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TitleStructural insights into DdCBE in action enable high-precision mitochondrial DNA editing.
Journal, issue, pagesMol Cell, Vol. 85, Issue 18, Page 3357-33372.e9, Year 2025
Publish dateSep 18, 2025
AuthorsJiangchao Xiang / Wenchao Xu / Jing Wu / Yaxin Luo / Chengyu Liu / Yaofeng Hou / Jia Chen / Bei Yang /
PubMed AbstractDddA-derived cytosine base editor (DdCBE) couples transcription activator-like effector (TALE) arrays and the double-stranded DNA (dsDNA)-specific cytidine deaminase DddA to target mitochondrial DNA ...DddA-derived cytosine base editor (DdCBE) couples transcription activator-like effector (TALE) arrays and the double-stranded DNA (dsDNA)-specific cytidine deaminase DddA to target mitochondrial DNA (mtDNA) for editing. However, structures of DdCBE in action are unavailable, impeding its mechanistic-based optimization for high-precision-demanding therapeutic applications. Here, we determined the cryo-electron microscopy (cryo-EM) structures of DdCBE targeting two native mitochondrial gene loci and combined editing data from systematically designed spacers to develop WinPred, a model that can predict DdCBE's editing outcome and guide its design to achieve high-precision editing. Furthermore, structure-guided engineering of DddA narrowed the editing window of DdCBE to 2-3 nt while minimizing its off-target (OT) editing to near-background levels, thereby generating accurate DdCBE (aDdCBE). Using aDdCBE, we precisely introduced a Leber hereditary optic neuropathy (LHON)-disease-related mutation into mtDNA and faithfully recapitulated the pathogenic conditions without interference from unintended bystander or OT mutations. Our work provides a mechanistic understanding of DdCBE and establishes WinPred and aDdCBE as useful tools for faithfully modeling or correcting disease-related mtDNA mutations.
External linksMol Cell / PubMed:40934924
MethodsEM (single particle)
Resolution3.0 Å
Structure data

61646

9jo8

EMDB-61646, PDB-9jo8:
Cryo-EM structure of the mono-DdCBE bound to a dsDNA substrate.
Method: EM (single particle) / Resolution: 3.0 Å

62637

9ky4

EMDB-62637, PDB-9ky4:
Cryo-EM structure of the mono-DdCBE bound TS substrate complex.
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

Source
  • burkholderia cenocepacia h111 (bacteria)
  • xanthomonas (bacteria)
  • homo sapiens (human)
  • Burkholderia cenocepacia (bacteria)
KeywordsDNA BINDING PROTEIN/DNA / TALE / DddA deaminase / DdCBE / dsDNA / ND4 / Mitochondrial base editor. / DNA BINDING PROTEIN-DNA complex / cytosine deaminase / Mitochondrial base editor

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