Probing the Formation Kinetics and Thermodynamics with Rationally Designed Analytical Tools Enables One-Pot Synthesis and Purification of a Tetrahedral DNA Nanostructure

A trivalent aptasensor by using DNA tetrahedron as scaffold for label-free determination of antibiotics

Owing to advantage in high sensitivity and fast response, aptamer based electrochemical biosensors have attracted much more attention. However, inappropriate interfacial engineering strategy leads to poor recognition performance, which ascribe to the following factors of immobilized oligonucleotide strand including steric hindrance, interchain entanglement, and unfavorable conformation. In this work, we proposed a DNA tetrahedron based diblock aptamer immobilized strategy for the construction of label-free electrochemical biosensor. The diblock aptamer sequence is composite of T-rich anchor domain and recognition domain, where T-rich domain enabling anchored on the edge of DNA tetrahedron via Hoogsteen hydrogen bond at neutral condition. The DNA tetrahedron scaffold offers an appropriate lateral space for target recognition of diblock aptamer. More importantly, this trivalent aptamer recognition interface can be regenerated by simply adjusting the pH environment to alkaline, resulting in the dissociation of diblock aptamer. Under the optimum condition, proposed electrochemical aptasensor manifested a satisfied sensitivity for aminoglycosides antibiotic, kanamycin with a limit of detection of 0.69 nM, which is 45-fold lower than traditional Au-S immobilization strategy. Moreover, the proposed aptasensor had also successfully been extended to ampicillin detection by changing the sequence of recognition domain in diblock aptamer. This work paves a new way for the rational design of aptamer-based electrochemical sensor.

Plasmonic nanocavity-modulated electrochemiluminescence sensor for gastric cancer exosomal miRNA detection

Plasmonic nanocavity possessing highly light field confinement and electromagnetic field enhancement can concentrate and enhance the luminescence signal. The plasmonic nanocavity has the great potential value in biosensing research and improve analytical sensitivity. In this work, we constructed a plasmonic nanocavity between circular Au nanoplate-film and spherical Au nanoparticle with tetrahedral DNA nanostructures. The nanocavity structure can regulate the local density of optical states and provide the field restriction to enhance the spontaneous ECL radiation of PEDOT-S dots. Additionally, Au nanoparticle acted as nanoantenna which localized and modulated ECL to directional emission. Because the plasmonic nanocavity effectively collected and redistributed ECL signal, the emission was enhanced by 5.9 times with polarized characteristics. The proposed plasmonic nanocavity-based ECL sensor was further used to detect exosomal miRNA-223-3p in ascites. The detection results indicated the novel sensing strategy can assist early diagnosis of peritoneal metastasis of gastric cancer.

Protein Nanotubes as Advanced Material Platforms and Delivery Systems

Protein nanotubes (PNTs) as state-of-the-art nanocarriers are promising for various potential applications both in the food and pharmaceutical industries. Derived from edible starting sources like α-lactalbumin, lysozyme, and ovalbumin, PNTs bear properties of biocompatibility and biodegradability. Their large specific surface area and hydrophobic core facilitate chemical modification and loading of bioactive substances, respectively. Moreover, their enhanced permeability and penetration ability across biological barriers such as intestinal mucus, extracellular matrix, and thrombus clot, make it promising platforms for health-related applications. Most importantly, their simple preparation processes enable large-scale production, supporting applications in the biomedical and nanotechnological fields. Understanding the self-assembly principles is crucial for controlling their morphology, size, and shape, and thus provides the ground to a multitude of applications. Here, the current state-of-the-art of PNTs including their building materials, physicochemical properties, and self-assembly mechanisms are comprehensively reviewed. The advantages and limitations, as well as challenges and prospects for their successful applications in biomaterial and pharmaceutical sectors are then discussed and highlighted. Potential cytotoxicity of PNTs and the need of regulations as critical factors for enabling in vivo applications are also highlighted. In the end, a brief summary and future prospects for PNTs as advanced platforms and delivery systems are included.

