A pure DNA hydrogel with stable catalytic ability produced by one-step rolling circle amplification

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.

DNA hydrogels and their derivatives in biomedical engineering applications

Deoxyribonucleotide (DNA) is uniquely programmable and biocompatible, and exhibits unique appeal as a biomaterial as it can be precisely designed and programmed to construct arbitrary shapes. DNA hydrogels are polymer networks comprising cross-linked DNA strands. As DNA hydrogels present programmability, biocompatibility, and stimulus responsiveness, they are extensively explored in the field of biomedicine. In this study, we provide an overview of recent advancements in DNA hydrogel technology. We outline the different design philosophies and methods of DNA hydrogel preparation, discuss its special physicochemical characteristics, and highlight the various uses of DNA hydrogels in biomedical domains, such as drug delivery, biosensing, tissue engineering, and cell culture. Finally, we discuss the current difficulties facing DNA hydrogels and their potential future development.

DNA-empowered synthetic cells as minimalistic life forms

Cells, the fundamental units of life, orchestrate intricate functions - motility, adaptation, replication, communication, and self-organization within tissues. Originating from spatiotemporally organized structures and machinery, coupled with information processing in signalling networks, cells embody the 'sensor-processor-actuator' paradigm. Can we glean insights from these processes to construct primitive artificial systems with life-like properties? Using de novo design approaches, what can we uncover about the evolutionary path of life? This Review discusses the strides made in crafting synthetic cells, utilizing the powerful toolbox of structural and dynamic DNA nanoscience. We describe how DNA can serve as a versatile tool for engineering entire synthetic cells or subcellular entities, and how DNA enables complex behaviour, including motility and information processing for adaptive and interactive processes. We chart future directions for DNA-empowered synthetic cells, envisioning interactive systems wherein synthetic cells communicate within communities and with living cells.

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.

CRISPR/Cas12a-Responsive Hydrogels for Conjugation-Free and Universal Indicator Release in Colorimetric Detection

Recent advances have demonstrated the significant potential and advantages to repurpose existing point-of-care reactions/devices to realize portable detection of nonoriginal targets, e.g., pathogen genes. However, pursuing this aim usually requires protein indicator-nucleic acid conjugation via a covalent bond, which may bring drawbacks such as high cost, complicated procedure, and annoying component rebuilding. Herein, we developed a conjugation-free, effective, and universal detection platform called CRIs-gel (CRISPR/Cas12a-Responsive Indicators@RCA hydrogels). Various protein indicators are pre-encapsulated into the hydrogels made of effective and high-yield rolling circle amplification (RCA). Upon a targeting sequence binding with its antisense crRNA, CRISPR/Cas12a starts its trans-cleavage activity to crush the hydrogel, which may directly release the indicator for downstream readout. Two proteins, amylase (GA) and human chorionic gonadotropin (hCG), are successfully used as model indicators to trigger the downstream amylum-I2 color change and pregnancy test strip response. After coupling with upstream isothermal nucleic acid amplification, both portable readouts may detect as few as 2 copies/μL genetic sequences of influenza A virus (FluA), human papilloma virus (HPV), SARS-CoV-2, and influenza B virus (FluB). This conjugation-free CRIs-gel platform is thus simple, sensitive, and universal and can provide innovative insights for portable point-of-care testing (POCT) development.

Smart G-quadruplex hydrogels: From preparations to comprehensive applications

In recent years, the accelerated development of G-quadruplexes and hydrogels has driven the development of intelligent biomaterials. Based on the excellent biocompatibility and special biological functions of G-quadruplexes, and the hydrophilicity, high-water retention, high water content, flexibility and excellent biodegradability of hydrogels, G-quadruplex hydrogels are widely used in various fields by combining the dual advantages of G-quadruplexes and hydrogels. Here, we provide a systematic and comprehensive classification of G-quadruplex hydrogels in terms of preparation strategies and applications. This paper reveals how G-quadruplex hydrogels skillfully utilize the special biological functions of G-quadruplexes and the skeleton structure of hydrogels, and expounds its applications in the fields of biomedicine, biocatalysis, biosensing and biomaterials. In addition, we deeply analyze the challenges in preparation, applications, stability and safety of G-quadruplex hydrogels, as well as potential future development directions.

Immunostimulatory DNA Hydrogel Enhances Protective Efficacy of Nanotoxoids against Bacterial Infection

While vaccines have been highly successful in protecting against various infections, there are still many high-priority pathogens for which there are no clinically approved formulations. To overcome this challenge, researchers have explored the use of nanoparticulate strategies for more effective antigen delivery to the immune system. Along these lines, nanotoxoids are a promising biomimetic platform that leverages cell membrane coating technology to safely deliver otherwise toxic bacterial antigens in their native form for antivirulence vaccination. Here, in order to further boost their immunogenicity, nanotoxoids formulated against staphylococcal α-hemolysin are embedded into a DNA-based hydrogel with immunostimulatory CpG motifs. The resulting nanoparticle-hydrogel composite is injectable and improves the in vivo delivery of vaccine antigens while simultaneously stimulating nearby immune cells. This leads to elevated antibody production and stronger antigen-specific cellular immune responses. In murine models of pneumonia and skin infection caused by methicillin-resistant Staphylococcus aureus, mice vaccinated with the hybrid vaccine formulation are well-protected. This work highlights the benefits of combining nanoparticulate antigen delivery systems with immunostimulatory hydrogels into a single platform, and the approach can be readily generalized to a wide range of infectious diseases.

