Silica surface features and their role in the adsorption of biomolecules: computational modeling and experiments

Ζ potential evidences silanol heterogeneity induced by metal contaminants at the quartz surface: Implications in membrane damage

Among the physico-chemical features responsible for the so-called "variability of quartz hazard", a key role has been assigned to the silica surface charge, evaluated by means of ζ potential measurement. The ζ potential of silica describes the protonation state of silanols which, in turn, determine interactions with cell membranes. To gain a molecular understanding of the role of silanols in silica pathogenicity, we conducted a systematic investigation of the variation of the ζ potential as a function of pH (ζ plot titration curve) on a large set of respirable quartz particles with different levels of metal contaminants. The membranolytic activity of the particles on red blood cells, used as a readout of pathogenic activity, was assessed in parallel. Pure quartz surfaces showed sigmoid-shaped ζ plots suggesting the presence of silanol families with similar acidity, whereas contaminated dusts exhibited convex-shaped ζ plots, indicating a higher silanol heterogeneity on contaminated surfaces with respect to the pure ones. The quartz particles with a higher surface heterogeneity related to metal contamination showed a higher membranolytic activity. By removing structural defects and chemical heterogeneity, the ζ plot shifted towards the typical shape of pure quartz and the membranolytic activity was reduced. We conclude that the ζ plot is a useful readout to measure the acid-base behavior of quartz surfaces and to describe the chemical heterogeneity of quartz silanols. Surface heterogeneity, here induced by metal contamination, is proposed as the main cause of quartz membranolytic activity, further supporting the hypothesis that surface silanol disorganization determines silica pathogenicity.

Glycine Polymerization on Oxide Minerals

It has long been suggested that mineral surfaces played an important role in peptide bond formation on the primitive Earth. However, it remains unclear which mineral species was key to the prebiotic processes. This is because great discrepancies exist among the reported catalytic efficiencies of minerals for amino acid polymerizations, owing to mutually different experimental conditions. This study examined polymerization of glycine (Gly) on nine oxide minerals (amorphous silica, quartz, α-alumina and γ-alumina, anatase, rutile, hematite, magnetite, and forsterite) using identical preparation, heating, and analytical procedures. Results showed that a rutile surface is the most effective site for Gly polymerization in terms of both amounts and lengths of Gly polymers synthesized. The catalytic efficiency decreased as rutile > anatase > γ-alumina > forsterite > α- alumina > magnetite > hematite > quartz > amorphous silica. Based on reported molecular-level information for adsorption of Gly on these minerals, polymerization activation was inferred to have arisen from deprotonation of the NH3+ group of adsorbed Gly to the nucleophilic NH2 group, and from withdrawal of electron density from the carboxyl carbon to the surface metal ions. The orientation of adsorbed Gly on minerals is also a factor influencing the Gly reactivity. The examination of Gly-mineral interactions under identical experimental conditions has enabled the direct comparison of various minerals' catalytic efficiencies and has made discussion of polymerization mechanisms and their relative influences possible Further systematic investigations using the approach reported herein (which are expected to be fruitful) combined with future microscopic surface analyses will elucidate the role of minerals in the process of abiotic peptide bond formation.

Ubiquitin immobilized on mesoporous MCM41 silica surfaces - Analysis by solid-state NMR with biophysical and surface characterization

Deriving the conformation of adsorbed proteins is important in the assessment of their functional activity when immobilized. This has particularly important bearings on the design of contemporary and new encapsulated enzyme-based drugs, biosensors, and other bioanalytical devices. Solid-state nuclear magnetic resonance (NMR) measurements can expand our molecular view of proteins in this state and of the molecular interactions governing protein immobilization on popular biocompatible surfaces such as silica. Here, the authors study the immobilization of ubiquitin on the mesoporous silica MCM41 by NMR and other techniques. Protein molecules are shown to bind efficiently at pH 5 through electrostatic interactions to individual MCM41 particles, causing their agglutination. The strong attraction of ubiquitin to MCM41 surface is given molecular context through evidence of proximity of basic, carbonyl and polar groups on the protein to groups on the silica surface using NMR measurements. The immobilized protein exhibits broad peaks in two-dimensional 13C dipolar-assisted rotational resonance spectra, an indication of structural multiplicity. At the same time, cross-peaks related to Tyr and Phe sidechains are missing due to motional averaging. Overall, the favorable adsorption of ubiquitin to MCM41 is accompanied by conformational heterogeneity and by a major loss of motional degrees of freedom as inferred from the marked entropy decrease. Nevertheless, local motions of the aromatic rings are retained in the immobilized state.

