Poly(L-lysine)-mediated immobilisation of oligonucleotides on carboxy-rich polymer surfaces

Efficient removal of ethidium bromide from aqueous solution by using DNA-loaded Fe3O4 nanoparticles

Ethidium bromide (EtBr) is widely used as DNA-staining dyes for the detection of nucleic acids in laboratories and known to be powerful mutagens and carcinogens. In the present paper, the removal of EtBr from aqueous solutions in a batch system using DNA-loaded Fe₃O₄ nanoparticles as a simple and efficient method was investigated. DNA was covalently loaded on the surface of Fe₃O₄ magnetic nanoparticles, which was confirmed by FT-IR analysis and zeta potential measurements. The morphology and crystal structure were characterized by SEM, TEM, and XRD. The influence factors on the removal efficiency such as initial EtBr concentration, contact time, adsorbent dose, pH, and temperature were also studied. The removal process of EtBr can be completed quickly within 1 min. The removal efficiency was more than 99% while the EtBr concentration was routinely used (0.5 mg L^-1) in biology laboratories and the dosages of nanoparticles were 1 g L^-1. For the different EtBr concentrations from 0.5 to 10 mg L^-1 in aqueous solution, the goal of optimized removal was achieved by adjusting the dosage of DNA-loaded Fe₃O₄ nanoparticles. The optimum pH was around 7 and the operational temperature from 4 to 35 °C was appropriate. Kinetic studies confirmed that the adsorption followed second-order reaction kinetics. Thermodynamic data revealed that the process was spontaneous and exothermic. The adsorption of EtBr on DNA-loaded Fe₃O₄ nanoparticles fitted well with the Freundlich isotherm model. These results indicated that DNA-loaded Fe₃O₄ nanoparticles are a promising adsorbent for highly efficient removal of EtBr from aqueous solution in practice.

Rapid Assay to Assess Bacterial Adhesion on Textiles

Textiles are frequently colonized by microorganisms leading to undesired consequences like hygienic problems. Biocidal coatings often raise environmental and health concerns, thus sustainable, biocide-free coatings are of interest. To develop novel anti-adhesive textile coatings, a rapid, reliable, and quantitative high-throughput method to study microbial attachment to fabrics is required, however currently not available. Here, a fast and reliable 96-well plate-based screening method is developed. The quantification of bacterial adhesion is based on nucleic acid staining by SYTO9, with Pseudomonas aeruginosa and Staphylococcus aureus as the model microorganisms. Subsequently, 38 commercially available and novel coatings were evaluated for their anti-bacterial adhesion properties. A poly(l-lysine)-g-poly(ethylene glycol) coating on polyester textile substratum revealed an 80% reduction of bacterial adhesion. Both the coating itself and the anti-adhesive property were stable after 20 washing cycles, confirmed by X-ray analysis. The assay provides an efficient tool to rapidly screen for non-biocidal coatings reducing bacterial attachment.

A handheld magnetic sensing platform for antigen and nucleic acid detection

A portable magnetic-based biosensing platform is introduced for antigen and nucleic acid detection utilizing the “magnetic freezing” technique.

High-throughput nano-biofilm microarray for antifungal drug discovery

Micro- and nanoscale technologies have radically transformed biological research from genomics to tissue engineering, with the relative exception of microbial cell culture, which is still largely performed in microtiter plates and petri dishes. Here, we present nanoscale culture of the opportunistic fungal pathogen Candida albicans on a microarray platform. The microarray consists of 1,200 individual cultures of 30 nl of C. albicans biofilms (“nano-biofilms”) encapsulated in an inert alginate matrix. We demonstrate that these nano-biofilms are similar to conventional macroscopic biofilms in their morphological, architectural, growth, and phenotypic characteristics. We also demonstrate that the nano-biofilm microarray is a robust and efficient tool for accelerating the drug discovery process: (i) combinatorial screening against a collection of 28 antifungal compounds in the presence of immunosuppressant FK506 (tacrolimus) identified six drugs that showed synergistic antifungal activity, and (ii) screening against the NCI challenge set small-molecule library identified three heretofore-unknown hits. This cell-based microarray platform allows for miniaturization of microbial cell culture and is fully compatible with other high-throughput screening technologies.

