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Mucus hyperconcentration in cystic fibrosis (CF) lung disease is marked by increases in both mucin and DNA concentration. Additionally, it has been shown that half of the mucins present in bronchial alveolar lavage fluid (BALF) from preschool-aged CF patients are present in as non-swellable mucus flakes. This motivates us to examine the utility of mucus flakes, as well as mucin and DNA concentrations in BALF as markers of infection and inflammation in CF airway disease.In this study, we examined the mucin and DNA concentration, as well as mucus flake abundance, composition, and biophysical properties in BALF from three groups; healthy adult controls, and two CF cohorts, one preschool aged and the other school aged. BALFs were characterized via refractometry, PicoGreen, immunofluorescence microscopy, particle tracking microrheology, and fluorescence image tiling.Mucin and DNA BALF concentrations increased progressively from healthy young adult controls to preschool-aged people and school-aged people with CF. Notably, mucin concentrations were increased in bronchoalveolar lavage fluid (BALF) from preschool-aged patients with CF prior to decreased pulmonary function. Infrequent small mucus flakes were identified in normal subjects. A progressive increase in the abundance of mucus flakes in preschool and school-aged CF patients was observed. Compositionally, MUC5B dominated flakes from normal subjects, whereas an increase in MUC5AC was observed in people with CF, reflected in a reduced flaked MUC5B/MUC5AC mucin ratio.These findings suggest mucus composition and flake properties are useful markers of inflammatory and infection-based changes in CF airways.

Viral variants of concern continue to arise for SARS-CoV-2, potentially impacting both methods for detection and mechanisms of action. Here, we investigate the effect of an evolving spike positive charge in SARS-CoV-2 variants and subsequent interactions with heparan sulfate and the angiotensin converting enzyme 2 (ACE2) in the glycocalyx. We show that the positively charged Omicron variant evolved enhanced binding rates to the negatively charged glycocalyx. Moreover, we discover that while the Omicron spike-ACE2 affinity is comparable to that of the Delta variant, the Omicron spike interactions with heparan sulfate are significantly enhanced, giving rise to a ternary complex of spike-heparan sulfate-ACE2 with a large proportion of double-bound and triple-bound ACE2. Our findings suggest that SARS-CoV-2 variants evolve to be more dependent on heparan sulfate in viral attachment and infection. This discovery enables us to engineer a second-generation lateral-flow test strip that harnesses both heparin and ACE2 to reliably detect all variants of concern, including Omicron.

Peptide amphiphiles (PAs) are a class of molecules comprised of short amino acid sequences conjugated to hydrophobic moieties that may exhibit self-assembly in water into supramolecular structures. We investigate here how mechanical properties of hydrogels formed by PA supramolecular nanofibers are affected by hydrogen bond densities within their internal structure by substituting glycine for aza-glycine (azaG) residues. We found that increasing the number of PA molecules that contain azaG up to 5 mol% in PA supramolecular nanofibers increases their persistence length fivefold and decreases their diffusion coefficients as measured by fluorescence recovery after photobleaching. When these PAs are used to create hydrogels, their bulk storage modulus (G') was found to increase as azaG PA content in the supramolecular assemblies increases up to a value of 10 mol% and beyond this value a decrease was observed, likely due to diminished levels of nanofiber entanglement in the hydrogels as a direct result of increased supramolecular rigidity. Interestingly, we found that the bioactivity of the scaffolds toward dopaminergic neurons derived from induced pluripotent stem cells can be enhanced directly by persistence length independently of storage modulus. We hypothesize that this is due to interactions between the cells and the extracellular environment across different size scales: from filopodia adhering to individual nanofiber bundles to cell adhesion sites that interact with the hydrogel as a bulk substrate. Fine tuning of hydrogen bond density in self-assembling peptide biomaterials such as PAs provides an approach to control nanoscale stiffness as part of an overall strategy to optimize bioactivity in these supramolecular systems. supramolecular biomaterials. STATEMENT OF SIGNIFICANCE: Hydrogen bonding is an important driving force for the self-assembly of peptides in both biological and artificial systems. Here, we increase the amount of hydrogen bonding within self-assembled peptide amphiphile (PA) nanofibers by substituting glycine for an aza-glycine (azaG). We show that increasing the molar concentration of azaG increases the internal order of individual nanofibers and increases their persistence length. We also show that these changes are sufficient to increase survival and tyrosine hydroxylase expression in induced pluripotent stem cell-derived dopaminergic neurons cultured in 3D gels made of these materials. Our strategy of tuning the number of hydrogen bonds in a supramolecular assembly provides mechanical customization for 3D cell culture and tissue engineering.

