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1.  Patterned Self-Assembled Monolayers: Efficient, Chemically Defined Tools for Cell Biology 
Self-assembled monolayers (SAMs) of alkanethiolates on gold can be used to carefully probe immobilized biomolecule interactions with cell-surface receptors. However, due to a lack of experimental throughput associated with labor-intensive production, specialized fabrication apparatus, and other practical challenges, alkanethiolate SAMs have not had widespread use by biological researchers. In this Minireview, we investigate a range of techniques that could enhance the throughput of SAM-based approaches by patterning substrates with arrays of different conditions. Here we highlight microfluidic, photochemical, localized removal, and backfilling techniques to locally pattern SAM substrates with biomolecules and also describe how these approaches have been applied in SAM-based screening systems. Furthermore we provide perspectives on several crucial barriers that need to be overcome to enable widespread use of SAM chemistry in biological applications.
doi:10.1002/cbic.201200226
PMCID: PMC3995495  PMID: 22807236
alkanethiolates; arrays; patterning; peptides; self-assembled monolayers
2.  Effect of Substratum Surface Chemistry and Surface Energy on Attachment of Marine Bacteria and Algal Spores 
Two series of self-assembled monolayers (SAMs) of ω-substituted alkanethiolates on gold were used to systematically examine the effects of varying substratum surface chemistry and energy on the attachment of two model organisms of interest to the study of marine biofouling, the bacterium Cobetia marina (formerly Halomonas marina) and zoospores of the alga Ulva linza (formerly Enteromorpha linza). SAMs were formed on gold-coated glass slides from solutions containing mixtures of methyl- and carboxylic acid-terminated alkanethiols and mixtures of methyl- and hydroxyl-terminated alkanethiols. C. marina attached in increasing numbers to SAMs with decreasing advancing water contact angles (θAW), in accordance with equation-of-state models of colloidal attachment. Previous studies of Ulva zoospore attachment to a series of mixed methyl- and hydroxyl-terminated SAMs showed a similar correlation between substratum θAW and zoospore attachment. When the hydrophilic component of the SAMs was changed to carboxylate, however, the profile of attachment of Ulva was significantly different, suggesting that a more complex model of interfacial energetics is required.
doi:10.1128/AEM.70.7.4151-4157.2004
PMCID: PMC444801  PMID: 15240295
3.  Patterning discrete stem cell culture environments via localized SAM replacement 
Self-assembled monolayers (SAMs) of alkanethiolates on gold have become an important tool for probing cell-material interactions. Emerging studies in stem cell biology are particularly reliant on well-defined model substrates, and rapid and highly controllable fabrication methods may be necessary to characterize the wide array of stem cell-material interactions. Therefore, this study describes a rapid method to create SAM cell culture substrates with multiple discrete regions of controlled peptide identity and density. The approach uses an NaBH4 solution to selectively remove regions of bio-inert, hydroxyl-terminated oligo(ethylene glycol) alkanethiolate SAM, then locally replace them with mixed SAMs of hydroxyl- and carboxylic acid-terminated oligo(ethylene glycol) alkanethiolates. The cell adhesion peptide Arg-Gly-Asp-Ser-Pro (RGDSP) was then covalently linked to carboxylic acid-terminated mixed SAM regions to create cell adhesive environments within a bio-inert background. SAM preparation and peptide immobilization were characterized using polarization modulation–infrared reflection-absorption spectroscopy (PMIRRAS), as well as assays to monitor conjugation of a fluorescently-labeled peptide. This “localized SAM replacement” method was achieved using an array of microchannels, which facilitated rapid and simple processing. Results indicate that immobilized RGDSP promoted spatially localized attachment of human mesenchymal stem cells (hMSCs) within specified regions, while maintaining a stable, bio-inert background in serum-containing cell culture conditions for up to 14 days. Cell attachment to patterned regions presenting a range of cell adhesion peptide densities demonstrated that peptide identity and density strongly influence hMSC spreading and focal adhesion density. These substrates contain discrete, well-defined microenvironments for stem cell culture, which could ultimately enable high-throughput screening for the effects of immobilized signals on stem cell phenotype.
doi:10.1021/la901938e
PMCID: PMC2769026  PMID: 19856996
4.  Role of Surface Chemistry in Protein Remodeling at the Cell-Material Interface 
PLoS ONE  2011;6(5):e19610.
Background
The cell-material interaction is a complex bi-directional and dynamic process that mimics to a certain extent the natural interactions of cells with the extracellular matrix. Cells tend to adhere and rearrange adsorbed extracellular matrix (ECM) proteins on the material surface in a fibril-like pattern. Afterwards, the ECM undergoes proteolytic degradation, which is a mechanism for the removal of the excess ECM usually approximated with remodeling. ECM remodeling is a dynamic process that consists of two opposite events: assembly and degradation.
