Coarse-grained modelling of the structural properties of DNA origami

TL;DR

This paper demonstrates that the oxDNA coarse-grained model accurately characterizes the structural properties of DNA origami, including helix bending and 3D structure, aligning well with experimental data and offering a tool for design pre-screening.

Contribution

The study shows that oxDNA can reliably predict the detailed structure of DNA origamis, bridging computational modeling with experimental validation.

Findings

oxDNA reproduces helix bending patterns in 2D origamis

The model's average structure deviates by 8.4 Å from cryo-EM data

oxDNA can be used to pre-screen DNA origami designs

Abstract

We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origamis, focussing on archetypal 2D and 3D origamis. The model reproduces well the characteristic pattern of helix bending in a 2D origami, showing that it stems from the intrinsic tendency of anti-parallel four-way junctions to splay apart, a tendency that is enhanced both by less screened electrostatic interactions and by increased thermal motion. We also compare to the structure of a 3D origami whose structure has been determined by cryo-electron microscopy. The oxDNA average structure has a root-mean-square deviation from the experimental structure of 8.4 Angstrom, which is of the order of the experimental resolution. These results illustrate that the oxDNA model is capable of providing detailed and accurate insights into the structure of DNA origamis, and has the potential to be used to routinely pre-screen putative origami designs.