Conformational fluctuations of supercoiled DNA molecules observed in real time with a scanning forcemicroscope

A scanning force microscope operating in a fluid was used to image the dynamics of supercoiled circular DNA molecules adsorbed on mica both under water and buffer. The time scales of the conformational equilibrations of molecules adsorbed on mica are controlled by frictional forces: these are modulated by the strength of adsorption that opposes the molecular mobility. We employ a method that permits the modulation of the adhesion, even to the point of completely immobilizing the molecules on the substrate and afterwards remobilizing them at will, so that their conformational fluctuations can start again. Thismethod was applied to the imaging of the conformational rearrangements that take place in native supercoiled DNA molecules. The motions that were captured in the images could be interpreted in terms of supercoiling tensions that fluctuate locally. © 1998 Springer-Verlag.