Strategies for patterning biomolecules with dip-pen nanolithography

Non-Centrosymmetric Single Crystalline Biomolecular Nano-Arrays for Responsive Electronics

Herein, a novel strategy is reported for synthesizing libraries of single crystalline amino acid (AA) nanocrystals with control over size, anisotropy, and polymorphism by leveraging dip-pen nanolithography (DPN) and recrystallization via solvent vapor annealing. The crystals are prepared by first depositing nanoreactors consisting of a solvent with AAs, followed by water vapor-induced recrystallization. This leads to isotropic structures that are non-centrosymmetric with strong piezoelectric (g33 coefficients >1000 mVm N-1), ferroelectric, and non-linear optical properties. However, recrystallizing arrays of isotropic DL-alanine nanodot features with a binary solvent (water and ethanol) leads to arrays of 1D piezoelectric nanorods with their long axis coincident with the polar axis. Moreover, positioning nanoreactors containing AAs (the nanodot features) between micro electrodes leads to capillary formation, making the reactors anisotropic and facilitating piezoelectric nanorod formation between the electrodes. This offers a facile route to device fabrication. These as-fabricated devices respond to ultrasonic stimulation in the form of a piezoelectric response. The technique described herein is significant as it provides a rapid way of investigating non-centrosymmetric nanoscale biocrystals, potentially pivotal for fabricating a new class of stimuli-responsive devices such as sensors, energy harvesters, and stimulators.

Mesenchymal cell migration on one-dimensional micropatterns

Quantitative studies of mesenchymal cell motion are important to elucidate cytoskeleton function and mechanisms of cell migration. To this end, confinement of cell motion to one dimension (1D) significantly simplifies the problem of cell shape in experimental and theoretical investigations. Here we review 1D migration assays employing micro-fabricated lanes and reflect on the advantages of such platforms. Data are analyzed using biophysical models of cell migration that reproduce the rich scenario of morphodynamic behavior found in 1D. We describe basic model assumptions and model behavior. It appears that mechanical models explain the occurrence of universal relations conserved across different cell lines such as the adhesion-velocity relation and the universal correlation between speed and persistence (UCSP). We highlight the unique opportunity of reproducible and standardized 1D assays to validate theory based on statistical measures from large data of trajectories and discuss the potential of experimental settings embedding controlled perturbations to probe response in migratory behavior.

Development of Meta-Chemical Surface by Dip-Pen Nanolithography for Precise Electrochemical Lead Sensing

Dip-pen nanolithography (DPN) is a powerful and unique technique for precisely depositing tiny nano-spherical cap shapes (nanoclusters) onto a desired surface. In this study, a meta-chemical surface (MCS; a pattern with advanced features) is developed by DPN and applied to electrochemical lead sensing, yielding a calibration curve in the ppb range. An ink mixture of PMMA and NTPH (which binds to Pb (II), as supported by DFT calculations) is patterned over a Pt surface. The average height of the nanoclusters is ≈13 nm with a high surface area-to-volume ratio, which depends on the ink composition and the MCS surface. This ratio affected the sensitivity of the MCS as a detecting tool. The results indicate that the sensor's features can be controlled by the ability to control the size of the nanoclusters, attributed to the unique properties of the DPN production method. These results are significant for the water-source purification industry.

Microarray fabrication techniques for multiplexed bioassay applications

Microarrays are powerful tools for high-throughput bioassays that can extract information from tens of thousands of micro-spots consisting of biomolecules. This information is invaluable to many applications, such as drug discovery and disease diagnostics. Different applications of these microarrays need spots of different shapes, sizes, and chemistries to achieve their goals. Micro/nano-fabrication techniques are used to make microarrays with different feature structures and array densities for required assay procedures. Understanding these fabrication methods is essential to creating an effective microarray. The purpose of this article is to critically review fabrication methods used in recent microarray-based bioassay studies. We summarized commonly used microarray fabrication techniques and filled the gap in recent literature on relevant topics. We discussed recent examples of how microarrays were fabricated and used in a variety of bioassays. Specifically, we examined microarray printing, various microlithography techniques, and microfluidics-based microarray fabrication. We evaluated how their application shaped the fabrication methods and compared their performance based on different applications. In the end, we discussed current challenges and outlined potential future directions. This review addressed the gap in literature and provided important insights for choosing appropriate fabrication techniques towards different applications.

