Effects of Design Choices on the Stiffness of Wireframe DNA Origami Structures

Benson, Erik; Mohammed, Abdulmelik; Rayneau-Kirkhope, Daniel; Gådin, Andreas; Orponen, Pekka; Högberg, Björn

doi:10.1021/acsnano.8b04148

Cited by 40 publications

(48 citation statements)

References 44 publications

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“…Our comparison to the 3D origami of (24), together with other recent studies of DNA origami using oxDNA (38,63–65,68,69), confirms the suitability of the oxDNA model for structural characterization of DNA origami. Structures that have been carefully characterised experimentally will give further opportunities to test and refine the structural predictions of the model, while for DNA origami that have only been visualized using low-resolution methods, oxDNA has the potential to provide more detailed structural insights, as has already been done for a number of examples (63,64,68,69). The model could also be used to pre-screen the properties of putative origami designs prior to experimental realization to aid the design process.…”

Section: Resultssupporting

confidence: 83%

“…OxDNA has previously been used to characterize a number of specific DNA origami nanostructures with good success (38,63–65,68,69). Here, our aim is to provide a detailed structural analysis of some of the basic features of DNA origami and to test the reliability of the oxDNA model by comparing to the most structurally detailed available experimental data.…”

Section: Introductionmentioning

confidence: 99%

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Coarse-grained modelling of the structural properties of DNA origami

Snodin¹,

Schreck

Romano

et al. 2019

Nucleic Acids Research

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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]

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Section: Resultssupporting

confidence: 83%

Section: Introductionmentioning

confidence: 99%

Coarse-grained modelling of the structural properties of DNA origami

Snodin¹,

Schreck

Romano

et al. 2019

Nucleic Acids Research

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“…We designed hexagonal, planar DNA nanostructures with single‐helix thickness and dimensions of 104 nm on two hexagonal axes and 140 nm on the third hexagonal axis using the vHelix framework (Figure S1, Supporting Information). Atomic force microscopy (AFM) images of structures ( Figure A,B) give a characteristic appearance of flatness, guided by adherence to underlying mica surface.…”

Section: Resultsmentioning

confidence: 99%

Solution‐Controlled Conformational Switching of an Anchored Wireframe DNA Nanostructure

Hoffecker

Chen²,

Gådin

et al. 2018

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Self‐assembled DNA origami nanostructures have a high degree of programmable spatial control that enables nanoscale molecular manipulations. A surface‐tethered, flexible DNA nanomesh is reported herein which spontaneously undergoes sharp, dynamic conformational transitions under physiological conditions. The transitions occur between two major macrostates: a spread state dominated by the interaction between the DNA nanomesh and the BSA/streptavidin surface and a surface‐avoiding contracted state. Due to a slow rate of stochastic transition events on the order of tens of minutes, the dynamic conformations of individual structures can be detected in situ with DNA PAINT microscopy. Time series localization data with automated imaging processing to track the dynamically changing radial distribution of structural markers are combined. Conformational distributions of tethered structures in buffers with elevated pH exhibit a calcium‐dependent domination of the spread state. This is likely due to electrostatic interactions between the structures and immobilized surface proteins (BSA and streptavidin). An interaction is observed in solution under similar buffer conditions with dynamic light scattering. Exchanging between solutions that promote one or the other state leads to in situ sample‐wide transitions between the states. The technique herein can be a useful tool for dynamic control and observation of nanoscale interactions and spatial relationships.

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“…A study on the effects of design choices on the stiffness of these wireframe structures was undertaken by the same research group in 2018 [72]. Through physical simulation with oxDNA software [41], synthesis, and TEM and AFM characterization of various test DNA meshes, they connected DNA wireframe stiffness with the persistence lengths of constituent double-helices and the salt concentrations of buffer solutions.…”

Section: Semi-automatic Top-down Polyhedral Dna Rendering With Vhelixmentioning

confidence: 99%

Increasing Complexity in Wireframe DNA Nanostructures

et al. 2020

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Structural DNA nanotechnology has recently gained significant momentum, as diverse design tools for producing custom DNA shapes have become more and more accessible to numerous laboratories worldwide. Most commonly, researchers are employing a scaffolded DNA origami technique by “sculpting” a desired shape from a given lattice composed of packed adjacent DNA helices. Albeit relatively straightforward to implement, this approach contains its own apparent restrictions. First, the designs are limited to certain lattice types. Second, the long scaffold strand that runs through the entire structure has to be manually routed. Third, the technique does not support trouble-free fabrication of hollow single-layer structures that may have more favorable features and properties compared to objects with closely packed helices, especially in biological research such as drug delivery. In this focused review, we discuss the recent development of wireframe DNA nanostructures—methods relying on meshing and rendering DNA—that may overcome these obstacles. In addition, we describe each available technique and the possible shapes that can be generated. Overall, the remarkable evolution in wireframe DNA structure design methods has not only induced an increase in their complexity and thus expanded the prevalent shape space, but also already reached a state at which the whole design process of a chosen shape can be carried out automatically. We believe that by combining cost-effective biotechnological mass production of DNA strands with top-down processes that decrease human input in the design procedure to minimum, this progress will lead us to a new era of DNA nanotechnology with potential applications coming increasingly into view.

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Effects of Design Choices on the Stiffness of Wireframe DNA Origami Structures

Cited by 40 publications

References 44 publications

Coarse-grained modelling of the structural properties of DNA origami

Coarse-grained modelling of the structural properties of DNA origami

Solution‐Controlled Conformational Switching of an Anchored Wireframe DNA Nanostructure

Increasing Complexity in Wireframe DNA Nanostructures

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