DNA Hydrogel Research Articles

DNA Adjuvant Hydrogel-Optimized Enzymatic Cascade Reaction for Tumor Chemodynamic-Immunotherapy.

Chemodynamic therapy (CDT) shows immense potential in cancer treatment as it not only directly kills tumor cells but also induces anti-tumor immune responses. However, the efficacy of CDT is hampered by challenges in targeting CDT catalysts specifically to tumors using nanomaterials, along with the limitations of low H2 O2 levels and short catalyst duration within the tumor microenvironment. In this study, DNA adjuvant hydrogel to arrange a glucose oxidase-ferrocene cascade for continuously generating reactive oxygen species (ROS) from glucose in situ for tumor CDT combined with immunotherapy is employed. By precisely tuning the catalyst spacing with DNA double helix, ROS production efficiency is elevated by up to nine times compared to free catalysts, resulting in stronger immunogenetic cell death. Upon intratumoral injection, the DNA hydrogel system elicited potent anti-tumor immune responses, thereby effectively inhibiting established tumors and rejecting re-challenged tumors. This work offers a novel platform for integrated CDT and immunotherapy in cancer treatment.

Liquid DNA Coacervates form Porous Capsular Hydrogels via Viscoelastic Phase Separation on Microdroplet Interface

AbstractLiquid–liquid phase separation (LLPS) droplets of biopolymers are known as functional microdroplets in living cells and have recently been used to construct protocells and artificial cells. The formation of DNA coacervates (also referred to as DNA droplets) from branched DNA nanostructures and the control of their physical properties via DNA nanostructure design are demonstrated previously. For the construction of artificial cells or protocells, however, even though physical effects such as surface tension, wetting, and viscoelasticity are more important in a tiny (micrometer‐sized), confined environment than in a bulk solution environment, they have not been explored yet. This study shows that a tiny, confined environment using a water‐in‐oil (W/O) microdroplet interface modulates the phase separation dynamics of DNA coacervates, leading to micrometer‐sized porous capsular structures. The porous structures are produced via two types of viscoelastic phase separation (VPS) processes in DNA coacervates: i) simple VPS and ii) cluster‐cluster aggregation after VPS. Finally, it is shown that environmental chemical stimulation can manipulate porous capsular DNA hydrogels extracted from W/O microdroplets. These results provide an approach for designing and fabricating artificial cells or protocells with complex structures and physicochemical properties.

An acid-responsive DNA hydrogel-mediated cascaded enzymatic nucleic acid amplification system for the sensitive imaging of alkaline phosphatase in living cells.

Alkaline phosphatase (ALP) is a class of hydrolase that catalyzes the dephosphorylation of phosphorylated species in biological tissues, playing an important role in many physiological and pathological processes. Sensitive imaging of ALP activity in living cells is contributory to the research on these processes. Herein, we propose an acid-responsive DNA hydrogel to deliver a cascaded enzymatic nucleic acid amplification system into cells for the sensitive imaging of intracellular ALP activity. The DNA hydrogel is formed by two kinds of Y-shaped DNA monomers and acid-responsive cytosine-rich linkers. The amplification system contained Bst DNA polymerase (Bst DP), Nt.BbvCI endonuclease, a Recognition Probe (RP, containing a DNAzyme sequence, a Nt.BbvCI recognition sequence, and a phosphate group at the 3'-end), and a Signal Probe (SP, containing a cleavage site for DNAzyme, Cy3 and BHQ2 at the two ends). The amplification system was trapped into the DNA hydrogel and taken up by cells, and the cytosine-rich linkers folded into a quadruplex i-motif in the acidic lysosomes, leading to the collapse of the hydrogel and releasing the amplification system. The phosphate groups on RPs were recognized and removed by the target ALP, triggering a polymerization-nicking cycle to produce large numbers of DNAzyme sequences, which then cleaved multiple SPs, restoring Cy3 fluorescence to indicate the ALP activity. This strategy achieved sensitive imaging of ALP in living HeLa, MCF-7, and NCM460 cells, and realized the sensitive detection of ALP in vitro with a detection limit of 2.0 × 10-5 U mL-1, providing a potential tool for the research of ALP-related physiological and pathological processes.

