Direct microcontact printing of oligonucleotides for biochip applications

Biofunctionalization of Multiplexed Silicon Photonic Biosensors

Silicon photonic (SiP) sensors offer a promising platform for robust and low-cost decentralized diagnostics due to their high scalability, low limit of detection, and ability to integrate multiple sensors for multiplexed analyte detection. Their CMOS-compatible fabrication enables chip-scale miniaturization, high scalability, and low-cost mass production. Sensitive, specific detection with silicon photonic sensors is afforded through biofunctionalization of the sensor surface; consequently, this functionalization chemistry is inextricably linked to sensor performance. In this review, we first highlight the biofunctionalization needs for SiP biosensors, including sensitivity, specificity, cost, shelf-stability, and replicability and establish a set of performance criteria. We then benchmark biofunctionalization strategies for SiP biosensors against these criteria, organizing the review around three key aspects: bioreceptor selection, immobilization strategies, and patterning techniques. First, we evaluate bioreceptors, including antibodies, aptamers, nucleic acid probes, molecularly imprinted polymers, peptides, glycans, and lectins. We then compare adsorption, bioaffinity, and covalent chemistries for immobilizing bioreceptors on SiP surfaces. Finally, we compare biopatterning techniques for spatially controlling and multiplexing the biofunctionalization of SiP sensors, including microcontact printing, pin- and pipette-based spotting, microfluidic patterning in channels, inkjet printing, and microfluidic probes.

Advances in Single-Cell Printing

Single-cell analysis is becoming an indispensable tool in modern biological and medical research. Single-cell isolation is the key step for single-cell analysis. Single-cell printing shows several distinct advantages among the single-cell isolation techniques, such as precise deposition, high encapsulation efficiency, and easy recovery. Therefore, recent developments in single-cell printing have attracted extensive attention. We review herein the recently developed bioprinting strategies with single-cell resolution, with a special focus on inkjet-like single-cell printing. First, we discuss the common cell printing strategies and introduce several typical and advanced printing strategies. Then, we introduce several typical applications based on single-cell printing, from single-cell array screening and mass spectrometry-based single-cell analysis to three-dimensional tissue formation. In the last part, we discuss the pros and cons of the single-cell strategies and provide a brief outlook for single-cell printing.

Lithographic Processes for the Scalable Fabrication of Micro- and Nanostructures for Biochips and Biosensors

Since the early 2000s, extensive research has been performed to address numerous challenges in biochip and biosensor fabrication in order to use them for various biomedical applications. These biochips and biosensor devices either integrate biological elements (e.g., DNA, proteins or cells) in the fabrication processes or experience post fabrication of biofunctionalization for different downstream applications, including sensing, diagnostics, drug screening, and therapy. Scalable lithographic techniques that are well established in the semiconductor industry are now being harnessed for large-scale production of such devices, with additional development to meet the demand of precise deposition of various biological elements on device substrates with retained biological activities and precisely specified topography. In this review, the lithographic methods that are capable of large-scale and mass fabrication of biochips and biosensors will be discussed. In particular, those allowing patterning of large areas from 10 cm² to m², maintaining cost effectiveness, high throughput (>100 cm² h^-1), high resolution (from micrometer down to nanometer scale), accuracy, and reproducibility. This review will compare various fabrication technologies and comment on their resolution limit and throughput, and how they can be related to the device performance, including sensitivity, detection limit, reproducibility, and robustness.

Evolution and applications of polymer brush hypersurface photolithography

Hypersurface photolithography creates arbitrary polymer brush patterns with independent control over feature diameter, height, and spacing between features, while controlling composition along a polymer chain and between features.

Fatty acids as biomimetic replication agents for luminescent metal-organic framework patterns

Luminescent metal-organic frameworks (MOFs) are known to spontaneously self-assemble on human fingerprints. Here, we investigate the different chemical components of fingerprints and determine that MOF growth is predominantly induced by insoluble fatty acids. This finding shows that these simple biomolecules can be employed for the precise positioning of luminescent MOFs.

Ultrasonic Microplotting of Microgel Bioinks

Material scaffolds that mimic the structure, function, and bioactivity of native biological tissues are in constant development. Recently, material scaffolds composed of microgel particles have shown promise for applications ranging from bone regeneration to spheroid cell growth. Previous studies with poly N-isopropylacrylamide microgel scaffolds utilized a layer-by-layer (LBL) technique where individual, uniform microgel layers are built on top of each other resulting in a multilayer scaffold. However, this technique is limited in its applications due to the inability to control microscale deposition or patterning of multiple particle types within a microgel layer. In this study, an ultrasonic microplotting technique is used to address the limitations of LBL fabrication to create patterned microgel films. Printing parameters, such as bioink formulation, surface contact angle, and print head diameter, are optimized to identify the ideal parameters needed to successfully print microgel films. It was found that bioinks composed of 2 mg/mL of microgels and 20% polyethylene glycol by volume (v/v), on bovine serum albumin-coated glass, with a print head diameter of 50 μm resulted in the highest quality prints. Patterned films were created with a maximum resolution of 50 μm with the potential for finer resolutions to be achieved with alternative bioink compositions and printing parameters. Overall, ultrasonic microplotting can be used to create more complex microgel films than is possible with LBL techniques and offers the possibility of greater printing resolution in 3D with further technology development.

