High-Contrast Aptamer-Based Merocyanine Displacement Assays for Sensitive Small Molecule Detection

Aptamer-based colorimetric dye-displacement assays offer a promising means for on-site detection due to their single-step mix-and-read procedure and rapid naked-eye readout. Here, analyte binding to non-covalent aptamer-dye complex triggers displacement of the dye into solution, resulting in the formation of aggregates with divergent optical absorbance properties from the monomeric aptamer-bound dye. However, these assays suffer from low sensitivity, poor color contrast, and to small absorbance wavelength shifts between the dye monomers and aggregates, as well as the large spectral overlaps between these two forms. Here, we introduce the solvatochromic coumarin-based merocyanine dye X-19539-107 as a novel indicator that enables highly sensitive detection of small-molecule targets in dye-displacement assays. In aqueous solution, the dye forms H-aggregates that absorb at 445 nm, whereas aptamer-bound dye monomers absorb at 610–625 nm—a difference of up to 180 nm, with minimal spectral overlap. We utilize X-19539-107 in dye-displacement assays with diverse aptamers to detect various small-molecule analytes with unprecedently high target-induced dye displacement efficiency and greater sensitivity than conventional cyanine indicators and excellent color contrast. We also demonstrate cocaine detection at toxicologically relevant levels in saliva, highlighting the real-world utility of these assays. We conclude that our merocyanine dye offers a powerful alternative to cyanine dyes for colorimetric aptamer-based sensing.