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protoSpaceJAM:一个开源的,可定制的和网页可访问的CRISPR/Cas插入敲进的设计平台

Duo Peng¹, Madhuri Vangipuram¹, Joan Wong¹

¹Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.

Nucleic acids research

|June 26, 2024

概括

本研究介绍了protoSpaceJAM,这是一种开源算法,可以优化CRISPR/Cas敲门实验的引导RNA和同质导向修复捐赠体设计,提高基因工程应用的效率和简化工作流程.

科学领域:

分子生物学分子生物学
生物信息学是一种生物信息学.
基因组工程是基因组工程.

背景情况:

克里斯普尔/卡斯技术允许精确的DNA插入,但在指导RNA (gRNA) 和同质导向修复 (HDR) 供体设计方面面临挑战.
优化gRNA选择和HDR捐赠体构造对于高效准确的CRISPR/Cas介导敲进来至关重要.

研究的目的:

开发一个自动化和优化的算法,protoSpaceJAM,用于设计CRISPR/Cas插入敲进的gRNA和HDR捐赠者.
通过改进设计策略,提高CRISPR/Cas敲门实验的效率和准确性.

主要方法:

开发了protoSpaceJAM,这是一个支持SpCas9,SpCas9-VQR和enAsCas12a酶的开源算法.
基于特异性,插入点的近距离和调节区域的定位来排列gRNA的生物规则.
嵌入了HDR捐赠体中的"记录"突变,以防止重新切割和通过实验验证的验证设计规则.

主要成果:

验证了protoSpaceJAM的设计规则,显示了重编码突变和最佳单链供体链选择的敲入效率提高.
通过优化 gRNA 选择和 HDR 供体设计,通过优化 gRNA 选择和 HDR 供体设计,证明了增强的敲门效率.
开发了一个额外的模块,用于设计基因型原型,用于编辑过的等位基因的深度测序.

结论:

protoSpaceJAM提供了一种精简,灵活和模块化解决方案,用于优化CRISPR/Cas的实验设计.
该算法通过提高基因组工程的效率和可靠性,有利于各种研究和治疗应用.
protoSpaceJAM可以作为一个开源的Web工具和Python包,促进可访问性和更广泛的采用.

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