Mechanochemical Approach to a Monocationic Asymmetric Monomethine Cyanine Dye for Nucleic Acid Analysis and Visualization

Cheshmedzhieva, Diana; Bozova, Nadezhda; Ilieva, Sonia; Novakov, Christo; Vasilev, Aleksey

doi:10.3390/molecules30193966

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Mechanochemical Approach to a Monocationic Asymmetric Monomethine Cyanine Dye for Nucleic Acid Analysis and Visualization

by

Diana Cheshmedzhieva

^1,*

,

Nadezhda Bozova

¹,

Sonia Ilieva

¹

,

Christo Novakov

²

and

Aleksey Vasilev

^1,2,*

¹

Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski”, 1 J. Bourchier Ave., 1164 Sofia, Bulgaria

²

Institute of Polymers, Bulgarian Academy of Sciences, Akad. G. Bonchev St., bl 103A, 1113 Sofia, Bulgaria

^*

Authors to whom correspondence should be addressed.

Molecules 2025, 30(19), 3966; https://doi.org/10.3390/molecules30193966

Submission received: 22 August 2025 / Revised: 19 September 2025 / Accepted: 24 September 2025 / Published: 2 October 2025

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Abstract

Using an environmentally friendly approach, we successfully synthesized an asymmetric monomethine cyanine dye, 7-chloro-1-ethyl-4-((3-ethylbenzo[d]thiazol-2(3H)-ylidene)methyl) quinolin-1-ium iodide, named CHLoris (CHL), via a modified Knoevenagel-type condensation. The reaction was carried out mechanochemically in an ethanol–water medium using 1-ethyl-2-methylbenzothiazolium iodide and 4,7-dichloro-1-ethylquinolin-1-ium iodide in the presence of sodium carbonate as a base and catalytic amounts of Hünig’s base. The UV/VIS absorption spectra of CHL in both the buffer solution and ethanol revealed the formation of aggregates in aqueous media. Density Functional Theory (DFT) and Time-Dependent DFT (TDDFT) calculations were employed to support the experimental findings further and provide insights into the self-association behavior of CHL in an aqueous solution. The photophysical properties of the dye were examined in the presence of DNA and RNA, and its performance was compared to that of the commercial dye Thiazole Orange (TO) under identical conditions. The results show that CHL is more sensitive towards RNA.

Keywords: monomethine cyanine dye; fluorogenic probes; RNA; DNA; biomolecular probes; aggregachromism

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MDPI and ACS Style

Cheshmedzhieva, D.; Bozova, N.; Ilieva, S.; Novakov, C.; Vasilev, A. Mechanochemical Approach to a Monocationic Asymmetric Monomethine Cyanine Dye for Nucleic Acid Analysis and Visualization. Molecules 2025, 30, 3966. https://doi.org/10.3390/molecules30193966

AMA Style

Cheshmedzhieva D, Bozova N, Ilieva S, Novakov C, Vasilev A. Mechanochemical Approach to a Monocationic Asymmetric Monomethine Cyanine Dye for Nucleic Acid Analysis and Visualization. Molecules. 2025; 30(19):3966. https://doi.org/10.3390/molecules30193966

Chicago/Turabian Style

Cheshmedzhieva, Diana, Nadezhda Bozova, Sonia Ilieva, Christo Novakov, and Aleksey Vasilev. 2025. "Mechanochemical Approach to a Monocationic Asymmetric Monomethine Cyanine Dye for Nucleic Acid Analysis and Visualization" Molecules 30, no. 19: 3966. https://doi.org/10.3390/molecules30193966

APA Style

Cheshmedzhieva, D., Bozova, N., Ilieva, S., Novakov, C., & Vasilev, A. (2025). Mechanochemical Approach to a Monocationic Asymmetric Monomethine Cyanine Dye for Nucleic Acid Analysis and Visualization. Molecules, 30(19), 3966. https://doi.org/10.3390/molecules30193966

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Mechanochemical Approach to a Monocationic Asymmetric Monomethine Cyanine Dye for Nucleic Acid Analysis and Visualization

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