Symposium SM04 : Understanding and Controlling the Structure and Function of Biomolecules at Material Interfaces

DNA has emerged as an exceptional molecular building block to engineer DNA nanostructures of increasing complexity. I will discuss our recent progress in designing complex DNA nanostructures and engineering 3D DNA crystals, and their applications in organizing proteins and nanoparticles for various functions.

A key challenge in nanotechnology is to design and fabricate nanostructures and nanodevices. Such systems can serve as platforms for basic science research (structural biology, molecular biology, for instance) at nanoscale, and for practical applications. Rational-designed self-assembly, particularly structural DNA nanotechnology has attracted significant attentions due to its programmability and its precise control of matter at nanoscale.

I am excited to have this opportunity to share some of our most recent research results (ke-lab.gatech.edu/publication.html). The tal will open with a brief introduction of structural DNA nanotechnology, followed by discussing our recent progress in making massive DNA nanostructures with complex shapes. In 2012, we invented a modular assembly strategy for constructing complex 3D shapes, up to 8 megadalton in size, using short synthetic DNA oligos — “DNA bricks”. Here, we will discuss this method and how a quantum leap in term of structure size and complexity was made recently. The next part of this talk will focus on reconfigurable DNA structures, particularly a new system that demonstrated controlling information transfer at molecular level using a DNA-based molecular network. The system’s transformation can be initiated at specific locations, and then propagate through prescribed pathways.

DNA and protein are the most significant biopolymers in nature – not only because of their important roles for life, but also because of their unique functions. Here, we demonstrate the extended applications of those two critical biomolecules with an avidin-biotin conjugation system. Successive and simple magnetic separation steps followed by randomly mixing traptavidin core proteins and four pre-programmed DNAs enable us to use a supramolecular nano-assembly platform to fabricate various functional and structural materials at the nanoscale. Traptavidin-DNA hybrid building-blocks with distinct tetravalency provide four independently programmable DNAs as well as a structurally rigid tetrahedral hub. Using this nano-assembly platform, we fabricate various plasmonic nanostructures with well-defined configurations and arrangements of nanoparticles in predetermined ways. Also, we synthesized dendrimer nanostructures using valency-controlled traptavidin-DNA hybrid molecules in programmable manner. We believe that these supramolecular building-blocks will contribute to the assembly of multicomponent and complicated nanostructures for contemporary applications from molecular imaging to biosensing.

The ability to design nanoscale bio-hybrid material surfaces with tailored morphology is crucial for the development of future devices for life science and molecular electronics. The creation of hierarchical nanostructures allows for a versatile approach to combine different materials classes into advanced functional nanopatterns. In this paper, we demonstrate the site-selective adsorption of DNA origami into hexagonally arranged nanoscale metallic surface pre-patterns.

DNA origami are widely used 2D-nanoobjects with tailored shape, which are fabricated by self-folding of designed DNA strands. DNA origami with triangular shape, as used in this work, tend to arrange themselves into close-packed layers if adsorbed onto solid surfaces, where they can be used as templates for molecular lithography, e.g. for the creation of protein or nanoparticle arrays. For the creation of protein or nanoparticle arrays with tailored periodicity, we investigate the DNA origami adsorption on pre-patterned surfaces.

To this end, we used nanosphere lithography to create self-arranged antidot pre-patterns with tailored feature sizes in the range of 100 - 400 nm on large substrate areas. The antidot patterns exhibit hexagonally arranged circular free substrate areas in metal thin films, creating simultaneously a periodical topography as well as a chemical contrast on the surface.
We demonstrate the positioning of single DNA triangles site-selectively inside these antidot-patterns in a gold thin film on a SiO2 surface. The influence of the adsorption conditions, i.e. buffer, salt and origami concentration and incubation time, on the yield of adsorbed DNA triangles is investigated. The functionalization of the origami prior to the deposition process is shown to allow for precise positioning of nanoparticles along with the origami. The created hierarchical nanopatterns of DNA with attached nanoparticles inside the antidots are investigated by AFM and SEM.

As the pre-patterning technique as well as the DNA origami positioning are easily applicable on large surface areas and the number of adsorbed origamis per antidot can be set by the pre-pattern dimensions, this approach largely enhances the flexibility of molecular lithography.

In this talk, I will present our latest progress in using nanomechanical interfaces to influence the adaptive biomechanics of living cells during cell migration, as a way to understand cell physiology and pathology. It is a research direction emerging at the interface of nanoscience, materials science, and biomechanics. We more focus on how the nano-mechanical components including soft and hard materials modulate the cell biomechanics and consequently cell physiology or pathology at the nanoscale level. Specifically, I will present the modulated cell migration by tailoring extracellular mechanical cues, mainly the topology and interfacial apparent stiffness of underlying substrates.

This communication reports the grafting onto iron oxide nanoparticles (IONPs) of recombinant polypeptides made of di-block elastin-like peptide (ELP_40-60) and cell-penetrating peptide (Tat) sequences.¹ The ELP₄₀ block is thermosensitive and undergoes a water de-swelling transition at a critical temperature around 42 °C in solution, the ELP₆₀ block is hydrophilic and provides colloidal stability to the resulting γ-Fe₂O₃@ELP_40-60-Tat core-shell IONPs. Magnetic cores were synthesized by a polyol pathway with controlled spherical morphology, size-dispersity and suitable heating efficiency under an alternating magnetic field (AMF).² The bio-functionalization of these IONPs with the di-block ELP_40-60-Tat was achieved by a convergent strategy through strong coordination bonding of a phosphonate group introduced near the N-terminus of the polypeptide. To the best of our knowledge, this is the first report on a thermosensitive ELP_m-n polypeptide brush grafting onto magnetic IONPs. Large temperature variations of the sample (up to 30 °C) could be obtained in a few minutes by applying an AMF. Fast size changes of the magnetic core-thermosensitive shell nanoparticles were measured by dynamic light-scattering (DLS) in situ while the AMF was on. Variations of the hydrodynamic size were compared to the classical polymer brush model revised for the highly curved surface of nanoparticles. Cellular internalization and toxicity assays were performed on a human glioblastoma (U87) cell line in view of applications for drug delivery activated magnetically. Superior cellular uptake of the IONPs@ELP_40-60-Tat was evidenced compared to IONPs@PEG control nanoparticles prepared from the same magnetic cores. The internalization pathway in lysosomes was monitored by electron microscopy on microtomes and confocal optical microscopy on live cells. Cellular toxicity after AMF application with these core-shell IONPs was ascribed to lysosomal membrane rupture and leakage into the cytosol. The intra-cellular fate of such IONPs, from their internalization to the effect of an AMF application, validates the use of thermosensitive peptide brushes on IONPs as drug delivery systems, addressing lysosomal compartments and triggering leakage of their content by external AMF application. Preliminary in vivo experiments evidenced the positive effect of the Tat peptide end-sequence compared to the PEG brush control on the bio-distribution, with similar contents in the liver and in U87 model tumor in mice. Long term fate (after 48 h) is discussed in view of the cell division with equal sharing of the magnetically loaded lysosomes among daughter cells, possibly envisioning the successive application of magnetic hyperthermia on time scales superior to the cellular life cycle.
¹ E Garanger, S MacEwan, O Sandre, A Brûlet, L Bataille, A Chilkoti, S Lecommandoux, Macromol. 2015, 48, 6617
² G Hemery, A Keyes, E Garaio, I Rodrigo, J A Garcia, F Plazaola, E Garanger, O Sandre, Inorg. Chem. 2017, 56, 8232

The significance of the overall fibrillar and porous nanoscale topography of the extracellular matrix (ECM) in promoting essential cellular processes has led to consideration of biomaterials with nanofibrous features. Of the many methods for fabricating fibers with micrometer and nanometer diameters, electrospinning is simplest, most straightforward and cost-effective. Fibers are produced by forcing a polymer melt or solution through a spinneret in the presence of a high electric field. This approach becomes intriguingly powerful when remarkable morphological features such as very large surface area to volume ratio and porosity are combined with unique chemical, physical, or mechanical functionalisation by adding desired components with ease and control. Our current research focuses on exploring new possibilities to fabricate three-dimensional Nano-biointerfaces that synergise the nanostructural induction and the bioactives signalling to affect cellular behaviours, such as cell adhesion and migration, proliferation and stem cell differentiation. The biomimetic nanofibers that are responsive to external stimuli, such as temperature, pH, light, and electric/magnetic field were also developed for therapeutic delivery and intervention.

Polymer/virus composite fibers have the potential to combine the structural properties of a polymer with the site-specific chemistry of viral proteins. Because viruses can be genetically modified to display a range of high affinity peptides, they can be tailored to different applications. One such virus, the filamentous M13 bacteriophage, has found utility in cellular scaffolds, biotemplates, biosensors and drug release. For these polymer/M13 composite fibers, enriching specific fiber interfaces can enhance functionality. For example, in biosensing and cellular scaffold applications, the surface of the fiber is the critical interface; biomolecule surface enrichment can improve sensor sensitivity and encourage cell growth. For controlled-release applications, the important interface is within the volume of the fiber; biomolecule core enrichment can help to sustain or delay drug delivery.
One method of producing polymer/M13 fibers is near-field electrospinning, a scalable direct write fabrication method utilizing a strong applied voltage to fabricate fibers quickly and precisely. The electric field generated during the near field electrospinning process has the potential to interact with the pH-modified surface charge of the M13 virus and enrich the fiber interface.
In this work, we characterized the spatial distribution of a streptavidin-binding M13 bacteriophage encapsulated within near-field electrospun polyvinyl alcohol (PVA) fibers as a function of spinning solution pH. The viral spatial distribution was evaluated with confocal fluorescence microscopy by covalently tagging M13 with fluorescent molecules. At pH values above the isoelectric point (pI), the electric field generated during electrospinning attracted the negatively charged M13 to the fiber surface, resulting in surface-enriched fibers. Conversely, at pH below the pI, the positively charged M13 were drawn to the fiber core, resulting in core-enriched fibers. To further evaluate the polymer/M13 interface, the fibers were crosslinked and incubated with streptavidin-conjugated gold nanoparticles. Surface-enriched PVA/M13 fibers demonstrated greater streptavidin affinity than core-enriched fibers. These results show that M13 virus distribution can be controlled via pH during the near-field electrospinning process to produce enhanced functional PVA/M13 fibers.

Detecting H₂S in living cells has attracted a lot of attention because H₂S is one of the most important gaseous mediator for regulation of cellular signal transduction pathways which is related to many diseases such as Alzheimer’s disease, Down’s syndrome, diabetes and liver cirrhosis. Two-dimensional (2D) nanomaterials possess the highest surface-to-volume ratio and have exceptional optical and electrical properties which make them extremely prospective for sensors applications. Previously, our group demonstrated the assembly of 2D membrane-mimetic nanomaterials from lipid-like peptoids (sequence-defined poly-N-substituted glycines). Large flexible surface area and good stability make these 2D nanomambranes have great potential in sensing probes. Due to the large side-chain diversity of peptoids, the surface functions of the 2D nanomembranes could be tuned and achieved easily through side-chain chemistry. Normally, fluorescent probes for H₂S have been developed based on specific chemical reactions by taking advantage of the reducing or nucleophilic properties of H₂S. In this work, the dinitrophenyl ether group were introduced into 3 position of 1, 8-naphthalimide to give the two-photo fluorescent group (Nap-NI), which acted as the H₂S reactive site. Compared to traditional fluorescent probes work with one photo microscopy, two-photon fluorescent probes reduced phototoxicity, increased specimen penetration, and negligible background fluorescence. The Nap-NI groups were modified on the peptoid sequences (Pep-Nap-NI) to achieve self-assembled 2D nanomembranes using as H₂S sensor. Atomic force microscopy (AFM), Transmission electron microscopy (TEM) and X-ray diffraction (XRD) results demonstrate that the assembled structures are highly crystalline and is similar with the model we developed in previous work. The absorption and fluorescence titration experiments of peptoid 2D probes with H₂S were recorded in aqueous solution with different dosage of H₂S. The selectivity of peptoid 2D probes for H₂S over reactive oxygen species (ROS), reactive nitrogen species (RNS) was also verified. We will also tested the ability of the peptoid 2D probes to be used to visualize and monitor the H₂S in live cells in the following experiments. In consequence, we developed a fluorescent probe for imaging H₂S based on 2D nanomembrane assembled from peptoids, which could rapidly react with H₂S in aqueous solution. It provides a new promising 2D platform as biosensor for imaging some biomarkers in living cells.

The design of new biomaterials for the targeted delivery of poorly water-soluble antimicrobial peptides that are sensitive to degradation is a major challenge in the biomedical field. In this context, antimicrobial peptides are gaining increasing attention as promising alternatives to conventional antibiotics in the light of the global emergence of antibiotic resistance. This presentation demonstrates the structural engineering of functional nanocarriers for antimicrobial peptides. These nanocarriers arise from the self-assembly of structure-forming biomolecules including amphiphilic lipids and nanocellulose. The comprehensive design of these functional nanomaterials requires an in-depth understanding of their structural and morphological characteristics. Small angle X-ray and neutron scattering (SAXS, SANS), dynamic light scattering (DLS) and cryogenic transmission electron microscopy (cryo-TEM) showed that the antimicrobial peptides actively and critically integrate into the self-assembled nanocarriers, where they contribute to alterations in the structural features. For instance, certain antimicrobial peptides together with the amphiphilic lipids glycerol monooleate and oleic acid self-assemble to bicontinuous cubic structures, hexagonal- and sponge phases in water, depending on the composition and pH.[1,2] The pH-induced phase transitions in this system can be applied to release the peptide on demand for targeted delivery to bacteria infected locations in the body. These pH-responsive lipid structures mimic the highly ordered nanostructures that were discovered to form in situ during milk digestion, where they function as carriers for essential, poorly water soluble food components in the digestive tract, securing human survival.[3,4,5] Briefly, this presentation sheds light on the formation and transformation of functional bio-nanostructures with the aim of designing biomimetic delivery systems for antimicrobial peptides as alternative to conventional antibiotics.
1. Gontsarik M., Buhmann M., Yaghmur A., Ren Q., Maniura W., Salentinig S. J. Phys. Chem. Lett. 2016, 7, 3482–3486.
2. Gontsarik M., Mohammadtaheri M., Yaghmur A., Salentinig S. Biomaterials Science 2018, accepted, DOI: 10.1039/C7BM00929A.
3. Salentinig S., Phan S., Khan J., Hawley A., Boyd B. ACS Nano, 2013, 23, 10904-10911.
4. Salentinig S., Phan S., Hawley A., Boyd B. Angew. Chem. Int. Ed., 2015, 5, 1600-1603.
5. Salentinig S., Amenitsch H., Yaghmur A., ACS Omega, 2017, 2, 1441–1446.

BACKGROUND
(photosynthetic proteins and its highly efficent energy harvesting)

Nano-scale patterns of LH (light-harvesting) pigment-protein complexes in a photosynthetic membrane are known to capture photons that is followed by an highly efficient excitation energy transfer[Ke, Photosynthesis]. A typical photosynthetic membrane takes a configuration of LH2 complexes surrounding LH1-RC (reaction center) complexes. In this distribution, excitation energy transfer from LH2 to LH1-RC are known to be accomplished in a high efficiency. One way to reveal how this protein distribution is contributing the excellent photon-electron conversion is to compare the photovoltaic signal from the actual co-assembled system of LH1-RC and LH2 in different distributing patterns.

