3D Freestanding DNA Nanostructure Hybrid as a Low-Density High-Strength Material

Rapid Silicification of a DNA Origami with Shape Fidelity

High-fidelity patterning of DNA origami nanostructures on various interfaces holds great potential for nanoelectronics and nanophotonics. However, distortion of a DNA origami often occurs due to the strong interface interactions, e.g., on two-dimensional (2D) materials. In this study, we discovered that the adsorption of silica precursors in rapid silicification can prevent the distortion caused by graphene and generates a high shape-fidelity DNA origami-silica composite on a graphene interface. We found that an incubation time of 1 min and silicification time of 16 h resulted in the formation of DNA origami-silica composites with the highest shape fidelity of 99%. By comparing the distortion of the DNA origami on the graphene interface with and without silicification, we observed that rapid silicification effectively preserved the integrity of the DNA origami. Statistical analysis of scanning electron microscopy data indicates that compared to bare DNA origami, the DNA origami-silica composite has an increased shape fidelity by more than two folds. Furthermore, molecular dynamics simulations revealed that rapid silicification effectively suppresses the distortion of the DNA origami through the interhelical insertion of silica precursors. Our strategy provides a simple yet effective solution to maintain the shape-fidelity DNA origami on interfaces that have strong interaction with DNA molecules, expanding the applicable interfaces for patterning 2D DNA origamis.

Toward three-dimensional DNA industrial nanorobots

Nanoscale industrial robots have potential as manufacturing platforms and are capable of automatically performing repetitive tasks to handle and produce nanomaterials with consistent precision and accuracy. We demonstrate a DNA industrial nanorobot that fabricates a three-dimensional (3D), optically active chiral structure from optically inactive parts. By making use of externally controlled temperature and ultraviolet (UV) light, our programmable robot, ~100 nanometers in size, grabs different parts, positions and aligns them so that they can be welded, releases the construct, and returns to its original configuration ready for its next operation. Our robot can also self-replicate its 3D structure and functions, surpassing single-step templating (restricted to two dimensions) by using folding to access the third dimension and more degrees of freedom. Our introduction of multiple-axis precise folding and positioning as a tool/technology for nanomanufacturing will open the door to more complex and useful nano- and microdevices.

Mechanics of dynamic and deformable DNA nanostructures

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. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration 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 transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. 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 their associated deformations and mechanics. 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.

Self-assembled endogenous DNA nanoparticles for auto-release and expression of the eGFP gene in Bacillus subtilis

The development of DNA delivery techniques is critical to promote the wider use of deoxyribonucleic acids as cellular transporters. The present study aimed to develop a type of DNA nanoparticle (citZ-box) to automatically load and release cargo. The restriction enzyme can cleave citZ-boxes at pro-designed sites, and the enhanced green fluorescent protein gene (eGFP) can be delivered into the B. subtilis protoplasts by them. The process of eGFP expression is recorded using a confocal microscope over 4 h. Here, multiscaffold and multimodular designs are used for citZ-box assembly with a DAEDALUS module, DX_cage_design and rem (edge_length, 21), to ensure the structure was predicted as B-type DNA. Finally the citZ-box is estimated to be a 50.7 nm cube. The 3D structure of the citZ-box particle is detected to be approximately 50.3 ± 0.3 nm. DNA nanoparticles prepared as citZ-boxes have great potential as drug carriers with automatic loading and releasing abilities.

Mechanical deformation behaviors and structural properties of ligated DNA crystals

DNA self-assembly has emerged as a powerful strategy for constructing complex nanostructures. While the mechanics of individual DNA strands have been studied extensively, the deformation behaviors and structural properties of self-assembled architectures are not well understood. This is partly due to the small dimensions and limited experimental methods available. DNA crystals are macroscopic crystalline structures assembled from nanoscale motifs via sticky-end association. The large DNA constructs may thus be an ideal platform to study structural mechanics. Here, we investigate the fundamental mechanical properties and behaviors of ligated DNA crystals made of tensegrity triangular motifs. We perform coarse-grained molecular dynamics simulations and confirm the results with nanoindentation experiments using atomic force microscopy. We observe various deformation modes, including untension, linear elasticity, duplex dissociation, and single-stranded component stretch. We find that the mechanical properties of a DNA architecture are correlated with those of its components. However, the structure shows complex behaviors which may not be predicted by components alone and the architectural design must be considered.

Engineering Inorganic Materials with DNA Nanostructures

Nucleic acid nanotechnology lays a foundation for the user-friendly design and synthesis of DNA frameworks of any desirable shape with extreme accuracy and addressability. Undoubtedly, such features make these structures ideal modules for positioning and organizing molecules and molecular components into complex assemblies. One of the emerging concepts in the field is to create inorganic and hybrid materials through programmable DNA templates. Here, we discuss the challenges and perspectives of such DNA nanostructure-driven materials science engineering and provide insights into the subject by introducing various DNA-based fabrication techniques including metallization, mineralization, lithography, casting, and hierarchical self-assembly of metal nanoparticles.

Mutations in artificial self-replicating tiles: A step toward Darwinian evolution

In nature, mutation is the first step of evolution, where it provides the genetic variation for the natural selection to act. Here we take a system of artificial self-replicating tiles, DNA origami, that exhibit templated reproduction. We can generate a small fraction of mutations by introducing a mismatch in hybridization between parent and daughter. We can modify the origami functionality to affect the growth rate of the mutated species, giving it less or more evolutionary advantage, and to become dominant in several generations. The introduction of mutations into an artificial self-replicating system provides new directions for research into self-assembly processes.

Artificial self-replication and exponential growth holds the promise of gaining a better understanding of fundamental processes in nature but also of evolving new materials and devices with useful properties. A system of DNA origami dimers has been shown to exhibit exponential growth and selection. Here we introduce mutation and growth advantages to study the possibility of Darwinian-like evolution. We seed and grow one dimer species, AB, from A and B monomers that doubles in each cycle. A similar species from C and D monomers can replicate at a controlled growth rate of two or four per cycle but is unseeded. Introducing a small mutation rate so that AB parents infrequently template CD offspring we show experimentally that the CD species can take over the system in approximately six generations in an advantageous environment. This demonstration opens the door to the use of evolution in materials design.