New approach to oligonucleotide microarrays using zirconium phosphonate-modified surfaces

A new approach to oligonucleotide arrays is demonstrated that utilizes zirconium phosphonate-derivatized glass slides. The active slides are prepared by binding Zr(4+) to surfaces terminated with organophosphonate groups previously deposited using either Langmuir-Blodgett or self-assembled monolayer methods. Oligonucleotide probes modified with a terminal phosphate bind strongly to the active zirconium phosphonate monolayer, and arrays for detecting fluorescent targets have been prepared using commercial spotting and scanning instruments. Preferred binding to the surface of the terminal phosphate of the modified probes instead of the internal phosphate diester groups is demonstrated and shown to yield increased fluorescence intensity after hybridization with labeled targets. A significant decrease in background signal is achieved by treating the slides with bovine serum albumin after spotting and before hybridization. A further increase in fluorescence after hybridization is observed when using a poly-guanine spacer between the probe oligomer and the terminal phosphate. Combining these modifications, an intensity ratio of nearly 1000 is achieved when comparing 5'-phosphate-modified 33-mer probes with unmodified probes upon hybridization with fluorescent targets.     

Electronic detection of single-base mismatches in DNA with ferrocene-modified probes.

Genotyping and gene-expression monitoring is critical to the study of the association between genetics and drug response (pharmacogenomics) and the association of sequence variation with heritable phenotypes. Recently, we developed an entirely electronic method for the detection of DNA hybridization events by the site-specific incorporation of ferrocenyl derivatives into DNA oligonucleotides. To perform rapid and accurate point mutation detection employing this methodology, two types of metal-containing signaling probes with varying redox potentials are required. In this report we describe a new ferrocene-containing phosphoramidite 9 that provides a range of detectable redox potentials. Using automated DNA/RNA synthesis techniques the two ferrocenyl complexes were inserted at various positions along oligonucleotide probes. Thermal stability analysis of these metal-containing DNA oligonucleotides indicates that incorporation of 9 resulted in no destabilization of the duplex. A mixture of oligonucleotides containing compounds 9 and I was analyzed by alternating current voltammetry (ACV) monitored at the 1st harmonic. The data demonstrate that the two ferrocenyl oligonucleotide derivatives can be distinguished electrochemically. A CMS-DNA array was prepared on an array of gold electrodes on a printed circuit board substrate with a self-assembled mixed monolayer, coupled to an electronic detection system. Experiments for the detection of a single-base match utilizing two signaling probes were carried out. The results demonstrate that rapid and accurate detection of a single-base mismatch can be achieved by using these dual-signaling probes on CMS-DNA chips.     

A mixed film composed of oligonucleotides and poly(2-hydroxyethyl methacrylate) brushes to enhance selectivity for detection of single nucleotide polymorphisms

Preliminary studies of mixed films composed of oligonucleotides and poly(2-hydroxyethyl methacrylate) (PHEMA) have recently been shown to enhance the selectivity for detection of 3 base-pair mismatched (3 bpm) oligonucleotide targets. Evaluation of selectivity for detection of single nucleotide polymorphisms (SNP) using such mixed films has now been completed. The selectivity was quantitatively determined by considering the sharpness of melt curves and melting temperature differences (ΔT_m) for fully complementary targets and SNPs. Stringency conditions were investigated, and it was determined that the selectivity was maximized when a moderate ionic strength was used (0.1-0.6 M). Increases of ΔT_m when using mixed films were up to 3-fold larger compared to surfaces containing only immobilized oligonucleotide probes. Concurrently, increases in sharpness of melt curves for 1 bpm targets were observed to be up to 2-fold greater for mixed films. The co-immobilization of PHEMA resulted in a more homogeneous distribution of oligonucleotide probes on surfaces. Lifetime measurements of fluorescence emission from immobilized oligonucleotide probes labeled with Cy3 dye indicated the difference in microenvironment of immobilized oligonucleotides in the presence of PHEMA.     

