YM155 (Sepantronium bromide) has been evaluated in clinical trials as a survivin suppressant but despite positive signals from early work later studies were negative. Clarifying the mechanism of action of YM155 is important to its further development. YM155 affects cells in a cell cycle specific manner. When cells are in G1, YM155 prevented their progression through S phase, leaving the cells at G1/S when exposed to YM155. Passage through mitosis from G2 is also defective following YM155 exposure. In this study, YM155 did not behave like a typical DNA intercalator in viscosity, circular dichroism (CD) and absorption spectroscopies studies. Additionally, molecular modeling experiments ruled out YM155 DNA interaction to produce DNA intercalation. We demonstrate that YM155 inhibited Top 2α decatenation and Top 1-mediated cleavage of DNA, suggesting that YM155 inhibits the enzyme function. Consistent with these findings, DNA double strand break repair was also inhibited by YM155.