Designing and Generating CRISPR-Cas Mutants

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Designing the Targeting Strategy

  • Determine where you want to target the gene and copy that DNA sequence. It needs to be the genomic DNA from that particular species that is targeted, so if your region of interest spans several introns, you need to copy the genomic DNA not the mRNA sequence. In other words, if you can design your CRISPR pairs to be within one exon that is best. In that case submit the exon to the CRISPR tool. If your target site is close to an exon boundary then you need to submit the genomic sequence around that exon. You do not want your CRISPR pairs to span an intron.
  • Paste this sequence into the CRISPR tool at and select your target species. When complete select Double Nickase Design for Guides and Off-Targets for non-Nickase
  • Based on where you want to cut the DNA select the one or two guide DNA sequences. Name those sequences based on the nucleotide it cuts after (see cuts after position in the CRISPR tool output). Use the actual nucleotide from the reference mRNA sequence, not the nucleotide based on the arbitrary region that you pasted into the CRISPR tool.
  • Print out, or sketch all of the targeting information into your notes.

Generating the CRISPR-Cas Plasmids

You will need to generate two nickase plasmids using the pX335 backbone, or a single gDNA using the pX459 backbone. Below is a schematic of the cloning taken from

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Desigining and Ordering Primers

  • For each guide DNA sequence you need to order a pair of primers to make this gDNA sequence.
  • To make the forward primer copy the sequence but remove the NGG site at the end. Add CACC to the 5' end of it to generate the appropriate overhang. If the gDNA does not start with a 'G' also add a G (CACCG-gDNA)
  • To make the reverse primer reverse transcribe the copied sequence (removing the NGG and the end, and not including the CACC at the other end). Add AAAC to the 5' end of that reverse transcribed sequence to make the appropriate overhang. If you had to add a G to the forward primer, end this primer with a 'C'
  • Name the primers as follows: mm-Pygm-gDNA-62-FWD where mm = species; Pygm = your gene name, 62 = where this nickase cuts, and FWD or REV is whether the primer is forward or reverse.