cyaninedyes

Cyanine dyes are a family of synthetic organic dyes widely used as fluorescent labels in biology and medicine. They consist of two nitrogen-containing heterocycles linked by a polymethine chain. The molecules are typically positively charged, and various substituents tune their water solubility and biocompatibility.

The optical properties of cyanine dyes are mainly determined by the length of the polymethine chain and the nature of the end groups. Increasing chain length shifts absorption and emission to longer wavelengths, enabling excitation and detection from the visible into the near-infrared region. This tunability, combined with high molar extinction coefficients and bright fluorescence for many derivatives, makes them versatile for labeling biomolecules and cells. Quantum yields vary among dyes and conditions.

Commonly encountered cyanine dyes include Cy3, Cy5, and Cy7, as well as indocyanine green (ICG). Cy dyes are frequently used to label nucleic acids, proteins, antibodies, and small molecules for fluorescence microscopy, flow cytometry, and diagnostic assays. ICG is notable for clinical use and imaging, including some FDA-approved applications.

Limitations and considerations include photobleaching and environmental sensitivity, particularly in nonpolar or highly fluorescent environments. Hydrophobic variants may require solubilizing groups, and some cyanine dyes can exhibit cytotoxicity at high concentrations. When multiplexing, spectral overlap and dye stability must be managed with appropriate controls and spectral planning.

Synthesis typically involves condensation reactions that form the polymethine bridge between heterocyclic components. Cyanine dyes remain popular due to their tunable spectra, strong brightness, and relative synthetic accessibility.