Nucleic acids can adopt non-duplex topologies, such as G-quadruplexes in vitro. Yet it has been challenging to establish their existence and function in vivo due to a lack of suitable tools. Recently, we identified the triangulenium compound DAOTA-M2 as a unique fluorescence probe for such studies. This probe's emission lifetime is highly dependent on the topology of the DNA it interacts with opening up the possibility of carrying out live-cell imaging studies. Herein, we describe the origin of its fluorescence selectivity for G-quadruplexes. Cyclic voltammetry predicts that the appended morpholino groups can act as intra- molecular photo-induced electron transfer (PET) quenchers. Photophysical studies show that a delicate balance between this effect and inter-molecular PET with nucleobases is key to the overall fluorescence enhancement observed upon nucleic acid binding. We utilised computational modelling to demonstrate a conformational dependence of intra-molecular PET. Finally, we performed orthogonal studies with a triangulenium compound, in which the morpholino groups were removed, and demonstrated that this change inverts triangulenium fluorescence selectivity from G-quadruplex to duplex DNA, thus highlighting the importance of fine tuning the molecular structure not only for target affinity, but also for fluorescence response. Photophysical, electrochemical, and computational studies were utilised to investigate the mode of action of a triangulenium-based G-quadruplex optical probe. A conformational dependence of the intramolecular photoinduced electron transfer (PET) mechanism is proposed. Orthogonal studies with a second triangulenium compound, lacking morpholino substituents, were performed. This change inverts triangulenium fluorescence selectivity from G-quadruplex to duplex DNA.
Shivalingam, A., Vyšniauskas, A., Albrecht, T., White, A. J. P., Kuimova, M. K., & Vilar, R. (2016). Trianguleniums as Optical Probes for G-Quadruplexes: APhotophysical, Electrochemical, and Computational Study. Chemistry - A European Journal, 22(12), 4129–4139. https://doi.org/10.1002/chem.201504099