Selective biomolecular nanoarrays for parallel single-molecule investigations

The ability to direct the self-assembly of biomolecules on surfaces with true nanoscale control is key for the creation of functional substrates. Herein we report the fabrication of nanoscale biomolecular arrays via selective self-assembly on nanopatterned surfaces and minimized nonspecific adsorption. We demonstrate that the platform developed allows for the simultaneous screening of specific protein-DNA binding events at the single-molecule level. The strategy presented here is generally applicable and enables high-throughput monitoring of biological activity in real time and with single-molecule resolution.

Multiscale fabrication of multiple proteins and topographical structures by combining capillary force lithography and microscope projection photolithography

We present new methods that enable the fabrication of multiscale, multicomponent protein-patterned surfaces and multiscale topologically structured surfaces by exploiting the merits of two well-established techniques: capillary force lithography (CFL) and microscope projection photolithography (MPP) based on a protein-friendly photoresist. We further demonstrate that, when hierarchically organized micro- and nanostructures were used as a cell culture platform, human colon cancer cells (cell line SW480) preferentially adhere and migrate onto the area with nanoscale topography over the one with microscale topography. These methods will provide many exciting opportunities for the study of cellular responses to multiscale physicochemical cues.

Illuminating intracellular signaling and molecules for single cell analysis

Fluorescent and bioluminescent proteins are now widely used for detection of small molecules and various intracellular events ranging from protein conformational change to cell death in living cells. To analyze the dynamics of molecular processes in real time at the level of single cells, engineered protein-based probes with higher sensitivity and selectivity are required. The probes can be entirely genetically encoded and can comprise fusions of different proteins or domains. This review specifically examines basic concepts of designing genetically encoded fluorescent and bioluminescent probes developed in the past decade, highlighting some potential applications for basic research and for drug discovery.

Models at the single cell level

Many cellular behaviors cannot be completely captured or appropriately described at the cell population level. Noise induced by stochastic chemical reactions, spatially polarized signaling networks, and heterogeneous cell-cell communication are among the many phenomena that require fine-grained analysis. Accordingly, the mathematical models used to describe such systems must be capable of single cell or subcellular resolution. Here, we review techniques for modeling single cells, including models of stochastic chemical kinetics, spatially heterogeneous intracellular signaling, and spatial stochastic systems. We also briefly discuss applications of each type of model.

Controlled confinement of DNA at the nanoscale: nanofabrication and surface bio-functionalization

Nanopatterned arrays of biomolecules are a powerful tool to address fundamental issues in many areas of biology. DNA nanoarrays, in particular, are of interest in the study of DNA-protein interactions and for biodiagnostic investigations. In this context, achieving a highly specific nanoscale assembly of oligonucleotides at surfaces is critical. In this chapter, we describe a method to control the immobilization of DNA on nanopatterned surfaces; the nanofabrication and the bio-functionalization involved in the process will be discussed.

Nanoscale surfacing for regenerative medicine

Cells in most tissues reside in microenvironment surrounded with specific three-dimensional features. The extracellular matrix or substratum with which cells interact often includes topography at the nanoscale. For example, the basement membrane of many tissues displays features of pores, fibers and ridges in the nanometer range. The nanoscale topography has significant effects on cellular behavior. Knowledge of the cell-substratum interactions is crucial to the understanding of many fundamental biological questions and to regenerative medicine. Rapid advances in nanotechnology enable cellular study on engineered nanoscale surfaces. Recent findings underscore the phenomenon that mammalian cells do respond to nanosized features on a synthetic surface. This review covers the commonly used techniques of engineering nanoscale surface and the techniques which have not been adapted but are of great potential in regenerative medicine, surveys the applications of nanoscale surface in regenerative medicine including vascular, bone, neural and stem cell tissue engineering, and discusses the possible mechanisms of cellular responses to nanoscale surface. A better understanding of the interactions between cells and nanoscale surfacing will help advance the field of regenerative medicine.

Biomimetic nanopatterns as enabling tools for analysis and control of live cells

It is becoming increasingly evident that cell biology research can be considerably advanced through the use of bioengineered tools enabled by nanoscale technologies. Recent advances in nanopatterning techniques pave the way for engineering biomaterial surfaces that control cellular interactions from the nano- to the microscale, allowing more precise quantitative experimentation capturing multi-scale aspects of complex tissue physiology in vitro. The spatially and temporally controlled display of extracellular signaling cues on nanopatterned surfaces (e. g., cues in the form of chemical ligands, controlled stiffness, texture, etc.) that can now be achieved on biologically relevant length scales is particularly attractive enabling experimental platform for investigating fundamental mechanisms of adhesion-mediated cell signaling. Here, we present an overview of bio-nanopatterning methods, with the particular focus on the recent advances on the use of nanofabrication techniques as enabling tools for studying the effects of cell adhesion and signaling on cell function. We also highlight the impact of nanoscale engineering in controlling cell-material interfaces, which can have profound implications for future development of tissue engineering and regenerative medicine.