Strategy based on multiplexed brush architectures for regulating the spatiotemporal immobilization of biomolecules

Functional surfaces that enable both spatial and temporal control of biomolecules immobilization have attracted enormous attention for various fields including smart biointerface materials, high-throughput bioarrays, and fundamental research in the biosciences. Here, a flexible and promising method was presented for regulating the spatiotemporal arrangement of multiple biomolecules by constructing the topographically and chemically diverse polymer brushes patterned surfaces. A series of polymer brushes patterned surfaces, including antifouling brushes patterned surface, epoxy-presenting brushes patterned surface without and with antifouling background layer, were fabricated to control the spatial distribution of protein and cell adhesion through specific and nonspecific means. The fluorescence measurements demonstrated the effectiveness of spatially regulating the density of surface-immobilized protein through controlling the areal thickness of the poly (glycidyl methacrylate) (PGMA) brush patterns, leading to various complex patterns featuring well-defined biomolecule concentration gradients. Furthermore, a multiplexed surface bearing epoxy groups and azido groups with various areal densities was fabricated for regulating the spatiotemporal arrangement of different proteins, enabling binary biomolecules patterns with higher degrees of functionality and complexity. The presented strategy for the spatiotemporal control of biomolecules immobilization would boost the development of dynamic and multifunctional biosystems.

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.

Multifunctional Structured Platforms: From Patterning of Polymer-Based Films to Their Subsequent Filling with Various Nanomaterials

There is an astonishing number of optoelectronic, photonic, biological, sensing, or storage media devices, just to name a few, that rely on a variety of extraordinary periodic surface relief miniaturized patterns fabricated on polymer-covered rigid or flexible substrates. Even more extraordinary is that these surface relief patterns can be further filled, in a more or less ordered fashion, with various functional nanomaterials and thus can lead to the realization of more complex structured architectures. These architectures can serve as multifunctional platforms for the design and the development of a multitude of novel, better performing nanotechnological applications. In this work, we aim to provide an extensive overview on how multifunctional structured platforms can be fabricated by outlining not only the main polymer patterning methodologies but also by emphasizing various deposition methods that can guide different structures of functional nanomaterials into periodic surface relief patterns. Our aim is to provide the readers with a toolbox of the most suitable patterning and deposition methodologies that could be easily identified and further combined when the fabrication of novel structured platforms exhibiting interesting properties is targeted.

High-resolution measurement of atomic force microscope cantilever resonance frequency

The atomic force microscope (AFM) is widely used in a wide range of applications due to its high scanning resolution and diverse scanning modes. In many applications, there is a need for accurate and precise measurement of the vibrational resonance frequency of a cantilever. These frequency shifts can be related to changes in mass of the cantilever arising from, e.g., loss of fluid due to a nanolithography operation. A common method of measuring resonance frequency examines the power spectral density of the free random motion of the cantilever, commonly known as a thermal. While the thermal is capable of reasonable measurement resolution and speed, some applications are sensitive to changes in the resonance frequency of the cantilever, which are small, rapid, or both, and the performance of the thermal does not offer sufficient resolution in frequency or in time. In this work, we describe a method based on a narrow-range frequency sweep to measure the resonance frequency of a vibrational mode of an AFM cantilever and demonstrate it by monitoring the evaporation of glycerol from a cantilever. It can be seamlessly integrated into many commercial AFMs without additional hardware modifications and adapts to cantilevers with a wide range of resonance frequencies. Furthermore, this method can rapidly detect small changes in resonance frequency (with our experiments showing a resolution of ∼0.1 Hz for cantilever resonances ranging from 70 kHz to 300 kHz) at a rate far faster than with a thermal. These attributes are particularly beneficial for techniques such as dip-pen nanolithography.

