A PCR problem

Z.Huang huang.zhong at med.kuleuven.ac.be
Thu Dec 4 19:29:08 EST 1997

Olivier Cochet wrote:
> I have a cDNA mixture containing the gene of interest (A) and an unwanted
> gene (B), highly homologous, excepted for an internal part. My 5' and 3'
> primers amplify A and B genes (300 bp). I want to get rid off gene B by
> designing an internal primer (anti sense) specific of B but degenerated at
> the 3' end in such a way that no amplification would be possible.
> So, in my PCR mixture, I will have 3 primers.


Maybe I didn't catch your question. But one thing seems certain that if 
you use a primer with degenerate at 3' end would result in high 
background and false signals. I have ever faced such situation that my 
primer(antisense) just has one mismatch at 3' end but failed to amplify 
the correct product.

Huang Z
Gut Hormone Lab

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