Submicron patterning of DNA oligonucleotides on silicon

Giant Magnetoresistance Biosensors in Biomedical Applications

The giant magnetoresistance (GMR) effect has seen flourishing development from theory to application in the last three decades since its discovery in 1988. Nowadays, commercial devices based on the GMR effect, such as hard-disk drives, biosensors, magnetic field sensors, microelectromechanical systems (MEMS), etc., are available in the market, by virtue of the advances in state-of-the-art thin-film deposition and micro- and nanofabrication techniques. Different types of GMR biosensor arrays with superior sensitivity and robustness are available at a lower cost for a wide variety of biomedical applications. In this paper, we review the recent advances in GMR-based biomedical applications including disease diagnosis, genotyping, food and drug regulation, brain and cardiac mapping, etc. The GMR magnetic multilayer structure, spin valve, and magnetic granular structure, as well as fundamental theories of the GMR effect, are introduced at first. The emerging topic of flexible GMR for wearable biosensing is also included. Different GMR pattern designs, sensor surface functionalization, bioassay strategies, and on-chip accessories for improved GMR performances are reviewed. It is foreseen that combined with the state-of-the-art complementary metal-oxide-semiconductor (CMOS) electronics, GMR biosensors hold great promise in biomedicine, particularly for point-of-care (POC) disease diagnosis and wearable devices for real-time health monitoring.

Random sequential adsorption on imprecise lattice

We report a surprising result, established by numerical simulations and analytical arguments for a one-dimensional lattice model of random sequential adsorption, that even an arbitrarily small imprecision in the lattice-site localization changes the convergence to jamming from fast, exponential, to slow, power-law, with, for some parameter values, a discontinuous jump in the jamming coverage value. This finding has implications for irreversible deposition on patterned substrates with pre-made landing sites for particle attachment. We also consider a general problem of the particle (depositing object) size not an exact multiple of the lattice spacing, and the lattice sites themselves imprecise, broadened into allowed-deposition intervals. Regions of exponential vs. power-law convergence to jamming are identified, and certain conclusions regarding the jamming coverage are argued for analytically and confirmed numerically.

Hierarchical-Multiplex DNA Patterns Mediated by Polymer Brush Nanocone Arrays That Possess Potential Application for Specific DNA Sensing

This paper provides a facile and cost-efficient method to prepare single-strand DNA (ssDNA) nanocone arrays and hierarchical DNA patterns that were mediated by poly(2-hydroxyethyl methacrylate) (PHEMA) brush. The PHEMA brush nanocone arrays with different morphology and period were fabricated via colloidal lithography. The hierarchical structure was prepared through the combination of colloidal lithography and traditional photolithography. The DNA patterns were easily achieved via grafting the amino group modified ssDNA onto the side chain of polymer brush, and the anchored DNA maintained their reactivity. The as-prepared ssDNA nanocone arrays can be applied for target DNA sensing with the detection limit reaching 1.65 nM. Besides, with the help of introducing microfluidic ideology, the hierarchical-multiplex DNA patterns on the same substrate could be easily achieved with each kind of pattern possessing one kind of ssDNA, which are promising surfaces for the preparation of rapid, visible, and multiplex DNA sensors.

Straightforward Micropatterning of Oligonucleotides in Microfluidics by Novel Spin-On ZrO₂ Surfaces

DNA biochip assays often require immobilization of bioactive molecules on solid surfaces. A simple biofunctionalization protocol and precise spatial binding represent the two major challenges in order to obtain localized region specific biopatterns into lab-on-a-chip (LOC) systems. In this work, a simple strategy to anchor oligonucleotides on microstructured areas and integrate the biomolecules patterns within microfluidic channels is reported. A photosensitive ZrO2 system is proposed as an advanced platform and versatile interface for specific positioning and oriented immobilization of phosphorylated DNA. ZrO2 sol-gel structures were easily produced on fused silica by direct UV lithography, allowing a simple and fast patterning process with different geometries. A thermal treatment at 800 °C was performed to crystallize the structures and maximize the affinity of DNA to ZrO2. Fluorescent DNA strands were selectively immobilized on the crystalline patterns inside polydimethylsiloxane (PDMS) microchannels, allowing high specificity and rapid hybridization kinetics. Hybridization tests confirmed the correct probe anchoring and the bioactivity retention, while denaturation experiments demonstrated the possibility of regenerating the surface.

