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Consequently, understanding RNA function is necessarily tied into an understanding of RNA folding and dynamics. A major challenge in this endeavor is that RNA folding is a dynamic, hierarchical process that often involves multiple sparse, transient states, which cannot be characterized by traditional high-resolution methods. In this work, I develop new NMR methods for characterizing RNA transient states and apply them to the study of riboswitch folding and ribozyme catalysis. First, I develop a new NMR method for the detection of relatively slow exchanging, sparsely populated NMR states. I then explore the limits of other NMR techniques in studying similar motions. Second, I develop a new NMR method for obtaining structural information about excited RNA conformational states through the detection of residual dipolar couplings. Third, I apply the techniques developed to understanding and mapping out the regulatory mechanism of fluoride riboswitch, revealing that it operates through the allosteric suppression of a transient state. Finally, in collaboration with a previous lab member, we apply these techniques to study hammerhead ribozyme catalysis, focusing on the pre-catalytic hammerhead ribozyme. We show that the cleavage rate of hammerhead ribozyme is intricately tied into its ability to pre-order through the transient sampling of a docked excited state. Together, the work presented here will provide new NMR tools for studying RNA excited states and demonstrate their importance RNA function. Winter 2017 2017 Biochemistry Dynamics, NMR, RNA, Structure eng Doctor of Philosophy Dissertation University of North Carolina at Chapel Hill Graduate School Degree granting institution Chemistry Qi Zhang Thesis advisor Gary Pielak Thesis advisor Kevin Weeks Thesis advisor Andrew Lee Thesis advisor Nikolay Dokholyan Thesis advisor text Bo Zhao Creator Department of Chemistry College of Arts and Sciences Development of NMR Methods for Characterizing Conformational Dynamics in RNA Folding and Catalysis RNA are highly dynamic molecules that often have to undergo multiple conformational transitions to achieve distinct structures resulting in unique functions. Consequently, understanding RNA function is necessarily tied into an understanding of RNA folding and dynamics. A major challenge in this endeavor is that RNA folding is a dynamic, hierarchical process that often involves multiple sparse, transient states, which cannot be characterized by traditional high-resolution methods. In this work, I develop new NMR methods for characterizing RNA transient states and apply them to the study of riboswitch folding and ribozyme catalysis. First, I develop a new NMR method for the detection of relatively slow exchanging, sparsely populated NMR states. I then explore the limits of other NMR techniques in studying similar motions. Second, I develop a new NMR method for obtaining structural information about excited RNA conformational states through the detection of residual dipolar couplings. Third, I apply the techniques developed to understanding and mapping out the regulatory mechanism of fluoride riboswitch, revealing that it operates through the allosteric suppression of a transient state. Finally, in collaboration with a previous lab member, we apply these techniques to study hammerhead ribozyme catalysis, focusing on the pre-catalytic hammerhead ribozyme. We show that the cleavage rate of hammerhead ribozyme is intricately tied into its ability to pre-order through the transient sampling of a docked excited state. Together, the work presented here will provide new NMR tools for studying RNA excited states and demonstrate their importance RNA function. 2017-12 2017 Biochemistry Dynamics, NMR, RNA, Structure eng Doctor of Philosophy Dissertation University of North Carolina at Chapel Hill Graduate School Degree granting institution Chemistry Qi Zhang Thesis advisor Gary Pielak Thesis advisor Kevin Weeks Thesis advisor Andrew Lee Thesis advisor Nikolay Dokholyan Thesis advisor text Bo Zhao Creator Department of Chemistry College of Arts and Sciences Development of NMR Methods for Characterizing Conformational Dynamics in RNA Folding and Catalysis RNA are highly dynamic molecules that often have to undergo multiple conformational transitions to achieve distinct structures resulting in unique functions. Consequently, understanding RNA function is necessarily tied into an understanding of RNA folding and dynamics. A major challenge in this endeavor is that RNA folding is a dynamic, hierarchical process that often involves multiple sparse, transient states, which cannot be characterized by traditional high-resolution methods. In this work, I develop new NMR methods for characterizing RNA transient states and apply them to the study of riboswitch folding and ribozyme catalysis. First, I develop a new NMR method for the detection of relatively slow exchanging, sparsely populated NMR states. I then explore the limits of other NMR techniques in studying similar motions. Second, I develop a new NMR method for obtaining structural information about excited RNA conformational states through the detection of residual dipolar couplings. Third, I apply the techniques developed to understanding and mapping out the regulatory mechanism of fluoride riboswitch, revealing that it operates through the allosteric suppression of a transient state. Finally, in collaboration with a previous lab member, we apply these techniques to study hammerhead ribozyme catalysis, focusing on the pre-catalytic hammerhead ribozyme. We show that the cleavage rate of hammerhead ribozyme is intricately tied into its ability to pre-order through the transient sampling of a docked excited state. Together, the work presented here will provide new NMR tools for studying RNA excited states and demonstrate their importance RNA function. 