Mechanical deformation behaviors and structural properties of ligated DNA crystals
Mechanical deformation behaviors and structural properties of ligated DNA crystals
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DOI：
10.1016/j.bpj.2022.09.036
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发表时间：
2022-11-01
影响因子：
3.4
通讯作者：
Choi, Jong Hyun
中科院分区：
文献类型：
--
作者：
Li, Ruixi;Zheng, Mengxi;Choi, Jong Hyun
DNA 自组装已成为构建复杂纳米结构的强大策略。虽然单个 DNA 链的力学已被广泛研究，但自组装结构的变形行为和结构特性尚不清楚。这部分是由于尺寸小和可用的实验方法有限。 DNA 晶体是由纳米级图案通过粘端缔合组装而成的宏观晶体结构。因此，大型 DNA 构建体可能是研究结构力学的理想平台。在这里，我们研究了由张拉整体三角形图案制成的连接 DNA 晶体的基本机械特性和行为。我们进行了粗粒度分子动力学模拟，并使用原子力显微镜通过纳米压痕实验证实了结果。我们观察到各种变形模式，包括无张力、线弹性、双链体解离和单链组分拉伸。我们发现 DNA 结构的机械特性与其组件的机械特性相关。然而，该结构表现出复杂的行为，这些行为可能无法仅通过组件来预测，因此必须考虑架构设计。
DNA self-assembly has emerged as a powerful strategy for constructing complex nanostructures. While the mechanics of individual DNA strands have been studied extensively, the deformation behaviors and structural properties of self-assembled architectures are not well understood. This is partly due to the small dimensions and limited experimental methods available. DNA crystals are macroscopic crystalline structures assembled from nanoscale motifs via sticky-end association. The large DNA constructs may thus be an ideal platform to study structural mechanics. Here, we investigate the fundamental mechanical properties and behaviors of ligated DNA crystals made of tensegrity triangular motifs. We perform coarse-grained molecular dynamics simulations and confirm the results with nanoindentation experiments using atomic force microscopy. We observe various deformation modes, including untension, linear elasticity, duplex dissociation, and single-stranded component stretch. We find that the mechanical properties of a DNA architecture are correlated with those of its components. However, the structure shows complex behaviors which may not be predicted by components alone and the architectural design must be considered.