Functionalization of self-assembled monolayers on glass and oxidized silicon wafers by surface reactions

Guided deposition of individual DNA nanostructures on silicon substrates

We demonstrate immobilization of DNA nanostructures (37 nm x 8 nm) on silicon by a combination of "top-down" fabrication and "bottom-up" self-assembly. Anchor lines and pads were defined using electron beam lithography and a cationic molecular monolayer. Individual DNA nanostructures bind in 85% yield onto the anchor pads and can be washed and imaged in air. The strength of the binding interaction between a DNA nanostructure and its anchor pad is at least -43 kJ/mol.

Discriminate crystallinities of tin doped indium oxide films on self-assembled monolayers modified glass substrates

Tin doped indium oxide (ITO) films have generated tremendous research interest and received widespread applications in optoelectronic devices due to a good combination of desired optical and electrical properties. Their electrical properties vary depending on the crystallinity of the film. A good quality ITO film should have low resistivity, which can be achieved with highly crystalline films deposited at very high temperature. Thus, film quality is sensitive to the deposition conditions. Generally, low-temperature deposition of ITO results in poor quality films due to amorphous growth. In this study, we have demonstrated that crystallinity of the ITO films can be improved even at room temperature (RT) using self-assembled monolayers (SAMs) modified glass substrates. The present study demonstrates that SAM with -SH terminal group is necessary for the high-quality ITO growth, while SAMs with other terminal groups (-NH(2) and -CH(3)) generate ITO films with moderate crystallinity. Various properties of such films were investigated using X-ray diffraction, X-ray photoelectron depth profile, four-point probe, and Hall measurements. It is confirmed from such measurements that ITO film deposited on -SH terminated SAM substrate has excellent crystallinity, conductivity, and optical transmission.

Investigations of chemical modifications of amino-terminated organic films on silicon substrates and controlled protein immobilization

Fourier transform infrared spectroscopy by grazing-angle attenuated total reflection (FTIR-GATR), ellipsometry, atomic force microscopy (AFM), UV-visible spectroscopy, and fluorescence microscopy were employed to investigate chemical modifications of amino-terminated organic thin films on silicon substrates, protein immobilization, and the biological activity and hydrolytic stability of immobilized proteins. Amino-terminated organic films were prepared on silicon wafers by self-assembling 3-aminopropyltriethoxysilane (APTES) in anhydrous toluene. Surface amino groups were derivatized into three different linkers: N-hydroxysuccinimide (NHS) ester, hydrazide, and maleimide ester groups. UV-visible absorption measurements and fluorescence microscopy revealed that more than 40% of surface amino groups were chemically modified. Protein immobilization was carried out on modified APTES films containing these linkers via coupling with primary amines (-NH(2)) in intact monoclonal rabbit immunoglobulin G (IgG), the aldehyde (-CHO) of an oxidized carbohydrate residue in IgG, or the sulfhydryl (-SH) of fragmented half-IgG, respectively. FTIR spectra contain vibrational signatures of these functional groups present in modified APTES films and immobilized IgGs. Changes in the APTES film thickness after chemical modifications and protein immobilization were also observed by ellipsometric measurements. The biological activity and long-term hydrolytic stability of immobilized IgGs on modified APTES films were estimated by fluorescence measurements of an adsorbed antigen, fluorescein isothiocyanate (FITC)-labeled goat anti-rabbit IgG (FITC-Ab). Our results indicate that the FITC-Ab binding capacity of half-IgG immobilized via maleimide groups is greater than that of the oxidized IgG and the intact IgG immobilized via hydrazide and NHS ester groups, respectively. In addition, IgGs immobilized using all coupling chemistries were hydrolytically stable in phosphate-buffered saline (PBS).

