We used the scanning tunneling microscope (STM) to examine single-stranded deoxyribonucleic acid (DNA) oligomers deposited on a metal surface. Because STM can be used to study the electrical properties of materials via the tunneling spectra, we used it to visualize DNA oligomers at the single molecule resolution. The 5'-hexachloro-fluorescein phosphoramidite (HEX)-labeled oligomers (sequence, AGCTTC) were observed on an atomically flat Cu(111) surface. At large tip-sample distances at large set-point biases, the lowest unoccupied molecular orbit (LUMO) peak of the empty state can be observed for the dye molecules on the tunneling spectra. When this distance becomes small, similar spectra as for the Cu substrate were observed for the dye molecule on the LUMO-related peak. Cu gave peaks at small bias voltages in the filled state. From comparison of these peaks on each subunit of the molecules, the measured values of dI/dVon HEX were smaller to those on Cu because of the large size of the HEX molecule, but the normalized values of dI/dV/(I/V) were apparently equal. We believe that the tunneling current is able to pass through the HEX molecules to the Cu substrate, thus reflecting the density of the Cu(111) surface. Molecular size therefore affects the intensity of dI/dV LUMO-related peaks sometimes cannot be observed for HEX because of conformational differences, but Cu peaks can almost always be observed for HEX molecules. These peaks for the counter ions are almost the same as those for the Cu substrate. Thus, tunneling spectra can assist in the molecular mapping of DNA. (c) 2005 Elsevier B.V. All rights reserved.