A pH-triggered, fast-responding DNA hydrogel

DNA Tetrahedra as Functional Nanostructures: From Basic Principles to Applications

Self-assembled supramolecular DNA tetrahedra composed of programmed sequence-engineered complementary base-paired strands represent elusive nanostructures having key contributions to the development and diverse applications of DNA nanotechnology. By appropriate engineering of the strands, DNA tetrahedra of tuneable sizes and chemical functionalities were designed. Programmed functionalities for diverse applications were integrated into tetrahedra structures including sequence-specific recognition strands (aptamers), catalytic DNAzymes, nanoparticles, proteins, or fluorophore. The article presents a comprehensive review addressing methods to assemble and characterize the DNA tetrahedra nanostructures, and diverse applications of DNA tetrahedra framework are discussed. Topics being addressed include the application of structurally functionalized DNA tetrahedra nanostructure for the assembly of diverse optical or electrochemical sensing platforms and functionalized intracellular sensing and imaging modules. In addition, the triggered reconfiguration of DNA tetrahedra nanostructures and dynamic networks and circuits emulating biological transformations are introduced. Moreover, the functionalization of DNA tetrahedra frameworks with nanoparticles provides building units for the assembly of optical devices and for the programmed crystallization of nanoparticle superlattices. Finally, diverse applications of DNA tetrahedra in the field of nanomedicine are addressed. These include the DNA tetrahedra-assisted permeation of nanocarriers into cells for imaging, controlled drug release, active chemodynamic/photodynamic treatment of target tissues, and regenerative medicine.

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.

In Vivo Interactions of Nucleic Acid Nanostructures With Cells

Nucleic acid nanostructures, derived from the assembly of nucleic acid building blocks (e.g., plasmids and oligonucleotides), are important intracellular carriers of therapeutic cargoes widely utilized in preclinical nanomedicine applications, yet their clinical translation remains scarce. In the era of "translational nucleic acid nanotechnology", a deeper mechanistic understanding of the interactions of nucleic acid nanostructures with cells in vivo will guide the development of more efficacious nanomedicines. This review showcases the recent progress in dissecting the in vivo interactions of four key types of nucleic acid nanostructures (i.e., tile-based, origami, spherical nucleic acid, and nucleic acid nanogel) with cells in rodents over the past five years. Emphasis lies on the cellular-level distribution of nucleic acid nanostructures in various organs and tissues and the cellular responses induced by their cellular entry. Next, in the spirit of preclinical translation, this review features the latest interactions of nucleic acid nanostructures with cells in large animals and humans. Finally, the review offers directions for studying the interactions of nucleic acid nanostructures with cells from both materials and biology perspectives and concludes with some regulatory updates.

Constructing Stiffness Tunable DNA Hydrogels Based on DNA Modules with Adjustable Rigidity

DNA hydrogel represents a potent material for crafting biological scaffolds, but the toolbox to systematically regulate the mechanical property is still limited. Herein, we have provided a strategy to tune the stiffness of DNA hydrogel through manipulating the rigidity of DNA modules. By introducing building blocks with higher molecular rigidity and proper connecting fashion, DNA hydrogel stiffness could be systematically elevated. These hydrogels showed excellent dynamic properties and biocompatibility, thus exhibiting great potential in three-dimensional (3D) cell culture. This study has offered a systematic method to explore the structure-property relationship, which may contribute to the development of more intelligent and personalized biomedical platforms.

Advanced Smart Biomaterials for Regenerative Medicine and Drug Delivery Based on Phosphoramidite Chemistry: From Oligonucleotides to Precision Polymers

Over decades of development, while phosphoramidite chemistry has been known as the leading method in commercial synthesis of oligonucleotides, it has also revolutionized the fabrication of sequence-defined polymers (SDPs), offering novel functional materials in polymer science and clinical medicine. This review has introduced the evolution of phosphoramidite chemistry, emphasizing its development from the synthesis of oligonucleotides to the creation of universal SDPs, which have unlocked the potential for designing programmable smart biomaterials with applications in diverse areas including data storage, regenerative medicine and drug delivery. The key methodologies, functions, biomedical applications, and future challenges in SDPs, have also been summarized in this review, underscoring the significance of breakthroughs in precisely synthesized materials.

Chemical and Photochemical-Driven Dissipative Fe3+/Fe2+-Ion Cross-Linked Carboxymethyl Cellulose Gels Operating Under Aerobic Conditions: Applications for Transient Controlled Release and Mechanical Actuation

A Fe3+-ion cross-linked carboxymethyl cellulose, Fe3+-CMC, redox-active gel exhibiting dissipative, transient stiffness properties is introduced. Chemical or photosensitized reduction of the higher-stiffness Fe3+-CMC to the lower-stiffness Fe2+-CMC gel, accompanied by the aerobic reoxidation of the Fe2+-CMC matrix, leads to the dissipative, transient stiffness, functional matrix. The light-induced, temporal, transient release of a load (Texas red dextran) and the light-triggered, transient mechanical bending of a poly-N-isopropylacrylamide (p-NIPAM)/Fe3+-CMC bilayer construct are introduced, thus demonstrating the potential use of the dissipative Fe3+-CMC gel for controlled drug release or soft robotic applications.

