How we simulate DNA origami

TL;DR

This paper presents a comprehensive tutorial on simulating DNA origami structures using the oxDNA coarse-grained model, aiding experimentalists in integrating computational tools into their design process.

Contribution

It introduces a general approach for simulating DNA origami with oxDNA, facilitating better understanding and design of nanoscale DNA structures.

Findings

Enhanced understanding of DNA origami shape and function through simulation

Streamlined design process using oxDNA ecosystem tools

Integration of computational analysis into experimental workflows

Abstract

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.