WHAT WE HAVE DONE
(patterning of two LH proteins and its photoelectric measurement)

We have prepared a co-immobilized LH1-RC and LH2 on a common substrate. Isolation and immobilization methods of each proteins are described in our previous reports [Yajima, Appl. Phys. Lett. 2012] [Kondo, Biomacromol., 2012]

Using this sample substrate, photoelectric signal was observed using different illuminating wavelengths that each correspond to the excitations of LH1 and LH2 pigments.

As a result, enhancement of photocurrent was observed from LH1-RC with the co-existence of adjacent LH2. In addition, enhancement was as well observed using LH2 excitation wavelength compared to the case using LH1 exciting wavelength. The result indicates that the rearranged organization of LH complexes onto an inorganic substrate was successful in exhibiting the characteristic of natural photosynthetic membrane.

The work is expected to be useful in providing guidelines for materials design for organic/inorganic solar cells as well as its contribution for photosynthetic study field.

Antimicrobial peptides (AMPs) have gained fast and growing interest in the past decades as they represent a viable alternative for the increasing bacterial resistance to conventional antibiotics. The cationic charge and amphipathicity of AMPs play an important role in their antimicrobial activity. The antimicrobial mechanism is still under debate, although a few models have been proposed to date, including barrel-stave, carpet, and toroidal-pore models. The secondary structure of cationic AMPs could highly affect the antimicrobial activity, which implies it has a significant role in the AMPs mechanism of action. Some artificially-designed AMPs can also form supramolecular assemblies. However, the specific and interconnected roles of the secondary structure and/or the self-assembled structures of AMPs on their antimicrobial activity and mechanism of action are not fully understood. Here, we explore the effect of pH and time on the secondary structure and the supramolecular assemblies of a well-studied AMP, GL13K (GKIIKLKASLKLL-NH₂). GL13K was derived from a potential host defense salivary protein BPIFA2, and it is bactericidal to Gram-negative and Gram-positive bacteria and their biofilms.
GL13K and its randomized non-antimicrobial sequence, GL13K-R (IGIKLLKSKLKAL-NH₂) were prepared in sodium borax buffers at increasing pH=8.0-10.6 to further investigate the effect of peptide charge on their structural changes. The calculated net charge of GL13K and GL13K-R is +5 at pH 7 and 0 at pH 14 (pI). Thus, the selected pH range has the highest change in net charge. The secondary structures of GL13K and GL13K-R were explored with circular dichroism (CD) spectroscopy at different times after peptide dissolution up to 9 days. To better understand the mechanism by which the secondary structures govern self-assembly of these peptides, the supramolecular structures were characterized by negative stained transmission electron microscopy (TEM) and dynamic light scattering (DLS).
The two peptides showed notable differences in structural conformations and assemblies as a function of both pH and time. Whereas the non-antimicrobial GL13K-R maintained unstructured configurations at all pH and times tested, the antimicrobial GL13K underwent a significant transformation to beta-sheet configurations at pH>9.6. These transformations occurred over time at pH=9.6-10.0, but at pH>10.0 stable beta-sheet configurations were detected right after peptide dissolution. TEM images showed that beta-sheet signal of GL13K at pH>9.6 was caused by the peptides self-assembly to twisted ribbons with thickness of 5-30 nm and length of as long as a few micrometers. DLS analysis confirmed the formation of these supramolecular assemblies. These results highlight the relevance of the secondary structure and supramolecular assemblies of the peptides formed as charge neutralization occur and how it might assist in the unraveling of the antimicrobial mechanism of these designed AMPs.

Amphiphilic coating has gained much attention due to its dual hydrophobic and hydrophilic properties. Due to their bifunctional nature, it has been suggested that the amphiphilic coatings resist the attachment of organisms and the adhesion of complex protein or glycoprotein adhesives secreted by the colonizing organisms. Most amphiphilic coatings are polymers based on oligo- and polyethylene glycols (OEG and PEG). Spontaneous self-assembled amphiphilic peptide brings advantages of the protease resistance property of the backbone sequencing, precise control of molecular weight and side chain composition versatility. In this work, we focus on the antifouling performance of a self-assembly amphiphilic tripeptide with rational positioning of the amino acids within the peptide chain and influence of the C and N terminus when the amino acids are in the same position. We have selected 3, 4-dihydroxy-L-phenylalanine (DOPA) as the binding amino acid to the surface, 4-fluoro-phenylalanine (Phe(4F)) as the hydrophobic amino acid due to its fluorinated side chain, and Lysine (Lys) as the hydrophilic amino acids. Our result indicates that the sequencing of amino acids affects the antifouling performance, particularly with lysine adjacent to a DOPA at the C terminal and Phe(4F) at the N terminal.

The response of polyelectrolytes to specific environmental conditions has attracted materials scientists for decades. Recently, end-grafted polyelectrolytes, denoted “polyelectrolyte brushes”, have flourished due to their relevance in biological systems and in various applications in materials science and nanotechnology. We combined the surface forces apparatus (SFA), atomic force microscopy (AFM) techniques, and coarse-grained molecular dynamics (MD) simulation method to study the structure of high-density polystyrene sulfonate (PSS) brushes in a variety of solvent conditions. Surface force and AFM measurements show that the presence of multivalent counterions, even at relatively low concentrations, can strongly affect the structure of polyelectrolyte brushes.Taken together, AFM, SFA, and MD in unison described a system in which solvophobic and multivalent ion induced effects together drive strong phase separation, with electrostatic bridging of polyelectrolyte chains playing an essential role in the collapsed structure formation. The subtle details of a polyelectrolyte brush’s environment can strongly dictate its structural features and potential applications.

Molecular assembly based on Watson-Crick base-pairing has enabled the construction of complex 2D and 3D DNA nanostructures to be used in widespread applications including photonics, biosensing, enzymatic catalysis, single-molecule fluorescence, and drug delivery. In particular, scaffolded DNA origami involves the cooperative binding of large numbers of short single-stranded DNA (ssDNA) helper strands to “staple” a long ssDNA into a predesigned object. However, the order of assembly and different folding pathways to assemble these DNA nanostructures still remain unclear. Recent efforts have utilized a combination of ex situ imaging techniques, i.e., transmission electron microscopy and atomic force microscopy (AFM) to observe the structures of intermediates formed at each annealing step. However, the transient intermediates may experience structural distortions and damages because these approaches require the DNA samples to be transferred from solutions and deposited onto mica surfaces for imaging. In addition, there is a lack of direct evidences as to how a particular DNA origami structure evolves from a random-coil scaffold strand.
Here, we utilized a recent DNA imaging method developed in our group to resolve the structures and kinetics of intermediates in situ along the DNA origami folding pathway. Thiolated DNA probes were inserted stochastically into the defect sites of negatively charged carboxylate-modified alkanethiol self-assembled monolayers (SAMs). These probes were then hybridized and crosslinked with double-stranded DNA precursors. Surface-tethered DNAs were then denatured to yield single-stranded scaffolds, enabling hybridization with DNA staples in the solution phase. Divalent cations were used to immobilize the surface-tethered intermediates onto the negatively charged SAMs for AFM visualization, while monovalent cation solutions enable intermediates to be released from the surface and hybridize with DNA staples. Because DNA scaffolds were tethered to surfaces, we were able to follow the evolution of each DNA origami with minimal structural distortion and damages. Using formamide to vary “effective” temperatures, we showed that the optimal folding temperature ranges not only agree with solution-phase studies, but could also be translated to surface-assisted folding of DNA origami structures. Moreover, we showed that the thiolated DNA probes act as surface seeds to nucleate different 2D origami structures, rectangles and crosses, simultaneously on the same substrate. Thus, our approach not only offers new insight into folding intermediates, but also provides a convenient method to generate single-stranded scaffolds from virtually any double-stranded DNAs, which can be mass-produced via polymerase chain reactions.

Advanced functional materials with stimuli-responsive and/or adaptive behaviors are highly promising for several applications (e.g., sensing, piezoelectronics, mechanical actuation, filtration). Although dynamic behavior has been demonstrated in both two-dimensional (2D) and 3D frameworks, the successful prediction and bottom-up design of these properties remains a formidable challenge. This is because dynamic behavior necessitates a free-energy landscape which is traversable in a prescribed manner, permitting the population of various functional states. In Nature, the thermodynamics of proteins and biomolecular assemblies have been evolutionarily optimized to carry out their functions, and thus the design of new materials which rival these systems requires a detailed understanding of how to appropriately balance thermodynamic factors to achieve the desired conformational flexibility. Here we report the calculated free-energy landscape of a previously characterized dynamic 2D protein crystal, rationalize its profile in terms of the constituent enthalpic and entropic components, and harness this information to rationally perturb the landscape, giving rise to a predictable modulation of the crystal dynamics which is confirmed experimentally. By careful selection of the identity and placement of these mutations, we demonstrate that this modification simultaneously affords a novel degree of control over the conformational state of the lattice via reversible metal coordination interactions.

Bone and dentin are composite materials with a high degree of hierarchical structure, which contributes largely to their biomechanical and biochemical properties. The tissues are composed of well-ordered self-assembled collagen fibrils as the organic template mineralized with uniaxially oriented and tightly packed HAP nanocrystals. It is widely accepted that unstructured acidic non-collagenous proteins (ANCPs) act as promoters or inhibitors of mineral deposition in the regulation of biomineralization. Osteocalcin (OCN) is a small, highly structured NCP that is found in abundance in bone. Recent findings have discovered that the partially carboxylated form of OCN is a multifunctional hormone, yet, surprisingly little is known about the detailed mechanisms by which the fully carboxylated form of OCN regulates mineralization. In this study, we focused on the potential roles of OCN in collagen fibrillogenesis and mineralization using various in vitro experimental methods. This NCP was found to regulate both collagen fibril formation and intrafibillar calcium-phosphate (Ca-PO₄) mineralization. Results of fibrillogenesis and immunogold labeling studies showed that OCN was localized primarily in the intrafibrillar collagen matrix, especially at the boundary between the overlap and hole zones where crosslinking of collagen occurs. The mineralization studies revealed that OCN modulates mineralization by inhibiting rapid extrafibrillar Ca-PO₄ particle precipitation. Transmission electron microscopy results showed that small, highly hydrated, OCN-stabilized spherical nanoclusters of Ca-PO₄ were found on the outer surface of the fibrils. The nanoclusters are proposed to infiltrate the fibrils ultimately resulting in intrafibrillar mineralization with HAP crystals aligned with the fibrils and, at the same time, retarding rapid extrafibrillar mineralization. This mechanism is similar to that observed for unstructured ANCPs. The present findings contribute to understanding the multiple roles of OCN in regulating mineralization, as well as elucidating design principles of small synthetic analogs of OCN for promoting bone biomaterials at a reduced cost.

Hierarchical assembly of nanostructures is a significant challenge in nanotechnology. Several excellent strategies, including employing DNA linkers, block co-polymers or patchy particles, have led to exquisite nanocrystal assemblies. Nevertheless, most efforts have been focusing on the discovery and utilization of the primary structure and chemical functions of these specific (bio)molecules. The higher order structures of biomolecules which play important roles in biomaterial growth and assembly, however, remain largely unexplored in material structure creation. In this presentation, we will share the important roles of primary and secondary structures of biomolecules in both the morphology controlled synthesis of nanocrystals growth and their following anisotropic assembly into long-range hierarchical structures.

An outstanding question in molecular recognition at interfaces is how the spatial organization of the ligand/probe molecules impacts the energetics and kinetics of this process. Unlike a ligand molecule in a dilute solution, the ability of an immobilized ligand (or probe) to recognize targets may be profoundly influenced by interactions with the local chemical environment, which consists of the neighboring probe molecules, the spacer molecules near the probe molecules, and the substrate. An increasing body of evidence suggests that the molecular components are often not uniformly distributed. It is difficult to derive molecular level insight from existing ensemble averaging measurement of highly heterogeneous systems.

We have focused on DNA functionalized self-assembled monolayers (DNA SAMs) as the model system to understand how the complex interactions between the probe molecules impact molecular recognition on biosensors. We have developed new atomic force microscopy (AFM) techniques to image the single DNA probe molecules on model E-DNA sensor surfaces with substantially improved spatial resolution (a few nanometers). For the first time, we can map the spatial organization of DNA probe molecules on DNA SAMs at probe densities relevant to electrochemical DNA sensors. Our in situ AFM has provided new insight into the conformational changes and hybridization of single molecules. We have developed and applied spatial statistical models that allow us to correlate the spatial patterns of molecular components to the hybridization kinetics as well as electrochemical signaling. Our results not only confirmed the “crowding” effect at short spatial scales<15nm but also revealed a surprising cooperative effect: a probe molecule may increase the rate of target capture of another probe molecule that is 20-30 nm away. The origin of this effect will be discussed.

The results from our single molecule measurement revealed a new level of complexity of interfacial molecular recognition on a simple model system. The findings showcase the importance of high resolution, in situ, single molecule studies of such heterogeneous systems. With the improved knowledge of how complex interactions at the interface impact molecular recognition, we may begin to rationally tailor interfacial properties to enable biosensors that are more sensitive, selective and reliable.

2D materials such as graphene exhibit unique electronic and mechanical properties that promise substantial advantages in applications ranging from nanoelectronics to human health. Such interfaces are often functionalized noncovalently with lying-down phases of functional molecules to avoid disrupting electronic structure with the basal plane. Structurally, such molecules are often very similar to amphiphiles found in biological cell membranes, though the overall surface chemistry is strikingly different -- in essence, a repeating cross-section of a lipid bilayer, with both hydrophilic and hydrophobic components exposed at the environmental interface in a structured manner. As 2D materials are integrated into hybrid materials and devices, this functionalization approach raises two classes of significant questions: (1) How do noncovalent lying-down phases of phospholipids and fatty acids respond to solution or thermal processing? More generally, to what extent can structural design principles from the cell membrane be invoked to control chemical functionality and reactions at the interface? (2) Can noncovalently-adsorbed layers be patterned to template further interactions with the environment? Lying-down phases of phospholipids and fatty acids present 1-nm-wide stripes of ordered chemical functional groups, suggesting the possibility of controlling processes such as crystallization, phase segregation, or analyte binding. We examine these questions, again integrating design principles from biological cell membranes, which use hundreds of structurally different amphiphiles to create a complex noncovalent interface of central biological importance.

