V. Cengiz Ozalp

Pathogen detection by core-shell type aptamer-magnetic preconcentration coupled to real-time PCR.

The presence of pathogenic bacteria is a major health risk factor in food samples and the commercial food supply chain is susceptible to bacterial contamination. Thus, rapid and sensitive identification methods are in demand for the food industry. Quantitative polymerase chain reaction (PCR) is one of the reliable specific methods with reasonably fast assay times. However, many constituents in food samples interfere with PCR, resulting in false results and thus hindering the usability of the method. Therefore, we aimed to develop an aptamer-based magnetic separation system as a sample preparation method for subsequent identification and quantification of the contaminant bacteria by real-time PCR. To achieve this goal, magnetic beads were prepared via suspension polymerization and grafted with glycidylmethacrylate (GMA) brushes that were modified into high quantities of amino groups. The magnetic beads were decorated with two different aptamer sequences binding specifically to Escherichia coli or Salmonella typhimurium. The results showed that even 1.0% milk inhibited PCR, but our magnetic affinity system capture of bacteria from 100% milk samples allowed accurate determination of bacterial contamination at less than 2.0 h with limit of detection around 100 CFU/mL for both bacteria in spiked-milk samples.

Label free optical sensor for Avidin based on single gold nanoparticles functionalized with aptamers.

Optical spectroscopy of a single gold nanoparticle, functionalized with an aptamer, is used to sense the specific binding of avidin. Herewith, the field of single noble metal nanoparticle biosensors is extended to the important field of aptamer based assays. The sensitivity of this initial, but not yet optimized apta-nano-sensor is in the range of 20 nM. Due to its nanoscopic size, this single nanoparticle based apta-sensor may be used in nanoscopic volumes such as in array type assays or even inside cells.

Melting temperature of surface-tethered DNA

A method for the accurate determination of the melting temperature (T(m)) of surface-immobilized DNA duplexes that exploits the fluorescence-quenching properties of gold is reported. A thiolated single-stranded DNA probe is chemisorbed onto a gold surface and then hybridized to a fluorophore-labeled complementary sequence. On formation of the duplex, the fluorescence of the label is effectively quenched by the gold surface. As the temperature is increased and the duplex denatures, the fluorophore label moves away from the gold surface and the fluorescence signal is again observed. The increase in fluorescence is measured as the temperature is ramped, and using first-derivative plots, the T(m) is determined. To demonstrate the approach, the T(m) of the cystic fibrosis DF508 mutation was determined in three different phases: in solution, in suspension immobilized on gold nanoparticles, and immobilized on gold film-coated substrate. The technique was further applied to optimize conditions for differentiation between a surface-immobilized DF508 mutant probe and a mutant/wild-type target exploiting increasing stringency in varying salt and formamide concentrations. The approach has application in optimization of assay conditions for biosensors that use gold substrates as well as in melting curve analysis.

Improvement stability and performance of invertase via immobilization on to silanized and polymer brush grafted magnetic nanoparticles

In this study, magnetic nanoparticles (Fe3O4) were modified sequentially with silica (Fe3O4@SiO2), glycidyl methacrylate (GMA) by surface initiated atom transfer radical polymerization (SI-ATRP) and hexamethylene diamine (as a spacer arm). The p(GMA) grafted and SA modified form (i.e., Fe3O4@SiO2@pGMA-SA-3) was used for covalent immobilization of invertase (EC 3.2.1.26). The amount of immobilized enzyme on Fe3O4@SiO2@p(GMA) and Fe3O4@SiO2@p(GMA)-SA-3 was 36.1±0.9 and 33.4±1.3mg/g, respectively. The Km and Vmax values of immobilized invertase were found to be 39.4mmol/L and 349.5mmol/L min, and not significantly changed compared with free form (34.3mmol/L and 387.2mmol/Lmin), respectively, revealed that the applied protocol did not have any detrimental effect on the retained activity of immobilized invertase.

Staphylococcus aureus detection in blood samples by silica nanoparticle-oligonucleotides conjugates.

A fast, specific and sensitive homogeneous assay for Staphylococcus aureus detection was developed by measuring the activity of secreted nuclease from the bacteria via a modified DNA oligonucleotide. As biosensor format, an effective system, Nanokeepers as previously reported, were used for triggered release of confined fluorophores, and hence specific detection of S. aureus on nuclease activity was obtained. The interference from blood components for fluorescent quantification was eliminated by a pre-purification by aptamer-functionalized silica magnetic nanoparticles. The reported assay system was exclusively formed by nucleic acid oligos and magnetic or mesoporous silica nanoparticles, that can be used on blood samples in a stepwise manner. The assay was successfully used as a sensing platform for the specific detection of S. aureus cells as low as 682 CFU in whole blood.

