Direct observation of the reversible unwinding of a single DNA molecule caused by the intercalation of ethidium bromide

Nucleic Acids Res. 2007;35(19):e125. doi: 10.1093/nar/gkm529. Epub 2007 Sep 28.


Ethidium bromide (EtBr) is the conventional intercalator for visualizing DNA. Previous studies suggested that EtBr lengthens and unwinds double-stranded DNA (dsDNA). However, no one has observed the unwinding of a single dsDNA molecule during intercalation. We developed a simple method to observe the twisting motions of a single dsDNA molecule under an optical microscope. A short dsDNA was attached to a glass surface of a flow chamber at one end and to a doublet bead as a rotation marker at the other end. After the addition and removal of EtBr, the bead revolved in opposite directions that corresponded to the unwinding and rewinding of a dsDNA, respectively. The amount of intercalating EtBr was estimated from the revolutions of the bead. EtBr occupied 57% of base pairs on a single dsDNA at 1 mM of EtBr, indicating that EtBr molecules could bind at contiguous sites to each other. The isotherm of intercalation showed that negative cooperativity existed between adjoining EtBr molecules. The association constant of EtBr and dsDNA (1.9 (+/-0.1) x 10(5) M(-1)) was consistent with that of previous results. Our system is useful to investigate the twisting of a single dsDNA interacting with various chemicals and biomolecules.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry*
  • Ethidium / chemistry*
  • Intercalating Agents / chemistry*
  • Kinetics
  • Microscopy
  • Nanospheres
  • Nucleic Acid Conformation
  • Rotation
  • Torque


  • Intercalating Agents
  • DNA
  • Ethidium