DNA hydrogels and nanogels for diagnostics, therapeutics, and theragnostics of various cancers

As an efficient class of hydrogel-based therapeutic drug delivery systems, deoxyribonucleic acid (DNA) hydrogels (particularly DNA nanogels) have attracted massive attention in the last five years. The main contributor to this is the programmability of these 3-dimensional (3D) scaffolds that creates fundamental effects, especially in treating cancer diseases. Like other active biological ingredients (ABIs), DNA hydrogels can be functionalized with other active agents that play a role in targeting drug delivery and modifying the half-life of the therapeutic cargoes in the body's internal environment. Considering the brilliant advantages of DNA hydrogels, in this survey, we intend to submit an informative collection of feasible methods for the design and preparation of DNA hydrogels and nanogels, and the responsivity of the immune system to these therapeutic cargoes. Moreover, the interactions of DNA hydrogels with cancer biomarkers are discussed in this account. Theragnostic DNA nanogels as an advanced species for both detection and therapeutic purposes are also briefly reviewed.

Construction of rolling circle amplification products-based pure nucleic acid nanostructures for biomedical applications

Nucleic acid nanomaterials with good biocompatibility, biodegradability, and programmability have important applications in biomedical field. Nucleic acid nanomaterials are usually combined with some inorganic nanomaterials to improve their biological stability. However, undefined toxic side effects of composite nanocarriers hamper their application in vivo. As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. RCA products with different functional parts can be customized by changing the sequence of the circular template, thereby generating complex multifunctional DNA nanostructures, such as DNA nanowire, nanoflower, origami, nanotube, nanoribbon, etc. More importantly, RCA products as nonnicked building blocks can enhance the biostability of DNA nanostructures, especially in vivo. These RCA products-based nucleic acid nanostructures can be used as scaffolds or nanocarriers to interact or load with metal nanoparticles, proteins, lipids, cationic polymers, therapeutic nucleic acids or drugs, etc. This paper reviews the assembly strategies of RCA based DNA nanostructures with different shape and their applications in biosensing, bioimaging and biomedicine. Finally, the development prospects of the nucleic acid nanomaterials in clinical diagnosis and treatment of diseases are described. STATEMENT OF SIGNIFICANCE: As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. This paper reviews the construction of various shapes of pure nucleic acid nanomaterials based on RCA products and their applications in biosensing, bioimaging and biomedicine. This will promote the development of biocompatible DNA nanovehicles and their further application in living systems, including bioimaging, molecular detection, disease diagnosis and drug delivery, finally producing a significant impact in the field of nanotechnology and nanomedicine.

Design and application of stimuli-responsive DNA hydrogels: A review

Deoxyribonucleic acid (DNA) hydrogels combine the properties of DNAs and hydrogels, and adding functionalized DNAs is key to the wide application of DNA hydrogels. In stimuli-responsive DNA hydrogels, the DNA transcends its application in genetics and bridges the gap between different fields. Specifically, the DNA acts as both an information carrier and a bridge in constructing DNA hydrogels. The programmability and biocompatibility of DNA hydrogel make it change macroscopically in response to a variety of stimuli. In order to meet the needs of different scenarios, DNA hydrogels were also designed into microcapsules, beads, membranes, microneedle patches, and other forms. In this study, the stimuli were classified into single biological and non-biological stimuli and composite stimuli. Stimuli-responsive DNA hydrogels from the past five years were summarized, including but not limited to their design and application, in particular logic gate pathways and signal amplification mechanisms. Stimuli-responsive DNA hydrogels have been applied to fields such as sensing, nanorobots, information carriers, controlled drug release, and disease treatment. Different potential applications and the developmental pro-spects of stimuli-responsive DNA hydrogels were discussed.

Programmable DNA Hydrogels as Artificial Extracellular Matrix

The cell microenvironment plays a crucial role in regulating cell behavior and fate in physiological and pathological processes. As the fundamental component of the cell microenvironment, extracellular matrix (ECM) typically possesses complex ordered structures and provides essential physical and chemical cues to the cells. Hydrogels have attracted much attention in recapitulating the ECM. Compared to natural and synthetic polymer hydrogels, DNA hydrogels have unique programmable capability, which endows the material precise structural customization and tunable properties. This review focuses on recent advances in programmable DNA hydrogels as artificial extracellular matrix, particularly the pure DNA hydrogels. It introduces the classification, design, and assembly of DNA hydrogels, and then summarizes the state-of-the-art achievements in cell encapsulation, cell culture, and tissue engineering with DNA hydrogels. Ultimately, the challenges and prospects for cellular applications of DNA hydrogels are delivered.

Construction of a Mass-Tagged Oligo Probe Set for Revealing Protein Ratiometric Relationship Associated with EGFR-HER2 Heterodimerization in Living Cells

Protein dimerization, as the most common form of protein-protein interaction, can manifest more significant roles in cellular signaling than individual monomers. For example, excessive formation of EGFR-HER2 dimer has been implicated in cancer development and therapeutic resistance in addition to the overexpression of EGFR and HER2 proteins. Thus, quantitative evaluation of these heterodimers in living cells and revelation of their ratiometric relationship with protein monomers in dimerization may provide insights into clinical cancer management. To achieve this goal, the prerequisite is protein heterodimer quantification. Given the current lack of quantitative methods, we constructed a mass-tagged oligo nanoprobe set for quantification of EGFR-HER2 dimer in living cells. The mass-tagged oligo nanoprobe set contained two targeting probes (nucleic acid aptamers), a connector probe, a hairpin probe, and a photocleavable mass-tagged probe. Two distinct aptamers can recognize target protein monomers and initiate the subsequent hybridization cascade involving binding to the connector probe, formation of an initiator strand, opening of a hairpin probe, and ensuing hybridization with a photocleavable mass-tagged probe. Ultimately, the mass tag was released under ultraviolet light and then subjected to mass spectrometric analysis. In this way, the information regarding the interaction between two protein monomers was successfully converted to the quantitative signal of the mass tag. Using the assay, the expression level of EGFR-HER2 dimer and its relationship with individual protein monomers were determined in four breast cancer cell lines. We are among the first to obtain the absolute level of protein heterodimer, and this quantitative information may be vital in understanding the molecular basis of cancer.

