Monomer motion in single- and double-stranded DNA coils

TL;DR

This paper refines the understanding of monomer dynamics in DNA coils by applying a joint Rouse-Zimm theory, revealing that both double- and single-stranded DNA predominantly exhibit Zimm-type behavior, with implications for polymer physics models.

Contribution

It introduces a joint Rouse-Zimm model to better interpret monomer motion in DNA, challenging previous assumptions of Rouse dominance in single-stranded DNA.

Findings

dsDNA exhibits Zimm-type kinetics consistent with literature

ssDNA also shows Zimm-like behavior, but with a larger Kuhn length

The model improves interpretation of fluorescence correlation data

Abstract

The dynamics of flexible polymers in dilute solution is usually described in terms of the pure Rouse or Zimm bead-spring models assuming continuous distribution of the internal relaxation modes. We show that this approach may lead to misleading interpretation of experimental data. The more correct description should come from the joint Rouse-Zimm (RZ) theory that contains the Rouse and Zimm models as limiting cases. The internal modes are discrete with respect to the mode number, and the type of the bead motion changes in the time from the Rouse to Zimm behavior. We demonstrate this interpreting the recent first observation of the kinetics of individual polymer monomers using the fluorescence correlation technique [R. Shusterman et al., Phys. Rev. Lett. 92, 048303 (2004)]. Optimizing the RZ theory to the data on double- and single-stranded DNA coils (dsDNA and ssDNA) the parameters for the statistical-mechanical description of the behavior of these polymers have been determined. The calculations indicate that dsDNA follows mainly the classical Zimm-type kinetics rather than the Rouse one as it was originally proposed. Single-stranded DNA also behaves predominantly as the Zimm polymer. For dsDNA the Kuhn length agrees with the commonly accepted value in the literature while in the case of ssDNA it takes a value much larger than it is usually cited in the literature.