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 Gquadruplexes.
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 where the
morpholino groups were removed and demonstrate 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.