Cyanines

Cyanines are a class of synthetic dyes and pigments characterized by two nitrogen-containing heterocycles linked by a polymethine chain. The length of the polymethine chain determines the color, with shorter chains producing yellow to red dyes and longer chains extending absorption into the near-infrared. Most cyanines are positively charged, which influences their solubility, binding properties, and interactions with biomolecules.

Chemically, the key feature is a polymethine chromophore that bridges two heterocyclic rings, such as indole, benzothiazole, or quinoline derivatives. The chain length and substituents tune the electronic structure, yielding high molar absorptivity and, for fluorescent variants, bright emission. Increasing chain length shifts both absorption and emission toward longer wavelengths, and hexamethine to heptamethine cyanines are commonly used to reach the near-infrared region.

Applications of cyanines are diverse. They are used as dyes and pigments for textiles, printing, and photography, and as laser dyes in optical systems. In biology and chemistry, cyanine dyes such as Cy3 and Cy5 are widely employed as fluorescent labels for nucleic acids, proteins, and other biomolecules, enabling fluorescence microscopy, flow cytometry, and imaging assays. Their brightness and tunable spectra contribute to their prominence as labeling reagents.

Synthesis typically involves condensation of heterocyclic precursors with reagents that form the polymethine bridge, allowing systematic adjustment of wavelength, brightness, and solubility. Practical use requires consideration of photostability, tendency to aggregate in solution, and sensitivity to solvent polarity and pH, which can affect performance.