Smart Free-Standing Bilayer Polyacrylamide/DNA Hybrid Hydrogel Film-Based Sensing System Using Changes in Bending Angles as a Visual Signal Readout

Stimuli-responsive DNA hydrogels have shown great potential in sensing applications due to their attractive properties such as programmable target responsiveness, excellent biocompatibility, and biodegradability. In contrast to the extensively developed DNA hydrogel sensing systems based on the stimuli-responsive hydrogel-to-solution phase transition of the hydrogel matrix, the quantitative sensing application of DNA hydrogels exhibiting smart shape deformations has rarely been explored. Moreover, bulk DNA hydrogel-based sensing systems also suffer from high material cost and slow response. Herein, free-standing bilayer polyacrylamide/DNA hybrid hydrogel films with programmable responsive properties directed by the sequence of functional DNA units have been constructed. Compared with bulk DNA hydrogels, these DNA hydrogel films with a thickness at the micrometer scale not only greatly reduce the consumption of DNA materials but also facilitate the mass transfer of biomacromolecular substances within the hydrogel network, thus favoring their sensing applications. Therefore, a target-responsive smart DNA hydrogel film-based sensor system is further demonstrated based on the large amplitude macroscopic shape deformation of the film as a visual signal readout. As a proof of concept, Pb2+ or UO22+ ion-responsive DNA units were introduced into the active layer of the bilayer hydrogel films. In the presence of Pb2+ or UO22+ ions, the occurrence of a cleavage reaction within the DNA units leads to the release of DNA segments from the hydrogel film, inducing a dramatic shape deformation of the film, and thus sensing of Pb2+ or UO22+ ions with high specificity is achieved based on measuring the bending angle changes of these smart free-standing films. These smart DNA hydrogel film sensors with target-programmable responsiveness, simple operation, and ease of storage may hold promise for future rapid on-site testing applications.

Programming the Assembly of Oligo-Adenine with Coralyne into a pH-Responsive DNA Hydrogel

External stimuli-responsive DNA hydrogels present interesting platforms for drug loading and triggered release. Typically, drug molecules are encapsulated within three-dimensionally hybridized DNA networks. However, the utilization of drug molecules as cofactors to facilitate the directed assembly of DNA strands into hydrogel frameworks and their subsequent controlled release remains to be explored. Herein, we introduce the guided assembly of oligo-adenine (A-strand) into an acidic pH-responsive DNA hydrogel using an anticancer drug, coralyne (COR), as a low-molecular-weight cofactor. At pH 7, COR orchestrates the assembly of A-strand into an antiparallel duplex configuration cross-linked by A-COR-A units at a stoichiometric ratio of one COR cofactor per four adenine bases, resulting in a DNA hydrogel characterized by A-COR-A duplex bridges. At pH 4-5, the instability of A-COR-A units results in the disintegration of the duplex into its constituent components, leading to the release of COR and simultaneous dissociation of the DNA hydrogel matrix. This study introduces a method by which drug molecules, exemplified here by COR, facilitate the direct formation of a supramolecular cofactor-DNA complex, subsequently leading to the creation of a stimuli-responsive DNA hydrogel. This approach may inspire future investigations into DNA hydrogels tailored for controlled drug encapsulation and release applications.

DNA Cryogels with Anisotropic Mechanical and Responsive Properties for Specific Cell Capture and Release

Due to their programmable stimuli-responsiveness, excellent biocompatibility, and water-rich and soft structures similar to biological tissues, smart DNA hydrogels hold great promise for biosensing and biomedical applications. However, most DNA hydrogels developed to date are composed of randomly oriented and isotropic polymer networks, and the resulting slow response to biotargets and lack of anisotropic properties similar to those of biological tissues have limited their extensive applications. Herein, anisotropic DNA hydrogels consisting of unidirectional void channels internally oriented up to macroscopic length scales were constructed by a directional cryopolymerization method, as exemplified by a DNA-incorporated covalently cross-linked DNA cryogel and a DNA duplex structure noncovalently cross-linked DNA cryogel. Results showed that the formation of unidirectional channels significantly improved the responsiveness of the gel matrix to biomacromolecular substances and further endowed the DNA cryogels with anisotropic properties, including anisotropic mechanical properties, anisotropic swelling/shrinking behaviors, and anisotropic responsiveness to specific biotargets. Moreover, the abundant oriented and long macroporous channels in the gel matrix facilitated the migration of cells, and through the introduction of aptamer structures and thermosensitive polymers, an anisotropic DNA cryogel-based platform was further constructed to achieve the highly efficient capture and release of specific cells. These anisotropic DNA hydrogels may provide new opportunities for the development of anisotropic separation and biosensing systems.

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.

Rational Design of DNA Hydrogels Based on Molecular Dynamics of Polymers

In recent years, DNA has emerged as a fascinating building material to engineer hydrogel due to its excellent programmability, which has gained considerable attention in biomedical applications. Understanding the structure-property relationship and underlying molecular determinants of DNA hydrogel is essential to precisely tailor its macroscopic properties at molecular level. In this review, the rational design principles of DNA molecular networks based on molecular dynamics of polymers on the temporal scale, which can be engineered via the backbone rigidity and crosslinking kinetics, are highlighted. By elucidating the underlying molecular mechanisms and theories, it is aimed to provide a comprehensive overview of how the tunable DNA backbone rigidity and the crosslinking kinetics lead to desirable macroscopic properties of DNA hydrogels, including mechanical properties, diffusive permeability, swelling behaviors, and dynamic features. Furthermore, it is also discussed how the tunable macroscopic properties make DNA hydrogels promising candidates for biomedical applications, such as cell culture, tissue engineering, bio-sensing, and drug delivery.

