CALCULATING HYDRODYNAMIC PROPERTIES OF DNA THROUGH A 2ND-ORDER BROWNIAN DYNAMICS ALGORITHM

We describe the application of a second-order Brownian dynamics algorithm (Iniesta, A.; Garcia de la Torre, J. J. Chem. Phys. 1990, 92 (3), 2015) to the calculation of hydrodynamic properties of simple bead-chain models of linear DNA, consisting of 2-17 circular beads of a diameter of 3.184 nm. Hydrodynamic interactions were incorporated using the Rotne-Prager tensor (Rotne, J.; Prager, S. J. Chem. Phys. 1969, 50 (11), 4831). The results of the computations were tested against properties of the model chains that could be calculated from other means, such as end-to-end distance, diffusion coefficient, or rotational relaxation time. Typical trajectory lengths were up to 11.4-mu-s for a 10 subunit (93 base pair) chain, which allowed us to predict the DLS structure factor to a maximum time of 1-2-mu-s. Compared with a first-order algorithm (Ermak, D. L.; McCammon, J. A. J. Chem. Phys. 1978, 69 (4), 1352), the second-order calculation achieves the same accuracy in 4-5 times less CPU time.