DNA probes on chip surfaces studied by scanning force microscopy using specific binding of colloidal gold

Functionalization of Phosphate and Tellurite Glasses and Spherical Whispering Gallery Mode Microresonators

Active whispering gallery mode resonators made as spherical microspheres doped with quantum dots or rare earth ions achieve high quality factors and are excellent candidates for biosensors capable of detecting biomolecules at low concentrations. However, to produce quantum dot-doped microspheres, new low melting temperature glasses are sought, which require surface functionalization and antibody immobilization for biosensor development. Here, we demonstrate the successful functionalization of three low melting point glasses and microspheres made of them. The glasses were made from sodium borophosphate, sodium aluminophosphate, and tellurite, and then, they were functionalized using (3-glycidyloxypropyl)trimethoxysilane in ethanol- and toluene-based protocols. Proper silanization was confirmed by energy-dispersive X-ray spectroscopy and fluorescence microscopy of an amino-modified luminescent oligonucleotide probe. Fluorescence imaging showed successful silanization for all tested samples and no degradation for aluminophosphate and tellurite glasses. The strongest signal was registered for tellurite glass samples functionalized using the toluene-based silanization protocol. This conclusion implies that this functionalization method is the most efficient and is highly recommended for future antibody immobilization and biosensing application.

Passive Control of Silane Diffusion for Gradient Application of Surface Properties

Liquid lithography represents a robust technique for fabricating three-dimensional (3D) microstructures on a two-dimensional template. Silanization of a surface is often a key step in the liquid lithography process and is used to alter the surface energy of the substrate and, consequently, the shape of the 3D microfeatures produced. In this work, we present a passive technique that allows for the generation of silane gradients along the length of a substrate. The technique relies on a secondary diffusion chamber with a single opening, leading to a directional introduction of silane to the substrate via passive diffusion. The secondary chamber geometry influences the deposited gradient, which is shown to be well captured by Monte Carlo simulations that incorporate the passive diffusion and grafting processes. The technique ultimately allows the user to generate a range of substrate wettabilities on a single chip, enhancing throughput for organ-on-a-chip applications by mimicking the spatial variability of tissue topographies present in vivo.

Optimizing Silanization to Functionalize Stainless Steel Wire: Towards Breast Cancer Stem Cell Isolation

Chemically modified metal surfaces have been used to recognize and capture specific cell types and biomolecules. In this work, stainless steel wires were functionalized with aptamers against breast cancer stem cell markers. Stainless steel wires were first electropolished and silanized via electrodeposition. Aptamers were then attached to the silanized surface through a cross-linker. The functionalized wires were able to capture the target cells in an in vitro test. During surface modification steps, wires were analyzed by atomic force microscopy, cyclic voltammetry, scanning electron and fluorescence microscopy to determine their surface composition and morphology. Optimized conditions of silanization (applied potential, solution pH, heat treatment temperature) for obtaining an aptamer-functionalized wire were determined in this work together with the use of several surface characterization techniques suitable for small-sized and circular wires. These modified wires have potential applications for the in vivo capture of target cells in blood flow, since their small size allows their insertion as standard guidewires in biomedical devices.

Etched Fiber Bragg Grating Biosensor Functionalized with Aptamers for Detection of Thrombin

A biosensor based on an etched Fiber Bragg Grating (EFBG) for thrombin detection is reported. The sensing system is based on a Fiber Bragg Grating (FBG) with a Bragg wavelength of 1550 nm, wet-etched in hydrofluoric acid (HF) for ~27 min, to achieve sensitivity to a refractive index (RI) of 17.4 nm/RIU (refractive index unit). Subsequently, in order to perform a selective detection of thrombin, the EFBG has been functionalized with silane-coupling agent 3-(aminopropyl)triethoxysilane (APTES) and a cross-linker, glutaraldehyde, for the immobilization of thrombin-binding aptamer. The biosensor has been validated for thrombin detection in concentrations ranging from 10 nM to 80 nM. The proposed sensor presents advantages with respect to other sensor configurations, based on plasmonic resonant tilted FBG or Long Period Grating (LPG), for thrombin detection. Firstly, fabricating an EFBG only requires chemical etching. Moreover, the functionalization method used in this study (silanization) allows the avoidance of complicated and expensive fabrications, such as thin film sputtering or chemical vapor deposition. Due to their characteristics, EFBG sensors are easier to multiplex and can be used in vivo. This opens new possibilities for the detection of thrombin in clinical settings.

