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Abstract

The effect of hydrodynamic coupling on the spatial orientation of rigid bent rods in electric fields has been analyzed by Brownian dynamics simulations. Bead models for smoothly bent rods were constructed with dimensions of DNA double helices, and established simulation procedures were used to calculate their diffusion tensor, including the translational-rotational coupling tensor. The electric and optical parameters were assigned on the basis of known properties of double helices. Brownian dynamics simulations of the orientation of these models in electric fields showed that both transients and amplitudes of the calculated dichroism are very strongly dependent on translational-rotational coupling over a wide range of electric field strengths. For example, the stationary dichroism of a smoothly bent 179 bp DNA fragment calculated at low field strengths is positive in the presence and negative in the absence of hydrodynamic coupling. The transients are converted from a biphasic to a monophasic shape, when hydrodynamic coupling is turned off. The large changes resulting from hydrodynamic coupling were controlled by calculations based on analytical expressions derived for electrooptical response curves in the limit of low electric field strengths; the results obtained by this independent approach are in very satisfactory agreement with our Brownian dynamics simulations. The effect is strongly dependent on the electric dipole and on its direction. In the absence of any dipole the coupling effect was not observed. The coupling effect increases with the size of the bent rods. Because most macromolecular structures are known to have induced and/or permanent dipole moments, large effects of hydrodynamic coupling on both the amplitudes and the transients of the electric dichroism/birefringence must be expected in general for structures with nonsymmetric shape.