Microorganisms are typically still grown in petri dishes, test tubes, and Erlenmeyer flasks in spite of the latest advances in miniaturization that have benefitted other allied research fields, including genomics and proteomics. Culturing microorganisms in small scale can be particularly valuable in cutting down time, cost, and reagent usage. This paper describes the development, characterization, and application of nanoscale culture of an opportunistic fungal pathogen, Candida albicans. Despite a more than 2,000-fold reduction in volume, the growth characteristics and drug response profiles obtained from the nanoscale cultures were comparable to the industry standards. The platform also enabled rapid identification of new drug candidates that were effective against C. albicans biofilms, which are a major cause of mortality in hospital-acquired infections.

Electrochemical detection of dihydromyricetin using a DNA immobilized ethylenediamine/polyglutamic modified electrode

A novel voltammetric sensor, based on DNA immobilized on the surface of an ethylenediamine/polyglutamic (En/PGA) modified glassy carbon electrode (GCE), was constructed and used for determination of dihydromyricetin (DMY). The electrochemical behaviour of DMY at this sensor was investigated in pH 3.6 NaAc-HAc buffer solutions by cyclic voltammetry (CV) and differential pulse anodic voltammetry (DPV). The oxidation of DMY is an adsorption-controlled irreversible process. The oxidation mechanism was proposed and discussed. It was found that the modified electrode exhibited a linear voltammetric response for DMY in the range of 4.0 × 10(-8) mol L(-1) to 2 × 10(-6) mol L(-1), with a detection limit of 2 × 10(-8) mol L(-1). The method was also applied successfully to detect DMY in an ampelopsis sample with satisfactory results.

Label-free target DNA recognition using oligonucleotide-functionalized polypyrrole nanotubes

Conjugated polymers for oligonucleotide immobilization offer extraordinary potential as transducers for detecting DNA duplex formation, because the electrical, optical, and electrochemical properties are strongly affected by relatively small perturbations. Moreover, carboxylated conducting polymer supports are an attractive alternative due to their versatile immobilization with DNA, protein, and enzyme using various pendant groups: -SH, -NH(2), and -COOH. Therefore, we report the fabrication of carboxylic acid-functionalized polypyrrole nanotubes (CPPy NTs) using oxidant-impregnated template synthesis. The diverse number of carboxylates on the surface of CPPy NTs was applied to binding sites for amino-terminal oligonucleotides. Conductance of single DNA strands (ssDNA) and hybridized DNA helix were readily measured by means of depositing DNA-functionalized nanotubes on gold leads, and indicated high sensitivity (DeltaR/R(0)=1.7) even at low concentration (1 nmol) of target DNA. In addition, target DNA concentration was distinguished up to a narrow difference of 2 nmol. The successful DNA immobilization on polymer nanotubes was confirmed and visualized by the photoluminescence of fluorescein isothiocyanate (FITC)-tagged target DNA using confocal laser scanning microscopy.

Initiated chemical vapor deposition of alternating copolymers of styrene and maleic anhydride

