You could do a nested PCR, using the PRC product made with the labeled primers as template, but this time with new primers without a labeling. This way you get rid of any problems with the labeling dye. Run the new product on a agarose gel, cut out the band and use a purification kit to clean it up. I have used a kit from Qiagen (QIAquick) for purification.

Thanks Britta, but I do not know the sequence of the DNA so how can I design the primers?

Thanks very much.

Hi Mahmoud!

You do not have to design new primers if you know the sequence of your labeled primers. Just order new primers without any modifications or if you know the sequence of the adapters that you use after the restriction enzyme step of AFLP.

Best Britta

Thanks very much. Mack