Biology subjects

Swett, A. A.

Publications and source records attributed to Swett, A. A..

3 recordsLinked to original sources

bioRxiv2025

Understanding Structural Mechanics of Ligated DNA Crystals via Molecular Dynamics Simulation

DNA self-assembly is a highly programmable method that can construct arbitrary architectures based on sequence complementarity. Among various constructs, DNA crystals are macroscopic crystalline materials formed by assembling motifs via sticky end association. Due to their high structural integrity and size ranging from tens to hundreds of micrometers, DNA crystals offer unique opportunities to study structural properties and deformation behaviors of DNA assemblies. For example, enzymatic ligation of sticky ends can selectively seal nicks resulting in more robust structures with enhanced mechanical properties. However, the research efforts have been mostly on experiments such as different motif designs, structural optimization, or new synthesis methods, while their mechanics are not fully understood. The complex properties of DNA crystals are difficult to study via experiment alone, and numerical simulation can complement and inform the experiment. Coarse-grained molecular dynamics (MD) simulation is a powerful tool that can probe the mechanics of DNA assemblies. Here, we investigate DNA crystals made of four different motif lengths with various ligation patterns (full ligation, major directions, connectors, and in-plane) using oxDNA, an open-source, coarse-grained MD platform. We find that several distinct deformation stages emerge in response to mechanical loading and that the number and the location of the ligated nucleotides can significantly modulate structural behaviors. These findings should be useful for predicting crystal properties and thus improving the design.

biophysics↗

bioRxiv2024

Realizing Mechanical Frustration at the Nanoscale Using DNA Origami

Structural designs inspired by physical and biological systems have been previously utilized to develop advanced mechanical metamaterials. These are based on the clever geometric arrangement of their building blocks, resulting in enhanced mechanical properties such as shape morphing and auxetic behavior. Until now, the benefits from such designs have yet to be leveraged at the nanoscale. Here, we use the DNA origami method to realize a nanoscale metastructure exhibiting mechanical frustration, the mechanical counterpart of the well-known phenomenon of magnetic frustration. We show that this DNA metastructure can be precisely controlled to adopt either frustrated or non-frustrated mechanical states, each characterized by a distinct free energy profile. Switching among the states is achieved by engineering reconfigurable struts into the structure. Actuation of the struts causes a global deformation of the metastructures. In the non-frustrated state, strain can be distributed homogeneously throughout the structure, while in the frustrated state, strain is concentrated at a specific location. Molecular dynamics simulations reconcile the contrasting behaviors of the two modes and provide detailed insights into the mechanics. Our work demonstrates how combining programmable DNA self-assembly with mechanical design principles can overcome engineering limitations encountered at the macroscale, enabling the development of dynamic, deformable nanostructures with tunable responses. These may lay the foundation for mechanical energy storage elements, nanomechanical computation, and allosteric mechanisms in DNA-based nanomachinery.

biophysics↗

bioRxiv2023

DNA Nanostar Structures with Tunable Auxetic Properties

Auxetic structures are unique with a negative Poissons ratio. Unlike regular materials, they response to external loading with simultaneous expansion or compression in all directions, rendering powerful properties advantageous in diverse applications from manufacturing to space engineering. The auxetic behaviors are determined by structural design and architecture. Such structures have been discovered in natural crystals and demonstrated synthetically with bulk materials. Recent development of DNA-based structures has pushed the unit cell size to nanometer scale. DNA nanotechnology utilizes sequence complementarity between nucleotides. By combining sequence designs with programmable self-assembly, it is possible to construct complex structures with nanoscale accuracy and to perform dynamic reconfigurations. Herein, we report a novel design of auxetic nanostars with sliding behaviors using DNA origami. Our proposed structure, inspired by an Islamic pattern, demonstrates a unit cell with two distinct reconfigurations by programming directed sliding mechanisms. Compared to previous metamaterials, the DNA nanostars show an architecture with tunable auxetic properties for the first time. We envision that this strategy may form the basis of novel metastructures with adaptability and open new possibilities in bioengineering.

biophysics↗