High-efficiency base editing for nuclear and mitochondrial DNA with an optimized DYW-like deaminase.

Mol Ther

Department of Cell and Genetic Engineering, BK21 Project, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea; Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea. Electronic address: yongsub1.ki

Published: August 2025


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Article Abstract

CRISPR-based cytosine base editors enable precise genome editing without inducing double-stranded DNA breaks yet traditionally depend on a limited selection of deaminases from the APOBEC/AID or TadA families. Here, we present SsCBE, a CRISPR-based cytosine base editor utilizing SsdA, a DYW-like deaminase derived from the toxin of Pseudomonas syringae. Strategic engineering of SsdA has led to remarkable improvements in the base editing efficiency (by up to 8.4-fold) and specificity for SsCBE, while concurrently reducing cytotoxicity. Exhibiting exceptional versatility, SsCBE was delivered and efficiently applied using diverse delivery methods, including engineered virus-like particles. Its application has enabled targeted cytosine base editing in mouse zygotes and pioneering edits in mitochondrial DNA. SsCBE expands the genome editing toolbox by introducing a distinct deaminase scaffold with broad utility for both basic research and potential therapeutic applications.

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http://dx.doi.org/10.1016/j.ymthe.2025.08.007DOI Listing

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