Variant-specific knockdown by siRNA
How to use the siDESIGN Center to design isoform or gene variant-specific siRNAs
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 siDESIGN Center offers a tool to confidently create custom, variant-specific siRNAs, by leveraging the Dharmacon 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
- 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:
- Click "Required" for any variant that must be targeted by the designs. Please note that at least one variant must remain "Required" for the design step to proceed.
- Click "Allowed" for any variant that will neither be required nor excluded by resulting siRNA designs.
- Click the "Excluded" radio button for any variant whose sequence record should NOT be targeted
Custom synthesis landing page
- View the online User Guide for help using siDESIGN Center tool.
- Use our online design tools and extensive synthesis options to create custom products specific to your application.
- Find product guides, FAQs and more.