Methodology/Principal Findings
This work investigates matrix protein dynamics on mixed self-assembled monolayers (SAMs) of –OH and –CH3 terminated alkanethiols. SAMs assembled on gold are highly ordered organic surfaces able to provide different chemical functionalities and well-controlled surface properties. Fibronectin (FN) was adsorbed on the different surfaces and quantified in terms of the adsorbed surface density, distribution and conformation. Initial cell adhesion and signaling on FN-coated SAMs were characterized via the formation of focal adhesions, integrin expression and phosphorylation of FAKs. Afterwards, the reorganization and secretion of FN was assessed. Finally, matrix degradation was followed via the expression of matrix metalloproteinases MMP2 and MMP9 and correlated with Runx2 levels. We show that matrix degradation at the cell material interface depends on surface chemistry in MMP-dependent way.
Conclusions/Significance
This work provides a broad overview of matrix remodeling at the cell-material interface, establishing correlations between surface chemistry, FN adsorption, cell adhesion and signaling, matrix reorganization and degradation. The reported findings improve our understanding of the role of surface chemistry as a key parameter in the design of new biomaterials. It demonstrates the ability of surface chemistry to direct proteolytic routes at the cell-material interface, which gains a distinct bioengineering interest as a new tool to trigger matrix degradation in different biomedical applications.
doi:10.1371/journal.pone.0019610
PMCID: PMC3090403  PMID: 21573010
5.  Role of SAM Chain Length in Enhancing the Sensitivity of Nanopillar Modified Electrodes for Glucose Detection 
Sensors (Basel, Switzerland)  2009;9(3):1295-1305.
In this report, alkanethiol self assembled monolayers (SAM) with two different chain lengths were used to immobilize the functionalizing enzyme (glucose oxidase) onto gold nanopillar modified electrodes and the electrochemical processes of these functionalized electrodes in glucose detection were investigated. First, the formation of these SAMs on the nanopillar modified electrodes was characterized by the cyclic voltammetry and electrochemical impedance spectroscopy techniques, and then the detection sensitivity of these functionalized electrodes to glucose was evaluated by the amperometry technique. Results showed that the SAM of alkanethiols with a longer chain length resulted in a higher degree of surface coverage with less defect and a higher electron transfer resistance, whereas the SAM of alkanethiols with a shorter chain length gave rise to a higher detection sensitivity to glucose. This study sheds some new insight into how to enhance the sensing performance of nanopillar modified electrodes.
doi:10.3390/s90301295
PMCID: PMC3345854  PMID: 22573954
Gold nanopillar modified electrodes; self assembled monolayer; alkanethiols; electrochemical processes; glucose detection; biosensors
6.  Surface polyethylene glycol enhances substrate-mediated gene delivery by nonspecifically immobilized complexes 
Acta biomaterialia  2007;4(1):26-39.
Substrate-mediated gene delivery describes the immobilization of gene therapy vectors to a biomaterial, which enhances gene transfer by exposing adhered cells to elevated DNA concentrations within the local microenvironment. Surface chemistry has been shown to affect transfection by nonspecifically immobilized complexes using self-assembled monolayers (SAMs) of alkanethiols on gold. In this report, SAMs were again used to provide a controlled surface to investigate whether the presence of oligo(ethylene glycol) (EG) groups in a SAM could affect complex morphology and enhance transfection. EG groups were included at percentages that did not affect cell adhesion. Nonspecific complex immobilization to SAMs containing combinations of EG- and carboxylic acid-terminated alkanethiols resulted in substantially greater transfection than surfaces containing no EG groups or SAMs composed of EG groups combined with other functional groups. Enhancement in transfection levels could not be attributed to complex binding densities or release profiles. Atomic force microscopy imaging of immobilized complexes revealed that EG groups within SAMs affected complex size and appearance and could indicate the ability of these surfaces to preserve complex morphology upon binding. The ability to control the morphology of the immobilized complexes and influence transfection levels through surface chemistry could be translated to scaffolds for gene delivery in tissue engineering and diagnostic applications.
doi:10.1016/j.actbio.2007.08.008
PMCID: PMC2170460  PMID: 17920004
Gene delivery; Reverse transfection; Atomic force microscopy (AFM); Self-assembled monolayers
7.  Substrate-mediated delivery from self-assembled monolayers: Effect of surface ionization, hydrophilicity, and patterning 
Acta biomaterialia  2005;1(5):511-522.
