Glen Report 20.27: 5'-Dichloro-Dimethoxy-Fluorescein (JOE™) Phosphoramidite

Fluorescent labelling is now at the forefront of DNA detection and sequencing. As such, Glen Research is always happy to expand our repertoire of fluorescent phosphoramidite reagents in order to help our customers find a fluorophore with just the spectral characteristics they desire. The latest addition to our line of dyes is 5’-Dichloro-dimethoxy-fluorescein Phosphoramidite.

Figure 1: Structure of dichloro-dimethoxy-fluorescein phosphoramidite

The 5’-Dichloro-dimethoxy-fluorescein dye is more commonly known as JOE™ to those familiar with the dye sets used in Applied Biosystems DNA PRISM sequencers - e.g., Dye Set 20 and 32, which contain FAM/JOE/TAMRA/ROX and FAM/JOE/NED/ROX, respectively.

As a dye, it gained popularity because its emission is nicely resolved from both FAM and TAMRA, falling squarely between them. This allows for multiplex detection without too much signal bleed through into other channels, making it extremely useful in automated DNA sequencing. In addition, because of the electron-withdrawing groups on the xanthene ring, the 5’-Dichloro-dimethoxy-fluorescein dye is less prone to quenching due to protonation. As such, its fluorescence is much less pH sensitive than its popular cousin, fluorescein. Even at pH 5, our in-house testing indicates 5’-Dichloro-dimethoxy-fluorescein’s signal dropped by only 30%.

With its high extinction coefficient of 75,000 L/, a quantum yield of fluorescence of 0.581, and excellent stability to standard deprotection conditions in ammonium hydroxide, we are sure the 5’-Dichloro-dimethoxy-fluorescein Phosphoramidite will be a popular addition to our ever-expanding selection of fluorophore phosphoramidites.

Spectral Characteristics
Absorbance 525 nm
Emission 548 nm
E260 12,000 L/mol•cm
Emax 75,000 L/mol•cm
QY 0.58


  1. J. Ju, C. Ruan, C.W. Fuller, A.N. Glazer, and R.A. Mathies, Proc Natl Acad Sci U S A, 1995, 92, 4347-51.

Product Information

5'-Dichloro-dimethoxy-Fluorescein has been discontinued, please see:

5'-Dichloro-dimethoxy-Fluorescein Phosphoramidite II (Joe II) (10-5906)