Date of Award

Spring 5-2014

Degree Type

Honors College Thesis


Chemistry and Biochemistry

First Advisor

Anthony Bell

Advisor Department

Chemistry and Biochemistry


The short-term goal of this research project is to employ small molecules as a means to stabilize four-way DNA junctions (4WJs) composed of natural DNA and chimeric nucleic acids. The long-term goal of the project is utilizing the 4WJs as extracellular therapeutic inhibitors of DNA binding proteins [i.e. Histones and High Mobility Group Protein B (HMGB1b)]. A number of studies have shown that classical intracellular DNA-binding proteins have a variety of deleterious side-effects when present in the extracellular milieu. In order to develop a successful 4WJ therapeutic, we are focused on using modified nucleic acids to enhance the stability of the resulting 4WJ. The nucleic acid of interest is PNA (peptide nucleic acid). PNA was selected because it is known to form DNA-PNA duplex/triplex structures with elevated thermo- and nuclease stability. 4WJs are prepared using fluorescently labeled DNA strands and a single PNA strand. Small molecules are currently being investigated as tools to potentially link the PNA-DNA strands to form 4WJs composed of multiple PNA strands. One molecule of interest is [Ru(bpy)2(dpp)PtCl2]Cl2. Electrophoretic mobility shift assays (EMSAs) have shown that stable 4WJs form in the presence of this molecule. The junctions were visualized using polyacrylamide gels. Circular dichroism studies will be employed to characterize the structural properties of hybrid of interest. Once a stable 4WJ structure is identified, the hybrid was used to study binding and inhibition of HMGB1 in cell-based assays.