RNA in nature is modified at many specific sites to order to gain extra functions or to expand the genetic code. One of such RNAs is ribosomal RNA (rRNA), which contains several modified bases, particularly around the functionally significant sites. We have focused on understanding the influences of modified base on RNA structure and function by employing helix 69 (H69), which is a good region to evaluate the roles of modified bases since it contains three pseudouridines in the loop region and exists at the core of the ribosome.
Previous model studies using small hairpin H69 showed the conformational differences of H69 loop under different conditions and revealed the significance of modified bases in H69 dynamics. Comparison of crystal structures of ribosomes indicates variable H69 conformations under different conditions. Based on these information, we performed dimethylsulfate (DMS) probing on 50S ribosomal subunits under different pHs, temperatures and Mg2+ concentrations, showing that H69 has a dynamic RNA loop component on the ribosome level as well as the models, and its multiple conformations are dependent on the presence of modified bases. In addition, footprintings in the presence of aminoglycoside antibiotics neomycin and paromomycin also show conformational variability in H69. These results indicate that H69 exists in multiple conformational states, which could be related to the function of the ribosome in the cell.
","abstract_html":"<p>RNA in nature is modified at many specific sites to order to gain extra functions or to expand the genetic code. One of such RNAs is ribosomal RNA (rRNA), which contains several modified bases, particularly around the functionally significant sites. We have focused on understanding the influences of modified base on RNA structure and function by employing helix 69 (H69), which is a good region to evaluate the roles of modified bases since it contains three pseudouridines in the loop region and exists at the core of the ribosome.</p> <p>Previous model studies using small hairpin H69 showed the conformational differences of H69 loop under different conditions and revealed the significance of modified bases in H69 dynamics. Comparison of crystal structures of ribosomes indicates variable H69 conformations under different conditions. Based on these information, we performed dimethylsulfate (DMS) probing on 50S ribosomal subunits under different pHs, temperatures and Mg2+ concentrations, showing that H69 has a dynamic RNA loop component on the ribosome level as well as the models, and its multiple conformations are dependent on the presence of modified bases. In addition, footprintings in the presence of aminoglycoside antibiotics neomycin and paromomycin also show conformational variability in H69. These results indicate that H69 exists in multiple conformational states, which could be related to the function of the ribosome in the cell.</p>","abstract_has_math":false,"creators":["Sakakibara, Yogo"],"institution":null,"degree_name":"Ph.D.","degree_level":"Open Access Dissertation","degree_discipline":"Chemistry","degree_department":null,"school":null,"contributors":["Christine S. Chow"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2012,"date_issued":"2012-01-01T08:00:00Z","date_published":"2012-01-01T08:00:00Z","updated_at":"2026-07-24T05:59:04Z","subjects":["Chemical probing, Fluorescent probing, Helix 69, Ribosomes, RNA","Biochemistry","Chemistry"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://digitalcommons.wayne.edu/oa_dissertations/494","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Christine S. Chow"]},{"key":"dc:creator","label":"Author","values":["Sakakibara, Yogo"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2012-01-01T08:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Chemistry"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Open Access Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Chemical probing, Fluorescent probing, Helix 69, Ribosomes, RNA","Biochemistry","Chemistry"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://digitalcommons.wayne.edu/oa_dissertations/494"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["RNA in nature is modified at many specific sites to order to gain extra functions or to expand the genetic code. One of such RNAs is ribosomal RNA (rRNA), which contains several modified bases, particularly around the functionally significant sites. We have focused on understanding the influences of modified base on RNA structure and function by employing helix 69 (H69), which is a good region to evaluate the roles of modified bases since it contains three pseudouridines in the loop region and exists at the core of the ribosome.
Previous model studies using small hairpin H69 showed the conformational differences of H69 loop under different conditions and revealed the significance of modified bases in H69 dynamics. Comparison of crystal structures of ribosomes indicates variable H69 conformations under different conditions. Based on these information, we performed dimethylsulfate (DMS) probing on 50S ribosomal subunits under different pHs, temperatures and Mg2+ concentrations, showing that H69 has a dynamic RNA loop component on the ribosome level as well as the models, and its multiple conformations are dependent on the presence of modified bases. In addition, footprintings in the presence of aminoglycoside antibiotics neomycin and paromomycin also show conformational variability in H69. These results indicate that H69 exists in multiple conformational states, which could be related to the function of the ribosome in the cell.
"]},{"key":"dc:title","label":"Title","values":["Exploring conformational variability of an rna domain in the ribosome: from structure and function to potential antibiotic targeting"]}]}],"canonical_facts":{"dc:contributor":["Christine S. Chow"],"dc:creator":["Sakakibara, Yogo"],"dc:date.available":["2012-01-01T08:00:00Z"],"dc:description.abstract":["RNA in nature is modified at many specific sites to order to gain extra functions or to expand the genetic code. One of such RNAs is ribosomal RNA (rRNA), which contains several modified bases, particularly around the functionally significant sites. We have focused on understanding the influences of modified base on RNA structure and function by employing helix 69 (H69), which is a good region to evaluate the roles of modified bases since it contains three pseudouridines in the loop region and exists at the core of the ribosome.
Previous model studies using small hairpin H69 showed the conformational differences of H69 loop under different conditions and revealed the significance of modified bases in H69 dynamics. Comparison of crystal structures of ribosomes indicates variable H69 conformations under different conditions. Based on these information, we performed dimethylsulfate (DMS) probing on 50S ribosomal subunits under different pHs, temperatures and Mg2+ concentrations, showing that H69 has a dynamic RNA loop component on the ribosome level as well as the models, and its multiple conformations are dependent on the presence of modified bases. In addition, footprintings in the presence of aminoglycoside antibiotics neomycin and paromomycin also show conformational variability in H69. These results indicate that H69 exists in multiple conformational states, which could be related to the function of the ribosome in the cell.
"],"dc:identifier":["https://digitalcommons.wayne.edu/oa_dissertations/494"],"dc:subject":["Chemical probing, Fluorescent probing, Helix 69, Ribosomes, RNA","Biochemistry","Chemistry"],"dc:title":["Exploring conformational variability of an rna domain in the ribosome: from structure and function to potential antibiotic targeting"],"thesis:degree_discipline":["Chemistry"],"thesis:degree_level":["Open Access Dissertation"],"thesis:degree_name":["Ph.D."]},"updated_at":"2026-07-24T05:59:04Z"}