Development of loop-mediated isothermal amplification (LAMP) based biosendor set for detection of genetically modified organisms (GMO) and Escherichia coli (E. Coli)

Official URL: https://risc01.sabanciuniv.edu/record=b2352879_(Table of contents)

The worldwide usage of products with genetically modified organisms (GMOs) is constrained by different legal frameworks. GMO's usage limits are determined by the related regulations in each countries. "Regulation on Genetically Modified Organisms and Products" named law – effective since 2010 – draws the aforementioned conditions in Turkey. As a consequence, a variety of products are monitored by undergoing a GMO detection and classification processes. Researchers have been proposing different works regarding the specifically important problem of GMO-based products’ detection. Various methods such as Polymerase Chain Reaction, Ligase Chain Reaction, Rotating Circle Amplification are commonly used for DNA amplification, a crucial preprocessing step of the detection process. In this work, the loop-based isothermal amplification (LAMP) method which provides fast results and requires fewer temperature cycles is used. For the LAMP method to be properly implemented, the sample should be kept at 60-65:C between 35-120 minutes. Conventional laboratory devices used for this purpose can be characterized - on average – to be heavy (1-12 kg), expensive (1300-15000 €), unmovable and only operable by trained experts. In this thesis, we present the design, implementation and performance analysis of two prototype GMO-based product and bacteria detection devices that are portable (108-240 g) , fast (<30-40 minutes), affordable (<25-30 €) and pocket-size (6x6x3-9.7x6.8x5 cm) provided with battery system that allows its functionality outside laboratory environment. The temperature level controller, heater design, feedback circuit and the exterior of the device are prepared via different mechanical and electronic design software. A Proportional control based feedback control scheme is used to adjust the temperature with a high accuracy of (± 0.2:C). In this work, we extended the devices uses to E.coli bacteria detection as well. The detection was done using the LAMP method and is presented as the second device with its customized design providing high output (105 microchannels). Roundup Ready Soybean (RRS), gts40-3-2) with 0%, 0.1%, 1% and 10% GMO content were used for GMO analysis part and E. Coli ATCC 10536 bacteria for bacterial analysis. Both GMO and Bacteria detection and analysis results were done by the proposed devices showed similar performance in terms of accuracy and sensitivity when compared to the laboratory or commercial correspondents in the market while successfully outperforming them in the other already mentioned aspects