Automated analysis of tethered DNA nanostructures using constraint solving
Automated analysis of tethered DNA nanostructures using constraint solving
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DOI：
10.1007/s11047-018-9693-y
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发表时间：
2018-12-01
影响因子：
2.1
通讯作者：
Phillips, Andrew
中科院分区：
文献类型：
--
作者：
Lakin, Matthew R.;Phillips, Andrew
使用链接到表面的组件实施DNA计算电路，而使用在散装解决方案中自由扩散的组件具有多个优点。但是，束缚电路的自动计算建模比解决方案回路更具挑战性，因为在确定两个束缚物种是否可以相互作用时，必须考虑分子几何形状。在这里，我们使用简单的生物物理模型将束缚的分子电路转换为构造组件可能物理构型的约束问题来解决此问题。我们使用满意度模量理论求解器来确定与给定结构相关的约束问题是否令人满意，这对应于该结构是否可以在物理上实现，鉴于链球几何形状所施加的约束。我们将此技术应用于文献的示例结构，并讨论如何将这种方法与反应枚举器集成以实现束缚分子计算系统的完全自动化分析。本文是会议出版物的大量修订和扩展版本：Lakin和Phillips（在Brijder and Qian（Eds）第23届国际DNA计算和分子编程会议上，计算机科学讲义，第10467卷，第1-1-1页。 16，2017）。
Implementing DNA computing circuits using components tethered to a surface offers several advantages over using components that freely diffuse in bulk solution. However, automated computational modeling of tethered circuits is far more challenging than for solution-phase circuits, because molecular geometry must be taken into account when deciding whether two tethered species may interact. Here, we tackle this issue by translating a tethered molecular circuit into a constraint problem that encodes the possible physical configurations of the components, using a simple biophysical model. We use a satisfaction modulo theories solver to determine whether the constraint problem associated with a given structure is satisfiable, which corresponds to whether that structure is physically realizable given the constraints imposed by the tether geometry. We apply this technique to example structures from the literature, and discuss how this approach could be integrated with a reaction enumerator to enable fully automated analysis of tethered molecular computing systems. This paper is a significantly revised and extended version of a conference publication: Lakin and Phillips (in Brijder and Qian (eds) Proceedings of the 23rd International Conference on DNA Computing and Molecular Programming. Lecture Notes in Computer Science, vol 10467, pp 1-16, 2017).