Outer-Membrane Protease (OmpT) Based E. coli Sensing with Anionic Polythiophene and Unlabeled Peptide Substrate.

E. coli and Salmonella are two of the most common bacterial pathogens involved in foodborne and waterborne related deaths. Hence, it is critical to develop rapid and sensitive detection strategies for near-outbreak applications. Reported is a simple and specific assay to detect as low as 1 CFU mL-1 of E. coli in water within 6 hours by targeting the bacteria's surface protease activity. The assay relies on polythiophene acetic acid (PTAA) as an optical reporter and a short unlabeled peptide (LL37FRRV ) previously optimized as a substrate for OmpT, an outer-membrane protease on E. coli. LL37FRRV interacts with PTAA to enhance its fluorescence while also inducing the formation of a helical PTAA-LL37FRRV construct, as confirmed by circular dichroism. However, in the presence of E. coli LL37FRRV is cleaved and can no longer affect the conformations and optical properties of PTAA. This ability to distinguish between an intact and cleaved peptide was investigated in detail using LL37FRRV sequence variants.

Label-Free Assay of Protein Tyrosine Phosphatase Activity in Single Cells.

Populations of cells exhibit variations in biochemical activity, resulting from many factors including random stochastic variability in protein production, metabolic and cell-cycle states, regulatory mechanisms, and external signaling. The development of methods for the analysis of single cells has allowed for the measurement and understanding of this inherent heterogeneity, yet methods for measuring protein activities on the single-cell scale lag behind their genetic analysis counterparts and typically report on expression rather than activity. This paper presents an approach to measure protein tyrosine phosphatase (PTP) activity in individual cells using self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry. Using flow cytometry, individual cells are first sorted into a well plate containing lysis buffer and a phosphopeptide substrate. After lysis and incubation-during which the PTP enzymes act on the peptide substrate-the reaction substrate and product are immobilized onto arrays of self-assembled monolayers, which are then analyzed using mass spectrometry. PTP activities from thousands of individual cells were measured and their distributions analyzed. This work demonstrates a general method for measuring enzyme activities in lysates derived from individual cells and will contribute to the understanding of cellular heterogeneity in a variety of contexts.

Sequential Photoactivation of Self-Assembled Monolayers to Direct Cell Adhesion and Migration.

Dynamic substrates for cell culture control the spatial and temporal presentation of extracellular matrix ligands that interact with adherent cells. This paper reports a photoactive surface chemistry that can repeatedly activate regions of the substrate for cell adhesion, spreading, and migration. The approach uses self-assembled monolayers presenting the integrin ligand RGD that is caged with a nitrophenyl-based photoprotecting group. The group is also modified with a maltoheptaose oligosaccharide to prevent nonspecific protein adsorption and cell attachment. The peptide is uncaged when irradiated with a laser source at 405 nm on a microscope to reveal micron-size regions for single cell attachment. This method is applied to studies of gap junction-mediated communication between two neighboring cells and requires the patterning of an initial receiver cell population and then the patterning of a second sender population to give a culture wherein each pair of cells are separated by 30 µm. Finally, activation of the region between the cells permits cell-cell contact and gap junction assembly between the sender and receiver cells. This example demonstrates the broad relevance of this method to studying complex phenotypes in cell culture.

Self-assembled monolayer facilitates epithelial-mesenchymal interactions mimicking odontogenesis.

Cell-cell interactions are vital for embryonic organ development and normal function of differentiated cells and tissues. In this study we have developed a self-assembled monolayer-based co-culture system to study tooth morphogenesis. Specifically, we designed a 2-D microenvironment present in the dental tissue by creating a well-structured, laterally organized epithelial and mesenchymal cell co-culture system by patterning the cell-attachment substrate. Chemical modifications were used to develop tunable surface patterns to facilitate epithelial-mesenchymal interactions mimicking the developing tooth. Such a design promoted interactions between monolayer's of the 2 cell types and provided signaling cues that resulted in cellular differentiation and mineralized matrix formation. Gene expression analysis showed that these co-cultures mimicked in-vivo conditions than monolayer cultures of a single cell type.

