Evans Foundation for Molecular Medicine and California Institute of Technology, Physics, Pasadena, CA, USA.
Chem Soc Rev. 2017 Jun 19;46(12):3808-3829. doi: 10.1039/c6cs00745g.
DNA tiles provide a promising technique for assembling structures with nanoscale resolution through self-assembly by basic interactions rather than top-down assembly of individual structures. Tile systems can be programmed to grow based on logical rules, allowing for a small number of tile types to assemble large, complex assemblies that can retain nanoscale resolution. Such algorithmic systems can even assemble different structures using the same tiles, based on inputs that seed the growth. While programming and theoretical analysis of tile self-assembly often makes use of abstract logical models of growth, experimentally implemented systems are governed by nanoscale physical processes that can lead to very different behavior, more accurately modeled by taking into account the thermodynamics and kinetics of tile attachment and detachment in solution. This review discusses the relationships between more abstract and more physically realistic tile assembly models. A central concern is how consideration of model differences enables the design of tile systems that robustly exhibit the desired abstract behavior in realistic physical models and in experimental implementations. Conversely, we identify situations where self-assembly in abstract models can not be well-approximated by physically realistic models, putting constraints on physical relevance of the abstract models. To facilitate the discussion, we introduce a unified model of tile self-assembly that clarifies the relationships between several well-studied models in the literature. Throughout, we highlight open questions regarding the physical principles for DNA tile self-assembly.
DNA 瓦片通过基本相互作用的自组装提供了一种很有前途的技术，用于以纳米级分辨率组装结构，而不是通过自上而下的单个结构组装。瓦片系统可以根据逻辑规则进行编程以进行生长，允许使用少量的瓦片类型来组装大型复杂的组件，这些组件可以保留纳米级分辨率。这样的算法系统甚至可以基于种子生长的输入，使用相同的瓦片来组装不同的结构。虽然瓦片自组装的编程和理论分析通常利用生长的抽象逻辑模型，但实验实现的系统受纳米级物理过程的控制，这些物理过程可能导致非常不同的行为，通过考虑在溶液中瓦片附着和脱离的热力学和动力学，可以更准确地对其进行建模。这篇综述讨论了更抽象和更物理现实的瓦片组装模型之间的关系。一个核心关注点是如何考虑模型差异，以便在现实物理模型和实验实现中设计出能够稳健地表现出所需抽象行为的瓦片系统。相反，我们确定了在抽象模型中自组装不能很好地被物理现实模型所逼近的情况，从而对抽象模型的物理相关性施加了限制。为了便于讨论，我们引入了瓦片自组装的统一模型，该模型阐明了文献中几个经过充分研究的模型之间的关系。在整个讨论中，我们强调了有关 DNA 瓦片自组装物理原理的开放性问题。
