DNA Sensing Platforms: Novel Insights into Molecular Grafting Using Low Perturbative AFM Imaging.

By using AFM as a nanografting tool, we grafted micrometer-sized DNA platforms into inert alkanethiol SAMs. Tuning the grafting conditions (surface density of grafting lines and scan rate) allowed us to tailor the molecular density of the DNA platforms. Following the nanografting process, AFM was operated in the low perturbative Quantitative Imaging (QI) mode. The analysis of QI AFM images showed the coexistence of molecular domains of different heights, and thus different densities, within the grafted areas, which were not previously reported using contact AFM imaging. Thinner domains corresponded to low-density DNA regions characterized by loosely packed, randomly oriented DNA strands, while thicker domains corresponded to regions with more densely grafted DNA. Grafting with densely spaced and slow scans increased the size of the high-density domains, resulting in an overall increase in patch height. The structure of the grafted DNA was compared to self-assembled DNA, which was assessed through nanoshaving experiments. Exposing the DNA patches to the target sequence produced an increase in the patch height, indicating that hybridization was accomplished. The relative height increase of the DNA patches upon hybridization was higher in the case of lower density patches due to hybridization leading to a larger molecular reorganization. Low density DNA patches were therefore the most suitable for targeting oligonucleotide sequences.

Insights in Cell Biomechanics through Atomic Force Microscopy.

We review the advances obtained by using Atomic Force Microscopy (AFM)-based approaches in the field of cell/tissue mechanics and adhesion, comparing the solutions proposed and critically discussing them. AFM offers a wide range of detectable forces with a high force sensitivity, thus allowing a broad class of biological issues to be addressed. Furthermore, it allows for the accurate control of the probe position during the experiments, providing spatially resolved mechanical maps of the biological samples with subcellular resolution. Nowadays, mechanobiology is recognized as a subject of great relevance in biotechnological and biomedical fields. Focusing on the past decade, we discuss the intriguing issues of cellular mechanosensing, i.e., how cells sense and adapt to their mechanical environment. Next, we examine the relationship between cell mechanical properties and pathological states, focusing on cancer and neurodegenerative diseases. We show how AFM has contributed to the characterization of pathological mechanisms and discuss its role in the development of a new class of diagnostic tools that consider cell mechanics as new tumor biomarkers. Finally, we describe the unique ability of AFM to study cell adhesion, working quantitatively and at the single-cell level. Again, we relate cell adhesion experiments to the study of mechanisms directly or secondarily involved in pathologies.

Silicone Oil Tamponade Removal: Which Technique Is More Effective? An X-Ray Photoemission Spectroscopy Study.

Purpose: To compare the efficacy of two surgical techniques used to remove silicone oil (SiO) emulsion tamponade after pars plana vitrectomy: triple air-fluid exchange (AFX) and balanced salt solution lavage (BSSL). Methods: X-ray photoemission spectroscopy measured silicon content of the dry residue of fluid samples taken during AFX and BSSL. Ten patients underwent AFX and five BSSL. Three fluid samples were taken per patient, and the dry residue of 10 drops per sample were analyzed. A fluid sample from a patient who never received SiO tamponade was also analyzed to set a "blank" reference sample. Results: Patients' demographics showed no significant difference. Sample 1 of the two groups contained comparable silicon content while samples 2 and 3 of the AFX group contained significantly more silicon than that of the BSSL group (15.0 ± 0.1 and 12.0 ± 0.9 for the AFX group vs. 10.7 ± 1.4 and 5.2 ± 0.6 for the BSSL group, respectively; P < 0.05). The cumulative amount of silicon in the three successive samples was also significantly higher for the AFX group (42.3 ± 1.6 vs. 32 ± 2; P < 0.0001). The average silicon content ratio of consecutive samples was significantly higher for the AFX group compared to the BSSL group (0.90 ± 0.01 vs. 0.58 ± 0.06; P = 0.006). Conclusions: Triple AFX removed more silicon than triple lavage. The eye wall actively interacts with silicon emulsion retaining silicon content rather than behaving as a neutral container. Translational Relevance: Triple air-fluid exchange removed more silicon than BSS lavage. Neither technique behaved as a well-mixed box dilution, suggesting the eye walls actively retain emulsion and a dynamic equilibrium is established between silicon dispersion and the eye wall surface.