Supramolecular DNA nanogels through host-guest interaction for targeted drug delivery.

DNA hydrogels have been demonstrated with the advantages of good stability, easy modification, and extraordinary biocompatibility, which enables their great application prospects in biosensing, tissue engineering, and biomedicine. Based on the host-guest recognition properties of cucurbit[8]uril (CB[8]), we proposed a general method for constructing functional supramolecular DNA nanogels. Guest molecules have been conjugated into the DNA building units, which could be further crosslinked with CB[8] to construct supramolecular DNA nanogels. At the same time, the aptamer has also been modified into the hydrogel network to achieve cell targeting. These supramolecular DNA nanogels have been demonstrated with a controllable size and multiple stimuli responses, in addition to the excellent biocompatibility, stability and good targeting drug transport ability. Such a host-guest based strategy will provide a molecular library as a "toolbox" for the functionalization of DNA nanogels.

Effects of monovalent and divalent cations on the rheology of entangled DNA.

In this paper we investigate the effects of varying cation valency and concentration on the rheology of entangled λDNA solutions. We show that monovalent cations moderately increase the viscoelasticty of the solutions mainly by stabilising linear concatenation of λDNA "monomers" via hybridisation of their sticky ends. On the contrary, divalent cations have a far more complex and dramatic effect on the rheology of the solution and we observe evidence of inter-molecular DNA-DNA bridging by Mg2+. We argue that these results may be interesting in the context of dense solutions of single and double stranded DNA, e.g. in vivo or in biotechnology applications such as DNA origami and DNA hydrogels.

Solar-powered simultaneous highly efficient seawater desalination and highly specific target extraction with smart DNA hydrogels.

Obtaining freshwater and important minerals from seawater with solar power facilitates the sustainable development of human society. Hydrogels have demonstrated great solar-powered water evaporation potential, but highly efficient and specific target extraction remains to be expanded. Here, we report the simultaneous highly efficient seawater desalination and specific extraction of uranium with smart DNA hydrogels. The DNA hydrogel greatly promoted the evaporation of water, with the water evaporation rate reached a high level of 3.54 kilograms per square meter per hour (1 kilowatt per square meter). Simultaneously, uranyl-specific DNA hydrogel exhibited a high capture capacity of 5.7 milligrams per gram for uranium from natural seawater due to the rapid ion transport driven by the solar powered interfacial evaporation and the high selectivity (10.4 times over vanadium). With programmable functions and easy-to-use devices, the system is expected to play a role in future seawater treatment.

Dual-mode biosensors for ultrasensitive detection of Legionella pneumophila using CRISPR/Cas12a integrated recombinase polymerase amplification

Legionella pneumophila (L. pneumophila) can cause respiratory disease in humans when it infects water sources, posing a major challenge to public health and the environment. Herein, we further explore the potential application of CRISPR/Cas12a and develop CRISPR/Cas12a-drived fluorescent and colorimetry dual-mode biosensors for detection L. pneumophila. In this design, Amplified part not only realizes fast and convenient operation, but also avoids aerosol pollution. Bi2Fe4O9 NSs have excellent colorimetric performance and Bi2Fe4O9 NSs-coated DNA hydrogel can serve as independent unit. Experimental results demonstrate that the limit of detection (LOD) for the fluorescent biosensor is 7.606 × 10−6 ng/μL (3.8 copies/μL) with 60 min, which is 10,000 times better than the industry standard (SN/T 2528 - 2010). While the colorimetry achieves a LOD is 7.606 × 10−3 ng/μL (3800 copies/μL) with 100 min, which is 10 times better than the industry standard. In the actual sample test, the selectivity of the detection scheme is 100%, and the positive detection rate is higher than the industry standard 10.71%. We take the lead in integrating RPA and CRISPR/Cas12a for detecting L. pneumophila, which has been further broadened the detection strategy by incorporating colorimetric sensing. Moreover, this biosensor demonstrates excellent repeatability and strong universality, along with practical applicability for various water environment monitoring purposes.

