Both primers worked equally well in my hands. For more info regarding the primers, please consult papers published by the two authors mentioned. Other dyes, like DEAC and the rhodamine derivatives, inhibit PCR amplification when added at the same concentration as FITC, biotin, digoxigenin. However, by performing parallel labeling reactions which use increasing or decreasing amounts of labeled nucleotide, a point of compromise can be identified, where DNA synthesis is not fully inhibited, and the DNA is sufficiently labeled to yield results. Yet other dyes, like the newly tested CMF is bulky and titration of the CMF-dUTP amount does not influence the overall amount of DNA produced in the reaction, indicating that this modified nucleotide is NOT used at all by the polymerase.
Various dyes influence the level of DNA amplification differently.
Simple method to verify DNA labeling. Because of the labeled nucleotide incorporation, the PCR products runs at slightly different speed in the gel. Whereas this is automatically taken care of in a nick translation, where the DNase amount is chosen so as to yield fragments shorter than 500 BP, in PCR, a partial DNase treatment is required after the reaction. The DNase solution can be added directly into the PCR vials. The short fragments yield best FISH signals.