DNA double helices with positive electric dichroism and permanent dipole moments: Non-symmetric charge distributions and “frozen” configurations

Abstract

The stationary electric dichroism of DNA restriction fragments with chain lengths of 399, 587 and 859 base pairs (bp) is shown to be positive at low electric field strengths in the range up to about 1 kV/cm; the dichroism is changed to values with the usual negative sign at higher electric field strengths. A positive dichroism at low field strengths has been observed in buffers with Na +-cations of various ionic strengths from 1 to 11 m M. Experiments with reversal of the electric field vector indicate that the alignment is induced by a permanent electric moment at low field strengths; when the field strength is increased, the contribution from an induced dipole moment increases and becomes dominant at high field strengths. Thus, the permanent dipole mechanism is prevailing in the range with positive values of the dichroism found at low electric fields, whereas the induced dipole mechanism is dominant in the range with negative values of the stationary dichroism found at high electric fields. In contrast to these results obtained in buffers containing only monovalent ions, the electric dichroism is negative in the whole accessible range of electric field strengths, when the buffer contained 100 μ M Mg 2+. The stationary values of the dichroism are negative under all tested conditions of buffer concentrations and electric field strengths for DNA double helices with 95, 179, 256, 4361 and 48502 bp. The positive dichroism found in the intermediate range of chain lengths is reduced and finally changed to the standard negative dichroism by UV irradiation. Positive values of the linear dichroism are predicted by Monte Carlo simulations for ensembles of wormlike chains with the charge density and optical parameters of DNA double helices, when the polarizability along the chain axis is negligible and when the internal mobility is frozen. The positive dichroism is due to the fact that virtually all DNA fragments are bent by thermal agitation; most of these bent DNA's are asymmetric and, thus, are associated with permanent dipole moments; the majority of dipole vectors in a given range of chain lengths is perpendicular to the end-to-end vector and, thus, leads to positive values of the linear dichroism at low degrees of bending. The model predicts a chain length dependence consistent with the experimental one due to a superposition of chain length dependences of the dipole moment and of the dichroism. The change from positive to negative values of the linear dichroism at increasing field strengths suggests some increase of the polarizability with the field strength, but may also be partly due to field induced stretching. The absence of the special effect in the presence of Mg 2+ indicates a particularly high compensation of the phosphate charges by this ion. The time constants of electrooptical rise curves observed in the range with the positive stationary dichroism are rather close to those of the decay curves. It is shown by Brownian dynamics simulations that this result is consistent with the existence of a permanent dipole moment. The deviation from the standard expected for permanent dipoles is due to the fact that in the present case the dipole vectors are mainly perpendicular to the long axis of the molecules. The decrease of the positive dichroism by UV irradiation is consistent with the interpretation of the data by a frozen ensemble of configurations and indicates that photoproducts introduce flexible joints into the DNA chains.