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siRNA Design Guidelines

Using siRNA for gene silencing is a rapidly evolving tool in molecular biology. There are several methods for preparing siRNA, such as chemical synthesis, in vitro transcription, siRNA expression vectors, and PCR expression cassettes. Irrespective of which method one uses, the first step in designing a siRNA is to choose the siRNA target site. The guidelines below for choosing siRNA target sites are based on both the current literature, and on empirical observations by scientists at Ambion. Using these guidelines, approximately half of all siRNAs yield >50% reduction in target mRNA levels.

For the Best Results, Let Us Design Your siRNAs

Ambion has recently partnered with Cenix BioScience, a leader in the field of RNAi. Cenix has developed a proprietary siRNA design algorithm that yields a much higher percentage of effective siRNAs when compared to siRNAs designed using the rules outlined below. For information on that algorithm, see Designing a Better siRNA. You can order chemically synthesized siRNAs pre-designed using the Cenix algorithm from Ambion. Designs are currently available for >98% of the human, mouse, and rat genes in the RefSeq database. See the Pre-designed siRNA Catalog Page for more information. In addition, Ambion offers Silencer Validated siRNAs to a number of important human g
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