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

Liquid-colloid-solid modular assembly for three-dimensional electrochemical biosensing of small molecules

Electrochemical biosensors hold promise for advanced analytical applications in modern life analysis due to their miniaturization and cost-effectiveness. Nevertheless, their implementation in complex biological systems necessitates overcoming challenges related to timeliness, sensitivity, and interference resistance. Here, we developed a novel DNA hydrogel three-dimensional electron transporter through liquid-colloid-solid assembly, integrating electronic mediators and employing porous electrode covers with 3D printing technology. Our approach facilitated the fabrication of a high-performance electrochemical sensor for small molecule detection, leveraging target-specific aptamers and catalytic hairpin assembly (CHA) elements within the DNA hydrogel, which exhibited outstanding selectivity, sensitivity, and universality, achieving detection limits of 0.047 nM for kanamycin and 2.67 pM for ATP. Furthermore, this sensor could detect kanamycin in real samples, demonstrating good accuracy and robust anti-interference capabilities in human serum. Our work not only possesses substantial application value in clinical sample analysis but also represents a breakthrough in traditional strategies, thereby contributing to advancements in the application of electrochemical biosensors for life analysis.

Metal-organic framework integrated hydrogel bioreactor for smart detection of metal ions

Bioreactors with environment responsiveness for smart detection has attracted widespread interest. Bioreactors that operate in liquid have excellent reaction speed and sensitivity, and those that operate at a solid interface have unique portability and stability. However, bioreactors that can simultaneously take advantage of both properties are still limited. Here, we developed a metal-organic framework (MOF) integrated hydrogel bioreactor that can accommodate both solid and liquid properties by using a hydrogel as a quasi-liquid medium. To enhance the stability and intelligence of the hydrogel bioreactor, we have opted for the utilization of europium metal-organic framework (Eu-MOF) as the optical output to withstand long-term storage challenges, and DNA as the highly programmable substance for intelligent target response. On this basis, smart detection of metal ions and biological micro-molecules have been achieved. Notably, this quasi-liquid hydrogel bioreactor has effectively tackled the intrinsic issues of inadequate dispersion stability of Eu-MOF in liquid systems and poor stability of DNA against environmental interference. Moreover, this MOF integrated hydrogel bioreactor has been applied to the construction of a portable hydrogel bioreactor, which enables platform-free and arrayed target detection via a smartphone, providing a new perspective for further promoting the application of quasi-liquid hydrogel bioreactors and intelligent nanobiological sensors.

An Intelligent DNA Nanoreactor for Easy-to-Read In Vivo Tumor Imaging and Precise Therapy

Nanomaterial-based in vivo tumor imaging and therapy have attracted extensive attention; however, they suffer from the unintelligent "always ON" or single-parameter responsive signal output, substantial off-target effects, and high cost. Therefore, achieving in vivo easy-to-read tumor imaging and precise therapy in a multi-parameter responsive and intelligent manner remains challenging. Herein, an intelligent DNA nanoreactor (iDNR) was constructed following the "AND" Boolean logic algorithm to address these issues. iDNR-mediated in situ deposition of photothermal substance polydopamine (PDA) can only be satisfied in tumor tissues with abundant membrane protein biomarkers "AND" hydrogen peroxide (H2 O2 ). Therefore, intelligent temperature-based in vivo easy-to-read tumor imaging is realized without expensive instrumentation, and its diagnostic performance matches with that of flow cytometry, and photoacoustic imaging. Moreover, precise photothermal therapy (PTT) of tumors could be achieved via intelligent heating of tumor tissues. The precise PTT of primary tumors in combination with immune checkpoint blockade (ICB) therapy suppresses the growth of distant tumors and inhibits tumor recurrence. Therefore, highly programmable iDNR is a powerful tool for intelligent biomedical applications.

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.

