Atomic force microscopy studies of intercalation-induced changes in plasmid DNA tertiary structure

Structural transitions in the tertiary structure of plasmid DNA have been i nvestigated using atomic force microscopy. Changes in superhelical stress w ere induced by ethidium bromide intercalation, and conformational effects m onitored by recording topographic images from DNA complexes of various ethi dium bromide : base pair stoichiometry. Significant changes in the tertiary structure of individual DNA molecules were observed with increasing ethidi um bromide concentration. The first distinct conformational transition was from a predominantly relaxed structure to one consisting solely of toroidal supercoils. A further increase in ethidium bromide concentration resulted in the formation of regions of plectonemic supercoiling. The ratio of plect onemic : toroidal supercoiling gradually increased until an extremely tight ly interwound structure of solely plectonemic supercoiling was finally adop ted. The toroidal form of supercoiling observed in this study is unusual as both atomic force microscopy and electron microscopy techniques have previ ously shown that plectonemic supercoiling is the predominant form adopted b y plasmid DNA.