Torison dynamics and depolarization of fluorescence of linear macromolecules. II. Fluorescence polarization anisotropy measurements on a clean viral phi 29 DNA.

Abstract

The decay of the fluorescence polarization anisotropy (FPA) of ethidium bromide bound to DNA has been studied over a range of time-spans from 18 ns to 120 ns with the aid of a picosecond dye laser. These FPA data have been fitted to three different functional forms: (1) the single-exponential-decay-plus-baseline employed by Wahl et al.; (2) the Initial Exponential Decay Zone formula of a recently developed rigid-rod and torsion spring model for the torsion dynamics of DNA; (3) the Intermediate Zone formula of that same model. At any fixed experimental time-span the formulas (2) and (3) provide slightly better fits than formula (1), but cannot be distinguished from each other by reduced chi-squared values alone, However, only the Intermediate Zone formula fits the data from all different time-spans with the same set of physical parameters The parameters determined for formulas (1) and (2) vary with the time-span of the experiment in a characteristic manner that can be rationalized in the event that the FPA actually follows the Intermediate Zone curve. The fact that the torsion dynamics for this DNA is well described by the Intermediate Zone formula discounts the possibility of distinct widely spaced torsion joints in such clean DNAs. We are able to provide the first reliable value for the torsional rigidity of DNA, C = 1.29 +/- 0.10 X 10(-19) dyne cm2 in 0.01 M NaCl at 25 degree C.