We develop the first molecular dynamics model of airway mucus based on the detailed physical properties and chemical structure of the predominant gel-forming mucin MUC5B. Our airway mucus model leverages the LAMMPS open-source code [https://lammps.sandia.gov], based on the statistical physics of polymers, from single molecules to networks. On top of the LAMMPS platform, the chemical structure of MUC5B is used to superimpose proximity-based, non-covalent, transient interactions within and between the specific domains of MUC5B polymers. We explore feasible ranges of hydrophobic and electrostatic interaction strengths between MUC5B domains with 9 nanometer spatial and 1 nanosecond temporal resolution. Our goal here is to propose and test a mechanistic hypothesis for a striking clinical observation with respect to airway mucus: a 10-fold increase in non-swellable, dense structures called flakes during progression of cystic fibrosis disease. Among the myriad possible effects that might promote self-organization of MUC5B networks into flake structures, we hypothesize and confirm that the clinically confirmed increase in mucin concentration, from 1.5 to 5 mg/mL, alone is sufficient to drive the structure changes observed with scanning electron microscopy images from experimental samples. We post-process the LAMMPS simulated datasets at 1.5 and 5 mg/mL, both to image the structure transition and compare with scanning electron micrographs and to show that the 3.33-fold increase in concentration induces closer proximity of interacting electrostatic and hydrophobic domains, thereby amplifying the proximity-based strength of the interactions.

The SARS-CoV-2 Omicron sub-lineage contains a significant number of mutations in the spike protein relative to earlier SARS-CoV-2 variants. Most notably, these mutations significantly increased the positive charge of the spike protein that is postulated to confer increased infectivity, potentially through enhanced interactions with cell surface receptors, and an altered host-cell entry mechanism. While heparan sulfate (HS) was shown to be a key co-receptor in the host-cell entry of SARS-CoV-2, the effect of spike charge on its interactions with heparan sulfate has not been clearly elucidated. Here, we investigate the role of evolving spike positive charge in accelerating long-range interactions to heparan sulfate and ACE2 in the glycocalyx. We show that the positively charged Omicron evolved enhanced binding rates to the negatively charged glycocalyx. Moreover, we discovered that while the Omicron spike-ACE2 affinity is comparable to Delta, the Omicron spike interactions with heparan sulfate are significantly enhanced, giving rise to a ternary complex of spike-HS-ACE2 with a larger proportion of double-bound and triple-bound ACE2. Our findings suggest that SARS-CoV-2 variants evolve to be more dependent on heparan sulfate in viral attachment and infection. We leveraged this understanding for the successful and sensitive detection of the Omicron variant. The evolving enhanced binding of SARS-Cov-2 to heparan sulfate presents new therapeutic and diagnostic opportunities.

The integration of proteins with DNA nanotechnology would enable materials with diverse applications in biology, medicine, and engineering. Here, we describe a method for the incorporation of bioactive fibronectin domain proteins with DNA nanostructures using two orthogonal coiled-coil peptides. One peptide from each coiled-coil pair is attached to a DNA origami cuboid in a multivalent fashion by attaching the peptides to DNA handles. These structures can then be assembled into one-dimensional arrays through the addition of a fibronectin domain linker genetically fused with the complementary peptides to those on the origami. We validate array formation using two different self-assembly protocols and characterize the fibers by atomic force and electron microscopy. Finally, we demonstrate that surfaces coated with the protein-DNA nanofibers can serve as biomaterial substrates for fibroblast adhesion and spreading with the nanofibers showing enhanced bioactivity compared to that of the monomeric protein.

