Abstract
Atomic force microscopy (AFM) has been used to view DNA shape, condensation, and protein binding at the nanometer scale. Intercalators, such as ethidium bromide and octahedral ruthenium complexes, induce changes in the superhelical shape of DNA, producing an extension, unwinding, and stiffening of the DNA helix. A few groups have demonstrated supercoiled characteristics using air and liquid AFM studies of pBR322 with ethidium bromide, but no one has yet studied the effect of intercalating octahedral metal complexes on DNA by AFM. Studies of the plasmid DNA, pBR322, will be conducted using TappingMode AFM in both air and liquid to observe these transformations, which are caused by the untwisting of base pairs and helical backbone needed to accommodate the intercalator between the DNA base pairs. We will investigate the structural transitions in the plasmid DNA in response to Ru<sup>+2</sup> intercalation. Currently, studies are in progress to determine a diverse set of images with and without the Ru<sup>2+</sup> intercalator, to determine what tertiary structures are formed, and whether this complex does indeed intercalate into DNA.
