BROWNIAN DYNAMICS SIMULATIONS OF WORMLIKE CHAINS - DYNAMIC LIGHT-SCATTERING FROM A 2311 BASE PAIR DNA FRAGMENT

The technique of Brownian dynamics simulation is used to study dynamic light scattering (DLS) from a linear 2311-bp fragment of DNA. A variety of different semistiff models are considered, and the simulation results are compared with actual experiments (Sorlie, S.; Pecora, R. Macromolecules 1988, 21, 1437). The parameters of the model are chosen subject to the constraints that the overall translational diffusion constant (D0) and mean-square radius of gyration ({S2}) match experimental values. Time correlation functions are analyzed by contin, which constructs the distribution of relaxation times, and by cumulant and average lifetime methods. At q2 = 2.684 × 1010 cm−2, contin analysis of simulations on 10 subunit chains with hydrodynamic interaction (HI) included is in better agreement with experiment than the corresponding free draining models. For the ensemble sizes employed in the simulations (300 trajectories), there is some uncertainty in the faster decay portion of the lifetime distribution. In the scattering vector range 4 × 1010 < q2 < 1011 cm−2, the contin analysis of models with sufficient stiffness to give the requisite 〈S2〉and D0 with HI give DLS results that are not very different from the Gaussian coil model with no HI and stiffness added indirectly via the 〈S2〉and D0 constraints. At higher values of the scattering vector, cumulant analysis is able to discriminate between models with different amounts of stiffness and the same 〈S2〉and D0. For stiff/flexible models there exists an intermediate range of scattering vector in which the first cumulant varies as q3/q4 for chains with and without intersubunit HI. DLS appears to be insensitive to the number of subunits in models that are subjected to similar constraints provided q < 5.0(b2)1/2 where 〈b2〉 is the mean-square intersubunit separation. © 1990, American Chemical Society. All rights reserved.