{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/105879"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/105879","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Photonic resonator absorption microscopy for biosensing with digital resolution","abstract":"Circulating exosomal miRNA represents a potentially useful class of blood-based biomarkers for cancer liquid biopsy. The detection of miRNA at a very low concentration and with single-base discrimination without the need for sophisticated equipment, large volumes, or elaborate sample processing is a challenge. To address this, we present an approach that is highly specific for a target miRNA sequence and has the ability to provide “digital” resolution of individual target molecules with high signal-to-noise ratio. Gold nanoparticle tags are prepared with thermodynamically optimized nucleic acid toehold probes that, when binding to a target miRNA sequence, displace a probe-protecting oligonucleotide and reveal a capture sequence that is used to selectively pull down the target-probe-nanoparticle complex to a photonic crystal (PC) biosensor surface. By matching the surface plasmon resonant wavelength of the nanoparticle tag to the resonant wavelength of the PC nanostructure, the reflected light intensity from the PC is dramatically and locally quenched by the presence of each individual nanoparticle, enabling a new form of biosensor microscopy that we call Photonic Resonator Absorption Microscopy (PRAM). Dynamic PRAM imaging of nanoparticle tag capture enables direct 100 aM limit of detection and single-base mismatch selectivity in a 2-hour kinetic discrimination assay. The PRAM assay demonstrates that ultrasensitivity (<1 pM) and high selectivity can be achieved on a direct read-out diagnostic.","abstract_html":"Circulating exosomal miRNA represents a potentially useful class of blood-based biomarkers for cancer liquid biopsy. The detection of miRNA at a very low concentration and with single-base discrimination without the need for sophisticated equipment, large volumes, or elaborate sample processing is a challenge. To address this, we present an approach that is highly specific for a target miRNA sequence and has the ability to provide “digital” resolution of individual target molecules with high signal-to-noise ratio. Gold nanoparticle tags are prepared with thermodynamically optimized nucleic acid toehold probes that, when binding to a target miRNA sequence, displace a probe-protecting oligonucleotide and reveal a capture sequence that is used to selectively pull down the target-probe-nanoparticle complex to a photonic crystal (PC) biosensor surface. By matching the surface plasmon resonant wavelength of the nanoparticle tag to the resonant wavelength of the PC nanostructure, the reflected light intensity from the PC is dramatically and locally quenched by the presence of each individual nanoparticle, enabling a new form of biosensor microscopy that we call Photonic Resonator Absorption Microscopy (PRAM). Dynamic PRAM imaging of nanoparticle tag capture enables direct 100 aM limit of detection and single-base mismatch selectivity in a 2-hour kinetic discrimination assay. The PRAM assay demonstrates that ultrasensitivity (&lt;1 pM) and high selectivity can be achieved on a direct read-out diagnostic.","abstract_has_math":false,"creators":["Li, Nantao"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Electrical & Computer Engr","degree_department":null,"school":null,"contributors":["Cunningham, Brian T"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2019,"date_issued":"2019-11-26T20:58:33Z","date_published":"2019-11-26T20:58:33Z","updated_at":"2026-07-22T22:24:45Z","subjects":["Photonic crystal","Diagnostics","MicroRNA","Microscopy","Label-free"],"languages":["en"],"rights":["Copyright 2019 Nantao Li"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/105879","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Cunningham, Brian T"]},{"key":"dc:creator","label":"Author","values":["Li, Nantao"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2019-11-26T20:58:33Z","2021-11-27T10:15:09Z","2019-06-28","2019-08"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Electrical & Computer Engr"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"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":["Photonic crystal","Diagnostics","MicroRNA","Microscopy","Label-free"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2019 Nantao Li"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/105879"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Circulating exosomal miRNA represents a potentially useful class of blood-based biomarkers for cancer liquid biopsy. The detection of miRNA at a very low concentration and with single-base discrimination without the need for sophisticated equipment, large volumes, or elaborate sample processing is a challenge. To address this, we present an approach that is highly specific for a target miRNA sequence and has the ability to provide “digital” resolution of individual target molecules with high signal-to-noise ratio. Gold nanoparticle tags are prepared with thermodynamically optimized nucleic acid toehold probes that, when binding to a target miRNA sequence, displace a probe-protecting oligonucleotide and reveal a capture sequence that is used to selectively pull down the target-probe-nanoparticle complex to a photonic crystal (PC) biosensor surface. By matching the surface plasmon resonant wavelength of the nanoparticle tag to the resonant wavelength of the PC nanostructure, the reflected light intensity from the PC is dramatically and locally quenched by the presence of each individual nanoparticle, enabling a new form of biosensor microscopy that we call Photonic Resonator Absorption Microscopy (PRAM). Dynamic PRAM imaging of nanoparticle tag capture enables direct 100 aM limit of detection and single-base mismatch selectivity in a 2-hour kinetic discrimination assay. The PRAM assay demonstrates that ultrasensitivity (<1 pM) and high selectivity can be achieved on a direct read-out diagnostic.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2021-08-01","The student, Nantao Li, accepted the attached license on 2019-06-26 at 11:52.","The student, Nantao Li, submitted this Thesis for approval on 2019-06-26 at 12:03.","This Thesis was approved for publication on 2019-06-28 at 11:11.","DSpace SAF Submission Ingestion Package generated from Vireo submission #14086 on 2019-11-26 at 14:00:27","Made available in DSpace on 2019-11-26T20:58:33Z (GMT). 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The detection of miRNA at a very low concentration and with single-base discrimination without the need for sophisticated equipment, large volumes, or elaborate sample processing is a challenge. To address this, we present an approach that is highly specific for a target miRNA sequence and has the ability to provide “digital” resolution of individual target molecules with high signal-to-noise ratio. Gold nanoparticle tags are prepared with thermodynamically optimized nucleic acid toehold probes that, when binding to a target miRNA sequence, displace a probe-protecting oligonucleotide and reveal a capture sequence that is used to selectively pull down the target-probe-nanoparticle complex to a photonic crystal (PC) biosensor surface. By matching the surface plasmon resonant wavelength of the nanoparticle tag to the resonant wavelength of the PC nanostructure, the reflected light intensity from the PC is dramatically and locally quenched by the presence of each individual nanoparticle, enabling a new form of biosensor microscopy that we call Photonic Resonator Absorption Microscopy (PRAM). Dynamic PRAM imaging of nanoparticle tag capture enables direct 100 aM limit of detection and single-base mismatch selectivity in a 2-hour kinetic discrimination assay. The PRAM assay demonstrates that ultrasensitivity (<1 pM) and high selectivity can be achieved on a direct read-out diagnostic.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2021-08-01","The student, Nantao Li, accepted the attached license on 2019-06-26 at 11:52.","The student, Nantao Li, submitted this Thesis for approval on 2019-06-26 at 12:03.","This Thesis was approved for publication on 2019-06-28 at 11:11.","DSpace SAF Submission Ingestion Package generated from Vireo submission #14086 on 2019-11-26 at 14:00:27","Made available in DSpace on 2019-11-26T20:58:33Z (GMT). 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