Diffusion and Segmental Dynamics of Double-Stranded DNA

Diffusion and segmental dynamics of the double-stranded $\lambda$-phage DNA polymer are quantitatively studied over the transition range from stiff to semiflexible chains. Spectroscopy of fluorescence fluctuations of single-end fluorescently labeled monodisperse DNA fragments unambiguously shows that double-stranded DNA in the length range of ${10}^2–2\times {10}^4$ base pairs behaves as a semiflexible polymer with segmental dynamics controlled by hydrodynamic interactions.

Figure 1

Normalized FCS correlation functions (a) and calculated reduced mean-square displacements (b) of freely diffusing Alexa 488 dye (D), labeled forward primer (P), and single-end-labeled $\lambda$-DNA fragments with lengths of 0.1 (I), 0.2 (II), 0.5 (III), 1 (IV), 2 (V), 5 (VI), 10 (VII), and 20 kbp (VIII). Also shown are the fit of Alexa 488 data to the free diffusion model (a) and the corresponding MSD (b). Panel (b) additionally shows intramolecular contributions to the MSD (gray curves) obtained by subtracting the contributions due to overall Fickian diffusion of dsDNA polymers from the corresponding data, as well as $t^{2/3}$ (long dashed line) and $t^{1/2}$ (short dashed line) power laws. The erratic deviations of the curves reflect statistical errors in the data.

Figure 2

Normalized FCS autocorrelation functions of 0.5, 1, 2, and 20 kbp DNA fragments (left to right) and their fits by Eqs. (1, 2) (dashed line).

Figure 3

Diffusion coefficients (a) and longest relaxation times (b) of dsDNA. Present work (corrected to $20°\mathrm{C}$) (●, ▪), data from Refs. 5a (□), 5b (▵), 6 (▿), 7 (⋄), 8a (○), 8b (▹). Predictions of the semiflexible polymer theory [4] for $l_p=50\mathrm{nm}$, ${\Lambda }_D=0.9$, and $\Lambda =0.6$ (solid line). Zimm-type [1] scaling $D\sim L^{-1/2}$ and ${\tau }_r\sim L^{3/2}$ (long dashed line). Rouse-type [1] scaling $D\sim L^{-1}$ and ${\tau }_r\sim L^2$ (short dashed line). Notes: For the two shortest DNA fragments, the intramolecular relaxation times could not be reliably resolved and are not presented. To account for the difference in experimental techniques, the TEB relaxation times from 8 are multiplied by a factor of 2. Insets show the ratios of our experimental results to the prediction of the semiflexible polymer theory.