Lipid mono- and bilayer supported on polymer films: composite polymer-lipid films on solid substrates.

We report the deposition of lipid monolayers and bilayers on polyacrylamide films deposited by radical chain reaction onto solid substrates in aqueous solutions. Polymer films of various degrees of monomer density and cross-linking are prepared. Lateral diffusion and fluorescent probe permeation measurements yield insight into the continuity of the lipid layers and show that monolayers exposed to air are much less sensitive towards polymer heterogeneities than bilayers below water, which is explained in terms of the wetting laws. The diffusion studies of lipid and lipopeptide probes yield absolute values of the frictional coefficients between the lipid layer and the polymer films and allow one to estimate the surface viscosity of the polymer film. The potential applications of supported membranes on soft thin polymer films for the preparation of biofunctionalized surfaces or biocompatible receptive surfaces for biosensors are discussed.     

Submicron patterning of DNA oligonucleotides on silicon

The covalent attachment of DNA oligonucleotides onto crystalline silicon (100) surfaces, in patterns with submicron features, in a straightforward, two-step process is presented. UV light exposure of a hydrogen-terminated silicon (100) surface coated with alkenes functionalized with N-hydroxysuccinimide ester groups resulted in the covalent attachment of the alkene as a monolayer on the surface. Submicron-scale patterning of surfaces was achieved by illumination with an interference pattern obtained by the transmission of 248 nm excimer laser light through a phase mask. The N-hydroxysuccinimide ester surface acted as a template for the subsequent covalent attachment of aminohexyl-modified DNA oligonucleotides. Oligonucleotide patterns, with feature sizes of 500 nm, were reliably produced over large areas. The patterned surfaces were characterized with atomic force microscopy, scanning electron microscopy, epifluorescence microscopy and ellipsometry. Complementary oligonucleotides were hybridized to the surface-attached oligonucleotides with a density of 7 × 10¹² DNA oligonucleotides per square centimetre. The method will offer much potential for the creation of nano- and micro-scale DNA biosensor devices in silicon.     

Immobilization of native membrane-bound rhodopsin on biosensor surfaces

In this paper, we evaluated the grafting of G-protein-coupled receptors (GPCRs) onto functionalized surfaces, which is a primary requirement to elaborate receptor-based biosensors, or to develop novel GPCR assays. Bovine rhodopsin, a prototypical GPCR, was used in the form of receptor-enriched membrane fraction. Quantitative immobilization of the membrane-bound rhodopsin either non-specifically on a carboxylated dextran surface grafted with long alkyl groups, or specifically on a surface coated with anti-rhodopsin antibody was demonstrated by surface plasmon resonance. In addition, a new substrate based on mixed self-assembled multilayer that anchors specific anti-receptor antibodies was developed. Electrochemical impedance spectroscopy performed upon deposition of membrane-bound rhodopsin of increasing concentration exhibited a significant change, until a saturation level was reached, indicating optimum receptor immobilization on the substrate. The structures obtained with this new immobilization procedure of the rhodopsin in its native membrane environment are stable, with a controlled density of specific anchoring sites. Therefore, such receptor immobilization method is attractive for a range of applications, especially in the field of GPCR biosensors.     

Supported membranes on soft polymer cushions: fabrication, characterization and applications

Soft biofunctional and biocompatible interfaces on solids designed by the deposition of ultrathin soft polymer films or supported membranes have numerous scientific and practical applications. These include the immobilization of glycolipids, membrane receptors and proteins to generate models of cell and tissue surfaces. Powerful surface-sensitive techniques can be applied to study protein-protein recognition processes at membranes and the control of cell adhesion by the interplay of specific 'lock-and-key' forces and universal interfacial forces. Potential practical applications include the design of smart biosensors based on electro-optical devices and the fabrication of biofunctional surfaces for the stimulation of cell proliferation and tissue growth, or for the suppression of apoptosis.     

A Simple Method to Functionalize PCL Surface by Grafting Bioactive Polymers Using UV Irradiation

Background

Polycaprolactone (PCL) is a biodegradable polymer which is used in tissue engineering applications thanks to its many favorable characteristics. However, PCL surfaces are known as hydrophobic leading to a lack of favorable cell response. To overcome this problem, PCL surfaces will undergo a surface functionalization by grafting bioactive polymers bearing ionic groups.

