This book describes the author’s work on the development of sequence-specific DNA binders for the therapy of mihondrial diseases. In the first chapter, the author provides a detailed background of pyrrole–imidazole polyamides (PIPs) and mihondrial disease research followed by chapters presenting the author's own research and discoveries. Firstly, the developed compounds called MITO-PIPs, which recognize specific sequences in mihondrial DNA, are presented. The following chapter demonstrates how, by introducing a DNA alkylating reagent into a MITO-PIP that recognizes the adjacent sequence to a target mutation, the copy number of mutated mihondrial DNA was successfully reduced in live cells. Furthermore, because nuclear DNA is another important target for treating mihondrial diseases, the author demonstrated that tri-arginine vectors can enhance nuclear uptake of PIPs and improve their biological activity in cells. This work willattract readers’ interest because it paves the way for a transgene-free chemical gene therapy for mihondrial diseases. The book includes a detailed description of experimental procedures, especially compound synthesis. This description helps readers to have a clear image of the author’s studies and to perform similar and extended studies themselves.