Understanding the interplay between nucleic acids and protein aggregation is integral to the understanding of proteostasis, aging, and neurodegenerative disease progression. Nucleic acids are known to modulate the aggregation of PrP, tau, ⍺-synuclein, and other disease relevant proteins. Although the interactions between misfolded protein and nucleic acids can play a role in disease, this interaction may potentially be beneficial as well. Our group and others have shown nucleic acids can be powerful chaperones. Previous work has shown both RNA and DNA can prevent protein aggregation and RNA can pass off protein clients to the heat shock protein (Hsp) system. Here we explore the underlying physical properties and kinetics of how nucleic acids prevent protein aggregation. We found that the concentration of bulk dsDNA can be tuned to roughly control the size of kinetically stable protein oligomers. DNA facilitates this oligomerization via the formation of “networks” to rapidly assimilate misfolded proteins to yield smaller oligomers at higher DNA concentrations or larger aggregates at lower DNA concentrations. In a follow up study, we found that G-quadruplexes were an even more powerful chaperone than bulk DNA (which on a per-weight basis was more powerful than any known protein-based chaperone). G-quadruplexes appear to be particularly adept at interacting with misfolded proteins and are also thought to play a role in a number of diseases related to protein aggregation. To find the source of G-quadruplex’s chaperoning ability, we systematically mutated two G-quadruplex forming sequences with solved structures. The solved structures allowed us to make structure function hypotheses, where we found several factors contributed to their remarkable chaperone activity. In particular: their structural topology, overall dynamics and G-quadruplex accessibility, and oligomerization state. Together, this work explores the structural, physical, and mechanistic features of nucleic acids that make them such adept chaperones.
","abstract_html":"<p>Understanding the interplay between nucleic acids and protein aggregation is integral to the understanding of proteostasis, aging, and neurodegenerative disease progression. Nucleic acids are known to modulate the aggregation of PrP, tau, ⍺-synuclein, and other disease relevant proteins. Although the interactions between misfolded protein and nucleic acids can play a role in disease, this interaction may potentially be beneficial as well. Our group and others have shown nucleic acids can be powerful chaperones. Previous work has shown both RNA and DNA can prevent protein aggregation and RNA can pass off protein clients to the heat shock protein (Hsp) system. Here we explore the underlying physical properties and kinetics of how nucleic acids prevent protein aggregation. We found that the concentration of bulk dsDNA can be tuned to roughly control the size of kinetically stable protein oligomers. DNA facilitates this oligomerization via the formation of “networks” to rapidly assimilate misfolded proteins to yield smaller oligomers at higher DNA concentrations or larger aggregates at lower DNA concentrations. In a follow up study, we found that G-quadruplexes were an even more powerful chaperone than bulk DNA (which on a per-weight basis was more powerful than any known protein-based chaperone). G-quadruplexes appear to be particularly adept at interacting with misfolded proteins and are also thought to play a role in a number of diseases related to protein aggregation. To find the source of G-quadruplex’s chaperoning ability, we systematically mutated two G-quadruplex forming sequences with solved structures. The solved structures allowed us to make structure function hypotheses, where we found several factors contributed to their remarkable chaperone activity. In particular: their structural topology, overall dynamics and G-quadruplex accessibility, and oligomerization state. Together, this work explores the structural, physical, and mechanistic features of nucleic acids that make them such adept chaperones.</p>","abstract_has_math":false,"creators":["Litberg, Theodore J."],"institution":null,"degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":null,"degree_department":null,"school":null,"contributors":["Scott Horowitz","Daniel Linseman","Michelle Knowles","Sunil Kumar","Martin Margittai"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2023,"date_issued":"2023-08-01T07:00:00Z","date_published":"2023-08-01T07:00:00Z","updated_at":"2026-07-24T02:01:39Z","subjects":["Chaperone","G-quadruplex","Nucleic acids","Protein aggregation","Biochemistry","Biochemistry, Biophysics, and Structural Biology","Biology","Biophysics","Life Sciences"],"languages":["English (eng)"],"rights":["Copyright is held by the author. User is responsible for all copyright compliance.
"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://digitalcommons.du.edu/etd/2291","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Scott Horowitz","Daniel Linseman","Michelle Knowles","Sunil Kumar","Martin Margittai"]},{"key":"dc:creator","label":"Author","values":["Litberg, Theodore J."]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2024-09-12T07:00:00Z"]},{"key":"thesis:degree_level","label":"Degree Level","values":["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":["Chaperone","G-quadruplex","Nucleic acids","Protein aggregation","Biochemistry","Biochemistry, Biophysics, and Structural Biology","Biology","Biophysics","Life Sciences"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["English (eng)"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright is held by the author. User is responsible for all copyright compliance.
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"]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Mechanisms Behind the Chaperone Activity of Nucleic Acids"]}]}],"canonical_facts":{"dc:contributor":["Scott Horowitz","Daniel Linseman","Michelle Knowles","Sunil Kumar","Martin Margittai"],"dc:creator":["Litberg, Theodore J."],"dc:date.available":["2024-09-12T07:00:00Z"],"dc:description.abstract":["Understanding the interplay between nucleic acids and protein aggregation is integral to the understanding of proteostasis, aging, and neurodegenerative disease progression. Nucleic acids are known to modulate the aggregation of PrP, tau, ⍺-synuclein, and other disease relevant proteins. Although the interactions between misfolded protein and nucleic acids can play a role in disease, this interaction may potentially be beneficial as well. Our group and others have shown nucleic acids can be powerful chaperones. Previous work has shown both RNA and DNA can prevent protein aggregation and RNA can pass off protein clients to the heat shock protein (Hsp) system. Here we explore the underlying physical properties and kinetics of how nucleic acids prevent protein aggregation. We found that the concentration of bulk dsDNA can be tuned to roughly control the size of kinetically stable protein oligomers. DNA facilitates this oligomerization via the formation of “networks” to rapidly assimilate misfolded proteins to yield smaller oligomers at higher DNA concentrations or larger aggregates at lower DNA concentrations. In a follow up study, we found that G-quadruplexes were an even more powerful chaperone than bulk DNA (which on a per-weight basis was more powerful than any known protein-based chaperone). G-quadruplexes appear to be particularly adept at interacting with misfolded proteins and are also thought to play a role in a number of diseases related to protein aggregation. To find the source of G-quadruplex’s chaperoning ability, we systematically mutated two G-quadruplex forming sequences with solved structures. The solved structures allowed us to make structure function hypotheses, where we found several factors contributed to their remarkable chaperone activity. In particular: their structural topology, overall dynamics and G-quadruplex accessibility, and oligomerization state. Together, this work explores the structural, physical, and mechanistic features of nucleic acids that make them such adept chaperones.
"],"dc:format":["application/pdf"],"dc:identifier":["https://digitalcommons.du.edu/etd/2291"],"dc:language":["English (eng)"],"dc:rights":["Copyright is held by the author. User is responsible for all copyright compliance.
"],"dc:subject":["Chaperone","G-quadruplex","Nucleic acids","Protein aggregation","Biochemistry","Biochemistry, Biophysics, and Structural Biology","Biology","Biophysics","Life Sciences"],"dc:title":["Mechanisms Behind the Chaperone Activity of Nucleic Acids"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."]},"updated_at":"2026-07-24T02:01:39Z"}