{"title":"提高准确性和安全性的肽插入碱基编辑器工程","authors":"Qi Chen, Yangning Sun, Jia Yao, Yingfan Lu, Ruikang Qiu, Fuling Zhou, Zixin Deng, Yuhui Sun","doi":"10.1002/smll.202411583","DOIUrl":null,"url":null,"abstract":"<p>Base editors are effective tools for introducing base conversions without double-strand breaks, showing broad applications in biotechnological and clinical areas. However, their non-negligible bystander mutations and off-target effects have raised extensive safety concerns. To address these issues, a novel method is developed by inserting specific peptide fragments into the substrate binding pocket of deaminases in base editors to modify these outcomes. It is validated that the composition and position of the inserted peptide can significantly impact the performance of A3A-based cytosine base editor and TadA-8e-based adenine base editor, leading to improved editing activity and precision in human HEK293T cells. Importantly, the TadA-8e variant with DPLVLRRRQ peptide inserted behind S116 residue showed a strong motif preference of Y<sub>4</sub>A<sub>5</sub>N<sub>6</sub>, which can accurately edit the A<sub>5</sub> base in targeted protospacer with minimized bystander and off-target effects in DNA and RNA-level. By summarizing the regularity during engineering, a set of systematic procedures is established, which can potentially be used to modify other types of base editors and make them more accurate and secure. In addition, the peptide insertion strategy is also proven to be compatible with traditional amino acid changes which have been reported, exhibiting excellent compatibility.</p>","PeriodicalId":228,"journal":{"name":"Small","volume":"21 14","pages":""},"PeriodicalIF":12.1000,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/smll.202411583","citationCount":"0","resultStr":"{\"title\":\"Engineering of Peptide-Inserted Base Editors with Enhanced Accuracy and Security\",\"authors\":\"Qi Chen, Yangning Sun, Jia Yao, Yingfan Lu, Ruikang Qiu, Fuling Zhou, Zixin Deng, Yuhui Sun\",\"doi\":\"10.1002/smll.202411583\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>Base editors are effective tools for introducing base conversions without double-strand breaks, showing broad applications in biotechnological and clinical areas. However, their non-negligible bystander mutations and off-target effects have raised extensive safety concerns. To address these issues, a novel method is developed by inserting specific peptide fragments into the substrate binding pocket of deaminases in base editors to modify these outcomes. It is validated that the composition and position of the inserted peptide can significantly impact the performance of A3A-based cytosine base editor and TadA-8e-based adenine base editor, leading to improved editing activity and precision in human HEK293T cells. Importantly, the TadA-8e variant with DPLVLRRRQ peptide inserted behind S116 residue showed a strong motif preference of Y<sub>4</sub>A<sub>5</sub>N<sub>6</sub>, which can accurately edit the A<sub>5</sub> base in targeted protospacer with minimized bystander and off-target effects in DNA and RNA-level. By summarizing the regularity during engineering, a set of systematic procedures is established, which can potentially be used to modify other types of base editors and make them more accurate and secure. In addition, the peptide insertion strategy is also proven to be compatible with traditional amino acid changes which have been reported, exhibiting excellent compatibility.</p>\",\"PeriodicalId\":228,\"journal\":{\"name\":\"Small\",\"volume\":\"21 14\",\"pages\":\"\"},\"PeriodicalIF\":12.1000,\"publicationDate\":\"2025-02-25\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1002/smll.202411583\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Small\",\"FirstCategoryId\":\"88\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/smll.202411583\",\"RegionNum\":2,\"RegionCategory\":\"材料科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Small","FirstCategoryId":"88","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/smll.202411583","RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
Engineering of Peptide-Inserted Base Editors with Enhanced Accuracy and Security
Base editors are effective tools for introducing base conversions without double-strand breaks, showing broad applications in biotechnological and clinical areas. However, their non-negligible bystander mutations and off-target effects have raised extensive safety concerns. To address these issues, a novel method is developed by inserting specific peptide fragments into the substrate binding pocket of deaminases in base editors to modify these outcomes. It is validated that the composition and position of the inserted peptide can significantly impact the performance of A3A-based cytosine base editor and TadA-8e-based adenine base editor, leading to improved editing activity and precision in human HEK293T cells. Importantly, the TadA-8e variant with DPLVLRRRQ peptide inserted behind S116 residue showed a strong motif preference of Y4A5N6, which can accurately edit the A5 base in targeted protospacer with minimized bystander and off-target effects in DNA and RNA-level. By summarizing the regularity during engineering, a set of systematic procedures is established, which can potentially be used to modify other types of base editors and make them more accurate and secure. In addition, the peptide insertion strategy is also proven to be compatible with traditional amino acid changes which have been reported, exhibiting excellent compatibility.
期刊介绍:
Small serves as an exceptional platform for both experimental and theoretical studies in fundamental and applied interdisciplinary research at the nano- and microscale. The journal offers a compelling mix of peer-reviewed Research Articles, Reviews, Perspectives, and Comments.
With a remarkable 2022 Journal Impact Factor of 13.3 (Journal Citation Reports from Clarivate Analytics, 2023), Small remains among the top multidisciplinary journals, covering a wide range of topics at the interface of materials science, chemistry, physics, engineering, medicine, and biology.
Small's readership includes biochemists, biologists, biomedical scientists, chemists, engineers, information technologists, materials scientists, physicists, and theoreticians alike.