Mismatch prime editing gRNA increased efficiency and reduced indels

Jidong Fei, Dongdong Zhao (), Caiyi Pang, Ju Li, Siwei Li, Wentao Qiao, Juan Tan, Changhao Bi () and Xueli Zhang ()
Additional contact information
Jidong Fei: Tianjin Normal University
Dongdong Zhao: Chinese Academy of Sciences
Caiyi Pang: Chinese Academy of Sciences
Ju Li: Tianjin Normal University
Siwei Li: Chinese Academy of Sciences
Wentao Qiao: Nankai University
Juan Tan: Nankai University
Changhao Bi: Chinese Academy of Sciences
Xueli Zhang: Chinese Academy of Sciences

Nature Communications, 2025, vol. 16, issue 1, 1-10

Abstract: Abstract Prime editing enables precise and efficient genome editing, but its efficacy is hindered by pegRNA’s 3’ extension, forming secondary structures due to high complementarity with the protospacer. The continuous presence of the prime editing system also leads to unintended indel formation, raising safety concerns for therapeutic applications. To address these challenges, we develop a mismatched pegRNA (mpegRNA) strategy that introduces mismatched bases into the pegRNA protospacer, reducing complementarity and secondary structure formation, and preventing sustained activity. Our findings show that mpegRNA enhances editing efficiency by up to 2.3 times and reduces indel levels by 76.5% without compromising performance. Combining mpegRNA with epegRNA further increases efficiency up to 14-fold, or 2.4-fold in PE4max/PE5max systems, underscoring its potential in research and therapy. AlphaFold 3 analysis suggests that the optimal mpegRNA structure contributes significantly to improved editing outcomes. Overall, mpegRNA advances prime editing technology, improving efficiency while reducing indels.

Date: 2025
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-024-55578-z Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-024-55578-z

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-024-55578-z

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().