DNA Nanotechnology-Based Supramolecular Assemblies for Targeted Biomedical Applications

DNA is a polyanionic, hydrophilic, and natural biopolymer that offers properties such as biodegradability, biocompatibility, non-toxicity, and non-immunogenicity. These properties of DNA as an ideal biopolymer offer modern-day researchers' reasons to exploit these to form high-order supramolecular assemblies. These structures could range from simple to complex and provide various applications. Among them, supramolecular assemblies like DNA hydrogels (DNA-HG) and DNA dendrimers (DNA-DS) show massive growth potential in the areas of biomedical applications such as cell biology, medical stream, molecular biology, pharmacology, and healthcare product manufacturing. The application of both of these assemblies has seen enormous growth in recent years. In this focused review on DNA-based supramolecular assemblies like hydrogels and dendrimers, we present the principles of synthesis and characterization, key developments with examples and applications, and conclude with a brief perspective on challenges and future outlook for such devices and their subsequent applications.

Designer DNA biomolecules as a defined biomaterial for 3D bioprinting applications

DNA has excellent features such as the presence of functional and targeted molecular recognition motifs, tailorability, multifunctionality, high-precision molecular self-assembly, hydrophilicity, and outstanding biocompatibility. Due to these remarkable features, DNA has emerged as a leading next-generation biomaterial of choice to make hydrogels by self-assembly. In recent times, novel routes for the chemical synthesis of DNA, advances in tailorable designs, and affordable production ways have made DNA as a building block material for various applications. These advanced features have made researchers continuously explore the interesting properties of pure and hybrid DNA for 3D bioprinting and other biomedical applications. This review article highlights the topical advancements in the use of DNA as an ideal bioink for the bioprinting of cell-laden three-dimensional tissue constructs for regenerative medicine applications. Various bioprinting techniques and emerging design approaches such as self-assembly, nucleotide sequence, enzymes, and production cost to use DNA as a bioink for bioprinting applications are described. In addition, various types and properties of DNA hydrogels such as stimuli responsiveness and mechanical properties are discussed. Further, recent progress in the applications of DNA in 3D bioprinting are emphasized. Finally, the current challenges and future perspectives of DNA hydrogels in 3D bioprinting and other biomedical applications are discussed.

Construction and Research of Multiple Stimuli-Responsive 2D Photonic Crystal DNA Hydrogel Sensing Platform with Double-Network Structure and Signal Self-Expression

The stimuli-responsive DNA hydrogel has attracted wide attention in the fields of chemical and biological sensing. However, it is still a challenge to integrate characteristics with low-cost, high mechanical strength, and signal self-expression into a DNA hydrogel simultaneously. Herein, a stimuli-responsive 2D photonic crystal double network DNA hydrogel (2D PhC DN-DNA hydrogel) sensing platform is developed via combining the signal self-expression of 2D PhC array with the selective recognition of polyacrylamide (PAM)/DNA DN hydrogel. The change of DNA configuration induced by specific target triggers the change of 2D PhC DN-DNA hydrogel volume, leading to a shift of the Debye diffraction ring diameter. In order to verify the feasibility of this strategy, the 2D PhC DN-DNA hydrogel with C-rich sequences is chosen as a proof-of-concept. The results indicate that the hydrogel has good detection performance for pH and Ag⁺/Cys. And the Debye diffraction ring diameter of the hydrogel is correlated with the concentration of the Ag⁺/Cys in the range of 0.5-20 μM. Compared with previously pure DNA hydrogel sensing platform, the 2D PhC DN-DNA hydrogel features low-cost preparation process and label-free determination. Meanwhile, only a laser pointer and a ruler are needed for the determination of targets, which shows that the hydrogel has application prospect in the development of portable response equipment.

Dual-Targeted Self-Assembled DNA Hydrogels Decorated With Multivalent Aptamers Loaded With DOX for Anticancer Therapy

Chemotherapy, as one of the principal modalities for cancer therapy, is limited by its non-specific and inefficient delivery to tumors. To overcome these limitations, we report herein a dual-targeted aptamer-decorated DNA hydrogel system (DTA-H) to achieve efficient, stable, and targeted delivery of drugs. Firstly, DNA hydrogel was formed by the rolling circle amplification. By reasonable design, double target and multivalent aptamers were decorated on DNA hydrogel to load DOX. The results confirmed that DTA-H can deliver chemotherapy drugs and aptamer nucleic acids drugs to target cells, inducing degradation of HER2 protein while chemotherapy is synergistic to inhibit HER2-positive breast cancer growth. The proposed drug delivery system has significant potential to achieve efficient, stable, and targeted delivery of drugs and cancer therapy.

