1
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Arora A, Kumar S, Kumar S, Dua A, Singh BK. Synthesis, characterization and photophysical studies of dual-emissive base-modified fluorescent nucleosides. Org Biomol Chem 2024. [PMID: 38808609 DOI: 10.1039/d4ob00749b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
A straightforward and efficient methodology has been employed for the synthesis of a diverse set of base-modified fluorescent nucleoside conjugates via Cu(I)-catalysed cycloaddition reaction of 5-ethynyl-2',3',5'-tri-O-acetyluridine/3',5'-di-O-acetyl-2'-deoxyuridine with 4-(azidomethyl)-N9-(4'-aryl)-9,10-dihydro-2H,8H-chromeno[8,7-e][1,3]oxazin-2-ones in tBuOH to afford the desired 1,2,3-triazoles in 92-95% yields. Treatment with NaOMe/MeOH resulted in the final deprotected nucleoside analogues. The synthesized 1,2,3-triazoles demonstrated a significant emission spectrum, featuring two robust bands in the region from 350-500 nm (with excitation at 300 nm) in fluorescence studies. Photophysical investigations revealed a dual-emissive band with high fluorescence intensity, excellent Stokes shift (140-164 nm) and superior quantum yields (0.068-0.350). Furthermore, the electronic structures of the synthesized triazoles have been further verified by DFT studies. Structural characterization of all synthesized compounds was carried out using various analytical techniques, including IR, 1H-NMR, 13C-NMR, 1H-1H COSY, 1H-13C HETCOR experiments, and HRMS measurements. The dual-emissive nature of these nucleosides would be a significant contribution to nucleoside chemistry as there are limited literature reports on the same.
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Affiliation(s)
- Aditi Arora
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India.
| | - Sumit Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India.
| | - Sandeep Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India.
- Department of Chemistry, Ramjas College, University of Delhi, Delhi-110007, India
| | - Amita Dua
- Department of Chemistry, Dyal Singh College, University of Delhi, Delhi-110007, India
| | - Brajendra K Singh
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India.
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2
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Le HN, Kuchlyan J, Baladi T, Albinsson B, Dahlén A, Wilhelmsson LM. Synthesis and photophysical characterization of a pH-sensitive quadracyclic uridine (qU) analogue. Chemistry 2024:e202303539. [PMID: 38230625 DOI: 10.1002/chem.202303539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/18/2024]
Abstract
Fluorescent base analogues (FBAs) have become useful tools for applications in biophysical chemistry, chemical biology, live-cell imaging, and RNA therapeutics. Herein, two synthetic routes towards a novel FBA of uracil named qU (quadracyclic uracil/uridine) are described. The qU nucleobase bears a tetracyclic fused ring system and is designed to allow for specific Watson-Crick base pairing with adenine. We find that qU absorbs light in the visible region of the spectrum and emits brightly with a quantum yield of 27 % and a dual-band character in a wide pH range. With evidence, among other things, from fluorescence lifetime measurements we suggest that this dual emission feature results from an excited-state proton transfer (ESPT) process. Furthermore, we find that both absorption and emission of qU are highly sensitive to pH. The high brightness in combination with excitation in the visible and pH responsiveness makes qU an interesting native-like nucleic acid label in spectroscopy and microscopy applications in, for example, the field of mRNA and antisense oligonucleotide (ASO) therapeutics.
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Affiliation(s)
- Hoang-Ngoan Le
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - Jagannath Kuchlyan
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
| | - Tom Baladi
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - Bo Albinsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
| | - Anders Dahlén
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
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3
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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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4
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Le HN, Brazard J, Barnoin G, Vincent S, Michel BY, Leonard J, Burger A. Control of Intermolecular Photoinduced Electron Transfer in Deoxyadenosine-Based Fluorescent Probes. Chemistry 2021; 27:1364-1373. [PMID: 32767410 DOI: 10.1002/chem.202003456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Indexed: 12/12/2022]
Abstract
In this work, we report on the Photoinduced Electron Transfer (PET) reaction between a donor (adenine analogue) and an acceptor (3-methoxychromone dye, 3MC) in the context of designing efficient fluorescent probes as DNA sensors. Firstly, Gibbs energy was investigated in disconnected donor-acceptor systems by Rehm-Weller equation. The oxidation potential of the adenine derivative was responsible for exergonicity of the PET reaction in separated combinations. Then, the PET reaction in donor-π-acceptor conjugates was investigated using steady-state fluorescence spectroscopy, acid-mediated PET inhibition and transient absorption techniques. In conjugated systems, PET is a favorable pathway of fluorescent quenching when an electron-rich adenine analogue (d7A) was connected to the fluorophore (3MC). We found that formation of ground-state complexes even at nm concentration range dominated the dye photophysics and generated poorly emissive species likely through intermolecular PET from d7A to 3MC. On the other hand, solution acidification disrupts complexation and turns on the dye emission. Bridging an electron-poor adenine analogue with high oxidation potential (8 d7A) to 3MC presenting low reduction potential is another alternative to prevent complex formation and produce highly emissive monomer conjugates.
