Single-step DNA immobilization on antifouling self-assembled monolayers covalently bound to silicon (111)

Hydrosilylation of alkenes with epoxide-terminated tri(ethylene oxide) moieties on Si-H surfaces yields homogeneous monolayers for the efficient coupling of biomolecules. The wetting properties of the epoxide-functionalized surface allow for the spotting of solutions of biomolecules, making the surface amenable to microarraying. Immobilization of thiolated DNA was achieved in a single step to fabricate biorecognition interfaces showing the hybridization of complementary DNA at low concentrations and negligible binding of noncomplementary DNA.     

Biofunctionalization on alkylated silicon substrate surfaces via "click" chemistry

Biofunctionalization of silicon substrates is important to the development of silicon-based biosensors and devices. Compared to conventional organosiloxane films on silicon oxide intermediate layers, organic monolayers directly bound to the nonoxidized silicon substrates via Si-C bonds enhance the sensitivity of detection and the stability against hydrolytic cleavage. Such monolayers presenting a high density of terminal alkynyl groups for bioconjugation via copper-catalyzed azide-alkyne 1,3-dipolar cycloaddition (CuAAC, a "click" reaction) were reported. However, yields of the CuAAC reactions on these monolayer platforms were low. Also, the nonspecific adsorption of proteins on the resultant surfaces remained a major obstacle for many potential biological applications. Herein, we report a new type of "clickable" monolayers grown by selective, photoactivated surface hydrosilylation of α,ω-alkenynes, where the alkynyl terminal is protected with a trimethylgermanyl (TMG) group, on hydrogen-terminated silicon substrates. The TMG groups on the film are readily removed in aqueous solutions in the presence of Cu(I). Significantly, the degermanylation and the subsequent CuAAC reaction with various azides could be combined into a single step in good yields. Thus, oligo(ethylene glycol) (OEG) with an azido tag was attached to the TMG-alkyne surfaces, leading to OEG-terminated surfaces that reduced the nonspecific adsorption of protein (fibrinogen) by >98%. The CuAAC reaction could be performed in microarray format to generate arrays of mannose and biotin with varied densities on the protein-resistant OEG background. We also demonstrated that the monolayer platform could be functionalized with mannose for highly specific capturing of living targets (Escherichia coli expressing fimbriae) onto the silicon substrates.     

Staphylococcus aureus adhesion to self-assembled monolayers: effect of surface chemistry and fibrinogen presence

Staphylococcus aureus adhesion on self-assembled monolayers (SAMs) formed by the adsorption of alkanethiols on transparent gold films has been studied in real time under well-defined flow conditions using a radial flow chamber and an automated videomicroscopy system. SAMs terminated with methyl, hydroxyl, carboxylic acid and tri(ethylene oxide) groups were investigated. SAMs were characterized using contact angle measurements, ellipsometry and X-ray photoelectron spectroscopy. Adhesion experiments using the Newman strain of S. aureus were performed on bare monolayers and monolayers pre-incubated with fibrinogen. Adhesion was found to be lowest on the ethylene oxide-bearing surfaces, followed by the hydroxyl surfaces. Adhesion on the carboxylic- and methyl-terminated SAMs was much higher. Bacterial adhesion was higher on the hydrophobic surfaces. Pre-incubation of surfaces with fibrinogen minimized the effect of the surface properties of the substrate. Adhesion was increased on all surfaces when fibrinogen was present and no significant differences were observed between adhesion to the different SAMs. This study showed that surfaces rich in ethylene oxide groups can be effectively used to prevent bacterial adhesion. However, under physiological conditions, most of the substrate properties are masked by the presence of the adsorbed protein layer and the effect of substrate properties on bacteria adhesion under flow is minimal.     

