DNA triplex-based fluorescence turn-on sensors for adenosine using a fluorescent molecular rotor 5-(3-methylbenzofuran-2-yl) deoxyuridine

Kanamori, Takashi; Yoshio, Masaki; Oda, Yuki; Ohzeki, Hiroki; Ohkubo, Akihiro; Sekine, Mitsuo; Seio, Kohji

doi:10.1039/c8ob02747a

Cited by 10 publications

(4 citation statements)

References 46 publications

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“…Similar working principles have been exploited to use environmentally sensitive probes to study base mismatches [140] and non‐canonical secondary structure of nucleic acids, [139a] including triplexes, [141] i‐motifs [142] or G‐quadruplexes (G4s). [ 130 , 143 ] G4s are non‐canonical nucleic acid structures that form in guanine‐rich regions of the genome, which are thought to have vital biological roles, acting as regulators of gene transcription, in replication and in telomere maintenance.…”

Section: Molecular Rotors For Biological Imagingmentioning

confidence: 99%

Molecular Rotors: Fluorescent Sensors for Microviscosity and Conformation of Biomolecules

Paez‐Perez,

Kuimova

2023

Angew Chem Int Ed

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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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Section: Molecular Rotors For Biological Imagingmentioning

confidence: 99%

Molecular Rotors: Fluorescent Sensors for Microviscosity and Conformation of Biomolecules

Paez‐Perez,

Kuimova

2023

Angew Chem Int Ed

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“…The use of non-denaturing PAGE is highly effective for both the qualitative and quantitative analyses of DNA triplexes but the use of radioactive material containing 32 P and/or other radionuclides requires expertise in handling, manufacture and the safe disposal of waste to protect against negative impact on the environment. Fluorescence-based [5] approaches provide potentially less expensive, greener methods for triplex DNA analysis. The use of a bifunctional triplex DNA sensor incorporating the 1,8-naphthilamide fluorophore and a naphthoquinoline motif was examined [6] and shown to be selective for triplex over duplex and single-stranded DNA, as judged by photoelectron transfer [7] (PET) assay.…”

Section: Introductionmentioning

confidence: 99%

Selectivity of a bromoacridine-containing fluorophore for triplex DNA

Sharma

Fraser

2021

Monatsh Chem

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Fluorophore 1,8-naphthilamide was linked to 2-bromoacridine through an ethylenediamine spacer using a succinct synthetic route to give a bromoacridine-linked, bifunctional fluorophore conjugate for the detection of triplex DNA. Acridine is well known to intercalate into duplex DNA whereas introduction of a bulky bromine atom at position C2 redirects specificity for triplex over duplex DNA. In this work, photoelectron transfer assay was used to demonstrate that the synthesised 2-bromoacridine-linked fluorophore conjugate had good selectivity for the representative triplex DNA target sequence d(T*A.T)20 compared with double-stranded d(T.A)20, single-stranded dT20 or d(G/A)19 DNA sequences. Graphic abstract

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“…Recently, it has been shown that probes belonging to molecular rotor group can result in a large increase in their emission intensity upon binding with DNA molecules. − Molecular rotors are characterized by an electron donor and electron acceptor moieties connected through a single bond. Such molecule upon photoexcitation undergoes very efficient torsional motion around that single bond and leads to the formation of a nonemissive twisted intramolecular charge transfer (TICT) state. − Due to such process, the emission yield of molecular rotors is extremely low (<10 –3 ) in solvents with low viscosity, such as water, methanol, etc. − However, upon association with biomolecules, the microviscosity around such molecular rotor increases and provides strong frictional forces toward the torsional motion in the excited state. ,− Hence, due to the binding, the nonradiative torsional process gets restricted and the emission quantum yield of such biomolecule-bound molecular rotor increases to a large extent.…”

Section: Introductionmentioning

confidence: 99%

Anthryl Benzothiazolium Molecular Rotor-Based Turn-On DNA Probe: Detailed Mechanistic Studies

et al. 2019

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An efficient turn-on fluorescence probe for biomolecules not only helps in its sensitive detection but is also useful to understand the different interactions that are operating between biomolecules and probes. Polycyclic aromatic molecules are known to be strong interacting ligand for DNA and extensively studied as a model cancer drug. However, these molecules show large decrease in their emission intensity, i.e., a turn-off probe for DNA. In the present work, we have synthesized a benzothiazole-based anthracene derivative and studied its interaction with a natural DNA with the aim of having a turn-on DNA probe with a polycyclic aromatic moiety. Our detailed spectroscopic studies show that the new probe strongly interacts with DNA molecules and results in a significant increase in its emission yield. Time-resolved studies show a large increase in probe’s excited-state lifetime in DNA solution. Detailed experiments have been performed to understand its mode of interaction with DNA molecules. The mode of interaction has also been supported by the blind molecular docking studies. Further, the viscosity-dependent photophysical properties and detailed quantum chemical calculations confirm that the new probe belongs to molecular rotor class of molecules. Association with DNA molecules results in a significant retardation in the nonradiative deactivation process due to the torsional motion in the excited state of the probe and leads to a significant increase in its emission yield. Thus, due its molecular rotor nature, despite with a turn-off fluorophore unit, anthracene, the new probe, acts as a sensitive turn-on fluorescence probe for DNA molecules.

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DNA triplex-based fluorescence turn-on sensors for adenosine using a fluorescent molecular rotor 5-(3-methylbenzofuran-2-yl) deoxyuridine

Abstract: Fluorescence turn-on detection of adenosine based on microenvironmental and conformational changes of a fluorescent molecular rotor in the DNA triplex is reported.

Cited by 10 publications

References 46 publications

Molecular Rotors: Fluorescent Sensors for Microviscosity and Conformation of Biomolecules

Molecular Rotors: Fluorescent Sensors for Microviscosity and Conformation of Biomolecules

Selectivity of a bromoacridine-containing fluorophore for triplex DNA

Anthryl Benzothiazolium Molecular Rotor-Based Turn-On DNA Probe: Detailed Mechanistic Studies

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