Gene transfer has many potential applications in basic and applied sciences. In vitro, DNA delivery can be enhanced by increasing the concentration of DNA in the cellular microenvironment through immobilization of DNA to a substrate that supports cell adhesion. Substrate-mediated delivery describes the immobilization of DNA, complexed with cationic lipids or polymers, to a biomaterial or substrate. As surface properties are critical to the efficiency of the surface delivery approach, self-assembled monolayers (SAMs) of alkanethiols on gold were used to correlate surface chemistry of the substrate to binding, release, and transfection of non-specifically immobilized complexes. Surface hydrophobicity and ionization were found to mediate both DNA complex immobilization and transfection, but had no effect on complex release. Additionally, SAMs were used in conjunction with soft lithographic techniques to imprint substrates with specific patterns, resulting in patterned DNA complex deposition and transfection, with transfection efficiencies in the patterns nearing 40%. Controlling the interactions between complexes and substrates, with the potential for patterned delivery, can be used to locally enhance or regulate gene transfer, with applications to tissue engineering scaffolds and transfected cell arrays.
doi:10.1016/j.actbio.2005.05.004
PMCID: PMC2648400  PMID: 16701831
Self-assembled monolayers; Gene delivery; Reverse transfection; Solid-phase delivery; Substrate mediated
8.  Fabrication of carbon nanomembranes by helium ion beam lithography 
Summary
The irradiation-induced cross-linking of aromatic self-assembled monolayers (SAMs) is a universal method for the fabrication of ultrathin carbon nanomembranes (CNMs). Here we demonstrate the cross-linking of aromatic SAMs due to exposure to helium ions. The distinction of cross-linked from non-cross-linked regions in the SAM was facilitated by transferring the irradiated SAM to a new substrate, which allowed for an ex situ observation of the cross-linking process by helium ion microscopy (HIM). In this way, three growth regimes of cross-linked areas were identified: formation of nuclei, one-dimensional (1D) and two-dimensional (2D) growth. The evaluation of the corresponding HIM images revealed the dose-dependent coverage, i.e., the relative monolayer area, whose density of cross-links surpassed a certain threshold value, as a function of the exposure dose. A complete cross-linking of aromatic SAMs by He+ ion irradiation requires an exposure dose of about 850 µC/cm2, which is roughly 60 times smaller than the corresponding electron irradiation dose. Most likely, this is due to the energy distribution of secondary electrons shifted to lower energies, which results in a more efficient dissociative electron attachment (DEA) process.
doi:10.3762/bjnano.5.20
PMCID: PMC3943867  PMID: 24605285
carbon nanomembranes; dissociative electron attachment; helium ion microscopy; ion beam-organic molecules interactions; self-assembled monolayers
9.  Peptide Arrays Identify Isoform-Selective Substrates for Profiling Endogenous Lysine Deacetylase Activity 
ACS Chemical Biology  2010;5(9):863-873.
This paper reports the development of a class of isoform-selective peptide substrates for measuring endogenous lysine deacetylase (KDAC) activities in cell culture. The peptides were first identified by comparing the substrate specificity profiles of the four KDAC isoforms KDAC2, KDAC3, KDAC8, and sirtuin 1 (SIRT1) on a 361-member hexapeptide array wherein the two C-terminal residues to the acetylated lysine were varied. The arrays were prepared by immobilizing the peptides to a self-assembled monolayer of alkanethiolates on gold and could therefore be analyzed by a mass spectrometry technique termed SAMDI (self-assembled monolayers for matrix assisted laser desorption/ionization time-of-flight mass spectrometry). Arrays presenting the selective substrates were treated with nuclear extracts from HeLa, Jurkat, and smooth muscle cells and analyzed to measure endogenous deacetylase activities. We then use the arrays to profile KDAC activity through the HeLa cell cycle. We find that the activity profile of the KDAC3 selective peptide closely mirrors the changing acetylation state of the H4 histone, suggesting a role for this enzyme in cell cycle regulation. This work is significant because it describes a general route for identifying selective substrates that can be used to understand the differential roles of members of the deacetylase enzyme family in complex biological processes and further because the label-free approach avoids perturbation of enzyme activity that has plagued fluorescence-based assays.
doi:10.1021/cb100088g
PMCID: PMC2941244  PMID: 20849068
10.  The Platelet Integrin αIIbβ3 Binds to the RGD and AGD Motifs in Fibrinogen 
Chemistry & biology  2009;16(9):990-1000.
SUMMARY
Fibrinogen (Fbg) mediates platelet aggregation through its binding to the αIIbβ3 integrin receptor. Despite the many studies of platelet aggregation and blood clotting, the interaction of Fbg with the platelet integrin has remained unresolved. This paper reports on the use of self-assembled monolayers (SAMs) of alkanethiolates on gold to study the adhesion of αIIbβ3 CHO K1 cells to the GRGDS and HHLGGAKQAGDV motifs within Fbg. The peptides were immobilized to a monolayer that otherwise prevented nonspecific interactions of the cells with the substrate. Monolayers presenting GRGDSC or HHLGGAKQAGDVC were effective at mediating αIIbβ3 CHO K1 cell adhesion and spreading and were comparable to the use of Fbg-coated substrates, suggesting that both sequences can bind the receptor independently. A comparison of cell adhesion to several peptide truncations revealed that AGD was the minimal binding sequence in HHLGGAKQAGDV, and inhibition experiments showed that AGD and RGD were competitive ligands for the receptor. A peptide array of GXGDSC peptides revealed that αIIbβ3 CHO K1 cells adhered to peptides containing basic or hydrophobic residues in the X position, revealing the relaxed specificity with which αIIbβ3 recognizes its ligands. This work therefore suggests that AGD and RGD interact with Fbg in a functionally similar manner and that the use of AGD peptides may lead to a new generation of anti-thrombotic agents.
doi:10.1016/j.chembiol.2009.08.012
PMCID: PMC2788794  PMID: 19778727
11.  Improving the Dielectric Properties of Ethylene-Glycol Alkanethiol Self-Assembled Monolayers 
Langmuir  2014;30(5):1321-1326.