Transmembrane photosynthetic proteins, Photosystem I (PSI) are nano-scale biological photodiodes that enable light-activated unidirectional electron flow. The robust photochemical properties make PSI a promising candidate for harnessing solar energy.^1-3 However, the role of natural membrane confinements of PSI in orchestrating this photoactivated charge separation with near unity quantum efficiency is ill-understood yet, imperative for the rational design of PSI-based energy conversion devices. Motivated by this lack of fundamental understanding, herein we investigate the photoactivity of biomimetic constructs of cyanobacterial PSI encapsulated within solid-supported lipid bilayers (SLB) assembled on electrodes. PSI-confined SLBs are assembled from PSI-proteoliposomes that are synthesized from our recently developed facile routes for engineering negatively charged phospholipid (DPhPG) bilayer membranes.⁴ Absorption/fluorescence spectroscopy and direct visualization using atomic force microscopy (AFM) have already demonstrated the formation of biomimetic PSI-proteoliposomes that indicate alterations in photo responses as evident from their unique emission signatures.⁵ In this talk, we present detailed chronoamperometry measurements to investigate the corresponding photocurrent variations arising from the aforementioned PSI confinements in SLBs supported on self-assembled monolayer (SAM) substrates. These measurements, in conjunction with cryo-transmission electron microscopy (cryo-TEM), AFM imaging and force spectroscopy, allow for direct visualizations and detection of SLBs of PSI-proteoliposomes on the substrates. Our results indicate the role of microenvironment alterations heretofore not considered in triggering ~ 4-5 fold enhancements in photocurrents generated from PSI complexes under SLB confinements as compared to those from a dense monolayer of equivalent concentrations of PSI on SAM substrates.⁶ Such studies provide deeper insight into the functional roles of membrane scaffoldings in optimizing charge transport efficiencies in photosynthetic proteins.
References:
(1) T. Bennett, H. Nirooman, R. Pamu, I. Ivanov, D. Mukherjee, B. Khomami; PCCP, 2016, 18, 8512.
(2) D. Mukherjee, M. May, B. Khomami; J. Coll. Interf. Sci., 2011, 358, 477.
(3) D. Mukherjee, M. May, M. Vaughn, B. D. Bruce, B. Khomami; Langmuir, 2010, 26, 16048.
(4) H. Niroomand, G. A. Venkatesan, S. A. Sarles, D. Mukherjee, B. Khomami; J. Membr. Biol., 2016, 249, 523.
(5) H. Niroomand, D. Mukherjee, B. Khomami; Scientific Rep., 2017, 7.
(6) H. Niroomand, R. Pamu, D. Mukherjee, B. Khomami; Nature Nanotech., 2017, Submitted.

Understanding the interaction between complex (bio)molecules and inorganic surfaces lies at the heart of a number of fundamental and industrial research areas with applications ranging from healthcare to energy, from food to environmental protection. In particular, the ability to characterise the resulting interfaces at high spatial resolution has been the key to significant advancements in the field and is thus a major investigation topic.
This talk will present recent advances in the use of high-resolution scanning tunnelling microscopy (STM) to analyse a number of (bio)molecule-surface model systems with increasing complexity. It will start from analysing how the two dimensional self-assembly of simple amino acids is already influenced by their conformational flexibility. It will then move onto dipeptides to show that, when interacting with metallic surfaces, these molecules can undergo reactions similar to those catalysed by enzymes with significant consequences for their structure, assembly and chirality. The discussion will then proceed to analyse the limits that standard molecular deposition techniques impose on the size of (bio)molecules that can by studied in surface science. Finally it will be demonstrated that these limitations can be overcome by using soft ionisation techniques capable to transfer thermolabile complex molecules in the gas phase and to soft land them intact onto surfaces under fully controlled depositions conditions. In particular, it will be shown that a combination of electrospray vacuum deposition and high-resolution STM allows the imaging of individual macromolecules with unprecedented detail, thereby unravelling structural and self-assembly characteristics that have so far been impossible to determine.

Noncovalent modification of graphene with biomolecules such as DNA/RNA, protein, peptides and others is a promising method for fabricating novel sensors with high biosensing performances on both sensitivity and selectivity. However, predicting and characterizing adsorbed biomolecules at graphitic interfaces raises substantial theoretical and experimental challenges.
In this presentation, I will introduce our recent results, which studies the structure of peptides and RNA molecules adsorbed on graphene and graphite interface by employing advanced atomic force microscopy (AFM) and molecular dynamics (MD) simulations.^1,2 For amyloid peptide adsorbed on hydrophobic graphite interface, the early Aβ peptide aggregates forming the molecular monolayer are investigated. The Aβ peptide molecular monolayer consisting of novel parallel β strand like structure is further revealed by means of a AFM based quantitative nanomechanical spectroscopy technique with force controlled in pico Newton range, combining with MD simulation. The identified parallel β strand like structure of molecular monolayer on graphite interface is distinct from the antiparallel β strand structure of Aβ amyloid fibril.¹ For RNA molecules adsorbed on graphene interface in water, the AFM results showed that the key parameters governing the RNA’s behavior on the graphene surface are the number of graphene layers, RNA concentration, and temperature. At high concentrations, the RNA forms a film on the graphene surface with entrapped nanobubbles. The density and the size of the bubbles depend on the number of graphene layers. At lower concentrations, unfolded RNA stacks on the graphene and forms molecular clusters on the surface.² Our findings on the structure of biomolecules adsorbed on graphitic interfaces would facilitate new applications of graphene derivatives in biosensors and biotechnology.

References:
[1] Identification of parallel β-stand conformation within molecular monolayer of amyloid peptide, Liu, L.†; Li, Q.†; Zhang, S†; Wang, X.F.;Hoffmann, S. V.; Li, J.Y.; Liu, Z.; Besenbacher, F.*; Dong, M.D.*, Advanced Science, 2016, 3, 1500369
[2] Tuning of RNA nanopatterning on graphene, Li, Q.; Froning, J.P.; Pykal, M.; Zhang, S.; Wang, Z.G.; Vondrák, M.; Banáš,P.; Čépe, K.; Jurečka P.; Šponer, J.; Zboril, R.; Dong, M.D.*; Otyepka, M.*
ACS Nano, 2017, under review,

Basic blocks of DNA are very interesting constituents for designing supramolecular single-layer and multilayer surface architectures. Our recent studies of self-assembly of nucleoside derivatives in monolayer films at the air-water interface (Langmuir films) reveal that guanosine derivatives exhibit very different behaviour from analogous derivatives containing other nucleobases [1]. We also demonstrated that the number of lipophilic chains attached to the sugar hydroxyl groups and the type/concentration of ions present in the water subphase strongly affected molecular organization of guanosine derivatives in Langmuir monolayers as well as in Langmuir-Blodgett (LB) films deposited on various solid substrates [2,3,4]. Modifications of these parameters hence provide a possibility of tuning intermolecular organization in thin film configurations.
An appealing strategy for control and manipulation of intermolecular organization is to use optical irradiation. To test the applicability of this method in case of guanosine derivatives we investigated Langmuir films of azo-functionalised guanosine molecules in which the isomerisation can be switched from trans to cis and vice versa by irradiation with UV and visible light. Photoinduced modifications within Langmuir films were studied by film balance experiments and by Brewster angle microscopy (BAM). We were able to revesibly induce changes in the surface pressure of the film by alternatingly irradiating with UV and blue light, indicating a light-induced change in the film structure. We also investigated effect of optical irradiation on binding properties of the film for different compounds added either to the water subphase or to the air-water interface.

[1] L. Čoga, T. Ilc, M. Devetak, S. Masiero, L. Gramigna, G. P. Spada, and I. Drevenšek Olenik, Colloid. Surface B 103, 45 – 51 (2013).
[2] M. Devetak, S. Masiero, S. Pieraccini, G. P. Spada, M. Čopič, and I. Drevenšek Olenik, Appl. Surf. Sci. 256, 2038 – 2043 (2010)
[3] L. Čoga, S. Masiero, and I. Drevenšek Olenik, Colloid. Surface B 121, 114 – 121 (2014)
[4] L. Čoga, S. Masiero, and I. Drevenšek Olenik, Langmuir 31, 4837 – 4843 (2015)

The known types of interactions between proteins and a surface include electrostatic, dipolar, van der Waals forces, steric forces or specific hybridization. To modify the interaction one would normally change the surface decoration or surface chemistry.
Remarkably, this is not the only way to control protein-surface interactions by surface science. As a new approach we use highly crosslinked polymer films that can be hydrated and can incorporate an intrinsic chemical nano-gradient that generates a surprisingly long-range modification of interaction. We elucidate the mechanisms of this effect and show that it is the water confined in such subsurface gradients that spawns a dipolar field that significantly affects the protein-surface interaction.
The required subsurface gradients are realized in form highly crosslinked polymer layer of typically ≈50nm thickness. Using neutron reflectometry we have scrutinized and quantified the hydration of such films. Then, using the transmission interferometric adsorption sensor (TInAS [1]) we have also studied how the adsorbed mass of bovine serum albumin (BSA) is modified [2]. Detailed analysis of water contact angles and their kinetics during hydration and dehydration suggest that there is subsurface layer of confined water molecules in a ferroelectric state. This subsurface hydration was further investigated using neutron reflectometry [3] and it could be shown that water is present in subsurface regions.
The adsorption of (BSA) onto TInAS sensors, coated with plasma polymer films [4], show that there is a significant reduction of adsorbed mass in presence of water in the subsurface gradient, as compared to reference samples.
Therefore, proteins adsorb differently, although the surface chemistry and solution parameters are identical.



[1] Heuberger, M. and T. Balmer, Journal of Physics D: Applied Physics, 2007. 40: p. 7245-7254
[2] Blanchard, N.E., et al., Plasma Processes and Polymers, 2015. 12(1): p. 32-41
[3] Blanchard, N.E., et al., Langmuir, 2015. 31(47): p. 12944-12953
[4] Hegemann, D., N.E. Blanchard, and M. Heuberger, Plasma Process. Polym. 2016, 13, p.494–498

We have developed a universal nanosensor array for biosystems analyses. The array is composed of non-specific nanoreceptors which were assembled using three types of two-dimensional (2D) nanoparticles; nGO, MoS₂, or WS₂; and various fluorescently labeled single stranded DNA (ssDNA) molecules. The array was first employed for the identification of three radically different biosystems; five proteins, three types of live breast cancer cells and a structure-switching event of a macromolecule. The data matrices for each system were processed using Partial Least Squares (PLS) discriminant analysis. In all of the systems, the sensor array was able to identify each entity as separate clusters with 95% confidence and without any overlap. Out of 15 unknown entities with unknown protein concentrations tested, 14 of them were predicted successfully with correct concentration. 8 breast cancer cell samples out of 9 unknown entities from three cell types were predicted correctly. Later the nanosensor array was used for the discrimination of nine miRNA analogs which belong to the same miRNA family. All nine targets are highly similar in sequence, differing by only a single or few nucleobases. Both the identity and concentration of the unknown targets were determined using double-blind tests with this combinatorial approach. Unlike the typical lock-and-key sensing strategy, which relies on the most dominant interactions between the probe and target, our sensor array takes every single; minor or major; non-specific interaction into account. Therefore, this approach is bias-free, in which the background or possible false-positive signals are already included in the large data set. The analysis of the comprehensive big data set enables simultaneous and precise identification of every single non-specific entity tested with our sensor array. Multiple compounds can be analyzed simultaneously with a single step and separation-free procedure. Though we have studied only four groups of biosystems, this approach is universal and can be applied to a wide-range of biological and environmental systems analyses.

Controlling ion and water transport on a molecular scale is important for applications ranging from industrial water treatment and membrane separations to bioelectronic interface design. Living systems move ions and small molecules across biological membranes using protein pores that rely on nanoscale confinement effects to achieve efficient and exquisitely-selective transport. I will show that carbon nanotube porins—pore channels formed by ultra-short carbon nanotubes assembled in a lipid membrane—can exploit similar physical principles to transport water, protons, and small ions with efficiency that rivals and sometimes exceeds that of biological channels. I will discuss the role of molecular confinement in these pores, and show how it can enhance water and proton transport efficiency, and influence the mechanisms of ion selectivity in these pores. Overall, carbon nanotube porins represent a simple and versatile biomimetic membrane pore that is ideal for studying nanoscale transport phenomena, and building the next generation of separation technologies and biointerfaces.

Proteins represent the most versatile building blocks available to living organisms or the laboratory scientist for constructing functional materials and molecular devices. Underlying this versatility is an immense structural and chemical heterogeneity that renders the programmable self-assembly of proteins an extremely challenging design task. To circumvent the challenge of designing extensive non-covalent interfaces for controlling protein self-assembly, our group has developed chemical bonding strategies based on fundamental principles of inorganic and supramolecular chemistry. These strategies have resulted in discrete or infinite, 1-, 2- and 3D protein architectures that display high structural order over large length scales (yet are dynamic/adaptive and stimuli-responsive) and possess new emergent chemical/physical properties.

One dimensional (1D) organic nanotubes (ONTs) have emerged as an important class of nanostructures with high aspect ratios and large internal surface areas for applications in nanotechnology and medicine, including catalysis, optics, electronics, chemical or biological sensors, and tissue engineering. In the past decades, a wide range of single-walled and multi-walled ONTs have been synthesized through the assembly of amphiphilic small molecules or macromolecules. Despite all these advances in ONT development, integration of sequence-defined engineering and dynamic response characteristics into ONTs is a challenging task. In addition, despite the continuing emergence of new applications of ONTs, fundamentals, such as the mechanism of the formation of ONTs that is crucial to ONT properties and applications, are still the missing piece of the puzzle.

Here we report a new family of highly-designable, dynamic and stiff nanotubes assembled from sequence-defined peptoids through a unique “rolling-up and closure of nanosheet” mechanism. During the assembly process, amorphous spherical particles of amphiphilic peptoid oligomers crystallize to form well-defined nanosheets before folding to form single-walled nanotubes. These nanotubes undergo a pH-triggered, reversible contraction-expansion motion. By varying the number of hydrophobic residues of peptoids, we demonstrate the tuning of nanotube wall thickness, diameter, and mechanical properties. Atomic force microscopy based mechanical measurements show PNTs are highly stiff (Young’s Modulus ~13-17 GPa). We further demonstrate the precise incorporation of functional groups within peptoid nanotubes and their applications in water decontamination and cellular adhesion and uptake. These nanotubes provide a robust platform for developing biomimetic materials tailored to specific applications.

Reference:
1. Jin, H. B.; Ding, Y.-H.; Wang, M.; Song, Y.; Liao, L.; Newcomb, C. J.; Wu, X.; Tang, X.-Q.; Li, Z.; Lin, Y.; Yan, F.; Jian, T.; Mu, P.; Chen, C. L. Designable and Dynamic Single-Walled Stiff Nanotubes Assembled from Sequenced-Defined Peptoids. Nature Commun. 2017, in press.

Development of synthetic membranes is an emerging field in biomaterials research because of its potential for creating artificial cells that can withstand a variety of environments and have augmented functions that are otherwise limited in natural cells. Silk fibroin has many benefits including robust mechanical properties, controllable degradation rate, ease of functionalization, and ability to undergo prolonged exposure to UV light without complete degradation. Due to these properties, silk fibroin is a promising material to create shells that encapsulate DNA, in order to take the first steps towards a synthetic membrane that minimizes DNA damage and denaturation. This study focused on the encapsulation of plasmid DNA with polylysine-functionalized silk fibroin, to provide enhanced protection of the plasmid DNA, and then subjecting it to damaging environments, specifically UV radiation. Encapsulation of the plasmid DNA was achieved using the layer-by-layer fabrication method to create polylysine-functionalized silk fibroin shells around individual plasmid DNA molecules and conducting an in-depth characterization before and after exposure to UV light, using UV spectroscopy, zeta potential, atomic force microscopy, and gel electrophoresis. Changes to the plasmid DNA structure without silk encapsulation were analyzed, i.e. from its native, supercoiled form to its damaged, open circular form, and compared to encapsulated plasmid DNA. This study demonstrated that plasmid DNA encapsulated in polylysine-functionalized silk fibroin shells incurred less damage than unprotected DNA when exposed to UV light.

Recent advances in the design and synthesis of DNA with programmable 3D nanostructures have stimulated new efforts to study charge transport in DNA, and to explore DNA as building blocks of electronic devices. We examine basic charge transport, electromechanical and thermoelectric properties in single DNA molecules, and study the dependence of these properties on the DNA length and sequence. We also demonstrate a molecular switch by inserting a redox group in between DNA bases. Electrically tuning of the redox group between reduced and oxidized states leads to reversible switching of the molecule between high and low conductivity states. We further show that this strategy allows tracking of single chemical reaction events, and examining of the thermodynamics and kinetics of the reaction at the single-molecule level.