Cytoskeletal assemblies produce functionality through multiscale structural reconfiguration by exploiting a family of protein crosslinkers. Inspired by these principles, we designed an array of complementary peptide-DNA monomers able to form multistranded junctions with different geometries and stabilities and tested their effect on the structural organization of co-polymerized filament-forming peptides. In striking similarity to their biological counterparts, the peptide-DNA crosslinkers organized fibers into bundled architectures with base-pair tunable aspect ratios. Controlling solvent or temperature drove assembly through distinct pathways to form different structural and mechanical states exhibiting multiple levels of hierarchy from the same set of components. The thermal reversibility of DNA crosslinks drove structures to form, disassemble, and rebuild over multiple cycles. Sequential transitioning between bundles and fibers using orthogonal triggers enabled the dosed release of proteins to modulate catalytic reactions. This programmable peptide-DNA nanotechnology framework will pave the way towards the design of hierarchical materials with reconfigurable properties.

Cytoskeletal assemblies produce functionality through multiscale structural reconfiguration by exploiting a family of protein crosslinkers. Inspired by these principles, we designed an array of complementary peptide-DNA monomers able to form multistranded junctions with different geometries and stabilities and tested their effect on the structural organization of co-polymerized filament-forming peptides. In striking similarity to their biological counterparts, the peptide-DNA crosslinkers organized fibers into bundled architectures with base-pair tunable aspect ratios. Controlling solvent or temperature drove assembly through distinct pathways to form different structural and mechanical states exhibiting multiple levels of hierarchy from the same set of components. The thermal reversibility of DNA crosslinks drove structures to form, disassemble, and rebuild over multiple cycles. Sequential transitioning between bundles and fibers using orthogonal triggers enabled the dosed release of proteins to modulate catalytic reactions. This programmable peptide-DNA nanotechnology framework will pave the way towards the design of hierarchical materials with reconfigurable properties.

Cystic fibrosis (CF) is characterized by abnormal transepithelial ion transport. However, a description of CF lung disease pathophysiology unifying superficial epithelial and submucosal gland (SMG) dysfunctions has remained elusive. We hypothesized that biophysical abnormalities associated with CF mucus hyperconcentration provide a unifying mechanism. Studies of the anion secretion–inhibited pig airway model of CF revealed elevated SMG mucus concentrations, osmotic pressures, and SMG mucus accumulation. Human airway studies revealed hyperconcentrated CF SMG mucus with raised osmotic pressures and cohesive forces predicted to limit SMG mucus secretion/release. Using proline-rich protein 4 (PRR4) as a biomarker of SMG secretion, CF sputum proteomics analyses revealed markedly lower PRR4 levels compared to healthy and bronchiectasis controls, consistent with a failure of CF SMGs to secrete mucus onto airway surfaces. Raised mucus osmotic/cohesive forces, reflecting mucus hyperconcentration, provide a unifying mechanism that describes disease-initiating mucus accumulation on airway surfaces and in SMGs of the CF lung.

We apply our mechanistic, within-host,pre-immunity, respiratory tract infection model for unvaccinated, previously uninfected, and immune-compromised individuals. Starting from published cell infection and viral replication data for the SARS-CoV-2 alpha variant, we explore variability in outcomes of viral load and cell infection due to three plausible mechanisms altered by SARS-CoV-2 mutations of delta and omicron. We seek a mechanistic explanation of clinical test results: delta nasal infections express ∼3 orders-of-magnitude higher viral load than alpha, while omicron infections express an additional 1 to 2 orders-of-magnitude rise over delta. Model simulations revealshortening of the eclipse phase(the time between cellular uptake of the virus and onset of infectious viral replication and shedding)alone can generate 3-5 orders-of-magnitude higher viral load within 2 days post initial infection. Higher viral replication rates by an infected cell can generate at most one order-of-magnitude rise in viral load, whereas higher cell infectability has minimal impact and lowers the viral load.

