basicsynbio and the BASIC SEVA collection: Software and vectors for an established DNA assembly method
basicsynbio and the BASIC SEVA collection: Software and vectors for an established DNA assembly method
复制标题
basicsynbio 和 BASIC SEVA 系列：用于已建立的 DNA 组装方法的软件和载体
DOI：
10.1101/2022.01.06.446575
复制
发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Haines M
中科院分区：
文献类型：
--
作者：
Haines M
利用模块化组件的标准化脱氧核糖核酸（DNA）组装方法提供了一个强大的框架，通过设计-构建-测试-学习循环来探索设计和优化。DNA组装使用模块化部件和接头，高度准确，易于自动化，可免费用于学术和商业用途，并通过幂等格式实现分层组装。这些功能使包括通路工程、核糖体结合位点（RBS）调整、融合蛋白工程和多重引导核糖核酸（RNA）表达的应用成为可能。在这项工作中，我们提出了basicsynbio，开源软件，包括一个Web应用程序（https：//basicsynbio.web.app/）和Python包（https：//github.com/LondonBiofoundry/basicsynbio），通过简单的拖放操作或编程实现BASIC结构设计。使用basicsynbio，用户可以在设计新部件和组件时访问常用的BASIC部件和链接器，并对常见错误进行异常处理。用户可以导出序列数据并为手动或声学液体处理平台创建说明。指令生成依赖于BasicBuild开放标准，该标准针对定制的工作流进行解析，并且可以在JavaScript Object Notation中序列化以进行传输和存储。我们展示了basicsynbio，组装30个载体使用的序列，包括模块的标准欧洲载体架构（SEVA）。BASIC SEVA矢量集合与使用BsaI的BASIC和Golden Gate兼容。载体含有六种抗生素抗性标记之一和来自不同相容性组的五个复制起点。该集合可通过Addgene根据OpenMTA协议提供。此外，在basicsynbio应用程序编程接口中还可以使用载体序列以及其他部件和连接器集合，为生物工程应用程序设计组件提供了强大的环境。图形摘要
Standardized deoxyribonucleic acid (DNA) assembly methods utilizing modular components provide a powerful framework to explore designs and iterate through Design–Build–Test–Learn cycles. Biopart Assembly Standard for Idempotent Cloning (BASIC) DNA assembly uses modular parts and linkers, is highly accurate, easy to automate, free for academic and commercial use and enables hierarchical assemblies through an idempotent format. These features enable applications including pathway engineering, ribosome binding site (RBS) tuning, fusion protein engineering and multiplexed guide ribonucleic acid (RNA) expression. In this work, we present basicsynbio, open-source software encompassing a Web App (https://basicsynbio.web.app/) and Python Package (https://github.com/LondonBiofoundry/basicsynbio), enabling BASIC construct design via simple drag-and-drop operations or programmatically. With basicsynbio, users can access commonly used BASIC parts and linkers while designing new parts and assemblies with exception handling for common errors. Users can export sequence data and create instructions for manual or acoustic liquid-handling platforms. Instruction generation relies on the BasicBuild Open Standard, which is parsed for bespoke workflows and is serializable in JavaScript Object Notation for transfer and storage. We demonstrate basicsynbio, assembling 30 vectors using sequences including modules from the Standard European Vector Architecture (SEVA). The BASIC SEVA vector collection is compatible with BASIC and Golden Gate using BsaI. Vectors contain one of six antibiotic resistance markers and five origins of replication from different compatibility groups. The collection is available via Addgene under an OpenMTA agreement. Furthermore, vector sequences are available from within the basicsynbio application programming interface with other collections of parts and linkers, providing a powerful environment for designing assemblies for bioengineering applications.Graphical Abstract