DNA Hydrogel Research Articles

Chromatin inspired bio-condensation between biomass DNA and guanosine monophosphate produces all-nucleic hydrogel as a hydrotropic drug carrier.

The integration of biomolecules into supramolecular nanostructures forms the basis of the natural world. Naturally occurring liquid-liquid phase separation resulting in biomolecular condensates has inspired the formation of biomolecule-based smart materials with multi-dimensional applications. A non-covalent bio-condensation between biomass DNA and guanosine monophosphate (GMP) has been described, mimicking chromatin folding and creating a unique "all-nucleic" DNA-GMP condensates. These condensates initiate the formation of G-quadruplex-based superstructures, assembling into super-helical fibres driven by synergistic hydrogen bonding and stacking, which have been thoroughly investigated. This simple, one-step method for the bio-condensation of biomass DNA leads to an "all-nucleic" hydrogel with higher-order self-assembly and excellent mechanical properties. While most of the reported DNA based biomaterials, including hydrogels, require precisely sequenced and molecularly architectured DNA building blocks, we have developed a simple, universal, and facile bio-condensation method that utilizes biomass DNA acquired from any bio-resource to fabricate DNA hydrogels. The hydrogel efficiently encapsulates and sustains the release of both hydrophilic and hydrophobic drugs, demonstrating its competency as a drug carrier. We believe this energy-efficient and low-cost method represents a new technique for using biomass DNA as building blocks for the next generation of soft materials.

Nanotech‐Enhanced Chemical Energy Storage with DNA

AbstractDNA nanotechnology has revolutionized materials science by harnessing DNA's programmable properties. DNA serves as a versatile biotemplate, facilitating the creation of novel materials such as electrode materials and DNA hydrogels for electrolytes and membranes. These advancements have significantly boosted the performance of energy storage devices. DNA biotemplates not only enhance supercapacitor capacitance and increase Li–S battery cycling stability but also improve metal ion transport in perovskite solar cells, enhancing power conversion efficiency. Additionally, DNA's addressable nature allows precise enzyme positioning in biofuel cells, enhancing enzyme cascade efficiency. Overall, DNA nanotechnology offers a potent strategy for enhancing electrochemical device performance and stability through structural engineering.

Printing Cell Embedded Sacrificial Strategy for Microvasculature using Degradable DNA Biolubricant

Microvasculature is essential for the continued function of cells in tissue and is fundamental in the fields of tissue engineering, organ repair and drug screening. However, the fabrication of microvasculature is still challenging using existing strategies. Here, we developed a general PRINting Cell Embedded Sacrificial Strategy (PRINCESS) and successfully fabricated microvasculatures using degradable DNA biolubricant. This is the first demonstration of direct cell printing to fabricate microvasculature, which eliminates the need for a subsequent cell seeding process and the associated deficiencies. Utilizing the shear‐thinning property of DNA hydrogels as a novel sacrificial, cell‐laden biolubricant, we can print a 70‐μm endothelialized microvasculature, breaking the limit of 100 μm. To our best knowledge, this is the smallest endothelialized microvasculature that has ever been bioprinted so far. In addition, the self‐healing property of DNA hydrogels allows the creation of continuous branched structures. This strategy provides a new platform for constructing complex hierarchical vascular networks and offers new opportunity towards engineering thick tissues. The extremely low volume of sacrificial biolubricant paves the way for DNA hydrogels to be used in practical tissue engineering applications. The high‐resolution bioprinting technique also exhibits great potential for printing lymphatics, retinas and neural networks in the future.

Printing Cell Embedded Sacrificial Strategy for Microvasculature using Degradable DNA Biolubricant.

Microvasculature is essential for the continued function of cells in tissue and is fundamental in the fields of tissue engineering, organ repair and drug screening. However, the fabrication of microvasculature is still challenging using existing strategies. Here, we developed a general PRINting Cell Embedded Sacrificial Strategy (PRINCESS) and successfully fabricated microvasculatures using degradable DNA biolubricant. This is the first demonstration of direct cell printing to fabricate microvasculature, which eliminates the need for a subsequent cell seeding process and the associated deficiencies. Utilizing the shear-thinning property of DNA hydrogels as a novel sacrificial, cell-laden biolubricant, we can print a 70-μm endothelialized microvasculature, breaking the limit of 100 μm. To our best knowledge, this is the smallest endothelialized microvasculature that has ever been bioprinted so far. In addition, the self-healing property of DNA hydrogels allows the creation of continuous branched structures. This strategy provides a new platform for constructing complex hierarchical vascular networks and offers new opportunity towards engineering thick tissues. The extremely low volume of sacrificial biolubricant paves the way for DNA hydrogels to be used in practical tissue engineering applications. The high-resolution bioprinting technique also exhibits great potential for printing lymphatics, retinas and neural networks in the future.