Self–assembly is a process by which molecules of fundamental importance for life, such as proteins and DNA, are formed. Apart from these examples of beneficial self–assembly, aberrant assembly of pathogenic proteins, such as amyloids, may occur. The latter is responsible for several highly–debilitating neurodegenerative disorders which remains currently incurable, such as Alzheimer’s and Parkinson’s diseases. On the other hand, biomaterials inspired by amyloids, such as the ones using diphenylalanine as the building block, are successfully employed in a large selection of functional materials. Delving into amyloid self–assembly is therefore highly relevant for both medical and engineering fields.

In this work, we show how acetylation of KLVFF, a fragment of the pathogenic β-amyloid protein considered to be an aggregation inhibitor, can turn this peptide into a fast self-assembling molecule, able to reach macroscopic size in seconds, even when mild incubation conditions are applied. The driving force for such assembly is a combination of local charge modification and diphenylalanine propensity to assemble into stable structures. We also describe the metastability of KLVFF and show that it can directed by chemical modifications as opposed to peptide length. To prove our hypothesis, we followed and compared the self–assembly of unmodified KLVFF with its amidated and acetylated counterparts. Amidated KLVFF can form amyloid fibrils; we observed folding events occurring in as little as 60 msec.

We exploited synchrotron radiation circular dichroism and a vaste array of microscopies including atomic force and electron microscopy, and scanning electron microscopy. We believe that the remarkable ability of single KLVFF molecules to assemble as highly ordered macroscopic structures in seconds will make it highly desirable for applications of acetylated KLVFF as a rapid–forming templating material.

Melanins are a family of heterogeneous polymeric pigments that provide UV protection, structural support, coloration and free radical scavenging. Formed by oxidative oligomerization of catecholic small molecules, the physical properties of these materials are influenced by covalent and non-covalent disorder. We report the use of tyrosine-containing tripeptides as tunable precursors for polymeric pigments. In these structures, phenols are presented in a (supra-)molecular context dictated by the peptide sequence by repositioning amino acids. Oxidative polymerization can be tuned in a sequence dependent manner resulting in peptide sequence-encoded properties such as UV absorbance, morphology, coloration and electrochemical properties over a considerable range. Short peptides have low barriers to application and can be easily scaled, suggesting near-term applications in cosmetics and biomedicine.

Scaffolded DNA origami has proven to be a powerful and efficient technique to fabricate functional nanomachines by programming the folding of a single-stranded DNA viral genome into three-dimensional (3D) nanostructures, designed to be precisely motion-controlled. Although two-dimensional (2D) imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic in 3D, geometric analysis based on 2D imaging was insufficient to uncover the exact motion in 3D. Here we use individual-particle electron tomography method and reconstruct 129 density maps from 129 individual DNA origami Bennett linkage mechanisms at ~6-14 nm resolution. The statistical analyses of these conformations lead to understanding the 3D structural dynamics of Bennett linkage mechanisms. Moreover, our effort provides, for the first-time, experimental verification of the theoretical kinematics model of DNA origami, which can be used as feedback to improve the design and control of motion via optimized DNA sequences.

Delivery of imaging agents and pharmaceutical payloads to the central nervous system (CNS) is essential for efficient diagnosis and treatment of brain diseases. However, therapeutic delivery is often restricted by the blood-brain barrier (BBB), which prevents transport of clinical compounds to their region of interest. For example, MRI contrast agents such as DOTA-Gd³⁺ are unable to enter the brain for imaging purposes unless the BBB has been compromised. Therefore, an innovative approach to facilitate transport of these molecules across the BBB and into the brain is a crucial area of research. A multifunctional nanoparticle (NP) system is needed that 1) can be loaded with functional molecules, 2) transport across the BBB, and 3) localize to specific regions in the brain.

Here, we investigate a delivery system based on the MS2 bacteriophage capsid. MS2 self-assembles into a protein cage structure with hundreds of reactive groups on its surface for conjugation of targeting moieties, making it an ideal NP platform. Angiopep-2 (AP2) is a 3kDa synthetic peptide capable of receptor-mediated transcytosis across the BBB. We report on the development of our multifunctional NP utilizing AP2 conjugated to MS2 bacteriophage capsids and evaluate transport over an in vitro BBB model, investigate the feasibility of dual modification of the MS2 surface with both AP2 and anti-NMDAR2D IgG, and evaluate nucleotide-mediated loading of a MRI contrast agent based on psoralen and DOTA-Gd³⁺ into MS2 NPs.

The targeting moieties were conjugated to the MS2 surface using the heterobifunctional reagent SMCC. Traut’s Reagent was used to activate IgG before conjugation to the MS2 capsid surface. The dually functionalized NP constructs were tested for the presence of the two targeting moieties using a dot blot. The particles were also tested for their ability to recognize NMDAR2D receptors in brain cell lysate using a Western blot. Confluent 2D monolayers of primary rat brain microvascular endothelial cells (RBMECs) on Transwell inserts were used to evaluate the ability of AP2-conjugated MS2 NPs to cross an in vitro BBB model. NP transport over the BBB model was monitored over 24 hours using real-time reverse transcriptase PCR. Samples were taken from the bottom compartment and amplified using probe sequences for MS2 RNA. Loading of the MRI contrast agent DOTA-Gd³⁺ via nucleotide driven interactions was evaluated using inductively coupled plasma mass spectrometry (ICP-MS).

Preliminary results show successful conjugation of the targeting moieties to the MS2 capsid surface and that the antibody is functional after reaction. Studies are currently ongoing to confirm in vitro BBB transport of MS2-AP2 NPs, the potential for using PCR in MS2 NP detection, and the ability to load MS2 with MRI contrast agent.

Driven by the serious consequences caused by biofouling, fouling-resistant coatings integrated ‘offense’ and ‘defense’ properties are developed for combating marine biofouling. In this work, polysaccharides (PSa)-based self-polishing multilayer coatings were prepared via layer-by-layer (LbL) deposition. Dextran aldehyde (Dex-CHO) and carboxymethyl chitosan (CMCS) were synthesized and alternatively incorporated via imine linkage into the multilayer coating. X-ray photoelectron spectroscopy (XPS), surface plasmon resonance (SPR) and ellipsometric thickness profiles were utilized to characterize the LbL assembly. Experimental observes showed that the antifouling and antimicrobial performances of the resulting multilayer coating against bovine serum albumin (BSA) adsorption, bacterial adhesion (S. aureus and E. coli), and Amphora coffeaeformis attachment improved steadily, with increasing number of assembled bilayers. More importantly, the pH-responsive imine linkages-triggered self-polishing ability was achieved via bond cleavage under acidic environments. Besides, dense bacterial adhesion also induced detachment of the outmost layer of the multilayer coating. The anti-adhesion and antimicrobial efficacies were thus enhanced by the self-detachable capability of the coating layers. Therefore, the LbL-deposited self-polishing dextran/chitosan coatings offer an environmentally friendly and sustainable alternative for biofouling inhibition in aqueous and marine environments.

Physical interactions of self-oligomerizing protein complexes are important in many biological processes such as intercellular communication and the self-assembly of biomaterials. Weakly self-associated protein complexes as physical crosslinkers are advantageous for constructing injectable and self-healing hydrogels for biomedical applications. Following injection, the weak strength of such crosslinkers result in relatively fast erosion that limits the hydrogel lifetime in vivo. Additional design strategies are necessary to improve mechanical reinforcement of injectable hydrogels.

In this study, we use streptavidin (SAv) tetramers as a model protein crosslinker and investigate the influence of biotin, a ligand known for its high affinity binding to SAv monomers at a 1:1 stoichiometric ratio, on the strength of SAv physical interactions in protein hydrogels. SAv tetramers are composed of four identical monomers with strongly associating monomer-monomer interfaces and a weaker dimer-dimer interface. Previous studies provide evidence that biotin enhances the thermal stability of SAv, however it is unknown whether biotin can reinforce SAv mechanical stability, in particular the weak dimer-dimer interface. Furthermore, biochemical and single-molecule mechanical studies indicate that correlation between protein thermal stability and mechanical stability is not guaranteed. Therefore, to evaluate whether SAv tetramers with biotin are proper physical crosslinkers for post-injection hydrogel reinforcement, we used atomic force microscope (AFM)-based single molecule force spectroscopy (SMFS) to investigate the effect of biotin on the mechanical strength of SAv tetramers. Subsequently, we engineered telechelic protein sequences, consisting of a polyelectrolyte-like protein with SAv monomer end groups, as building blocks to form protein hydrogels by SAv tetramer oligomerization. Then, we performed rheological characterization of protein hydrogels to correlate biotin-mediated SAv strengthening at single-molecule and macroscopic levels.

Characterization of individual SAv tetramers and SAv self-assembled hydrogels captured mechanical strengthening induced by biotin binding. AFM-based SMFS results reveal that increasing biotin concentrations enhance the mechanical stability of the weak SAv dimer-dimer interface, increasing its rupture force approximately 200%. At the macroscopic level, rheology results indicate that biotin, a vitamin available in over the counter dietary supplements, can modulate the stress-relaxation properties of physical hydrogels, presenting a potential post-injection mechanism for controlling the in vivo lifetime of injectable hydrogels. We propose the fabrication of telechelic proteins, consisting of proteins of interest with SAv monomer end groups, together with biotin for the customizable design of biomaterial matrices for potential applications in advanced drug delivery systems, internal wound dressing, and tissue engineering.

The epidermal growth factor receptor (EGFR) pathway plays an important role in the progression of colorectal cancer (CRC). Anti-EGFR drugs based on antibodies have been widely used for treating CRC through inducing the cell death pathway. However, the majority of CRC patients will inevitably develop drug resistance during anti-EGFR drug treatment, which is mainly caused by point mutation in the KRAS oncogene as single-nucleotide polymorphisms. To address this problem, we developed a nanoliposomal (NL) particle containing a Cas9 nuclease protein and single-guide RNA (sgRNA) complex (Cas9 ribonuclease protein, Cas9-RNP) for genomic editing of the KRAS mutation. The NL particle is composed of a bio-compatible lipid compounds that can effectively encapsulate Cas9-RNP complexes. By modifying the NL particle to include the appropriate antibody, it can specifically recognize EGFR expressing CRC and effectively delivered the gene-editing complexes. The conditions of NL treatment were optimized using a KRAS mutated CRC in vivo mouse model. Mice with KRAS-mutated CRC showed drug resistance against Cetuximab, a therapeutic antibody drug. After treating the mice with the KRAS gene-editing NL particles, the implanted tumors showed a dramatic decrease in size. Our results demonstrated that this genomic editing complex has great potential as a therapeutic carrier system for treating of drug-resistant cancer caused by a point mutation.

Synchrotron-generated X-ray crystallography have been used for identifying structures of proteins, but it has not been able to solve many kinds of structures. X-ray free-electron lasers (XFELs) is emerging as a next-generation technology for solving structures of proteins. XFELs have extremely high luminance, femtosecond-region X-ray pulses, and perfect optical coherence in contrast to synchrotron-generated X-rays. The femtosecond X-ray pulse is tremendously short, so high-resolution diffraction patterns of proteins can be obtained without deformation or destruction of proteins. Protein crystallography by using XFELs is based on serial femtosecond crystallography (SFX), collecting huge amount of single diffraction pattern of proteins in femtoseconds. Therefore, SFX can investigate crystal structures of proteins that have not solved before. Sample delivery system is one of the significant issue for collecting diffraction data in SFX. Injection systems, such as lipidic cubic phase (LCP) injector, liquid jet or acoustic injector are currently used in SFX experiments. The velocity of injected solution must be very high because of thin flow of crystals, therefore most of crystals are wasted without hitting by X-ray beam, that indicates low hitting rates of X-rays. Besides, injector exerts high pressure on the mother liquor to maintain the thin flow of crystals, so it can be the damage to the protein crystals. Low hitting rates of X-ray beam and the waste of the protein crystals are huge barrier for protein crystallography.
In this work, we implemented an attractive sample delivery system of SFX to reduce the waste of crystals and to improve hitting rates of X-ray beam, called fixed-target matrix. Fixed-target matrix is successfully fabricated by low-cost fabrication process, using ultra violet photolithography and chemical etching. Additionally, surface treatment using oxygen plasma is applied to fixed-target matrix for hydrophilic surface. Polar energy of the matrix is drastically enhanced from 3.25mN/m to 40.14mN/m, resulting in zero contact angle of water. Therefore, mother liquor with protein crystals can be spread well, and protein crystals can enter the hole efficiently. This fixed-target matrix can attend significant role to demonstrate the crystal structure of proteins.

In this work, an integrated nucleic acid test, which includes cell lysing, nucleic acid extraction, amplification, and detection, was developed on a centrifugal platform. In the conventional approach, molecular diagnostic methods were often conducted manually by trained and experienced technicians and the task is usually labor-intensive and time-consuming. In addition, cross contamination often occurred during sample transferring between operations. Therefore, an integrated and automated nucleic acid testing system is desired.
In our platform, sample preparation procedures were integrated on a disk and the assay procedure were carried out by the coordination of the disk spinning control, microfluidic structures on the disk, and the magnetic module. Magnetic beads were used as the nucleic acid carriers and they were transported between various reagent reservoirs under a programmable spinning control. During the test, the cell sample was loaded into the disk and was lysed by the lysis buffer. The nucleic acid was released from the cell sample and was captured by the magnetic beads. To reduce the background signals, the magnetic beads were transferred through immiscible phases so that the unbounded materials were filtered at the immiscible interface. Then the magnetic beads were transferred to the elution buffer reservoir to elute the nucleic acid to the buffer. Then the nucleic acid was replicated by the recombinase polymerase amplification (RPA) process at a constant temperature.
To evaluate the performance of the nucleic acid test on the centrifugal platform, a commercial nucleic acid extraction kits was used and the test results between the two systems were compared. The test results from the centrifugal platform showed good consistency and is in good agreement with the commercial kit.

The functionalization of metal oxide photoelectrodes with biological motifs with photosynthetic properties is interesting for the performance enhancement in photovoltaic (PV) cells and for photoelectrochemical cells (PEC) for solar fuel production. The energy and charge transfer between the biological motif and the photoelectrodes is important for the operability of the bio-hybrid device. We have decorated iron oxide photoanodes with phycocyanin with various anchoring and deposition methods and subjected it to electro-analytic measurements for the AC and DC photocurrent and with iron resonant in situ valence band photoemission spectroscopy (PES). The anchoring method has a noticeable effect on the photocurrent amplitude and on the valence band shift of the PES spectra. In an extension of the bio-interface studies, we grew a biofilm from anabaena spirulina on iron oxide and subjected it to resonant PES while the entire bio-electrode assembly was set under 150 mTorr water vapor partial pressure, illumination and a DC bias. This different exposure to thermodynamic parameters had corresponding effects on the shift of the valence band of the bio-electrode interface. This approach could allow in the future to find a quantitative correlation between the electric transport properties and electronic structure of bio-interfaces and yield information on their suitability and optimization for energy conversion and storage <!--[endif]---->^{1, 2}.<!--![endif]---->
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1. A. Braun, F. Boudoire, D.K. Bora, G. Faccio, Y. Hu, A. Kroll, B.S. Mun and S.T. Wilson: Biological components and bioelectronic interfaces of water splitting photoelectrodes for solar hydrogen production. Chemistry 21, 4188 (2015).
2. G. Faccio, K. Gajda-Schrantz, J. Ihssen, F. Boudoire, Y. Hu, B.S. Mun, D.K. Bora, L. Thöny-Meyer and A. Braun: Charge transfer between photosynthetic proteins and hematite in bio-hybrid photoelectrodes for solar water splitting cells. Nano Convergence 2, 1 (2015).

