Selection Criteria

Please note that siRNA candidates produced by this wizard are not guaranteed to work. However, they do have a higher probability than randomly selected candidates.

Standard search

This section uses default selection criteria.
  1. Sequence submitted - siRNA directed against any mRNA regions (UTRs or coding sequence) are renowned to be functionnal, but we advise to submit only the coding sequence (from ATG to stop codon) for better results.
  2. Starting nucleotide - The first nucleotide of the siRNA sequence is an A or G, which corresponds to the transcription initiation point of the human H1 and 7SK promoter (see Guidelines for more details).
  3. GC content of the siRNA sequence - Default GC content ranges from 30% to 55%. Sequences with lower GC content seem to be more active than those with higher GC content.
  4. Excluded sequences - Sequences with a stretch of 4+ T, or a set of 6+ G and C (eg GCCGGC) or G and T (eg GGTGTT) are excluded. Sequences containing a palindrome are also omitted to avoid unwanted hairpin structures. Sequences GTCCTTCAA, TGTGT and CTGAATT, known to induce immune response (1,2,3) are also excluded.
  5. Thermodynamic properties of siRNA - Only siRNA sequences with optimal internal stability are selected (see Guidelines for more details).

References: 1- Hornung V. et al.,2005. Sequence-specific potent induction of INF-α by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat. Med. 2005 Mar;11(3):263-70
2- Judge A. et al., 2005. Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat Biotechnol. 2005 Apr;23(4):457-62
3- Lan T et al., 2009. Synthetic oligoribonucleotides-containing secondary structure acr as agonists of Toll-like receptors 7 and 8. Biochem Biophys Res Commun. [AOP]

Advanced search

This section allows you to select your own criteria to find a candidate siRNA sequence. We recommend that you choose your selection criteria following the siRNA design guidelines based on the results from various laboratories including ours.