A portable and partitioned DNA hydrogel chip for multitarget detection

A DNA hydrogel, owing to its dual properties of liquid and solid, is considered to be an ideal material for constructing biosensors that can integrate the advantages of both wet chemistry and dry chemistry. Nevertheless, it has struggled to cope with the demands of high-throughput analysis. A partitioned and chip-based DNA hydrogel is a potential avenue to achieve this, but currently remains a formidable challenge. Here, we developed a portable and partitioned DNA hydrogel chip that can be used for multitarget detection. The partitioned and surface-immobilized DNA hydrogel chip was formed by inter-crosslinking amplification by incorporating target-recognizing fluorescent aptamer hairpins into multiple rolling circle amplification products, which can achieve portable and simultaneous detection of multiple targets. This approach expands the application of semi-dry chemistry strategies, which can realize high throughput and point of care testing (POCT) of different targets, improving the development of hydrogel-based bioanalysis and providing new potential solutions for biomedical detection.

Nanomaterial-based biohybrid hydrogel in bioelectronics

Despite the broadly applicable potential in the bioelectronics, organic/inorganic material-based bioelectronics have some limitations such as hard stiffness and low biocompatibility. To overcome these limitations, hydrogels capable of bridging the interface and connecting biological materials and electronics have been investigated for development of hydrogel bioelectronics. Although hydrogel bioelectronics have shown unique properties including flexibility and biocompatibility, there are still limitations in developing novel hydrogel bioelectronics using only hydrogels such as their low electrical conductivity and structural stability. As an alternative solution to address these issues, studies on the development of biohybrid hydrogels that incorporating nanomaterials into the hydrogels have been conducted for bioelectronic applications. Nanomaterials complement the shortcomings of hydrogels for bioelectronic applications, and provide new functionality in biohybrid hydrogel bioelectronics. In this review, we provide the recent studies on biohybrid hydrogels and their bioelectronic applications. Firstly, representative nanomaterials and hydrogels constituting biohybrid hydrogels are provided, and next, applications of biohybrid hydrogels in bioelectronics categorized in flexible/wearable bioelectronic devices, tissue engineering, and biorobotics are discussed with recent studies. In conclusion, we strongly believe that this review provides the latest knowledge and strategies on hydrogel bioelectronics through the combination of nanomaterials and hydrogels, and direction of future hydrogel bioelectronics.

Stimuli-Responsive Self-Degradable DNA Hydrogels: Design, Synthesis, and Applications

DNA hydrogels play an increasingly important role in biomedicine and bioanalysis applications. Due to their high programmability, multifunctionality and biocompatibility, they are often used as effective carriers for packing drugs, cells, or other bioactive cargoes in vitro and in vivo. However, the stability of the DNA hydrogels prevents their in-demand rapid release of cargoes to achieve a full therapeutic effect in time. For bioanalysis, the generation of signals sometimes needs the DNA hydrogel to be rapidly degraded when sensing target molecules. To meet these requirements, stimulus-responsive DNA hydrogels are designed. By responding to different stimuli, self-degradable DNA hydrogels can switch from gel to solution for quantitative bioanalysis and precision cargo delivery. This review summarizes the recently developed innovative methods for designing stimuli-responsive self-degradable DNA hydrogels and showed their applications in the bioanalysis and biomedicines fields. Challenges, as well as prospects, are also discussed.

Advances in the Translation of Electrochemical Hydrogel-Based Sensors

Novel biomaterials for bio- and chemical sensing applications have gained considerable traction in the diagnostic community with rising trends of using biocompatible and lowly cytotoxic material. Hydrogel-based electrochemical sensors have become a promising candidate for their swellable, nano-/microporous, and aqueous 3D structures capable of immobilizing catalytic enzymes, electroactive species, whole cells, and complex tissue models, while maintaining tunable mechanical properties in wearable and implantable applications. With advances in highly controllable fabrication and processability of these novel biomaterials, the possibility of bio-nanocomposite hydrogel-based electrochemical sensing presents a paradigm shift in the development of biocompatible, "smart," and sensitive health monitoring point-of-care devices. Here, recent advances in electrochemical hydrogels for the detection of biomarkers in vitro, in situ, and in vivo are briefly reviewed to demonstrate their applicability in ideal conditions, in complex cellular environments, and in live animal models, respectively, to provide a comprehensive assessment of whether these biomaterials are ready for point-of-care translation and biointegration. Sensors based on conductive and nonconductive polymers are presented, with highlights of nano-/microstructured electrodes that provide enhanced sensitivity and selectivity in biocompatible matrices. An outlook on current challenges that shall be addressed for the realization of truly continuous real-time sensing platforms is also presented.

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.

