RT-PCR primer design at 3'-UTR or ORF? - (Jan/26/2006 )
Hi! Everyone,
When doing RT-PCR or Northern blot of a know gene to analysis the expression pattern, which region of the mRNA sequence you will choose to amplify?
It's said that using 3'-UTR will be better for the multi-gene family. But if we don't use the ORF region of the gene, the expression will be affected or not?
What's your opion?
-WendyGuo-
QUOTE (WendyGuo @ Jan 26 2006, 05:40 AM)
Hi! Everyone,
When doing RT-PCR or Northern blot of a know gene to analysis the expression pattern, which region of the mRNA sequence you will choose to amplify?
It's said that using 3'-UTR will be better for the multi-gene family. But if we don't use the ORF region of the gene, the expression will be affected or not?
What's your opion?
When doing RT-PCR or Northern blot of a know gene to analysis the expression pattern, which region of the mRNA sequence you will choose to amplify?
It's said that using 3'-UTR will be better for the multi-gene family. But if we don't use the ORF region of the gene, the expression will be affected or not?
What's your opion?
What sort of gene expression are you studiying. Is a organism gene of viral genome?
Actually it all depend on what you want to do. 3'-UTR or 5'UTR normally is conserved among the same family, allowing you to study expression pattern of whole gene family. But it might couses unspecificity as well. Design primer on ORF will be highly specific.
Hadrian
-Hadrian-
Thank you for your reply. I am studying in stress-induced genes in higher plants.You thought that ORF region will be highly specific, really?
-WendyGuo-