Electrochemical sensor for detection of unmodified nucleic acids

We have developed a nucleic acid (NA) sensor based on mediated electrochemical oxidation of guanine residues. In this method, oligonucleotide probes are bound to a tin-doped indium oxide (ITO) electrode through a self-assembled phosphonate monolayer. The end carboxyl moiety of the monolayer is activated with carbodiimide and reacted with the amine group of a C6 alkyl linker which has been added to the 5'-end of the oligonucleotide probe. Upon hybridization of the complementary target NA, the hybrid is detected using a redox-active mediator, tris(2,2'-bipyridyl) ruthenium(II). We speculate that the monolayer does not impede electron-transfer since it contains many defect sites when assembled on a polycrystalline ITO surface. These defect sites are accessible to the mediator, but not to NA or proteins. The electrocatalytic current was a linear function of the amount of guanine bound at the electrode surface, with a detection limit of 120 amoles of guanine cm(-2) at 0.28 cm(2) ITO electrodes.     

微孔尼龙-6膜的催化水解改性和DNA芯片的原位合成

基因芯片常用的载体有玻璃片、硅片、聚丙烯膜、硝酸纤维膜和尼龙膜等[1～ 4 ] .其中有机高分子膜载体由于自身荧光背景较强 ,寡核苷酸探针或 c DNA片段通常用点样法固定 ,并以同位素标记的靶基因与其杂交 ,用放射显影进行检测 ,探针密度不高且损害人体健康 .生物分子纳米标记和时间分辨荧光等检测技术可以非常有效地克服载体荧光背景[5,6 ] .因此 ,若将高分子材料进行改性 ,使其表面带有羟基、氨基和巯基等活性基团并应用于 DNA的原位合成 ,再结合新开发的生物分子标记和检测方法 ,将拓展生物芯片基材选择范围 ,并开发出新的生物芯片制…     

Immobilization of the nanoparticle monolayer onto self-assembled monolayers by combined sterically enhanced hydrophobic and electrophoretic forces

The immobilization of surface-derivatized gold nanoparticles onto methyl-terminated self-assembled monolayers (SAMs) on gold surface was achieved by the cooperation of hydrophobic and electrophoretic forces. Electrochemical and scanning probe microscopy techniques were utilized to explore the influence of the SAM's structure and properties of the nanoparticle/SAM/gold system. SAMs prepared from 1-decanethiol (DT) and 2-mercapto-3-n-octylthiophene (MOT) were used as hydrophobic substrates. The DT SAM is a closely packed and organized monolayer, which can effectively block the underlying gold and inhibit a variety of solution species including organic and inorganic molecules from penetrating, whereas the MOT monolayer is poorly packed or disorganized (because of a large difference in dimension between the thiophene head and the alkylchain tail) and permeable to many organic probes in aqueous solution but not to inorganic probes. Thus, the MOT monolayer provides a more energetically favorable hydrophobic surface for the penetration and adsorption of organic species than the DT monolayer. This hypothesis is supported by experiments in which the density of hydrophobically immobilized nanoparticles on the MOT SAM is much larger than that on the DT SAM. The results also suggest new approaches for modification of macroscopic surfaces with nanoscopic particles.     

Controlling DNA orientation on mixed ssDNA/OEG SAMs

We present and characterize a mixed self-assembled monolayer (SAM) consisting of single-stranded oligonucleotide (ssDNA)- and oligo(ethylene glycol) (OEG)-terminated thiols. The ssDNA/OEG SAMs are prepared by simultaneous coadsorption from a common thiol solution over a broad range of compositions. Electron spectroscopy for chemical analysis (ESCA) is used to measure the surface coverage of ssDNA, whereas surface plasmon resonance (SPR) sensor is used to measure the hybridization of complementary ssDNA and protein resistance. Through the complementary use of these techniques, we find that the composition of OEG in the assembly solution controls a key parameter: the surface coverage of ssDNA on the surface. There is evidence that it influences the orientation of the immobilized ssDNA probes. Lower OEG concentrations yield a surface with higher ssDNA coverage and less favorable orientation, whereas higher OEG concentrations produce a surface with lower DNA coverage and more favorable orientation. Competition between these two effects controls the hybridization efficiency of the ssDNA surface. Compared to ssDNA surfaces prepared with other diluent thiols, the use of OEG improves the protein resistance of the surface, making it more broadly applicable.     

