Self-assembled DNA-conjugated polymer for novel DNA chip.

We developed DNA-conjugated polymer for DNA chip fabrication. A 30 mer probe DNA and disulfide bridges were covalently attached to the polymer side chain. The DNA-conjugated polymer can be specifically adsorbed on a gold substrate surface by a self-assembly technique. The interaction between fully matched DNA and DNA-conjugated polymer was investigated by surface plasmon resonance (SPR) technique. The DNA-conjugated polymer-modified gold surface highly recognized fully matched DNA, rather than unmatched DNA. Therefore, DNA-conjugated polymer can be used for novel DNA chip fabrication.     

Friction of single polymers at surfaces

Atomic force microscope (AFM) single molecule force spectroscopy has been used to investigate the friction coefficient of individual polymers adsorbed onto a solid support. The polymer chains were covalently attached to an AFM tip and were allowed to adsorb on a mica surface. Different polymers (ssDNA, polyallylamine) were chosen to cover a range of friction coefficients. During the experiment, the AFM tip was retracted in- and off-plane which results, depending on the chosen conditions, in a desorption of the polymer from the surface, a sliding across the surface, or a combination of both. Thus, the obtained force-extension spectra reveal detailed information on the mobility of a polymer chain on a surface under experimentally accessible conditions. This study demonstrates that absorbed polymers with comparable desorption forces may exhibit drastically different in plane mobility.     

Three-dimensional organization of block copolymers on "DNA-minimal" scaffolds

Here, we introduce a 3D-DNA construction method that assembles a minimum number of DNA strands in quantitative yield, to give a scaffold with a large number of single-stranded arms. This DNA frame is used as a core structure to organize other functional materials in 3D as the shell. We use the ring-opening metathesis polymerization (ROMP) to generate block copolymers that are covalently attached to DNA strands. Site-specific hybridization of these DNA-polymer chains on the single-stranded arms of the 3D-DNA scaffold gives efficient access to DNA-block copolymer cages. These biohybrid cages possess polymer chains that are programmably positioned in three dimensions on a DNA core and display increased nuclease resistance as compared to unfunctionalized DNA cages.     

Towards the optimization of an optical DNA sensor: control of selectivity coefficients and relative surface affinities

Short single-stranded DNA (ssDNA) oligonucleotides can be grown on the surface of fused silica by automated nucleic acid synthesis. The immobilized ssDNA can be deposited at a desired average density. The density of ssDNA provides a controlled parameter that in combination with temperature, ionic strength and pH, can be used to define the selectivity of hybridization. Furthermore, the density of ssDNA can be used to control the affinity of complementary DNA so that it associates with the nucleic acids on the surface rather than areas that are not coated with ssDNA. The characteristic melt temperature observed for immobilized double-stranded DNA (dsDNA) 20mer shifts by up to 10 °C when a single base pair mismatch is present in the center of a target oligonucleotide. Optimization of quantitative analysis of such single base pair mismatches requires use of select experimental conditions to maximize the formation of the fully matched target duplex while minimizing the formation of the mismatched duplex. Results based on fiber optic biosensors that are used to study binding of fluorescein-labeled complementary DNA demonstrate that it is possible to achieve a selectivity coefficient of fully matched to single base pair mismatch of approximately 85-1, while maintaining >55% of the maximum possible signal that can be obtained from the fully matched target duplex.     

Detection of mRNA from Escherichia coli in drinking water on nanostructured polymeric surfaces using liquid crystals

In this study, we demonstrate the detection of mRNA from Escherichia coli in drinking water using thermotropic liquid crystals (LCs). After hybridization of complementary mRNA with the single-stranded DNA immobilized on a polymer substrate containing periodic sinusoidal wave patterns, the orientation of LCs transits from a uniform to a non-uniform state, thereby inducing a change in the optical response of LCs. The periodic sinusoidal features of the polymer substrate are obtained through buckling the poly-(dimethylsiloxane) slide on a cylindrical surface, followed by replicating the associated relief structures on a poly-(urethaneacrylate) surface, where a film of gold was deposited. Then, thiol-modified single-stranded DNA was functionalized on the gold film as an mRNA receptor. The formation of mRNA–single-stranded DNA complex, which covers the sinusoidal nanostructures on the surface, induces the orientational transition of LCs. This result indicates that LCs can be used to report the specific hybridization of mRNA with single-stranded DNA, which holds promise for the sensitive and label-free detection of viable bacterial pathogens in drinking water.

