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Is there any information on the stability of fluorescently labeled oligos and the fluorescent modifications?
The stability of fluorescently labeled oligos and fluorophore function is similar to the stability of a standard oligo. For optimal stability, oligos that are to be stored long term should be stored frozen, at -20°C. If the oligos are going to be resuspended, storage in a TE buffer (10 mM Tris, 0.1 mM EDTA, pH 7.5–8.0; such as IDTE) is better than using water (non-DEPC treated). The impact from the type of storage medium used is marginal at -20°C, but becomes more important at higher temperatures (see the Technical Report, Oligonucleotide Stability Study,for the data).
With fluorophores, it's important to remember that exposure to natural light or ozone can negatively impact stability.