Immobilization techniques for microarray: challenges and applications

The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials) on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.

Covalent immobilization of microtubules on glass surfaces for molecular motor force measurements and other single-molecule assays

Rigid attachment of microtubules (MTs) to glass cover slip surfaces is a prerequisite for a variety of microscopy experiments in which MTs are used as substrates for MT-associated proteins, such as the molecular motors kinesin and cytoplasmic dynein. We present an MT-surface coupling protocol in which aminosilanized glass is formylated using the cross-linker glutaraldehyde, fluorescence-labeled MTs are covalently attached, and the surface is passivated with highly pure beta-casein. The technique presented here yields rigid MT immobilization while simultaneously blocking the remaining glass surface against nonspecific binding by polystyrene optical trapping microspheres. This surface chemistry is straightforward and relatively cheap and uses a minimum of specialized equipment or hazardous reagents. These methods provide a foundation for a variety of optical tweezers experiments with MT-associated molecular motors and may also be useful in other assays requiring surface-immobilized proteins.

DNA hybridization assay at individual, biofunctionalized zinc oxide nanowires

Reliable and efficient identification of DNA is a major goal in on-site diagnostics. One dimensional nanostructures like nanowires (NW) represent potential sensor structures due to their extreme surface-to-bulk ratio, enabling enhanced biomolecule binding which results in optimal signals. While silicon NW are already well studied, NW made from other materials with promising properties like ZnO are not yet established as NW sensor material for bioanalytics. Here we demonstrate the DNA functionalization of ZnO NW even at the single NW level and their successful application in a DNA hybridization assay.

Detection of single tumor cell resistance with aptamer biochip

In this study, a novel RNA aptamer biochip was developed for tumor cell capture and detection of single cell resistance. This biochip consists of a polydimethylsiloxane (PDMS) cover containing a channel for introducing cells and sustaining their activity and microelectrode matrix on a silicon dioxide layer. Epidermal growth factor receptor (EGFR) aptamers which specifically identify and isolate tumor cells were attached in the gap between two electrodes. After cell biochip incubation, surplus tumor cells were removed, and those dwelling on the intervals were further analyzed. When resistance measurement was completed, these cells were flushed away via controlled flow acceleration, and were collected for further analysis. The results demonstrate the convenience and efficiency of using anti-EGFR aptamer biochips for the detection of single cell resistance. This novel aptamer biochip may be used for the isolation of circulating tumor cells from peripheral blood and cell counting, or be assembled with other lab-on-a-chip components for follow-up gene and protein analysis.

Comparison of adsorption of mercaptopropyltrimethoxysilane on amphiphilic TiO2 and hydroxylated SiO2

Alkylsilane 3-mercaptopropyltrimethoxysilane (3MPT) monolayers with a functional end group -SH were used to immobilize Ag colloidal nanoparticles on photoinduced amphiphilic TiO(2) and hydroxylated SiO(2) surfaces. The differences in the adsorption of 3MPT and the immobilization of Ag colloids on both surfaces were studied. Under identical experimental conditions, 3MPT islands were formed on UV-exposed TiO(2) surfaces compared to continuous and flat monolayers formed on SiO(2). The significant structural differences found for monolayers of 3MPT on TiO(2) could be explained in terms of the different densities of hydroxyl groups and the microstructure of hydrophilic domains induced by UV irradiation. The surface properties were characterized using contact angle measurements and XPS. XPS showed an increase in the hydroxyl group's density and a decrease in the number of adsorbed hydrocarbon films on the TiO(2) surface as a function of the UV irradiation time. The density of the adsorbed 3MPT on TiO(2) surfaces as a function of the UV irradiation time was quantitatively related to the cosine of the water contact angles. Such a 3MPT distribution influenced the subsequent adsorption of Ag colloids and resulted in more isolated nanoparticles on the modified TiO(2) with a narrower size distribution.

