Electrostatically directed visual fluorescence response of DNA-functionalized monolithic hydrogels for highly sensitive Hg²+ detection

One-step and label-free ratiometric fluorescence assay for the detection of plasma exosome towards cancer diagnosis

Exosomes are closely associated with tumor development and are regarded as viable biomarkers for cancer. Here, a ratiometric fluorescence method was proposed for the one-step and label-free detection of plasma exosomes. A bicolor streptavidin magnetic beads were specifically created with an immobilized Cy5-labeled hairpin aptamer for CD63 (Cy5-Apt) on its surface to identify exosome, and a green color SYBR Green I (SGI) embedded in the stem of Cy5-Apt to respond to exosomes. After exosome capture, the Cy5-Apt could undergo a conformational shift and release the encapsulated SGI, allowing exosome measurement based on the fluorescence ratio of Cy5 and SGI. The enrichment, separation and detection of exosomes in proposed method could be completed in one step (30 min), which is a significant improvement over previous method. Furthermore, the use of ratiometric fluorescence and magnetic separation allows for exosome enrichment and interference elimination from complex matrices, improving accuracy and sensitivity. Particularly, the assay could detect exosomes in plasma and has potential to distinguish lung cancer patients from healthy volunteers with an area under the receiver operator characteristic curve of 0.85. Besides, the study provided an efficient method for analyzing the various divisions of exosomes by merely modifying the aptamer, which holds great promise for point-of-care applications.

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.

Hydrogel-Based Biosensors

There is an increasing interest in sensing applications for a variety of analytes in aqueous environments, as conventional methods do not work reliably under humid conditions or they require complex equipment with experienced operators. Hydrogel sensors are easy to fabricate, are incredibly sensitive, and have broad dynamic ranges. Experiments on their robustness, reliability, and reusability have indicated the possible long-term applications of these systems in a variety of fields, including disease diagnosis, detection of pharmaceuticals, and in environmental testing. It is possible to produce hydrogels, which, upon sensing a specific analyte, can adsorb it onto their 3D-structure and can therefore be used to remove them from a given environment. High specificity can be obtained by using molecularly imprinted polymers. Typical detection principles involve optical methods including fluorescence and chemiluminescence, and volume changes in colloidal photonic crystals, as well as electrochemical methods. Here, we explore the current research utilizing hydrogel-based sensors in three main areas: (1) biomedical applications, (2) for detecting and quantifying pharmaceuticals of interest, and (3) detecting and quantifying environmental contaminants in aqueous environments.

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.

Tailoring the Photoelectrochemical Activity of Hexametaphosphate-Capped CdS Quantum Dots by Ca2+-Triggered Surface Charge Regulation: A New Signaling Strategy for Sensitive Immunoassay

The development of efficient signaling strategies is highly important for photoelectrochemical (PEC) immunoassay. We report here a new and efficient strategy for sensitive PEC immunoassay by tailoring the electrostatic interaction between the photoactive material and the electron donor. The photoelectric conversion of hexametaphosphate (HMP)-capped CdS quantum dots (QDs) in Na₂SO₃ solution is significantly boosted after Ca²⁺ incubation. The negative surface charges on CdS@HMP QDs decrease because of the complexation reaction between HMP and Ca²⁺, and the electrostatic repulsion between CdS@HMP QDs and electron donor (SO₃^2-) becomes weak accordingly, leading to an improved electron-hole separation efficiency. Inspired by the PEC response of CdS@HMP QDs to Ca²⁺, a novel "signal-on" PEC immunoassay platform is established by employing CaCO₃ nanoparticles as labels. By regulating the surface charge of CdS@HMP QDs with in situ-generated Ca²⁺ from CaCO₃ labels, sensitive detection of the carcinoembryonic antigen (CEA) is achieved. The linear detection range is 0.005-50 ng mL^-1 and the detection limit is 1 pg mL^-1 for CEA detection. Our work not only provides a facile route to tailor the photoelectric conversion but also lays the foundation for sensitive PEC immunoassay by simply regulating the surface charge of photoactive materials.

Hydrogel-Based Optical Ion Sensors: Principles and Challenges for Point-of-Care Testing and Environmental Monitoring

Hydrogel is a unique family of biocompatible materials with growing applications in chemical and biological sensors. During the past few decades, various hydrogel-based optical ion sensors have been developed aiming at point-of-care testing and environmental monitoring. In this Perspective, we provide an overview of the research field including topics such as photonic crystals, DNAzyme cross-linked hydrogels, ionophore-based ion sensing hydrogels, and fluoroionophore-based optodes. As the different sensing principles are summarized, each strategy offers its advantages and limitations. In a nutshell, developing optical ion sensing hydrogels is still in the early stage with many opportunities lying ahead, especially with challenges in selectivity, assay time, detection limit, and usability.

