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  1. Article ; Online: Synthesis and Photophysical Characterization of a pH-Sensitive Quadracyclic Uridine (qU) Analogue.

    Le, Hoang-Ngoan / Kuchlyan, Jagannath / Baladi, Tom / Albinsson, Bo / Dahlén, Anders / Wilhelmsson, L Marcus

    Chemistry (Weinheim an der Bergstrasse, Germany)

    2024  Volume 30, Issue 18, Page(s) e202303539

    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/ ... ...

    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.
    MeSH term(s) Uridine/chemistry ; Fluorescent Dyes/chemistry ; Nucleic Acids ; Hydrogen-Ion Concentration ; Uracil
    Chemical Substances Uridine (WHI7HQ7H85) ; Fluorescent Dyes ; Nucleic Acids ; Uracil (56HH86ZVCT)
    Language English
    Publishing date 2024-02-09
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1478547-X
    ISSN 1521-3765 ; 0947-6539
    ISSN (online) 1521-3765
    ISSN 0947-6539
    DOI 10.1002/chem.202303539
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: An Expeditious Approach towards the Synthesis and Application of Water-Soluble and Photostable Fluorogenic Chromones for DNA Detection.

    Vincent, Steve / Mallick, Suman / Barnoin, Guillaume / Le, Hoang-Ngoan / Michel, Benoît Y / Burger, Alain

    Molecules (Basel, Switzerland)

    2022  Volume 27, Issue 7

    Abstract: The intensive research for hybridization probes based on organic molecules with fluorogenic properties is currently attracting particular attention due to their potential to efficiently recognize different DNA conformations and the local environment. ... ...

    Abstract The intensive research for hybridization probes based on organic molecules with fluorogenic properties is currently attracting particular attention due to their potential to efficiently recognize different DNA conformations and the local environment. However, most established organic chromophores do not meet the requirements of this task, as they do not exhibit good brightness in aqueous buffer media, develop aggregation and/or are not easily conjugated to oligodeoxynucleotides (ODNs) while keeping their photophysics intact. Herein, an important modification strategy was employed for a well-known fluorophore, 2-(4-(diethylamino)phenyl)-3-hydroxychromone (
    MeSH term(s) Chromones ; DNA ; DNA Probes ; Fluorescent Dyes ; Water
    Chemical Substances Chromones ; DNA Probes ; Fluorescent Dyes ; Water (059QF0KO0R) ; DNA (9007-49-2)
    Language English
    Publishing date 2022-03-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules27072267
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.MO 81: Show issues

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  3. Article ; Online: Multiphoton characterization and live cell imaging using fluorescent adenine analogue 2CNqA.

    Nilsson, Jesper R / Benitez-Martin, Carlos / Sansom, Henry G / Pfeiffer, Pauline / Baladi, Tom / Le, Hoang-Ngoan / Dahlén, Anders / Magennis, Steven W / Wilhelmsson, L Marcus

    Physical chemistry chemical physics : PCCP

    2023  Volume 25, Issue 30, Page(s) 20218–20224

    Abstract: Fluorescent nucleobase analogues (FBAs) are established tools for studying oligonucleotide structure, dynamics and interactions, and have recently also emerged as an attractive option for labeling RNA-based therapeutics. A recognized drawback of FBAs, ... ...

    Abstract Fluorescent nucleobase analogues (FBAs) are established tools for studying oligonucleotide structure, dynamics and interactions, and have recently also emerged as an attractive option for labeling RNA-based therapeutics. A recognized drawback of FBAs, however, is that they typically require excitation in the UV region, which for imaging in biological samples may have disadvantages related to phototoxicity, tissue penetration, and out-of-focus photobleaching. Multiphoton excitation has the potential to alleviate these issues and therefore, in this work, we characterize the multiphoton absorption properties and detectability of the highly fluorescent quadracyclic adenine analogue 2CNqA as a ribonucleotide monomer as well as incorporated, at one or two positions, into a 16mer antisense oligonucleotide (ASO). We found that 2CNqA has a two-photon absorption cross section that, among FBAs, is exceptionally high, with values of
    MeSH term(s) Fluorescent Dyes/chemistry ; Oligonucleotides ; Spectrometry, Fluorescence/methods ; Purine Nucleosides ; Adenine/chemistry
    Chemical Substances Fluorescent Dyes ; Oligonucleotides ; Purine Nucleosides ; Adenine (JAC85A2161)
    Language English
    Publishing date 2023-08-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d3cp01147j
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Intermolecular dark resonance energy transfer (DRET): upgrading fluorogenic DNA sensing.

    Barnoin, Guillaume / Shaya, Janah / Richert, Ludovic / Le, Hoang-Ngoan / Vincent, Steve / Guérineau, Vincent / Mély, Yves / Michel, Benoît Y / Burger, Alain

    Nucleic acids research

    2021  Volume 49, Issue 12, Page(s) e72

    Abstract: The sensitivity of FRET-based sensing is usually limited by the spectral overlaps of the FRET donor and acceptor, which generate a poor signal-to-noise ratio. To overcome this limitation, a quenched donor presenting a large Stokes shift can be combined ... ...

    Abstract The sensitivity of FRET-based sensing is usually limited by the spectral overlaps of the FRET donor and acceptor, which generate a poor signal-to-noise ratio. To overcome this limitation, a quenched donor presenting a large Stokes shift can be combined with a bright acceptor to perform Dark Resonance Energy Transfer (DRET). The consequent fluorogenic response from the acceptor considerably improves the signal-to-noise ratio. To date, DRET has mainly relied on a donor that is covalently bound to the acceptor. In this context, our aim was to develop the first intermolecular DRET pair for specific sensing of nucleic acid sequences. To this end, we designed DFK, a push-pull probe based on a fluorenyl π-platform that is strongly quenched in water. DFK was incorporated into a series of oligonucleotides and used as a DRET donor with Cy5-labeled complementary sequences. In line with our expectations, excitation of the dark donor in the double-labeled duplex switched on the far-red Cy5 emission and remained free of cross-excitation. The DRET mechanism was supported by time-resolved fluorescence measurements. This concept was then applied with binary probes, which confirmed the distance dependence of DRET as well as its potency in detecting sequences of interest with low background noise.
    MeSH term(s) Fluorescence Resonance Energy Transfer ; Fluorescent Dyes/chemical synthesis ; Fluorescent Dyes/chemistry ; Oligonucleotides/chemistry ; Spectrometry, Fluorescence/methods
    Chemical Substances Fluorescent Dyes ; Oligonucleotides
    Language English
    Publishing date 2021-04-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkab237
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Control of Intermolecular Photoinduced Electron Transfer in Deoxyadenosine-Based Fluorescent Probes.

    Le, Hoang-Ngoan / Brazard, Johanna / Barnoin, Guillaume / Vincent, Steve / Michel, Benoît Y / Leonard, Jérémie / Burger, Alain

    Chemistry (Weinheim an der Bergstrasse, Germany)

    2020  Volume 27, Issue 4, Page(s) 1364–1373

    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 ... ...

    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.
    Language English
    Publishing date 2020-12-07
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1478547-X
    ISSN 1521-3765 ; 0947-6539
    ISSN (online) 1521-3765
    ISSN 0947-6539
    DOI 10.1002/chem.202003456
    Database MEDical Literature Analysis and Retrieval System OnLINE

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