Controlling cell behavior through the design of polymer surfaces

Polymers have gained a remarkable place in the biomedical field as materials for the fabrication of various devices and for tissue engineering applications. The initial acceptance or rejection of an implantable device is dictated by the crosstalk of the material surface with the bioentities present in the physiological environment. Advances in microfabrication and nanotechnology offer new tools to investigate the complex signaling cascade induced by the components of the extracellular matrix and consequently allow cellular responses to be tailored through the mimicking of some elements of the signaling paths. Patterning methods and selective chemical modification schemes at different length scales can provide biocompatible surfaces that control cellular interactions on the micrometer and sub-micrometer scales on which cells are organized. In this review, the potential of chemically and topographically structured micro- and nanopolymer surfaces are discussed in hopes of a better understanding of cell-biomaterial interactions, including the recent use of biomimetic approaches or stimuli-responsive macromolecules. Additionally, the focus will be on how the knowledge obtained using these surfaces can be incorporated to design biocompatible materials for various biomedical applications, such as tissue engineering, implants, cell-based biosensors, diagnostic systems, and basic cell biology. The review focusses on the research carried out during the last decade.

Engineering extracellular matrix through nanotechnology

The goal of tissue engineering is the creation of a living device that can restore, maintain or improve tissue function. Behind this goal is a new idea that has emerged from twentieth century medicine, science and engineering. It is preceded by centuries of human repair and replacement with non-living materials adapted to restore function and cosmetic appearance to patients whose tissues have been destroyed by disease, trauma or congenital abnormality. The nineteenth century advanced replacement and repair strategies based on moving living structures from a site of normal tissue into a site of defects created by the same processes. Donor skin into burn wounds, tendon transfers, intestinal replacements into the urinary tract, toes to replace fingers are all examples. The most radical application is that of vital organ transplantation in which a vital part such as heart, lung or liver is removed from one donor, preserved for transfer and implanted into a patient dying of end-stage organ failure. Tissue engineering and regenerative medicine have advanced a general strategy combining the cellular elements of living tissue with sophisticated biomaterials to produce living structures of sufficient size and function to improve patients' lives. Multiple strategies have evolved and the application of nanotechnology can only improve the field. In our era, by necessity, any medical advance must be successfully commercialized to allow widespread application to help the greatest number of patients. It follows that business models and regulatory agencies must adapt and change to enable these new technologies to emerge. This brief review will discuss the science of nanotechnology and how it has been applied to this evolving field. We will then briefly summarize the history of commercialization of tissue engineering and suggest that nanotechnology may be of use in breeching the barriers to commercialization although its primary mission is to improve the technology by solving some remaining and vexing problems in its science and engineering aspects.

Transwells with microstamped membranes produce micropatterned two-dimensional and three-dimensional co-cultures

This article describes a simple and rapid cell patterning method to form co-culture microarrays in commercially available Transwells. A thin poly(dimethylsiloxane) (PDMS) layer is printed on the underside of a Transwell using a PDMS stamp. Arbitrary cellular patterns are generated according to the geometric features of the thin PDMS layer through hydrodynamic forces that guide cells onto the membrane only over the PDMS-uncoated regions. Micropatterns of surface-adhered cells (we refer to this as two-dimensional) or non-surface-adhered clusters of cells (we refer to this as three-dimensional) can be generated depending on the surface treatment of the filter membrane. Additionally, co-cultures can be established by introducing different types of cells on the membrane or in the bottom chamber of the Transwell. We show that this co-culture method can evaluate mouse embryonic stem (mES) cell differentiation based on heterogeneous cell-cell interactions. Co-culture of mES cells and HepG2 cells decreased SOX17 expression of mES cells, and direct cell-cell contact further decreased SOX17 expression, indicating that co-culture with HepG2 cells inhibits endoderm differentiation through soluble factors and cell-cell contact. This method is simple and user-friendly and should be broadly useful to study cell shapes and cell-cell interactions.

Addressable micropatterning of multiple proteins and cells by microscope projection photolithography based on a protein friendly photoresist

We report a new method for the micropatterning of multiple proteins and cells with micrometer-scale precision. Microscope projection photolithography based on a new protein-friendly photoresist, poly(2,2-dimethoxy nitrobenzyl methacrylate-r-methyl methacrylate-r-poly(ethylene glycol) methacrylate) (PDMP), was used for the fabrication of multicomponent protein/cell arrays. Microscope projection lithography allows precise registration between multiple patterns as well as facile fabrication of microscale features. Thin films of PDMP became soluble in near-neutral physiological buffer solutions upon UV exposure and exhibited excellent resistance to protein adsorption and cell adhesion. By harnessing advantages in microscope projection photolithography and properties of PDMP thin films, we could successfully fabricate protein arrays composed of multiple proteins. Furthermore, we could extend this method for the patterning of two different types of immune cells for the potential study of immune cell interactions. This technique will in general be useful for protein chip fabrication and high-throughput cell-cell communication study.