Smartphone-Based Pure DNAzyme Hydrogel Platform for Visible and Portable Colorimetric Detection of Cell-Free DNA

Cell-free DNA (cfDNA), as a tumor marker, is of great importance for the diagnosis of cancer and targeted therapy. However, the need for huge analytical instruments for cfDNA analysis has restricted its practical applications, especially in rural areas and third-world countries. Herein, a portable and visual smartphone-based DNAzyme hydrogel platform is developed for cfDNA detection. The target cfDNA triggers rolling circle amplification to produce a G-quadruplex-comprised DNA hydrogel with an horseradish peroxidase (HRP)-like catalytic function, which further catalyzes the chromogenic substrate to generate a visible output signal. Notably, the naked-eye detection of cfDNA can be realized by the macroscale visibility and catalytic ability of the DNA hydrogel. The linear range of the DNAzyme hydrogel platform for cfDNA detection is 0.1 pM-1500 nM with a detection limit of 0.042 pM. Moreover, this platform is exploited for the detection of cfDNA in spiked human serum with favorable sensitivity and recovery. Therefore, the DNAzyme hydrogel platform provides highly promising potential for testing other nucleic acid biomarkers.

Recent Advances in Stimuli-Responsive DNA-Based Hydrogels

Stimuli-responsive DNA-based hydrogels are attracting growing interest because of their smart responsiveness, excellent biocompatibility, regulated biodegradability, and programmable design properties. Integration of reconfigurable DNA architectures and switchable supramolecular moieties (as cross-linkers) in hydrogels by responding to external stimuli provides an ideal approach for the reversible tuning structural and mechanical properties of the hydrogels, which can be exploited in the development of intelligent DNA-based materials. This review highlights recent advances in the design of responsive pure DNA hydrogels, DNA-polymer hybrid hydrogels, and autonomous DNA-based hydrogels with transient behaviors. A variety of chemically and physically triggered DNA-based stimuli-responsive hydrogels and their versatile applications in biosensing, biocatalysis, cell culture and separation, drug delivery, shape memory, self-healing, and robotic actuators are summarized. Finally, we address the key challenges that the field will face in the coming years, and future prospects are identified.

Stimuli-responsive DNA-based hydrogels for biosensing applications

The base sequences of DNA are endowed with the rich structural and functional information and are available for the precise construction of the 2D and 3D macro products. The hydrogels formed by DNA are biocompatible, stable, tunable and biologically versatile, thus, these have a wide range of promising applications in bioanalysis and biomedicine. In particular, the stimuli-responsive DNA hydrogels (smart DNA hydrogels), which exhibit a reversible and switchable hydrogel to sol transition under different triggers, have emerged as smart materials for sensing. Thus far, the combination of the stimuli-responsive DNA hydrogels and multiple sensing platforms is considered as biocompatible and is useful as the flexible recognition components. A review of the stimuli-responsive DNA hydrogels and their biosensing applications has been presented in this study. The synthesis methods to prepare the DNA hydrogels have been introduced. Subsequently, the current status of the stimuli-responsive DNA hydrogels in biosensing has been described. The analytical mechanisms are further elaborated by the combination of the stimuli-responsive DNA hydrogels with the optical, electrochemical, point-of-care testing (POCT) and other detection platforms. In addition, the prospects of the application of the stimuli-responsive DNA hydrogels in biosensing are presented.

Smart Nucleic Acid Hydrogels with High Stimuli-Responsiveness in Biomedical Fields

Due to their hydrophilic, biocompatible and adjustability properties, hydrogels have received a lot of attention. The introduction of nucleic acids has made hydrogels highly stimuli-responsiveness and they have become a new generation of intelligent biomaterials. In this review, the development and utilization of smart nucleic acid hydrogels (NAHs) with a high stimulation responsiveness were elaborated systematically. We discussed NAHs with a high stimuli-responsiveness, including pure NAHs and hybrid NAHs. In particular, four stimulation factors of NAHs were described in details, including pH, ions, small molecular substances, and temperature. The research progress of nucleic acid hydrogels in biomedical applications in recent years is comprehensively discussed. Finally, the opportunities and challenges facing the future development of nucleic acid hydrogels are also discussed.

Selective and Nongenetic Peroxidase Tag of Membrane Protein: a Nucleic Acid Tool for Proximity Labeling

The protein nanoenvironment on the plasma membrane is intimately linked to cellular biological functions. Elucidation of the protein nanoenvironment contributes to understanding the pathological mechanism and discovery of disease biomarkers. However, methods enabling characterization of the protein nanoenvironment in the endogenous biological environment have been rarely developed. Toward this end, we created a nucleic acid tool called Apt-Gq/h for proximity labeling to decipher the endogenous protein nanoenvironment. Here, the aptamer acts as an anchor for binding the protein of interest (POI). The G-quadruplex/hemin complex induces proximity labeling of POI via catalyzing the conversion of inert small-molecule substrates into short-lived reactive species. The labeled proteins enable the subsequent affinity-based enrichment and proteomic analysis. We first characterized Apt-Gq/h-mediated POI labeling in vitro and tested its utility by interrogating the protein nanoenvironment of POI in living cells. Taking advantage of the nongenetic, multiple reaction sites, and rapid proximity labeling, Apt-Gq/h was further utilized to imaging the cell-cell connection and amplification detection of biomarkers in living cells and tissue sections. We believe that Apt-Gq/h will be a potential tool for basic science and clinical applications.