Conductive AFM patterning on oligo(ethylene glycol)-terminated alkyl monolayers on silicon substrates: proposed mechanism and fabrication of avidin patterns

Micro- and nanopatterns of biomolecules on inert, ultrathin platforms on nonoxidized silicon are ideal interfaces between silicon-based microelectronics and biological systems. We report here the local oxidation nanolithography with conductive atomic force microscopy (cAFM) on highly protein-resistant, oligo(ethylene glycol) (OEG)-terminated alkyl monolayers on nonoxidized silicon substrates. We propose a mechanism for this process, suggesting that it is possible to oxidize only the top ethylene glycol units to generate carboxylic acid and aldehyde groups on the film surface. We show that avidin molecules can be attached selectively to the oxidized pattern and the density can be varied by altering the bias voltage during cAFM patterning. Biotinylated molecules and nanoparticles are selectively immobilized on the resultant avidin patterns. Since one of the most established methods for immobilization of biomolecules is based on avidin-biotin binding and a wide variety of biotinylated biomolecules are available, this approach represents a versatile means for prototyping any nanostructures presenting these biomolecules on silicon substrates.     

New deuterated oligo(ethylene glycol) building blocks and their use in the preparation of surface active lipids possessing labeled hydrophilic tethers

For the introduction of additional analysis protocols of tethered molecules, a method is presented to prepare functionalized, deuterated oligo(ethylene glycols) from ethylene glycol-d4. Partial oligomerization of ethylene glycol-d4 and conversion to ditosylates is accompanied by coupling reactions to prepare doubly benzyl protected oligo(ethylene glycols) with two to five repeating units. The tetramer bearing 16 deuteria was elaborated at both ends to eventually prepare 2,3-di-O-phytanyl-sn-glycerol-1-tetraethylene glycol-d,l-alpha-lipoic acid ester (DPTL), which bears a fully deuterated tetra(ethylene glycol) spacer group. Through linking of functionalized components, an analogue of DPTL possessing an octa(ethylene glycol) spacer group was prepared, both in deuterated and unlabeled form.     

Nanoscale water condensation on click-functionalized self-assembled monolayers

We have examined the nanoscale adsorption of molecular water under ambient conditions onto a series of well-characterized functionalized surfaces produced by Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC or "click") reactions on alkyne-terminated self-assembled monolayers on silicon. Water contact angle (CA) measurements reveal a range of macroscopic hydrophilicity that does not correlate with the tendency of these surfaces to adsorb water at the molecular level. X-ray reflectometry has been used to follow the kinetics of water adsorption on these "click"-functionalized surfaces, and also shows that dense continuous molecular water layers are formed over 30 h. For example, a highly hydrophilic surface, functionalized by an oligo(ethylene glycol) moiety (with a CA = 34°) showed 2.9 ? of adsorbed water after 30 h, while the almost hydrophobic underlying alkyne-terminated monolayer (CA = 84°) showed 5.6 ? of adsorbed water over the same period. While this study highlights the capacity of X-ray reflectometry to study the structure of adsorbed water on these surfaces, it should also serve as a warning for those intending to characterize self-assembled monolayers and functionalized surfaces to avoid contamination by even trace amounts of water vapor. Moreover, contact angle measurements alone cannot be relied upon to predict the likely degree of moisture uptake on such surfaces.     

One-step photochemical introduction of nanopatterned protein-binding functionalities to oligo(ethylene glycol)-terminated self-assembled monolayers

Exposure of oligo(ethylene glycol) (OEG)-terminated self-assembled monolayers (SAMs) to UV light leads to the formation of aldehyde groups, leading to a simple one-step method for the introduction of reactive functional groups to protein-resistant surfaces. X-ray photoelectron spectroscopy has been used to demonstrate binding of amines to the modified surfaces, while surface plasmon resonance has shown that proteins are covalently bound. Modified OEG monolayers bind streptavidin at least as well as N-hydroxysuccinimidyl ester functionalized monolayers. Micrometer and nanometer-scale patterns are conveniently fabricated by exposing the monolayers using, respectively, a mask and a scanning near-field optical microscope.     