DNA修饰电极的研究(Ⅸ)--DNA探针在金基底上的固定、表征及其表面分子杂交

采用疏基化合的自组装／共价键合反应的逐层固定方法将双链DNA固定到金表面得到DNA修饰电极,并对该电极表面进行了电化学和X射线光电子能谱表征。研究了电极表面固定化DNA的表面分子杂交。对开发电化学基因诊断芯片和基因传感器具有一定意义。     

DNA修饰电极的研究(ⅠΧ)——DNA探针在金基底上的固定、表征及其表面分子杂交

采用巯基化合物自组装 /共价键合反应的逐层固定方法将双链 DNA固定到金表面得到 DNA修饰电极 ,并对该电极表面进行了电化学和 X射线光电子能谱表征 .研究了电极表面固定化 DNA的表面分子杂交 .对开发电化学基因诊断芯片和基因传感器具有一定意义     

DNA sensor based on an Escherichia coli lac Z gene probe immobilization at self-assembled monolayers-modified gold electrodes

A novel approach to construct an electrochemical DNA sensor based on immobilization of a 25 base single-stranded probe, specific to E. coli lac Z gene, onto a gold disk electrode is described. The capture probe is covalently attached using a self-assembled monolayer of 3,3′-dithiodipropionic acid di(N-succinimidyl ester) (DTSP) and mercaptohexanol (MCH) as spacer. Hybridization of the immobilized probe with the target DNA at the electrode surface was monitored by square wave voltammetry (SWV), using methylene blue (MB) as electrochemical indicator. Variables involved in the sensor performance, such as the DTSP concentration in the modification solution, the self-assembled monolayers (SAM) formation time, the DNA probe drying time atop the electrode surface and the amount of probe immobilized, were optimized.

A good stability of the single- and double-stranded oligonucleotides immobilized on the DTSP-modified electrode was demonstrated, and a target DNA detection limit of 45 nM was achieved without signal amplification. Hybridization specificity was checked with non-complementary and mismatch oligonucleotides. A single-base mismatch oligonucleotide gave a hybridization response only 7 ± 3%, higher than the signal obtained for the capture probe before hybridization. The possibility of reusing the electrochemical genosensor was also tested.     

Immobilization of single-stranded deoxyribonucleic acid on gold electrode with self-assembled aminoethanethiol monolayer for DNA electrochemical sensor applications

A synthesized 24-mer single-stranded deoxyribonucleic acid (ssDNA) was covalently immobilized onto a self-assembled aminoethanethiol monolayer modified gold electrode, using water-soluble 1-ethyl-3(3-dimethylaminopropyl)-carbodiimide (EDC). The covalently immobilized ssDNAs were hybridized with complementary ssDNA (cDNA) or yAL(3) gene in solution, forming double-stranded DNAs (dsDNA). Meanwhile, daunomycin as an electrochemical active intercalator in the hybridization buffer solution was intercalated into the dsDNA to form a dsDNA/daunomycin system on the gold electrode surface, which was used for DNA electrochemical sensor. The cathodic waves of daunomycin bound to the double-stranded DNA (dsDNA) by linear sweep voltammetry were utilized to detect the cDNA. The cathodic peak current (i(pc)) of duanomycin was linearly related to the concentrations of cDNA between 0.1 mug ml(-1) and 0.1 ng ml(-1). The detection limit was about 30 pg ml(-1).     

