DNA microarray: a high throughput approach for methylation detection

We described a DNA microarray-based method combined with bisulphite treatment of DNA and regular PCR to examine hyper-methylation in promoter 1A of APC gene. A set of oligonucleotide probes were designed and immobilized on the aldehyde-coated glass slides for detecting the methylation pattern of 15 selected CpG sites in the region. The methylation status of 30 colorectal tumor samples have been examined by both of methylation-specific PCR (MS-PCR) and the present microarray method. The methylation pattern of the 15 CpG sites for the samples have been obtained with the microarray. A total of 19 samples out of 30 were methylated by microarray, in which five samples cannot be detected by MS-PCR due to the methylated CpG patterns not accordant to the MS-PCR primers. The detecting ratio for methylation of APC gene of colorectal tumor samples increased from 46.7% with MS-PCR to 63.3% with the microarray, which successfully demonstrated that DNA microarray-based method not only can obtained the methylation patterns for the related genes, but also decrease the false-negative results of methylation status by the conventional MS-PCR for the investigated genes.     

Effect of oligonucleotide probes substituted by deoxyinosines on the specificity of SNP detection on the DNA microarray

One of the main factors that can affect the quality of microarray results is the microarray hybridization specificity. The key factor that affects hybridization specificity is the design of the probes. In this paper, we described a novel oligonucleotide probe containing deoxyinosines aimed at improving DNA hybridization specificity. We compared different probes to determine the distance between deoxyinosine base and SNPs site and the number of deoxyinosine bases. The new probe sequences contained two set of deoxyinosines (each set had two deoxyinosines), in which the interval between SNP site and each set of deoxyinosines was two bases. The new probes could obtain the highest hybridization specificity. The experimental results showed that probes containing deoxyinosines hybridized effectively to the perfectly matched target and improved the hybridization specificity of DNA microarray. By including a simple washing step after hybridization, these probes could distinguish matched targets from single‐base‐mismatched sequences perfectly. For the probes containing deoxyinosines, the fluorescence intensity of a match sequence was more than eight times stronger than that of a mismatch. However, the intensity ratio was only 1.3 times or less for the probes without deoxyinosines. Finally, using hybridization of the PCR product microarrays, we successfully genotyped SNP of 140 samples using these new labeled probes. Our results show that this is a useful new strategy for modifying oligonucleotide probes for use in DNA microarray analysis.     

A modified uridine for the synthesis of branched DNA

Branched DNA constructs have found wide application in DNA-based nanotechnology. Several reports describe the generation of branched DNA structures with variable numbers of arms to self-assemble with pre-designed architectures. Branched DNA is generated by using designed rigid crossover DNA molecules as building blocks. Alternatively, branched DNAs can also be generated by using synthetic branch points derived either from nucleoside or non-nucleoside building blocks. Herein, we report the synthesis of modified uridine derivatives as branching monomer for the synthesis of branched DNA and first studies of their self-assembling properties.     

Synthesis of highly modified DNA by a combination of PCR with alkyne-bearing triphosphates and click chemistry

We report the combination of "click chemistry" with PCR by using alkyne-modified triphosphates for efficient and homogeneous labeling of DNA. A series of modified PCR products of different lengths (300, 900, and 2000 base pairs) were prepared by using a variety of alkyne- and azide-containing triphosphates and different polymerases. After intensive screening of real-time PCR methods, protocols were developed that allow the amplification of genes by using these modified triphosphates with similar efficiency to that of standard PCR. The click reaction on the highly modified PCR fragments provided conversion rates above 90 % and resulted in the functionalization of hundreds of alkynes on large DNA fragments with superb selectivity and efficiency.     

Cationic polymer coatings for design of electroosmotic flow and control of DNA adsorption

A difficulty with the design and operation of an electrokinetically operated DNA hybridization microfluidic chip is the opposite direction of the electroosmotic flow and electrophoretic mobility of the oligonucleotides. This makes it difficult to simultaneously deliver targets and an appropriate hybridization buffer simultaneously to the probe sites. In this work we investigate the possibility of coating the inner walls of the microfluidic system with hexadimentrine bromide (polybrene, PB) and other cationic polymers in order to reverse the direction of electroosmotic flow so that it acts in the same direction as the electrophoretic transport of the oligonucleotides. The results indicated that the electroosmotic flow (EOF) in channels that were coated with the polymer could be reversed in 1× TBE buffer or 1× SSC buffer. Under these conditions, the DNA and EOF move in the same direction, and the flow can be used to deliver DNA to an area for selective hybridization within the channel. The effects of coating the surface of a nucleic acid microarray with polybrene were also studied to assess non-selective adsorption and stability. The polybrene coating significantly reduced the extent of non-selective adsorption of oligonucleotides in comparison to adsorption onto a glass surface, and the coating did not alter the extent of hybridization. The results suggest that use of the coating makes it possible to achieve semi-quantitative manipulation of nucleic acid oligomers for delivery to an integrated microarray or biosensor.     