Functional monolayers for improved resistance to protein adsorption: oligo(ethylene glycol)-modified silicon and diamond surfaces

The interaction of proteins with semiconductors such as silicon and diamond is of great interest for applications such as electronic biosensing. We have investigated the use of covalently bound oligo(ethylene glycol), EG, monolayers on diamond and silicon to minimize nonspecific protein adsorption. Protein adsorption was monitored by fluorescence scanning as a function of the length of the ethylene glycol chain (EG3 through EG6) and the terminal functional group (methyl- versus hydroxyl-terminated EG3 monolayer). More quantitative measurements were made by eluting adsorbed avidin from the surface and measuring the intensity of fluorescence in the solution. The attachment chemistry of the tri(ethylene glycol) molecules and monolayer orientation was studied by X-ray photoelectron spectroscopy. Improvement in the selectivity of surfaces modified with EG functionality was demonstrated in two model biosensing assays. We find that high-quality EG monolayers are formed on silicon and diamond and that these EG3 monolayers are as effective as EG3 self-assembled monolayers on gold at resisting nonspecific avidin adsorption. These results show promise for use of silicon and diamond materials in many potential applications such as biosensing and medical implants.     

Covalent attachment of organic monolayers to silicon carbide surfaces

This work presents the first alkyl monolayers covalently bound on HF-treated silicon carbide surfaces (SiC) through thermal reaction with 1-alkenes. Treatment of SiC with diluted aqueous HF solutions removes the native oxide layer (SiO2) and provides a reactive hydroxyl-covered surface. Very hydrophobic methyl-terminated surfaces (water contact angle theta = 107 degrees ) are obtained on flat SiC, whereas attachment of omega-functionalized 1-alkenes also yields well-defined functionalized surfaces. Infrared reflection absorption spectroscopy, ellipsometry, and X-ray photoelectron spectroscopy measurements are used to characterize the monolayers and show their covalent attachment. The resulting surfaces are shown to be extremely stable under harsh acidic conditions (e.g., no change in theta after 4 h in 2 M HCl at 90 degrees C), while their stability in alkaline conditions (pH = 11, 60 degrees C) also supersedes that of analogous monolayers such as those on Au, Si, and SiO2. These results are very promising for applications involving functionalized silicon carbide.     

Control of protein structure and function through surface recognition by tailored nanoparticle scaffolds

Thioalkyl and thioalkylated oligo(ethylene glycol) (OEG) ligands with chain-end functionality were used to fabricate water-soluble CdSe nanoparticle scaffolds. Surface recognition of chymotrypsin (ChT) was achieved using these functionalized nanoparticle scaffolds, with three levels of interaction demonstrated: no interaction (OEG terminated with hydroxyl group), inhibition with denaturation (carboxylate-terminated thioalkyl ligands), and inhibition with retention of structure (carboxylate-terminated OEG). The latter process was reversible upon an increase in ionic strength, with essentially complete restoration of enzymatic activity.     

Tandem "click" reactions at acetylene-terminated Si(100) monolayers

We demonstrate a simple method for coupling alkynes to alkynes. The method involves tandem azide-alkyne cycloaddition reactions ("click" chemistry) for the immobilization of 1-alkyne species onto an alkyne modified surface in a one-pot procedure. In the case presented, these reactions take place on a nonoxidized Si(100) surface although the approach is general for linking alkynes to alkynes. The applicability of the method in the preparation of electrically well-behaved functionalized surfaces is demonstrated by coupling an alkyne-tagged ferrocene species onto alkyne-terminated Si(100) surfaces. The utility of the approach in biotechnology is shown by constructing a DNA sensing interface by derivatization of the acetylenyl surface with commercially available alkyne-tagged oligonucleotides. Cyclic voltametry, electrochemical impedance spectroscopy, X-ray photoelectron spectroscopy, and X-ray reflectometry are used to characterize the coupling reactions and performance of the final modified surfaces. These data show that this synthetic protocol gives chemically well-defined, electronically well-behaved, and robust (bio)functionalized monolayers on silicon semiconducting surfaces.     

