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 c oefficient and internal motions of narrow topoisomer distributions of pUC18 DNA (2687 base pairs) as a function of linking number. The topoi somer distributions were prepared by C-18 reversed phase high performa nce liquid chromatography separation of topoisomerase I/ethidium-gener ated topoisomer families. The measured diffusion coefficients agree we ll with those predicted by a Monte Carlo model for the generation of e quilibrium 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 independent ly from other techniques. Two different values for the torsional rigid ity, alpha = 4.10(-12) and 8.8.10(-12) dyn cm, were used. Intrachain i nteractions in the DNA were taken into account by using an ''effective DNA radius,'' which was varied between r(DNA) = 1-8 nm. The best agre ement between the measured and calculated values was obtained for alph a = 4.10(-12) dyn cm, r(DNA) = 4 nm. The internal motions of the DNA t opoisomers were characterized by the amplitude of the fast relaxation of the DLS autocorrelation function. Our earlier result that supercoil ing leads to a decrease in the amplitude of internal motion was confir med. In addition, we see a characteristic maximum-of the internal moti on amplitude at a superhelix density of sigma = -0.03. The maximum occ urs in the same range as a structural transition in pUC8 dimers previo usly described by L. Song et al. (1990 J. Mol. Biol. 214, 307-326). (C ) 1994 John Wiley and Sons, Inc.