Directing stem cell fate by controlling the affinity and density of ligand-receptor interactions at the biomaterials interface.

Sticky situation: the differentiation of mesenchymal stem cells can be influenced by the affinity and density of an immobilized ligand for the integrin receptors. Cells adherent to monolayers that present the high-affinity, cyclic-RGD peptide (left) show increased expression of osteogenic markers, while cells on monolayers presenting the lower-affinity, linear-RGD peptide (right) express early markers of myogenesis at a high density and neurogenesis at a low density of the ligand.

Micropatterned dynamically adhesive substrates for cell migration.

We present a novel approach to examine cell migration using dynamically adhesive substrates consisting of three spatially and functionally distinct regions: the first is permanently nonadhesive to cells, the second is permanently adhesive, and the final region is electrochemically switched from nonadhesive to adhesive. We applied a double microcontact printing approach to pattern gold surfaces with carboxylic acid-terminated self-assembled monolayers (SAMs) that permit initial cell adhesion, with methyl-terminated SAMs that permit adsorption of a nonadhesive, and with tri(ethylene glycol)-terminated SAMs that can be electrochemically "switched" to permit cell migration from a prespecified pattern onto a new pattern. Using these substrates, we investigated the migration of epithelial cells from monolayers onto narrow, branching tracks of extracellular matrix in order to characterize how lead cells influence the direction of movement of followers. Time-lapse imaging revealed that, on average, five cells consistently chose one branch before other cells entered the second branch, providing evidence to suggest that intercellular communication plays an important role in guiding the cohesive movement of epithelial sheets. This platform may be of use in furthering our understanding of the mechanisms underlying cellular decision-making during migration in both individual and multicellular contexts.

Subcellular Control over Focal Adhesion Anisotropy, Independent of Cell Morphology, Dictates Stem Cell Fate.

Although microscale patterning techniques have been used to control cell morphology and shape, they only provide indirect control over the formation of the subcellular cytoskeletal elements that determine contractility. This paper addresses the hypotheses that nanoscale anisotropic features of a patterned matrix can direct the alignment of internal cytoskeletal actin fibers within a confined shape with an unbiased aspect ratio, and that this enhanced control over cytoskeletal architecture directs programmed cell behaviors. Here, large-area polymer pen lithography is used to pattern substrates with nanoscale extracellular matrix protein features and to identify cues that can be used to direct cytoskeletal organization in human mesenchymal stem cells. This nanopatterning approach is used to identify how anisotropic focal adhesions around the periphery of symmetric patterns yield an organized and contractile actin cytoskeleton. This work reports the important finding that anisotropic cues that increase cell contractility within a circular shape redirect cell differentiation from an adipogenic to an osteogenic fate. Together, these experiments introduce a programmable approach for using subcellular spatial cues to control cell behavior within defined geometries.

Exploration of the nanomedicine-design space with high-throughput screening and machine learning.

Only a tiny fraction of the nanomedicine-design space has been explored, owing to the structural complexity of nanomedicines and the lack of relevant high-throughput synthesis and analysis methods. Here, we report a methodology for determining structure-activity relationships and design rules for spherical nucleic acids (SNAs) functioning as cancer-vaccine candidates. First, we identified ~1,000 candidate SNAs on the basis of reasonable ranges for 11 design parameters that can be systematically and independently varied to optimize SNA performance. Second, we developed a high-throughput method for making SNAs at the picomolar scale in a 384-well format, and used a mass spectrometry assay to rapidly measure SNA immune activation. Third, we used machine learning to quantitatively model SNA immune activation and identify the minimum number of SNAs needed to capture optimum structure-activity relationships for a given SNA library. Our methodology is general, can reduce the number of nanoparticles that need to be tested by an order of magnitude, and could serve as a screening tool for the development of nanoparticle therapeutics.

Immunoisolating pancreatic islets by encapsulation with selective withdrawal.

