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Abstract: Reliable RNA integrity assay is important for a wide range of applications in genomics and diagnostics, yet the existing technologies have certain limitations such as large amount of sample required, high cost of equipment and/or long turnaround times. I report a simple assay method to analyze bacterial ribosomal RNA (rRNA) from complex total RNA samples utilizing shape-encoded and singl... read moree-stranded DNA-conjugated hydrogel microparticle suspension arrays with no need for target amplification and under standard fluorescence imaging conditions. I show that this simple microparticle-based sensing scheme is reliable, sequence-specific and presents a responsive binding behavior to target RNA concentrations. Moreover, the relative stability of 16S and 23S rRNA can be assessed in a simple shape encoding-based multiplexed format. Combined, these findings represent a significant step toward cheap, fast, simple, and reliable assays for the analysis of rRNA and general RNA integrity.
Thesis (M.S.)--Tufts University, 2015.
Submitted to the Dept. of Chemical and Biological Engineering.
Advisor: Hyunmin Yi.
Committee: Qiaobing Xu, and Ayse Asatekin.
Keywords: Chemical engineering, and Molecular biology.read less
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