DESIGNS AND MECHANICS OF ARCHITECTURED DNA ASSEMBLIES
Creators: name: Li, Ruixin
Publisher: name: Purdue University Graduate School
Year: 2023
Subjects: Numerical modelling and mechanical characterisation

description: Architectured metamaterials are artificial systems with unique structural characteristics. They show distinct deformation behaviors and improved mechanical properties compared to regular materials. For example, mechanical metamaterials demonstrate negative Poisson's ratios, whereas regular materials have positive values. In theory, the auxetic behaviors arise from periodic cellular architectures regardless of the materials utilized. While this premise is mostly true for macroscopic metamaterials, it may not work well at a very small lengthscale since chemistry may play a critical role in nanostructures. However, this fundamental idea has not been addressed due to the lack of powerful manufacturing strategies at the nanoscale. The majority of architectured metamaterials are manufactured from top down with their unit size of microns or larger. On the other hand, there are also molecular auxetics which are natural crystals and thus are not designable. Therefore, there is a significant gap in lengthscale from 10 nm to 1 µm. DNA self-assembly is a bottom-up approach that can construct complex nanostructures based on sequence complementarity. Examples include DNA origami structures and DNA tile assemblies. This dissertation bridges the gap in the lengthscale by introducing nanoscale auxetic units from DNA and investigates relevant structural properties and mechanical behaviors. This study addresses the premise of metamaterials and elucidates the structure-property relation. The findings from this work formulate design principles for DNA based auxetic metastructures. In this work, we built several two-dimensional (2D) auxetic nanostructures from wireframe DNA origami. They serve as the model systems to demonstrate the feasibility of constructing nanoscale auxetics via DNA self-assembly. DNA origami structures are commonly constructed by a long ‘scaffold’ strand with many ‘staple’ oligonucleotides. Since the DNA metastructures are too small to directly apply external forces, we implemented chemical deformation by inserting ‘jack’ edges. Like a car jack, the length of the jack edges can be modulated via two-step DNA reactions: toehold-mediated strand displacement and annealing with a new set of jack staples. The DNA nanostructures reconfigure accordingly. To complement the experiment, we performed molecular dynamics (MD) simulations based on coarse-grained models using an open-source oxDNA platform. In the numerical computation, external loads were directly applied to deform the metastructures, providing details of structural deformation. We discovered that the auxetic behaviors of DNA metamaterials can be estimated by architectural designs, however the material properties are also crucial in the structures and deformations. Our mechanistic study provided general design guidelines for 2D auxetic DNA metamaterials. We also designed and constructed a Hoberman flight ring from DNA, a simplified planar version of Hoberman sphere. This structure consists of six equilateral triangles that are topologically organized into two layers, resembling a trefoil knot. The DNA flight ring deploys upon external forces, expanding (open state) or contracting (closed state) by sliding the two layers of triangles. This is the first synthetic deployable nanostructure and offers a versatile platform for topological research. This thesis also investigates 3D effects in DNA assemblies and related mechanics. We used a DNA origami tile designed with an intrinsic twist as a model system and explored its cyclization process using MD simulations. The numerical computation revealed the detailed process where the structure untwists and curves for cyclization simultaneously under external forces. The force and energy required to overcome the initial curvature and cause the 3D deformation were also calculated. The results agree well with the previous experiment and theory, further verifying the simulation method. Direct mechanical forces and DNA responses were realized experimentally with 3D DNA crystals built from triangular DNA tiles. Nanoindentation was performed on macroscopic ligated crystals using atomic force microscopy (AFM). MD simulations were performed in parallel, which revealed the full spectrum of several distinct deformation modes from linear elasticity to structural failure. The combined experiment, computation, and theoretical calculation showed that the complex behaviors can only be understood fully by considering the structure and its components. The scientific findings from this thesis should contribute to the construction of auxetic metastructures, the design methods for DNA based metamaterials as well as the prediction of their structural properties and mechanical behaviors. This thesis will pave the way for building architectured materials from DNA with tailored properties and functionalities, opening the door for new opportunities and unique applications.