Monitoring single-cell infectivity from virus-particle nanoarrays fabricated by parallel dip-pen nanolithography

Nanopatterned Extracellular Matrices Enable Cell-Based Assays with a Mass Spectrometric Readout

Cell-based assays are finding wider use in evaluating compounds in primary screens for drug development, yet it is still challenging to measure enzymatic activities as an end point in a cell-based assay. This paper reports a strategy that combines state-of-the-art cantilever free polymer pen lithography (PPL) with self-assembled monolayer laser desorption-ionization (SAMDI) mass spectrometry to guide cell localization and measure cellular enzymatic activities. Experiments are conducted with a 384 spot array, in which each spot is composed of ∼400 nanoarrays and each array has a 10 × 10 arrangement of 750 nm features that present extracellular matrix (ECM) proteins surrounded by an immobilized phosphopeptide. Cells attach to the individual nanoarrays, where they can be cultured and treated with small molecules, after which the media is removed and the cells are lysed. Phosphatase enzymes in the proximal lysate can then act on the immobilized phosphopeptide substrate to convert it to the dephosphorylated form. After the lysate is removed, the array is analyzed by SAMDI mass spectrometry to identify the extent of dephosphorylation and, therefore, the amount of enzyme activity in the cell. This novel approach of using nanopatterning to mediate cell adhesion and SAMDI to record enzyme activities in the proximal lysate will enable a broad range of cellular assays for applications in drug discovery and research not possible with conventional strategies.

Hard Transparent Arrays for Polymer Pen Lithography

Patterning nanoscale features across macroscopic areas is challenging due to the vast range of length scales that must be addressed. With polymer pen lithography, arrays of thousands of elastomeric pyramidal pens can be used to write features across centimeter-scales, but deformation of the soft pens limits resolution and minimum feature pitch, especially with polymeric inks. Here, we show that by coating polymer pen arrays with a ∼175 nm silica layer, the resulting hard transparent arrays exhibit a force-independent contact area that improves their patterning capability by reducing the minimum feature size (∼40 nm), minimum feature pitch (<200 nm for polymers), and pen to pen variation. With these new arrays, patterns with as many as 5.9 billion features in a 14.5 cm(2) area were written using a four hundred thousand pyramid pen array. Furthermore, a new method is demonstrated for patterning macroscopic feature size gradients that vary in feature diameter by a factor of 4. Ultimately, this form of polymer pen lithography allows for patterning with the resolution of dip-pen nanolithography across centimeter scales using simple and inexpensive pen arrays. The high resolution and density afforded by this technique position it as a broad-based discovery tool for the field of nanocombinatorics.

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

Multiple-allergen testing for high throughput and high sensitivity requires the development of miniaturized immunoassays that allow for a large test area and require only a small volume of the test analyte, which is often available only in limited amounts. Developing such miniaturized biochips containing arrays of test allergens needs application of a technique able to deposit molecules at high resolution and speed while preserving its functionality. Lipid dip-pen nanolithography (L-DPN) is an ideal technique to create such biologically active surfaces, and it has already been successfully applied for the direct, nanoscale deposition of functional proteins, as well as for the fabrication of biochemical templates for selective adsorption. The work presented here shows the application of L-DPN for the generation of arrays of the ligand 2,4-dinitrophenyl[1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[6-[(2,4-dinitrophenyl)amino]hexanoyl] (DNP)] onto glass surfaces as a model system for detection of allergen-specific Immunoglobin E (IgE) antibodies and for mast cell activation profiling.

Nanobiochips

The actual progress towards biological chip devices consisting of nanostructured functional entities is summarized. The practical aspects of molecular nanobiochips are discussed, including the main surface chemistry platforms, as well as conventional and unconventional fabrication tools. Several successful biological demonstrations of the first generation of nanobiochip devices (mainly, different nanoarrays) are highlighted with the aim of revealing the potential of this technology in life sciences, medicine, and related areas.