This manuscript reports the application of the selective-withdrawal coating technique to the microencapsulation of insulin-producing pancreatic islets within thin poly(ethylene glycol) coatings. These polymer coatings permit the islets to respond to changes in glucose concentration by producing insulin with a dose-response profile that is substantially similar to that of unencapsulated islets. Furthermore, the hydrogel capsules exclude the large molecules of the immune system. These results suggest that the microencapsulation technique-which combines droplet formation from a flow of two immiscible fluids with polymerization chemistries-has the characteristics required for the transplantation of islets for the treatment of Type I diabetes.

Micropatterning Facilitates the Long-Term Growth and Analysis of iPSC-Derived Individual Human Neurons and Neuronal Networks.

The discovery of induced pluripotent stem cells (iPSCs) and their application to patient-specific disease models offers new opportunities for studying the pathophysiology of neurological disorders. However, current methods for culturing iPSC-derived neuronal cells result in clustering of neurons, which precludes the analysis of individual neurons and defined neuronal networks. To address this challenge, cultures of human neurons on micropatterned surfaces are developed that promote neuronal survival over extended periods of time. This approach facilitates studies of neuronal development, cellular trafficking, and related mechanisms that require assessment of individual neurons and specific network connections. Importantly, micropatterns support the long-term stability of cultured neurons, which enables time-dependent analysis of cellular processes in living neurons. The approach described in this paper allows mechanistic studies of human neurons, both in terms of normal neuronal development and function, as well as time-dependent pathological processes, and provides a platform for testing of new therapeutics in neuropsychiatric disorders.

Carbohydrate arrays for the evaluation of protein binding and enzymatic modification.

This paper reports a chemical strategy for preparing carbohydrate arrays and utilizes these arrays for the characterization of carbohydrate-protein interactions. Carbohydrate chips were prepared by the Diels-Alder-mediated immobilization of carbohydrate-cyclopentadiene conjugates to self-assembled monolayers that present benzoquinone and penta(ethylene glycol) groups. Surface plasmon resonance spectroscopy showed that lectins bound specifically to immobilized carbohydrates and that the glycol groups prevented nonspecific protein adsorption. Carbohydrate arrays presenting ten monosaccharides were then evaluated by profiling the binding specificities of several lectins. These arrays were also used to determine the inhibitory concentrations of soluble carbohydrates for lectins and to characterize the substrate specificity of beta-1,4-galactosyltransferase. Finally, a strategy for preparing arrays with carbohydrates generated on solid phase is shown. This surface engineering strategy will permit the preparation and evaluation of carbohydrate arrays that present diverse and complex structures.

A gene expression-based comparison of cell adhesion to extracellular matrix and RGD-terminated monolayers.

This work uses global gene expression analysis to compare the extent to which model substrates presenting peptide adhesion motifs mimic the use of conventional extracellular matrix protein coated substrates for cell culture. We compared the transcriptional activities of genes in cells that were cultured on matrix-coated substrates with those cultured on self-assembled monolayers presenting either a linear or cyclic RGD peptide. Cells adherent to cyclic RGD were most similar to those cultured on native ECM, while cells cultured on monolayers presenting the linear RGD peptide had transcriptional activities that were more similar to cells cultured on the uncoated substrates. This study suggests that biomaterials presenting the cyclic RGD peptide are substantially better mimics of extracellular matrix than are uncoated materials or materials presenting the common linear RGD peptide.

Combinatorial screening of mesenchymal stem cell adhesion and differentiation using polymer pen lithography.

The extracellular matrix (ECM) is a complex, spatially inhomogeneous environment that is host to myriad cell-receptor interactions that promote changes in cell behavior. These biological systems can be probed and simulated with engineered surfaces, but doing so demands careful control over the arrangement of ligands. Here, we describe how such surfaces can be fabricated by utilizing polymer pen lithography (PPL), which is a cantilever-free scanning probe lithographic method that utilizes polymeric pen arrays to generate patterns over large areas. With the advent of PPL, fundamental questions in cell biology can be answered by recapitulating cell-ECM interactions to explore how these interactions lead to changes in cell behavior. Here, we describe an approach for the combinatorial screening of cell adhesion behavior to gain understanding of how ECM protein feature size dictates osteogenic differentiation of mesenchymal stem cells. The technique outlined here is generalizable to other biological systems and can be paired with quantitative analytical methods to probe important processes such as cell polarization, proliferation, signaling, and differentiation.