Surface characterization of 3-glycidoxypropyltrimethoxysilane films on silicon-based substrates

Silane coupling agents are commonly used to activate surfaces for subsequent immobilization of biomolecules. The homogeneity and surface morphology of silane films is important for controlling the structural order of immobilized single-stranded DNA probes based on oligonucleotides. The surfaces of silicon wafers and glass slides with covalently attached 3-glycidoxypropyltrimethoxysilane (GOPS) have been characterized by using angularly dependent X-ray photoelectron spectroscopy (XPS), time-of-flight secondary-ion mass spectrometry (ToF–SIMS), atomic force microscopy (AFM), scanning electron microscopy (SEM), and monochromatic and spectroscopic ellipsometry. XPS and ToF–SIMS data provided evidence of complete surface coverage by GOPS. Data from angularly resolved XPS and ellipsometry methods suggested that the GOPS films were of monolayer thickness. AFM and SEM data indicated the presence of films that consisted of nodules approximately 50–100 nm in diameter. Modeling suggested that the nodules may lead to a nanoscale structural morphology that might influence the hybridization kinetics and thermodynamics of immobilized oligonucleotides.     

Application of self-assembly techniques in the design of biocompatible protein microarray surfaces

This review focuses on the application of novel technologies for generating biocompatible surfaces for high-throughput screening (HTS) of proteins. Various methods of coupling and spotting proteins on self-assembled monolayer (SAM) surfaces will be described along with the protein chip challenges pertaining to spot homogeneity, morphology, biocompatibility and reproducibility.     

Organic modification and subsequent biofunctionalization of porous anodic alumina using terminal alkynes

Porous anodic alumina (PAA) is a well-defined material that has found many applications. The range of applications toward sensing and recognition can be greatly expanded if the alumina surface is covalently modified with an organic monolayer. Here, we present a new method for the organic modification of PAA based on the reaction of terminal alkynes with the alumina surface. The reaction results in the the formation of a monolayer within several hours at 80 °C and is dependent on both oxygen and light. Characterization with X-ray photoelectron spectroscopy and infrared spectroscopy indicates formation of a well-defined monolayer in which the adsorbed species is an oxidation product of the 1-alkyne, namely, its α-hydroxy carboxylate. The obtained monolayers are fairly stable in water and at elevated temperatures, as was shown by monitoring the water contact angle. Modification with 1,15-hexadecadiyne resulted in a surface that has alkyne end groups available for further reaction, as was demonstrated by the subsequent reaction of N-(11-azido-3,6,9-trioxaundecyl)trifluoroacetamide with the modified surface. Biofunctionalization was explored by coupling 11-azidoundecyl lactoside to the surface and studying the subsequent adsorption of the lectin peanut agglutinin (PNA) and the yeast Candida albicans, respectively. Selective and reversible binding of PNA to the lactosylated surfaces was demonstrated. Moreover, PNA adsorption was higher on surfaces that exposed the β-lactoside than on those that displayed the α anomer, which was attributed to surface-associated steric hindrance. Likewise, the lactosylated surfaces showed increased colonization of C. albicans compared to unmodified surfaces, presumably due to interactions involving the cell wall β-glucan. Thus, this study provides a new modification method for PAA surfaces and shows that it can be used to induce selective adsorption of proteins and microorganisms.     

Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers

Microarray-based technology is in need of flexible and cost-effective chemistry for fabrication of oligonucleotide microarrays. We have developed a novel method for the fabrication of oligonucleotide microarrays with unmodified oligonucleotide probes on nanoengineered three-dimensional thin films that are deposited on glass slides by consecutive layer-to-layer adsorption of polyelectrolytes. Unmodified oligonucleotide probes were spotted and immobilized on these multilayered polyelectrolyte thin films (PET) by electrostatic adsorption and entrapment on the porous structure of the PET film. The PET provides higher probe binding capacity and thus higher hybridization signal than that of the traditional two-dimensional aminosilane and poly-L-lysine coated slides. Immobilized probe densities of 3.4 x 10(12)/cm2 were observed for microarray spots on PET with unmodified 50-mer oligonucleotide probes, which is comparable to the immobilized probe densities of alkyamine-modified 50-mer probes end-tethered on an aldehyde-functionalized slide. The study of hybridization efficiency showed that 90% of immobilized probes on PET film are accessible to target DNA to form duplex format in hybridization. The DNA microarray fabricated on PET film has wider dynamic range (about 3 orders of magnitude) and lower detection limit (0.5 nM) than the conventional amino- and aldehyde-functionalized slides. Oligonucleotide microarrays fabricated on these PET-coated slides also had consistent spot morphology. In addition, discrimination of single nucleotide polymorphism of 16S rRNA genes was achieved with the PET-based oligonucleotide microarrays. The PET microarrays constructed by our self-assembly process is cost-effective, versatile, and well suited for immobilizing many types of biological active molecules so that a wide variety of microarray formats can be developed.     

Covalent strategy for immobilization of DNA-microspots suitable for microarrays with label-free and time-resolved optical detection of hybridization

Sequence-specific detection and quantification of nucleic acids are central steps in many molecular biology procedures which have also been transferred to chip-based procedures. Hybridization-based assays can be used to quantify and discriminate between DNA target sequences down to the level of single base mismatches. Arrays of DNA probes immobilized on a support enable simultaneous testing of multiple sequences of a single sample. DNA arrays can be produced either by in-situ synthesis of oligonucleotides or by immobilization of pre-assembled DNA probes. Covalent and directed immobilization improves the reproducibility and stability of DNA arrays. This is especially interesting with repeated use of transducers or chips. Procedures are described for effective covalent immobilization of pre-assembled amino-linked oligonucleotides, by use of ink-jet techniques, on a modified and heated glass surface, with addressable surface areas ranging from 0.01 mm2 to a few mm2. Almost immediate evaporation of the spotted droplets on the heated surfaces leads to very high surface hybridization capacities. The surfaces are suitable for use with a label-free detection method - reflectometric interference spectroscopy (RIfS). It is shown that hybridization capacity and non-specific interaction at these DNA-surfaces can be characterized by use of RIfS. With a consumption of less than 80 ng mm(-2) oligonucleotide and a specific hybridization capacity of more than 300 fmol mm(-2), the activated aminodextran procedure was usually suitable for setting up a DNA array with label-free detection. Non-specific interactions with random oligomers or protein (ovalbumin) were low. Up to 150 repeated regenerations (stripping) of the surfaces by acid treatment and denaturing agents, and 50 days of storage, have been possible without significant loss of hybridization capacity.     

Surface-initiated growth of poly d(A-T) by Taq DNA polymerase

In this paper, we report surface-initiated d(A-T) polymerization by Taq DNA polymerase as a method for constructing DNA-tethered surfaces using an enzyme. The enzymatic polymerization was conducted successfully via two steps: tethering of oligo d(A-T)s onto the surface presenting carboxylic acids by amide coupling and surface-initiated polymerization using Taq DNA polymerase. In this enzymatic polymerization process, the design and construction of carboxylic acid-presenting surfaces were found to be an important factor: DNA growth did not occur on the gold surface coated only with the self-assembled monolayer (SAM) of 16-mercaptohexadecanoic acid (MHDA), but effectively proceeded on the surfaces presenting mixed SAMs of MHDA and 1-pentadecanethiol. The coupling of oligo d(A-T)s and the subsequent DNA polymerization reaction were characterized by polarized infrared external reflectance spectroscopy, ellipsometry, X-ray photoelectron spectroscopy, and atomic force microscopy.     