Characterization of single- and double-stranded DNA on gold surfaces

Single- and double-stranded deoxy ribonucleic acid (DNA) molecules attached to self-assembled monolayers (SAMs) on gold surfaces were characterized by a number of optical and electronic spectroscopic techniques. The DNA-modified gold surfaces were prepared through the self-assembly of 6-mercapto-1-hexanol and 5'-C(6)H(12)SH -modified single-stranded DNA (ssDNA). Upon hybridization of the surface-bound probe ssDNA with its complimentary target, formation of double-stranded DNA (dsDNA) on the gold surface is observed and in a competing process, probe ssDNA is desorbed from the gold surface. The competition between hybridization of ssDNA with its complimentary target and ssDNA probe desorption from the gold surface has been investigated in this paper using X-ray photoelectron spectroscopy, chronocoulometry, fluorescence, and polarization modulation-infrared reflection absorption spectroscopy (PM-IRRAS). The formation of dsDNA on the surface was identified by PM-IRRAS by a dsDNA IR signature at approximately 1678 cm(-)(1) that was confirmed by density functional theory calculations of the nucleotides and the nucleotides' base pairs. The presence of dsDNA through the specific DNA hybridization was additionally confirmed by atomic force microscopy through colloidal gold nanoparticle labeling of the target ssDNA. Using these methods, strand loss was observed even for DNA hybridization performed at 25 degrees C for the DNA monolayers studied here consisting of attachment to the gold surfaces by single Au-S bonds. This finding has significant consequence for the application of SAM technology in the detection of oligonucleotide hybridization on gold surfaces.     

Stable immobilization of an oligonucleotide probe on a gold substrate using tripodal thiol derivatives

We proposed an interface molecule for immobilization of DNA probes on solid substrates of DNA chips. We have designed and synthesized tripodal thiol derivatives for stable immobilization of oligonucleotide probes on a gold surface. On the basis of the tetrahedral structure of tripod, the tripodal thiol derivatives were bonded upright to the gold substrate, which would control the orientation of oligonucleotide probes. When the gold substrate with oligonucleotide probes tethered using the thiol derivatives was exposed to deionized water at higher temperatures, the tripodal interface molecules were attached to the gold surface more stably than the single contact molecules. The DNA chip platform combined with the functional interface molecule is suitable for a reproducible, inexpensive, and high-throughput detection system for genetic analyses in clinical diagnostics.     

Effects of gold nanoparticle and electrode surface properties on electrocatalytic silver deposition for electrochemical DNA hybridization detection

In this paper we report the catalytic effects of various gold nanoparticles for silver electrodeposition on indium tin oxide (ITO)-based electrodes, and successfully apply this methodology for signal amplification of the hybridization assay. The most widely used gold nanoparticle-based hybridization indicators all promote silver electrodeposition on the bare ITO electrodes, with decreasing catalytic capability in order of 10 nm gold, DNA probe-10 nm gold conjugate, streptavidin-5 nm gold, and streptavidin-10 nm gold. Of greater importance, these electrocatalytic characteristics are affected by any surface modifications of the electrode surfaces. This is illustrated by coating the ITO with an electroconducting polymer, poly(2-aminobenzoic acid)(PABA), as well as avidin molecules, which are promising immobilization platforms for DNA biosensors. The catalytic silver electrodeposition of the gold nanoparticles on the PABA-coated ITO surfaces resembles that on the bare surfaces. With avidin covalently bound to the PABA, it is interesting to note that the changes in electrocatalytic performance vary for different types of gold nanoparticles. For the streptavidin-5 nm gold, the silver electrodeposition profile is unaffected by the presence of the avidin layer, whereas for both the 10 nm Au and DNA probe-10 nm gold conjugate, the deposition profiles are suppressed. The streptavidin-5 nm gold is employed as the hybridization indicator, with avidin-modified (via PABA) ITO electrode as the immobilization platform, to enable signal amplification by the silver electrodeposition process. Under the conditions, this detection strategy offers a signal-to-noise ratio of 20. We believe that this protocol has great potential for simple, reproducible, highly selective and sensitive DNA detection on fully integrated microdevices in clinical diagnostics and environmental monitoring applications.     

