FlexiPlate siRNA

Cutting-edge siRNA design

Advances in the siRNA design process ensure that QIAGEN's highly innovative and sophisticated HP OnGuard siRNA Design delivers potent and specific siRNA. siRNAs are designed using neural-network technology based on an extremely large set of data from RNAi experiments. siRNA design is then checked for homology to all other sequences of the genome using an up-to-date, nonredundant sequence database and a proprietary homology analysis tool. HP OnGuard siRNA Design incorporates many unique and advanced features (see table).

3' UTR/seed region analysis

Several studies have shown that off-target effects may be caused by matches of the seed region of the siRNA antisense strand with the 3' untranslated region of unintended mRNA targets (see table). The seed region comprises 6 nucleotides in positions 2–7 of the antisense siRNA strand of the siRNA duplex. Matches such as these can contribute to downregulation of unintended targets due to the siRNA mimicking the action of an miRNA. siRNA designed at QIAGEN is analyzed for 3' UTR/seed region complementarity using a proprietary set of 3' UTR sequences derived from the human, rat, and mouse RefSeq databases. Each siRNA is aligned against these sequences to check for any homology that could contribute to miRNA-like, off-target effects.

Matches of 6 out of 6 nucleotides of the siRNA seed region with an unrelated target 3' UTR sequence are common and it is not necessary or practical to eliminate siRNAs showing such matches. More rarely, seed region matches in combination with 10 or more bases of additional homology are observed in an siRNA sequence. Such homologies have greater potential to result in off-target effects, and where possible these siRNAs are rejected in favor of others with less significant homology to unintended target genes.

For some targets, it is not possible to select siRNAs that do not show any such homologies. In these cases, EntrezGene IDs of the unrelated genes that could be unintended targets of the siRNA are provided at GeneGlobe. Observation of this type of homology does not necessarily mean that these genes will be affected by the siRNA. However, they can be considered potential unintended targets for follow up analysis, if warranted.

FlexiPlate siRNA allows design of RNAi screening experiments to suit specific requirements. siRNAs for any human or mouse gene can be selected as well as any positive and negative controls required. With the user-friendly Web interface, siRNAs and controls can be placed in any of the wells of a 96-well or 384-well plate, or plate layout can be selected from a range of predefined layout patterns. siRNAs are provided in 0.1 nmol, 0.25 nmol, or 1 nmol scales, enabling economical screening using low or higher siRNA amounts, as required. The 0.1 nmol, 0.25 nmol, and 1 nmol scales are available in 96-well plates. The 0.1 nmol and 0.25 nmol scales are available in 384-well plates.

The GeneGlobe Web portal makes it easy to search for siRNAs for genes of interest and to arrange plate layouts to suit screening experiments. Lists of gene names, Entrez Gene IDs, RefSeq IDs, siRNA names, or catalog numbers can be uploaded, making the process of plate ordering fast and easy. Order plates immediately or save for later changes and ordering. Easily download plate layouts for your records.

FlexiPlate siRNA enables RNAi applications including:

• Pathway analysis
• Follow-up screening experiments