机械双稳态的DNA折纸的自由能景观
The free-energy landscape of a mechanically bistable DNA origami
摘要：
使用粗粒度模型的分子模拟允许DNA折纸的结构，动力学和力学得到全面表征。在这里，我们专注于自由能景观的联合DNA折纸，已被设计为表现出两个机械稳定的状态和双稳态景观已推断出从合奏的结构可视化电子显微镜。令人惊讶的是，使用oxDNA模型的模拟预测，无缺陷的折纸具有单一的自由能最小值。预期的第二状态是不稳定的，因为铰链接头不简单地允许自由角运动，而是在接近与第二状态相关的接头角度时导致增加的自由能量损失。这就提出了一些有趣的问题，即模拟和实验之间存在差异的原因，例如组装缺陷如何影响实验观察到的结构系综。
英文摘要：
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.
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