A novel aptasensor based on DNA hydrogel for sensitive visual detection of ochratoxin A

A novel visual detection mode is proposed to improve the detection sensitivity for the determination of ochratoxin A (OTA). The mode is based on aptamer recognition and the signal amplification of rolling circle amplification (RCA) products self-assembled DNA hydrogel. Moreover, gold nanoparticles (AuNPs) were directly assembled inside the DNA hydrogel by adjusting the padlock probe sequences to achieve a stronger binding force between the DNA hydrogel and AuNPs; this avoids the need for modification of AuNPs with DNA sequences. In the presence of OTA, DNA hydrogel is formed. With higher concentrations of OTA, a larger amount of DNA hydrogel is formed. When AuNPs are added to the DNA hydrogel, AuNPs can be enclosed inside the DNA hydrogel. With more DNA hydrogel, there is less AuNPs in the supernatant. Thus, the absorbance of the supernatant is anti-correlated with the concentration of OTA. After optimization of the experimental conditions, the change in the absorbance of the supernatant was linearly correlated with the concentration of OTA, in the range 0.05 to 10 ng/mL; the limit of detection was 0.005 ng/mL. The good specificity of the developed biosensor was confirmed in the presence of other mycotoxins that are coexistent with or analogues of OTA. By comparing the developed method with the ELISA method, the accuracy and stability of this new method were also verified, with good performance obtained in real samples. Diagram of the principle of the colorimetric aptasensor for OTA detection based on rolling circle amplification product self-assembled DNA hydrogel.

Smart and Functionalized Development of Nucleic Acid-Based Hydrogels: Assembly Strategies, Recent Advances, and Challenges

Nucleic acid-based hydrogels that integrate intrinsic biological properties of nucleic acids and mechanical behavior of their advanced assemblies are appealing bioanalysis and biomedical studies for the development of new-generation smart biomaterials. It is inseparable from development and incorporation of novel structural and functional units. This review highlights different functional units of nucleic acids, polymers, and novel nanomaterials in the order of structures, properties, and functions, and their assembly strategies for the fabrication of nucleic acid-based hydrogels. Also, recent advances in the design of multifunctional and stimuli-responsive nucleic acid-based hydrogels in bioanalysis and biomedical science are discussed, focusing on the applications of customized hydrogels for emerging directions, including 3D cell cultivation and 3D bioprinting. Finally, the key challenge and future perspectives are outlined.

Development, Preparation, and Biomedical Applications of DNA-Based Hydrogels

Hydrogels have outstanding research and application prospects in the biomedical field. Among them, the design and preparation of biomedical hydrogels with deoxyribonucleic acid (DNA) as building blocks have attracted increasing research interest. DNA-based hydrogel not only has the skeleton function of hydrogel, but also retains its biological functions, including its excellent selection specificity, structural designability, precise molecular recognition ability, outstanding biocompatibility, and so on. It has shown important application prospects in the biomedical field, such as drug delivery, biosensing, and tissue engineering. In recent years, researchers have made full use of the characteristics of DNA molecules and constructed various pure DNA-based hydrogels with excellent properties through various crosslinking methods. Moreover, via introducing functional molecules or elements, or combining with other functional materials, a variety of multifunctional DNA-based hybrid hydrogels have also been constructed, which expand the breadth and depth of their applications. Here, we described the recent development trend in the area of DNA-based hydrogels and highlighted various preparation methods of DNA-based hydrogels. Representative biomedical applications are also exemplified to show the high performance of DNA-based hydrogels. Meanwhile, the existing problems and prospects are also summarized. This review provided references for the further development of DNA-based hydrogels.

Harnessing the physicochemical properties of DNA as a multifunctional biomaterial for biomedical and other applications

The biological purpose of DNA is to store, replicate, and convey genetic information in cells. Progress in molecular genetics have led to its widespread applications in gene editing, gene therapy, and forensic science. However, in addition to its role as a genetic material, DNA has also emerged as a nongenetic, generic material for diverse biomedical applications. DNA is essentially a natural biopolymer that can be precisely programed by simple chemical modifications to construct materials with desired mechanical, biological, and structural properties. This review critically deciphers the chemical tools and strategies that are currently being employed to harness the nongenetic functions of DNA. Here, the primary product of interest has been crosslinked, hydrated polymers, or hydrogels. State-of-the-art applications of macroscopic, DNA-based hydrogels in the fields of environment, electrochemistry, biologics delivery, and regenerative therapy have been extensively reviewed. Additionally, the review encompasses the status of DNA as a clinically and commercially viable material and provides insight into future possibilities.

Melanin-loaded CpG DNA hydrogel for modulation of tumor immune microenvironment

Photothermal immunotherapy has emerged as one of the most potent approaches for cancer treatment, but this strategy has suffered from the lack of biodegradability of the photoresponsive materials. In this study, we aimed to develop biodegradable materials for photothermal immunotherapy. To this end, we designed a DNA CpG hydrogel (DH, generated by rolling-circle amplification), loaded it with bis-(3'-5')-cyclic dimeric guanosine monophosphate (G/DH), and coated the formulation with melanin (Mel/G/DH). Mel/G/DH exhibited a temperature increase upon near infrared (NIR) illumination. In vitro, Mel/G/DH plus NIR (808 nm) irradiation, induced the exposure of calreticulin on CT26 cancer cells, and significantly activated the maturation of dendritic cells (DC). In vivo, local administration of Mel/G/DH (+NIR) exerted photothermal killing of primary tumors and induced maturation of DC in lymph nodes. Treatment of primary tumors with Mel/G/DH(+NIR) prevented the growth of rechallenged tumors at a distant site. Survival was 100% in mice treated with Mel/G/DH(+NIR), 5-fold higher than the group treated with Mel/G(+NIR). Mel/G/DH(+NIR) treatment remodeled the immune microenvironment of distant tumors, increasing cytotoxic T cells and decreasing Treg cells. Taken together, the results of this study suggest the potential of Mel/G/DH as a platform for modulating tumor immune microenvironment aimed at preventing the recurrence of distant tumors.

