Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland.
J Biol Eng. 2014 Feb 2;8(1):6. doi: 10.1186/1754-1611-8-6.
In our previous computational work, we showed that gene digital circuits can be automatically designed in an electronic fashion. This demands, first, a conversion of the truth table into Boolean formulas with the Karnaugh map method and, then, the translation of the Boolean formulas into circuit schemes organized into layers of Boolean gates and Pools of signal carriers. In our framework, gene digital circuits that take up to three different input signals (chemicals) arise from the composition of three kinds of basic Boolean gates, namely YES, NOT, and AND. Here we present a library of YES, NOT, and AND gates realized via plasmidic DNA integration into the yeast genome. Boolean behavior is reproduced via the transcriptional control of a synthetic bipartite promoter that contains sequences of the yeast VPH1 and minimal CYC1 promoters together with operator binding sites for bacterial (i.e. orthogonal) repressor proteins. Moreover, model-driven considerations permitted us to pinpoint a strategy for re-designing gates when a better digital performance is required. Our library of well-characterized Boolean gates is the basis for the assembly of more complex gene digital circuits. As a proof of concepts, we engineered two 2-input OR gates, designed by our software, by combining YES and NOT gates present in our library.
在我们之前的计算工作中，我们展示了基因数字电路可以以电子方式自动设计。这首先需要将真值表转换为具有 Karnaugh 图方法的布尔公式，然后将布尔公式转换为组织成布尔门层和信号载体池的电路方案。在我们的框架中，最多可以从三种基本布尔门，即 YES、NOT 和 AND 组合中生成三个不同输入信号（化学物质）的基因数字电路。在这里，我们提出了一个通过质粒 DNA整合到酵母基因组中来实现 YES、NOT 和 AND 门的库。通过包含酵母 VPH1 和最小 CYC1 启动子序列以及细菌（即正交）抑制剂蛋白的结合位点的合成二部分启动子的转录控制来再现布尔行为。此外，模型驱动的考虑使我们能够确定当需要更好的数字性能时重新设计门的策略。我们的功能齐全的布尔门库是组装更复杂基因数字电路的基础。作为概念验证，我们通过组合我们库中存在的 YES 和 NOT 门，设计了两个 2 输入 OR 门。
