DNA Assembly of Modular Components into a Rotary Nanodevice

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.

DNA-Based Molecular Machines: Controlling Mechanisms and Biosensing Applications

The rise of DNA nanotechnology has driven the development of DNA-based molecular machines, which are capable of performing specific operations and tasks at the nanoscale. Benefitting from the programmability of DNA molecules and the predictability of DNA hybridization and strand displacement, DNA-based molecular machines can be designed with various structures and dynamic behaviors and have been implemented for wide applications in the field of biosensing due to their unique advantages. This review summarizes the reported controlling mechanisms of DNA-based molecular machines and introduces biosensing applications of DNA-based molecular machines in amplified detection, multiplex detection, real-time monitoring, spatial recognition detection, and single-molecule detection of biomarkers. The challenges and future directions of DNA-based molecular machines in biosensing are also discussed.

Bubble DNA tweezer: A triple-conformation sensor responsive to concentration-ratios

DNA tweezers, with their elegant simplicity and flexibility, have been pivotal in biosensing and DNA computing. However, conventional tweezers are confined to a binary transformation pre/post target signal recognition, limiting them to presence/absence judgments. This study introduces bubble DNA tweezers (BDT), capable of three distinct conformations based on variable target signal ratios. In contrast to traditional compact tweezers, BDT features a looser structure centered around a non-complementary bubble domain located between the tweezer arms' connecting axis and target signal recognition jaws. This bubble triggers toehold-free DNA strand displacement, leading to three conformational changes at different target signal concentrations. BDT detects presence/absence and true concentration with remarkable specificity and sensitivity. This adaptability is not confined to ideal scenarios, proving valuable in complex, noisy environments. Our method facilitates target DNA/miRNA signal quantification within a specific length range, promising applications in clinical research and environmental detection, while inspiring future biological assay innovations.

Twisted DNA Origami-Based Chiral Monolayers for Spin Filtering

DNA monolayers with inherent chirality play a pivotal role across various domains including biosensors, DNA chips, and bioelectronics. Nonetheless, conventional DNA chiral monolayers, typically constructed from single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA), often lack structural orderliness and design flexibility at the interface. Structural DNA nanotechnology has emerged as a promising solution to tackle these challenges. In this study, we present a strategy for crafting highly adaptable twisted DNA origami-based chiral monolayers. These structures exhibit distinct interfacial assembly characteristics and effectively mitigate the structural disorder of dsDNA monolayers, which is constrained by a limited persistence length of ∼50 nm of dsDNA. We highlight the spin-filtering capabilities of seven representative DNA origami-based chiral monolayers, demonstrating a maximal one-order-of-magnitude increase in spin-filtering efficiency per unit area compared with conventional dsDNA chiral monolayers. Intriguingly, our findings reveal that the higher-order tertiary chiral structure of twisted DNA origami further enhances the spin-filtering efficiency. This work paves the way for the rational design of DNA chiral monolayers.

Nucleotide-based regenerated fiber production using salmon (Oncorhynchus keta) milt waste by solution spinning

The use of nucleic acid-derived fibers has not been developed in contrast to the traditional use of polysaccharide- and protein-based fibers in daily life. Salmon, Oncorhynchus keta, is an abundant fishery resource, and its milt contains a huge amount of DNA. Most of the milt is discarded because it degrades easily and is unsuitable for food consumption. DNA-based fibers are expected to possess functionality and mechanical strength because DNA is a polyanion with a high molecular weight. Here, using DNA extracted from the salmon milt, we produced nucleotide-based fibers. A solution spinning system was applied using ethanol as a coagulant. Adding the salt to the dope solution reduced the solubility of DNA, which was essential for the successful spinning of DNA-based fibers. The obtained fibers became insoluble in water by ultraviolet (UV) exposure. Fibril-like structures were detected on the fracture surface, and humidity influenced the conformational structure. This study focuses on the bulk-scale production of biodegradable DNA-based fibers. Therefore, it can be used not only for clothing and filters but also as a functional material to remove harmful pollutants released into the ocean, such as heavy metal ions and aromatic derivatives.