Accumulated detection of ethidium bromide using a UV-irradiated DNA film modified electrode and its application for electrochemical detection of an environmental pollutant

In this study, DNA was first fabricated on a glassy carbon electrode by UV-irradiation. Through this process, water-soluble DNA was converted into insoluble materials, and a stable DNA film formed on the electrode. Ethidium bromide (EtBr), a typical model substance for harmful chemicals having planer structure, was used as an electroactive intercalator. This allowed our group to investigate the electrochemical and accumulative behaviors of the intercalator in UV-irradiated DNA film on the electrode. The UV-irradiated, DNA film-modified electrode (UV-DNA-FE) made it possible to accumulate electroactive EtBr on the electrode and detect it after accumulation. The modified electrode was used to detect dibenzofuran (DBF) as an environmental pollutant. The measurements were successfully obtained by focusing on the variation of the electrode response of EtBr, based on the competitive reaction between EtBr and DBF for the intercalating sites of DNA. The results indicated the possibility of using UV-DNA film as a sensing mechanism.     

A DNA Origami-based Bactericide for Efficient Healing of Infected Wounds

Bacteria infection is a significant obstacle in the clinical treatment of exposed wounds facing widespread pathogens. Herein, we report a DNA origami-based bactericide for efficient anti-infection therapy of infected wounds in vivo. In our design, abundant DNAzymes (G4/hemin) can be precisely organized on the DNA origami for controllable generation of reactive oxygen species (ROS) to break bacterial membranes. After the destruction of the membrane, broad-spectrum antibiotic levofloxacin (LEV, loaded in the DNA origami through interaction with DNA duplex) can be easily delivered into the bacteria for successful sterilization. With the incorporation of DNA aptamer targeting bacterial peptidoglycan, the DNA origami-based bactericide can achieve targeted and combined antibacterial therapy for efficiently promoting the healing of infected wounds. This tailored DNA origami-based nanoplatform provides a new strategy for the treatment of infectious diseases in vivo.     

Detection of processed genetically modified food using CIM monolithic columns for DNA isolation

The availability of sufficient quantities of DNA of adequate quality is crucial in polymerase chain reaction (PCR)-based methods for genetically modified food detection. In this work, the suitability of anion-exchange CIM (Convective Interaction Media; BIA Separations, Ljubljana, Slovenia) monolithic columns for isolation of DNA from food was studied. Maize and its derivates corn meal and thermally pretreated corn meal were chosen as model food. Two commercially available CIM disk columns were tested: DEAE (diethylaminoethyl) and QA (quaternary amine). Preliminary separations were performed with standard solution of salmon DNA at different pH values and different NaCl concentrations in mobile phase. DEAE groups and pH 8 were chosen for further isolations of DNA from a complex matrix-food extract. The quality and quantity of isolated DNA were tested on agarose gel electrophoresis, with UV-scanning spectrophotometry, and by amplification with real-time PCR. DNA isolated in this way was of suitable quality for further PCR analyses. The described method is also applicable for DNA isolation from processed foods with decreased DNA content. Furthermore, it is more effective and less time-consuming in comparison with the existing proposed methods for isolation of DNA from plant-derived foods.     

Polyurethane Molecular Stamps for the in situ Synthesis of DNA Microarray

Fabrication of polyurethane molecular stamps (PU stamps) based on polypropylene glycol (PPG) and toluene dissocyanate (TDI), using 3,3′-dichloro-4,4′-methylenedianiline (MOCA) as the crosslinker ,is reported. It was shown from the contact angle measurement that PU stamps surface has good affinity with acetonitrile,guaranteeing the well distribution of DNA monomers on patterned stamps. Laser confocal fluorescence microscopy images of oligonucleotide arrays after hybridization confirmed polyurethane is an excellent material for molecular stamps when ransferring polar chemicals and conducting rections on interfaces by stamping.     

