Journal
OLIGONUCLEOTIDES
Volume 20, Issue 4, Pages 199-206Publisher
MARY ANN LIEBERT, INC
DOI: 10.1089/oli.2010.0239
Keywords
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Funding
- [PBZ-MNiSW-07/1/2007]
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Short interfering RNAs (siRNAs) are valuable reagents for sequence-specific inhibition of gene expression via the RNA interference (RNAi) pathway. Recently, it was suggested that 16-bp siRNAs are effective RNAi triggers and superior to classical 19-bp siRNAs. This contradiction with generally accepted knowledge prompted us to reinvestigate this issue. Here, in a series of experiments performed with siRNA duplexes of various lengths (from 19 to 15 bp) designed to silence either overexpressed enhanced green fluorescent protein or endogenously expressed CDK9, we demonstrate that 19-bp siRNAs are more active silencers than shorter corresponding duplexes. The discrepancy between our results and those questioned appears to be due to different modes of shortening the duplex (either at the 3'-end or at the 5'-end, with respect to polarity of the guide strand). Importantly, duplexes with intact 5'-ends but shortened at their 3'-ends retain target site specificity, whereas those shortened at the 5'-end are complementary to different target sites located upstream.
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