Self-assembled monolayers (SAMs) can be formed at the interface between solids and fluids, and are often used to modify the surface properties of the solid. One of the most widely employed SAM systems is exploiting thiol-gold chemistry, which, together with alkane-chain-based molecules, provides a reliable way of SAM formation to modify the surface properties of electrodes. Oligo ethylene-glycol (OEG) terminated alkanethiol monolayers have shown excellent antifouling properties and have been used extensively for the coating of biosensor electrodes to minimize nonspecific binding. Here, we report the investigation of the dielectric properties of COOH-capped OEG monolayers and demonstrate a strategy to improve the dielectric properties significantly by mixing the OEG SAM with small concentrations of 11-mercaptoundecanol (MUD). The monolayer properties and composition were characterized by means of impedance spectroscopy, water contact angle, ellipsometry and X-ray photoelectron spectroscopy. An equivalent circuit model is proposed to interpret the EIS data and to determine the conductivity of the monolayer. We find that for increasing MUD concentrations up to about 5% the resistivity of the SAM steadily increases, which together with a considerable decrease of the phase of the impedance, demonstrates significantly improved dielectric properties of the monolayer. Such monolayers will find widespread use in applications which depend critically on good dielectric properties such as capacitive biosensor.
doi:10.1021/la403983b
PMCID: PMC4065163  PMID: 24447311
12.  Immobilization of peptides with distinct biological activities onto stem cell culture substrates using orthogonal chemistries 
We have used the orthogonal carbodiimide condensation and Copper-catalyzed azide-alkyne “click” cycloaddition (CuAAC) reactions to prepare self-assembled monolayers that present distinct peptides to stem cells in a bio-inert background. The approach involved first forming mixed SAMs with three components: i) an azide-terminated hexaethylene glycol alkanethiolate (HS---EG6---N3), ii) a carboxylate-terminated hexaethylene glycol alkanethiolate (HS---EG6---COOH), and iii) a triethylene glycol alkanethiolate (HS---EG3). An acetylene-bearing peptide and an amine-terminated peptide were then immobilized to these substrates using a “click” CuAAC reaction and a carbodiimide condensation reaction, respectively. Polarization-modulated infrared reflectance-absorbance spectroscopic analysis demonstrated formation of well-ordered, close-packed SAMs, chemoselective conjugation of amine-terminated peptides to surface carboxylate groups, and subsequent conjugation of acetylene-terminated peptides to the azide groups on SAMs. Varying the mole fraction of HS---EG6---N3, HS---EG6---COOH, and HS---EG3 during SAM formation allowed for control over the densities of each peptide on the substrate. Substrates presenting varying surface densities of RGESP (a non-functional peptide), RGDSP (a cell adhesion peptide) or TYRSRKY (a heparin/heparan sulfate-binding peptide) were then used to characterize the relationship between peptide surface density and human mesenchymal stem cell (hMSC) adhesion. Results demonstrate that RGESP does not influence RGDSP-mediated adhesion of hMSCs, which indicates that a second peptide with distinct bio-activity can be immobilized alongside RGDSP to characterize the influence of two peptides on hMSC behavior. Our results also demonstrate that RGDSP and TYRSRKY act synergistically to promote hMSC adhesion in the absence of serum. Interestingly, heparin sequestered by TYRSRKY inhibits cell adhesion on substrates presenting RGDSP = 0.1% and > 0.1% TYRSRKY or RGDSP = 1% and > 0.5% TYRSRKY. Taken together, these results indicate that two peptides can be controllably presented to stem cells on the same otherwise bio-inert SAM substrate, and that multiple, distinct extracellular moieties act in concert to regulate hMSC adhesion.
doi:10.1021/la1008208
PMCID: PMC2860651  PMID: 20353153
13.  Automated scanning probe lithography with n-alkanethiol self assembled monolayers on Au(111): Application for teaching undergraduate laboratories 
Journal of Laboratory Automation  2011;16(2):112-125.
