions of base pair mismatches (0.1-10 ns). These properties enable unprecedented sensitivity in detecting local dynamics of nucleic acids.
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Affiliation(s)
- Ashkan Karimi
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland.,Department of Chemistry, McGill University, H3A-0B8 Montreal, Canada
| | - Richard Börner
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland.,Laserinstitut Hochschule Mittweida, University of Applied Sciences, 09648 Mittweida, Germany
| | - Guillaume Mata
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Nathan W Luedtke
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland.,Department of Chemistry, McGill University, H3A-0B8 Montreal, Canada.,Department of Pharmacology and Therapeutics, McGill University, H3A-1A3 Montreal, Canada
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19
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Kuba M, Kraus T, Pohl R, Hocek M. Nucleotide-Bearing Benzylidene-Tetrahydroxanthylium Near-IR Fluorophore for Sensing DNA Replication, Secondary Structures and Interactions. Chemistry 2020; 26:11950-11954. [PMID: 32633433 PMCID: PMC7361531 DOI: 10.1002/chem.202003192] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Indexed: 12/16/2022]
Abstract
Thymidine triphosphate bearing benzylidene‐tetrahydroxanthylium near‐IR fluorophore linked to the 5‐methyl group via triazole was synthesized through the CuAAC reaction and was used for polymerase synthesis of labelled DNA probes. The fluorophore lights up upon incorporation to DNA (up to 348‐times) presumably due to interactions in major groove and the fluorescence further increases in the single‐stranded oligonucleotide. The labelled dsDNA senses binding of small molecules and proteins by a strong decrease of fluorescence. The nucleotide was used as a light‐up building block in real‐time PCR for detection of SARS‐CoV‐2 virus.
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Affiliation(s)
- Miroslav Kuba
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
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20
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A near-infrared azadipyrromethene dye: Photophysical properties under different acidity conditions. INORG CHEM COMMUN 2020. [DOI: 10.1016/j.inoche.2020.107942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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