Document Type



Doctor of Philosophy


Chemistry, Biochemistry

Date of Defense


Graduate Advisor

Dr. Cynthia M. Dupureur


Dr. Michael R. Nichols

Dr. James K. Bashkin

Dr. Chung F. Wong


Human papillomavirus (HPV) is a common sexually transmitted virus responsible for cervical cancers, and its infection is currently incurable. Only a few vaccines against high-risk HPV strains are available. Hairpin polyamides (PAs) in different sizes (8-20 units long) bind DNA in different lengths. They have been shown to have different anti-HPV activities in cell culture.

The interaction between PA and DNA is stabilized by two types of molecular forces: attractive and repulsive forces. Attractive forces include hydrogen bonds, van der Waals contacts and electrostatic forces between PA and DNA. Repulsive forces include the hydrophobic effect, which forces the PA out of the solvent into the DNA minor groove. These forces contribute to the enthalpy change (ΔH) and the entropy change (ΔS) differently. Analyzing how different forces contribute to a PA-DNA interaction provides a way to characterize the binding mode of that PA.

To understand this molecular interaction, van’t Hoff analysis was performed: binding affinities of different sized PAs towards DNA were measured using a fluorescence assay with different perturbations (temperatures, salt concentration, etc.). We have observed that binding affinities of PA-DNA interactions are not sensitive to salt, which indicates that electrostatic forces do not contribute significantly to these interactions.

Binding affinities at different temperatures were analyzed to determine which binding forces dominates. The results indicate that the hydrophobic effect contributes significantly to large PA-DNA interactions. This contrasts with small PAs, the DNA binding of which, are dominated by hydrogen bonds.

Binding between small PAs and different DNA sequences has been observed to have different binding driving forces. And how large PAs behave is unknown. The hypothesis is that different DNA sequence patterns (e.g., ATAT vs. TTTT) have different degrees of hydration. Thus, in the bound state, PAs displaced different amount of water to provide different ΔS upon binding. Our results confirm the hypothesis. As d(TT) pattern is more hydrated than d(AT) pattern, the PA-d(TT) interaction has a more favorable ΔS than the PA-d(AT) interaction.

These studies are conducive to understanding the binding mode of different PAs. They could also provide valuable information for the optimization and development of new PAs.