• SMARTselection siRNA Design

    Effective gene silencing by the RNA interference (RNAi) pathway requires a comprehensive understanding of the elements that influence small interfering RNA (siRNA) functionality and specificity. Our scientists were the first to establish siRNA design rules for high potency silencing and continue to drive innovations in this area.

    The principles of SMARTselection design:

    To identify optimal sequences for siRNA targeting, it is necessary to delineate target gene sequence space and build a representative candidate list.

    siRNA Smart Selection Flowchart

    siRNA Smart Selection Flowchart

    Adapted from A. Birmingham et. al., A protocol for designing siRNAs with high functionality and specificity, Nature Methods., Aug 2007; 9: 2068-2078

    1. Build list of candidate 19mers that target the appropriate region(s) of the target gene.
    2. Filter to remove candidates with known functionality or specificity issues (G/C content, SNP, toxic or miRNA-like seed motifs, etc.)
    3. Score remaining candidates with proprietary algorithm – (high score = high silencing potential)
    4. Crop list of candidates to eliminate low scores and increase efficiency of downstream analyses.
    5. BLAST both strands to identify potential unintended targets. These results, combined with upstream scoring, provide an indicator of whether the siRNA design should be synthesized with a chemical modification (ON-TARGET) to inhibit sense-strand uptake. This is indicated when:
      1. The sense strand has fewer than 2 mismatches to a (non-self) sequence record in the BLAST database or
      2. analysis indicates that the design favors sense strand over antisense strand entry into RISC
    6. Pick the four best siRNA with a proprietary set of criteria for seed-region frequency, Score, BLAST results, and targeting region.