Primer design (long transcripts) - (Feb/20/2008 )

Hello,

I am wondering: if I am trying to amplify a long transcript 3kb, does it matter which part of the gene I chose to design primers for?

I am worried about the efficacy of reverse-transcription. Is it better to pick a primer with less complimentation that is at the 5' end of the gene, or a primer with more complimentation that is at the 3' end of the gene?

Thanks so much!

Hi,

If you wouldn't ask I'd never know that there is such a problem.
I've recently amplified a transcript of 3.5kb without any problems, may be my primers were a little bit longer than a standard (26-30bp), but the rest was pretty the same.