QCM-based DNA biosensor for detection of genetically modified organisms (GMOs)

Karamollaoglu, Irem
Oektem, Hueseyin Avni
Mutlu, Mehmet Kayhan
Development of a mass sensitive quartz crystal microbalance (QCM)-based DNA biosensor for the detection of the hybridization of CaMV 35S promoter sequence (P35S) was investigated for the screening of genetically modified organisms (GMOs). Attention was focused on the choice of the coating chemistry that could be used for the immobilization of probe sequences on the gold surface of the quartz crystal. Two immobilization procedures were tested and compared considering the amount of the immobilized P35S probe and the extent of the hybridization reaction with the target oligonucleotide. In wet chemistry procedure, the interaction between the thiol and gold for the immobilization of a thiolated probe was employed. Direct surface functionalization of piezoelectric quartz crystals were achieved in 13.56 MHz plasma polymerization reactor utilising ethylenediamine (EDA) precursors for the immobilization of amined probes. Results indicated that immobilization of a thiolated probe provides better immobilization characteristics and higher sensitivity for the detection of the hybridization reaction. The thiolated probe was used for the detection of P35S sequence in PCR-amplified DNAs and in real samples of pflp (ferrodoxin like protein)-gene inserted tobacco plants. Fragmentation of the genomic DNAs were achieved by digestion with restriction endonucleases and ultrasonication. The results obtained from the fragmented genomic DNAs demonstrated that it is possible to detect the target sequence directly in non-amplified genomic DNAs by using the developed QCM-based DNA biosensor system. The developed QCM-based DNA biosensor represented promising results for a real-time, label-free, direct detection of DNA samples for the screening of GMOs.


Analyses of extracellular protein production in Bacillus subtilis - I: Genome-scale metabolic model reconstruction based on updated gene-enzyme-reaction data
KOCABAŞ, PINAR; Çalık, Pınar; ÇALIK GARCİA, GÜZİDE; Ozdamar, Tuncer H. (Elsevier BV, 2017-11-15)
Bacillus subtilis genome-scale model (GEM) reconstruction was stimulated by the recent sequencing and consequent re-annotations. The updated gene-enzyme-reaction data were collected from databases to reconstruct B. subtilis reaction network BsRN-2016 containing 1144 genes linked to 1955 reactions and 1103 metabolites. Thermodynamic analysis was conducted to identify reversibility and directionality of the reactions. By elimination of unconnected-reactions from BsRN-2016, reconstruction process of the first ...
Analyses of extracellular protein production in Bacillus subtilis - II: Responses of reaction network to oxygen transfer at transcriptional level
KOCABAŞ, PINAR; ÇALIK GARCİA, GÜZİDE; Çalık, Pınar; Ozdamar, Tuncer H. (Elsevier BV, 2017-11-15)
Oxygen transfer influences intracellular fluxes which are orchestrated by genome and its transcription in Bacillus subtilis throughout fermentation in recombinant human growth hormone (rhGH) production. Responses of B. subtilis reaction network to oxygen transfer were analysed at transcriptional level with determined transcriptome and calculated intracellular fluxes by the reconstructed genome scale model iBsu1144(rhGH) based on updated gene-enzyme-reaction data. iBsu1144(rhGH) employing 1067 reactions link...
Covalent immobilization of chloroperoxidase onto magnetic beads: Catalytic properties and stability
Bayramoglu, Guelay; Kiralp, Senem; Yilmaz, Meltem; Toppare, Levent Kamil; Arica, M. Yakup (Elsevier BV, 2008-02-15)
Amino groups containing magnetic beads were used in covalent immobilization of the enzyme "chloroperoxidase (CPO)" which is one of a few enzymes that can catalyse the peroxide dependent oxidation of a wide spectrum of organic and inorganic compounds. The magnetic poly(glycidylmethacrylate-methylmethacrylate-etbyleneglycol dimethacrylate), magnetic p(GMA-MMA-EGDMA) beads were prepared via suspension polymerization in the presence of ferric ions. The magnetic beads were characterized with scanning electron mi...
Carbon sources affect metabolic capacities of Bacillus species for the production of industrial enzymes: theoretical analyses for serine and neutral proteases and alpha-amylase
Çalık, Pınar (Elsevier BV, 2001-07-01)
The metabolic fluxes through the central carbon pathways were calculated for the genus Bacillus separately for the enzymes serine alkaline protease (SAP), neutral protease (NP) and alpha -amylase (AMY) on five carbon sources that have different reduction degrees (gamma), to determine the theoretical ultimate limits of the production capacities of Bacillus species and to predict the selective substrate for the media design. Glucose (gamma = 4.0), acetate (gamma = 4.0), and the TCA cycle organic-acids succina...
Biodegradation of 4-CP and 2,4-DCP mixture in a rotating biological contactor (RBC)
şahinkaya, Erkan; Dilek, Filiz Bengü (Elsevier BV, 2006-09-01)
In this study, the performance of a two stage rotating biological contactor (RBC) was evaluated for the treatment of synthetic wastewater containing peptone, 4-chlorophenol (4-CP) and 2,4-dichlorophenol (2,4-DCP) at 5 rpm. Also, the effect of biogenic substrate (peptone) concentration on the reactor performance was investigated. High chlorophenols (> 98%) and COD (> 94%) removals were achieved throughout the reactor operation in the first stage and the second stage behaved as a polishing step. The observed ...
Citation Formats
I. Karamollaoglu, H. A. Oektem, and M. K. Mutlu, “QCM-based DNA biosensor for detection of genetically modified organisms (GMOs),” BIOCHEMICAL ENGINEERING JOURNAL, pp. 142–150, 2009, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/58010.