Mechanical properties of a reversible, DNA-crosslinked polyacrylamide hydrogel

Programming gel automata shapes using DNA instructions

The ability to transform matter between numerous physical states or shapes without wires or external devices is a major challenge for robotics and materials design. Organisms can transform their shapes using biomolecules carrying specific information and localize at sites where transitions occur. Here, we introduce gel automata, which likewise can transform between a large number of prescribed shapes in response to a combinatorial library of biomolecular instructions. Gel automata are centimeter-scale materials consisting of multiple micro-segments. A library of DNA activator sequences can each reversibly grow or shrink different micro-segments by polymerizing or depolymerizing within them. We develop DNA activator designs that maximize the extent of growth and shrinking, and a photolithography process for precisely fabricating gel automata with elaborate segmentation patterns. Guided by simulations of shape change and neural networks that evaluate gel automata designs, we create gel automata that reversibly transform between multiple, wholly distinct shapes: four different letters and every even or every odd numeral. The sequential and repeated metamorphosis of gel automata demonstrates how soft materials and robots can be digitally programmed and reprogrammed with information-bearing chemical signals.

Hydrogels and Aerogels for Versatile Photo-/Electro-Chemical and Energy-Related Applications

The development of photo-/electro-chemical and flexible electronics has stimulated research in catalysis, informatics, biomedicine, energy conversion, and storage applications. Gels (e.g., aerogel, hydrogel) comprise a range of polymers with three-dimensional (3D) network structures, where hydrophilic polyacrylamide, polyvinyl alcohol, copolymers, and hydroxides are the most widely studied for hydrogels, whereas 3D graphene, carbon, organic, and inorganic networks are widely studied for aerogels. Encapsulation of functional species with hydrogel building blocks can modify the optoelectronic, physicochemical, and mechanical properties. In addition, aerogels are a set of nanoporous or microporous 3D networks that bridge the macro- and nano-world. Different architectures modulate properties and have been adopted as a backbone substrate, enriching active sites and surface areas for photo-/electro-chemical energy conversion and storage applications. Fabrication via sol-gel processes, module assembly, and template routes have responded to professionalized features and enhanced performance. This review presents the most studied hydrogel materials, the classification of aerogel materials, and their applications in flexible sensors, batteries, supercapacitors, catalysis, biomedical, thermal insulation, etc.

Substrate stress relaxation regulates neural stem cell fate commitment

Adult neural stem cells (NSCs) reside in the dentate gyrus of the hippocampus, and their capacity to generate neurons and glia plays a role in learning and memory. In addition, neurodegenerative diseases are known to be caused by a loss of neurons and glial cells, resulting in a need to better understand stem cell fate commitment processes. We previously showed that NSC fate commitment toward a neuronal or glial lineage is strongly influenced by extracellular matrix stiffness, a property of elastic materials. However, tissues in vivo are not purely elastic and have varying degrees of viscous character. Relatively little is known about how the viscoelastic properties of the substrate impact NSC fate commitment. Here, we introduce a polyacrylamide-based cell culture platform that incorporates mismatched DNA oligonucleotide-based cross-links as well as covalent cross-links. This platform allows for tunable viscous stress relaxation properties via variation in the number of mismatched base pairs. We find that NSCs exhibit increased astrocytic differentiation as the degree of stress relaxation is increased. Furthermore, culturing NSCs on increasingly stress-relaxing substrates impacts cytoskeletal dynamics by decreasing intracellular actin flow rates and stimulating cyclic activation of the mechanosensitive protein RhoA. Additionally, inhibition of motor-clutch model components such as myosin II and focal adhesion kinase partially or completely reverts cells to lineage distributions observed on elastic substrates. Collectively, our results introduce a unique system for controlling matrix stress relaxation properties and offer insight into how NSCs integrate viscoelastic cues to direct fate commitment.

Actuation of Soft Thermoresponsive Hydrogels Mechanically Stimulates Osteogenesis in Human Mesenchymal Stem Cells without Biochemical Factors

Mesenchymal stem cells (MSCs) have the potential to differentiate into multiple lineages and can be harvested relatively easily from adults, making them a promising cell source for regenerative therapies. While it is well-known how to consistently differentiate MSCs into adipose, chondrogenic, and osteogenic lineages by treatment with biochemical factors, the number of studies exploring how to achieve this with mechanical signals is limited. A relatively unexplored area is the effect of cyclic forces on the MSC differentiation. Recently, our group developed a thermoresponsive N-ethyl acrylamide/N-isopropylacrylamide (NIPAM/NEAM) hydrogel supplemented with gold nanorods that are able to convert near-infrared light into heat. Using light pulses allows for local hydrogel collapse and swelling with physiologically relevant force and frequency. In this study, MSCs are cultured on this hydrogel system with a patterned surface and exposed to intermittent or continuous actuation of the hydrogel for 3 days to study the effect of actuation on MSC differentiation. First, cells are harvested from the bone marrow of three donors and tested for their MSC phenotype, meeting the following criteria: the harvested cells are adherent and demonstrate a fibroblast-like bipolar morphology. They lack the expression of CD34 and CD45 but do express CD73, CD90, and CD105. Additionally, their differentiation potential into adipogenic, chondrogenic, and osteogenic lineages is validated by the addition of standardized differentiation media. Next, MSCs are exposed to intermittent or continuous actuation, which leads to a significantly enhanced cell spreading compared to nonactuated cells. Moreover, actuation results in nuclear translocation of Runt-related transcription factor 2 and the Yes-associated protein. Together, these results indicate that cyclic mechanical stimulation on a soft, ridged substrate modulates the MSC fate commitment in the direction of osteogenesis.

