Free energy landscape of salt-actuated reconfigurable DNA nanodevices
Free energy landscape of salt-actuated reconfigurable DNA nanodevices
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DOI：
10.1093/nar/gkz1137
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发表时间：
2019-12
影响因子：
14.9
通讯作者：
Ze Shi;G. Arya
中科院分区：
文献类型：
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作者：
Ze Shi;G. Arya
摘要实现DNA结构的快速、非侵入性致动对于扩展DNA纳米技术的功能至关重要。一种有前景的驱动方法涉及将多对短单链DNA突出端引入结构的组分，并通过溶液离子条件的变化触发突出端的杂交或解离以驱动结构转变。在这里，我们揭示了这种新方法的基础，通过分子模拟计算的自由能景观的DNA折纸铰链之间的开放和关闭状态。我们的研究结果揭示了悬突如何共同引入一个尖锐的自由能最小值在封闭状态和开放和封闭状态之间的广泛的能量障碍，以及如何在离子条件的变化调制这些功能的景观驱动驱动朝向开放或封闭状态。我们证明了铰链限制在稳定的杂交状态的突出和放大的能量势垒解离发挥的关键作用。通过分析突出端的分布及其长度和序列如何调节能量景观，我们获得了用于调整驱动行为的设计规则。在这里获得的分子的见解应该适用于广泛的系统，涉及DNA杂交在封闭的系统。
Abstract Achieving rapid, noninvasive actuation of DNA structures is critical to expanding the functionality of DNA nanotechnology. A promising actuation approach involves introducing multiple, short pairs of single-stranded DNA overhangs to components of the structure and triggering hybridization or dissociation of the overhangs via changes in solution ionic conditions to drive structural transitions. Here, we reveal the underlying basis of this new approach by computing via molecular simulations the free energy landscape of DNA origami hinges actuated between open and closed states. Our results reveal how the overhangs collectively introduce a sharp free-energy minimum at the closed state and a broad energy barrier between open and closed states and how changes in ionic conditions modulate these features of the landscape to drive actuation towards the open or closed state. We demonstrate the critical role played by hinge confinement in stabilizing the hybridized state of the overhangs and magnifying the energy barrier to dissociation. By analyzing how the distribution of overhangs and their length and sequence modulate the energy landscape, we obtain design rules for tuning the actuation behavior. The molecular insights obtained here should be applicable to a broad range of systems involving DNA hybridization within confined systems.