In this thesis, a novel approach for species-specific genomic DNA extraction based on the utilization of surface modified magnetic nanoparticles (MNPs) is reported. Two extraction methods, liquid-phase and sandwich hybridization, are investigated relying on species-specific hybridization. In the liquid-phase approach, a biotinylated oligo-probe, which is complementary to the genomic DNA, hybridizes with the genomic DNA and then binds on MNP surface through biotin-streptavidin interaction. In the sandwich approach, a linking sequence is designed that one end of it is complementary to the oligo-probe on MNP and the other end contains complementary sequence to the genome DNA. The genomic DNA, therefore, can be captured through two steps of hybridization. DNA captured on MNPs can be easily...[ Read more ]

In this thesis, a novel approach for species-specific genomic DNA extraction based on the utilization of surface modified magnetic nanoparticles (MNPs) is reported. Two extraction methods, liquid-phase and sandwich hybridization, are investigated relying on species-specific hybridization. In the liquid-phase approach, a biotinylated oligo-probe, which is complementary to the genomic DNA, hybridizes with the genomic DNA and then binds on MNP surface through biotin-streptavidin interaction. In the sandwich approach, a linking sequence is designed that one end of it is complementary to the oligo-probe on MNP and the other end contains complementary sequence to the genome DNA. The genomic DNA, therefore, can be captured through two steps of hybridization. DNA captured on MNPs can be easily separated with the presence of external magnetic field. The extraction of Bacillus subtilis genome was successfully demonstrated using this ‘sandwich approach’ extraction technique and the performance is comparable to the commercial DNA extraction kit. Different factors influencing the extraction efficiency are also studied for the enhancement to the extraction efficiency. The captured DNA is amplified by polymerase chain reaction (PCR) and then quantified by PicoGreen^® double-stranded (ds) quantification dye which provides more reliable and accurate results than the conventional measurement of relative band intensity in gel after gel electrophoresis. This emerging DNA extraction method is an alternative, providing rapid and user-friendly procedure of sample preparation for many biological applications.