Synthetic Transient Crosslinks Program the Mechanics of Soft, Biopolymer-Based Materials

DNA Crosslinked Mucin Hydrogels Allow for On-Demand Gel Disintegration and Triggered Particle Release

Whereas hydrogels created from synthetic polymers offer a high level of control over their stability and mechanical properties, their biomedical activity is typically limited. In contrast, biopolymers have evolved over billions of years to integrate a broad range of functionalities into a single design. Thus, biopolymeric hydrogels can show remarkable capabilities such as regulatory behavior, selective barrier properties, or antimicrobial effects. Still, despite their widespread use in numerous biomedical applications, achieving a meticulous control over the physical properties of macroscopic biopolymeric networks remains a challenge. Here, a macroscopic, DNA-crosslinked mucin hydrogel with tunable viscoelastic properties that responds to two types of triggers: temperature alterations and DNA displacement strands, is presented. As confirmed with bulk rheology and single particle tracking, the hybridized base pairs governing the stability of the hydrogel can be opened, thus allowing for a precise control over the hydrogel stiffness and even enabling a full gel-to-sol transition. As those DNA-crosslinked mucin hydrogels possess tunable mechanical properties and can be disintegrated on demand, they can not only be considered for controlled cargo release but may also serve as a role model for the development of smart biomedical materials in applications such as tissue engineering and wound healing.

Highly flexible PEG-LifeAct constructs act as tunable biomimetic actin crosslinkers

In vitro studies of actin filament networks crosslinked with dynamic actin binding proteins provide critical insights into cytoskeletal mechanics as well as inspiration for new adaptive materials design. However, discontinuous variance in the physiochemical properties of actin binding proteins impedes holistic relationships between crosslinker molecular parameters, network structure, and mechanics. Bio-synthetic constructs composed of synthetic polymer backbones and actin binding motifs would enable crosslinkers with engineered physiochemical properties to directly target the desired structure-property relationships. As a proof of concept, bio-synthetic crosslinkers composed of highly flexible polyethylene glycol (PEG) polymers functionalized with the actin binding peptide LifeAct, are explored as actin crosslinkers. Using bulk rheology and fluorescence microscopy, these constructs are shown to modulate actin filament network structure and mechanics in a contour length dependent manner, while maintaining the stress-stiffening behavior inherent to actin filament networks. These results encourage the design of more diverse and complex peptide-polymer crosslinkers to interrogate and control semi-flexible polymer networks.

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.

Heavy water induces bundling in entangled actin networks

Heavy water is known to affect many different biological systems, with the most striking effects observed at the cellular level. Many dynamic processes, such as migration or invasion, but also central processes of cell proliferation are measurably inhibited by the presence of deuterium oxide (D2O). Furthermore, individual cell deformabilities are significantly decreased upon D2O treatment. In order to understand the origin of these effects, we studied entangled filamentous actin networks, a commonly used model system for the cytoskeleton, which is considered a central functional element for dynamic cellular processes. Using bulk shear rheology to extract rheological signatures of reconstituted actin networks at varying concentrations of D2O, we found a non-monotonic behavior, which is explainable by a drastic change in the actin network architecture. Applying light scattering and fluorescence microscopy, we were able to demonstrate that the presence of deuterium oxide induces bundling in reconstituted entangled networks of filamentous actin. This constitutes an entirely novel and previously undescribed actin bundling mechanism.

Integration of functional peptides into nucleic acid-based nanostructures

In many applications such as diagnostics and therapy development, small peptide fragments consisting of only a few amino acids are often attractive alternatives to bulky proteins. This is due to factors such as the ease of scalable chemical synthesis and numerous methods for their discovery. One drawback of using peptides is that their activity can often be negatively impacted by the lack of a rigid, 3D stabilizing structure provided by the rest of the protein. In many cases, this can be alleviated by different methods of rational templating onto nanomaterials, which provides additional possibilities to use concepts of multivalence or rational nano-engineering to enhance or even create new types of function or structure. In recent years, nanostructures made from the self-assembly of DNA strands have been used as scaffolds to create functional arrangements of peptides, often leading to greatly enhanced biological activity or new material properties. This review will give an overview of nano-templating approaches based on the combination of DNA nanotechnology and peptides. This will include both bioengineering strategies to control interactions with cells or other biological systems, as well as examples where the combination of DNA and peptides has been leveraged for the rational design of new functional materials.

