arXiv 2110.014772021-10cond-mat.softcond-mat.stat-mechphysics.bio-phphysics.chem-ph

DNA纳米结构力学性能的研究

Probing the mechanical properties of DNA nanostructures with metadynamics

W. T. Kaufhold, W. Pfeifer, C. E. Castro, L. Di Michele

备注：: 4 figures, 7 SI figures, 3 SI tables, 2 SI discussions, methods

摘要：

分子动力学模拟经常被用于在DNA纳米结构的设计工作流程中提供反馈。然而，即使使用粗粒度模型，无偏模拟的分布收敛也很慢，限制了平衡结构特性的应用。鉴于对动态、可重构和可变形装置的兴趣日益增加，迫切需要能够有效量化大范围运动、构象转变和机械变形的方法。Metadaptics是一种自动偏置技术，通过平坦化自由能景观，可以快速获取分子构象分布。在这里，我们利用这种方法来采样DNA纳米结构的自由能景观，其无偏动力学是非遍历的，包括Holliday junctions和部分holliday折纸。以一个折纸柔性关节为例，我们进一步证明了元粘附学可以预测一个完整的DNA折纸装置对施加的力的机械响应，与实验结果吻合良好。我们的研究结果建立了一个有效的框架来研究DNA纳米器件中的自由能景观和力响应，这可以应用于迭代设计工作流程中的快速反馈，并通常促进模拟和实验的集成。元adaptics将是特别有用的，以指导纳米机器人，生物传感，或纳米制造应用的动态设备的设计。

英文摘要：

Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, convergence of distributions from unbiased simulation is slow, limiting applications to equilibrium structural properties. Given the increasing interest in dynamic, reconfigurable, and deformable devices, methods that enable efficient quantification of large ranges of motion, conformational transitions, and mechanical deformation are critically needed. Metadynamics is an automated biasing technique that enables the rapid acquisition of molecular conformational distributions by flattening free energy landscapes. Here we leveraged this approach to sample the free energy landscapes of DNA nanostructures whose unbiased dynamics are non-ergodic, including bistable Holliday junctions and part of a bistable origami. Taking an origami compliant joint as a case study, we further demonstrate that metadynamics can predict the mechanical response of a full DNA origami device to an applied force, showing good agreement with experiments. Our results establish an efficient framework to study free energy landscapes and force response in DNA nanodevices, which could be applied for rapid feedback in iterative design workflows and generally facilitate the integration of simulation and experiments. Metadynamics will be particularly useful to guide the design of dynamic devices for nanorobotics, biosensing, or nanomanufacturing applications.

机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。

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