Deposition of DNA-functionalized gold nanospheres into nanoporous surfaces

We report the deposition of DNA-conjugated gold nanospheres into arrays of surface nanopores obtained from hexagonally ordered thin polystyrene-b-poly(methyl methacrylate) (PS-b-PMMA) diblock copolymer films on silicon. The deposition occurs spontaneously from aqueous solution and is driven by either electrostatic interactions or specific DNA hybridization events between the DNA nanospheres and the surface nanopores. To mitigate this spontaneous deposition, we have chemically modified the nanopores with either positively charged aminosilanes or oligonucleotide probe sequences. The deposition of DNA nanospheres into the surface nanopores was characterized by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). We have observed preferential immobilization of individual DNA nanospheres within the nanopores, based on the size matching between the two entities. The inclusion density and selectivity of DNA nanosphere deposition into the surface nanopores was found to depend predominantly on the methods through which the nanoporous surfaces were prepared and chemically functionalized.     

Surface plasmon resonance sensor for lysozyme based on molecularly imprinted thin films

Molecularly imprinted polymers (MIPs) selective for lysozyme were prepared on SPR sensor chips by radical co-polymerization with acrylic acid and N,N′-methylenebisacrylamide. Gold-coated SPR sensor chips were modified with N,N′-bis(acryloyl)cystamine, on which MIP thin films were covalently conjugated. The presence of NaCl during the polymerization and the re-binding tests affected the selectivity and the optimization of NaCl concentration in the pre-polymerization mixture and the re-binding buffer could enhance the selectivity in the target protein sensing. When the lysozyme-imprinted polymer thin films were prepared in the presence of 40 mM NaCl, the selectivity factor (target protein bound/reference protein bound) of MIP in the re-binding buffer containing 20 mM NaCl was 9.8, meanwhile, that of MIP in the re-binding buffer without NaCl was 1.2. A combination of SPR sensing technology with protein-imprinted thin films is a promising tool for the construction of selective protein sensors.     

Preparation of analyte-sensitive polymeric supports for biochemical sensors

The preparation and use of multiple polymers attached to a surface plasmon resonance (SPR) sensor for optimization of signal enhancement and minimization of fouling during sensing of biological species has been achieved. These polymers are advantageous compared to the current practice of carboxymethylated-dextran (CM-dextran). The polymers offer a wide range of functionalities and different molecular weights. Using these polymers, the SPR sensors can be fabricated as fast or faster than the CM-dextran sensor. In this study, we investigated the use of nine polymers for SPR biosensors. Polysaccharides, including CM-dextran, CM-hyaluronic acid, hyaluronic acid, and alginic acid, were investigated. Humic acid, polylactic acid, polyacrylic acid, orthopyridyldisulfide-polyethyleneglycol-N-hydroxysuccinimide (OPSS-PEG-NHS) and a synthesized polymer; polymethacrylic-acid-co-vinyl-acetate (PMAVA), were also used. The polymers were chemically attached to a thiol monolayer on the SPR biosensor using carbodiimide chemistry. The polymers were functionalized for binding of anti-myoglobin (anti-MG). The sensor performance was measured using myoglobin (MG) at 25 ng ml⁻¹, a biologically relevant level for myocardial infarction detection. Most polymers offered similar performance to CM-dextran for MG detection in HEPES buffer saline pH 7.4 (HBS). In preliminary studies in bovine serum, each of the candidate polymers demonstrated better performance than CM-dextran.     

Synthesis of ferrocene-grafted poly(p-phenylene-ethynylenes) and control of electrochemical behaviors of their thin films

New ferrocene-coated poly(p-phenylene-ethynylenes) (PPEs) with end capping groups of protected thiol were prepared by a palladium-catalyzed Sonogashira coupling reaction. Ferrocene groups were covalently attached to polymers A and B through ethylene oxide tethers and to polymer C through methylene tethers. Polymers A and B are soluble in common solvents such as tetrahydrofuran (THF), chloroform, methylene chloride, acetone, dimethylformamide (DMF), and dimethyl sulfoxide (DMSO), and polymer C is soluble in toluene, THF, chloroform, and methylene chloride. Polymers A-C display low quantum yield, caused by electron-transfer quenching of ferrocene groups as electron donors. The polymer thin films were prepared through incubation of gold electrodes in THF solutions containing the polymers for 2 days. Ferrocene in thin films of polymers A and B display significantly faster electron-transfer rate than that of polymer C. Hydrophilic ethylene oxide side chains of polymers A and B decrease formal potential of tethered ferrocene groups because of electron-donating effect from ethylene oxide side chains, which stabilizes the ferrocenium ion and leads to a cathodic shift of the redox wave.     