Highly Efficient Fumed Silica Nanoparticles for Peptide Bond Formation: Converting Alanine to Alanine Anhydride

In this work, thermal condensation of alanine adsorbed on fumed silica nanoparticles is investigated using thermal analysis and multiple spectroscopic techniques, including infrared (IR), Raman, and nuclear magnetic resonance (NMR) spectroscopies. Thermal analysis shows that adsorbed alanine can undergo thermal condensation, forming peptide bonds within a short time period and at a lower temperature (∼170 °C) on fumed silica nanoparticle surfaces than that in bulk (∼210 °C). Spectroscopic results further show that alanine is converted to alanine anhydride with a yield of 98.8% during thermal condensation. After comparing peptide formation on solution-derived colloidal silica nanoparticles, it is found that fumed silica nanoparticles show much better efficiency and selectivity than solution-derived colloidal silica nanoparticles for synthesizing alanine anhydride. Furthermore, Raman spectroscopy provides evidence that the high efficiency for fumed silica nanoparticles is likely related to their unique surface features: the intrinsic high population of strained ring structures present at the surface. This work indicates the great potential of fumed silica nanoparticles in synthesizing peptides with high efficiency and selectivity.

Low concentration DNA extraction and recovery using a silica solid phase

DNA extraction from clinical samples is commonly achieved with a silica solid phase extraction column in the presence of a chaotrope. Versions of these protocols have been adapted for point of care (POC) diagnostic devices in miniaturized platforms, but commercial kits require a high amount of input DNA. Thus, when the input clinical sample contains less than 1 μg of total DNA, the target-specific DNA recovery from most of these protocols is low without supplementing the sample with exogenous carrier DNA. In fact, many clinical samples used in the development of POC diagnostics often exhibit target DNA concentrations as low as 3 ng/mL. With the broader goal of improving the yield and efficiency of nucleic acid-based POC devices for dilute samples, we investigated both DNA adsorption and recovery from silica particles by using 1 pg- 1 μg of DNA with a set of adsorption and elution buffers ranging in pH and chaotropic presence. In terms of adsorption, we found that low pH and the presence of chaotropic guanidinium thiocyanate (GuSCN) enhanced DNA-silica adsorption. When eluting with a standard low-salt, high-pH buffer, > 70% of DNA was unrecoverable, except when DNA was initially adsorbed with 5 M GuSCN at pH 5.2. Unrecovered DNA was either not initially adsorbed or irreversibly bound on the silica surface. Recovery was improved when eluting with 95°C formamide and 1 M NaOH, which suggested that DNA-silica-chaotrope interactions are dominated by hydrophobic interactions and hydrogen bonding. While heated formamide and NaOH are non-ideal elution buffers for practical POC devices, the salient results are important for engineering a set of optimized reagents that could maximize nucleic acid recovery from a microfluidic DNA-silica-chaotrope system.

Structure and Function of Adsorbed Hemoglobin on Silica Nanoparticles: Relationship between the Adsorption Process and the Oxygen Binding Properties

The connection between the mechanisms of protein adsorption on nanoparticles and the structural and functional properties of the adsorbed protein often remains unclear. We investigate porcine hemoglobin adsorption on silica nanoparticles, and we analyze the structural and functional modifications of adsorbed hemoglobin by UV-vis spectrophotometry, circular dichroism, and oxygen binding measurement. The structural analysis of adsorbed hemoglobin on silica nanoparticles reveals a significant loss of secondary structure and a preservation of the heme electronic structure. However, adsorbed hemoglobin retains its quaternary structure and exhibits an enhanced oxygen affinity with cooperative binding. Moreover, the structural and functional modifications are fully reversible after complete desorption from silica nanoparticles at pH 8.7. The tunable adsorption and desorption of hemoglobin on SNPs with pH change, and the full control of hemoglobin activity by pH, temperature, and the addition of inorganic phosphate effectors opens the way to an interesting system whereby protein adsorption on nanoparticles can allow for full control over hemoglobin oxygen binding activity. Our results suggest that adsorption of hemoglobin on silica nanoparticles leads to a new structural, functional, and dynamic state with full reversibility in a way that significantly differs from protein denaturation.

