Haggenmueller Sarah, Matthies Michael, Sample Matthew, Šulc Petr
School of Natural Sciences, Department of Bioscience, Technical University Munich, 85748, Garching, Germany.
School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, 85287, USA.
Small Methods. 2025 Jun;9(6):e2401526. doi: 10.1002/smtd.202401526. Epub 2025 Feb 5.
DNA origami consists of a long scaffold strand and short staple strands that self-assemble into a target 2D or 3D shape. It is a widely used construct in nucleic acid nanotechnology, offering a cost-effective way to design and create diverse nanoscale shapes. With promising applications in areas such as nanofabrication, diagnostics, and therapeutics, DNA origami has become a key tool in the bionanotechnology field. Simulations of these structures can offer insight into their shape and function, thus speeding up and simplifying the design process. However, simulating these structures, often comprising thousands of base pairs, poses challenges due to their large size. OxDNA, a coarse-grained model specifically designed for DNA nanotechnology, offers powerful simulation capabilities. Its associated ecosystem of visualization and analysis tools can complement experimental work with in silico characterization. This tutorial provides a general approach to simulating DNA origami structures using the oxDNA ecosystem, tailored for experimentalists looking to integrate computational analysis into their design workflow.
DNA折纸由一条长的支架链和短的订书钉链组成,它们自组装成目标二维或三维形状。它是核酸纳米技术中广泛使用的构建体,提供了一种经济高效的方式来设计和创建各种纳米级形状。由于在纳米制造、诊断和治疗等领域有着广阔的应用前景,DNA折纸已成为生物纳米技术领域的关键工具。对这些结构进行模拟可以深入了解它们的形状和功能,从而加快并简化设计过程。然而,模拟这些通常包含数千个碱基对的结构,因其尺寸较大而带来挑战。OxDNA是一种专门为DNA纳米技术设计的粗粒度模型,具有强大的模拟能力。其相关的可视化和分析工具生态系统可以通过计算机模拟表征来补充实验工作。本教程提供了一种使用OxDNA生态系统模拟DNA折纸结构的通用方法,适用于希望将计算分析集成到其设计工作流程中的实验人员。