In an aqueous solution, ultrasonic irradiation is known to produce hydrogen peroxide which oxidizes thiols to disulfides. By utilizing the reaction, we designed novel functional molecules with ultrasound-induced structural changes. Two functional molecules, 1 and 2, were prepared by introducing alkyl thiol moieties into diaminoacridine and diaminopyridine, which were known as DNA intercalators. [chemical formula][chemical formula] By ultrasonic irradiation for several hours under alkaline condition, linear functional molecules were converted into cyclic ones with intramolecular disulfide bond. Such structural changes were confirmed by ^1H-NMR method. Chemical shifts of α-protons to thiol groups shifted to downfield and multiplicity changed from double doublet to triplet. These functional molecules have the potential for cancer treatment. After intercalation into DNA and successive ultrasonic irradiation, functional molecules can be expected to form irreversible complexes, which may cause damages on DNA duplication.