A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures
A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures
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DOI：
10.1098/rsif.2019.0866
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发表时间：
2020-06-24
影响因子：
3.9
通讯作者：
Winfree, Erik
中科院分区：
文献类型：
--
作者：
Badelt, Stefan;Grun, Casey;Winfree, Erik
信息技术使程序员和工程师能够设计和综合令人震惊的复杂性系统，尽管如此，这些系统仍以预期的方式行事。正式抽象的层次结构从高级编程语言到低级实现规范，使这种复杂性的掌握成为可能。 DNA纳米技术向我们提供了一种新的分子信息技术，其潜力尚未以这种方式完全解锁。开发有效的抽象层次结构对于增加可编程DNA系统的复杂性至关重要。在这里，我们以先验的实践为基础，为DNA链位移系统的“域级”表示形式提供了新的形式化，该系统与核酸生物物理具有自然连接，同时仍适合正式分析。单分子和双分子反应的枚举为可编程分子相互作用提供了一种语义，并通过近似生物物理模型给出动力学。反应凝结提供了尊重总体动力学特性的详细反应的可探讨简化。该模型的适用性和准确性将在广泛的工程DNA链位移系统上进行评估。因此，我们的工作可以用作在核苷酸序列水平运行的低级DNA模型与在抽象物种之间相互作用水平下运行的高级化学反应网络模型之间的界面。
Information technologies enable programmers and engineers to design and synthesize systems of startling complexity that nonetheless behave as intended. This mastery of complexity is made possible by a hierarchy of formal abstractions that span from high-level programming languages down to low-level implementation specifications, with rigorous connections between the levels. DNA nanotechnology presents us with a new molecular information technology whose potential has not yet been fully unlocked in this way. Developing an effective hierarchy of abstractions may be critical for increasing the complexity of programmable DNA systems. Here, we build on prior practice to provide a new formalization of 'domain-level' representations of DNA strand displacement systems that has a natural connection to nucleic acid biophysics while still being suitable for formal analysis. Enumeration of unimolecular and bimolecular reactions provides a semantics for programmable molecular interactions, with kinetics given by an approximate biophysical model. Reaction condensation provides a tractable simplification of the detailed reactions that respects overall kinetic properties. The applicability and accuracy of the model is evaluated across a wide range of engineered DNA strand displacement systems. Thus, our work can serve as an interface between lower-level DNA models that operate at the nucleotide sequence level, and high-level chemical reaction network models that operate at the level of interactions between abstract species.