Electric dichroism transients of aqueous solutions of DNA

Abstract

In this work we develop a theory of reduced electric linear dichroism transients of DNA fragments in aqueous solution. The DNA fragments are modelled as rigid 'bent-rod molecules' (BRM) with the following physical parameters: electric charge, electric polarizability tensors and hydrodynamical ones, and the average transition probability tensor per molecule. In order to study the growth and decay of electric dichroism transients, the orientational distribution function of the molecules is needed. This function is obtained by solving the time-dependent Fokker-Planck equation in the presence of a low electric field E, using a perturbation method and the Fourier method with time-dependent coefficients. In our calculations the origin of the coordinate system is the mass centre of the BRM. With respect to this centre, the electric dipole moment of the molecule is zero. The developed theory adequately explains the experimental results. We show that the theoretical approach used in this work is equivalent to the one applied in the Brownian dynamics simulation work performed by Porschke and co-workers. We also analyse the effect of a possible electric dipole moment on the transients of the reduced electric linear dichroism in DNA bent fragments.

Electric linear dichroism transients of bent DNA fragments

“…The combination of both contributions results in the curve of Figure 2. In Figure 3 we can see that curves calculated with the MDF and those analytic curves reported by Bertolotto et al 13 are in agreement. Figure 4 shows the different contributions to RELD for an arc with the same parameters used in Figure 3 in presence of an electric field with strength equal to 60 kV/cm.…”

“…Figure 2 shows the RELD curves versus time obtained for BRM with bending angle 116 o and an electric field strength E = 2 kV/cm. Figure 2 also shows the RELD curves calculated through approximate analytic results reported by Bertolotto et al 13 valid in the limit of low electric field strength (up to 2 kV/cm, approximately). Both calculations are in satisfactory agreement.…”

“…The molecular parameters here used are the same implemented by Bertolotto et al 13 in a previous work. The principal elements of electric polarizability tensor are α E x x = 7.311 × 10 −33 Fm 2 , α E y y = 5.341 × 10 −33 Fm 2 , and α E z z = 2.397 × 10 −32 Fm 2 .…”

“…One of them is due to the interaction between the induce dipole moment and the electric field and the other is owned to the hydrodynamic coupling between the translational and rotational movements. 13 Always positive curves represent the contribution owned to hydrodynamic coupling and always negative curves those owned to polarization. The middle curves correspond to both contributions together.…”

“…Nowadays, the influence of hydrodynamic coupling on the electro-optical effects (electric birefringence and dichroism) of DNA fragments has been studied through Brownian dynamic simulation [3][4][5] and theoretical methods. [6][7][8][9][10][11][12][13][14][15] Theoretical analytic results have been reported only for the limit of low electric field strength because the study of the orientational process induced by electric field has mathematical difficulties. Simulation studies early made are applied for arbitrary electric field strength but they have a disadvantage; they require computer simulations that are too extensive.…”