Allergen arrays for antibody screening and immune cell activation profiling generated by parallel lipid dip-pen nanolithography

Rapid Capture of Cancer Extracellular Vesicles by Lipid Patch Microarrays

Extracellular vesicles (EVs) contain various bioactive molecules such as DNA, RNA, and proteins, and play a key role in the regulation of cancer progression. Furthermore, cancer-associated EVs carry specific biomarkers and can be used in liquid biopsy for cancer detection. However, it is still technically challenging and time consuming to detect or isolate cancer-associated EVs from complex biofluids (e.g., blood). Here, a novel EV-capture strategy based on dip-pen nanolithography generated microarrays of supported lipid membranes is presented. These arrays carry specific antibodies recognizing EV- and cancer-specific surface biomarkers, enabling highly selective and efficient capture. Importantly, it is shown that the nucleic acid cargo of captured EVs is retained on the lipid array, providing the potential for downstream analysis. Finally, the feasibility of EV capture from patient sera is demonstrated. The demonstrated platform offers rapid capture, high specificity, and sensitivity, with only a small need in analyte volume and without additional purification steps. The platform is applied in context of cancer-associated EVs, but it can easily be adapted to other diagnostic EV targets by use of corresponding antibodies.

Dip-Pen Nanolithography(DPN): from Micro/Nano-patterns to Biosensing

Dip-pen nanolithography is an emerging and attractive surface modification technique that has the capacity to directly and controllably write micro/nano-array patterns on diverse substrates. The superior throughput, resolution, and registration enable DPN an outstanding candidate for biological detection from the molecular level to the cellular level. Herein, we overview the technological evolution of DPN in terms of its advanced derivatives and DPN-enabled versatile sensing patterns featuring multiple compositions and structures for biosensing. Benefitting from uniform, reproducible, and large-area array patterns, DPN-based biosensors have shown high sensitivity, excellent selectivity, and fast response in target analyte detection and specific cellular recognition. We anticipate that DPN-based technologies could offer great potential opportunities to fabricate multiplexed, programmable, and commercial array-based sensing biochips.

Antibody Printing Technologies

Antibody microarrays are routinely employed in the lab and in the clinic for studying protein expression, protein-protein, and protein-drug interactions. The microarray format reduces the size scale at which biological and biochemical interactions occur, leading to large reductions in reagent consumption and handling times while increasing overall experimental throughput. Specifically, antibody microarrays, as a platform, offer a number of different advantages over traditional techniques in the areas of drug discovery and diagnostics. While a number of different techniques and approaches have been developed for creating micro and nanoscale antibody arrays, issues relating to sensitivity, cost, and reproducibility persist. The aim of this review is to highlight current state-of the-art techniques and approaches for creating antibody arrays by providing latest accounts of the field while discussing potential future directions.

Enhanced Stability of Lipid Structures by Dip-Pen Nanolithography on Block-Type MPC Copolymer

Biomimetic lipid membranes on solid supports have been used in a plethora of applications, including as biosensors, in research on membrane proteins or as interfaces in cell experiments. For many of these applications, structured lipid membranes, e.g., in the form of arrays with features of different functionality, are highly desired. The stability of these features on a given substrate during storage and in incubation steps is key, while at the same time the substrate ideally should also exhibit antifouling properties. Here, we describe the highly beneficial properties of a 2-methacryloyloxyethyl phosphorylcholine (MPC) copolymer for the stability of supported lipid membrane structures generated by dip-pen nanolithography with phospholipids (L-DPN). The MPC copolymer substrates allow for more stable and higher membrane stack structures in comparison to other hydrophilic substrates, like glass or silicon oxide surfaces. The structures remain highly stable under immersion in liquid and subsequent incubation and washing steps. This allows multiplexed functionalization of lipid arrays with antibodies via microchannel cantilever spotting (µCS), without the need of orthogonal binding tags for each antibody type. The combined properties of the MPC copolymer substrate demonstrate a great potential for lipid-based biomedical sensing and diagnostic platforms.

