The merocyanine family of dyes was first introduced in the 1950s as photosensitizing agents for the development of colour photographs. Since this time, this family of chromophores has gained much more attention in the realms of materials science, dye chemistry as well as in biotechnology. Demonstrating impressive optical changes as a function of pH, solvent polarity, and solvent viscosity, these dyes present as prime candidates for use in a wide variety of detection platforms. Herein, novel phenolic merocyanine dye derivatives were synthesized and characterized based on changes observed in the dyes’ absorbance and fluorescence capabilities as a function of acid-base exchange in aqueous environments and their ability to undergo tautomeric exchange processes in a number of polar protic solvents. Additionally, molecular rotor examples of these dyes were synthesized and assessed for their ability to undergo fluorescence emission enhancement in high viscosity solvents as well as in the presence of guanine-quadruplex (GQ) DNA. It was observed that these dye derivatives were capable of undergoing an energy transfer process in the presence of a DNA GQ, providing a means to determine the binding affinity of the dyes with various GQ topologies. This was achieved through the use the human telomeric repeat sequence, a sequence demonstrating high polymorphism in its ability adopt a variety of GQ topologies. Finally, this energy transfer phenomenon was applied to the detection of Ochratoxin A (OTA) with a GQ forming 36-mer DNA aptamer. In this label free assay, energy transfer from the aptamer to the toxin allowed for a 3-fold enhancement in the visible fluorescence of OTA, providing a sensitive, simple and elegant strategy for the detection of this small molecule target.