Monomer Dynamics in Double- and Single-Stranded DNA Polymers

We present the first measurements of the kinetics of random motion of individual monomers within large polymer coils. We use double- and single-stranded DNA (dsDNA and ssDNA) as models of semiflexible and flexible polymers, respectively. Fluorescence fluctuations of DNA fragments labeled specifically at a single position reveal the time dependence of the DNA monomer’s mean-square displacement $⟨r^2(t)⟩$. The monomer motions within dsDNA and ssDNA coils are characterized by two qualitatively different kinetic regimes: close to $⟨r^2(t)⟩\propto t^{2/3}$ for ssDNA and $⟨r^2(t)⟩\propto \sqrt{t}$ for dsDNA. While the kinetic behavior of ssDNA is consistent with the generally accepted Zimm theory of polymer dynamics, the kinetic behavior of dsDNA monomers is in good agreement with the Rouse model.

Figure 1

FCS correlation functions for the end-labeled 6700 bp dsDNA fragment (red solid line) and 6700 base ssDNA (blue dashed line). To facilitate comparison, the correlation functions were normalized to have the same level $\sim 1$ at short time scales.

Figure 2

The mean square displacement as a function of time for the end monomers of 6700 bp dsDNA fragment (red open circles) and 6700 base ssDNA (blue full circles) as extracted from measured FCS correlation functions. The long-time portion of the data corresponds to the diffusion of a polymer coil as a whole and $⟨r^2⟩\propto t$ (dashed lines). The short-time data correspond to the monomer motion inside the coil. The best power fits $⟨r^2⟩\propto t^{\alpha }$ to the low-time portion of the data give $\alpha =0.50\pm 0.01$ for dsDNA and $\alpha =0.69\pm 0.01$ for ssDNA (solid lines).

Figure 3

The kinetics of random motion $⟨r^2(t)⟩$ of the end monomer of ssDNA (a) and dsDNA (b) fragments of different lengths (in units of bases for ssDNA, base pairs for dsDNA): 2400 (blue dashed line) and 23 100 (red solid line). Thick solid lines are the theoretical predictions by (a) Zimm theory Eq. (4) and (b) Rouse model Eq. (3). Inset in (b): blowup of the data region for 23 100 bp dsDNA showing Zimm dynamics. Red solid line: the best power fit through these data ($\alpha =0.64\pm 0.01$); dashed line: Zimm dynamics given by Eq. (4) (with $\eta =1\mathrm{m}\mathrm{P}\mathrm{a}\mathrm{s}$ at $T=293\mathrm{K}$).