Detection of disease specific biomarkers is of great importance in diagnosis and treatment of diseases. Modern bioanalytical techniques, such as liquid chromatography with mass spectrometry (LC-MS), have the ability to identify biomarkers, but their cost and scalability are two main drawbacks. Enzyme-linked immunosorbent assay (ELISA) is another potential tool, but it works best for proteins, rather than peptide biomarkers. Recently, microfluidics has emerged as a promising technique due to its small fluid volume consumption, rapidness, low fabrication cost, portability and versatility. Therefore, it shows prominent potential in the analysis of disease specific biomarkers. In this thesis, microfluidic systems that integrate monolith columns for preconcentration and on-chip labeling are developed to analyze several protein biomarkers. I have successfully fabricated cyclic olefin copolymer (COC) microfluidic devices with standard micromachining techniques. Monoliths are prepared in situ in microchannels via photopolymerization, and the physical properties of monoliths are optimized by varying the composition and concentration of monomers to achieve better flow and extraction. On-chip labeling of protein biomarkers is achieved by driving solution through the monolith using voltage and incubating fluorescent dye with protein retained in the monolith. Subsequently, the labeled proteins are eluted by applying voltages to reservoirs on the microdevice and detected by laser-induced fluorescence. Finally, automation of on-chip preconcentration and labeling is successfully demonstrated.

My dissertation work integrates the techniques of microfabrication, micro/nanofluidics, and bioanalytical chemistry to develop miniaturized devices for healthcare applications. Semiconductor processing techniques including photolithography, physical and chemical vapor deposition, and wet etching are used to build these devices in silicon and polymeric materials. On-chip micro-/nanochannels, pumps, and valves are used to manipulate the flow of fluid in these devices. Analytical techniques such as size-based filtration, solid-phase extraction (SPE), sample enrichment, on-chip labeling, microchip electrophoresis (µCE), and laser induced fluorescence (LIF) are utilized to analyze biomolecules. Such miniaturized devices offer the advantages of rapid analysis, low cost, and lab-on-a-chip scale integration that can potentially be used for point-of-care applications.The first project involves construction of sieving devices on a silicon substrate, which can separate sub-100-nm biostructures based on their size. Devices consist of an array of 200 parallel nanochannels with a height step in each channel, an injection reservoir, and a waste reservoir. Height steps are used to sieve the protein mixture based on size as the protein solution flows through channels via capillary action. Proteins smaller than the height step reach the end of the channels while larger proteins stop at the height step, resulting in separation. A process is optimized to fabricate 10-100 nm tall channels with improved reliability and shorter fabrication time. Furthermore, a protocol is developed to reduce the electrostatic interaction between proteins and channel walls, which allows the study of size-selective trapping of five proteins in this system. The effects of protein size and concentration on protein trapping behavior are evaluated. A model is also developed to predict the trapping behavior of different size proteins in these devices. Additionally, the influence of buffer ionic strength, which can change the effective cross-sectional area of nanochannels and trapping of proteins at height steps, is explored in nanochannels. The ionic strength inversely correlates with electric double layer thickness. Overall, this work lays a foundation for developing nanofluidic-based sieving systems with potential applications in lipoprotein fractionation, protein aggregate studies in biopharmaceuticals, and protein preconcentration. The second project focuses on designing and developing a microfluidic-based platform for preterm birth (PTB) diagnosis. PTB is a pregnancy complication that involves delivery before 37 weeks of gestation, and causes many newborn deaths and illnesses worldwide. Several serum PTB biomarkers have recently been identified, including three peptides and six proteins. To provide rapid analysis of these PTB biomarkers, an integrated SPE and µCE device is assembled that provides sample enrichment, on-chip labeling, and separation. The integrated device is a multi-layer structure consisting of polydimethylsiloxane valves with a peristaltic pump, and a porous polymer monolith in a thermoplastic layer. The valves and pump are fabricated using soft lithography to enable pressure-based sample actuation, as an alternative to electrokinetic operation. Porous monolithic columns are synthesized in the SPE unit using UV photopolymerization of a mixture consisting of monomer, cross-linker, photoinitiator, and various porogens. The hydrophobic surface and porous structure of the monolith allow both protein retention and easy flow. I have optimized the conditions for ferritin retention, on-chip labelling, elution, and µCE in a pressure-actuated device. Overall functionality of the integrated device in terms of pressure-controlled flow, protein retention/elution, and on-chip labelling and separation is demonstrated using a PTB biomarker (ferritin). Moreover, I have developed a µCE protocol to separate four PTB biomarkers, including three peptides and one protein. In the future, an immunoaffinity extraction unit will be integrated with SPE and µCE to enable rapid, on-chip analysis of PTB biomarkers. This integrated system can be used to analyze other disease biomarkers as well.

Microfluidics is a vibrant and expanding field that has the potential for solving many analytical challenges. Microfluidics shows promise to provide rapid, inexpensive, efficient, and portable diagnostic solutions that can be used in resource-limited settings. Microfluidic devices have gained immense interest as diagnostic tools for various diseases through biomarker analysis. My dissertation work focuses on developing electrokinetically operated integrated microfluidic devices for the analysis of biomarkers indicative of preterm birth risk. Preterm birth (PTB), a birth prior to 37 weeks of gestation, is the most common complication of pregnancy and the leading cause of neonatal deaths and newborn illnesses. In this dissertation, I have designed, fabricated and developed several microfluidic devices that integrate various sample preparation processes like immunoaffinity extraction, preconcentration, fluorescent labeling, and electrophoretic separation of biomarkers indicative of PTB risk. I developed microchip electrophoresis devices for separation of selected PTB biomarkers. I further optimized multiple reversed-phase porous polymer monoliths UV-polymerized in microfluidic device channels for selective retention and elution of fluorescent dyes and PTB biomarkers to facilitate on-chip labeling. Successful on-chip fluorescent labeling of multiple PTB biomarkers was reported using these microfluidic devices. These devices were further developed using a pH-mediated approach for solid-phase extraction, resulting in a ~50 fold enrichment of a PTB biomarker. Additionally, this approach was integrated with microchip electrophoresis to develop a combined enrichment and separation device that yielded 15-fold preconcentration for a PTB peptide. I also developed an immunoaffinity extraction device for analyzing PTB biomarkers directly from a human serum matrix. A glycidyl methacrylate monolith was characterized within microfluidic channels for immobilization of antibodies to PTB biomarkers. Antibody immobilization and captured analyte elution protocols were optimized for these monoliths, and two PTB biomarker proteins were successfully extracted using these devices. This approach was also integrated with microchip electrophoresis for combined extraction and separation of two PTB biomarkers in spiked human serum in <30 min. In the future, these optimized microfluidic components can be integrated into a single platform for automated immunoaffinity extraction, preconcentration, fluorescent labeling, and separation of PTB biomarkers. This integrated microfluidic platform could significantly improve human health by providing early diagnosis of PTBs.