( and nucleotide distribution over the ...)IMPROVE SILENCING SUCCESS: siRNAs THAT WORK BETTER!

, and nucleotide distribution over the length of the siRNA (including 5' duplex end composition shown to be important in recent publications (1,2)) to name just a few. Those characteristics that correlated with high siRNA potency were incorporated into the algorithm. As specificity is critical, a key step in the design process is a stringent comparison of each siRNA sequence to the target organism's genome sequence to eliminate those siRNAs that have a high probability of cross reaction.

Figure 1 demonstrates the high success rate of the Cenix siRNA design algorithm. In this initial experiment, 79 siRNAs designed with the algorithm were transfected into HeLa cells and mRNA levels were analyzed by real-time RT-PCR 48 hours later to assess siRNA effectiveness. Of the siRNAs tested, 74 (94%) reduced target mRNA levels by >70%. To date, more than 900 siRNAs designed using the Cenix algorithm, targeting hundreds of individual human genes, have been functionally tested. These studies demonstrate that the algorithm is robust and that it successfully addresses gene-to-gene variability in susceptibility to RNAi.

Figure 1. The Effectiveness of Cenix Designed siRNAs. siRNAs targeting 79 human genes, designed using the Cenix algorithm, were transfected into HeLa cells at a 100 nM final concentration. Target gene expression was quantified by real-time RT-PCR 48 hours post-transfection. Relative reduction in mRNA expression was measured against cells transfected with a negative control siRNA. Sample size was normalized by measuring 18S rRNA.

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