Immobilization of silanized DNA on glass: influence of the silane tether on the DNA hybridization

Two trifunctional (trimethoxy and triethoxy) and one difunctional (methyldimethoxy) 3-mercaptopropyl-alkoxysilanes were covalently tethered to thiolated DNA oligonucleotides in solution. After deposition as microarrays onto glass, the immobilized DNA probes were tested for hybridization ability by a florescence-based method. The results demonstrate a large enhancement in the fluorescence signal when the functionality of the silane tether is reduced from three to two. An XPS analyses revealed that this is not due to a higher DNA surface density. FTIR spectra of the spin-coated silanes showed that the trifunctional silanes form branched and cyclic siloxane moieties, whereas the difunctional silane generates predominantly short straight siloxane chains. Therefore, the propensity of trifunctional silanes to form more complex networks leads to conformations of the bound DNA which are less favorable for the specific interaction with the complementary strand. The data implicate that further significant improvements in the DNA hybridization ability are possible by adroit choice of the silane system.

Synthesis and characterization of Au-attached single-walled carbon nanotube bundles

We synthesized suspended single-walled carbon nanotubes (SWNTs) by the thermal chemical vapor deposition method and functionalized them with Au nanoparticles (NPs). We used 3-(aminopropyl)triethoxysilane as a linker and controlled the Au NP density on the SWNT surface by changing the reaction time. In the Raman scattering spectra of the Au-functionalized SWNTs, an enhanced peak frequency and peak intensity were observed in the non-resonant region. A significant enhancement of the metallic character in the high frequency region was also observed, especially when we used a 633 nm laser. By measuring the electric properties using a standard field effect transistor configuration, we found that charge transfer occurred during the functionalization processes. It is expected that the charge transfer related optical enhancement may affect the observed change in the Raman profiles.

Flexible biochips for detection of biomolecules

Miniaturization of biosensors is envisaged by the development of biochips consisting of parallel microarray patterns of binding sites on rigid substrates, such as glass or silicon. Thin plastic substrates are promising flexible alternatives because of the possibility for large-area roll-to-roll manufacturing of disposable chips at lower costs. Mature optical lithography technology faces many challenges when used to pattern flexible foils as a result of the substrate instabilities, especially at higher temperatures. In this work, flexible biochips with gold electrode patterns were fabricated on thin polyethylene naphthalate (PEN) foils using photolithography. The gold electrode structures of the chips were manufactured by direct metal patterning and by lift-off processing. Both methodologies resulted in well-defined electrode patterns as concluded from optical microscopy and scanning electron microscopy (SEM) characterization and resistance measurements. The biochips were successfully employed for the electrical and optical detection of DNA molecules. The DNA detection was based on the immobilization of capture DNA between electrode gaps, hybridization with biotin-labeled target DNA, and enzymatic silver enhancement.

Directed self-organization of single DNA molecules in a nanoslit via embedded nanopit arrays

We show that arrays of nanopit structures etched in a nanoslit can control the positioning and conformation of single DNA molecules in nanofluidic devices. By adjusting the spacing, organization and placement of the nanopits it is possible to immobilize DNA at predetermined regions of a device without additional chemical modification and achieve a high degree of control over local DNA conformation. DNA can be extended between two nanopits and in closely spaced arrays will self-assemble into "connect-the-dots" conformations consisting of locally pinned segments joined by fluctuating linkers. These results have broad implications for nanotechnology fields that require methods for the nanoscale positioning and manipulation of DNA.

Quantitation of surface coverage of oligonucleotides bound to chip surfaces: a fluorescence-based approach using alkaline phosphatase digestion

Silanized chip surfaces provide a reliable substrate for immobilization of oligonucleotides. The ability for rapid and sensitive detection of oligonucleotide surface coverage on these chips is crucial for their wide and effective applications in biotechnology. In this paper, two different silanization procedures were used to covalently bind fluorescent-labeled single-stranded DNA onto silicon dioxide or nitride chip surfaces. Effects of surface functionalization techniques for different surfaces, and immobilization conditions, including buffers and solution ionic strength, on surface probe coverage were investigated, quantifying the endpoint probe density by fluorescent measurement upon digestion with alkaline phosphatase (ALP). Digestion of surface-immobilized oligonuleotides with ALP released the fluorophore-tagged probe fragments back into the solution. The detection of DNA was accomplished by laser-induced fluorescence detection of the solution containing those cleaved fragments. The probe surface density on gold thin film, determined by ALP-digestion, was found to coincide well with that measured using the conventional alkanethiol-based fluorescence-displacement technique for the same system. The developed method has important implications for evaluating the performance of different oligonucleotide immobilization strategies. Also, it has the potential to serve as a sample-thrifty, time saving, and therefore routine tool to realize more realistic, practical quantification of the surface coverage of oligonucleotides immobilized on any solid surfaces.