Stable Halide Perovskite CsPbBr3 Nanocrystals Assisted by Covalent-Organic Frameworks for Electrochemiluminescence Analysis in an Aqueous Medium.

Lead halide perovskites have garnered attention as promising electrochemiluminescence (ECL) emitters owing to their superior photophysical characteristics. However, their poor water stability severely restricts their application in aqueous media for ECL. In this study, inorganic perovskite CsPbBr3 was assembled in situ in the imine-linked covalent-organic framework (COF-LZU1) as a novel ECL emitter. The expansive surface area and robust hydrophobic architecture of COF-LZU1 not only improved the water stability of CsPbBr3 but also guaranteed its exceptional ECL performance. The novel composite nanoluminescent material was coated onto an indium tin oxide (ITO) electrode via spin-coating and calcination processes to serve as an electrochemiluminescence (ECL) platform. A sensor was developed by combining a DNA hydrogel target-induced release system with a platform using ascorbic acid (AA) as a coreactant and T-2 toxin as the target analyte model. This method achieved a detection limit as low as 3.56 fg·mL-1 and was successfully applied to the analysis of the T-2 toxin content in corn samples. This study offers a novel path for the advancement of perovskite-based ECL emitters and their utilization in aqueous environments within the ECL field.

A novel double-door-opening sensor for visual determination of cardiac troponin I based on DNA hydrogel and bimetallic nanozyme

Cardiac troponin I (cTnI), as a cardiac biomarker, holds significant importance in the diagnosis of acute myocardial infarction. However, the current detection methods mostly require specialized personnel and large analytical instruments, making it difficult to achieve convenient and on-site testing. This situation leads to delayed disease diagnosis and treatment, that increases patient suffering, and reduces the cure rate. This strategy presents the development of a portable visual DNA hydrogel colorimetric sensing platform based on a smartphone. Utilizing dual-mode detection with ultraviolet signals and solution colorimetry, the platform achieves ultra-sensitive and real-time detection of cTnI. Furthermore, optimization of detection conditions, such as the amount of polyacrylamide, reaction time, aptamer concentration, encapsulation of the nanozyme, incubation time, and reaction temperature, were performed based on this platform. The proposed ultraviolet and visual detection platforms exhibited good linear relationships with the signal within the ranges of 0.003 ng mL−1 to 10.00 ng mL−1 and 0.01 ng mL−1 to 7.00 ng mL−1, with detection limits of 2.57 pg mL−1 and 0.013 pg mL−1, respectively. Additionally, utilizing 3D printing technology, a portable detection device was designed and employed for the detection of cTnI concentrations in human serum samples. Whatever in the initial and spiked samples, the results showed high sensitivities. The sensitivity and convenience of the sensor in detecting cTnI make it promising for home testing of patients, with broad market prospects.

A smart DNA hydrogel for isolation of bacterial outer membrane vesicles and localized cancer immunotherapy

A smart DNA hydrogel for isolation of bacterial outer membrane vesicles and localized cancer immunotherapy

A Critical View on the Use of DNA Hydrogels in Cell‐Free Protein Synthesis

Numerous studies have reported in the past that the use of protein‐encoding DNA hydrogels as templates for cell‐free protein synthesis (CFPS) leads to better yields than the use of conventional templates such as plasmids or PCR fragments. Systematic investigation of different types of bulk materials from pure DNA hydrogels and DNA hydrogel composites using a commercially available CFPS kit showed no evidence of improved expression efficiency. However, protein‐coding DNA hydrogels were advantageously used in microfluidic reactors as immobilized templates for repetitive protein production, suggesting that DNA‐based materials offer potential for future developments in high‐throughput profiling or rapid in situ characterization of proteins.

A Critical View on the Use of DNA Hydrogels in Cell-Free Protein Synthesis.