Chemical and Biological Engineering Strategies to Make and Modify Next-Generation Hydrogel Biomaterials

There is a growing interest in the development of technologies to probe and direct in vitro cellular function for fundamental organoid and stem cell biology, functional tissue and metabolic engineering, and biotherapeutic formulation. Recapitulating many critical aspects of the native cellular niche, hydrogel biomaterials have proven to be a defining platform technology in this space, catapulting biological investigation from traditional two-dimensional (2D) culture into the 3D world. Seeking to better emulate the dynamic heterogeneity characteristic of all living tissues, global efforts over the last several years have centered around upgrading hydrogel design from relatively simple and static architectures into stimuli-responsive and spatiotemporally evolvable niches. Towards this end, advances from traditionally disparate fields including bioorthogonal click chemistry, chemoenzymatic synthesis, and DNA nanotechnology have been co-opted and integrated to construct 4D-tunable systems that undergo preprogrammed functional changes in response to user-defined inputs. In this Review, we highlight how advances in synthetic, semisynthetic, and bio-based chemistries have played a critical role in the triggered creation and customization of next-generation hydrogel biomaterials. We also chart how these advances stand to energize the translational pipeline of hydrogels from bench to market and close with an outlook on outstanding opportunities and challenges that lay ahead.

On-Demand Aligned DNA Hydrogel Via Light Scanning

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

Novel Vectors and Administrations for mRNA Delivery

mRNA therapy has shown great potential in infectious disease vaccines, cancer immunotherapy, protein replacement therapy, gene editing, and other fields due to its central role in all life processes. However, mRNA is challenging to pass through the cell membrane due to its significant negative charges and degradation from RNase, so the key to mRNA therapy is efficient packaging and delivery of it with appropriate vectors. Presently researchers have developed various vectors such as viruses and liposomes, but these conventional vectors are now difficult to meet the growing requirement like safety, efficiency, and targeting, so many novel delivery vectors with unique advantages have emerged recently. This review mainly introduces two categories of novel vectors: biomacromolecules and inorganic nanoparticles, as well as two novel methods of control and administration based on these novel vectors: controlled-release administration and non-invasive administration. These novel delivery strategies have the advantages of high safety, biocompatibility, versatility, intelligence, and targeting. This paper analyzes the challenges faced by the field of mRNA delivery in depth, and discusses how to use the characteristics of novel vectors and administrations to solve these problems.

AMP Aptamer Programs DNA Tile Cohesion without Canonical Base Pairing

Tile-based DNA self-assembly provides a versatile approach for the construction of a wide range of nanostructures for various applications such as nanomedicine and advanced materials. The inter-tile interactions are primarily programmed by base pairing, particularly Watson-Crick base pairing. To further expand the tool box for DNA nanotechnology, herein, we have designed DNA tiles that contain both ligands and aptamers. Upon ligand-aptamer binding, tiles associate into geometrically well-defined nanostructures. This strategy has been demonstrated by the assembly of a series of DNA nanostructures, which have been thoroughly characterized by gel electrophoresis and atomic force microscopy. This new inter-tile cohesion could bring new potentials to DNA self-assembly in the future. For example, the addition of free ligand could modulate the nanostructure formation. In the case of biological ligands, DNA self-assembly could be related to the presence of certain ligands.

Stimuli-Responsive DNA-Based Hydrogels on Surfaces for Switchable Bioelectrocatalysis and Controlled Release of Loads

The assembly of enzyme [glucose oxidase (GOx)]-loaded stimuli-responsive DNA-based hydrogels on electrode surfaces, and the triggered control over the stiffness of the hydrogels, provides a means to switch the bioelectrocatalytic functions of the hydrogels. One system includes the assembly of GOx-loaded, pH-responsive, hydrogel matrices cross-linked by two cooperative nucleic acid motives comprising permanent duplex nucleic acids and "caged" i-motif pH-responsive duplexes. Bioelectrocatalyzed oxidation of glucose leads to the formation of gluconic acid that acidifies the hydrogel resulting in the separation of the i-motif constituents and lowering the hydrogel stiffness. Loading of the hydrogel matrices with insulin results in the potential-triggered, glucose concentration-controlled, switchable release of insulin from the hydrogel-modified electrodes. The switchable bioelectrocatalyzed release of insulin is demonstrated in the presence of ferrocenemethanol as a diffusional electron mediator or by applying an electrically wired integrated matrix that includes ferrocenyl-modified GOx embedded in the hydrogel. The second GOx-loaded, stimuli-responsive, DNA-based hydrogel matrix associated with the electrode includes a polyacrylamide hydrogel cooperatively cross-linked by duplex nucleic acids and "caged" G-quadruplex-responsive duplexes. The hydrogel matrix undergoes K+-ions/crown ether-triggered stiffness changes by the cyclic K+-ion-stimulated formation of G-quadruplexes (lower stiffness) and the crown ether-induced separation of the G-quadruplexes (higher stiffness). The hydrogel matrices demonstrate switchable bioelectrocatalytic functions guided by the stiffness properties of the hydrogels.

DNA Materials Assembled from One DNA Strand

Due to the specific base-pairing recognition, clear nanostructure, programmable sequence and responsiveness of the DNA molecule, DNA materials have attracted extensive attention and been widely used in controlled release, drug delivery and tissue engineering. Generally, the strategies for preparing DNA materials are based on the assembly of multiple DNA strands. The construction of DNA materials using only one DNA strand can not only save time and cost, but also avoid defects in final assemblies generated by the inaccuracy of DNA ratios, which potentially promote the large-scale production and practical application of DNA materials. In order to use one DNA strand to form assemblies, the sequences have to be palindromes with lengths that need to be controlled carefully. In this review, we introduced the development of DNA assembly and mainly summarized current reported materials formed by one DNA strand. We also discussed the principle for the construction of DNA materials using one DNA strand.

