Conformation and Dynamics of DNA Confined in Slitlike Nanofluidic Channels

Using laser fluorescence microscopy, we study the shape and dynamics of individual DNA molecules in slitlike nanochannels confined to a fraction of their bulk radius of gyration. With a confinement size spanning 2 orders of magnitude, we observe a transition from the de Gennes regime to the Odijk regime in the scaling of both the radius of gyration and the relaxation time. The radius of gyration and the relaxation time follow the predicted scaling in the de Gennes regime, while, unexpectedly, the relaxation time shows a sharp decrease in the Odijk regime. The radius of gyration remains constant in the Odijk regime. Additionally, we report the first measurements of the effect of confinement on the shape anisotropy.

Figure 1

Overview of the experimental setup with (a) the etched channel before bonding, (b) the bonded channel with plexiglass holder and o rings, and (c),(d) side views of the DNA confined in channels of height $h$ in different regimes.

Figure 2

Typical images of $\lambda$ DNA in $1.3\mu \mathrm{m}$ and 33 nm high channels.

Figure 3

Histograms of the size of the major axis ($R_M$) and the minor axis ($R_m$) where $h=107\mathrm{nm}$. Solid lines are fits of Eq. (6). In the inset a snapshot of a molecule is shown with $R_M$ and $R_m$ as calculated with Eqs. (1, 2).

Figure 4

Dependence of polymer extension and relaxation time on confinement in a slitlike nanochannel, with (a) the radius of gyration parallel to the channel walls, scaled by its bulk value of $0.84\mu \mathrm{m}$. The dashed line represents the scaling of Eq. (7), while the dash-dotted line is a fit to the points in the Odijk regime. Data points indicated with open circles were measured in channels that were bonded using silicate bonding, while the solid circles represent the directly bonded channels. (b) The relaxation time, scaled by its bulk value of 0.2 s. The dashed line represents the scaling of Eq. (8), and the dash-dotted line denotes $\tau \sim (R_{\mathrm{bulk}}/h{)}^{-0.63}$. In the inset, time autocorrelation functions $C$ of $R_{\parallel }$ are shown for different channel heights, fitted with exponential functions.

Figure 5

Anisotropy of the molecules as a function of confinement, with symbols as in Fig. 4. The solid line is a guide to the eye. The confinement of the bulk measurement is an estimate based on the amount of liquid used and the size of the glass plates. In the insets, an ellipsoidal polymer coil is depicted schematically in bulk (left) and in confinement (right).