Spatial organization and signal transduction at intercellular junctions

The coordinated organization of cell membrane receptors into diverse micrometre-scale spatial patterns is emerging as an important theme of intercellular signalling, as exemplified by immunological synapses. Key characteristics of these patterns are that they transcend direct protein-protein interactions, emerge transiently and modulate signal transduction. Such cooperativity over multiple length scales presents new and intriguing challenges for the study and ultimate understanding of cellular signalling. As a result, new experimental strategies have emerged to manipulate the spatial organization of molecules inside living cells. The resulting spatial mutations yield insights into the interweaving of the spatial, mechanical and chemical aspects of intercellular signalling.

Nanoscale resolution, multicomponent biomolecular arrays generated by aligned printing with parylene peel-off

We present "Print-and-Peel", a high-throughput method to generate multicomponent biomolecular arrays with sub-100 nm nanoscale feature width. An inkjet printer is first aligned to a parylene template containing nanoscale openings. After printing, the parylene is peeled off to reveal uniformly patterned nanoscale features, despite the imperfect morphologies of the original inkjet spots. We further patterned combinatorial nanoarrays by performing a second print-run superimposed over the first, thereby extending the multiplexing capability of the technique.

Early T-cell activation biophysics

The T-cell is one of the main players in the mammalian immune response. It ensures antigen recognition at the surface of antigen-presenting cells in a complex and highly sensitive and specific process, in which the encounter of the T-cell receptor with the agonist peptide associated with the major histocompatibility complex triggers T-cell activation. While signaling pathways have been elucidated in increasing detail, the mechanism of TCR triggering remains highly controversial despite active research published in the past 10 years. In this paper, we present a short overview of pending questions on critical initial events associated with T-cell triggering. In particular, we examine biophysical approaches already in use, as well as future directions. We suggest that the most recent advances in fluorescence super-resolution imaging, coupled with the new classes of genetic fluorescent probes, will play an important role in elucidation of the T-cell triggering mechanism. Beyond this aspect, we predict that exploration of mechanical cues in the triggering process will provide new clues leading to clarification of the entire mechanism.

Roles for SH2 and SH3 domains in Lyn kinase association with activated FcepsilonRI in RBL mast cells revealed by patterned surface analysis

In mast cells, antigen-mediated cross-linking of IgE bound to its high-affinity surface receptor, FcepsilonRI, initiates a signaling cascade that culminates in degranulation and release of allergic mediators. Antigen-patterned surfaces, in which the antigen is deposited in micron-sized features on a silicon substrate, were used to examine the spatial relationship between clustered IgE-FcepsilonRI complexes and Lyn, the signal-initiating tyrosine kinase. RBL mast cells expressing wild-type Lyn-EGFP showed co-redistribution of this protein with clustered IgE receptors on antigen-patterned surfaces, whereas Lyn-EGFP containing an inhibitory point mutation in its SH2 domain did not significantly accumulate with the patterned antigen, and Lyn-EGFP with an inhibitory point mutation in its SH3 domain exhibited reduced interactions. Our results using antigen-patterned surfaces and quantitative cross-correlation image analysis reveal that both the SH2 and SH3 domains contribute to interactions between Lyn kinase and cross-linked IgE receptors in stimulated mast cells.

Focal adhesion proteins connect IgE receptors to the cytoskeleton as revealed by micropatterned ligand arrays

Patterned surfaces that present specific ligands in spatially defined arrays are used to examine structural linkages between clustered IgE receptors (IgE-Fc epsilonRI) and the cytoskeleton in rat basophilic leukemia (RBL) mast cells. We showed with fluorescence microscopy that cytoskeletal F-actin concentrates in the same regions as cell surface IgE-Fc epsilonRI that bind to the micrometer-size patterned ligands. However, the proteins mediating these cytoskeletal connections and their functional relevance were not known. We now show that whereas the adaptor proteins ezrin and moesin do not detectably concentrate with the array of clustered IgE-Fc epsilonRI, focal adhesion proteins vinculin, paxillin, and talin, which are known to link F-actin with integrins, accumulate in these regions on the same time scale as F-actin. Moreover, colocalization of these focal adhesion proteins with clustered IgE-Fc epsilonRI is enhanced after addition of fibronectin-RGD peptides. Significantly, the most prominent rat basophilic leukemia cell integrin (alpha5) avoids the patterned regions occupied by the ligands and associates preferentially with exposed regions of the silicon substrate. Thus, spatial separation provided by the patterned surface reveals that particular focal adhesion proteins, which connect to the actin cytoskeleton, associate with ligand-cross-linked IgE-Fc epsilonRI, independently of integrins. We investigated the functional role of one of these proteins, paxillin, in IgE-Fc epsilonRI-mediated signaling by using small interfering RNA. From these results, we determine that paxillin reduces stimulated phosphorylation of the Fc epsilonRI beta subunit but enhances stimulated Ca(2+) release from intracellular stores. The results suggest that paxillin associated with clustered IgE-Fc epsilonRI has a net positive effect on Fc epsilonRI signaling.