{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/34548"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/34548","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"The development of new sensing methodologies for nucleic acids using arrays of silicon photonic microring resonators","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.","abstract_html":"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.","abstract_has_math":false,"creators":["Qavi, Abraham"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Chemistry","degree_department":null,"school":null,"contributors":["Bailey, Ryan C.","Ceman, Stephanie S.","Suslick, Kenneth S.","Sweedler, Jonathan V."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2012,"date_issued":"2012-09-18T21:25:07Z","date_published":"2012-09-18T21:25:07Z","updated_at":"2026-07-22T22:25:31Z","subjects":["microRibonucleic acid (microRNA)","Sensors","Photonic Resonators","Biosensors"],"languages":["en"],"rights":["Copyright Abraham Jaleel Qavi, 2012"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/34548","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Bailey, Ryan C.","Ceman, Stephanie S.","Suslick, Kenneth S.","Sweedler, Jonathan V."]},{"key":"dc:creator","label":"Author","values":["Qavi, Abraham"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2012-09-18T21:25:07Z","2014-09-18T10:00:36Z","2012-08"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Chemistry"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["microRibonucleic acid (microRNA)","Sensors","Photonic Resonators","Biosensors"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright Abraham Jaleel Qavi, 2012"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/34548"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["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.","Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2012-06-28T17:58:11Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 Qavi_Abraham.pdf: 5370679 bytes, checksum: 8593e695a4aaaba75e2a29ae98441540 (MD5)","Made available in DSpace on 2012-09-18T21:25:07Z (GMT). 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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.","Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2012-06-28T17:58:11Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 Qavi_Abraham.pdf: 5370679 bytes, checksum: 8593e695a4aaaba75e2a29ae98441540 (MD5)","Made available in DSpace on 2012-09-18T21:25:07Z (GMT). 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