Automated sequence design of 2D wireframe DNA origami with honeycomb edges
Automated sequence design of 2D wireframe DNA origami with honeycomb edges
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DOI：
10.1038/s41467-019-13457-y
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发表时间：
2019-11-28
影响因子：
16.6
通讯作者：
Bathe, Mark
中科院分区：
文献类型：
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作者：
Jun, Hyungmin;Wang, Xiao;Bathe, Mark
线框DNA折纸已成为一种在纳米尺度上制造几乎任意二维和三维几何形状的强大方法。然而，设计线框DNA折纸物体所需的复杂支架和订书钉路径，使得基于几何形状的全自动序列设计方法对其合成至关重要。而且线框DNA折纸的结构保真度可能会受到仅由一个或两个双链组成的线框边缘的限制。在此我们引入一种全自动计算方法，该方法使用由六个平行双链组成的蜂窝状边缘对二维线框折纸组件进行编程。与使用双双链边缘编程的相同几何形状相比，这些线框组件从基于电子显微镜的编程角度测量中显示出更高的结构保真度。分子动力学为所观察到的结构保真度提高提供了额外的理论支持。将我们的自上而下的序列设计程序应用于各种复杂物体，证明了它在可编程二维纳米材料方面的广泛用途。
Wireframe DNA origami has emerged as a powerful approach to fabricating nearly arbitrary 2D and 3D geometries at the nanometer-scale. Complex scaffold and staple routing needed to design wireframe DNA origami objects, however, render fully automated, geometry-based sequence design approaches essential for their synthesis. And wireframe DNA origami structural fidelity can be limited by wireframe edges that are composed only of one or two duplexes. Here we introduce a fully automated computational approach that programs 2D wireframe origami assemblies using honeycomb edges composed of six parallel duplexes. These wireframe assemblies show enhanced structural fidelity from electron microscopy-based measurement of programmed angles compared with identical geometries programmed using dual-duplex edges. Molecular dynamics provides additional theoretical support for the enhanced structural fidelity observed. Application of our top-down sequence design procedure to a variety of complex objects demonstrates its broad utility for programmable 2D nanoscale materials.