Dynamic matrices with DNA-encoded viscoelasticity for cell and organoid culture

Three-dimensional cell and organoid cultures rely on the mechanical support of viscoelastic matrices. However, commonly used matrix materials lack control over key cell-instructive properties. Here we report on fully synthetic hydrogels based on DNA libraries that self-assemble with ultrahigh-molecular-weight polymers, forming a dynamic DNA-crosslinked matrix (DyNAtrix). DyNAtrix enables computationally predictable and systematic control over its viscoelasticity, thermodynamic and kinetic parameters by changing DNA sequence information. Adjustable heat activation allows homogeneous embedding of mammalian cells. Intriguingly, stress-relaxation times can be tuned over four orders of magnitude, recapitulating mechanical characteristics of living tissues. DyNAtrix is self-healing, printable, exhibits high stability, cyto- and haemocompatibility, and controllable degradation. DyNAtrix-based cultures of human mesenchymal stromal cells, pluripotent stem cells, canine kidney cysts and human trophoblast organoids show high viability, proliferation and morphogenesis. DyNAtrix thus represents a programmable and versatile precision matrix for advanced approaches to biomechanics, biophysics and tissue engineering.

Multiscale Biofabrication: Integrating Additive Manufacturing with DNA-Programmable Self-Assembly

Structure and hierarchical organization are crucial elements of biological systems and are likely required when engineering synthetic biomaterials with life-like behavior. In this context, additive manufacturing techniques like bioprinting have become increasingly popular. However, 3D bioprinting, as well as other additive manufacturing techniques, show limited resolution, making it difficult to yield structures on the sub-cellular level. To be able to form macroscopic synthetic biological objects with structuring on this level, manufacturing techniques have to be used in conjunction with biomolecular nanotechnology. Here, a short overview of both topics and a survey of recent advances to combine additive manufacturing with microfabrication techniques and bottom-up self-assembly involving DNA, are given.

Nanocomposite Hydrogels as Functional Extracellular Matrices

Over recent years, nano-engineered materials have become an important component of artificial extracellular matrices. On one hand, these materials enable static enhancement of the bulk properties of cell scaffolds, for instance, they can alter mechanical properties or electrical conductivity, in order to better mimic the in vivo cell environment. Yet, many nanomaterials also exhibit dynamic, remotely tunable optical, electrical, magnetic, or acoustic properties, and therefore, can be used to non-invasively deliver localized, dynamic stimuli to cells cultured in artificial ECMs in three dimensions. Vice versa, the same, functional nanomaterials, can also report changing environmental conditions-whether or not, as a result of a dynamically applied stimulus-and as such provide means for wireless, long-term monitoring of the cell status inside the culture. In this review article, we present an overview of the technological advances regarding the incorporation of functional nanomaterials in artificial extracellular matrices, highlighting both passive and dynamically tunable nano-engineered components.

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.

Distant migration of gel filler: imaging findings following breast augmentation

Recently, many attempts have been made to use injectable materials in the subcutaneous fat layer anywhere in the body, including the breast and face, for cosmetic purposes. A 56-year-old woman presented with multiple palpable lumps without tenderness or skin color changes on the anterior and lateral chest and the abdominal walls. Magnetic resonance imaging showed fluid-like collections without surrounding soft tissue inflammatory changes in the chest wall, abdominal wall, and deeper within the abdomen. The lesions penetrated the peritoneum and were observed adjacent to the liver dome. Ultrasonography also showed hypoechogenicity suggestive of fluid collection in the left axilla and trunk. The differential diagnosis based on radiologic findings included parasite manifestation, non-specific inflammatory conditions, and chronic granulomatous infections such as tuberculosis or non-tuberculous mycobacterial infections. However, these conditions are usually accompanied by changes in the adjacent subcutaneous fat layers, but our patient did not show any other abnormalities in the adjacent soft tissue. After biopsy and aspiration analysis, the patient was found to have a history of filler injection for breast augmentation approximately 17 years prior. It is often difficult to make a differential diagnosis without detailed knowledge of the patient's medical history. Here we describe a rare case of distant migration of the filler to the axilla, chest wall, abdominal wall, and peritoneum following breast augmentation with filler injection. Knowledge of the radiologic characteristics and migration patterns of gel fillers and their related complications is useful for making an accurate diagnosis.

Engineering DNA-based synthetic condensates with programmable material properties, compositions, and functionalities

Biomolecular condensates participate in diverse cellular processes, ranging from gene regulation to stress survival. Bottom-up engineering of synthetic condensates advances our understanding of the organizing principle of condensates. It also enables the synthesis of artificial systems with novel functions. However, building synthetic condensates with a predictable organization and function remains challenging. Here, we use DNA as a building block to create synthetic condensates that are assembled through phase separation. The programmability of intermolecular interactions between DNA molecules enables the control over various condensate properties including assembly, composition, and function. Similar to the way intracellular condensates are organized, DNA clients are selectively partitioned into cognate condensates. We demonstrate that the synthetic condensates can accelerate DNA strand displacement reactions and logic gate operation by concentrating specific reaction components. We envision that the DNA-based condensates could help the realization of the high-order functions required to build more life-like artificial systems.

Functionalized-DNA nanostructures as potential targeted drug delivery systems for cancer therapy

Seeman's pioneer idea has led to the foundation of DNA nanostructures, resulting in a remarkable advancement in DNA nanotechnology. Over the last few decades, remarkable advances in drug delivery techniques have resulted in the self-assembly of DNA for encapsulating candidate drug molecules. The nuclear targeting capability of DNA nanostructures is lies within their high spatial addressability and tremendous potential for active targeting. However, effective programming and assembling those DNA molecules remains a challenge, making the path to DNA nanostructures for real-world applications difficult. Because of their small size, most nanostructures are self-capable of infiltrating into the tumor cellular environment. Furthermore, to enable controlled and site-specific delivery of encapsulated drug molecules, DNA nanostructures are functionalized with special moieties that allow them to bind specific targets and release cargo only at targeted sites rather than non-specific sites, resulting in the prevention/limitation of cellular toxicity. In light of this, the current review seeks to shed light on the versatility of the DNA molecule as a targeting and encapsulating moiety for active drugs in order to achieve controlled and specific drug release with spatial and temporal precision. Furthermore, this review focused on the challenges associated with the construction of DNA nanostructures as well as the most recent advances in the functionalization of DNA nanostructures using various materials for controlled and targeted delivery of medications for cancer therapy.

