DNA i-motif Stabilization by Ligand Binding to Loop Regions

Davis, Harrison Reed (2015) DNA i-motif Stabilization by Ligand Binding to Loop Regions. Undergraduate thesis, under the direction of Randy Wadkins from Chemistry and Biochemistry, The University of Mississippi.

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Abstract

DNA i-motifs are a secondary structure of DNA that can be useful in a variety of ways, but this experiment investigates the maximum potential to stabilize i-motifs artificially with a small molecule binding to loop regions. DNA with different position and number of loops was tested to see to what extent the i-motif could be stabilized . A drug, Actinomycin D, was used for its known high affinity for a particular DNA sequence, which we used to make the loops of the i-motif. The binding constant for the drug to the DNA was determined through fluorescense spectroscopy while the presence of the i-motif structure was confirmed using Circular Dichroism spectra. The resulting dissociation constants showed that AMD had a higher affinity for the DNA strands when in the i-motif conformation at pH 5.4. The small molecule had the greatest binding constant when more than one binding site was present except in the case of L13HP due to steric hindrance by the nature of the i-motif structure.

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