Rotational dynamics of curved DNA fragments studied by fluorescence polarization anisotropy

The rotational dynamics of short DNA fragments with or without intrinsic cu rvature were studied using time-resolved phase fluorimetry of intercalated ethidium with detection of the anisotropy. Parameters determined were the s pinning diffusion coefficient of the DNA fragments about the long axis and the zero-time ethidium fluorescence anisotropy. We find a significant decre ase in the spinning diffusion coefficient for all curved fragments compared to the straight controls. This decrease is likewise evident in rotational diffusion coefficients computed from DNA structures obtained by a curvature prediction program for these sequences. Using: a hinged-cylinder model, we can identify the change in rotational diffusion coefficient with a permane nt bend of 13-16 degrees per helix turn for the sequences studied. Moreover , for some of the curved fragments an increased flexibility has to be assum ed in addition to the permanent bend in order to explain the data.