Rupture of Liquid Bridges on Porous Tips: Competing Mechanisms of Spontaneous Imbibition and Stretching

Liquid bridges are commonly encountered in nature and the liquid transfer induced by their rupture is widely used in various industrial applications. In this work, with the focus on the porous tip, we studied the impacts of capillary effects on the liquid transfer induced by the rupture through numerical simulations. To depict the capillary effects of a porous tip, a time scale ratio, R_T, is proposed to compare the competing mechanisms of spontaneous imbibition and external drag. In terms of R_T, we then develop a theoretical model for estimating the liquid retention ratio considering the geometry, porosity, and wettability of tips. The mechanism presented in this work provides a possible approach to control the liquid transfer with better accuracy in microfluidics or microfabrications.

Rupture of a Liquid Bridge between a Cone and a Plane

In this work, a systematic experimental study of the rupture of an axially symmetric liquid bridge between a cone and a plane was performed, with focus on the volume distribution after break up. A model based on the Young-Laplace equation is presented, and its solutions are compared to experimental data. Cones and conical cavities with different aperture angles were used in our experiments. We found that this aperture influences the potential pinning of the contact line, the meniscus shape, and therefore the liquid transfer. For half aperture angles α < 70°, where no pinning was observed, the liquid bridge slips off from the cone and almost no transfer to the cone is observed. However, at α > 70°, contact line pinning on the cone induces a net liquid transfer to the cone at rupture. In the case of conical cavities, a maximum of liquid transfer is observed for at α = 110°. The distance at which the rupture of the liquid bridge occurs is also discussed. The model can fairly predict the transfer ratio and the rupture height of the liquid bridge.

Covalently bound monolayer patterns obtained by plasma etching on glass surfaces

Micropatterns of β-cyclodextrin (β-CD) monolayers on glass are obtained by using a plasma etching approach with polydimethylsiloxane (PDMS) stamps. This simple and versatile approach provides a promising alternative to current techniques for creating patterns of covalently bound molecules. It is also possible to fabricate sub-10 μm sized features.

Development of Dip-Pen Nanolithography (DPN) and Its Derivatives

Dip-pen nanolithography (DPN) is a unique nanofabrication tool that can directly write a variety of molecular patterns on a surface with high resolution and excellent registration. Over the past 20 years, DPN has experienced a tremendous evolution in terms of applicable inks, a remarkable improvement in fabrication throughput, and the development of various derivative technologies. Among these developments, polymer pen lithography (PPL) is the most prominent one that provides a large-scale, high-throughput, low-cost tool for nanofabrication, which significantly extends DPN and beyond. These developments not only expand the scope of the wide field of scanning probe lithography, but also enable DPN and PPL as general approaches for the fabrication or study of nanostructures and nanomaterials. In this review, a focused summary and historical perspective of the technological development of DPN and its derivatives, with a focus on PPL, in one timeline, are provided and future opportunities for technological exploration in this field are proposed.

Polymer Pen Lithography-Fabricated DNA Arrays for Highly Sensitive and Selective Detection of Unamplified Ganoderma Boninense DNA

There is an increasing demand for lithography methods to enable the fabrication of diagnostic devices for the biomedical and agri-food sectors. In this regard, scanning probe lithography methods have emerged as a possible approach for this purpose, as they are not only convenient, robust and accessible, but also enable the deposition of “soft” materials such as complex organic molecules and biomolecules. In this report, the use of polymer pen lithography for the fabrication of DNA oligonucleotide arrays is described, together with the application of the arrays for the sensitive and selective detection of Ganoderma boninense, a fungal pathogen of the oil palm. When used in a sandwich assay format with DNA-conjugated gold nanoparticles, this system is able to generate a visually observable result in the presence of the target DNA. This assay is able to detect as little as 30 ng of Ganoderma-derived DNA without any pre-amplification and without the need for specialist laboratory equipment or training.

