Edinburgh Genome Foundry, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
Methods Mol Biol. 2025;2850:61-77. doi: 10.1007/978-1-0716-4220-7_4.
Golden Gate cloning enables the modular assembly of DNA parts into desired synthetic genetic constructs. The "one-pot" nature of Golden Gate reactions makes them particularly amenable to high-throughput automation, facilitating the generation of thousands of constructs in a massively parallel manner. One potential bottleneck in this process is the design of these constructs. There are multiple parameters that must be considered during the design of an assembly process, and the final design should also be checked and verified before implementation. Doing this by hand for large numbers of constructs is neither practical nor feasible and increases the likelihood of introducing potentially costly errors. In this chapter we describe a design workflow that utilizes bespoke computational tools to automate the key phases of the construct design process and perform sequence editing in batches.
金标准克隆使 DNA 片段的模块化组装成所需的合成遗传构建体成为可能。金标准反应的“一锅法”性质使它们特别适合高通量自动化，以大规模并行的方式生成数千个构建体。在这个过程中，一个潜在的瓶颈是这些构建体的设计。在组装过程的设计中，必须考虑多个参数，并且在实施之前，最终设计也应该进行检查和验证。对于大量的构建体，手动完成这一点既不实际也不可行，并且增加了引入潜在昂贵错误的可能性。在本章中，我们描述了一个设计工作流程，该流程利用定制的计算工具来自动化构建体设计过程的关键阶段，并批量执行序列编辑。