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DNA hydrogel, favored by researchers, combines properties of DNA and hydrogels.

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Both DNA and skeleton, having many response characteristics, can respond to stimuli.

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Sensing, nano robots, information carriers, drug delivery, and disease treatment uses.

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Three stimulus response types: single biological, single abiotic and compound.

Hydrogel Nanoarchitectonics: An Evolving Paradigm for Ultrasensitive Biosensing

The integration of nanoarchitectonics and hydrogel into conventional biosensing platforms offers the opportunities to design physically and chemically controlled and optimized soft structures with superior biocompatibility, better immobilization of biomolecules, and specific and sensitive biosensor design. The physical and chemical properties of 3D hydrogel structures can be modified by integrating with nanostructures. Such modifications can enhance their responsiveness to mechanical, optical, thermal, magnetic, and electric stimuli, which in turn can enhance the practicality of biosensors in clinical settings. This review describes the synthesis and kinetics of gel networks and exploitation of nanostructure-integrated hydrogels in biosensing. With an emphasis on different integration strategies of hydrogel with nanostructures, this review highlights the importance of hydrogel nanostructures as one of the most favorable candidates for developing ultrasensitive biosensors. Moreover, hydrogel nanoarchitectonics are also portrayed as a promising candidate for fabricating next-generation robust biosensors.

Cytidine-rich hydrogel as an electrochemical signal amplification strategy for microRNA detection

Signal amplification strategies increase the complexities of biosensors while improving the response signals. Herein, a novel electrochemical biosensor was developed based on a DNA hydrogel for sensitive analysis using microRNA-21 (miRNA-21) as a detection model. Poly C sequences combined with C-Ag(I)-C hydrogel formed a DNA hydrogel by the unique interaction between the cytosines and silver ions. Thus, with a three-way conjunction structure of DNA, this C-Ag(I)-C hydrogel was constructed as a novel biosensor for the detection of miRNAs. With the assistance of this hydrogel, numerous silver ions gathered around DNA strands, which would amplify the signal. Under these conditions, the silver ions produced distinct square wave voltammetry oxidation peak currents. This electrochemical biosensor we designed exhibited a great linear relationship for the logarithm of the concentration of miRNA-21 from 1 fM to 100 pM with a detection limit of 0.117 fM. Furthermore, our sensors were able to differentiate miRNA-21 from its homologous family with satisfactory responsiveness in the dilute bovine serum system.

A smart microhydrogel membrane sensor realized by pipette tip

In this paper, we describe a simple and practical way to prepare hydrogel membranes in a conical channel (pipette tip). We used a pipette to create a gas pressure difference on both sides of the gel precursor, which drove the gel precursor to move in the pipette tip. During movement, the shape of the hydrogel precursor gradually becomes thinner as the radius of the tapered channel becomes larger. We use this principle to realize the highly controllable preparation of the hydrogel membrane structure (130 μm at its thinnest). Moreover, we fabricated a hydrogel membrane sensor in one step by implanting smart molecules in the hydrogel, which achieved rapid and sensitive detection of 0.5 μM-500 mM potassium ions. This method of preparing the hydrogel membrane sensor does not rely on professional membrane production equipment and complex molecular design processes, has high gel utilization and simple and controllable membrane thickness, and has a wide range of application value in the field of intelligent hydrogel-based analysis technology.

Smart DNA-gold nanoparticle hybrid hydrogel film based portable, cost-effective and storable biosensing system for the colorimetric detection of lead (II) and uranyl ions

