Department of Chemistry, Indian Institute of Technology Roorkee , Roorkee, 247667, India.
Department of Chemical Engineering, Columbia University , New York, New York 10027, United States.
ACS Nano. 2017 Dec 26;11(12):12426-12435. doi: 10.1021/acsnano.7b06470. Epub 2017 Nov 3.
As detailed structural characterizations of large complex DNA nanostructures are hard to obtain experimentally, particularly if they have substantial flexibility, coarse-grained modeling can potentially provide an important complementary role. Such modeling can provide a detailed view of both the average structure and the structural fluctuations, as well as providing insight into how the nanostructure's design determines its structural properties. Here, we present a case study of jointed DNA nanostructures using the oxDNA model. In particular, we consider archetypal hinge and sliding joints, as well as more complex structures involving a number of such coupled joints. Our results highlight how the nature of the motion in these structures can sensitively depend on the precise details of the joints. Furthermore, the generally good agreement with experiments illustrates the power of this approach and suggests the use of such modeling to prescreen the properties of putative designs.
由于大型复杂 DNA 纳米结构的详细结构特征很难通过实验获得，特别是如果它们具有很大的柔韧性，粗粒度建模可能会提供一个重要的补充作用。这种建模可以提供平均结构和结构波动的详细视图，并深入了解纳米结构的设计如何决定其结构特性。在这里，我们使用 oxDNA 模型对连接 DNA 纳米结构进行了案例研究。特别是，我们考虑了典型的铰链和滑动接头，以及涉及多个这种耦合接头的更复杂结构。我们的结果强调了这些结构中运动的性质如何敏感地取决于接头的精确细节。此外，与实验的一般良好一致性说明了这种方法的强大功能，并建议使用这种建模来预先筛选假定设计的特性。
