Controlling Silicification on DNA Origami with Polynucleotide Brushes

Diverse applications of DNA origami as a cross-disciplinary tool

As knowledge from a single discipline is no longer sufficient to keep pace with the growing complexity of technological advancements, interdisciplinary collaboration has become a crucial driver of innovation. DNA nanotechnology exemplifies this integration, serving as a field where cross-disciplinary communication is particularly prominent. Since its introduction by Rothemund in 2006, DNA origami has proved to be a powerful tool for interdisciplinary research, offering exceptional structural stability, programmability, and addressability. This review provides an overview of the development of DNA origami technology, highlights its major advances, and explores its innovative applications across various disciplines in recent years, showcasing its vast potential and future prospects. We believe DNA origami is poised for even broader applications, driving progress across multiple fields.

Two-Dimensional, Chiral Colloidal Superlattices Engineered with DNA Origami

Colloidal crystal engineering is widely recognized as a superior method for creating novel materials in multiple fields. However, achieving chiral superlattices of nanoparticles remains a considerable challenge so far. Here, we spread a two-dimensional (2D), microscale DNA origami array on substrate surfaces to maintain its planar conformation onto which DNA-encoded metal nanoparticles are attached to designated positions, thereby creating 2D chiral superlattices. By designing programmable chiral patterns of DNA sticky ends within the DNA origami units, we realize a variety of 2D chiral superlattices over large areas with well-defined chiral configurations of nanoparticle arrangements. The underlying chiral optical mechanism of the superlattices is revealed, showing the essential role of local plasmonic couplings within the repeating units. This research represents the first example of DNA-programmed 2D chiral superlattices of nanoparticles assembled directly on a substrate surface, with the potential to impact future studies in on-chip integrated metamaterials, photonics, optoelectronics, and related fields.

Crystalline Assemblies of DNA Nanostructures and Their Functional Properties

Self-assembly presents a remarkable approach for creating intricate structures by positioning nanomaterials in precise locations, with control over molecular interactions. For example, material arrays with interplanar distances similar to the wavelength of light can generate structural color through complex interactions like scattering, diffraction, and interference. Moreover, enzymes, plasmonic nanoparticles, and luminescent materials organized in periodic lattices are envisioned to create functional materials with various applications. Focusing on structural DNA nanotechnology, here, we summarized the recent developments of two- and three-dimensional lattices made purely from DNA nanostructures. We review DNA-based monomer design for different lattices, guest molecule assembly, and inorganic material coating techniques and discuss their functional properties and potential applications in photonic crystals, nanoelectronics, and bioengineering as well as future challenges and perspectives.

Silica-Biomacromolecule Interactions: Toward a Mechanistic Understanding of Silicification

Silica-organic composites are receiving renewed attention for their versatility and environmentally benign compositions. Of particular interest is how macromolecules interact with aqueous silica to produce functional materials that confer remarkable physical properties to living organisms. This Review first examines silicification in organisms and the biomacromolecule properties proposed to modulate these reactions. We then highlight findings from silicification studies organized by major classes of biomacromolecules. Most investigations are qualitative, using disparate experimental and analytical methods and minimally characterized materials. Many findings are contradictory and, altogether, demonstrate that a consistent picture of biomacromolecule-Si interactions has not emerged. However, the collective evidence shows that functional groups, rather than molecular classes, are key to understanding macromolecule controls on mineralization. With recent advances in biopolymer chemistry, there are new opportunities for hypothesis-based studies that use quantitative experimental methods to decipher how macromolecule functional group chemistry and configuration influence thermodynamic and kinetic barriers to silicification. Harnessing the principles of silica-macromolecule interactions holds promise for biocomposites with specialized applications from biomedical and clean energy industries to other material-dependent industries.

Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies

Chemo-mechanical deformation of structured DNA assemblies driven by DNA-binding ligands has offered promising avenues for biological and therapeutic applications. However, it remains elusive how to effectively model and predict their effects on the deformation and mechanical properties of DNA structures. Here, we present a computational framework for simulating chemo-mechanical change of structured DNA assemblies. We particularly quantify the effects of ethidium bromide (EtBr) intercalation on the geometry and mechanical properties of DNA base-pairs through molecular dynamics simulations and integrated them into finite-element-based structural analysis to predict the shape and properties of DNA objects. The proposed model captures various structural changes induced by EtBr-binding such as shape variation, flexibility modulation, and supercoiling instability. It enables a rational design of structured DNA assemblies with tunable shapes and mechanical properties by binding molecules.

Proximity-Induced Bipedal DNA Walker for Accurately Visualizing microRNA in Living Cancer Cell

DNA walker, a type of dynamic DNA device that is capable of moving progressively along prescribed walking tracks, has emerged as an ideal and powerful tool for biosensing and bioimaging. However, most of the reported three-dimensional (3D) DNA walker were merely designed for the detection of a single target, and they were not capable of achieving universal applicability. Herein, we reported for the first time the development of a proximity-induced 3D bipedal DNA walker for imaging of low abundance biomolecules. As a proof of concept, miRNA-34a, a biomarker of breast cancer, is chosen as the model system to demonstrate this approach. In our design, the 3D bipedal DNA walker can be generated only by the specific recognition of two proximity probes for miRNA-34a. Meanwhile, it stochastically and autonomously traveled on 3D tracks (gold nanoparticles) via catalytic hairpin assembly (CHA), resulting in the amplified fluorescence signal. In comparison with some conventional DNA walkers that were utilized for living cell imaging, the 3D DNA walkers induced by proximity ligation assay can greatly improve and ensure the high selectivity of bioanalysis. By taking advantage of these unique features, the proximity-induced 3D bipedal DNA walker successfully realizes accurate and effective monitoring of target miRNA-34a expression levels in living cells, affording a universal, valuable, and promising platform for low-abundance cancer biomarker detection and accurate identification of cancer.

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.