Examination of Groove Binding and Intercalation into DNA by Atomic Force Microscopy

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 induce changes in the superhelical shape of DNA, producing an extension, unwinding, and stiffening of the DNA helix. Groove-binding agents induce little change in the length or shape of DNA in solution; however, on a surface, these same cations can cause condensation of the DNA. We have used Tapping Mode AFM to examine the binding of a family of Ru²⁺ octahedral metal complexes to DNA. Based on solution measurements, some of these complexes are proposed to intercalate, others bind to the groove of DNA via electrostatics, and still others have multiple binding modes. By measuring the length, height, and shape of hundreds of plasmid molecules at a variety of Ru²⁺ concentrations, we have observed that the nature of the metal ligands affects the mode of DNA binding, and have found that the metal complex-DNA interactions at a surface can be more complex than those in solution.