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Engineered Sdd7 cytosine base editors with enhanced specificity

Author

Listed:
  • Hye-Yeon Hwang

    (Sungkyunkwan University School of Medicine)

  • Minyoung Lee

    (Sungkyunkwan University School of Medicine)

  • Hwalin Yi

    (Sungkyunkwan University School of Medicine)

  • Cheong Seok

    (Sungkyunkwan University School of Medicine)

  • Kayeong Lim

    (Korea Institute of Science and Technology (KIST))

  • Yi Rang Na

    (Seoul National University Hospital
    Seoul National University Hospital
    Seoul National University College of Medicine)

  • Jong-Sun Kang

    (Sungkyunkwan University School of Medicine)

  • Jae-Hyun Park

    (Sungkyunkwan University School of Medicine)

  • Daesik Kim

    (Sungkyunkwan University School of Medicine
    Sungkyunkwan University)

Abstract

Cytosine base editors (CBEs) revolutionize genome editing by enabling precise C-to-T conversions without double-strand breaks. Sdd7, a recently developed cytosine deaminase, exhibits high activity across a broad protospacer range but induces unintended off-target effects, including bystander mutations within and upstream of the protospacer and both gRNA-dependent and independent deamination. Here, we report that BE4max and Sdd7 induce bystander editing upstream of the protospacer. To overcome this, we engineer two Sdd7 variants, Sdd7e1 and Sdd7e2, enhancing specificity while preserving on-target efficiency. These variants display reduced bystander editing, narrowed editing windows, and significantly lower off-target activity. Delivery as ribonucleoproteins via engineered virus-like particles (eVLPs) further improves specificity, nearly eliminating bystander edits and increasing precise single-point mutations. Our findings establish Sdd7e1 and Sdd7e2, especially when delivered via eVLP, as high-fidelity CBEs poised for safe, precise therapeutic genome editing.

Suggested Citation

  • Hye-Yeon Hwang & Minyoung Lee & Hwalin Yi & Cheong Seok & Kayeong Lim & Yi Rang Na & Jong-Sun Kang & Jae-Hyun Park & Daesik Kim, 2025. "Engineered Sdd7 cytosine base editors with enhanced specificity," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-60789-z
    DOI: 10.1038/s41467-025-60789-z
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    References listed on IDEAS

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