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.     

Microscale plasma-initiated patterning (muPIP)

A novel technique to create biomolecular micropatterns of varying complexity on several types of polymer substrates is presented. This method uses a patterned PDMS stamp to preferentially expose or protect areas of an underlying polymer substrate from oxygen plasma. Following plasma treatment, the substrate is immersed in a biomolecular ink, whereby molecules preferentially adsorb to either the plasma-exposed or plasma-protected substrate regions, depending on the particular substrate/ink combination. Using this method, polyethylene (PE), polystyrene (PS), poly(methyl methacrylate) (PMMA), poly(dimethylsiloxane) (PDMS), and poly(hydroxybutyrate/hydroxyvalerate) (PHBV) were micropatterned with different aqueous-based biomolecular inks (i.e., goat anti-rabbit immunoglobulin G, poly-l-lysine, and bovine serum albumin (BSA)). Water contact angle measurements performed on substrates after oxygen plasma exposure showed that the hydrophilicity of substrate areas exposed to plasma was significantly greater than that of areas protected from plasma by the PDMS stamp. In addition, scanning electron microscopy results demonstrated that substrate areas exposed to plasma were physically modified (e.g., roughened) compared to adjacent, protected areas. Areas in contact with a patterned PDMS stamp during plasma exposure were found to be physically unaffected by plasma treatment, and exhibited spatial features/dimensions consistent with the corresponding features of the patterned stamp. Last, protein patterns of BSA on the polymer substrates were stable and distinct after 4 weeks of incubation at 37 degrees C.     

Hydrophilic elastomers for microcontact printing of polar inks

A moderately hydrophilic, thermoplastic elastomer (poly(ether-ester)) was investigated as a stamp material for microcontact printing of a polar ink: pentaerythritol-tetrakis-(3-mercaptopropionate). Stamps with a relief structure were produced from this polymer by hot embossing, and a comparison was made with conventional poly(dimethylsiloxane) (PDMS) and oxygen-plasma-treated PDMS. It is shown that the hydrophilic stamps can be used for the repetitive printing (without re-inking) of at least 10 consecutive patterns, which preserve their etch resistance, and this in rather sharp contrast to conventional and oxygen plasma-treated PDMS stamps. It is argued that these enhanced printing characteristics of the hydrophilic stamps originate from an improved wetting and solubility of polar inks in the hydrophilic stamp.     

Surface modification of elastomeric stamps for microcontact printing of polar inks

Chemical modification of the surface of a stamp used for microcontact printing (microCP) is interesting for controling the surface properties, such as the hydrophilicity. To print polar inks, plasma polymerization of allylamine (PPAA) was employed to render the surface of poly(dimethylsiloxane) (PDMS), polyolefin plastomers (POP), and Kraton elatomeric stamps hydrophilic for long periods of time. A thin PPAA film of about 5 nm was deposited on the stamps, which increased the hydrophilicity, and which remained stable for at least several months. These surface-modified stamps were used to transfer polar inks by microCP. The employed microCP schemes are as follows: (a) a second generation of dendritic ink having eight dialkyl sulfide end groups to fabricate patterns on gold substrates by positive microCP, (b) fluorescent guest molecules on beta-cyclodextrin (beta-CD) printboards on glass employing host-guest recognition, and (c) Lucifer Yellow ethylenediamine resulting in covalent patterning on an aldehyde-terminated glass surface. All experiments resulted in an excellent performance of all three PPAA-coated stamp materials to transfer the polar inks from the stamp surface to gold and glass substrates by microCP, even from aqueous solutions.     