Microscale Objects via Restructuring of Large, Double-Stranded DNA Molecules

As the interest in DNA nanotechnology increases, so does the need for larger and more complex DNA structures. In this work, we describe two methods of using large, double-stranded (ds) DNA to self-assemble sequence-specific, nonrepetitive microscale structures. A model system restructures T7 DNA (40 kb) through sequence-specific biotinylation followed by intramolecular binding to a 40 nm diameter neutravidin bead to create T7 "rosettes". This model system informed the creation of "nodal DNA" where "nodes" with single-stranded DNA flaps are attached to a large dsDNA insert so that a complementary oligonucleotide "strap" bridges the two nodes for restructuring to form a DNA "bolo". To do this in high yield, several methodologies were developed, including a protection/deprotection scheme using RNA/RNase H and dialysis chambers, which remove excess straps while retaining large DNA molecules. To assess these restructuring processes, the DNA was adsorbed onto supported lipid bilayers, allowing for a visual assay of their structure using single-molecule fluorescence microscopy. Good agreement between the expected and observed fluorescence intensity measurements of the individual features of restructured DNA for both the DNA rosettes and bolos gives us a high degree of confidence that both processes give sequence-specific restructuring of large, dsDNA molecules to create microscale objects.

Manipulating Femtoliter to Picoliter Droplets by Pins for Single Cell Analysis and Quantitative Biological Assay

Herein, we developed an automated and flexible system for performing miniaturized liquid-liquid reactions and assays in the femtoliter to picoliter range, by combining the contact printing and the droplet-based microfluidics techniques. The system mainly consisted of solid pins and an oil-covered hydrophilic micropillar array chip fixed on an automated x- y- z translation stage. A novel droplet manipulation mode called "dipping-depositing-moving" (DDM) was proposed, which was based on the programmable combination of three basic operations, dipping liquids and depositing liquids with the solid pins and moving the two-dimensional oil-covered hydrophilic pillar microchip. With the DDM mode, flexible generation and manipulation of small droplets with volumes down to 179 fL could be achieved. For overcoming the scale phenomenon specially appeared in picoliter-scale droplets, we used a design of water moat to protect the femtoliter to picoliter droplets from volume loss through the cover oil during the droplet generation, manipulation, reaction and assay processes. Moreover, we also developed a precise quantitative method, quantitative droplet dilution method, to accurately measure the volumes of femtoliter to picoliter droplets. To demonstrate its feasibility and adaptability, we applied the present system in the determination of kinetics parameter for matrix metalloproteinases (MMP-9) in 1.81 pL reactors and the measurement the activity of β-galactosidase in single cells (HepG2 cells) in picoliter droplet array. The ultrasmall volumes of the droplet reactors avoided the excessive dilution to the reaction solutions and enabled the highly sensitive measurement of enzyme activity in the single cell level.

Recent advances in hybrid measurement methods based on atomic force microscopy and surface sensitive measurement techniques

This review summaries the recent progress of the combination of optical and non-optical surface sensitive techniques with the atomic force microscopy.

How cells respond to environmental cues - insights from bio-functionalized substrates

Biomimetic materials have long been the (he)art of bioengineering. They usually aim at mimicking in vivo conditions to allow in vitro culture, differentiation and expansion of cells. The past decade has witnessed a considerable amount of progress in soft lithography, bio-inspired micro-fabrication and biochemistry, allowing the design of sophisticated and physiologically relevant micro- and nano-environments. These systems now provide an exquisite toolbox with which we can control a large set of physicochemical environmental parameters that determine cell behavior. Bio-functionalized surfaces have evolved from simple protein-coated solid surfaces or cellular extracts into nano-textured 3D surfaces with controlled rheological and topographical properties. The mechanobiological molecular processes by which cells interact and sense their environment can now be unambiguously understood down to the single-molecule level. This Commentary highlights recent successful examples where bio-functionalized substrates have contributed in raising and answering new questions in the area of extracellular matrix sensing by cells, cell-cell adhesion and cell migration. The use, the availability, the impact and the challenges of such approaches in the field of biology are discussed.

