{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/24412"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/24412","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Single stranded DNA: A new model system for single molecule polymer dynamics","abstract":"The study of polymer dynamics has been an active area of research for many years. For nearly two decades, fluorescently-labeled double stranded DNA (dsDNA) has been the model system for studying single molecule polymer dynamics in non-equilibrium conditions. However, dsDNA is a semiflexible polymer with markedly different local molecular properties compared to flexible polymer chains, such as synthetic organic polymers. In this work, we developed a new model system for single molecule studies of flexible polymers based on single stranded DNA (ssDNA). Using a biochemical synthesis scheme called rolling circle replication, long strands (>25 µm) of ssDNA containing “designer sequences” have been generated to prevent intramolecular base pairing. Polymer chains are synthesized with amine modified bases incorporated along the backbone to facilitate labeling with fluorescent dyes. As proof-of-principle demonstration of this new chemical platform, we use epifluorescence microscopy to image individual ssDNA molecules stretching in an extensional flow generated inside a microfluidic device. It is anticipated that the model polymer system presented here will serve to promote further investigations of flexible polymer dynamics at the molecular level.","abstract_html":"The study of polymer dynamics has been an active area of research for many years. For nearly two decades, fluorescently-labeled double stranded DNA (dsDNA) has been the model system for studying single molecule polymer dynamics in non-equilibrium conditions. However, dsDNA is a semiflexible polymer with markedly different local molecular properties compared to flexible polymer chains, such as synthetic organic polymers. In this work, we developed a new model system for single molecule studies of flexible polymers based on single stranded DNA (ssDNA). Using a biochemical synthesis scheme called rolling circle replication, long strands (>25 µm) of ssDNA containing “designer sequences” have been generated to prevent intramolecular base pairing. Polymer chains are synthesized with amine modified bases incorporated along the backbone to facilitate labeling with fluorescent dyes. As proof-of-principle demonstration of this new chemical platform, we use epifluorescence microscopy to image individual ssDNA molecules stretching in an extensional flow generated inside a microfluidic device. It is anticipated that the model polymer system presented here will serve to promote further investigations of flexible polymer dynamics at the molecular level.","abstract_has_math":false,"creators":["Brockman, Christopher A."],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Chemical Engineering","degree_department":null,"school":null,"contributors":["Schroeder, Charles M."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2011,"date_issued":"2011-05-25T14:40:33Z","date_published":"2011-05-25T14:40:33Z","updated_at":"2026-07-22T22:25:23Z","subjects":["single molecule","polymer dynamics","rolling circle replication","fluorescence microscopy"],"languages":["en"],"rights":["Copyright 2011 Christopher A. Brockman"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/24412","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Schroeder, Charles M."]},{"key":"dc:creator","label":"Author","values":["Brockman, Christopher A."]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2011-05-25T14:40:33Z","2013-05-26T10:00:25Z","2011-05"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Chemical Engineering"]},{"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":["single molecule","polymer dynamics","rolling circle replication","fluorescence microscopy"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2011 Christopher A. Brockman"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/24412"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["The study of polymer dynamics has been an active area of research for many years. For nearly two decades, fluorescently-labeled double stranded DNA (dsDNA) has been the model system for studying single molecule polymer dynamics in non-equilibrium conditions. However, dsDNA is a semiflexible polymer with markedly different local molecular properties compared to flexible polymer chains, such as synthetic organic polymers. In this work, we developed a new model system for single molecule studies of flexible polymers based on single stranded DNA (ssDNA). Using a biochemical synthesis scheme called rolling circle replication, long strands (>25 µm) of ssDNA containing “designer sequences” have been generated to prevent intramolecular base pairing. Polymer chains are synthesized with amine modified bases incorporated along the backbone to facilitate