Dual-functional DNA nanogels for anticancer drug delivery

DNA hydrogels with unique sequence programmability on nucleic acid framework manifest remarkable attributes, such as high payload capacities, biocompatibility and biosafety. The availability of DNA nanogels with multimodal functionalities remains limited due to the absence of facile gelation methods applicable at the nanometer scale. Here, we developed a one-step assembly of DNA dendrimers into nanogels (DNG) with couple hundred nanometers size. DNG showed robust stability against physical forces and biological degradation for easy purification and sustainable drug release. Long-term stability either in powder or aqueous solution endows DNG easy for shipping, handling and storage. By encoding dual functionalities into separate branches on DNA dendrimers, DNG can accommodate chemodrugs and aptamers with distinctive loading moduli. DNG significantly enhanced the drug efficacy against cancerous cells while minimizing cytotoxicity towards somatic cells, as demonstrated in vitro and in xenografted mice models of breast cancer. Thus, due to their facile assembly and storage, bi-entity encoding, and inherent biocompatibility, DNG exhibits immense prospects as nanoscale vesicles for the synergistic delivery of multimodal theranostics in anticancer treatments. Statement of significanceDNA nanogels were self-assembled via a facile protocol utilizing a DNA dendrimer structure. These nanogels displayed robust stability against physical forces, permitting long term storage in concentrated solutions or as a powder. Furthermore, they exhibited resilience to biological degradation, facilitating sustained drug release. The bi-entity encoded dendritic branches conferred dual functionalities, enabling both chemodrug encapsulation and the presentation of aptamers as targeting motifs. In vivo investigations confirmed the nanogels provide high efficacy in tumor targeting and chemotherapy with enhanced drug efficacy and reduced side effects.

A G-quadruplex-assisted target-responsive dual-mode aptasensor based on copper nanoclusters synthesized in situ in a DNA hydrogel for ultrasensitive detection of ochratoxin A

Developing ultrasensitive sensing platforms for trace ochratoxin A (OTA) in food safety is still challenging. Herein, we presented a novel dual-mode sensing strategy for fluorescence and colorimetric detection of OTA by combining the target-responsive hemin-encapsulated and copper nanoclusters (CuNCs) functionalized DNA hydrogel. Through simple assembly and in situ synthesis methods, fluorescence CuNCs are synthesized and modified on the 3D hydrophilic network structure of DNA cross-linked. OTA specifically recognized by Apt-linker can control the collapse of hydrogel, resulting in the fluorescence quenching of CuNCs and release of coated hemin. Interestingly, OTA could trigger Apt-linker conformational changes to form G-quadruplex structures, allowing the released hemin to form G-quadruplex/hemin DNAzyme via self-assembly. Fluorescence signal amplification could be achieved through further fluorescence quenching of CuNCs caused by DNAzyme-catalyzed hydrogen peroxide (H2O2) because of the peroxidase activity of DNAzyme. Simultaneously, DNAzyme could catalyze the H2O2-mediated oxidation of TMB to provide colorimetric signal. Thereafter, the DNA-CuNCs hydrogel exhibited low detection limits of 3.49 pg/mL in fluorescence mode and 0.25 ng/mL in colorimetric modality. Real sample analyses of foodstuffs showed satisfactory results, providing prospective potential for monitoring mycotoxin contaminant.

Hierarchical Mechanical Transduction of Precision-Engineered DNA Hydrogels with Sacrificial Bonds.