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Affiliation(s)
- Hoang-Ngoan Le
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
| | - Johanna Brazard
- Université de Strasbourg, Institut de Physique et Chimie, des Matériaux de Strasbourg and Labex NIE, UMR 7504, CNRS, 67200, Strasbourg, France.,Present address: Université de Genève, Département de Chimie Physique, 1211, Genève, France
| | - Guillaume Barnoin
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
| | - Steve Vincent
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
| | - Benoît Y Michel
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
| | - Jérémie Leonard
- Université de Strasbourg, Institut de Physique et Chimie, des Matériaux de Strasbourg and Labex NIE, UMR 7504, CNRS, 67200, Strasbourg, France
| | - Alain Burger
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
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5
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Kaczmarek R, Twardy DJ, Olson TL, Korczyński D, Andrei G, Snoeck R, Dolot R, Wheeler KA, Dembinski R. Extension of furopyrimidine nucleosides with 5-alkynyl substituent: Synthesis, high fluorescence, and antiviral effect in the absence of free ribose hydroxyl groups. Eur J Med Chem 2020; 209:112884. [PMID: 33039724 PMCID: PMC7521880 DOI: 10.1016/j.ejmech.2020.112884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/15/2020] [Accepted: 09/23/2020] [Indexed: 11/24/2022]
Abstract
A novel methodology to access alkynyl nucleoside analogues is elaborated. Highly fluorescent 5-alkynylfuropyrimidines were synthesized (97-46%) and their antiviral properties investigated in vitro. Regiochemistry of the functionalization was achieved with the aid of 5-endo-dig electrophilic halocyclization of acetyl 5-p-tolyl- or 5-p-pentylphenyl-2'-deoxyuridine. Structure of one of the resulting nucleosides, 6-p-tolyl-5-iodo-2'-deoxyribofuranosyl-furo[2,3-d]pyrimidin-2-one, was confirmed by X-ray crystallography, and its conformation was compared to related nucleosides. Diverse alkynyl substituents were introduced at the heterobicyclic base C-5 position via Sonogashira coupling of 5-iodo-2'-deoxyribofuranosyl-furo[2,3-d]pyrimidin-2-ones. The resulting compounds had fluorescence emissions of 452-481 nm. High quantum yields of 0.53-0.60 were observed for 9-ethynyl-9-fluorenol and propargyl alcohol/methyl ether-modified furopyrimidines. These modified nucleosides, designed in the form of ribose acetyl esters, are potential tools for fluorescent tagging, studying nucleoside metabolism, 2'-deoxyribonucleoside kinase activity, and antiviral activity. Antiviral assays against a broad spectrum of DNA and RNA viruses showed that in human embryonic lung (HEL) cell cultures some of the compounds posess antiviral activity (EC50 1.3-13.2 μM) against varicella-zoster virus (VZV). The alkynyl furopyrimidine with two p-pentylphenyl substituents emerged as the best compound with reasonable and selective anti-VZV activity, confirming p-pentylphenyl potency as a pharmacophore.
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Affiliation(s)
- Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Dylan J Twardy
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI, 48309-4479, USA
| | - Trevor L Olson
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI, 48309-4479, USA
| | - Dariusz Korczyński
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Graciela Andrei
- Rega Institute, Department of Microbiology, Immunology and Transplantation, Herestraat 49, 3000, Leuven, Belgium
| | - Robert Snoeck
- Rega Institute, Department of Microbiology, Immunology and Transplantation, Herestraat 49, 3000, Leuven, Belgium
| | - Rafał Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Kraig A Wheeler
- Department of Chemistry, Whitworth University, 300 W. Hawthorne Rd., Spokane, WA, 99251, USA
| | - Roman Dembinski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland; Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI, 48309-4479, USA.
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6
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Michel BY, Dziuba D, Benhida R, Demchenko AP, Burger A. Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels. Front Chem 2020; 8:112. [PMID: 32181238 PMCID: PMC7059644 DOI: 10.3389/fchem.2020.00112] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).
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Affiliation(s)
- Benoît Y. Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
| | - Dmytro Dziuba
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Mohamed VI Polytechnic University, UM6P, Ben Guerir, Morocco
| | - Alexander P. Demchenko
- Laboratory of Nanobiotechnologies, Palladin Institute of Biochemistry, Kyiv, Ukraine
- Institute of Physical, Technical and Computer Science, Yuriy Fedkovych National University, Chernivtsi, Ukraine
| | - Alain Burger
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
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7
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Kaczmarek R, Korczyński D, Green JR, Dembinski R. Extension of the 5-alkynyluridine side chain via C-C-bond formation in modified organometallic nucleosides using the Nicholas reaction. Beilstein J Org Chem 2020; 16:1-8. [PMID: 31976010 PMCID: PMC6964655 DOI: 10.3762/bjoc.16.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/14/2019] [Indexed: 01/15/2023] Open
Abstract
Dicobalt hexacarbonyl nucleoside complexes of propargyl ether or esters of 5-substituted uridines react with diverse C-nucleophiles. Synthetic outcomes confirmed that the Nicholas reaction can be carried out in a nucleoside presence, leading to a divergent synthesis of novel metallo-nucleosides enriched with alkene, arene, arylketo, and heterocyclic functions, in the deoxy and ribo series.
