Recent Advances in Stimuli-Responsive DNA-Based Hydrogels

Distance-based paper device coupled with uracil-rich DNA hydrogel for visual quantification of Uracil-DNA glycosylase

Uracil-DNA glycosylase (UDG), an enzyme for repairing uracil-containing DNA damage, is crucial for maintaining genomic stability. Simple and fast quantification of UDG activity is essential for biological assay and clinical diagnosis, since its aberrant level is associated with DNA damage and various diseases. Herein, we developed a fully integrated "sample in-signal out" distance-based paper analytical device (dPAD) for visual quantification of UDG using a flow-controlled uracil-rich DNA hydrogel (URDH). The uracil base sites contained in the DNA hydrogel are mis-incorporated with dUTP by rolling circle amplification (RCA), which simplifies the preparation process of the functionalized hydrogel. In the presence of UDG, the uracil in URDH can be recognized and removed to induce the permeability change of URDH, resulting in the visible distance signal along the paper channel. Using dPAD, as low as 6.4 × 10-4 U/mL of UDG (within 80 min) is visually identified without any instruments and complicated operations. This integrated dPAD is advantageous for its simplicity, cost effectiveness, and ease of use. We envision that it has the great potential for point-of-care testing (POCT) in DNA damage testing, personalized healthcare assessment, and biomedical applications.

DNA-Based Complexes and Composites: A Review of Fabrication Methods, Properties, and Applications

Deoxyribonucleic acid (DNA), a macromolecule that stores genetic information in organisms, has recently been gradually developed into a building block for new materials due to its stable chemical structure and excellent biocompatibility. The efficient preparation and functional integration of various molecular complexes and composite materials based on nucleic acid skeletons have been successfully achieved. These versatile materials possess excellent physical and chemical properties inherent to certain inorganic or organic molecules but are endowed with specific physiological functions by nucleic acids, demonstrating unique advantages and potential applications in materials science, nanotechnology, and biomedical engineering in recent years. However, issues such as the production cost, biological stability, and potential immunogenicity of DNA have presented some unprecedented challenges to the application of these materials in the field. This review summarizes the cutting-edge manufacturing techniques and unique properties of DNA-based complexes and composites and discusses the trends, challenges, and opportunities for the future development of nucleic acid-based materials.

DNA microbeads for spatio-temporally controlled morphogen release within organoids

Organoids are transformative in vitro model systems that mimic features of the corresponding tissue in vivo. However, across tissue types and species, organoids still often fail to reach full maturity and function because biochemical cues cannot be provided from within the organoid to guide their development. Here we introduce nanoengineered DNA microbeads with tissue mimetic tunable stiffness for implementing spatio-temporally controlled morphogen gradients inside of organoids at any point in their development. Using medaka retinal organoids and early embryos, we show that DNA microbeads can be integrated into embryos and organoids by microinjection and erased in a non-invasive manner with light. Coupling a recombinant surrogate Wnt to the DNA microbeads, we demonstrate the spatio-temporally controlled morphogen release from the microinjection site, which leads to morphogen gradients resulting in the formation of retinal pigmented epithelium while maintaining neuroretinal cell types. Thus, we bioengineered retinal organoids to more closely mirror the cell type diversity of in vivo retinae. Owing to the facile, one-pot fabrication process, the DNA microbead technology can be adapted to other organoid systems for improved tissue mimicry.

From Bioreactor to Bulk Rheology: Achieving Scalable Production of Highly Concentrated Circular DNA

DNA serves as a model system in polymer physics due to its ability to be obtained as a uniform polymer with controllable topology and nonequilibrium behavior. Currently, a major obstacle in the widespread adoption of DNA is obtaining it on a scale and cost basis that accommodates bulk rheology and high-throughput screening. To address this, recent advancements in bioreactor-based plasmid DNA production is coupled with anion exchange chromatography producing a unified approach to generating gram-scale quantities of monodisperse DNA. With this method, 1.1 grams of DNA is obtained per batch to generate solutions with concentrations up to 116 mg mL-1. This solution of uniform supercoiled and relaxed circular plasmid DNA, is roughly 69 times greater than the overlap concentration. The utility of this method is demonstrated by performing bulk rheology measurements at sample volumes up to 1 mL on DNA of different lengths, topologies, and concentrations. The measured elastic moduli are orders of magnitude larger than those previously reported for DNA and allowed for the construction of a time-concentration superposition curve that spans 12 decades of frequency. Ultimately, these results can provide important insights into the dynamics of ring polymers and the nature of highly condensed DNA dynamics.