Systematic altering of semiflexible DNA-based polymer networks via tunable crosslinking

In order to understand and predict the mechanical behaviours of complex, soft biomaterials such as cells or stimuli-responsive hydrogels, it is important to connect how the nanoscale properties of their constituent components impact those of the bulk material. Crosslinked networks of semiflexible polymers are particularly ubiquitous, being underlying mechanical components of biological systems such as cells or ECM, as well as many synthetic or biomimetic materials. Cell-derived components such as filamentous biopolymers or protein crosslinkers are readily available and well-studied model systems. However, as evolutionarily derived materials, they are constrained to a fixed set of structural parameters such as the rigidity and size of the filaments, or the valency and strength of binding of crosslinkers forming inter-filament connections. By implementing a synthetic model system based on the self-assembly of DNA oligonucleotides into nanometer-scale tubes and simple crosslinking constructs, we used the thermodynamic programmability of DNA hybridization to explore the impact of binding affinity on bulk mechanical response. Stepwise tuning the crosslinking affinity over a range from transient to thermodynamically stable shows an according change in viscoelastic behaviour from loosely entangled to elastic, consistent with models accounting for generalized inter-filament interactions. While characteristic signatures of concentration-dependent changes in network morphology found in some other natural and synthetic filament-crosslinker systems were not apparent, the presence of a distinct elasticity increase within a narrow range of conditions points towards potential subtle alterations of crosslink-filament architecture. Here, we demonstrate a new synthetic approach for gaining a deeper understanding of both biological as well as engineered hydrogel systems.

Nonlinear Microscale Mechanics of Actin Networks Governed by Coupling of Filament Crosslinking and Stabilization

Actin plays a vital role in maintaining the stability and rigidity of biological cells while allowing for cell motility and shape change. The semiflexible nature of actin filaments-along with the myriad actin-binding proteins (ABPs) that serve to crosslink, bundle, and stabilize filaments-are central to this multifunctionality. The effect of ABPs on the structural and mechanical properties of actin networks has been the topic of fervent investigation over the past few decades. Yet, the combined impact of filament stabilization, stiffening and crosslinking via ABPs on the mechanical response of actin networks has yet to be explored. Here, we perform optical tweezers microrheology measurements to characterize the nonlinear force response and relaxation dynamics of actin networks in the presence of varying concentrations of α-actinin, which transiently crosslinks actin filaments, and phalloidin, which stabilizes filamentous actin and increases its persistence length. We show that crosslinking and stabilization can act both synergistically and antagonistically to tune the network resistance to nonlinear straining. For example, phalloidin stabilization leads to enhanced elastic response and reduced dissipation at large strains and timescales, while the initial microscale force response is reduced compared to networks without phalloidin. Moreover, we find that stabilization switches this initial response from that of stress stiffening to softening despite the increased filament stiffness that phalloidin confers. Finally, we show that both crosslinking and stabilization are necessary to elicit these emergent features, while the effect of stabilization on networks without crosslinkers is much more subdued. We suggest that these intriguing mechanical properties arise from the competition and cooperation between filament connectivity, bundling, and rigidification, shedding light on how ABPs with distinct roles can act in concert to mediate diverse mechanical properties of the cytoskeleton and bio-inspired polymeric materials.

Large and stable: actin aster networks formed via entropic forces

Biopolymer networks play a major role as part of the cytoskeleton. They provide stable structures and act as a medium for signal transport. These features encourage the application of such networks as organic computation devices. While research on this topic is not advanced yet, previous results are very promising. The protein actin in particular appears advantageous. It can be arranged to various stable structures and transmit several signals. In this study aster shaped networks were self-assembled via entropic forces by the crowding agent methyl cellulose. These networks are characterised by a regular and uniquely thick bundle structure, but have so far only been accounted in droplets of 100 μm diameter. We report now regular asters in an area of a few mm² that could be observed even after months. Such stability outside of an organism is striking and underlines the great potential actin aster networks display.

Characterization of binding interactions of SARS-CoV-2 spike protein and DNA-peptide nanostructures

Binding interactions of the spike proteins of the severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) to a peptide fragment derived from the human angiotensin converting enzyme 2 (hACE2) receptor are investigated. The peptide is employed as capture moiety in enzyme linked immunosorbent assays (ELISA) and quantitative binding interaction measurements that are based on fluorescence proximity sensing (switchSENSE). In both techniques, the peptide is presented on an oligovalent DNA nanostructure, in order to assess the impact of mono- versus trivalent binding modes. As the analyte, the spike protein and several of its subunits are tested as well as inactivated SARS-CoV-2 and pseudo viruses. While binding of the peptide to the full-length spike protein can be observed, the subunits RBD and S1 do not exhibit binding in the employed concentrations. Variations of the amino acid sequence of the recombinant full-length spike proteins furthermore influence binding behavior. The peptide was coupled to DNA nanostructures that form a geometric complement to the trimeric structure of the spike protein binding sites. An increase in binding strength for trimeric peptide presentation compared to single peptide presentation could be generally observed in ELISA and was quantified in switchSENSE measurements. Binding to inactivated wild type viruses could be shown as well as qualitatively different binding behavior of the Alpha and Beta variants compared to the wild type virus strain in pseudo virus models.

