Copper(II) ion-bound CysGly dipeptides linked by an azobenzene derivative were photoisomerized between the trans and cis forms. The two copper(II) ion centers were positioned close to each other in the cis form, whereas they were far away from each other in the trans form. The copper complex in the cis form exhibited DNA cleavage activity, whereas the activity in the trans form was negligible. The DNA cleavage activity of the cis form is attributed to the cooperation of the closely located copper(II) centers. The present results show the photocontrol of the cooperation of metal ions for DNA cleavage.