Enzymatic Dissociation of DNA-Histone Condensates in an Electrophoretic Setting: Modulating DNA Patterning and Hydrogel Viscoelasticity

Development of an energy-driven self-assembly process is a matter of interest for understanding and mimicking diverse ranges of biological and environmental patterns in a synthetic system. In this article, first we demonstrate transient and temporally controlled self-assembly of a DNA-histone condensate where trypsin (already present in the system) hydrolyzes histone, resulting in disassembly. Upon performing this dynamic self-assembly process in a gel matrix under an electric field, we observe diverse kinds of DNA patterning across the gel matrix depending on the amount of trypsin, incubation time of the reaction mixture, and gel porosity. Notably, here, the micrometer-sized DNA-histone condensate does not move through the gel and only free DNA can pass; therefore, transport and accumulation of DNA at different zones depend on the release rate of DNA by trypsin. Furthermore, we show that the viscoelasticity of the native gel increases in the presence of DNA and a pattern over gel viscoelasticity at different zones can be achieved by tuning the amount of enzyme, i.e., the dissociation rate of the DNA-histone condensate. We believe enabling spatiotemporally controlled DNA patterning by applying an electric field will be potentially important in designing different kinds of spatiotemporally distinct dynamic materials.

A stimuli-responsive hydrogel for reversible information storage, encryption and decryption

Smart hydrogel materials, known for their sensitivity to external stimuli, exhibit a reversible dynamic response and find applications in diverse fields, particularly in information storage. Despite significant efforts in this domain, developing a hydrogel with high-resolution, repeatable recording, and robust information encryption/decryption capabilities still remains a challenge. In this study, we synthesized a polymer hydrogel, namely polyvinyl alcohol-n-isopropylacrylamide-octadecyl polyoxyethylene ether acrylate hydrogel (PPNS), which features multiple hydrogen bonds through copolymerization, by using N-isopropylacrylamide, polyvinyl alcohol, and octadecyl polyoxyethylene ether acrylate (SGA15) as raw materials. The PPNS hydrogel demonstrated outstanding high-resolution, repeatable recording capabilities, enabling reversible recording, encryption, and decryption of information using anhydrous ethanol as the inducer. Varying the SGA15 monomer concentration revealed that the PPNS-2% hydrogel, prepared with 2% SGA15, outperformed the other hydrogels in terms of information recording and encryption/decryption when immersed in anhydrous ethanol and deionized water. Furthermore, the PPNS-2% hydrogel exhibited the ability to undergo multiple information cycles while maintaining excellent mechanical properties even after 25 cycles. Notably, ethanol served as a specialized ink for inscribing different patterns on the hydrogel surface for information recording. The recorded information could be erased through water wiping or ethanol volatilization, enabling reversible information recording, encryption, and decryption. Due to their responsive and dynamic nature of PPNS hydrogels are positions them as promising candidates for use as innovative information storage platforms.

On-Demand Aligned DNA Hydrogel Via Light Scanning

DNA is an anisotropic, water-attracting, and biocompatible material, an ideal building block for hydrogel. The alignment of the anisotropic DNA chains is essential to maximize hydrogel properties, which has been little explored. Here, we present a method to fabricate the anisotropic DNA hydrogel that allows precise control for the polymerization process of photoreactive cationic monomers. Scanning ultraviolet light enables the uniaxial alignment of DNA chains through the polymerization-induced diffusive mass flow using a concentration gradient. While studying anisotropic mechanical properties and orientation recovery according to the DNA chain alignment direction, we demonstrate the potential of directionally controlled DNA hydrogels as smart materials.