Anchoring energies of liquid crystals measured on surfaces presenting oligopeptides

We report a methodology that permits quantitation of the azimuthal anchoring energy of the nematic liquid crystal 4-cyano-4'-pentyl-biphenyl on surfaces patterned with oligopeptides. The oligopeptide (IYGEFKKKC), an optimized substrate for the Src protein kinase, was covalently immobilized via the terminal cysteine to monolayers of amine-terminated tetra(ethylene glycol) formed on gold films. The measurements of anchoring energies, which were based on a torque-balance method, revealed a systematic decrease in anchoring energy from 3.7 +/- 0.6 microJ/m2 with increasing surface density of oligopeptide. We calculate that a mass density of oligopeptide of less than 1 ng/cm2 can lead to a measurable change in the anchoring energy of the nematic liquid crystal. These results suggest that measurements of anchoring energies of liquid crystals on surfaces may offer the basis of quantitative and label-free methods for detecting biomolecules on surfaces.     

"Click" immobilization on alkylated silicon substrates: model for the study of surface bound antimicrobial peptides

We describe an effective approach for the covalent immobilization of antimicrobial peptides (AMPs) to bioinert substrates via Cu(I) -catalyzed azide-alkyne cycloaddition (CuAAC). The bioinert substrates were prepared by surface hydrosilylation of oligo(ethylene glycol) (OEG) terminated alkenes on hydrogen-terminated silicon surfaces. To render the OEG monolayers "clickable", mixed monolayers were prepared using OEG-alkenes with and without a terminal alkyne protected by a trimethylgermanyl (TMG) group. The mixed monolayers were characterized by X-ray photoelectron spectroscopy (XPS), elliposometry and contact angle measurement. The TMG protecting group can be readily removed to yield a free terminal alkyne by catalytic amounts of Cu(I) in an aqueous media. This step can then be combined with the subsequent CuAAC reaction. Thus, the immobilization of an azide modified AMP (N3-IG-25) was achieved in a one-pot deprotection/coupling reaction. Varying the ratio of the two alkenes in the deposition mixture allowed for control over the density of the alkynyl groups in the mixed monolayer, and subsequently the coverage of the AMPs on the monolayer. These samples allowed for study of the dependence of antimicrobial activities on the AMP density. The results show that a relative low coverage of AMPs (～1.6×10(13) molecule per cm(2)) is sufficient to significantly suppress the viability of Pseudomonas aeruginosa, while the surface presenting the highest density of AMPs (～2.8×10(13) molecule per cm(2)) is still cyto-compatible. The remarkable antibacterial activity is attributed to the long and flexible linker and the site-specific "click" immobilization, which may facilitate the covalently attached peptides to interact with and disrupt the bacterial membranes.     

Surface-immobilized PAMAM-dendrimers modified with cationic or anionic terminal functions: physicochemical surface properties and conformational changes after application of liquid interface stress

Functionalization of surfaces with highly branched dendrimer molecules has gained attractiveness for various applications because the number of functional groups exceeds those of surfaces functionalized with self-assembled monolayers. So far, little is known about the physicochemical properties of dendrimer functionalized surfaces, especially if the flexibility of dendrimer structure remains after covalent immobilization. Therefore, the purpose of this study was to covalently immobilize polyamidoamine (PAMAM) dendrimer molecules exhibiting terminal amine and carboxyl groups to silicon model surfaces and to explore their properties and structure at the solid-air and solid-liquid interface. Our results show that the surface free energy is higher for PAMAM coatings than for analogously terminated SAMs and also higher for carboxyl than amine functionalized coatings. Furthermore, several findings suggest that conformational freedom of the dendrimers was preserved after surface immobilization. Wet compared to dry PAMAMNH(2) surfaces show reduced hydrophilicity and increased contact angle hysteresis, whereas PAMAMCOOH surfaces become more hydrophilic and showed decreased hysteresis. Streaming current measurements showed an unexpected behavior for PAMAMCOOH surfaces in that they reveal a net positive surface charge over a wide pH range in spite of the carboxylated periphery. All of these results indicate a certain degree of masking, burrowing, back-folding and unfolding of functional groups upon environmental changes.     

