A p-calculus Model of Supercoiling DNA Circuits
A p-calculus Model of Supercoiling DNA Circuits
复制标题
超螺旋 DNA 电路的 p 微积分模型
DOI：
10.1162/isal_a_00582
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Rainford P
中科院分区：
文献类型：
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作者：
Rainford P
合成生物学是人工生命的一个方面，它设计新的生物成分，如DNA，RNA，膜，以产生新的行为。在这里，我们感兴趣的是DNA“电路”：DNA工程具有特定的计算属性。在基因转录过程中，DNA双螺旋发生超螺旋变化，从而影响附近基因的转录。相对于物理，DNA电路的数学建模有限，并且不考虑超螺旋。在许多目前的合成回路中，必须小心地去除超螺旋，特别是在体内系统中，以防止未建模的副作用。然而，超螺旋是影响基因表达的DNA固有特性，如果包括在模型中，可以利用。在这里，我们提出了一个新的π演算形式主义建模DNA电路与超螺旋，并证明其使用一个简单的遗传电路。通常与π演算相关联的状态转移图在状态数变大时是不可访问的。我们提出了一个新的圆形可视化的π演算电路组件，更直观，可读的生物学家熟悉的圆形可视化的质粒。
Synthetic biology is one facet of Artificial Life which designs novel biological components, eg DNA, RNA, membranes, to produce new behaviours. Here, we are interested in DNA “circuits”: DNA engineered to have particular computational properties. During gene transcription, the DNA double-helix undergoes supercoiling changes, which affects transcription of nearby genes. There is limited mathematical, as opposed to physical, modelling of DNA circuits, and supercoiling is not considered. In many current synthetic circuits, supercoiling has to be carefully removed, particularly in in vivo systems, to prevent unmodelled side effects. However, supercoiling is an intrinsic property of DNA that impacts gene expression, and could be exploited if included in models. Here, we present a new π-calculus formalism for modelling DNA circuits with supercoiling, and demonstrate its use on a simple genetic circuit. The state transition diagrams normally associated with π-calculus are not accessible when the number of states becomes large. We present a new circular visualisation of the π-calculus circuit components that is more intuitive and readable for biologists familiar with the circular visualisations of plasmids.