Graduation Year

Spring 2012

Document Type

Open Access Senior Thesis

Degree Name

Bachelor of Arts



Second Department


Reader 1

Mary Hatcher-Skeers

Reader 2

Kathleen Purvis-Roberts

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Terms of Use for work posted in Scholarship@Claremont.

Rights Information

© 2012 Kelly A. Garton


The Cre sequence (ACGT) is a site responsible for the binding of specific transcription factors that determine the activation of genes. Due to its major role in gene transcription, it has become a subject of immense research. The binding of transcription factors to the Cre binding site has been determined to be dependent on DNA conformation. In this study, the effects of flanking sequence around the Cre binding site on the conformation and the dynamics of DNA were investigated. The Cre binding site was studied in its native form with differing flanking sequences to determine the BI/BII profile (conformation) and the magnitude of the energy transition barrier (dynamics) between the BI and BII conformations of each phosphate step of the following three dodecamer sequences: CreACAG, CreGGAG, and CreTATA. In order to obtain the BI/BII profile of each phosphate step, 2D 31P-NMR NOESY and HSQC experiments at various temperatures were utilized. Based of the basic principles of kinetics, the lower the energy barrier between the two conformations, the easier the transition between the BI and BII conformation. Therefore, it was hypothesized that low and high %BII character lead to a large energy barrier (high ∆G values), whereas average %BII character leads to a small energy barrier (low ∆G values). The results of the 2D 31P-NMR experiments of the three dodecamer sequences confirmed this relationship between the %BII character and the magnitude of the energy barrier (∆G). However, further conformation and dynamics studies must be conducted to further understand the correlation.