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Extracellular Matrix (ECM) is a collective matrix surrounded by cells that allows structural and biochemical support. ECM is being extensively researched as a promising biomaterial in tissue engineering and biomedical field, due to its biocompatibility that prevents any adverse host response. Many researchers have obtained clean and effective ECM material through various decellularization processes which completely remove all DNA and cellular contents from a tissue. Although decellularized ECM has already being used successfully in clinical applications, it has not yet been applied for real use in vivo. This is because the typical decellularization process often corrupts distinct characteristics of ECM if the chemicals used are not adequately removed. In this study, supercritical fluid (SCF) extraction system was used as post-cleaning of conventional decellularization process. SC-CO₂ extraction is already being used in many industrial fields, as an extraction or cleaning system. In order to remove the chemicals and the cell residues efficiently, and to preserve the distinct properties of ECM, CO₂ was set into a supercritical state, over 73 atm of pressure and over 31 ^oC, at which point it has unique and beneficial properties of sterilization. The decellularized ECM using conventional process and post-cleaned by SCF extraction system has been evaluated and compared with the specimen without the SCF post-cleaning process. The study has shown that this novel method of using supercritical fluid extraction system has properly removed the chemicals and all cell residues from the ECM completely. Considering the superior results compared with the ECM without post-cleaning, SC-CO₂ prepared ECM shows a very high potential to be actually applied for real use in vivo.

This work contributes to the development of bio-sensitized solar cells (BSSC) by studying the photoactive protein bacteriorhodopsin (BR) as the photoanode sensitizer to replace the common expensive and toxic Ru dyes. Substrates of ZnO nanoparticles (NPs) spread over fluorione-doped tin oxide (FTO)-coated glass or graphene-coated glass are used to immobilized BR by three different techniques: dropcasting, pheniltriethoxysilane (PTES) chemical functionalization, and electrophoretic sedimentation. The photoactive functionality of the protein after immobilization is assessed through ultraviolet visible absorption spectroscopy (UV-VIS). The performance of the photoanodes is determined by chronopotentiometry, linear sweep voltammetry and electrochemical impedance spectroscopy (EIS) under illumination. Preliminary results show a high charge transfer resistance of the photoanodes in the iodide electrolyte extracted from EIS provided relative high values (10⁵ Ω.cm²) for the three methods, in comparison with the values commonly reported for photoanodes prepared with Ru-based dyes (10² Ω.cm²). The molecular layer of PTES has been found to reduce the time required to impregnate BR, but increased the resistance and slowed down the kinetics of charge transfer, thus it is not appropriate for the desired application. The photoanodes prepared by electrophoretic method provide higher photovoltage than those prepared by dropcasting, indicating that the orientation of the protein on ZnO is determinant in the photovoltaic performance. In electrophoresis the electric field applied causes the protein molecules to orient uniformly according to their electric dipole, but with the dropcasting technique, the orientation is random and uncontrollable, resulting in counteracting of individual charge transfer processes. We are working on reducing the large charge transfer resistance, for example by using different electrolyte system, optimize a monolayer formation and increasing the surface area coated with BR.

Mechanical and biological deterioration of articular cartilage is an irreversible process retarded by lubricin (PRG4) —a mucinous glycoprotein that naturally forms a protective coating on the cartilage surface. Drawing inspiration from lubricin’s structure, we designed a new set of bioconjugates with protein-based binding domains and antifouling brush polymers. We synthesizedf these bioconjugates by combining ATRP and copper-catalyzed click chemistry, and characterized them by NMR, IR, GPC, SLS, and SDS-PAGE. Our click-based modular synthesis approach allows for compatibility with a large variety of proteins and functional polymers. Furthermore, we studied the adsorption behavior of our brush copolymers onto collagen by quartz crystal microbalance (QCM) and, investgated their conformatinal mechanics by colloidal probe atomic force microscopy (CP-AFM). We will discuss our findings in the context of our previous work on the conformational mechanics of PRG4. Our results contribute to the rational design of innovative, bio-inspired, polymers for the treatment of osteoarthritis.

The rapid development of nanomaterials has led to an increase in the number and variety of engineered nanomaterials (ENMs) in the environment. We are continuously exposed to products containing ENMs such as batteries, catalysts, chemical coatings, biomedicines and cosmetics. The expanding production of ENMs has led to serious concerns regarding their impact on human health and the environment (for example the considerable investment made by the EU in nanosafety research in the H2020 programme). Given this degree of exposure, it is striking that implications for environmental and human health remain mostly unknown or poorly understood. Identifying ENMs hazardous to natural organisms is difficult, given the wide variety of NPs, their diverse properties (e.g. particle material, size, shape, surface, charge, corona) and the complexity of biological entities (e.g. membrane and media composition, type of cell, cell cycle). The interaction of inorganic NPs with biological systems can lead to severe cytotoxic effects. Although there is a vast literature that highlight the biological impact of the NP exposure, a detailed physicochemical description of nanoparticle and cell interactions and adverse outcomes relevant to predict in vivo behaviour does not exist. In fact, most of the published studies offer no conclusive nanotoxicological data for in vitro models which might make it possible to predict an in vivo response. In order to be able to distinguish between harmless and harmful nanomaterials significant progress must be made in understanding the relevant interactions or key initiating events at nano bio interfaces and determining the NM properties relevant for these interactions.
One route to being able to predict nanotoxicological responses is through in silico approaches that, based on a detailed understanding of toxicity pathways and nano biomolecular structure and dynamics, correlate materials descriptors (physical properties such as size, shape, electronic energy levels, lipid adsorption energies) with toxicological outcomes. Such a model is only possible if there exist reliable physical property data either from experiment and nanoscale simulation. Since one of the first steps in a toxicological response will be the nanoparticle meeting the cell membrane, it is clear that, prominent amongst the materials descriptors, will be the nanomaterial and lipid interaction characterised by its heat of adsorption. In this work, we will present the first experimental quantification data and thermodynamic properties of NP and lipid interaction obtained via calorimetry, coupled with TEM and DLS physical chemical analysis. Studies that could be used for the construction of an in silico model able to predict potential membrane perturbations and consequently, cytotoxic effects. For the experiments, NPs made with different inorganic materials, surface charge and size have been used, while the lipid considered were both in free and assembled (liposome) state.

In Nature, sequence-specific interactions between proteins and inorganic materials lead to formation of hierarchical structures exhibiting complex functions. Achieving the same level of hierarchy and function in synthetic materials requires an understanding of how sequence combines with macromolecular-solvent-surface interactions to control assembly dynamics and materials architecture. Here we report the results of in situ AFM investigations aimed at gaining that understanding for two systems: synthetic proteins designed via Rosetta de novo design software to assemble on mica (001) and synthetic peptides with sequences selected via phage display to bind to MoS₂ (0001). The synthetic proteins consisted of nanorods of repeating cross-helical subunits designed to give an epitaxial match between carboxylic side chains and the K⁺ sub-lattice of mica. As K⁺ solution concentration was varied from 10 mM to 3M, protein coverage and order increased, going from sparse, non-interacting nanorods to small domains of co-aligned nanorods to highly-ordered 2D smectic crystals extending across many mm. The development of order was highly dynamic and cooperative with ordered domains initially forming and disappearing rapidly (~1-10s). The time for stable, ordered structures to emerge depended on K⁺ and protein concentrations and the degree of order depended on the number of sub-units in a nanorod. Short repeats (2-4) exhibited poor order and long repeats (18) produced highly ordered arrays. Introduction of end-to-end interactions further modified assembly to produce long, continuous, co-aligned protein nanowires. The results suggest these proteins exhibit many features of colloidal systems due to their rigidity and high surface charge. However, the ability to vary protein-protein, protein-substrate, and solution-protein interactions by design enables the assembly dynamics and order to be tuned. The phage-selected MoS₂-binding peptides also assembled into highly-ordered 2D arrays. These arrays consisted of monomer-high rows of dimers exhibiting an epitaxial match to the underlying MoS₂ substrate. During assembly, peptides first joined to form dimers as the smallest building blocks. These small units then packed closely to generate rows with a width of 4.1nm and aligning at 30° to the densest S-atom packing direction of the MoS₂ lattice. High-resolution structural images and comparison between different sequences indicate the existence and position of phenyl groups play an important role in surface attachment and the inter-molecular interactions leading to assembly. MD simulations predict binding energies are on the order ~100 kcal/mol and that the dimers are further stabilized via hydrogen bonds. Although the final arrays are 2D, due to the 1D nature of the constituent rows, there is no free energy barrier to nucleation and no critical size. Thus, nucleation rates vary linearly with concentration and are finite for all concentrations above the solubility limit

Bone is a natural biocomposite with an intricate, hierarchical organization that results in structural properties ideal for protecting and supporting the body’s soft tissues. For more effective treatment of severe bone injuries, which affect millions of people worldwide, we need implantable scaffolds that can replace bone’s supportive function while facilitating regeneration of new bone at the implant site. Synthetic fibers that can mimic the nanostructure of natural bone show promise to replicate bone’s structural and biological function, yet few materials have been able to recreate the precise mineral organization of bone. In particular, control over the spatial distribution and orientation of mineral crystals in fibers remains a challenge for biomimicry. In order to achieve this, a method is needed to guide mineralization to occur with periodic distribution and alignment within a polymeric matrix. The objective of this work is to direct the biomineralization of a nanofibrous scaffold using hierarchically nanostructured polymers. We achieve this by using poly(acrylic acid) (PAA) as a recruiter of calcium ions to initiate the nucleation and growth of hydroxyapatite within a poly(caprolactone) (PCL) scaffold. To create the hierarchical composite, we crystallize a block copolymer of PCL-b-PAA onto the surface of electrospun PCL nanofibers. This creates a nanofiber shish-kebab morphology that nucleates hydroxyapatite into periodic PAA domains for a repeating mineral structure with orientation induced by nanoscale confinement. We have shown that calcium phosphate will form within nanoscale PAA domains first as an amorphous calcium phosphate phase before crystallizing into hydroxyapatite. Wide-angle X-ray diffraction and transmission electron microscopy have been used to confirm that the mineral crystals form in repeating lamellae oriented perpendicular to the fiber backbone. By altering the copolymer domain location and size, we direct the formation kinetics, orientation, and amount of minerals in the composite. PAA can additionally be incorporated into the nanofiber backbones for further possible mineral content and structure. Compared to other mineralization-directing techniques such as surface modification and polymer-induced liquid precursors, our block copolymer-directed mineralization gives us greater control over the possible composite morphologies that can be achieved. Through this system, we more closely mimic the nanoscale bone structure to achieve better mechanical performance.

Biomineral-occluded proteins are known to play an important role in precursor phase stabilization, hierarchical structuring, and strengthening of the forming mineral. Obviously, these influences occur at the protein interface with the forming nuclei. Quantifying these effects may help us understanding the mechanisms behind the natural production of biominerals and open the door for more efficient fabrication methods and new engineering tools. One example is the process of S. purpuratus sea urchin spiculogenesis, which exhibits smooth and controlled single crystal growth in its embryonic endoskeleton stage. It is thought that the small amount of protein inclusions (1% w/w) causes these extremely different traits then in-vitro inorganic grown calcite. Unfortunately, our understanding on the specific function of these proteins is very limited. Herein we focus on the spicule matrix (SM)30 protein, which is the most abundant acidic glycoprotein involved in S. purpuratus spiculogenesis, and study the effect of protein concentration on the nucleation kinetics, polymorph selection, and morphology using a state-of-the-art microfluidic chip. Interestingly, our experiments suggest decreasing the protein concentration increases the nucleation rate, and favors vaterite formation. On the other hand, high protein concentration yields exclusively calcite, providing evidence that the protein plays a significant role in polymorph selection. Further studies will reveal the protein location in the forming crystals, giving us additional insight into the role of SM30 in calcium carbonate crystal formation.

Mineralization of inorganic materials in (bio)polymers became one of the most fruitful approaches towards designing materials with outstanding properties in the past decades. The concept of biomieralization is adapted from nature and has witnessed numerous fascinating developments, which in many cases have changed our lives. Among those functional materials hybrid materials play an increasingly important role. Hybrid materials are in most cases blends of inorganic and organic materials and are considered to be key for the next generation of materials research. The main goal while fabricating such materials is to bridge the worlds of polymers and ceramics, ideally uniting the most desirable properties within a singular material.
In our work, we extend the concept of biomineralization towards fabrication of (bio)polymer-inorganic hybrid materials by applying a solvent-free vapor phase infiltration (VPI) process rather than making use of wet chemistry. The VPI process can be seen as a chemical reactor that allows precise dosing of a chemical, allowing for chemical interaction and modification of the subsurface area of a substrate.
In this talk, some approaches will be discussed that show great promise for establishing VPI as the method-of-choice for innovation. The VPI process allows infusing metals or ceramics into polymeric substrates, which leads to novel material blends that cannot easily be obtained in other ways. The chemical or physical properties of the initial substrate are improved or new functionalities added. With some showcases, this talk will discuss approaches towards fabrication of novel materials with great promise in personal protection or flexible electronics.

Viruses are widely known biological macromolecules with self-assembly and molecular recognition capabilities. Genetic modification of viruses to include high affinity peptide fusions allows templating of a variety of materials, and formation of hierarchical nanoarchitectures. Despite the success of biotemplate employment, there is a significant disadvantage: the geometry of the scaffold cannot be drastically changed. A different virus with the required architecture must be individually engineered. The desire to develop a viral scaffold with geometry tuning capability, while preserving its material binding properties has led us to study M13 bacteriophage transformation. The M13 bacteriophage is a high aspect ratio, 880 nm long and 6.5 nm diameter filamentous virus. It contains approximately 2700 copies of p8 major coat protein along its length and 5 copies of p3 minor coat protein at the proximal end of the filament. An extensive collection of peptides with affinity for an array of materials has been developed for and is compatible with this biotemplate. Moreover, the M13 can contract from nanowire to rod and spheroidal structures upon exposure to nonpolar media. This is a considerable advantage, since it enables low-cost manufacturing of variable nanoarchitectures under mild conditions. In this work, genetically-modified bacteriophage with Au- and ZnS-binding peptides displayed on the p8 and p3 sites, respectively, have been transformed via chloroform treatment into 250 nm long and 15 nm diameter rod structures, known as intermediate- or i-forms. Circular dichroism and UV-vis absorption spectroscopy were employed to study the structural changes which accompanied the morphological modification. I-form peptide fusion functionality was compared with that of the filamentous and spheroidal geometries through templated Au and ZnS synthesis. Size, growth rate and crystallinity of the resulting Au and ZnS nanostructures were investigated by transmission electron microscopy and electron diffraction techniques. Optical absorbance and photoluminescence were measured and correlated to viral scaffold architecture. This research shows that fine-tuning of the virus geometry allows assembly of inorganic materials with desired morphological and optical properties.