DNA-Based Gold Nanoparticle Assemblies: From Structure Constructions to Sensing Applications

Gold nanoparticles (Au NPs) have become one of the building blocks for superior assembly and device fabrication due to the intrinsic, tunable physical properties of nanoparticles. With the development of DNA nanotechnology, gold nanoparticles are organized in a highly precise and controllable way under the mediation of DNA, achieving programmability and specificity unmatched by other ligands. The successful construction of abundant gold nanoparticle assembly structures has also given rise to the fabrication of a wide range of sensors, which has greatly contributed to the development of the sensing field. In this review, we focus on the progress in the DNA-mediated assembly of Au NPs and their application in sensing in the past five years. Firstly, we highlight the strategies used for the orderly organization of Au NPs with DNA. Then, we describe the DNA-based assembly of Au NPs for sensing applications and representative research therein. Finally, we summarize the advantages of DNA nanotechnology in assembling complex Au NPs and outline the challenges and limitations in constructing complex gold nanoparticle assembly structures with tailored functionalities.

Engineering DNA-based cytoskeletons for synthetic cells

The development and bottom-up assembly of synthetic cells with a functional cytoskeleton sets a major milestone to understand cell mechanics and to develop man-made machines on the nano- and microscale. However, natural cytoskeletal components can be difficult to purify, deliberately engineer and reconstitute within synthetic cells which therefore limits the realization of multifaceted functions of modern cytoskeletons in synthetic cells. Here, we review recent progress in the development of synthetic cytoskeletons made from deoxyribonucleic acid (DNA) as a complementary strategy. In particular, we explore the capabilities and limitations of DNA cytoskeletons to mimic functions of natural cystoskeletons like reversible assembly, cargo transport, force generation, mechanical support and guided polymerization. With recent examples, we showcase the power of rationally designed DNA cytoskeletons for bottom-up assembled synthetic cells as fully engineerable entities. Nevertheless, the realization of dynamic instability, self-replication and genetic encoding as well as contractile force generating motors remains a fruitful challenge for the complete integration of multifunctional DNA-based cytoskeletons into synthetic cells.

A Review on Self-Assembly of Colloidal Nanoparticles into Clusters, Patterns, and Films: Emerging Synthesis Techniques and Applications

The colloidal synthesis of functional nanoparticles has gained tremendous scientific attention in the last decades. In parallel to these advancements, another rapidly growing area is the self-assembly or self-organization of these colloidal nanoparticles. First, the organization of nanoparticles into ordered structures is important for obtaining functional interfaces that extend or even amplify the intrinsic properties of the constituting nanoparticles at a larger scale. The synthesis of large-scale interfaces using complex or intricately designed nanostructures as building blocks, requires highly controllable self-assembly techniques down to the nanoscale. In certain cases, for example, when dealing with plasmonic nanoparticles, the assembly of the nanoparticles further enhances their properties by coupling phenomena. In other cases, the process of self-assembly itself is useful in the final application such as in sensing and drug delivery, amongst others. In view of the growing importance of this field, this review provides a comprehensive overview of the recent developments in the field of nanoparticle self-assembly and their applications. For clarity, the self-assembled nanostructures are classified into two broad categories: finite clusters/patterns, and infinite films. Different state-of-the-art techniques to obtain these nanostructures are discussed in detail, before discussing the applications where the self-assembly significantly enhances the performance of the process.

Recent Advances in DNA Origami-Engineered Nanomaterials and Applications

DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.

Ordered Assembly of DNA on Topological Insulator Bi2Se3 and Octadecylamine for a Sensitive Biosensor