Low Cost and Lithography-free Stamp fabrication for Microcontact Printing

Microcontact printing (µCP) is a commonly used technique for patterning proteins of interest on substrates. The cells take the shape of these printed patterns. This technique is used to explore the effect of cellular morphology on their various functions such as survival, differentiation, migration, etc. An essential step for µCP is to fabricate a stamp from a silicon mould, prepared using lithography. Lithography is cost intensive and needs a high level of expertise to handle the instrumentation. Also, one stamp can be used to print patterns of one size and shape. Here, to overcome these limitations, we devised a low-cost fabrication technique using readily available objects such as injection needles and polystyrene beads. We patterned the C2C12, myoblasts cells on the shapes printed using lithography-free fabricated stamps. We further exploited the surface curvature of the stamp to vary the size of the print either by changing the applied load and/or the substrate stiffness. We showed that the print dimension could be predicted well by using JKR theory of contact mechanics. Moreover, some innovative improvisations enabled us to print complex shapes, which would be otherwise difficult with conventional lithography technique. We envisage that this low cost and easy to fabricate method will allow many research laboratories with limited resources to perform exciting research which is at present out of their reach.

DNA-Hybridization Detection on Si(100) Surfaces Using Light-Activated Electrochemistry: A Comparative Study between Bovine Serum Albumin and Hexaethylene Glycol as Antifouling Layers

Light can be used to spatially resolve electrochemical measurements on a semiconductor electrode. This phenomenon has been explored to detect DNA hybridization with light-addressable potentiometric sensors and, more recently, with light-addressable amperometric sensors based on organic-monolayer-protected Si(100). Here, a contribution to the field is presented by comparing sensing performances when bovine serum albumin (BSA) and hexaethylene glycol (OEG₆) are employed as antifouling layers that resist nonspecific adsorption to the DNA-modified interface on Si(100) devices. What is observed is that both sensors based on BSA or OEG₆ initially allow electrochemical distinction among complementary, noncomplementary, and mismatched DNA targets. However, only surfaces based on OEG₆ can sustain electroactivity over time. Our results suggest that this relates to accelerated SiO _x formation occasioned by BSA proteins adsorbing on monolayer-protected Si(100) surfaces. Therefore, DNA biosensors were analytically explored on low-doped Si(100) electrodes modified on the molecular level with OEG₆ as an antifouling layer. First, light-activated electrochemical responses were recorded over a range of complementary DNA target concentrations. A linear semilog relation was obtained from 1.0 × 10^-11 to 1.0 × 10^-6 mol L^-1 with a correlation coefficient of 0.942. Then, measurements with three independent surfaces indicated a relative standard deviation of 4.5%. Finally, selectivity tests were successfully performed in complex samples consisting of a cocktail mixture of four different DNA sequences. Together, these results indicate that reliable and stable light-activated amperometric DNA sensors can be achieved on Si(100) by employing OEG₆ as an antifouling layer.

Fabrication of Biomolecule Microarrays for Cell Immobilization Using Automated Microcontact Printing

Biomolecule microarrays are generally produced by conventional microarrayer, i.e., by contact or inkjet printing. Microcontact printing represents an alternative way of deposition of biomolecules on solid supports but even if various biomolecules have been successfully microcontact printed, the production of biomolecule microarrays in routine by microcontact printing remains a challenging task and needs an effective, fast, robust, and low-cost automation process. Here, we describe the production of biomolecule microarrays composed of extracellular matrix protein for the fabrication of cell microarrays by using an automated microcontact printing device. Large scale cell microarrays can be reproducibly obtained by this method.

Rapid real-time recirculating PCR using localized surface plasmon resonance (LSPR) and piezo-electric pumping

Rapid detection and characterization of pathogens in patients with bloodstream infections (BSIs) is a persistent problem for modern medicine, as current techniques are slow or provide incomplete diagnostic information. Real-time polymerase chain reaction (qPCR) allows specific detection of a wide range of targets and quantification of pathogenic burdens to aid in treatment planning. However, new technological advances are required for a rapid and multiplex implementation of qPCR in clinical applications. In this paper, the feasibility of a novel microfluidic platform for qPCR is presented, integrating highly sensitive, label-free localized surface plasmon resonance (LSPR) imaging of DNA hybridization into a recirculating chip design for real-time analysis. Single target and multiplex detection of DNA target amplification are demonstrated, with a limit of detection of 5 fg μL^-1 of E. coli DNA for single target PCR, correlating with approximately 300 bacteria per mL. The results of this study demonstrate the potential of this platform for simultaneous real-time detection of multiple target genes within 15 minutes that could provide live saving benefits in patients with BSIs.

