Tuning the DNA binding properties of phenolic hemicyanine dyes for host-guest fluorescent aptasensor applications

Fluorescent dyes that bind specifically to DNA aptamers with turn-on emission serve as powerful tools for biosensor development. DNA three-way junctions (3WJs) consisting of a Y-shaped hydrophobic branch point connecting three double-stranded stems serve as recognition elements for DNA aptasensors for a wide variety of diagnostic applications. Herein, we highlight the tunability of phenolic hemicyanine dyes for host-guest fluorescent aptasensor applications using the cocaine-binding aptamer (MN4) as a representative 3WJ-aptamer substrate. The DNA aptamer MN4 exhibits ligand binding promiscuity and binds the alkaloid quinine with ∼26-fold greater affinity than its intended cocaine target. Combining the cationic N-methylbenzothiazolium (Btz) acceptor with a 2-fluoro-phenolic (FPhO) donor through a vinyl-linkage creates the FPhOBtz hemicyanine as a universal fluorescent turn-on probe for DNA 3WJs. The FPhOBtz dye binds MN4 with higher affinity than cocaine, but with weaker affinity than quinine. Consequently, FPhOBtz displacement from the 3WJ with turn-off fluorescence is effectively mediated by quinine, but not cocaine, resulting in poor detection of cocaine by the dye-displacement assay. Our current results demonstrate superior cocaine detection by replacing the planar cationic Btz group with the non-planar indolenium (Ind) acceptor to afford FPhOInd as the signaling fluorescent probe. This simple change in dye structure strongly diminishes MN4 binding affinity (19-fold) with cocaine now possessing stronger affinity for the 3WJ of MN4 compared to FPhOInd. Consequently, FPhOInd displacement from MN4 is effectively mediated by cocaine to provide a 13-fold improvement in cocaine detection in undiluted urine using the host-guest biosensing platform.