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.

Extracellular Matrix Stiffness in Lung Health and Disease

The extracellular matrix (ECM) provides structural support and imparts a wide variety of environmental cues to cells. In the past decade, a growing body of work revealed that the mechanical properties of the ECM, commonly known as matrix stiffness, regulate the fundamental cellular processes of the lung. There is growing appreciation that mechanical interplays between cells and associated ECM are essential to maintain lung homeostasis. Dysregulation of ECM-derived mechanical signaling via altered mechanosensing and mechanotransduction pathways is associated with many common lung diseases. Matrix stiffening is a hallmark of lung fibrosis. The stiffened ECM is not merely a sequelae of lung fibrosis but can actively drive the progression of fibrotic lung disease. In this article, we provide a comprehensive view on the role of matrix stiffness in lung health and disease. We begin by summarizing the effects of matrix stiffness on the function and behavior of various lung cell types and on regulation of biomolecule activity and key physiological processes, including host immune response and cellular metabolism. We discuss the potential mechanisms by which cells probe matrix stiffness and convert mechanical signals to regulate gene expression. We highlight the factors that govern matrix stiffness and outline the role of matrix stiffness in lung development and the pathogenesis of pulmonary fibrosis, pulmonary hypertension, asthma, chronic obstructive pulmonary disease (COPD), and lung cancer. We envision targeting of deleterious matrix mechanical cues for treatment of fibrotic lung disease. Advances in technologies for matrix stiffness measurements and design of stiffness-tunable matrix substrates are also explored. © 2022 American Physiological Society. Compr Physiol 12:3523-3558, 2022.

Cation-Responsive and Photocleavable Hydrogels from Noncanonical Amphiphilic DNA Nanostructures

Thanks to its biocompatibility, versatility, and programmable interactions, DNA has been proposed as a building block for functional, stimuli-responsive frameworks with applications in biosensing, tissue engineering, and drug delivery. Of particular importance for in vivo applications is the possibility of making such nanomaterials responsive to physiological stimuli. Here, we demonstrate how combining noncanonical DNA G-quadruplex (G4) structures with amphiphilic DNA constructs yields nanostructures, which we termed "Quad-Stars", capable of assembling into responsive hydrogel particles via a straightforward, enzyme-free, one-pot reaction. The embedded G4 structures allow one to trigger and control the assembly/disassembly in a reversible fashion by adding or removing K+ ions. Furthermore, the hydrogel aggregates can be photo-disassembled upon near-UV irradiation in the presence of a porphyrin photosensitizer. The combined reversibility of assembly, responsiveness, and cargo-loading capabilities of the hydrophobic moieties make Quad-Stars a promising candidate for biosensors and responsive drug delivery carriers.

Modulation of hydrogel stiffness by external stimuli: soft materials for mechanotransduction studies

Mechanotransduction is an important process in determining cell survival, proliferation, migration and differentiation. The extracellular matrix (ECM) is the component of natural tissue that provides structural support and biochemical signals to adhering cells. The ECM is dynamic and undergoes physical and biochemical changes in response to various stimuli and there is an interest in understanding the effect of dynamic changes in stiffness on cell behaviour and fate. Therefore, stimuli-responsive hydrogels have been developed to mimic the cells' microenvironment in a controlled fashion. Herein, we review strategies for dynamic modulation of stiffness using various stimuli, such as light, temperature and pH. Special emphasis is placed on conducting polymer (CP) hydrogels and their fabrication procedures. We believe that the redox properties of CPs and hydrogels' biological properties make CPs hydrogels a promising substrate to investigate the effect of dynamic stiffness changes and mechanical actuation on cell fate in future studies.

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

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

Cascaded pattern formation in hydrogel medium using the polymerisation approach

Reaction-diffusion systems are one of the models of the formation process with various patterns found in nature. Inspired by natural pattern formation, several methods for designing artificial chemical reaction-diffusion systems have been proposed. DNA is a suitable building block to build such artificial systems owing to its programmability. Previously, we reported a line pattern formed due to the reaction and diffusion of synthetic DNA; however, the width of the line was too wide to be used for further applications such as parallel and multi-stage pattern formations. Here, we propose a novel method to programme a reaction-diffusion system in a hydrogel medium to realise a sharp line capable of forming superimposed and cascaded patterns. The mechanism of this system utilises a two-segment polymerisation of DNA caused by hybridisation. To superimpose the system, we designed orthogonal DNA sequences that formed two lines in different locations on the hydrogel. Additionally, we designed a reaction to release DNA and form a cascade pattern, in which the third line appears between the two lines. To explain the mechanism of our system, we modelled the system as partial differential equations, whose simulation results agreed well with the experimental data. Our method to fabricate cascaded patterns may inspire combinations of DNA-based technologies and expand the applications of artificial reaction-diffusion systems.

Stimuli Responsive, Programmable DNA Nanodevices for Biomedical Applications

Of the multiple areas of applications of DNA nanotechnology, stimuli-responsive nanodevices have emerged as an elite branch of research owing to the advantages of molecular programmability of DNA structures and stimuli-responsiveness of motifs and DNA itself. These classes of devices present multiples areas to explore for basic and applied science using dynamic DNA nanotechnology. Herein, we take the stake in the recent progress of this fast-growing sub-area of DNA nanotechnology. We discuss different stimuli, motifs, scaffolds, and mechanisms of stimuli-responsive behaviours of DNA nanodevices with appropriate examples. Similarly, we present a multitude of biological applications that have been explored using DNA nanodevices, such as biosensing, in vivo pH-mapping, drug delivery, and therapy. We conclude by discussing the challenges and opportunities as well as future prospects of this emerging research area within DNA nanotechnology.

