ArticleNature communications2025
Insights into the compact CRISPR-Cas9d system.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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Who cites it
12 citing papers in PubMed.
- Visualizing structural dynamics during nuclease activation across evolutionarily diverse IscB and CRISPR-Cas9 enzymes.Research square · 2026Article
- Compact 9dBEs Enable Efficient and Precise Genome Editing in Mammalian Cells and In Vivo.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- On-target and off-target activities of CRISPR therapeutics across scales.Trends in biotechnology · 2026Review
- Molecular basis of single-mismatch-induced nuclease-to-nickase conversion in TIGR-TasH.Nucleic acids research · 2026Article
- Structure basis for single-strand nucleic acid targeting by IscB and variants.Nucleic acids research · 2026Article
- Allosteric activation mechanism of the type VII CRISPR-Cas system.Nucleic acids research · 2026Article
- A Programmable Eukaryotic Argonaute Nuclease with Dual DNA and RNA Cleavage Activity from Thermophilic FungusSmall science · 2026Article
- Structural visualization of the molecular evolution of CRISPR-Cas9.Nature structural & molecular biology · 2026Article
- And… cut! - how conformational regulation of CRISPR-Cas effectors directs nuclease activity.The Biochemical journal · 2025Review
- Structural insights into Type II-D Cas9 and its robust cleavage activity.Nature communications · 2025Article
- Expanding the CRISPR/Cas toolkit: applications in proteomics and theranostics.Frontiers in bioengineering and biotechnology · 2025Review
- Advances and challenges of CRISPR/Cas gene editing for corneal diseases.Advances in ophthalmology practice and researchReview
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cas9d, the smallest known member of the Cas9 family, employs a compact domain architecture for effective target cleavage. However, the underlying mechanism remains unclear. Here, we present the cryo-EM structures of the Cas9d-sgRNA complex in both target-free and target-bound states. Biochemical assays elucidated the PAM recognition and DNA cleavage mechanisms of Cas9d. Structural comparisons revealed that at least 17 base pairs in the guide-target heteroduplex is required for nuclease activity. Beyond its typical role as an adaptor between Cas9 enzymes and targets, the sgRNA also provides structural support and functional regulation for Cas9d. A segment of the sgRNA scaffold interacts with the REC domain to form a functional target recognition module. Upon target binding, this module undergoes a coordinated conformational rearrangement, enabling heteroduplex propagation and facilitating nuclease activity. This hybrid functional module precisely monitors heteroduplex complementarity, resulting in a lower mismatch tolerance compared to SpyCas9. Moreover, structure-guided engineering in both the sgRNA and Cas9d protein led to a more compact Cas9 system with well-maintained nuclease activity. Altogether, our findings provide insights into the target recognition and cleavage mechanisms of Cas9d and shed light on the development of high-fidelity mini-CRISPR tools.
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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.