Selective recognition of G-quadruplexes by a dimeric carbocyanine dye

A novel dimeric carbocyanine dye is found to recognise G-quadruplex structures selectively compared to mixed sequence or double-stranded DNA molecules. The dye exhibits a preference for G3-bearing parallel quadruplexes and results in a nearly 1400-fold enhancement compared to the absence of DNA and a nearly 30-fold fluorescence enhancement compared to duplex and single stranded DNA molecules. Study of the dye binding with various quadruplex-forming sequences points towards an end-stacking mechanism of interaction. The number of G-quartets and spacer sequences along with the identity of monovalent ions strongly influence the interaction of quadruplexes with the dye.