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.
Ryan D Chow  #  1  2  3  4 ,  Jennifer S Chen  #  4  5  6  7 ,  Johanna Shen  1  2  3 ,  Sidi Chen  8  9  10  11  12  13  14  15  16  17  18  19
Affiliations
  • 1. Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
  • 2. Systems Biology Institute, Yale University, West Haven, CT, USA.
  • 3. Center for Cancer Systems Biology, Yale University, West Haven, CT, USA.
  • 4. M.D.-Ph.D. Program, Yale University, New Haven, CT, USA.
  • 5. Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA.
  • 6. Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
  • 7. Immunobiology Program, Yale University, New Haven, CT, USA.
  • 8. Department of Genetics, Yale University School of Medicine, New Haven, CT, USA. [email protected].
  • 9. Systems Biology Institute, Yale University, West Haven, CT, USA. [email protected].
  • 10. Center for Cancer Systems Biology, Yale University, West Haven, CT, USA. [email protected].
  • 11. M.D.-Ph.D. Program, Yale University, New Haven, CT, USA. [email protected].
  • 12. Immunobiology Program, Yale University, New Haven, CT, USA. [email protected].
  • 13. Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA. [email protected].
  • 14. Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA. [email protected].
  • 15. Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA. [email protected].
  • 16. Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA. [email protected].
  • 17. Yale Liver Center, Yale University School of Medicine, New Haven, CT, USA. [email protected].
  • 18. Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA. [email protected].
  • 19. Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA. [email protected].
  • # Contributed equally.
PMID: 32989284 DOI: 10.1038/s41551-020-00622-8
Abstract

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.