The development and characterization of lab-on-a-chip devices for the analysis of DNA and proteins

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Fozdar, David Yash

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The polymerase chain reaction (PCR) is a biochemical assay utilized to chemically amplify specific regions of DNA. An attempt to resolve issues with traditional PCR thermal cyclers has sparked the development of a myriad of microchip-based PCR devices in substrates including silicon, glass, and a variety of polymers using well-established integrated circuit (IC) and micro-electromechanical systems (MEMS) fabrication technologies. Chapter I reviews fundamental aspects of traditional PCR and explores the development and characteristics of PCR microchip technology. An introduction to lab-on-a-chip (LOC) / micro-total-analysis systems (μTAS) technologies is given towards the end of chapter I. Chapter II presents a novel continuous-flow PCR microchip with regional velocity control developed by our research group here at The University of Texas at Austin. Design considerations, microfabrication processes, theoretical and experimental investigations, and flow-through experimental procedures are divulged in detail. Novel semi-analytical and finite element simulations, employed to optimize microchip performance, are described. Successful efficient amplification of a 90 bp DNA bacillus anthracis fragment was achieved in our flow-through experiments indicating the viability or our biochip for use in point-of-care diagnostics applications. Chapter III presents two Poly(dimethylsiloxane)-based ad hoc packaging systems, also developed by our research group here at UT-Austin, serving as an infrastructure for enzyme-linked immunosorbent assays (ELISA) using previously reported “electronic taste” chips. One design is capable of hosting a single “taste” chip for single analyte identification while the other has the capacity of handling four “taste” chips for analysis of up to four analytes. The devices utilize microfluidics for ligand transport in liquid-phase media and contain windows for optical signal detection based on the absorption and emission of probe-conjugated agarose beads. An established C-reactive protein (CRP) assay was performed to evaluate the performance of the packaging systems. Detection limits of the “electronic taste” chips when supported by our packaging systems were found to be very low indicating the possibility and feasibility of “taste” chip detection of proteins and amplified DNA by PCR for on-site genetic screening applications. Chapter IV concludes this thesis by succinctly summarizing the information presented in chapters I, II, and III. The main goal of the chapter is to connect the ideas behind our foregoing research by putting in perspective how each work fits into our ultimate goal, to create a complete lab-on-a-chip device incorporating all the investigative tools necessary for biomolecular (DNA, protein, etc.) analysis. An explanation of the goals and purpose of our work are highlighted and linked to pertinent future research projects


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