Spongelike Porous Silica Nanosheets: From "Soft" Molecular Trapping to DNA Delivery

Spongelike porous silica nanosheets, with nanometer thicknesses and pores whose diameters are on the hundreds-of-nanometers scale, have been used as a novel carrier for molecular immobilization of different guests. Enhanced properties of encapsulation were shown for drug molecules of different dimensions due to "softness" caused by the specific nanometric features of the porous structure. The encapsulating effect of the structure results in sustained and stimuli-responsive release behavior of immobilized guest molecules. By studying the adsorption process of DNA molecules on spongelike porous nanosheets or on solid nanoparticles by use of a quartz crystal microbalance, we show that better elasticity of surfaces of the porous nanosheets over that of solid nanoparticles can improve the immobilization of guest molecules. The coating of porous silica nanosheets onto various substrates was also found to effectively mediate DNA delivery to mammalian cells.

p-TsOH-Catalyzed one-pot transformation of di- and trihydroxy steroids towards diverse A/B-ring oxo-functionalization

A milder, facile, and greener transformative protocol, specifically on solid supports, to yield A-ring and/or B-ring oxo-functionalized steroids has been accomplished.

Models for biomedical interfaces: a computational study of quinone-functionalized amorphous silica surface features

The structural and IR features of amorphous silica surfaces, functionalized by ortho-benzoquinone groups, were computed to obtain a deeper knowledge of multifunctional coatings with antimicrobial properties.

A molecular dynamics study of the interaction of water with the external surface of silicalite-1

The modeling study of the interaction of water with the external surface of silicalite-1 reveals retention of H₂O molecules at the interface because of the formation of a structured water layer.

Insights into Silica Bilayer Hydroxylation and Dissolution

Hydroxylation and dissolution of well-structured silica bilayer films grown on a ruthenium single-crystal support (SiO₂/Ru(0001)) was studied by temperature programmed desorption and X-ray photoelectron spectroscopy (XPS). Water desorption signals from SiO₂/Ru(0001) hydroxylated by electron-bombardment of adsorbed ice at 100 K were found to be comparable to those of hydroxylated bulk silica samples and attributed to adsorbed molecular water and silanol groups (vicinal and terminal). Isotopic exchange between ¹⁸O-labeled SiO₂ and ¹⁶O-labeled water suggests the occurrence of dynamic siloxane bond cleavage and re-formation during electron bombardment. Together with the observed strong dependence of hydroxylation activity on ice coverage, which is found to increase with increasing thickness of the ice layer, a hydroxylation mechanism based on the activation of siloxane bonds by water radiolysis products (e.g. hydroxyls) and subsequent water dissociation is proposed. Dissolution rates obtained from the attenuation of Si 2p and O 1s XPS signal intensities upon exposure of bilayer SiO₂/Ru(0001) to alkaline conditions at various temperatures are in agreement with the proposed rate model for bulk silica dissolution by OH⁻ attack and provide further corroboration of the proposed hydroxylation mechanism.

Dynamic behaviour of the silica-water-bio electrical double layer in the presence of a divalent electrolyte

Molecular dynamics simulation of the electric double layer at the silica-water-bio interface in mixed electrolyte. Water orientation and charge distribution showed a significant effect on the electrostatics at the interface.

The elusive silica/water interface: isolated silanols under water as revealed by vibrational sum frequency spectroscopy

Isolated surface silanols are unambiguously identified under water. They are found to be not easily deprotonated and their populations to be clearly dependent on the surface pre-treatment method.

