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.     

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.     

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.     

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.     

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.     

A method of printing uniform protein lines by using flat PDMS stamps

In this paper, we report a method of printing uniform protein lines on glass slides by using UV-treated flat PDMS stamps. Unlike traditional microcontact printing (μCP) which requires microstructured PDMS stamps, this μCP method only requires a flat PDMS stamp, an UV lamp and a number of straight needles. Our results show that lines of bovine serum albumin (BSA), immunoglobin (IgG), anti-biotin, anti-human IgG and anti-mouse IgG can be printed evenly on glass slides by using this μCP method. We also demonstrate that the printed protein lines are suitable for applications such as microfluidic immunoassays.     

Oxygen plasma-treatment effects on Si transfer

Oxygen plasma-treatment is commonly used to increase the hydrophilicity of poly(dimethylsiloxane) (PDMS) stamps used for microcontact printing (muCP) aqueous-based inks. Review of the literature reveals that a wide range of plasma parameters are currently employed to modify stamp surfaces. However, little is known about the effect of these parameters (e.g., power, chamber pressure, duration) on the undesirable transfer of low-molecular-weight silicon-containing fragments from the stamps that commonly occurs during muCP. To study the effect of oxygen plasma-treatment on Si transfer, unpatterned PDMS stamps were treated with oxygen plasma under various conditions and used to stamp deionized water on plasma-activated poly(methyl methacrylate) (PMMA) substrates. Once stamped, the PMMA substrates were analyzed with X-ray photoelectron spectroscopy (XPS) to quantify and characterize silicon present on the substrate surface. In addition, used PDMS stamps were analyzed with scanning electron microscopy (SEM) to observe topographical changes that occur during oxygen plasma-treatment. XPS results show that all plasma treatments studied significantly reduced the amount of Si transfer from the treated stamps during muCP as compared to untreated PDMS stamps and that the source of transfer is residual PDMS fragments not removed by oxygen plasma. SEM results show that, although the treated stamps undergo a variety of topographical changes, no correlation exists between stamp topography and extent of Si transfer from the stamps.     

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.     

Covalent microcontact printing of proteins for cell patterning

We describe a straightforward approach to the covalent immobilization of cytophilic proteins by microcontact printing, which can be used to pattern cells on substrates. Cytophilic proteins are printed in micropatterns on reactive self-assembled monolayers by using imine chemistry. An aldehyde-terminated monolayer on glass or on gold was obtained by the reaction between an amino-terminated monolayer and terephthaldialdehyde. The aldehyde monolayer was employed as a substrate for the direct microcontact printing of bioengineered, collagen-like proteins by using an oxidized poly(dimethylsiloxane) (PDMS) stamp. After immobilization of the proteins into adhesive "islands", the remaining areas were blocked with amino-poly(ethylene glycol), which forms a layer that is resistant to cell adhesion. Human malignant carcinoma (HeLa) cells were seeded and incubated onto the patterned substrate. It was found that these cells adhere to and spread selectively on the protein islands, and avoid the poly(ethylene glycol) (PEG) zones. These findings illustrate the importance of microcontact printing as a method for positioning proteins at surfaces and demonstrate the scope of controlled surface chemistry to direct cell adhesion.     

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.     

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.     

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.     

Chemically patterned flat stamps for microcontact printing

Locally oxidized patterns on flat poly(dimethylsiloxane) stamps for microcontact printing were used as a platform for the transfer of a hydrophilic fluorescent ink to a glass substrate. The contrast was found to be limited. These locally oxidized patterns were conversely used as barriers for the transfer of hydrophobic n-octadecanethiol. In this case a good contrast was obtained, but the pattern was found to be susceptible to defects (cracks) in the barrier layer. Local stamp surface oxidation and subsequent modification with 1H,1H,2H,2H-perfluorodecyltrichlorosilane, for use as a barrier in the transfer of n-octadecanethiol, 16-mercaptohexadecanoic acid, and octanethiol, resulted in remarkably good contrast and stable patterns. The improved ink transfer control is ascribed to the reduction of undesired surface spreading and a superior mechanical stability of the stamp pattern. This new approach substantially expands the applicability of microcontact printing and provides a tool for the faithful reproduction of even extremely low filling ratio patterns.     

Microcontact printing of Alzheimer’s β-amyloid monomers and fibrils

Adsorption of the 40-residue Alzheimer’s β-amyloid peptide (Aβ40) on a hydrophobic surface leads to formation of potentially disease-relevant aggregates. Existing techniques are limited in characterizing the adsorbed Aβ40 and producing potentially useful Aβ40 microstructures such as microarrays and microparticles. In this paper, a novel approach based on microcontact printing (μCP) to studying and utilizing adsorption of Aβ40 monomers and fibril fragments on hydrophobic surface of polydimethylsiloxane (PDMS) stamps has been developed. By transferring the adsorbed layer from the stamp to a glass substrate, this approach allows easy measurement of thickness of the adsorbed layer. It also enables characterization of the face of the adsorbed layer in contact with the stamp surface. This face exhibits significant higher thioflavin T fluorescence than the face exposed to water, suggesting β-sheet formation induced by the PDMS surface. The intrinsic stability of the adsorbed layer is evaluated by printing the layer on a water-soluble substrate and exposing it to water vapor or water. Stable particulate microstructures in water are obtained by chemically crosslinking the adsorbed peptides. Moreover, co-micropatterning of the different states of Aβ40 (monomers and fibril fragments) is demonstrated. This μCP-based approach is simple, versatile, and holds potential for various applications.     

Site-selective surface modification using enzymatic soft lithography

Surface modification with functional polymers or molecules offers great promise for the development of smart materials and applications. Here, we describe a versatile and easy-to-use method of site-selective surface modification based on the ease of microcontact printing and the exquisite selectivity of enzymatic degradation. A micropatterned poly-L-lysine (PLL) layer on solid substrates was prepared by enzymatic degradation using trypsin enzyme immobilized on a prestructured poly(dimethlylsiloxane) (PDMS) stamp. After the enzymatic degradation of PLL and the removal of the degradation products, very well defined patterning was revealed over a large scale by fluorescence microscopy and atomic force microscopy (AFM). We investigate the advantage of our method by comparison with traditional microcontact printing and found that lateral diffusion was reduced, yielding a more accurate reproduction of the master. We also demonstrate that the stamp can be reused without reinking. The patterned surface was used for site-selective modification. The strategy was applied to two applications: the first is dedicated to the creation of amino-silane patterned surfaces, and the second illustrates the possibility of patterning polyelectrolyte multilayered thin films.     

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.     

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.     

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.     

Surface patterning by microcontact chemistry

In this Feature Article we describe recent progress in covalent surface patterning by microcontact chemistry. Microcontact chemistry is a variation of microcontact printing based on the transfer of reactive "ink" molecules from a microstructured, elastomeric stamp onto surfaces modified with complementary reactive groups, leading to a chemical reaction in the area of contact. In comparison with other lithographic methods, microcontact chemistry has a number of advantageous properties including very short patterning times, low consumption of ink molecules, high resolution and large area patterning. During the past 5 years we and many others have investigated a set of different reactions that allow the modification of flat and also spherical surfaces in an effective way. Especially click-type reactions were found to be versatile for substrate patterning by microcontact chemistry and were applied for chemical modification of reactive self-assembled monolayers and polymer surfaces. Microcontact chemistry has already found broad application for the production of functional surfaces and was also used for the preparation of DNA, RNA, and carbohydrate microarrays, for the immobilization of proteins and cells and for the development of sensors.