Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model.
Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model.
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DOI：
10.1021/acsnano.5b07664
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发表时间：
2016-03
期刊：
影响因子：
17.1
通讯作者：
J. Schreck;F. Romano;M. Zimmer;A. Louis;J. Doye
中科院分区：
文献类型：
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作者：
J. Schreck;F. Romano;M. Zimmer;A. Louis;J. Doye
我们使用oxDNA，一种核苷酸水平的DNA粗粒度模型，来模拟由多臂星形瓷砖组成的大纳米裂缝，其中已被纳入瓷砖设计的凸起环的大小被用来控制瓷砖的灵活性。OxDNA模型预测了几种不同纳米设计的平衡结构，这些结构与CryoTEM测量的实验结构非常吻合。特别是，我们复制了纳米棱镜顶面和底面的手性扭曲，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不同。随着棱镜的组装，我们也能够观察到星形瓷砖的性质是如何演变的。单个星形瓷砖非常灵活，但随着它们被合并到更大的组件中，它们的结构变得越来越明确和僵硬。OxDNA还发现，实验中观察到的棱镜比倒置的棱镜更稳定，但有趣的是，这种让瓷砖的手臂向给定方向弯曲的偏好只有在它们是更大的组装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。
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.