Aptamer-functionalized hydrogels: An emerging class of biomaterials for protein delivery, cell capture, regenerative medicine, and molecular biosensing

Molecular recognition is essential to the development of biomaterials. Aptamers are a unique class of synthetic ligands interacting with not only their target molecules with high affinities and specificities but also their complementary sequences with high fidelity. Thus, aptamers have recently attracted significant attention in the development of an emerging class of biomaterials, that is, aptamer-functionalized hydrogels. In this review, we introduce the methods of incorporating aptamers into hydrogels as pendant motifs or crosslinkers. We further introduce the functions of these hydrogels in recognizing proteins, cells, and analytes through four applications including protein delivery, cell capture, regenerative medicine, and molecular biosensing. Notably, as aptamer-functionalized hydrogels have the characteristics of both aptamers and hydrogels, their potential applications are broad and beyond the scope of this review. This article is categorized under: Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Implantable Materials and Surgical Technologies > Nanomaterials and Implants Therapeutic Approaches and Drug Discovery > Emerging Technologies.

(Macro)molecular self-assembly for hydrogel drug delivery

Hydrogels prepared via self-assembly offer scalable and tunable platforms for drug delivery applications. Molecular-scale self-assembly leverages an interplay of attractive and repulsive forces; drugs and other active molecules can be incorporated into such materials by partitioning in hydrophobic domains, affinity-mediated binding, or covalent integration. Peptides have been widely used as building blocks for self-assembly due to facile synthesis, ease of modification with bioactive molecules, and precise molecular-scale control over material properties through tunable interactions. Additional opportunities are manifest in stimuli-responsive self-assembly for more precise drug action. Hydrogels can likewise be fabricated from macromolecular self-assembly, with both synthetic polymers and biopolymers used to prepare materials with controlled mechanical properties and tunable drug release. These include clinical approaches for solubilization and delivery of hydrophobic drugs. To further enhance mechanical properties of hydrogels prepared through self-assembly, recent work has integrated self-assembly motifs with polymeric networks. For example, double-network hydrogels capture the beneficial properties of both self-assembled and covalent networks. The expanding ability to fabricate complex and precise materials, coupled with an improved understanding of biology, will lead to new classes of hydrogels specifically tailored for drug delivery applications.

Reversible Control of Gelatin Hydrogel Stiffness by Using DNA Crosslinkers*

Biomaterials with dynamically tunable properties are critical for a range of applications in regenerative medicine and basic biology. In this work, we show the reversible control of gelatin methacrylate (GelMA) hydrogel stiffness through the use of DNA crosslinkers. We replaced some of the inter-GelMA crosslinks with double-stranded DNA, allowing for their removal through toehold-mediated strand displacement. The crosslinks could be restored by adding fresh dsDNA with complementary handles to those on the hydrogel. The elastic modulus (G') of the hydrogels could be tuned between 500 and 1000 Pa, reversibly, over two cycles without degradation of performance. By functionalizing the gels with a second DNA strand, it was possible to control the crosslink density and a model ligand in an orthogonal fashion with two different displacement strands. Our results demonstrate the potential for DNA to reversibly control both stiffness and ligand presentation in a protein-based hydrogel, and will be useful for teasing apart the spatiotemporal behavior of encapsulated cells.

Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials

DNA hydrogels are self-assembled biomaterials that rely on Watson–Crick base pairing to form large-scale programmable three-dimensional networks of nanostructured DNA components. The unique mechanical and biochemical properties of DNA, along with its biocompatibility, make it a suitable material for the assembly of hydrogels with controllable mechanical properties and composition that could be used in several biomedical applications, including the design of novel multifunctional biomaterials. Numerous studies that have recently emerged, demonstrate the assembly of functional DNA hydrogels that are responsive to stimuli such as pH, light, temperature, biomolecules, and programmable strand-displacement reaction cascades. Recent studies have investigated the role of different factors such as linker flexibility, functionality, and chemical crosslinking on the macroscale mechanical properties of DNA hydrogels. In this review, we present the existing data and methods regarding the mechanical design of pure DNA hydrogels and hybrid DNA hydrogels, and their use as hydrogels for cell culture. The aim of this review is to facilitate further study and development of DNA hydrogels towards utilizing their full potential as multifeatured and highly programmable biomaterials with controlled mechanical properties.

DNA hydrogel-based gene editing and drug delivery systems

Deoxyribonucleic acid (DNA) is a promising synthesizer for precisely constructing almost arbitrary geometry in two and three dimensions. Among various DNA-based soft materials, DNA hydrogels are comprised of hydrophilic polymeric networks of crosslinked DNA chains. For their properties of biocompatibility, porosity, sequence programmability and tunable multifunctionality, DNA hydrogels have been widely studied in bioanalysis and biomedicine. In this review, recent developments in DNA hydrogels and their applications in drug delivery systems are highlighted. First, physical and chemical crosslinking methods for constructing DNA hydrogels are introduced. Subsequently, responses of DNA hydrogels to nonbiological and biological stimuli are described. Finally, DNA hydrogel-based delivery platforms for different types of drugs are detailed. With the emergence of gene therapy, this review also gives future prospects for combining DNA hydrogels with the gene editing toolbox.

