A novel dimeric carbocyanine dye is found to recognise G-quadruplex structures selectively compared to mixed sequence or double-stranded DNA molecules.

Symmetrical dicarbocyanine dyes are known to cooperatively assemble on DNA templates. With the goal of developing dyes that are capable of template‐free self‐assembly, two N‐linked dimeric benzothiazole containing pentamethine cyanine dyes have been synthesized. UV‐visible spectroscopy of the dimeric dyes reveals very strong propensities for self‐assembly unlike their monomeric dye counterparts. The N‐propyl linked dye exhibits pronounced H‐aggregation at micromolar dye concentrations with the absorption maxima blue‐shifted by nearly 200 nm. In contrast, an N‐hexyl linked dye preferentially folds into H‐dimers. Similar aggregates of the monomeric dicarbocyanine dyes are known to be observed at much higher dye concentrations or in presence of suitable templates such as DNA molecules. The aggregate species of the dimeric dyes are identified based on shifts in their absorbance maxima and quenched fluorescence. The calculated electronic structure of the dimeric dyes supports their observed aggregation behaviour. Further, introduction of DNA molecules with AT‐tracts leads to transformation of the spontaneously formed dimeric dye H‐aggregates and H‐dimers into DNA‐bound dye species.

Dimeric cyanine dyes self-assemble into H-dimers and H-aggregates, which experience de-aggregation with specific biomolecules.

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