Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
Bioengineering, Computing + Mathematical Sciences, and Computation & Neural Systems, California Institute of Technology, Pasadena, CA, USA.
Nat Chem. 2021 Jun;13(6):549-558. doi: 10.1038/s41557-021-00679-1. Epub 2021 May 10.
RNA origami is a framework for the modular design of nanoscaffolds that can be folded from a single strand of RNA and used to organize molecular components with nanoscale precision. The design of genetically expressible RNA origami, which must fold cotranscriptionally, requires modelling and design tools that simultaneously consider thermodynamics, the folding pathway, sequence constraints and pseudoknot optimization. Here, we describe RNA Origami Automated Design software (ROAD), which builds origami models from a library of structural modules, identifies potential folding barriers and designs optimized sequences. Using ROAD, we extend the scale and functional diversity of RNA scaffolds, creating 32 designs of up to 2,360 nucleotides, five that scaffold two proteins, and seven that scaffold two small molecules at precise distances. Micrographic and chromatographic comparisons of optimized and non-optimized structures validate that our principles for strand routing and sequence design substantially improve yield. By providing efficient design of RNA origami, ROAD may simplify the construction of custom RNA scaffolds for nanomedicine and synthetic biology.
RNA 折纸术是一种模块化设计纳米支架的框架，可从单链 RNA 折叠而成，并用于以纳米级精度组织分子组件。可遗传表达的 RNA 折纸术的设计必须在共转录时折叠，这需要建模和设计工具来同时考虑热力学、折叠途径、序列约束和假结优化。在这里，我们描述了 RNA 折纸术自动化设计软件（ROAD），它可以从结构模块库中构建折纸模型，识别潜在的折叠障碍，并设计优化的序列。使用 ROAD，我们扩展了 RNA 支架的规模和功能多样性，创建了 32 个多达 2360 个核苷酸的设计，其中 5 个支架两个蛋白质，7 个支架两个小分子，距离精确。优化和非优化结构的显微和色谱比较验证了我们在链路由和序列设计方面的原则可以大大提高产量。通过提供 RNA 折纸术的高效设计，ROAD 可能会简化用于纳米医学和合成生物学的定制 RNA 支架的构建。