Adsorption of the rhNGF Protein on Polypropylene with Different Grades of Copolymerization.

The surface properties of drug containers should reduce the adsorption of the drug and avoid packaging surface/drug interactions, especially in the case of biologically-derived products. Here, we developed a multi-technique approach that combined Differential Scanning Calorimetry (DSC), Atomic Force Microscopy (AFM), Contact Angle (CA), Quartz Crystal Microbalance with Dissipation monitoring (QCM-D), and X-ray Photoemission Spectroscopy (XPS) to investigate the interactions of rhNGF on different pharma grade polymeric materials. Polypropylene (PP)/polyethylene (PE) copolymers and PP homopolymers, both as spin-coated films and injected molded samples, were evaluated for their degree of crystallinity and adsorption of protein. Our analyses showed that copolymers are characterized by a lower degree of crystallinity and lower roughness compared to PP homopolymers. In line with this, PP/PE copolymers also show higher contact angle values, indicating a lower surface wettability for the rhNGF solution on copolymers than PP homopolymers. Thus, we demonstrated that the chemical composition of the polymeric material and, in turn, its surface roughness determine the interaction with the protein and identified that copolymers may offer an advantage in terms of protein interaction/adsorption. The combined QCM-D and XPS data indicated that protein adsorption is a self-limiting process that passivates the surface after the deposition of roughly one molecular layer, preventing any further protein adsorption in the long term.

Biofunctionalization of Porous Titanium Oxide through Amino Acid Coupling for Biomaterial Design.

Porous transition metal oxides are widely studied as biocompatible materials for the development of prosthetic implants. Resurfacing the oxide to improve the antibacterial properties of the material is still an open issue, as infections remain a major cause of implant failure. We investigated the functionalization of porous titanium oxide obtained by anodic oxidation with amino acids (Leucine) as a first step to couple antimicrobial peptides to the oxide surface. We adopted a two-step molecular deposition process as follows: self-assembly of aminophosphonates to titanium oxide followed by covalent coupling of Fmoc-Leucine to aminophosphonates. Molecular deposition was investigated step-by-step by Atomic Force Microscopy (AFM) and X-ray Photoemission Spectroscopy (XPS). Since the inherent high roughness of porous titanium hampers the analysis of molecular orientation on the surface, we resorted to parallel experiments on flat titanium oxide thin films. AFM nanoshaving experiments on aminophosphonates deposited on flat TiO2 indicate the formation of an aminophosphonate monolayer while angle-resolved XPS analysis gives evidence of the formation of an oriented monolayer exposing the amine groups. The availability of the amine groups at the outer interface of the monolayer was confirmed on both flat and porous substrates by the following successful coupling with Fmoc-Leucine, as indicated by high-resolution XPS analysis.

A Two-Step Approach to Tune the Micro and Nanoscale Morphology of Porous Niobium Oxide to Promote Osteointegration.

We present a two-step surface modification process to tailor the micro and nano morphology of niobium oxide layers. Niobium was firstly anodized in spark regime in a Ca- and P-containing solution and subsequently treated by acid etching. The effects of anodizing time and applied potential on the surface morphology is investigated with SEM and AFM, complemented by XPS compositional analysis. Anodizing with a limiting potential of 250 V results in the fast growth of oxide layers with a homogeneous distribution of micro-sized pores. Cracks are, however, observed on 250 V grown layers. Limiting the anodizing potential to 200 V slows down the oxide growth, increasing the anodizing time needed to achieve a uniform pore coverage but produces fracture-free oxide layers. The surface nano morphology is further tuned by a subsequent acid etching process that leads to the formation of nano-sized pits on the anodically grown oxide surface. In vitro tests show that the etching-induced nanostructure effectively promotes cell adhesion and spreading onto the niobium oxide surface.