Regular Nanoscale Protein Patterns via Directed Adsorption through Self-Assembled DNA Origami Masks

DNA origami has become a widely used method for synthesizing well-defined nanostructures with promising applications in various areas of nanotechnology, biophysics, and medicine. Recently, the possibility to transfer the shape of single DNA origami nanostructures into different materials via molecular lithography approaches has received growing interest due to the great structural control provided by the DNA origami technique. Here, we use ordered monolayers of DNA origami nanostructures with internal cavities on mica surfaces as molecular lithography masks for the fabrication of regular protein patterns over large surface areas. Exposure of the masked sample surface to negatively charged proteins results in the directed adsorption of the proteins onto the exposed surface areas in the holes of the mask. By controlling the buffer and adsorption conditions, the protein coverage of the exposed areas can be varied from single proteins to densely packed monolayers. To demonstrate the versatility of this approach, regular nanopatterns of four different proteins are fabricated: the single-strand annealing proteins Redβ and Sak, the iron-storage protein ferritin, and the blood protein bovine serum albumin (BSA). We furthermore demonstrate the desorption of the DNA origami mask after directed protein adsorption, which may enable the fabrication of hierarchical patterns composed of different protein species. Because selectivity in adsorption is achieved by electrostatic interactions between the proteins and the exposed surface areas, this approach may enable also the large-scale patterning of other charged molecular species or even nanoparticles.

Reactions in ultra-small droplets by tip-assisted chemistry

The confinement of chemical reactions within small droplets has received much attention in the last few years. This approach has been proved successful for the in-depth study of naturally occurring chemical processes as well as for the synthesis of different sets of nanomaterials with control over their size, shape and properties. Different approaches such as the use of self-contained structures or microfluidic generated droplets have been followed over the years with success. However, novel approaches have emerged during the last years based on the deposition of femtolitre-sized droplets on surfaces using tip-assisted lithographic methods. In this feature article, we review the advances made towards the use of these ultra-small droplets patterned on surfaces as confined nano-reactors.

Nanomanufacturing: A Perspective

Nanomanufacturing, the commercially scalable and economically sustainable mass production of nanoscale materials and devices, represents the tangible outcome of the nanotechnology revolution. In contrast to those used in nanofabrication for research purposes, nanomanufacturing processes must satisfy the additional constraints of cost, throughput, and time to market. Taking silicon integrated circuit manufacturing as a baseline, we consider the factors involved in matching processes with products, examining the characteristics and potential of top-down and bottom-up processes, and their combination. We also discuss how a careful assessment of the way in which function can be made to follow form can enable high-volume manufacturing of nanoscale structures with the desired useful, and exciting, properties.

Bottom-Up Synthesis and Sensor Applications of Biomimetic Nanostructures

The combination of nanotechnology, biology, and bioengineering greatly improved the developments of nanomaterials with unique functions and properties. Biomolecules as the nanoscale building blocks play very important roles for the final formation of functional nanostructures. Many kinds of novel nanostructures have been created by using the bioinspired self-assembly and subsequent binding with various nanoparticles. In this review, we summarized the studies on the fabrications and sensor applications of biomimetic nanostructures. The strategies for creating different bottom-up nanostructures by using biomolecules like DNA, protein, peptide, and virus, as well as microorganisms like bacteria and plant leaf are introduced. In addition, the potential applications of the synthesized biomimetic nanostructures for colorimetry, fluorescence, surface plasmon resonance, surface-enhanced Raman scattering, electrical resistance, electrochemistry, and quartz crystal microbalance sensors are presented. This review will promote the understanding of relationships between biomolecules/microorganisms and functional nanomaterials in one way, and in another way it will guide the design and synthesis of biomimetic nanomaterials with unique properties in the future.

