Resonance energy transfer between ethidium bromide molecules bound to nucleic acids: Does intercalation wind or unwind the DNA helix?

Abstract

The computer simulation of energy transfer between ethidium bromide molecules bound to DNA allows the calculation of the theoretical depolarization of the fluorescence emitted by ethidium. Since the energy transfer is very dependent on orientation, the angle between two ethidium molecules and, therefore, the local change in the winding angle of the DNA helix caused by intercalation, can be determined. We infer that the DNA helix is wound by 13 ° ± 4 °, and not unwound, as previously assumed, after the intercalation of one ethidium bromide molecule. This unexpected result contradicts the conclusions derived previously from physical-chemical studies of closed circular DNA in solution, but agrees with X-ray diffraction results. A critical re-examination of the experiments in agreement and in disagreement with this result are presented. A new molecular model for intercalation is presented. It would follow from this work that the tertiary turns in natural closed circular DNA are positive.