2017-12 2017 Biochemistry Dynamics, NMR, RNA, Structure eng Doctor of Philosophy Dissertation University of North Carolina at Chapel Hill Graduate School Degree granting institution Chemistry Qi Zhang Thesis advisor Gary Pielak Thesis advisor Kevin Weeks Thesis advisor Andrew Lee Thesis advisor Nikolay Dokholyan Thesis advisor text Bo Zhao Creator Department of Chemistry College of Arts and Sciences Development of NMR Methods for Characterizing Conformational Dynamics in RNA Folding and Catalysis RNA are highly dynamic molecules that often have to undergo multiple conformational transitions to achieve distinct structures resulting in unique functions. Consequently, understanding RNA function is necessarily tied into an understanding of RNA folding and dynamics. A major challenge in this endeavor is that RNA folding is a dynamic, hierarchical process that often involves multiple sparse, transient states, which cannot be characterized by traditional high-resolution methods. In this work, I develop new NMR methods for characterizing RNA transient states and apply them to the study of riboswitch folding and ribozyme catalysis. First, I develop a new NMR method for the detection of relatively slow exchanging, sparsely populated NMR states. I then explore the limits of other NMR techniques in studying similar motions. Second, I develop a new NMR method for obtaining structural information about excited RNA conformational states through the detection of residual dipolar couplings. Third, I apply the techniques developed to understanding and mapping out the regulatory mechanism of fluoride riboswitch, revealing that it operates through the allosteric suppression of a transient state. Finally, in collaboration with a previous lab member, we apply these techniques to study hammerhead ribozyme catalysis, focusing on the pre-catalytic hammerhead ribozyme. We show that the cleavage rate of hammerhead ribozyme is intricately tied into its ability to pre-order through the transient sampling of a docked excited state. Together, the work presented here will provide new NMR tools for studying RNA excited states and demonstrate their importance RNA function. 2017-12 2017 Biochemistry Dynamics, NMR, RNA, Structure eng Doctor of Philosophy Dissertation University of North Carolina at Chapel Hill Graduate School Degree granting institution Chemistry Qi Zhang Thesis advisor Gary Pielak Thesis advisor Kevin Weeks Thesis advisor Andrew Lee Thesis advisor Nikolay Dokholyan Thesis advisor text Bo Zhao Creator Department of Chemistry College of Arts and Sciences Development of NMR Methods for Characterizing Conformational Dynamics in RNA Folding and Catalysis RNA are highly dynamic molecules that often have to undergo multiple conformational transitions to achieve distinct structures resulting in unique functions. Consequently, understanding RNA function is necessarily tied into an understanding of RNA folding and dynamics. A major challenge in this endeavor is that RNA folding is a dynamic, hierarchical process that often involves multiple sparse, transient states, which cannot be characterized by traditional high-resolution methods. In this work, I develop new NMR methods for characterizing RNA transient states and apply them to the study of riboswitch folding and ribozyme catalysis. First, I develop a new NMR method for the detection of relatively slow exchanging, sparsely populated NMR states. I then explore the limits of other NMR techniques in studying similar motions. Second, I develop a new NMR method for obtaining structural information about excited RNA conformational states through the detection of residual dipolar couplings. Third, I apply the techniques developed to understanding and mapping out the regulatory mechanism of fluoride riboswitch, revealing that it operates through the allosteric suppression of a transient state. Finally, in collaboration with a previous lab member, we apply these techniques to study hammerhead ribozyme catalysis, focusing on the pre-catalytic hammerhead ribozyme. We show that the cleavage rate of hammerhead ribozyme is intricately tied into its ability to pre-order through the transient sampling of a docked excited state. Together, the work presented here will provide new NMR tools for studying RNA excited states and demonstrate their importance RNA function. 2017-12 2017 Biochemistry Dynamics, NMR, RNA, Structure eng Doctor of Philosophy Dissertation Chemistry Qi Zhang Thesis advisor Gary J. Pielak Thesis advisor Kevin Weeks Thesis advisor Andrew Lee Thesis advisor Nikolay Dokholyan Thesis advisor text University of North Carolina at Chapel Hill Degree granting institution Bo Zhao Creator Department of Chemistry College of Arts and Sciences Development of NMR Methods for Characterizing Conformational Dynamics in RNA Folding and Catalysis RNA are highly dynamic molecules that often have to undergo multiple conformational transitions to achieve distinct structures resulting in unique functions. Consequently, understanding RNA function is necessarily tied into an understanding of RNA folding and dynamics. A major challenge in this endeavor is that RNA folding is a dynamic, hierarchical process that often involves multiple sparse, transient states, which cannot be characterized by traditional high-resolution methods. In this work, I develop new NMR methods for characterizing RNA transient states and apply them to the study of riboswitch folding and ribozyme catalysis. First, I develop a new NMR method for the detection of relatively slow exchanging, sparsely