Directional Assembly of Nanoparticles by DNA Shapes: Towards Designed Architectures and Functionality

Dynamic Gold Nanostructures Based on DNA Self Assembly

The combination of DNA nanotechnology and Nano Gold (NG) plasmon has opened exciting possibilities for a new generation of functional plasmonic systems that exhibit tailored optical properties and find utility in various applications. In this review, the booming development of dynamic gold nanostructures are summarized, which are formed by DNA self-assembly using DNA-modified NG, DNA frameworks, and various driving forces. The utilization of bottom-up strategies enables precise control over the assembly of reversible and dynamic aggregations, nano-switcher structures, and robotic nanomachines capable of undergoing on-demand, reversible structural changes that profoundly impact their properties. Benefiting from the vast design possibilities, complete addressability, and sub-10 nm resolution, DNA duplexes, tiles, single-stranded tiles and origami structures serve as excellent platforms for constructing diverse 3D reconfigurable plasmonic nanostructures with tailored optical properties. Leveraging the responsive nature of DNA interactions, the fabrication of dynamic assemblies of NG becomes readily achievable, and environmental stimulation can be harnessed as a driving force for the nanomotors. It is envisioned that intelligent DNA-assembled NG nanodevices will assume increasingly important roles in the realms of biological, biomedical, and nanomechanical studies, opening a new avenue toward exploration and innovation.

Tetrahedral framework nucleic acids for improving wound healing

Wounds are one of the most common health issues, and the cost of wound care and healing has continued to increase over the past decade. In recent years, there has been growing interest in developing innovative strategies to enhance the efficacy of wound healing. Tetrahedral framework nucleic acids (tFNAs) have emerged as a promising tool for wound healing applications due to their unique structural and functional properties. Therefore, it is of great significance to summarize the applications of tFNAs for wound healing. This review article provides a comprehensive overview of the potential of tFNAs as a novel therapeutic approach for wound healing. In this review, we discuss the possible mechanisms of tFNAs in wound healing and highlight the role of tFNAs in modulating key processes involved in wound healing, such as cell proliferation and migration, angiogenesis, and tissue regeneration. The targeted delivery and controlled release capabilities of tFNAs offer advantages in terms of localized and sustained delivery of therapeutic agents to the wound site. In addition, the latest research progress on tFNAs in wound healing is systematically introduced. We also discuss the biocompatibility and biosafety of tFNAs, along with their potential applications and future directions for research. Finally, the current challenges and prospects of tFNAs are briefly discussed to promote wider applications.

Utilizing peptide-anchored DNA templates for novel programmable nanoparticle assemblies in biological macromolecules: A review

Biological macromolecules such as proteins and DNA are known to self-assemble into various structural moieties with distinct functions. While nucleic acids are the structural building blocks, peptides exemplify diversity as tailorable biochemical units. Thus, combining the scaffold properties of the biomacromolecule DNA and the functionality of peptides could evolve into a powerful method to obtain tailorable nano assemblies. In this review, we discuss the assembly of non-DNA-coated colloidal NPs on DNA/peptide templates using functional anchors. We begin with strategies for directly attaching metallic NPs to DNA templates to ascertain the functional role of DNA as a scaffold. Followed by methods to assemble peptides onto DNA templates to emphasize the functional versatility of biologically abundant DNA-binding peptides. Next, we focus on studies corroborating peptide self-assembling into macromolecular templates onto which NPs can attach to emphasize the properties of NP-binding peptides. Finally, we discuss the assembly of NPs on a DNA template with a focus on the bifunctional DNA-binding peptides with NP-binding affinity (peptide anchors). This review aims to highlight the immense potential of combining the functional power of DNA scaffolds and tailorable functionalities of peptides for NP assembly and the need to utilize them effectively to obtain tailorable hierarchical NP assemblies.

DNA Origami-Based Letterpress Printing of Gold Nanostructures with Predesigned Morphologies

Creating customizable metallic nanostructures in a simple and controllable manner has been a long-standing goal in nanoscience. In this study, we use DNA origami as a letterpress printing plate and gold nanoparticles as ink to produce predesigned gold nanostructures. The letterpress plate is reusable, enabling the repetitive production of predesigned gold nanostructures. Furthermore, by modifying the DNA origami letterpress plate on magnetic beads, we can simplify the printing processes. We have successfully printed gold nanoparticle dimers, trimers, straight and quadrilateral tetramers, and other nanostructures. Our approach improves the flexibility and stability of metallic nanostructures, simplifying both their design and their operation. It promises universal applicability in the fabrication of metamaterials, biosensors, and surface plasma nanooptics.

