Sequence-dependent folding of monolayered DNA origami domains

Gambietz, Sabrina; Stenke, Lena J; Saccá, Barbara

doi:10.1039/d3nr02537c

Cited by 2 publications

(1 citation statement)

References 43 publications

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“…An in-plane angle of π/3 rad (60°) is a commonly accepted value in biological contexts [58,59]. This angle is likely to be lower in DNA nanostructures, and may vary between designs, particularly for 2D and 3D structures, and quantification of these angles in origami or other DNA nanostructures has been a subject of few publications, typically in the context of mechanical properties [60], ion dependent reconfiguration [61,62], novel characterization [63][64][65], and bistable physical isomorphs [66,67]. It is worth noting that both the schematics in figure 12, and in most CAD tools, can visually imply larger spacings than occur practically.…”

Section: Decoration Accuracymentioning

confidence: 99%

DNA nanostructure decoration: a how-to tutorial

Piantanida,

Liddle,

Hughes

et al. 2024

Nanotechnology

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DNA Nanotechnology is being applied to multiple research fields. The functionality of DNA nanostructures is significantly enhanced by decorating them with heterogeneous nanoscale moieties including: proteins, metallic nanoparticles, quantum dots, and chromophores. Decoration is a complex process and protocols for reliable attachment routinely require trial and error. Additionally, the granular nature of scientific communication makes it difficult to see the forest for the trees in DNA nanostructure decoration. This tutorial is a guidebook to limit experimental bottlenecks and avoid dead-ends when decorating DNA nanostructures. We supplement the reference material on available technical tools and procedures with a conceptual framework required to make efficient and effective decisions in the lab. Together these resources should aid both the novice and the expert to develop and execute a rapid, reliable decoration protocol.

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Section: Decoration Accuracymentioning

confidence: 99%

DNA nanostructure decoration: a how-to tutorial

Piantanida,

Liddle,

Hughes

et al. 2024

Nanotechnology

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ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems

Tosti Guerra,

Poppleton,

Šulc

et al. 2024

The Journal of Chemical Physics

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The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales and system sizes involved. In this article, we present a new coarse-grained model for investigating the folding dynamics of nucleic acids. Our model represents three nucleotides with a patchy particle and is parameterized using well-established nearest-neighbor models. Thanks to the reduction of degrees of freedom and to a bond-swapping mechanism, our model allows for simulations at timescales and length scales that are currently inaccessible to more detailed models. To validate the performance of our model, we conducted extensive simulations of various systems: We examined the thermodynamics of DNA hairpins, capturing their stability and structural transitions, the folding of an MMTV pseudoknot, which is a complex RNA structure involved in viral replication, and also explored the folding of an RNA tile containing a k-type pseudoknot. Finally, we evaluated the performance of the new model in reproducing the melting temperatures of oligomers and the dependence on the toehold length of the displacement rate in toehold-mediated displacement processes, a key reaction used in molecular computing. All in all, the successful reproduction of experimental data and favorable comparisons with existing coarse-grained models validate the effectiveness of the new model.

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Sequence-dependent folding of monolayered DNA origami domains

Abstract: Current models of DNA origami folding can explain the yield of the assembly process and the isomerization of the structure upon application of mechanical forces. Nevertheless, the role of sequence...

Cited by 2 publications

References 43 publications

DNA nanostructure decoration: a how-to tutorial

DNA nanostructure decoration: a how-to tutorial

ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems

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