Numerous studies have reported in the past that the use of protein-encoding DNA hydrogels as templates for cell-free protein synthesis (CFPS) leads to better yields than the use of conventional templates such as plasmids or PCR fragments. Systematic investigation of different types of bulk materials from pure DNA hydrogels and DNA hydrogel composites using a commercially available CFPS kit showed no evidence of improved expression efficiency. However, protein-coding DNA hydrogels were advantageously used in microfluidic reactors as immobilized templates for repetitive protein production, suggesting that DNA-based materials offer potential for future developments in high-throughput profiling or rapid in situ characterization of proteins.

Construction of Aptamer-Functionalized DNA Hydrogels for Effective Inhibition of Shiga Toxin II Toxicity.

Bacterial infections have been seriously endangering public health and life, making it imperative to explore novel anti-infection strategies for their control. Herein, we constructed a DNA hydrogel encoded with aptamers (Apt-hydrogel) to inhibit Shiga toxin II (Stx2) toxicity, thereby alleviating Escherichia coli (EHEC) infection. The Apt-hydrogel was formed by two Y-shaped DNA scaffolds through rational design, where one end of Y was encoded with an aptamer sequence targeting the B subunit of Shiga toxin II (Stx2B). The Apt-hydrogel not only retained the high affinity of the aptamer but also provided protection for the aptamer, endowing it with better stability and biocompatibility. The results from in vitro and in vivo demonstrated good mediation effects of the Apt-hydrogel on Stx2 toxicity and confirmed its excellent inhibition activity. We hypothesized that the mechanism could be attributed to the high affinity of Apt-hydrogel for Stx2B, which effectively occupies the active site of Stx2B and its receptor Gb3. This interaction enhanced steric hindrance, thereby mediating their interaction and preventing Stx2 from entering the cell to exert toxicity. We anticipate that the novel Apt-hydrogel will expand the usage of aptamers and provide a new dimension for the Apt-hydrogel as a promising blocking assistant to inhibit Shiga toxin infections via a strong steric hindrance effect.

Engineering Phi29-DNAP Variants for Customized DNA Hydrogel Materials.

DNA hydrogels, which hold potential for use in medicine, biosensors, and tissue engineering, can be produced through enzymatic rolling circle amplification (RCA) using phi29 DNA polymerase (DNAP). This paper introduces new DNAP variants designed for RCA-based DNA hydrogel production, featuring enzymes with modified DNA binding, enhanced thermostability, reduced exonuclease activity, and protein tags for fluorescence detection or specific immobilization. We evaluated these enzymes by quantifying DNA output via quantitative PCR (qPCR) and assessing hydrogel mechanical properties through micromechanical indentation. The results showed that most variants generated similar DNA amounts and hydrogels with comparable mechanical properties. Additionally, all variants successfully incorporated non-natural nucleotides, such as base-modified dGTP derivatives and 2'-fluoro-dGTP, during RCA. This study's robust analytical approach offers a strong foundation for selecting new enzymes and producing DNA hydrogels with tailored material properties.

Oligo-Adenine Derived Secondary Nucleic Acid Frameworks: From Structural Characteristics to Applications.

Oligo-adenine (polyA) is primarily known for its critical role in mRNA stability, translational status, and gene regulation. Beyond its biological functions, extensive research has unveiled the diverse applications of polyA. In response to environmental stimuli, single polyA strands undergo distinctive structural transitions into diverse secondary configurations, which are reversible upon the introduction of appropriate counter-triggers. In this review, we systematically summarize recent advances of noncanonical structures derived from polyA, including A-motif duplex, A-cyanuric acid triplex, A-coralyne-A duplex, and T ⋅ A-T triplex. The structural characteristics and mechanisms underlying these conformations under specific external stimuli are addressed, followed by examples of their applications in stimuli-responsive DNA hydrogels, supramolecular fibre assembly, molecular electronics and switches, biosensing and bioengineering, payloads encapsulation and release, and others. A detailed comparison of these polyA-derived noncanonical structures is provided, highlighting their distinctive features. Furthermore, by integrating their stimuli-responsiveness and conformational characteristics, advanced material development, such as pH-cascaded DNA hydrogels and supramolecular fibres exhibiting dynamic structural transitions adapting environmental cues, are introduced. An outlook for future developments is also discussed. These polyA derived, stimuli-responsive, noncanonical structures enrich the arsenal of DNA "toolbox", offering dynamic DNA frameworks for diverse future applications.