Hybridization-Driven Adsorption of Polyadenine DNA onto Gold Nanoparticles

The attachment of functional DNA to gold nanoparticles via polyadenine adsorption is a well-established technology. This approach was mainly viewed through the lens of changing the DNA charge in order to reduce the electrostatic barrier created by a similarly charged gold surface. However, altering the DNA charge results in the loss of its functionality. This work considers the adsorption process of polyadenines by force that artificially brings them closer to the surface. As a force source, we used the hybridization of a DNA strand carrying polyadenines with a complementary strand already attached to the surface. It was shown that the hybridization forces facilitated the adsorption of polyadenines. We believe that this approach is applicable in various areas where it is essential to preserve the functionality of DNA during conjugation with nanoparticles.

Rapid DNA origami nanostructure detection and classification using the YOLOv5 deep convolutional neural network

The intra-image identification of DNA structures is essential to rapid prototyping and quality control of self-assembled DNA origami scaffold systems. We postulate that the YOLO modern object detection platform commonly used for facial recognition can be applied to rapidly scour atomic force microscope (AFM) images for identifying correctly formed DNA nanostructures with high fidelity. To make this approach widely available, we use open-source software and provide a straightforward procedure for designing a tailored, intelligent identification platform which can easily be repurposed to fit arbitrary structural geometries beyond AFM images of DNA structures. Here, we describe methods to acquire and generate the necessary components to create this robust system. Beginning with DNA structure design, we detail AFM imaging, data point annotation, data augmentation, model training, and inference. To demonstrate the adaptability of this system, we assembled two distinct DNA origami architectures (triangles and breadboards) for detection in raw AFM images. Using the images acquired of each structure, we trained two separate single class object identification models unique to each architecture. By applying these models in sequence, we correctly identified 3470 structures from a total population of 3617 using images that sometimes included a third DNA origami structure as well as other impurities. Analysis was completed in under 20 s with results yielding an F1 score of 0.96 using our approach.

How to design an icosahedral quasicrystal through directional bonding

Icosahedral quasicrystals (IQCs) are materials that exhibit long-range order but lack periodicity in any direction. Although IQCs were the first reported quasicrystals¹, they have been experimentally observed only in metallic alloys², not in other materials. By contrast, quasicrystals with other symmetries (particularly dodecagonal) have now been found in several soft-matter systems^3-5. Here we introduce a class of IQCs built from model patchy colloids that could be realized experimentally using DNA origami particles. Our rational design strategy leads to systems that robustly assemble in simulations into a target IQC through directional bonding. This is illustrated for both body-centred and primitive IQCs, with the simplest systems involving just two particle types. The key design feature is the geometry of the interparticle interactions favouring the propagation of an icosahedral network of bonds, despite this leading to many particles not being fully bonded. As well as furnishing model systems in which to explore the fundamental physics of IQCs, our approach provides a potential route towards functional quasicrystalline materials.

Programming patchy particles to form three-dimensional dodecagonal quasicrystals

Model patchy particles have been shown to be able to form a wide variety of structures, including symmetric clusters, complex crystals, and even two-dimensional quasicrystals. Here, we investigate whether we can design patchy particles that form three-dimensional quasicrystals, in particular targeting a quasicrystal with dodecagonal symmetry that is made up of stacks of two-dimensional quasicrystalline layers. We obtain two designs that are able to form such a dodecagonal quasicrystal in annealing simulations. The first is a one-component system of seven-patch particles but with wide patches that allow them to adopt both seven- and eight-coordinated environments. The second is a ternary system that contains a mixture of seven- and eight-patch particles and is likely to be more realizable in experiments, for example, using DNA origami. One interesting feature of the first system is that the resulting quasicrystals very often contain a screw dislocation.

Resilient three-dimensional ordered architectures assembled from nanoparticles by DNA

Rapid developments of DNA-based assembly methods provide versatile capabilities in organizing nanoparticles (NPs) in three-dimensional (3D) organized nanomaterials, which is important for optics, catalysis, mechanics, and beyond. However, the use of these nanomaterials is often limited by the narrow range of conditions in which DNA lattices are stable. We demonstrate here an approach to creating an inorganic, silica-based replica of 3D periodic DNA-NP structures with different lattice symmetries. The created ordered nanomaterials, through the precise 3D mineralization, maintain the spatial topology of connections between NPs by DNA struts and exhibit a controllable degree of the porosity. The formed silicated DNA-NP lattices exhibit excellent resiliency. They are stable when exposed to extreme temperatures (>1000°C), pressures (8 GPa), and harsh radiation conditions and can be processed by the conventional nanolithography methods. The presented approach allows the use of a DNA assembly strategy to create organized nanomaterials for a broad range of operational conditions.

