{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/98248"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/98248","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Transport properties of DNA nanostructures","abstract":"Besides the role of genetic information storage, DNA has been proposed as a new material in nanotechnology. The idea came from the nature-occurring Holliday junction (HJ) which allows more than 2 DNA strands to be assembled. Multiple HJs can be combined with desired orientation to form complex 2- or 3-dimensional objects. One of the most popular methods that realize this concept is the DNA origami. The basic principle of DNA origami is the programmed folding of a long (tens of thousands of nucleotides) DNA strand into a custom shape, guided by multiple specially designed short DNA strands which connect different parts of the long DNA strand through HJs. Since its first demonstration in 2006, not only large (up to hundreds of nanometers) and complex 3D objects with sub-nanometer precision have been produced, but some of them were able to perform active functions. Experimental techniques, including atomic force spectroscopy, small-angle X-ray scattering, transmission electron microscopy (TEM), super-resolution optical imaging, FRET and magnetic tweezers, have been applied to study the global structure and dynamics of the DNA nanostructures. Recently, an atomic-level model of DNA origami in situ has also been obtained, which showed considerable deviation from the idealized structure. A few experimental studies reported the ionic permeability of DNA origami constructs placed on top of a solid-state support or embedded in a lipid bilayer membrane. However, the transport properties of DNA nanostructures and the underlying mechanism have remained relatively unexplored. Here, several simulation studies focusing on the transport properties of DNA nanostructures are pre- sented. Specifically, a comprehensive study on the ionic conductivity and mechanical properties of DNA plates of different lattice type, the number of layers, nucleotide content and cross-over pattern in the electric field were performed. The ionic conductances of a range of DNA channels embedded in lipid membrane were obtained. Several factors were found to affect the ionic conductances of DNA channels, including channel aggregation, channel unfolding and blocking by lipid molecules. The smallest and the largest DNA channels so far were developed. The first DNA scramblase which facilitates the translocation of lipid molecules across the membrane was developed. These works represent potential applications of DNA nanostructures in biosensing, nanofluidics, drug delivery and biomedical engineering.","abstract_html":"Besides the role of genetic information storage, DNA has been proposed as a new material in nanotechnology. The idea came from the nature-occurring Holliday junction (HJ) which allows more than 2 DNA strands to be assembled. Multiple HJs can be combined with desired orientation to form complex 2- or 3-dimensional objects. One of the most popular methods that realize this concept is the DNA origami. The basic principle of DNA origami is the programmed folding of a long (tens of thousands of nucleotides) DNA strand into a custom shape, guided by multiple specially designed short DNA strands which connect different parts of the long DNA strand through HJs. Since its first demonstration in 2006, not only large (up to hundreds of nanometers) and complex 3D objects with sub-nanometer precision have been produced, but some of them were able to perform active functions. Experimental techniques, including atomic force spectroscopy, small-angle X-ray scattering, transmission electron microscopy (TEM), super-resolution optical imaging, FRET and magnetic tweezers, have been applied to study the global structure and dynamics of the DNA nanostructures. Recently, an atomic-level model of DNA origami in situ has also been obtained, which showed considerable deviation from the idealized structure. A few experimental studies reported the ionic permeability of DNA origami constructs placed on top of a solid-state support or embedded in a lipid bilayer membrane. However, the transport properties of DNA nanostructures and the underlying mechanism have remained relatively unexplored. Here, several simulation studies focusing on the transport properties of DNA nanostructures are pre- sented. Specifically, a comprehensive study on the ionic conductivity and mechanical properties of DNA plates of different lattice type, the number of layers, nucleotide content and cross-over pattern in the electric field were performed. The ionic conductances of a range of DNA channels embedded in lipid membrane were obtained. Several factors were found to affect the ionic conductances of DNA channels, including channel aggregation, channel unfolding and