遗传逻辑电路定时分析的仿真方法

Simulation Approach for Timing Analysis of Genetic Logic Circuits.

作者信息

Baig Hasan, Madsen Jan

机构信息

Department of Applied Mathematics and Computer Science, Technical University of Denmark , 2800 Kongens Lyngby, Denmark.

出版信息

ACS Synth Biol. 2017 Jul 21;6(7):1169-1179. doi: 10.1021/acssynbio.6b00296. Epub 2017 Feb 1.

Abstract

Constructing genetic logic circuits is an application of synthetic biology in which parts of the DNA of a living cell are engineered to perform a dedicated Boolean function triggered by an appropriate concentration of certain proteins or by different genetic components. These logic circuits work in a manner similar to electronic logic circuits, but they are much more stochastic and hence much harder to characterize. In this article, we introduce an approach to analyze the threshold value and timing of genetic logic circuits. We show how this approach can be used to analyze the timing behavior of single and cascaded genetic logic circuits. We further analyze the timing sensitivity of circuits by varying the degradation rates and concentrations. Our approach can be used not only to characterize the timing behavior but also to analyze the timing constraints of cascaded genetic logic circuits, a capability that we believe will be important for design automation in synthetic biology.

摘要

构建基因逻辑电路是合成生物学的一项应用,其中活细胞的部分DNA经过改造,以执行由特定蛋白质的适当浓度或不同遗传成分触发的专用布尔函数。这些逻辑电路的工作方式类似于电子逻辑电路,但它们具有更大的随机性,因此更难进行特性描述。在本文中,我们介绍一种分析基因逻辑电路阈值和定时的方法。我们展示了如何使用这种方法来分析单个和级联基因逻辑电路的定时行为。我们通过改变降解速率和浓度进一步分析电路的定时敏感性。我们的方法不仅可用于描述定时行为,还可用于分析级联基因逻辑电路的定时约束,我们认为这一能力对于合成生物学中的设计自动化将非常重要。

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