Controllers for scanning probe instruments can be programmed for automated lithography to generate desired surface arrangements of nanopatterns of organic thin films, such as n-alkanethiol self-assembled monolayers (SAMs). In this report, atomic force microscopy (AFM) methods of lithography known as nanoshaving and nanografting are used to write nanopatterns within organic thin films. Commercial instruments provide software to control the length, direction, speed, and applied force of the scanning motion of the tip. For nanoshaving, higher forces are applied to an AFM tip to selectively remove regions of the matrix monolayer, exposing bare areas of the gold substrate. Nanografting is accomplished by force-induced displacement of molecules of a matrix SAM, followed immediately by the surface self-assembly of n-alkanethiol molecules from solution. Advancements in AFM automation enable rapid protocols for nanolithography, which can be accomplished within the tight time restraints of undergraduate laboratories. Example experiments with scanning probe lithography (SPL) will be described in this report that were accomplished by undergraduate students during laboratory course activities and research internships in the chemistry department of Louisiana State University. Students were introduced to principles of surface analysis and gained “hands-on” experience with nanoscale chemistry.
doi:10.1016/j.jala.2010.06.003
PMCID: PMC3072817  PMID: 21483651
14.  An Adaptor Domain-Mediated Auto-Catalytic Interfacial Kinase Reaction 
This paper describes a model system for studying the auto-catalytic phosphorylation of an immobilized substrate by a kinase enzyme. This work uses self-assembled monolayers (SAMs) of alkanethiolates on gold to present the peptide substrate on a planar surface. Treatment of the monolayer with Abl kinase results in phosphorylation of the substrate. The phosphorylated peptide then serves as a ligand for the SH2 adaptor domain of the kinase and thereby directs the kinase activity to nearby peptide substrates. This directed reaction is intramolecular and proceeds with a faster rate than does the initial, intermolecular reaction, making this an auto-catalytic process. The kinetic non-linearity gives rise to properties that have no counterpart in the corresponding homogeneous phase reaction: in one example, the rate for phosphorylation of a mixture of two peptides is faster than the sum of the rates for phosphorylation of each peptide when presented alone. This work highlights the use of an adaptor domain in modulating the activity of a kinase enzyme for an immobilized substrate and offers a new approach for studying biochemical reactions in spatially inhomogeneous settings.
doi:10.1002/chem.200901345
PMCID: PMC2856317  PMID: 19821459
Adaptor domain; autocatalysis; interfacial; SAMDI; phosphorylation
15.  Selective patterning of ZnO nanorods on silicon substrates using nanoimprint lithography 
Nanoscale Research Letters  2011;6(1):159.
In this research, nanoimprint lithography (NIL) was used for patterning crystalline zinc oxide (ZnO) nanorods on the silicon substrate. To fabricate nano-patterned ZnO nanorods, patterning of an n-octadecyltrichlorosilane (OTS) self-assembled monolayers (SAMs) on SiO2 substrate was prepared by the polymer mask using NI. The ZnO seed layer was selectively coated only on the hydrophilic SiO2 surface, not on the hydrophobic OTS SAMs surface. The substrate patterned with the ZnO seed layer was treated with the oxygen plasma to oxidize the silicon surface. It was found that the nucleation and initial growth of the crystalline ZnO were proceeded only on the ZnO seed layer, not on the silicon oxide surface. ZnO photoluminescence spectra showed that ZnO nanorods grown from the seed layer treated with plasma showed lower intensity than those untreated with plasma at 378 nm, but higher intensity at 605 nm. It is indicated that the seed layer treated with plasma produced ZnO nanorods that had a more oxygen vacancy than those grown from seed layer untreated with plasma. Since the oxygen vacancies on ZnO nanorods serve as strong binding sites for absorption of various organic and inorganic molecules. Consequently, a nano-patterning of the crystalline ZnO nanorods grown from the seed layer treated with plasma may give the versatile applications for the electronics devices.
doi:10.1186/1556-276X-6-159
PMCID: PMC3211210  PMID: 21711665
16.  Inhibition of Escherichia coli Biofilm Formation by Self-Assembled Monolayers of Functional Alkanethiols on Gold▿ † 
Applied and Environmental Microbiology  2007;73(13):4300-4307.
Bacterial biofilms cause serious problems, such as antibiotic resistance and medical device-related infections. To further understand bacterium-surface interactions and to develop efficient control strategies, self-assembled monolayers (SAMs) of alkanethiols presenting different functional groups on gold films were analyzed to determine their resistance to biofilm formation. Escherichia coli was labeled with green florescence protein, and its biofilm formation on SAM-modified surfaces was monitored by confocal laser scanning microscopy. The three-dimensional structures of biofilms were analyzed with the COMSTAT software to obtain information about biofilm thickness and surface coverage. SAMs presenting methyl, l-gulonamide (a sugar alcohol tethered with an amide bond), and tri(ethylene glycol) (TEG) groups were tested. Among these, the TEG-terminated SAM was the most resistant to E. coli biofilm formation; e.g., it repressed biofilm formation by E. coli DH5α by 99.5% ± 0.1% for 1 day compared to the biofilm formation on a bare gold surface. When surfaces were patterned with regions consisting of methyl-terminated SAMs surrounded by TEG-terminated SAMs, E. coli formed biofilms only on methyl-terminated patterns. Addition of TEG as a free molecule to growth medium at concentrations of 0.1 and 1.0% also inhibited biofilm formation, while TEG at concentrations up to 1.5% did not have any noticeable effects on cell growth. The results of this study suggest that the reduction in biofilm formation on surfaces modified with TEG-terminated SAMs is a result of multiple factors, including the solvent structure at the interface, the chemorepellent nature of TEG, and the inhibitory effect of TEG on cell motility.
