Generation of plasmonic Au nanostructures in the visible wavelength using two-dimensional parallel dip-pen nanolithography.

The fabrication and characterization of over millimeter (mm)-scale Au plasmonic structures are reported. Fishnet structures of Au are fabricated by the "bottom-up (direct deposition of alkanethiol)" and "top-down (wet-etching of Au)" combined approach using massively parallel dip-pen nanolithography (DPN). An array of two-dimensional (2D) parallel 55,000 pens was used for the DPN writing of 1-octadecanethiol (ODT) on an Au film in an area of 10 mm × 10 mm. The plasmonic resonance of the over millimeter-scale Au fishnet structures is shown at the visible region around 500 nm, which is measured by ellipsometrical experiments and theoretical finite-difference time-domain (FDTD) calculation. It was demonstrated that massive metal plasmonic structures can be conveniently obtained by using DPN, complementary with both e-beam lithography and nanoimprint lithography.

Femtolitre chemistry assisted by microfluidic pen lithography.

Chemical reactions at ultrasmall volumes are becoming increasingly necessary to study biological processes, to synthesize homogenous nanostructures and to perform high-throughput assays and combinatorial screening. Here we show that a femtolitre reaction can be realized on a surface by handling and mixing femtolitre volumes of reagents using a microfluidic stylus. This method, named microfluidic pen lithography, allows mixing reagents in isolated femtolitre droplets that can be used as reactors to conduct independent reactions and crystallization processes. This strategy overcomes the high-throughput limitations of vesicles and micelles and obviates the usually costly step of fabricating microdevices and wells. We anticipate that this process enables performing distinct reactions (acid-base, enzymatic recognition and metal-organic framework synthesis), creating multiplexed nanoscale metal-organic framework arrays, and screening combinatorial reactions to evaluate the crystallization of novel peptide-based materials.

Targeted delivery to single cells in precisely controlled microenvironments.

The heterogeneous nature of cells can be an issue for in vitro analysis of cell function due to cell type differences within a population. Observations are most often averaged and dependent on the homogeneity or lack thereof for most cell types. Patterning of features at the sub-cellular scale (< 10 µm) allows for single cell manipulation. Additionally, the ability to pattern multiple materials simultaneously with nanoscale precision enables facile fabrication of multiplexed cellular microenvironment arrays. Here we use this ability to deliver different materials to single or few cells within hundreds of microns of each other on the same substrate. Calcein AM, Calcein Red AM and quantum dots are delivered to live single or few cells. This allows for exposing limited cell numbers to many well defined conditions, thus opening the possibility of single cell based assays.

Subcellular scaled multiplexed protein patterns for single cell cocultures.

Tip-based direct protein printing is a relatively new technique that is useful for controlling the cellular microenvironment with subcellular resolution. Coculture studies have been useful for mimicking the in vivo environment and studying effects on stem or progenitor cell function. However, there are many experimental variables that cannot be properly controlled and may lead to confounding results. Here we demonstrate a technique that allows spatial control of multiple cell types at single cell levels on a substrate. Specifically, 3T3 fibroblasts and C2C12 myoblasts and their respective binding dynamics with fibronectin and laminin demonstrate the single cell coculture concept.

Immobilization method of yeast cells for intermittent contact mode imaging using the atomic force microscope.

The atomic force microscope (AFM) is widely used for studying the surface morphology and growth of live cells. There are relatively fewer reports on the AFM imaging of yeast cells [1] (Kasas and Ikai, 1995), [2] (Gad and Ikai, 1995). Yeasts have thick and mechanically strong cell walls and are therefore difficult to attach to a solid substrate. In this report, a new immobilization technique for the height mode imaging of living yeast cells in solid media using AFM is presented. The proposed technique allows the cell surface to be almost completely exposed to the environment and studied using AFM. Apart from the new immobilization protocol, for the first time, height mode imaging of live yeast cell surface in intermittent contact mode is presented in this report. Stable and reproducible imaging over a 10-h time span is observed. A significant improvement in operational stability will facilitate the investigation of growth patterns and surface patterns of yeast cells.

Detection and quantification of protein biomarkers from fewer than 10 cells.

The use of antibody microarrays continues to grow rapidly due to the recent advances in proteomics and automation and the opportunity this combination creates for high throughput multiplexed analysis of protein biomarkers. However, a primary limitation of this technology is the lack of PCR-like amplification methods for proteins. Therefore, to realize the full potential of array-based protein biomarker screening it is necessary to construct assays that can detect and quantify protein biomarkers with very high sensitivity, in the femtomolar range, and from limited sample quantities. We describe here the construction of ultramicroarrays, combining the advantages of microarraying including multiplexing capabilities, higher throughput, and cost savings with the ability to screen very small sample volumes. Antibody ultramicroarrays for the detection of interleukin-6 and prostate-specific antigen (PSA), a widely used biomarker for prostate cancer screening, were constructed. These ultramicroarrays were found to have a high specificity and sensitivity with detection levels using purified proteins in the attomole range. Using these ultramicroarrays, we were able to detect PSA secreted from 100 LNCaP cells in 3 h and from just four LNCaP cells in 24 h. Cellular PSA could also be detected from the lysate of an average of just six cells. This strategy should enable proteomic analysis of materials that are available in very limited quantities such as those collected by laser capture microdissection, neonatal biopsy microspecimens, and forensic samples.

