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Alkyl side chain engineering of thiazole orange derivates for improved G-Quadruplex DNA binding selectivity and live-cell fluorescence imaging.

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Title: Alkyl side chain engineering of thiazole orange derivates for improved G-Quadruplex DNA binding selectivity and live-cell fluorescence imaging.
Authors: Li, Lu-Yu1 (AUTHOR), Zhao, Yi-Ran1 (AUTHOR), Guo, Haoran2 (AUTHOR), Fan, Xu-Bo1 (AUTHOR), Li, Ze-Kai1 (AUTHOR), Shu, Jing1 (AUTHOR), Zhou, Si-Hong1 (AUTHOR), Huang, Gui-Chuan1 (AUTHOR), Yang, Fa1,2 (AUTHOR) yangfa@fmmu.edu.cn, Wang, Ming-Qi1 (AUTHOR) wmq3415@163.com
Source: Dyes & Pigments. Mar2026:Part 1, Vol. 246, pN.PAG-N.PAG. 1p.
Subjects: Quadruplex nucleic acids, Fluorescent probes, Cell imaging, Fluorescence microscopy, Thiazole derivatives, Ligand binding (Biochemistry)
Abstract: Fluorescent probes derived from the thiazole orange (TO) scaffold have made significant advances in the recognition and detection of G-Quadruplex (G4) DNA. However, the reported probes of this type still have some limitations. For instance, they often exhibit limited binding affinity toward nuclear DNA, resulting in non-specific cytoplasmic retention. Moreover, their cellular imaging process typically requires extended incubation times, hindering their application in real-time imaging. To address these limitations, we propose a molecular side-chain engineering strategy based on the TO scaffold to modulate the G4 DNA binding affinity, cellular permeability, and nuclear anchoring capability. Herein, a series of dyes designated as TOQ-C n (where n is the number of carbons), derived from the (Z)-2-ethylidene-3-methyl-2,3-dihydrobenzo[ d ]thiazole (2TO) scaffold with different lengths of side chains were designed and synthesized. Results indicated that they all exhibited binding selectivity toward G4 DNA over single- and double-stranded DNA structures. Among them, the medium-chain derivative TOQ-C 5 demonstrated the highest binding affinity for G4 DNA, identifying it as the most promising candidate. Combining spectroscopic and computational approaches, binding studies revealed that TOQ-C 5 bound to G4 DNA with a 2:1 stoichiometry via end-stacking, demonstrating a notable preference for the 3′ terminus. Moreover, the distinct optical responses of TOQ-C 5 upon binding to G4 DNA enabled the construction of a label-free binary INHIBIT logic gate, illustrating its potential for application in molecular-scale logic circuits. Fluorescence imaging studies in live HeLa cells showed that medium-chain TOQ-C 5 could quickly enter the living cells and localize to both mitochondria and the nucleus, enabling rapid imaging of DNA within the nucleus. In contrast, short-chain and long-chain dyes exhibit poor cellular permeability, making it difficult for them to enter the nucleus. This study provides an effective design strategy for developing fluorescent dyes that can tune both G4 DNA binding affinity and cell internalization efficiency through side-chain modulation. [Display omitted] • A series of TO derivatives with varying alkyl chain lengths as promising fluorescent dyes for G4 DNA structures is outlined. • TOQ-C 5 with medium chain length had the highest affinity for G4 DNA. • A label-free binary INHIBIT gate was achieved by TOQ-C 5. • TOQ-C 5 rapidly entered cells within approximately 2 min and localized to both mitochondrial and nuclear regions. [ABSTRACT FROM AUTHOR]
Copyright of Dyes & Pigments is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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Header DbId: egs
DbLabel: Engineering Source
An: 189497020
AccessLevel: 6
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PubTypeId: academicJournal
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  Data: Alkyl side chain engineering of thiazole orange derivates for improved G-Quadruplex DNA binding selectivity and live-cell fluorescence imaging.