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Affiliation(s)
- Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Dariusz Korczyński
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - James R Green
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, N9B 3P4, Canada
| | - Roman Dembinski
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland.,Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309-4479, USA
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8
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Lee SY, Hong SW, Yeo H, Hwang GT. The linkers in fluorene-labeled 2′-deoxyuridines affect fluorescence discriminating phenomena upon duplex formation. RSC Adv 2020; 10:18853-18859. [PMID: 35518342 PMCID: PMC9053879 DOI: 10.1039/d0ra01651a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/08/2020] [Indexed: 11/29/2022] Open
Abstract
Three fluorene-labeled 2′-deoxyuridines that differ in terms of their linkers—UF (without linker), UFL (with ethynyl linker), and UDF (with diethynyl linker)—have been introduced at the central positions of oligodeoxynucleotides to examine the effects that their linkers have on the fluorescence emission properties upon duplex formation with fully matched and single-base-mismatched targets. Here, we describe the influence of the linkers on the emission behavior, the intramolecular electron transfer between the fluorene moiety and the uracil base after photoexcitation, and the structural stability upon duplex formation. The probe containing the UFL residue (with an ethynyl linker) and cytosine residues as flanking bases exhibited the greatest fluorescence turn-on selective behavior toward the perfectly matched target. Three fluorene-labeled 2′-deoxyuridines that differ in terms of their linkers have been introduced at the central positions of oligodeoxynucleotides to examine the effects that their linkers have on the emission properties upon duplex formations.![]()
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Affiliation(s)
- So Young Lee
- Department of Chemistry and Green-Nano Materials Research Center
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Seung Woo Hong
- Department of Chemistry and Green-Nano Materials Research Center
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Hyeonuk Yeo
- Department of Chemistry Education
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center
- Kyungpook National University
- Daegu 41566
- Republic of Korea
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9
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Chatterjee S, Ahire K, Karuso P. Room-Temperature Dual Fluorescence of a Locked Green Fluorescent Protein Chromophore Analogue. J Am Chem Soc 2019; 142:738-749. [PMID: 31846319 DOI: 10.1021/jacs.9b05096] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A structurally locked green fluorescent protein (GFP) chromophore with a phenyl group at C(2) of the imidazolone has been synthesized. Rotation around the exocyclic double bond is hindered, resulting in room-temperature fluorescence. The quantum yield in water is 500 times greater than that of unlocked analogues. Unlike the methyl-substituted analogue, the phenyl analogue exhibits a dual emission (cyan and red) that can be used for ultrasensitive ratiometric measurements and fluorescence microscopy. To explain this dual emission, DFT calculations were carried out along with fluorescence upconversion experiments. The Z-isomer was found to be emissive, while the origin of the dual emission was dependent on the phenyl group in the Z-isomer, which stabilizes the Franck-Condon state, resulting in a cyan fluorescence, while the zwitterionic tautomer fluoresces red. These results bring important new insights into the photophysics of the GFP chromophore and provide a new scaffold capable of dual emission with utility in biotechnology.
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Affiliation(s)
- Soumit Chatterjee
- Department of Molecular Sciences , Macquarie University , Sydney , NSW 2109 , Australia
| | - Ketan Ahire
- Department of Molecular Sciences , Macquarie University , Sydney , NSW 2109 , Australia
| | - Peter Karuso
- Department of Molecular Sciences , Macquarie University , Sydney , NSW 2109 , Australia
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10
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Teppang KL, Lee RW, Burns DD, Turner MB, Lokensgard ME, Cooksy AL, Purse BW. Electronic Modifications of Fluorescent Cytidine Analogues Control Photophysics and Fluorescent Responses to Base Stacking and Pairing. Chemistry 2018; 25:1249-1259. [PMID: 30338571 DOI: 10.1002/chem.201803653] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Indexed: 11/07/2022]
Abstract
The rational design of fluorescent nucleoside analogues is greatly hampered by the lack of a general method to predict their photophysics, a problem that is especially acute when base pairing and stacking change fluorescence. To better understand these effects, a series of tricyclic cytidine (tC and tCO ) analogues ranging from electron-rich to electron-deficient was designed and synthesized. They were then incorporated into oligonucleotides, and photophysical responses to base pairing and stacking were studied. When inserted into double-stranded DNA oligonucleotides, electron-rich analogues exhibit a fluorescence turn-on effect, in contrast with the electron-deficient compounds, which show diminished fluorescence. The magnitude of these fluorescence changes is correlated with the oxidation potential of nearest neighbor nucleobases. Moreover, matched base pairing enhances fluorescence turn-on for the electron-rich compounds, and it causes a fluorescence decrease for the electron-deficient compounds. For the tCO compounds, the emergence of vibrational fine structure in the fluorescence spectra in response to base pairing and stacking was observed, offering a potential new tool for studying nucleic acid structure and dynamics. These results, supported by DFT calculations, help to rationalize fluorescence changes in the base stack and will be useful for selecting the best fluorescent nucleoside analogues for a desired application.
