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Difficutly go separate product from primer dimers


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#1 Deepa

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Posted 21 March 2005 - 11:39 AM

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

#2 pcrman

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Posted 21 March 2005 - 04:29 PM

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.




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