Local Optical Properties in CVD-Grown Monolayer WS2 Flakes.

Excitons dominate the light absorption and re-emission spectra of monolayer transition-metal dichalcogenides (TMD). Microscopic investigations of the excitonic response in TMD almost invariably extract information from the radiative recombination step, which only constitutes one part of the picture. Here, by exploiting imaging spectroscopic ellipsometry (ISE), we investigate the spatial dependence of the dielectric function of chemical vapor deposition (CVD)-grown WS2 flakes with a microscopic lateral resolution, thus providing information about the spatially varying, exciton-induced light absorption in the monolayer WS2. Comparing the ISE results with imaging photoluminescence spectroscopy data, the presence of several correlated features was observed, along with the unexpected existence of a few uncorrelated characteristics. The latter demonstrates that the exciton-induced absorption and emission features are not always proportional at the microscopic scale. Microstructural modulations across the flakes, having a different influence on the absorption and re-emission of light, are deemed responsible for the effect.

Correlative nanoscopy: A multimodal approach to molecular resolution.

Atomic force microscopy (AFM) is a nano-mechanical tool uniquely suited for biological studies at the molecular scale. AFM operation is based on mechanical interaction between the tip and the sample, a mechanism of contrast capable of measuring different information, including surface topography, mechanical, and electrical properties. However, the lack of specificity highlights the need to integrate AFM data with other techniques providing compositional hints. In particular, optical microscopes based on fluorescence as a mechanism of contrast can access the local distribution of specific molecular species. The coupling between AFM and super-resolved fluorescence microscopy solves the resolution mismatch between AFM and conventional fluorescence optical microscopy. Recent advances showed that also the inherently label-free imaging capabilities of the AFM are fundamental to complement the fluorescence images. In this review, we have presented a brief historical view on correlative microscopy, and, finally, we have summarized the progress of correlative AFM-super-resolution microscopy in biological research.

Morphological and Mechanical Characterization of DNA SAMs Combining Nanolithography with AFM and Optical Methods.

The morphological and mechanical properties of thiolated ssDNA films self-assembled at different ionic strength on flat gold surfaces have been investigated using Atomic Force Microscopy (AFM). AFM nanoshaving experiments, performed in hard tapping mode, allowed selectively removing molecules from micro-sized regions. To image the shaved areas, in addition to the soft contact mode, we explored the use of the Quantitative Imaging (QI) mode. QI is a less perturbative imaging mode that allows obtaining quantitative information on both sample topography and mechanical properties. AFM analysis showed that DNA SAMs assembled at high ionic strength are thicker and less deformable than films prepared at low ionic strength. In the case of thicker films, the difference between film and substrate Young's moduli could be assessed from the analysis of QI data. The AFM finding of thicker and denser films was confirmed by X-Ray Photoelectron Spectroscopy (XPS) and Spectroscopic Ellipsometry (SE) analysis. SE data allowed detecting the DNA UV absorption on dense monomolecular films. Moreover, feeding the SE analysis with the thickness data obtained by AFM, we could estimate the refractive index of dense DNA films.

Reproducibility warning: The curious case of polyethylene glycol 6000 and spheroid cell culture.

Reproducibility of results is essential for a well-designed and conducted experiment. Several reasons may originate failure in reproducing data, such as selective reporting, low statistical power, or poor analysis. In this study, we used PEG6000 samples from different distributors and tested their capability inducing spheroid formation upon surface coating. MALDI-MS, NMR, FTIR, and Triple SEC analysis of the different PEG60000s showed nearly identical physicochemical properties different, with only minor differences in mass and hydrodynamic radius, and AFM analysis showed no significant differences in the surface coatings obtained with the available PEG6000s. Despite these similarities, just one showed a highly reproducible formation of spheroids with different cell lines, such as HT-29, HeLa, Caco2, and PANC-1. Using the peculiar PEG6000 sample and a reference PEG6000 chosen amongst the others as control, we tested the effect of the cell/PEG interaction by incubating cells in the PEG solution prior to cell plating. These experiments indicate that the spheroid formation is due to direct interaction of the polymer with the cells rather than by interaction of cells with the coated surfaces. The experiments point out that for biological entities, such as cells or tissues, even very small differences in impurities or minimal variations in the starting product can have a very strong impact on the reproducibility of data.