Controlling the assembly of DNA in order on a suitable electrode surface is of great significance for biosensors and disease diagnosis, but it is full of challenges. In this work, we creatively assembled DNA on the surface of octadecylamine (ODA)-modified topological insulator (Tls) Bi₂Se₃ and developed an electrochemical biosensor to detect biomarker DNA of coronavirus disease 2019 (COVID-19). A high-quality Bi₂Se₃ sheet was obtained from a single crystal synthesized in our lab. A uniform ODA layer was coated in argon by chemical vapor deposition (CVD). We observed and analyzed the assembly and mechanism of single-strand DNA (ssDNA) and double-strand DNA (dsDNA) on the Bi₂Se₃ surface through atomic force microscopy (AFM) and molecular dynamics (MD) simulations. The electrochemical signal revealed that the biosensor based on the DNA/ODA/Bi₂Se₃ electrode has a wide linear detection range from 1.0 × 10^-12 to 1.0 × 10^-8 M, with the limit of detection as low as 5 × 10^-13 M. Bi₂Se₃ has robust surface states and improves the electrochemical signal-to-noise ratio, while the uniform ODA layer guides high-density ordered DNA, enhancing the sensitivity of the biosensor. Our work demonstrates that the ordered DNA/ODA/Bi₂Se₃ electrode surface has great application potential in the field of biosensing and disease diagnosis.

Controllable dynamics of complex DNA nanostructures

In the past four decades, a variety of self-assembly design frameworks have led to the construction of versatile DNA nanostructures with increasing complexity and controllability. The controllable dynamics of DNA nanostructures has garnered much interest and emerged as a powerful tool for conducting sophisticated tasks at the molecular level. In this minireview, we summarized the controllable reconfigurations of complex DNA nanostructures induced by nucleic acid strands, environmental stimuli and enzymatic treatments. We also envisioned that with the optimization of response time, sensitivity and specificity, dynamic DNA nanostructures have great promise in applications ranging from nanorobotics to life sciences.

Transformable Plasmonic Helix with Swinging Gold Nanoparticles

Control over multiple optical elements that can be dynamically rearranged to yield substantial three-dimensional structural transformations is of great importance to realize reconfigurable plasmonic nanoarchitectures with sensitive and distinct optical feedback. In this work, we demonstrate a transformable plasmonic helix system, in which multiple gold nanoparticles (AuNPs) can be directly transported by DNA swingarms to target positions without undergoing consecutive stepwise movements. The swingarms allow for programmable AuNP translocations in large leaps within plasmonic nanoarchitectures, giving rise to tailored circular dichroism spectra. Our work provides an instructive bottom-up solution to building complex dynamic plasmonic systems, which can exhibit prominent optical responses through cooperative rearrangements of the constituent optical elements with high fidelity and programmability.

Aluminum(III)-Based Organic Nanofibrous Gels as an Aggregation-Induced Electrochemiluminescence Emitter Combined with a Rigid Triplex DNA Walker as a Signal Magnifier for Ultrasensitive DNA Assay

Due to effective tackling of the problems of aggregation-caused quenching of traditional ECL emitters, aggregation-induced electrochemiluminescence (AIECL) has emerged as a research hotspot in aqueous detection and sensing. However, the existing AIECL emitters still encounter the bottlenecks of low ECL efficiency, poor biocompatibility, and high cost. Herein, aluminum(III)-based organic nanofibrous gels (AOGs) are used as a novel AIECL emitter to construct a rapid and ultrasensitive sensing platform for the detection of Flu A virus biomarker DNA (fDNA) with the assistance of a high-speed and hyper-efficient signal magnifier, a rigid triplex DNA walker (T-DNA walker). The proposed AOGs with three-dimensional (3D) nanofiber morphology are assembled in one step within about 15 s by the ligand 2,2':6',2″-terpyridine-4'-carboxylic acid (TPY-COOH) and cheap metal ion Al³⁺, which demonstrates an efficient ECL response and outstanding biocompatibility. Impressively, on the basis of loop-mediated isothermal amplification-generated hydrogen ions (LAMP-H⁺), the target-induced pH-responsive rigid T-DNA walker overcomes the limitations of conventional single or duplex DNA walkers in walking trajectory and efficiency due to the entanglement and lodging of leg DNA, exhibiting high stability, controllability, and walking efficiency. Therefore, AOGs with excellent AIECL performance were combined with a CG-C⁺ T-DNA nanomachine with high walking efficiency and stability, and the proposed "on-off" ECL biosensor displayed a low detection limit down to 23 ag·μL^-1 for target fDNA. Also, the strategy provided a useful platform for rapid and sensitive monitoring of biomolecules, considerably broadening its potential applications in luminescent molecular devices, clinical diagnosis, and sensing analysis.