Promoter G-Quadruplex Binding Styryl Benzothiazolium Derivative for Applications in Ligand Affinity Ranking and as Ethidium Bromide Substitute in Gel Staining

Fluorescent compounds that can preferentiallyinteract with certainnucleic acids are of great importance in new drug discovery in a multitudeof functions including fluorescence-based displacement assays andgel staining. Here, we report the discovery of an orange emissivestyryl-benzothiazolium derivative (compound 4) whichinteracts preferentially with Pu22 G-quadruplex DNAamong a pool of nucleic acid structures containing G-quadruplex, duplex,and single-stranded DNA structures as well as RNA structures. Fluorescence-basedbinding 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 thisinteraction was found to be 1.12 (+/- 0.15) x 10(6) M-1. Circular dichroism studies showed that thebinding of the probe does not cause changes in the overall parallelG-quadruplex conformation; however, signs of higher-order complexformation were seen in the form of exciton splitting in the chromophoreabsorption region. UV-visible spectroscopy studies confirmedthe stacking nature of the interaction of the fluorescent probe withthe G-quadruplex which was further complemented by heat capacity measurementstudies. Finally, we have shown that this fluorescent probe can beused toward G-quadruplex-based fluorescence displacement assays forligand affinity ranking and as a substitute for ethidium bromide ingel staining.