Diffusional spinning as a probe of DNA fragments conformation

The dependence of the spinning diffusion coefficient of a wormlike chain upon contour length L, persistence length P, and radius R is shown here to follow a ''Lorentzian'' law of width Gamma vs sigma(beta)L/R, where sigma(beta)(2)=l(0)/P is the variance of the bending angles distribution of Monte Carlo simulated chains with bond length l(0). This description is equivalent to that of a spinning cylinder of length L and effective radius R(eff)=R(L,P), with R(eff)greater than or equal to R. When considering experimental data it is found that fluorescence polarization anisotropy (FPA), a technique very sensitive to spinning, also yields apparent DNA radii depending upon fragment length. In order to derive DNA parameters which are independent of fragment length, we introduce a procedure for fitting FPA data which takes into account thermal distortions and employs the parametric expressions for rigid body rotations, spinning and tumbling, depending only upon L, P, and the actual DNA radius, R. Then the apparent persistence length P can be estimated once a value of R is assumed together with the value of the dynamic persistence length, the latter affecting the internal bending motions of the fragments. Fitting the FPA data is easily accomplished with the value of R=10 Angstrom as suggested by a number of recent measurements. (C) 1996 American Institute of Physics.