Whole-cell biochips for bio-sensing: integration of live cells and inanimate surfaces

Recent advances in the convergence of the biological, chemical, physical, and engineering sciences have opened new avenues of research into the interfacing of diverse biological moieties with inanimate platforms. A main aspect of this field, the integration of live cells with micro-machined platforms for high throughput and bio-sensing applications, is the subject of the present review. These unique hybrid systems are configured in a manner that ensures positioning of the cells in designated patterns, and enables cellular viability maintenance, and monitoring of cellular functionality. Here we review both animate and inanimate surface properties and how they affect cellular attachment, describe relevant modifications of both types of surfaces, list technologies for platform engineering and for cell deposition in the desired configurations, and discuss the influence of various deposition and immobilization methods on the viability and performance of the immobilized cells.     

Accelerated formation of multicellular 3-D structures by cell-to-cell cross-linking

The three-dimensional (3-D) arrangement of cells within tissues is integral to their development and function. Advances in stem cell science and regenerative medicine have stimulated interest in the replication of this architecture in vitro. We have developed a versatile method for controlling short-term cell-cell and cell-matrix interactions via a facile cell surface engineering process that enables the rapid formation of specific 3-D interactions for a range of cell types. We demonstrate that chemical modification of cell surfaces and matrix proteins can artificially accelerate the cell adhesion process and confirm the ability to control the formation of multicellular aggregates with defined architectures and heterotypic cell types. Direct comparison with a natural aggregation process seen during differentiation of embryonic stem (ES) cells revealed increased expression of developmental regulatory proteins and a concomitant enhancement of ES cell differentiation. Furthermore, this new methodology has numerous applications in generating layered structures. For example, we demonstrate improved transfer of therapeutic human keratinocytes onto a dermal layer in a skin repair model.     

Conducting polymer nanowires-based label-free biosensors

Label-free sensing technologies have recently attracted a great deal of interest for sensitive, rapid and facile analysis for applications in health care, environmental monitoring, food safety and homeland security. One-dimensional (1-D) nanostructures such as nanowires, configured as field-effect transistors (FETs)/chemiresistors that change conductance upon binding of charged macromolecules to receptors linked to the device surfaces are extremely attractive for label-free biosensors. Herein, we review recent advances in label-free biosensors based on conducting polymer nanowires based FET/chemiresistor. Specifically, we address the fabrication, functionalization, assembly/alignment and sensing applications of FET/chemiresistor based on these nanomaterials. The advantages and disadvantages of various fabrication, functionalization, and assembling procedures of these nanosensors are reviewed and discussed.     

Acousto-optic laser-scanning cytometer

An instrument has been developed that uses a computer-controlled rapidly scanning laser beam to make cytometric measurements on cells or particles and which can measure low levels of fluorescence when using low-power lasers (Gershman, Hoffman, and O'Connell, "Methods and Apparatus for Analysis of Particles and Cells.") The method used is based upon acousto-optic principles of light diffraction. A vertically polarized 5-mW He-Ne laser is directed into an acousto-optic Bragg cell in which a portion of the incident light undergoes a small angular variation or deflection. Suitable optics focus the beam to a 25 microns diameter spot, at the 1/e2 point, in a sample cuvette while translating the angular variation into a linear scan. The cuvette enclosing the sample is slowly moved (approximately 1 micron/ms) via a stepper drive into the scanning beam while the forward angle light scatter sensor is monitored for the presence of valid signal events. When an event occurs, appropriate software optimizes the position of the focused laser beam onto the cell. Subsequently, scanning is stopped to allow for cell interrogation times that last for milliseconds or longer.     

Effects of surface functionalization on the surface phage coverage and the subsequent performance of phage-immobilized magnetoelastic biosensors

One of the important applications for which phage-immobilized magnetoelastic (ME) biosensors are being developed is the wireless, on-site detection of pathogenic bacteria for food safety and bio-security. Until now, such biosensors have been constructed by immobilizing a landscape phage probe on gold-coated ME resonators via physical adsorption. Although the physical adsorption method is simple, the immobilization stability and surface coverage of phage probes on differently functionalized sensor surfaces need to be evaluated as a potential way to enhance the detection capabilities of the biosensors. As a model study, a filamentous fd-tet phage that specifically binds streptavidin was adsorbed on either bare or surface-functionalized gold-coated ME resonators. The surface functionalization was performed through the formation of three self-assembled monolayers with a different terminator, based on the sulfur-gold chemistry: AC (activated carboxy-terminated), ALD (aldehyde-terminated), and MT (methyl-terminated). The results, obtained by atomic force microscopy, showed that surface functionalization has a large effect on the surface phage coverage (46.8%, 49.4%, 4.2%, and 5.2% for bare, AC-, ALD-, and MT-functionalized resonators, respectively). In addition, a direct correlation of the observed surface phage coverage with the quantity of subsequently captured streptavidin-coated microbeads was found by scanning electron microscopy and by resonance frequency measurements of the biosensors. The differences in surface phage coverage on the differently functionalized surfaces may then be used to pattern the phage probe layer onto desired parts of the sensor surface to enhance the detection capabilities of ME biosensors.     

