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Small interfering RNA (siRNA)

Predesigned siRNA product lines

Guaranteed to silence target gene expression by at least 75%

  • ON-TARGETplus siRNA

    Silence gene function and reduce off-target effects by up to 90%. ON-TARGETplus guarantees functional knockdown with optimal specificity.

  • Accell siRNA

    Deliver siRNA into difficult-to-transfect cells without a transfection reagent, Accell self-delivering siRNA enables non-viral RNAi in neuronal, immune, and stem cells.

  • siGENOME siRNA

    Highly potent siRNA for all human, mouse, and rat genes. siGENOME has provided the longest standing siRNA silencing guarantee on the market.

  • Lincode siRNA

    siRNAs for efficient knockdown of long, noncoding RNA (lncRNA) genes with modifications to ensure specificity.

Custom siRNA

Use our online design tool to create and order a custom siRNA specific for your application.

siRNA knockdown experiments are the gold standard for transiently assessing a protein’s function. Researchers employing this powerful technology need confidence in 1) the functional silencing of their gene of interest and 2) careful mitigation of off-target effects.

The principles of SMARTselection design

Scientists from Dharmacon™ (now part of the Horizon team) pioneered siRNA design rules 20 years ago and have been perfecting algorithms for high potency silencing ever since. Horizon continues to innovate the siRNA product portfolio to offer unmatched efficiency, accuracy, and deliverability.

Our SMARTselection algorithm designs highly functional and specific siRNAs, with guaranteed functional knockdown for ON-TARGETplus, siGENOME and Accell reagents.

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

sirna smart selection flowchart
  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:
    • the sense strand has fewer than 2 mismatches to a (non-self) sequence record in the BLAST database or
    • 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.

All siRNA reagents are available individually, as sets of 4 individual siRNAs, or as a SMARTpool.

SMARTpool technology

The SMARTpool combines four gene-specific siRNAs into a single reagent. Research has shown that pooled siRNAs:

  • Minimize sequence-specific off-targeting by lowering the relative concentration of each siRNA
  • Improve the likelihood of effective gene silencing
  • Better mimic the natural RNAi pathway
  • Reduce false negatives caused by inaccessible binding sites

Reducing off-targets for better specificity

siRNA knockdown experiments only advance your research when there is a high degree of confidence that the desired gene is the only gene silenced. The primary source of siRNA-mediated off-targets is the seed region (nucleotides 2-7) which uses the microRNA pathway to induce non-specific gene silencing via interactions within the 3' UTR. Horizon’s SMARTselection algorithm incorporates comprehensive bioinformatic strategies like seed region filters and seed frequency analysis within its design strategy to reduce microRNA-like off-target activity.

  • Conserved microRNA seed regions filtered from siRNA designs
  • Frequency analysis of siRNA seed complements (how often this occurs in the 3' UTR transcriptome) performed, with preference given to siRNA designs with low-frequency seeds

siRNA format selection

Choosing a Dharmacon siRNA product line and format

siRNA control recommendations

This technical note discusses the function and features of a variety of control siRNAs.

Accell siRNA silencing workflow

Experimental workflow for gene silencing with Dharmacon Accell siRNA.