RNAi's Minor Setback - RNAi - Protein Synthesis

Early on, researchers assumed that a single RNAi knocked down a single gene causing a phenotype. "What we know now is that single siRNA was probably affecting tens if not hundreds of genes," says David Brown of Austin, Texas-based Ambion, an siRNA supplier. One way to overcome this problem is to use multiple, single siRNAs targeting different regions of the gene of interest as a control, with the expectation that each of the siRNAs will have different off-target effects because they have different sequences. "If each of the siRNAs causes the same phenotype ... the effect that you're seeing is specific to the target gene, and not to the single siRNAs that you're using," Brown says. Another potential way to control off-target effects is to mitigate them through chemical modifications to the siRNA backbone at critical locations, according to Jackson.
Choosing the correct sequence or delivery system could help as well. "There may be potential to design siRNAs that avoid the induction of innate immunity, yet are effective at mediating RNAi, and that's what we've shown in our paper," says MacLachlan.
Davis cautions that the RNAi picture is still "muddy" and that concentration, delivery, and sequence all need to be considered in the further development of the technology and its application to therapeutics. "I think it's too early to say that there are any global conclusions yet."
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