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.

Constraint Release for Reptating Filaments in Semiflexible Networks Depends on Background Fluctuations

Entangled semiflexible polymer networks are usually described by the tube model, although this concept has not been able to explain all experimental observations. One of its major shortcomings is neglecting the thermal fluctuations of the polymers surrounding the examined test filament, such that disentanglement effects are not captured. In this study, we present experimental evidence that correlated constraint release which has been predicted theoretically occurs in entangled, but not in crosslinked semiflexible polymer networks. By tracking single semiflexible DNA nanotubes embedded both in entangled and crosslinked F-actin networks, we observed different reptation dynamics in both systems, emphasizing the need for a revision of the classical tube theory for entangled polymer solutions.

From Strain Stiffening to Softening—Rheological Characterization of Keratins 8 and 18 Networks Crosslinked via Electron Irradiation

Networks of crosslinked keratin filaments are abundant in epithelial cells and tissues, providing resilience against mechanical forces and ensuring cellular integrity. Although studies of in vitro models of reconstituted keratin networks have revealed important mechanical aspects, the mechanical properties of crosslinked keratin structures remain poorly understood. Here, we exploited the power of electron beam irradiation (EBI) to crosslink in vitro networks of soft epithelial keratins 8 and 18 (k8–k18) filaments with different irradiation doses (30 kGy, 50 kGy, 80 kGy, 100 kGy, and 150 kGy). We combined bulk shear rheology with confocal microscopy to investigate the impact of crosslinking on the mechanical and structural properties of the resultant keratin gels. We found that irradiated keratin gels display higher linear elastic modulus than the unirradiated, entangled networks at all doses tested. However, at the high doses (80 kGy, 100 kGy, and 150 kGy), we observed a remarkable drop in the elastic modulus compared to 50 kGy. Intriguingly, the irradiation drastically changed the behavior for large, nonlinear deformations. While untreated keratin networks displayed a strong strain stiffening, increasing irradiation doses shifted the system to a strain softening behavior. In agreement with the rheological behavior in the linear regime, the confocal microscopy images revealed fully isotropic networks with high percolation in 30 kGy and 50 kGy-treated keratin samples, while irradiation with 100 kGy induced the formation of thick bundles and clusters. Our results demonstrate the impact of permanent crosslinking on k8–k18 mechanics and provide new insights into the potential contribution of intracellular covalent crosslinking to the loss of mechanical resilience in some human keratin diseases. These insights will also provide inspiration for the synthesis of new keratin-based biomaterials.

Putting DNA to Work as Generic Polymeric Materials

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

Cells in Slow Motion: Apparent Undercooling Increases Glassy Behavior at Physiological Temperatures

Solvent conditions are unexpectedly sufficient to drastically and reversibly slow down cells. In vitro on the molecular level, protein-solvent interactions drastically change in the presence of heavy water (D2 O) and its stronger hydrogen bonds. Adding D2 O to the cell medium of living cells increases the molecular intracellular viscosity. While cell morphology and phenotype remain unchanged, cellular dynamics transform into slow motion in a changeable manner. This is exemplified in the slowdown of cell proliferation and migration, which is caused by a reversible gelation of the cytoplasm. In analogy to the time-temperature superposition principle, where temperature is replaced by D2 O, an increase in viscosity slows down the effective time. Actin networks, crucial structures in the cytoplasm, switch from a power-law-like viscoelastic to a more rubber-like elastic behavior. The resulting intracellular resistance and dissipation impair cell movement. Since cells are highly adaptive non-equilibrium systems, they usually respond irreversibly from a thermodynamic perspective. D2 O induced changes, however, are fully reversible and their effects are independent of signaling as well as expression. The stronger hydrogen bonds lead to glass-like, drawn-out intramolecular dynamics, which may facilitate longer storage times of biological matter, for instance, during transport of organ transplants.