Rapid immunostaining method for three-dimensional volume imaging of biological tissues by magnetic force-induced focusing of the electric field

Recent surges in tissue clearing technology have greatly advanced 3-dimensional (3D) volume imaging. Cleared tissues need to be stained with fluorescence probes for imaging but the current staining methods are too laborious and inefficient for thick 3D samples, which impedes the broad application of clearing technology. To overcome these limitations, we developed an advanced staining platform named EFIC in which a magnetic force focuses the electric field by bending it onto the sample. Such that EFIC applies a significantly lower electric field to maintain nanoscale structural integrity while effectively drives staining probes into pre-cleared 3D samples. We found that EFIC achieved a rapid and uniform staining of various proteins and vascular networks of the brain as well as other organs over the entire depth of imaging. EFIC stained tau deposits and the vascular structure in the post-mortem human brain of Alzheimer's disease and intracerebral hemorrhage, respectively, enabling quantitative analysis. The effectiveness of EFIC was further extended by the successful staining of various targets in non-cleared 3D brain samples. Together, EFIC represents a versatile and reliable staining platform for rapidly analyzing 3D molecular signatures and can be applied to sectioning-free 3D histopathology for diagnostic purposes.

Advanced polymeric nanotechnology to augment therapeutic delivery and disease diagnosis

Therapeutic and diagnostic payloads are usually associated with properties that compromise their efficacy, such as poor aqueous solubility, short half-life, low bioavailability, nonspecific accumulation and diverse side effects. Nanotechnological solutions have emerged to circumvent some of these drawbacks, augmenting therapeutic and/or diagnostic outcomes. Nanotechnology has benefited from the rise in polymer science research for the development of novel nanosystems for therapeutic and diagnostic purposes. Polymers are a widely used class of biomaterials, with a considerable number of regulatory approvals for application in clinics. In addition to their versatility in production and functionalization, several synthetic and natural polymers demonstrate biocompatible properties that dictate their successful biological performance. This article highlights the physicochemical characteristics of a variety of natural and synthetic biocompatible polymers, as well as their role in the manufacture of nanotechnology-based systems, state-of-art applications in disease treatment and diagnosis, and current challenges in finding a way to clinics.

Breast reconstruction after complications following breast augmentation with massive filler injections

INTRODUCTION

Breast filler injections are less commonly used due to their associated complications, such as pain and foreign body reactions. Yet, these fillers are often administered illegally, resulting in aesthetic or life-threatening complications. These are treated by removing the foreign material, and the breasts are reconstructed using silicone implants or autologous tissue/fat injection.

PATIENT CONCERNS

Case 1. A 45-year-old woman with polyacrylamide gel injections in both breasts visited our clinic for breast pain and tenderness. Grade I ptosis was observed in each breast, without skin necrosis and discoloration. Case 2. A 51-year-old woman, with unknown breast filler injections, visited our clinic for painful masses. Intraoperatively, massive amounts of foreign material had severely infiltrated the nearby tissues; thus, an immediate breast reconstruction could not be performed. Three months later, severe deformities including shrinkage and irregular breast skin surfaces were observed.

DIAGNOSIS

Case 1. Multiple cystic lesions, fluid collection in the retromammary spaces, and diffuse infiltration were observed on mammography, computed tomography, and ultrasonography. Case 2. Multiple cystic lesions, calcified areas, and diffuse infiltrations in the axillae and retromammary spaces were observed on mammography, computed tomography, and ultrasonography.

INTERVENTIONS

Case 1. The foreign material was removed and the breasts were reconstructed using silicone implants into subpectoral pocket with acellular dermal matrices (Alloderm, Lipocell Corporation). Case 2. A delayed reconstruction was undertaken using silicone implants covered by latissimus dorsi muscle flaps, 3 months after the foreign material removal.

OUTCOMES

Case 1. The foreign material was removed and there were no complications such as foreign body reaction, capsular contracture. Ptosis was corrected and both breasts were symmetric with proper projection. Case 2. Residual foreign material was removed and there were no complications such capsular contracture, implant malposition.

CONCLUSION

Massive injections of foreign materials into the breast can cause severe infiltration and associated foreign body reactions. By a near-complete removal of the foreign materials and breast reconstruction using silicone implants, we achieved satisfactory results, without complications such as wound disruption, capsular contracture, and implant malposition.

Stimuli-Responsive Biomaterials for Vaccines and Immunotherapeutic Applications

The immune system is the key target for vaccines and immunotherapeutic approaches aimed at blunting infectious diseases, cancer, autoimmunity, and implant rejection. However, systemwide immunomodulation is undesirable due to the severe side effects that typically accompany such strategies. In order to circumvent these undesired, harmful effects, scientists have turned to tailorable biomaterials that can achieve localized, potent release of immune-modulating agents. Specifically, "stimuli-responsive" biomaterials hold a strong promise for delivery of immunotherapeutic agents to the disease site or disease-relevant tissues with high spatial and temporal accuracy. This review provides an overview of stimuli-responsive biomaterials used for targeted immunomodulation. Stimuli-responsive or "environmentally responsive" materials are customized to specifically react to changes in pH, temperature, enzymes, redox environment, photo-stimulation, molecule-binding, magnetic fields, ultrasound-stimulation, and electric fields. Moreover, the latest generation of this class of materials incorporates elements that allow for response to multiple stimuli. These developments, and other stimuli-responsive materials that are on the horizon, are discussed in the context of controlling immune responses.

Programming Diffusion and Localization of DNA Signals in 3D-Printed DNA-Functionalized Hydrogels

Additive manufacturing enables the generation of 3D structures with predefined shapes from a wide range of printable materials. However, most of the materials employed so far are static and do not provide any intrinsic programmability or pattern-forming capability. Here, a low-cost 3D bioprinting approach is developed, which is based on a commercially available extrusion printer that utilizes a DNA-functionalized bioink, which allows to combine concepts developed in dynamic DNA nanotechnology with additive patterning techniques. Hybridization between diffusing DNA signal strands and immobilized anchor strands can be used to tune diffusion properties of the signals, or to localize DNA strands within the gel in a sequence-programmable manner. Furthermore, strand displacement mechanisms can be used to direct simple pattern formation processes and to control the availability of DNA sequences at specific locations. To support printing of DNA-functionalized gel voxels at arbitrary positions, an open source python script that generates machine-readable code (GCODE) from simple vector graphics input is developed.