DNA hydrogels for bone regeneration

DNA-based biomaterials have been proposed for tissue engineering approaches due to their predictable assembly into complex morphologies and ease of functionalization. For bone tissue regeneration, the ability to bind Ca2+ and promote hydroxyapatite (HAP) growth along the DNA backbone combined with their degradation and release of extracellular phosphate, a known promoter of osteogenic differentiation, make DNA-based biomaterials unlike other currently used materials. However, their use as biodegradable scaffolds for bone repair remains scarce. Here, we describe the design and synthesis of DNA hydrogels, gels composed of DNA that swell in water, their interactions in vitro with the osteogenic cell lines MC3T3-E1 and mouse calvarial osteoblast, and their promotion of new bone formation in rat calvarial wounds. We found that DNA hydrogels can be readily synthesized at room temperature, and they promote HAP growth in vitro, as characterized by Fourier transform infrared spectroscopy, X-ray diffraction, scanning electron microscopy, atomic force microscopy, and transmission electron microscopy. Osteogenic cells remain viable when seeded on DNA hydrogels in vitro, as characterized by fluorescence microscopy. In vivo, DNA hydrogels promote the formation of new bone in rat calvarial critical size defects, as characterized by micro-computed tomography and histology. This study uses DNA hydrogels as a potential therapeutic biomaterial for regenerating lost bone.

Target response controlled enzyme activity switch for multimodal biosensing detection

How to achieve delicate regulation of enzyme activity and empower it with more roles is the peak in the field of enzyme catalysis research. Traditional proteases or novel nano-enzymes are unable to achieve stimulus-responsive activity modulation due to their own structural limitations. Here, we propose a novel Controllable Enzyme Activity Switch, CEAS, based on hemin aggregation regulation, to deeply explore its regulatory mechanism and develop multimodal biosensing applications. The core of CEAS relies on the dimerizable inactivation of catalytically active center hemin and utilizes a DNA template to orderly guide the G4-Hemin DNAzyme to tightly bind to DNA-Hemin, thereby shutting down the catalytic ability. By customizing the design of the guide template, different target stimulus responses lead to hemin dimerization dissociation and restore the synergistic catalysis of G4-Hemin and DNA-Hemin, thus achieving a target-regulated enzymatic activity switch. Moreover, the programmability of CEAS allowed it easy to couple with a variety of DNA recognition and amplification techniques, thus developing a series of visual protein detection systems and highly sensitive fluorescent detection systems with excellent bioanalytical performance. Therefore, the construction of CEAS is expected to break the limitation of conventional enzymes that cannot be targetable regulated, thus enabling customizable enzymatic reaction systems and providing a new paradigm for controllable enzyme activities.

Small Molecule-Templated DNA Hydrogel with Record Stiffness Integrates and Releases DNA Nanostructures and Gene Silencing Nucleic Acids

Deoxyribonucleic acid (DNA) hydrogels are a unique class of programmable, biocompatible materials able to respond to complex stimuli, making them valuable in drug delivery, analyte detection, cell growth, and shape-memory materials. However, unmodified DNA hydrogels in the literature are very soft, rarely reaching a storage modulus of 10³  Pa, and they lack functionality, limiting their applications. Here, a DNA/small-molecule motif to create stiff hydrogels from unmodified DNA, reaching 10⁵  Pa in storage modulus is used. The motif consists of an interaction between polyadenine and cyanuric acid-which has 3-thymine like faces-into multimicrometer supramolecular fibers. The mechanical properties of these hydrogels are readily tuned, they are self-healing and thixotropic. They integrate a high density of small, nontoxic molecules, and are functionalized simply by varying the molecule sidechain. They respond to three independent stimuli, including a small molecule stimulus. These stimuli are used to integrate and release DNA wireframe and DNA origami nanostructures within the hydrogel. The hydrogel is applied as an injectable delivery vector, releasing an antisense oligonucleotide in cells, and increasing its gene silencing efficacy. This work provides tunable, stimuli-responsive, exceptionally stiff all-DNA hydrogels from simple sequences, extending these materials' capabilities.

End-ligation can dramatically stabilize i-motifs at neutral pH

Stabilizing i-motif structures at neutral pH and physiological temperature remains a major challenge. Here, we demonstrate the use of chemical end-ligation to stabilize intramolecular i-motifs at both acidic and neutral pH. We also demonstrate that combining 2'-deoxy-2'-fluoroarabinocytidine substitutions and end-ligation results in an i-motif with an unparalleled thermal stability of 54 °C at neutral pH. Overall, the ligated i-motifs presented herein may be used in screens for selective i-motif ligands and proteins and could find important applications in nanotechnology.

Polymeric DNA Hydrogels and Their Applications in Drug Delivery for Cancer Therapy

The biomolecule deoxyribonucleic acid (DNA), which acts as the carrier of genetic information, is also regarded as a block copolymer for the construction of biomaterials. DNA hydrogels, composed of three-dimensional networks of DNA chains, have received considerable attention as a promising biomaterial due to their good biocompatibility and biodegradability. DNA hydrogels with specific functions can be prepared via assembly of various functional sequences containing DNA modules. In recent years, DNA hydrogels have been widely used for drug delivery, particularly in cancer therapy. Benefiting from the sequence programmability and molecular recognition ability of DNA molecules, DNA hydrogels prepared using functional DNA modules can achieve efficient loading of anti-cancer drugs and integration of specific DNA sequences with cancer therapeutic effects, thus achieving targeted drug delivery and controlled drug release, which are conducive to cancer therapy. In this review, we summarized the assembly strategies for the preparation of DNA hydrogels on the basis of branched DNA modules, hybrid chain reaction (HCR)-synthesized DNA networks and rolling circle amplification (RCA)-produced DNA chains, respectively. The application of DNA hydrogels as drug delivery carriers in cancer therapy has been discussed. Finally, the future development directions of DNA hydrogels in cancer therapy are prospected.

