Coarse-grained modelling of the structural properties of DNA origami.

Benedict E K Snodin,Ard A Louis,Jonathan P K Doye,Flavio Romano,John S Schreck

doi:10.1093/nar/gky1304

Benedict E K Snodin, Ard A Louis + Show 3 more

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https://doi.org/10.1093/nar/gky1304

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Abstract

We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origami, focussing on archetypal 2D and 3D origami. 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 Å, 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 origami, and has the potential to be used to routinely pre-screen putative origami designs and to investigate the molecular mechanisms that regulate the properties of DNA origami.

Highlights

DNA nanotechnology seeks to use the specificity of the Watson–Crick base pairing and the programmability possible through the DNA sequence to design self-assembling nanoscale DNA structures and devices
There are a number of such models at this level of detail [47,48,49], here we explore in detail the description of DNA origami nanostructures provided by the oxDNA model [36,37,38]
Before we directly address origami structure, we first consider the properties of a single four-way junction, known as a Holliday junction, as they are an essential feature of origami designs

Summary

Introduction

DNA nanotechnology seeks to use the specificity of the Watson–Crick base pairing and the programmability possible through the DNA sequence to design self-assembling nanoscale DNA structures and devices. The increasing usage of DNA origami was facilitated by the development of computer-aided design tools, such as caDNAno [7]. These original approaches produced structures involving mainly bundles of locally parallel double helices held together by four-way junctions. Scaffolded origami approaches have been developed that generate more open ‘wireframe’ structures [8,9,10,11], aided by the vHelix [8] and DAEDALUS [9] design programmes. The structural control and the addressability provided by the DNA origami technique naturally have led to many types of applications [12], in the areas of biosensing [13], drug delivery [14,15] and nanofabrication [16,17]

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