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The siDESIGN Center is an advanced, user-friendly siRNA design tool which significantly improves the likelihood of identifying functional siRNA. One-of-a-kind options are available to enhance target specificity and adapt siRNA designs for more sophisticated experimental design.
Note: Candidates produced using the siDESIGN Center do not carry the an siRNA product performance guarantee. However, siRNAs designed using this tool are more likely to provide potent and specific knockdown than those designed with conventional methods.
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There are four options for identifying the target sequence of interest for evaluation by the siDESIGN Center:
This option supports isoform or gene variant-specific siRNA design. Please note that using this option may greatly reduce the number of siRNA designs generated due to the increased stringency of the design parameters.
The Target Gene Variants table displays the Accession number(s) for all know RefSeq variants associated with the target gene (based on the Gene ID, GI number, or Accession number entered in Step 1). As a default, all variants will be targeted by the siRNA designs.
This option supports (a) the design of cross-species siRNA to target homologous genes in multiple organisms and (b) the design of siRNA to target conserved gene family members within an organism. Please note that using this option may greatly reduce the number of siRNA designs generated due to the increased stringency of the design parameters.
Up to 10 Accession numbers may be entered (separated by spaces or line breaks) in the field provided. These gene targets will be "Required" by the design tool along with the original target gene provided in Step 1.
Note: This option is not available if a Nucleotide Sequence is used as the Identifier in Step 1.
This step is only required when Nucleotide Sequence is used as an Identifier in Step 1. The organism will be populated automatically from the RefSeq record if Gene ID, GI number, or Accession number is used.
Select the corresponding organism from the drop-down list for human, mouse, or rat sequences. Any other organism should be set to "Other", and will not be analyzed for seed region frequency.
Seed region analysis determines the number of exact matches of the siRNA seed region (nucleotides 2-7) to the 3'UTRs of all genes in the chosen genome (only performed for human, mouse, and rat). siRNAs with low seed region frequency will have reduced likelihood of seed-region mediated off-target effects compared to those with higher frequencies1 .
This analysis will not limit the number of designs generated, but instead provides you with an indicator on the Results Page of the designs with low frequency of seed matches.
1Anderson, E, et al., "Low Genomic 3' UTR Seed Complement Frequency Predicts siRNA Target Specificity". Poster at Keystone Symposia: MicroRNAs and siRNAs: Biological Functions and Mechanism. (January 2007)
This value is calculated using the core 19 nucleotide target sequence and does not include the dinucleotide leader sequence. Early research suggested that siRNA should have a G/C content of approximately 50%. For genes that are G/C poor or rich, the range of G/C content be expanded to include other ranges.
A BLAST step is required when using Advanced Options to exclude target gene variants.
The following species-specific BLAST databases are available for analyses of candidate siRNAs: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Zebrafish (Danio rerio), Fruitfly (Drosophila melanogaster), Worm (Caenorhabditis elegans), Cow (Bos taurus), Rhesus monkey (Macaca mulatta), Chimpanzee (Pan troglodytes), Dog (Canis familiaris), and Chicken (Gallus gallus).
Two combined databases are also available to support cross-species designs: Human/Mouse, and Human/Rat.
If your species does not appear in this list, we recommend using a database most closely associated with the species of interest and/or performing an additional blastn analysis at NCBI with the candidate siRNAs.
In addition to user-specified design criteria, candidate siRNA design regions are also selected for the required target(s) with other important criteria. Several of these key criteria include the exclusion of:
Following analysis, up to 50 of the top-scoring candidates are presented as a list. This page also includes details of the designated target for verification of the search.
The output may be sorted by category by selecting the desired column heading:
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