Controlling Matter at the Molecular Scale with DNA Circuits

In recent years, a diverse set of mechanisms have been developed that allow DNA strands with specific sequences to sense information in their environment and to control material assembly, disassembly, and reconfiguration. These sequences could serve as the inputs and outputs for DNA computing circuits, enabling DNA circuits to act as chemical information processors to program complex behavior in chemical and material systems. This review describes processes that can be sensed and controlled within such a paradigm. Specifically, there are interfaces that can release strands of DNA in response to chemical signals, wavelengths of light, pH, or electrical signals, as well as DNA strands that can direct the self-assembly and dynamic reconfiguration of DNA nanostructures, regulate particle assemblies, control encapsulation, and manipulate materials including DNA crystals, hydrogels, and vesicles. These interfaces have the potential to enable chemical circuits to exert algorithmic control over responsive materials, which may ultimately lead to the development of materials that grow, heal, and interact dynamically with their environments.

Viscoelastic and Thermoreversible Networks Crosslinked by Non-covalent Interactions Between "Clickable" Nucleic Acids Oligomers and DNA

An approach to efficient and scalable production of oligonucleotide-based gel networks is presented. Specifically, a new class of xenonucleic acid (XNA) synthesized through a scalable and efficient thiol-ene polymerization mechanism, "Clickable" Nucleic Acids (CNAs), were conjugated to a multifunctional poly(ethylene glycol), PEG. In the presence of complementary single stranded DNA (ssDNA), the macromolecular conjugate assembled into a crosslinked 3D gel capable of achieving storage moduli on the order of 1 kPa. Binding studies between the PEG-CNA macromolecule and complementary ssDNA indicate that crosslinking is due to the CNA/DNA interaction. Gel formation was specific to the base sequence and length of the ssDNA crosslinker. The gels were fully thermoreversible, completely melting at temperatures above 60°C and re-forming upon cooling over multiple cycles and with no apparent hysteresis. Shear stress relaxation experiments revealed that relaxation dynamics are dependent on crosslinker length, which is hypothesized to be an effect of the polydisperse CNA chains. Arrhenius analysis of characteristic relaxation times was only possible for shorter crosslinker lengths, and the activation energy for these gels was determined to be 110 ± 20 kJ/mol. Overall, the present work demonstrates that CNA is capable of participating in stimuli-responsive interactions that would be expected from XNAs, and that these interactions support 3D gels that have potential uses in biological and materials science applications.

Programmable patterns in a DNA-based reaction-diffusion system

Biology offers compelling proof that macroscopic "living materials" can emerge from reactions between diffusing biomolecules. Here, we show that molecular self-organization could be a similarly powerful approach for engineering functional synthetic materials. We introduce a programmable DNA embedded hydrogel that produces tunable patterns at the centimeter length scale. We generate these patterns by implementing chemical reaction networks through synthetic DNA complexes, embedding the complexes in the hydrogel, and triggering with locally applied input DNA strands. We first demonstrate ring pattern formation around a circular input cavity and show that the ring width and intensity can be predictably tuned. Then, we create patterns of increasing complexity, including concentric rings and non-isotropic patterns. Finally, we show "destructive" and "constructive" interference patterns, by combining several ring-forming modules in the gel and triggering them from multiple sources. We further show that computer simulations based on the reaction-diffusion model can predict and inform the programming of target patterns.

New Developments in Medical Applications of Hybrid Hydrogels Containing Natural Polymers

New trends in biomedical applications of the hybrid polymeric hydrogels, obtained by combining natural polymers with synthetic ones, have been reviewed. Homopolysaccharides, heteropolysaccharides, as well as polypeptides, proteins and nucleic acids, are presented from the point of view of their ability to form hydrogels with synthetic polymers, the preparation procedures for polymeric organic hybrid hydrogels, general physico-chemical properties and main biomedical applications (i.e., tissue engineering, wound dressing, drug delivery, etc.).

Tailoring DNA Self-assembly to Build Hydrogels

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

Photolithographic shape control of DNA hydrogels by photo-activated self-assembly of DNA nanostructures

We report a photolithographic method for the shape control of DNA hydrogels based on photo-activated self-assembly of Y-shaped DNA nanostructures (Y-motifs). To date, various methods to control the shape of DNA hydrogels have been developed to enhance the functions of the DNA hydrogel system. However, photolithographic production of shape-controlled DNA hydrogels formed through the self-assembly of DNA nanostructures without the use of radical polymerizations has never been demonstrated, although such a method is expected to be applied for the shape-control of DNA hydrogels encapsulating sensitive biomolecules, such as proteins. In this study, we used a photo-activated linker to initiate the self-assembly of Y-motifs, where the cross-linker DNA was at first inactive but was activated after UV light irradiation, resulting in the formation of shape-controlled DNA hydrogels only at the UV-exposed area produced by photomasks. We believe that this method will be applied for the construction of biohybrid machines, such as molecular robots and artificial cells that contain intelligent biomolecular devices, such as molecular sensors and computers.

Programmable CRISPR-responsive smart materials

Stimuli-responsive materials activated by biological signals play an increasingly important role in biotechnology applications. We exploit the programmability of CRISPR-associated nucleases to actuate hydrogels containing DNA as a structural element or as an anchor for pendant groups. After activation by guide RNA-defined inputs, Cas12a cleaves DNA in the gels, thereby converting biological information into changes in material properties. We report four applications: (i) branched poly(ethylene glycol) hydrogels releasing DNA-anchored compounds, (ii) degradable polyacrylamide-DNA hydrogels encapsulating nanoparticles and live cells, (iii) conductive carbon-black-DNA hydrogels acting as degradable electrical fuses, and (iv) a polyacrylamide-DNA hydrogel operating as a fluidic valve with an electrical readout for remote signaling. These materials allow for a range of in vitro applications in tissue engineering, bioelectronics, and diagnostics.