An intriguing question in biomineralization is as how living organisms build smoothly curving single crystals that are perfectly adapted to their biological function. While intensive research has been dedicated to CaCO₃ single crystal formation, as in in sea urchins or coccolithophores, many other biominerals remain rather poorly understood. Sulfate biominerals (BaSO₄, SrSO₄), as found in desmid green algae, are promising candidates for bioremediation of strontium-90 radioisotopes from nuclear waste ^{1 2}.
A prime example of biological single crystal engineering is the delicate endoskeleton in the single-celled protozoa Acantharea that typically consists of 20 spicules of single crystalline celestite (SrSO₄) ³. While for each species, spicule shape and arrangement follows a stereotypical pattern, there are very significant differences between species. In addition, the deviation of the spicule habit from equilibrium morphology of SrSO4, and strong crystallographic orientation indicate exquisite control over the crystal growth process. In many other systems a variety of ions, small molecules, and biomacromolecules are thought to play a role in controlling phase transformations, stabilize metastable amorphous intermediates, guide crystal growth, and modulate mechanical properties. We are working to explore the role of such additives in celestite biomineralization.
Towards this goal, we investigated the single-crystalline structure of Acantharea spicules using synchrotron powder XRD and laboratory single-crystal single crystal diffraction. We will further report on an in-depth characterization of the biominerals composition, using synchrotron-based X-ray fluorescence microscopy and atom probe tomography. Finally we will discuss results from electron-optical methods and confocal Raman microscopy that we used to investigate the distribution of organic matter in the biomineral and at the inorganic/soft tissue interface.


1. M. R. Krejci, L. Finney, S. Vogt, D. Joester, Selective Sequestration of Strontium in Desmid Green Algae by Biogenic Co-precipitation with Barite. ChemSusChem 2011, 4 (4), 470-473.
2. M. R. Krejci, B. Wasserman, L. Finney, I. McNulty, D. Legnini, S. Vogt, D. Joester, Selectivity in biomineralization of barium and strontium. Journal of Structural Biology 2011, 176 (2), 192-202.
3. J. R. Wilcock, C. C. Perry, R. J. P. Williams, R. F. C. Mantoura, Crystallographic and morphological studies of the celestite skeleton of the acantharian species Phyllostaurus siculus. Proceedings of the Royal Society Series B-Biological Sciences 1988, 233 (1273), 393-405.

We report for the first time the biomimetic mineralization of metal-organic frameworks from biomolecules and living cells. This bioinspired mineralization process leads to the formation of ultra-porous crystal coatings around bioentities, showing promise in various biotechnological applications.
Metal-organic frameworks (MOFs) have attracted tremendous research efforts in the last two decades. This ultra-porous, organic-inorganic hybrid material exhibits extraordinary degree of variability of their chemical structures and physiochemical properties and has shown promise in clean energy and catalysis applications[1]. However, the application in biotechnology is still in its infancy, largely owing to their harsh synthetic conditions that makes them incompatible to most of the biomolecules of interest.
Inspired by biological biominerlization processes, scientists have been trying to adopt and transform this natural process into ‘biomimetic’ strategies for the preparation of the next generation of functional materials[2]. Here, we present the first example of unconventional biomineralization of MOFs[3]. This biologically induced self-assembly process leads to the formation of a highly porous, protective MOF shell around biomacromolecules (e.g. proteins, enzymes, polysaccharides, and DNA)[3-6], and around living entities (e.g. prokaryotic and eukaryotic cells)[7-8]. As a result, the porous MOF shell allows selective transport of small molecules, enabling selective interaction of the encapsulated biomolecules and cells with the external environment, while significantly enhancing their stability. Moreover, the biomineralized MOF coatings can be engineered responsive to biological triggers, which enable them to release cargo at target site on demand. This discovery proposes MOFs as ideal candidate materials for a range of biotechnological applications, such as industrial biocatalysis, drug delivery, biomedical lab-on-a-chip device fabrication, and cell manipulation[2-8].

References
H.-C. Zhou, J.R. Long, and O.M. Yaghi, Chem. Rev. 2012, 112, pp. 673−674.
F.C. Meldrum and H. Cölfen. Chem. Rev. 2008, 108, pp. 4332-4432.
K. Liang, R. Ricco, C.M. Doherty, M.J. Styles, S. Bell, N. Kirby, S. Mudie, D. Haylock, A.J. Hill, C.J. Doonan, and P. Falcaro, Nat. Commun. 2015, 6, 7240.
K. Liang, C.J. Coghlan, S. Bell, C. Doonan, and P. Falcaro. Chem. Commun. 2016, 52, 473-476.
K. Liang, R. Wang, M. Boutter, C.M. Doherty, X. Mulet, and J.J. Richardson, Chem. Commun. 2017, 53, pp. 1249-1252.
K. Liang, J.J. Richardson, J. Cui, F. Caruso, C.J. Doonan, and P. Falcaro, Adv. Mater. 2016, 28, 7910-7914.
K. Liang, C. Carbonell, M.J. Styles, R. Ricco, J. Cui, J.J. Richardson, D. Maspoch, F. Caruso, and P. Falcaro, Adv. Mater. 2015, 27, 7293-7298.
K. Liang, J.J. Richardson, C.J. Doonan, X. Mulet, Y. Ju, J. Cui, F. Caruso, and P. Falcaro, Angew. Chemie. Int. Ed. 2017, 56, 8510-8515.

Bacterial surface layers (S-layers) are highly ordered 2D protein layers that form the outermost cell wall of many bacterial and cyanobacterial species. Cyanobacteria are known to mineralize CaCO₃ on their surfaces, a process which is linked to so-called ‘whiting events’ in lakes where diffusion of CO₂ to solution is the main source of carbon. This identifies whiting events as a natural way for atmospheric carbon sequestration.
The formation of CaCO₃ on crystalline S-layers (Lysinibacillus sphaericus – ATCC 4525, MW 132 kDa) is analyzed using complementary surface science techniques. Structural information is obtained using continuous flow in situ Atomic Force Microscopy (AFM) whereas chemical information is obtained by collecting X-ray Absorption Spectra (XAS) of the calcium L_II and L_III absorption edge. The use of continuous liquid flow cells that are compatible with the Ultra High Vacuum (UHV) conditions necessary during XAS measurements, makes it possible to mimic the typical concentrations of Ca²⁺ and CO₂ in lakes. By using liquid flow cells for both XAS and AFM, their complementary data can be easily integrated.
Experimental results of both ex situ as well as continuous flow in situ XAS show the presence of a stable layer of amorphous CaCO₃ on S-layers after exposure to standard concentrations of CaCl₂ and NaHCO₃. No such CaCO₃ formation is found in for S-layers alone, or for S-layers in the absence of CaCl₂ and NaHCO₃.
These results are consistent with complementary continuous flow in situ AFM measurements that were done under the same experimental conditions. In situ AFM images show the presence of a stable layer of amorphous calcium carbonate (ACC) at the S-layer-liquid interface. As bulk ACC is not stable under these conditions, this indicates the stabilization of ACC by the S-layer biointerface. Furthermore, the growth of crystalline calcite (the thermodynamically most stable form of CaCO₃) has been observed in situ on top of this amorphous ACC layer.
Our results indicate that S-layers are able to stabilize ACC and catalyze the formation of crystalline calcite ex vivo, at naturally occurring concentrations. This suggests that the catalytic properties of many cyanobacteria are at least in part due to the specific functional properties of the biointerface expressed at their outer surface.

Chiral surfaces can be created by the adsorption of intrinsically chiral molecules, with the handedness defined by the molecule [1-4]. Additionally, a second manifestation of chirality may arise due to the molecule-substrate interaction in the form of a chiral adsorption footprint. Thus, chiral surfaces may possess both handedness and ‘footedness’ [5-8]. How both these aspects unfold and express themselves in organized molecular layers is little understood. This talk will illustrate how the ordering of handedness and footedness within organised assemblies of amino-acids on a Cu(110) surface can be tracked at the single-molecule level. The complex behaviour observed can be understood on the basis of three simple generic rules [9]. Using these rules, it is possible to generate every possible footprint and enantiomer arrangement that could be expressed by an amino-acid monolayer. A truly surprising level of complexity in chiral ordering behavior emerges, with a manifold of possible outputs, ranging from segregations of chirality into separate enantiopure assemblies, to ordered racemic compounds with heterochiral unit cells, to solid solutions where chirality is randomly distributed. This complexity in output can emerge at either the handed or the footed levels, leading to highly complex combinations and permutations.


[1] M.Ortega-Lorenzo, C.J.Baddeley, C.Muryn and R.Raval, ‘Extended Surface Chirality from Supramolecular Assemblies of Adsorbed Chiral Molecules’, Nature, 404 (2000) 376.
[2] R.Raval, 'Molecular Assembly at Surfaces: Progress and Challenges', Faraday Discussions, 204 (2017) 9-33
[3] P. Donovan, A. Robin, M. S. Dyer, M. Persson, R. Raval, ‘Unexpected Deformations Induced by Surface Interaction and Chiral Self-Assembly of Co(II)-Tetraphenylporphyrin adsorbed on Cu(110): A combined STM and Periodic DFT study’. Chemistry, A European Journal, 16 (2010) 11641.
[4] S.Haq, N. Liu, V.Humblot. A.P.J.Jansen, R.Raval, ‘Drastic Symmetry Breaking in Supramolecular Organization of Enantiomerically Unbalanced Monolayers at Surfaces’. Nature Chemistry, 1 (2009) 409-414.
[5] M. Forster, M. Dyer, M. Persson and R.Raval, ‘Probing Conformers and Adsorption Footprints at the Single-Molecule Level in a Highly Organized Amino Acid Assembly of (S)-Proline on Cu(110)’. J. Am. Chem. Soc., 131 (2009) 10173-10181.
[6] M. Forster, M. Dyer, M. Persson and R.Raval, ‘2-D Random Organization of Racemic Amino-Acid Monolayers Driven by Nanoscale Adsorption Footprints: Proline on Cu(110)’, Angewandte Chemie Int. Ed., 2010 (49), 2344-47.
[7] A.G. Mark, M. Forster, R. Raval, Recognition and Ordering at Surfaces: The Importance of Handedness and Footedness. ChemPhysChem 12 (2011)1474.
[8] M.Forster, M.S. Dyer, M. Persson, R.Raval, Tailoring Homochirality at Surfaces: Going Beyond Molecular Handedness. J. Am. Chem. Soc. 133 (2011) 15992.
[9] M. Forster and R. Raval, Simple rules and the emergence of complexity in surface chirality
Chemical Communications, 52 (2016) 14075.

Biointerfaces are ubiquitous in nature as well as in technological applications such as biosensors and medical implants. Their structure and response to stimuli are ultimately determined by intra- and intermolecular interactions at the nanoscale. In order to achieve functional biointerfaces at the nanoscale over macroscopic areas, bottom-up fabrication through self-assembly is one of the few viable fabrication pathways. However, the rational use of self-assembly requires a deep understanding of the underlying forces that drive the interactions between individual building blocks and their surroundings.
We present a systematical study of self-assembly at the nanoscale using model systems such as synthetic peptides and self-assembling proteins. Synthetic peptides are highly tunable due to their modular nature, large variety of functional groups and well-established techniques for synthesis. Additionally, 2D self-assembling protein layers (S-layers) present a robust and biomimetic approach to surface functionalization.
Electrospray Ion Beam Deposition (ES-IBD) enables full control over the transfer of large biomolecules to the solid-vacuum interface. By comparing ES-IBD and in situ drop casting techniques, a direct comparison is possible between self-assembly at the solid-vacuum interface (UHV conditions) and self-assembly at the solid-liquid interface.
In this way, the self-assembly of alanine-based peptides was locally studied in different environments, i.e. gas phase, solid-vacuum and solid-liquid interface. Thus enabling the underlying intra- and intermolecular interactions to be elucidated. By carefully choosing both deposition and imaging conditions, specific self-assembling behavior can be selected. This control over the conformational output allows us to tune the function exposed at the biointerface. Furthermore, high-speed in situ Atomic Force Microscopy is used to resolve the intermolecular dynamics of biomolecular self-assembly on a variety of surfaces.

In recent years, viruses have been investigated as versatile, hierarchical templates with site-specific affinity. Peptides displayed via genetic or chemical modification can facilitate the selective synthesis of one or more inorganic materials on viral surface proteins, while viral structure can control the long-range assembly of these materials. In particular, the M13 bacteriophage, measuring approximately one micron in length and 6 nm in diameter, has been studied extensively. This virus is composed of five structural proteins including the p3 located at its proximal tip and the p8 found along its length. Each of these proteins can be modified to create a comparatively low-symmetry template with peptide affinity for two different materials. Moreover, using simple chemical exposure, this filamentous template can undergo a shape transformation to form 60 nm spheres, while maintaining peptide affinity. The capacity for extreme modification of morphology combined with the asymmetric placement of the p3 and p8 on the viral surface make the M13 bacteriophage a potentially powerful scaffold for metal-semiconductor Janus particle assembly. Unlike core-shell metal-semiconductor structures in which the core material is isolated from the surrounding environment (and therefore chemically inactive), two-faced particles preserve the chemical activity of both materials. Exposure of both the metal and semiconductor to the surrounding environment is beneficial for photocatalytic processes as it allows for electron/hole exchange between catalyst and reactant. While the filamentous form has seen extensive use as a template, its spheroidal counterpart is relatively unstudied. This work characterized the shape change transformation then employed the spheroid as a template for a Janus-like particle composed of ZnS and Au. The novel nanoparticle was used in the photo-degradation of methylene blue, and the photo-generated electron pathway was studied. This work represents one of the first examples of application of the genetically and morphologically modified M13.

Adsorption and self-assembly of (bio)-organic molecules at surfaces is a key issue in nanoscience and nanotechnology for the many possible uses of the hybrid organic-inorganic interfaces. Depending on the nature of the molecules, applications are foreseen in the fields of molecular electronics, sensoristics, pharmacology, bio-compatibility, hygiene and bio-fouling.
In this frame, amino acids (AA) have a key role since they are the basic constituents of peptides and proteins and are simple enough to bring information on the chemical interaction of some biological functions with the surface. They are therefore among the most used molecules in fundamental studies aiming at the characterization of the hybrid organic-inorganic interface at the molecular level [1].

In my talk, I will discuss our recent results on AA adsorption at Ag surfaces. The self-assembly of glutamic acid and of cysteine molecules on different Ag substrates [1] is described by combining microscopic and spectroscopic techniques with density functional theory calculations. Particular attention is given to the determination of the chemical state of the adsorbed molecules, to the explanation of the observed geometries and to the understanding of the self-assembly mechanism [2,3]. Both glutamic acid and of cysteine layers organize on Ag surfaces in different phases depending on surface temperature, suggesting the existence of several local minima in the energy diagram of these systems [4]. The peculiarities introduced by the weak interaction with a poorly reactive substrate are critically discussed by comparison with literature cases.

[1] Dominique Costa, Claire Marie Pradier, Frederik Tielens, Letizia Savio, Surf. Sci. Rep. 70, 449 (2015).
[2] Marco Smerieri, Luca Vattuone, Dominique Costa, Frederick Tielens, Letizia Savio, Langmuir 26, 7208 (2010).
[3] Dominique Costa, Marco Smerieri, Ionut Tranc, Letizia Savio, Luca Vattuone, Frederik Tielens, J. Phys. Chem. C 118, 29874 (2014).
[4] Marco Smerieri, Luca Vattuone, Tatiana Kravchuk, Dominique Costa, Letizia Savio, Langmuir 27, 2393 (2011).