Mechanistic insight into the structure, thermodynamics and dynamics of equilibrium gels of multi-armed DNA nanostars

The unique sequence specificity rule of DNA makes it an ideal molecular building block for constructing periodic arrays and devices with nanoscale accuracy and precision. Here, we present the self-assembly of DNA nanostars having three, four and five arms into a gel phase using a simplistic coarse-grained bead-spring model developed by Z. Xing, C. Ness, D. Frenkel and E. Eiser (Macromolecules, 2019, 52, 504-512). Our simulations show that the DNA nanostars form a thermodynamically stable fully bonded gel phase from an unstructured liquid phase with the lowering of temperature. We characterize the phase transition by calculating several structural features such as the radial distribution function and structure factor. The thermodynamics of gelation is quantified by the potential energy and translational pair-entropy of the system. The phase transition from an arrested gel phase to an unstructured liquid phase has been modelled using a two-state theoretical model. We find that this transition is enthalpy driven, and loss of configuration and translational entropy is counterpoised by enthalpic interaction of the DNA sticky-ends, which gives rise to a gel phase at low temperature. The absolute rotational and translational entropy of the systems, measured using a two-phase thermodynamic model, also substantiates the gel transition. The slowing down of the dynamics upon approaching the transition temperature from a high temperature demonstrates the phase transition to a gel phase. A detailed numerical simulation study of the morphology, dynamics and thermodynamics of DNA gelation can provide guidance for future experiments, is easily extensible to other polymeric systems, and is expected to help in understanding the physics of self-assembly.

Cellulose based self-healing hydrogel through Boronic Ester connections for wound healing and antitumor applications

The application of biodegradable hydrogels in medical field has drawn great attention because their networked structure provided ideal spaces for drug loading and cell growth. In this research, the boronic acid was coupled onto carboxyethyl cellulose (CMC) to synthesize boronic acid grafted CMC (CMC-BA) conveniently and self-healing hydrogel was fabricated with polyvinyl alcohol (PVA) crosslinking through dynamic boronic ester bond. The CMC-BA/PVA hydrogel showed good biocompatibility and could be degraded by cellulase and in vivo. The hydrogel formed fast fit for localized injection to cover the irregular wounds and localize the antitumor drugs to the tumor site. The in vivo wound repairing experiment revealed the hydrogel could form airtight adhesion to the wound site to reduce blood loss and accelerate the wound repairing rate. The hydrogel as a drug release carrier also reduced the acute in vivo toxicity of DOX with antitumor performance well preserved through a controlled release profile. Based on the above advantages, the CMC-based hydrogel with boronic ester connection should have great potential in biomedical areas with profitable future.

A Strong Acid-Induced DNA Hydrogel Based on pH-Reconfigurable A-Motif Duplex

Under a pH value lower than the pK_a of adenine (3.5), adenine-rich sequences (A-strand) form a unique parallel A-motif duplex due to the protonation of A-strand. At a pH above 3.5, deprotonation of adenines leads to the dissolution of A-motif duplex to A-strand single coil. This pH-reconfigurable A-motif duplex has been developed as a novel pH-responsive DNA hydrogel, termed A-hydrogel. The hydrogel state is achieved at pH 1.2 by the A-motif duplex bridging units, which are cross-linked by both reverse Hoogsteen interaction and electrostatic attraction. Hydrogel-to-solution transition is triggered by pH 4.3 due to the deprotonation-induced separation of A-motif duplex. The A-hydrogel system undergoes reversible hydrogel-solution transitions by subjecting the system to cyclic pH shifts between 1.2 and 4.3. An anti-inflammatory medicine, sulfasalazine (SSZ), which intercalates into A-motif duplex, is loaded into A-hydrogel. Its pH-controlled release from A-hydrogel is successfully demonstrated. The strong acid-induced A-hydrogel may fill the gap that other mild acid-responsive DNA hydrogels cannot do, such as protection of orally delivered drug in hostile stomach environment against strong acid (pH ~ 1.2) and digestive enzymes.

DNA Droplets: Intelligent, Dynamic Fluid

Breathtaking advances in DNA nanotechnology have established DNA as a promising biomaterial for the fabrication of programmable higher-order nano/microstructures. In the context of developing artificial cells and tissues, DNA droplets have emerged as a powerful platform for creating intelligent, dynamic cell-like machinery. DNA droplets are a microscale membrane-free coacervate of DNA formed through phase separation. This new type of DNA system couples dynamic fluid-like property with long-established DNA programmability. This hybrid nature offers an advantageous route to facile and robust control over the structures, functions, and behaviors of DNA droplets. This review begins by describing programmable DNA condensation, commenting on the physical properties and fabrication strategies of DNA hydrogels and droplets. By presenting an overview of the development pathways leading to DNA droplets, it is shown that DNA technology has evolved from static, rigid systems to soft, dynamic systems. Next, the basic characteristics of DNA droplets are described as intelligent, dynamic fluid by showcasing the latest examples highlighting their distinctive features related to sequence-specific interactions and programmable mechanical properties. Finally, this review discusses the potential and challenges of numerical modeling able to connect a robust link between individual sequences and macroscopic mechanical properties of DNA droplets.

