In this screen, you select from a list of up to 10 top-scoring siRNA designs generated from your target sequence. The designs have been generated from a statistical analysis of multiple validated siRNA sets and a proprietary algorithm.
Information about the target sequence is listed at the top of the page. If you copied and pasted a nucleotide sequence, only the sequence length will be listed. Information about the gene is included if you entered an accession number.
To view the results of the BLAST search selected in Step 3 of the previous page, including which regions of the sequence were masked due to known homologies, click on View BLAST Results.
In the results table, each design is listed with a selection checkbox. If you entered an accession number for the target sequence, the Gene Region of each design will be listed. The GC% column lists the GC percentage of the design. The Tuschl's Pattern Match column lists the Tuschl's patterns that the design matches. Finally, the design ranking (in stars) is listed next to each design.
Note: We recommend selecting 2–4 designs for experimental testing; the number of designs you select will depend on their probability rankings.
Select the checkbox next to each design that you want to order and click on Continue. In the following screen, you will be prompted to select any Negative Control Sequences that you want to order with your siRNA molecules.
If the Designer is unable to generate a suitable number of siRNA designs for your target sequence, you can click on the Back button on your browser to return to the design parameters screen. You can then change some or all of the following parameters:
Target sequence — If you entered a partial gene sequence in the Nucleotide Sequence field in Step 1, entering more of the sequence may enable the Designer to generate more designs. Also consider entering an accession number in Step 1 to ensure that the complete gene sequence is reviewed for designs. (We recommend entering accession numbers in RefSeq format, e.g., NT_123456, to ensure that each sequence is also screened for SNPs).
Regions for target design — If you entered an accession number for the target sequence in Step 1, selecting more than one region checkbox (Open Reading Frame, 5' UTR, and/or 3' UTR) in Step 2 may enable the Designer to generate more designs.
Minimum and maximum G/C percentage — Expanding this range in Step 4 may enable the Designer to generate more designs.
Design option — If you select Tuschl's motif pattern as your design option, consider selecting the Default motif pattern instead. The default proprietary design algorithm will frequently give more results with a High probability of success. The results using this algorithm may include some Tuschl's patterns; these will be noted on the results page.