GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology
GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology
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DOI：
10.1104/pp.113.217661
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发表时间：
2013-07-01
期刊：
影响因子：
7.4
通讯作者：
Orzaez, Diego
中科院分区：
文献类型：
--
作者：
Sarrion-Perdigones, Alejandro;Vazquez-Vilar, Marta;Orzaez, Diego
植物合成生物学旨在将工程原理应用于植物遗传设计。植物合成生物学的一个战略要求是采用通用的标准化技术，促进在DNA水平上构建日益复杂的多基因结构，同时使植物生物工程师之间能够交换遗传构建模块。在这里，我们描述了GoldenBraid 2.0（GB2.0），这是一个全面的技术框架，旨在促进植物合成生物学标准DNA部分的交换。GB2.0依赖于使用IIS型限制性内切酶进行DNA组装，并提出了一种类似于自然语言语法的位置符号的模块化克隆模式。除了提供优化的克隆策略，为多基因工程生成完全可交换的遗传元件外，GB2.0工具包还提供了不断增长的DNA部分开放集合，包括一组经过功能测试的预制遗传模块，以构建常用的模块，如组成型和诱导型表达盒，内源性基因沉默和蛋白质-蛋白质相互作用工具，GB2.0框架的使用由许多网络资源促进，所述网络资源包括公开可用的数据库、教程和软件包，所述软件包提供用于GB2.0部分驯化和多基因工程的计算机模拟和实验室方案。简而言之，GB2.0提供了一个在生物工程师之间交换信息和物理DNA元素的框架，以帮助实施植物合成生物学项目。
Plant synthetic biology aims to apply engineering principles to plant genetic design. One strategic requirement of plant synthetic biology is the adoption of common standardized technologies that facilitate the construction of increasingly complex multigene structures at the DNA level while enabling the exchange of genetic building blocks among plant bioengineers. Here, we describe GoldenBraid 2.0 (GB2.0), a comprehensive technological framework that aims to foster the exchange of standard DNA parts for plant synthetic biology. GB2.0 relies on the use of type IIS restriction enzymes for DNA assembly and proposes a modular cloning schema with positional notation that resembles the grammar of natural languages. Apart from providing an optimized cloning strategy that generates fully exchangeable genetic elements for multigene engineering, the GB2.0 toolkit offers an ever-growing open collection of DNA parts, including a group of functionally tested, premade genetic modules to build frequently used modules like constitutive and inducible expression cassettes, endogenous gene silencing and protein-protein interaction tools, etc. Use of the GB2.0 framework is facilitated by a number of Web resources that include a publicly available database, tutorials, and a software package that provides in silico simulations and laboratory protocols for GB2.0 part domestication and multigene engineering. In short, GB2.0 provides a framework to exchange both information and physical DNA elements among bioengineers to help implement plant synthetic biology projects.