Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)



First Advisor

W. David Wilson, PhD

Second Advisor

David W. Boykin, PhD

Third Advisor

Markus W. Germann, PhD


A common approach to treating many illnesses is through targeting a specific protein. Gene-related illnesses, however, are particularly difficult to treat and targeting the gene with small molecules for drug development is an alternative approach. This is an attractive area because it provides new and potential methods for regulating the expression of diseased-genes. Dicationic diamidines are a class of small molecules which bind in the DNA minor groove where most gene control proteins, such as transcription factors, do not interact. These small molecules can modulate various processes through allosteric interactions and provide therapeutic potential. Typically, these compounds have an inherent selectivity towards sites rich in A∙T base pairs (bps). Many synthetic efforts are used to design diamidines specific to target mixed-site sequences (G∙C-containing) but these efforts remain challenging. To overcome this obstacle, our recognition repertoire must be extended to include G∙C bps and distinguishability among A∙T bp sites. Many biophysical methods can be used to investigate small molecule-DNA interactions and the development of competition mass spectrometry, in particular, has helped do this. Competition electrospray ionization mass spectrometry (ESI-MS) is a powerful, novel screening technique used to identify biomolecular interactions. This method identifies important information such as stoichiometry, relative binding affinity, and cooperativity and can be used for a number of analyses. It is particularly useful when applied as a competition assay to quickly and accurately pinpoint the preferred target site of a compound among many DNA sequences. Our competition ESI-MS methodology has been used to investigate the sequence specific interaction of diamidines with DNA and discover binding sites for synthetic compounds. Combining ESI-MS with other biophysical techniques has successfully identified patterns of recognition and the selectivity of DNA minor groove binding compounds. With this information, we have developed a detailed understanding of the variations in sequences and their effects on compound recognition. This will ultimately lead to more sequence specific, rationally designed compounds with fewer off-target effects.