A robust DNA interface on a silicon electrode

Schematic of a DNA sensing interface formed on oxide-free silicon electrodes that both resist nonspecific adsorption of DNA and maintains stable electrical properties in biological media.

Efficient self-assembly of DNA-functionalized fluorophores and gold nanoparticles with DNA functionalized silicon surfaces: the effect of oligomer spacers

Although strategies for the immobilization of DNA oligonucleotides onto surfaces for bioanalytical and top-down bio-inspired nanobiofabrication approaches are well developed, the effect of introducing spacer molecules between the surface and the DNA oligonucleotide for the hybridization of nanoparticle–DNA conjugates has not been previously assessed in a quantitative manner. The hybridization efficiency of DNA oligonucleotides end-labelled with gold nanoparticles (1.4 or 10 nm diameter) with DNA sequences conjugated to silicon surfaces via hexaethylene glycol phosphate diester oligomer spacers (0, 1, 2, 6 oligomers) was found to be independent of spacer length. To quantify both the density of DNA strands attached to the surfaces and hybridization with the surface-attached DNA, new methodologies have been developed. Firstly, a simple approach based on fluorescence has been developed for determination of the immobilization density of DNA oligonucleotides. Secondly, an approach using mass spectrometry has been created to establish (i) the mean number of DNA oligonucleotides attached to the gold nanoparticles and (ii) the hybridization density of nanoparticle–oligonucleotide conjugates with the silicon surface–attached complementary sequence. These methods and results will be useful for application with nanosensors, the self-assembly of nanoelectronic devices and the attachment of nanoparticles to biomolecules for single-molecule biophysical studies.

Reductive surface synthesis of gold nanoparticles on silicate glass and their biochemical sensor applications

Gold nanoparticles (Au NPs) were directly synthesized on the surface of polyvinylsilazane (PVSZ, -[(vinyl)SiH-NH2]-) without use of extra reductive additives. The reductive Si-H functional groups on the surface of cured PVSZ acted as surface bound reducing agents to form gold metal when contacted with an aqueous Au precursor (HAuCl4) solution, leading to formation of Au NPs adhered to silicate glass surface. The Au NPs-silicate platforms were preliminarily tested to detect Rhodamine B (1 μM) by surface enhanced Raman scattering. Furthermore, gold microelectrode obtained by post-chemical plating was used as an integrated amperometric detection element in the polydimethylsilane-glass hybrid microfluidic chip.

MicroRNAs as newer therapeutic targets: A big hope from a tiny player

MicroRNAs (miRNAs) are a novel group of universally present small noncoding endogenous RNAs that regulate gene expression and protein coding by base pairing with the 3’ untranslated region (UTR) of target mRNAs. So they have been associated with several physiological processes and play an important role in the manifestation of diverse diseases. miRNAs expression is associated with the normal and diverse pathophysiological state including cardiac hypertrophy, neurodegenerative diseases, diabetes and its complication, and cancer because individual miRNAs are associated with the regulation of the expression of multiple target genes. Modulating the expression of a single miRNA can influence an entire gene network and thereby modify complex disease phenotypes. From recent studies, it has been confirmed that miRNA has a potential physiological role in various body systems. But in some specialized condition over expression of miRNA within the cytoplasm also leads to some pathological condition in the body. Here, we summarize the roles of miRNAs in various pathological conditions and consider the advantages and potential challenges of miRNA-based therapeutic approaches compared to conventional drug-based therapies.

Micro- and nanopatterning of functional organic monolayers on oxide-free silicon by laser-induced photothermal desorption

The photothermal laser patterning of functional organic monolayers, prepared on oxide-free hydrogen-terminated silicon, and subsequent backfilling of the laser-written lines with a second organic monolayer that differs in its terminal functionality, is described. Since the thermal monolayer decomposition process is highly nonlinear in the applied laser power density, subwavelength patterning of the organic monolayers is feasible. After photothermal laser patterning of hexadecenyl monolayers, the lines freed up by the laser are backfilled with functional acid fluoride monolayers. Coupling of cysteamine to the acid fluoride groups and subsequent attachment of Au nanoparticles allows easy characterization of the functional lines by atomic force microscopy (AFM) and scanning electron microscopy (SEM). Depending on the laser power and writing speed, functional lines with widths between 1.1 μm and 250 nm can be created. In addition, trifluoroethyl-terminated (TFE) monolayers are also patterned. Subsequently, the decomposed lines are backfilled with a nonfunctional hexadecenyl monolayer, the TFE stripes are converted into thiol stripes, and then finally covered with Au nanoparticles. By reducing the lateral distance between the laser lines, Au-nanoparticle stripes with widths close to 100 nm are obtained. Finally, in view of the great potential of this type of monolayer in the field of biosensing, the ease of fabricating biofunctional patterns is demonstrated by covalent binding of fluorescently labeled oligo-DNA to acid-fluoride-backfilled laser lines, which--as shown by fluorescence microscopy--is accessible for hybridization.