β-Cristobalite (001) surface as 4-formaminoantipyrine adsorbent: First principle study of the effect on adsorption of surface modification

Silica based materials find applications as excipients and particularly as drug delivery agents for pharmaceutical drugs. Their performance can be crucially affected by surface treatments, as it can modify the adsorption (and release) of these formulations. The role of surface modification on the features of 4-formaminoantipyrine (FAA) adsorbed on β-cristobalite (001) surface is studied by means of simulations based on the Density Functional Theory (DFT). Starting from the results of FAA in interaction with a dehydroxylated surface; a fully hydroxylated surface and a functionalized surface with benzalkonium chloride (BC) surfactant have been added to study the configurational landscape. Calculations suggest that the trend for FAA preferential adsorption on silica surfaces is: dehydroxylated>hydroxylated>BC-functionalized. The potential for hydrogen bonding causes the main contribution to the bonding while dispersion forces present an additional contribution independently of whether the drug is hydrogen-bonded or BC-bonded to the surface. Adsorption takes mainly place through nitrogen atoms in the heterocyclic ring, the carbonyl and amine functional groups. Associated mode's shifts and concurrent changes in bond length are also observed showing accordance between electronic and geometrical structure results. BC surfactant reduces the number of formed H-bonds and lowers the attractive molecule-surface interaction being it useful to prevent particle agglomeration and could favor drug release in therapies that requires faster but controlled delivery.

Agarose and Its Derivatives as Supports for Enzyme Immobilization

Agarose is a polysaccharide obtained from some seaweeds, with a quite particular structure that allows spontaneous gelation. Agarose-based beads are highly porous, mechanically resistant, chemically and physically inert, and sharply hydrophilic. These features-that could be further improved by means of covalent cross-linking-render them particularly suitable for enzyme immobilization with a wide range of derivatization methods taking advantage of chemical modification of a fraction of the polymer hydroxyls. The main properties of the polymer are described here, followed by a review of cross-linking and derivatization methods. Some recent, innovative procedures to optimize the catalytic activity and operational stability of the obtained preparations are also described, together with multi-enzyme immobilized systems and the main guidelines to exploit their performances.

Probing Silica-Biomolecule Interactions by Solid-State NMR and Molecular Dynamics Simulations

Understanding the molecular interactions between inorganic phases such as silica and organic material is fundamental for chromatographic applications, for tailoring silica-enzyme interactions, and for elucidating the mechanisms of biomineralization. The formation, structure, and properties of the organic/inorganic interface is crucial in this context. Here, we investigate the interaction of selectively ¹³C-labeled choline with ²⁹Si-labeled monosilicic acid/silica at the molecular level. Silica/choline nanocomposites were analyzed by solid-state NMR spectroscopy in combination with extended molecular dynamics (MD) simulations to understand the silica/organic interface. Cross-polarization magic angle spinning (CP MAS)-based NMR experiments like ¹H-¹³C CP-REDOR (rotational-echo double resonance), ¹H-¹³C HETCOR (heteronuclear correlation), and ¹H-²⁹Si-¹H double CP are employed to determine spatial parameters. The measurement of ²⁹Si-¹³C internuclear distances for selectively ¹³C-labeled choline provides an experimental parameter that allows the direct verification of MD simulations. Atomistic modeling using classical MD methodologies is performed using the INTERFACE force field. The modeling results are in excellent agreement with the experimental data and reveal the relevant molecular conformations as well as the nature and interplay of the interactions between the choline cation and the silica surface. Electrostatic interactions and hydrogen bonding are both important and depend strongly on the hydration level as well as the charge state of the silica surface.