Simple and rapid methods for the fabrication of polymeric and glass chips for using in analytical chemistry

This paper describes simple and rapid methods for the fabrication of glass and polymeric chips for routine analytical applications. The methods are easily interfaced to the general laboratory environment and do not require special clean room facilities or expensive instruments. Glass microchips were fabricated by etching with HF solution. Microfluidic channels were designed with CAD program and transferred onto a sheet of commercial polymeric self-adhesive (PSA) film by a cutter plotter. The PSA film was used as a mask for etching process. The etching rate was about 7 μm min⁻¹. A cover glass plate was sealed on the top of etched substrate by using polycellulose (cellophane). Polymeric microchips were fabricated by sawing with a jigsaw. Commercial polycarbonate (PC) was used as a substrate and two iron sheets were used as leader masks. While this restricts us to the fabrication of straight channels, it is however, much faster and less complicated than the other methods. The chip comprised three polymeric plates and the channels were created in the middle plate. Thermal bonding was used to bond three layers of the microfluidic chip. With this method, we could achieve simple channels with the width of about 200 μm. The channel depth depends on the polymeric plate thickness. Fabricated channels were accurate without any sinuosity or sideshow.     

A novel detection of single-stranded DNA binding protein based on ss-DNA modified chip using surface plasmon resonance microscopy

An ss-DNA gold chip was prepared based on self-assembly of the thiol-derivatized oligonucleotide,and used for thedetermination of single-stranded binding protein(SSB)by surface plasmon resonance microscopy(SPR).The experiment resultsshowed that SSB binds ss-DNA with high specificity,and relative signal of SPR response is proportional to the concentration of SSBin the range of 0.1-100 ng/mL with a detection limit(S/N=3)of 0.07 ng/mL.     

Microwave assisted fabrication of polymethyl methacrylate-graphene composite nanoparticles applied for the preparation of SBS modified asphalt with enhanced high temperature performance

In order to improve the high temperature rutting resistance ability and stability of styrene-butadiene-styrene (SBS) modified asphalt, microwave heating emulsion polymerization strategy was used to prepare polymethyl methacrylate (PMMA) and graphene nanoparticles (GNPs) composite (PMMA-GNPs) which was used to prepare PMMA-GNPs/SBS modified asphalt. Fourier transform infrared spectroscopy, X-ray diffraction, scanning electron microscopy and thermogravimetric analysis characterizations showed that PMMA-GNPs particles were successfully prepared having a weight ratio of GNPs: PMMA of 1:9. Microwave heating reduced the reaction time from 5 h to 30 min compared to conventional oil bath heating. Dynamic shear rheological test and multi-stress creep recovery test confirmed that 0.06% PMMA-GNPs/SBS modified asphalt (0.06% PMMA-GNPs of the mass of base asphalt) exhibited an increase of 14.2% in elastic modulus (G′), while rutting resistance was enhanced and sensitivity to stress changes was reduced as compared to those of 5% SBS modified asphalt. Fluorescence microscopy analysis and phase separation test revealed that an appropriate amount of PMMA-GNPs can be uniformly dispersed in SBS modified asphalt and enhance the mutual interaction of SBS with base asphalt. Based on the results of mechanical tests and characterizations, a suitable modification mechanism of PMMA-GNPs particles in the original SBS modified asphalt was described in detail. This study proposes a simple, cost effective and fast strategy for the preparation of PMMA-GNPs incorporated SBS modified asphalt and hence can be envisioned of great promise in construction and highway industries.     

Tin oxide nanoparticles-polymer modified single-use sensors for electrochemical monitoring of label-free DNA hybridization

In this study, SnO₂ nanoparticles (SNPs)-poly(vinylferrocenium) (PVF⁺) modified single-use graphite electrodes were developed for electrochemical monitoring of DNA hybridization. The surfaces of polymer modified and polymer-SNP modified pencil graphite electrodes (PGEs) were firstly characterized by using SEM analysis. The electrochemical behaviours of these electrodes were also investigated using the differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS) techniques. The polymer-SNP modified PGEs were then tested for the electrochemical sensing of DNA based on the changes at the guanine oxidation signals. Experimental parameters, such as; different modifications in DNA oligonucleotides, DNA probe concentrations were examined to obtain more sensitive and selective electrochemical signals for nucleic acid hybridization. After optimization studies, DNA hybridization was investigated in the case of complementary of hepatitis B virus (HBV) probe, mismatch (MM), and noncomplementary (NC) sequences.