Solution structure and dynamics of DNA topoisomers: Dynamic light scattering studies and Monte Carlo simulations

Using dynamic light scattering (DLS), we have measured the diffusion coefficient and internal motions of narrow topoisomer distributions of pUCl8 DNA (2687 base pairs) as a function of linking number. The topoisomer distributions were prepared by C-18 reversed phase high performance liquid chromatography separation of topoisomerase I/ethidium-generated topoisomer families. The measured diffusion coefficients agree well with those predicted by a Monte Carlo model for the generation of equilibrium ensembles of DNA topoisomers of defined linking number. The only parameters used in the model were the bending persistence length, torsional rigidity, and hydrodynamic radius of DNA known independently from other techniques. Two different values for the torsional rigidity, α = 4 · 10−12 and 8.8 · 10−12 dyn cm, were used. Intrachain interactions in the DNA were taken into account by using an “effective DNA radius,” which was varied between rDNA = 1–8 nm. The best agreement between the measured and calculated values was obtained for α = 4 · 10−12 dyn cm, rDNA = 4 nm. The internal motions of the DNA topoisomers were characterized by the amplitude of the fast relaxation of the DLS autocorrelation function. Our earlier result that supercoiling leads to a decrease in the amplitude of internal motion was confirmed. In addition, we see a characteristic maximum of the internal motion amplitude at a superhelix density of σ = −0.03. The maximum occurs in the same range as a structural transition in pUC8 dimers previously described by L. Song et al. (1990 J. Mol. Biol. 214, 307–326). © 1994 John Wiley & Sons, Inc.