Hemicyanine-linked pyrimidine mimics as solvatochromic fluorophores with visible excitation wavelengths

The design of solvatochromic fluorescent nucleosides with visible excitation wavelengths is a goal towards the generation of modified oligonucleotides for fluorimetry-based molecular imaging. Herein, two hemicyanine-linked C5-2′-deoxyuridine nucleosides (PyI-dU and APPy-dU) have been synthesized by first generating hemicyanine-alkyne precursors that were attached via the alkyne moiety to 5-iodo-2′-deoxyuridine (5-I-dU) by Sonogashira coupling. The photophysical properties of the hemicyanine-linked dU probes have been characterized and compared to the corresponding properties of the hemicyanine-alkyne precursors. The nucleoside probe PyI-dU exhibits optical features that mimic the properties of the free hemicyanine-alkyne precursor, while the APPy-dU probe displays more favorable optical properties (longer excitation wavelength, brighter emission in water) than its precursor that is ascribed to π-stacking interactions between the hemicyanine dye with the dU nucleobase. Overall, probe APPy-dU is a superior solvatochromic fluorophore than PyI-dU suggesting its greater utility for fluorescent imaging applications.