Direct Measurement of Aqueous Mercury(II): Combining DNA-Based Sensing with Diffusive Gradients in Thin Films

A highly specific DNA-functionalized hydrogel sensing layer was integrated with the diffusive gradients in thin films (DGT) technique for the direct determination of aqueous mercury(II). The DNA-functionalized layer in the DGT unit exhibited both high affinity (complexation constant K_c = 10^19.8 at 25 °C) and high binding capacity (9.5 mg Hg disk^-1) toward Hg²⁺. The diffusion coefficient for Hg²⁺ complexed with common inorganic ligands was an order of magnitude higher than that for Hg²⁺ complexed with natural dissolved organic matter: 9.0 × 10^-6 versus 9.8 × 10^-7 cm² s^-1 at 25 °C. The performance of the DNA-DGT sensor was further assessed under variable pH (3-10) and temperature (5-40 °C) conditions, as well as across a range of hydrochemically diverse artificial and natural freshwaters. The observed effects of the environmental and solution compositional variables on Hg²⁺ binding to the DNA in the sensing layer were successfully accounted for by equilibrium speciation calculations and temperature-corrected, multicomponent diffusion coefficients for aqueous Hg(II). The results therefore support the use of the DNA-DGT sensor as an alternative to traditional sampling and analysis methods for measuring aqueous Hg(II) concentrations down to the nanomolar level in freshwater environments.

Toehold Length of Target ssDNA Affects Its Reaction-Diffusion Behavior in DNA-Responsive DNA-co-Acrylamide Hydrogels

In the present study, we expand on the understanding of hydrogels with embedded deoxyribonucleic acid (DNA) cross-links, from the overall swelling to characterization of processes that precede the swelling. The hydrogels respond to target DNA strands because of a toehold-mediated strand displacement reaction in which the target strand binds to and opens the dsDNA cross-link. The spatiotemporal evolution of the diffusing target ssDNA was determined using confocal laser scanning microscopy (CLSM). The concentration profiles revealed diverse partitioning of the target DNA inside the hydrogel as compared with the immersing solution: excluding a nonbinding DNA, while accumulating a binding target. The data show that a longer toehold results in faster cross-link opening but reduced diffusion of the target, thus resulting in only a moderate increase in the overall swelling rate. The parameters obtained by fitting the data using a reaction-diffusion model were discussed in view of the molecular parameters of the target ssDNA and hydrogels.

Rhodamine-immobilized optical hydrogels with shape deformation and Hg2+-sensitive fluorescence behaviors

A highly effective method for the research and development of a novel macroscopic hydrogel sensor and bilayer hydrogel is reported. Based on Rhodamine 6G, an Hg2+ sensitive fluorescent functional monomer was synthesized, then the monomer was utilized to synthesize hydrogel sensors and bilayer hydrogels. Hydrogel sensor has prominent selectivity to Hg2+, the bilayer hydrogel has shape changing function additionally. By combining a thermoresponsive hydrogel layer, poly N-isopropylacrylamide (PNIPAM), with an Hg2+ selective hydrogel layer via macroscopic supramolecular assembly, a bilayer hydrogel is obtained that can be tailored and reswells. The bilayer hydrogel sensor can show complex shape deformation caused by the PNIPAM layer and the Hg2+-responsive characteristic of hydrogel sensor layer can be observed under visible light or UV light. This work will provide novel insights for the design and synthesis of novel smart materials with synergistic functions.

A DNA-based biosensor for aqueous Hg(II): Performance under variable pH, temperature and competing ligand composition

Mercury (Hg) is a toxic metal posing major health risks to human beings and wildlife. The characterization of Hg fate and transport in aquatic environments is hindered by a lack of sensitive, selective and easily field-deployable analytical techniques. Here we assess the reliability and performance of a Hg²⁺ sensor based on the selective binding of Hg²⁺ to a thymine-rich DNA under environmentally-relevant conditions. Experimental results indicate that the interactions between the DNA and SYBR Green I, which produce the detection fluorescence signal, are significantly impacted by pH, metal ligands and natural dissolved organic matter (NDOM). These interferences are largely eliminated by immobilizing the DNA in a polyacrylamide hydrogel, although high concentrations of NDOM, such as fulvic acids, still affect the sensor's performance due to competitive binding of Hg²⁺. The binding of Hg²⁺ to NDOM, however, can be accounted for via equilibrium speciation calculations, which also yield the complexation constant for Hg²⁺ binding to the DNA in the hydrogel. The equilibrium calculations reproduce the results for the entire set of experimental conditions, from simple electrolyte solutions to complex aqueous compositions mimicking natural lake waters, and across large ranges of pH (3-10) and temperature (5-50 °C).