An Optical Urate Biosensor Based on Urate Oxidase and Long-Lifetime Metalloporphyrins

Gout is a condition that affects over 8 million Americans. This condition is characterized by severe pain, and in more advanced cases, bone erosion and joint destruction. This study explores the fabrication and characterization of an optical, enzymatic urate biosensor for gout management, and the optimization of the biosensor response through the tuning of hydrogel matrix properties. Sensors were fabricated through the co-immobilization of oxygen-quenched phosphorescent probes with an oxidoreductase within a biocompatible copolymer hydrogel matrix. Characterization of the spectral properties and hydrogel swelling was conducted, as well as evaluation of the response sensitivity and long-term stability of the urate biosensor. The findings indicate that increased acrylamide concentration improved the biosensor response by yielding an increased sensitivity and reduced lower limit of detection. However, the repeatability and stability tests highlighted some possible areas of improvement, with a consistent response drift observed during repeatability testing and a reduction in response seen after long-term storage tests. Overall, this study demonstrates the potential of an on-demand, patient-friendly gout management tool, while paving the way for a future multi-analyte biosensor based on this sensing platform.

From design to applications of stimuli-responsive hydrogel strain sensors

Stimuli-responsive hydrogel strain sensors that synergize the advantages of both hydrogel and smart functional materials have attracted increasing interest from material design to emerging applications in health monitors and human–machine interfaces.

Functional DNA-based hydrogel intelligent materials for biomedical applications

Multifunctional intelligent DNA hydrogels have been reviewed for many biomedical applications.

Design strategies for programmable oligonucleotide nanotherapeutics

A systematic review on how to design different programmable nanotherapeutics using oligonucleotides as building blocks or as surface and matrix modifiers for controlled and targeted delivery of various therapeutic agents in presented.

Digital Maskless Photolithographic Patterning of DNA-Functionalized Poly(ethylene glycol) Diacrylate Hydrogels with Visible Light Enabling Photodirected Release of Oligonucleotides

Soft biomaterials possessing structural hierarchy have growing applications in lab-on-chip devices, artificial tissues, and micromechanical and chemomechanical systems. The ability to integrate sets of biomolecules, specifically DNA, within hydrogel substrates at precise locations could offer the potential to form and modulate complex biochemical processes with DNA-based molecular switches in such materials and provide a means of creating dynamic spatial patterns, thus enabling spatiotemporal control of a wide array of reaction-diffusion phenomena prevalent in biological systems. Here we develop a means of photopatterning two-dimensional DNA-functionalized poly(ethylene glycol) diacrylate (PEGDA) hydrogel architectures with an aim toward these applications. While PEGDA photopatterning methods are well-established for the fabrication of hydrogels, including those containing oligonucleotides, the photoinitiators typically used have significant crosstalk with many UV-photoswitchable chemistries including nitrobenzyl derivatives. We demonstrate the digital photopatterning of PEGDA-co-DNA hydrogels using a blue light-absorbing (470 nm peak) photoinitiator system and macromer comprised of camphorquinone, triethanolamine, and poly(ethylene glycol) diacrylate (M_n = 575) that minimizes absorption in the UV-A wavelength range commonly used to trigger photoswitchable chemistries. We demonstrate this method using digital maskless photolithography within microfluidic devices that allows for the reliable construction of multidomain structures. The method achieves feature resolutions as small as 25 μm, and the resulting materials allow for lateral isotropic bulk diffusion of short single-stranded (ss) DNA oligonucleotides. Finally, we show how the use of these photoinitiators allows for orthogonal control of photopolymerization and UV-photoscission of acrylate-modified DNA containing a 1-(2-nitrophenyl) ethyl spacer to selectively cleave DNA from regions of a PEGDA substrate.

Cellular responses to beating hydrogels to investigate mechanotransduction

Cells feel the forces exerted on them by the surrounding extracellular matrix (ECM) environment and respond to them. While many cell fate processes are dictated by these forces, which are highly synchronized in space and time, abnormal force transduction is implicated in the progression of many diseases (muscular dystrophy, cancer). However, material platforms that enable transient, cyclic forces in vitro to recreate an in vivo-like scenario remain a challenge. Here, we report a hydrogel system that rapidly beats (actuates) with spatio-temporal control using a near infra-red light trigger. Small, user-defined mechanical forces (~nN) are exerted on cells growing on the hydrogel surface at frequencies up to 10 Hz, revealing insights into the effect of actuation on cell migration and the kinetics of reversible nuclear translocation of the mechanosensor protein myocardin related transcription factor A, depending on the actuation amplitude, duration and frequency.

From DNA Nanotechnology to Material Systems Engineering

In the past 35 years, DNA nanotechnology has grown to a highly innovative and vibrant field of research at the interface of chemistry, materials science, biotechnology, and nanotechnology. Herein, a short summary of the state of research in various subdisciplines of DNA nanotechnology, ranging from pure "structural DNA nanotechnology" over protein-DNA assemblies, nanoparticle-based DNA materials, and DNA polymers to DNA surface technology is given. The survey shows that these subdisciplines are growing ever closer together and suggests that this integration is essential in order to initiate the next phase of development. With the increasing implementation of machine-based approaches in microfluidics, robotics, and data-driven science, DNA-material systems will emerge that could be suitable for applications in sensor technology, photonics, as interfaces between technical systems and living organisms, or for biomimetic fabrication processes.