Engineering the response to external signals in mechanically switchable hydrogels is important to promote smart materials applications. However, comparably little attention has focused on embedded precision mechanisms for autonomous nonlinear response in mechanical profiles in hydrogels, and we lack understanding of how the behavior from the molecular scale transduces to the macroscale. Here, we design a nonlinear stress-strain response into hydrogels by engineering sacrificial DNA hairpin loops into model network hydrogels formed from star-shaped building blocks. We characterize the force-extension response of single DNA hairpins and are able to describe how the specific topology influences the nonlinear mechanical behavior at different length scales. For this purpose, we utilize force spectroscopy as well as microscopic and macroscopic deformation tests. This study contributes to a better understanding of designing nonlinear strain-adaptive features into hydrogel materials.

Programmable DNA Hydrogel Assisting Microcrystal Formulations for Sustained Locoregional Drug Delivery in Surgical Residual Tumor Lesions and Lymph Node Metastasis.

Surgical residual tumor lesions (R1 resection of surgical procedures (e.g., liver cancer infiltrating the diaphragm, surgical residual breast cancer, postoperative residual ovarian cancer) or boundary residual after ablation) and lymph node metastasis that cannot be surgically resected (retroperitoneal lymph nodes) significantly affect postoperative survival of tumor patients. This clinical conundrum poses three challenges for local drug delivery systems: stable and continuous delivery, good biocompatibility, and the ability to package new targeted drugs that can synergize with other treatments. Here, a drug-laden hydrogel generated from pure DNA strands and highly programmable in adjusting its mesh size is reported. Meanwhile, the DNA hydrogel can assist the microcrystallization of novel radiosensitizing drugs, ataxia telangiectasia and rad3-related protein (ATR) inhibitor (Elimusertib), further facilitating its long-term release. When applied to the tumor site, the hydrogel system demonstrates significant antitumor activity, minimized systemic toxicity, and has a modulatory effect on the tumor-immune cell interface. This drug-loaded DNA-hydrogel platform represents a novel modality for adjuvant therapy in patients with surgical residual tumor lesions and lymph node metastasis.

Rational Design of DNA Hydrogels Based on Molecular Dynamics of Polymers.

In recent years, DNA has emerged as a fascinating building material to engineer hydrogel due to its excellent programmability, which has gained considerable attention in biomedical applications. Understanding the structure-property relationship and underlying molecular determinants of DNA hydrogel is essential to precisely tailor its macroscopic properties at molecular level. In this review, the rational design principles of DNA molecular networks based on molecular dynamics of polymers on the temporal scale, which can be engineered via the backbone rigidity and crosslinking kinetics, are highlighted. By elucidating the underlying molecular mechanisms and theories, it is aimed to provide a comprehensive overview of how the tunable DNA backbone rigidity and the crosslinking kinetics lead to desirable macroscopic properties of DNA hydrogels, including mechanical properties, diffusive permeability, swelling behaviors, and dynamic features. Furthermore, it is also discussed how the tunable macroscopic properties make DNA hydrogels promising candidates for biomedical applications, such as cell culture, tissue engineering, bio-sensing, and drug delivery.

Injectable DNA Hydrogels with Intrinsic Antioxidant and Anti-inflammatory Functions for Effectively Healing Bacteria-Infected Diabetic Wounds

Injectable DNA Hydrogels with Intrinsic Antioxidant and Anti-inflammatory Functions for Effectively Healing Bacteria-Infected Diabetic Wounds

Preparation Strategies, Functional Regulation, and Applications of Multifunctional Nanomaterials-Based DNA Hydrogels.

With the extensive attention of DNA hydrogels in biomedicine, biomaterial, and other research fields, more and more functional DNA hydrogels have emerged to match the various needs. Incorporating nanomaterials into the hydrogel network is an emerging strategy for functional DNA hydrogel construction. Surprisingly, nanomaterials-based DNA hydrogels can be engineered to possess favorable properties, such as dynamic mechanical properties, excellent optical properties, particular electrical properties, perfect encapsulation properties, improved magnetic properties, and enhanced antibacterial properties. Herein, the preparation strategies of nanomaterials-based DNA hydrogels are first highlighted and then different nanomaterial designs are used to demonstrate the functional regulation of DNA hydrogels to achieve specific properties. Subsequently, representative applications in biosensing, drug delivery, cell culture, and environmental protection are introduced with some selected examples. Finally, the current challenges and prospects are elaborated. The study envisions that this review will provide an insightful perspective for the further development of functional DNA hydrogels.