Enhanced portable detection for Sars-CoV-2 utilizing DNA tetrahedron-tethered aptamers and a pressure meter

Tethering oligonucleotide aptamers to a DNA tetrahedron structure can enhance the recognition of SARS-CoV-2 spike protein to effectively overcome challenges with its detection in current diagnostic assays. Building on this framework, we have developed a unique portable detection method for COVID-19 that provides exceptional sensitivity and selectivity via pressure meter readout. This innovative assay streamlines the detection process, providing a rapid, sensitive, cost-effective, and user-friendly diagnostic tool. This point-of-care test exhibits high sensitivity and specificity, achieving an impressive detection limit of 0.1 pg mL-1 for the spike protein. The effectiveness of this method was validated using pseudoviruses and oropharyngeal swab samples, and its utility for environmental monitoring is demonstrated by testing sewage samples. With a wide linear range and strong potential for clinical or home application, our assay represents a major innovation in point-of-care diagnostics and provides a vital contribution to the current toolkit for controlling the impacts of COVID-19.

Nucleic acid nanostructures for in vivo applications: The influence of morphology on biological fate

The development of programmable biomaterials for use in nanofabrication represents a major advance for the future of biomedicine and diagnostics. Recent advances in structural nanotechnology using nucleic acids have resulted in dramatic progress in our understanding of nucleic acid-based nanostructures (NANs) for use in biological applications. As the NANs become more architecturally and functionally diverse to accommodate introduction into living systems, there is a need to understand how critical design features can be controlled to impart desired performance in vivo. In this review, we survey the range of nucleic acid materials utilized as structural building blocks (DNA, RNA, and xenonucleic acids), the diversity of geometries for nanofabrication, and the strategies to functionalize these complexes. We include an assessment of the available and emerging characterization tools used to evaluate the physical, mechanical, physiochemical, and biological properties of NANs in vitro. Finally, the current understanding of the obstacles encountered along the in vivo journey is contextualized to demonstrate how morphological features of NANs influence their biological fates. We envision that this summary will aid researchers in the designing novel NAN morphologies, guide characterization efforts, and design of experiments and spark interdisciplinary collaborations to fuel advancements in programmable platforms for biological applications.

Probing the self-assembly process of amphiphilic tetrahedral DNA frameworks

Herein we utilized the thermal hysteresis method to directly probe the self-assembly process of amphiphilic DNA nanostructures, with the use of an amphiphilic tetrahedral DNA framework (am-TDF) as a model system. The analysis of the reaction rate surfaces under different ionic strengths revealed that strands of amphiphilic DNA first formed metastable micelles via an entropy-driven process, which were then enthalpically transformed into am-TDF.

Characterization of DNA nanostructure stability by size exclusion chromatography

DNA-based nanostructures (DNs) are advantageous for the design of functional materials for biology and medicine due to the nanoscale control provided by their predictable self-assembly. However, the use of DNs in vivo has been limited due to structural instability in biofluids. As the stability of a particular DN sets the scope of its potential biological applications, efficient methods to characterize stability are required. Here, we apply size exclusion chromatography (SEC) to study the stability of a tetrahedron DNA nanostructure (TDN) and demonstrate the analytical capabilities of our method in characterizing degradation by enzymes and a diluted human serum matrix. We show that SEC analysis can reliably assay TDN degradation by a nuclease through direct injection and peak integration. Furthermore, data analysis using a ratio chromatogram technique enables TDN peak deconvolution from the matrix of serum proteins. Using our method, we found that TDNs exhibit half-lives of 23.9 hours and 10.1 hours in 20% and 50% diluted human serum, respectively, which is consistent with reported stability studies in 10% fetal bovine serum. We anticipate that this method can be broadly applicable to characterize a variety of DNs and serve as an efficient technique toward analysis of the stability of new DN designs in complex biological matrixes.

Recent Progress of Magnetically Actuated DNA Micro/Nanorobots

In the past few decades, the field of DNA origami-based micro/nanotechnology has developed dramatically and spawned attention increasingly, as its high integrality, rigid structure, and excellent resistance ability to enzyme digestion. Many two-dimensional and three-dimensional DNA nanostructures coordinated with optical, chemical, or magnetic triggers have been designed and assembled, extensively used as versatile templates for molecular robots, nanosensors, and intracellular drug delivery. The magnetic field has been widely regarded as an ideal driving and operating system for micro/nanomaterials, as it does not require high-intensity lasers like light control, nor does it need to change the chemical composition similar to chemical activation. Herein, we review the recent achievements in the induction and actuation of DNA origami-based nanodevices that respond to magnetic fields. These magnetic actuation-based DNA nanodevices were regularly combined with magnetic beads or gold nanoparticles and applied to generate single-stranded scaffolds, assemble various DNA nanostructures, and purify specific DNA nanostructures. Moreover, they also produced artificial magnetism or moved regularly driven by external magnetic fields to explain deeper scientific issues.