Protocol Online logo
Top : Forum Archives: : siRNA, microRNA and RNAi

Position of RNAi target on mRNA - How important is the location (Mar/20/2006 )

Hi all,

I'm going to try and knock-down some genes, and I am curious to know if there is any effect of targetting your siRNA to the 5' or 3' end. I have heard that targetting to the 3' end can be effective, though I'm not sure as to how this works. Wouldn't it still leave the majority of the mRNA intact?

Similarly, say I target the middle of the mRNA molecule, will the 5' end be expressed until the point where the mRNA was cleaved?

Any thoughts?


i use a targetr that is in exon sequence.
Regarding degradation, mRNA is not or totally degraded.
If partial 3' digestion would have occured as you mention, the stability of this non polyA resulting mRNA would be very ery low, and you'll will probably not have any translation of this mRNA


That makes a lot of sense,

Thank you kindly!