CRISPR Design Tool Workflow

Online tool to design & order custom guide RNAs

Quickly and easily design and order custom guide RNAs for targeted gene knockout or HDR-mediated genome editing. Choose from lentiviral single guide RNA (sgRNA), synthetic sgRNA, or synthetic CRISPR RNA (crRNA).

  • Rigorous specificity checking identifies designs with potential off-targets
  • Target protein coding, microRNA, or lncRNA genes for over 30 species
  • Synthetic guide RNAs provided in tubes or plates, lentiviral sgRNA as glycerol stock or concentrated lentiviral particles
  • Advanced options enable transcript-specific designs or designs for a novel sequence

The flexibility and utility of the CRISPR Design Tool provides an intuitive one-stop location for custom guide RNA design and ordering. Our bioinformatics team is constantly making improvements and expanding the capabilities of this resource, so click the Feedback link if you don’t see what you need!

Need to design a guide RNA?

  • Choose from over 30 model organisms; simply enter a gene identifier!
  • Support for protein coding, long noncoding, or microRNA genes
  • Target a specific region for optimal HDR knock-in studies
  • Unparalleled specificity checking for reduced off-target cleavage
  • Intuitive interface lets you visualize guide RNA designs along your gene

Already have a guide RNA design?

  • Enter a target sequence(s) to easily order lentiviral or synthetic guide RNAs for use with S. pyogenes Cas9 nuclease
  • Guide RNAs for other Cas9 species (Cpf1, S. aureus, etc.) may be entered and ordered as synthetic sgRNA or crRNA

Looking for functional knockout without a design step?

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

The CRISPR Design Tool has four options for designing and/or ordering custom guide RNAs. Choose the best option for your experiment and get started!

Input gene ID or gene symbol: design anywhere within gene: This option is to design guide RNAs for knockout of protein coding, microRNA, or lncRNA genes for over 30 different species.

Input gene ID or gene symbol: specific cleavage location for HDR: This enables design of guide RNA in a specific region to facilitate HDR and knock-in studies. Weighted functionality and specificity ranking is provided.

Provide a DNA region for design: For designs in regions outside of defined genes, other model organisms, or to target a very particular genomic region.

Input my own guide RNA sequence: No design assistance needed? Simply enter a target sequence or the entire length of your synthetic crRNA or sgRNA

Advanced options

Advanced Options for the CRISPR Design Tool

By selecting the “Advanced options” link prior to initiating the design step, you have the option to select particular transcript(s) to exclude from guide RNA targeting (default is to target all transcripts)

There are also options to adjust default setting for the purpose of opening up design space when few or no results are returned:

  • Turn off the specificity check
  • Permit target site to lie outside of the coding region (CDS)
  • Adjust the GC content of the target sequence

Adding to cart

When the desired designs have been entered or selected, simply choose the appropriate guide RNA product(s) from one or more of the tabbed lists and click the Add to Cart button (See Products tab for details). If you select Add to Plate for synthetic crRNA or sgRNA, you will be taken to a separate interface to configure your 96-well plate.