I am currently in my experimental design on RNAi work. In one of the steps, i would like to measure RNAi efficacy by using qRT-PCR method. Do i need to consider the amplification region in cDNA? It is because i am worried if the amplification region is outside of RISC cleavage site, the partially degraded mRNA (after RISC cleavage) will interfere my results.
Or this is something that i think too much, where partially degraded mRNA is insignificant and neglectable, or even absent in nature?
Edited by dcch, 18 May 2009 - 06:44 PM.