Functionalizing gold with single strand DNA: novel insight into optical properties via combined spectroscopic ellipsometry and nanolithography measurements.

We have studied the self-assembly of 22-base oligonucleotides bound by a short alkyl thiol linker (C6-ssDNA) on flat Au films. The self-assembled monolayer (SAM) was modified by addition of a spacer (mercaptohexanol, MCH). Molecular depositions were monitored in situ by spectroscopic ellipsometry (SE). SAMs were characterized in a liquid environment by coupling SE (difference spectra method) with Atomic Force Microscope (AFM) measurements. We exploited the biofilm thickness obtained by AFM nanolithography and imaging to solve the refractive index/thickness correlation in optical measurements on ultrathin molecular layers. The combined SE/AFM analysis provided reliable estimates of the thickness and the refractive index of the biofilm in the NIR region (650-1300 nm) and revealed new aspects of DNA molecular organization: exposure to MCH leads to an increase of both film thickness and refractive index, which points to a reorganization of C6-ssDNA film. We show that the contribution of the thiol/Au interface has to be included in the optical model to obtain a more reliable determination of the refractive index of the biofilm in a liquid. The careful, correlative characterization of the mixed C6-ssDNA/MCH SAM represents a key step towards the optimization of a robust detection scheme based on helix-helix hybridization.

Investigating organic multilayers by spectroscopic ellipsometry: specific and non-specific interactions of polyhistidine with NTA self-assembled monolayers.

BACKGROUND: A versatile strategy for protein-surface coupling in biochips exploits the affinity for polyhistidine of the nitrilotriacetic acid (NTA) group loaded with Ni(II). Methods based on optical reflectivity measurements such as spectroscopic ellipsometry (SE) allow for label-free, non-invasive monitoring of molecule adsorption/desorption at surfaces. RESULTS: This paper describes a SE study about the interaction of hexahistidine (His6) on gold substrates functionalized with a thiolate self-assembled monolayer bearing the NTA end group. By systematically applying the difference spectra method, which emphasizes the small changes of the ellipsometry spectral response upon the nanoscale thickening/thinning of the molecular film, we characterized different steps of the process such as the NTA-functionalization of Au, the adsorption of the His6 layer and its eventual displacement after reaction with competitive ligands. The films were investigated in liquid, and ex situ in ambient air. The SE investigation has been complemented by AFM measurements based on nanolithography methods (nanografting mode). CONCLUSION: Our approach to the SE data, exploiting the full spectroscopic potential of the method and basic optical models, was able to provide a picture of the variation of the film thickness along the process. The combination of Î´Δ i +1 ,i (λ), Î´Ψ i +1 ,i (λ) (layer-addition mode) and δΔ(†) i ', i +1(λ), δΨ(†) i ', i +1(λ) (layer-removal mode) difference spectra allowed us to clearly disentangle the adsorption of His6 on the Ni-free NTA layer, due to non specific interactions, from the formation of a neatly thicker His6 film induced by the Ni(II)-loading of the NTA SAM.

Spectroscopic ellipsometry meets AFM nanolithography: about hydration of bio-inert oligo(ethylene glycol)-terminated self assembled monolayers on gold.

