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We do not recommend PAGE purification of Cy-labeled oligonucleotides. Ammonium persulfate, a cross linking agent used in place of urea, is a component of the acrylamide gel that can damage the dye.
Ammonium persulfate oxidizes the double bonds in the chain between the rings, affecting the dye's ability to fluoresce when excited. HPLC purification, however, does not oxidize Cy dyes and is required for these modifications.