Date of Award

Spring 2014

First Advisor

Dr. Chrystal Bruce


Biologically relevant short sequences of DNA have previously been shown to possess high affinity and specificity for binding of small polyamide structures to their minor groove. These structures, or minor groove binders, have the potential to control access to specific regulatory regions of DNA. Before modeling the binding of these polyamides to the DNA, the small segments of DNA must be characterized for better understanding of the impact the minor groove binder will have on the structure of the DNA. The method for such a characterization is a molecular dynamics computer simulation including the solvent effects for a length of 50 ns. The three DNA segments to be characterized include 5’-ATGCAA-3’, 5’-TAGCTA-3’, and 5’-TACGAT-3’. All three segments were characterized by the slide, twist, and roll helical parameters, the zeta-epsilon backbone angles, and the alpha-gamma backbone angles. The results of the characterization indicate that the molecular dynamics simulation was stable and successful.

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Biology Commons