Nanostructured porous Si (PSi) has emerged as an attractive and versatile material for optical biosensing applications due to its large internal surface area and tunable optical properties. Numerous biosensing schemes have been reported, demonstrating the advantages of these nanosystems over conventional bio-analytical techniques in terms of improved detection sensitivity, label-free, and real-time rapid analysis. However, a key challenge in designing PSi-based biosensors arises from the relative chemical instability of the Si scaffold in biologically-relevant environments. Specifically, PSi oxidation and dissolution in aqueous environments lead to significant changes in its optical and electrical properties, e.g., luminescence, refractive index and absorption coefficient, and may ultimately result in the structural collapse of the matrix. Several chemical routes are used to enhance PSi stability, including thermal oxidation, hydrosilylation, electrochemical alkylation, and thermal hydrocarbonization. Thermal oxidation is frequently utilized for PSi biosensors passivation, owing to the wide repertoire of chemical modifications available for Si oxide surfaces. The present work explores the effect of thermal oxidation conditions on the stability and sensitivity of PSi-based optical biosensor for label-free and real-time monitoring of enzymatic activity. We compare three oxidation temperatures (400, 600, and 800 °C) and their effect on the enzyme immobilization efficiency and the intrinsic stability of the resulting oxidized porous Si (PSiO₂), Fabry–Pérot thin films. Importantly, we show that the thermal oxidation profoundly affects the biosensing performance in terms of greater optical sensitivity, by monitoring the catalytic activity of horseradish peroxidase and trypsin-immobilized PSiO₂. Despite the significant decrease in porous volume and specific surface area (confirmed by nitrogen gas adsorption–desorption studies) with elevating the oxidation temperature, higher content and surface coverage of the immobilized enzymes is attained. This in turn leads to greater optical stability and sensitivity of PSiO₂ nanostructures. Specifically, films produced at 800 °C exhibit stable optical readout in aqueous buffers combined with superior biosensing performance. Thus, by proper control of the oxide layer formation, we can eliminate the aging effect, thus achieving efficient immobilization of different biomolecules, optical signal stability, and sensitivity.

Two-dimensional (2D) materials have rich and unique functional properties, but many are susceptible to corrosion under ambient conditions. Here we show that linear alkylamines n-C_mH_2m+1NH₂, with m = 4 to 11, are highly effective in protecting the optoelectronic properties of 2D materials such as black phosphorous (BP) and transition metal dichalcogenides (TMDs: WS₂, 1T’-MoTe₂, WTe₂, WSe₂, TaS₂, and NbSe₂). The material lifetime of BP is prolonged from a few hours to several months. As a representative example, n-hexylamine (m = 6) can be applied easily in the form of self-assembled ~1 nm coatings on BP and its devices to effectively preserve their optoelectronic properties under extended exposure to air, H₂O, and even H₂O₂. The coating is also stable under air or H₂ heating and stable in organic solvents, but can be removed by certain organic acids in a reversible manner.

Soft-hard material integration is ubiquitous in biological materials and structures in nature and has also attracted growing attention in the bio-inspired design of advanced functional materials, structures and devices. The inherent physical distinction between these soft and hard phases has led to fundamental differences in their mechanical behavior (e.g. usually more than two orders of magnitude difference in Young’s modulus) but is harnessed well in biological structures through elegant and facile integrated organizations with unprecedented functions as a whole. In essence, the unique properties of soft-hard integrated natural or man-made materials, structures and devices are closely underpinned by the soft-hard interactions, where the rotation of hard phases in a soft matrix has been considered to be very critical and plays a significant role in the entire mechanical properties and functionalities. In the present study, inspired by the Nacre, a typical hard-soft material integrated structure, where the hard inorganic aragonite is embedded into the organic biopolymer soft matrix, we design a soft-hard composite that exhibits a negative Poisson’s ratio by leveraging the unique rotation of hard particles in the soft matrix. A mechanics theory is established to quantitatively describe the rotation of hard particles in a soft elastic matrix and to incorporate with the overall negative Poisson’s ratio of soft-hard composites. The designed soft-hard composites are manufactured using 3D printing technique to validate the structural design and mechanical performance.

Bacteria often populate environments where fluid flow is present on both natural and synthetic polymeric materials. Pseudomonas aeruginosa is an opportunistic biofilm forming bacterium that exhibits the ability to twitch upstream in fluid flow environments such as the vasculature of plants, respiratory tracts of mammals, and medical devices. The upstream movement is facilitated by the retraction and extension of their type iv pili mechanosensor ATPase motors pilT and pilU when adhered to a surface. Such surface motility modalities of P. aeruginosa lead to bacterial colonization and infectious biofilm formation. Here, motility prohibition and detachment of P. aeruginosa are studied on polymer biomaterial surfaces structures with arrays of nanopillared geometries under fluid flow. Nanopillared surfaces structures are fabricated using thermal nanoimprint lithography on synthetic polymers used in medical devices such as poly(methyl methacrylate) (PMMA) and biopolymers with inherently antimicrobial chemistries such as chitin and chitosan. The arrays of nanopillars range in periodicity from 200, 300, to 600 nanometers. Upstream movement direction, detachment, and velocity of wild-type P. aeruginosa expressing GFP were monitored in flow channels of flat and nanopillared surfaces and quantified using fluorescence microscopy. The cell motility prohibition and detachment under shear stress was observed to have a nanopillar surfaced periodicity dependence. This bacteria-interface interaction phenomenon allows us to tailor our surface interfaces with specific nanopillared geometries for structurally controlling cell motility and detachment under fluid flow. The disruption of surface attached bacterium upstream movement that lead to colonization and biofilm formation is crucial in preventing harmful infection from contaminated medical devices such as catheters.

Biological functions in livings occurs by interactions, which ultimately imply stereo- and chemical-complementarity between the binding partners. In protein interaction, definite protein segments, such as exposed loops, helix-loop-helix motifs, etc. are involved in the formation of complexes that ultimately trigger the physiological responses.
Here, as a mimic of protein interactors, we attempted the synthesis of molecularly imprinted nanogels (nanoMIPs), performed by means of the molecular imprinting technique [1] and in precipitation polymerization conditions [2], that were addressed at the recognition of a structured peptide: the loop-shaped 9mer peptide with sequence C₁-(X)_n=7-C₉ and fixed by a disulphyde bond.
The nanoMIPs were about 50 nm in size and 2 10⁶ Da of mean molecular weight. They exhibited high affinity (Kd = 9 10^-9 M) and structural selectivity for the loop-shaped peptide. Additionally, it was observed that the nanoMIPs promoted a fast formation of the loop-shaped peptide, by the oxidation of the linear precursor peptide [3].
These results demonstrated the feasibility of the structural imprinting and hinted at a possible role of the nanoMIPs to assist the refolding of peptide segments into defined structures, anticipating polymeric nanomachines for counteracting folding defects.

References
[1] G. Wulff and A. Sarhan, Angew. Chem. Int. Ed. 11, 341(1972); R. Arshady and K. Mosbach, Die Makromoleculare Chemie, 182, 687 (1981).
[2] N. Perez-Moral and A. G. Mayes, Anal. Chim. Acta 504, 15 (2004).
[3] L. Cenci, G. Guella, E. Andreetto, E. Ambrosi, A. Anesi, A.M. Bossi. Nanoscale 8, 15665 (2016).

Herein, we present a simple and versatile method for morphological enhanced stabilization and transcription of beta-lactoglobulin (ßlg). This globular protein spontaneously self-assemble to soluble spherical aggregate (ca. 80-300 nm) upon heat treatment at definite pH. Our approach involves the construction of π-conjugated co-polymer coating around the outer surface of protein spheres. Here we used for the first time, 1,5-dihydroxynapthalene and 1,3,5-trimethyl-1,3,5-triazinane for surface modification of ßlg amphiphilic protein, which crosslinked on the protein surface with extension of π-conjugated structures by in situ co-polymerization at room temperature (298 K). Further the obtained core-shell structure composed of π-conjugated polymer-coated ßlg protein sphere was transformed to hollow carbon nanosphere with tailored properties by carbonization at high temperature. The hollow spheres were characterized by using transmission electron microscopy (TEM). The cross sectional analysis with field emission scanning electron microscopy (FE SEM) of core-shell structure revealed polymer coating on the ßlg protein surface. The obtained conjugated polymer and carbon hollow sphere were further characterized by energy dispersive x-ray spectroscopy (EDS), solid state NMR, dynamic light scattering (DLS). The surface properties of prepared organic and carbon nanosphere can be adjusted by hybridization of different types of functional materials and provides interesting platform for nanoarchitectonics.

In-vitro metabolite detection relies on designed materials based analytical platforms and is universally employed in biomedical research and clinical practice. However, metabolite analysis in bio-samples always need tedious pre-treatment, due to the sample complexity and low molecular abundance. What is more challenging is to construct diagnostic tools by materials based platforms. Herein, we developed several novel platforms using plasmonic nanoshells. We synthesized SiO₂@Ag and SiO₂@Au with tunable shell structures using both chemical and physical method. Optimized nanoshells facilitated metabolome fingerprinting in 0.5 μL of bio-fluids by direct laser desorption/ionization mass spectrometry. We applied these nanoshells for disease diagnosis and therapeutic evaluation. We identified patients with postoperative brain infection through daily monitoring and glucose quantitation in cerebrospinal fluid (CSF). We measured drug distribution in blood and CSF systems and validated the function of blood-brain/CSF-barriers for pharmacokinetics. Our work sheds light on the design of nanomaterials for advanced metabolite analysis and precision diagnostics.

Double stranded DNA and dAMP (2′-Deoxyadenosine 5′-monophosphate) were encapsulated in silica by sol-gel route. The microstructure of the biomolecule-hostings gels and the chemical interactions between biomolecules and silica host have been investigated. Ethidium bromide (EtBr) intercalation and leach out tests showed revearled a high hydraulic reactivity for encapsulated DNA and dAMP gels due to presence of more silanol groups than plain silica gel. For both biomolecules, no chemical binding occurred with Si core of the silica network. The chemical association between DNA/dAMP and silica host was through phosphate groups and molecular water attached to silanols, acting as a barrier around biomolecules. The helix morphology was found not to be essential for such interaction. BET analyses showed that interconnected, inkbottle shaped mesoporous silica network with an average pore size of 5.6 nm for DNA and 4.8 nm for dAMP containing bulk gels, respectively.

Silver clusters ‘grown’ in single-stranded DNA are promising new fluorophores for applications in bio-labels and bio-imaging, due to their highly emissive properties from visible to the near-infrared range and good biocompatibility. However, their photophysics is sensitive to their geometry, size, and interactions with the DNA nucleotides. The small silver cluster could also form the dimer and its photophysical properties largely depend on dimer formation mechanism. We have performed Density Functional Theory (DFT) calculations to study Ag clusters of 5 and 6 atoms in sizes passivated by three different nucleotides- cytosine, guanine, and thymine bases. Our calculations show that the geometry of clusters, the interaction between the cluster and bases depend on the oxidation state of the system, while different base-cluster binding trends are observed for mixed capping instead of only cytosine or only guanine passivation. It is also reported that dimer also could form, which has distinct photophysical properties. Time-dependent DFT (TD-DFT) calculations predict the red-shifted lower intensity peak in absorption spectra of both clusters, which originates from doublet transitions. The second more intensive absorption band appears nearly at the same energies for both singlet and doublet transitions but its intensity is largely ligand dependent. In case of the dimer, energy of the absorption peaks is almost same, but intensity depends on the dimer formation mechanism. It is shown that first peak is almost independent of dimer size and bridging but 2^nd peak intensity is decreased if pi-pi stacking was formed during the dimer formation.

Mammalian teeth are a composite product of biomineralization consisting of an inorganic component, hydroxyapatite (HA), and an organic component, predominantly collagen. Biologically formed HA can be described as precisely adjusted Ca-deficient carbonate containing apatite with minor amounts of Mg, Na, K and Zn [1]. Teeth are structured with three unique hard tissues – enamel, dentine and cementum. The most voluminous mineralized tissue forming the bulk of the tooth is dentine, constituted of 70 wt% of inorganic HA platelets, 20 wt% of organic material and 10 wt% of water [2]. Dentinal tubules (DT) penetrate through the dentine, turning it into a highly permeable tissue [2,3]. Properties of biological functional composites are modulated starting at the nanoscale, making their characterization very demanding, especially as they are very beam sensitive.
The microstructure and chemistry of intertubular dentine (ID) and dentinal tubules (DT) of human teeth [4], continuously growing rodents (Myocastor coypus) incisors and molars [5] were inspected by advanced analytical and imaging transmission electron microscopy (TEM) techniques. Microstructural investigations have revealed relatively dense rim of peritubular dentine (PD) surrounding the DT in human teeth. Bulk of the tooth dentine between the DT is composed of ID. Average Ca/P at% ratios measured in ID are higher compared to PD and are combined with greatly higher Mg/P at% ratios (~1.4 times) obtained in PD. Considering the crystal chemistry perspective, there is a high probability for Mg incorporation into HA lattice by substituting Ca. In addition, smaller HA crystals in PD could be linked to higher Mg concentrations. Interestingly, ID of rodents molars is chemically identical to ID in human teeth. DT of rodents incisors appear to be partially filled with flake-like amorphous material. Surprisingly, the amount of Mg in ID of incisors is notably higher, and the Mg/P at% ratio is 2-4 times higher compared to ID in rodents molars or human teeth. The flake-like material within the incisors DT had an unprecedentedly high amount of Mg, that is around 5 times higher compared to the values in ID, suggesting the presence of an amorphous (Mg,Ca)-phosphate phase. The presence of such high Mg concentrations only in continuously growing incisors but in not molars could be closely associated with the permanent growth of incisors.
Living organisms have ability to precisely adjust organic and inorganic components into masterpiece compounds. Detailed knowledge of such natural biocomposites is important for better understanding of the functionality of human dental tissues and in preventive and restorative dentistry.

[1] S Mann, Biomineralization; Oxford University Press: Oxford, UK, 2001
[2] JK Avery, Essentials of Oral Histology and Embryology; Mosby Elsevier, USA, 2006
[3] IA Mjör and I Nordahl, Arch Oral Biol 41 (1996), 401
[4] V Srot et al., Microsc Microanal 18 (2012), 509
[5] V Srot et al., ACS Nano 11 (2017), 239

Multivalency is a ubiquitous phenomenon in nature. Over the past decades, the fields of nanoparticle and nano-engineering have utilised this concept to achieve targeted delivery, increased specificity and selectivity of therapeutic and diagnostic ligand-functionalized nanoparticles. Numerous systems have been developed yet the translation to clinical success is rare. It has been recognised that a certain threshold concentration / density of ligands on a nanoparticle surface is required to activate or engage biologically relevant signalling; however, detailed quantitative assays on enhanced binding affinities through multivalent ligand presentation are rare.

With a system that is so abundant in nature, and functions flawlessly in amongst others cell signalling and immune protection, it is clear that fundamental design principles for the mechanistic translation of (heterogeneous) multivalency into targeted therapeutic nanoparticles are missing. To understand how to improve these design parameters, we need new analysis methods, better control in nanoparticle ligand presentation and advances in or theoretical models and simulations.

In this study, we started with a proof of concept where fully programmable dendritic nanoparticles interact with well-defined multivalent targets. We choose DNA as material backbone of our particles to ensure perfect programmable control over size, shape and ligand functionality. By spatially matching ligand presentation versus surface receptor density, we demonstrate that control in design outperforms random ligand presentation. In a second next step, we present heterogeneous ligands to target complex multivalency, defined by us as the multivalent interaction between heterogeneous ligand/receptor molecules. We compare these systems with bispecific antibodies and our models will be used to mechanistically and quantitatively study the potential synergy in thier heterogeneous multivalent binding. The system will then be gradually expanded to program more ligands and understand the role of spatial control in cell-matrix binding and cell signalling using integrin targeting ligands. Our novel insights in multivalent binding has the potential to be translated toward improved design of biomaterials and superior diagnostic / therapeutic nanoparticles.