labeling with fluorescent dyes. As proof-of-principle demonstration of this new chemical platform, we use epifluorescence microscopy to image individual ssDNA molecules stretching in an extensional flow generated inside a microfluidic device. It is anticipated that the model polymer system presented here will serve to promote further investigations of flexible polymer dynamics at the molecular level.","Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2011-04-28T17:28:32Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 2 Brockman_Christopher.docx: 2771208 bytes, checksum: 25b2aa8f45d07c262ad51ad950265a97 (MD5) Brockman_Christopher.pdf: 3520987 bytes, checksum: 3e5e20446f38d7012be439c9c03322e3 (MD5)","Made available in DSpace on 2011-05-25T14:40:33Z (GMT). No. of bitstreams: 2 Brockman_Christopher.pdf: 3521508 bytes, checksum: 8e830b5f3d8e41f9881c118bce1180a8 (MD5) license.txt: 4070 bytes, checksum: 6f3492e72a06aecd72663582cd111ca6 (MD5)","Item marked as restricted to the 'UIUC Users [automated]' Group (id=2) by William Ingram (wingram2@illinois.edu) on 2011-05-25T14:42:04Z Item is restricted until 2013-05-25T14:41:28Z","Item reinstated by Sarah Shreeves (sshreeve@illinois.edu) on 2013-05-26T10:00:25Z Item was in collections: University of Illinois Dissertations and Theses (ID: 204) Dissertations and Theses - Chemical and Biomolecular Engineering (ID: 591) No. of bitstreams: 2 Brockman_Christopher.pdf: 3521508 bytes, checksum: 8e830b5f3d8e41f9881c118bce1180a8 (MD5) license.txt: 4070 bytes, checksum: 6f3492e72a06aecd72663582cd111ca6 (MD5)","Item released from any restrictions by Sarah Shreeves (sshreeve@illinois.edu) on 2013-05-26T10:00:25Z"]},{"key":"dc:title","label":"Title","values":["Single stranded DNA: A new model system for single molecule polymer dynamics"]}]}],"canonical_facts":{"dc:contributor":["Schroeder, Charles M."],"dc:creator":["Brockman, Christopher A."],"dc:date":["2011-05-25T14:40:33Z","2013-05-26T10:00:25Z","2011-05"],"dc:description":["The study of polymer dynamics has been an active area of research for many years. For nearly two decades, fluorescently-labeled double stranded DNA (dsDNA) has been the model system for studying single molecule polymer dynamics in non-equilibrium conditions. However, dsDNA is a semiflexible polymer with markedly different local molecular properties compared to flexible polymer chains, such as synthetic organic polymers. In this work, we developed a new model system for single molecule studies of flexible polymers based on single stranded DNA (ssDNA). Using a biochemical synthesis scheme called rolling circle replication, long strands (>25 µm) of ssDNA containing “designer sequences” have been generated to prevent intramolecular base pairing. Polymer chains are synthesized with amine modified bases incorporated along the backbone to facilitate labeling with fluorescent dyes. As proof-of-principle demonstration of this new chemical platform, we use epifluorescence microscopy to image individual ssDNA molecules stretching in an extensional flow generated inside a microfluidic device. It is anticipated that the model polymer system presented here will serve to promote further investigations of flexible polymer dynamics at the molecular level.","Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2011-04-28T17:28:32Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 2 Brockman_Christopher.docx: 2771208 bytes, checksum: 25b2aa8f45d07c262ad51ad950265a97 (MD5) Brockman_Christopher.pdf: 3520987 bytes, checksum: 3e5e20446f38d7012be439c9c03322e3 (MD5)","Made available in DSpace on 2011-05-25T14:40:33Z (GMT). No. of bitstreams: 2 Brockman_Christopher.pdf: 3521508 bytes, checksum: 8e830b5f3d8e41f9881c118bce1180a8 (MD5) license.txt: 4070 bytes, checksum: 6f3492e72a06aecd72663582cd111ca6 (MD5)","Item marked as restricted to the 'UIUC Users [automated]' Group (id=2) by William Ingram (wingram2@illinois.edu) on 2011-05-25T14:42:04Z Item is restricted until 2013-05-25T14:41:28Z","Item reinstated by Sarah Shreeves (sshreeve@illinois.edu) on 2013-05-26T10:00:25Z Item was in collections: University of Illinois Dissertations and Theses (ID: 204) Dissertations and Theses - Chemical and Biomolecular Engineering (ID: 591) No. of bitstreams: 2 Brockman_Christopher.pdf: 3521508 bytes, checksum: 8e830b5f3d8e41f9881c118bce1180a8 (MD5) license.txt: 4070 bytes, checksum: 6f3492e72a06aecd72663582cd111ca6 (MD5)","Item released from any restrictions by Sarah Shreeves (sshreeve@illinois.edu) on 2013-05-26T10:00:25Z"],"dc:identifier":["http://hdl.handle.net/2142/24412"],"dc:language":["en"],"dc:rights":["Copyright 2011 Christopher A. Brockman"],"dc:subject":["single molecule","polymer dynamics","rolling circle replication","fluorescence microscopy"],"dc:title":["Single stranded DNA: A new model system for single molecule polymer dynamics"],"thesis:degree_discipline":["Chemical Engineering"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:23Z"}