Synthesis and characterization of bioconjugates of S-layer proteins

The self-assembling proteins that form crystalline surface layers (S-layers) on many microbial species have found numerous applications due to their nanostructured nature. To devise a new method to construct surface displays that exploit S-layer self-assembly activity and nanostructural properties, we have constructed polymer bioconjugates of S-layer proteins. The conjugates formed are similar in function to the monomer alkanethiols that form self-assembled monolayers (SAMs) on gold surfaces. However, the self-assembly is driven by the protein "headgroup" that positions polymer-tethered endgroups on a surface. This paper examines the integration of protein purification, conjugation, and surface assembly that has led to the development of this new method for the formation of nanostructured surfaces. Purified S-layer proteins from Lactobacillus brevis were conjugated with small molecule probes and polymers using amine-based reactions. To keep multiple labeling of protein amine groups to acceptable levels, the conjugations were performed at pH 6.5, allowing for limited yields (24-39%) as determined by mass spectrometry and SDS-polyacrylamide gel electrophoresis. As the presence of high levels of unlabeled S-layer proteins is undesired, we have developed a protocol for further purification that employs monomeric avidin affinity chromatography. The surface self-assembly of the polymer bioconjugates onto amine-terminated microspheres was studied using epi-fluorescence, confocal, and scanning electron microscopy. The surfaces obtained exhibited homogeneous distributions of tethered molecules. Also, in cases where the modular assembly of two distinct types of tethered endgroups was accomplished, there was no evidence for phase separation in the surfaces. The modular assembly method will provide a potential route to controlling surface display density as the starting assembly conditions guide displayed endgroup concentrations in mixed molecular monolayers.     

The mechanism of two-photon photochemical laser-induced deposition of silicon thin films from silane

We have investigated the mechanism of silicon thin film deposition by ArF excimer laser irradiation of silane gas diluted with argon. The Si films were deposited by a focused laser beam irradiating in parallel to silicon and silicon dioxide substrates at a gas flow rate of 20 SCCM, total pressure of 60 Torr and repetition rate of 15 Hz. At laser energy fluences higher than 160 mJ/cm² the deposition rate was almost independent of the incident laser energy, while at a lower energy the deposition rate depended strongly on the laser energy. A 3/2 power law was found for absorption measurements carried out at the same pressure under flow conditions and for several repetition rates at average laser power above 300 mW, regardless of the laser repetition rate. This kind of behavior is typical of a multiphoton absorption process involving saturation effects caused by focusing of the laser beam. Below 300 mW the power dependence indicated a two-photon absorption process. From the observed photochemical yield we found the value 5.7×10^-44 cm⁴ s molec^-1 for the two-photon absorption cross section.A Gaussian-shaped transverse thickness distribution of the deposited layer was obtained with a maximum value corresponding to the center of the laser beam spatial profile. This distribution depended on the deposition parameters, and was attributed to the diffusion process of silane decomposition products in the gas phase in the substrate. Analysis of the adsorption features of the process showed that the major product adsorbed on the substrate surface is silicon.An Arrhenius plot of the deposition rate versus the substrate temperature exhibits two regimes, each associated with a different activation energy. Between 340°C and 460°C the activation energy is 0.25–0.3 e. V, while between 500°C and 560°C it is 1.1 e. V. The activation energy in the higher temperature regime is similar to that found for thermal nonlaser assisted chemical vapor deposition. However, in the lower temperature regime the deposition process is mainly laser induced, and the value of the activation energy is due to the process of adsorption of the gas species on the substrate.     

