Department of Computer Science, Aalto University, 00076 Aalto, Finland.
Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland.
ACS Nano. 2022 Oct 25;16(10):16608-16616. doi: 10.1021/acsnano.2c06035. Epub 2022 Sep 30.
We address the problem of de novo design and synthesis of nucleic acid nanostructures, a challenge that has been considered in the area of DNA nanotechnology since the 1980s and more recently in the area of RNA nanotechnology. Toward this goal, we introduce a general algorithmic design process and software pipeline for rendering 3D wireframe polyhedral nanostructures in single-stranded RNA. To initiate the pipeline, the user creates a model of the desired polyhedron using standard 3D graphic design software. As its output, the pipeline produces an RNA nucleotide sequence whose corresponding RNA primary structure can be transcribed from a DNA template and folded in the laboratory. As case examples, we design and characterize experimentally three 3D RNA nanostructures: a tetrahedron, a triangular bipyramid, and a triangular prism. The design software is openly available and also provides an export of the targeted 3D structure into the molecular dynamics simulator for easy simulation and visualization.
我们解决了从头设计和合成核酸纳米结构的问题，自 20 世纪 80 年代以来，这一挑战一直被认为是 DNA 纳米技术领域的一个挑战，最近在 RNA 纳米技术领域也是如此。为此，我们引入了一种用于在单链 RNA 中呈现 3D 线框多面体纳米结构的通用算法设计流程和软件管道。为了启动该管道，用户使用标准的 3D 图形设计软件创建所需多面体的模型。作为其输出，该管道生成一个 RNA 核苷酸序列，其对应的 RNA 一级结构可以从 DNA 模板转录并在实验室中折叠。作为案例示例，我们设计并通过实验表征了三种 3D RNA 纳米结构：四面体、三角双锥和三棱柱。设计软件是公开可用的，还提供了将目标 3D 结构导出到分子动力学模拟器的功能，便于模拟和可视化。
