论文标题
机械双向DNA折纸的自由能景观
The free-energy landscape of a mechanically bistable DNA origami
论文作者
论文摘要
使用粗粒模型的分子模拟允许全面表征DNA折纸的结构，动力学和力学。在这里，我们专注于旨在展示两个机械稳定的状态的连接DNA折纸的自由能景观，并从通过电子显微镜可视化的结构的集合中推断出了双态景观。出乎意料的是，使用OxDNA模型的模拟预测，无缺陷折纸的最小自由能最小。预期的第二个状态不稳定，因为铰链接头不仅允许自由角运动，而且会导致随着与第二个状态相关的关节角度的增加而导致自由能的惩罚。这就提出了有关模拟和实验之间这种差异的原因的有趣问题，例如，组装缺陷如何影响实验观察到的结构集合。
Molecular simulations using coarse-grained models allow the structure, dynamics and mechanics of DNA origamis to be comprehensively characterized. Here, we focus on the free-energy landscape of a jointed DNA origami that has been designed to exhibit two mechanically stable states and for which a bistable landscape has been inferred from ensembles of structures visualized by electron microscopy. Surprisingly, simulations using the oxDNA model predict that the defect-free origami has a single free-energy minimum. The expected second state is not stable because the hinge joints do not simply allow free angular motion but instead lead to increasing free-energetic penalties as the joint angles relevant to the second state are approached. This raises interesting questions about the cause of this difference between simulations and experiment, such as how assembly defects might affect the ensemble of structures observed experimentally.
