A magnetic bead-based DNA extraction and purification device has been designed to be used for extraction of the target DNA molecules from whole blood sample. Mixing and separation steps are performed using functionalised superparamagnetic beads suspended in the cell lysis buffer in a circular chamber that is sandwiched between two electromagnets. Non-uniform nature of the magnetic field causes temporal and spatial distribution of the beads within the chamber. This process efficiently mixes the lysis buffer and whole blood in order to extract DNA from target cells. Functionalized surface of the magnetic beads then attract the exposed DNA molecules. Finally, DNA-attached magnetic beads are attracted to the bottom of the chamber by activating the bottom electrode. DNA molecules are extracted from the magnetic beads by washing and re-suspension processes. The numerical simulation approach has been adopted in order to design the magnetic field source. The performance of the magnetic field source has been investigated against different physical and geometrical parameters and optimised dimensions are obtained with two different magnetic field sources; integrated internal source and external source. A new magnetic field pattern has been introduced in order to efficiently control the bulk of magnetic beads inside the mixing chamber by dynamic shifting of magnetic field regions from the centre of the coils to the outer edge of the coils and vice versa. A Matlab code has been developed to simulate beads trajectories inside the designed extraction chip in order to investigate the efficiency of the magnetic mixing. A preliminary target molecule capturing simulation has also been performed using the simulated bead trajectories to evaluate the DNA-capturing efficiency of the designed extraction chip. The performance of the designed extraction chip has been tested by conducting a series of biological experiments. Different magnetic bead-based extraction kits have been used in a series of preliminary experiments in order to extract a more automation friendly extraction protocol. The efficiency of the designed device has been evaluated using the spiked bacterial DNA and non-pathogenic bacterial cell cultures (B. subtilis, Gram positive bacteria and E. coli, Gram negative bacteria) into the blood sample. Excellent DNA yields and recovery rates are obtained with the designed extraction chip through a simple and fast extraction protocol.

<div> <div> <div> <p>Microfluidics is a new and emerging field that has applications in a myriad of microfluidic industrial applications such as biochemical engineering, analytical processing, biomedical engineering and separation of cells. Microfluidics operations are carried out in microfluidic chips, and the traditional method of fabrication is carried out in a cleanroom. However, this fabrication method is very costly and also requires professional trained personnel. In this thesis, a low-cost fabrication platform was developed based on soft-lithography technique developed to fabricate the microfluidic devices with resolution at microscale. This fabrication method is advantageous and novel because it is able to achieve the microscale fabrication capability with simple steps and lower-level laboratory configuration. In the developed fabrication platform, an array of ultraviolet light was illuminated onto a photoresist film that has a negative photomask with a microfluidic design on it. The photoresist film is then developed, and a silicon polymer of polydimethylsiloxane (PDMS) is chosen to be the material for the device. In this work, the performance and resolution of the fabrication system was evaluated using scanning electron microscopy (SEM), polymer resolution test and light intensity analysis. </p> <p>Based on the success of the development of microfluidics fabrication platform, various experiment of mixing and separation was conducted and studied because the utilization of the microfluidic device for mixing and separation is very valuable in biomedical and chemical engineering. Although there are a lot of applications reported, the precise separation and mixing at microscale still meet some difficulties. Mixing in micromixers is extremely time-consuming and requires very long microchannels due to laminar flow and low Reynolds number. Particle separation is also hard to be achieved because the size of micron bioparticles is very small and thus the force is not strong enough to manipulate their motion. The integration of magnetic field is an active method to strengthen both mixing and separation that has been widely applied in the biomedical industry overcome these difficulties because of its compatibility with organic particles. However, most magnetic mixing and separation use bulky permanent magnets that leave a large footprint or electromagnets that generate harmful Joule heat to organic and bio-particles. In this work, microscale magnet made of a mixture of neodymium powder and polydimethylsiloxane was developed and integrated into microfluidic system to achieve both rapid mixing of ferrofluids and separation of microparticles. Systematic experiments were conducted to discuss the effect of various parameters on the performance of magnetic mixing and separation of microparticles. It was found that channel geometry, flow filed, and magnetic properties will affect the transport phenomena of ferrofluid and microparticles, and thus mixing and separation efficiency. These findings are of great significance for the high throughput sorting of cancer cells and its mixing between drug for therapy treatment.</p></div></div></div>