The brain is one of the softest tissues in the body with storage moduli (G') that range from hundreds to thousands of pascals (Pa) depending upon the anatomic region. Furthermore, pathological processes such as injury, aging and disease can cause subtle changes in the mechanical properties throughout the central nervous system. However, these changes in mechanical properties lie within an extremely narrow range of moduli and there is great interest in understanding their effect on neuron biology. We report here the design of supramolecular hydrogels based on anionic peptide amphiphile nanofibers using oligo-L-lysines of different molecular lengths to precisely tune gel stiffness over the range of interest and found that G' increases by 10.5 Pa for each additional lysine monomer in the oligo-L-lysine chain. We found that small changes in storage modulus on the order of 70 Pa significantly affect survival, neurite growth and tyrosine hydroxylase-positive population in dopaminergic neurons derived from induced pluripotent stem cells. The work reported here offers a strategy to tune mechanical stiffness of hydrogels for use in 3D neuronal cell cultures and transplantation matrices for neural regeneration.

Inspired by the role of cell-surface glycoproteins as coreceptors for pathogens, we report the development of GlycoGrip: a glycopolymer-based lateral flow assay for detecting SARS-CoV-2 and its variants. GlycoGrip utilizes glycopolymers for primary capture and antispike antibodies labeled with gold nanoparticles for signal-generating detection. A lock-step integration between experiment and computation has enabled efficient optimization of GlycoGrip test strips which can selectively, sensitively, and rapidly detect SARS-CoV-2 and its variants in biofluids. Employing the power of the glycocalyx in a diagnostic assay has distinct advantages over conventional immunoassays as glycopolymers can bind to antigens in a multivalent capacity and are highly adaptable for mutated strains. As new variants of SARS-CoV-2 are identified, GlycoGrip will serve as a highly reconfigurable biosensor for their detection. Additionally, via extensive ensemble-based docking simulations which incorporate protein and glycan motion, we have elucidated important clues as to how heparan sulfate and other glycocalyx components may bind the spike glycoprotein during SARS-CoV-2 host-cell infection. GlycoGrip is a promising and generalizable alternative to costly, labor-intensive RT-PCR, and we envision it will be broadly useful, including for rural or low-income populations that are historically undertested and under-reported in infection statistics., The cell surface is covered with a “sugary” glycocalyx matrix. We use this knowledge to develop a sensor that can detect SARS-CoV-2 and its rapidly emerging variants.

Mechanistic insights into human respiratory tract (RT) infections from SARS-CoV-2 can inform public awareness as well as guide medical prevention and treatment for COVID-19 disease. Yet the complexity of the RT and the inability to access diverse regions pose fundamental roadblocks to evaluation of potential mechanisms for the onset and progression of infection (and transmission). We present a model that incorporates detailed RT anatomy and physiology, including airway geometry, physical dimensions, thicknesses of airway surface liquids (ASLs), and mucus layer transport by cilia. The model further incorporates SARS-CoV-2 diffusivity in ASLs and best-known data for epithelial cell infection probabilities, and, once infected, duration of eclipse and replication phases, and replication rate of infectious virions. We apply this baseline model in the absence of immune protection to explore immediate, short-term outcomes from novel SARS-CoV-2 depositions onto the air-ASL interface. For each RT location, we compute probability to clear versus infect; per infected cell, we compute dynamics of viral load and cell infection. Results reveal that nasal infections are highly likely within 1-2 days from minimal exposure, and alveolar pneumonia occurs only if infectious virions are deposited directly into alveolar ducts and sacs, not via retrograde propagation to the deep lung. Furthermore, to infect just 1% of the 140 m

