The oxDNA coarse-grained model as a tool to simulate DNA origami

Doye, Jonathan P. K.; Fowler, Hannah; Prešern, Domen; Bohlin, Joakim; Rovigatti, Lorenzo; Romano, Flavio; Šulc, Petr; Wong, Chak Kui; Louis, Ard A.; Schreck, John S.; Engel, Megan Clare; Matthies, Michael; Benson, Erik; Poppleton, Erik; Snodin, Benedict E. K.

doi:10.48550/arxiv.2004.05052

Cited by 3 publications

(6 citation statements)

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“…5). The oxDNA2 coarse-grained model was used because it accurately represents the thermodynamic and mechanical properties of DNA while enabling long time scale simulations at lower computational cost compared with classical all-atom models (44,45). As the largest and most complex wireframe origami folded in this study, the hexagonal and pentagonal DNA origami objects with internal meshes were first chosen for oxDNA2 simulation (figs.…”

Section: Molecular Simulation Of 2d Origami Objectsmentioning

confidence: 99%

“…Coarse-grained molecular dynamics simulations using the oxDNA2 model MD simulations of DNA nanostructures were performed using the oxDNA2 model and simulation software (44,45,56,57). The oxDNA model is a coarse-grained approximation to study the thermodynamic and mechanical properties of DNA, enabling longer time scales and larger system sizes to be simulated (44,45). Fully atomistic DNA nanostructures from ATHENA were converted into oxDNA file format using tacoxDNA (58).…”

Section: Cryo-em Imaging Without 3d Reconstructionmentioning

confidence: 99%

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Planar 2D wireframe DNA origami

Wang

Jun

et al. 2022

Sci. Adv.

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Two-dimensional (2D) DNA origami is widely used for applications ranging from excitonics to single-molecule biophysics. Conventional, single-layer 2D DNA origami exhibits flexibility and curvature in solution; however, that may limit its suitability as a 2D structural template. In contrast, 2D wireframe DNA origami rendered with six-helix bundle edges offers local control over duplex orientations with enhanced in-plane rigidity. Here, we investigate the 3D structure of these assemblies using cryo–electron microscopy (cryo-EM). 3D reconstructions reveal a high degree of planarity and homogeneity in solution for polygonal objects with and without internal mesh, enabling 10-Å resolution for a triangle. Coarse-grained simulations were in agreement with cryo-EM data, offering molecular structural insight into this class of 2D DNA origami. Our results suggest that these assemblies may be valuable for 2D material applications and geometries that require high structural fidelity together with local control over duplex orientations, rather than parallel duplex assembly.

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Section: Molecular Simulation Of 2d Origami Objectsmentioning

confidence: 99%

Section: Cryo-em Imaging Without 3d Reconstructionmentioning

confidence: 99%

Planar 2D wireframe DNA origami

Wang

Jun

et al. 2022

Sci. Adv.

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“…In particular, there is a vector that is perpendicular to the notional plane FIG. 1: Structure and interactions of the oxDNA model (adapted from [51,99]). a) Three strands forming a nicked duplex as represented by oxDNA2.0, with the central section of the complex illustrating key interactions from Eq.…”

Section: The Oxdna Modelmentioning

confidence: 99%

“…A more detailed primer on setting up these simulations can be fund in Ref. [99]; here we focus only on technical aspects of the simulations.…”

Section: Simulation Of Large Structuresmentioning

confidence: 99%

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A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results

Sengar,

Ouldridge,

Henrich

et al. 2021

Preprint

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The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly-documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of -and feed into our understanding of -less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.

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Sequence-Dependent Kink Formation in Short DNA Loops: Theory and Molecular Dynamics Simulations

Park

Cho

Jung

2021

J. Chem. Theory Comput.

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Kink formation is essential in highly bent DNA complexed with gene regulatory proteins such as histones to release the bending stress stored within the DNA duplex. Local opening of the double-stranded DNA creates a sharp turn along the specific sequence, which leads to the global bending of the DNA strand. Despite the critical role of kink formation, it is still challenging to predict the position of kink formation for a given DNA sequence. In this study, we propose a theoretical model and perform molecular dynamics simulations to quantify the sequence-dependent kink probability of a strongly bent DNA. By incorporating the elastic bending energy and the sequence-specific thermodynamic parameters, we investigate the importance of the DNA sequence on kink formation. We find that the sequence with TA dinucleotide repeats flanked by GC steps increases the kink propensity by more than an order of magnitude under the same bending stress. The number of base pairs involved in the local opening is found to be coupled with the sequence-specific bubble formation free energy. Our study elucidates the molecular origin of the sequence heterogeneity on kink formation, which is fundamental to understanding protein–DNA recognition.

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The oxDNA coarse-grained model as a tool to simulate DNA origami

Cited by 3 publications

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Planar 2D wireframe DNA origami

Planar 2D wireframe DNA origami

A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results

Sequence-Dependent Kink Formation in Short DNA Loops: Theory and Molecular Dynamics Simulations

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