Prime editor with rational design and AI-driven optimization for reverse editing window and enhanced fidelity

Chao Yang (), Qingxiao Fang, Mengyu Li, Jin Zhang, Rui Li, Tianxing Zhou, Keshan Wang, Jie Deng, Xiuchao Wang, Chongbiao Huang, Yukuan Feng, Xiaoping Zhang, Lei Shi (), Changhao Bi (), Xueli Zhang (), Jun Yu () and Jihui Hao ()
Additional contact information
Chao Yang: Tianjin Medical University Cancer Institute and Hospital
Qingxiao Fang: Tianjin Medical University Cancer Institute and Hospital
Mengyu Li: Tianjin Medical University Cancer Institute and Hospital
Jin Zhang: Tianjin Medical University Cancer Institute and Hospital
Rui Li: Tianjin University of Science and Technology
Tianxing Zhou: Tianjin Medical University Cancer Institute and Hospital
Keshan Wang: Huazhong University of Science and Technology
Jie Deng: Huazhong University of Science and Technology
Xiuchao Wang: Tianjin Medical University Cancer Institute and Hospital
Chongbiao Huang: Tianjin Medical University Cancer Institute and Hospital
Yukuan Feng: Tianjin Medical University Cancer Institute and Hospital
Xiaoping Zhang: Huazhong University of Science and Technology
Lei Shi: State Key Laboratory of Experimental Hematology
Changhao Bi: Chinese Academy of Sciences
Xueli Zhang: Chinese Academy of Sciences
Jun Yu: Tianjin Medical University Cancer Institute and Hospital
Jihui Hao: Tianjin Medical University Cancer Institute and Hospital

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract Prime editing (PE) is a precise tool for introducing genetic mutations in eukaryotes. Extending the efficient editing scope and mitigating undesired byproducts are possible. We introduce reverse PE (rPE), a SpCas9-directed variant that enabled DNA editing at the 3′ direction of HNH-mediated nick site. The rPE leveraging nCas9-D10A and rPE gRNA targeting the 5′ direction of HNH-mediated nick site inscribes genetic alterations, achieving a reverse editing window and potentially high fidelity. HNH and reverse transcriptase engineered using protein language models in conjunction with La facilitate circular erPEmax and erPE7max, achieving editing efficiency up to 44.41% without nick gRNA or positive selection. Furthermore, our findings underscore the capability of rPE in inserting functionally enhanced variant (PIK3CDE527G) for cell therapy. By expanding the editing scope and enhancing genomic manipulability, rPE represents a meaningful advancement in prime editing, improving its utility for research and therapeutic applications.

Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-60495-w 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_s41467-025-60495-w

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

DOI: 10.1038/s41467-025-60495-w

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 ().