Design of DNA microarrays for pathogen detection

• Main Author: Lau, Yi Xiang.
• Other Authors: Chang Wook, Matthew
• Format: Final Year Project
• Language: English
• Published: 2010
• Subjects: DRNTU::Engineering::Chemical engineering::Biotechnology
• Online Access: http://hdl.handle.net/10356/39369
• Institution: Nanyang Technological University

A method using DNA Microarrays following PCR amplification of 12 selected unique genes has been proposed for the specific detection of Escherichia coli O157:H7, Salmonella Typhimurium, Salmonella Typhi, Salmonella Enteritidis and Yersinia Enterocolitica in drinking water sample. The use of specific literature PCR primers amplifying the unique rfbE sequence as well as hybridization of amplicons with specific DNA Microarray probes was proven to be able to provide a specific detection of E. coli O157:H7 in theory. 3 other genes, with primers and DNA probes derived from these genes (fliC, stx1 and stx2) were used as confirmation to detection results. Moreover, the STM4497 gene was unique and its primer set was also proven to be specific to S. Typhimurium. Also, since the STM4497 Microarray probe was specific for the same pathogen, it should provide a specific detection of S. Typhimurium, using the STM4492 primer sets and Microarray probe as confirmation. In addition, it was also proven theoretically that the use of the viaB primer set to amplify the unique viaB gene sequence allowed the specific detection of Salmonella Typhi using specific DNA Microarray probes. Tyv PCR primer set and its DNA Microarray probe provided a good confirmation of the presence of S. Typhi. Also, the amplification of the unique gene of S. Enteritidis – the spvA gene, using specific PCR primer set was able to allow the specific detection of S. Enteritidis by DNA Microarray. Finally, the ail and yst genes were proven to be unique to Y. Enterocolitica. The PCR primer sets used were proven to be specific and their use provided a theoretically specific detection of Y. Enterocolitica through hybridization with DNA Microarray probes. The virF primers and DNA Microarray probes are expected to give a good confirmation of the hybridization results.