A portable, cost-effective and storable DNA-gold nanoparticle (AuNP) hybrid hydrogel film based biosensing system was developed, with AuNPs serving as both the crosslinking units of the film and the signaling units. Using a layer-by-layer assembly method, hydrogel film composed of three-dimensional hydrophilic network of densely packed AuNPs interconnected by responsive DNA structures was constructed onto a glass slide. By programming the sequence of DNA structures, target-responsive hybrid films were constructed. As a proof of concept, the sequence of a substrate DNA which can be identified and cleaved by Pb²⁺-dependent DNAzyme was encoded to construct Pb²⁺-responsive DNA-AuNP hybrid hydrogel film. The high-density packing of AuNPs as signal substances significantly improved the sensitivity of the ultrathin film biosensing system while reduced the cost of expensive DNA materials. A hydrogel film composed of 10 layers of assembled DNA-AuNP structures generated sufficient visual colorimetric signals for Pb²⁺ detection, with a detection limit of 2.6 nM. By introducing UO₂²⁺-dependent DNAzyme, the system could be further applied in the sensitive and selective detection of UO₂²⁺, with a detection limit of 10.3 nM. Compared with bulk-sized DNA hydrogel biosensing systems, the DNA-AuNP hydrogel film biosensing system exhibited faster response thanks to the sub-micrometer ultrathin film structures. Moreover, the protection of fragile non-covalently crosslinked DNA films with solid slides also facilitated the portable application and long-term storage of the resulting biosensing system, with 95% of the response signal retained after three months of storage. The DNA-AuNPs hydrogel film biosensing system is highly promising for future rapid on-site detection applications.

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.

Putting DNA to Work as Generic Polymeric Materials

DNA is a true polymer that stores the genetic information of an organism. With its amazing biological and polymeric characteristics, DNA has been regarded as a universal building block for the construction of diverse materials for real-world applications. Through various approaches including ligation, polymerization, chemical crosslinking, and physical crosslinking, both pure and hybrid DNA gels have been developed as generic materials. This Review discusses recent advances in the construction of DNA-based networks without considering any of DNA's genetic properties. In addition, we highlight the biomedical and non-biomedical applications of DNA as generic materials. Owing to the superb molecular recognition, self-assembly, and responsiveness of DNA, a mushrooming number of DNA materials with various properties have been developed for general utilization.

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.

A Carbon-Based Antifouling Nano-Biosensing Interface for Label-Free POCT of HbA1c

Electrochemical biosensing relies on electron transport on electrode surfaces. However, electrode inactivation and biofouling caused by a complex biological sample severely decrease the efficiency of electron transfer and the specificity of biosensing. Here, we designed a three-dimensional antifouling nano-biosensing interface to improve the efficiency of electron transfer by a layer of bovine serum albumin (BSA) and multi-walled carbon nanotubes (MWCNTs) cross-linked with glutaraldehyde (GA). The electrochemical properties of the BSA/MWCNTs/GA layer were investigated using both cyclic voltammetry and electrochemical impedance to demonstrate its high-efficiency antifouling nano-biosensing interface. The BSA/MWCNTs/GA layer kept 92% of the original signal in 1% BSA and 88% of that in unprocessed human serum after a 1-month exposure, respectively. Importantly, we functionalized the BSA/MWCNTs/GA layer with HbA1c antibody (anti-HbA1c) and 3-aminophenylboronic acid (APBA) for sensitive detection of glycated hemoglobin A (HbA1c). The label-free direct electrocatalytic oxidation of HbA1c was investigated by cyclic voltammetry (CV). The linear dynamic range of 2 to 15% of blood glycated hemoglobin A (HbA1c) in non-glycated hemoglobin (HbAo) was determined. The detection limit was 0.4%. This high degree of differentiation would facilitate a label-free POCT detection of HbA1c.

Enzymatical biomineralization of DNA nanoflowers mediated by manganese ions for tumor site activated magnetic resonance imaging

DNA nanoflower has been demonstrated as a promising DNA nanostructure for therapeutics and bioimaging primarily because of the programmable DNA sequence and unique structure. Herein, we report manganese ions mediated enzymatic biomineralization to prepare DNA-Mn hybrid nanoflower (DMNF). Paramagnetic Mn²⁺ was explored as the co-factor of DNA polymerase for the extension of long strand DNA. The biomimetic synthesis of DMNF was performed using the long strand DNA as template via nucleation and growth of Mn₂PPi. The morphology and size of DMNF were controllable by tuning reaction time and Mn²⁺ concentration. The aptamer sequence was encoded into circle template to achieve tumor-targeted DMNF, and cellular uptake assay demonstrated obvious aptamer-mediated internalization. DMNF showed enhanced T₁-weighted magnetic resonance (MR) imaging effect in acid environment for high tumor-specific MR imaging, and high spatial resolution imaging of kidneys and liver. Our work provides a facile enzymatically biomineral strategy to integrate multifunctional modules into one DNA structure and promotes the development of DNA nanostructure for precision medicine.