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

Nat Biomed Eng. 2021 Feb;5(2):190-194. doi: 10.1038/s41551-020-00622-8. Epub 2020 Sep 28.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • CRISPR-Associated Protein 9 / genetics
  • CRISPR-Cas Systems*
  • Gene Editing / methods*
  • HEK293 Cells
  • Humans
  • Internet
  • RNA, Guide, CRISPR-Cas Systems / genetics*
  • Software*


  • RNA, Guide, CRISPR-Cas Systems
  • CRISPR-Associated Protein 9