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Engineered CRISPR-Cas9 nuclease with expanded targeting space
Open accessAbstract
Cas9 enzyme (SpCas9) requires an NGG protospacer adjacent motif (PAM) for target recognition, thereby restricting the targetable genomic loci. Here, we report a rationally engineered SpCas9 variant (SpCas9-NG) that can recognize relaxed NG PAMs. The crystal structure revealed that the loss of the base-specific interaction with the third nucleobase is compensated by newly introduced non-base-specific interactions, thereby enabling the NG PAM recognition. We showed that SpCas9-NG induces indels at endogenous target sites bearing NG PAMs in human cells. Furthermore, we found that the fusion of SpCas9-NG and the activation-induced cytidine deaminase (AID) mediates the C-to-T conversion at target sites with NG PAMs in human cells.
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“These can be targeted in combination with evolved Cas9 variants such as SpCas9-NG20 or SpG.19”
From Protocol to create isogenic disease models from adult stem cell-derived organoids using next-generation CRISPR tools (2024) · cites this paper as [20]
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“A rationally engineered SpCas9 variant (SpCas9-NG) generated based on the reduced interaction between the third nucleobase of PAMs and the gRNA-Cas9 complex could edit the target site with NG PAMs.”
From Machine learning-based prediction models to guide the selection of Cas9 variants for efficient gene editing (2024) · cites this paper as [28]
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“Cas9 genomic localization is delimited by the protospacer adjacent motif (PAM), which is NGG for SpCas9 while evolved variants of SpCas9 tolerate a broader range of PAM sequences17–21.”
From One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids (2023) · cites this paper as [19]
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Jeong, Y. Y., Han, J. H., Yu, J., Bae, S., & Seo, P. J. (2025) · BMB Reports · doi:10.5483/bmbrep.2024-0102 · Cited by 4
Visualization of a multi-turnover Cas9 after product release
Kiernan, K. A., & Taylor, D. W. (2025) · Nature Communications · doi:10.1038/s41467-025-60668-7 · Cited by 4
Off-target interactions in the CRISPR-Cas9 Machinery: mechanisms and outcomes
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Application and Research Prospects of CRISPR/Cas Gene Editing Technology in Lactic Acid Bacteria
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Metadata
- Authors
- Nishimasu, H., Shi, X., Ishiguro, S., Gao, L., Hirano, S., Okazaki, S., Noda, T., Abudayyeh, O. O., Gootenberg, J. S., Mori, H., Oura, S., Holmes, B., Tanaka, M., Seki, M., Hirano, H., Aburatani, H., Ishitani, R., Ikawa, M., Yachie, N., Zhang, F., & Nureki, O.
- Affiliations
- The University of Tokyo (JP)
- Broad Institute (US)
- Keio University (JP)
- Research Institute for Microbial Diseases, The University of Osaka (JP)
- Research Center for Advanced Science and Technology, The University of Tokyo (JP)
- Institute of Medical Science, The University of Tokyo (JP)
- Corresponding author
- Nishimasu, Hiroshi
- Nureki, Osamu
- ORCID
- Venue
- Science
- Published
- 2018-09-21
- Volume
- 361
- Issue
- 6408
- Pages
- 1259-1262
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC6368452
- OpenAlex
- W2889513238
- Cited by
- 1,100
- References
- 25
- Citations by year
- 2026: 81 · 2025: 113 · 2024: 143 · 2023: 134 · 2022: 167 · 2021: 169 · 2020: 156 · 2019: 125 · 2018: 11
- FWCI
- 41.07
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- PMC
- Funders
- Japan Agency for Medical Research and Development
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Health Sciences › Medicine › Oncology › CAR-T cell therapy research
- Keywords
- CRISPR/Cas9, SpCas9, protospacer adjacent motif, crystal structure, indels, C-to-T conversion, activation-induced cytidine deaminase, targeted mutagenesis
- MeSH terms
- Gene Editing, CRISPR-Associated Protein 9, Bacterial Proteins, Endonucleases, Humans, Protein Engineering, Crystallography, X-Ray, HEK293 Cells, CRISPR-Cas Systems
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