We are developing a method of chemical modifications in living cells which will detect non-canonical DNA structures, such as those associated with GAA repeats, responsible for Friedreich’s ataxia, and GATA repeats, known to be unstable in colon cancer cells and a FoxE1 region, which was hypothesized to be involved in evolution. This research will shed light on the mechanism of their instability, which may be important for treatment development and understanding of disease evolution.