Amphotericin B channels in phospholipid membrane-coated nanoporous silicon surfaces: implications for photovoltaic driving of ions across membranes

The antimycotic agent amphotericin B (AmB) functions by forming complexes with sterols to form ion channels that cause membrane leakage. When AmB and cholesterol mixed at 2:1 ratio were incorporated into phospholipid bilayer membranes formed on the tip of patch pipettes, ion channel current fluctuations with characteristic open and closed states were observed. These channels were also functional in phospholipid membranes formed on nanoporous silicon surfaces. Electrophysiological studies of AmB-cholesterol mixtures that were incorporated into phospholipid membranes formed on the surface of nanoporous (6.5 nm pore diameter) silicon plates revealed large conductance ion channels ( approximately 300 pS) with distinct open and closed states. Currents through the AmB-cholesterol channels on nanoporous silicon surfaces can be driven by voltage applied via conventional electrical circuits or by photovoltaic electrical potential entirely generated when the nanoporous silicon surface is illuminated with a narrow laser beam. Electrical recordings made during laser illumination of AmB-cholesterol containing membrane-coated nanoporous silicon surfaces revealed very large conductance ion channels with distinct open and closed states. Our findings indicate that nanoporous silicon surfaces can serve as mediums for ion-channel-based biosensors. The photovoltaic properties of nanoporous silicon surfaces show great promise for making such biosensors addressable via optical technologies.     

Protein surface representation and analysis by dimension reduction

Background

Protein structures are better conserved than protein sequences, and consequently more functional information is available in structures than in sequences. However, proteins generally interact with other proteins and molecules via their surface regions and a backbone-only analysis of protein structures may miss many of the functional and evolutionary features. Surface information can help better elucidate proteins' functions and their interactions with other proteins. Computational analysis and comparison of protein surfaces is an important challenge to overcome to enable efficient and accurate functional characterization of proteins.

Methods

In this study we present a new method for representation and comparison of protein surface features. Our method is based on mapping the 3-D protein surfaces onto 2-D maps using various dimension reduction methods. We have proposed area and neighbor based metrics in order to evaluate the accuracy of this surface representation. In order to capture functionally relevant information, we encode geometric and biochemical features of the protein, such as hydrophobicity, electrostatic potential, and curvature, into separate color channels in the 2-D map. The resulting images can then be compared using efficient 2-D image registration methods to identify surface regions and features shared by proteins.

Results

We demonstrate the utility of our method and characterize its performance using both synthetic and real data. Among the dimension reduction methods investigated, SNE, LandmarkIsomap, Isomap, and Sammon's mapping provide the best performance in preserving the area and neighborhood properties of the original 3-D surface. The enriched 2-D representation is shown to be useful in characterizing the functional site of chymotrypsin and able to detect structural similarities in heat shock proteins. A texture mapping using the 2-D representation is also proposed as an interesting application to structure visualization.

     

Antimicrobial activity of argon fluoride (ArF) excimer laser on gram-negative bacteria

The objective of this study was to evaluate the antibacterial activity of argon fluoride (ArF) excimer laser radiation on clinically important strains of gram-negative bacteria. The antibacterial activity of ArF excimer laser radiation was evaluated on two Acinetobacter baumannii, one Enterobacter cloacae, three Escherichia coli, two Helicobacter pylori, one Klebsiella pneumoniae and two Pseudomonas aeruginosa strains. The strains were isolated from clinical specimens and typed by the usual biochemical procedures. Square agar plates of 12 x 12 cm were divided into rectangular (2 x 3 cm) regions and spread with 0.5x 10(4) colony forming units (CFU)/ml of bacterial suspension. The excess liquid was removed and the plates were allowed to dry for 30 min. A total of 96 rectangular (2x3 cm) regions were used for each strain, in order to test an equal number of laser parameters. Each rectangular region was irradiated with different laser parameters, using a 193 nm ArF excimer laser, linked with a simple Galilean afocal system and a rectangular diaphragm of the same dimensions as the original laser beam cross-section, at a distance of 10 cm from the irradiated surface. This system was used in order to keep the laser pulse energy under 80 mJ and to cut-out the non-transverse electromagnetic mode branches of the laser beam. We then studied the bacterial survival ratio versus the number of laser pulses, the repetition frequency and the total laser beam fluence. Our results showed that the total laser beam fluence was the most important parameter to consider in evaluating the bactericidal effect of ArF excimer laser radiation. A critical value of the total fluence was determined for each strain, such that, for laser beam fluences greater than this critical value, no colonies appeared to survive while, for laser fluences less than this critical value, the survival ratio did not exceed 2 x 10(7) CFU (2 x 10(-5)%). These critical values were found to vary between 8 J/cm2 and 16 J/cm2 for the bacterial species studied. Under these conditions, ArF laser irradiation is promising for the sterilisation of hard surfaces and for in situ application.     