Adhesion mechanisms of curli subunit CsgA to abiotic surfaces

Curli fibers are functional amyloids that play a key role in biofilm structure and adhesion to various surfaces. Strong bioinspired adhesives comprising curli fibers have recently been created; however, the mechanisms curli uses to attach onto abiotic surfaces are still uncharacterized. Toward a materials-by-design approach for curli-based adhesives and multifunctional materials, we examine curli subunit adsorption onto graphene and silica surfaces through atomistic simulation. We find that both structural features and sequence influence adhesive strength, enabling the CsgA subunit to adhere strongly to both polar and nonpolar surfaces. Specifically, flexible regions facilitate adhesion to both surfaces, charged and polar residues (Arg, Lys, and Gln) enable strong interactions with silica, and six-carbon aromatic rings (Tyr and Phe) adsorb strongly to graphene. We find that adsorption not only lowers molecular mobility but also leads to loss of secondary structure, factors that must be well balanced for effective surface attachment. Both events appear to propagate through the CsgA structure as correlated motion between clusters of residues, often H-bonded between rows on adjacent β strands. To quantify this, we present a correlation analysis approach to detecting collective motion between residue groups. We find that certain clusters of residues have a higher impact on the stability of the rest of the protein structure, often polar and bulky groups within the helix core. These findings lend insight into bacterial adhesion mechanisms and reveal strategies for theory-driven design of engineered curli fibers that harness point mutations and conjugates for stronger adhesion.

Residue-Specific Interactions of an Intrinsically Disordered Protein with Silica Nanoparticles and their Quantitative Prediction

Elucidation of the driving forces that govern interactions between nanoparticles and intrinsically disordered proteins (IDP) is important for the understanding of the effect of nanoparticles in living systems and for the design of new nanoparticle-based assays to monitor health and combat disease. The quantitative interaction profile of the intrinsically disordered transactivation domain of p53 and its mutants with anionic silica nanoparticles is reported at atomic resolution using nuclear magnetic spin relaxation experiments. These profiles are analyzed with a novel interaction model that is based on a quantitative nanoparticle affinity scale separately derived for the 20 natural amino acids. The results demonstrate how the interplay of attractive and repulsive Coulomb interactions with hydrophobic effects is responsible for the sequence-dependent binding of a disordered protein to nanoparticles.

Modeling and simulation of protein-surface interactions: achievements and challenges

Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

Characterizations of the Formation of Polydopamine-Coated Halloysite Nanotubes in Various pH Environments

Recent studies demonstrated that polydopamine (PDA) coating is universal to nearly all substrates, and it endows substrates with biocompatibility, postfunctionality, and other useful properties. Surface chemistry of PDA coating is important for its postmodifications and applications. However, there is less understanding of the formation mechanism and surface functional groups of PDA layers generated in different conditions. Halloysite is a kind of clay mineral with tubular nanostructure. Water-swellable halloysite has unique reactivity. In this study, we have investigated the reaction of dopamine in the presence of water-swellable halloysite. We have tracked the reaction progresses in different pH environments by using UV-vis spectroscopy and surface-enhanced Raman spectroscopy (SERS). The surface properties of PDA on halloysite were clarified by X-ray photoelectron spectroscopy (XPS), SERS, Fourier transform infrared (FTIR) characterizations, zeta potential, surface wettability, and morphological characterizations. We noticed that the interaction between halloysite surface and dopamine strongly influences the surface functionality of coated PDA. In addition, pH condition further modulates surface functional groups, resulting in less content of secondary/aromatic amine in PDA generated in weak acidic environment. This study demonstrates that the formation mechanism of polydopamine becomes complex in the presence of inorganic nanomaterials. Substrate property and reaction condition dominate the functionality of obtained PDA together.

Integrated Modeling and Experimental Approaches to Control Silica Modification of Design Silk-Based Biomaterials

Mineralized polymeric biomaterials provide useful options toward mechanically robust systems for some tissue repairs. Silks as a mechanically robust protein-based material provide a starting point for biomaterial options, particularly when combined with silica toward organic-inorganic hybrid systems. To further understand the interplay between silk proteins and silica related to material properties, we systematically study the role of three key domains in bioengineered spider silk fusion proteins with respect to β-sheet formation and mineralization: (i) a core silk domain for materials assembly, (ii) a histidine tag for purification, and (iii) a silicification domain for mineralization. Computational simulations are used to identify the effect of each domain on the protein folding and accessibility of positively charged amino acids for silicification and predictions are then compared with experimental data. The results show that the addition of the silica and histidine domains reduces β-sheet structure in the materials, and increases solvent-accessible surface area to the positive charged amino acids, leading to higher levels of silica precipitation. Moreover, the simulations show that the location of the charged biomineralization domain has small effect on the protein folding and consequently surface exposure of charged amino acids. Those surfaces display correlation with the amount of silicification in experiments. The results demonstrate that the exposure of the positively charged amino acids impacts protein function related to mineralization. In addition, processing parameters (solvating agent, the method of β-sheet induction and temperature) affect protein secondary structure, folding and function. This integrated modeling and experimental approach provides insight into sequence-structure-function relationships for control of mineralized protein biomaterial structures.

