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  1. Abstract

    Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable forceĀ field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.

     
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  2. Free, publicly-accessible full text available February 19, 2025
  3. In this work, we describe the development of a computational model for arrays of rotary DNA origami elements which can self-organize on a large scale and explore the interesting morphologies and orderā€“disorder transition behavior of these systems.

     
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  4. Structural DNA nanotechnology has enabled the design and construction of complex nanoscale structures with precise geometry and programmable dynamic and mechanical properties. Recent efforts have led to major advances in the capacity to actuate shape changes of DNA origami devices and incorporate DNA origami into larger assemblies, which open the prospect of using DNA to design shape-morphing assemblies as components of micro-scale reconfigurable or sensing materials. Indeed, a few studies have constructed higher order assemblies with reconfigurable devices; however, these demonstrations have utilized structures with relatively simple motion, primarily hinges that open and close. To advance the shape changing capabilities of DNA origami assemblies, we developed a multi-component DNA origami 6-bar mechanism that can be reconfigured into various shapes and can be incorporated into larger assemblies while maintaining capabilities for a variety of shape transformations. We demonstrate the folding of the 6-bar mechanism into four different shapes and demonstrate multiple transitions between these shapes. We also studied the shape preferences of the 6-bar mechanism in competitive folding reactions to gain insight into the relative free energies of the shapes. Furthermore, we polymerized the 6-bar mechanism into tubes with various cross-sections, defined by the shape of the individual mechanism, and we demonstrate the ability to change the shape of the tube cross-section. This expansion of current single-device reconfiguration to higher order scales provides a foundation for nano to micron scale DNA nanotechnology applications such as biosensing or materials with tunable properties. 
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  5. null (Ed.)
  6. Dynamic DNA nanotechnology involves the creation of nanoscale devices made of DNA whose primary function arises from their ability to undergo controlled motion or reconfiguration. In the past two decades, dynamic DNA nanotechnology has evolved to the point where it is now being employed in devices intended for applications in sensing, drug delivery, computation, nanorobotics, and more. In this review article, we discuss the design of dynamic DNA nanodevices and the characterization and prediction of device behavior. We also identify a number of continuing challenges in dynamic DNA nanotechnology and discuss potential solutions to those challenges. 
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  7. Abstract Achieving rapid, noninvasive actuation of DNA structures is critical to expanding the functionality of DNA nanotechnology. A promising actuation approach involves introducing multiple, short pairs of single-stranded DNA overhangs to components of the structure and triggering hybridization or dissociation of the overhangs via changes in solution ionic conditions to drive structural transitions. Here, we reveal the underlying basis of this new approach by computing via molecular simulations the free energy landscape of DNA origami hinges actuated between open and closed states. Our results reveal how the overhangs collectively introduce a sharp free-energy minimum at the closed state and a broad energy barrier between open and closed states and how changes in ionic conditions modulate these features of the landscape to drive actuation towards the open or closed state. We demonstrate the critical role played by hinge confinement in stabilizing the hybridized state of the overhangs and magnifying the energy barrier to dissociation. By analyzing how the distribution of overhangs and their length and sequence modulate the energy landscape, we obtain design rules for tuning the actuation behavior. The molecular insights obtained here should be applicable to a broad range of systems involving DNA hybridization within confined systems. 
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