Dynamic and static quenching of 6-(2′,7′-dimethoxy-4′,5′-dichloro)carboxyfluorescein (JOE) by nucleosides (deoxyadenosine, deoxycytidine, deoxyguanosine, thymidine, and deoxyuridine) in Tris-acetate buffer solution was analyzed using the Stern–Volmer equation. Only one of the five nucleosides, deoxyguanosine, exhibited predominantly static quenching. The fluorescence quantum yields in buffer solution of 5- and 6-carboxyfluorescein (FAM) and 5-and 6-JOE bound covalently to the oligonucleotide by a rigid linker (4-trans-aminocyclohexanol) were greater than those of their analogs with a flexible linker (6-aminohexanol). It was shown that fluorescence quenching in systems with a flexible linker occurred mainly through van-der-Waals contact of the fluorophore with guanine. An increase in the number of consecutively located guanines in the oligonucleotides and their duplexes bound to the dye by a linker decreased the fluorescence quantum yield. Quantum-chemical calculations using the Gaussian 09 program provided an interpretation for the low-frequency shifts of 5-FAM and 5-JOE absorption and fluorescence spectra relative to those of the 6-isomers.
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Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 84, No. 3, pp. 434–442, May–June, 2017.
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Povedailo, V.A., Stupak, A.P., Tsybulsky, D.A. et al. Fluorescence Quenching of Carboxyfluoresceins Conjugated Convalently to Oligonucleotides. J Appl Spectrosc 84, 452–459 (2017). https://doi.org/10.1007/s10812-017-0491-6
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DOI: https://doi.org/10.1007/s10812-017-0491-6