A Programmable DNA Double-Write Material: Synergy of Photolithography and Self-Assembly Nanofabrication

We demonstrate a DNA double-write process that uses UV to pattern a uniquely designed DNA write material, which produces two distinct binding identities for hybridizing two different complementary DNA sequences. The process requires no modification to the DNA by chemical reagents and allows programmed DNA self-assembly and further UV patterning in the UV exposed and nonexposed areas. Multilayered DNA patterning with hybridization of fluorescently labeled complementary DNA sequences, biotin probe/fluorescent streptavidin complexes, and DNA patterns with 500 nm line widths were all demonstrated.

Automated and Multiplexed Soft Lithography for the Production of Low-Density DNA Microarrays

Microarrays are established research tools for genotyping, expression profiling, or molecular diagnostics in which DNA molecules are precisely addressed to the surface of a solid support. This study assesses the fabrication of low-density oligonucleotide arrays using an automated microcontact printing device, the InnoStamp 40(®). This automate allows a multiplexed deposition of oligoprobes on a functionalized surface by the use of a MacroStamp(TM) bearing 64 individual pillars each mounted with 50 circular micropatterns (spots) of 160 µm diameter at 320 µm pitch. Reliability and reuse of the MacroStamp(TM) were shown to be fast and robust by a simple washing step in 96% ethanol. The low-density microarrays printed on either epoxysilane or dendrimer-functionalized slides (DendriSlides) showed excellent hybridization response with complementary sequences at unusual low probe and target concentrations, since the actual probe density immobilized by this technology was at least 10-fold lower than with the conventional mechanical spotting. In addition, we found a comparable hybridization response in terms of fluorescence intensity between spotted and printed oligoarrays with a 1 nM complementary target by using a 50-fold lower probe concentration to produce the oligoarrays by the microcontact printing method. Taken together, our results lend support to the potential development of this multiplexed microcontact printing technology employing soft lithography as an alternative, cost-competitive tool for fabrication of low-density DNA microarrays.

Surface-enhanced Raman spectroscopy on porous silicon membranes decorated with Ag nanoparticles integrated in elastomeric microfluidic chips

An elastomeric microfluidic chip integrating SERS active silver-coated porous silicon membranes is developed, which performs label free and calibrated SERS analysis in a multi-analyte configuration.

Improved single-cell culture achieved using micromolding in capillaries technology coupled with poly (HEMA)

Cell studies at the single-cell level are becoming more and more critical for understanding the complex biological processes. Here, we present an optimization study investigating the positioning of single cells using micromolding in capillaries technology coupled with the cytophobic biomaterial poly (2-hydroxyethyl methacrylate) (poly (HEMA)). As a cytophobic biomaterial, poly (HEMA) was used to inhibit cells, whereas the glass was used as the substrate to provide a cell adhesive background. The poly (HEMA) chemical barrier was obtained using micromolding in capillaries, and the microchannel networks used for capillarity were easily achieved by reversibly bonding the polydimethylsiloxane mold and the glass. Finally, discrete cell adhesion regions were presented on the glass surface. This method is facile and low cost, and the reagents are commercially available. We validated the cytophobic abilities of the poly (HEMA), optimized the channel parameters for higher quality and more stable poly (HEMA) patterns by investigating the effects of changing the aspect ratio and the width of the microchannel on the poly (HEMA) grid pattern, and improved the single-cell occupancy by optimizing the dimensions of the cell adhesion regions.

Spatial regulation of controlled bioactive factor delivery for bone tissue engineering

Limitations of current treatment options for critical size bone defects create a significant clinical need for tissue engineered bone strategies. This review describes how control over the spatiotemporal delivery of growth factors, nucleic acids, and drugs and small molecules may aid in recapitulating signals present in bone development and healing, regenerating interfaces of bone with other connective tissues, and enhancing vascularization of tissue engineered bone. State-of-the-art technologies used to create spatially controlled patterns of bioactive factors on the surfaces of materials, to build up 3D materials with patterns of signal presentation within their bulk, and to pattern bioactive factor delivery after scaffold fabrication are presented, highlighting their applications in bone tissue engineering. As these techniques improve in areas such as spatial resolution and speed of patterning, they will continue to grow in value as model systems for understanding cell responses to spatially regulated bioactive factor signal presentation in vitro, and as strategies to investigate the capacity of the defined spatial arrangement of these signals to drive bone regeneration in vivo.