Multifunctional DNA-Based Hydrogel Promotes Diabetic Alveolar Bone Defect Reconstruction.

Diabetic alveolar bone defect (DABD) causes persistent bacterial infection, prolonged inflammation, and delayed bone healing, making it a considerable clinical challenge. In this study, by integrating silver nanoclusters (AgNCs) and M2 macrophage-derived extracellular vesicles (M2EVs), a multifunctional DNA-based hydrogel, called Agevgel, is developed with antibacterial, anti-inflammatory, immunomodulatory, and osteogenic properties to promote DABD rebuilding. AgNCs are tightly embedded into the DNA scaffolds and exhibit effective anti-bacterial activity, while immunomodulatory M2EVs are encapsulated within the shape-variable DNA scaffolds and exhibit potent anti-inflammatory and osteogenic properties. The results reveal that Agevgel effectively prolongs the local retention time and bioactivity of M2EVs in vivo. In particular, the sustained release of M2EVs can last for at least 7 days when applying Agevgel to DABD. Compared to free M2EVs or Aggel (AgNCs encapsulated within the DNA hydrogel) treatments, the Agevgel treatment accelerates the defect healing rate of alveolar bone and dramatically improves the trabecular architecture. Mechanistically, Agevgel plays a key role in regulating macrophage polarization and promoting the expression of proliferative and osteogenic factors. In summary, Agevgel provides a comprehensive treatment strategy for DABD with a great clinical translational value, highlighting the application of DNA hydrogels as an ideal bioscaffolds for periodontal diseases.

Programmable all-DNA hydrogels based on rolling circle and multiprimed chain amplification products.

Soft, biocompatible, and tunable materials offer biomedical engineers and material scientists programmable matrices for a variety of biomedical applications. In this regard, DNA hydrogels have emerged as highly promising biomaterials that offer programmable self-assembly, superior biocompatibility, and the presence of specific molecular identifiable structures. Many types of DNA hydrogels have been developed, yet the programmability of the DNA building blocks has not been fully exploited, and further efforts must be directed toward understanding how to finely tune their properties in a predictable manner. Herein, we develop physically crosslinked all-DNA hydrogels with tunable morphology and controllable biodegradation, based on rolling circle amplification and multiprimed chain amplification products. Through molecular engineering of the DNA sequences and their nano-/microscale architectures, the precursors self-assemble in a controlled manner to produce soft hydrogels in an efficient, cost-effective, and highly tunable manner. Notably, we develop a novel DNA microladder architecture that serves as a framework for modulating the hydrogel properties, including over an order of magnitude change in pore size and up to 50% change in biodegradation rate. Overall, we demonstrate how the properties of this DNA-based biomaterial can be tuned by modulating the amounts of rigid double-stranded DNA chains compared to flexible single-stranded DNA chains, as well as through the precursor architecture. Ultimately, this work opens new avenues for the development of programmable and biodegradable soft materials in which DNA functions not only as a store of genetic information but also as a versatile polymeric biomaterial and molecularly engineered macroscale scaffold.

A recipe for tunable DNA hydrogels

Changing the structure of microscopic DNA ladders tailors hydrogels properties for potential applications in drug delivery, biosensing, and tissue engineering.