For the first time, to our knowledge, spectroscopic ellipsometry (SE) has been combined with state-of-the-art AFM differential height measurements conducted after shaving nano-lithography of ultrathin, soft-matter films for thickness determination. We investigated self-assembled monolayers of SH-(CH2)11-EGn-OH molecules on gold, where EG is ethylene glycol units and n = 3 and 6, a prototypical non-fouling system. We performed SE measurements (245-1200 nm) focusing on the changes induced by the formation of the film (difference spectra). SE measurements, analysed by simple models, confirm the formation of the S-Au interface, transparency of the SAMs and provide a sharp picture of the ability of the EG functionality to protect the surface from unspecific adsorption of proteins. A quantitative assessment of the film thickness by SE was carried out ex situ, thanks to the optical contrast between the film and the ambient, and by AFM in liquid. The cross-check between SE and AFM height measurements combined with the comparison between in-liquid and ex situ SE measurements allowed obtaining non-perturbative information about the vertical density profile of the SAM. The in-liquid SE measurements indicate a refractive index matching between the aqueous medium and the outer part of the SAM, consistent with a disordered configuration of OEG and/or the penetration of water amid the OEG strands. A critical discussion provides a detailed insight into the subtle issues and pitfalls related to the thickness determination of soft-matter films to the monolayer limit.

Spectroscopic ellipsometry of self assembled monolayers: interface effects. The case of phenyl selenide SAMs on gold.

This work focuses on the quantitative application of spectroscopic ellipsometry to the study of optical properties and thickness of self assembled monolayers (SAMs) of phenyl selenide deposited from the liquid phase on gold. STM, XPS and cyclic voltammetry measurements provide additional chemical and morphological characterization of the SAMs. While routine ellipsometry analysis of SAMs often relies on the film-induced Î´Δ change in the Δ ellipsometric angle and discards SAM-substrate interface effects, the present data show a distinctive behaviour of the Î´Ψ data that we assign to interface effects, stronger than those previously found for densely packed alkanethiol SAMs. An inaccurate modelling of the variations in Ψ related to the nano-structured SAM-substrate interface leads to a large overestimation of the film thickness. A simple model, which takes into account an effective approximation for the interface layer between the film and the substrate, and the molecular optical absorptions, provides a good agreement between the data and a reliable thickness estimate of the SAM.

Interaction of L-cysteine with naked gold nanoparticles supported on HOPG: a high resolution XPS investigation.

We report the results of a synchrotron-based high-resolution XPS study of the interaction of L-cysteine (Cys) with well-characterized colloidal gold nanoparticles (NPs, typical size 3-4 nm), which were pre-deposited on highly oriented pyrolytic graphite and then brought into contact with the aqueous solution of Cys by drop-casting. By comparison with data previously obtained for Cys deposition on flat Au substrates (single crystals and high quality films), we demonstrate the formation of a strong Cys/NP thiolate bond. The analysis of the line shape and adsorbate-induced Au 4f core level shift, backed by simulations of the NP structure, reveals the interaction of Cys with low-coordinated Au atoms belonging to the NP edge and corners. The analysis of the N 1s core-level indicates that neutral molecules are the most abundant species. The small facet size limits the formation of extended networks of zwitterionic molecules, typical of single crystal surfaces. This study provides a spectroscopic insight into the intense poisoning effect caused by a limited amount of Cys on Au catalysts described in previous reports.

Optical properties of Yeast Cytochrome c monolayer on gold: an in situ spectroscopic ellipsometry investigation.

The adsorption of Yeast Cytochrome c (YCC) on well defined, flat gold substrates has been studied by Spectroscopic Ellipsometry (SE) in the 245-1000 nm wavelength range. The investigation has been performed in aqueous ambient at room temperature, focusing on monolayer-thick films. In situ Î´Ψ and Î´Δ difference spectra have shown reproducibly well-defined features related to molecular optical absorptions typical of the so-called heme group. The data have been reproduced quantitatively by a simple isotropic optical model, accounting for the molecular absorption spectrum and film-substrate interface effects. The simulations allowed a reliable estimate of the film thickness and the determination of the position and the shape of the so-called Soret absorption peak that, within the experimental uncertainty, is the same found for molecules in liquid. These findings suggest that YCC preserves its native structure upon adsorption. The same optical model was able to reproduce also ex situ results on rinsed and dried samples, dominated by the spectral features associated to the polypeptide chain that tend to overwhelm the heme absorption features.

