siRNA designation for different genes - (Nov/17/2008 )
trying to design siRNA to knock down endogenous A protein expression in mouse cells and texpress human mutant A protein in this knock-down cells.
I designed several siRNA (21nt) and checked the difference of them with human A protein cDNA in order to avoid inhibit human A protein expression. I want to ask how many different bps are necessary to knock down mouse A protein and no interfere on human A protein expression? 3, 4, 5, 6 out of 21? how many are enough?
Make sure the seed sequence (2-8 nucleotide counted from the 3' end of the siRNA duplex) differ from human sequence.