Topoisomerases are ubiquitous proteins that alter supercoiling in double stranded DNA (dsDNA) during transcription and replication and. vaccinia and the closely related poxvirus variola virus, at 314 amino acids in length, encode the smallest of the type I topoisomerases(TopIB). TopIB is a two domain protein that recognizes the sequence 5’-T/CCCTT, cleaves at the 3’-end and relaxes supercoiling through rotation. The C-terminal domain (CTD) alone contains the catalytic activity and specificity. Deletion of the N-terminal domain results in a greatly reduced rate of relaxation and rapid dissociation. Biochemical data suggests that the N-terminal domain (NTD) is important for pre-cleavage binding and affinity for the target site. A combination of NMR-based interaction studies, the measurement of backbone dynamics using 15N relaxation measurements, and isothermal calorimetry (ITC) is used in this work to show that the NTD is capable of independently binding to DNA. Additionally, it is shown that the nature of the engagement of dsDNA by the NTD, in terms of affinity and characteristics of the binding modes, differs between sequences containing the 5’-CCCTT segment from those that do not. An attempt is made to extend these observations to the full length protein.
","abstract_html":"<p>Topoisomerases are ubiquitous proteins that alter supercoiling in double stranded DNA (dsDNA) during transcription and replication and. <em>vaccinia</em> and the closely related poxvirus <em>variola</em> virus, at 314 amino acids in length, encode the smallest of the type I topoisomerases(TopIB). TopIB is a two domain protein that recognizes the sequence 5’-T/CCCTT, cleaves at the 3’-end and relaxes supercoiling through rotation. The C-terminal domain (CTD) alone contains the catalytic activity and specificity. Deletion of the N-terminal domain results in a greatly reduced rate of relaxation and rapid dissociation. Biochemical data suggests that the N-terminal domain (NTD) is important for pre-cleavage binding and affinity for the target site. A combination of NMR-based interaction studies, the measurement of backbone dynamics using <sup>15</sup>N relaxation measurements, and isothermal calorimetry (ITC) is used in this work to show that the NTD is capable of independently binding to DNA. Additionally, it is shown that the nature of the engagement of dsDNA by the NTD, in terms of affinity and characteristics of the binding modes, differs between sequences containing the 5’-CCCTT segment from those that do not. An attempt is made to extend these observations to the full length protein.</p>","abstract_has_math":false,"creators":["Reed, Benjamin R"],"institution":"The Graduate School and University Center of The City University of New York","degree_name":"Doctor of Philosophy","degree_level":"Doctoral","degree_discipline":"Chemistry","degree_department":null,"school":null,"contributors":[],"advisors":["Ranajeet Ghose"],"committee_chairs":[],"committee_members":["Ruth Stark","Nancy Greenbaum","Stewart Shuman","David Cowburn"],"year":2016,"date_issued":"2016-09-30T07:00:00Z","date_published":"2016-09-30T07:00:00Z","updated_at":"2026-07-24T01:58:31Z","subjects":["Analytical Chemistry","Biochemistry","Microbiology","Molecular Biology","Other Chemistry","Structural Biology","Protein NMR","Protein-DNA binding","DNA","DNA binding specificity","isothermal titration calorimetry","chemical shift perturbation","NMR relaxation","rotational correlation time","binding electrostatics"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://academicworks.cuny.edu/gc_etds/1493","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Ranajeet Ghose"]},{"key":"dc:contributor.committeemember","label":"Committee Member","values":["Ruth Stark","Nancy Greenbaum","Stewart Shuman","David Cowburn"]},{"key":"dc:creator","label":"Author","values":["Reed, Benjamin R"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2017-08-18T07:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Chemistry"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Doctoral"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Doctor of Philosophy"]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["The Graduate School and University Center of The City University of New