Fibrous polymer grafted magnetic chitosan beads with strong poly(cation-exchange) groups for single step purification of lysozyme

Lysozyme is an important polypetide used in medical and food applications. We report a novel magnetic strong cation exchange beads for efficient purification of lysozyme from chicken egg white. Magnetic chitosan (MCHT) beads were synthesized via phase inversion method, and then grafted with poly(glycidyl methacrylate) (p(GMA)) via the surface-initiated atom transfer radical polymerization (SI-ATRP). Epoxy groups of the grafted polymer, were modified into strong cation-exchange groups (i.e., sulfonate groups) in the presence of sodium sulfite. The MCTH and MCTH-g-p(GMA)-SO3H beads were characterized by ATR-FTIR, SEM, and VSM. The sulphonate groups content of the modified MCTH-g-p(GMA)-4 beads was found to be 0.53mmolg(-1) of beads by the potentiometric titration method. The MCTH-g-p(GMA)-SO3H beads were first used as an ion-exchange support for adsorption of lysozyme from aqueous solution. The influence of different experimental parameters such as pH, contact time, and temperature on the adsorption process was evaluated. The maximum adsorption capacity was found to be 208.7mgg(-1) beads. Adsorption of lysozyme on the MCTH-g-p(GMA)-SO3H beads fitted to Langmuir isotherm model and followed the pseudo second-order kinetic. More than 93% of the adsorbed lysozyme was desorbed using Na2CO3 solution (pH 11.0). The purity of the lysozyme was checked by HPLC and SDS gel electrophoresis. In addition, the MCTH-g-p(GMA)-SO3H beads prepared in this work showed promising potential for separation of various anionic molecules.

Design of a core–shell type immuno-magnetic separation system and multiplex PCR for rapid detection of pathogens from food samples

We report an immuno-magnetic separation system developed by the immobilization of pathogen-specific antibodies on the core–shell magnetic beads. The magnetic beads were grafted with glycidylmethacrylate (GMA) using surface-initiated atom transfer radical polymerization (SI-ATRP). For immuno-magnetic separation (IMS) of target bacterial cells from others, antibodies for Escherichia coli and Salmonella enterica serovar Typhimurium cells were immobilized on the magnetic beads via glutaraldehyde coupling reaction. Our IMS system successfully separated Salmonella cells when the concentrations of target (i.e., Salmonella) and interfering (i.e., E. coli) cells were at the same level. Polymerase chain reaction (PCR) assays amplifying the rfb/rfbE region of the E. coli genome and a 647-bp fragment of the invA region of Salmonella were performed as the specific selection to accurately confirm the presence of E. coli and Salmonella, respectively. IMS and multiplex PCR methods can be used for specific and quantitative detection of pathogens from food samples. Thus, this study developed a reliable and direct system for rapid detection of Salmonella and E. coli in food samples. In addition, IMS method could be easily adapted to detect other pathogens by selecting the pertinent antibody.

Adsorption and separation of immunoglobulins by novel affinity core-shell beads decorated with Protein L and l-histidine.

A novel core shell beaded chromatographic materials was prepared by grafting of glycidyl methacrylate (GMA) on to the surface of poly(hydoxypropyl methacrylate/ethyleneglycol dimethacrylate), p(HPMA/EGDMA) beads via surface-initiated atom transfer radical polymerization (SI-ATRP). For grafting GMA, p(HPMA/EGDMA) beads were first modified with an ATRP initiator. A reaction with 2-bromo-2-methylpropionyl bromide of the hydroxyl groups of the beads led to ATRP initiator-covered surfaces. The grafted p(GMA) fibrous chains on the beads were decorated with two different ligands (i.e., Protein L and l-histidine) for separation of Immunoglobulins (Igs) from aqueous solution in batch system. The maximum Igs adsorptions on the p(HPMA/EGDMA)-g-p(GMA)-Protein L and p(HPMA/EGDMA)-g-p(GMA)-l-histidine affinity beads were found to be 81.8 and 112.3mg/g at pH 7.5 and 5.5, respectively. The purity of Igs from human serum was analyzed by HPLC. The Protein L immobilized affinity beads provided purity about 98%. The novel core shell polymeric beads decorated with Protein L showed a good selectivity for Igs molecules from diluted human serum. Adsorption studies of Igs onto Protein L and l-histidine immobilized affinity beads were also carried out in a continuous system.

Magnetic silica nanoparticle–Taq polymerase hybrids for multiple uses in polymerase chain reaction

Enzyme-magnetic nanoparticle hybrids have been employed as a strategy to improve the biocatalytic usability of biological molecules. For this purpose, we synthesized magnetic core–silica shell nanoparticles for direct one-step easy immobilization of Taq polymerase from a crude extract preparation. The hybrid magnetic particles were synthesized by a magnetic co-precipitation method. The magnetic particles were then coated with a 3-(triethoxysilyl)-propylamine (APTES)/tetraethoxysilane (TEOS) mixture, and the pendant –NH2 groups subsequently functionalized with glutaraldehyde for simultaneous immobilization of Taq-polymerase. The magnetic properties of the particles contributed to fast purification to eliminate inhibitory elements present in the crude extract during Taq polymerase isolation. The Taq–silica hybrid material performed with a similar efficiency to the solution-phase enzyme. Additionally, the new hybrid material allowed reuse of the enzyme multiple times. The silica–Taq polymerase hybrid lost 16% of its activity after 6 cycles. Most importantly, the silica microparticle immobilization extended the functional life of Taq polymerase at room temperature by facilitating a fast cleaning procedure.

Development of a paper‐type tyrosinase biosensor for detection of phenolic compounds

A low‐cost, portable, and disposable paper‐type tyrosinase biosensor was developed for determination of phenolic compounds, using a paper‐strip absorption method. Tyrosinase and a chromophore (3‐methyl‐2‐benzothiazolinone hydrazone) were immobilized on paper strips to manufacture the biosensor, which was tested on a nontoxic substrate (l‐dopamine). The biosensor was responsive to phenolic compounds such as 4‐chlorophenol, catechol, m‐cresol, and p‐cresol. The sensor showed stability for 70 days. The developed biosensor can be used for remote on‐site qualitative monitoring of phenolic compounds in wastewater samples.