Reactive surface coatings based on polysilsesquioxanes: controlled functionalization for specific protein immobilization

The key designing in reliable biosensors is the preparation of thin films in which biomolecular functions may be immobilized and addressed in a controlled and reproducible manner. This requires the controlled preparation of specific binding sites on planar surfaces. Poly(methylsilsesquioxane)-poly(pentafluorophenyl acrylates) (PMSSQ-PFPA) are promising materials to produce stable and adherent thin reactive coatings on various substrates. Those reactive surface coatings could be applied onto various materials, for example, gold, polycarbonate (PC), poly(tetrafluoroethylene) (PTFE), and glass. By dipping those substrates in a solution of a desired amine, specific binding sites for protein adsorption could be immobilized on the surface. The versatile strategy allowed the attachment of various linkers, for example, biotin, l-thyroxine, and folic acid. The adsorption processes of streptavidin, pre-albumin, and folate-binding protein were monitored using surface plasmon resonance (SPR), Fourier transform infrared (FTIR) spectroscopy, fluorescence spectroscopy, and atomic force microscopy (AFM). The presented protein immobilization strategy, consisting of four steps (a) spin-coating of PMSSQ-PFPA hybrid polymer from tetrahydrofuran (THF) solution, (b) annealing at 130 degrees C for 2 h to induce thermal cross-linking of the PMSSQ part, (c) surface analogues reaction with different amino-functionalized specific binding sites for proteins, and (d) controlled assembly of proteins on the surface, may find various applications in future biosensor design.

Enhancement of second-harmonic generation from self-assembled monolayers on gold by excitation with a radially polarized beam

We have studied the enhancement of second-harmonic generation (SHG) from self-assembled monolayers on Au surfaces excited by radially polarized beams. The electric field at the metal surface was enhanced by constructive interference between the incident and the reflected beams due to a longitudinal field, which is the field parallel to the optical axis, generated around the focus by the radially polarized beam. Since even-order nonlinear phenomena are surface sensitive, the combination of SHG and a radially polarized beam has the potential to be a powerful new imaging tool for characterization of metal surfaces. The SHG signal excited by the radially polarized beam was about 3 times higher than that excited by a linearly polarized beam; in addition, the SHG from a 7-(dimethylamino)-4-methylcoumarin-3-isothiocyanate monolayer was about 1.3 times higher than that from a bare Au substrate.

Aminosilane multilayer formed on a single-crystalline diamond surface with controlled nanoscopic hardness and bioactivity by a wet process

Diamond could be an excellent support for nanodevices utilizing biomolecules if it is covered with a polymer layer immobilizing a variety of biomolecules. We report a wet method to form a 3-aminopropyltriethoxysilane (APTES) multilayer with a controlled hardness, roughness, and capacity for immobilizing protein. The method is feasible in typical biochemical laboratories where biomolecules are prepared. Atomic force microscopy (AFM) revealed that the surface geometries and nanoscopic hardness of the multilayers on an oxygen-terminated single-crystalline diamond surface depended on the dielectric constant of the solvent; the smaller the constant, the harder the layer. The hard multilayers had holes and APTES aggregates on the surfaces, while less hard ones had homogeneous surfaces with rare holes and little aggregates. The secondary deposition of APTES in a solvent with a large dielectric constant on a hard multilayer removed the holes, and further treatment of the multilayer in acidic ethanol solution diminished the aggregates. Such a surface can immobilize streptavidin with enough specificity against nonspecific adsorption using a combination of polyethylene glycol reagents. The results of a scratching test and nanoindentation test with AFM provided consistent results, suggesting some universality of the scratching test independent of the tip structure of the cantilever. The mechanism of formation of multilayers on the diamond surface and their binding to it is discussed.

Anisotropic demineralization and oriented assembly of hydroxyapatite crystals in enamel: smart structures of biominerals

It is interesting to note that the demineralization of natural enamel does not happen as readily as that of the synthesized hydroxyapatite (HAP), although they share a similar chemical composition. We suggest that the hierarchical structure of enamel is an important factor in the preservation of the natural material against dissolution. The anisotropic demineralization of HAP is revealed experimentally, and this phenomenon is understood by the different interfacial structures of HAP-water at the atomic level. It is found that HAP {001} facets can be more resistant against dissolution than {100} under acidic conditions. Although {100} is the largest surface of the typical HAP crystal, it is {001}, the smallest habit face, that is chosen by the living organisms to build the outer surface of enamel by an oriented assembly of the rodlike crystals. We reveal that such a biological construction can confer on enamel protections against erosion, since {001} is relatively dissolution-insensitive. Thus, the spontaneous dissolution of enamel surface can be retarded in biological milieu by such a smart construction. The current study demonstrates the importance of hierarchical structures in the functional biomaterials.

