Silly question - primer design (Feb/05/2008 )

Hello all,

I'm wondering is it all right to design primers that anneal to the 3' or 5' untranslated region of the gene that I am interested in? I'm designing primers for p16/INK4a as well as p19/ARF mRNA transcripts, and since the two transcripts there is only a limited amount of sequence in the coding sequence of the mRNAs that are different. I'm thinking that if I include the UTRs in my primer search engine then I'll be able to get better primers.

Am I getting real-time confused with siRNA, or is there a reason to avoid the UTRs when designing primer for real-time.

A million thank yous.

The UTRs should be fine targets as long as you are sure they really are transcribed.