Morpholino Target Molecular Properties Affect the Swelling Process of Oligomorpholino-Functionalized Responsive Hydrogels

Responsive hydrogels featuring DNA as a functional unit are attracting increasing interest due to combination of versatility and numerous applications. The possibility to use nucleic acid analogues opens for further customization of the hydrogels. In the present work, the commonly employed DNA oligonucleotides in DNA-co-acrylamide responsive hydrogels are replaced by Morpholino oligonucleotides. The uncharged backbone of this nucleic acid analogue makes it less susceptible to possible enzymatic degradation. In this work we address fundamental issues related to key processes in the hydrogel response; such as partitioning of the free oligonucleotides and the strand displacement process. The hydrogels were prepared at the end of optical fibers for interferometric size monitoring and imaged using confocal laser scanning microscopy of the fluorescently labeled free oligonucleotides to observe their apparent diffusion and accumulation within the hydrogels. Morpholino-based hydrogels' response to Morpholino targets was compared to DNA hydrogels' response to DNA targets of the same base-pair sequence. Non-binding targets were observed to be less depleted in Morpholino hydrogels than in DNA hydrogels, due to their electroneutrality, resulting in faster kinetics for Morpholinos. The electroneutrality, however, also led to the total swelling response of the Morpholino hydrogels being smaller than that of DNA, since their lack of charges eliminates swelling resulting from the influx of counter-ions upon oligonucleotide binding. We have shown that employing nucleic acid analogues instead of DNA in hydrogels has a profound effect on the hydrogel response.

DNA Hydrogels and Microgels for Biosensing and Biomedical Applications

DNA hydrogels, which take advantage of the unique properties of functional DNA motifs, such as specific molecular recognition, programmable and high-precision assembly, multifunctionality, and excellent biocompatibility, have attracted increasing research interest in the past two decades in diverse fields, especially in biosensing and biomedical applications. The responsiveness of smart DNA hydrogels to external stimuli by changing their swelling volume, crosslinking density, and optical or mechanical properties has facilitated the development of DNA-hydrogel-based in vitro biosensing systems and actuators. Furthermore, reducing the sizes of DNA hydrogels to the micro- and nanoscale leads to better responsiveness and delivery capacity, thereby making them excellent candidates for rapid detection, in vivo real-time sensing, and drug release applications. Here, the recent progress in the development of smart DNA hydrogels and DNA microgels for biosensing and biomedical applications is summarized, and the current challenges as well as future prospects are also discussed.

Adsorption of DNA Oligonucleotides by Boronic Acid-Functionalized Hydrogel Nanoparticles

Boronic acid-functionalized hydrogels were commonly used for covalent binding of cis-diol-contained molecules such as glucose, but noncovalent adsorption by boronic acids was less studied. DNA as an important polymer has been used to enhance the function of hydrogels including boronic acid-containing gels. In this work, noncovalent interactions between DNA oligonucleotides and boronic acid-containing hydrogel nanoparticles were studied in detail. The gels were composed of either poly(N-isopropylacrylamide) or with additional 5.6 mol % of 3-acrylamidophenylboronic acid (AAPBA). DNA adsorption on the AAPBA-containing gels was achieved with a high salt concentration, which can be explained by electrostatic repulsion between DNA and boronic acid. The critical role of boronic acid was confirmed by adding competing cis-diol-containing molecules such as glucose, fructose, and cytidine. Hydrogen bonding and hydrophobic interactions are important for DNA adsorption based on inhibited adsorption by urea and dimethyl sulfoxide. Polycytosine DNA showed a higher adsorption capacity compared to the other three types of DNA homopolymers. When T₁₅ and T₁₄-rU were compared, no covalent binding was detected for T₁₄-rU, suggesting that a single terminal diol was insufficient to support covalent binding at the low concentration of DNA used. Finally, the boronic acid-containing gels were able to adsorb an aptamer and inhibit its binding function. Binding was rescued by adding glucose to block the boronic acids. This study demonstrates noncovalent boronic acid interactions with DNA, and this information could be useful for designing and optimization of related biosensors and materials.