New challenges for pharmaceutical formulations and drug delivery systems characterization using isothermal titration calorimetry

Long viewed as the 'method of choice' for characterizing thermodynamics and stoichiometry of molecular interactions, with high sensitivity, isothermal titration calorimetry (ITC) has been applied to many areas of pharmaceutical analysis. This review highlights ITC employment to measure binding thermodynamics and their use for pharmaceutical formulations and drug delivery system characterization particularly cyclodextrin-guest interactions, investigation of micellar-based systems, polyelectrolytes, nucleic acid interactions with multivalent cations and the optimization of DNA targeting and delivery. Furthermore, the potential of ITC for the characterization of different functionalities carried by nanoparticles as well as their interaction with living systems was outlined.

Construction of oligonucleotide microarrays (biochip) using heterobifunctional reagents

A number of hetero- and homobifunctional reagents have been reported to immobilize biomolecules on a variety of supports. However, efforts are on to search for a method, which is relatively simple, involving minimum of steps, cost effective, easy to reproduce, and that produces stable oligonucleotide arrays. Two new reagents, viz., [N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine], and [N-(3-trifluoroethanesulfonyloxypropyl)anthraquinone-2-carboxamide] have been designed considering the above points. These reagents contain different functional groups at their two ends. In [N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine], one end (triethoxysilyl) is capable of binding to the virgin glass surface and the other one consists of trifluoroethanesulfonate (tresyl) function specific toward aminoalkyl and mercaptoalkyl functionalities, which are easy to introduce at the 3'- or 5'-end of oligonucleotides. Likewise, in [N-(3-trifluoroethanesulfonyloxypropyl)anthraquinone-2-carboxamide], one end consists of photoactivatable moiety (anthraquinone) capable of reacting to a C-H containing surface and the tresyl function at the other end reacts specifically with aminoalkyl and mercaptoalkyl functionalities in modified oligonucleotides. These reagents have successfully been utilized to construct a number of oligonucleotide arrays and subsequently used for the detection of mismatches.

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

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

Performance characteristics of 65-mer oligonucleotide microarrays

Microarray fabrication using presynthesized long oligonucleotide is becoming increasingly important, but a study of large-scale array productions has not yet been published. We addressed the issue of fabricating oligonucleotide microarrays by spotting commercial presynthesized 65-mers with 5' amines representing 7500 murine genes. Amine-modified oligonucleotides were immobilized on glass slides having aldehyde groups via transient Schiff base formation followed by reduction to produce a covalent conjugate. When RNA derived from the same source was used for Cy3 and Cy5 labeling and hybridized to the same array, signal intensities spanning three orders of magnitude were observed and the coefficient of variance (CV) between the two channels for all spots was 8 to 10%. To ascertain the reproducibility of ratio determination of these arrays, two triplicate hybridizations (with fluorochrome reversal) comparing RNAs from a fibroblast (NIH3T3) and a breast cancer (JC) cell line were carried out. The 95% confidence interval for all spots in the six hybridizations was 0.60 to 1.66. This level of reproducibility allows use of the full range of pattern finding and discriminant analysis typically applied to complementary DNA (cDNA) microarrays. Further comparative testing was carried out with oligonucleotide microarrays, cDNA microarrays, and reverse transcription (RT)-PCR assays to examine the comparability of results across these different methodologies.