Writing Behavior of Phospholipids in Polymer Pen Lithography (PPL) for Bioactive Micropatterns

Lipid-based membranes play crucial roles in regulating the interface between cells and their external environment, the communication within cells, and cellular sensing. To study these important processes, various lipid-based artificial membrane models have been developed in recent years and, indeed, large-area arrays of supported lipid bilayers suit the needs of many of these studies remarkably well. Here, the direct-write scanning probe lithography technique called polymer pen lithography (PPL) was used as a tool for the creation of lipid micropatterns over large areas via polymer-stamp-mediated transfer of lipid-containing inks onto glass substrates. In order to better understand and control the lipid transfer in PPL, we conducted a systematic study of the influence of dwell time (i.e., duration of contact between tip and sample), humidity, and printing pressure on the outcome of PPL with phospholipids and discuss results in comparison to the more often studied dip-pen nanolithography with phospholipids. This is the first systematic study in phospholipid printing with PPL. Biocompatibility of the obtained substrates with up to two different ink compositions was demonstrated. The patterns are suitable to serve as a platform for mast cell activation experiments.

Liposomes and lipid bilayers in biosensors

Biosensors for the rapid, specific, and sensitive detection of analytes play a vital role in healthcare, drug discovery, food safety, and environmental monitoring. Although a number of sensing concepts and devices have been developed, many longstanding challenges to obtain inexpensive, easy-to-use, and reliable sensor platforms remain largely unmet. Nanomaterials offer exciting possibilities for enhancing the assay sensitivity and for lowering the detection limits down to single-molecule resolution. In this review, we present an overview of liposomes and lipid bilayers in biosensing applications. Lipid assemblies in the form of spherical liposomes or two-dimensional planar membranes have been widely used in the design of biosensing assays; in particular, we highlight a number of recent promising developments of biosensors based on liposomes in suspension, liposome arrays, and lipid bilayers arrays. Assay sensitivity and specificity are discussed, advantages and drawbacks are reviewed, and possible further developments are outlined.

Polymer Pen Lithography with Lipids for Large-Area Gradient Patterns

Gradient patterns comprising bioactive compounds over comparably (in regard to a cell size) large areas are key for many applications in the biomedical sector, in particular, for cell screening assays, guidance, and migration experiments. Polymer pen lithography (PPL) as an inherent highly parallel and large area technique has a great potential to serve in the fabrication of such patterns. We present strategies for the printing of functional phospholipid patterns via PPL that provide tunable feature size and feature density gradients over surface areas of several square millimeters. By controlling the printing parameters, two transfer modes can be achieved. Each of these modes leads to different feature morphologies. By increasing the force applied to the elastomeric pens, which increases the tip-surface contact area and boosts the ink delivery rate, a switch between a dip-pen nanolithography (DPN) and a microcontact printing (μCP) transfer mode can be induced. A careful inking procedure ensuring a homogeneous and not-too-high ink-load on the PPL stamp ensures a membrane-spreading dominated transfer mode, which, used in combination with smooth and hydrophilic substrates, generates features with constant height, independently of the applied force of the pens. Ultimately, this allows us to obtain a gradient of feature sizes over a mm² substrate, all having the same height on the order of that of a biological cellular membrane. These strategies allow the construction of membrane structures by direct transfer of the lipid mixture to the substrate, without requiring previous substrate functionalization, in contrast to other molecular inks, where structure is directly determined by the printing process itself. The patterns are demonstrated to be viable for subsequent protein binding, therefore adding to a flexible feature library when gradients of protein presentation are desired.

Biomimetic Phospholipid Membrane Organization on Graphene and Graphene Oxide Surfaces: A Molecular Dynamics Simulation Study

Supported phospholipid membrane patches stabilized on graphene surfaces have shown potential in sensor device functionalization, including biosensors and biocatalysis. Lipid dip-pen nanolithography (L-DPN) is a method useful in generating supported membrane structures that maintain lipid functionality, such as exhibiting specific interactions with protein molecules. Here, we have integrated L-DPN, atomic force microscopy, and coarse-grained molecular dynamics simulation methods to characterize the molecular properties of supported lipid membranes (SLMs) on graphene and graphene oxide supports. We observed substantial differences in the topologies of the stabilized lipid structures depending on the nature of the surface (polar graphene oxide vs nonpolar graphene). Furthermore, the addition of water to SLM systems resulted in large-scale reorganization of the lipid structures, with measurable effects on lipid lateral mobility within the supported membranes. We also observed reduced lipid ordering within the supported structures relative to free-standing lipid bilayers, attributed to the strong hydrophobic interactions between the lipids and support. Together, our results provide insight into the molecular effects of graphene and graphene oxide surfaces on lipid bilayer membranes. This will be important in the design of these surfaces for applications such as biosensor devices.