Cystic fibrosis (CF) is characterized by abnormal transepithelial ion transport. However, a description of CF lung disease pathophysiology unifying superficial epithelial and submucosal gland (SMG) dysfunctions has remained elusive. We hypothesized that biophysical abnormalities associated with CF mucus hyperconcentration provide a unifying mechanism. Studies of the anion secretion-inhibited pig airway CF model revealed elevated SMG mucus concentrations, osmotic pressures, and SMG mucus accumulation. Human airway studies revealed hyperconcentrated CF SMG mucus with raised osmotic pressures and cohesive forces predicted to limit SMG mucus secretion/release. Utilizing proline-rich protein 4 (PRR4) as a biomarker of SMG secretion, proteomics analyses of CF sputum revealed markedly lower PRR4 levels compared to healthy and bronchiectasis controls, consistent with a failure of CF SMGs to secrete mucus onto airway surfaces. Raised mucus osmotic/cohesive forces, reflecting mucus hyperconcentration, provide a unifying mechanism that describes disease-initiating mucus accumulation on airway surfaces and within SMGs of the CF lung. One Sentence Summary Hyperconcentrated Mucus Unifies Submucosal Gland and Superficial Airway Dysfunction in Cystic Fibrosis

COVID-19 remains an ongoing issue across the globe, highlighting the need for a rapid, selective, and accurate sensor for SARS-CoV-2 and its emerging variants. The chemical specificity and signal amplification of surface-enhanced Raman spectroscopy (SERS) could be advantageous for developing a quantitative assay for SARS-CoV-2 with improved speed and accuracy over current testing methods. Here, we have tackled the challenges associated with SERS detection of viruses. As viruses are large, multicomponent species, they can yield different SERS signals, but also other abundant biomolecules present in the sample can generate undesired signals. To improve selectivity in complex biological environments, we have employed peptides as capture probes for viral proteins and developed an angiotensin-converting enzyme 2 (ACE2) mimetic peptide-based SERS sensor for SARS-CoV-2. The unique vibrational signature of the spike protein bound to the peptide-modified surface is identified and used to construct a multivariate calibration model for quantification. The sensor demonstrates a 300 nM limit of detection and high selectivity in the presence of excess bovine serum albumin. This work provides the basis for designing a SERS-based assay for the detection of SARS-CoV-2 as well as engineering SERS biosensors for other viruses in the future.

Supramolecular biomaterials are promising systems to bind or deliver therapeutic growth factors given their great structural versatility and tunability of properties by simply mixing molecules. In this work, we have investigated this approach for the growth factor cytokine TGFβ-1, which is potentially important in the regeneration of damaged cartilage or in the prevention of fibrinogenesis of organs and the progression of tumors. Our previous work identified a peptide sequence capable of binding TGFβ-1 and supramolecular peptide amphiphile (PA) nanofiber hydrogels that displayed the sequence were found to enhance regeneration of cartilage in a rabbit model. In this work, we have synthesized novel PA molecules motivated by the tendency of the original bioactive peptide to undergo deamidation during purification procedures, thus interfering with synthesis of molecularly well-defined structures. We report here on novel PA nanofibers that can be purified without deamidation to establish if the chemical reaction affects chondrogenesis. Interestingly, we found that gels formed from nanofibers displaying a fully deamidated sequence by introducing an asparagine to aspartic acid mutation retain 25% more growth factor relative to those displaying the original bioactive peptide even though the individual peptides have similar affinity for the cytokine. We attribute this difference in growth factor retention to bundling of nanofibers displaying the original asparagine-containing sequence, thus masking the growth factor-binding structure. Improved retention of the growth factor resulted in chondrogenesis of cells encapsulated in the gels as indicated by a more than 50% increase in Sox 9 expressing cells at 3 days and a 100% increase in glycosaminoglycan production at 21 days. We have therefore been able to design a more effective bioactive supramolecular biomaterial to bind TGFβ-1, and also demonstrated how bioactive peptide sequences in supramolecular biomaterials can have impact on their structure at larger length scales that change their biological functions.

