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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

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

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

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

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

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

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

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

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

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