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Study of the interaction of fluorescent dyes with several DNA structures

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Treballs Finals de Grau de Química, Facultat de Química, Universitat de Barcelona, Any: 2026, Tutor: Raimundo Gargallo Gómez

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This project studies the interaction of four cyanine organic dyes (ID1-ID4) with different DNA structures, including the double helix, the G-quadruplex and the i-motif. For the characterisation of these interactions, molecular spectroscopic techniques such as UV-visible absorption, fluorescence and circular dichroism were used together with high-performance liquid chromatography.
UV-visible absorption provides relevant information on the aggregation of the dyes in aqueous solution, while fluorescence and circular dichroism allowed insight into the general modes of interaction of the ligands with the DNA structures.
The results show that the behaviour of the dyes varies depending on the substituents, although all four ligands can form H-dimers, only ID1 and ID3 form other H-type aggregates, such as trimers or tetramers.
Regarding DNA binding, ID1 and ID3 interact via an ordered π-π stacking with the terminal tetrads of Pu22T14T23, which is a parallel G-quadruplex, whereas ID2 and ID4 exhibit a disordered interaction due to steric hindrance from their substituents. In the case of the Py39wt i-motif, all ligands show a disordered interaction.
Thermal denaturation measurements indicate that dyes ID3 and ID4 significantly stabilise Pu22T14T23, whereas no ligand stabilises the Py39wt sequence.
HPLC analysis also confirms the formation of DNA:dye complexes and that this binding does not produce significant conformational changes in the DNA structure.
In summary, this study demonstrates that ligands can stabilise non-canonical DNA structures, particularly G-quadruplexes, making them interesting for future studies on the selective detection of G-quadruplexes and for the development of new therapeutic strategies for diseases such as cancer

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Study of the interaction of fluorescent dyes with several DNA structures

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Estudi de la interacció de marcadors fluorescents amb diverses estructures de l’ADN