Imaging of oligonucleotide-metal complexes by scanning tunneling microscopy

Abstract

Scanning tunneling microscopy (STM) has been used to image synthetic oligonucleotide duplexes alone or with an intercalatively bound metal complex with submolecular resolution. The sizes of 12 and 24 base pair (bp) oligonucleotides determined from STM images are in agreement with expected values, and images of isolated duplexes resolve the two nucleotide strands of these molecules. 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 Å from the 12-bp duplex end. This new feature corresponds well to the metal binding sites 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 and other macromolecules could serve as useful labels in STM structural studies.