Date of Award

Fall 2012

Degree Type


Degree Name

Master of Applied Science (MASc)


Mechanical Engineering


P. R. Selvaganapathy




Continuous monitoring of pathogens that may be present in water is one of the key preventive measures that can be used in rural areas of developed countries and developing countries to reduce chances of the water borne diseases outbreak. Off-site testing of microbiological contamination of water is conventionally done for monitoring water quality. However, such a process is time consuming and involves using a variety of hazardous reagents. To address these issues, a portable device for rapid detection of unsafe water is needed.

One of the key components in this system is to extract DNA from the pathogens. The primary consideration for DNA extraction is to separate DNA from proteins and other cell debris in the lysate solution. The pure population of DNA molecules are then sent downstream for subsequent processing such as real-time PCR (Polymerase Chain Reaction) and BioFET sensors for further identification and analysis.

The focus of the thesis will be on the fabrication of a microfluidic DNA extraction system that can achieve high DNA extraction efficiency and a good repeatability. It can also be easily automated, and integrated with other components of the DNA analysis system. The high surface-to-volume macro/mesoporous silica DNA binding column was synthesized using sol-gel silica technology and triblock copolymer F127 was added to form a crack-free mesoporous silica network. Furthermore, a monodispersed polystyrene microspheres soft-template was assembled using a simple but novel technique that employs controlled suction to enhance self-assembly into a periodically patterned structure in the extraction chamber/chambers. In combination of heat annealing treatment of this assembled polystyrene template, one can easily control the size of the macropores in the final macro/mesoporous silica structure to allow a lower pressure resistance for DNA sample flow at elution stage. The final macro/mesoporous silica structure synthesized using heat annealing temperature of 115oC for 10 minutes was determined to have a porosity of 83.6%. Mesopores of this silica monolith was determined by BET test to be 3.65 nm and the macroporous ranging from 0.5μm to 0.86μm were observed. In addition, the fabrication of porous silica monolith can be easily integrated with the microfluidic system for achieving DNA extraction purposes

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