Scanning tunneling microscopy imaging of synthetic oligonucleotides and oligonucleotide-metal complexes

Scanning tunneling microscopy (STM) has been used to image 12- and 24-base pair (bp) synthetic oligonucleotide duplexes alone or with intercalatively-bound metal complexes with submolecular resolution. The sizes of the 12- and 24-bp oligonucleotides determined from STM images are close to expected values, and images of isolated duplexes resolve the two nucleotide strands of these molecules. The variation of duplex size in our images demonstrates that these features are not due to surface artifacts. In addition, images of the 12-bp duplex in the presence of bis(9,10-phenanthrenequinone diimine)(2,2'-bipyridyl)rhodium(III) exhibit a new structural feature at 14 +/- 2 A from the duplex ends. This new feature corresponds well to the metal binding site determined from DNA cleavage and molecular modeling studies. These results indicate that STM can be used to image directly transition metal complexes bound to DNA, and thus suggest that metal complexes bound specifically to biological molecules could serve as labels in STM structural studies.