A web tool for the design of prime-editing guide RNAs

Prime editing enables diverse genomic alterations to be written into target sites without requiring double-strand breaks or donor templates. The design of prime-editing guide RNAs (pegRNAs), which must be customized for each edit, can however be complex and time consuming. Compared with single guide RNAs (sgRNAs), pegRNAs have an additional 3 ' extension composed of a primer binding site and a reverse-transcription template. Here we report a web tool, which we named pegFinder (http://pegfinder.sidichenlab.org), for the rapid design of pegRNAs from reference and edited DNA sequences. pegFinder can incorporate sgRNA on-target and off-target scoring predictions into its ranking system, and nominates secondary nicking sgRNAs for increasing editing efficiency. CRISPR-associated protein 9 variants with expanded targeting ranges are also supported. To facilitate downstream experimentation, pegFinder produces a comprehensive table of candidate pegRNAs, along with oligonucleotide sequences for cloning.

Automated summary

Prime editing allows diverse genomic alterations to be made at target sites without double-strand breaks or donor templates. However, designing pegRNAs can be complex and time-consuming, as they require customization for each edit. The web tool pegFinder facilitates the rapid design of pegRNAs for downstream experimentation, with the incorporation of sgRNA predictions and nomination of secondary nicking sgRNAs for improved editing efficiency.