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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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Kanagawa T, Tachibana S, Masaki Y, Seio K. Synthesis and Conformational Analyses of Cyclonucleoside Having 13-Membered Ring Bridging Nucleobase and 5'-Position via a Linker Containing Sulfonamide. Org Lett 2023; 25:7868-7872. [PMID: 37857270 DOI: 10.1021/acs.orglett.3c03094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
A cyclic nucleoside has been designed and synthesized to serve as a conformationally fixed building block for the development of functional oligonucleotides. The bridge was introduced between the nucleobase and the 5'-position to fix the rotation around the C4'-C5' bond, the base orientation, and the sugar puckering all at once. The 13-membered cyclic structure was introduced using a sulfonamide linkage, which retains an N-H group that can be used to attach an additional nucleoside moiety. The sulfonamide linkage was formed through the end-to-end cyclization of an intermediate that contained both a sulfonyltriazole and amino groups. Both 1H NMR and computational studies revealed that the sugar conformation, base orientation, and γ torsion angle were S-type, anti, and trans, respectively. As such, cyclic nucleosides show promise for introducing these specific distorted conformations into functional nucleic acids.
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Affiliation(s)
- Takayuki Kanagawa
- Department of Life Sciences and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama Kanagawa 226-8501, Japan
| | - Shigetoshi Tachibana
- Department of Life Sciences and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama Kanagawa 226-8501, Japan
| | - Yoshiaki Masaki
- Department of Life Sciences and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama Kanagawa 226-8501, Japan
- JST PRESTO, Kawaguchi 332-0012, Japan
| | - Kohji Seio
- Department of Life Sciences and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama Kanagawa 226-8501, Japan
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Ozturk SE, Isci R, Faraji S, Sütay B, Majewski LA, Ozturk T. Synthesis, Photophysical Properties and OFET Application of Thienothiophene and Benzothiadiazole Based Donor-π-Acceptor- π (D- π -A- π) Type Conjugated Polymers. Eur Polym J 2023. [DOI: 10.1016/j.eurpolymj.2023.112028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Copolymers of 3-Arylthieno[3,2-b]thiophenes Bearing Different Substituents: Synthesis, Electronic, Optical, Sensor and Memory Properties. Eur Polym J 2022. [DOI: 10.1016/j.eurpolymj.2022.111167] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Isci R, Unal M, Kucukcakir G, Gurbuz NA, Gorkem SF, Ozturk T. Triphenylamine/4,4'-Dimethoxytriphenylamine-Functionalized Thieno[3,2- b]thiophene Fluorophores with a High Quantum Efficiency: Synthesis and Photophysical Properties. J Phys Chem B 2021; 125:13309-13319. [PMID: 34807616 DOI: 10.1021/acs.jpcb.1c09448] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A wide series of 10 new triphenylamine (TPA)/4,4'-dimethoxytriphenylamine (TPA(OMe)2)-functionalized thieno[3,2-b]thiophene (TT) fluorophores, 4a-e and 5a-e, bearing different electron-donating and electron-withdrawing substituents (-PhCN, -PhF, -PhOMe, -Ph, and -C6H13) at the terminal thienothiophene units were designed and synthesized by the Suzuki coupling reaction. Their optical and electrochemical properties were investigated by experimental and computational studies. Solid-state fluorescent quantum yields were recorded to be from 20 to 69%, and the maximum solution-state quantum efficiency reached 97%. Moreover, the photophysical characterization of the novel chromophores demonstrated a significant Stokes shift, reaching 179 nm with a bathochromic shift. They exhibited tuning color emission from orange to dark blue in solution and showed fluorescence lifetime reaching 4.70 ns. The relationship between triphenylamine (TPA)/4,4'-dimethoxytriphenylamine (TPA(OMe)2)-derived triarylamines and different functional groups on thieno[3,2-b] thiophene units was discussed.