A methodology for preparing nanostructured biomolecular interfaces with high enzymatic activity

The development of a novel method for functionalizing nanopatterned surfaces with catalytically active proteins is reported. This method involves using dip-pen nanolithography (DPN) and polymer pen lithography (PPL) to generate nanoscale patterns of coenzyme A, followed by a phosphopantetheinyl transferase-mediated coupling between coenzyme A and proteins fused to the ybbR-tag. By exploiting the ability to generate protein features over large areas afforded by DPN and PPL, it was now possible to measure protein activity directly on these surfaces. It was found that proteins immobilized on the nanoscale features not only display higher activity per area with decreasing feature size, but are also robust and can be used for repeated catalytic cycles. The immobilization method is applicable to a variety of proteins and gives rise to superior activity compared to proteins attached in random orientations on the surface.

Chemically functionalized surface patterning

Patterning substrates with versatile chemical functionalities from micro- to nanometer scale is a long-standing and interesting topic. This review provides an overview of a range of techniques commonly used for surface patterning. The first section briefly introduces conventional micropatterning tools, such as photolithography and microcontact printing. The second section focuses on the currently used nanolithographic techniques, for example, scanning probe lithography (SPL), and their applications in surface patterning. Their advantages and disadvantages are also demonstrated. In the last section, dip-pen nanolithography (DPN) is emphatically illustrated, with a particular stress on the patterning and applications of biomolecules.

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.

Temperature controlled dip-pen nanolithography

Dip-pen nanolithography (DPN) has emerged as a powerful tool for creating sophisticated micron- and nanoscale features of various molecules, such as small organic molecules, on a variety of substrates. Despite significant advances in recent years, the influence of temperature on molecular transport for nanostructure fabrication has not been fully explored. Herein, it is shown how the dimensions of patterned organic nanostructures can be controlled by using a cooling/heating module. This method allows nanometer-sized feature fabrication of a variety of small organic molecules, including 'inks' that have been deemed very difficult to write under ambient conditions. Features with dimensions as small as 30 nm have been successfully reproduced using the newly developed temperature control device in conjunction with DPN.

Large-scale arrays of aligned single viruses

The fabrication of single virus arrays is herein demonstrated using the direct printing of unmodified anti-M13 bacteriophage antibodies on silicon with nanometer resolution, widely variable feature pitch, and flow alignment of the viruses. Organization of virus-based systems into functional, addressable arrays has many technological applications, including micro-array technology and bottom-up nano-assemblies.

Dip-pen nanolithography on SiOx and tissue-derived substrates: comparison with multiple biological inks

There has been extensive interest in the micro and nanoscale manipulation of various substrates in the past few decades. One promising technique is dip-pen nanolithography which has shown the capability to pattern substrates of all forms including, tissue-derived substrates. Patterning of tissue-derived substrates is of particular interest, as it would facilitate studies into controlling cell morphology and cell-substrate interaction. To expand the field into this area both peptides and bioactive collagen-binding peptide-linked biomolecules were patterned to the inner collagenous zone of the Bruch's membrane (BM). Collagen-binding peptide, and extra cellular matrix (ECM) proteins laminin and fibronectin were patterned on the BM and SiO(x). The lithographic protocol was facilitated by Triton X-100 which was used to clean the tissue-derived construct after harvesting. This produced a collagen-exposed BM which was more hydrophilic (contact angle 67 degrees +/-8.49 degrees) surface compared with other cleaning methods but it maintained similar surface roughness (root-mean-square) 80+/-18 nm and collagen exposure. This type of surface can be readily patterned with the chosen inks under lower humidity conditions.

