| | Re: Suppression of Protein Levels but not mRNA using siRNA
It sounds like your siRNA might not be completely complementary to the target mRNA for which you are assaying the corresponding protein. Translation inhibition is the usual miRNA effect, and generally accompanies siRNA knockdowns as inhibition of translation from off-target genes.
Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells. Scacheri PC, Rozenblatt-Rosen O, Caplen NJ, Wolfsberg TG, Umayam L, Lee JC, Hughes CM, Shanmugam KS, Bhattacharjee A, Meyerson M, Collins FS. Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):1892-7. Epub 2004 Feb 09.