Microcontact printing of proteins inside microstructures

Microfluidic devices are well suited for the miniaturization of biological assays, in particular when only small volumes of samples and reagents are available, short time to results is desirable, and multiple analytes are to be detected. Microfluidic networks (MFNs), which fill by means of capillary forces, have already been used to detect important biological analytes with high sensitivity and in a combinatorial fashion. These MFNs were coated with Au, onto which a hydrophilic, protein-repellent monolayer of thiolated poly(ethyleneglycol) (HS-PEG) was self-assembled, and the binding sites for analytes were present on a poly(dimethylsiloxane) (PDMS) sealing cover. We report here a set of simple methods to extend previous work on MFNs by integrating binding sites for analytes inside the microstructures of MFNs using microcontact printing (muCP). First, fluorescently labeled antibodies (Abs) were microcontact-printed from stamps onto planar model surfaces such as glass, Si, Si/SiO2, Au, and Au derivatized with HS-PEG to investigate how much candidate materials for MFNs would quench the fluorescence of printed, labeled Abs. Au coated with HS-PEG led to a fluorescence signal that was approximately 65% weaker than that of glass but provided a convenient surface for printing Abs and for rendering the microstructures of the MFNs wettable. Then, proteins were inked from solution onto the surface of PDMS (Sylgard 184) stamps having continuous or discontinuous micropatterns or locally inked onto planar stamps to investigate how the aspect ratio (depth:width) of microstructures and the printing conditions affected the transfer of protein and the accuracy of the resulting patterns. By applying a controlled pressure to the back of the stamp, Abs were accurately microcontact-printed into the recessed regions of MFNs if the aspect ratio of the MFN microstructures was lower than approximately 1:6. Finally, the realization of a simple assay between Abs (used as antigens) microcontact-printed in microchannels and Abs from solution suggests that this method could become useful to pattern proteins in microstructures for advanced bioanalytical purposes.     

Bifunctional, chemically patterned flat stamps for microcontact printing of polar inks

Different methods to create chemically patterned, flat PDMS stamps with two different chemical functionalities were compared. The best method for making such stamps, functionalized with 1H,1H,2H,2H-perfluorodecyltrichlorosilane (PFDTS) and 3-(aminopropyl)triethoxysilane (APTS), appeared to be full functionalization of a freshly oxidized flat PDMS stamp with either adsorbate, followed by renewed oxidation through a mask and attachment of the other adsorbate. These stamps were used to transfer polar inks (a thioether-functionalized dendrimer and a fluorescent dye) by microcontact printing. The PFDTS monolayer was used as a barrier against ink transfer, while the APTS SAM areas functioned as an ink reservoir for polar inks. The printing results confirmed the excellent transfer of hydrophilic inks with these stamps to gold and glass substrates, even from aqueous solutions. Attachment of a fluorescent dye on the amino-functionalized regions shows the possibility of the further modification of the chemically patterned stamps for tailoring of the stamps' properties.     

Diffusion of alkanethiols in PDMS and its implications on microcontact printing (muCP)

n-Alkanethiols HS-(CH2)n-CH3 such as hexadecanethiol (HDT, n = 15), octadecanethiol (ODT, n = 17), and eicosanethiol (ECT, n = 19) have been shown to provide highly protective etch resists on microcontact-printed noble metals. As the quality of the printed pattern strongly depends on the mobility of the ink compound, we focused on understanding the diffusion behavior of HDT, ODT, and ECT in poly(dimethylsiloxane) (PDMS) stamps. We used a commercial PDMS material (Sylgard184), which is commonly used for microcontact printing (muCP), and a custom-synthesized one with a higher modulus. On the basis of linear-diffusion experiments, which maintained realistic printing conditions, we showed that the ink transport in the stamp follows Fick's law of diffusion. We then determined the diffusion coefficient by analytical and numerical modeling of the diffusion experiments. Numerical calculations were carried out with the finite-difference method applying more realistic boundary conditions (ink adsorption). Values for the diffusion coefficients of the three ink compounds in the two different PDMS materials all are on the order of (4-7) x 10(-7) cm2 s(-1). The scope and limits of the mathematical models are discussed. To demonstrate the potential of such models for microcontact printing, we simulate multiple printing cycles of an inked stamp and compare the results with experimental data.     

A Simple Method for Fabricating Patterned Curvilinear Microstructures in Poly(dimethylsiloxane) by Selective Wetting

The fabrication of patterned microstructures in poly(dimethylsiloxane) (PDMS) is a prerequisite for soft lithography. Herein, curvilinear surface relief microstructures in PDMS are fabricated through a simple three‐stage approach combining microcontact printing (μCP), selective surface wetting/dewetting and replica molding (REM). First, using an original PDMS stamp (first‐generation stamp) with linear relief features, a chemical pattern on gold substrate is generated by μCP using hexadecanethiol (HDT) as an ink. Then, by a dip‐coating process, an ordered polyethylene glycol (PEG) polymer‐dot array forms on the HDT‐patterned gold substrate. Finally, based on a REM process, the PEG‐dot array on gold substrate is used to fabricate a second‐generation PDMS stamp with microcavity array, and the second‐generation PDMS stamp is used to generate third‐generation PDMS stamp with microbump array. These fabricated new‐generation stamps are utilized in μCP and in micromolding in capillaries (MIMIC), allowing the generation of surface micropatterns which cannot be obtained using the original PDMS stamp. The method will be useful in producing new‐generation PDMS stamps, especially for those who want to use soft lithography in their studies but have no access to the microfabrication facilities.     