Measuring structural parameters of crosslinked and entangled semiflexible polymer networks with single-filament tracing

Single-filament tracing has been a valuable tool to directly determine geometrical and mechanical properties of entangled polymer networks. However, systematically verifying how the stiffness of the tracer filament or its molecular interactions with the surrounding network impacts the measurement of these parameters has not been possible with the established experimental systems. Here we use mechanically programmable DNA nanotubes embedded in crosslinked and entangled F-actin networks, as well as in synthetic DNA networks, in order to measure fundamental, structural network properties like tube width and mesh size with respect to the stiffness of the tracers. While we confirm some predictions derived from models based purely on steric interactions, our results indicate that these models should be expanded to account for additional interfilament interactions, thereby describing the behavior of real polymer networks.

DNA Nanostructures in the Fight Against Infectious Diseases

Throughout history, humanity has been threatened by countless epidemic and pandemic outbreaks of infectious diseases, from the Justinianic Plague to the Spanish flu to COVID-19. While numerous antimicrobial and antiviral drugs have been developed over the last 200 years to face these threats, the globalized and highly connected world of the 21st century demands for an ever-increasing efficiency in the detection and treatment of infectious diseases. Consequently, the rapidly evolving field of nanomedicine has taken up the challenge and developed a plethora of strategies to fight infectious diseases with the help of various nanomaterials such as noble metal nanoparticles, liposomes, nanogels, and virus capsids. DNA nanotechnology represents a comparatively recent addition to the nanomedicine arsenal, which, over the past decade, has made great progress in the area of cancer diagnostics and therapy. However, the past few years have seen also an increasing number of DNA nanotechnology-related studies that particularly focus on the detection and inhibition of microbial and viral pathogens. Herein, a brief overview of this rather young research field is provided, successful concepts as well as potential challenges are identified, and promising directions for future research are highlighted.

Cellulose/Collagen Dressings for Diabetic Foot Ulcer: A Review

Diabetic foot ulcer (DFU) is currently a global concern and it requires urgent attention, as the cost allocation by the government for DFU increases every year. This review was performed to provide scientific evidence on the advanced biomaterials that can be utilised as a first-line treatment for DFU patients. Cellulose/collagen dressings have a biological property on non-healing wounds, such as DFU. This review aims to analyse scientific-based evidence of cellulose/collagen dressing for DFU. It has been proven that the healing rate of cellulose/collagen dressing for DFU patients demonstrated a significant improvement in wound closure as compared to current standard or conventional dressings. It has been scientifically proven that cellulose/collagen dressing provides a positive effect on non-healing DFU. There is a high tendency for cellulose/collagen dressing to be used, as it highly promotes angiogenesis with a rapid re-epithelisation rate that has been proven effective in clinical trials.

Influence of hyaluronic acid binding on the actin cortex measured by optical forces

Melanoma cells are often surrounded by hyaluronic acid (HA) rich environments, which are considered to promote tumor progression and metastasis. Induced effects in compound materials consisting of cells embedded in an extracellular matrix have been studied, however, alterations of the single cells have never been addressed. Here, we explicitly addressed single cell properties and measured HA-induced biomechanical changes via deformations induced solely by optical forces. With the optical stretcher setup, cells were deformed after culturing them in either the presence or absence of HA revealing the crucial interplay of HA with the CD44 receptor. To assess the role of CD44 in transducing effects of HA, we compared a CD44 expressing variant of the melanoma cell line RPM-MC to its natural CD44-negative counterpart. Our measurements revealed a significant stiffness change, which we attribute to changes of the actin cytoskeleton.

Influence of Network Topology on the Viscoelastic Properties of Dynamically Crosslinked Hydrogels