populated NMR states. I then explore the limits of other NMR techniques in studying similar motions. Second, I develop a new NMR method for obtaining structural information about excited RNA conformational states through the detection of residual dipolar couplings. Third, I apply the techniques developed to understanding and mapping out the regulatory mechanism of fluoride riboswitch, revealing that it operates through the allosteric suppression of a transient state. Finally, in collaboration with a previous lab member, we apply these techniques to study hammerhead ribozyme catalysis, focusing on the pre-catalytic hammerhead ribozyme. We show that the cleavage rate of hammerhead ribozyme is intricately tied into its ability to pre-order through the transient sampling of a docked excited state. Together, the work presented here will provide new NMR tools for studying RNA excited states and demonstrate their importance RNA function. 2017-12 2017 Biochemistry Dynamics; NMR; RNA; Structure eng Doctor of Philosophy Dissertation Chemistry Qi Zhang Thesis advisor Gary J. Pielak Thesis advisor Kevin Weeks Thesis advisor Andrew Lee Thesis advisor Nikolay Dokholyan Thesis advisor text University of North Carolina at Chapel Hill Degree granting institution Bo Zhao Creator Department of Chemistry College of Arts and Sciences Development of NMR Methods for Characterizing Conformational Dynamics in RNA Folding and Catalysis RNA are highly dynamic molecules that often have to undergo multiple conformational transitions to achieve distinct structures resulting in unique functions. Consequently, understanding RNA function is necessarily tied into an understanding of RNA folding and dynamics. A major challenge in this endeavor is that RNA folding is a dynamic, hierarchical process that often involves multiple sparse, transient states, which cannot be characterized by traditional high-resolution methods. In this work, I develop new NMR methods for characterizing RNA transient states and apply them to the study of riboswitch folding and ribozyme catalysis. First, I develop a new NMR method for the detection of relatively slow exchanging, sparsely populated NMR states. I then explore the limits of other NMR techniques in studying similar motions. Second, I develop a new NMR method for obtaining structural information about excited RNA conformational states through the detection of residual dipolar couplings. Third, I apply the techniques developed to understanding and mapping out the regulatory mechanism of fluoride riboswitch, revealing that it operates through the allosteric suppression of a transient state. Finally, in collaboration with a previous lab member, we apply these techniques to study hammerhead ribozyme catalysis, focusing on the pre-catalytic hammerhead ribozyme. We show that the cleavage rate of hammerhead ribozyme is intricately tied into its ability to pre-order through the transient sampling of a docked excited state. Together, the work presented here will provide new NMR tools for studying RNA excited states and demonstrate their importance RNA function. 2017-12 2017 Biochemistry Dynamics, NMR, RNA, Structure eng Doctor of Philosophy Dissertation University of North Carolina at Chapel Hill Graduate School Degree granting institution Chemistry Qi Zhang Thesis advisor Gary J. Pielak Thesis advisor Kevin Weeks Thesis advisor Andrew Lee Thesis advisor Nikolay Dokholyan Thesis advisor text Bo Zhao Creator Department of Chemistry College of Arts and Sciences Development of NMR Methods for Characterizing Conformational Dynamics in RNA Folding and Catalysis RNA are highly dynamic molecules that often have to undergo multiple conformational transitions to achieve distinct structures resulting in unique functions. Consequently, understanding RNA function is necessarily tied into an understanding of RNA folding and dynamics. A major challenge in this endeavor is that RNA folding is a dynamic, hierarchical process that often involves multiple sparse, transient states, which cannot be characterized by traditional high-resolution methods. In this work, I develop new NMR methods for characterizing RNA transient states and apply them to the study of riboswitch folding and ribozyme catalysis. First, I develop a new NMR method for the detection of relatively slow exchanging, sparsely populated NMR states. I then explore the limits of other NMR techniques in studying similar motions. Second, I develop a new NMR method for obtaining structural information about excited RNA conformational states through the detection of residual dipolar couplings. Third, I apply the techniques developed to understanding and mapping out the regulatory mechanism of fluoride riboswitch, revealing that it operates through the allosteric suppression of a transient state. Finally, in collaboration with a previous lab member, we apply these techniques to study hammerhead ribozyme catalysis, focusing on the pre-catalytic hammerhead ribozyme. We show that the cleavage rate of hammerhead ribozyme is intricately tied into its ability to pre-order through the transient sampling of a docked excited state. Together, the work presented here will provide new NMR tools for studying RNA excited states and demonstrate their importance RNA function. 2017-12 2017 Biochemistry Dynamics; NMR; RNA; Structure eng Doctor of Philosophy Dissertation University of North Carolina at Chapel Hill Graduate School Degree granting institution Qi Zhang Thesis advisor Gary J. Pielak Thesis advisor Kevin Weeks Thesis advisor Andrew Lee Thesis advisor Nikolay Dokholyan Thesis advisor text Zhao_unc_0153D_17457.pdf uuid:328a7950-2124-4fc6-ba64-1448135a925b 2019-12-31T00:00:00 2017-12-05T23:10:24Z proquest application/pdf 18380221