Control of Triboelectrification by Engineering Surface Dipole and Surface Electronic State

Although triboelectrification is a well-known phenomenon, fundamental understanding of its principle on a material surface has not been studied systematically. Here, we demonstrated that the surface potential, especially the surface dipoles and surface electronic states, governed the triboelectrification by controlling the surface with various electron-donating and -withdrawing functional groups. The functional groups critically affected the surface dipoles and surface electronic states followed by controlling the amount of and even the polarity of triboelectric charges. As a result, only one monolayer with a thickness of less than 1 nm significantly changed the conventional triboelectric series. First-principles simulations confirmed the atomistic origins of triboelectric charges and helped elucidate the triboelectrification mechanism. The simulation also revealed for the first time where charges are retained after triboelectrification. This study provides new insights to understand triboelectrification.

Adsorption of Amino Acids and Peptides on Metal and Oxide Surfaces in Water Environment: A Synthetic and Prospective Review

Amino acids and peptides are often used as "model" segments of proteins for studying their behavior in various types of environments, and/or elaborating functional surfaces. Indeed, though the protein behavior is much more complex than that of their isolated segments, knowledge of the binding mode as well as of the chemical structure of peptides on metal or oxide surfaces is a significant step toward the control of materials in a biological environment. Such knowledge has considerably increased in the past few years, thanks to the combination of advanced characterization techniques and of modeling methods. Investigations of biomolecule-surface interactions in water/solvent environments are quite numerous, but only in a few cases is it possible to reach an understanding of the molecule-(water)-surface interaction with a level of detail comparable to that of the UHV studies. This contribution aims at reviewing the recent data describing the amino acid and peptide interaction with metal or oxide surfaces in the presence of water.

Extraction and Purification of DNA from Complex Biological Sample Matrices Using Solid-Phase Microextraction Coupled with Real-Time PCR

The determination of extremely small quantities of DNA from complex biological sample matrices represents a significant bottleneck in nucleic acid analysis. In this study, polymeric ionic liquid (PIL)-based solid-phase microextraction (SPME) was applied for the extraction and purification of DNA from crude bacterial cell lysate with subsequent quantification by real-time PCR (qPCR) analysis. Using an on-fiber ultraviolet initiated polymerization technique, eight different PIL sorbent coatings were generated and their DNA extraction performance evaluated using qPCR. The PIL sorbent coating featuring halide anions and carboxylic acid groups in the cationic portion exhibited superior DNA extraction capabilities when compared to the other studied PILs and a commercial polyacrylate SPME fiber. Electrostatic interactions as well as an ion-exchange mechanism were identified as the driving forces in DNA extraction by the PIL sorbents. The selectivity of the PIL sorbent coating for DNA was demonstrated in the presence of PCR inhibitors at high concentration, where a quantifiable amount of template DNA was extracted from aqueous samples containing CaCl2 and FeCl3. Furthermore, the PIL-based SPME method was successfully applied for the extraction of DNA from crude bacterial cell lysate spiked with 1 pg mL(-1) template DNA without requiring the use of organic solvents or centrifugation steps. Following PIL-based SPME of DNA from a dilute cell lysate, the qPCR amplification efficiency was determined to be 100.3%, demonstrating the feasibility of the developed method to extract high purity DNA from complex sample matrices.