Molecularly Imprinted Sites Translate into Macroscopic Shape-Memory Properties of Hydrogels

The polymerization of acrylamide, dopamine methacrylamide, and bis-acrylamide in the presence of one of the electron acceptors, N,N'-dimethyl-4,4'-bipyridinium, (1), N,N'-dimethylbipyridinium-4,4'-ethylene, (2), or bipyridinium dithienylethene, (3), yields hydrogel matrices of high stiffness that are cooperatively cross-linked by bis-acrylamide and electron donor (dopamine)-acceptor complexes. Washing off the diffusional electron acceptor units yields molecularly imprinted matrices of lower stiffness, stabilized only by the bis-acrylamide bridges that include specific binding sites for the selective association of the electron acceptor (1), (2), or (3). These imprinted hydrogel matrices show selective recovery of the stiff properties upon binding the respective electron acceptor units to the imprinted sites. The control over the stiffness properties enables the development of shape-memory, molecularly imprinted hydrogels and stiffness-based sensors. The results show how molecularly imprinted sites translate into macroscopic shape-memory properties of hydrogels.

DNA-Based Hydrogels Loaded with Au Nanoparticles or Au Nanorods: Thermoresponsive Plasmonic Matrices for Shape-Memory, Self-Healing, Controlled Release, and Mechanical Applications

Gold nanoparticles (AuNPs) or gold nanorods (AuNRs) are loaded in polyacrylamide hydrogels cooperatively cross-linked by bis-acrylamide and nucleic acid duplexes or boronate ester-glucosamine and nucleic acid duplexes. The thermoplasmonic properties of AuNPs and AuNRs are used to control the stiffness of the hydrogels. The irradiation of the AuNP-loaded (λ = 532 nm) or the AuNR-loaded (λ = 808 nm) hydrogels leads to thermoplasmonic heating of the hydrogels, the dehybridization of the DNA duplexes, and the formation of hydrogels with lower stiffness. By ON/OFF irradiation, the hydrogels are switched between low- and high-stiffness states. The reversible control over the stiffness properties of the hydrogels is used to develop shape-memory hydrogels and self-healing soft materials and to tailor thermoplasmonic switchable drug release. In addition, by designing bilayer composites of AuNP- and AuNR-loaded hydrogels, a reversible thermoplasmonic, light-induced bending is demonstrated, where the bending direction is controlled by the stress generated in the respective bilayer composite.

Novel Membrane Detector Based on Smart Nanogels for Ultrasensitive Detection of Trace Threat Substances

A novel membrane detector is developed by a facile strategy combining commercialized membrane and smart nanogels for ultrasensitive and highly selective real-time detection of trace threat substances. On the basis of nanogel filtration and polydopamine adhesion, the membrane detector is fabricated by simply immobilizing smart nanogels onto the multiple pores of a commercialized membrane as the nanosensors and nanovalves. This is demonstrated by incorporating Pb²⁺-responsive poly( N-isopropylacrylamide- co-acryloylamidobenzo-18-crown-6) nanogels in the straight pores of a commercialized polycarbonate membrane for ultrasensitive and highly selective real-time detection of trace Pb²⁺. When selectively recognizing the Pb²⁺ in solution, the smart nanogels in the membrane pores swell, which lead to trans-membrane flux change. Quantitative detection of Pb²⁺ concentration can be achieved by simply measuring the flow rate of the trans-membrane flow. Due to the multiple nanochannels of nanogel-immobilized pores in the membrane for Pb²⁺ sensing and flux regulating, ultrasensitive and highly selective real-time detection of trace Pb²⁺ with concentration as low as 10^-10 mol L^-1 can be achieved. The nanogel-immobilized membrane detector offers a flexible platform to create versatile new membrane detectors by incorporating diverse smart nanogels for ultrasensitive and highly selective real-time detection of different trace threat substances.

How to Construct DNA Hydrogels for Environmental Applications: Advanced Water Treatment and Environmental Analysis

With high binding affinity, porous structures, safety, green, programmability, etc., DNA hydrogels have gained increasing recognition in the environmental field, i.e., advanced treatment technology of water and analysis of specific pollutants. DNA hydrogels have been demonstrated as versatile potential adsorbents, immobilization carriers of bioactive molecules, catalysts, sensors, etc. Moreover, altering components or choosing appropriate functional DNA optimizes environment-oriented hydrogels. However, the lack of comprehensive information hinders the continued optimization. The principle used to fabricate the most suitable hydrogels in terms of the requirements is the focus of this Review. First, different fabrication strategies are introduced and the ideal characteristic for environmental applications is in focus. Subsequently, recent environmental applications and the development of diverse DNA hydrogels regarding their synthesis mechanism are summarized. Finally, the Review provides an insight into the remaining challenging and future perspectives in environmental applications.

