RNAi induced in mammalian and Drosophila cells via transfection of dimers and trimers of small interfering RNA

Twenty one base pair long small interfering RNAs (siRNAs) are widely in use in mammalian RNAi experiments. The present study assesses the capability of 43 and 63bp dsRNAs with two 2nt long 3′-overhangs to induce RNAi in mammalian and Drosophila cells. Human Dicer was found to cleave these dsRNAs from their ends to generate two or three monomeric siRNA units, each 21-22bp in length. When, in 43bp dsRNA, there was present a highly-effective siRNA sequence in frame with respect to the Dicer digestion, considerably high RNAi activity was noted to be induced in mouse embryonic stem E14TG2a, human HeLa, Chinese hamster CHO-K1 or Drosophila S2 cells. In contrast, RNAi depending on 63bp dsRNA, containing a highly effective siRNA sequence in frame with respect to Dicer digestion, varied considerably depending on cell lines used. While there was no appreciable RNAi in HeLa cells associated with relatively strong interferon response, a significant level of RNAi was noted in E14TG2a, CHO-K1 and S2 cells, in all of which interferon response induction was but slight, if at all. It would thus follow that siRNA oligomers with sequence of a highly functional siRNA monomer unit in frame with respect to dicer digestion should serve as a good RNAi agent in Drosophila and certain mammalian cells.