Undergraduate Honors Theses

Thesis Defended

Spring 2017

Document Type


Type of Thesis

Departmental Honors



First Advisor

Robert Kuchta

Second Advisor

Bob Garcea

Third Advisor

Joe Falke


The binding of streptavidin to biotin is one of the strongest non-covalent interactions observed in nature. However, we have observed that streptavidin rapidly dissociates from biotinylated double stranded DNA in the presence of free biotin. In contrast, streptavidin does not rapidly dissociate from single stranded biotinylated DNA under identical conditions. Due to the ubiquitous exploitation of the streptavidin-biotin system in the laboratory, we investigated this phenomenon in greater detail. To study the dissociation of streptavidin from biotinylated DNA, we used fluorescence polarization and electrophoretic mobility shift assays. We found that the binding of streptavidin to double stranded DNA can be stabilized by one or more mismatches across from the biotinylated site. Moreover, molecular modeling of the interaction suggests that steric and electrostatic effects may play a role in catalyzing streptavidin dissociation. We propose that the weaker interaction between streptavidin and double stranded DNA is stabilized by mismatches because they make the DNA more locally fluid, and thus allow the DNA to adopt a more sterically and electrostatically favorable orientation in relation to streptavidin. More investigation is necessary to validate these speculations, but, regardless, these findings are valuable to the scientific community.

Included in

Biochemistry Commons