Because the positioning and clustering of biomolecules within the extracellular matrix dictates cell behaviors, the engineering of biomaterials incorporating bioactive epitopes with spatial organization tunable at the nanoscale is of primary importance. Here we used a highly modular composite approach combining peptide amphiphile (PA) nanofibers and silica nanoparticles, which are both easily functionalized with one or several bioactive signals. We show that the surface of silica nanoparticles allows the clustering of RGDS bioactive signals leading to improved adhesion and spreading of fibroblast cells on composite hydrogels at an epitope concentration much lower than in PA-only based matrices. Most importantly, by combining the two integrin-binding sequences RGDS and PHSRN on nanoparticle surfaces, we improved cell adhesion on the PA nanofiber/particle composite hydrogels, which is attributed to synergistic interactions known to be effective only for peptide intermolecular distance ofca. 5 nm. Such composites with soft and hard nanostructures offer a strategy for the design of advanced scaffolds to display multiple signals and control cell behavior.

A new class of hybrid biomaterials has recently evolved from the combination of peptides and DNA. In this chapter, we survey the unique systems and properties made possible by merging the bioactivity and mechanical properties of peptides with the programmability and reversibility of DNA. We explore peptide–DNA probes and switches, peptide-decorated DNA scaffolds and DNA-decorated peptide structures. We illustrate the rich variety of architectures made from the interplay of orthogonal peptide and DNA assembly motifs in cooperative assemblies, with examples of peptide-directed or DNA-directed hybrid structures. We present systems with hierarchical organization and dynamic assembly, presenting fascinating emergent properties made possible by peptide–DNA combinations. Finally, we discuss the future possibilities and open challenges presented by this intriguing class of hybrid biomaterials.

The single stranded DNA oligonucleotides known as aptamers have the capacity to bind proteins and other molecules and offer great therapeutic potential. Further work is required to optimize their function and to diminish their susceptibility to nuclease degradation. We report here on the synthesis and supramolecular self-assembly of DNA-peptide amphiphiles that form high aspect ratio nanofibers and display aptamers for platelet-derived growth factor. The nanofibers were found to bind the growth factor with an affinity that was fivefold greater than the free aptamer. We also observed that the aptamer displayed by the supramolecular nanostructures was eight times more nuclease resistant than free aptamer. In order to highlight the therapeutic potential of these supramolecular systems, we demonstrated the improved inhibition of proliferation when the growth factor was bound to aptamers displayed by the nanofibers.

Hierarchical assemblies of proteins into fibrillar structures occur in both physiologic and pathologic extracellular spaces and often involve interactions between oppositely charged peptide domains. However, the interplay between tertiary structure dynamics and quaternary hierarchical structure formation remains unclear. In this work, we investigate supramolecular mimics of these systems by mixing one-dimensional assemblies of small alkylated peptides bearing opposite charge and varying in peptide sequence. We found that assemblies with weak cohesive interactions readily create fibrous superstructures of bundled filaments as molecules redistribute upon mixing. Low cohesion allows molecules to escape from the original assemblies and exchange dynamics help them reassemble into electrostatically stable bundles. However, we also found that kinetic barriers can be encountered in these systems and limit formation of the hierarchical structures at pH values where charge densities are high. Increasing intermolecular cohesion using longer peptide sequences that form stable β-sheets was found to suppress superstructure formation. Our findings suggest that low internal cohesion in protein systems could facilitate the conformational rearrangements required to create hierarchical structures.

Because the positioning and clustering of biomolecules within the extracellular matrix dictates cell behaviors, the engineering of biomaterials incorporating bioactive epitopes with spatial organization tunable at the nanoscale is of primary importance. Here we used a highly modular composite approach combining peptide amphiphile (PA) nanofibers and silica nanoparticles, which are both easily functionalized with one or several bioactive signals. We show that the surface of silica nanoparticles allows the clustering of RGDS bioactive signals leading to improved adhesion and spreading of fibroblast cells on composite hydrogels at an epitope concentration much lower than in PA-only based matrices. Most importantly, by combining the two integrin-binding sequences RGDS and PHSRN on nanoparticle surfaces, we improved cell adhesion on the PA nanofiber/particle composite hydrogels, which is attributed to synergistic interactions known to be effective only for peptide intermolecular distance of ca. 5 nm. Such composites with soft and hard nanostructures offer a strategy for the design of advanced scaffolds to display multiple signals and control cell behavior.