Tungsten disulfide nanosheets-based colorimetric assay for glucose sensing

We have developed a glucose oxidase (GOx)-mediated strategy for glucose detection, which is based on the intrinsic peroxidase-like activity of WS₂ as a catalyst for the 3,3',5,5'-tetramethylbenzidine‑hydrogen peroxide (TMB-H₂O₂) reaction. The colorimetric assay involves two parts: generation of H₂O₂ from the oxidation of glucose catalyzed by GOx, and WS₂ nanosheets that catalyze the reaction between TMB and H₂O₂. In this colorimetric assay, the enhancement of colorimetric signals depends directly on the increased H₂O₂ concentration, which, in turn, relies on the glucose concentration. The results show that the concentrations of the glucose were directly proportional to absorbance of the TMB solutions over a range of 1 nM-500 μM with a limit of detection of 0.1445 nM. In addition, this new colorimetric assay has been utilized for glucose detection in human serum with a satisfactory result.

Programmable 3D rigid clathrate hydrogels based on self-assembly of tetrahedral DNA and linker PCR products

A clathrate tetrahedral DNA gel was assembled by combining tetrahedral DNA and rigid linker PCR products to achieve visible detection of Salmonella spp. This method overcame the shortcomings of AuNPs in coloration and enriched the use of tetrahedral DNA for the visible detection of virtually any target concerned with pathogens.

A Simple Blocking PCR-Based Method for the Synthesis of High-Copy dsDNA Tandem Repeats

DNA tandem repeats are frequently found in eukaryotic genomes. High-copy DNA repeats can serve as building blocks of complex DNA structures, but the in vitro synthesis of DNA repeats has been challenging due to complicated procedures and the high cost. Here, a new, simple method is developed using the strategy of blocking polymerase chain reaction for highly efficient DNA repeat expansion (BPRE). With BPRE, dsDNA fragments composed of more than 40 copies of the repeat sequence can be quickly produced, while the cost is reduced by at least 90%. As a typical application, reannealing of the dsDNA repeats generates elastic hydrogels, which shows a high capacity for doxycycline absorption and prolonged release.

DNA Hydrogel-Based Three-Dimensional Electron Transporter and Its Application in Electrochemical Biosensing

Electrochemical biosensing relies on electron transport on the electrode surface. However, the limited functional area of the two-dimensional electrode prevents the qualitative breakthrough in the efficiency of electron transfer. Here, a three-dimensional electron transporter was constructed to improve the efficiency of electron transfer by using an interface-immobilized DNA hydrogel. A three-dimensional pure DNA hydrogel is constructed and used as a scaffold for electron transfer. Then, an electron mediator is embedded in the DNA hydrogel through intercalative binding, and DNAzyme with intrinsic peroxidase-like activity is introduced at the node of the hydrogel scaffold to fabricate an electrochemical biosensor. The conduction of the electron mediator in the scaffold enables the acquisition of long-distance DNAzyme catalytic signals, thereby overcoming the limitation of two-dimensional electrodes. This three-dimensional electron transporter is significant for enriching the toolbox of electrochemical biosensing and can provide potential support for the development of highly sensitive biosensors.

Dynamic DNA Assemblies in Biomedical Applications

Deoxyribonucleic acid (DNA) has been widely used to construct homogeneous structures with increasing complexity for biological and biomedical applications due to their powerful functionalities. Especially, dynamic DNA assemblies (DDAs) have demonstrated the ability to simulate molecular motions and fluctuations in bionic systems. DDAs, including DNA robots, DNA probes, DNA nanochannels, DNA templates, etc., can perform structural transformations or predictable behaviors in response to corresponding stimuli and show potential in the fields of single molecule sensing, drug delivery, molecular assembly, etc. A wave of exploration of the principles in designing and usage of DDAs has occurred, however, knowledge on these concepts is still limited. Although some previous reviews have been reported, systematic and detailed reviews are rare. To achieve a better understanding of the mechanisms in DDAs, herein, the recent progress on the fundamental principles regarding DDAs and their applications are summarized. The relative assembly principles and computer-aided software for their designing are introduced. The advantages and disadvantages of each software are discussed. The motional mechanisms of the DDAs are classified into exogenous and endogenous stimuli-triggered responses. The special dynamic behaviors of DDAs in biomedical applications are also summarized. Moreover, the current challenges and future directions of DDAs are proposed.

DNAzymes as Catalysts for l-Tyrosine and Amyloid β Oxidation

Single-stranded deoxyribonucleic acids have an enormous potential for catalysis by applying tailored sequences of nucleotides for individual reaction conditions and substrates. If such a sequence is guanine-rich, it may arrange into a three-dimensional structure called G-quadruplex and give rise to a catalytically active DNA molecule, a DNAzyme, upon addition of hemin. Here, we present a DNAzyme-mediated reaction, which is the oxidation of l-tyrosine toward dityrosine by hydrogen peroxide. With an optimal stoichiometry between DNA and hemin of 1:10, we report an activity of 101.2 ± 3.5 μUnits (μU) of the artificial DNAzyme Dz-00 compared to 33.0 ± 1.8 μU of free hemin. Exemplarily, DNAzymes may take part in neurodegeneration caused by amyloid beta (Aβ) aggregation due to l-tyrosine oxidation. We show that the natural, human genome-derived DNAzyme In1-sp is able to oxidize Aβ peptides with a 4.6% higher yield and a 33.3% higher velocity of the reaction compared to free hemin. As the artificial DNAzyme Dz-00 is even able to catalyze Aβ peptide oxidation with a 64.2% higher yield and 337.1% higher velocity, an in-depth screening of human genome-derived DNAzymes may identify further candidates with similarly high catalytic activity in Aβ peptide oxidation.

