Web Server with a Simple Interface for Coarse-grained Molecular Dynamics of DNA Nanostructures

Yamashita, Yudai; Watanabe, Kotaro; Murata, Satoshi; Kawamata, Ibuki

doi:10.1273/cbij.21.28

Cited by 3 publications

(2 citation statements)

References 29 publications

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“…The downside of that approach is that the simulation of systems is stochastic and would thus neither generate an actual CRN nor prove the absence of interesting structures in a given system. Simulations are extremely costly and can take up to 5 days for 300 ns of simulated time on a dedicated computing server for large structures [ 58 ], preventing the application of that simulator at an earlier stage of the exploration. Alternatively, a different enumerator might be plugged in the framework instead of Peppercorn, or as an additional refinement stage for the CRN exploration.…”

Section: Discussionmentioning

confidence: 99%

Automated exploration of DNA-based structure self-assembly networks

2021

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Finding DNA sequences capable of folding into specific nanostructures is a hard problem, as it involves very large search spaces and complex nonlinear dynamics. Typical methods to solve it aim to reduce the search space by minimizing unwanted interactions through restrictions on the design (e.g. staples in DNA origami or voxel-based designs in DNA Bricks). Here, we present a novel methodology that aims to reduce this search space by identifying the relevant properties of a given assembly system to the emergence of various families of structures (e.g. simple structures, polymers, branched structures). For a given set of DNA strands, our approach automatically finds chemical reaction networks (CRNs) that generate sets of structures exhibiting ranges of specific user-specified properties, such as length and type of structures or their frequency of occurrence. For each set, we enumerate the possible DNA structures that can be generated through domain-level interactions, identify the most prevalent structures, find the best-performing sequence sets to the emergence of target structures, and assess CRNs' robustness to the removal of reaction pathways. Our results suggest a connection between the characteristics of DNA strands and the distribution of generated structure families.

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Section: Discussionmentioning

confidence: 99%

Automated exploration of DNA-based structure self-assembly networks

2021

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“…Using reported methods 45 , 46 , we defined the oxDNA parameters such as total steps: 3 × 10 8 , temperature: 0.00938 (298.15 K), salt concentration: 0.5, cutoff radius: 2.0, max backbone force: 5, Verlet skin: 0.05, diffusion coefficient: 2.5, simulation type: MD, interaction type: DNA2, thermostat: John, all of which are written in oxDNA units. Assuming the time unit of oxDNA is 3.03 ps 47 , simulations of 3 µs were performed in each computation.…”

Section: Methodsmentioning

confidence: 99%

Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies

Karna,

Mano,

et al. 2023

Nat Commun

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The intrinsic complexity of many mesoscale (10–100 nm) cellular machineries makes it challenging to elucidate their topological arrangement and transition dynamics. Here, we exploit DNA origami nanospring as a model system to demonstrate that tens of piconewton linear force can modulate higher-order conformation dynamics of mesoscale molecular assemblies. By switching between two chemical structures (i.e., duplex and tetraplex DNA) in the junctions of adjacent origami modules, the corresponding stretching or compressing chemo-mechanical stress reversibly flips the backbone orientations of the DNA nanosprings. Both coarse-grained molecular dynamics simulations and atomic force microscopy measurements reveal that such a backbone conformational switch does not alter the right-handed chirality of the nanospring helix. This result suggests that mesoscale helical handedness may be governed by the torque, rather than the achiral orientation, of nanospring backbones. It offers a topology-based caging/uncaging concept to present chemicals in response to environmental cues in solution.

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DNA nanomachine tutorial

2024

BIOPHYSICS

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Web Server with a Simple Interface for Coarse-grained Molecular Dynamics of DNA Nanostructures

Abstract: Licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0)

Cited by 3 publications

References 29 publications

Automated exploration of DNA-based structure self-assembly networks

Automated exploration of DNA-based structure self-assembly networks

Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies

DNA nanomachine tutorial

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