Mechanical deformation behaviors and structural properties of ligated DNA crystals

Li, Ruixin; Zheng, Mengxi; Madhvacharyula, Anirudh Sampath; Du, Yancheng; Mao, Chengde; Choi, Jong Hyun

doi:10.1016/j.bpj.2022.09.036

Cited by 4 publications

(12 citation statements)

References 57 publications

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“…External forces are applied by multiple tools including optical tweezers, 100-102 magnetic tweezers, 63,103,104 electric fields, [105][106][107] and AFM. [108][109][110] These devices can add forces or torques precisely and used for studying deformation mechanisms as well as mechanical properties.…”

Section: Reconfiguration Methodsmentioning

confidence: 99%

“…AFM can also be used for external loading studies. 108 A DNA crystal was constructed and nanoindentation was performed using AFM. The mechanical deformation behaviors and elastic properties were probed successfully.…”

Section: External Loadingmentioning

confidence: 99%

“…Fundamental structural properties such as Young's modulus of DNA constructs were measured in nanoindentation experiment using AFM. 108,109,142 During indentation, the force with respect to the separation between the AFM tip and the deepest indented point of the sample is recorded and used to calculate the Young's modulus (Figure 7(b)). The tip can also cut, fold, and stretch the surface of DNA structure.…”

Section: Experimental Characterizationmentioning

confidence: 99%

“…The separation is the displacement from the lowest indented point. The indentation depth is approximately 100 nm 108. (c) Manipulation of DNA origami using AFM through cutting 143.…”

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confidence: 99%

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Mechanics of Dynamic and Deformable DNA Nanostructures

Madhvacharyula

et al. 2022

Preprint

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In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations, whose design strategies have been studied extensively. Dynamic structures reconfigure in response to external cues. Such transformational mechanisms have been explored to create dynamic nanodevices for environmental sensing, payload delivery, and other applications. However, the precise control of reconfigurable dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during reconfiguration. These structures often have better controls in programmed deformation. However, related deformability and mechanics, as well as deformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable nanostructures from the mechanics perspectives. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding the deformations and mechanics, including commonly used elasticity theory, finite element method, and coarse-grained molecular dynamics models. Other special models are also introduced. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers. After presenting unique applications, we conclude with current challenges in dynamic and deformable structures and outlook for the development of the field.

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Section: Reconfiguration Methodsmentioning

confidence: 99%

Section: External Loadingmentioning

confidence: 99%

Section: Experimental Characterizationmentioning

confidence: 99%

“…The separation is the displacement from the lowest indented point. The indentation depth is approximately 100 nm 108. (c) Manipulation of DNA origami using AFM through cutting 143.…”

mentioning

confidence: 99%

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Mechanics of Dynamic and Deformable DNA Nanostructures

Madhvacharyula

et al. 2022

Preprint

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“…(e) The force-strain behaviors of dsDNA component (ds-l-DNA, top) and architectured structures (DNA crystal, bottom). 67,74,155,245,246 The reference length for the strain is the length of B-form DNA. The force in the DNA crystal is the force per loaded dsDNA.…”

Section: (C) Tomentioning

confidence: 99%

Mechanics of dynamic and deformable DNA nanostructures

Madhavacharyula

et al. 2023

Chem. Sci.

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Exploring the Potential of Three‐Dimensional DNA Crystals in Nanotechnology: Design, Optimization, and Applications

Kong

Sun

et al. 2023

Advanced Science

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DNA has been used as a robust material for the building of a variety of nanoscale structures and devices owing to its unique properties. Structural DNA nanotechnology has reported a wide range of applications including computing, photonics, synthetic biology, biosensing, bioimaging, and therapeutic delivery, among others. Nevertheless, the foundational goal of structural DNA nanotechnology is exploiting DNA molecules to build three‐dimensional crystals as periodic molecular scaffolds to precisely align, obtain, or collect desired guest molecules. Over the past 30 years, a series of 3D DNA crystals have been rationally designed and developed. This review aims to showcase various 3D DNA crystals, their design, optimization, applications, and the crystallization conditions utilized. Additionally, the history of nucleic acid crystallography and potential future directions for 3D DNA crystals in the era of nanotechnology are discussed.

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Mechanical deformation behaviors and structural properties of ligated DNA crystals

Cited by 4 publications

References 57 publications

Mechanics of Dynamic and Deformable DNA Nanostructures

Mechanics of Dynamic and Deformable DNA Nanostructures

Mechanics of dynamic and deformable DNA nanostructures

Exploring the Potential of Three‐Dimensional DNA Crystals in Nanotechnology: Design, Optimization, and Applications

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