DNA Hydrogels as Functional Materials and Their Biomedical Applications

AbstractWith the remarkable development of DNA nanotechnology, interest in DNA molecules has expanded beyond its biological role to building blocks in materials science. As a unique branch of DNA‐based materials, DNA hydrogels have exhibited many fascinating characteristics, including broad biocompatibility, precise programmability, convenient modification, and tunable mechanical properties, which make DNA hydrogels ideal biomaterials. Moreover, by combining with functional nucleic acids, such as aptamers, i‐motif nanostructures, CpG oligodeoxynucleotides, and DNAzymes, DNA hydrogels can be further tailored to provide additional target recognition, therapeutic potential, and catalytic activities, allowing them to play important roles in biosensing and medical applications. This review, aims to provide readers with an up‐to‐date overview of the important developments of biomedical DNA hydrogels. First, it introduces different synthetic strategies of hydrogels that utilize DNA as building materials and functional units within the hydrogel networks and discuss their advantages in biomedical applications. Subsequently, new approaches and applications of biomedical DNA hydrogels in the recent years are highlighted, such as therapeutic systems, cell culture platforms, tissue engineering materials, and biosensors. Finally, future perspectives and remaining challenges of DNA hydrogels in biomedicine are presented.

Thermoresponsive DNA hydrogels through hydrophilic pre-polymer cross-linker and self-assembly

Denatured DNA molecules were used as building blocks to fabricate thermoresponsive hydrogels by cross-linking DNA strands with an isocyanate (NCO) end-capped star-shaped poly(EO-stat-PO) cross-linker. The NCO groups reacted with the amine groups of DNA’s bases through urea links while base pairing between the matching strands of DNA led to the self-assembly of DNA into a three-dimensional hydrogel network. Analysis of the ultrastructure by scanning force microscopy (SFM) revealed the temperature-mediated transition from the rod-to-coil structure as a result of the destabilization of double-stranded DNA (dsDNA) to form a single-stranded DNA (ssDNA), which eventually resulted in a DNA network due to base pairing, along with hairpin loops due to mismatches between nucleotides. Dynamic oscillatory and large deformation creep tests, as well as stress relaxation tests, revealed the formation of robust cross-linked gels: A ten-fold rise in the elastic modulus was observed for the covalent DNA gel compared to the physical gel at the identical DNA concentration. The thermoresponsiveness of the hydrogels was confirmed by a heating–cooling cycle while the non-porous internal morphology of the hydrogel was demonstrated through scanning electron microscopic analysis. Overall, this is the first study showing the fabrication of covalent DNA hydrogels using an NCO-end-capped hydrophilic prepolymer. Such gels have a high potential to be exploited in many fields to benefit from the structural properties of DNA molecules.

Programmable DNA hydrogel provides suitable microenvironment for enhancing autophagy-based therapies in intervertebral disc degeneration treatment

The pathogenesis of intervertebral disc degeneration (IVDD) is attributed to metabolic dysregulation within the extracellular matrix and heightened apoptosis of nucleus pulposus cells (NPC). Therefore, a potential therapeutic strategy for managing IVDD involves the reestablishment of metabolic equilibrium within the extracellular matrix and the suppression of excessive myeloid cell apoptosis. The microRNA, miR-5590, displays marked differential expression in degenerative nucleus pulposus (NP) tissues and exerts a direct influence on the regulation of DDX5 expression. This, in turn, modulates mammalian target of rapamycin (mTOR) phosphorylation, thereby impacting autophagy and apoptosis. However, ensuring the smooth delivery of miRNA to a specific injury site poses a significant challenge. To address this issue, a multifunctional DNA hydrogel was developed and subsequently loaded with miR-5590 via spherical nucleic acids (SNAs) for the treatment of IVDD. The hydrogel, which exhibits versatility, has the potential to be administered through injection at the site of injury, resulting in a consistent and prolonged release of miR-5590. This leads to the creation of a genetic microenvironment within the NP, which triggers the onset of autophagy in NPCs and subsequently suppresses apoptosis. As a result, this process regulates the metabolic equilibrium within the extracellular matrix, thereby impeding the in vitro and in vivo progression of IVDD. The amalgamation of miRNAs and biomaterials offers a promising therapeutic strategy for the management of IVDD in clinical settings.