DNA and peptides are two of the most commonly used biomolecules for building self-assembling materials, but few examples exist of hybrid nanostructures that contain both components. Here we report the modification of two peptides that comprise a coiled-coil heterodimer pair with unique DNA handles in order to link DNA origami nanostructures bearing complementary strands into micrometer-long one-dimensional arrays. We probed the effect of number of coils on self-assembly and demonstrated the formation of structures through multiple routes: one-pot assembly, formation of dimers and trimers and an alternating copolymer of two different origami structures, and stepwise assembly of purified structures with coiled-coil conjugates. Our results demonstrate the successful merging of two distinct self-assembly modes to create hybrid bionanomaterials expected to have a range of potential applications in the future.

DNA and peptides are two of the most commonly used biomolecules for building self-assembling materials, but few examples exist of hybrid nanostructures that contain both components. Here we report the modification of two peptides that comprise a coiled-coil heterodimer pair with orthogonal DNA handles in order to link DNA origami nanostructures bearing complementary strands into micrometer long one-dimensional arrays. We probed the effect of number of coils on self-assembly and demonstrated the formation of self-assembled structures through multiple routes, to form dimers and trimers, an alternating copolymer of two different origami bundles, and stepwise assembly of purified structures with coiled-coil conjugates. Our results demonstrate the successful merging of two distinct self-assembly modes to create hybrid bionanomaterials expected to have a range of potential applications in the future.

Creating soft materials with the tunable hierarchical structures observed in nature remains an enormous challenge. Synthetic hierarchical systems have been reported, yet strategies to reversibly modulate their structure and function are scarce. We report on the programmable self-assembly of peptide-DNA brush copolymers into supramolecular architectures that can be tuned with changes in temperature, pH, or addition of a soluble trigger. A fiber to bundle transition occurs upon mixing peptides bearing complementary oligonucleotides. These hierarchical structures can be reversed using the programmable nature of DNA-DNA interactions. The ability to encode the final assemblies in the composition of both amino acid and DNA building blocks provides a strategy for constructing a unique class of reconfigurable supramolecular materials.

In this chapter, we will outline key applications for DNA as a scaffold for interfacing with and guiding the activity of biological systems. DNA is a highly programmable molecular building block but generally lacks activity for signaling cells. However, by synthesizing hybrid molecules of DNA linked to biologically active molecules like proteins or peptides, it is possible to imbue them with bioactivity. We will focus on two main categories of DNA-based materials: (1) three-dimensional hydrogels for cell encapsulation and/or delivery and (2) two-dimensional surfaces for studying cell-matrix interactions. Critically, we will restrict ourselves to systems that incorporate cells and strive to mimic the extracellular environment. These materials are highly promising for a broad range of applications in biology, bioengineering, and medicine.

We report the construction of DNA nanotubes covalently functionalized with the cell adhesion peptide RGDS as a bioactive substrate for neural stem cell differentiation. Alteration of the Watson–Crick base pairing program that builds the nanostructures allowed us to probe independently the effect of nanotube architecture and peptide bioactivity on stem cell differentiation. We found that both factors instruct synergistically the preferential differentiation of the cells into neurons rather than astrocytes.

Protein- and peptide-based structural biopolymers are abundant building blocks of biological systems. Either in their natural forms, such as collagen, silk, and fibronectin, or as related synthetic materials, they can be used in various technologies. An emerging area is that of biomimetic materials inspired by protein-based biopolymers, which are made up of small molecules rather than macromolecules and can therefore be described as supramolecular polymers. These materials are very useful in biomedical applications because of their ability to imitate the extracellular matrix in both architecture and the capacity to signal cells. This article describes important features of the natural extracellular matrix and highlights how these features are being incorporated into biomaterials composed of biopolymers and supramolecular polymers. We particularly focus on the structures, properties, and functions of collagen, fibronectin, and silk, and the supramolecular polymers inspired by them as biomaterials for regenerative medicine.