Paper-based lateral flow immunoassays (LFIAs) are one of the most widely used point-of-care (PoC) devices. However, their application in early disease diagnostics is often limited due to insufficient sensitivity for the requisite sample sizes and the short time frames of PoC testing.¹ To address this, we developed a serum-stable, nanoparticle catalyst-labeled LFIA with sensitivity surpassing that of both current commercial and published sensitivities for paper-based detection of p24, one of the earliest and most conserved biomarkers of HIV.²

Due to their high catalytic efficiency and extraordinary stability in harsh environments, such as high temperature and extreme pH, mixed noble-metal catalytic nanoparticles have emerged as promising materials for signal amplification in colorimetric immunoassays.³ We report the synthesis and characterization of peroxidase-mimicking porous platinum core-shell nanocatalysts (PtNCs), which retain high catalytic activity when exposed to complex human blood serum samples. We explored the application of antibody functionalized PtNCs with strategically and orthogonally modified nanobodies with high affinity and specificity toward p24, and establish the key larger nanoparticle size regimes needed for efficient amplification and performance in LFIA. Harnessing the catalytic amplification of PtNCs to generate an intensely colored product at the test line enabled naked-eye detection of p24 spiked into sera in the low femtomolar range (ca. 0.8 pg/mL).

The PtNC-labeled LFIA exhibits a dual dynamic range spanning over four orders of magnitude, which arises from both the inherent coloration of the nanomaterials and their catalytic ability. The 100-fold signal amplification provided by the PtNCs allowed for the detection of acute phase HIV in clinical human plasma samples in under 20 minutes. This provides a versatile absorbance-based and rapid LFIA with sensitivity capable of significantly reducing the HIV acute phase detection window. This diagnostic may be readily adapted for detection of other biomolecules; as an ultrasensitive screening tool for infectious and non-communicable diseases, and can be capitalized upon in PoC settings for early disease detection.

1. Howes, P. D., Chandrawati, R. & Stevens, M. M. Colloidal nanoparticles as advanced biolgical sensors. Science 346, 1247390-1-1247390–10 (2014).
2. Loynachan, C. N., Thomas, M. R. et al. Platinum Nanocatalyst Amplification: Redefining the Gold Standard for Lateral Flow Immunoassays with Ultrabroad Dynamic Range. ACS Nano (2017). doi:10.1021/acsnano.7b06229
3. Xia, X. et al. Pd-Ir Core-Shell Nanocubes: A Type of Highly Efficient and Versatile Peroxidase Mimic. ACS Nano 9, 9994–10004 (2015).

Peptoids, structural isomers of peptides, can self-assemble into extended, flat nanostructures at an air-water interface. Our molecular dynamics simulations predict that the flatness of nanosheets is made possible by peptoids' ability to associate in a linear and untwisted manner, which in turn is made possible by the ability of residues along the peptoid backbone to adopt alternating, twist-opposed rotational states (by contrast, peptides in beta sheets tend to adopt a single type of rotational state that is slightly twisted, a property transmitted to the sheet as a whole). I will discuss how the choice of rotational state-pairs in the peptoid nanosheet substantially infuences its emergent order, and discuss strategies for functionalizing nanosheets in order to promote mineralization and catalysis. In this sense the nanosheet itself can be considered to be an interface at which reactions occur.

Dynamic manipulation of wetting behavior of a surface can be used to trigger attachment or detachment of biomolecules and cells, induce changes to affinity for tissue, and diffusion behavior. A biocompatible biomaterial, whose interface can be dynamically modulated, therefore can find potential application in bio-adhesives, bio-patches, biosensors, actuators, cell delivery and lab on chip. We have developed a family of biodegradable and biocompatible segmented thermoplastic polyester (STEP), which are capable of undergoing change in shape and wetting behavior upon exposure to an external stimulus, which is compatible with physiological environments. By surface engineering the aligned segregated hydrophobic segments, a system with an activatable surface wetting behavior has been realized. As an example, a 15 degree change in static contact angle was triggered in a mechanically programmed STEP device by illumination with infra-red light. By prescribing a shape during the mechanical programming shape-change devices possessing hydrophilic properties in a strained state and hydrophobic properties in a relaxed state have been achieved. In addition to practical applications the role of strain, chain relaxation, time, and temperature in STEP polymers with dynamically tunable interface will be presented.


Keywords: engineered biomaterials, dynamic bio-interface, programmable wettability

SM04: Understanding and Controlling the Structure and Function of Biomolecules at Material Interfaces.

Photosynthesis, the model system for energy conversion, uses CO₂ as its starting reactant to convert solar energy into chemical energy, i.e. organic molecules or biomass. The ratedetermining step of this process is the immobilization and activation of CO₂, a carboxylation reaction catalyzed by the enzyme RuBisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase). Inspired by the active site of RuBisCO, we design nanostructures that self-assemble on solid surfaces. Here we show the fabrication of the first hybrid networks using an alkaline earth metal (Group 2): magnesium (Mg) and organic molecules of terephthalic acid (TPA) and 2,4,6-tris(4-aminophenyl)-1,3,5-triazine (TAPT) by direct deposition onto clean metal substrates [Cu (100) and Mg (0001)] under Ultra High Vacuum (UHV) conditions at room temperature (RT). We track their reactivity and dynamic response to CO₂ and O₂ in situ by Scanning tunneling microscopy (STM) and X-Ray Photoelectron Spectroscopy (XPS), supported by density functional theory (DFT) calculations. Specific phase transformations and active sites are identified with atomic resolution upon gas exposure at RT. Our study shows that is possible to reverse the structure-function equation to design selfassembled 2D functional networks inspired in biological active centers.

Sound can be music to please the ear, however, the waves produced can be utilized as “Acoustic Tweezers” for the manipulation of cells and particles in a fluid medium. The acoustofluidics technology, combining sound waves with fluidics, becomes a revolutionary way to dexterously and noninvasively manipulate biological specimens. Firstly, this technique manipulates cells or particles using gentle mechanical vibrations. These vibrations create a pressure gradient in the medium to move suspended micro-objects yielding a contamination-free, contactless, and label-free manipulation. Secondly, acoustofluidics has minimal impact on cell viability and function. Thirdly, this technology can operate in a single micro-device without any external moving parts or complicated setups, which offer additional advantages in ease of use, versatility, and portability. Here, we report a series of acoustic tweezers for the manipulation of micro-objects in a liquid medium or the microfluidic environment to address the problems in the field of biomedicine including tissue engineering, cell-cell interaction, disease diagnostics, and point-of-care testing.

Biological membranes contain a sizeable fraction of charged lipids and proteins that separate into domains essential to cell functions. Phase separated lipid bilayers are routinely prepared in vitro, and the average surface charge or surface potential is characterized by methods such as electrophoresis, streaming potential or electroacoustics. The local charge of individual domains has however not previously been quantitatively described. This stands in stark contrast to a widespread focus on zeta potential values, especially for drug delivery.

In this work we prepare phase separated lipid bilayers by mixing an unsaturated lipid of distinct charge (DOPG, DOPC or DOTAP) with a zwitterionic saturated lipid (DPPC). Electrostatic repulsion between lipids of same charge favors a uniform mixing of the two lipids, while lipids with similar tail groups are attracted by an entropically favored packing configuration. The two lipids are mixed at a temperature above T_M and slowly cooled, leading to a demixing and formation of micrometer sized domains with distinct charge. We then characterize these domains using the recently developed method Quantitative Surface Charge Microscopy (QSCM). QSCM is based on scanning ion conductance microscopy (SICM), and uses fluctuations in ionic current passing through a nanopipette as it is placed near the lipid bilayer.

Lipid domains are clearly distinguishable from both topography and charge maps in all three model membranes. We furthermore find that the standard sample preparation, where a mixture of lipids with different T_M is slowly cooled to induce mixing, will not produce a complete division between the lipids. Instead we estimate that at least 30% of disordered domains in DOPG:DPPC and DOTAP:DPPC will be composed of DPPC. This ratio could present a limit for the formation of charged domains in lipid membranes. In summary we demonstrate that QSCM is capable of distinguishing domains of charged and uncharged lipids with spatial resolution on the nanoscale, and we show that the precision of the measured charge is good enough to deduce the mixing ratios between charged and uncharged lipids.

With advances in electron microscopy and image analysis over the past decade has come the ability to determine the structure of biomolecules with nanometer or better resolution. But what about their dynamics? When biomolecules self-assemble or carry out their function, motion is involved! We are using liquid-phase transmission electron microscopy (TEM), a recently developed imaging technique that combines the nanometer resolution of TEM with the ability to observe the continuous motions of individual particles preserved in solution, to investigate the nanoscale dynamics of biomolecules. In particular, we are using liquid-phase TEM to study the conformational dynamics of ryanodine receptor—a membrane protein ion channel involved in muscle contraction and calcium signaling—and the aggregation and disaggregation of amyloids—fibrillar structures formed from misfolded proteins—in the presence of a polymer-based inhibitor, in the hopes of shedding new light on the relationship between structure, dynamics, and function in these systems.

Since the milestone of bubbles management at 1776, when the steam engine was produced by James Watt, this area has been considerably extended, and many industrial practices got involved, including drinks (e.g. carbonated beverages), petro-chemical industry (e.g. expanded plastic) and glass-making. Electrolysis and fuel cells, which consume or generate electric power, and generate or consume gases at the same time, are also important gas-involved procedures. To improve the reaction rate, tremendous efforts have been devoted to novel catalysts design for low onset potential, high surface, while bubble management is of much less attention.
In previous investigation, we have been engaged in tailoring the interfacial wettability to control the detachment/bursting of bubble on electrode, to promote the gas evolution/consumption reactions and concepts like superaerophobicity or superaerophilicity have been developed. However, to design better nano-electrodes, deeper insights into the bubble behavior on eletrodes are critical which demands advanced in situ monitoring techniques. Since the bubble generation/consumption usually happens at interface of solid (electrode) and liquid (electrolyte), where three-phase (vapor, liquid and solid) coexist, only high-speed camera and atomic force microscope (AFM) are applied and only top-view or side-view can be acchieved. To get multi-scale observation (from nm to mm), it is highly appealing to obtain the whole information of bubble behavior and besides primary parameters including diameter, volume and contact angle, etc.
Surface plasmon resonance (SPR) techniques are widely use in biological binding/recognition investigations, which is sensitive down to molecule scale. Due to the excellent electric conductivity of gold film substrate and the high sensitivity to the charge density, we develop SPR technique to a powerful “view-from-bottom” label-free method to study interfacial electrochemical reactions, especially bubble-involved electro-catalysis. We show here some advances of utilizing SPR to invest the bubble behavior at the “bottom” (the interface of electrode and electrolyte) in our group.

References
[1] Z. Lu, W. Zhu, X. Yu, H. Zhang, Y. Li, X. Sun, X. Wang, H. Wang, J. Wang, J. Luo, X. Lei, L. Jiang. Adv. Mater. 26(2014) 2683-2687.
[2] Y. Li, H. Zhang, T. Xu, Z. Lu, X. Wu, P. Wan, X. Sun, L. Jiang. Adv. Funct. Mater. 25( 2015) 1737-1744.
[3] Z. Lu, M. Sun, T. Xu, Y. Li, W. Xu, Z. Chang, Y. Ding, X. Sun, L. Jiang. Adv. Mater. 27(2015) 2361-2366.
[4] X. Liu, Z. Chang, L. Luo, T. Xu, X. Lei, J. Liu, X. Sun. Chem. Mater., 26(2014) 1889-1895.

Understanding the role of interfaces is critical to catalysis, surface physics, corrosion, nanoscience, tribology, geochemistry and electrochemistry, and energy production. Resonant X-ray Scattering (RXS) offers a unique element, site and valence specific probe to study spatial modulations of molecular orbital degrees of freedom on the nanoscopic length scale. This unique sensitivity is achieved by merging small angle x-ray scattering and x-ray absorption spectroscopy into a single experiment, where the scattering provides information about spatial modulations and the spectroscopy provides sensitivity to the molecular anisotropy. We applied RXS to biomimetic poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) zwitterionic polymer (ZWP) brushes at solid-liquid interfaces. ZWPs, on which each monomer segment bears both a positive and a negative charge, are an understudied class of polyelectrolyte macromolecules, most of which are simple polyelectrolytes (SPE) that bear a single sign of charge on each monomer. As each monomer has no net charge, the chains are not in extended configurations at low salt concentrations. In contrast to SPE, they expand when salt is added since the local attractions between positive and negative ions are screened, thereby producing a rich science base in understanding the configurations, ionic distribution, and in interfacial interactions of ZWP brushes in a variety of relevant and important ionic environments. The technical opportunity stems from observations that ZWP surface layers are particularly resistant to the nonspecific accumulation of proteins and microorganisms, making them excellent candidates for a wide range of antifouling applications, ranging from biocompatible medical devices to marine coatings. PMPC is a unique member in polyzwitterionic families and it has an ultrahigh affinity to water, leading to no detectable shrinks in aqueous solutions even with low ionic strengths, in contrast to those sulfobetaine and carboxybetaine polymer brushes. In this work, we systemically synthesized highly dense PMPC brushes via surface initiated atom transfer radical polymerization and thoroughly characterized the configurational behavior and lateral charge correlation of PMPC ZWPs at interfaces under a variety of ionic (mono- and multivalent) conditions with different concentrations. PMPC polymers only weakly interact with biomembranes via van der Waals forces as seen in force and neutron spin echo measurements, indicative of the nonspecific binding nature of PMPC polymers. The ion-induced changes of PMPC chain configurations are not apparent, in contrast to common polyelectrolytes and other ZWPs, such as poly(carboxybetaine) and poly(sulfobetaine). This, in turn, establishes structure-property relationships between surface chemistry and the ability of a thin film to resist biofoulant adhesion for the design and optimization of antifouling materials.

Enamel is consider as one of nature’s hardest materials. It is formed extracellularly by a complex process involving multiple proteins. The most common protein present during enamel formation is amelogenin (>90%). Amelogenin’s dominance in the extracellular matrix along with a multitude of both in vivo and in vitro studies demonstrate that it can strongly influence the shape and properties of the resulting crystals. This influence is so controlled, that even single amino acid modifications in the primary structure can result in severely dysfunctional enamel. While amelogenin’s role in enamel formation is widely agreed upon, the mechanism of growth and control at a molecular level is less clear. Studies by Beniash and coworkers have proposed a growth mechanism based on cryo-EM studies which identify amelogenin dimers as a design group upon which the larger hierarchical structures are built.
In this work, we extend the use of solid state NMR to study large biomineralization proteins a step further, to probe intermolecular interactions which dominate the proposed secondary structure of this protein. Based on the overlapping tail-to-tail interactions of amelogenin dimers in the presence of calcium phosphate deduced by the cryo-EM study, we propose that the dimer conformations are stabilized by salt bridges. We selected a specific stable isotope labeling (¹³C and ¹⁵N) scheme to probe this bridging interaction that fit two criteria: 1) residues that do not “scramble” excessively during biological synthesis, i.e. the biosynthetic pathway does not result in additional residues being labeled; and 2) residues that should be close enough in space to detect if salt bridges are present. Using detail 2D-solid state NMR study, we have identified a unique atomic level intermolecular interaction stabilizing amelogenin dimers. The demonstration of atomic level intermolecular interactions for a biomineralization protein bound to its biologically relevant surface is an important advancement in this field and allows us to further define mechanistic details for the formation of hard tissues such as enamel.