Three-dimensional parallel holographic micropatterning using a spatial light modulator

We present a micropatterning method for the automatic transfer and arbitrary positioning of computer-generated three-dimensional structures within a substrate. The Gerchberg-Saxton algorithm and an electrically addressed spatial light modulator (SLM) are used to create and display phase holograms, respectively. A holographic approach to light manipulation enables arbitrary and efficient parallel photo-patterning. Multiple pyramidal microstructures were created simultaneously in a photosensitive adhesive. A scanning electron microscope was used to confirm successful replication of the desired microscale structures.

One-step photochemical attachment of NHS-terminated monolayers onto silicon surfaces and subsequent functionalization

N-Hydroxysuccinimide (NHS)-ester-terminated monolayers were covalently attached in one step onto silicon using visible light. This mild photochemical attachment, starting from omega-NHS-functionalized 1-alkenes, yields a clean and flat monolayer-modified silicon surface and allows a mild and rapid functionalization of the surface by substitution of the NHS-ester moieties with amines at room temperature. Using a combination of analytical techniques (infrared reflection absorption spectroscopy (IRRAS), extensive X-ray photoelectron spectroscopy (XPS) in combination with density functional theory calculations of the XPS chemical shifts of the carbon atoms, atomic force microscopy (AFM), and static contact angle measurements), it was shown that the NHS-ester groups were attached fully intact onto the surface. The surface reactivity of the NHS-ester moieties toward amines was qualitatively and quantitatively evaluated via the reaction with para-trifluoromethyl benzylamine and biotin hydrazide.

Direct immobilization of cholesteryl-TEG-modified oligonucleotides onto hydrophobic SU-8 surfaces

We introduce a rapid, simple one-step procedure for the high-yield immobilization of cholesteryl-tetraethyleneglycol-modified oligonucleotides (chol-DNA) at hydrophobic sites made of SU-8 photoresist. Topographic structures of SU-8 were microfabricated on microscope glass coverslips sputtered with a Ti/Au layer. Upon application, chol-DNA adsorbed to the SU-8 structures from solution, leaving the surrounding gold surface free of chol-DNA. chol-DNA immobilization is complete within 15 min and yields a surface coverage in the range of 20-95 pmol/cm(2), which corresponds to a film density of 10(12)-10(13) molecules/cm(2). chol-DNA immobilization is stable and can be sustained despite rinsing, drying, dry storage for several hours, and rehydration of chips. Furthermore, complementary DNA in solution hybridizes efficiently to immobilized chol-DNA.

An improved gel-based DNA microarray method for detecting single nucleotide mismatch

3-D polyacrylamide gel-based DNA microarray platforms provide a high capacity for nucleic acids immobilization and a solution-mimicking environment for hybridization. However, several technological bottlenecks still remain in these platforms, such as difficult microarray preparation and high fluorescent background, which limit their application. In this study, two new approaches have been developed to improve the convenience in microarray preparation and to reduce the background after hybridization. To control the polymerization process, solutions containing acrylamide-modified oligonucleotide, acrylamide, glycerol and ammonium persulfate are spotted onto a functionalized glass slide, and then the slide is transferred to a vacuum chamber with TEMED, so that TEMED is vaporized and diffused into the spots to induce polymerization. By applying an electric field across a hybridized microarray to remove the nonspecifically bound labeled targets, this approach can solve the problem of high fluorescent background of the gel-based microarray after hybridization. Experimental results show that our immobilization method can be used to construct high quality microarrays and exhibits good reproducibility. Moreover, the polymerization is not affected by PCR medium, so that PCR products can be used for microarray construction without being treated by commercial purification cartridges. Electrophoresis can improve the signal-to-noise significantly and has the ability to differentiate single nucleotide variation between two homozygotes and a heterozygote. Our results demonstrated that this is a reliable novel method for high-throughput mutation analysis and disease diagnosis.