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Affiliation(s)
- Kristine L Teppang
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Raymond W Lee
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Dillon D Burns
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - M Benjamin Turner
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Melissa E Lokensgard
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Andrew L Cooksy
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Byron W Purse
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
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11
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Hemicyanine-linked pyrimidine mimics as solvatochromic fluorophores with visible excitation wavelengths. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Lawson CP, Füchtbauer AF, Wranne MS, Giraud T, Floyd T, Dumat B, Andersen NK, H El-Sagheer A, Brown T, Gradén H, Wilhelmsson LM, Grøtli M. Synthesis, oligonucleotide incorporation and fluorescence properties in DNA of a bicyclic thymine analogue. Sci Rep 2018; 8:13970. [PMID: 30228309 PMCID: PMC6143597 DOI: 10.1038/s41598-018-31897-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/23/2018] [Indexed: 12/26/2022] Open
Abstract
Fluorescent base analogues (FBAs) have emerged as a powerful class of molecular reporters of location and environment for nucleic acids. In our overall mission to develop bright and useful FBAs for all natural nucleobases, herein we describe the synthesis and thorough characterization of bicyclic thymidine (bT), both as a monomer and when incorporated into DNA. We have developed a robust synthetic route for the preparation of the bT DNA monomer and the corresponding protected phosphoramidite for solid-phase DNA synthesis. The bT deoxyribonucleoside has a brightness value of 790 M−1cm−1 in water, which is comparable or higher than most fluorescent thymine analogues reported. When incorporated into DNA, bT pairs selectively with adenine without perturbing the B-form structure, keeping the melting thermodynamics of the B-form duplex DNA virtually unchanged. As for most fluorescent base analogues, the emission of bT is reduced inside DNA (4.5- and 13-fold in single- and double-stranded DNA, respectively). Overall, these properties make bT an interesting thymine analogue for studying DNA and an excellent starting point for the development of brighter bT derivatives.
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Affiliation(s)
- Christopher P Lawson
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296, Gothenburg, Sweden
| | - Anders F Füchtbauer
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Tristan Giraud
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Thomas Floyd
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Blaise Dumat
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Nicolai K Andersen
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Henrik Gradén
- Cardiovascular, Renal and Metabolic Diseases IMED Biotech Unit, AstraZeneca Gothenburg, Pepparedsleden 1, Molndal, SE-431 83, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden.
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296, Gothenburg, Sweden.
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13
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Bag SS, Gogoi H. Design of "Click" Fluorescent Labeled 2'-deoxyuridines via C5-[4-(2-Propynyl(methyl)amino)]phenyl Acetylene as a Universal Linker: Synthesis, Photophysical Properties, and Interaction with BSA. J Org Chem 2018; 83:7606-7621. [PMID: 29877080 DOI: 10.1021/acs.joc.7b03097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microenvironment-sensitive fluorescent nucleosides present attractive advantages over single-emitting dyes for sensing inter-biomolecular interactions involving DNA. Herein, we report the rational design and synthesis of triazolyl push-pull fluorophore-labeled uridines via the intermediacy of C5-[4-(2-propynyl(methyl)amino)]phenyl acetylene as a universal linker. The synthesized nucleosides showed interesting solvatochromic characteristic and/or intramolecular charge transfer (ICT) features. A few of them also exhibited dual-emitting characteristics evidencing our designing concept. The HOMO-LUMO distribution showed that the emissive states of these nucleosides were characterized with more significant electron redistribution between the C5-[4-(2-propynyl(methyl)amino)]phenyl triazolyl donor moiety and the aromatic chromophores linked to it, leading to modulated emission property. The solvent polarity sensitivity of these nucleosides was also tested. The synthesized triazolyl benzonitrile (10C), naphthyl (10E), and pyrenyl (10G) nucleosides were found to exhibit interesting ICT and dual (LE/ICT) emission properties. The dual-emitting pyrenyl nucleoside maintained a good ratiometric response in the BSA protein microenvironment, enabling the switch-on ratiometric sensing of BSA as the only protein biomolecule. Thus, it is expected that the new fluorescent nucleoside analogues would be useful in designing DNA probes for nucleic acid analysis or studying DNA-protein interactions via a drastic change in fluorescence response due to a change in micropolarity.
