Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom.
Dipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca' Foscari Venezia , I-30123 Venezia, Italy.
ACS Nano. 2016 Apr 26;10(4):4236-47. doi: 10.1021/acsnano.5b07664. Epub 2016 Mar 30.
We use oxDNA, a coarse-grained model of DNA at the nucleotide level, to simulate large nanoprisms that are composed of multi-arm star tiles, in which the size of bulge loops that have been incorporated into the tile design is used to control the flexibility of the tiles. The oxDNA model predicts equilibrium structures for several different nanoprism designs that are in excellent agreement with the experimental structures as measured by cryoTEM. In particular we reproduce the chiral twisting of the top and bottom faces of the nanoprisms, as the bulge sizes in these structures are varied due to the greater flexibility of larger bulges. We are also able to follow how the properties of the star tiles evolve as the prisms are assembled. Individual star tiles are very flexible, but their structures become increasingly well-defined and rigid as they are incorporated into larger assemblies. oxDNA also finds that the experimentally observed prisms are more stable than their inverted counterparts, but interestingly this preference for the arms of the tiles to bend in a given direction only emerges after they are part of larger assemblies. These results show the potential for oxDNA to provide detailed structural insight as well as to predict the properties of DNA nanostructures and hence to aid rational design in DNA nanotechnology.
我们使用 oxDNA，一种基于核苷酸水平的 DNA 粗粒模型，来模拟由多臂星形瓷砖组成的大型纳米棱柱体，其中嵌入瓷砖设计的凸起环的大小用于控制瓷砖的柔韧性。oxDNA 模型预测了几种不同的纳米棱镜设计的平衡结构，这些结构与 cryoTEM 测量的实验结构非常吻合。特别是，我们重现了纳米棱柱体顶部和底部的手性扭曲，因为这些结构中的凸起大小由于较大凸起的更大灵活性而发生变化。我们还能够随着棱柱体的组装，跟踪星形瓷砖的性质如何演变。单个星形瓷砖非常灵活，但随着它们被纳入更大的组装体，它们的结构变得越来越明确和刚性。oxDNA 还发现，实验观察到的棱柱体比它们的倒置对应物更稳定，但有趣的是，这种对瓷砖臂在给定方向弯曲的偏好只有在它们成为更大组装体的一部分后才会出现。这些结果表明 oxDNA 有可能提供详细的结构洞察力，以及预测 DNA 纳米结构的性质，从而有助于 DNA 纳米技术的合理设计。