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Affiliation(s)
- Recep Isci
- Chemistry Department, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
| | - Melis Unal
- Chemistry Department, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
| | - Gizem Kucukcakir
- Chemistry Department, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
| | - Naime A Gurbuz
- Chemistry Department, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
| | - Sultan F Gorkem
- Chemistry Department, Eskisehir Technical University, 26470 Eskisehir, Turkey
| | - Turan Ozturk
- Chemistry Department, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey.,Chemistry Group Laboratories, TUBITAK UME, 41470 Gebze, Kocaeli, Turkey
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Hirashima S, Sugiyama H, Park S. Construction of a FRET System in a Double-Stranded DNA Using Fluorescent Thymidine and Cytidine Analogs. J Phys Chem B 2020; 124:8794-8800. [DOI: 10.1021/acs.jpcb.0c06879] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Shingo Hirashima
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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Kladova OA, Kuznetsova AA, Barthes NPF, Michel BY, Burger A, Fedorova OS, Kuznetsov NA. New Fluorescent Analogs of Nucleotides Based on 3-Hydroxychromone for Recording Conformational Changes of DNA. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019060220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Saady A, Böttner V, Meng M, Varon E, Shav-Tal Y, Ducho C, Fischer B. An oligonucleotide probe incorporating the chromophore of green fluorescent protein is useful for the detection of HER-2 mRNA breast cancer marker. Eur J Med Chem 2019; 173:99-106. [PMID: 30991278 DOI: 10.1016/j.ejmech.2019.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/05/2019] [Accepted: 04/04/2019] [Indexed: 01/15/2023]
Abstract
Diagnosis and treatment of breast cancer can be greatly enhanced and personalized based on the quantitative detection of mRNA markers. Here, we targeted the development of a fluorescent oligonucleotide probe to detect specifically the HER-2 mRNA breast cancer marker. We have selected the chromophore of the Green Fluorescent Protein (GFP), 4-hydroxybenzylidene imidazolinone (HBI), as a fluorophore covalently bound to an oligonucleotide probe and potentially capable of intercalating within a probe-mRNA duplex. We first synthesized the two-ring scaffold of the HBI chromophore 5 and coupled it to 2'-deoxyuridine at C5-position via a 7-atom-spacer, to give 4. Indeed, in the highly viscous glycerol used to mimic the reduced conformational flexibility of the intercalated HBI, chromophore 4 displayed a quantum yield of 0.29 and brightness of 20600 M-1cm-1, while no fluorescent signal was observed in methanol. Next, we synthesized a 20-mer oligonucleotide probe incorporating 4 at position 6 (5'-CCCGTUTCAACAGGAGTTTC-3'), ONHBI, targeting nucleotides 1233-1253 of HER-2 mRNA. A 16-fold enhancement of ONHBI emission intensity upon hybridization with the complementary RNA vs that of the oligonucleotide probe alone indicated the presence of target oligonucleotide and proved the intercalation of the chromophore (quantum yield 0.52; brightness 23500 M-1cm-1). Even more, an 11-fold enhancement of ONHBI emission (quantum yield 0.50; brightness 23200 M-1cm-1) was observed when the probe was mixed with total RNA extract from a human cell line that has high levels of HER2 mRNA expression. Thus, we propose ONHBI as a promising probe potentially useful for the sensitive and specific detection of HER2 mRNA breast cancer marker.
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Affiliation(s)
- Abed Saady
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Verena Böttner
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Melissa Meng
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Eli Varon
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Yaron Shav-Tal
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Bilha Fischer
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel.
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Tachallait H, Safir Filho M, Marzag H, Bougrin K, Demange L, Martin AR, Benhida R. A straightforward and versatile FeCl3 catalyzed Friedel–Crafts C-glycosylation process. Application to the synthesis of new functionalized C-nucleosides. NEW J CHEM 2019. [DOI: 10.1039/c8nj06300a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rapid and straightforward access to C-nucleosides using an inexpensive FeCl3 catalyst.
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Affiliation(s)
- Hamza Tachallait
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique
- URAC23
- Faculté des Sciences
- 1014 Rabat
- Morocco
| | - Mauro Safir Filho
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Hamid Marzag
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Khalid Bougrin
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique
- URAC23
- Faculté des Sciences
- 1014 Rabat
- Morocco
| | - Luc Demange
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Anthony R. Martin
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Rachid Benhida
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
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Mesoscopic modelling of Cy3 and Cy5 dyes attached to DNA duplexes. Biophys Chem 2017; 230:62-67. [DOI: 10.1016/j.bpc.2017.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/21/2017] [Accepted: 08/27/2017] [Indexed: 11/19/2022]
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