Versatile Stamps in Microcontact Printing: Transferring Inks by Molecular Recognition and from Ink Reservoirs

Microcontact printing is a heavily used surface modification method in materials and life science applications. This concept article focuses on the development of versatile stamps for microcontact printing that can be used to bind and release inks through molecular recognition or through an ink reservoir, the latter being used for the transfer of heavy inks, such as biomolecules and particles. Conceptually, such stamp properties can be introduced at the stamp surface or by changing the bulk stamp material; both lines of research will be reviewed here. Examples include supramolecular stamps with affinity properties, polymer‐layer‐grafted PDMS stamps, and porous multilayer‐grafted PDMS stamps for the first case, and hydrogel stamps and porous stamps made by phase‐separation micromolding for the second. Potential directions for future advancement of this field are also discussed.     

Micro/nanopatterning of proteins via contact printing using high aspect ratio PMMA stamps and nanoimprint apparatus

Micro- and nanoscale protein patterns have been produced via a new contact printing method using a nanoimprint lithography apparatus. The main novelty of the technique is the use of poly(methyl methacrylate) (PMMA) instead of the commonly used poly(dimethylsiloxane) (PDMS) stamps. This avoids printing problems due to roof collapse, which limits the usable aspect ratio in microcontact printing to 10:1. The rigidity of the PMMA allows protein patterning using stamps with very high aspect ratios, up to 300 in this case. Conformal contact between the stamp and the substrate is achieved because of the homogeneous pressure applied via the nanoimprint lithography instrument, and it has allowed us to print lines of protein approximately 150 nm wide, at a 400 nm period. This technique, therefore, provides an excellent method for the direct printing of high-density sub-micrometer scale patterns, or, alternatively, micro-/nanopatterns spaced at large distances. The controlled production of these protein patterns is a key factor in biomedical applications such as cell-surface interaction experiments and tissue engineering.     

Microcontact printing of monodiamond nanoparticles: an effective route to patterned diamond structure fabrication

By combining microcontact printing with a nanodiamond seeding technique, a precise micrometer-sized chemical vapor deposition (CVD) diamond pattern have been obtained. On the basis of the guidance of basic theoretical calculations, monodisperse detonation nanodiamonds (DNDs) were chosen as an "ink" material and oxidized poly(dimethylsiloxane) (PDMS) was selected to serve as a stamp because it features a higher interaction energy with the DNDs compared to that of the original PDMS. The adsorption kinetics shows an approximately exponential law with a maximum surface DND density of 3.4 × 10(10) cm(-2) after 20 min. To achieve a high transfer ratio of DNDs from the PDMS stamp to a silicon surface, a thin layer of poly(methyl methacrylate) (PMMA) was spin coated onto the substrates. A microwave plasma chemical vapor deposition system was used to synthesize the CVD diamond on the seeded substrate areas. Precise diamond patterns with a low expansion ratio (3.6%) were successfully prepared after 1.5 h of deposition. Further increases in the deposition time typically lead to a high expansion rate (～0.8 μm/h). The general pattern shape, however, did not show any significant change. Compared with conventional diamond pattern deposition methods, the technique described here offers the advantages of being simple, inexpensive, damage-free, and highly compatible, rendering it attractive for a broad variety of industrial applications.     

Light stamping lithography: microcontact printing without inks

We report a new patterning method, called light-stamping lithography (LSL), that uses UV-induced adhesion of poly(dimethylsiloxane) (PDMS). LSL is based on the direct transfer of the contact surface of the PDMS stamp to a substrate via a UV (254 nm)-induced surface bonding between the stamp and the substrate. This procedure can be adopted in automated printing machines that generate patterns with a wide range of feature sizes on diverse substrates. To demonstrate its usefulness, the LSL method was applied to prepare several PDMS patterns on a variety of substrates. The PDMS patterns were then used as templates for selective deposition of TiO2 thin film using atomic layer deposition as well as resists for selective wet etching.     

