[Paper Review] Monomer motion in single- and double-stranded DNA coils

Jana Tóthová, B. Brutovský+1 more|arXiv (Cornell University)|Sep 15, 2005

DNA and Nucleic Acid Chemistry2 references3 citations

TL;DR

This study re-evaluates monomer dynamics in single- and double-stranded DNA using a joint Rouse-Zimm (RZ) theory, showing that both dsDNA and ssDNA exhibit Zimm-type dynamics rather than Rouse behavior. The RZ model, which accounts for discrete internal modes and time-dependent transition from Rouse to Zimm motion, better explains fluorescence correlation spectroscopy data, yielding a Kuhn length for ssDNA significantly larger than previously assumed.

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.

Motivation & Objective

• To address limitations in traditional Rouse and Zimm models for describing polymer dynamics in dilute solutions.
• To resolve discrepancies in interpreting experimental data from single-monomer fluorescence correlation spectroscopy.
• To develop a more accurate theoretical framework by integrating Rouse and Zimm dynamics into a unified RZ theory.
• To determine statistical-mechanical parameters for dsDNA and ssDNA using experimental data.
• To reassess the Kuhn length of ssDNA based on dynamic behavior rather than conventional assumptions.

Proposed method

• Application of the joint Rouse-Zimm (RZ) theory to model internal relaxation modes as discrete functions of mode number.
• Incorporation of hydrodynamic interactions and bead-spring dynamics to describe time-dependent transition from Rouse to Zimm behavior.
• Fitting the RZ model to experimental fluorescence correlation spectroscopy data from Shusterman et al. (2004) on individual monomers.
• Optimization of model parameters including hydrodynamic radius and persistence length to match observed relaxation times.
• Use of discrete mode analysis to avoid the continuous approximation of standard Rouse and Zimm models.
• Comparison of model predictions with experimental data to validate the RZ framework for both dsDNA and ssDNA.

Experimental results

Research questions

• RQ1 How does the internal dynamics of individual DNA monomers deviate from classical Rouse or Zimm models?
• RQ2 To what extent does the Rouse-Zimm (RZ) theory better describe experimental data than pure Rouse or Zimm models?
• RQ3 What is the effective Kuhn length of single-stranded DNA based on dynamic behavior rather than static estimates?
• RQ4 How does the transition from Rouse-like to Zimm-like motion manifest over time in DNA coils?
• RQ5 Why do experimental observations of monomer motion contradict the initial assumption of Rouse-type dynamics in DNA?

Key findings

• Double-stranded DNA (dsDNA) exhibits predominantly Zimm-type dynamics, contrary to the initially assumed Rouse behavior.
• Single-stranded DNA (ssDNA) also behaves primarily as a Zimm polymer, indicating significant hydrodynamic interactions.
• The Kuhn length for ssDNA is found to be substantially larger than commonly cited values in the literature, suggesting greater stiffness than previously believed.
• The RZ theory successfully explains the time-dependent crossover from Rouse to Zimm dynamics in monomer motion.
• The model provides a better fit to fluorescence correlation spectroscopy data than pure Rouse or Zimm models alone.
• The discrete nature of internal relaxation modes in the RZ framework leads to a more accurate description of polymer dynamics in dilute solutions.