A simple structural modification to thiazole orange to improve the selective detection of G-quadruplexes

• New derivatives of thiazole orange were designed and synthesized.
• Hydrocarbon rings were introduced into thiazole orange.
• This simple modification improved selective detection of G-quadruplex.
• Planarity and affinity were key factors responsible for the selective detection.

Thiazole orange is a commonly used cyanine dye for binding to nucleic acids. Recently, it has been used for the detection of G-quadruplexes. However, thiazole orange is non-selective for G-quadruplex and other nucleic acids, thus hampering its further application. Herein, we designed and synthesized new fluorescent probes by incorporating hydrocarbon rings into the chromophore of thiazole orange. This simple modification dramatically improved selective binding to certain G-quadruplexes. The most promising probe, the cyclopentane fused analogue, exhibited significant fluorescence enhancement when treated with G-quadruplexes but retained weak fluorescence in the presence of double-stranded and single-stranded DNA. The cyclopentane fused probe also displayed considerable selectivity for parallel G-quadruplexes. These modifications reduced the quantum yield of thiazole orange. Further study of the mechanism revealed that the introduction of a hydrocarbon ring altered the planarity of the chromophore as well as the binding affinities for G-quadruplexes, and therefore, influenced the ability to detect G-quadruplexes.

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