doi:10.1128/AEM.02633-06
PMCID: PMC1932777  PMID: 17483274
17.  Nanoscale patterning of a self-assembled monolayer by modification of the molecule–substrate bond 
Summary
The intercalation of Cu at the interface of a self-assembled monolayer (SAM) and a Au(111)/mica substrate by underpotential deposition (UPD) is studied as a means of high resolution patterning. A SAM of 2-(4'-methylbiphenyl-4-yl)ethanethiol (BP2) prepared in a structural phase that renders the Au substrate completely passive against Cu-UPD, is patterned by modification with the tip of a scanning tunneling microscope. The tip-induced defects act as nucleation sites for Cu-UPD. The lateral diffusion of the metal at the SAM–substrate interface and, thus, the pattern dimensions are controlled by the deposition time. Patterning down to the sub-20 nm range is demonstrated. The difference in strength between the S–Au and S–Cu bond is harnessed to develop the latent Cu-UPD image into a patterned binary SAM. Demonstrated by the exchange of BP2 by adamantanethiol (AdSH) this is accomplished by a sequence of reductive desorption of BP2 in Cu free areas followed by adsorption of AdSH. The appearance of Au adatom islands upon the thiol exchange suggests that the interfacial structures of BP2 and AdSH SAMs are different.
doi:10.3762/bjnano.5.28
PMCID: PMC3999799  PMID: 24778947
copper; electrodeposition; gold adatoms; nanolithography; negative resist
18.  X-ray spectroscopy characterization of self-assembled monolayers of nitrile-substituted oligo(phenylene ethynylene)s with variable chain length 
Summary
Self-assembled monolayers (SAMs) of nitrile-substituted oligo(phenylene ethynylene) thiols (NC-OPEn) with a variable chain length n (n ranging from one to three structural units) on Au(111) were studied by synchrotron-based high-resolution X-ray photoelectron spectroscopy and near-edge absorption fine-structure spectroscopy. The experimental data suggest that the NC-OPEn molecules form well-defined SAMs on Au(111), with all the molecules bound to the substrate through the gold–thiolate anchor and the nitrile tail groups located at the SAM–ambient interface. The packing density in these SAMs was found to be close to that of alkanethiolate monolayers on Au(111), independent of the chain length. Similar behavior was found for the molecular inclination, with an average tilt angle of ~33–36° for all the target systems. In contrast, the average twist of the OPEn backbone (planar conformation) was found to depend on the molecular length, being close to 45° for the films comprising the short OPE chains and ~53.5° for the long chains. Analysis of the data suggests that the attachment of the nitrile moiety, which served as a spectroscopic marker group, to the OPEn backbone did not significantly affect the molecular orientation in the SAMs.
doi:10.3762/bjnano.3.2
PMCID: PMC3304316  PMID: 22428092
nitrile substitution; oligo(phenylene ethynylene); self-assembled monolayers; twist angle; X-ray absorption spectroscopy
19.  Site-selective growth of surface-anchored metal-organic frameworks on self-assembled monolayer patterns prepared by AFM nanografting 
Summary
Surface anchored metal-organic frameworks, SURMOFs, are highly porous materials, which can be grown on modified substrates as highly oriented, crystalline coatings by a quasi-epitaxial layer-by-layer method (liquid-phase epitaxy, or LPE). The chemical termination of the supporting substrate is crucial, because the most convenient method for substrate modification is the formation of a suitable self-assembled monolayer. The choice of a particular SAM also allows for control over the orientation of the SURMOF. Here, we demonstrate for the first time the site-selective growth of the SURMOF HKUST-1 on thiol-based self-assembled monolayers patterned by the nanografting technique, with an atomic force microscope as a structuring tool. Two different approaches were applied: The first one is based on 3-mercaptopropionic acid molecules which are grafted in a 1-decanethiolate SAM, which serves as a matrix for this nanolithography. The second approach uses 16-mercaptohexadecanoic acid, which is grafted in a matrix of an 1-octadecanethiolate SAM. In both cases a site-selective growth of the SURMOF is observed. In the latter case the roughness of the HKUST-1 is found to be significantly higher than for the 1-mercaptopropionic acid. The successful grafting process was verified by time-of-flight secondary ion mass spectrometry and atomic force microscopy. The SURMOF structures grown via LPE were investigated and characterized by atomic force microscopy and Fourier-transform infrared microscopy.
doi:10.3762/bjnano.4.71
PMCID: PMC3817682  PMID: 24205458
atomic force microscopy (AFM); metal-organic frameworks; nanografting; nanoshaving; SURMOF
20.  Solid-State Densification of Spun-Cast Self-Assembled Monolayers for Use in Ultra-Thin Hybrid Dielectrics 
Applied surface science  2012;261:10.1016/j.apsusc.2012.09.013.
