A wealth of small molecule compounds exist that may inhibit cancer or virus-causing diseases, and a wide array of experiments must be performed to narrow down the hundreds of thousands of possible candidates to a few biologically relevant compounds that could serve as ideal drug candidates. Microscale systems have the ability to duplicate benchtop screening experiments with the same fidelity at much smaller scales. Microscale experiments also have the benefit of using very little precious reagent, giving the economic value of low volume usage.;In order to develop high density microscale experimental combinatorics, a new valve was developed that is passively closed at rest, termed Actuate-to-Open (AtO) valves. Chapter 2 reports new design rules for AtO valve operation, both in single valve studies and in large on-chip arrays. The AtO valves are also employed in a combinatorial screening chip with a reversible seal that allows for interchangeable sensing capabilities. In Chapter 3, the combinatorial screening chip is integrated with a photonic crystal biosensor capable of screening for binding events in a label free fashion. A proof-of-principle protein-antibody assay was performed to validate the combinatorial features of the chip. In Chapter 4, the combinatorial chip was integrated with a molecular beacon patterned glass cover slip capable of detecting complementary DNA fragments. Total internal reflection fluorescence (TIRF) microscopy is used for read out of the chip. Four virus-like oligomer targets with sequences corresponding to key fragments of the viruses HIV, HPV, Hepatitis A and Hepatitis B were tested against four different molecular beacons, each complementary to one of the four virus target oligonucleotides. The result of this combinatorial screening chip indicated strong fluorescent values for the matching beacon-target pairs, with statistically insignificant values for non-matching targets. This experiment not only established proof of principle of on-chip virus detection, it also demonstrated the high specificity of surface immobilized molecular beacons used in combination with TIRF.
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