Stretching DNA origami: effect of nicks and Holliday junctions on the axial stiffness.
Stretching DNA origami: effect of nicks and Holliday junctions on the axial stiffness.
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DOI：
10.1093/nar/gkaa985
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发表时间：
2020-12-02
影响因子：
14.9
通讯作者：
Chen Y
中科院分区：
文献类型：
--
作者：
Jung WH;Chen E;Veneziano R;Gaitanaros S;Chen Y
DNA折纸的轴向硬度是由关键的纳米结构特征决定的。合成了不同结构的具有特定密度的Nicks和Holliday结的双螺旋纳米棒，并通过流体流动拉伸。通过实施单粒子跟踪来提取力-位移曲线，可以在热弹性区域(即大于15pN的力)测量DNA折纸硬挺值。对比结扎螺旋和刻痕螺旋，发现后者的轴向刚度降低了近两倍。将DNA螺旋视为弹性杆的数值模型被用来评估Nicks结和Holliday结处的局部刚度损失。结果表明，模型准确地再现了实验数据，表明这两种设计特征产生的局部刚度都比完整双螺旋的对应值小两个数量级。这种局部退化反过来导致宏观上的刚性损失，这是对多螺旋DNA束进行数值评估的结果。
The axial stiffness of DNA origami is determined as a function of key nanostructural characteristics. Different constructs of two-helix nanobeams with specified densities of nicks and Holliday junctions are synthesized and stretched by fluid flow. Implementing single particle tracking to extract force–displacement curves enables the measurement of DNA origami stiffness values at the enthalpic elasticity regime, i.e. for forces larger than 15 pN. Comparisons between ligated and nicked helices show that the latter exhibit nearly a two-fold decrease in axial stiffness. Numerical models that treat the DNA helices as elastic rods are used to evaluate the local loss of stiffness at the locations of nicks and Holliday junctions. It is shown that the models reproduce the experimental data accurately, indicating that both of these design characteristics yield a local stiffness two orders of magnitude smaller than the corresponding value of the intact double-helix. This local degradation in turn leads to a macroscopic loss of stiffness that is evaluated numerically for multi-helix DNA bundles.
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