Fluorescent probes to target nucleic acids

Abstract

Guanine-quadruplexes (G-quadruplexes) are non-canonical nucleic acid structures that consist of two or more stacked G-tetrads further stabilized by monovalent-cations. These structures are stable under physiological conditions and form in vivo in the genome of mammalian cells, particularly at telomere region of chromosomes, oncogene transcription sites, in genes connected with neurological conditions, as well as in some parasites and viruses. Since the G-quadruplex formation has been linked to genome instability, G-quadruplexes have been a subject of great research interest. Various molecules have been synthesized as probes to target G-quadruplexes. However, the major problem remains the lack of selectivity for binding to G-quadruplexes over dsDNA. Taking the topology of targeted G-quadruplexes into account is essential for the design and fine-tuning of G-quadruplex probes.

During the last 15 years Professor Rozas' group has prepared a large number of diaromatic bis-guanidinium-like derivatives that strongly bind to the minor-groove of DNA. Recently, Rozas and co-workers have prepared a series of novel G-quadruplex conjugates by combining a porphyrin core ('warhead') with diaromatic guanidinium systems ('arms') by means of a semi-flexible amidinourea linker. These compounds have exhibited strong selectivity for several G-quadruplexes over the double stranded DNA. The computational docking of some of these compounds with the c-Kit-2 G-quadruplex showed the stacking of the porphyrin moiety on top of the upper G-tetrad and the interaction of the cationic diaromatic guanidine 'arm' with the G-quadruplex side groove. Based on this previous work, we have studied the semi-flexible linked conjugates as well as developed novel conjugates with flexible linkers. The docking studies of two previously prepared semi-flexible linked conjugates and a novel conjugate proposed were carried out with the structures of G-quadruplexes of different topologies. The synthesis of the previously prepared semi-flexible linked conjugates has been optimized and the novel compound proposed has been prepared. Binding to the c-Kit-2 G-quadruplex of previously prepared tetrasubstituted porphyrin derivatives connected to diaromatic guanidine systems by semi-flexible linkers was studied by means of UV DNA thermal denaturation. A new family of conjugates of mono-substituted porphyrins and diaryl guanidinium systems connected by di-ether alkyl linkers has been designed, computationally studied by molecular docking, and their synthetic pathway has been explored.