Functionalized silicone nanofilaments: a novel material for selective protein enrichment

We present a simple and versatile technique of tailoring functionalized surface structures for protein enrichment and purification applications based on a superhydrophobic silicone nanofilament coating. Using amino and carboxyl group containing silanes, silicone nanofilament templates were chemically modified to mimic anionic and cationic exchange resins. Investigations on the selectivity of the functionalized surfaces toward adsorption of charged model proteins were carried out by means of fluorescence techniques. Due to a high contact area resulting from the nanoroughness of the coating, excellent protein retention characteristics under various conditions were found. The surfaces were shown to be highly stable and reusable over several retention-elution cycles. Especially the full optical transparency and the possibility to use glass substrates as support material open new opportunities for the development of optical biosensors, open geometry microfluidics, or lab-on-a-chip devices.

Probing the effects of cholesterol on pyrene-functionalized interfacial adlayers

We have synthesized a novel set of pyrene-functionalized, covalently bound surface adlayers with and without cholesterol derivatives coadded to the adlayer. We have deposited these adlayers on quartz, oxidized silicon wafers, and indium-doped tin oxide coated substrates. The addition of tethered cholesterol to the adlayer creates a hydrophobic, likely disordered, microenvironment in which the surface-bound pyrene resides. X-ray photoelectron spectroscopy measurements demonstrate the covalent attachment of both cholesterol and pyrene in our adlayers. The presence of the cholesterol moieties gives rise to a reduction in film thickness, as measured ellipsometrically, and contact angle data indicate significant surface heterogeneity. Steady-state fluorescence data show that the presence of cholesterol moieties reduces the extent of pyrene excimer formation and provides a less polar environment for the chromophore. Fluorescence lifetime measurements on surface-bound pyrene were biexponential, consistent with multiple local environments, regardless of whether tethered cholesterol was present or not. Cyclic voltammetry reveals competition between the pyrene and cholesterol moieties for binding to available surface sites on the epoxide-terminated surface-binding layer we use.

Base sequence- and T m-dependent DNA oligomer separation by open tubular capillary columns carrying complementary DNA oligomers as probes

DNA chips prepared on a flat glass surface have unavoidable drawbacks when used for quantitative analysis. In an attempt to overcome this problem, we constructed an HPLC-type system suitable for quantitative analysis that enables base sequence- and T (m)-dependent DNA oligomer separation in a flow system. A small open tubular capillary column (300-mm x 100-microm I.D.) was used. The DNA oligomers used as probes had an amino group at the 5'-end and were immobilized on the inner silica surface of the capillary column which had been sequentially treated with 3-aminopropyltriethoxysilane, butyltrimethoxysilane, and disuccinimidylglutarate. Using the combination of probe-immobilized column placed in a column oven equipped with temperature gradient function, a nano-flow-controllable pump, a small sample-loading injector, and a capillary-fitted UV detector, we succeeded in separating complementary and non-complementary DNA oligomers in specific and quantitative modes. We also designed a temperature gradient strategy for efficient separation of target DNA oligomers in DNA mixture samples. Using a column carrying two different probes with similar T (m) values, their complementary target DNA oligomers were also separated and detected. The developed DNA open tubular capillary column system investigated in the present study could be further improved as an alternative tool to DNA chips to be used for the quantitative analysis of DNA or mRNA samples.

