Fluorescent compounds that can preferentially
interact with certain
nucleic acids are of great importance in new drug discovery in a multitude
of functions including fluorescence-based displacement assays and
gel staining. Here, we report the discovery of an orange emissive
styryl-benzothiazolium derivative (compound 4) which
interacts preferentially with Pu22 G-quadruplex DNA
among a pool of nucleic acid structures containing G-quadruplex, duplex,
and single-stranded DNA structures as well as RNA structures. Fluorescence-based
binding analysis revealed that compound 4 interacts with Pu22 G-quadruplex DNA in a 1:1 DNA to ligand binding stoichiometry.
The association constant (K
a) for this
interaction was found to be 1.12 (±0.15) × 106 M–1. Circular dichroism studies showed that the
binding of the probe does not cause changes in the overall parallel
G-quadruplex conformation; however, signs of higher-order complex
formation were seen in the form of exciton splitting in the chromophore
absorption region. UV–visible spectroscopy studies confirmed
the stacking nature of the interaction of the fluorescent probe with
the G-quadruplex which was further complemented by heat capacity measurement
studies. Finally, we have shown that this fluorescent probe can be
used toward G-quadruplex-based fluorescence displacement assays for
ligand affinity ranking and as a substitute for ethidium bromide in
gel staining.