Engineered Silicon Carbide Three-Dimensional Frameworks through DNA-Prescribed Assembly

The ability to create nanoengineered silicon carbide (SiC) architectures is important for the diversity of optical, electronic, and mechanical applications. Here, we report a fabrication of periodic three-dimensional (3D) SiC nanoscale architectures using a self-assembled and designed 3D DNA-based framework. The assembly is followed by the templating into silica and subsequent conversion into SiC using a lower temperature pathway (<700 °C) via magnesium reduction. The formed SiC framework lattice has a unit size of about 50 nm and domains over 5 μm, and it preserves the integrity of the original 3D DNA lattice. The spectroscopic and electron microscopy characterizations reveal SiC crystalline morphology of 3D nanoarchitectured lattices, whereas electrical probing shows 2 orders of magnitude enhancements of electrical conductivity over the precursor silica framework. The reported approach offers a versatile methodology toward creating highly structured and spatially prescribed SiC nanoarchitectures through the DNA-programmable assembly and the combination of templating processes.

Toehold-Mediated Selective Assembly of Compact Discrete DNA Nanostructures

Production of small discrete DNA nanostructures containing covalent junctions requires reliable methods for the synthesis and assembly of branched oligodeoxynucleotide (ODN) conjugates. This study reports an approach for self-assembly of hard-to-obtain primitive discrete DNA nanostructures-"nanoethylenes", dimers formed by double-stranded oligonucleotides using V-shaped furcate blocks. We scaled up the synthesis of V-shaped oligonucleotide conjugates using pentaerythritol-based diazide and alkyne-modified oligonucleotides using copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) and optimized the conditions for "nanoethylene" formation. Next, we designed nanoethylene-based "nanomonomers" containing pendant adapters. They demonstrated smooth and high-yield spontaneous conversion into the smallest cyclic product, DNA tetragon aka "nano-methylcyclobutane". Formation of DNA nanostructures was confirmed using native polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM) and additionally studied by molecular modeling. The proposed facile approach to discrete DNA nanostructures using precise adapter-directed association expands the toolkit for the realm of DNA origami.

DNA-Functionalized Nanoparticles for Targeted Biosensing and Biological Applications

Nanoscale systems have increasingly been used in biomedical applications, enhancing the demand for the development of biomolecule-functionalized nanoparticles for targeted applications. Such designer nanosystems hold great prospective to refine disease diagnosis and treatment. To completely investigate their potential for bioapplications, nanoparticles must be biocompatible and targetable toward explicit receptors to guarantee particular detecting, imaging, and medication conveyance in complex organic milieus, for example, living cells, tissues, and organisms. We present recent works that explore enhanced biocompatibility and biorecognition of nanoparticles functionalized with DNA and different DNA entities such as aptamers, DNAzymes, and aptazymes. We sum up the methods utilized in the amalgamation of complex nanostructures, survey the significant types of multifunctional nanoparticles that have been developed in the course of recent years, and give a perceptual vision of the significant field of nanomedicine. The field of DNA-functionalized nanoparticles holds an incredible guarantee in rising biomedical zones, for example, multimodal imaging, theranostics, and picture-guided treatments.

Stepwise Strategy for One-Pot Synthesis of Single-Stranded DNA Rings from Multiple Short Fragments

Cyclic rings of single-stranded (ss) DNA have various unique properties, but wider applications have been hampered by their poor availability. This paper reports a convenient one-pot method in which these rings are efficiently synthesized by using T4 DNA ligase through convergent cyclization of easily available short DNA fragments. The key to the present method is to separate all the splint oligonucleotides into several sets, and add each set sequentially at an appropriate interval to the solutions containing all the short DNA fragments. Compared with simple one-pot strategies involving simultaneous addition of all the splints at the beginning of the reaction, both the selectivity and the yields of target ssDNA rings are greatly improved. This convergent method is especially useful for preparing large-sized rings that are otherwise hard to obtain. By starting from six short DNA fragments (71-82 nt), prepared by a DNA synthesizer, a ssDNA ring of 452-nt size was synthesized in 35 mol % yield and in high selectivity. Satisfactorily pure DNA rings were obtainable simply by treating the crude products with exonuclease.