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Affiliation(s)
- Subhendu Sekhar Bag
- Bioorganic Chemistry Laboratory, Department of Chemistry , Indian Institute of Technology Guwahati 781039 , India
| | - Hiranya Gogoi
- Bioorganic Chemistry Laboratory, Department of Chemistry , Indian Institute of Technology Guwahati 781039 , India
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14
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Grytsai O, Druzhenko T, Demange L, Ronco C, Benhida R. Cyanoguanidine as a versatile, eco-friendly and inexpensive reagent for the synthesis of 2-aminobenzoxazoles and 2-guanidinobenzoxazoles. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.03.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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15
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Zhang M, Yang W, Gong T, Zhou W, Xue R. Tunable AIEE fluorescence constructed from a triphenylamine luminogen containing quinoline - application in a reversible and tunable pH sensor. Phys Chem Chem Phys 2018; 19:21672-21682. [PMID: 28767113 DOI: 10.1039/c7cp03234j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Herein, tunable emissions in aggregation processes of triphenylamine derivatives (TPAQs) and their protonated cations, as well as protonated processes have been described. In this study, three triphenylamine-based compounds (TPAQs) were synthesized and their optical properties were investigated. Initially, the TPAQs displayed aggregation-induced emission enhancement (AIEE) properties via the restricted intramolecular charge transfer (ICT) state. Interestingly, the single-branched fluorophore (STPAQ) and its protonated cation emitted different color fluorescence in the solution and aggregation state. They emitted green fluorescence, which originated from the intramolecular charge transfer (ICT) state in a strong polar solvent, but the fluorescence bands turned blue, which was attributed to the LE state in the aggregated state. However, the cations of triple-branched fluorophores (TTPAQs) exhibited an inverse tunable emission process from bluish violet fluorescence of the LE state in a weak polar solvent (e.g., THF) to green fluorescence of the ICT state in the aggregated state. In a THF/water mixture solution (fw = 10%), the STPAQ could switch its emission between blue and green in the pH range of 10.0-0.5. This phenomenon enabled STPAQ to serve as a fluorescent pH sensor in solution. In the powder state, double-branched fluorophores (DTPAQs) could be used as a fluorescent sensor for the detection of acidic and basic organic vapors in the solid state.
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Affiliation(s)
- Mengmeng Zhang
- School of Chemistry & Chemical Engineering and Material Science, Soochow University, 199 Ren'ai Road, Suzhou, 215123, People's Republic of China.
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16
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Qiao N, Wei NN, Zhang J, Hao C. The dual-luminescence mechanism of the ESIPT chemosensor tetrasubstituted imidazole core compound: a TDDFT study. NEW J CHEM 2018. [DOI: 10.1039/c8nj01162a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The dual-luminescence mechanism of the tetrasubstituted imidazole core (TIC) compound was theoretically explored by considering the excited-state intramolecular proton transfer (ESIPT) process in the present study.
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Affiliation(s)
- Na Qiao
- School of Life Science and Medicine
- Dalian University of Technology
- Panjin 124221
- P. R. China
| | - Ning-Ning Wei
- School of Life Science and Medicine
- Dalian University of Technology
- Panjin 124221
- P. R. China
| | - Jianing Zhang
- School of Life Science and Medicine
- Dalian University of Technology
- Panjin 124221
- P. R. China
| | - Ce Hao
- State Key Laboratory of Fine Chemicals
- School of Petroleum and Chemical Engineering
- Dalian University of Technology
- Panjin 124221
- P. R. China
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17
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Londesborough MGS, Dolanský J, Jelínek T, Kennedy JD, Císařová I, Kennedy RD, Roca-Sanjuán D, Francés-Monerris A, Lang K, Clegg W. Substitution of the laser borane anti-B18H22 with pyridine: a structural and photophysical study of some unusually structured macropolyhedral boron hydrides. Dalton Trans 2018; 47:1709-1725. [DOI: 10.1039/c7dt03823b] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One-step derivatization of the laser borane, anti-B18H22, with pyridine gives three uniquely structured macropolyhedral boranes with interesting photophysical properties.
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Affiliation(s)
| | - Jiří Dolanský
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- Husinec-Řež
- Czech Republic
- Charles University in Prague
- Department of Inorganic Chemistry
| | - Tomáš Jelínek
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- Husinec-Řež
- Czech Republic
- Katchem s.r.o
- 278 01 Kralupy nad Vltavou
| | - John D. Kennedy
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- Husinec-Řež
- Czech Republic
- The School of Chemistry of the University of Leeds
- Leeds
| | - Ivana Císařová
- Charles University in Prague
- Department of Inorganic Chemistry
- 128 43 Prague 2
- Czech Republic
| | | | | | | | - Kamil Lang
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- Husinec-Řež
- Czech Republic
| | - William Clegg
- Chemistry
- The School of Natural and Environmental Sciences of Newcastle University
- Newcastle upon Tyne
- UK
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18
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Alaoui S, Dufies M, Driowya M, Demange L, Bougrin K, Robert G, Auberger P, Pagès G, Benhida R. Synthesis and anti-cancer activities of new sulfonamides 4-substituted-triazolyl nucleosides. Bioorg Med Chem Lett 2017; 27:1989-1992. [PMID: 28325600 DOI: 10.1016/j.bmcl.2017.03.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 12/11/2022]
Abstract
Nucleoside analogues are among the most known drugs commonly used in antiviral and anticancer chemotherapies. Among them, those featuring a five-membered ring nucleobase are of utmost interest such as the anti-cancer agent AICAR or the anti-viral drug ribavirin. Despite its low activity in vitro in different cell lines, AICAR is under clinical development for several pathologies, thanks to its original mode of action. Indeed, AICAR induced autophagy cell death and is able, following this mechanism, to circumvent resistance to apoptotic drugs including kinase inhibitors currently on the market. To improve the activity of AICAR, we report herein an efficient synthesis of new series of sulfonamide-4-substituted-1,2,3-triazolyl nucleosides using a Cu-catalyzed 1,3-dipolar cycloaddition. All these molecules have been fully characterized and evaluated against two aggressive tumor cell lines, RCC4 and MDA-MB-231. Among them, nucleoside analogue 5i belonging to the ribose series was found to be 19 to 66-fold more active than AICAR. Western blot analyses on RCC4 cells showed that 5i displayed an interesting mode of action by inducing both apoptosis and autophagy cell death, making therefore this class of molecules highly promising for further hit-to-lead optimization.