N-(3-Triethoxysilylpropyl)-4-(N'-maleimidylmethyl)cyclohexanamide (TPMC): a heterobifunctional reagent for immobilization of oligonucleotides on glass surface

A new heterobifunctional reagent, namely, N-(3-triethoxysilylpropyl)-4-(N'-maleimidylmethyl)cyclohexanamide (TPMC) was developed and its potentiality for fixing of thiol (-SH) modified oligonucleotides were tested. The covalent attachment of oligonucleotides with the reagent was achieved through its maleimide functionality at one end via stable thioether linkage while the other end bearing triethoxysilyl functionality has been utilized for coupling with the virgin glass surface with simplified methodologies. Immobilization of oligonucleotides was achieved by two alternating ways. The PATH-1 involves formation of conjugate of reagent and SH-modified oligonucleotides through thioether linkage and was subsequently immobilized on unmodified glass surface through triethoxysilyl group and alternatively, PATH-2 involves reaction of reagent first with unmodified glass surface to get maleimide functionality on the surface and then the SH-modified oligonucleotides were immobilized via thioether linkage. The specificity of immobilization was tested by hybridization study with complementary fluorescein labeled oligonucleotide strand.

A parallel approach for subwavelength molecular surgery using gene-specific positioned metal nanoparticles as laser light antennas

An optical technique for the parallel manipulation of nanoscale structures with molecular resolution is presented. Bioconjugated metal nanoparticles are thereby positioned at the location of interest, such as, e.g., certain DNA sequences along metaphase chromosomes, prior to pulsed laser light irradiation of the whole sample. The nanoparticles are designed to absorb the introduced energy highly efficiently, in that way acting as nanoantenna. As result of the interaction, structural changes of the sample with subwavelength dimensions and nanoscale precision are observed at the location of the particles. The process leading to the nanolocalized destruction is caused by particle ablation as well as thermal damage of the surrounding material.

N-(3-Triethoxysilylpropyl)-6-(N-maleimido)-hexanamide: An efficient heterobifunctional reagent for the construction of oligonucleotide microarrays

Synthesis of a new heterobifunctional reagent, N-(3-triethoxysilylpropyl)-6-(N-maleimido)-hexanamide (TPMH), for the preparation of oligonucleotide microarrays is described. Its triethoxysilyl function is specific toward virgin glass surface and maleimide function undergoes conjugate addition to 3'- or 5'-thiol-modified oligonucleotides. The construction of microarrays using TPMH has been realized via two routes. In Route A, TPMH was reacted first with 3'- or 5'-thiol-modified oligonucleotide under microwaves, thereby producing oligonucleotide-triethoxysilyl conjugate in 15min, which was then brought in contact with virgin glass microslide, resulting in immobilization of an oligonucleotide sequence. In Route B, immobilization involves generation of maleimide functions on virgin glass surface by the reaction with TPMH, followed by coupling with thiol-modified oligonucleotides under microwaves in 15 min to produce surface-bound oligonucleotides. The microarrays constructed using both routes were analyzed by hybridizing with tetrachlorofluorescein-labeled complementary oligonucleotide. Subsequently, these microarrays were successfully used in the discrimination of single and double nucleotide mismatches based on fluorescence intensity.

A real-time PCR-based method for determining the surface coverage of thiol-capped oligonucleotides bound onto gold nanoparticles

Here we report a real-time PCR-based method for determining the surface coverage of dithiol-capped oligonucleotides bound onto gold nanoparticles alone and in tandem with antibody. The detection of gold nanoparticle-bound DNA is accomplished by targeting the oligonucleotide with primer and probe binding sites, amplification of the oligonucleotide by PCR, and real-time measurement of the fluorescence emitted during the reaction. This method offers a wide dynamic range and is not dependant on the dissociation of the oligonucleotide strands from the gold nanoparticle surface; the fluorophore is not highly quenched by the gold nanoparticles in solution during fluorescence measurements. We show that this method and a fluorescence-based method give equivalent results for determining the surface coverage of oligonucleotides bound onto 13 or 30 nm gold nanoparticles alone and in tandem with antibody. Quantifying the surface coverage of immobilized oligonucleotides on metallic nanoparticle surfaces is important for optimizing the sensitivity of gold nanoparticle-based detection methods and for better understanding the interactions between thiol-functionalized oligonucleotides and gold nanoparticles.

