The interaction of a structural flexible small molecule with nucleic acid structures: Investigation of the origin of fluorescence signal discrimination in sensing and the utilization in live cell imaging

Abstract

Thiazole orange (TO) stains most nucleic acids giving strong fluorescence signal non-specifically. To resolve the poor discriminating ability of TO among tertiary structures of DNAs, a planar and rotatable π–conjugated small molecule designed by replacing the methylene bridge with an ethylene that slightly increases its structural flexibility, while maintain the crucial conjugated co-planar two-ring system. The study addressed the origin of signal discrimination for the molecule upon binding with different DNA structures and the results demonstrate that the molecule exhibits excellent fluorescence signal discrimination between the DNA G-quadruplexes and other DNA tertiary structures. In a typical staining assay, the molecule induced 30-fold greater fluorescence signal upon binding with Pu27 than that of ssDNA and dsDNA. Molecular modelling studies also support that the flexible ethylene bridge between the two-ring system is the crucial factor for inducing selectivity towards G-quadruplexes. Furthermore, the selectivity, sensitivity, and stability of the molecule were investigated with various techniques. The application of the molecule as a selective staining agent for imaging of G-quadruplex in human prostate cancer cells PC3 and mouse fibroblast L929 was also investigated. The strongly observed green fluorescence signal in the cell nucleus suggests that the molecule is able to enter into the nucleus and then binding with G-quadruplexes.