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Affiliation(s)
- Soukaina Alaoui
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272, 06108 Nice, France; Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique, URAC23, Faculté des Sciences, Université Mohammed V, B.P. 1014 Rabat, Morocco
| | - Maeva Dufies
- Université Côte d'Azur, CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
| | - Mohsine Driowya
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique, URAC23, Faculté des Sciences, Université Mohammed V, B.P. 1014 Rabat, Morocco
| | - Luc Demange
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272, 06108 Nice, France; Département de Chimie, Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Pharmaceutiques, 4 avenue de l'Observatoire & UFR Biomédicale des Saints Pères, 45 rue des Saints Pères, Paris Fr-75006, France
| | - Khalid Bougrin
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique, URAC23, Faculté des Sciences, Université Mohammed V, B.P. 1014 Rabat, Morocco
| | - Guillaume Robert
- Université Côte d'Azur, INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Bâtiment ARCHIMED, 151 Route de Saint-Antoine de Ginestière, BP 2 3194, 06204 Nice Cedex 3, France
| | - Patrick Auberger
- Université Côte d'Azur, INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Bâtiment ARCHIMED, 151 Route de Saint-Antoine de Ginestière, BP 2 3194, 06204 Nice Cedex 3, France
| | - Gilles Pagès
- Université Côte d'Azur, CNRS UMR 7284 and INSERM U 1081, Institute for Research on Cancer and Aging (IRCAN), 28 Avenue de Valombrose, 06107 Nice, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272, 06108 Nice, France.
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19
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Szakács Z, Kállay M, Kubinyi M. Theoretical study on the photooxygenation and photorearrangement reactions of 3-hydroxyflavone. RSC Adv 2017. [DOI: 10.1039/c7ra04590e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The mechanisms of three photodegradation reactions of 3-hydroxyflavone – its photosensitized oxygenation, photooxygenation with 3O2 and photorearrangement into an indanedione derivative – have been investigated by computing the free energy profiles.
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Affiliation(s)
- Zoltán Szakács
- Department of Physical Chemistry and Materials Science
- Budapest University of Technology and Economics
- 1521 Budapest
- Hungary
| | - Mihály Kállay
- MTA-BME Lendület Quantum Chemistry Research Group
- Department of Physical Chemistry and Materials Science
- Budapest University of Technology and Economics
- 1521 Budapest
- Hungary
| | - Miklós Kubinyi
- Department of Physical Chemistry and Materials Science
- Budapest University of Technology and Economics
- 1521 Budapest
- Hungary
- Institute of Materials and Environmental Chemistry
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20
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Naito H, Nishino K, Morisaki Y, Tanaka K, Chujo Y. Solid-State Emission of the Anthracene-o-Carborane Dyad from the Twisted-Intramolecular Charge Transfer in the Crystalline State. Angew Chem Int Ed Engl 2016; 56:254-259. [PMID: 27911472 DOI: 10.1002/anie.201609656] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Indexed: 02/04/2023]
Abstract
The emission process of the o-carborane dyad with anthracene originating from the twisted intramolecular charge transfer (TICT) state in the crystalline state is described. The anthracene-o-carborane dyad was synthesized and its optical properties were investigated. Initially, the dyad had aggregation- and crystallization-induced emission enhancement (AIEE and CIEE) properties via the intramolecular charge transfer (ICT) state. Interestingly, the dyad presented the dual-emissions assigned to both locally excited (LE) and ICT states in solution. From the mechanistic studies and computer calculations, it was indicated that the emission band from the ICT should be attributable to the TICT emission. Surprisingly, even in the crystalline state, the TICT emission was observed. It was proposed from that the compact sphere shape of o-carborane would allow for rotation even in the condensed state.