Revisiting the paradigm of silica pathogenicity with synthetic quartz crystals: the role of crystallinity and surface disorder

BACKGROUND

Exposure to some - but not all - quartz particles is associated to silicosis, lung cancer and autoimmune diseases. What imparts pathogenicity to any single quartz source is however still unclear. Crystallinity and various surface features are implied in toxicity. Quartz dusts used so far in particle toxicology have been obtained by grinding rocks containing natural quartz, a process which affects crystallinity and yields dusts with variable surface states. To clarify the role of crystallinity in quartz pathogenicity we have grown intact quartz crystals in respirable size.

METHODS

Quartz crystals were grown and compared with a fractured specimen obtained by grinding the largest synthetic crystals and a mineral quartz (positive control). The key physico-chemical features relevant to particle toxicity - particle size distribution, micromorphology, crystallinity, surface charge, cell-free oxidative potential - were evaluated. Membranolysis was assessed on biological and artificial membranes. Endpoints of cellular stress were evaluated on RAW 264.7 murine macrophages by High Content Analysis after ascertaining cellular uptake by bio-TEM imaging of quartz-exposed cells.

RESULTS

Quartz crystals were grown in the submicron (n-Qz-syn) or micron (μ-Qz-syn) range by modulating the synthetic procedure. Independently from size as-grown quartz crystals with regular intact faces did not elicit cellular toxicity and lysosomal stress on RAW 264.7 macrophages, and were non-membranolytic on liposome and red blood cells. When fractured, synthetic quartz (μ-Qz-syn-f) attained particle morphology and size close to the mineral quartz dust (Qz-f, positive control) and similarly induced cellular toxicity and membranolysis. Fracturing imparted a higher heterogeneity of silanol acidic sites and radical species at the quartz surface.

CONCLUSIONS

Our data support the hypothesis that the biological activity of quartz dust is not due to crystallinity but to crystal fragmentation, when conchoidal fractures are formed. Besides radical generation, fracturing upsets the expected long-range order of non-radical surface moieties - silanols, silanolates, siloxanes - which disrupt membranes and induce cellular toxicity, both outcomes associated to the inflammatory response to quartz.

Photoswitched Cell Adhesion on Azobenzene-Containing Self-Assembled Films

Stimuli-responsive surfaces that can regulate and control cell adhesion have attracted much attention for their great potential in diverse biomedical applications. Unlike for pH- and temperature-responsive surfaces, the process of photoswitching requires no additional input of chemicals or thermal energy. In this work, two different photoresponsive azobenzene films are synthesized by chemisorption and electrostatic layer-by-layer (LbL) assembly techniques. The LbL film exhibits a relatively loose packing of azobenzene chromophores compared with the chemisorbed film. The changes in trans/cis isomer ratio of the azobenzene moiety and the corresponding wettability of the LbL films are larger than those of the chemisorbed films under UV light irradiation. The tendency for cell adhesion on the LbL films decreases markedly after UV light irradiation, whereas adhesion on the chemisorbed films decreases only slightly, because the azobenzene chromophores stay densely packed. Interestingly, the tendency for cell adhesion can be considerably increased on rough substrates, the roughness being introduced by use of photolithography and inductively coupled plasma deep etching techniques. For the chemisorbed films on rough substrates, the amount of cells that adhere also changes slightly after UV light irradiation, whereas, the amount of cells that adhere to LbL films on rough substrates decreases significantly.

Stereochemically Distinct Cyclotetrasiloxanes Containing 3-Pyridyl Moieties and Their Functional Coordination Polymers