Specificity and sensitivity of fluorescence labeling of surface species

FLOSS (fluorescence labeling of surface species) enables one to identify and quantify very low concentrations of surface functional groups. Unlike most surface analytical techniques, FLOSS can provide absolute, as well as relative, surface coverage determination. However, as with any other surface derivatization technique, FLOSS provides a lower limit to surface coverage. The specificity of FLOSS for a particular functional group is the key to this application. In one FLOSS protocol, amine-modified dyes are used to label surface aldehyde groups. However, amine-modified dyes, in principle, can bind to both aldehyde and carboxyl groups, limiting specificity. In this paper, we report that the FLOSS protocol devised results in less than 0.5 % of the carboxyl-modified dyes binding to the surface amine groups. Therefore, the presence of carboxyl groups on the surface should have a limited effect on the detection of aldehyde groups by amine-modified dye. Quenching of fluorescence can potentially affect quantitative measurements. To address this issue, the densities of surface functional groups of CHO-, NH2-, and epoxy-coated glass surfaces were quantified using FLOSS and compared to surface densities estimated by other methods. The FLOSS technique was extended to glass surfaces by using visible absorbing and emitting dyes. The lower detection limit is on the order of 10(9) groups/cm2.

Optimization of silica silanization by 3-aminopropyltriethoxysilane

Thin films of 3-aminopropyltriethoxysilane (APTES) are commonly used to promote adhesion between silica substrates and organic or metallic materials with applications ranging from advanced composites to biomolecular lab-on-a-chip. Unfortunately, there is confusion as to which reaction conditions will result in consistently aminated surfaces. A wide range of conflicting experimental methods are used with researchers often assuming the creation of smooth self-assembled monolayers. A range of film morphologies based on the film deposition conditions are presented here to establish an optimized method of APTES film formation. The effect of reaction temperature, solution concentration, and reaction time on the structure and morphology was studied for the system of APTES on silica. Three basic morphologies were observed: smooth thin film, smooth thick film, and roughened thick film.

Deposition of DNA rafts on cationic SAMs on silicon [100]

We demonstrate a guided self-assembly approach to the fabrication of DNA nanostructures on silicon substrates. DNA oligonucleotides self-assemble into "rafts" 8 x 37 x 2 nm in size. The rafts bind to cationic SAMs on silicon wafers. Electron-beam lithography of a thin poly(methyl methacrylate) (PMMA) resist layer was used to define trenches, and (3-aminopropyl)triethoxysilane (APTES), a cationic SAM precursor, was deposited from aqueous solution onto the exposed silicon dioxide at the trench bottoms. The remaining PMMA can be cleanly stripped off with dichloromethane, leaving APTES layers 0.7-1.2 nm in thickness and 110 nm in width. DNA rafts bind selectively to the resulting APTES stripes. The coverage of DNA rafts on adjacent areas of silicon dioxide is 20 times lower than on the APTES stripes. The topographic features of the rafts, measured by AFM, are identical to those of rafts deposited on wide-area SAMs. Binding to the APTES stripes appears to be very strong as indicated by "jamming" of the rafts at a saturation coverage of 42% and the stability to repeated AFM scanning in air.

Assembly of coordination nanostructures via ligand derivatization of oxide surfaces

A scheme is presented for the construction of coordination nanostructures on oxide surfaces (glass, Si/SiO2, quartz), based on application of epoxy-terminated monolayers as anchors for covalent grafting of ligands. Two ligands bearing amine groups were reacted with epoxysilane monolayers on oxide surfaces, providing ligand-terminated substrates. The ligands employed were (i) a pyridine moiety, used for subsequent binding of cobalt tetraphenylporphine (CoTPP), and (ii) deferoxamine (DFX), which contains hydroxamic acid moieties, used for subsequent construction of various Zr4+-based coordination layers. The results suggest that a dense ligand layer was obtained in both cases, allowing the formation of coordination overlayers on the oxide surfaces. The growth of coordinated layers was similar to analogous overlayers assembled on Au substrates, indicating that high ligand coverage is achieved by the epoxy-amine surface reaction. Epoxy-based functionalization of oxide substrates is a mild and efficient method for preparing high-quality coordination overlayers. Moreover, the method makes use of commercially available silane and amine reactants, providing the basis for wide application.

