Single molecule analysis of structural fluctuations in DNA nanostructures
Single molecule analysis of structural fluctuations in DNA nanostructures
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DOI：
10.1039/c9nr03826d
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发表时间：
2019-10-21
期刊：
影响因子：
6.7
通讯作者：
Birkedal, Victoria
中科院分区：
文献类型：
--
作者：
Jepsen, Mette D. E.;Sorensen, Rasmus Scholer;Birkedal, Victoria
DNA折纸是构建复杂人工纳米结构的绝佳工具。这些结构的功能化提供了在纳米尺度上精确组织物质的可能性。在实践中，这种努力可能会受到静电排斥或分子尺度上的其他动力学的阻碍，导致不合规的局部结构。使用单分子FRET显微镜结合粗粒度布朗动力学模拟，我们在这里研究了DNA折纸盒的盖子周围的局部结构，它可以由特定的DNA钥匙打开。我们发现，封闭盒的FRET信号取决于缓冲液离子浓度和DNA结构设计的微小变化。模拟提供了一个全局和局部结构的视图，并表明盒壁和盖之间的距离经历波动。这些结果提供了可视化和改善三维DNA折纸组件的局部结构的方法，并为控制化学基团和配体的位置提供了指导。
DNA origami is an excellent tool for building complex artificial nanostructures. Functionalization of these structures provides the possibility of precise organization of matter at the nanoscale. In practice, efforts in this endeavour can be impeded by electrostatic repulsion or other dynamics at the molecular scale, resulting in uncompliant local structures. Using single molecule FRET microscopy combined with coarse-grained Brownian dynamics simulations, we investigated here the local structure around the lid of a DNA origami box, which can be opened by specific DNA keys. We found that FRET signals for the closed box depend on buffer ion concentrations and small changes to the DNA structure design. Simulations provided a view of the global and local structure and showed that the distance between the box wall and lid undergoes fluctuations. These results provide methods to vizualise and improve the local structure of three-dimensional DNA origami assemblies and offer guidance for exercising control over placement of chemical groups and ligands.