Highly Stretchable DNA/Clay Hydrogels with Self-Healing Ability

We present mechanically strong and self-healable clay hydrogels containing 2-8 w/v % ds-DNA together with a synthetic biocompatible polymer, poly( N, N-dimethylacrylamide). Clay nanoparticles in the hydrogels act like a chemical cross-linker and promote their elastic behavior, whereas DNA contributes to their viscoelastic energy dissipation. The extent of mechanical hysteresis during cyclic tensile tests reveals that the strength of intermolecular bonds in DNA/clay hydrogels is in the range of the strength of hydrogen bonds. The hydrogels exhibit a high stretchability (up to 1500%) and a tensile strength between 20 and 150 kPa. They have the ability to self-heal, which is induced by heating the damaged gel samples above the melting temperature of ds-DNA. When comparing the mechanical properties of the hydrogels before and after healing, the healing efficiency is greater than 100%. We also demonstrate that ds-DNA molecules entrapped in the gel network undergoes thermal denaturation/renaturation cycles, leading to a further improvement in the mechanical properties of the hydrogels.

Redox-triggered hydrogels revealing switchable stiffness properties and shape-memory functions

Metal-ion terpyridine-crosslinked acrylamide hydrogels or metal-ion-bridged carboxymethylcellulose hydrogels reveal redox-switchable stiffness and shape-memory properties.

Stimuli-Responsive DNA-Based Hydrogels: From Basic Principles to Applications

The base sequence of nucleic acids encodes structural and functional information into the DNA biopolymer. External stimuli such as metal ions, pH, light, or added nucleic acid fuel strands provide triggers to reversibly switch nucleic acid structures such as metal-ion-bridged duplexes, i-motifs, triplex nucleic acids, G-quadruplexes, or programmed double-stranded hybrids of oligonucleotides (DNA). The signal-triggered oligonucleotide structures have been broadly applied to develop switchable DNA nanostructures and DNA machines, and these stimuli-responsive assemblies provide functional scaffolds for the rapidly developing area of DNA nanotechnology. Stimuli-responsive hydrogels undergoing signal-triggered hydrogel-to-solution transitions or signal-controlled stiffness changes attract substantial interest as functional matrices for controlled drug delivery, materials exhibiting switchable mechanical properties, acting as valves or actuators, and "smart" materials for sensing and information processing. The integration of stimuli-responsive oligonucleotides with hydrogel-forming polymers provides versatile means to exploit the functional information encoded in the nucleic acid sequences to yield stimuli-responsive hydrogels exhibiting switchable physical, structural, and chemical properties. Stimuli-responsive DNA-based nucleic acid structures are integrated in acrylamide polymer chains and reversible, switchable hydrogel-to-solution transitions of the systems are demonstrated by applying external triggers, such as metal ions, pH-responsive strands, G-quadruplex, and appropriate counter triggers that bridge and dissociate the polymer chains. By combining stimuli-responsive nucleic acid bridges with thermosensitive poly(N-isopropylacrylamide) (pNIPAM) chains, systems undergoing reversible solution ↔ hydrogel ↔ solid transitions are demonstrated. Specifically, by bridging acrylamide polymer chains by two nucleic acid functionalities, where one type of bridging unit provides a stimuli-responsive element and the second unit acts as internal "bridging memory", shape-memory hydrogels undergoing reversible and switchable transitions between shaped hydrogels and shapeless quasi-liquid states are demonstrated. By using stimuli-responsive hydrogel cross-linking units that can assemble the bridging units by two different input signals, the orthogonally-triggered functions of the shape-memory were shown. Furthermore, a versatile approach to assemble stimuli-responsive DNA-based acrylamide hydrogel films on surfaces is presented. The method involves the activation of the hybridization chain-reaction (HCR) by a surface-confined promoter strand, in the presence of acrylamide chains modified with two DNA hairpin structures and appropriate stimuli-responsive tethers. The resulting hydrogel-modified surfaces revealed switchable stiffness properties and signal-triggered catalytic functions. By applying the method to assemble the hydrogel microparticles, substrate-loaded, stimuli-responsive microcapsules are prepared. The signal-triggered DNA-based hydrogel microcapsules are applied as drug carriers for controlled release. The different potential applications and future perspectives of stimuli responsive hydrogels are discussed. Specifically, the use of these smart materials and assemblies as carriers for controlled drug release and as shape-memory matrices for information storage and inscription and the use of surface-confined stimuli-responsive hydrogels, exhibiting switchable stiffness properties, for catalysis and controlled growth of cells are discussed.