Molecular recognition of surface-immobilized carbohydrates by a synthetic lectin

The molecular recognition of carbohydrates and proteins mediates a wide range of physiological processes and the development of synthetic carbohydrate receptors (“synthetic lectins”) constitutes a key advance in biomedical technology. In this article we report a synthetic lectin that selectively binds to carbohydrates immobilized in a molecular monolayer. Inspired by our previous work, we prepared a fluorescently labeled synthetic lectin consisting of a cyclic dimer of the tripeptide Cys-His-Cys, which forms spontaneously by air oxidation of the monomer. Amine-tethered derivatives of N-acetylneuraminic acid (NANA), β-D-galactose, β-D-glucose and α-D-mannose were microcontact printed on epoxide-terminated self-assembled monolayers. Successive prints resulted in simple microarrays of two carbohydrates. The selectivity of the synthetic lectin was investigated by incubation on the immobilized carbohydrates. Selective binding of the synthetic lectin to immobilized NANA and β-D-galactose was observed by fluorescence microscopy. The selectivity and affinity of the synthetic lectin was screened in competition experiments. In addition, the carbohydrate binding of the synthetic lectin was compared with the carbohydrate binding of the lectins concanavalin A and peanut agglutinin. It was found that the printed carbohydrates retain their characteristic selectivity towards the synthetic and natural lectins and that the recognition of synthetic and natural lectins is strictly orthogonal.

High-precision robotic microcontact printing (R-μCP) utilizing a vision guided selectively compliant articulated robotic arm

Increased realization of the spatial heterogeneity found within in vivo tissue microenvironments has prompted the desire to engineer similar complexities into in vitro culture substrates. Microcontact printing (μCP) is a versatile technique for engineering such complexities onto cell culture substrates because it permits microscale control of the relative positioning of molecules and cells over large surface areas. However, challenges associated with precisely aligning and superimposing multiple μCP steps severely limits the extent of substrate modification that can be achieved using this method. Thus, we investigated the feasibility of using a vision guided selectively compliant articulated robotic arm (SCARA) for μCP applications. SCARAs are routinely used to perform high precision, repetitive tasks in manufacturing, and even low-end models are capable of achieving microscale precision. Here, we present customization of a SCARA to execute robotic-μCP (R-μCP) onto gold-coated microscope coverslips. The system not only possesses the ability to align multiple polydimethylsiloxane (PDMS) stamps but also has the capability to do so even after the substrates have been removed, reacted to graft polymer brushes, and replaced back into the system. Plus, non-biased computerized analysis shows that the system performs such sequential patterning with <10 μm precision and accuracy, which is equivalent to the repeatability specifications of the employed SCARA model. R-μCP should facilitate the engineering of complex in vivo-like complexities onto culture substrates and their integration with microfluidic devices.

A Simple Nanoscale Interface Directs Alignment of a Confluent Cell Layer on Oxide and Polymer Surfaces

Templating of cell spreading and proliferation is described that yields confluent layers of cells aligned across an entire two-dimensional surface. The template is a reactive, two-component interface that is synthesized in three steps in nanometer thick, micron-scaled patterns on silicon and on several biomaterial polymers. In this method, a volatile zirconium alkoxide complex is first deposited at reduced pressure onto a surface pattern that is prepared by photolithography; the substrate is then heated to thermolyze the organic ligands to form surface-bound zirconium oxide patterns. The thickness of this oxide layer ranges from 10 to 70 nanometers, which is controlled by alkoxide complex deposition time. The oxide layer is treated with 1,4-butanediphosphonic acid to give a monolayer pattern whose composition and spatial conformity to the photolithographic mask are determined spectroscopically. NIH 3T3 fibroblasts and human bone marrow-derived mesenchymal stem cells attach and spread in alignment with the pattern without constraint by physical means or by arrays of cytophilic and cytophobic molecules. Cell alignment with the pattern is maintained as cells grow to form a confluent monolayer across the entire substrate surface.

Microdevices for nanomedicine

This review surveys selected methods of manufacture and applications of microdevices-miniaturized functional devices capable of handling cell and tissue cultures or producing particles-and discusses their potential relevance to nanomedicine. Many characteristics of microdevices such as miniaturization, increased throughput, and the ability to mimic organ-specific microenvironments are promising for the rapid, low-cost evaluation of the efficacy and toxicity of nanomaterials. Their potential to accurately reproduce the physiological environments that occur in vivo could reduce dependence on animal models in pharmacological testing. Technologies in microfabrications and microfluidics are widely applicable for nanomaterial synthesis and for the development of diagnostic devices. Although the use of microdevices in nanomedicine is still in its infancy, these technologies show promise for enhancing fundamental and applied research in nanomedicine.

