Dicyanomethylene-Functionalized Squaraine as a Highly Selective Probe for Parallel G-Quadruplexes

DNA sequences that can form G-quadruplexes (G4s) are highly prevalent in the genome. However, the structures and functions of most G4-forming sequences in the genome are poorly understood. Therefore, the development of molecular probes for G4 recognition in biological samples, especially probes with long wavelength, are important for the basic research of G4s. Squaraines dyes exhibit sharp and intense absorption and strong emission in the red to NIR region, but very few of them have been reported as probes for the recognition of nucleic acids. Here we report the interactions of two squaraine dyes, STS and CSTS, with different kinds of DNA. The dicyanomethylene-functionalized squaraine dye, CSTS, exhibits strong interaction with the parallel G4s, but no interaction with other DNA. In aqueous conditions, this interaction causes the transformation of CSTS from H-aggregates to monomers, which results in decline and growth of the absorption spectra of both forms. The parallel G4s enhance the fluorescence of both STS and CSTS, but the fluorescence enhancement of CSTS is much higher than that of STS. CSTS is demonstrated to bind to G4s through end-stacking model on G-quartet surface. The high selectivity of CSTS to parallel G4s is attributed to its V-shaped rigid planar It scaffold. The high selectivity, very low background fluorescence, large absorption coefficient, and high fluorescence quantum yield make CSTS hold great promise as a long-wavelength probe for parallel G4 detection in biological samples or in vivo.