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Are siRNA Pools Smart?


Screening with small interfering RNAs (siRNAs) is an important method for identifying genes involved in biological pathways. This article analyzes the effectiveness of two strategies--transfection of individual siRNAs and transfection of pools of siRNAs--for large-scale screening experiments. The increased effectiveness of testing at least two distinct, algorithm-derived siRNAs to the same target results in decreased use of resources required to screen false positive targets, and more importantly, minimizes the risk of missing valid targets.

In initial RNA interference studies, many researchers opted to combine multiple small interfering RNAs (siRNAs) that targeted distinct regions of the same gene to facilitate degradation of the target mRNA. The desire to mix siRNAs arose primarily from the finding that less than 50% of random-designed siRNAs significantly reduced target gene expression. These experiments showed that combinations of siRNAs did not appear to function synergistically to affect target gene expression, and on occasion less active siRNAs interfered with the activities of the higher efficacy siRNAs. Nevertheless, the pooling strategy increased the chances of reducing target gene expression of random-designed siRNAs.

The realization that potent siRNAs share sequence characteristics has led to siRNA design algorithms that significantly improve the percentage of effective siRNA sequences. For in
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