{"id":{"repo_id":"cambridge","oai_identifier":"oai:www.repository.cam.ac.uk:1810/379247"},"canonical_url":"https://search.dev.ndltd.org/etd/cambridge/oai:www.repository.cam.ac.uk:1810/379247","repository":{"repo_id":"cambridge","name":"Cambridge University","base_url":"https://api.repository.cam.ac.uk/server/oai/request"},"display":{"title":"Decoding the Fabric of Life: Nanopore Sensing of Nucleic Acid Structure from the Primary to the Quaternary","abstract":"Nucleic acids exhibit a great variety of structures at all levels of organisation. These range from chemical modifications on nucleotides at the primary level through non-canonical tertiary structures like triplexes, and to quaternary structures such as naturally occurring ribosomes and artificially induced DNA/RNA nanostructures. The structure of nucleic acids is also intimately linked to their biological function. In this thesis, I leveraged RNA/DNA nanotechnology and solid-state nanopore sensing to detect RNA structural modifications and to characterise the kinetics of nanostructure formation. Additionally, I aimed to directly identify triplexes solely using nanopore sensing. The group’s RNA Single-nucleotide Characterisation and Analysis Nanolatch (RNA-SCAN) system, a type of RNA/DNA nanotechnology, takes advantage of the effect of RNA modifications on duplex binding. This system was able to detect the m5C1407 modification in E. coli 16S rRNA. I developed a two-state model for this system and used it to extract thermodynamic data from various modifications that were used, such as 5-methylcytosine, 2’-deoxyinosine and 2’-O-methoxyethyl . The data acquired agreed well with values from the nearest neighbour model. Furthermore, I validated the assumption that the RNA-SCAN system is in equilibrium during measurements and attempted to quantitatively track RNA-SCAN dynamics. Lastly, I investigated the current signals in nanopores for suspected triplexes in plasmids with GAA/TTC mirror repeats in various topologies, such as supercoiled, nicked and linearised. I did so by comparing their current traces to ones produced by control plasmids with poly (A/T) repeats or no repeats. I demonstrated that there are two distinct populations in the GAA/TTC plasmids compared to one in the control plasmids, and I sought to show that the second population were indeed triplexes. The work here shows the promise of nanopore sensing to characterise nucleic acid structures at various levels of organisation.","abstract_html":"Nucleic acids exhibit a great variety of structures at all levels of organisation. These range from chemical modifications on nucleotides at the primary level through non-canonical tertiary structures like triplexes, and to quaternary structures such as naturally occurring ribosomes and artificially induced DNA/RNA nanostructures. The structure of nucleic acids is also intimately linked to their biological function. In this thesis, I leveraged RNA/DNA nanotechnology and solid-state nanopore sensing to detect RNA structural modifications and to characterise the kinetics of nanostructure formation. Additionally, I aimed to directly identify triplexes solely using nanopore sensing. The group’s RNA Single-nucleotide Characterisation and Analysis Nanolatch (RNA-SCAN) system, a type of RNA/DNA nanotechnology, takes advantage of the effect of RNA modifications on duplex binding. This system was able to detect the m5C1407 modification in E. coli 16S rRNA. I developed a two-state model for this system and used it to extract thermodynamic data from various modifications that were used, such as 5-methylcytosine, 2’-deoxyinosine and 2’-O-methoxyethyl . The data acquired agreed well with values from the nearest neighbour model. Furthermore, I validated the assumption that the RNA-SCAN system is in equilibrium during measurements and attempted to quantitatively track RNA-SCAN dynamics. Lastly, I investigated the current signals in nanopores for suspected triplexes in plasmids with GAA/TTC mirror repeats in various topologies, such as supercoiled, nicked and linearised. I did so by comparing their current traces to ones produced by control plasmids with poly (A/T) repeats or no repeats. I demonstrated that there are two distinct populations in the GAA/TTC plasmids compared to one in the control plasmids, and I sought to show that the second population were indeed triplexes. The work here shows the promise of nanopore sensing to characterise nucleic acid structures at various levels of organisation.","abstract_has_math":false,"creators":["Meng, Siong Chen"],"institution":"University of Cambridge","degree_name":"Master of Philosophy (MPhil)","degree_level":"Masters","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Keyser, Ulrich"],"committee_chairs":[],"committee_members":[],"year":2024,"date_issued":"2024-02-09","date_published":"2024-02-09","updated_at":"2026-07-22T22:24:25Z","subjects":[],"languages":[],"rights":[],"rights_urls":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/a6a15e88-b75f-41c8-996c-8ff7a6a8c3ac/download","https://creativecommons.org/licenses/by-nc/4.0/"],"identifier_entries":[]},"links":{"outbound_url":"https://doi.org/10.17863/CAM.115402","outbound_label":"DOI","outbound_source":"dc:identifier.doi"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Keyser, Ulrich"]},{"key":"dc:creator","label":"Author","values":["Meng, Siong Chen"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.issued","label":"Date","values":["2024-02-09"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Cambridge"]},{"key":"dc:relation.isreferencedby.uri","label":"Dc Relation Isreferencedby URI","values":["https://www.repository.cam.ac.uk/handle/1810/379247"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Masters"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["Master