Short PCR product

Duncan Clark junk at
Tue Jan 8 08:48:37 EST 2002

In message <a1egi1$aha$1 at>, aes <ali at> writes 
on the Tue, 8 Jan 2002
>I am going to attempt to do quantitative PCR with degenerate primers, I can
>make the primers so that they should amplify all the genes I want, but again
>the primers end up being 28 bp long with 8 bases (in the middle) having
>degenerate composition (R,K and Y). Do you think it is possible to get these
>primers working in a semi quantitative experiment?

I would think you are looking for trouble with false priming and/or 
primer dimers. You would need to verify the product you are seeing is 
correct before trusting the screen result.

The only way to find out is to try it.

Is there no way you can use degenerate primers with a common Taqman 
probe or other probe system in the middle?

The problem with being on the cutting edge is that you occasionally get
sliced from time to time....

Duncan Clark
GeneSys Ltd.

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