Effect of Intermolecular Electrostatic Interactions on the End-over-End Rotational Dynamics of 200-Base-Pair DNAs

Abstract

The self-rotational diffusion coefficients (DR) of 200 bp DNAs were measured by a new transient polarization grating method. Measurements were performed over a range of added ionic strengths from 4 to 47 mM at a DNA concentration of 1.5 g/L, where the prevailing intermolecular electrostatic interactions begin to significantly affect the self-rotational relaxation times (τR ≡ (6DR)-1). With decreasing added ionic strength from 20 to 4 mM, τR is observed to increase by 12% from 3800 to 4260 ns. Abolition of this increase, when the DNA concentration is reduced by 2-fold to 0.75 g/L, demonstrates the intermolecular origin of this phenomenon. The strengths of the intermolecular interactions are characterized by the second virial term, ρB2, where ρ is the DNA rod density and B2 is the second virial coefficient. This second virial term takes the values 0.27, 0.37, 0.46, and 1.53 at respectively 47, 26, 20, and 4 mM added ionic strength. The rise in τR between 20 and 4 mM added ionic strength is associated with a large increase in the second (and third) virial terms that reflects a shift from primarily two-rod to multirod interactions. A theory is formulated for the enhancement of rotational friction via reflected hydrodynamic interactions from the neighbors around a given diffusor. The increase in τR with decreasing added ionic strength from 20 to 4 mM is attributed to increasingly parallel alignment of neighboring rods over this range. Because perpendicular orientations are favored when two-rod interactions dominate the virial series, it is inferred that parallel orientations must be favored by multirod interactions. According to the second virial terms, the rise in τR of the present 200 bp DNA sample on one hand and the decrease in scattered intensity and change in translational dynamics of the 150 bp DNA sample studied by Fulmer et al. on the other appear to occur over similar ranges of corresponding states. These intermolecular structural transitions evidently are not true isotropic to nematic transitions but may correspond to a thwarted transition of that kind.