Self-leveling two-dimensional probe arrays for Dip Pen Nanolithography

Scanning probe lithography (SPL) has witnessed a dramatic transformation with the advent of two-dimensional (2D) probe arrays. Although early work with single probes was justifiably assessed as being too slow to practically apply in a nanomanufacturing context, we have recently demonstrated throughputs up to 3x10(7) microm(2)/h--in some cases exceeding e-beam lithography--using centimeter square arrays of 55,000 tips tailored for Dip Pen Nanolithography (DPN). Parallelizing DPN has been critical because there exists a need for a lithographic process that is not only high throughput, but also high resolution (DPN has shown line widths down to 14 nm) with massive multiplexing capabilities. Although previous methods required non-trivial user manipulation to bring the 2D array level to the substrate, we now demonstrate a self-leveling fixture for NanoInk's 2D nano PrintArray. When mounted on NanoInk's NLP 2000, the 55,000 tip array can achieve a planarity of <0.1 degrees with respect to the substrate in a matter of seconds, with no user manipulation required. Additional fine-leveling routines (<2 min of user interaction) can improve this planarity to <0.002 degrees with respect to the substrate-a Z-difference of less than 600 nm across 1 cm(2) of surface area. We herein show highly homogeneous etch-resist nanostructure results patterned from a self-leveled array of DPN pens, with feature size standard deviation of <6% across a centimeter square sample. We illustrate the mechanisms and methods of the self-leveling fixture, and detail the advantages thereof. Finally, we emphasize that this methodology brings us closer to the goal of true nanomanufacturing by automating the leveling process, reducing setup time by at least a factor of 10, enhancing the ease of the overall printing process, and ultimately ensuring a more level device with subsequently homogeneous nanostructures.

Molecular printing

Molecular printing techniques, which involve the direct transfer of molecules to a substrate with submicrometre resolution, have been extensively developed over the past decade and have enabled many applications. Arrays of features on this scale have been used to direct materials assembly, in nanoelectronics, and as tools for genetic analysis and disease detection. The past decade has witnessed the maturation of molecular printing led by two synergistic technologies: dip-pen nanolithography and soft lithography. Both are characterized by material and substrate flexibility, but dip-pen nanolithography has unlimited pattern design whereas soft lithography has limited pattern flexibility but is low in cost and has high throughput. Advances in DPN tip arrays and inking methods have increased the throughput and enabled applications such as multiplexed arrays. A new approach to molecular printing, polymer-pen lithography, achieves low-cost, high-throughput and pattern flexibility. This Perspective discusses the evolution and future directions of molecular printing.

Porphyrin-based photocatalytic nanolithography: a new fabrication tool for protein arrays

Nanoarray fabrication is a multidisciplinary endeavor encompassing materials science, chemical engineering, and biology. We formed nanoarrays via a new technique, porphyrin-based photocatalytic nanolithography. The nanoarrays, with controlled features as small as 200 nm, exhibited regularly ordered patterns and may be appropriate for (a) rapid and parallel proteomics screening of immobilized biomolecules, (b) protein-protein interactions, and/or (c) biophysical and molecular biology studies involving spatially dictated ligand placement. We demonstrated protein immobilization utilizing nanoarrays fabricated via photocatalytic nanolithography on silicon substrates where the immobilized proteins are surrounded by a non-fouling polymer background.

Multifunctional Polypeptide EQCN Sensors: Probing the Cysteamine-Glutathione Film Permeability with Hg(II) Ions

Multifunctional films are the basis of biosensors and play an important role in the emerging field of nanobioelectronics. In this work, films of a tripeptide glutathione (GSH) immobilized on a self-assembled monolayer of cysteamine (CA-SAM) on a quartz crystal Au piezosensor have been synthesized and characterized using electrochemical quartz crystal nanogravimetry (EQCN) with a Hg(II) ion probe. It has been found that in contrast to previously studied Au/GSH films, the Au/CA-GSH films strongly hinder the formation of Hg⁰ with bulk properties while still allowing for relatively easy permeation by Hg(II) ions. This results in complete disappearance of the sharp Hg⁰ electrodissolution peak which is observed on bare Au and Au/GSH piezosensors. The multiple-peak anodic behavior of Au/CA and bare Au is replaced by a single high-field anodic peak of mercury reoxidation in the case of Au/CA-GSH sensors. The mass-to-charge plots indicate predominant ingress/egress of Hg(II) to/from the film. The strong hindrance of CA-SAM to bulk-Hg⁰ formation is attributed to film-stabilizing formation of surface (CA)₂Hg²⁺ complexes with conformation evaluated by ab initio quantum mechanical calculations of electronic structure using Hartree-Fock methods. The associates CA-GSH provide an additional functionality of the side sulfhydryl group which is free for interactions, e.g. with heavy metals. It is proposed that in the film, the CA-GSH molecules can assume open (extended) conformation or bent hydrogen-bonded conformation with up to four possible internal hydrogen bonds.