Programmed pH-Responsive Microcapsules for the Controlled Release of CdSe/ZnS Quantum Dots

Two methods for the preparation of pH-responsive all-DNA microcapsules loaded with CdSe/ZnS quantum dots (QDs) are discussed. One approach involves the construction of DNA microcapsules composed of nucleic acid layers that include, at pH 7.2, "dormant" C-G·C(+) triplex sequences. The formation of the C-G·C(+) triplex structures at pH 5.0 leads to the cleavage of the microcapsules and to the release of the QDs. A second approach involves the synthesis of CdSe/ZnS QD-loaded DNA microcapsules, stabilized at pH 7.2 by T-A·T interlayer triplex bridges. The dissociation of the bridges at pH 9.0 separates the bridging triplex units, resulting in the degradation of the microcapsules and to the release of the QDs. The programmed pH-stimulated release of luminescent QDs, emitting at 620 and 560 nm, from the C-G·C(+) or T-A·T triplex-responsive microcapsules is demonstrated by subjecting the QD-loaded microcapsule mixtures to pH 5.0 or pH 9.0, respectively.

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

Hydrogels are crosslinked hydrophilic polymers that can absorb a large amount of water. By their hydrophilic, biocompatible and highly tunable nature, hydrogels can be tailored for applications in bioanalysis and biomedicine. Of particular interest are DNA-based hydrogels owing to the unique features of nucleic acids. Since the discovery of the DNA double helical structure, interest in DNA has expanded beyond its genetic role to applications in nanotechnology and materials science. In particular, DNA-based hydrogels present such remarkable features as stability, flexibility, precise programmability, stimuli-responsive DNA conformations, facile synthesis and modification. Moreover, functional nucleic acids (FNAs) have allowed the construction of hydrogels based on aptamers, DNAzymes, i-motif nanostructures, siRNAs and CpG oligodeoxynucleotides to provide additional molecular recognition, catalytic activities and therapeutic potential, making them key players in biological analysis and biomedical applications. To date, a variety of applications have been demonstrated with FNA-based hydrogels, including biosensing, environmental analysis, controlled drug release, cell adhesion and targeted cancer therapy. In this review, we focus on advances in the development of FNA-based hydrogels, which have fully incorporated both the unique features of FNAs and DNA-based hydrogels. We first introduce different strategies for constructing DNA-based hydrogels. Subsequently, various types of FNAs and the most recent developments of FNA-based hydrogels for bioanalytical and biomedical applications are described with some selected examples. Finally, the review provides an insight into the remaining challenges and future perspectives of FNA-based hydrogels.

Dual signal amplification by an “on-command” pure DNA hydrogel encapsulating HRP for colorimetric detection of ochratoxin A

A pure DNA hydrogel, consisting of two kinds of Y-scaffold nucleic acid subunits and the aptamer domain of ochratoxin A, undergoes a switchable gel-to-sol transition in the presence of ochratoxin A.

Multitriggered Shape-Memory Acrylamide-DNA Hydrogels

Acrylamide-acrylamide nucleic acids are cross-linked by two cooperative functional motives to form shaped acrylamide-DNA hydrogels. One of the cross-linking motives responds to an external trigger, leading to the dissociation of one of the stimuli-responsive bridges, and to the transition of the stiff shaped hydrogels into soft shapeless states, where the residual bridging units, due to the chains entanglement, provide an intrinsic memory for the reshaping of the hydrogels. Subjecting the shapeless states to counter stimuli restores the dissociated bridges, and regenerates the original shape of the hydrogels. By the cyclic dissociation and reassembly of the stimuli-responsive bridges, the reversible switchable transitions of the hydrogels between stiff shaped hydrogel structures and soft shapeless states are demonstrated. Shaped hydrogels bridged by K(+)-stabilized G-quadruplexes/duplex units, by i-motif/duplex units, or by two different duplex bridges are described. The cyclic transitions of the hydrogels between shaped and shapeless states are stimulated, in the presence of appropriate triggers and counter triggers (K(+) ion/crown ether; pH = 5.0/8.0; fuel/antifuel strands). The shape-memory hydrogels are integrated into shaped two-hydrogel or three-hydrogel hybrid structures. The cyclic programmed transitions of selective domains of the hybrid structures between shaped hydrogel and shapeless states are demonstrated. The possible applications of the shape-memory hydrogels for sensing, inscription of information, and controlled release of loads are discussed.