Thermoresponsive Stiffness Softening of Hierarchically Porous Nanohybrid Membranes Promotes Niches for Mesenchymal Stem Cell Differentiation

Despite the attention given to the development of novel responsive implants for regenerative medicine applications, the lack of integration with the surrounding tissues and the mismatch with the dynamic mechanobiological nature of native soft tissues remain in the current products. Hierarchical porous membranes based on a poly (urea-urethane) (PUU) nanohybrid have been fabricated by thermally induced phase separation (TIPS) of the polymer solution at different temperatures. Thermoresponsive stiffness softening of the membranes through phase transition from the semicrystalline phase to rubber phase and reverse self-assembly of the quasi-random nanophase structure is characterized at body temperature near the melting point of the crystalline domains of soft segments. The effects of the porous structure and stiffness softening on proliferation and differentiation of human bone-marrow mesenchymal stem cells (hBM-MSCs) are investigated. The results of immunohistochemistry, histological, ELISA, and qPCR demonstrate that hBM-MSCs maintain their lineage commitment during stiffness relaxation; chondrogenic differentiation is favored on the soft and porous scaffold, while osteogenic differentiation is more prominent on the initial stiff one. Stiffness relaxation stimulates more osteogenic activity than chondrogenesis, the latter being more influenced by the synergetic coupling effect of softness and porosity.

Advances in immunotherapy delivery from implantable and injectable biomaterials

Macroscale biomaterials, such as preformed implantable scaffolds and injectable soft materials, possess powerful synergies with anti-cancer immunotherapies. Immunotherapies on their own typically have poor delivery properties, and often require repeated high-dose injections that result in serious off-tumor effects and/or limited efficacy. Rationally designed biomaterials allow for discrete localization and controlled release of immunotherapeutic agents, and have been shown in a large number of applications to improve outcomes in the treatment of cancers via immunotherapy. Among various strategies, macroscale biomaterial delivery systems can take the form of robust tablet-like scaffolds that are surgically implanted into a tumor resection site, releasing programmed immune cells or immunoregulatory agents. Alternatively they can be developed as soft gel-like materials that are injected into solid tumors or sites of resection to stimulate a potent anti-tumor immune response. Biomaterials synthesized from diverse components such as polymers and peptides can be combined with any immunotherapy in the modern toolbox, from checkpoint inhibitors and stimulatory adjuvants, to cancer antigens and adoptive T cells, resulting in unique synergies and improved therapeutic efficacy. The field is growing rapidly in size as publications continue to appear in the literature, and biomaterial-based immunotherapies are entering clinical trials and human patients. It is unarguably an exciting time for cancer immunotherapy and biomaterial researchers, and further work seeks to understand the most critical design considerations in the development of the next-generation of immunotherapeutic biomaterials. This review will discuss recent advances in the delivery of immunotherapies from localized biomaterials, focusing on macroscale implantable and injectable systems. STATEMENT OF SIGNIFICANCE: Anti-cancer immunotherapies have shown exciting clinical results in the past few decades, yet they suffer from a few distinct limitations, such as poor delivery kinetics, narrow patient response profiles, and systemic side effects. Biomaterial systems are now being developed that can overcome many of these problems, allowing for localized adjuvant delivery, focused dose concentrations, and extended therapy presentation. The field of biocompatible carrier materials is uniquely suited to be combined with immunotherapy, promising to yield significant improvements in treatment outcomes and clinical care. In this review, the first pioneering efforts and most recent advances in biomaterials for immunotherapeutic applications are explored, with a specific focus on implantable and injectable biomaterials such as porous scaffolds, cryogels, and hydrogels.

Dynamically Programmed Switchable DNA Hydrogels Based on a DNA Circuit Mechanism

Biological stimuli-responsive DNA hydrogels have attracted much attention in the field of medical engineering owing to their unique phase transitions from gel to sol through cleavage of DNA cross-linking points in response to specific biomolecular inputs. In this paper, a new class of biological stimuli-responsive DNA hydrogels with a dynamically programmed DNA system that relies on a DNA circuit system through cascading toehold-mediated DNA displacement reactions is constructed, allowing the catalytic cleavage of cross-linking points and main chains in response to an appropriate DNA input. The dynamically programmed DNA hydrogels exhibit a significant sharp phase transition from gel to sol in comparison to another DNA hydrogel showing noncatalytic cleavage of cross-linking points due to synchronization of the catalytic cleavage of cross-linking points and the main chains. Further, the sol-gel phase transitions of the DNA hydrogels in response to the DNA input are easily tunable by changing the cross-linking density. Additionally, with a structure-switching aptamer, DNA hydrogels encapsulating PEGylated gold nanoparticles can be used as enzyme-free signal amplifiers for the colorimetric detection of adenosine 5'-triphosphate (ATP); this detection system provides simplicity and higher sensitivity (limit of detection: 5.6 × 10^-6 m at 30 min) compared to other DNA hydrogel-based ATP detection systems.

Emerging applications of peptide-oligonucleotide conjugates: bioactive scaffolds, self-assembling systems, and hybrid nanomaterials

Peptide-oligonucleotide conjugates (POCs) are covalent constructs that link a molecule like DNA to a synthetic peptide sequences. These materials merge the programmable self-assembly of oligonucleotides with the bioactivity and chemical diversity of polypeptides. Recent years have seen the widespread use of POCs in a range of fields, driven the by relative advantages of each molecular type. In this review, we will present an overview of the synthesis and application of POCs, with an emphasis on emerging areas where these molecules will have a unique impact. We first discuss two main strategies for synthesizing POCs from synthetic monomers such as phosphoramidites and functionalized amino acids. We then describe four key fields of research in POCs: (1) biomaterials for interfacing with, and controlling the behavior of cells; (2) hybrid self-assembling systems that balance peptide and oligonucleotide intermolecular forces; (3) template-enhanced coupling of POCs into larger molecules; and (4) display of peptides on self-assembled oligonucleotide scaffolds. We also highlight several promising areas for future applications in each of these four directions, and anticipate ever increasing uses of POCs in interdisciplinary research.