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Silencer Validated siRNAs

les for siRNA Design
On average, 50% of the siRNAs featuring the Tuschl design rules (3' UU overhangs, <50% G/C content; 2-4) provide at least 50% reduction in target gene expression. An early goal for Cenix was to improve the percentage of effective siRNAs by improving the design rules for siRNAs. To accomplish this, Cenix tested several hundred siRNAs targeting a number of endogenous human gene products that were expressed at detectable levels in several different cell lines. The effective and ineffective siRNAs were used to judge the impact of a number of physical characteristics on siRNA activity, including Tm, predicted RNA secondary structure, nucleotide position effects, nucleotide content of the 3' overhangs, siRNA length, and nucleotide distribution over the length of the siRNA. Those characteristics that correlated with siRNA effectiveness were incorporated into a design algorithm. The final step of designing the algorithm was a BLAST search to ensure that the siRNA was specific to the gene of interest.

The algorithm was then tested for its capacity to identify effective siRNAs. siRNAs targeting 60 human genes were designed, prepared, and tested across as many as four cell lines. Of the genes whose expression could be reduced without causing cell death, 89% of the designed siRNAs provided greater than 70% reduction in target gene expression (Figure 1).

The design algorithm is now being tested on hundreds of human genes. The first siRNA sequences validated during this collaborative study are being made available by Ambion and Cenix BioScience as part of the Silencer Validated siRNA product line. As the study progresses, many more additional sequences will be added to this line. '"/>

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