Transfer printing techniques for materials assembly and micro/nanodevice fabrication

Transfer printing represents a set of techniques for deterministic assembly of micro-and nanomaterials into spatially organized, functional arrangements with two and three-dimensional layouts. Such processes provide versatile routes not only to test structures and vehicles for scientific studies but also to high-performance, heterogeneously integrated functional systems, including those in flexible electronics, three-dimensional and/or curvilinear optoelectronics, and bio-integrated sensing and therapeutic devices. This article summarizes recent advances in a variety of transfer printing techniques, ranging from the mechanics and materials aspects that govern their operation to engineering features of their use in systems with varying levels of complexity. A concluding section presents perspectives on opportunities for basic and applied research, and on emerging use of these methods in high throughput, industrial-scale manufacturing.

DNA-nanostructure-assembly by sequential spotting

BACKGROUND

The ability to create nanostructures with biomolecules is one of the key elements in nanobiotechnology. One of the problems is the expensive and mostly custom made equipment which is needed for their development. We intended to reduce material costs and aimed at miniaturization of the necessary tools that are essential for nanofabrication. Thus we combined the capabilities of molecular ink lithography with DNA-self-assembling capabilities to arrange DNA in an independent array which allows addressing molecules in nanoscale dimensions.

RESULTS

For the construction of DNA based nanostructures a method is presented that allows an arrangement of DNA strands in such a way that they can form a grid that only depends on the spotted pattern of the anchor molecules. An atomic force microscope (AFM) has been used for molecular ink lithography to generate small spots. The sequential spotting process allows the immobilization of several different functional biomolecules with a single AFM-tip. This grid which delivers specific addresses for the prepared DNA-strand serves as a two-dimensional anchor to arrange the sequence according to the pattern. Once the DNA-nanoarray has been formed, it can be functionalized by PNA (peptide nucleic acid) to incorporate advanced structures.

CONCLUSIONS

The production of DNA-nanoarrays is a promising task for nanobiotechnology. The described method allows convenient and low cost preparation of nanoarrays. PNA can be used for complex functionalization purposes as well as a structural element.

Cell patterning using molecular vapor deposition of self-assembled monolayers and lift-off technique

This paper reports a precise, live cell-patterning method by means of patterning a silicon or glass substrate with alternating cytophilic and cytophobic self-assembled monolayers (SAMs) deposited via molecular vapor deposition. Specifically, a stack of hydrophobic heptadecafluoro-1,1,2,2-tetrahydrodecyltrichlorosilane SAMs and a silicon oxide adhesion layer were patterned on the substrate surface, and a hydrophilic SAM derived from 3-trimethoxysilyl propyldiethylenetriamine was coated on the remaining non-treated areas on the substrate surface to promote cell growth. The primary characteristics of the reported method include: (i) single-cell resolution; (ii) easy alignment of the patterns with the pre-existing patterns on the substrate; (iii) easy formation of nanoscale patterns (depending on the exposure equipment); (iv) long shelf life of the substrate pattern prior to cell culturing; (v) compatibility with conventional, inverted, optical microscopes for simple visualization of patterns formed on a glass wafer; and (vi) the ability to support patterned cell (osteoblast) networks for at least 2 weeks. Here, we describe the deposition technique and the characterization of the deposited layers, as well as the application of this method in the fabrication of multielectrode arrays supporting patterned neuronal networks.

Carbohydrate microarrays by microcontact printing

This Article describes the preparation of carbohydrate microarrays by the immobilization of carbohydrates via microcontact printing (microCP) on glass and silicon substrates. To this end, diene-modified carbohydrates (galactose, glucose, mannose, lactose, and maltose) were printed on maleimide-terminated self-assembled monolayers (SAMs). A Diels-Alder reaction occurred exclusively in the contact area between stamp and substrate and resulted in a carbohydrate pattern on the substrate. It was found that cyclopentadiene-functionalized carbohydrates could be printed within minutes at room temperature, whereas furan-functionalized carbohydrates required long printing times and high temperatures. By successive printing, microstructured arrays of up to three different carbohydrates could be produced. Immobilization and patterning of the carbohydrates on the surfaces was investigated with contact angle measurements, X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (TOF-SIMS), and fluorescence microscopy. Furthermore, the lectins concanavalin A (ConA) and peanut agglutinin (PNA) bind to the microarrays, and the printed carbohydrates retain their characteristic selectivity toward these proteins.

Probing differential Ag+-nucleobase interactions with isothermal titration calorimetry (ITC): Towards patterned DNA metallization

DNA has been successfully used as a scaffold for the fabrication of metallic nanowires, primarily based on the electrostatic complexation and reduction of the metal cations on the negatively charged sugar-phosphate backbone. Here, we probe the differential binding affinities of nucleobases for silver ions using sensitive isothermal titration calorimetry (ITC) measurements of the reaction enthalpies, which go in order: C > G > A > or = T. Using the disparity between the interaction of cytosine (strong binding) and thymine (weak binding) with silver ions, we have successfully generated silver nanoparticle doublets and triplets on custom-made oligonucleotides, C(30)-T(40)-C(30) and C(20)-T(20)-C(20)-T(20)-C(20), respectively. Thus, a new and simple method of generating metallized DNA wires is presented, based entirely on the nucleotide sequence of DNA. The concept could be extended to other cations and complex DNA sequences in order to achieve intricately patterned DNA constructs.

