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Choosing Fluorescent Dyes for FCS Assays

When selecting a fluorescent dye to use in a fluorescence correlation spectroscopy assay, the first consideration should be compatibility with the biological or chemical system to be studied.

Ideal FCS Dye Properties:
  • Little or no nonspecific binding to your probe or target.
  • Resistant to irreversible photobleaching.
  • Resistant to triplet state excitation
  • Large emission at low intensity excitation (e.g. high quantum yield)

The dyes listed below have been used successfully in FCS Assays, and are compatible with the QuantumXpert FCS Spectrometer. Although we have not yet compiled a comprehensive characterization of all of these dyes, we are working on it!

Fluorescent Dyes for Covalent Conjugation
  • Rhodamine 6G
  • Alexa Dyes (488, 532, 568)
  • Cy 3.5 and Cy 3.5b
  • Tetramethyl Rhodamine
  • Texas Red
  • Quantum Dots (525, 565, 605)
Intrinsically Fluorescent Proteins
  • GFP
  • CFP
  • YFP
Dyes That Selectively Bind or Intercalate
  • DiI