ArticleNature biomedical engineering2025
Structure-guided discovery of highly efficient cytidine deaminases with sequence-context independence.
Article in Nature biomedical engineering, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed.
- An endonuclease V protectsbioRxiv : the preprint server for biology · 2026Article
- Harnessing mitochondrial genome editing for crop improvement: principles and applications.aBIOTECH · 2026Review
- Structural mining and engineering of metagenome-derived Cas12a orthologs expands the CRISPR genome editing and multiplex diagnostics toolkit.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- Therapeutic adenine base editor with minimized off-target effects.Protein & cell · 2026Article
- Discovery and engineering of bacterial P450s for C-14 hydroxylation in ent-kaurane diterpenoids.Nature communications · 2026Article
- Rationally and in silico guided APOBEC3F-directed CBE for enhanced PDAC genetic therapy.Communications biology · 2026Article
- Harnessing artificial intelligence to advance CRISPR-based genome editing technologies.Nature reviews. Genetics · 2026Review
- Deep learning-based semantic matching of cis-regulatory DNA sequences facilitates the prediction of gene function.Nature plants · 2026Article
- Protein-nucleic acid language model-assisted design of precise and compact adenine base editor.Nature communications · 2025Article
- High-efficiency base editing for nuclear and mitochondrial DNA with an optimized DYW-like deaminase.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- Structural basis for sequence context-independent single-stranded DNA cytosine deamination by the bacterial toxin SsdA.Nature communications · 2025Article
- Development of cytosine and adenine base editors for maize precision breeding.Journal of integrative plant biology · 2025Article
- AlphaCD: a machine learning model capable of highly accurate characterization for 21,335 cytidine deaminases.Cell research · 2025Article
- Correcting a patient-specific Rhodopsin mutation with adenine base editor in a mouse model.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- Charting the development and engineering of CRISPR base editors: lessons and inspirations.Cell chemical biology · 2025Review
- Harnessing novel cytidine deaminases from the animal kingdom for robust multiplexed base editing in rice.Plant biotechnology journal · 2025Article
- Review
- Single-cell RNA sequencing data analysis of the inner ear in gentamicin-treated mice via intraperitoneal injection.Open medicine (Warsaw, Poland) · 2025Article
- From bench to bedside: cutting-edge applications of base editing and prime editing in precision medicine.Journal of translational medicine · 2024Review
- Research on Artificial-Intelligence-Assisted Medicine: A Survey on Medical Artificial Intelligence.Diagnostics (Basel, Switzerland) · 2024Review
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
The applicability of cytosine base editors is hindered by their dependence on sequence context and by off-target effects. Here, by using AlphaFold2 to predict the three-dimensional structure of 1,483 cytidine deaminases and by experimentally characterizing representative deaminases (selected from each structural cluster after categorizing them via partitional clustering), we report the discovery of a few deaminases with high editing efficiencies, diverse editing windows and increased ratios of on-target to off-target effects. Specifically, several deaminases induced C-to-T conversions with comparable efficiency at AC/TC/CC/GC sites, the deaminases could introduce stop codons in single-copy and multi-copy genes in mammalian cells without double-strand breaks, and some residue conversions at predicted DNA-interacting sites reduced off-target effects. Structure-based generative machine learning could be further leveraged to expand the applicability of base editors in gene therapies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.