Nanopatterned polymer brushes: conformation, fabrication and applications

Surfaces with end-grafted, nanopatterned polymer brushes that exhibit well-defined feature dimensions and controlled chemical and physical properties provide versatile platforms not only for investigation of nanoscale phenomena at biointerfaces, but also for the development of advanced devices relevant to biotechnology and electronics applications. In this review, we first give a brief introduction of scaling behavior of nanopatterned polymer brushes and then summarize recent progress in fabrication and application of nanopatterned polymer brushes. Specifically, we highlight applications of nanopatterned stimuli-responsive polymer brushes in the areas of biomedicine and biotechnology.

Catalyst-free site-specific surface modifications of nanocrystalline diamond films via microchannel cantilever spotting

Microchannel cantilever spotting is combined with a copper-free click chemistry ligation to achieve the patterning of nanocrystalline diamond films.

Ultrahigh resolution, serial fabrication of three dimensionally-patterned protein nanostructures by liquid-mediated non-contact scanning probe lithography

Sub-100 nm and 3D-patterned structures of protein are fabricated on Au surface in solution by liquid-mediated non-contact scanning probe lithography.

Spatially-controlled laser-induced decoration of 2D and 3D substrates with plasmonic nanoparticles

We demonstrate a new approach which can be used for targeted imparting of plasmonic properties for wide range of different substrates which may have any 2D or 3D topological structure created independently in a prior step with some other technology.

Current Trends and Challenges in Biointerfaces Science and Engineering

The cellular microenvironment is extremely complex, and a plethora of materials and methods have been employed to mimic its properties in vitro. In particular, scientists and engineers have taken an interdisciplinary approach in their creation of synthetic biointerfaces that replicate chemical and physical aspects of the cellular microenvironment. Here the focus is on the use of synthetic materials or a combination of synthetic and biological ligands to recapitulate the defined surface chemistries, microstructure, and function of the cellular microenvironment for a myriad of biomedical applications. Specifically, strategies for altering the surface of these environments using self-assembled monolayers, polymer coatings, and their combination with patterned biological ligands are explored. Furthermore, methods for augmenting an important physical property of the cellular microenvironment, topography, are highlighted, and the advantages and disadvantages of these approaches are discussed. Finally, the progress of materials for prolonged stem cell culture, a key component in the translation of stem cell therapeutics for clinical use, is featured.

Planar bioadhesive microdevices: a new technology for oral drug delivery

The oral route is the most convenient and least expensive route of drug administration. Yet, it is accompanied by many physiological barriers to drug uptake including low stomach pH, intestinal enzymes and transporters, mucosal barriers, and high intestinal fluid shear. While many drug delivery systems have been developed for oral drug administration, the physiological components of the gastro intestinal tract remain formidable barriers to drug uptake. Recently, microfabrication techniques have been applied to create micron-scale devices for oral drug delivery with a high degree of control over microdevice size, shape, chemical composition, drug release profile, and targeting ability. With precise control over device properties, microdevices can be fabricated with characteristics that provide increased adhesion for prolonged drug exposure, unidirectional release which serves to avoid luminal drug loss and enhance drug permeation, and protection of a drug payload from the harsh environment of the intestinal tract. Here we review the recent developments in microdevice technology and discuss the potential of these devices to overcome unsolved challenges in oral drug delivery.

Nanotechnologies in protein microarrays

Protein microarray technology became an important research tool for study and detection of proteins, protein-protein interactions and a number of other applications. The utilization of nanoparticle-based materials and nanotechnology-based techniques for immobilization allows us not only to extend the surface for biomolecule immobilization resulting in enhanced substrate binding properties, decreased background signals and enhanced reporter systems for more sensitive assays. Generally in contemporarily developed microarray systems, multiple nanotechnology-based techniques are combined. In this review, applications of nanoparticles and nanotechnologies in creating protein microarrays, proteins immobilization and detection are summarized. We anticipate that advanced nanotechnologies can be exploited to expand promising fields of proteins identification, monitoring of protein-protein or drug-protein interactions, or proteins structures.

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.