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  Data: <searchLink fieldCode="AR" term="%22Li%2C+Lu-Yu%22">Li, Lu-Yu</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Zhao%2C+Yi-Ran%22">Zhao, Yi-Ran</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Guo%2C+Haoran%22">Guo, Haoran</searchLink><relatesTo>2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Fan%2C+Xu-Bo%22">Fan, Xu-Bo</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Li%2C+Ze-Kai%22">Li, Ze-Kai</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Shu%2C+Jing%22">Shu, Jing</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Zhou%2C+Si-Hong%22">Zhou, Si-Hong</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Huang%2C+Gui-Chuan%22">Huang, Gui-Chuan</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Yang%2C+Fa%22">Yang, Fa</searchLink><relatesTo>1,2</relatesTo> (AUTHOR)<i> yangfa@fmmu.edu.cn</i><br /><searchLink fieldCode="AR" term="%22Wang%2C+Ming-Qi%22">Wang, Ming-Qi</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> wmq3415@163.com</i>
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  Data: <searchLink fieldCode="JN" term="%22Dyes+%26+Pigments%22">Dyes & Pigments</searchLink>. Mar2026:Part 1, Vol. 246, pN.PAG-N.PAG. 1p.
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  Data: Fluorescent probes derived from the thiazole orange (TO) scaffold have made significant advances in the recognition and detection of G-Quadruplex (G4) DNA. However, the reported probes of this type still have some limitations. For instance, they often exhibit limited binding affinity toward nuclear DNA, resulting in non-specific cytoplasmic retention. Moreover, their cellular imaging process typically requires extended incubation times, hindering their application in real-time imaging. To address these limitations, we propose a molecular side-chain engineering strategy based on the TO scaffold to modulate the G4 DNA binding affinity, cellular permeability, and nuclear anchoring capability. Herein, a series of dyes designated as TOQ-C n (where n is the number of carbons), derived from the (Z)-2-ethylidene-3-methyl-2,3-dihydrobenzo[ d ]thiazole (2TO) scaffold with different lengths of side chains were designed and synthesized. Results indicated that they all exhibited binding selectivity toward G4 DNA over single- and double-stranded DNA structures. Among them, the medium-chain derivative TOQ-C 5 demonstrated the highest binding affinity for G4 DNA, identifying it as the most promising candidate. Combining spectroscopic and computational approaches, binding studies revealed that TOQ-C 5 bound to G4 DNA with a 2:1 stoichiometry via end-stacking, demonstrating a notable preference for the 3′ terminus. Moreover, the distinct optical responses of TOQ-C 5 upon binding to G4 DNA enabled the construction of a label-free binary INHIBIT logic gate, illustrating its potential for application in molecular-scale logic circuits. Fluorescence imaging studies in live HeLa cells showed that medium-chain TOQ-C 5 could quickly enter the living cells and localize to both mitochondria and the nucleus, enabling rapid imaging of DNA within the nucleus. In contrast, short-chain and long-chain dyes exhibit poor cellular permeability, making it difficult for them to enter the nucleus. This study provides an effective design strategy for developing fluorescent dyes that can tune both G4 DNA binding affinity and cell internalization efficiency through side-chain modulation. [Display omitted] • A series of TO derivatives with varying alkyl chain lengths as promising fluorescent dyes for G4 DNA structures is outlined. • TOQ-C 5 with medium chain length had the highest affinity for G4 DNA. • A label-free binary INHIBIT gate was achieved by TOQ-C 5. • TOQ-C 5 rapidly entered cells within approximately 2 min and localized to both mitochondrial and nuclear regions. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: <i>Copyright of Dyes & Pigments is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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      – Type: doi
        Value: 10.1016/j.dyepig.2025.113404
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      – Code: eng
        Text: English
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    Subjects:
      – SubjectFull: Quadruplex nucleic acids
        Type: general
      – SubjectFull: Fluorescent probes
        Type: general
      – SubjectFull: Cell imaging
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      – SubjectFull: Fluorescence microscopy
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      – SubjectFull: Thiazole derivatives
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      – SubjectFull: Ligand binding (Biochemistry)
        Type: general
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      – TitleFull: Alkyl side chain engineering of thiazole orange derivates for improved G-Quadruplex DNA binding selectivity and live-cell fluorescence imaging.
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              M: 03
              Text: Mar2026:Part 1
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