Micrometer-scale domains in fibroblast plasma membranes

We have used the technique of fluorescence photobleaching recovery to measure the lateral diffusion coefficients and the mobile fractions of a fluorescent lipid probe, 1-acyl-2-(12-[(7-nitro-2-1, 3-benzoxadiazol-4-yl)aminododecanoyl]) phosphatidylcholine (NBD-PC), and of labeled membrane proteins of human fibroblasts. Values for mobile fractions decrease monotonically with increasing size of the laser spot used for the measurements, over a range of 0.35-5.0 microns. Values for NBD-PC diffusion coefficients increase in part of this range to reach a plateau at larger laser spots. This variation is not an artifact of the measuring system, since the effects are not seen if diffusion of the probe is measured in liposomes. We also find that the distribution of diffusion coefficients measured with small laser spots is heterogeneous indicating that these small spots can sample different regions of the membrane. These regions appear to differ in protein concentration. Our data strongly indicate that fibroblast surface membranes consist of protein-rich domains approximately 1 micron in diameter, embedded in a relatively protein-poor lipid continuum. These features appear in photographs of labeled cell surfaces illuminated by the expanded laser beam.     

Spatially controlled electro-stimulated DNA adsorption and desorption for biochip applications

The manipulation of biomolecules at solid/liquid interfaces is important for the enhanced performance of a number of biomedical devices, including biochips. This study focuses on the spatial control of surface interactions of DNA as well as the electro-stimulated adsorption and desorption of DNA by appropriate surface modification of highly doped p-type silicon. Surface modification by plasma polymerisation of allylamine resulted in a surface that supported DNA adsorption and sustained cell attachment. Subsequent high-density grafting of poly(ethylene oxide) formed a low fouling layer resistant to biomolecule adsorption and cell attachment. Spatially controlled excimer laser ablation of the surface produced patterns of re-exposed plasma polymer with high-resolution. On patterned surfaces, preferential electro-stimulated adsorption of DNA to the allylamine plasma polymer surface and subsequent desorption by the application of a negative bias was observed. Furthermore, the concept presented here was investigated for use in transfection chips. Cell culture experiments with human embryonic kidney cells, using the expression of green fluorescent protein as a reporter, demonstrated efficient and controlled transfection of cells. Electro-stimulated desorption of DNA was shown to yield significantly enhanced solid phase transfection efficiencies to values of up to 30%. The ability to spatially control DNA adsorption combined with the ability to control the binding and release of DNA by application of a controlled voltage enables an advanced level of control over DNA bioactivity on solid substrates and lends itself to biochip applications.     

Poly(vinylpyrrolidone) for bioconjugation and surface ligand immobilization

Poly(vinylpyrrolidone) (PVP), a nonionic and nontoxic polymer with antifouling properties, has been synthesized via RAFT polymerization to obtain thiol-terminated PVP. We demonstrate that when the polymer is adsorbed onto the surface of colloidal silica particles, the terminal thiol groups of PVP remain accessible for chemical modification and lend themselves to the immobilization of ligands. We show that ligand attachment onto the surface via conjugation to PVP is reversible, as the polymer can be desorbed from the surface for conjugate and surface recovery. We present the conjugation of a model peptide and an oligonucleotide to PVP via the polymer terminal thiol and demonstrate that conjugates remain functional in molecular recognition assay. The developed technique offers a novel method to functionalize low-fouling surfaces for a variety of biomedical applications and presents opportunities to use PVP as a macromolecular drug carrier.     

Denaturing and refolding of protein molecules on surfaces

Keeping protein molecules in the active state on a solid surface is essential to protein microarrays and other protein-based biosensors. Here, we show that the 2-D chemical environment controls the refolding of the denatured green fluorescent proteins tethered to solid surfaces. Refolding occurs readily on the repulsive PEG functionalized surface but is inhibited on the attractive--NH(2) functionalized surface. This result shows the critical importance of the 2-D chemical environment in the maintenance and revival of protein activity on surfaces and opens the door to designing 2-D molecular chaperones for protein folding.