Three-component reaction discovery enabled by mass spectrometry of self-assembled monolayers.

Multicomponent reactions are employed extensively in many areas of organic chemistry. Despite significant progress, the discovery of such enabling transformations remains challenging. Here, we present the development of a parallel, label-free reaction-discovery platform that can be used in the identification of new multicomponent transformations. Our approach is based on parallel mass spectrometric screening of interfacial chemical reactions on arrays of self-assembled monolayers. This strategy enabled the identification of a simple organic phosphine that can catalyse a previously unknown condensation of siloxyalkynes, aldehydes and amines to produce 3-hydroxyamides with high efficiency and diastereoselectivity. The reaction was further optimized using solution-phase methods.

Electroactive self-assembled monolayers that permit orthogonal control over the adhesion of cells to patterned substrates.

This article describes an electroactive substrate that displays two independent dynamic functions for controlling the adhesion of cells. The approach is based on self-assembled monolayers on gold that are patterned into regions presenting the Arg-Gly-Asp peptide cell adhesion ligand. The patterned regions differ in the electrochemical properties of the linkers that tether the peptides to the monolayer. In this work, three distinct chemistries are employed that provide for release of the ligand on application of a negative potential, release of the ligand on application of a positive potential, and no change in response to a potential. Cells were allowed to attach to a monolayer patterned into circular regions comprising the three chemistries. Treatment with electric potentials of 650 or -650 mV resulted in the selective release of adherent cells only from regions that display the relevant electroactive groups. This example establishes the preparation of dynamic substrates with multiple functions and will be important to preparing model cultures derived from multiple cell types, with control over the temporal interactions of each cell population.

A photochemical method for patterning the immobilization of ligands and cells to self-assembled monolayers.

This work describes a chemically well defined method for patterning ligands to self-assembled monolayers (SAMs) of alkanethiolates on gold. This method begins with monolayers presenting a nitroveratryloxycarbonyl (NVOC)-protected hydroquinone which is photochemically irradiated to reveal a hydroquinone group. The resulting hydroquinone is then oxidized to the corresponding benzoquinone, providing a site for the Diels-Alder mediated immobilization of ligands. The rate constant for the photochemical deprotection is 0.032 s(-1) (with an intensity of approximately 100 mW/cm(2) between 355 and 375 nm), corresponding to a half-life of 21 s. The hydroquinone is oxidized to the benzoquinone using either electrochemical or chemical oxidation and then functionalized by reaction with a cyclopentadiene-tagged ligand. Two methods for patterning the immobilization of ligands are described. In the first, the substrate is illuminated through a mask to generate a pattern of hydroquinone groups, which are elaborated with ligands. In the second method, an optical microscope fit with a programmable translational stage is used to write patterns of deprotection which are then again elaborated with ligands. This technique is characterized by the use of well-defined chemical reactions to control the regions and densities of ligand immobilization and will be important for a range of applications that require patterned ligands for biospecific interactions.

Patterning multiple aligned self-assembled monolayers using light.

This work describes a method for patterning a gold substrate with multiple, aligned self-assembled monolayers (SAMs) using light at different wavelengths. It describes the synthesis and characterization of an alkanethiolate SAM that is photosensitive to light at both 220 and 365 nm. A photomask acts as an area-selective filter for light at 220 and 365 nm, and a single set of exposures at these two wavelengths through one photomask, without steps of alignment between the exposures, can produce three aligned SAMs on one gold substrate. We demonstrate the versatility of this method of photopatterning by modifying individual aligned SAMs chemically to produce surfaces having different properties. We characterize the modified SAMs using immunolabeling, matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy, and surface plasmon resonance spectroscopy. We also describe the patterning of two aligned SAMs that resist the adsorption of proteins and a third region that does not resist the adsorption of proteins. The ability to produce multiple, aligned patterns of SAMs in a single step, without alignment of photomasks in separate steps, increases the versatility of SAMs for studying a range of physical phenomena.