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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 ... read moresingle-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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