Monomer dynamics in single- and double-stranded DNA coils

Abstract

In our paper (Tothova et al., Czech. J. Phys. 55, 221 (2005)), the first observation of the kinetics of individual polymer monomers using the fluorescence correlation technique (R. Shusterman et al., Phys. Rev. Lett. 92, 048303 (2004)) has been interpreted within the bead-spring theory. Optimizing the joint Rouse-Zimm model to the experimental data, the phenomenological parameters for the statistical-mechanical description of the universal behavior of double- and single-stranded DNA and the dominant types of their dynamics have been determined. Recently, these data have been corrected (R. Shusterman et al., Phys. Rev. Lett. 98, 029901 (2007)). In the present work, the fits of the theory to the new data are given. The main conclusions of our preceding paper remain unchanged but some of the polymer parameters have changed. The new data allow a significantly better agreement with the theory than the previous ones. Our calculations confirm that dsDNA follows mainly the classical Zimm-type kinetics rather than the Rouse one as it was proposed by Shusterman et al. Single-stranded DNA also behaves predominantly as the Zimm polymer. To support these conclusions, we analyze the draining effects on the monomer dynamics and the applicability of simple "universal" laws, according to which the monomer mean square displacement scales with the time as t 1/2 and t 2/3 for the Rouse and Zimm polymers, respectively.

A Bead-Spring Model and Mean Field Theory Based Re-Calculation Reveals Uncertainty of Rouse-Type Dna Dynamics in Dilute Solution

“…This seems to be a combined dynamics of Rouse-and Zimm-type which can be explained by the so called RouseÀZimm model. 10 But the results we get are rather di®erent with that of Tothova et al 10,11 while their calculation suggested a strong HI applicable to Zimm model. Up to now, we do not know why this would happen for a relatively weak HI which can be interpreted by neither model, perhaps partially owing to processes related to the internal dynamics of the°uorophore or the semi-°exible nature of dsDNA.…”

“…Up to now, we do not know why this would happen for a relatively weak HI which can be interpreted by neither model, perhaps partially owing to processes related to the internal dynamics of the°uorophore or the semi-°exible nature of dsDNA. 10 As for a new model beyond Rouse and Zimm 6 or nonlinear HI, 4,9 more experimental and theoretical work need to be done.…”

“…Theoretical methods have also been used to give insight into the controversy. For example, Tothova et al 10,11 used a joint RouseÀZimm model with the argument the dynamics of polymers in solution is not of the pure Rouse or Zimm type, thus the experimental data needed to be interpreted in a general model containing both models. Optimizing the theory to the experimental data, they found strong HI which may be more inclined to Zimm model.…”

The joint Rouse-Zimm theory of the dynamics of polymers in dilute solutions

“…Here we shall briefly focus on the simplest (but observable [6]) motion of the end monomer within a polymer coil and calculate its mean square displacement (MSD). The MSD part due to internal modes is [4,11] …”

“…In the literature, following de Gennes [10], it is assumed that at θ conditions, the Zimm modes with the dispersion of relaxation times τ pZ ∼ p −3/2 , where p is the mode number, at low frequencies, should always dominate the Rouse modes with τ pR ∼ p −2 ; we show that these both contributions to the polymer characteristics should be taken into account. Next, the internal modes are distributed discretely (the assumption of their continuous distribution with respect to p is true only in a restricted time domain and often leads to incorrect interpretation of experimental data [11]. The formalism from our theory with the time-dependent hydrodynamics of polymers has been adopted [9,12] and, finally, the Brinkman's theory [13,14] for the flow in porous media is used in order to take into account the effect of other coils on the test polymer.…”