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Updated: May 8, 2026

Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes
Published on: July 6, 2016
Photochemical properties of squarylium cyanine dyes
D P Ferreira1, D S Conceição, V R A Ferreira
1CQFM-Centro de Química-Física Molecular and IN-Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade Técnica de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal. luisfilipevf@ist.utl.pt.
Abstract:
This study presents several new squarylium dyes derived from benzothiazole and benzoselenazole with several structural variations, namely the nature of the heteroaromatic ring and the length of the N,N'-dialkyl groups. Before being investigated in connection with their effect on living cells and/or tissues, these novel compounds were characterized, namely with respect to the determination of their main photophysical parameters. Therefore, a study of the ground state absorption, fluorescence emission (quantum yields and lifetimes) and singlet oxygen generation quantum yields was performed for all the compounds synthesized in order to evaluate their efficiency as photosensitizers. An increase of the alkyl chain length from ethyl to hexyl did not produce a clear change in the fluorescence quantum yields, showing no influence on the photoisomerization process. Heavy atom inclusion (Se instead of S) enhanced the singlet oxygen generation efficiency and decreased the intensity of the fluorescence emission. The external heavy atom effect (I(-) as a counterion instead of CF3SO3(-)) produced a significant increase in the singlet oxygen formation quantum yield (about 20%). Transient absorption studies in aerated and oxygen free samples revealed that the photoisomerization process, which could compete with the triplet state formation for all dyes in solution, is a negligible pathway for the excited state deactivation, in accordance with the rigidity introduced by the squaric ring into the polymethine chain of the dye, both in chloroform and ethanol. However, in the case of the chloroform solution a new transient was detected in air equilibrated solutions, resulting from a reaction of the excited squarylium dye in the singlet state with CHCl3˙, and assigned to the radical cation (SQ(+)˙) of the dye.
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