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Are siRNA Pools Smart?

stance, the Cenix siRNA design algorithm--upon which Ambion's Silencer Pre-designed siRNAs are based--has a success rate of >80%, with the majority of the siRNAs providing >85% reduction in target gene expression (Figure 1). Given the success rate of individual algorithm-designed siRNAs, the benefits of siRNA pooling have decreased (Figure 2). Furthermore, the recent observations of off-target effects by siRNAs [1] suggest that combining multiple siRNAs might actually increase the chances that genes other than the target are being affected.

Figure 1. Efficacy of Silencer Pre-designed siRNAs. More than 1100 siRNAs targeting nearly 400 endogenously expressed human genes were tested for target mRNA reduction. More than 82% of the siRNAs reduced target gene expression by at least 70% and more than 61% reduced target gene expression by at least 85%. All siRNA designs were based on an algorithm developed by Cenix BioScience.

Figure 2. Target mRNA Reduction by Single siRNAs and siRNA Pools. Cells transfected with three individual Silencer Pre-designed siRNAs (30 nM) or a pool of all three siRNAs (10 nM each) were monitored for target mRNA reduction by real-time RT-PCR 48 h post-transfection. Relative target mRNA expression was taken as a percentage of mRNA expressed in cells transfected with Silencer Negative Control #1 siRNA (Ambion). All real-time
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