blocking by lipid molecules. The smallest and the largest DNA channels so far were developed. The first DNA scramblase which facilitates the translocation of lipid molecules across the membrane was developed. These works represent potential applications of DNA nanostructures in biosensing, nanofluidics, drug delivery and biomedical engineering.","abstract_has_math":false,"creators":["Li, Chen-Yu"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Biophysics & Computnl Biology","degree_department":null,"school":null,"contributors":["Schleife, André","Shukla, Diwakar","Aksimentiev, Aleksei","Lu, Yi"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2017,"date_issued":"2017-09-29T16:39:17Z","date_published":"2017-09-29T16:39:17Z","updated_at":"2026-07-22T22:24:35Z","subjects":["Deoxyribonucleic acid (DNA) origami","Molecular dynamics simulation"],"languages":["en"],"rights":["Copyright 2017 Chen-Yu Li"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/98248","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Schleife, André","Shukla, Diwakar","Aksimentiev, Aleksei","Lu, Yi"]},{"key":"dc:creator","label":"Author","values":["Li, Chen-Yu"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2017-09-29T16:39:17Z","2019-09-30T09:15:08Z","2017-07-10","2017-08"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biophysics & Computnl Biology"]},{"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":["Deoxyribonucleic acid (DNA) origami","Molecular dynamics simulation"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2017 Chen-Yu Li"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/98248"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Besides the role of genetic information storage, DNA has been proposed as a new material in nanotechnology. The idea came from the nature-occurring Holliday junction (HJ) which allows more than 2 DNA strands to be assembled. Multiple HJs can be combined with desired orientation to form complex 2- or 3-dimensional objects. One of the most popular methods that realize this concept is the DNA origami. The basic principle of DNA origami is the programmed folding of a long (tens of thousands of nucleotides) DNA strand into a custom shape, guided by multiple specially designed short DNA strands which connect different parts of the long DNA strand through HJs. Since its first demonstration in 2006, not only large (up to hundreds of nanometers) and complex 3D objects with sub-nanometer precision have been produced, but some of them were able to perform active functions. Experimental techniques, including atomic force spectroscopy, small-angle X-ray scattering, transmission electron microscopy (TEM), super-resolution optical imaging, FRET and magnetic tweezers, have been applied to study the global structure and dynamics of the DNA nanostructures. Recently, an atomic-level model of DNA origami in situ has also been obtained, which showed considerable deviation from the idealized structure. A few experimental studies reported the ionic permeability of DNA origami constructs placed on top of a solid-state support or embedded in a lipid bilayer membrane. However, the transport properties of DNA nanostructures and the underlying mechanism have remained relatively unexplored. Here, several simulation studies focusing on the transport properties of DNA nanostructures are pre- sented. Specifically, a comprehensive study on the ionic conductivity and mechanical properties of DNA plates of different lattice type, the number of layers, nucleotide content and cross-over pattern in the electric field were performed. The ionic conductances of a range of DNA channels embedded in lipid membrane were obtained. Several factors were found to affect the ionic conductances of DNA channels, including channel aggregation, channel unfolding and blocking by lipid molecules. The smallest and the largest DNA channels so far were developed. The first DNA scramblase which facilitates the translocation of lipid molecules across the membrane was developed. These works represent potential applications of DNA nanostructures in biosensing, nanofluidics, drug delivery and biomedical engineering.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2019-08-01","The student, Chen-Yu Li, accepted the attached license on 2017-06-28 at 14:06.","The student, Chen-Yu Li, submitted this Dissertation for approval on 2017-06-28 at 15:20.","This Dissertation was approved for publication on 2017-07-10 at 14:46.","DSpace SAF Submission Ingestion Package generated from Vireo submission #11276 on 2017-09-29 at 11:14:10","Made available in DSpace on 2017-09-29T16:39:17Z (GMT). No. of bitstreams: 4 LI-DISSERTATION-2017.pdf: 78770513 bytes, checksum: d12826c56bfa1739309e9df749a462e5 (MD5) LI2015_permission.pdf: 71181 bytes, checksum: 91bc2fc04a8bca400158567743b575e8 (MD5) LICENSE.txt: 4207 bytes, checksum: edbc7b614817bbc822153a60843bf50a (MD5) PROQUEST_LICENSE.txt: 4553 bytes, checksum: e80dc261d2faf61e3a6a8d66235034d9 (MD5) Previous issue date: 2017-07-10","Embargo set by: Colleen Fallaw for item 103395 Lift date: 2019-09-29T16:39:52Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Embargo set by: Colleen Fallaw for item 103395 Lift date: 2019-09-29T17:52:45Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Limited Restriction Lifted for Item 103395 on 2019-09-30T09:15:08Z."