Ultrathin monolayer of rubrene on Au(111) induced by charge transfer

An ultrathin self‐assembly monolayer of rubrene on Au(111) has been fabricated and studied by scanning tunneling microscopy. The apparent thickness of such monolayer is 0.08 nm and close to the radius of a carbon atom. Moreover, the rubrene molecules within the second layer prefer adsorbing on to the positions corresponding to the herringbone structure underneath the Au(111)–() while the Au surface is fully covered by a monolayer of rubrene. With the assistant with theoretical simulations, we reveal that small apparent height of such monolayer is due to the coupling between the molecular orbitals and the gold surface. About 0.237 electron per rubrene molecule is transferred to the surface, and as a consequence, an interfacial dipole is formed on the rubrene/Au interface. The formation of such interfacial dipole induced by charge transfer from molecules to surfaces is believed to be applied in organic molecules adsorbed on metal surfaces. Copyright © 2011 John Wiley & Sons, Ltd.     

A bipolar electrochemical approach to constructive lithography: metal/monolayer patterns via consecutive site-defined oxidation and reduction

Experimental evidence is presented, demonstrating the feasibility of a surface-patterning strategy that allows stepwise electrochemical generation and subsequent in situ metallization of patterns of carboxylic acid functions on the outer surfaces of highly ordered OTS monolayers assembled on silicon or on a flexible polymeric substrate. The patterning process can be implemented serially with scanning probes, which is shown to allow nanoscale patterning, or in a parallel stamping configuration here demonstrated on micrometric length scales with granular metal film stamps sandwiched between two monolayer-coated substrates. The metal film, consisting of silver deposited by evaporation through a patterned contact mask on the surface of one of the organic monolayers, functions as both a cathode in the printing of the monolayer patterns and an anodic source of metal in their subsequent metallization. An ultrathin water layer adsorbed on the metal grains by capillary condensation from a humid atmosphere plays the double role of electrolyte and a source of oxidizing species in the pattern printing process. It is shown that control over both the direction of pattern printing and metal transfer to one of the two monolayer surfaces can be accomplished by simple switching of the polarity of the applied voltage bias. Thus, the patterned metal film functions as a consumable "floating" stamp capable of two-way (forward-backward) electrochemical transfer of both information and matter between the contacting monolayer surfaces involved in the process. This rather unusual electrochemical behavior, resembling the electrochemical switching in nanoionic devices based on the transport of ions in solid ionic-electronic conductors, is derived from the nanoscale thickness of the water layer acting as an electrolyte and the bipolar (cathodic-anodic) nature of the water-coated metal grains in the metal film. The floating stamp concept introduced in this report paves the way to a series of unprecedented capabilities in surface patterning, which are particularly relevant to nanofabrication by chemical means and the engineering of a new class of molecular nanoionic systems.     

Covalent assembly and micropatterning of functionalized multiwalled carbon nanotubes to monolayer-modified Si(111) surfaces

Multiwalled carbon nanotubes (MWNTs) covalently bound to monocrystalline p-type Si(111) surfaces have been prepared by attaching soluble amine-functionalized MWNTs onto a preassembled undecanoic acid monolayer using carbodiimide coupling. SEM analysis of these functionalized surfaces shows that the bound MWNTs are parallel to the surface rather than perpendicular. The voltammetric and electrochemical impedance spectroscopy measurements reveal that the electron transfer at the MWNT-modified surface is faster than that observed at a MWNT-free alkyl monolayer. We have also demonstrated that it is possible to prepare MWNT micropatterns using this surface amidation reaction and a "reagentless" UV photolithography technique. Following this approach, MWNT patterns surrounded by n-dodecyl areas have been produced and the local electrochemical properties of these micropatterned surfaces have been examined by scanning electrochemical microscopy. In particular, it is demonstrated that the MWNT patterns allow a faster charge transfer which is consistent with the results obtained for the uniformly modified surfaces.     

Hydrophobic monolayer preparation by Langmuir-Blodgett and chemical adsorption techniques