Initiated chemical vapor deposition (iCVD) of alternating copolymer thin films has been achieved for the first time. Copolymerization is desirable for maleic anhydride (Ma) since this monomer does not homopolymerize to an appreciable extent. At conditions where the observed deposition rates for styrene (S) and Ma homopolymers were only 0 and 5.5 nm/min, respectively, combining the two monomers resulted in a much higher deposition rate of 75.4 nm/min. iCVD processes utilize low energy (<30 W) to generate peroxy radicals from initiator molecules while avoiding degradation of functional groups in the monomers. Indeed, full retention of the anhydride functionality from the Ma monomer and avoidance of undesirable side reactions was observed in iCVD of poly(styrene-alt-maleic anhydride) (PSMa) copolymer films. Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and 13C nuclear magnetic resonance (NMR) conclusively demonstrate that all of the copolymer films contain 50% styrene and 50% Ma (within experimental error), irrespective of gas feed ratios employed during the deposition. The 13C NMR signal in the 136-140 ppm region from the quaternary carbon in styrene and additional distortionless enhancement polarization transfer experiments confirmed that the copolymers are strictly alternating. Varying the gas feed ratio of Ma to styrene provided control over deposition rates and number-average molecular weights. Number-average molecular weights varied from 1380 to 4680 g/mol, and deposition rates varied from 6.3 to 75.4 nm/min.

Oligonucleotide chip for the diagnosis of HNF-1α mutations

Mutations in HNF-1 alpha cause maturity-onset diabetes of the young (MODY) type 3, which is the most prevalent MODY subtype in most countries. In the present study, we investigated an oligonucleotide microchip for the detection of the known HNF-1 alpha mutations. We first optimized the coupling chemistries for covalent immobilization of allele-specific oligonucleotides on aldehyde (CHO)- and thiocyanate (NCS)-activated glass slides and compared their hybridization efficiencies. CHO-glass was found to provide a more favorable environment for hybridization than NCS-glass, whereas the binding capacity of NCS-glass for amine-activated oligonucleotide was much greater than with CHO-glass. We also investigated the effects of the length of the capture probes on the hybridized signals. To determine the presence of HNF-1 alpha mutations in a human sample, we prepared an oligonucleotide chip from selected mutation sites of exon2 from HNF-1 alpha. Cy3-labeled RNA target probes were obtained by in vitro transcription of promoter-tagged PCR products from a wild-type blood sample and subsequent fragmentation. Hybridization of the chip with the RNA target probes successfully identified all of the genotypes for the tested sites. This work demonstrates that oligonucleotide chip-based analysis is a good candidate for routine clinical testing for HNF-1 alpha mutations.

Detecting minimal traces of DNA using DNA covalently attached to superparamagnetic nanoparticles and direct PCR-ELISA

A single bond covalent immobilization of aminated DNA probes on magnetic particles suitable for selective molecular hybridization of traces of DNA samples has been developed. Commercial superparamagnetic nanoparticles containing amino groups were activated by coating with a hetero-functional polymer (aldehyde-aspartic-dextran). This new immobilization procedure provides many practical advantages: (a) DNA probes are immobilized far from the support surface preventing steric hindrances; (b) the surface of the nanoparticles cannot adsorb DNA ionically; (c) DNA probes are bound via a very strong covalent bond (a secondary amine) providing very stable immobilized probes (at 100 degrees C, or in 70% formamide, or 0.1N NaOH). Due to the extreme sensitivity of this purification procedure based on DNA hybridization, the detection of hybridized products could be coupled to a PCR-ELISA direct amplification of the DNA bond to the magnetic nanoparticles. As a model system, an aminated DNA probe specific for detecting Hepatitis C Virus cDNA was immobilized according to the optimised procedure described herein. Superparamagnetic nanoparticles containing the immobilized HCV probe were able to give a positive result after PCR-ELISA detection when hybridized with 1 mL of solution containing 10(-18) g/mL of HCV cDNA (two molecules of HCV cDNA). In addition, the detection of HCV cDNA was not impaired by the addition to the sample solution of 2.5 million-fold excess of non-complementary DNA. The experimental data supports the use of magnetic nanoparticles containing DNA probes immobilized by the procedure here described as a convenient and extremely sensitive procedure for purification/detection DNA/RNA from biological samples. The concentration/purification potential of the magnetic nanoparticles, its stability under a wide range of conditions, coupled to the possibility of using the particles directly in amplification by PCR greatly reinforces this methodology as a molecular diagnostic tool.