Self-aligned immobilization of proteins utilizing PEG patterns

A novel self-aligned method to selectively immobilize proteins on a silicon dioxide surface is developed in conjunction with a standard lift-off patterning technique of a PEG layer. The approach is designed to photolithographically pattern regions that specifically bind target proteins and particles, surrounded by regions that suppress non-specific attachment of bio-species. The physical and biological properties of the derivatized surfaces at the end of the fabrication process are characterized.

DNA conformation on surfaces measured by fluorescence self-interference

The conformation of DNA molecules tethered to the surface of a microarray may significantly affect the efficiency of hybridization. Although a number of methods have been applied to determine the structure of the DNA layer, they are not very sensitive to variations in the shape of DNA molecules. Here we describe the application of an interferometric technique called spectral self-interference fluorescence microscopy to the precise measurement of the average location of a fluorescent label in a DNA layer relative to the surface and thus determine specific information on the conformation of the surface-bound DNA molecules. Using spectral self-interference fluorescence microscopy, we have estimated the shape of coiled single-stranded DNA, the average tilt of double-stranded DNA of different lengths, and the amount of hybridization. The data provide important proofs of concept for the capabilities of novel optical surface analytical methods of the molecular disposition of DNA on surfaces. The determination of DNA conformations on surfaces and hybridization behavior provide information required to move DNA interfacial applications forward and thus impact emerging clinical and biotechnological fields.

Chip devices for miniaturized biotechnology

Chip devices were introduced in chemistry and molecular biology to improve the read-out of information from molecular systems by efficient analytical procedures and to organize automated experiments. Biochips and chip reactor systems are of interest for cellular processes, too, and can be regarded as components in interfaces for the information exchange between living nature and digital electronic systems. In this minireview, different types of chip reactors for biotechnological applications like nanotiterplates, chip thermocyclers and devices for segmented flow operations are discussed. Finally, an outlook is given on the application of chip reactor systems, which are promising tools for automated experiments with highly parallelized screening procedures, for artificial microcompartmentation, cell analogue systems, micro-ecological studies, investigations on modulated morphogenesis, and for a bioanalogue molecular nanotechnology.

Isothermal titration calorimetry studies on the binding of DNA bases and PNA base monomers to gold nanoparticles

An isothermal titration calorimetric (ITC) investigation of the interaction of DNA bases and PNA base monomers with gold nanoparticles is described revealing a binding sequence in the order C > G > A > T. Direct measurement of the strength of interaction of ligands with nanogold by ITC has important implications in surface modification strategies for biomedical, catalysis, and nanoarchitecture applications.

DNA Codes for Nanoscience

The nanometer scale is a special place where all sciences meet and develop a particularly strong interdisciplinarity. While biology is a source of inspiration for nanoscientists, chemistry has a central role in turning inspirations and methods from biological systems to nanotechnological use. DNA is the biological molecule by which nanoscience and nanotechnology is mostly fascinated. Nature uses DNA not only as a repository of the genetic information, but also as a controller of the expression of the genes it contains. Thus, there are codes embedded in the DNA sequence that serve to control recognition processes on the atomic scale, such as the base pairing, and others that control processes taking place on the nanoscale. From the chemical point of view, DNA is the supramolecular building block with the highest informational content. Nanoscience has therefore the opportunity of using DNA molecules to increase the level of complexity and efficiency in self-assembling and self-directing processes.

Construction of oligonucleotide arrays on a glass surface using a heterobifunctional reagent, N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine (NTMTA)

A rapid method for construction of oligonucleotide arrays on a glass surface, using a novel heterobifunctional reagent, N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine (NTMTA), has been described. The heterobifunctional reagent, NTMTA, carries two different thermoreactive groups. The triethoxysilyl group on one end is specific towards silanol functions on the virgin glass surface, while the trifluoroethanesulfonyl (tresyl) group on the other end of the reagent reacts specifically with aminoalkyl- or mercaptoalkyl- functionalized oligonucleotides. Immobilization of oligonucleotides on a glass surface has been realized via two routes. In the first one (A), 5'- aminoalkyl- or mercaptoalkyl-functionalized oligonucleotides were allowed to react with NTMTA to form a oligonucleotide-triethoxysilyl conjugate which, in a subsequent reaction with unmodified (virgin) glass microslide, results in surface-bound oligonucleotides. In the second route (B), the NTMTA reagent reacts first with a glass microslide whereby it generates trifluoroethanesulfonate ester functions on it, which in a subsequent step react with 5'-aminoalkyl or mercaptoalkyl oligonucleotides to generate support-bound oligonucleotides. Subsequently, the oligonucleotide arrays prepared by both routes were analyzed by hybridization experiments with complementary oligonucleotides. The constructed microarrays were successfully used in single and multiple nucleotide mismatch detection by hybridizing these with fluorescein-labeled complementary oligonucleotides. Further more, the proposed method was compared with the existing methods with respect to immobilization efficiency of oligonucleotides.