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Affiliation(s)
- Hirofumi Naito
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Kenta Nishino
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Yasuhiro Morisaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Department of Applied Chemistry for Environment, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan
| | - Kazuo Tanaka
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Yoshiki Chujo
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
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21
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Naito H, Nishino K, Morisaki Y, Tanaka K, Chujo Y. Solid‐State Emission of the Anthracene‐
o
‐Carborane Dyad from the Twisted‐Intramolecular Charge Transfer in the Crystalline State. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609656] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Hirofumi Naito
- Department of Polymer Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
| | - Kenta Nishino
- Department of Polymer Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
| | - Yasuhiro Morisaki
- Department of Polymer Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
- Department of Applied Chemistry for Environment School of Science and Technology Kwansei Gakuin University 2-1 Gakuen, Sanda Hyogo 669-1337 Japan
| | - Kazuo Tanaka
- Department of Polymer Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
| | - Yoshiki Chujo
- Department of Polymer Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
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22
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Barthes NPF, Gavvala K, Bonhomme D, Dabert-Gay AS, Debayle D, Mély Y, Michel BY, Burger A. Design and Development of a Two-Color Emissive FRET Pair Based on a Photostable Fluorescent Deoxyuridine Donor Presenting a Mega-Stokes Shift. J Org Chem 2016; 81:10733-10741. [DOI: 10.1021/acs.joc.6b01807] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Nicolas P. F. Barthes
- Institut
de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Krishna Gavvala
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Dominique Bonhomme
- Institut
de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Anne Sophie Dabert-Gay
- Institut
de Pharmacologie Moléculaire et Cellulaire, UMR 6097, Université Côte d'Azur, CNRS, 660 Route des Lucioles, 06560 Valbonne, France
| | - Delphine Debayle
- Institut
de Pharmacologie Moléculaire et Cellulaire, UMR 6097, Université Côte d'Azur, CNRS, 660 Route des Lucioles, 06560 Valbonne, France
| | - Yves Mély
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Benoît Y. Michel
- Institut
de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Alain Burger
- Institut
de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
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23
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Dziuba D, Pospíšil P, Matyašovský J, Brynda J, Nachtigallová D, Rulíšek L, Pohl R, Hof M, Hocek M. Solvatochromic fluorene-linked nucleoside and DNA as color-changing fluorescent probes for sensing interactions. Chem Sci 2016; 7:5775-5785. [PMID: 30034716 PMCID: PMC6021979 DOI: 10.1039/c6sc02548j] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 06/20/2016] [Indexed: 12/16/2022] Open
Abstract
A nucleoside bearing a solvatochromic push-pull fluorene fluorophore (dCFL ) was designed and synthesized by the Sonogashira coupling of alkyne-linked fluorene 8 with 5-iodo-2'-deoxycytidine. The fluorene building block 8 and labeled nucleoside dCFL exerted bright fluorescence with significant solvatochromic effect providing emission maxima ranging from 421 to 544 nm and high quantum yields even in highly polar solvents, including water. The solvatochromism of 8 was studied by DFT and ADC(2) calculations to show that, depending on the polarity of the solvent, emission either from the planar or the twisted conformation of the excited state can occur. The nucleoside was converted to its triphosphate variant dCFLTP which was found to be a good substrate for DNA polymerases suitable for the enzymatic synthesis of oligonucleotide or DNA probes by primer extension or PCR. The fluorene-linked DNA can be used as fluorescent probes for DNA-protein (p53) or DNA-lipid interactions, exerting significant color changes visible even to the naked eye. They also appear to be suitable for time-dependent fluorescence shift studies on DNA, yielding information on DNA hydration and dynamics.
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Affiliation(s)
- Dmytro Dziuba
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Petr Pospíšil
- J. H eyrovský Institute of Physical Chemistry , Czech Academy of Sciences , Dolejskova 3 , CZ-182 23 Prague , Czech Republic
| | - Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Martin Hof
- J. H eyrovský Institute of Physical Chemistry , Czech Academy of Sciences , Dolejskova 3 , CZ-182 23 Prague , Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
- Department of Organic Chemistry , Faculty of Science , Charles University in Prague , Hlavova 8 , CZ-12843 Prague 2 , Czech Republic
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24
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Shaya J, Fontaine-Vive F, Michel BY, Burger A. Rational Design of Push-Pull Fluorene Dyes: Synthesis and Structure-Photophysics Relationship. Chemistry 2016; 22:10627-37. [PMID: 27304218 DOI: 10.1002/chem.201600581] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Indexed: 12/22/2022]
Abstract
Our work surveyed experimental and theoretical investigations to construct highly emissive D-π-A (D=donor, A=acceptor) fluorenes. The synthetic routes were optimised to be concise and gram-scalable. The molecular design was first rationalised by varying the electron-withdrawing group from an aldehyde, ketotriazole or succinyl to methylenemalonitrile or benzothiadiazole. The electron-donating group was next varied from aliphatic or aromatic amines to saturated cyclic amines ranging from aziridine to azepane. Spectroscopic studies correlated with TD-DFT calculations provided the optimised structures. The selected push-pull dyes exhibited visible absorptions, significant brightness, important solvatofluorochromism, mega-Stokes shifts (>250 nm) and dramatic shifts in emission to the near-infrared. The current library includes the comprehensive characterization of 16 prospective dyes for fluorescence applications. Among them, several fluorene derivatives bearing different conjugation anchors were tested for coupling and demonstrated to preserve the photophysical responses once further bound.
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Affiliation(s)
- Janah Shaya
- Institut de Chimie de Nice, UMR 7272, Université de Nice Sophia Antipolis, CNRS, Parc Valrose, 06108, Nice Cedex 2, France
| | - Fabien Fontaine-Vive
- Institut de Chimie de Nice, UMR 7272, Université de Nice Sophia Antipolis, CNRS, Parc Valrose, 06108, Nice Cedex 2, France
| | - Benoît Y Michel
- Institut de Chimie de Nice, UMR 7272, Université de Nice Sophia Antipolis, CNRS, Parc Valrose, 06108, Nice Cedex 2, France
| | - Alain Burger
- Institut de Chimie de Nice, UMR 7272, Université de Nice Sophia Antipolis, CNRS, Parc Valrose, 06108, Nice Cedex 2, France.