Integration of Switchable DNA-Based Hydrogels with Surfaces by the Hybridization Chain Reaction

A novel method to assemble acrylamide/acrydite DNA copolymer hydrogels on surfaces, specifically gold-coated surfaces, is introduced. The method involves the synthesis of two different copolymer chains consisting of hairpin A, HA, modified acrylamide copolymer and hairpin B, HB, acrylamide copolymer. In the presence of a nucleic acid promoter monolayer associated with the surface, the hybridization chain reaction between the two hairpin-modified polymer chains is initiated, giving rise to the cross-opening of hairpins HA and HB and the formation of a cross-linked hydrogel on the surface. By the cofunctionalization of the HA- and HB-modified polymer chains with G-rich DNA tethers that include the G-quadruplex subunits, hydrogels of switchable stiffness are generated. In the presence of K(+)-ions, the hydrogel associated with the surface is cooperatively cross-linked by duplex units of HA and HB, and K(+)-ion-stabilized G-quadruplex units, giving rise to a stiff hydrogel. The 18-crown-6-ether-stimulated elimination of the K(+)-ions dissociates the bridging G-quadruplex units, resulting in a hydrogel of reduced stiffness. The duplex/G-quadruplex cooperatively stabilized hydrogel associated with the surface reveals switchable electrocatalytic properties. The incorporation of hemin into the G-quadruplex units electrocatalyzes the reduction of H2O2. The 18-crown-6-ether stimulated dissociation of the hemin/G-quadruplex bridging units leads to a catalytically inactive hydrogel.

Hemin-G-quadruplex-crosslinked poly-N-isopropylacrylamide hydrogel: a catalytic matrix for the deposition of conductive polyaniline

A G-rich nucleic acid-tethered acrylamide/N-isopropylacrylamide (NIPAM) copolymer is prepared. The nucleic acid-modified pNIPAM chains assemble, in the presence of K⁺ ions, into a stimuli-responsive G-quadruplex-crosslinked pNIPAM hydrogel undergoing cyclic and reversible solution/hydrogel/solid transitions. Addition of kryptofix [2.2.2], CP, to the K⁺-stabilized G-quadruplex-crosslinked hydrogel eliminates the K⁺ ions from the crosslinking units, resulting in the transition of the hydrogel into a pNIPAM solution. In turn, heating the pNIPAM hydrogel from 25 °C to 40 °C results in the transition of the hydrogel to the solid state, and cooling the solid to 25 °C restores the hydrogel state. Incorporation of hemin into the G-quadruplex-crosslinked hydrogel results in a catalytic hydrogel that catalyzes the oxidation of aniline by H₂O₂ to form polyaniline. The polyaniline/pNIPAM hydrogel hybrid doped with 2 M HCl forms an emeraldine salt, which exhibits an electrical conductivity of 9 × 10^-4 [cm Ω]^-1.

pH-responsive and switchable triplex-based DNA hydrogels

New methods for the preparation of reversible pH-responsive DNA hydrogels based on Hoogsteen triplex structures are described. One system consists of a hydrogel composed of duplex DNA units that bridge acrylamide chains at pH = 7.4 and undergoes dissolution at pH = 5.0 through the reconfiguration of one of the duplex bridging units into a protonated CG·C+ triplex structure. The second system consists of a hydrogel consisting of acrylamide chains crosslinked in the presence of an auxiliary strand by Hoogsteen TA·T triplex interaction at pH = 7.0. The hydrogel transforms into a liquid phase at pH = 10.0 due to the separation of the triplex bridging units. The two hydrogel systems undergo reversible and cyclic hydrogel/solution transitions by subjecting the systems to appropriate pH values. The anti-cancer drug, coralyne, binds specifically to the TA·T triplex-crosslinked hydrogel thereby increasing its stiffness. The pH-controlled release of the coralyne from the hydrogel is demonstrated.

Programmed DNAzyme-Triggered Dissolution of DNA-Based Hydrogels: Means for Controlled Release of Biocatalysts and for the Activation of Enzyme Cascades

Acrylamide/acrylamide-modified nucleic acid copolymer chains provide building units for the construction of acrylamide-DNA hydrogels. Three different hydrogels are prepared by the cross-linking of the acrylamide-DNA chains with metal ion-dependent DNAzyme sequences and their substrates. The metal ion-dependent DNAzyme sequences used in the study include the Cu(2+)-, Mg(2+)-, and Zn(2+)-dependent DNAzymes. In the presence of the respective metal ions, the substrates of the respective DNAzymes are cleaved, leading to the separation of the cross-linking units and to the dissolution of the hydrogel. The different hydrogels were loaded with a fluorophore-modified dextran or with a fluorophore-functionalized glucose oxidase. Treatment of the different hydrogels with the respective ions led to the release of the loaded dextran or the enzyme, and the rates of releasing of the loaded macromolecules followed the order of Cu(2+) > Mg(2+) > Zn(2+). Also, the different hydrogels were loaded with the enzymes β-galactosidase (β-Gal), glucose oxidase (GOx), or horseradish peroxidase (HRP). In the presence of the appropriate metal ions, the respective hydrogels were dissolved, resulting in the activation of the β-Gal/GOx or GOx/HRP bienzyme cascades and of the β-Gal/GOx/HRP trienzyme cascade.

pH-stimulated DNA hydrogels exhibiting shape-memory properties

Nucleic acid-functionalized polyacrylamide chains that are cooperatively cross-linked by i-motif and nucleic acid duplex units yield, at pH 5.0, DNA hydrogels exhibiting shape-memory properties. Separation of the i-motif units at pH 8.0 dissolves the hydrogel into a quasi-liquid phase. The residual duplex units provide, however, a memory code in the quasi-liquid allowing the regeneration of the hydrogel shape at pH 5.0.

