J. Langowski et al., SOLUTION STRUCTURE AND DYNAMICS OF DNA TOPOISOMERS - DYNAMIC LIGHT-SCATTERING-STUDIES AND MONTE-CARLO SIMULATIONS, Biopolymers, 34(5), 1994, pp. 639-646
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.