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