Will polyacrylamide gel electrophoresis damage a Cy3 labeled oligo?
We do not recommend PAGE purification of Cy labeled oligos. The component of the acrylamide gel that causes damage to the Cy 3 is ammonium persulfate, a cross linking agent, rather than urea. The ammonium persulfate oxidizes the double bonds in the chain between the rings. For Cy dyes we require HPLC purification since it works the best with these modifications.