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.

中文翻译：

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MrDNA：用于预测DNA系统结构和动力学的多分辨率模型。

尽管结构DNA纳米技术领域以惊人的速度向前发展，但是复杂的3D纳米结构和功能设备的从头设计仍然是一项费时费力的过程。其原因之一是需要进行多个实验表征周期，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，我们演示了多分辨率模拟框架mrdna，该框架在30分钟或更短的时间内即可产生自组装DNA纳米系统的原子分辨率结构。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，证明了我们的mrdna框架的真实性。此外，我们表明，我们的方法可以表征动态DNA纳米结构采用的构象的整体，利用离格自组装原理（即线框DNA对象）构建的DNA对象的平衡结构和动力学，并研究在一定条件下的DNA对象的特性。各种环境条件，例如施加的电场。作为一个开源Python软件包实施，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。