Bifunctional DNA–gold nanoparticle conjugates as building blocks for the self-assembly of cross-linked particle layers

The DNA-directed self-assembly of surface-bound layers of gold nanoparticles offers a broad range of applications in biomedical analyses as well as in materials science. We here describe a new concept for the assembly of substrate-bound nanoparticle monolayers which employs bifunctional nanoparticles as building blocks, containing two independently addressable DNA oligomer sequences. One of the sequences was utilized for attaching the particle at the solid support, while the other sequence was used to establish cross-links between adjacently immobilized particles. AFM analyses proved the functionality of inter-particle cross-links leading to enhanced surface coverages and the formation of monolayered supramolecular aggregates attached to the substrate. We anticipate that further refinement of this approach will enable applications, for instance, the assembly of ordered layers useful as transducers in biosensing.

Quantitative detection of protein arrays

We introduce a quantitative method that utilizes scanning electron microscopy for the analysis of protein chips (SEMPC). SEMPC is based upon counting target-coated gold particles interacting specifically with ligands or proteins arrayed on a derivative microscope glass slide by utilizing backscattering electron detection. As model systems, we quantified the interactions of biotin and streptavidin and of an antibody with its cognate hapten. Our method gives quantitative molecule-counting capabilities with an excellent signal-to-noise ratio and demonstrates a broad dynamic range while retaining easy sample preparation and realistic automation capability. Increased sensitivity and dynamic range are achieved in comparison to currently used array detection methods such as fluorescence, with no signal bleaching, affording high reproducibility and compatibility with miniaturization. Thus, our approach facilitates the determination of the absolute number of molecules bound to the chip rather than their relative amounts, as well as the use of smaller samples.

Hybridization and enzymatic extension of au nanoparticle-bound oligonucleotides

We have investigated the impact of steric effects on the hybridization and enzymatic extension of oligonucleotides bound to 12-nm colloidal Au particles. In these experiments, a nanoparticle-bound 12-mer sequence is hybridized either to its solution phase 12-mer complement or to an 88-mer template sequence. The particle-bound oligonucleotide serves as a primer for enzymatic extension reactions, in which covalent incorporation of nucleotides to form the complement of the template is achieved by the action of DNA polymerase. Primers were attached via-C(6)H(12)SH, -C(12)H(24)SH, and -TTACAATC(6)H(12)SH linkers attached at the 5' end. Primer coverage on the nanoparticles was varied by dilution with (5')HSC(6)H(12)AAA AAA(3'). Hybridization efficiencies were determined as a function of linker length, primer coverage, complement length (12-mer vs 88-mer), and primer:complement concentration ratio. In all cases, hybridization for the 88-mer was less efficient than for the 12-mer. Low primer surface coverage, greater particle-primer separation, and higher primer:complement ratios led to optimal hybridization. Hybridization efficiencies as high as 98% and 75% were observed for the 12-mer and 88-mer, respectively. Enzymatic extension of particle-bound primers was observed under all conditions tested; however, the efficiency of the reaction was strongly affected by linker length and primer coverage. Extension of primers attached by the longest linker was as efficient as the solution-phase reaction.

Gold nanoparticles as novel label for DNA diagnostics

The growing interest in DNA diagnostics, especially in combination with the need for highly-paralleled and miniaturized hybridization assays, is today addressed by fluorescence DNA chips. Fluorescence detection is approved and highly developed, however, it has also problematic aspects, e.g., the low stability of the dyes, the influence of the physicochemical environment onto the signal intensity and the expensive set-up for detection. A novel detection scheme based on metal nanoparticles was proposed to overcome these problems and is discussed in this review.