Phospholipid arrays on porous polymer coatings generated by micro-contact spotting

Nanoporous poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate) (HEMA-EDMA) is used as a 3D mesh for spotting lipid arrays. Its porous structure is an ideal matrix for lipid ink to infiltrate, resulting in higher fluorescent signal intensity as compared to similar arrays on strictly 2D substrates like glass. The embedded lipid arrays show high stability against washing steps, while still being accessible for protein and antibody binding. To characterize binding to polymer-embedded lipids we have applied Streptavidin as well as biologically important biotinylated androgen receptor binding onto 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(cap biotinyl) (Biotinyl Cap PE) and anti-DNP IgE recognition of 2,4-dinitrophenyl[1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[6-[(2,4-dinitrophenyl)amino]hexanoyl] (DNP)] antigen. This approach adds lipid arrays to the range of HEMA polymer applications and makes this solid substrate a very attractive platform for a variety of bio-applications.

Analytical approaches to study domain formation in biomimetic membranes

Novel characterization methods open new horizons in the study of membrane mixtures.

Click-Chemistry Based Allergen Arrays Generated by Polymer Pen Lithography for Mast Cell Activation Studies

The profiling of allergic responses is a powerful tool in biomedical research and in judging therapeutic outcome in patients suffering from allergy. Novel insights into the signaling cascades and easier readouts can be achieved by shifting activation studies of bulk immune cells to the single cell level on patterned surfaces. The functionality of dinitrophenol (DNP) as a hapten in the induction of allergic reactions has allowed the activation process of single mast cells seeded on patterned surfaces to be studied following treatment with allergen specific Immunoglobulin E antibodies. Here, a click-chemistry approach is applied in combination with polymer pen lithography (PPL) to pattern DNP-azide on alkyne-terminated surfaces to generate arrays of allergen. The large area functionalization offered by PPL allows an easy incorporation of such arrays into microfluidic chips. In such a setup, easy handling of cell suspension, incubation process, and read-out by fluorescence microscopy will allow immune cell activation screening to be easily adapted for diagnostics and biomedical research.

Self-limiting multiplexed assembly of lipid membranes on large-area graphene sensor arrays

Phospholipid membranes of different functionalities were simultaneously assembled on arrays of graphene surfaces in a parallel manner using multi-pen lipid dip-pen nano-lithography. The graphene patch facilitates and restricts the spreading of lipids within itself, obviating the need to scan the writing probes and reducing writing time. Binding studies establish that the lipids retain the functionality.

Selective Binding of DNA Origami on Biomimetic Lipid Patches

Arrays of biomimetic lipid patches for studying the binding of DNA origami structures can be tailored in size, shape, and composition with the aid of lipid-dip pen nanolithography. This approach allows for analysis of the effects of lipid composition with high throughput which could be applied for the targeted presentation of functional DNA origami structures on surfaces.

Ultra-large scale AFM of lipid droplet arrays: investigating the ink transfer volume in dip pen nanolithography

There are only few quantitative studies commenting on the writing process in dip-pen nanolithography with lipids. Lipids are important carrier ink molecules for the delivery of bio-functional patters in bio-nanotechnology. In order to better understand and control the writing process, more information on the transfer of lipid material from the tip to the substrate is needed. The dependence of the transferred ink volume on the dwell time of the tip on the substrate was investigated by topography measurements with an atomic force microscope (AFM) that is characterized by an ultra-large scan range of 800 × 800 μm(2). For this purpose arrays of dots of the phospholipid1,2-dioleoyl-sn-glycero-3-phosphocholine were written onto planar glass substrates and the resulting pattern was imaged by large scan area AFM. Two writing regimes were identified, characterized of either a steady decline or a constant ink volume transfer per dot feature. For the steady state ink transfer, a linear relationship between the dwell time and the dot volume was determined, which is characterized by a flow rate of about 16 femtoliters per second. A dependence of the ink transport from the length of pauses before and in between writing the structures was observed and should be taken into account during pattern design when aiming at best writing homogeneity. The ultra-large scan range of the utilized AFM allowed for a simultaneous study of the entire preparation area of almost 1 mm(2), yielding good statistic results.

