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Enhancing homology-directed repair efficiency with HDR-boosting modular ssDNA donor

Author

Listed:
  • Ying-Ying Jin

    (Chinese Academy of Medical Sciences & Peking Union Medical College)

  • Peng Zhang

    (Chinese Academy of Medical Sciences & Peking Union Medical College)

  • Le-Le Liu

    (Chinese Academy of Medical Sciences & Peking Union Medical College)

  • Xiang Zhao

    (Chinese Academy of Medical Sciences & Peking Union Medical College)

  • Xiao-Qing Hu

    (Chinese Academy of Medical Sciences & Peking Union Medical College)

  • Si-Zhe Liu

    (Chinese Academy of Medical Sciences & Peking Union Medical College)

  • Ze-Kun Li

    (Chinese Academy of Medical Sciences & Peking Union Medical College)

  • Qian Liu

    (Chinese Academy of Medical Sciences & Peking Union Medical College)

  • Jian-Qiao Wang

    (Chinese Academy of Medical Sciences & Peking Union Medical College)

  • De-Long Hao

    (Chinese Academy of Medical Sciences & Peking Union Medical College)

  • Zhu-Qin Zhang

    (Chinese Academy of Medical Sciences & Peking Union Medical College)

  • Hou-Zao Chen

    (Chinese Academy of Medical Sciences & Peking Union Medical College
    Chinese Academy of Medical Sciences)

  • De-Pei Liu

    (Chinese Academy of Medical Sciences & Peking Union Medical College
    Chinese Academy of Medical Sciences
    Haihe Laboratory of Cell Ecosystem)

Abstract

Despite the potential of small molecules and recombinant proteins to enhance the efficiency of homology-directed repair (HDR), single-stranded DNA (ssDNA) donors, as currently designed and chemically modified, remain suboptimal for precise gene editing. Here, we screen the biased ssDNA binding sequences of DNA repair-related proteins and engineer RAD51-preferred sequences into HDR-boosting modules for ssDNA donors. Donors with these modules exhibit an augmented affinity for RAD51, thereby enhancing HDR efficiency across various genomic loci and cell types when cooperated with Cas9, nCas9, and Cas12a. By combining with an inhibitor of non-homologous end joining (NHEJ) or the HDRobust strategy, these modular ssDNA donors achieve up to 90.03% (median 74.81%) HDR efficiency. The HDR-boosting modules targeting an endogenous protein enable a chemical modification-free strategy to improve the efficacy of ssDNA donors for precise gene editing.

Suggested Citation

  • Ying-Ying Jin & Peng Zhang & Le-Le Liu & Xiang Zhao & Xiao-Qing Hu & Si-Zhe Liu & Ze-Kun Li & Qian Liu & Jian-Qiao Wang & De-Long Hao & Zhu-Qin Zhang & Hou-Zao Chen & De-Pei Liu, 2024. "Enhancing homology-directed repair efficiency with HDR-boosting modular ssDNA donor," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50788-x
    DOI: 10.1038/s41467-024-50788-x
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