An Investigation of Protein-DNA Binding Characteristics by Fluorescence Anisotropy

Nobile, Danna (2015) An Investigation of Protein-DNA Binding Characteristics by Fluorescence Anisotropy. Undergraduate thesis, under the direction of Randy Wadkins from Chemistry and Biochemistry, University of Mississippi.

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Abstract

Recent studies have illustrated the presence of several secondary, non-B DNA structures that are associated with the promoter regions of several oncogenes, such as the intensely studied MYC gene. Two such secondary structures, G-quadruplexes and i-Motifs, have become topics of interest due to their prevalence within oncogenic promoters and their potential accessibility for future drug targeting due to their globular natures. Though fairly extensive research has been conducted to understand different factors affecting G-quadruplex formation and stability, similar studies for i-Motifs, particularly related to thermodynamics, are still evolving. One factor known to contribute to the additional energy required for duplex DNA to transition to its single-stranded form capable of forming i-Motifs is protein-DNA binding. This has been observed using EMSA, providing an estimated equilibrium binding constant. Therefore, other methods should be explored to acquire a truer equilibrium binding constant and determination of the energy contributed by protein binding to i-Motif DNA. This thesis explores the method of fluorescence anisotropy as an alternative way of examining the thermodynamic effects protein-DNA binding has on i-Motif stability by using a sequence within the c-MYC promoter and one domain of a Poly Cytosine Binding Protein. Because of the problems incurred throughout various experimental techniques, however, further studies are needed to explore the usefulness of fluorescence anisotropy with this particular protein and DNA sequence.

Item Type: Thesis (Undergraduate)
Creators: Nobile, Danna
Student's Degree Program(s): B.A. in Biochemistry
Thesis Advisor: Randy Wadkins
Thesis Advisor's Department: Chemistry and Biochemistry
Institution: University of Mississippi
Subjects: Q Science > QD Chemistry
Depositing User: Unnamed user with email dknobile@go.olemiss.edu
Date Deposited: 07 May 2015 20:14
Last Modified: 07 May 2015 20:14
URI: http://thesis.honors.olemiss.edu/id/eprint/403

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