• CRISPR Design Tool

    Our CRISPR Design Tool provides an intuitive one-stop location for guide RNA design and ordering. Use the design tool to order guide RNAs for targeted gene knockout or HDR-mediated genome editing.

    Features of the Dharmacon CRISPR Design Tool include:

    • Multiple guide RNA formats - synthetic single guide RNA (sgRNA), crRNA (+ tracrRNA), lentiviral sgRNA, or All-in-one vector
    • Custom guide RNA designs for over 40 species – simply provide the Gene ID
    • Design to protein coding, long noncoding, or microRNAs
    • Specific guide RNA design track for CRISPR Cas9 HDR knock-in
    • Most thorough specificity check to reduce off-targeting
    • Design guide RNA for S.pyogenes Cas9, MAD7, and other CRISPR-Cas systems

    Visit the CRISPR Design Tool Workflow page if you need to learn more about designing a custom guide RNA. Otherwise, select an option below to get started!

    You may also choose highly functional predesigned synthetic crRNA or lentiviral sgRNA to knockout your human or mouse gene target.

  • Start

    Design your guide RNA

    The Dharmacon CRISPR Design Tool allows you to select CRISPR targeting sequences for incorporation into synthetic crRNAs and single guide RNAs (sgRNAs).

    Start by choosing a design option

    See the S. pyogenes Cas9 User Guide or the Alternative CRISPR Nuclease User Guide for detailed instructions.

    Select design option

    Input gene ID or gene symbol: design for gene knockout
    Help Tooltip
    Select this option to generate guide RNA designs for gene knockout or across the entire gene. Edit-R functionality is applied for human, mouse and rat gene knockout designs.
    Input gene ID or gene symbol: targeted gene cleavage
    Help Tooltip
    Generate guide RNA designs in a specific region to facilitate HDR and knock-in experiments. Weighted functionality and specificity scoring is applied.
    Provide a DNA region for design
    Help Tooltip
    If you have any DNA sequence of interest and wish to generate a list of potential guide RNAs.
    Input my own guide RNA sequence

    In some cases, no design results are returned using the default parameters. Below are potential causes and suggestions for modifying the default settings to obtain designs:

    • Your gene may have non-overlapping transcripts. The default CRISPR Design Tool settings require targeting of all transcripts. In Advanced Options, specific transcripts may be Excluded or Allowed, rather than Required, to loosen the design criteria.
    • You might be using protein-coding gene settings with a noncoding gene target. Go back to the Design Purpose and select: Long non-coding RNA locus.
    • Your gene does not contain a NGG PAM. In Advanced Options, try including NAG PAM or uncheck “Require cuts to be in CDS”.
    • All potential target sites have GC percentages outside the default parameters. In Advanced Options, expand the GC Percentage settings.
    • Your gene does not contain target sites with more than two mismatches to PAM-adjacent sites in the selected genome. Deselect the Specificity Check. Keep in mind that the designs without Specificity Check are very likely to off-target.

    In some cases, no crRNA design results are returned using the default parameters. Below are examples of why the default settings may return no crRNA designs, and suggestions for obtaining designs:

    • Your DNA sequence does not contain a NGG PAM. In advanced options, try including NAG PAM.
    • Your DNA sequence has target sites with GC percentages outside the default parameters. In Advanced Options, expand the default GC Percentage settings.
    • Your DNA sequence only contains target sites that have possible off-targets to the selected genome. Expand the provided DNA sequence or deselect the Specificity Check.

    The CRISPR Design Tool service is experiencing high traffic. Please try again.

    The CRISPR Design Tool has timed out while working on your gene. Please try your design again in a few minutes. If timeouts persist, please contact Dharmacon Technical Support.

    Please try again in a few minutes. If problem persists, contact Technical Support.

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