Mechanics of Dynamic and Deformable DNA Nanostructures

Abstract

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.

Realizing Mechanical Frustration at the Nanoscale Using DNA Origami

“…These patterns indicate the mechanism of strain distributions within the structure. The edges in e and f are also colored on the basis of relative position, highlighted by the inset in f. The edges experiencing significant flexure (37) and buckling (27) are highlighted. The complete numbering of all edges is given in Fig.…”

“…Given the excellent programmability and structural predictability, DNA self-assembly has demonstrated both static and dynamic nanostructures including 2D lattices 16,17 , 3D polyhedra 18 , reconfigurable switches 19 , kinematic mechanisms 20,21 , and nanomachines powered by electric fields and chemical potentials [22][23][24] . Most deformable DNA constructs fall under the umbrella of adaptability where their components interact in synchrony to exhibit overall deformations or even negative Poisson's ratios [25][26][27] . Recent reports used computational mechanics to understand relevant properties and thermodynamic models to elucidate free energy landscapes 28,29 .…”

DNA Nanostar Structures with Tunable Auxetic Properties

“…26,30,43,44 We envision that DNA-based structural design can be used to build metamaterials with multimode reconfigurability that can detect and respond to complex surroundings and show adaptive mechanical properties. For example, combined with aptamers, i-motifs or enzymatic reactions, [45][46][47][48][49][50] DNA-based metamaterials will have strong potential to respond to environmental changes (e.g., pH change or the presence/absence of target molecules) with mechanical responses (e.g., changing stiffness, young's modulus, etc). The strategy may be extended to various applications such as wound healing and vascular scaffolds.…”

DNA nanostar structures with tunable auxetic properties

“…27,31,49,50 In addition, DNA-based structural design can be used to build metamaterials with multimode reconfigurability that can detect and respond to complex surroundings and show adaptive mechanical properties. For example, combined with aptamers, i-motifs or enzymatic reactions, [51][52][53][54][55][56] DNA-based metamaterials will have strong potential to respond to environmental changes (e.g., pH change or the presence/ absence of target molecules) with mechanical responses (e.g., changing stiffness, Young's modulus, etc.). The strategy may be extended to various applications such as wound healing and vascular scaffolds.…”