Search

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:

Molden, Rosalynn Conniff

Title:

Enhancing RNA catalysis through compartmentalization

Graduate Program:

Chemistry

Keywords:

model cell
aqueous two-phase systems
hammerhead ribozyme kinetics
RNA
cellular compartmentalization

File:

Download ThesisETD.pdf

Committee Members:

Christine Dolan Keating, Thesis Advisor/Co-Advisor
Christine Dolan Keating, Thesis Advisor/Co-Advisor

Author:

Reigh, Stephanie Ann

Title:

Syn Bases: Their Prevalence, Relevance, and Functional Utility in Functional RNA

Graduate Program:

Chemistry

Keywords:

RNA

File:

Download Reigh_Final_Thesis.pdf

Committee Members:

Philip C. Bevilacqua, Thesis Advisor/Co-Advisor
Philip C. Bevilacqua, Thesis Advisor/Co-Advisor

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

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

Author:

Kranick, Joshua Christian-issiah

Title:

Toward a More Complete Understanding of Microprocessing

Graduate Program:

Chemistry

Keywords:

RNAi
miRNA
RNA
Microprocessing
Drosha
DGCR8
RNA Interference
miRNA Maturation

File:

Download KranickFinalThesisV3.pdf

Committee Members:

Scott A Showalter, Thesis Advisor/Co-Advisor

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

Author:

Penrod, Katheryn Anne

Title:

Exploring RNA Flexibility Using Molecular Dynamics

Graduate Program:

Chemistry

Keywords:

RNA
Molecular Dynamics
MD
miRNA
microRNA

File:

Download 06-11-17_KAP_MS_Thesis_CV.pdf

Committee Members:

Dr. Scott A. Showalter, Thesis Advisor/Co-Advisor
Dr. William G. Noid, Committee Member
Dr. Edward P. O'Brien, Committee Member
Dr. Paul S. Cremer, Committee Member
Dr. Costas D. Maranas, Committee Member

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

Author:

Bingaman, Jamie Lee

Title:

Identification of novel catalytic strategies of small ribozymes

Graduate Program:

Chemistry

Keywords:

ribozyme
glmS
RNA
catalysis

File:

Download Bingaman_dissertation_2017.pdf

Committee Members:

Philip C. Bevilacqua, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Squire J Booker, Committee Member
David D Boehr, Committee Member
Song Tan, Outside Member

Author:

Schwalm, Erica Lynne

Title:

Investigation of the Radical SAM RNA Methylases RlmN and Cfr

Graduate Program:

Chemistry

Keywords:

radical SAM
RNA
enzymes
methylation

File:

Download Schwalm_Dissertation.pdf

Committee Members:

Squire J Booker, Dissertation Advisor/Co-Advisor
Squire J Booker, Committee Chair/Co-Chair
Amie Kathleen Boal, Committee Member
Carsten Krebs, Committee Member
William O Hancock, Outside Member

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

Author:

Walker, Michael

Title:

Development and Implementation of a Novel CRISPR/Cas9 System to Investigate Translational Repression Mechanisms in Plasmodium yoelii.

Graduate Program:

Molecular, Cellular and Integrative Biosciences

Keywords:

Malaria
CRISPR
Plasmodium
yoelii
TRIBE
Translational Repression
RNA
DNA
RGR

File:

Download Michael_P._Walker_Dissertation-Finalformat.pdf

Committee Members:

Scott E. Lindner, Dissertation Advisor/Co-Advisor
Scott E. Lindner, Committee Chair/Co-Chair
Melissa Rolls, Committee Member
Manuel Llinas, Committee Member
Howard M Salis, Outside Member
Maciej F Boni, Committee Member
Melissa Rolls, Program Head/Chair

Author:

Gontu, Abhinay

Title:

Broad-spectrum RNA prophylactic and therapeutic interventions for SARS-CoV-2

Graduate Program:

Pathobiology

Keywords:

RNA
SARS-CoV-2
Trans-amplifying mRNA vaccine
RNA mini-genome
SARS-CoV-2 variants

File:

Download Abhinay_Gontu_03142024.pdf

Committee Members:

Anthony Schmitt, Professor in Charge/Director of Graduate Studies
Costas Maranas, Outside Unit Member
Marco Archetti, Outside Field Member
Bhushan Jayarao, Co-Chair & Major Field Member
Suresh Kuchipudi, Chair & Dissertation Advisor
Alberto Gino Lorenzoni Calvo, Outside Field Member

Author:

Vezeau, Grace

Title:

Developing Nucleic Acid-Based Biosensor Platforms

Graduate Program:

Agricultural and Biological Engineering

Keywords:

synthetic biology
biosensors
RNA
riboswitch
CRISPR-Cas9
cell-free expression systems
biophysics
nucleic acid secondary structure

File:

Download Grace_Vezeau_dissertation.pdf

Committee Members:

Jeffrey Catchmark, Major Field Member
Howard Salis, Chair & Dissertation Advisor
Philip Bevilacqua, Outside Unit Member
Paul Heinemann, Program Head/Chair
Andrew Zydney, Outside Field Member

Author:

Dollinger, Roberta

Title:

The role of Spt5-nucleic acid contacts in promoter proximal pausing of RNA polymerase II

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

RNA polymerase II
DSIF
NELF
transcription
promoter proximal pausing
RNA
DNA
NGN
NusG
KOW
elongation factors
Spt5

File:

Login to Download

Committee Members:

Melissa Rolls, Major Field Member
David Gilmour, Chair & Dissertation Advisor
Scott Showalter, Outside Unit & Field Member
Song Tan, Major Field Member
Katsuhiko Murakami, Major Field Member
Wendy Hanna-Rose, Program Head/Chair

Author:

Xu, Jiansong

Title:

Reconsidering the czcD (NiCo) riboswitch as iron (II) riboswitch

Graduate Program:

Chemistry

Keywords:

Irving-William series
metalloregulation
RNA
iron
metal selectivity
riboswitch
metal sensor
czcD riboswitch
NiCo riboswitch
metal overload

File:

Login to Download

Committee Members:

Xin Zhang, Major Field Member
Joseph Cotruvo, Chair & Dissertation Advisor
Philip Bevilacqua, Major Field Member
Philip Bevilacqua, Program Head/Chair
Emily Weinert, Outside Unit & Field Member

Author:

Veenis, Andrew

Title:

Towards a Better Understanding of the Influence of Noncovalent Interactions on RNA Catalysis and the Properties of RNA Moieties

Graduate Program:

Chemistry

Keywords:

RNA
Ribozyme
pKa
Cheminformatics
Bioinformatics
Molecular Dynamics

File:

Login to Download

Committee Members:

Lasse Jensen, Major Field Member
Song Tan, Outside Unit & Field Member
Joseph Cotruvo, Major Field Member
Philip Bevilacqua, Chair & Dissertation Advisor
Philip Bevilacqua, Program Head/Chair

Author:

Sieg, Jacob

Title:

Thermodynamic Corrections to RNA Folding Models in Cells

Graduate Program:

Chemistry

Keywords:

RNA
metabolites
Magnesium
Thermodynamics
Nearest neighbor model

File:

Login to Download

Committee Members:

Andrew Patterson, Outside Field Member
Paul Babitzke, Outside Unit & Field Member
Scott Showalter, Major Field Member
Edward O'Brien, Major Field Member
Philip Bevilacqua, Chair & Dissertation Advisor
Philip Bevilacqua, Program Head/Chair

Author:

Douds, Catherine

Title:

Approaches to improve in vivo RNA structure prediction through chemical structure probing

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

RNA
RNA structure
structure probing
E. coli ribosome

File:

Login to Download

Committee Members:

Paul Babitzke, Major Field Member
Sarah Assmann, Outside Field Member
Shaun Mahony, Outside Unit Member
Lu Bai, Major Field Member
Philip Bevilacqua, Chair & Dissertation Advisor
Santhosh Girirajan, Program Head/Chair