Coarse-grained modelling of the structural properties of DNA origami

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 8.4Å, 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. arXiv:1809.08430v1 [cond-mat.soft]

Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure

“…System setup and simulation details The model used to parametrize the DNA is oxDNA [23,24,32], a coarsegrained model in which each nucleotide is represented by three rigidly connected interaction centers, developed to quantitatively reproduce the structural and kinetic experimental properties of DNA [24,[33][34][35][36]. Simulations were carried out with T = 300K and at 1M monovalent salt concentration.…”

Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation

“…As noted in 23 , averaging methods that use full structure alignment work very well for rigid structures; However, there are some caveats. Large planar structures frequently appear to have the smallest RMSF in a ring midway between the center and the edge (Fig.…”

“…Molecular simulations have proved indispensable in the field of nucleic acid nanotechnology, providing detailed information about bulk structural characteristics 19,20 , folding pathway kinetics 21,22 , conformational space and kinetics of complex nanostructures [23][24][25] , and active devices such as DNA walkers 26,27 . Due to the size of the designed nanostructures and the laboratory timescales involved, traditional fully atomistic simulation methods are often infeasible for nucleic acid nanotechnology applications.…”

“…To remedy this, several coarsegrained models have been developed [28][29][30][31][32][33][34][35][36] , each of which with a unique focus on a specific part of the DNA nanostructural design and characterization pipeline. In particular, the oxDNA/oxRNA models have grown in popularity in recent years and have been used for studying DNA/RNA nanostructures and devices 23,32,[37][38][39] as well as RNA/DNA biophysics 30,40,41 . The models represent each nucleotide as a single rigid body, where the interactions between nucleotides are empirically parameterized to reproduce basic structural, mechanical and thermodynamic properties of DNA and RNA FIG.…”

Understanding DNA interactions in crowded environments with a coarse-grained model

“…The oxDNA model [32][33][34] is a coarsegrained DNA model that captures the structural, thermodynamic and mechanical properties of both single-stranded DNA and double-stranded DNA. Where available, the model has been able to quantitatively reproduce experimental measurements of DNA properties and has been successfully applied to the study of duplex and hairpin formation 26,32,35 , DNA behavior under a pulling force and torque 36,37 , DNA origami assembly [38][39][40] , properties of polyhedral and tile-based nanostructures [41][42][43] , and other complex processes such as strand displacement kinetics 44 and DNA walkers 9,45 . We extend the oxDNA model by introducing inert crowding particles, which are represented by spheres interacting with excluded volume (schematically shown in Fig.…”