Creating patterned carbon nanotube catalysts through the microcontact printing of block copolymer micellar thin films

We report a route for synthesizing patterned carbon nanotube (CNT) catalysts through the microcontact printing of iron-loaded poly(styrene-block-acrylic acid) (PS-b-PAA) micellar solutions onto silicon wafers coated with thin aluminum oxide (Al(2)O(3)) layers. The amphiphilic block copolymer, PS-b-PAA, forms spherical micelles in toluene that can form quasi-hexagonal arrays of spherical PAA domains within a PS matrix when deposited onto a substrate. In this report, we dip a poly(dimethylsiloxane) (PDMS) molded stamp into an iron-loaded micellar solution to create a thin film on the PDMS features. The PDMS stamp is then put in contact with a substrate, and uniaxial compressive stress is applied to transfer the micellar thin film from the PDMS stamp onto the substrate in a defined pattern. The polymer is then removed by oxygen plasma etching to leave a patterned iron oxide nanocluster array on the substrate. Using these catalysts, we achieve patterned vertical growth of multiwalled CNTs, where the CNTs maintain the fidelity of the patterned catalyst, forming high-aspect-ratio standing structures.     

Characterization of supported membranes on topographically patterned polymeric elastomers and their applications to microcontact printing

This article describes the fluorescence microscopy and imaging ellipsometry-based characterization of supported phospholipid bilayer formation on elastomeric substrates and its application in microcontact printing of spatially patterned phospholipid bilayers. Elastomeric stamps, displaying a uniformly spaced array of square wells (20, 50, and 100 mum linear dimensions), are prepared using poly(dimethyl)siloxane from photolithographically derived silicon masters. Exposing elastomeric stamps, following UV/ozone-induced oxidation, to a solution of small unilamellar phospholipid vesicles results in the formation of a 2D contiguous, fluid phospholipid bilayers. The bilayer covers both the elevated and depressed regions of the stamp and exhibits a lateral connectivity allowing molecular transport across the topographic boundaries. Applications of these bilayer-coated elastomeric stamps in microcontact printing of lipid bilayers reveal a fluid-tearing process wherein the bilayer in contact regions selectively transfers with 75-90% efficiency, leaving behind unperturbed patches in the depressed regions of the stamp. Next, using cholera-toxin binding fluid POPC bilayers that have been asymmetrically doped with ganglioside Gm1 ligand in the outer leaflets, we examine whether the microcontact transfer of bilayers results in the inversion of the lipid leaflets. Our results suggest a complex transfer process involving at least partial bilayer reorganization and molecular re-equilibration during (or upon) substrate transfer. Taken together, the study sheds light on the structuring of lipid inks on PDMS elastomers and provides clues regarding the mechanism of bilayer transfer. It further highlights some important differences in stamping fluid bilayers from the more routine applications of stamping in the creation of patterned self-assembled monolayers.     

Fishing DNA targets in DNA solutions by using affinity microcontact printing

In this paper, we report the application of affinity microcontact printing (αCP) for "fishing" DNA targets in aqueous solutions and transferring them to solid surfaces for detection purposes. Affinity stamps used in this experiment were made of poly(dimethylsiloxane) (PDMS) with DNA probes covalently immobilized on their surface. When these stamps were immersed in DNA solutions, DNA targets with a perfect-match (PM) sequence to the probes can selectively hybridize to the stamp surfaces and then be transferred to solid surfaces. However, to distinguish PM DNA from single base-pair mismatch (1MM) DNA targets, 10 mM of NaCl must be added to the hybridization buffer. Under the optimized conditions, this αCP can lead to a surface density of PM which is 15 times higher than that of 1MM. The affinity stamp is also able to "fish" PM DNA targets from a mixture of PM/1MM DNA targets and transfer them to solid surfaces. Because DNA probes and targets are separated after printing, we also applied this technique for label-free detection of DNA targets by using liquid crystals.     