York"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Analytical Chemistry","Biochemistry","Microbiology","Molecular Biology","Other Chemistry","Structural Biology","Protein NMR","Protein-DNA binding","DNA","DNA binding specificity","isothermal titration calorimetry","chemical shift perturbation","NMR relaxation","rotational correlation time","binding electrostatics"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://academicworks.cuny.edu/gc_etds/1493"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Topoisomerases are ubiquitous proteins that alter supercoiling in double stranded DNA (dsDNA) during transcription and replication and. vaccinia and the closely related poxvirus variola virus, at 314 amino acids in length, encode the smallest of the type I topoisomerases(TopIB). TopIB is a two domain protein that recognizes the sequence 5’-T/CCCTT, cleaves at the 3’-end and relaxes supercoiling through rotation. The C-terminal domain (CTD) alone contains the catalytic activity and specificity. Deletion of the N-terminal domain results in a greatly reduced rate of relaxation and rapid dissociation. Biochemical data suggests that the N-terminal domain (NTD) is important for pre-cleavage binding and affinity for the target site. A combination of NMR-based interaction studies, the measurement of backbone dynamics using 15N relaxation measurements, and isothermal calorimetry (ITC) is used in this work to show that the NTD is capable of independently binding to DNA. Additionally, it is shown that the nature of the engagement of dsDNA by the NTD, in terms of affinity and characteristics of the binding modes, differs between sequences containing the 5’-CCCTT segment from those that do not. An attempt is made to extend these observations to the full length protein.
"]},{"key":"dc:title","label":"Title","values":["Specific Binding Affinity of the Non-Catalytic Domain of Eukaryotic Like Type IB Topoisomerase of vaccinia Virus"]}]}],"canonical_facts":{"dc:contributor.advisor":["Ranajeet Ghose"],"dc:contributor.committeemember":["Ruth Stark","Nancy Greenbaum","Stewart Shuman","David Cowburn"],"dc:creator":["Reed, Benjamin R"],"dc:date.available":["2017-08-18T07:00:00Z"],"dc:description.abstract":["Topoisomerases are ubiquitous proteins that alter supercoiling in double stranded DNA (dsDNA) during transcription and replication and. vaccinia and the closely related poxvirus variola virus, at 314 amino acids in length, encode the smallest of the type I topoisomerases(TopIB). TopIB is a two domain protein that recognizes the sequence 5’-T/CCCTT, cleaves at the 3’-end and relaxes supercoiling through rotation. The C-terminal domain (CTD) alone contains the catalytic activity and specificity. Deletion of the N-terminal domain results in a greatly reduced rate of relaxation and rapid dissociation. Biochemical data suggests that the N-terminal domain (NTD) is important for pre-cleavage binding and affinity for the target site. A combination of NMR-based interaction studies, the measurement of backbone dynamics using 15N relaxation measurements, and isothermal calorimetry (ITC) is used in this work to show that the NTD is capable of independently binding to DNA. Additionally, it is shown that the nature of the engagement of dsDNA by the NTD, in terms of affinity and characteristics of the binding modes, differs between sequences containing the 5’-CCCTT segment from those that do not. An attempt is made to extend these observations to the full length protein.
"],"dc:identifier":["https://academicworks.cuny.edu/gc_etds/1493"],"dc:subject":["Analytical Chemistry","Biochemistry","Microbiology","Molecular Biology","Other Chemistry","Structural Biology","Protein NMR","Protein-DNA binding","DNA","DNA binding specificity","isothermal titration calorimetry","chemical shift perturbation","NMR relaxation","rotational correlation time","binding electrostatics"],"dc:title":["Specific Binding Affinity of the Non-Catalytic Domain of Eukaryotic Like Type IB Topoisomerase of vaccinia Virus"],"thesis:degree_discipline":["Chemistry"],"thesis:degree_level":["Doctoral"],"thesis:degree_name":["Doctor of Philosophy"],"thesis:institution_name":["The Graduate School and University Center of The City University of New York"]},"updated_at":"2026-07-24T01:58:31Z"}