Submicron streptavidin patterns for protein assembly

Micron and submicron-scale features of aldehyde functionality were fabricated in polymer films by photolithography to develop a platform for protein immobilization and assembly at a biologically relevant scale. Films containing the pH-reactive polymer poly(3,3'-diethoxypropyl methacrylate) and a photoacid generator (PAG) were patterned from 500 nm to 40 mum by exposure to 365 nm (i-line) light. Upon PAG activation and hydrolysis of acetals, aldehyde groups formed. After the films were incubated with a biotinylated aldehyde reactive probe, the X-ray photoelectron spectroscopy results were consistent with biotin being attached to the surface. The background was subsequently passivated by flood exposure and incubation with an aminooxy-terminated poly(ethylene glycol), resulting in a 98% reduction in nonspecific protein adsorption. Protein patterning and assembly was demonstrated using streptavidin, biotinylated anthrax toxin receptor-1, and the protective antigen moiety of anthrax toxin and confirmed by fluorescence microscopy and atomic force microscopy (AFM). AFM demonstrated that 500 nm protein features were achieved. Because of the abundance of biotinylated proteins, this methodology provides a platform for protein immobilization and assembly for various applications in biotechnology.

Detecting the chemoselective ligation of peptides to silicon with the use of cobalt-carbonyl labels

While fluorescent-based methods are generally used to detect the immobilization and the interactions of biomolecules to solid supports, recent studies have shown their limitations in the case of silicon surfaces. As an alternative, we investigated the synthesis of peptides labeled with a metal transition complex and their subsequent immobilization to the silicon surfaces. The feasibility of using such probes has been explored by Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). By starting with hydrogen-terminated or oxidized silicon surfaces, we functionalized those surfaces with semicarbazide groups and showed the site-specific linkage of glyoxylyl peptides labeled with a Co2(CO)6 moiety.

Formation of tetra(ethylene oxide) terminated Si-C linked monolayers and their derivatization with glycine: an example of a generic strategy for the immobilization of biomolecules on silicon

Surface modification with oligo(ethylene oxide) functionalized monolayers terminated with reactive headgroups constitutes a powerful strategy to provide specific coupling of biomolecules with simultaneous protection from nonspecific adsorption on surfaces for the preparation of biorecognition interfaces. To date, oligo(ethylene oxide) functionalized monolayer-forming molecules which can be activated for attachment of biomolecules but which can selectively form monolayers onto hydrogen terminated silicon have yet to be developed. Here, self-assembled monolayers (SAMs) containing tetra(ethylene oxide) moieties protected with tert-butyl dimethylsilyl groups were formed by thermal hydrosilylation of alkenes with single-crystal Si(111)-H. The protection group was used to avoid side reactions with the hydride terminated silicon surface. Monolayer formation was carried out using solutions of the alkene in the high-boiling-point solvent 1,3,5-triethylbenzene. The protecting group was removed under very mild acidic conditions to yield a free hydroxyl functionality, a convenient surface moiety for coupling of biological entities via carbamate bond formation. The chemical composition and structure of the monolayers before and after deprotection were characterized by X-ray photoelectron spectroscopy (XPS) and X-ray reflectometry. To demonstrate the utility of this surface for covalent modification, two reagents were compared and contrasted for their ability to activate the surface hydroxyl groups for coupling of free amines, carbonyl diimidazole (CDI), and disuccinimidyl carbonate (DSC). Analysis of XP spectra before and after activation by CDI or DSC, and after subsequent reaction with glycine, provided quantitative information on the extent of activation and overall coupling efficiencies. CDI activated surfaces gave poor coupling yields under various conditions, whereas DSC mediated activation followed by aminolysis at neutral pH was found to be an efficient method for the immobilization of amines on tetra(ethylene oxide) modified surfaces.

Evidence for Why Tri(ethylene oxide) Functionalized Si-C Linked Monolayers on Si(111) Have Inferior Protein Antifouling Properties Relative to the Equivalent Alkanethiol Monolayers Assembled on Gold

High quality methoxy-terminated monolayers containing a tri(ethylene oxide) moiety were formed on Si(111)–H surfaces in thermal hydrosilylation reactions. X-ray photoelectron spectroscopy, contact angle, and X-ray reflectivity measurements suggested that the suboptimal protein anti-fouling properties of these Si–C linked monolayers were due to a reduced lateral packing density of the chains resulting in a disordered layer with insufficient internal and external hydrophilicity.