The chemical name of the fluorescent dye Joe is 4,5-dichloro-dimethoxy-fluorescein (Figure 1).
JOE is a chlorinated derivative of fluorescein and belongs to the class of xanthene dyes in the yellow range of the spectrum characterised by a high fluorescence quantum yield (number of photons emitted per photon absorbed) as a result of the fluoroscein dye being less susceptible to quenching by protonation, exhibiting a low pH sensitivity, a high quenching coefficient and resistance to deprotection with ammonium hydroxide.
JOE can be used as an alternative to VIC® or as a replacement for Alexa Fluor®532 or CAL Fluor®Gold 540 dyes due to their comparable spectral features. The emission of JOE ranks among the other dyes employed in automated sequencing, enabling it to be separated from FAM and TAMRA, and is therefore extremely suitable for automated DNA sequencing. Consequently, it is often used in multiplex PCR in combination with FAM with minimal signal bleed across other channels. Alkynyl or azido-bonded JOE dyes can be employed for click chemistry reactions with azides or alkynes.
Figure 1. Structure of 5'-Joe (R = sequence).
metabion offers the Joe modification in its DNA and RNA portfolio: