DNA-Based Daisy Chain Rotaxane Nanocomposite Hydrogels as Dual-Programmable Dynamic Scaffolds for Stem Cell Adhesion

Mechanically Tunable DNA Hydrogels as Prospective Biosensing Modules

Sequence-programmable DNA building blocks offer high degree of freedom in designing arbitrarily complex networks of tunable viscoelastic properties. Yet, the deployment of DNA-based functional materials remains limited due to insufficient control over the emerging structures and their mechanics. In an ongoing effort to place structure-property relations in stimuli-responsive DNA materials on a firm foundation, here a systematic rheological study of self-assembling DNA networks is presented, comprised of short DNA nanomotifs, namely trivalent nanostars and bivalent linkers, where the latter differ in their composition on a single base-pair level. Notably, we found through combining conventional bulk rheology with diffusing wave spectroscopy (DWS-based) passive microrheology a relationship between the melting temperature of a DNA hydrogel and its DNA sequence composition. By providing a use case, we demonstrated how the determination of such empirical relations could impact the areas of biosensing and mechanical computing, where control over the system state and target identification are key.

DNA-encoded dynamic hydrogels for 3D bioprinted cartilage organoids

Articular cartilage, composed of chondrocytes within a dynamic viscoelastic matrix, has limited self-repair capacity, posing a significant challenge for regeneration. Constructing high-fidelity cartilage organoids through three-dimensional (3D) bioprinting to replicate the structure and physiological functions of cartilage is crucial for regenerative medicine, drug screening, and disease modeling. However, commonly used matrix bioinks lack reversible cross-linking and precise controllability, hindering dynamic cellular regulation. Thus, encoding bioinks adaptive for cultivating cartilage organoids is an attractive idea. DNA, with its ability to be intricately encoded and reversibly cross-linked into hydrogels, offers precise manipulation at both molecular and spatial structural levels. This endows the hydrogels with viscoelasticity, printability, cell recognition, and stimuli responsiveness. This paper elaborates on strategies to encode bioink via DNA, emphasizing the regulation of predictable dynamic properties and the resulting interactions with cell behavior. The significance of these interactions for the construction of cartilage organoids is highlighted. Finally, we discuss the challenges and future prospects of using DNA-encoded hydrogels for 3D bioprinted cartilage organoids, underscoring their potential impact on advancing biomedical applications.

DNA-based hydrogels for bone regeneration: A promising tool for bone organoids

DNA-based hydrogels stand out for bone regeneration due to their exceptional biocompatibility and programmability. These hydrogels facilitate the formation of spatial bone structures through bulk hydrogel fabricating, microsphere formatting, and 3D printing. Furthermore, the bone microenvironment can be finely tuned by leveraging the degradation products, nanostructure, targeting, and delivery capabilities inherent to DNA-based materials. In this review, we underscore the advantages of DNA-based hydrogels, detailing their composition, gelation techniques, and structure optimization. We then delineate three critical elements in the promotion of bone regeneration using DNA-based hydrogels: (i) osteogenesis driven by phosphate ions, plasmids, and oligodeoxynucleotides (ODNs) that enhance mineralization and promote gene and protein expression; (ii) vascularization facilitated by tetrahedral DNA nanostructures (TDNs) and aptamers, which boosts gene expression and targeted release; (iii) immunomodulation achieved through loaded factors, TDNs, and bound ions that stimulate macrophage polarization and exhibit antibacterial properties. With these advantages and properties, these DNA-based hydrogels can be used to construct bone organoids, providing an innovative tool for disease modeling and therapeutic applications in bone tissue engineering. Finally, we discuss the current challenges and future prospects, emphasizing the potential impacts and applications in regenerative medicine.

Enhanced liquid-liquid phase separation of stress granules in a reconstructed model and their cytoplasmic targeting using a DNA nanodevice

Biomolecular condensates (BCs) are crucial membraneless organelles formed through the process of liquid-liquid phase separation (LLPS) involving proteins and nucleic acids. These LLPS processes are tightly linked with essential cellular activities. Stress granules (SGs), functioning as cytoplasmic BCs, play indispensable roles in maintaining cellular homeostasis and are implicated in diseases like cancers and neurodegenerative disorders. However, devices that can regulate SG LLPS are lacking. Herein, a triangular prism-shaped DNA nanostructure containing polythymidine (ΔDNA(polyT)) is presented as a nanodevice to investigate the LLPS process of in vitro reconstructed SGs (rSGs), a mixture of marker protein G3BP1 and total RNAs. Our observations reveal that the concentration threshold required for rSG LLPS decreases upon addition of ΔDNA(polyT), suggesting an enhancement in SG LLPS efficiency. It is speculated that ΔDNA(polyT) can concentrate mRNAs onto its surface via polyT hybridization with poly-adenosine sequences (polyA) in mRNAs. This alteration in the spatial distribution of mRNAs subsequently affects the multivalency interactions between G3BP1 and mRNAs. Furthermore, ΔDNA(polyT) exhibits excellent colocalization with cytoplasmic SGs under stressed conditions. This DNA-based nanodevice presents a new artificial approach for the targeted regulation of BC LLPS and holds promise for future studies focusing on BCs.

Biomedical Utility of Non-Enzymatic DNA Amplification Reaction: From Material Design to Diagnosis and Treatment

Nucleic acid nanotechnology has become a promising strategy for disease diagnosis and treatment, owing to remarkable programmability, precision, and biocompatibility. However, current biosensing and biotherapy approaches by nucleic acids exhibit limitations in sensitivity, specificity, versatility, and real-time monitoring. DNA amplification reactions present an advantageous strategy to enhance the performance of biosensing and biotherapy platforms. Non-enzymatic DNA amplification reaction (NEDAR), such as hybridization chain reaction and catalytic hairpin assembly, operate via strand displacement. NEDAR presents distinct advantages over traditional enzymatic DNA amplification reactions, including simplified procedures, milder reaction conditions, higher specificity, enhanced controllability, and excellent versatility. Consequently, research focusing on NEDAR-based biosensing and biotherapy has garnered significant attention. NEDAR demonstrates high efficacy in detecting multiple types of biomarkers, including nucleic acids, small molecules, and proteins, with high sensitivity and specificity, enabling the parallel detection of multiple targets. Besides, NEDAR can strengthen drug therapy, cellular behavior control, and cell encapsulation. Moreover, NEDAR holds promise for constructing assembled diagnosis-treatment nanoplatforms in the forms of pure DNA nanostructures and hybrid nanomaterials, which offer utility in disease monitoring and precise treatment. Thus, this paper aims to comprehensively elucidate the reaction mechanism of NEDAR and review the substantial advancements in NEDAR-based diagnosis and treatment over the past five years, encompassing NEDAR-based design strategies, applications, and prospects.

Daisy chain architectures: from discrete molecular entities to polymer materials

Daisy chain architectures, made by the self-complementary threading of an axle covalently linked to a macrocycle, represent a particularly intriguing family of supramolecular and mechanically interlocked (macro)molecules. In this review, we discuss their recent history, their modular chemical structures, and the various synthetic strategies to access them. We also detail how their internal sliding motions can be controlled and how their integration within polymers can amplify that motions up to the macroscopic scale. This overview of the literature demonstrates that the peculiar structure and dynamics of daisy chains have already strongly influenced the research on artificial molecular machines, with the potential to be implemented from nanometric switchable devices to mechanically active soft-matter materials.

Investigation of the Impact of Hydrogen Bonding Degree in Long Single-Stranded DNA (ssDNA) Generated with Dual Rolling Circle Amplification (RCA) on the Preparation and Performance of DNA Hydrogels

DNA hydrogels have gained significant attention in recent years as one of the most promising functional polymer materials. To broaden their applications, it is critical to develop efficient methods for the preparation of bulk-scale DNA hydrogels with adjustable mechanical properties. Herein, we introduce a straightforward and efficient molecular design approach to producing physically pure DNA hydrogel and controlling its mechanical properties by adjusting the degree of hydrogen bonding in ultralong single-stranded DNA (ssDNA) precursors, which were generated using a dual rolling circle amplification (RCA)-based strategy. The effect of hydrogen bonding degree on the performance of DNA hydrogels was thoroughly investigated by analyzing the preparation process, morphology, rheology, microstructure, and entrapment efficiency of the hydrogels for Au nanoparticles (AuNPs)-BSA. Our results demonstrate that DNA hydrogels can be formed at 25 °C with simple vortex mixing in less than 10 s. The experimental results also indicate that a higher degree of hydrogen bonding in the precursor DNA resulted in stronger internal interaction forces, a more complex internal network of the hydrogel, a denser hydrogel, improved mechanical properties, and enhanced entrapment efficiency. This study intuitively demonstrates the effect of hydrogen bonding on the preparation and properties of DNA hydrogels. The method and results presented in this study are of great significance for improving the synthesis efficiency and economy of DNA hydrogels, enhancing and adjusting the overall quality and performance of the hydrogel, and expanding the application field of DNA hydrogels.