Circular Nucleic Acids: Discovery, Functions and Applications

Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.

Tailoring DNA Self-assembly to Build Hydrogels

DNA hydrogels are crosslinked polymeric networks in which DNA is used as the backbone or the crosslinker. These hydrogels are novel biofunctional materials that possess the biological character of DNA and the framed structure of hydrogels. Compared with other kinds of hydrogels, DNA hydrogels exhibit not only high mechanical strength and controllable morphologies but also good recognition ability, designable responsiveness, and programmability. The DNA used in this type of hydrogel acts as a building block for self-assembly or as a responsive element due to its sequence recognition ability and switchable structural transitions, respectively. In this review, we describe recent developments in the field of DNA hydrogels and discuss the role played by DNA in these hydrogels. Various synthetic strategies for and a range of applications of DNA hydrogels are detailed.

The sweet detection of rolling circle amplification: Glucose-based electrochemical genosensor for the detection of viral nucleic acid

Herein, an isothermal padlock probe-based assay for the simple and portable detection of pathogens coupled with a glucose oxidase (GOx)-based electrochemical readout is reported. Infectious diseases remain a constant threat on a global scale, as in recurring pandemics. Rapid and portable diagnostics hold the promise to tackle the spreading of diseases and decentralising healthcare to point-of-care needs. Ebola, a hypervariable RNA virus causing fatalities of up to 90% for recent outbreaks in Africa, demands immediate attention for bedside diagnostics. The design of the demonstrated assay consists of a rolling circle amplification (RCA) technique, responsible for the generation of nucleic acid amplicons as RCA products (RCPs). The RCPs are generated on magnetic beads (MB) and subsequently, connected via streptavidin-biotin bonds to GOx. The enzymatic catalysis of glucose by the bound GOx allows for an indirect electrochemical measurement of the DNA target. The RCPs generated on the surface of the MB were confirmed by scanning electron microscopy, and among other experimental conditions such as the type of buffer, temperature, concentration of GOx, sampling and measurement time were evaluated for the optimum electrochemical detection. Accordingly, 125 μg mL^-1 of GOx with 5 mM glucose using phosphate buffer saline (PBS), monitored for 1 min were selected as the ideal conditions. Finally, we assessed the analytical performance of the biosensing strategy by using clinical samples of Ebola virus from patients. Overall, this work provides a proof-of-concept bioassay for simple and portable molecular diagnostics of emerging pathogens using electrochemical detection, especially in resource-limited settings.

DNA-scaffold copper nanoclusters integrated into a cerium(III)-triggered Fenton-like reaction for the fluorometric and colorimetric enzymatic determination of glucose

A fluorometric and colorimetric method are described for the determination of hydrogen peroxide and glucose by integrating copper nanoclusters (CuNCs) into a Fenton-like reaction. The mechanism mainly depends on the fast formation of long-strand DNA-templated CuNCs with strong red fluorescence (with excitation/emission maxima at 340/640 nm) in the absence of H₂O₂. The DNA can be cleaved into short-oligonucleotide fragments by hydroxy radicals as formed in the Ce(III)-triggered Fenton-like reaction in the presence of H₂O₂. As a result, short-strand DNA loses the ability as a template for the formation of CuNCs. This leads to a decrease of fluorescence. The colorimetric assay, in turn, is based on the oxidation of colorless Ce(III) ions to the distinctly yellow Ce(IV) ions (with an absorption maximum at 400 nm) by H₂O₂. Compared with those assays based on the use of enzyme mimics, this method does not require any chromogenic substrates such as ABTS and TMB. Based on the dual-signal readout platform, we successfully achieved the detection of H₂O₂ and glucose. LODs are as low as 0.266 μM and 2.92 μM. The methods were applied to the sensitive determination of glucose by using glucose oxidase (GOx) which catalyzes the oxidization of glucose to produce H₂O₂. The practical application was demonstrated by determination of glucose in human serum, with apparent recoveries of 98.4-101.9% and 99.1-105.6%, respectively. The concentration of glucose ranges from 1 to 500 μM and 50 to 600 μM based on the dual-signal readout platform, respectively. This fluorometric and colorimetric dual-mode strategy will pave a new avenue for constructing effective assays for H₂O₂-related analytes in biochemical and clinical applications. Graphical abstractSchematic representation of a fluorometric and colorimetric dual-readout strategy for the sensitive determination of hydrogen peroxide and glucose. The assay has been designed by integrating copper nanoclusters into a Ce(III)-triggered Fenton-like reaction.

Application of DNA Quadruplex Hydrogels Prepared from Polyethylene Glycol-Oligodeoxynucleotide Conjugates to Cell Culture Media

Application of Na+-responsive DNA quadruplex hydrogels, which utilize G-quadruplexes as crosslinking points of poly(ethylene glycol) (PEG) network as cell culture substrate, has been examined. PEG-oligodeoxynucleotide (ODN) conjugate, in which four deoxyguanosine (dG4) residues are tethered to both ends of PEG, was prepared by modified high-efficiency liquid phase (HELP) synthesis of oligonucleotides and used as the macromonomer. When mixed with equal volume of cell culture media, the solution of PEG-ODN turned into stiff hydrogel (G-quadruplex hydrogel) as the result of G-quadruplex formation by the dG4 segments in the presence of Na+. PEG-ODN itself did not show cytotoxicity and the resulting hydrogel was stable enough under cell culture conditions. However, L929 fibroblast cells cultured in G-quadruplex hydrogel remained spherical for a week, yet alive, without proliferation. The cells gradually sedimented through the gel day by day, probably due to the reversible nature of G-quadruplex formation and the resulting slow rearrangement of the macromonomers. Once they reached the bottom glass surface, the cells started to spread and proliferate.

