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Primer for 4 genes sharing short consensus sequence - (Dec/17/2005 )

Hi, everybody. I would like to ask a question about the primer design. I am going to design a set of primer to amplify 4 different genes from the same family. I have done the sequence alignment and found that there were only some short regions which were consensus among these 4 genes. May i know that at least how many nucleotides at the 3' of each primer must be consensus for the genes to be annealed and amplified?

Thank you very much.


Hello Angel,

I am sorry I don't quite understand your question. You are trying to amplify the 4 genes by using a common pair of primer which bind to the consensus region of the four. I think it is hard to predict the minimum number of base-pairings between the 3' portion of a primer and a target region that ensures amplification by the primer. Certainly the shorter the base-pairing is, the higher the possibility that it will also amplify other undesired targets. If there is a number for it, I guess a minimum of 10 bp matches is needed to achieve stable binding between the primer and the target.


Thanks a lot, pcrman. You have answered what I wanted to ask, actually. (Eventhough you said you don't quite see the question). tongue.gif At least i know the minimum number should be around 10bp. I'll try to get the best primer. And one more question, can you suggest me any webpage that discuss about the primer design for multiple genes?
Thank in advance.