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1. Studies of the Molecular Origins of Thermodynamic Stability in RNA Secondary Structure

open_access
Open Access
Author:
Proctor, David James
Title:
Studies of the Molecular Origins of Thermodynamic Stability in RNA Secondary Structure
Graduate Program:
Chemistry
Keywords:
RNA
biophysics
structure
thermodynamics
File:
Download thesis.pdf
Committee Members:
Philip C. Bevilacqua, Committee Chair/Co-Chair
Juliette T J Lecomte, Committee Member
George I Makhatadze, Committee Member
Paul Lee Babitzke, Committee Member

2. Stability in Nucleic Acid Hairpins: 1. Molecular Determinants of Cooperativity and 2. Linkage between Proton Binding and Folding

open_access
Open Access
Author:
Moody, Ellen Marie
Title:
Stability in Nucleic Acid Hairpins: 1. Molecular Determinants of Cooperativity and 2. Linkage between Proton Binding and Folding
Graduate Program:
Chemistry
Keywords:
RNA
DNA
pKa shifting
cooperativity
expandability
thermodynamics
File:
Download EMM_thesis.pdf
Committee Members:
Philip C. Bevilacqua, Committee Chair/Co-Chair
Christopher Falzone, Committee Member
Juliette T J Lecomte, Committee Member
James Gregory Ferry, Committee Member

3. Calorimetric Studies of Site-Specific Ligand Binding By RNA

open_access
Open Access
Author:
Sokoloski, Joshua Edward
Title:
Calorimetric Studies of Site-Specific Ligand Binding By RNA
Graduate Program:
Chemistry
Keywords:
Isothermal Titration Calorimetry
RNA
File:
Download JES_Sokoloski_Dissertation_F11_Corrected.pdf
Committee Members:
Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Scott A Showalter, Committee Member
David Lawrence Allara, Committee Member
Song Tan, Committee Member

4. ELUCIDATING THERMODYNAMIC RELATIONSHIPS IN THE RNA STRUCTURAL HIERARCHY: MOLECULAR ORIGINS OF STABILITY

open_access
Open Access
Author:
Blose, Joshua Matthew
Title:
ELUCIDATING THERMODYNAMIC RELATIONSHIPS IN THE RNA STRUCTURAL HIERARCHY: MOLECULAR ORIGINS OF STABILITY
Graduate Program:
Chemistry
Keywords:
Cooperative Folding
Thermophilic Adaptation
Tetraloop
RNA
Nonlinear Poisson-Boltzmann
NLPB
Electrostatics
File:
Download JMB_Dissertation_082009.pdf
Committee Members:
Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Sharon Hammes Schiffer, Committee Member
Tae Hee Lee, Committee Member
Kenneth Charles Keiler, Committee Member

5. Regulation of the protein kinase PKR by higher-order RNA secondary and tertiary structures

open_access
Open Access
Author:
Heinicke, Laurie Ann
Title:
Regulation of the protein kinase PKR by higher-order RNA secondary and tertiary structures
Graduate Program:
Chemistry
Keywords:
innate immune response
kinase
RNA
PKR
File:
Download Heinicke_04_26_10_Thesis.pdf
Committee Members:
Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Christine Dolan Keating, Committee Member
Scott A Showalter, Committee Member
Andrey S Krasilnikov, Committee Member

6. Arabidopsis thaliana under stress: Functional implications of G-quadruplex and non-coding RNA structure

open_access
Open Access
Author:
Mullen, Melissa Ann
Title:
Arabidopsis thaliana under stress: Functional implications of G-quadruplex and non-coding RNA structure
Graduate Program:
Chemistry
Keywords:
RNA
Arabidopsis
G-quadruplex
drought stress
File:
Download Mullen_Thesis_071511.pdf
Committee Members:
Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Sarah Mary Assmann, Committee Chair/Co-Chair
Christine Dolan Keating, Committee Member
David D Boehr, Committee Member
Paul Lee Babitzke, Committee Member

7. Folding Cooperativity and Its Influence on pKa Shifting in Nucleic Acids

open_access
Open Access
Author:
Siegfried, Nathan A.
Title:
Folding Cooperativity and Its Influence on pKa Shifting in Nucleic Acids
Graduate Program:
Chemistry
Keywords:
pKa shift
RNA
DNA
nucleic acids
cooperativity
acid base catalysis
File:
Download Siegfried_Thesis.pdf
Committee Members:
Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Squire J Booker, Committee Member
Scott A Showalter, Committee Member
Katsuhiko Murakami, Committee Member