Fabrication of protein dot arrays via particle lithography

The ability to pattern a surface with proteins on both the nanometer and the micrometer scale has attracted considerable interest due to its applications in the fields of biomaterials, biosensors, and cell adhesion. Here, we describe a simple particle lithography technique to fabricate substrates with hexagonally patterned dots of protein surrounded by a protein-repellent layer of poly(ethylene glycol). Using this bottom-up approach, dot arrays of three different proteins (fibrinogen, P-selectin, and human serum albumin) were fabricated. The size of the protein dots (450 nm to 1.1 microm) was independent of the protein immobilized but could be varied by changing the size of the latex spheres (diameter=2-10 microm) utilized in assembling the lithographic bead monolayer. These results suggest that this technique can be extended to other biomolecules and will be useful in applications where arrays of protein dots are desired.

Grafting of antibodies inside integrated microfluidic-microoptic devices by means of automated microcontact printing

A novel approach to integrating biochip and microfluidic devices is reported in which microcontact printing is a key fabrication technique. The process is performed using an automated microcontact printer that has been developed as an application-specific tool. As proof-of-concept the instrument is used to consecutively and selectively graft patterns of antibodies at the bottom of a glass channel for use in microfluidic immunoassays. Importantly, feature collapse due to over compression of the PDMS stamp is avoided by fine control of the stamp's compression during contact. The precise alignment of biomolecules at the intersection of microfluidic channel and integrated optical waveguides has been achieved, with antigen detection performed via fluorescence excitation. Thus, it has been demonstrated that this technology permits sequential microcontact printing of isolated features consisting of functional biomolecules at any position along a microfluidic channel and also that it is possible to precisely align these features with existing components.

Nanoscale patterns of oligonucleotides formed by electrohydrodynamic jet printing with applications in biosensing and nanomaterials assembly

The widespread use of DNA in microarrays for applications in biotechnology, combined with its promise in programmed nanomaterials assembly, unusual electronic devices, and other areas has created interest in methods for patterning DNA with high spatial resolution. Techniques based on thermal or piezoelectric inkjet printing are attractive due to their noncontacting nature and their compatibility with diverse materials and substrate types; their modest resolution (i.e., 10-20 microm) represents a major limitation for certain systems. Here we demonstrate the use of an operationally similar printing approach that exploits electrohydrodynamic forces, rather than thermal or acoustic energy, to eject DNA inks through fine nozzles, in a controlled fashion. This DNA printer is capable of resolution approaching 100 nm. A range of experiments on patterns of DNA formed with this printer demonstrates its key features. Example applications in DNA-directed nanoparticle assembly and DNA aptamer-based biosensing illustrate two representative uses of the patterns that can be formed.

A microcontact printing approach to the immobilization of oligonucleotide brushes

Solution hybridized oligonucleotides were immobilized onto surfaces via micro-contact printing. Besides micro-patterning of the substrate, sequential dehybridization and rehybridization were monitored via laser scanning microscopy, which assess the surface tethering of the oligonucleotides into a brush.

Immunological identification of fibrinogen in dual-component protein films by AFM imaging

The success of long-term blood-contacting implanted devices is largely dependent upon the interaction of the blood components with the device biomaterial surface. The ability to study these interactions has been hindered by a lack of methods to measure single-molecule interactions in complex multi-protein environments similar to the environment found in vivo. In this paper, we demonstrate the use of atomic force microscopy (AFM) in conjunction with gold nanolabels to detect the protein fibrinogen under aqueous conditions without the topographical clues usually necessary for high resolution visualization. BSA was patterned onto both muscovite mica and plasma-treated polydimethylsiloxane (PDMS) substrates and these test substrates were subsequently backfilled with fibrinogen to yield a featureless protein layer. The fibrinogen in this dual-protein layer was detected using high resolution AFM imaging following infusion of anti-fibrinogen conjugated with nanogold particles. This AFM immuno-detection technique will potentially be applicable to complex multi-component protein films adsorbed on clinically relevant polymers used in medical devices.

