We describe adsorption and identification of the binding sites of [Ru(NH3)(6)](3+) (RuHex) molecules in a closely packed monolayer of a 13-base ss-DNA on Au(111) electrodes by electrochemical in situ scanning tunneling microscopy (STM), cyclic voltammetry and interfacial capacitance data. In situ STM at single-molecule resolution shows that RuHex adsorbs only at the domain borders and near defects. Together with the electrochemical data that show a negative redox potential shift for RuHex adsorbed to DNA strands, this strongly suggests that RuHex binds only to the exposed phosphate groups in the DNA backbone.