Tumor Microenvironment-Responsive Hydrogel for Direct Extracellular ATP Imaging-Guided Surgical Resection with Clear Boundaries

Most solid tumors are clinically treated using surgical resection, and the presence of residual tumor tissues at the surgical margins often determines tumor survival and recurrence. Herein, a hydrogel (Apt-HEX/Cp-BHQ1 Gel, termed AHB Gel) is developed for fluorescence-guided surgical resection. AHB Gel is constructed by tethering a polyacrylamide hydrogel and ATP-responsive aptamers together. It exhibits strong fluorescence under high ATP concentrations corresponding to the TME (100-500 µm) but shows little fluorescence at low ATP concentrations (10-100 nm) such as those in normal tissues. AHB Gel can rapidly (within 3 min) emit fluorescence after exposure to ATP, and the fluorescence signal only occurs at sites exposed to high ATP, resulting in a clear boundary between the ATP-high and ATP-low regions. In vivo, AHB Gel exhibits specific tumor-targeting capacity with no fluorescence response in normal tissue, providing clear tumor boundaries. In addition, AHB Gel has good storage stability, which is conducive to its future clinical application. In summary, AHB Gel is a novel tumor microenvironment-targeted DNA-hybrid hydrogel for ATP-based fluorescence imaging. It can enable the precise imaging of tumor tissues, showing promising application in fluorescence-guided surgeries in the future.

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.

Stimulus-Responsive DNA Hydrogel Biosensors for Food Safety Detection

Food safety has always been a major global challenge to human health and the effective detection of harmful substances in food can reduce the risk to human health. However, the food industry has been plagued by a lack of effective and sensitive safety monitoring methods due to the tension between the cost and effectiveness of monitoring. DNA-based hydrogels combine the advantages of biocompatibility, programmability, the molecular recognition of DNA molecules, and the hydrophilicity of hydrogels, making them a hotspot in the research field of new nanomaterials. The stimulus response property greatly broadens the function and application range of DNA hydrogel. In recent years, DNA hydrogels based on stimulus-responsive mechanisms have been widely applied in the field of biosensing for the detection of a variety of target substances, including various food contaminants. In this review, we describe the recent advances in the preparation of stimuli-responsive DNA hydrogels, highlighting the progress of its application in food safety detection. Finally, we also discuss the challenges and future application of stimulus-responsive DNA hydrogels.

Current state of knowledge on intelligent-response biological and other macromolecular hydrogels in biomedical engineering: A review

Because intelligent hydrogels have good biocompatibility, a rapid response, and good degradability as well as a stimulus response mode that is rich, hydrophilic, and similar to the softness and elasticity of living tissue, they have received widespread attention and are widely used in biomedical engineering. In this article, we conduct a systematic review of the use of smart hydrogels in biomedical engineering. First, we introduce the properties and applications of hydrogels and compare the similarities and differences between traditional hydrogels and smart hydrogels. Secondly, we summarize the intelligent hydrogel types, the mechanisms of action used by different hydrogels, and the materials for preparing different types of hydrogels, such as the materials for the preparation of temperature-responsive hydrogels, which mainly include gelatin, carrageenan, agarose, amylose, etc.; summarize the morphologies of different hydrogels, such as films, fibers and microspheres; and summarize the application of smart hydrogels in biomedical engineering, such as for the delivery of proteins, antibiotics, deoxyribonucleic acid, etc. Finally, we summarize the shortcomings of current research and present future prospects for smart hydrogels. The purpose of this paper is to provide researchers engaged in related fields with a systematic review of the application of intelligent hydrogels in biomedical engineering. We hope that they will get some inspiration from this work to provide new directions for the development of related fields.

Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies

Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.

pH and light dual stimuli-responses of mixed system of 2-hydroxyl-propanediyl-α,ω-bis(dimethyldodecyl ammonium bromide) and trans-ortho-hydroxyl cinnamic acid