Stimulus-Responsive DNA Hydrogel Biosensors for Food Safety Detection

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

i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F···H and O···H hydrogen bonds

G-quadruplex and i-motif nucleic acid structures are believed to fold through kinetic partitioning mechanisms. Such mechanisms explain the structural heterogeneity of G-quadruplex metastable intermediates which have been extensively reported. On the other hand, i-motif folding is regarded as predictable, and research on alternative i-motif folds is limited. While TC₅ normally folds into a stable tetrameric i-motif in solution, we report that 2'-deoxy-2'-fluoroarabinocytidine (araF-C) substitutions can prompt TC₅ to form an off-pathway and kinetically-trapped dimeric i-motif, thereby expanding the scope of i-motif folding landscapes. This i-motif is formed by two strands, associated head-to-head, and featuring zero-nucleotide loops which have not been previously observed. Through spectroscopic and computational analyses, we also establish that the dimeric i-motif is stabilized by fluorine and non-fluorine hydrogen bonds, thereby explaining the superlative stability of araF-C modified i-motifs. Comparative experimental findings suggest that the strength of these interactions depends on the flexible sugar pucker adopted by the araF-C residue. Overall, the findings reported here provide a new role for i-motifs in nanotechnology and also pose the question of whether unprecedented i-motif folds may exist in vivo.

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.

pH-feedback systems to program autonomous self-assembly and material lifecycles

pH-responsive systems have gained importance for the development of smart materials and for biomedical applications because they can switch between different states by simple acid/base triggers. However, such equilibrium systems lack the autonomous behaviour that is so ubiquitous in living systems that self-regulate out of equilibrium. As a contribution to the emerging field of autonomous chemical systems, we have developed pH-feedback systems (pH-FS) based on the coupling of acid- and base-producing steps in chemical reaction networks. The resulting autonomous nonlinear pH curves can be coupled with a variety of pH-sensitive building blocks to program the lifecycles of the associated transient state at the level of self-assemblies and material systems. In this article, we discuss the different generations of such pH-feedback systems, the principles of their coupling to self-assemblies with lifecycles and highlight emerging concepts for the design of autonomous functional materials. The specificity, robustness, and flexible operation of such pH-FS can also be used to realize chemo-structural and chemo-mechanical feedbacks that extend the behaviour of such materials systems toward complex and functional life-like systems.

Fast Transport and Transformation of Biomacromolecular Substances via Thermo-Stimulated Active "Inhalation-Exhalation" Cycles of Hierarchically Structured Smart pNIPAM-DNA Hydrogels

Although smart hydrogels hold great promise in biosensing and biomedical applications, their response to external stimuli is governed by the passive diffusion-dependent substance transport between hydrogels and environments and within the 3D hydrogel matrices, resulting in slow response to biomacromolecules and limiting their extensive applications. Herein, inspired by the respiration systems of organisms, an active strategy to achieve highly efficient biomolecular substance transport through the thermo-stimulated "inhalation-exhalation" cycles of hydrogel matrices is demonstrated. The cryo-structured poly(N-isopropylacrylamide) (pNIPAM)-DNA hydrogels, composed of functional DNA-tethered pNIPAM networks and free-water-containing macroporous channels, exhibit thermally triggered fast and reversible shrinking/swelling cycles with high-volume changes, which drive the formation of dynamic water stream to accelerate the intake of external substances and expelling of endogenous substances, thus promoting the functional properties of hydrogel systems. Demonstrated by catalytic DNAzyme and CRISPR-Cas12a-incorporating hydrogels, significantly enhanced catalytic efficiency with up to 280% and 390% is achieved, upon the introduction of active "inhalation-exhalation" cycles, respectively. Moreover, remotely near-infrared (NIR)-triggering of "inhalation-exhalation" cycles is achieved after the introduction of NIR-responsive MXene nanosheets into the hydrogel matrix. These hydrogel systems with enhanced substance transport and transformation properties hold promise in the development of more effective biosensing and therapeutic systems.

Stimuli-responsive nucleic acid nanostructures for efficient drug delivery

Based on complementary base pairing, nucleic acid molecules have acted as engineerable building blocks to prepare versatile nanostructures with unique shapes and sizes. Benefiting from excellent programmability and biocompatibility, rationally designed nucleic acid nanostructures have been widely employed in biomedical applications. With the development of the chemical biology of nucleic acids, various stimuli-responsive nucleic acid nanostructures have been constructed by tailored chemical modification with multifunctional components. In this minireview, we summarize the representative and latest research about the employment of stimuli-responsive nucleic acid nanostructures for drug delivery in response to endogenous and exogenous stimuli (redox gradient, pH, nuclease, biomacromolecule, and light). We also discuss the broad prospects and remaining challenges of nucleic acid nanotechnology in biomedical applications.

Advances in DNA Supramolecular Hydrogels for Tissue Engineering

Deoxyribonucleic acid (DNA) is a biological macromolecule that plays a genetic role in cells. DNA molecules with specific recognition, self-assembly capabilities, and sequence programmability have become an excellent construction material for micro- and nanostructures. Based on DNA self-assembly technology, a series of molecular devices and materials are constructed. Among them, DNA hydrogels with the advantages of good biocompatibility, biodegradability, and containing designable stimuli-responsive units have attracted much attention. This review introduces the formation strategy of DNA supramolecular hydrogels, and focuses on its applications in tissue engineering, including cell encapsulation, cell culture, cell capture and release, wound dressings, and tissue growth. The unique properties and application prospects of DNA supramolecular hydrogels in tissue engineering are also discussed.

pH-Induced Symmetry Conversion of DNA Origami Lattices

DNA nanotechnology has provided credible approaches for assembly of three-dimensional (3D) lattices with complex patterns. However, the symmetries are strictly dependent on their initial configurations and difficult to alter via non-thermal treatments. While switchable nucleic acid structures have been employed to construct deformable DNA motifs, it remains challenging to arrange them anisotropically in 3D lattices to trigger directed collective shape transition and dynamic symmetry conversion. In this work, we used octahedral DNA origami frames to synthesize four DNA origami lattices by placing the pH-reactive i-motif sequences in the desired dimensions. Thereinto, lattices with an anisotropic design can switch between simple cubic (SC) and simple tetragonal (ST) upon pH change. Small angle X-ray scattering (SAXS) results reveal the feasibility of obtaining 3D lattices with sensitive responses to external stimuli, expanding the way to obtain low-symmetry lattices.