Sustained Release of Minor-Groove-Binding Antibiotic Netropsin from Calcium-Coated Groove-Rich DNA Particles

Control of the release properties of drugs has been considered a key factor in the development of drug delivery systems (DDSs). However, drug delivery has limitations including cytotoxicity, low loading efficiency, and burst release. To overcome these challenges, nano or micro-particles have been suggested as carrier systems to deliver chemical drugs. Herein, nano-sized DNA particles (DNAp) were manufactured to deliver netropsin, which is known to bind to DNA minor grooves. The rationally designed particles with exposed rich minor grooves were prepared by DNAp synthesis via rolling circle amplification (RCA). DNAp could load large quantities of netropsin in its minor grooves. An analytical method was also developed for the quantification of netropsin binding to DNAp by UV–visible spectrometry. Moreover, controlled release of netropsin was achieved by forming a layer of Ca²⁺ on the DNAp (CaDNAp). As a proof of concept, the sustained release of netropsin by CaDNAp highlights the potential of the DNAp-based delivery approach.

Label-free visual biosensor based on cascade amplification for the detection of Salmonella

Salmonella is a widely distributed, extremely harmful bacteria, the presence of which requires confirmation via an on-site visual biosensor. In this study, we constructed a label-free, cascade amplification visualization biosensor for the sensitive and rapid detection of Salmonella enterica subsp. enterica serovar typhimurium based on the RDTG principle (recombinase polymerase amplification (RPA), duplex-specific enzyme (DSN) cleavage, terminal deoxynucleotidyl transferase (TdT) extension and G-quadruplexes output). Following DNA extraction of Salmonella spp., the first step in the construction involved the recognition and amplification of nucleic acids, carried out by RPA, to achieve the first signal amplification within 10 min. This RPA product was then specifically cleaved by DSN to produce a large number of small double-stranded DNA (dsDNA) products with 3'-OH within 15 min to achieve the second signal amplification. Thereafter, TdT was employed to empower these small 3'-OH dsDNA products to extend and produce a large number of long G-rich single-stranded DNAs (ssDNAs) within 20 min, thus realizing the third signal increase. These long G-rich ssDNA products displayed a color change that could be directly observed through the naked eye by adding H₂O₂/3,3',5,5'-tetramethylbenzidine (TMB). The RDTG biosensor for the detection of Salmonella spp. has several advantages, including a low limit of 6 cfu/mL. It is an isothermal-free instrument, simple to operate, with a rapid detection time of less than 1.5 h. Furthermore, it can be visually characterized and quantified by a microplate reader to detect Salmonella spp., in food and environmental samples, and it has broad application prospects.

A rapidly self-assembling soft-brush DNA hydrogel based on RCA products

A rapid self-assembly strategy was developed for fabricating a novel soft-brush DNA hydrogel in one minute by introducing a pair of L-type probes into the RCA products. The L-type probes with universality achieved a controllable size and morphology of the DNA hydrogel, providing deeper insight into variability and probability in functional biomaterials.

Glucose Oxidase-Instructed Fluorescence Amplification Strategy for Intracellular Glucose Detection

The accurate detection of glucose at cellular level remains a big challenge. In this study, a signal amplification strategy mediated by silver nanocube (AgNC), glucose oxidase (GOx), and silver ion fluorescence probe (denoted as AgNC-GOx/Ag⁺-FP) is proposed for amplified intracellular glucose detection. The AgNC is oxidized into Ag⁺ by H₂O₂ generated from GOx-catalyzed glucose oxidation reaction, and Ag⁺ remarkably enhances the red fluorescence of Ag⁺-FP. Our results show that AgNC-GOx/Ag⁺-FP is highly sensitive and specific to glucose and H₂O₂. Afterward, the feasibility of using AgNC-GOx/Ag⁺-FP to detect intracellular glucose is verified in five different cell lines. In summary, a sensitive and specific fluorescence amplification strategy has been developed for intracellular glucose detection.

Target-responsive DNA hydrogel for non-enzymatic and visual detection of glucose

We have successfully developed a target-responsive aptamer cross-linked hydrogel for the visual detection of glucose, an important biomedical analyte. In this work, the glucose-responsive hydrogel was prepared using the target aptamer and its two short complementary DNA strands grafted onto a linear polyacrylamide chain as cross-linkers. Gold nanoparticles (AuNPs) modified with thiol-PEG were encapsulated in the gel and used as the output signal for visible detection. The complex of glucose and its ligand of boronic acid derivatives (Shinkai's receptor) can bind with the aptamer to disrupt the hydrogel, leading to the release of AuNPs with a distinct red colour in the supernatant. By this method glucose can be detected with the naked eye, and the sensor has a detection limit of 0.44 mM in buffer with the help of UV-Vis spectrophotometry. Furthermore, glucose spiked in 50% urine and 30% serum could also be detected respectively with the naked eye, and glucose was quantitatively detected in 50% urine. The hydrogel system provides a non-enzymatic and visual method for glucose detection, and offers promising applications in biotechnology and biomedicine.