Multiplexed lipid dip-pen nanolithography on subcellular scales for the templating of functional proteins and cell culture

Molecular patterning processes taking place in biological systems are challenging to study in vivo because of their dynamic behavior, subcellular size, and high degree of complexity. In vitro patterning of biomolecules using nanolithography allows simplification of the processes and detailed study of the dynamic interactions. Parallel dip-pen nanolithography (DPN) is uniquely capable of integrating functional biomolecules on subcellular length scales due to its constructive nature, high resolution, and high throughput. Phospholipids are particularly well suited as inks for DPN since a variety of different functional lipids can be readily patterned in parallel. Here DPN is used to spatially pattern multicomponent micro- and nanostructured supported lipid membranes and multilayers that are fluid and contain various amounts of biotin and/or nitrilotriacetic acid functional groups. The patterns are characterized by fluorescence microscopy and photoemission electron microscopy. Selective adsorption of functionalized or recombinant proteins based on streptavidin or histidine-tag coupling enables the semisynthetic fabrication of model peripheral membrane bound proteins. The biomimetic membrane patterns formed in this way are then used as substrates for cell culture, as demonstrated by the selective adhesion and activation of T-cells.

Solvent-mediated repair and patterning of surfaces by AFM

A tip-based approach to shaping surfaces of soluble materials with nanometer-scale control is reported. The proposed method can be used, for example, to eliminate defects and inhomogeneities in surface shape, repair mechanical or laser induced damage to surfaces, or perform 3D lithography on the length scale of an AFM tip. The phenomenon that enables smoothing and repair of surfaces is based on the transport of material from regions of high to low curvature within the solution meniscus formed in a solvent-containing atmosphere between the surface in question and an AFM tip scanned over the surface. Using in situ AFM measurements of the kinetics of surface remodeling on KDP (KH(2)PO(4)) crystals in humid air, we show that redistribution of solute material during relaxation of grooves and mounds is driven by a reduction in surface free energy as described by the Gibbs-Thomson law. We find that the perturbation from a flat interface evolves according to the diffusion equation, where the effective diffusivity is determined by the product of the surface stiffness and the step kinetic coefficient. We also show that, surprisingly, if the tip is instead scanned over or kept stationary above an atomically flat area of the surface, a convex structure is formed, with a diameter that is controlled by the dimensions of the meniscus, indicating that the presence of the tip and meniscus reduces the substrate chemical potential beneath that of the free surface. This allows one to create nanometer-scale 3D structures of arbitrary shape without the removal of substrate material or the use of extrinsic masks or chemical compounds. Potential applications of these tip-based phenomena are discussed.

Dip Pen Nanolithography: a "Desktop Nanofab" approach using high-throughput flexible nanopatterning

The ability to perform controllable nanopatterning with a broad range of "inks" at ambient conditions is a key aspect of the dip pen nanolithography (DPN) technique. The traditional ink system to demonstrate DPN is n-alkanethiols on a gold substrate, but the DPN method has found numerous other applications since. This article is meant to outline recent advances in the DPN toolkit, both in terms of research and patterning technology, and to discuss applications of DPN as a viable nanofabrication method. We will summarize new DPN developments, and introduce our concept of the "Desktop Nanofab." In addition, we outline our efforts to commercialize DPN as a viable nanofabrication technique by demonstrating massively parallel nanopatterning with the 55,000 tip 2D nano PrintArray. This demonstrates our ability to overcome the serial nature of DPN patterning and enable high-throughput nanofabrication.