电化学石英晶体微天平实时表征和定量检测短序列DNA

利用电化学石英晶体微天平(EQCM)这一灵敏的质量和电化学传感器测定特定序列DNA。应用自组装膜技术在压电石英晶振表面自组装一带羧基的α－硫辛酸单层膜,通过盐酸1-乙基-3-(3-二甲基氨基丙基)碳二亚胺(EDC)及N-羟基琥珀酰亚胺(NHS)共价固化寡聚核苷酸为探针,用于测定与其碱基序列互补的DNA。实验中EQCM实时监测了α-硫辛酸的自组装过程、探针固化过程及其与cDNA杂交过程。定量得出了探针固化量及cDNA杂交量。在酸性、中性和碱性条件下,分别对固化和杂交过程进行表征,实验发现探针固化及DNA杂交都受pH影响,本文对此现象进行了解释。同时,利用染料Hoechst33258的电化学活性,使其与双链DNA嵌合,通过测量Hoechst33258的电化学信息进一步验证了DNA杂交关键步骤。     

Label-Free DNA Biosensor for Electrochemical Detection of Short DNA Sequences Related to Human Papilloma Virus

Abstract

Highly sensitive label-free techniques of DNA determination are particularly interesting in relation to the present development of an electrochemical hybridization biosensor for the detection of short DNA fragments specific to the human papilloma virus (HPV). Unlabeled DNA probes have been immobilized by spontaneous coadsorption of thiolated single-stranded oligonucleotides (HS-ssDNA) onto the sensing surface of a screen-printed gold electrode (SPGE). The covalently immobilized single-stranded DNA probe (HS-ssDNA) could selectively hybridize with its complementary DNA (cDNA) in solution to form double-stranded DNA (dsDNA) on the surface. DNA is treated with acid (e.g., 0.5 M chloridric acid), and the acid-released purine bases are directly determined by square wave voltammetry (SWV).

Variables of the probe-immobilization and hybridization steps are optimized to offer convenient quantitation of HPV DNA target, in connection with a short hybridization time. Peak currents were found to increase in the following order: hybrid-modified SPGE, 11-base mismatched modified SPGE, 18-base mismatched SPGE, and the probe modified SPGE. Control experiments with noncomplementary oligonucleotides were carried out to assess whether the suggested DNA sensor responds selectively to the target. The effect of the target DNA concentration on the hybridization signal was also studied. Under optimal conditions, this sensor has a good calibration range with HPV DNA sequence detection limit of 2 pg · ml^?1 (S/N = 3).     

Modification of Escherichia coli single-stranded DNA binding protein with gold nanoparticles for electrochemical detection of DNA hybridization

The unique binding event between Escherichia coli single-stranded DNA binding protein (SSB) and single-stranded oligonucleotides conjugated to gold (Au) nanoparticles is utilized for the electrochemical detection of DNA hybridization. SSB was attached onto a self-assembled monolayer (SAM) of single-stranded oligonucleotide modified Au nanoparticle, and the resulting Au-tagged SSB was used as the hybridization label. Changes in the Au oxidation signal was monitored upon binding of Au tagged SSB to probe and hybrid on the electrode surface. The amplified oxidation signal of Au nanoparticles provided a detection limit of 2.17 pM target DNA, which can be applied to genetic diagnosis applications. This work presented here has important implications with regard to combining a biological binding event between a protein and DNA with a solid transducer and metal nanoparticles.     

Electrochemical detection of a Vibrio parahaemolyticus sequence-specific gene based on a gold electrode modified with a single stranded probe

An electrochemical DNA biosensor for specific-sequences detection of Vibrio parahaemolyticus (VP) was fabricated. A single-stranded 20-mer oligonucleotide (ssDNA) and 6-mercapto-1-hexanol (MCH) were immobilized via a thiol linker on gold disk electrodes by self-assembling. The ssDNA underwent hybridization in a hybridization solution containing complementary or non-complementary or single base pair mismatched DNA sequences of VP. Examination of changes in response to these three target DNAs showed that the developed biosensor had a high selectivity and sensitivity.