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25
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Freeman NS, Moore CE, Wilhelmsson LM, Tor Y. Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes. J Org Chem 2016; 81:4530-9. [PMID: 27128151 PMCID: PMC5493935 DOI: 10.1021/acs.joc.6b00310] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nucleodyes, visibly colored chromophoric nucleoside analogues, are reported. Design criteria are outlined and the syntheses of cytidine and uridine azo dye analogues derived from 6-aminouracil are described. Structural analysis shows that the nucleodyes are sound structural analogues of their native nucleoside counterparts, and photophysical studies demonstrate that the nucleodyes are sensitive to microenvironmental changes. Quantum chemical calculations are presented as a valuable complementary tool for the design of strongly absorbing nucleodyes, which overlap with the emission of known fluorophores. Förster critical distance (R0) calculations determine that the nucleodyes make good FRET pairs with both 2-aminopurine (2AP) and pyrrolocytosine (PyC). Additionally, unique tautomerization features exhibited by 5-(4-nitrophenylazo)-6-oxocytidine (8) are visualized by an extraordinary crystal structure.
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Affiliation(s)
- Noam S. Freeman
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
| | - Curtis E. Moore
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
| | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry
and Biochemistry, Chalmers University of Technology, Gothenburg 41296, Sweden
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
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26
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Gavvala K, Barthes NPF, Bonhomme D, Dabert-Gay AS, Debayle D, Michel BY, Burger A, Mély Y. A turn-on dual emissive nucleobase sensitive to mismatches and duplex conformational changes. RSC Adv 2016. [DOI: 10.1039/c6ra19061h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Herein, we demonstrate the on–off dual emissive behaviour of a fluorescent nucleoside sensitive towards DNA hybridization and conformational changes as well as detection of single nucleotide polymorphisms.
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Affiliation(s)
- Krishna Gavvala
- Laboratoire de Biophotonique et Pharmacologie
- UMR 7213
- Faculté de Pharmacie
- Université de Strasbourg
- CNRS
| | - Nicolas P. F. Barthes
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- Parc Valrose
| | - Dominique Bonhomme
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- Parc Valrose
| | - Anne Sophie Dabert-Gay
- Institut de Pharmacologie Moléculaire et Cellulaire
- UMR 6097
- Université de Nice Sophia Antipolis
- 660 Route des Lucioles
- 06560 Valbonne
| | - Delphine Debayle
- Institut de Pharmacologie Moléculaire et Cellulaire
- UMR 6097
- Université de Nice Sophia Antipolis
- 660 Route des Lucioles
- 06560 Valbonne
| | - Benoît Y. Michel
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- Parc Valrose
| | - Alain Burger
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- Parc Valrose
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie
- UMR 7213
- Faculté de Pharmacie
- Université de Strasbourg
- CNRS
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Dziuba D, Jurkiewicz P, Cebecauer M, Hof M, Hocek M. A Rotational BODIPY Nucleotide: An Environment-Sensitive Fluorescence-Lifetime Probe for DNA Interactions and Applications in Live-Cell Microscopy. Angew Chem Int Ed Engl 2015; 55:174-8. [PMID: 26768820 DOI: 10.1002/anie.201507922] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/20/2015] [Indexed: 12/16/2022]
Abstract
Fluorescent probes for detecting the physical properties of cellular structures have become valuable tools in life sciences. The fluorescence lifetime of molecular rotors can be used to report on variations in local molecular packing or viscosity. We used a nucleoside linked to a meso-substituted BODIPY fluorescent molecular rotor (dC(bdp)) to sense changes in DNA microenvironment both in vitro and in living cells. DNA incorporating dC(bdp) can respond to interactions with DNA-binding proteins and lipids by changes in the fluorescence lifetimes in the range 0.5-2.2 ns. We can directly visualize changes in the local environment of exogenous DNA during transfection of living cells. Relatively long fluorescence lifetimes and extensive contrast for detecting changes in the microenvironment together with good photostability and versatility for DNA synthesis make this probe suitable for analysis of DNA-associated processes, cellular structures, and also DNA-based nanomaterials.
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Affiliation(s)
- Dmytro Dziuba
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, 16610 Prague 6 (Czech Republic) http://www.uochb.cas.cz/hocekgroup
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 3, 18223 Prague 8 (Czech Republic) http://www.hof-fluorescence-group.weebly.com/
| | - Marek Cebecauer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 3, 18223 Prague 8 (Czech Republic) http://www.hof-fluorescence-group.weebly.com/
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejskova 3, 18223 Prague 8 (Czech Republic) http://www.hof-fluorescence-group.weebly.com/.
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, 16610 Prague 6 (Czech Republic) http://www.uochb.cas.cz/hocekgroup. .,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843 Prague 2 (Czech Republic).
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Dziuba D, Jurkiewicz P, Cebecauer M, Hof M, Hocek M. A Rotational BODIPY Nucleotide: An Environment-Sensitive Fluorescence-Lifetime Probe for DNA Interactions and Applications in Live-Cell Microscopy. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507922] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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