The influence of thiolate readsorption on the quality of mixed monolayers formed through an electrochemcial method

Lateral Force Microscopy (LFM) was used to probe the quality of binary mixed monolayers formed on planar polycrystalline gold through an electrochemical method. In the approach, portions of a self-assembled monolayer (SAM) composed of 2-aminoethanethiol (AET) were removed from the Au(111) surface facets by selective reductive desorption which maintained undisrupted regions of AET elsewhere on the polycrystalline surface. Monolayer voids created by this method were backfilled with 11-mercaptoundecanoic acid (MUA) and the interface characterized with ex situ LFM. This produced images with domains of high and low friction corresponding to isolated zones of MUA and AET respectively. Reverse sequence mixed monolayers were also prepared with MUA as the starting layer and rendered LFM images that mirrored the AET based layers. This demonstrates flexibility of the electrochemical method to produce heterogeneous binary SAMs, and to further probe the quality of mixed monolayers, a number of experimental conditions including desorption time, electrode configuration, and initial incubation period were studied. AET/MUA layers that produced the most enhanced LFM images were formed on a planar electrode that was vertically submerged into the electrolyte while maintaining a selective desorption potential for 5 min before backfilling with MUA. This condition allowed for the effective diffusion of AET away from the interface and created well-defined monolayer voids for backfilling. At desorption times lower than 1 min, some of the AET molecules that remained near the interface would readsorb onto the surface and interfere with the backfilling process thereby creating lower contrast LFM images. Structural features of these layers were independent of initial incubation time (10 min and 16 h); however, the contrast between domains was improved when using AET layers formed over a longer incubation period. Interestingly, the contrast was significantly reduced when mixed layers were created on electrodes set in a hanging meniscus with the electrolyte. Here, electrochemical evidence pointed to prolonged readsorption of thiolates creating less well-defined voids for backfilling, and the event was most pronounced for MUA based layers.

Design of surface modifications for nanoscale sensor applications

Nanoscale biosensors provide the possibility to miniaturize optic, acoustic and electric sensors to the dimensions of biomolecules. This enables approaching single-molecule detection and new sensing modalities that probe molecular conformation. Nanoscale sensors are predominantly surface-based and label-free to exploit inherent advantages of physical phenomena allowing high sensitivity without distortive labeling. There are three main criteria to be optimized in the design of surface-based and label-free biosensors: (i) the biomolecules of interest must bind with high affinity and selectively to the sensitive area; (ii) the biomolecules must be efficiently transported from the bulk solution to the sensor; and (iii) the transducer concept must be sufficiently sensitive to detect low coverage of captured biomolecules within reasonable time scales. The majority of literature on nanoscale biosensors deals with the third criterion while implicitly assuming that solutions developed for macroscale biosensors to the first two, equally important, criteria are applicable also to nanoscale sensors. We focus on providing an introduction to and perspectives on the advanced concepts for surface functionalization of biosensors with nanosized sensor elements that have been developed over the past decades (criterion (iii)). We review in detail how patterning of molecular films designed to control interactions of biomolecules with nanoscale biosensor surfaces creates new possibilities as well as new challenges.

Patterning of supported lipid bilayers and proteins using material selective nitrodopamine-mPEG

We present a generic patterning process by which biomolecules in a passivated background are patterned directly from physiological buffer to microfabricated surfaces without the need for further processing.

Atomic force microscopy in biomaterials surface science

Recent progress in surface science, nanotechnology and biophysics has cast new light on the correlation between the physicochemical properties of biomaterials and the resulting biological response. One experimental tool that promises to generate an increasingly more sophisticated knowledge of how proteins, cells and bacteria interact with nanostructured surfaces is the atomic force microscope (AFM). This unique instrument permits to close in on interfacial events at the scale at which they occur, the nanoscale. This perspective covers recent developments in the exploitation of the AFM, and suggests insights on future opportunities that can arise from the exploitation of this powerful technique.