Alkylsiloxane and perfluoroalkylsiloxane monolayers are prepared on siliceous surfaces using the techniques of Langmuir-Blodgett deposition and solid-liquid chemical adsorption. Acid-catalyzed hydrolysis and polycondensation reactions provide two-dimensional siloxane networks at the liquid-vapor interface, which can be compressed to mean molecular areas of approximately 22 and approximately 32 A(2) for pendent hydrocarbon and fluorocarbon chains, respectively. Subsequent Langmuir-Blodgett transfer onto glass substrates at moderate surface pressures leads to compact monolayers for single-component precursors, while mixed alkyl- and perfluoroalkylsilanes produce nonhomogeneous films characterized by transfer ratios greater than unity. As an alternate monolayer preparation technique, silane polymerization was performed directly on siliceous surfaces via a chemical adsorption mechanism. XPS analysis of a chemically adsorbed 1H,1H,2H,2H-perfluorodecylsiloxane film confirms a single adsorbed monolayer thickness in which the pendent fluoroalkyl chains align nonperpendicularly with respect to the surface. The surface free energy was determined to be 11.4 dyn cm(-1) based on static contact angle measurements. AFM imaging shows the presence of surface defects due to oligomer deposition during the drying process. The use of solubilized trichloro-based silane coupling agents under anhydrous conditions is shown to produce surfaces with a minimal number of surface defects. The presence of undissolved silane material in the bulk solution significantly increases the number of surface defects.     

Electrochemical pathway for the quantification of SERS enhancement factor

This communication presents a new pathway for the more precise quantification of surface-enhanced Raman scattering (SERS) enhancement factor via deducing resonance Raman scattering (RRS) effect from surface-enhanced resonance Raman scattering (SERRS). To achieve this, a self-assembled monolayer of 1,8,15,22-tetraaminophthalocyanatocobalt(II) (4α-Co^IITAPc) is formed on plasmon inactive glassy carbon (GC) and plasmon active GC/AuNP surface. The surfaces are subsequently used as common probes for electrochemical and Raman (RRS and SERRS) studies. The most crucial parameters required for the quantification of SERS substrate enhancement factor (SSEF) such as real surface area of GC/AuNPs substarte and the number of 4α-Co^IITAPc molecules contributing to RRS (on GC) and SERRS (on GC/AuNPs) are precisely estimated by cyclic voltammetry experiments. The present approach of SSEF quantification can be applied to varieties of surfaces by choosing an appropriate laser line and probe molecule for each surface.     

Visualizing and tuning thermodynamic dispersion in metalloprotein monolayers

In coupling the redox state of an adsorbed molecule to its spectral characteristics redox profiles can be directly imaged by means of far-field fluorescence. At suitable levels of dilution, on optically transparent electrode surfaces, reversible interfacial electron transfer processes can be followed pixel by pixel down to scales which approach the molecular. In mapping out switching potentials across a surface population, thermodynamic dispersion, related to variance in the orientation, electronic coupling, protein fold, electric field drop, and general surface order, can be quantified. The self-assembled monolayer buffering the protein from the underlying metallic electrode surface not only acts to tune electronic coupling between the two but also potentially provides a variable more easily segmented from other contributions to molecular dispersion. We have, specifically, considered the possibility that the supporting monolayer crystallinity is a significant contributor to the subsequently observed spread in half-wave potentials. We report here that this is indeed the case and that this spread diminishes from 17 to 12 mV for the blue copper protein azurin as the supporting alkanethiol layer crystallinity increases. The work herein, then, presents not only a direct determination of submonolayer scale variance in redox character but also a means of tuning this through gross surface and entirely standard chemical means.     

Electrochemical Characterization of the Self-Assembled Monolayer of 8-Mercaptoquinoline on Polycrystalline Gold Electrode

Self-assembled monolayer of 8-mercaptoquinoline (MQ) on the surface of gold from MQ dilute ethanolic solutions is investigated by electrochemical methods. Some aqueous redox probes, such as ferrocene carboxylic acid and Fe(CN)₆ ^4–/3– can sufficiently diffuse into the monolayer because significant diffusion-limited current peaks are observed when the redox reactions take place, showing that the monolayer is very loosely packed or dominated by defects. However, the study on the electron transfer of other aqueous probes, such as Cu²⁺ and Ru(NH₃)₆ ^3+/2+, confirm that the monolayer can block the electron transfer on the gold electrode surface rather effectively for its low ratio of pinhole defects. These studies show that the MQ monolayer on the electrode can provide an excellent barrier for penetration of some probes but cannot resist the penetration of other probes effectively. The unusual properties of the self-assembled monolayers are attributed to the entity of the very large heterocyclic moiety.