of Philosophy (MPhil)"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/a6a15e88-b75f-41c8-996c-8ff7a6a8c3ac/download","https://creativecommons.org/licenses/by-nc/4.0/"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.17863/CAM.115402"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/34d776e1-fe0d-44de-bed1-0b985944d07b/download"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Nucleic acids exhibit a great variety of structures at all levels of organisation. These range from chemical modifications on nucleotides at the primary level through non-canonical tertiary structures like triplexes, and to quaternary structures such as naturally occurring ribosomes and artificially induced DNA/RNA nanostructures. The structure of nucleic acids is also intimately linked to their biological function. In this thesis, I leveraged RNA/DNA nanotechnology and solid-state nanopore sensing to detect RNA structural modifications and to characterise the kinetics of nanostructure formation. Additionally, I aimed to directly identify triplexes solely using nanopore sensing. The group’s RNA Single-nucleotide Characterisation and Analysis Nanolatch (RNA-SCAN) system, a type of RNA/DNA nanotechnology, takes advantage of the effect of RNA modifications on duplex binding. This system was able to detect the m5C1407 modification in E. coli 16S rRNA. I developed a two-state model for this system and used it to extract thermodynamic data from various modifications that were used, such as 5-methylcytosine, 2’-deoxyinosine and 2’-O-methoxyethyl . The data acquired agreed well with values from the nearest neighbour model. Furthermore, I validated the assumption that the RNA-SCAN system is in equilibrium during measurements and attempted to quantitatively track RNA-SCAN dynamics. Lastly, I investigated the current signals in nanopores for suspected triplexes in plasmids with GAA/TTC mirror repeats in various topologies, such as supercoiled, nicked and linearised. I did so by comparing their current traces to ones produced by control plasmids with poly (A/T) repeats or no repeats. I demonstrated that there are two distinct populations in the GAA/TTC plasmids compared to one in the control plasmids, and I sought to show that the second population were indeed triplexes. The work here shows the promise of nanopore sensing to characterise nucleic acid structures at various levels of organisation."]},{"key":"dc:format.checksum.md5","label":"Dc Format Checksum Md5","values":["e92749df7cee8831570623ab27f1fd55","eb9d2d75cbfff5683a827dd2229be5c0"]},{"key":"dc:title","label":"Title","values":["Decoding the Fabric of Life: Nanopore Sensing of Nucleic Acid Structure from the Primary to the Quaternary"]}]}],"canonical_facts":{"dc:contributor.advisor":["Keyser, Ulrich"],"dc:creator":["Meng, Siong Chen"],"dc:date.issued":["2024-02-09"],"dc:description.abstract":["Nucleic acids exhibit a great variety of structures at all levels of organisation. These range from chemical modifications on nucleotides at the primary level through non-canonical tertiary structures like triplexes, and to quaternary structures such as naturally occurring ribosomes and artificially induced DNA/RNA nanostructures. The structure of nucleic acids is also intimately linked to their biological function. In this thesis, I leveraged RNA/DNA nanotechnology and solid-state nanopore sensing to detect RNA structural modifications and to characterise the kinetics of nanostructure formation. Additionally, I aimed to directly identify triplexes solely using nanopore sensing. The group’s RNA Single-nucleotide Characterisation and Analysis Nanolatch (RNA-SCAN) system, a type of RNA/DNA nanotechnology, takes advantage of the effect of RNA modifications on duplex binding. This system was able to detect the m5C1407 modification in E. coli 16S rRNA. I developed a two-state model for this system and used it to extract thermodynamic data from various modifications that were used, such as 5-methylcytosine, 2’-deoxyinosine and 2’-O-methoxyethyl . The data acquired agreed well with values from the nearest neighbour model. Furthermore, I validated the assumption that the RNA-SCAN system is in equilibrium during measurements and attempted to quantitatively track RNA-SCAN dynamics. Lastly, I investigated the current signals in nanopores for suspected triplexes in plasmids with GAA/TTC mirror repeats in various topologies, such as supercoiled, nicked and linearised. I did so by comparing their current traces to ones produced by control plasmids with poly (A/T) repeats or no repeats. I demonstrated that there are two distinct populations in the GAA/TTC plasmids compared to one in the control plasmids, and I sought to show that the second population were indeed triplexes. The work here shows the promise of nanopore sensing to characterise nucleic acid structures at various levels of organisation."],"dc:format.checksum.md5":["e92749df7cee8831570623ab27f1fd55","eb9d2d75cbfff5683a827dd2229be5c0"],"dc:identifier.doi":["https://doi.org/10.17863/CAM.115402"],"dc:identifier.uri":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/34d776e1-fe0d-44de-bed1-0b985944d07b/download"],"dc:publisher.institution":["University of Cambridge"],"dc:relation.isreferencedby.uri":["https://www.repository.cam.ac.uk/handle/1810/379247"],"dc:rights":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/a6a15e88-b75f-41c8-996c-8ff7a6a8c3ac/download","https://creativecommons.org/licenses/by-nc/4.0/"],"dc:title":["Decoding the Fabric of Life: Nanopore Sensing of Nucleic Acid Structure from the Primary to the Quaternary"],"dc:type":["Thesis"],"dc:type.qualificationlevel":["Masters"],"dc:type.qualificationname":["Master of Philosophy (MPhil)"]},"updated_at":"2026-07-22T22:24:25Z"}