Intelligent Software & Systems, Raytheon BBN Technologies, 10 Moulton Street, Cambridge, Massachusetts 02138, United States.
iGEM Foundation, 45 Prospect Street, Cambridge, Massachusetts 02139, United States.
ACS Synth Biol. 2023 Dec 15;12(12):3646-3655. doi: 10.1021/acssynbio.3c00418. Epub 2023 Nov 13.
The design and construction of genetic systems, in silico, in vitro, or in vivo, often involve the handling of various pieces of DNA that exist in different forms across an assembly process: as a standalone "part" sequence, as an insert into a carrier vector, as a digested fragment, etc. Communication about these different forms of a part and their relationships is often confusing, however, because of a lack of standardized terms. Here, we present a systematic terminology and an associated set of practices for representing genetic parts at various stages of design, synthesis, and assembly. These practices are intended to represent any of the wide array of approaches based on embedding parts in carrier vectors, such as BioBricks or Type IIS methods (e.g., GoldenGate, MoClo, GoldenBraid, and PhytoBricks), and have been successfully used as a basis for cross-institutional coordination and software tooling in the iGEM Engineering Committee.
遗传系统的设计和构建，无论是在计算机模拟、体外实验还是体内实验中，通常都涉及到处理各种不同形式的 DNA 片段，这些片段在组装过程中可能以独立的“部件”序列、插入载体、消化片段等形式存在。然而，由于缺乏标准化术语，这些部件的不同形式及其关系的交流往往会令人困惑。在这里，我们提出了一种系统的术语和相关的实践，用于表示设计、合成和组装各个阶段的遗传部件。这些实践旨在表示基于将部件嵌入载体的各种方法，例如 BioBricks 或 Type IIS 方法（例如 GoldenGate、MoClo、GoldenBraid 和 PhytoBricks），并且已经成功地用作 iGEM 工程委员会中跨机构协调和软件工具的基础。
