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理解 DNA 折纸瓦片的力学性质,并控制其折叠和展开的动力学重构。

Understanding the mechanical properties of DNA origami tiles and controlling the kinetics of their folding and unfolding reconfiguration.

机构信息

School of Mechanical Engineering, Birck Nanotechnology Center, Bindley Bioscience Center, Purdue University , West Lafayette, Indiana 47907, United States.

出版信息

J Am Chem Soc. 2014 May 14;136(19):6995-7005. doi: 10.1021/ja500612d. Epub 2014 May 2.

Abstract

DNA origami represents a class of highly programmable macromolecules that can go through conformational changes in response to external signals. Here we show that a two-dimensional origami rectangle can be effectively folded into a short, cylindrical tube by connecting the two opposite edges through the hybridization of linker strands and that this process can be efficiently reversed via toehold-mediated strand displacement. The reconfiguration kinetics was experimentally studied as a function of incubation temperature, initial origami concentration, missing staples, and origami geometry. A kinetic model was developed by introducing the j factor to describe the reaction rates in the cyclization process. We found that the cyclization efficiency (j factor) increases sharply with temperature and depends strongly on the structural flexibility and geometry. A simple mechanical model was used to correlate the observed cyclization efficiency with origami structure details. The mechanical analysis suggests two sources of the energy barrier for DNA origami folding: overcoming global twisting and bending the structure into a circular conformation. It also provides the first semiquantitative estimation of the rigidity of DNA interhelix crossovers, an essential element in structural DNA nanotechnology. This work demonstrates efficient DNA origami reconfiguration, advances our understanding of the dynamics and mechanical properties of self-assembled DNA structures, and should be valuable to the field of DNA nanotechnology.

摘要

DNA 折纸术代表了一类高度可编程的大分子,它们可以对外界信号做出构象变化的响应。在这里,我们展示了通过连接两条相对边缘的连接链的杂交,二维 origami 矩形可以有效地折叠成短的圆柱形管,并且这个过程可以通过链置换的引发点介导有效地逆转。我们将该重配置动力学作为孵育温度、初始 origami 浓度、缺失的 staples 和 origami 几何形状的函数进行了实验研究。通过引入 j 因子,我们建立了一个动力学模型来描述环化过程中的反应速率。我们发现,环化效率(j 因子)随温度急剧增加,并且强烈依赖于结构的灵活性和几何形状。我们使用一个简单的机械模型将观察到的环化效率与 origami 结构细节相关联。机械分析表明 DNA 折纸折叠的能量障碍有两个来源:克服全局扭曲并将结构弯曲成圆形构象。它还为 DNA 分子间交叉的刚性提供了第一个半定量估计,这是结构 DNA 纳米技术的一个基本要素。这项工作展示了有效的 DNA origami 重配置,推进了我们对自组装 DNA 结构的动力学和力学性质的理解,并且应该对 DNA 纳米技术领域有价值。

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