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.

Switchable and dynamic G-quadruplexes and their applications

G-Quadruplexes attract growing interest as functional constituents in biology, chemistry, nanotechnology, and material science. In particular, the reversible dynamic reconfiguration of G-quadruplexes provides versatile means to switch DNA nanostructures, reversibly control catalytic functions of DNA assemblies, and switch material properties and functions. The present review article discusses the switchable dynamic reconfiguration of G-quadruplexes as central functional and structural motifs that enable diverse applications in DNA nanotechnology and material science. The dynamic reconfiguration of G-quadruplexes has a major impact on the development of DNA switches and DNA machines. The integration of G-quadruplexes with enzymes yields supramolecular assemblies exhibiting switchable catalytic functions guided by dynamic G-quadruplex topologies. In addition, G-quadruplexes act as important building blocks to operate constitutional dynamic networks and transient dissipative networks mimicking complex biological dynamic circuitries. Furthermore, the integration of G-quadruplexes with DNA nanostructures, such as origami tiles, introduces dynamic and mechanical features into these static frameworks. Beyond the dynamic operation of G-quadruplex structures in solution, the assembly of G-quadruplexes on bulk surfaces such as electrodes or nanoparticles provides versatile means to engineer diverse electrochemical and photoelectrochemical devices and to switch the dynamic aggregation/deaggregation of nanoparticles, leading to nanoparticle assemblies that reveal switchable optical properties. Finally, the functionalization of hydrogels, hydrogel microcapsules, or nanoparticle carriers, such as SiO₂ nanoparticles or metal-organic framework nanoparticles, yields stimuli-responsive materials exhibiting shape-memory, self-healing, and controlled drug release properties. Indeed, G-quadruplex-modified nanomaterials find growing interest in the area of nanomedicine. Beyond the impressive G-quadruplex-based scientific advances achieved to date, exciting future developments are still anticipated. The review addresses these goals by identifying the potential opportunities and challenges ahead of the field in the coming years.

Enzyme-manipulated hydrogelation of small molecules for biomedical applications

Enzyme-manipulated hydrogelation based on self-assembly of small molecules is an attractive methodology for development of functional biomaterials. Upon the catalysis of enzymes, small-molecular precursors are converted into assemblable building blocks, which arrange into high-ordered nanofibers via non-covalent interactions at the molecular level, and further trap water to form hydrogels at the macroscopic level. Such approach has numerous advantages of region- and enantioselectivity, and mild reaction conditions for encapsulation of biomedications or cells that are fragile to environmental change. In addition to the common applications as drug reservoirs or cell scaffolds, the utilization of endogenous enzymes as stimuli to initiate self-assembly in the living cells and tissue is considered as an intelligent spatiotemporally controllable hydrogelation strategy for biomedical applications. The enzyme-instructed in situ self-assembly and hydrogelation can modulate the cell behavior, and even present therapeutic bioactivities, which provides a new perspective in the field of disease treatment. In this review, we categorize distinct enzymatic stimuli and elaborate substrate design, catalytic characteristics, and mechanisms of self-assembly and hydrogelation. The biomedical applications in drug delivery, tissue engineering, bioimaging, and in situ gelation-produced bioactivity are outlined. Advantages and limitations regarding the state-of-the-art enzyme-driven hydrogelation technologies and future perspectives are also discussed. STATEMENT OF SIGNIFICANCE: Hydrogel is a semi-solid soft material containing a large amount of water. Due to the features of adjustable flexibility, extremely porous architecture, and the high similarity of structure to natural extracellular matrices, the hydrogel has broad application prospects in biomedicine. In recent 20 years, enzyme-manipulated hydrogelation based on self-assembly of small molecules has developed rapidly as an attractive methodology for the construction of functional biomaterials. Upon the catalysis of enzymes, small-molecular precursors are converted into assemblable building blocks, which arrange into high-ordered nanofibers via non-covalent interactions at the molecular level, and further trap water to form hydrogels at the macroscopic level. This review summarized the characteristics of enzymatic hydrogel, as well as the traditional application and emerging prospect of enzyme-instructed self-assembly and hydrogelation.

Cytosine-rich oligonucleotides incorporating a non-nucleotide loop: A further step towards the obtainment of physiologically stable i-motif DNA

i-Motifs, also known as i-tetraplexes, are secondary structures of DNA occurring in cytosine-rich oligonucleotides (CROs) that recall increasing interest in the scientific community for their relevance in various biological processes and DNA nanotechnology. This study reports the design of new structurally modified CROs, named Double-Ended-Linker-CROs (DEL-CROs), capable of forming stable i-motif structures. Here, two C-rich strands having sequences d(AC₄A) and d(C₆) have been attached, in a parallel fashion, to the two linker's edges by their 3' or 5' ends. The resulting DEL-CROs have been investigated for their capability to form i-motif structures by circular dichroism, poly-acrylamide gel electrophoresis, HPLC-size-exclusion chromatography, and NMR studies. This investigation established that DEL-CROs could form more stable i-motif structures than the corresponding unmodified CROs. In particular, the i-motif formed by DEL-5'-d(C₆)₂ resulted stable enough to be detected even at near physiological conditions (37 °C, pH 7.0). The results open the way to developing pH-switchable nanocarriers and aptamers based on suitably functionalized DEL-CROs.