A critical comparison of protein microarray fabrication technologies

Of the diverse analytical tools used in proteomics, protein microarrays possess the greatest potential for providing fundamental information on protein, ligand, analyte, receptor, and antibody affinity-based interactions, binding partners and high-throughput analysis. Microarrays have been used to develop tools for drug screening, disease diagnosis, biochemical pathway mapping, protein-protein interaction analysis, vaccine development, enzyme-substrate profiling, and immuno-profiling. While the promise of the technology is intriguing, it is yet to be realized. Many challenges remain to be addressed to allow these methods to meet technical and research expectations, provide reliable assay answers, and to reliably diversify their capabilities. Critical issues include: (1) inconsistent printed microspot morphologies and uniformities, (2) low signal-to-noise ratios due to factors such as complex surface capture protocols, contamination, and static or no-flow mass transport conditions, (3) inconsistent quantification of captured signal due to spot uniformity issues, (4) non-optimal protocol conditions such as pH, temperature, drying that promote variability in assay kinetics, and lastly (5) poor protein (e.g., antibody) printing, storage, or shelf-life compatibility with common microarray assay fabrication methods, directly related to microarray protocols. Conventional printing approaches, including contact (e.g., quill and solid pin), non-contact (e.g., piezo and inkjet), microfluidics-based, microstamping, lithography, and cell-free protein expression microarrays, have all been used with varying degrees of success with figures of merit often defined arbitrarily without comparisons to standards, or analytical or fiduciary controls. Many microarray performance reports use bench top analyte preparations lacking real-world relevance, akin to "fishing in a barrel", for proof of concept and determinations of figures of merit. This review critiques current protein-based microarray preparation techniques commonly used for analytical and function-based proteomics and their effects on array-based assay performance.

Patterning of Quantum Dots by Dip-Pen and Polymer Pen Nanolithography

We present a direct way of patterning CdSe/ ZnS quantum dots by dip-pen nanolithography and polymer pen lithography. Mixtures of cholesterol and phospholipid 1,2-dioleoyl-sn-glycero-3 phosphocholine serve as biocompatible carrier inks to facilitate the transfer of quantum dots from the tips to the surface during lithography. While dip-pen nanolithography of quantum dots can be used to achieve higher resolution and smaller pattern features (approximately 1 μm), polymer pen lithography is able to address intermediate pattern scales in the low micrometre range. This allows us to combine the advantages of micro contact printing in large area and massive parallel patterning, with the added flexibility in pattern design inherent in the DPN technique.

Effects of Glucocorticoids in the Immune System

Glucocorticoids (GCs) are steroid hormones with widespread effects. They control intermediate metabolism by stimulating gluconeogenesis in the liver, mobilize amino acids from extra hepatic tissues, inhibit glucose uptake in muscle and adipose tissue, and stimulate fat breakdown in adipose tissue. They also mediate stress response. They exert potent immune-suppressive and anti-inflammatory effects particularly when administered pharmacologically. Understanding these diverse effects of glucocorticoids requires a detailed knowledge of their mode of action. Research over the years has uncovered several details on the molecular action of this hormone, especially in immune cells. In this chapter, we have summarized the latest findings on the action of glucocorticoids in immune cells with a view of identifying important control points that may be relevant in glucocorticoid therapy.

Large-scale parallel surface functionalization of goblet-type whispering gallery mode microcavity arrays for biosensing applications

A novel surface functionalization technique is presented for large-scale selective molecule deposition onto whispering gallery mode microgoblet cavities. The parallel technique allows damage-free individual functionalization of the cavities, arranged on-chip in densely packaged arrays. As the stamp pad a glass slide is utilized, bearing phospholipids with different functional head groups. Coated microcavities are characterized and demonstrated as biosensors.

Localization and dynamics of glucocorticoid receptor at the plasma membrane of activated mast cells

In addition to their actions in the cell nucleus, glucocorticoids exhibit rapid non-nuclear responses that are mechanistically not well understood. To explain these effects, the localization of a glucocorticoid receptor (GR) expressed in mast cells as a GFP fusion was analyzed after activation of the cells on allergenic lipid arrays. These arrays were produced on glass slides by dip-pen nanolithography (DPN) and total internal reflection (TIRF) microscopy was used to visualize the GR. A rapid glucocorticoid-independent and -dependent recruitment of the GR-GFP to the plasma cell membrane was observed following contact of the cells with the allergenic array. In addition, the mobility of the GR at the membrane was monitored by fluorescence recovery after photobleaching (FRAP) and shown to follow binding kinetics demonstrating interactions of the receptor with membrane-bound factors. Furthermore the recruitment of the GR to the cell membrane was shown to result in a glucocorticoid-mediated increase in Erk phosphorylation. This is evidenced by findings that destruction of the membrane composition of the mast cells by cholesterol depletion impairs the membrane localization of the GR and subsequent glucocorticoid-mediated enhancement of Erk phosphorylation. These results demonstrate a membrane localization and function of the GR in mast cell signaling.