Engineering Silicon Oxide Surfaces Using Self-Assembled Monolayers

Although a molecular monolayer is only a few nanometers thick it can completely change the properties of a surface. Molecular monolayers can be readily prepared using the Langmuir-Blodgett methodology or by chemisorption on metal and oxide surfaces. This Review focuses on the use of chemisorbed self-assembled monolayers (SAMs) as a platform for the functionalization of silicon oxide surfaces. The controlled organization of molecules and molecular assemblies on silicon oxide will have a prominent place in "bottom-up" nanofabrication, which could revolutionize fields such as nanoelectronics and biotechnology in the near future. In recent years, self-assembled monolayers on silicon oxide have reached a high level of sophistication and have been combined with various lithographic patterning methods to develop new nanofabrication protocols and biological arrays. Nanoscale control over surface properties is of paramount importance to advance from 2D patterning to 3D fabrication.

Liquid mechanical behavior of mixed monolayers of amino and alkyl silanes by atomic force microscopy

The adsorption of mixed terminally aminated organosilyl compounds with long-chain n-alkyltrichlorosilanes on silica substrates has been studied by FTIR and AFM to deposit and study DNA. By optimization of deposition conditions, the mixed monolayers were found to be well organized and homogeneous. The amino group was protected to obtain a reproducible grafting and then deprotected after the film formation. In addition, atomic force microscopy (AFM) studies in both dynamical modes, amplitude modulation and frequency modulation, reveal that the layer behaves as a fluid as measured by the tip-cantilever and has a smaller characteristic time than the tip-cantilever. For three amplitudes, the experimental frequency shifts have been modeled for a fluidlike layer crossed by the tip. Finally, we show that this new fluidlike monolayer is suitable for DNA deposition and AFM studies.

Mechanism of UV Photoreactivity of Alkylsiloxane Self-Assembled Monolayers

A molecular level understanding of the photoreactivity of self-assembled monolayers (SAMs) becomes increasingly important as the spatial resolution starts to be limited by the size of the resist and the spatial extent of the photochemical reactions in photoresist micropatterning. To this end, a number of surface characterization techniques were combined to understand the reactive agents, reactive sites, kinetics, and reaction pathways in the UV photoreactivity of octadecylsiloxane (ODS) SAMs. Quantitative analysis of our results provides evidence that ground state atomic oxygen is the primary reactive agent for the UV degradation of ODS SAMs. UV degradation, which follows zero-order kinetics, results in the scission of alkyl chains instead of the siloxane headgroups. Our results suggest that the top of the ODS SAMs is the preferential reactive site. Using a novel, highly surface sensitive technique, fluorescence labeling of surface species, we identified the presence of submonolayer quantities chemical functional groups formed by the UV degradation. These groups are intermediates in a proposed mechanism based on hydrogen abstraction.

Stability of lipid films formed on gamma-aminopropyl monolayers

The stability of supported lipid membranes (SLMs) deposited on planar substrates derivatized with (gamma-aminopropyl)silane (GAPS) was examined. Ellipsometry, fluorescence microscopy, and atomic force microscopy were used to characterize SLMs exposed to repeated drying and rehydration. Vesicle fusion on GAPS-coated substrates produced SLMs with a thickness significantly greater than that of a single lipid bilayer. Exposure to even one cycle of drying/rehydration significantly decreased the thickness of a SLM on GAPS, and repeated drying/rehydration resulted in near quantitative lipid desorption. Thus SLMs on GAPS do not appear to be significantly more stable than the single bilayer SLM that is formed on bare glass or SiO2 under equivalent conditions.

Interfacial pH at an Isolated Silica−Water Surface

Tethering a pH-sensitive dye to a silica surface enables the interfacial pH to be measured optically and is found to be 2 pH units lower than that of the bulk. The positive H+ ions are attracted by the surface potential and have an enhanced concentration consistent with the previously determined surface potential of order -120 mV, with respect to zero in the bulk. A stable near-surface charged layer once formed is not disrupted by the bulk pH.

Fluorescence Detection of Surface-Bound Intermediates Produced from UV Photoreactivity of Alkylsiloxane SAMs

Detection and quantification of submonolayer coverage surface species is not trivial. We have developed a novel method sensitive to surface-bound chemical functional groups as low as 10(11) molecules/cm(2) by specific covalent attachment of fluorescent chromophores. This enables the intermediates of the UV photochemistry of alkylsiloxane self-assembled monolayers to be identified.