A new instrument for automated microcontact printing with stamp load adjustment

An instrument for automated microcontact printing (microCP) on microscope slides is described. The movement of the stamp, which is actuated by a computer controlled pneumatic actuator, is precisely guided until it makes contact with the substrate. As a consequence, the absolute position of the microprinted patterns is reproducible over a series of substrates with 1 mum standard deviation. Exchange of substrates and stamps is a quick and simple procedure. This makes possible the microprinting of adjacent or superimposable patterns, with different products, in a reproducible manner. Furthermore, a novel approach is described for adjusting the load on the stamp during contact. Two adjustable screws are set up so that their length (with reference to the substrate holder) limits the stamp compression during contact. The load on the stamp is proportional to the stamp compression and from the experimental point of view, this is controlled by the operator adjusting the screws. This makes possible the microCP with stamps incorporating large surface features as well as stamps with isolated features raised on the surface. For proof of concept, automated microCP of a single parallelepiped polydimethylsiloxane feature, with a surface of 2 cm x 30 microm and a height of 25 mum, is demonstrated inside a microfluidic channel without roof collapse. A second example is provided with a single cross feature, possessing an overall surface of 140 x 140 microm(2) and a height of 14 microm. Potential applications of this versatile, inexpensive and compact instrument are discussed. The machine's potential for high throughput also makes it suitable for mass production applications.

Use of gamma-aminopropyl-coated glass surface for the patterning of oligonucleotides through oxime bond formation

The present work reports on the preparation of glass surfaces coated with NPPOC-protected aminooxy groups and their use for the patterning of oligonucleotides on glass slides and in capillary tubes. The method involves the use of surfaces coated with amino groups using (gamma-aminopropyl)triethoxy silane and subsequent grafting of the aminooxy groups by using the activated ester 1. The NPPOC-protected aminooxy groups on the surfaces can be cleaved upon irradiation. The free aminooxy groups so obtained are subsequently reacted with aldehyde-containing oligonucleotides to achieve efficient surface patterning.

Magnetic assembly of high-density DNA arrays for genomic analyses

A method for rapidly assembling high-density DNA arrays with near-perfect order is described. Photolithography is used to generate a wafer-scale array of microwells in a layer of photoresist on a chemically functionalized glass coverslip. The array is enclosed within a microfluidic device, and a suspension of superparamagnetic microbeads conjugated to DNA molecules is introduced into the chamber. A permanent magnet is used to direct the rapid assembly of the beads into the wells, with each well containing a single bead. These beads are immobilized on the glass surface via affinity binding, and excess beads can be recycled or washed away. Nonspecifically bound beads are removed by dissolving the photoresist. The result is a high-density array of beads with virtually no background. This method can be used to produce protein arrays for chip-based assays and DNA arrays for genotyping or genome sequencing.

Poly(dimethylsiloxane) contamination in microcontact printing and its influence on patterning oligonucleotides

It is well-established that, during microcontact printing (muCP) using poly(dimethylsiloxane) (PDMS)-based stamps, some unexpected siloxane fragments can be transferred from the stamp to the surface of the sample. This so-called contamination effect coexists with the delivery of the molecules constituting the ink and by this way influences the printing process. The real impact of this contamination for the muCP technique is still partially unknown. In this work, we investigate the kinetics of this contamination process through the surface characterization of both the sample and the stamp after imprinting. The way both the curing conditions of the PDMS material and the contact time influence the degree of contamination of the surface is investigated on silicon and glass substrates. We propose a cleaning process of the stamp during several hours which eliminates any trace of contamination during printing. We show that hydrophobicity recovery of PDMS surfaces after hydrophilic treatment using oxygen plasma is considerably slowed down when the PDMS material is cleaned using our procedure. Finally, by comparing cleaned and uncleaned PDMS stamps, we show the influence of contamination on the quality of muCP using fluorescent DNA molecules as an ink. Surprisingly, we observe that the amount of DNA molecules transferred during muCP is higher for the uncleaned stamp, highlighting the positive impact of the presence of low molecular weight siloxane fragments on the muCP process. This result is attributed to the better adsorption of oligonucleotides on the stamp surface in presence of these contaminating molecules.

Dendrimer-Mediated Transfer Printing of DNA and RNA Microarrays

This paper describes a new method to replicate DNA and RNA microarrays. The technique, which facilitates positioning of DNA and RNA with submicron edge resolution by microcontact printing (muCP), is based on the modification of poly(dimethylsiloxane) (PDMS) stamps with dendrimers ("dendri-stamps"). The modification of PDMS stamps with generation 5 poly(propylene imine) dendrimers (G5-PPI) gives a high density of positive charge on the stamp surface that can attract negatively charged oligonucleotides in a "layer-by-layer" arrangement. DNA as well as RNA is transfer printed from the stamp to a target surface. Imine chemistry is applied to immobilize amino-modified DNA and RNA molecules to an aldehyde-terminated substrate. The labile imine bond is reduced to a stable secondary amine bond, forming a robust connection between the polynucleotide strand and the solid support. Microcontact printed oligonucleotides are distributed homogeneously within the patterned area and available for hybridization. By using a robotic spotting system, an array of hundreds of oligonucleotide spots is deposited on the surface of a flat, dendrimer-modified stamp that is subsequently used for repeated replication of the entire microarray by microcontact printing. The printed microarrays are characterized by homogeneous probe density and regular spot morphology.

