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The development of new sensing methodologies for nucleic acids using arrays of silicon photonic microring resonators

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Title: The development of new sensing methodologies for nucleic acids using arrays of silicon photonic microring resonators
Author(s): Qavi, Abraham
Director of Research: Bailey, Ryan C.
Doctoral Committee Chair(s): Bailey, Ryan C.
Doctoral Committee Member(s): Ceman, Stephanie; Suslick, Kenneth S.; Sweedler, Jonathan V.
Department / Program: Chemistry
Discipline: Chemistry
Degree Granting Institution: University of Illinois at Urbana-Champaign
Degree: Ph.D.
Genre: Dissertation
Subject(s): Sensors microRibonucleic acid (microRNA) Photonic Resonators Biosensors
Abstract: With the sequencing of the human genome effectively complete, the development of high throughput and rapid biomarker assays has become a major focus of research as the biomedical community seeks to translate genomic insight into clinical improvements in patient care. One class of molecules that has attracted considerable attention is microRNAs (miRNAs). miRNAs are 19-24 nucleotide, short post-transcriptional regulators, involved in a number of cellular processes including proliferation, apoptosis, and development. They are also implicated in a variety of diseases, such as cancer, neurodegenerative disorders, and diabetes. Despite their importance in a variety of cellular functions as well as their potential for disease diagnostics, miRNAs are incredibly difficult to detect. Their short length makes it difficult to attach any label (fluorescent or radioactive) without introducing a signal bias to the measurement. Additionally, traditional PCR-based methods for RNA detection cannot be utilized, as the primers themselves are often the lengths of the miRNAs. To further complicate matters, miRNAs act in highly complex fashion. A single gene can be regulated by multiple miRNAs, and a single miRNA can regulate multiple genes. In order to fully understand the role miRNAs play, as well as utilize their potential as informative biomarkers, a multiplexed analysis is necessary. We have developed a sensing platform based on arrays of silicon photonic microring resonators that is highly amenable for the quantitative, multiplexed detection of nucleic acids, in particular, miRNAs. We begin by demonstrating a label-free method for the quantitative, multiplexed detection of miRNAs. We further extend this technique by utilizing S9.6, an unique antibody against DNA:RNA heteroduplexes, that significantly improves both our sensitivity and specificity without the introduction of a signal bias. Furthermore, we present an incredibly simple but elegant, method for distinguish single-nucleotide polymorphisms based on isothermal desorption. This not only offers potential applications for screening genomic SNPs, but more importantly, provides a framework to begin to distinguish closely related miRNAs. Future work will focus on the development of new amplification schemes to further increase the sensitivity of the microring resonator platform towards miRNAs, as well as applying this work towards a variety of interesting biological systems and clinical situations.
Issue Date: 2012-09-18
URI: http://hdl.handle.net/2142/34548
Rights Information: Copyright Abraham Jaleel Qavi, 2012
Date Available in IDEALS: 2012-09-18
Date Deposited: 2012-08
 

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