Diamidines are compounds with antiparasitic properties that target the minor groove of DNA. The mechanism of action of these compounds is unknown, but topological changes to DNA structure are a possibility. In this study, we have developed a polyacrylamide gel based screening method to determine topological effects of diamidines on four target sequences: AAAAA, TTTAA, AAATT, and ATATA. The changes caused are sequence dependent, but generally the effect on AAAAA and AAATT is the same while the effect on TTTAA and ATATA is the same. A few compounds show interesting sequence dependent topological effects in the polyacrylamide screening method that could be caused by the compound forming a dimer. Mass spectrometry is used to determine the stoichiometry of DNA-compound complexes. Once compounds show topological effects in the screening method, a bent fragment of kinetoplast DNA is isolated to determine if the same effects occur with DNA from a parasite.