Nanostars planarity modulates the elasticity of DNA hydrogels
Nanostars planarity modulates the elasticity of DNA hydrogels
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Nanostars 平面度调节 DNA 水凝胶的弹性
DOI：
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Y. G. Fosado
中科院分区：
文献类型：
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作者：
Y. G. Fosado
与网络和框架的经典刚性问题类似，由DNA纳米星（DNAn）制成的水凝胶的弹性特性预计将强烈依赖于其构建块的精确几何形状。然而，目前不可能通过实验确定DNAn的形状。计算粗粒度模型可以保留DNA纳米星的正确几何形状，并解释最近实验中观察到的整体性质，这可能会提供缺失的见解。在这项研究中，我们进行metadaptics模拟，以获得与oxDNA模型模拟的三臂DNA nanostars的首选配置。基于这些结果，我们引入了一个粗粒度的计算模型的纳米星，可以自组装成复杂的三维纳米网络。我们比较了两种不同设计的系统，其中使用平面或非平面纳米星。结构和网络分析揭示了两种情况下完全不同的功能，导致两个对比的弹性性能。在非平面的情况下，分子的流动性较大，这与平衡时从Green-Kubo模拟测量的较低粘度一致。据我们所知，这是第一次将DNAn的几何形状与DNA水凝胶的整体流变学性质联系起来，并可能为未来基于DNA的材料的设计提供信息。
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently not possible to determine DNAns shape experimentally. Computational coarse-grained models that can retain the correct geometry of DNA nanostars and account for the bulk properties observed in recent experiments could provide missing insights. In this study, we perform metadynamics simulations to obtain the preferred configuration of three-armed DNA nanostars simulated with the oxDNA model. Based on these results we introduce a coarse-grained computational model of nanostars that can self assemble into complex three dimensional percolating networks. We compare two systems with different designs, in which either planar or non-planar nanostars are used. Structural and network analysis reveal completely different features for the two cases, leading to two contrasting elastic properties. The mobility of molecules is larger in the non-planar case, which is consistent with a lower viscosity measured from Green-Kubo simulations in equilibrium. To the best of our knowledge, this is the first work connecting the geometry of DNAns with the bulk rheological properties of DNA hydrogels and may inform the design of future DNA based materials.