Modeling dynamic light scattering of supercoiled DNA

A new computational scheme, based on the Brownian dynamics and Monte Carlo techniques, was used to calculate the dynamic structure factor of supercoil ed SV40 DNA (5243 base pairs) in 0.1 M sodium chloride solution. All model parameters are known independently, and none are fitted. The results are in good agreement with earlier dynamic light scattering measurements. The cal culated dynamic structure factor, as a function of time, could be very well approximated by a simple analytical formula. The analysis of the experimen tal data based on this formula allows one to obtain the distribution functi on for relaxation times of intramolecular motions, if additional informatio n about the DNA structure is available from Monte Carlo simulations. The ra nge of relaxation times for supercoiled SV40 DNA comprises approximately 2 orders of magnitude, with the upper boundary exceeding 1 ms.