Photothermal laser fabrication of micro- and nanostructured chemical templates for directed protein immobilization

Photothermal patterning of poly(ethylene glycol) terminated organic monolayers on surface-oxidized silicon substrates is carried out using a microfocused beam of a CW laser operated at a wavelength of 532 nm. Trichlorosilane and trimethoxysilane precursors are used for coating. Monolayers from trimethoxysilane precursors show negligible unspecific protein adsorption in the background, i.e., provide platforms of superior protein repellency. Laser patterning results in decomposition of the monolayers and yields chemical templates for directed immobilization of proteins at predefined positions. Characterization is carried out via complementary analytical methods including fluorescence microscopy, atomic force microscopy, and scanning electron microscopy. Appropriate labeling techniques (fluorescent markers and gold clusters) and substrates (native and thermally oxidized silicon substrates) are chosen in order to facilitate identification of protein adsorption and ensure high sensitivity and selectivity. Variation of the laser parameters at a 1/e(2) spot diameter of 2.8 μm allows for fabrication of protein binding domains with diameters on the micrometer and nanometer length scale. Minimum domain sizes are about 300 nm. In addition to unspecific protein adsorption on as-patterned monolayers, biotin-streptavidin coupling chemistry is exploited for specific protein binding. This approach represents a novel facile laser-based means for fabrication of protein micro- and nanopatterns. The routine is readily applicable to femtosecond laser processing of glass substrates for the fabrication of transparent templates.

Hierarchically ordered nanopatterns for spatial control of biomolecules

The development and study of a benchtop, high-throughput, and inexpensive fabrication strategy to obtain hierarchical patterns of biomolecules with sub-50 nm resolution is presented. A diblock copolymer of polystyrene-b-poly(ethylene oxide), PS-b-PEO, is synthesized with biotin capping the PEO block and 4-bromostyrene copolymerized within the polystyrene block at 5 wt %. These two handles allow thin films of the block copolymer to be postfunctionalized with biotinylated biomolecules of interest and to obtain micropatterns of nanoscale-ordered films via photolithography. The design of this single polymer further allows access to two distinct superficial nanopatterns (lines and dots), where the PEO cylinders are oriented parallel or perpendicular to the substrate. Moreover, we present a strategy to obtain hierarchical mixed morphologies: a thin-film coating of cylinders both parallel and perpendicular to the substrate can be obtained by tuning the solvent annealing and irradiation conditions.

Classic, liquid, and matrix-assisted dip-pen nanolithography for materials research

As a powerful atomic force microscopy-based nanotechnological tool, dip-pen nanolithography (DPN) has provided an ideal direct-write "constructive" lithographic tool that allows materials to be patterned from DPN tips onto a surface with high registration and sub-15 nm resolution. In the past few decades, DPN has been enormously developed for studying the patterning of inorganic, organic, and biological materials onto a variety of substrates. The focus of this review is on the development of three types of DPN: classic, liquid, and matrix-assisted DPN. Such development mainly includes the following aspects: the comparisons of three types of DPN, the effect factors and basic mechanisms of three types of DPN, and the application progress of three types of DPN.

Ink-on-probe hydrodynamics in atomic force microscope deposition of liquid inks

The controlled deposition of attolitre volumes of liquids may engender novel applications such as soft, nano-tailored cell-material interfaces, multi-plexed nano-arrays for high throughput screening of biomolecular interactions, and localized delivery of reagents to reactions confined at the nano-scale. Although the deposition of small organic molecules from an AFM tip, known as dip-pen nanolithography (DPN), is being continually refined, AFM deposition of liquid inks is not well understood, and is often fraught with inconsistent deposition rates. In this work, the variation in feature-size over long term printing experiments for four model inks of varying viscosity is examined. A hierarchy of recurring phenomena is uncovered and there are attributed to ink movement and reorganisation along the cantilever itself. Simple analytical approaches to model these effects, as well as a method to gauge the degree of ink loading using the cantilever resonance frequency, are described. In light of the conclusions, the various parameters which need to be controlled in order to achieve uniform printing are dicussed. This work has implications for the nanopatterning of viscous liquids and hydrogels, encompassing ink development, the design of probes and printing protocols.

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.