Benchtop to at-home test: Amplicon-depleted CRISPR-regulated loop mediated amplification at skin-temperature for viral load monitoring

CoRPLA (CRISPR-regulated One-pot Recombinase Polymerase Loop-mediated Amplification) is an amplicon-depleted skin-temperature operated iNAAT designed for at-home testing. It uses specially designed loop primers to enhance isothermal amplification, triggering Cas12 for in-situ amplicon depletion and signal amplification. This method addresses issues like amplicon-derived aerosol contamination and complex assay formats, enabling quantitative detection with sub-attomolar sensitivity (0.5 cps/μL). CoRPLA employs a DNA hydrogel wearable tape for real-time, colorimetric readout, allowing visual differentiation of pathogen loads. It was validated with clinical samples for SARS-CoV-2, RSV, influenza A, and HPV, successfully identifying multi-level viral loads of the positive cases with results consistent with qPCR. Offering high sensitivity while eliminating false positives from aerosol contamination, CoRPLA bridges the molecular assay from benchtop to home for daily viral infections monitoring.

CRISPR-Responsive RCA-Based DNA Hydrogel Biosensing Platform with Customizable Signal Output for Rapid and Sensitive Nucleic Acid Detection.

Current nucleic acid-responsive DNA hydrogels face significant challenges, such as the requirement for high target concentrations, frequent redesigns, and increased costs, which limit their practical applications in biosensing. To address these issues, we developed a novel biosensing platform integrating a CRISPR/Cas12a system into an RCA-based DNA hydrogel. The hydrogel used in the platform could preencapsulate diverse signal molecules comprising GelRed, methylene blue, and gold nanoparticles, which were released upon Cas12a-mediated cleavage. This design enabled customizable signal output, including fluorescence, electrochemistry, and colorimetry, thereby ensuring the platform's adaptability to various detection scenarios. Our platform was highly specific for methicillin-resistant Staphylococcus aureus, with a mecA gene detection limit of 10 copies/μL, and provided fast and accurate results within 2 h for clinical samples. Hence, based on these advantages, the proposed biosensing platform exhibits promising application prospects in the field of nucleic acid detection.

DNA Nanostructures: Advancing Cancer Immunotherapy

AbstractCancer immunotherapy is a groundbreaking medical revolution and a paradigm shift from traditional cancer treatments, harnessing the power of the immune system to target and destroy cancer cells. In recent years, DNA nanostructures have emerged as prominent players in cancer immunotherapy, exhibiting immense potential due to their controllable structure, surface addressability, and biocompatibility. This review provides an overview of the various applications of DNA nanostructures, including scaffolded DNA, DNA hydrogels, tetrahedral DNA nanostructures, DNA origami, spherical nucleic acids, and other DNA‐based nanostructures in cancer immunotherapy. These applications explore their roles in vaccine development, immune checkpoint blockade therapies, adoptive cellular therapies, and immune‐combination therapies. Through rational design and optimization, DNA nanostructures significantly bolster the immunogenicity of the tumor microenvironment by facilitating antigen presentation, T‐cell activation, tumor infiltration, and precise immune‐mediated tumor killing. The integration of DNA nanostructures with cancer therapies ushers in a new era of cancer immunotherapy, offering renewed hope and strength in the battle against this formidable foe of human health.

Self-cleavage of genetically encoded Zn2+-dependent deoxyribozymes for low-cost biotechnological production of programable responsive DNA hydrogels

Despite the emergence of sequence-programable responsive DNA hydrogels, their further development is still hampered by the limited availability of chemically synthesized nucleic acid constituents. We herein developed a cost-efficient biotechnological approach for general production of programable responsive DNA hydrogels by harnessing bacteria as cell factories. Programmable pseudogenes of responsive DNA hydrogels were designed by interleaving Y-unit strand sequences with Zn2+-dependent self-cleaving deoxyribozymes. After in vivo amplification, self-cleavage of these deoxyribozymes in extracted precursor ssDNAs were systematically investigated. The versatility of this approach was demonstrated by preparing a unitary Y-unit system of pH-responsive DNA hydrogel and a binary Y-unit system of Cas12a-responsive hydrogel. This low-cost biotechnological approach requires only standard molecular biology equipment and inexpensive consumables, which may encourage further exploration of responsive DNA hydrogels.

Responsive DNA hydrogels: design strategies and prospects for biosensing.

