Variant-specific knockdown by siRNA

As our knowledge of the transcriptome has become more sophisticated, so has our experimental design. Dharmacon™ catalog siRNAs are designed to give complete knockdown by targeting all transcripts of a gene, but what options are available for a researcher that needs to target just one specific transcript variant?

The Dharmacon siDESIGN Center offers a tool to confidently create custom, variant-specific siRNAs, by leveraging our proprietary siRNA design algorithm and RNA synthesis expertise with NCBI’s genomic database of information. Here are some considerations and a step-by-step guide for creating an isoform-specific siRNA for your gene of interest.

  • Target transcript must have a stretch of sequence that is unique from the non-targeted isoforms
  • The NCBI accession number or gene ID of the targeted isoform is required
To design your isoform-specific siRNA
  1. Starting at the siDESIGN Center page, enter the gene identifier information for your target of interest (e.g.: Accession NM_005211 for human CSF1R) and press the “Advanced Options” button. Once related NCBI RefSeq accession information appears, use the radio buttons to choose the targets of interest, and exclude unwanted transcripts:

    sidesign center step 1
  2. To maximize the number of results, check boxes to expand the design parameters to include all regions (5’UTR, ORF, and 3’UTR).

    sidesign center step 2
  3. Accept default G/C percentage, unless otherwise required.

    sidesign center step 3
  4. An alignment step is required when using Advanced Options, so choose the BLAST sequence database from the pull-down that matches your species of interest and click the “Design siRNA” button. If your species is not represented, please contact Scientific Support for further instructions.

    sidesign center step 4
  5. Once results have been returned, siRNA designs are ranked with the top scoring designs on the top of the list. The Score represents a compilation of different factors created by the Dharmacon siRNA design algorithm as an indicator of the likelihood of successful silencing with a specific design. Further details about the data fields in this list can be found on the Custom siRNA Design Tool User Guide.

    sidesign center step 5
  6. Select the ones you want and add them to your cart, and your custom designs are ready to be checked out. Once the order is placed, you can expect to receive your high-quality, transcript-specific siRNA within just 4 business days (for North America)!

Written by Jennifer Abarca PhD, Lead Scientific Support Specialist

Jennifer Abarca, PhD

Jennifer Abarca has been assisting customers with their questions regarding our product portfolios for over a decade. She believes CRISPRa is one of the most exciting technologies introduced in recent time, "For years we've had researchers requesting an easier way to perform gain-of-function screens, and this CRISPRa platform finally delivers a solution that eliminates the difficulties associated with lentiviral and ORF-based methods." When not guiding customers through their experimental journey, Jennifer enjoys building neighborhood camaraderie by acting as director of the local community garden.


Ready to design your own variant specific siRNAs?
Get started with the siDESIGN Center

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