ArticleNature structural & molecular biology2023
Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA.
Article in Nature structural & molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 25 citations in OpenAlex.
- Base Editing: Mechanisms and Therapeutic Applications.Methods in molecular biology (Clifton, N.J.) · 2027Review
- Article
- Structural basis for double-stranded DNA cytosine deamination by BaDTF3 and its application in mitochondrial genome editing.Nature communications · 2026Article
- Efficient mitochondrial A-to-G base editors for the generation of mitochondrial disease models.Nature biotechnology · 2026Article
- Leveraging base excision repair for efficient adenine base editing of mitochondrial DNA.Nature biotechnology · 2026Article
- Advances in gene therapy for mitochondrial genetic disorders: current status and clinical implementation challenges.Journal of translational medicine · 2025Review
- Mapping single-cell diploid chromatin fiber architectures using DAF-seq.Nature biotechnology · 2025Article
- Computational design of a high-precision mitochondrial DNA cytosine base editor.Nature structural & molecular biology · 2025Article
- Structural basis for sequence context-independent single-stranded DNA cytosine deamination by the bacterial toxin SsdA.Nature communications · 2025Article
- Engineering a bacterial toxin deaminase from the DYW-family into a novel cytosine base editor for plants and mammalian cells.Genome biology · 2025Article
- MitoEdit: A pipeline for optimizing mtDNA base editing and predicting bystander effects.Computational and structural biotechnology journal · 2025Article
- Reducing off-target effects of DdCBEs by reversing amino acid charge near DNA interaction sites.Cell research · 2024Article
- Accelerated discovery and miniaturization of novel single-stranded cytidine deaminases.Nucleic acids research · 2024Article
- Strand-preferred base editing of organellar and nuclear genomes using CyDENT.Nature biotechnology · 2024Article
- Mitochondrial genome editing: strategies, challenges, and applications.BMB reports · 2024Review
- Mitochondrial Base Editing: Recent Advances towards Therapeutic Opportunities.International journal of molecular sciences · 2023Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The interbacterial deaminase toxin DddA catalyzes cytosine-to-uracil conversion in double-stranded (ds) DNA and enables CRISPR-free mitochondrial base editing, but the molecular mechanisms underlying its unique substrate selectivity have remained elusive. Here, we report crystal structures of DddA bound to a dsDNA substrate containing the 5'-TC target motif. These structures show that DddA binds to the minor groove of a sharply bent dsDNA and engages the target cytosine extruded from the double helix. DddA Phe1375 intercalates in dsDNA and displaces the 5' (-1) thymine, which in turn replaces the target (0) cytosine and forms a noncanonical T-G base pair with the juxtaposed guanine. This tandem displacement mechanism allows DddA to locate a target cytosine without flipping it into the active site. Biochemical experiments demonstrate that DNA base mismatches enhance the DddA deaminase activity and relax its sequence selectivity. On the basis of the structural information, we further identified DddA mutants that exhibit attenuated activity or altered substrate preference. Our studies may help design new tools useful in genome editing or other applications.
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