Honors Theses

Date of Award

Spring 5-8-2022

Document Type

Undergraduate Thesis



First Advisor

Randy Wadkins

Second Advisor

Wayne Gray

Relational Format



Deoxyribonucleic acid (DNA) is the hereditary material in all living organisms. According to the Watson and Crick model, DNA exists as two long strands coiled into a double helix. However, DNA has been found to have the potential to exist in secondary forms known as G-Quadruplexes and i-motifs. I-motifs (intercalated-motif or iM) are formed under acidic conditions when sets of cytosines pair with protonated cytosines and are looped around each other. The pKa value for iMs in dilute solutions is approximately 6.5, but iMs can potentially exist at a higher, physiological pH value under crowded conditions. Within the interior of a cell, a large percentage of total cellular volume is a dense mixture of macromolecules and solutes. A typical environment for an in vitro biochemical experiment is a dilute solution however what is actually present in cells is crowded. To best mimic this “crowding” in an in vitro environment, crowding agents like Ficoll, Polyethylene Glycol (PEG), and Dextran can be used. Over the years, crowding agents have been studied primarily PEG because it is cost-efficient and synthetically made. Dextran is a natural polymer that has been explored little because of the high cost. In this study, Dextran was explored to try and understand if it could be an effective crowding agent in the formation of i-motifs. However, a contaminate was found in some sources of Dextran which became the basis for further studies to determine its cause and solution which became the subject of this thesis. We found that Dextran from Alfa Aesar was highly contaminated with a potential microbe, but Dextran from alternative manufacturers was not.

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