Hydrogels are considered to be in the class of smart materials that find application in diagnostic, therapeutic,and fundamental science tools for miniaturized total analysis systems. In this thesis, the focus is on three major applications of patterned hydrogels, which are explored as an alternative strategy to expensive and low throughput systems for preparative DNA fractionation, in vitro compartmentalization of human gut epithelium, and desalination by microelectrodialysis. The use of patterned hydrogels in closed fluidic microchips or different research fields depends crucially on the ease and accessibility of their fabrication technology. In this work, two simple fabrication procedures are developed to pattern hydrogel microarrays. First, intermittent illumination is applied on mechanically polished microchips or the photopatterning of hydrogels. Second, capillary pressure barriers are used for controlling the position of the liquid-air meniscus in microchip channels, allowing the subsequent patterning of hydrogels by photopolymerization and thermo-gelation. Both fabrication techniques differ from previous studies in terms of versatility and high reproducibility. Preparative fractionation and purification of small-sized DNA fragments play an important role for second-generation sequencing and personalized medicine, and it is the first major application of hydrogels explored. We describe a novel method for concurrent continuous flow fractionation and purification of DNA fragments in a microfluidic device filled with agarose gel. The innovation of this work is twofold. Firstly, a new principle for continuous flow DNA fractionation is demonstrated. We exploit the variation in the field-dependent mobility of DNA molecules with DNA length for the fractionation, which is a separation mechanism that has hitherto gone unnoticed. Secondly, since this new mechanism can be applied using agarose gel, it provides a low-cost, robust, and versatile separation matrix. The theoretical advancement in combination with the practical advantages can lead to new developments in the gield of sample preparation of biological samples. Baseline fractionation of a 0.5-10 kbp DNA ladder is achieved within 2 minutes, which is ~15 times faster than in commercially available devices. Furthermore, the gel technology is easily adaptable; for example, changing the gel type can enable the fractionation of protein molecules. Thus, the microfluidic device is of broad interest for second generation sequencing and clinical diagnosis applications. The second major application of hydrogels reported in this thesis is the use of multicompartmental hydrogel arrays for 3D culturing of human intestine epithelial cells. Engineering in vitro microenvironments that mimic in vivo tissue systems is crucial for improving our understanding of tissue physiology, as well as curtailing the high costs and complexities associated with the existing techniques. We propose and demonstrate an in vitro microfluidic cell culture platform that consists of periodic 3D hydrogel structures. The compartmentalized nature of the microchip architecture and fluid delivery enable culturing of human intestine cells which spontaneously grow into 3D structures on the 3rd day of cell culturing. On the 8th day of culture, Caco-2 cells are co-cultured for 36 hours with intestinal bacteria E.coli, which adhered to the cells without affecting the cell viability. Continuous fluidic perfusion also enables the preliminary screening of chloramphenicol treatment on the intestinal epithelial cells. Finally, we find that different compartment geometries with large and small hydrogel interfaces lead to a difference in the proliferation and cell spread profile of Caco-2 cells. The microchip enables facile fluidic control that allows dynamic regulation of culture conditions. Microelectrodialysis is explored as the last major application of hydrogels in this thesis. Common methods used to construct microelectrodialysis devices rely on incorporation of membranes into microchips, which is challenging in terms of robustness, consistency, and ease of fabrication. Hydrogels are more promising candidates for desalination by electrodialysis, than membranes due to their ion selective and hydrophilic matrix, which is also versatile, inexpensive, and easily tailorable. Patterning ion selective hydrogels at small scales is therefore used to miniaturize the electrodialysis process in microfluidic devices, and subsequently provides more insight into the ion transport phenomena. In this work, we firstly show that parallel streams of concentrated and ion-depleted water are formed in continuous flow when a potential difference is applied across the microchip containing alternating rows of patterned cation- and anion-selective hydrogels. The device could remove approximately 75% of the 1 mM sodium chloride salt introduced via the inlet streams. We demonstrate different currents and flow rates in the microchip for desalination purposes. Secondly, the microchip enables ion transport visualization in the ion selective hydrogels and microchannels when a charged fluorescent dye is utilized. For sufficiently high potential differences, vortex formation is observed near the hydrogel-liquid interfaces, contributing to an enhanced convective transport towards the hydrogels in the overlimiting current regime.
|Award date||15 Sep 2016|
|Place of Publication||Enschede|
|Publication status||Published - 15 Sep 2016|