Fluorinated squaraine as near-IR label with improved properties for the labeling of oligonucleotides

A new squaraine dye with fluorinated benzothiazole rings was synthesized. This new label possesses improved photophysical properties and chemical stability as compared to the corresponding non-fluorinated and the dicyanosquaraines. These squaraines were used for the labeling of a series of oligonucleotides with various sequences, lengths, and chemistries. The conjugates involving the fluorinated squaraine possess the best properties: emission wavelength >670 nm, high quantum yields (0.27–0.39).