Difficutly go separate product from primer dimers - Methylation specific PCR (Mar/21/2005 )

Hi everybody,
My name is Deepa and I have just joined the forum.

I have a question,

I have been working on Methylation specific PCR recently. As far as I know I have been following the protocol perfectly.

I am fishing for 105 bp and 107 bp bands in my methylated and unmethylated control samples.

I feel that as the size of the band is almost close to 100 bp the actual band and the primer dimers are combining not giving me the actual band.

I think so because all i could see on my gel is a strong intensity band at about the 100 bp band of the marker.

So suggest me how u think i should separate this if at all the band is forming.

Thank you
Deepa

Hi Deepa,

You should be able to separate your product from primer dimer if you use higher pcrcentage gel 2-3% with longer run. Also try to optimize your PCR condition to minimize the interferring dimer bands.

good luck.