8. CATALYTIC AND STRUCTURAL ROLES OF NUCLEOBASES AND METAL IONS IN SMALL RIBOZYMES: NEW INSIGHTS FROM CALCULATIONS AND COMPARISON TO EXPERIMENTS

open_access
Open Access
Author:
Veeraraghavan, Narayanan
Title:
CATALYTIC AND STRUCTURAL ROLES OF NUCLEOBASES AND METAL IONS IN SMALL RIBOZYMES: NEW INSIGHTS FROM CALCULATIONS AND COMPARISON TO EXPERIMENTS
Graduate Program:
Integrative Biosciences
Keywords:
NLPB
reverse GU wobble
wobble
ribozyme
RNA
molecular dynamics
HDV
File:
Download NVeeraraghavan-eTD.pdf
Committee Members:
Prof Sharon Hammes Schiffer, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Sharon Hammes Schiffer, Committee Chair/Co-Chair
William George Noid, Committee Member
Andrey S Krasilnikov, Committee Member
Reka Z Albert, Committee Member

11. Development and utilization of spectroscopic and chemical methodologies for investigating pKa shifting in nucleic acids

open_access
Open Access
Author:
Wilcox, Jennifer Lynn
Title:
Development and utilization of spectroscopic and chemical methodologies for investigating pKa shifting in nucleic acids
Graduate Program:
Chemistry
Keywords:
RNA
nucleic acids
2-aminopurine fluorescence
pKa shifting
File:
Download Wilcox_Thesis.pdf
Committee Members:
Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Squire J Booker, Committee Member
Scott A Showalter, Committee Member
Andrey S Krasilnikov, Committee Member

12. Structural and Functional Roles of RNA Structure in Regulatory Processes in Plants

open_access
Open Access
Author:
Kwok, Chun Kit
Title:
Structural and Functional Roles of RNA Structure in Regulatory Processes in Plants
Graduate Program:
Chemistry
Keywords:
RNA
RNA structure
RNA folding
Plants
Arabidopsis thaliana
G-quadruplex
regulation
DMS
SHAPE
LMPCR
Structure-Seq
File:
Download Thesis_CKK_2014.pdf
Committee Members:
Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Sarah Mary Assmann, Dissertation Advisor/Co-Advisor
Scott A Showalter, Committee Member
Tae Hee Lee, Committee Member
Song Tan, Committee Member

13. toward understanding RNA structure, folding, and function in cells

open_access
Open Access
Author:
Strulson, Christopher A
Title:
toward understanding RNA structure, folding, and function in cells
Graduate Program:
Chemistry
Keywords:
RNA
ribozyme
molecular crowding
macromolecular crowding
catalysis
compartmentalization
folding cooperativity
File:
Download Christoper_Strulson_Thesis_Toward_Understanding_RNA__Structure_Folding_and_Function_in_Cells.pdf
Committee Members:
Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Christine Dolan Keating, Dissertation Advisor/Co-Advisor
Squire J Booker, Committee Member
Tae Hee Lee, Committee Member
Kenneth Charles Keiler, Committee Member

15. Mechanistic Investigation Of Activation Of The Innate Immune Sensor Pkr By Various Levels And Types Of Rna Structure

open_access
Open Access
Author:
Hull, Chelsea Michelle
Title:
Mechanistic Investigation Of Activation Of The Innate Immune Sensor Pkr By Various Levels And Types Of Rna Structure
Graduate Program:
Chemistry
Keywords:
PKR
RNA
bacterial RNA
riboswitch
ribozyme
innate immunity
File:
Download Hull_CM_2016.pdf
Committee Members:
Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Scott A Showalter, Committee Member
Christine Dolan Keating, Committee Member
Craig Eugene Cameron, Committee Member

17. Towards Investigation of RNA Catalysis and Compartmentalization

open_access
Open Access
Author:
Frankel, Erica Ann
Title:
Towards Investigation of RNA Catalysis and Compartmentalization
Graduate Program:
Chemistry
Keywords:
RNA
Catalysis
Compartmentalization
Cooperativity
Origins of Life
File:
Download Frankel_Dissertation_Final.pdf
Committee Members:
Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Scott A Showalter, Committee Member
Amie Kathleen Boal, Committee Member
James Kasting, Outside Member
Christine Dolan Keating, Dissertation Advisor/Co-Advisor
Christine Dolan Keating, Committee Chair/Co-Chair

20. Influence of biological small molecules on the twister ribozyme and development of methodologies to study and discover small ribozymes

open_access
Open Access
Author:
Messina, Kyle
Title:
Influence of biological small molecules on the twister ribozyme and development of methodologies to study and discover small ribozymes
Graduate Program:
Chemistry
Keywords:
RNA
Twister Ribozyme
Kinetics
Small Molecule
Cryo-EM
Bioinformatics
File:
Download Messina_KJ_2019_Dissertation.pdf
Committee Members:
Philip C Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C Bevilacqua, Committee Chair/Co-Chair
Carsten Krebs, Committee Member
David D Boehr, Committee Member
Craig Eugene Cameron, Outside Member
Philip C Bevilacqua, Program Head/Chair