Hydrogels, water-filled networks that can adapt to external stimuli by altering their volume, are known for their high flexibility and biocompatibility. DNA, a critical biomolecule renowned for its exceptional characteristics including information transmission, molecular recognition, and editability, has found widespread applications in the biosensing field as well. The integration of these two biomaterials offers promising opportunities for the development of novel biosensors with enhanced sensitivity, specificity, and adaptability. Therefore, by virtue of the collective features, researchers have recently focused on the construction of responsive DNA hydrogel systems. This feature article describes recent developments in fabricating DNA hydrogels and their applications in the biosensing area. Initially, it focuses on the design strategies employed in preparing DNA hydrogels, encompassing both pure DNA hydrogels and hybridized DNA hydrogels. Subsequently, it summarizes the use of DNA hydrogels in biosensing applications, highlighting their applications in visual detection, electrochemical sensing, and optical biosensing analyses. Furthermore, the underlying responsive mechanisms within these biosensing systems are also described. Lastly, this article presents a comprehensive discussion on the existing challenges and prospects of responsive DNA hydrogels, offering insights into their potential to revolutionize the field of biosensing.

Programmable soft DNA hydrogels stimulate cellular endocytic pathways and proliferation

Hydrogels are pivotal in tissue engineering, regenerative medicine, and drug delivery applications. Existing hydrogel platforms are not easily customizable and often lack precise programmability, making them less suited for 3D tissue culture and programming of cells. DNA molecules stand out among other promising biomaterials due to their unparalleled precision, programmability, and customization. In this study, we introduced a palette of novel cellular scaffolding platforms made of pure DNA-based hydrogel systems while improving the shortcomings of the existing platforms. We showed a quick and easy one step synthesis of DNA hydrogels using thermal annealing based on sequence specific hybridization strategy. We also demonstrated the formation of multi-armed branched supramolecular scaffolds with custom mechanical stiffness, porosity, and network density by increasing or decreasing the number of branching arms. These mechanically tuneable DNA hydrogels proved to be a suitable suitable platform for modulating the physiological processes of retinal pigment epithelial cells (RPE1). In-vitro studies showed dynamic changes at multiple levels, ranging from a change in morphology to protein expression patterns, enhanced membrane traffic, and proliferation. The soft DNA hydrogels explored here are mechanically compliant and pliable, thus excellently suited for applications in cellular programming and reprogramming. This research lays the groundwork for developing a DNA hydrogel system with a higher dynamic range of stiffness, which will open exciting avenues for tissue engineering and beyond.

Quantitative Characterization of RCA-Based DNA Hydrogels - Towards Rational Materials Design.

DNA hydrogels hold significant promise for biomedical applications and can be synthesized through enzymatic Rolling Circle Amplification (RCA). Due to the exploratory nature of this emerging field, standardized RCA protocols specifying the impact of reaction parameters are currently lacking. This study varied template sequences and reagent concentrations, evaluating RCA synthesis efficiency and hydrogel mechanical properties through quantitative PCR (qPCR) and indentation measurements, respectively. Primer concentration and stabilizing additives showed minimal impact on RCA efficiency, while changes in polymerase and nucleotide concentrations had a stronger effect. Concentration of the circular template exerted the greatest influence on RCA productivity. An exponential correlation between hydrogel viscosity and DNA amplicon concentration was observed, with nucleobase sequence significantly affecting both amplification efficiency and material properties, particularly through secondary structures. This study suggests that combining high-throughput experimental methods with structural folding prediction offers a viable approach for systematically establishing structure-property relationships, aiding the rational design of DNA hydrogel material systems.

DNA Hydrogels for Cancer Diagnosis and Therapy.

Nucleic acids, because of their precise pairing and simple composition, have emerged as excellent materials for the formation of gels. The application of DNA hydrogels in the diagnosis and therapy of cancer has expanded significantly through research on the properties and functions of nucleic acids. Functional nucleic acids (FNAs) such as aptamers, Small interfering RNA (siRNA), and DNAzymes have been incorporated into DNA hydrogels to enhance their diagnostic and therapeutic capabilities. This review discusses various methods for forming DNA hydrogels, with a focus on pure DNA hydrogels. We then explore the innovative applications of DNA hydrogels in cancer diagnosis and therapy. DNA hydrogels have become essential biomedical materials, and this review provides an overview of current research findings and the status of DNA hydrogels in the diagnosis and therapy of cancer, while also exploring future research directions.