A covalently conjugated branched DNA aptamer cluster-based nanoplatform for efficiently targeted drug delivery

Targeted delivery of therapeutic drugs is essential for precise treatment of various diseases to reduce possible serious side-effects. A screened DNA aptamer has been widely developed for active targeting delivery. Herein, we report a facile strategy for the construction of a branched DNA aptamer cluster-based nanoplatform for efficiently targeted drug delivery. In our design, the terminal-modified DNA aptamer can be covalently conjugated to form a branched aptamer cluster by click reaction easily. The branched aptamer cluster-modified DNA tetrahedron (TET) demonstrates highly targeted cellular uptake with the modification of only one site. After loading the chemotherapeutic drug (doxorubicin, DOX), the DNA aptamer cluster-based nanoplatform elicits a remarkable and selective inhibition of tumor cell proliferation by much-enhanced targeted delivery. This covalently conjugated branched DNA aptamer cluster-based nanoplatform provides a new strategy for the development of targeted drug delivery.

Nanomaterial based PVA nanocomposite hydrogels for biomedical sensing: Advances toward designing the ideal flexible/wearable nanoprobes

In today's world, the progress of wearable tools has gained increasing momentum. Notably, the demand for stretchable strain sensors has considerably increased owing to various potential and emerging applications like human motion monitoring, soft robotics, prosthetics, and electronic skin. Hydrogels possess excellent biocompatibility, flexibility, and stretchability that render them ideal candidates for flexible/wearable substrates. Among them, enormous efforts were focused on the progress of polyvinyl alcohol (PVA) hydrogels to realize multifunctional wearable sensing through using additives/nanofillers/functional groups to modify the hydrogel network. Herein, this review offers an up-to-date and comprehensive summary of the research progress of PVA hydrogel-based wearable sensors in view of their properties, strain sensory efficiency, and potential applications, followed by specifically highlighting their probes using metallic/non-metallic, liquid metal (LM), 2D materials, bio-nanomaterials, and polymer nanofillers. Indeed, flexible electrodes and strain/pressure sensing performance of designed PVA hydrogels for their effective sensing are described. The representative cases are carefully selected and discussed regarding the construction, merits and demerits, respectively. Finally, the necessity and requirements for future advances of conductive and stretchable hydrogels engaged in the wearable strain sensors are also presented, followed by opportunities and challenges.

Injectable DNA Hydrogel-Based Local Drug Delivery and Immunotherapy

Regulated drug delivery is an important direction in the field of medicine and healthcare research. In recent years, injectable hydrogels with good biocompatibility and biodegradability have attracted extensive attention due to their promising application in controlled drug release. Among them, DNA hydrogel has shown great potentials in local drug delivery and immunotherapy. DNA hydrogel is a three-dimensional network formed by cross-linking of hydrophilic DNA strands with extremely good biocompatibility. Benefiting from the special properties of DNA, including editable sequence and specificity of hybridization reactions, the mechanical properties and functions of DNA hydrogels can be precisely designed according to specific applications. In addition, other functional materials, including peptides, proteins and synthetic organic polymers can be easily integrated with DNA hydrogels, thereby enriching the functions of the hydrogels. In this review, we first summarize the types and synthesis methods of DNA hydrogels, and then review the recent research progress of injectable DNA hydrogels in local drug delivery, especially in immunotherapy. Finally, we discuss the challenges facing DNA hydrogels and future development directions.

DNA Hydrogels in the Perspective of Mechanical Properties

Tailoring the mechanical properties has always been a key to the field of hydrogels in terms of different applications. Particularly, deoxyribonucleic acid (DNA) hydrogels offer an unambiguous way to precisely tune the mechanical properties, largely on account of their programmable sequences, abundant responding toolbox, and various ligation approaches. In this review, DNA hydrogels from the perspective of mechanical properties, from synthetic standpoint to different applications are introduced. The relationship between the structure and their mechanical properties in DNA hydrogels and the methods of regulating the mechanical properties of DNA hydrogels are specifically summarized. Furthermore, several recent applications of DNA hydrogels in relation to their mechanical properties are discussed. Benefiting from the tunability and flexibility, rational design of mechanical properties in DNA hydrogels provided unheralded interest from fundamental science to extensive applications. This article is protected by copyright. All rights reserved.

Formation of non-base-pairing DNA microgels using directed phase transition of amphiphilic monomers

Programmability of DNA sequences enables the formation of synthetic DNA nanostructures and their macromolecular assemblies such as DNA hydrogels. The base pair-level interaction of DNA is a foundational and powerful mechanism to build DNA structures at the nanoscale; however, its temperature sensitivity and weak interaction force remain a barrier for the facile and scalable assembly of DNA structures toward higher-order structures. We conducted this study to provide an alternative, non-base-pairing approach to connect nanoscale DNA units to yield micrometer-sized gels based on the sequential phase transition of amphiphilic unit structures. Strong electrostatic interactions between DNA nanostructures and polyelectrolyte spermines led to the formation of giant phase-separated aggregates of monomer units. Gelation could be initiated by the addition of NaCl, which weakened the electrostatic DNA-spermine interaction while attractive interactions between cholesterols created stable networks by crosslinking DNA monomers. In contrast to the conventional DNA gelation techniques, our system used solid aggregates as a precursor for DNA microgels. Therefore, in situ gelation could be achieved by depositing aggregates on the desired substrate and subsequently initiating a phase transition. Our approach can expand the utility and functionality of DNA hydrogels by using more complex nucleic acid assemblies as unit structures and combining the technique with top-down microfabrication methods.