Multiplexed biomimetic lipid membranes on graphene by dip-pen nanolithography

The application of graphene in sensor devices depends on the ability to appropriately functionalize the pristine graphene. Here we show the direct writing of tailored phospholipid membranes on graphene using dip-pen nanolithography. Phospholipids exhibit higher mobility on graphene compared with the commonly used silicon dioxide substrate, leading to well-spread uniform membranes. Dip-pen nanolithography allows for multiplexed assembly of phospholipid membranes of different functionalities in close proximity to each other. The membranes are stable in aqueous environments and we observe electronic doping of graphene by charged phospholipids. On the basis of these results, we propose phospholipid membranes as a route for non-covalent immobilization of various functional groups on graphene for applications in biosensing and biocatalysis. As a proof of principle, we demonstrate the specific binding of streptavidin to biotin-functionalized membranes. The combination of atomic force microscopy and binding experiments yields a consistent model for the layer organization within phospholipid stacks on graphene.

The sensitivity and selectivity of graphene-based biosensors depends on attaching various functional groups to graphene. Hirtz et al. use dip-pen nanolithography to directly write phospholipid membranes on graphene, which enables multiplexed and heterogeneous non-covalent functionalization.

Mesopattern of immobilised bone morphogenetic protein-2 created by microcontact printing and dip-pen nanolithography influence C2C12 cell fate

Making meso matter: bone morphogenetic protein-2 (BMP-2) mesopattern created by dip-pen nanolithography and microcontact printing were applied to cell differentiation.

Interdigitated multicolored bioink micropatterns by multiplexed polymer pen lithography

Multiplexing, i.e., the application and integration of more than one ink in an interdigitated microscale pattern, is still a challenge for microcontact printing (μCP) and similar techniques. On the other hand there is a strong demand for interdigitated patterns of more than one protein on subcellular to cellular length scales in the lower micrometer range in biological experiments. Here, a new integrative approach is presented for the fabrication of bioactive microarrays and complex multi-ink patterns by polymer pen lithography (PPL). By taking advantage of the strength of microcontact printing (μCP) combined with the spatial control and capability of precise repetition of PPL in an innovative way, a new inking and writing strategy is introduced for PPL that enables true multiplexing within each repetitive subpattern. Furthermore, a specific ink/substrate platform is demonstrated that can be used to immobilize functional proteins and other bioactive compounds over a biotin-streptavidin approach. This patterning strategy aims specifically at application by cell biologists and biochemists addressing a wide range of relevant pattern sizes, easy pattern generation and adjustment, the use of only biofriendly, nontoxic chemicals, and mild processing conditions during the patterning steps. The retained bioactivity of the fabricated cm(2) area filling multiprotein patterns is demonstrated by showing the interaction of fibroblasts and neurons with multiplexed structures of fibronectin and laminin or laminin and ephrin, respectively.

On-chip microlasers for biomolecular detection via highly localized deposition of a multifunctional phospholipid ink

We report on a novel approach to realize on-chip microlasers, by applying highly localized and material-saving surface functionalization of passive photonic whispering gallery mode microresonators. We apply dip-pen nanolithography on a true three-dimensional structure. We coat solely the light-guiding circumference of pre-fabricated poly(methyl methacrylate) resonators with a multifunctional molecular ink. The functionalization is performed in one single fabrication step and simultaneously provides optical gain as well as molecular binding selectivity. This allows for a direct and flexible realization of on-chip microlasers, which can be utilized as biosensors in optofluidic lab-on-a-chip applications. In a proof-of-concept we show how this highly localized molecule deposition suffices for low-threshold lasing in air and water, and demonstrate the capability of the ink-lasers as biosensors in a biotin-streptavidin binding experiment.

The role of viscosity on polymer ink transport in dip-pen nanolithography

Understanding how ink transfers to a surface in dip-pen nanolithography (DPN) is crucial for designing new ink materials and developing the processes to pattern them. Herein, we investigate the transport of block copolymer inks with varying viscosities, from an atomic force microscope (AFM) tip to a substrate. The size of the patterned block copolymer features was determined to increase with dwell time and decrease with ink viscosity. A mass transfer model is proposed to describe this behaviour, which is fundamentally different from small molecule transport mechanisms due to entanglement of the polymeric chains. The fundamental understanding developed here provides mechanistic insight into the transport of large polymer molecules, and highlights the importance of ink viscosity in controlling the DPN process. Given the ubiquity of polymeric materials in semiconducting nanofabrication, organic electronics, and bioengineering applications, this study could provide an avenue for DPN to expand its role in these fields.