Highly effective silencing of endogenous genes by class Ia siRNAs (A and B), RNAi caused by an non-cognate siRNA (C) and class Ia siRNA-dependent RNAi in chick embryos (D). The sequences of siRNAs examined here are depicted in the right margin (see Fig. for coloration and box). (A) Silencing of vimentin, a human endogenous gene, by class Ia and class III siRNAs. Ten class Ia (VIM-270, -368, -596, -812, -857, -1097, -1128, -1148, -1235 and -1298) and three class III siRNAs (VIM-35, -155 and -491) were designed and their RNAi activity was examined in HeLa cells subjected to three cycles of 50 nM siRNA transfection. On day 3, cells were stained for vimentin (target) and Yes (control). Vimentin and Yes protein signals are colored in yellow and green, respectively. Note that all class Ia but not class III siRNAs significantly reduced vimentin signals. (B) Effects of siRNA transfection on the expression of Oct 4, a mouse endogenous gene. E14TG2a (mouse ES) cells were transfected with class Ia (Oct-670, -797 and -821) or class III (Oct-161 and -566). The four pictures on the left are phase contrast photographs. Note that class Ia siRNAs (Oct-670 and -797) induced a flat morphology typical of trophectoderm cells. Class Ia siRNA-specific degradation of Oct 4 mRNA visualized with RT–PCR is also shown. Gapd was used as a control. (C) ECFP RNAi caused by an non-cognate EGFP siRNA. EGFP-441 is a class Ia EGFP siRNA but not identical in sequence to ECFP-441, a class II ECFP siRNA possessing G at the 5′ AS end. While ECFP-441 did not abolish ECFP signals 2 days after transfection (on day 2 of transfection), non-cognate EGFP-441 virtually completely eliminated ECFP signals. Note that RNAi effects 1 day after transfection (on day 1) indicate that EGFP is a better target for EGFP-441 than ECFP. Blue and red arrows indicate that EGFP and ECFP mRNA possess a base substitution at the position corresponding to the 5′ AS end of EGFP-441 or ECFP-441. (D) In ovo RNAi in chick embryo. EGFP and DsRed expression plasmids were co-electroporated into chick spinal cord with class Ia siRNAs (EGFP-416, -441 and DsRed-399) or class III siRNAs (EGCFP-666 and DsRed-383). Class Ia siRNAs significantly abolished the targeted fluorescence, while class III siRNAs did not. Expression of EGFP and DsRed is colored in yellow and red, respectively. Dotted lines show left (L) and right (R) portions of the spinal cords. The 5′ ends of SS and AS, and the 5′ region of the AS (7 bp) are boxed and colored as described in Figure .