Ultra-thin self-assembled monolayer (SAM)-oxide hybrid dielectrics have gained significant interest for their application in low-voltage organic thin film transistors (OTFTs). A [8-(11-phenoxy-undecyloxy)-octyl]phosphonic acid (PhO-19-PA) SAM on ultrathin AlOx (2.5 nm) has been developed to significantly enhance the dielectric performance of inorganic oxides through reduction of leakage current while maintaining similar capacitance to the underlying oxide structure. Rapid processing of this SAM in ambient conditions is achieved by spin coating, however, as-cast monolayer density is not sufficient for dielectric applications. Thermal annealing of a bulk spun-cast PhO-19-PA molecular film is explored as a mechanism for SAM densification. SAM density, or surface coverage, and order are examined as a function of annealing temperature. These SAM characteristics are probed through atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and near edge X-ray absorption fine structure spectroscopy (NEXAFS). It is found that at temperatures sufficient to melt the as-cast bulk molecular film, SAM densification is achieved; leading to a rapid processing technique for high performance SAM-oxide hybrid dielectric systems utilizing a single wet processing step. To demonstrate low-voltage devices based on this hybrid dielectric (with leakage current density of 7.7×10−8 A cm−2 and capacitance density of 0.62 µF cm−2 at 3 V), pentacene thin-film transistors (OTFTs) are fabricated and yield sub 2 V operation and charge carrier mobilites of up to 1.1 cm2 V−1 s−1.
doi:10.1016/j.apsusc.2012.09.013
PMCID: PMC3840438  PMID: 24288423
Self Assembled Monolayer (SAM); SAM Dielectric; Hybrid Dielectric; SAM Processing; Organic Field Effect Transistor (OFET); Organic Thin Film Transistor (OTFT)
21.  Increased Stability of Glycol-Terminated Self-Assembled Monolayers for Long-Term Patterned Cell Culture 
Langmuir  2012;28(9):4318-4324.
Self-assembled monolayers (SAMs) are widely used to confine proteins and cells to a pattern in order to study cellular processes and behavior. In order to fully explore some of these phenomena, it is necessary to control cell growth and confinement for several weeks. Here we present a simple method by which protein and cellular confinement to a pattern can be maintained for more than 35 days. This represents a significant increase in pattern stability compared to previous monolayer systems and is achieved by using an amide-linked glycol monomer on 50 Å titanium/100 Å gold-coated glass coverslips. In addition, this study provides insight into the method of SAM degradation and excludes interfacial mixing of the monomers and blooming of the adlayer as major mechanisms for SAM degradation.
doi:10.1021/la2035533
PMCID: PMC3295894  PMID: 22316394
Self-Assembled Monolayer (SAM); patterned cell culture; monolayer stability; pattern fidelity; microcontact printing
22.  Modulation of electrochemical hydrogen evolution rate by araliphatic thiol monolayers on gold 
Electrochimica acta  2013;90:10.1016/j.electacta.2012.11.116.
Electroreductive desorption of a highly ordered self-assembled monolayer (SAM) formed by the araliphatic thiol (4-(4-(4-pyridyl)phenyl)phenyl)methanethiol leads to a concurrent rapid hydrogen evolution reaction (HER). The desorption process and resulting interfacial structure were investigated by voltammetric techniques, in situ spectroscopic ellipsometry, and in situ vibrational sum–frequency–generation (SFG) spectroscopy. Voltammetric experiments on SAM-modified electrodes exhibit extraordinarily high peak currents, which di er between Au(111) and polycrystalline Au substrates. Association of reductive desorption with HER is shown to be the origin of the observed excess cathodic charges. The studied SAM preserves its two–dimensional order near Au surface throughout a fast voltammetric scan even when the vertex potential is set several hundred millivolt beyond the desorption potential. A model is developed for the explanation of the observed rapid HER involving ordering and pre–orientation of water present in the nanometer–sized reaction volume between desorbed SAM and the Au electrode, by the structurally extremely stable monolayer, leading to the observed catalysis of the HER.
