3'UTR-siRNA - (Jul/06/2006 )
I have used the sequences from RNAicodex for my target of interest and made stable expression of the same using lentivirus. Since good antibodies to detect the endogenous protein are not available i used real time PCR (SybrGreen) to confirm the effect. I see only 20% reduction at mRNA levels. However, I do see one of the target genes' expression going down by atleast 50% by western blot! The cell line I am using is a germ cell tumor line.
Is it possible that the siRNA against 3'UTR only blocks the translation and not the levels of mRNA significantly, or is there smtg to do with the germ cell status. My target is a secreted protein.
Any help appreciated.
If the siRNA matches perfectly with your target mRNA (no matter 3UTR or coding region), the end effect would be the destroy of the mRNA, which is different from the effect of miRNA which matches with their targets imperfectly, leading to translation inhibition. Not every siRNA can induce RNAi with equal efficiency due to many factors such as siRNA design, local RNA secondary structure, etc.