Biological materials combine stress relaxation and self-healing with non-linear stress-strain responses. These characteristic features are a direct result of hierarchical self-assembly, which often results in fiber-like architectures. Even though structural knowledge is rapidly increasing, it has remained a challenge to establish relationships between microscopic and macroscopic structure and function. Here, we focus on understanding how network topology determines the viscoelastic properties, i.e., stress relaxation, of biomimetic hydrogels. We have dynamically crosslinked two different synthetic polymers with one and the same crosslink. The first polymer, a polyisocyanopeptide (PIC), self-assembles into semi-flexible, fiber-like bundles, and thus displays stress-stiffening, similar to many biopolymer networks. The second polymer, 4-arm poly(ethylene glycol) (starPEG), serves as a reference network with well-characterized structural and viscoelastic properties. Using one and the same coiled coil crosslink allows us to decouple the effects of crosslink kinetics and network topology on the stress relaxation behavior of the resulting hydrogel networks. We show that the fiber-containing PIC network displays a relaxation time approximately two orders of magnitude slower than the starPEG network. This reveals that crosslink kinetics is not the only determinant for stress relaxation. Instead, we propose that the different network topologies determine the ability of elastically active network chains to relax stress. In the starPEG network, each elastically active chain contains exactly one crosslink. In the absence of entanglements, crosslink dissociation thus relaxes the entire chain. In contrast, each polymer is crosslinked to the fiber bundle in multiple positions in the PIC hydrogel. The dissociation of a single crosslink is thus not sufficient for chain relaxation. This suggests that tuning the number of crosslinks per elastically active chain in combination with crosslink kinetics is a powerful design principle for tuning stress relaxation in polymeric materials. The presence of a higher number of crosslinks per elastically active chain thus yields materials with a slow macroscopic relaxation time but fast dynamics at the microscopic level. Using this principle for the design of synthetic cell culture matrices will yield materials with excellent long-term stability combined with the ability to locally reorganize, thus facilitating cell motility, spreading, and growth.

Actin networks voltage circuits

Filaments of the cellular protein actin can form bundles, which can conduct ionic currents as well as mechanical and voltage solitons. These inherent properties can be utilized to generate computing circuits solely based on self-assembled actin bundle structures. Starting with experimentally observed networks of actin bundles, we model their network structure in terms of edges and nodes. We compute and discuss the main electrical parameters, considering the bundles as electrical wires with either low or high filament densities. A set of equations describing the network is solved with several initial conditions. Input voltages, which can be considered as information bits, are applied in a set of points and output voltages are computed in another set of positions. We consider both an idealized situation, where pointlike electrodes can be inserted in any points of the bundles and a more realistic case, where electrodes lay on a surface and have typical dimensions available in the industry. We find that in both cases such a system can implement the main logical gates and a finite state machine.

Actin droplet machine

The actin droplet machine is a computer model of a three-dimensional network of actin bundles developed in a droplet of a physiological solution, which implements mappings of sets of binary strings. The actin bundle network is conductive to travelling excitations, i.e. impulses. The machine is interfaced with an arbitrary selected set of k electrodes through which stimuli, binary strings of length k represented by impulses generated on the electrodes, are applied and responses are recorded. The responses are recorded in a form of impulses and then converted to binary strings. The machine's state is a binary string of length k: if there is an impulse recorded on the ith electrode, there is a '1' in the ith position of the string, and '0' otherwise. We present a design of the machine and analyse its state transition graphs. We envisage that actin droplet machines could form an elementary processor of future massive parallel computers made from biopolymers.

Computing on actin bundles network

Actin filaments are conductive to ionic currents, mechanical and voltage solitons. These travelling localisations can be utilised to generate computing circuits from actin networks. The propagation of localisations on a single actin filament is experimentally unfeasible to control. Therefore, we consider excitation waves propagating on bundles of actin filaments. In computational experiments with a two-dimensional slice of an actin bundle network we show that by using an arbitrary arrangement of electrodes, it is possible to implement two-inputs-one-output circuits.

Pinpointed Stimulation of EphA2 Receptors via DNA-Templated Oligovalence

DNA nanostructures enable the attachment of functional molecules to nearly any unique location on their underlying structure. Due to their single-base-pair structural resolution, several ligands can be spatially arranged and closely controlled according to the geometry of their desired target, resulting in optimized binding and/or signaling interactions. Here, the efficacy of SWL, an ephrin-mimicking peptide that binds specifically to EphrinA2 (EphA2) receptors, increased by presenting up to three of these peptides on small DNA nanostructures in an oligovalent manner. Ephrin signaling pathways play crucial roles in tumor development and progression. Moreover, Eph receptors are potential targets in cancer diagnosis and treatment. Here, the quantitative impact of SWL valency on binding, phosphorylation (key player for activation) and phenotype regulation in EphA2-expressing prostate cancer cells was demonstrated. EphA2 phosphorylation was significantly increased by DNA trimers carrying three SWL peptides compared to monovalent SWL. In comparison to one of EphA2’s natural ligands ephrin-A1, which is known to bind promiscuously to multiple receptors, pinpointed targeting of EphA2 by oligovalent DNA-SWL constructs showed enhanced cell retraction. Overall, we show that DNA scaffolds can increase the potency of weak signaling peptides through oligovalent presentation and serve as potential tools for examination of complex signaling pathways.