Capture of a Transition State Using Molecular Dynamics: Creation of an Intercalation Site in dsDNA with Ethidium Cation
Figure 1
Three snapshots along the dynamics simulation movie, found at http://www.youtube.com/watch?v=ItSyPPH4T8g. (a) Initial placement of ethidium ligand with respect to the dsDNA decamer, (b) image captured as ethidium rotated and the base pairs began to rupture their directed hydrogen bonds, (c) the final, intercalated state. The movie and these graphics were produced from the original dynamics data by Dr. Michael Dolan.
