Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation
Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation
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DOI：
10.1093/nar/gkaa417
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发表时间：
2020-07-09
影响因子：
14.9
通讯作者：
Sulc, Petr
中科院分区：
文献类型：
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作者：
Poppleton, Erik;Bohlin, Joakim;Sulc, Petr
这项工作旨在弥补目前的核酸纳米技术软件环境中的两个不足之处：缺乏一个快速和用户友好的可视化工具和模拟系统的结构分析的标准。我们在这里介绍oxView，一个基于Web浏览器的可视化工具，可以加载超过100万个核苷酸的结构，从模拟轨迹创建视频，并允许用户对DNA和RNA设计进行基本编辑。我们还介绍了开源软件工具，用于提取常见的结构参数，以表征大的DNA/RNA纳米结构模拟使用粗粒度的建模工具，oxDNA，近年来越来越受欢迎，经常用于原型新的核酸纳米结构设计，DNA/RNA过程的生物物理模型，并合理化实验结果。新推出的软件工具通过提供多种分析脚本，包括平均结构和结构灵活性表征、氢键磨损和双链体间角度，促进了DNA/RNA设计的计算表征。这些工具的输出可以加载到oxView中，允许用户在3D图形环境中与模拟结构进行交互，并修改结构以实现所需的属性。我们通过将这些新开发的工具应用于设计和分析一系列DNA/RNA纳米结构来展示它们。
This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with over 1 million nucleotides, create videos from simulation trajectories, and allow users to perform basic edits to DNA and RNA designs. We additionally introduce open-source software tools for extracting common structural parameters to characterize large DNA/RNA nanostructures simulated using the coarse-grained modeling tool, oxDNA, which has grown in popularity in recent years and is frequently used to prototype new nucleic acid nanostructural designs, model biophysics of DNA/RNA processes, and rationalize experimental results. The newly introduced software tools facilitate the computational characterization of DNA/RNA designs by providing multiple analysis scripts, including mean structures and structure flexibility characterization, hydrogen bond fraying, and interduplex angles. The output of these tools can be loaded into oxView, allowing users to interact with the simulated structure in a 3D graphical environment and modify the structures to achieve the required properties. We demonstrate these newly developed tools by applying them to design and analysis of a range of DNA/RNA nanostructures.