Responsive DNA-based hydrogels and their applications

The term hydrogel describes a type of soft and wet material formed by cross-linked hydrophilic polymers. The distinct feature of hydrogels is their ability to absorb a large amount of water and swell. The properties of a hydrogel are usually determined by the chemical properties of their constituent polymer(s). However, a group of hydrogels, called "smart hydrogels," changes properties in response to environmental changes or external stimuli. Recently, DNA or DNA-inspired responsive hydrogels have attracted considerable attention in construction of smart hydrogels because of the intrinsic advantages of DNA. As a biological polymer, DNA is hydrophilic, biocompatible, and highly programmable by Watson-Crick base pairing. DNA can form a hydrogel by itself under certain conditions, and it can also be incorporated into synthetic polymers to form DNA-hybrid hydrogels. Functional DNAs, such as aptamers and DNAzymes, provide additional molecular recognition capabilities and versatility. In this Review, DNA-based hydrogels are discussed in terms of their stimulus response, as well as their applications.

Responsive hydrogels--structurally and dimensionally optimized smart frameworks for applications in catalysis, micro-system technology and material science

Although the technological and scientific importance of functional polymers has been well established over the last few decades, the most recent focus that has attracted much attention has been on stimuli-responsive polymers. This group of materials is of particular interest due to its ability to respond to internal and/or external chemico-physical stimuli, which is often manifested as large macroscopic responses. Aside from scientific challenges of designing stimuli-responsive polymers, the main technological interest lies in their numerous applications ranging from catalysis through microsystem technology and chemomechanical actuators to sensors that have been extensively explored. Since the phase transition phenomenon of hydrogels is theoretically well understood advanced materials based on the predictions can be prepared. Since the volume phase transition of hydrogels is a diffusion-limited process the size of the synthesized hydrogels is an important factor. Consistent downscaling of the gel size will result in fast smart gels with sufficient response times. In order to apply smart gels in microsystems and sensors, new preparation techniques for hydrogels have to be developed. For the up-coming nanotechnology, nano-sized gels as actuating materials would be of great interest.

Regenerable multifunctional mesoporous silica nanocomposites for simultaneous detection and removal of mercury(II)

Mercury (Hg(2+)) is a highly toxic and widespread environmental pollutant. Herein, a regenerable and highly selective core-shell structured magnetic mesoporous silica nanocomposite with functionalization of thymine (T) and T-rich DNA (denoted as Fe3O4@nSiO2@mSiO2-T-TRDNA nanocomposite) has been developed for simultaneous detection and removal of Hg(2+). In this work, the thymine and T-rich DNA were immobilized onto the interior and exterior surface of outermost mesoporous silica, respectively. The detection mechanism is based on Hg(2+)-mediated hairpin structure formed by T-rich DNA functionalized on the exterior surface of the nanocomposites, where, upon addition of SYBR Green I dye, strong fluorescence is observed. In the absence of Hg(2+), however, addition of the dye results in low fluorescence. The limit of detection for Hg(2+) in a buffer is 2 nM by fluorescence spectroscopy. Simultaneously, the Fe3O4@nSiO2@mSiO2-T-TRDNA nanocomposite features a selective binding with Hg(2+) between two thymines immobilized at the interior surface of the mesopores and exhibits efficient and convenient Hg(2+) removal by a magnet. Kinetic study reveals that the Hg(2+) removal is a rapid process with over 80% of Hg(2+) removed within approximately 1 h. The applicability of the developed nanocomposites is demonstrated to detect and remove Hg(2+) from samples of Xiangjiang river water spiked with Hg(2+). In addition, distinguishing aspects of the Fe3O4@nSiO2@mSiO2-T-TRDNA nanocomposites for Hg(2+) detection and removal also include the regeneration using a simple acid treatment and resistance to nuclease digestion. Similar process can be used to functionalize the Fe3O4@nSiO2@mSiO2 nanocomposites with other nucleic acids and small molecules for environmental and biomedical applications.