Facilitating crRNA Design by Integrating DNA Interaction Features of CRISPR-Cas12a System
文献类型： 外文期刊
作者： Yao, Zhihao 1 ; Li, Wanglu 2 ; He, Kaiyu 2 ; Wang, Hongmei 2 ; Xu, Yan 1 ; Wu, Qun 1 ; Wang, Liu 2 ; Nie, Yao 1 ;
作者机构： 1.Jiangnan Univ, Sch Biotechnol, Key Lab Ind Biotechnol, State Key Lab Food Sci & Resources,Minist Educ, Wuxi 214122, Jiangsu, Peoples R China
2.Zhejiang Acad Agr Sci, Inst Agroprod Safety & Nutr, State Key Lab Managing Biot & Chem Threats Qual &, Hangzhou 310021, Peoples R China
3.Minist Agr & Rural Affairs, Key Lab Informat Traceabil Agr Prod, Hangzhou 310021, Peoples R China
关键词： activity prediction; CRISPR-Cas12a; deep learning; molecular dynamics simulation; trans-cleavage
期刊名称：ADVANCED SCIENCE （ 影响因子：14.1； 五年影响因子：15.6 ）
ISSN：
年卷期： 2025 年
页码：
收录情况： SCI
摘要： The CRISPR-Cas12a system has gained significant attention as a rapid nucleic acid diagnostic tool due to its crRNA-guided trans-cleavage activity. Accurately predicting the activity of different targets is significant to facilitate the crRNA availability but remains challenging. In this study, a novel approach is presented that combines molecular dynamics simulations and neural network modeling to predict the trans-cleavage activity. Unlike conventional tools that rely solely on the base sequences, our method integrated sequence features and molecular interaction features of DNA in the CRISPR-Cas12a system, significantly improving prediction accuracy. Through feature importance analysis, key sequence features that influence Cas12a trans-cleavage activity are identified. Additionally, a crRNA-DNA library with over 23 456 feature sequences from representative viruses and bacteria is established, and validated the high predictive accuracy of the model (Pearson's r = 0.9328) by screening crRNAs from reference targets. This study offers new insights into the molecular interactions of Cas12a/crRNA-DNA and provides a reliable framework for optimizing crRNA design, facilitating the application of the CRISPR-Cas12a in rapid nucleic acid diagnostics.
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