Monolayer-derivative functionalization of non-oxidized silicon surfaces

This article describes a variety of monolayers anchored directly onto silicon surfaces without an oxide interlayer, their formation mechanisms, their technological applications, and our personal views on the future prospects for this field. The chemical modification of non-oxidized silicon surfaces utilizing monolayers was first reported in 1993. The basic finding that a non-oxidized silicon surface could be neutralized with alkyl chains through direct covalent linkage, i.e., silicon-carbon, has offered chemical scientists ease of handling even in an ambient environment and, thus, research has been predictably focused on forming anti-stiction coating films for nano- and micro-electromechanical systems (NEMS/MEMS). Such surface reforming has also been achieved by using other monolayers, which form interfacial bonds, e.g., silicon-nitrogen and silicon-oxygen. The resultant monolayer surfaces are useful for silicon-based applications including molecular electron transfer films, monolayer templates, molecular insulators, capsulators, and bioderivatives. Such monolayers are applicable not only for surface modification, but also for manipulating individual nanomaterials. By modifying the terminal groups of monolayers with nanomaterials including nanocrystals and biomolecules, the nanomaterials can remarkably be immobilized directly onto non-oxidized silicon surfaces based on the formation mechanisms of the monolayer. Such immobilizations will revolutionize the analysis of the specific features and capabilities of individual nanomaterials. Furthermore, the path will be opened for the development of more advanced monolayer-derived chip technology. To achieve this goal, it is extremely important to thoroughly understand the functionalization processes on silicon, since the resultant internal structures and properties of monolayer-derivative silicon may strongly depend on their course of formation.     

Probing proteins on functionalized silicon surfaces using matrix-assisted laser desorption/ionization mass spectrometry

Flat H-terminated Si(111) substrates modified with alkyl monolayers terminated with hydrophobic and hydrophilic functional groups were prepared using known surface functionalization methods and characterized by FTIR, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). The surfaces were then used for the study of non-specific binding of proteins from complex mixtures (using standard mixture of proteins with average molecular weight approximately 6-66 kDa) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Protein adsorption on these surfaces (following on-probe fractionation of the mixture) was found to be dependent on the nature of surface functional groups, and nature and pH of rinsing solutions used. The results obtained in this work demonstrate that simple silicon-based surface modifications can be effective for direct analysis of complex mixtures by MALDI-MS. Preliminary results obtained using similarly functionalized porous silicon substrates proved that such substrates are (due to their increased surface areas) better performing than flat silicon.     

Mixed self-assembled monolayers (SAMs) consisting of methoxy-tri(ethylene glycol)-terminated and alkyl-terminated dimethylchlorosilanes control the non-specific adsorption of proteins at oxidic surfaces

Monolayers from the newly synthesized compound methoxy-tri(ethylene glycol)-undecenyldimethylchlorosilane (CH3O(CH2CH2O)3(CH2)11Si(CH3)2Cl, MeO(EG)3C11DMS) and dodecyldimethylchlorosilane (DDMS), both pure and mixed, were prepared by self-assembly from organic solution in the presence of an organic base. The films obtained were characterized by advancing and receding contact angle measurements and ellipsometry to confirm the formation of self-assembled monolayers (SAMs). The resulting data on the covalently attached dimethylsilanes were compared to known oligo(ethylene glycol) (OEG)-terminated SAM systems based on terminal alkenes, thiolates or trihydrolyzable silanes. The composition of the mixed SAMs was found to depend directly and linearly on the composition of the silanization solution. Enhanced protein repellent properties were found for the SAMs using a variety of proteins, including the Ras Binding Domain (RBD), a protein with high relevance for cancer diagnostics. Roughly a RBD protein monolayer amount was adsorbed to silicon oxide surfaces silanized with DDMS or non-silanized silicon wafers, and in contrast, no RBD was adsorbed to surfaces silanized with MeO(EG)3C11DMS or to mixed monolayers consisting of DDMS and MeO(EG)3C11DMS if the content of OEG-silane overcame a critical content of X(EG) approximately 0.9.     

