Integrated computer-aided engineering and design for DNA assemblies
Integrated computer-aided engineering and design for DNA assemblies
复制标题
DNA组装的集成计算机辅助工程和设计
DOI：
10.1038/s41563-021-00978-5
复制
发表时间：
2021-04-19
期刊：
影响因子：
41.2
通讯作者：
Castro, Carlos E.
中科院分区：
文献类型：
--
作者：
Huang, Chao-Min;Kucinic, Anjelica;Castro, Carlos E.
最近，DNA已被用于制造纳米器件，用于医学、纳米制造、合成生物学、生物传感和生物物理学等领域的无数应用。然而，目前的DNA纳米器件主要依赖于几何设计，并且合理设计功能特性（如力响应或驱动行为）仍然具有挑战性。在这里，我们报告了DNA组装的迭代设计管道，该管道将基于粗粒度分子动力学的计算机辅助工程与通用的计算机辅助设计方法相结合，该方法将自上而下的自动化与自下而上的几何控制相结合。这种直观的框架允许从三维模型快速构建大型多组件组件，并以自动化的方式对DNA结构的几何、机械和动态特性进行更精细的控制。这种方法扩展了结构复杂性的范围，增强了DNA组件的机械和动态设计。一种将基于分子动力学的计算机辅助工程与计算机辅助设计相结合的方法允许快速构建大型三维DNA组装并控制其几何、力学和动力学。
Recently, DNA has been used to make nanodevices for a myriad of applications across fields including medicine, nanomanufacturing, synthetic biology, biosensing and biophysics. However, current DNA nanodevices rely primarily on geometric design, and it remains challenging to rationally design functional properties such as force-response or actuation behaviour. Here we report an iterative design pipeline for DNA assemblies that integrates computer-aided engineering based on coarse-grained molecular dynamics with a versatile computer-aided design approach that combines top-down automation with bottom-up control over geometry. This intuitive framework allows for rapid construction of large, multicomponent assemblies from three-dimensional models with finer control over the geometrical, mechanical and dynamical properties of the DNA structures in an automated manner. This approach expands the scope of structural complexity and enhances mechanical and dynamic design of DNA assemblies.An approach integrating molecular dynamics-based computer-aided engineering with computer-aided design allows for the rapid construction of large three-dimensional DNA assemblies and control over their geometry, mechanics and dynamics.