{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/121185"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/121185","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Methods and applications of using DNA-cleaving DNAzymes to cleave double-stranded DNA","abstract":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-12-01","abstract_html":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-12-01","abstract_has_math":false,"creators":["Lyu, Mingkuan"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Chemistry","degree_department":null,"school":null,"contributors":["Lu, Yi","Chan, Jefferson","Silverman, Scott K.","Zhao, Huimin"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-12","date_published":"2022-12","updated_at":"2026-07-22T22:24:57Z","subjects":["Dnazyme","Peptide Nucleic Acid","Genetic Engineering","Gene Editing","Cccdna"],"languages":["en","eng"],"rights":["Copyright 2022 Mingkuan Lyu"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/121185","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Lu, Yi","Chan, Jefferson","Silverman, Scott K.","Zhao, Huimin"]},{"key":"dc:creator","label":"Author","values":["Lyu, Mingkuan"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2022-12","2022-11-29"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"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":["Dnazyme","Peptide Nucleic Acid","Genetic Engineering","Gene Editing","Cccdna"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2022 Mingkuan Lyu"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/121185"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-12-01","The student, Mingkuan Lyu, accepted the attached license on 2022-11-16 at 09:09.","The student, Mingkuan Lyu, submitted this Dissertation for approval on 2022-11-16 at 09:42.","This Dissertation was approved for publication on 2022-11-29 at 17:16.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18585 on 2023-12-04 at 17:29:48","DNAzymes are DNA molecules that can catalyze specific reactions. Like protein-based enzymes, DNAzymes have high efficiency and specificity, yet they also own additional advantages such as more feasible customizability and lower cost. Particularly, DNAzymes that catalyze the cleavage of another DNA molecule, called DNA-cleaving DNAzymes, may specifically recognize and cleave user-defined DNA sequences with high efficiency. However, there are only limited applications of DNA-cleaving DNAzymes, because they could only recognize and cleave single-stranded DNA (ssDNA), whereas most DNA targets of interest (such as eukaryotic genomic DNA) are double-stranded DNA (dsDNA). To overcome this limitation, methods that can expand the substrate scope of DNA-cleaving DNAzymes from ssDNA to dsDNA are investigated. Here, a system called peptide nucleic acid (PNA)-assisted dsDNA nicking by DNAzymes (PANDA) is proven to be the first example of using DNA-cleaving DNAzymes to cleave dsDNA. PANDA may recognize almost any user-defined target sequences and cleave the target in a sequence-specific manner. The application of PANDA to mimic restriction enzymes is proven by using PANDA systems in molecular cloning. The potential and barriers of using PANDA systems in genome editing are investigated and discussed. Then, another system called ssDNA-assisted dsDNA nicking by DNAzymes (DANDA) is described, which proves that PANDA is not the only method to expand the substrate scope. The unique feature of DANDA to selectively cleave negatively supercoiled dsDNA rather than relaxed dsDNA has inspired a novel DNA detection method that has specificity on the target superhelicity. These results have proved that using DNA-cleaving DNAzymes to cleave dsDNA is feasible and has huge potential for further applications."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Methods and applications of using DNA-cleaving DNAzymes to cleave double-stranded DNA"]}]}],"canonical_facts":{"dc:contributor":["Lu, Yi","Chan, Jefferson","Silverman, Scott K.","Zhao, Huimin"],"dc:creator":["Lyu, Mingkuan"],"dc:date":["2022-12","2022-11-29"],"dc:description":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-12-01","The student, Mingkuan Lyu, accepted the attached license on 2022-11-16 at 09:09.","The student, Mingkuan Lyu, submitted this Dissertation for approval on 2022-11-16 at 09:42.","This Dissertation was approved for publication on 2022-11-29 at 17:16.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18585 on 2023-12-04 at 17:29:48","DNAzymes are DNA molecules that can catalyze specific reactions. Like protein-based enzymes, DNAzymes have high efficiency and specificity, yet they also own additional advantages such as more feasible customizability and lower cost. Particularly, DNAzymes that catalyze the cleavage of another DNA molecule, called DNA-cleaving DNAzymes, may specifically recognize and cleave user-defined DNA sequences with high efficiency. However, there are only limited applications of DNA-cleaving DNAzymes, because they could only recognize and cleave single-stranded DNA (ssDNA), whereas most DNA targets of interest (such as eukaryotic genomic DNA) are double-stranded DNA (dsDNA). To overcome this limitation, methods that can expand the substrate scope of DNA-cleaving DNAzymes from ssDNA to dsDNA are investigated. Here, a system called peptide nucleic acid (PNA)-assisted dsDNA nicking by DNAzymes (PANDA) is proven to be the first example of using DNA-cleaving DNAzymes to cleave dsDNA. PANDA may recognize almost any user-defined target sequences and cleave the target in a sequence-specific manner. The application of PANDA to mimic restriction enzymes is proven by using PANDA systems in molecular cloning. The potential and barriers of using PANDA systems in genome editing are investigated and discussed. Then, another system called ssDNA-assisted dsDNA nicking by DNAzymes (DANDA) is described, which proves that PANDA is not the only method to expand the substrate scope. The unique feature of DANDA to selectively cleave negatively supercoiled dsDNA rather than relaxed dsDNA has inspired a novel DNA detection method that has specificity on the target superhelicity. These results have proved that using DNA-cleaving DNAzymes to cleave dsDNA is feasible and has huge potential for further applications."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/121185"],"dc:language":["en","eng"],"dc:rights":["Copyright 2022 Mingkuan Lyu"],"dc:subject":["Dnazyme","Peptide Nucleic Acid","Genetic Engineering","Gene Editing","Cccdna"],"dc:title":["Methods and applications of using DNA-cleaving DNAzymes to cleave double-stranded DNA"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Chemistry"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:57Z"}