Transferring complementary target DNA from aqueous solutions onto solid surfaces by using affinity microcontact printing

In this paper, we report a method of transferring complementary target DNA from an aqueous solution onto a solid surface by using affinity microcontact printing. In this approach, the probe DNA is first immobilized on the surface of an aminated poly(dimethylsiloxane) (PDMS) stamp. After a complementary target DNA hybridizes with the probe DNA on the stamp surface, the PDMS stamp is printed on an aminated glass slide. By using fluorescent microscopy, we show that only complementary target DNA, but not noncomplementary DNA, can be captured onto the surface of the stamp and then transferred to the aminated glass slide. The transfer of DNA can be attributed to the stronger electrostatic attraction between DNA and amine groups compared to the hydrogen bonds between the hybridized DNA molecules. We also investigate several factors that may influence the transfer of DNA, such as the surface density of amine groups, hybridization conditions, and contamination from unreacted PDMS monomers.

Immobilization of oligonucleotides on glass surface using an efficient heterobifunctional reagent through maleimide-thiol combination chemistry

An efficient heterobifunctional reagent, N-(3-triethoxysilylpropyl)-4-(N'-maleimidylmethyl) cyclohexanamide (TPMC), was developed for the immobilization of thiol-modified oligonucleotides on an unmodified glass surface. The heterobifunctionality of the reagent was used for the construction of a DNA microarray in which the triethoxysilyl functionality has specificity toward a glass surface, whereas the maleimide functionality has thiol-modified oligonucleotides via a stable thioether linkage. Immobilization of DNA was achieved by two alternative approaches. In the first approach, the reagent TPMC was treated with oligonucleotides to get triethoxysilyl-oligonucleotide conjugate, which was then covalently attached via specific triethoxysilyl functionality to an unmodified glass surface. In the second approach, the reagent was first covalently linked with an unmodified glass surface to get maleimide functionality on a glass surface, which was then used for the immobilization of oligonucleotides via a stable thioether linkage. The applicability of the reagent was explored by hybridization studies with the fluorescein-labeled complementary DNA strand and in mismatch discrimination.

Efficient surface patterning of oligonucleotides inside a glass capillary through oxime bond formation

The efficient surface patterning of oligonucleotides was accomplished onto the inner wall of fused-silica capillary tubes as well as on the surface of glass slides through oxime bond formation. The robustness of the method was demonstrated by achieving the surface immobilization of up to three different oligonucleotide sequences inside the same capillary tube. The method involves the preparation of surfaces grafted with reactive aminooxy functionalities masked with the photocleavable protecting group, 2-(2-nitrophenyl) propyloxycarbonyl group (NPPOC). Briefly, NPPOC-aminooxy silane 1 was prepared and used to silanize the glass surfaces. The NPPOC group was cleaved under brief irradiation to unmask the reactive aminooxy group on surfaces. These reactive aminooxy groups were allowed to react with aldehyde-containing oligonucleotides to achieve an efficient surface immobilization. The advantage associated with the present approach is that it combines the high-coupling efficiency of oxime bond formation with the convenience associated with the use of photolabile groups. The present strategy thus offers an alternative approach for the immobilization of biomolecules in the microchannels of "labs on a chip" devices.

Microcontact printing: A tool to pattern

Microcontact printing has proven to be a useful technique in the patterned functionalization of certain chemicals onto surfaces. It has been particularly valuable in the patterning of biological materials. In this review, we describe the basic principles of the technology as well as its use in several applications, with an emphasis on biological ones. We also discuss the limitations and future directions of this method.

Increasing the sensitivity of DNA microarrays by metal-enhanced fluorescence using surface-bound silver nanoparticles

The effects of metal-enhanced fluorescence (MEF) have been measured for two dyes commonly used in DNA microarrays, Cy3 and Cy5. Silver island films (SIFs) grown on glass microscope slides were used as substrates for MEF DNA arrays. We examined MEF by spotting biotinylated, singly-labeled 23 bp DNAs onto avidin-coated SIF substrates. The fluorescence enhancement was found to be dependent on the DNA spotting concentration: below approximately 12.5 muM, MEF increased linearly, and at higher concentrations MEF remained at a constant maximum of 28-fold for Cy5 and 4-fold for Cy3, compared to avidin-coated glass substrates. Hybridization of singly-labeled oligonucleotides to arrayed single-stranded probes showed lower maximal MEF factors of 10-fold for Cy5 and 2.5-fold for Cy3, because of the smaller amount of immobilized fluorophores as a result of reduced surface hybridization efficiencies. We discuss how MEF can be used to increase the sensitivity of DNA arrays, especially for far red emitting fluorophores like Cy5, without significantly altering current microarray protocols.