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:10.1007/978-1-0716-3028-0_6

Cited by 8 publications

(3 citation statements)

References 38 publications

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“…The analysis of coarse-grained models based on OxDNA molecular dynamics (MD) simulations − reveals that dsDNAs within TDOs achieve stable conformations and spatial orientations when compared to ssDNA or dsDNA of equivalent length. First, we established a coarse-grained model for ssDNA and dsDNA, each with a length of 120 base pairs.…”

Section: Resultsmentioning

confidence: 99%

Twisted DNA Origami-Based Chiral Monolayers for Spin Filtering

Wang,

Yin,

et al. 2024

J. Am. Chem. Soc.

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DNA monolayers with inherent chirality play a pivotal role across various domains including biosensors, DNA chips, and bioelectronics. Nonetheless, conventional DNA chiral monolayers, typically constructed from singlestranded DNA (ssDNA) or double-stranded DNA (dsDNA), often lack structural orderliness and design flexibility at the interface. Structural DNA nanotechnology has emerged as a promising solution to tackle these challenges. In this study, we present a strategy for crafting highly adaptable twisted DNA origami-based chiral monolayers. These structures exhibit distinct interfacial assembly characteristics and effectively mitigate the structural disorder of dsDNA monolayers, which is constrained by a limited persistence length of ∼50 nm of dsDNA. We highlight the spin-filtering capabilities of seven representative DNA origami-based chiral monolayers, demonstrating a maximal one-order-of-magnitude increase in spin-filtering efficiency per unit area compared with conventional dsDNA chiral monolayers. Intriguingly, our findings reveal that the higher-order tertiary chiral structure of twisted DNA origami further enhances the spin-filtering efficiency. This work paves the way for the rational design of DNA chiral monolayers.

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Section: Resultsmentioning

confidence: 99%

Twisted DNA Origami-Based Chiral Monolayers for Spin Filtering

Wang,

Yin,

et al. 2024

J. Am. Chem. Soc.

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“…Rigid body dynamics in oxView were used to bend the arms into a rough initial configuration. Relaxation was then performed using the method described previously 64 . After relaxation, the dsDNA template was built using oxView’s editing tools and a further round of relaxation performed.…”

Section: Methodsmentioning

confidence: 99%

A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower

Centola,

Poppleton,

Ray

et al. 2023

Nat. Nanotechnol.

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Molecular engineering seeks to create functional entities for modular use in the bottom-up design of nanoassemblies that can perform complex tasks. Such systems require fuel-consuming nanomotors that can actively drive downstream passive followers. Most artificial molecular motors are driven by Brownian motion, in which, with few exceptions, the generated forces are non-directed and insufficient for efficient transfer to passive second-level components. Consequently, efficient chemical-fuel-driven nanoscale driver–follower systems have not yet been realized. Here we present a DNA nanomachine (70 nm × 70 nm × 12 nm) driven by the chemical energy of DNA-templated RNA-transcription-consuming nucleoside triphosphates as fuel to generate a rhythmic pulsating motion of two rigid DNA-origami arms. Furthermore, we demonstrate actuation control and the simple coupling of the active nanomachine with a passive follower, to which it then transmits its motion, forming a true driver–follower pair.

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“…Coarse-grained DNA modelse.g. the oxDNA model , can simulate one DNA origami nanostructure, but can not simulate hundreds of DNA origamis. To simulate colloidal crystal self-assembling the Glotzer group developed the HOOMD-blue molecular dynamics and Monte Carlo package.…”

Section: Introductionmentioning

confidence: 99%

Binding Site Programmable Self-Assembly of 3D Hierarchical DNA Origami Nanostructures

Wei,

Chen,

Popov

et al. 2024

J. Phys. Chem. A

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The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami

Cited by 8 publications

References 38 publications

Twisted DNA Origami-Based Chiral Monolayers for Spin Filtering

Twisted DNA Origami-Based Chiral Monolayers for Spin Filtering

A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower

Binding Site Programmable Self-Assembly of 3D Hierarchical DNA Origami Nanostructures

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