Self-assembly of 1,4-benzenedimethanethiol self-assembled monolayers on gold.

A study of the self-assembly of 1,4-benzenedimethanethiol (BDMT; HS-CH(2)-(C(6)H(4))-CH(2)-SH) monolayers on gold is presented. Self-assembled monolayers (SAMs) are characterized by reflection-absorption infrared spectroscopy (RAIRS), X-ray photoelectron spectroscopy (XPS), and spectroscopic ellipsometry (SE) measurements. The ensemble of measurements consistently shows that well-organized BDMT SAMs, with "standing-up" molecules, can be obtained on high quality gold films with incubation in n-hexane provided that N(2)-degassed solutions are used and all preparation steps are performed at 60 degrees C in the absence of ambient light. SE data indicate that the optical interface properties of the BDMT-Au system are different from those of simple alkanethiol SAMs. A possible mechanism for the formation of the "standing-up" phase from the lying-down phase via a hydrogen exchange reaction involving chemisorbed lying-down and free dithiol molecules is discussed.

The two-fold aspect of the interplay of amyloidogenic proteins with lipid membranes.

Investigating the pathways leading to the formation of amyloid protein aggregates and the mechanism of their cytotoxicity is fundamental for a deeper understanding of a broad range of human diseases. Increasing evidence indicates that early aggregates are responsible for the cytotoxic effects. This paper addresses the catalytic role of lipid surfaces in promoting aggregation of amyloid proteins and the permeability changes that these aggregates induce on lipid membranes. Effects of amyloid aggregates on model systems such as monolayers, vesicles, liposomes and supported lipid bilayers are reviewed. In particular, the relevance of atomic force microscopy in detecting both kinetics of amyloid formation and amyloid-membrane interactions is emphasized.

Nanopatterning by protein unfolding.

Molecular layers patterned on the nanoscale, with long-range order properties extending over the microscopic scale, have been obtained upon adsorption of commonly available proteins onto the hydrophobic and long-range ordered surface of pyrolytic graphite (HOPG). Proteins lose their native folding and polypeptide chains re-assemble on the surface in a layered fashion, forming a molecular bilayer. This behaviour is rather general since it is observed for different proteins irrespective of their specific structural properties.

Heparin strongly enhances the formation of beta2-microglobulin amyloid fibrils in the presence of type I collagen.

The tissue specificity of fibrillar deposition in dialysis-related amyloidosis is most likely associated with the peculiar interaction of beta2-microglobulin (beta2-m) with collagen fibers. However, other co-factors such as glycosaminoglycans might facilitate amyloid formation. In this study we have investigated the role of heparin in the process of collagen-driven amyloidogenesis. In fact, heparin is a well known positive effector of fibrillogenesis, and the elucidation of its potential effect in this type of amyloidosis is particularly relevant because heparin is regularly given to patients subject to hemodialysis to prevent blood clotting. We have monitored by atomic force microscopy the formation of beta2-m amyloid fibrils in the presence of collagen fibers, and we have discovered that heparin strongly accelerates amyloid deposition. The mechanism of this effect is still largely unexplained. Using dynamic light scattering, we have found that heparin promotes beta2-m aggregation in solution at pH 6.4. Morphology and structure of fibrils obtained in the presence of collagen and heparin are highly similar to those of natural fibrils. The fibril surface topology, investigated by limited proteolysis, suggests that the general assembly of amyloid fibrils grown under these conditions and in vitro at low pH is similar. The exposure of these fibrils to trypsin generates a cleavage at the C-terminal of lysine 6 and creates the 7-99 truncated form of beta2-m (DeltaN6beta2-m) that is a ubiquitous constituent of the natural beta2-m fibrils. The formation of this beta2-m species, which has a strong propensity to aggregate, might play an important role in the acceleration of local amyloid deposition.