doi:10.1016/j.electacta.2012.11.116
PMCID: PMC3825286  PMID: 24235778
Reductive SAM desorption; Hydrogen evolution; Catalysis; Sum frequency generation spectroscopy; Spectroscopic ellipsometry
23.  Effect of functional end groups of silane self assembled monolayer surfaces on apatite formation, fibronectin adsorption and osteoblast cell function 
Bioactive glass (BG) can directly bond to living bone without fibrous tissue encapsulation. Key mechanistic steps of BG’s activity are attributed to calcium phosphate formation, surface hydroxylation and fibronectin (FN) adsorption. In the present study, self-assembled monolayers (SAMs) of alkanesilanes with different surface chemistry (OH, NH2, and COOH) were used as a model system to mimic BG’s surface activity. Calcium phosphate (Ca-P) was formed on SAMs by immersion in a solution which simulates the electrolyte content of physiological fluids. FN adsorption kinetics and monolayer coverage was determined on SAMs with or without Ca-P coating. The surface roughness was also examined on these substrates before and after FN adsorption. The effects of FN-adsorbed, Ca-P coated SAMs on the function of MC3T3-E1 were evaluated by cell growth, expression of alkaline phosphatase activity, and actin cytoskeleton formation. We demonstrate that, although the FN monolayer coverage and the rms roughness are similar on −OH and −COOH terminated SAMs with or without Ca-P coating, higher levels of ALP activity, more actin cytoskeleton formation and more cell growth are obtained on −OH and −COOH terminated SAMs with Ca-P coating. In addition, although the FN monolayer coverage is higher on Ca-P coated −NH2 terminated SAMs and SiOx surfaces, higher levels of ALP activity and more cell growth are obtained on Ca-P coated −OH and −COOH terminated SAMs. Thus with same Ca-P coatings, different surface functional groups have different effects on the function of osteoblastic cells. These findings represent new insights into the mechanism of bioactivity of BG and, thereby, may lead to designing superior constructs for bone grafting.
doi:10.1002/term.131
PMCID: PMC2610238  PMID: 19012271
self assembled monolayers; calcium phosphate; protein adsorption; cell attachment; proliferation; alkaline phosphatase activity
24.  SP19 Label-Free Detection of Kinase Activities and Protein-Protein Interactions on BioChips 
This talk describes an approach to using mass spectrometry to analyze biochips—including enzyme-mediated reaction of immobilized biomolecules and protein-protein interactions. The method is based on self-assembled monolayers of alkanethiolates on gold that present proteins and small molecules with control over the densities, patterns, and orientations of these species. Of particular interest is the development of fusion protein capture strategies that give selective and covalent immobilization of proteins. In one example, the serine esterase cutinase reacts with phosphonate capture ligands to give an active-site covalent adduct. Application of a cutinase fusion protein with a monolayer presenting the capture ligand results in immobilization of the display protein, with strict control over both the orientation and the density of this reagent. The chips are compatible with matrix-assisted laser desorption ionization mass spectrometry, and therefore do not require fluorescent or radioisotopic labels for analysis. This technique, termed SAMDI MS, can efficiently monitor a broad class of enzyme activities, including kinase, protease, methyltransferase, and carbohydrate-directed modifications, and can detect proteins having molecular weights up to 100 kDa. The talk will describe examples in assays of endogeneous cellular activities and protein-protein interaction mapping.
PMCID: PMC2291925
25.  A chemically-defined screening platform reveals behavioral similarities between primary human mesenchymal stem cells and endothelial cells 
Chemically defined substrates, which rigorously control protein-surface and cell-surface interactions, can be used to probe the effects of specific biomolecules on cell behavior. Here we combined a chemically-defined, array-based format with automated, time-lapse microscopy to efficiently screen cell-substrate interactions. Self-assembled monolayers (SAMs) of alkanethiolates bearing oligo(ethylene glycol) units and reactive terminal groups were used to present cell adhesion peptides while minimizing non-specific protein interactions. Specifically, we describe rapid fabrication of arrays of 1 mm spots, which present varied densities of the integrin-binding ligand Gly-Arg-Gly-Asp-Ser-Pro (GRGDSP). Results indicate that cell attachment, cell spreading, and proliferation exhibit strong dependencies on GRGDSP density for both human mesenchymal stem cells (hMSCs) and human umbilical vein endothelial cells (HUVECs). Furthermore, relative spreading and proliferation over a broad range of GRGDSP densities are similar for both primary cell types, and detailed comparison between cell behaviors identified a 1:1 correlation between spreading and proliferation for both HUVECs and hMSCs. Finally, time-lapse microscopy of SAM arrays revealed distinct adhesion-dependent migratory behaviors for HUVECs and hMSCs. These results demonstrate the benefits of using an array-based screening platform for investigating cell function. While the proof-of-concept focuses on simple cellular properties, the quantitative similarities observed for hMSCs and HUVECs provides a direct example of how phenomena that would not easily be predicted can be shown to correlate between different cell types.
doi:10.1039/c2ib20029e
PMCID: PMC3543770  PMID: 23147838
self-assembled monolayers; RGD; mesenchymal stem cells; umbilical vein endothelial cells; array

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