MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems
MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems
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DOI：
10.1093/nar/gkaa200
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发表时间：
2020-05-21
影响因子：
14.9
通讯作者：
Aksimentiev, Aleksei
中科院分区：
文献类型：
--
作者：
Maffeo, Christopher;Aksimentiev, Aleksei
虽然结构DNA纳米技术领域一直在以惊人的速度前进，但复杂的3D纳米结构和功能器件的从头设计仍然是一个费力且耗时的过程。其中一个原因是需要多个周期的实验表征，以阐明设计选择对自组装物体的实际形状和功能的影响。在这里，我们展示了一个多分辨率的模拟框架，mrdna，在30分钟或更短的时间内，可以产生一个原子级分辨率的自组装DNA纳米系统的结构。我们通过直接比较模拟结果与多个3D DNA折纸对象的冷冻电子显微镜（cryo-EM）重建结果来展示我们的mrdna框架的保真度。此外，我们表明，我们的方法可以表征动态DNA纳米结构所采用的构象的集合，使用非晶格自组装原理构建的DNA对象的平衡结构和动力学，即线框DNA对象，并研究在各种环境条件下，如外加电场的DNA对象的属性。作为一个开源Python包实现，我们的框架可以由社区扩展，并与DNA设计和分子图形工具集成。
Although the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of experimental characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resolution simulation framework, mrdna, that, in 30 min or less, can produce an atomistic-resolution structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equilibrium structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e. wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied electric field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and molecular graphics tools.