Properties of a Fluorescent Deoxycytidine Analog in i-Motif Dna

Wingate, Sara E. (2015) Properties of a Fluorescent Deoxycytidine Analog in i-Motif Dna. Undergraduate thesis, under the direction of Randy Wadkins from Chemistry and Biochemistry, The University of Mississippi.

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Abstract

Experiments to determine fluorescence lifetimes and fluorescence quenching constants were performed using oligonucleotides of DNA containing PdC, a fluorescent analog of cytidine, at five different locations in the i-motif. My experiments were chosen in order to better understand the structural characteristics of i-motif DNA, which are thought to have biological importance in cancer and drug delivery. Fluorescent lifetime experiments were carried out using an ISS K2 fluorescence instrument with a modulated LED light source in order to determine if the cytidine bases in DNA replaced by PdC were paired or unpaired in the i-motif structure. The resulting data allowed us to relate the degree of quenching present at a position to its location in the i-motif. For example, the central paired locations in the i-motif stem were quenched the most. My research, along with other research performed by members of the Wadkins research team, allowed for a determination of the folding pathway of an i-motif structure. Further research into this folding pathway could determine specific intermediates in the folding structure of i-motifs; researchers might then be able to target the intermediates of folding and stop i-motif formation, thereby preventing cancer growth.

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