Cyanine dyes

Contents

Background

Cyanines have been used for many years as dyes, for example in photographic emulsions. Cyanine dyes began to be used widely as labels for nucleic acids in the early 1990s, when Cyanine-3, Cyanine-5 and Cyanine-7 (Figure 1) were made commercially available as succinimidyl esters. These Cyanine dyes were different from previous cyanine dyes in that they contain sulfonate groups, which makes the Cyanine dyes soluble in water (and also reduce fluorescence-quenching which can arise from dye–dye interactions). Since their introduction the Cyanine dyes have found widespread use in DNA and RNA labelling.

Cyanine dyes

Figure 1 | Cyanine dyesR = SO3- for aqueous solubility; R = H (or alkyl) for solubility in organic solvents.

Quasar dyes

The Quasar® dyes, manufactured and sold by Biosearch Technologues, are replacements for the Cyanine dyes. The Quasar dyes are chemically very similar to the Cyanine dyes (Figure 2). As such, the properties of the Quasar dyes are practically identical to those of the Cyanine dyes.

Quasar® dyes

Figure 2 | Quasar® dyes

Some physical properties of the Quasar dyes are compared with those of the Cyanine dyes in Table 1.

Table 1Common fluorescent dyes; their associated wavelengths of absorption (excitation) and emission, and colours

Nameλmax / nm (absorption)λmax / nm (emission)ColourE at λmaxΦτ / ns
Cyanine-3550570Dark pink136 0000.15-
Cyanine-3.5591604-116 0000.15< 0.3
Cyanine-3b558572-130 0000.672.8
Cyanine-5649670Blue250 0000.3-
Cyanine-5.5675695Blue209,0000.3-
Quasar 570548566Dark pink115 000--
Quasar 670647670Blue187 000--
Quasar 705690705Blue206 000--

See also

Our free online Nucleic Acids Book contains information on all aspects of nucleic acids chemistry and biology.