Characterization of testudine melanomacrophage linear, membrane extension processes--cablepodia--by phase and atomic force microscopy.

Melanomacrophages (MMs) are a component of an internal, pigmented cell system in liver and splenic tissues of some fishes, anurans, and reptiles. The cells have been found in centers or aggregates in sinusoids and are associated with cells capable of producing a peptide cytokine and immunoglobulins. A unique cell extension process has been observed in turtle MMs placed into cell culture, and this process has been studied by light and atomic force microscopy. These structures, referred to as cablepodia, are uniquely straight, narrow, and unbranching and appear to originate from growth cones opposite lamellipodia. Cablepodia were found to connect with other turtle MMs and fibroblasts forming cell networks. Dividing fibroblasts to which a cablepodium attached ceased cell division. The observations collectively suggest that a principal reason for aggregations of MMs in internal organs of lower vertebrates is their ability to form interconnected networks of cell processes for trapping and processing of particulate matter, cells, and infectious organisms and, possibly, for the communication of cell signals and transfer of intracellular materials.

Label-free protein and pathogen detection using the atomic force microscope.

The atomic force microscope (AFM) uses a sharp micron-scale tip to scan and amplify surface features, providing exceptionally detailed topographical information with magnification on the order of x10(6). This instrument is used extensively for quality control in the computer and semiconductor industries and is becoming a progressively more important tool in the biological sciences. Advantages of the AFM for biological application include the ability to obtain information in a direct, label-free manner and the ability to image in solution, providing real-time data acquisition under physiologically relevant conditions. A novel application of the AFM currently under development combines its surface profiling capabilities with fixed immuno-capture using antibodies immobilized in a nanoarray format. This provides a distinctive platform for direct, label-free detection and characterization of viral particles and other pathogens.

Functional protein nanoarrays for biomarker profiling.

The use of microarrays for parallel screening of nucleic acid profiles has become an industry standard. Similar efforts for screening protein-protein interactions are gaining momentum, however, they remain limited by the requirement for relatively large sample volumes. One strategy for overcoming this problem is to significantly decrease the size and consequently the sample volume of the protein interaction assay. We report here on our progress over the last two years in the construction of ultraminiaturized, functional protein capture assays. Each one micron spot in these array-based assays covers less than 1/1000(th) of the surface area of a conventional microarray spot while still maintaining enough antibodies to provide a useful dynamic range. These nanoarray assays can be read by conventional optical fluorescence microscopy as well as by novel label-free methods such as atomic force microscopy. The size reduction realized by functional protein nanoarrays also creates opportunities for novel applications including highly multiplexed single cell analysis and integration with microfluidics and other "lab-on-a-chip" technologies.

Analysis of solid-phase immobilized antibodies by atomic force microscopy.

Antibody adsorption to solid surfaces creates a number of constraints that may interfere with epitope recognition and ligand-antibody interaction. By optimizing the conditions of adsorption, one may minimize these constraints. We have studied several factors that affect the antibody adsorption using atomic force microscopy (AFM) as a readout mechanism. AFM provides a highly sensitive, label-free method for detecting and analyzing molecular interactions. In this report, AFM was used to study antibody properties, the efficiency of particle capture and ligand-antibody interaction using anti-bacteriophage fd antibodies in a solid phase assay format. The capture efficiencies of anti-fd preparations adsorbed onto gold surfaces under various conditions including pH and antibody concentration were determined and compared. The relative sensitivities of each antibody for the capture of phage fd as a function of applied phage concentrations was evaluated. The collective data indicates that AFM is effective as an analytical instrument for studying the functionality of surface adsorbed antibodies in particle capture assays. This method of analysis can be extended to rapidly screen and select antibodies or other ligands with a specific set of characteristics. As the number and complexity of chip-based analytical platforms in proteomics increases, rapid selection/screening processes such as that described here will become invaluable.

Virus particle detection by solid phase immunocapture and atomic force microscopy.

A novel application of atomic force microscopy (AFM) in the rapid, label-free detection and identification of viruses is described. Multiplexed, miniaturized antibody domains were constructed using "ink-jet" protein arraying technology. The solid-phase affinity substrate termed the "ViriChip" was used in the immunocapture of bacteriophage fd, canine parvoviruses, and coxsackieviruses and analyzed by AFM. Immunocapture was found to be antibody-specific with a sensitivity of 10(8)pfu/ml in 30min. Virus binding was found to be linear for concentration between 10(8) and 10(10)pfu/ml and did not reach saturation through 4h.