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Transport properties of DNA nanostructures"]}]}],"canonical_facts":{"dc:contributor":["Schleife, André","Shukla, Diwakar","Aksimentiev, Aleksei","Lu, Yi"],"dc:creator":["Li, Chen-Yu"],"dc:date":["2017-09-29T16:39:17Z","2019-09-30T09:15:08Z","2017-07-10","2017-08"],"dc:description":["Besides the role of genetic information storage, DNA has been proposed as a new material in nanotechnology. The idea came from the nature-occurring Holliday junction (HJ) which allows more than 2 DNA strands to be assembled. Multiple HJs can be combined with desired orientation to form complex 2- or 3-dimensional objects. One of the most popular methods that realize this concept is the DNA origami. The basic principle of DNA origami is the programmed folding of a long (tens of thousands of nucleotides) DNA strand into a custom shape, guided by multiple specially designed short DNA strands which connect different parts of the long DNA strand through HJs. Since its first demonstration in 2006, not only large (up to hundreds of nanometers) and complex 3D objects with sub-nanometer precision have been produced, but some of them were able to perform active functions. Experimental techniques, including atomic force spectroscopy, small-angle X-ray scattering, transmission electron microscopy (TEM), super-resolution optical imaging, FRET and magnetic tweezers, have been applied to study the global structure and dynamics of the DNA nanostructures. Recently, an atomic-level model of DNA origami in situ has also been obtained, which showed considerable deviation from the idealized structure. A few experimental studies reported the ionic permeability of DNA origami constructs placed on top of a solid-state support or embedded in a lipid bilayer membrane. However, the transport properties of DNA nanostructures and the underlying mechanism have remained relatively unexplored. Here, several simulation studies focusing on the transport properties of DNA nanostructures are pre- sented. Specifically, a comprehensive study on the ionic conductivity and mechanical properties of DNA plates of different lattice type, the number of layers, nucleotide content and cross-over pattern in the electric field were performed. The ionic conductances of a range of DNA channels embedded in lipid membrane were obtained. Several factors were found to affect the ionic conductances of DNA channels, including channel aggregation, channel unfolding and blocking by lipid molecules. The smallest and the largest DNA channels so far were developed. The first DNA scramblase which facilitates the translocation of lipid molecules across the membrane was developed. These works represent potential applications of DNA nanostructures in biosensing, nanofluidics, drug delivery and biomedical engineering.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2019-08-01","The student, Chen-Yu Li, accepted the attached license on 2017-06-28 at 14:06.","The student, Chen-Yu Li, submitted this Dissertation for approval on 2017-06-28 at 15:20.","This Dissertation was approved for publication on 2017-07-10 at 14:46.","DSpace SAF Submission Ingestion Package generated from Vireo submission #11276 on 2017-09-29 at 11:14:10","Made available in DSpace on 2017-09-29T16:39:17Z (GMT). No. of bitstreams: 4 LI-DISSERTATION-2017.pdf: 78770513 bytes, checksum: d12826c56bfa1739309e9df749a462e5 (MD5) LI2015_permission.pdf: 71181 bytes, checksum: 91bc2fc04a8bca400158567743b575e8 (MD5) LICENSE.txt: 4207 bytes, checksum: edbc7b614817bbc822153a60843bf50a (MD5) PROQUEST_LICENSE.txt: 4553 bytes, checksum: e80dc261d2faf61e3a6a8d66235034d9 (MD5) Previous issue date: 2017-07-10","Embargo set by: Colleen Fallaw for item 103395 Lift date: 2019-09-29T16:39:52Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Embargo set by: Colleen Fallaw for item 103395 Lift date: 2019-09-29T17:52:45Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Limited Restriction Lifted for Item 103395 on 2019-09-30T09:15:08Z."],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/2142/98248"],"dc:language":["en"],"dc:rights":["Copyright 2017 Chen-Yu Li"],"dc:subject":["Deoxyribonucleic acid (DNA) origami","Molecular dynamics simulation"],"dc:title":["Transport properties of DNA nanostructures"],"dc:type":["text"],"thesis:degree_discipline":["Biophysics & Computnl Biology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:35Z"}