Microscale features and surface chemical functionality patterned by electron beam lithography: a novel route to poly(dimethylsiloxane) (PDMS) stamp fabrication

Poly(dimethylsiloxane) (PDMS) has become a ubiquitous material for microcontact printing, yet there are few methods available to pattern a completed PDMS stamp in a single step. It is shown here that electron beam lithography (EBL) is effective in writing patterns directly onto cured PDMS stamps, thus overcoming the need for multiple patterning steps. Not only does this method allow the modification of an existing lithographic pattern, but new 3D features such as cones, pits, and channels can also be fabricated. EBL can also be used to fabricate PDMS masks for photolithography whereby 1:1 pattern transfer into a photoresist is achieved. Additionally, direct EBL writing of surface chemical features has been achieved using a PDMS stamp coated with a self-assembled monolayer. An electrostatic mechanism appears to be operative in the EBL patterning process, as supported by calculations, thermogravimetric analysis, time-of-flight secondary ion mass spectroscopy, optical and atomic force microscopy, and chemical functionalization assays.     

Duplication of photoinduced azo polymer surface-relief gratings through a soft lithographic approach

In this work, a soft lithographic approach has been developed to duplicate photoinduced surface-relief-gratings (SRGs) of azo polymer films to generate the surface pattern replicas composed of different materials on various substrates. For this purpose, thin films of an epoxy-based azo polymer (BP-AZ-CA) were prepared by spin-coating, and SRGs with different structures were inscribed by exposing the films to interference patterns of Ar(+) laser beams at modest intensity (150 mW/cm(2)). Using the azo polymer films as masters, stamps of poly(dimethylsiloxane) (PDMS) were prepared by replica molding. The PDMS stamps were then used to transfer the solutions of poly(3-hexylthiophene) (P3HT), multiwalled carbon nanotube (MWNT), and BP-AZ-CA to different substrates by contact printing. Through this process, surface pattern replicas made of the functional materials were obtained. The pattern formation and quality depended on the factors such as the solution concentration, contacting time in the printing process, and printing pressure. Under the proper conditions, the printed patterns showed the same grating periods as the masters and the same relief depths as the stamps (replicas of the masters). This approach, showing some attractive characteristics such as the easiness of master preparation and the versatility of soft fabrication processes, can be applied to the fabrications of optical functional surfaces, sensors, and photonic devices.     

Analysis of Dynamic and Thermodynamic Adsorption of Nanoparticles on Solid Surfaces by Dark‐Field Light Scattering Measurements

We have constructed a dark‐field light scattering microscope using a very low‐cost digital camera to investigate the adsorption of gold nanoparticles (AuNPs) on four different substrates at various pH values. The substrates used are glass, polycarbonate (PC), poly(dimethylsiloxane) (PDMS), and poly(methyl methacrylate) (PMMA). The coverage of AuNPs on hydrophobic substrates such as PDMS is greater than that on hydrophilic substrates like glass. The adsorption and aggregation of AuNPs on a particular substrate increased upon decreasing the pH (from 9.0 to 4.0). A greater coverage percentage of AuNPs, but less aggregation, occurs on glass treated with poly(diallyldimethylammonium) (PDDA) than on bare glass. The scattering intensity increases upon increasing the number of layers of adsorbed AuNPs on glass that was treated sequentially with AuNPs and PDDA. When compared to UV‐Vis absorption, dark‐field microscope provides greater sensitivity and qualitative surface information.     

Direct printing of self-assembled lipid tubules on substrates

Lipid tubules formed by rolled-up bilayer sheets have shown promise in drug delivery systems, nanofluidics, and microelectronics. Here we report a method for directly printing lipid tubules on substrates. Preformed lipid tubules of 1,2-bis(tricosa-10,12-diynoyl)-sn-glycero-3-phosphocholine are aligned in the recessed channels of a thin poly(dimethylsiloxane) (PDMS) stamp. The aligned lipid tubules then serve as an "ink" for microcontact printing. We demonstrate that two-dimensional (2-D) arrays of aligned lipid tubules can be transferred onto planar, patterned, and curved substrates from the recessed channels of the PDMS stamp by bringing the tubule-inked PDMS stamp into contact with these substrates. We show that the 2-D array of aligned lipid tubules can be transcribed into a 2-D array of aligned silica cylinders through templated sol-gel condensation of tetraethoxysilane.