One step growth of protein antifouling surfaces: monolayers of poly(ethylene oxide) (PEO) derivatives on oxidized and hydrogen-passivated silicon surfaces

We compare two routes for creating protein adsorption-resistant self-assembled monolayers (SAMs) by chemical modification of silicon surfaces with poly(ethylene oxide) (PEO) oligomeric derivatives. The first route involves the assembly of 2-methyl[(polyethyleneoxy)propyl]trichlorosilane (Cl3SiMPEO) films onto oxidized silicon surfaces (OH-SiO(x)) either by a liquid-phase process at room temperature or by a gas-phase process at 423 K, producing Si-O-Si bonds between the substrate and the organic layer. The second pathway makes use of the assembly of poly(ethylene glycol methyl ether) (MPEG) films onto hydrogen-passivated silicon surfaces (H-Si) using a liquid-phase process at 353 or 423 K, leading to the formation of Si-O-C bonds between the substrate and the organic layer. Structural investigation by X-ray reflectometry (XRR) reveals that the thickness and surface densities of the grafted PEO monolayers strongly depend on experimental conditions such as temperature and grafting time. Atomic force microscopy (AFM) shows that very smooth and homogeneous monolayers can be obtained with average roughnesses close to those measured on the corresponding bare substrates. Finally, the antifouling properties of the modified silicon surfaces were evaluated by X-ray photoelectron spectroscopy (XPS), using a membrane protein (P.69 antigen) as model protein. Both types of PEO monolayers exhibit excellent protein repellency, as soon as the grafting density is equal to or higher than 1.7 chains/nm2.     

Self-assembled monolayers of novel surface-bound dendrons: peripheral structure determines surface organization

The synthetic and functional versatility of dendrimers and their well-defined shapes make them attractive molecules for surface modification. We synthesized six structurally very similar surface-bound dendrons and used them as building blocks for the preparation of self-assembled monolayers (SAMs) on a gold surface. We studied the effects of the surface-bound dendron's main structure, peripheral substituents, and the coadsorption process on its self-assembling behavior. Using scanning tunneling microscopy (STM), we observed nanostripes for SAMs of the surface-bound dendron consisting of symmetrical benzene rings. When we changed the symmetrical dendron's structure slightly, by increasing or decreasing the numbers of benzene rings at one wedge, we found no ordered structures were formed by the asymmetrical dendrons. We also introduced two kinds of substituents, heptane chains and oligo(ethylene oxide) chains, to the symmetrical dendron's periphery. Heptane chains appear to enhance the interaction between symmetrical backbones, leading to the formation of stripes, while oligo(ethylene oxide) chains appear to weaken the interaction between symmetrical backbones, resulting in a homogeneous structure. Dendrons with both heptane and oligo(ethylene oxide) chains exhibit nanophase separation in a confined state, leading to the formation of a honeycomb structure. Electrochemical studies provide additional evidence for understanding the resulting surface organizations: surface-bound dendrons with symmetrical structures form denser monolayers than their asymmetrical analogues; SAMs comprising peripherally substituted dendrons exhibit blocking effects proportionate to their hydrophilic fraction.     

Nanoscale Biomolecular Structures on Self‐Assembled Monolayers Generated from Modular Pegylated Disulfides

A solid‐phase synthetic strategy was developed that uses modular building blocks to prepare symmetric oligo(ethylene glycol)‐terminated disulfides with a variety of lengths and terminal functionalities. The modular disulfides, composed of alkyl amino groups linked by an amide group to oligoethylene chains were used to generate self‐assembled monolayers (SAMs), which were characterised to determine their applicability for biomolecular applications. X‐ray photoelectron spectroscopy (XPS) of the SAMs obtained from these molecules demonstrated improved stability towards displacement by 16‐hexadecanethiol, while surface plasmon resonance (SPR) analyses of SAMs prepared with the hydroxy‐terminated oligoethylene disulfide showed equal resistance to non‐specific protein adsorption in comparison to 11‐mercaptoundecyl tri(ethylene glycol). SAMs made from these adsorbates were amenable to nanoscale patterning by scanning near‐field photolithography (SNP), facilitating the fabrication of nanopatterned, protein‐functionalised surfaces. Such SAMs may be further developed for bionanotechnology applications such as the fabrication of nanoscale biological arrays and sensor devices.