Synthesis of new cyclotetrasiloxane scaffolds containing peripherally functionalized 3-pyridyl moieties, [MeSiO(CH═CH(3)Py)]4 (L(1)) and [MeSiO(CH2CH2(3)Py)]4 (L(2)), and their reactivity studies with certain d(10) metal ions are reported. The ligand L(1) is obtained by the Heck-coupling reaction of tetramethyl tetravinyl tetrasiloxane (D4(vi)) and 3-bromopyridine in the presence of the Pd(0) catalysts. The as-synthesized ligand L(1) shows the presence of three stereoisomers, cis-trans-cis (L(1A)), cis-cis-trans (L(1B)), and all-trans (L(1C)), which are quantitatively separated by column chromatography. Subsequent reduction of L(1A), L(1B), and L(1C) with triethylsilane in the presence of catalytic amounts of Pd/C leads to the formation of the ligands L(2A), L(2B), and L(2C) with retention of stereochemistry due to the precursor moieties. Treatment of ZnI2 with L(1A) gives a one-dimensional coordination framework [(L(1A))4(ZnI2)2]∞, 1. These 1D-chains are further connected by π-π stacking interactions between the pyridyl groups of the adjacent chains leading to the formation of a three-dimensional network with the topology of a PtS net. The reaction of silver nitrate with ligand L(1B) gives a chain like one-dimensional cationic coordination polymer {[(L(1B))4Ag2]·2NO3·H2O·CH3OH }∞, 2, consisting of two different kinds of 32-membered macrocycles. Treatment of the all-trans ligand L(2C) with copper(I) iodide salt results in the formation of a cubane-type Cu4I4 cluster MOF [(L(2C))4Cu4I4]∞, 3, in a two-dimensional 4-connected uninodal sql/Shubnikov tetragonal plane net topology represented by the Schläfli symbol {4(4).6(2)}. This MOF displays a thermochromic luminescence behavior due to Cu4I4 clusters showing an orange emission at 298 K and a blue emission at 77 K.

Conjugation of A and B Blood Group Structures to Silica Microparticles for the Detection of Antigen-Specific B Cells

Silica microparticles were functionalized with A and B blood group carbohydrate antigens (A type I, A type II, B type I, and B type II) to enable the detection and monitoring of ABO antigen-specific B cells. Microparticles were prepared via the Stöber synthesis, labeled with an Alexafluor fluorescent dye, and characterized via TEM and fluorescence microscopy. The silica microparticles were functionalized with (3-aminopropyl)trimethoxysilane (APTMS), followed by the use of an established fluorenylmethyloxycarbonyl (Fmoc)-protected PEG-based linker. The terminal Fmoc moiety of the PEG-based linker was then deprotected, yielding free amino groups, to which the A and B antigens were coupled. The carbohydrate antigens were synthesized with a p-nitrophenol ester to enable conjugation to the functionalized silica microparticles via an amide bond. The number of free amine groups available for coupling for a given mass of PEG-functionalized silica microparticles was quantified via reaction with Fmoc-glycine. The antigen-functionalized microparticles were then evaluated for their specificity in binding to A and B antigen-reactive B-cells via flow cytometry, and for blocking of naturally occurring antibodies in human serum. Selective binding of the functionalized microparticles to blood group-reactive B cells was observed by flow cytometry and fluorescence microscopy. The modular approach outlined here is applicable to the preparation of silica microparticles containing any carbohydrate antigen and alternative fluorophores or labels. This approach therefore comprises a novel, general platform for screening B cell populations for binding to carbohydrate antigens, including, in this case, the human A and B blood group antigens.

Glyco-nano-oncology: Novel therapeutic opportunities by combining small and sweet

Recent efforts toward defining the molecular features of the tumor microenvironment have revealed dramatic changes in the expression of glycan-related genes including glycosyltransferases and glycosidases. These changes affect glycosylation of proteins and lipids not only in cancer cells themselves, but also in cancer associated-stromal, endothelial and immune cells. These glycan alterations including increased frequency of β1,6-branched N-glycans and bisecting N-glycans, overexpression of tumor-associated mucins, preferred expression of T, Tn and sialyl-Tn antigen and altered surface sialylation, may contribute to tumor progression by masking or unmasking specific ligands for endogenous lectins, including members of the C-type lectin, siglec and galectin families. Differential expression of glycans or glycan-binding proteins could be capitalized for the identification of novel biomarkers and might provide novel opportunities for therapeutic intervention. This review focuses on the biological relevance of lectin-glycan interactions in the tumor microenvironment (mainly illustrated by the immunosuppressive and pro-angiogenic activities of galectin-1) and the design of functionalized nanoparticles for pharmacological delivery of multimeric glycans, lectins or selective inhibitors of lectin-glycan interactions with antitumor activity.