Stimuli-responsive smart supramolecular self-assembly with controllable morphology and adjustable rheological property has attracted widespread concern of scientists in recent years due to the great potential application in microfluidics, controlled release, biosensors and so on. In this study, a pH and UV light dual stimuli-responsive system was constructed by combining Gemini surfactant 2-hydroxyl-propanediyl-α,ω-bis(dimethyldodecyl ammonium bromide) (12-3(OH)-12·2Br^-) with trans-ortho-hydroxyl cinnamic acid (trans-OHCA) in aqueous solution. The phase behavior and stimuli-responsive behavior of the system including the microstructural transition, rheological property, intermolecular interaction, and isomerization reaction were explored by various experiment techniques such as rheometer, UV-vis spectrum, polarized optical microscopy (POM), transmission electron microscopy (TEM), dynamic light scattering (DLS) as well as theoretical calculation. The system displays abundant phase behaviors that supramolecular self-assemblies of different morphologies in different states such as spherical micelle, wormlike micelle, lamellar liquid crystal, and aqueous two phase system (ATPS) were observed even at lower concentration, which provide the research basis on the abundant stimuli-responsiveness of the system. The results prove that the multiple ionization and the photo-isomerization of trans-OHCA endow the system with plentiful responses to pH and UV light stimuli. It is expected that this study on the dual stimuli-responsive system with abundant self-assembly behaviors and adjustable rheological behaviors would be of theoretical and practical importance, which would provide essential guidance in designing and constructing smart materials with multiple stimuli-responses.

A Label-Free Photoelectrochemical Biosensor Based on CRISPR/Cas12a System Responsive Deoxyribonucleic Acid Hydrogel and "Click" Chemistry

A novel label-free photoelectrochemical (PEC) biosensor is presented in this work. As a barrier, the DNA hydrogel could block the coupling between g-C₃N₄ and CdS quantum dots (QDs). Therefore, extremely low photocurrent signals were obtained. The presence of target microRNA-21 can initiate the rolling circle amplification (RCA) reaction, which in turn produces many repeated sequences to activate the CRISPR/Cas12a system. The trans-cleavage activity of the CRISPR/Cas12a system led to the degradation of DNA hydrogels efficiently. As a result, the g-C₃N₄/CdS QDs heterojunction was formed through "click" chemistry. Through the amplification of the RCA and CRISPR/Cas12a system, the sensitivity of the PEC biosensor was improved significantly with the detection limit of 3.2 aM. The proposed sensor also showed excellent selectivity and could be used to detect actual samples. In addition, the modular design could facilitate the detection of different objects. Thus, the proposed CRISPR/Cas12a system responsive DNA hydrogel provides a simple, sensitive, and flexible way for label-free PEC analysis.

Advances in the Structural Strategies of the Self-Assembly of Photoresponsive Supramolecular Systems

Photosensitive supramolecular systems have garnered attention due to their potential to catalyze highly specific tasks through structural changes triggered by a light stimulus. The tunability of their chemical structure and charge transfer properties provides opportunities for designing and developing smart materials for multidisciplinary applications. This review focuses on the approaches reported in the literature for tailoring properties of the photosensitive supramolecular systems, including MOFs, MOPs, and HOFs. We discuss relevant aspects regarding their chemical structure, action mechanisms, design principles, applications, and future perspectives.

Self-Assembled ATP-Responsive DNA Nanohydrogel for Specifically Activated Fluorescence Imaging and Chemotherapy in Cancer Cells

Tumor marker-responsive drug delivery systems have been developed for cancer imaging and chemotherapy. However, improving their ability of controlled drug release remains a challenge. In this study, we have developed an adenosine triphosphate (ATP)-responsive DNA nanohydrogel for specifically activated fluorescence imaging and chemotherapy in cancer cells. Acrylamide and acrydite-modified DNAs were polymerized to obtain DNA-grafted polyacrylamide copolymers. Then, the copolymers acted as the backbone of the nanohydrogel and were assembled by base complementation with ATP aptamer linkers to construct an ATP-responsive nanohydrogel. Meanwhile, the chemotherapeutic drug doxorubicin (DOX) was added and loaded into the ATP-responsive nanohydrogel during the assembly process. After endocytosis by cancer cells and response to a high intracellular ATP level, the DOX-loaded nanohydrogel disassembled due to the formation of aptamer/ATP complexes. Subsequently, the released DOX played a role in fluorescence imaging and chemotherapy of cancer cells. Through the ATP-responsive property and satisfying drug delivery capability, this nanohydrogel realized fluorescence imaging and specific cancer cell killing capabilities due to different intracellular ATP levels in normal and cancer cell lines. In summary, this study has provided a novel strategy of constructing a tumor microenvironment-responsive drug delivery system triggered by the tumor markers for tumor intracellular imaging and chemotherapy.