Collapse of DNA in ac Electric Fields

We report that double-stranded DNA collapses in the presence of ac electric fields at frequencies of a few hundred Hertz, and does not stretch as commonly assumed. In particular, we show that confinement-stretched DNA can collapse to about one quarter of its equilibrium length. We propose that this effect is based on finite relaxation times of the counterion cloud, and the subsequent partitioning of the molecule into mutually attractive units. We discuss alternative models of those attractive units.

Figure 1

Schematics of device structures. (a) Microfluidic device with molecule of actual size. (b) Nanofluidic device with schematic molecule in nanochannel (center) bridging two microchannels (left and right).

Figure 2

Collapse of DNA in an ac electric field at 300 Hz. (a)–(c) Time traces of intensity along nanochannel-stretched DNA vs time ((A) $210\mathrm{V}/\mathrm{cm}$, (b) $420\mathrm{V}/\mathrm{cm}$, (c) $780\mathrm{V}/\mathrm{cm}$). Each line is a instantaneous intensity along the nanochannel axis, which have a cross-section of $80\times 100{\mathrm{nm}}^2$. The small panels are individual movie frames. The horizontal scale is $10\mu \mathrm{m}$, and the total time is 50 sec. The ac field was applied at the arrow. (d) and (e) Molecules in microchannel without and with electric field of $700\mathrm{V}/\mathrm{cm}$, respectively. Scale bar $5\mu \mathrm{m}$.

Figure 3

(a) Fractional length vs field strength in $80\times 100{\mathrm{nm}}^2$ nanochannels. Data shows spread of individual points. (b) Standard deviation within individual single-molecule traces.

Figure 4

Influence of frequency on contraction. (A) Fractional extension in $80\mathrm{nm}\times 100\mathrm{nm}$ channels. Symbols: 100 (■), 300 (○), 500 (×), and 700 Hz (△). The inset show the contraction at $1.4\mathrm{kV}/\mathrm{cm}$ over a large range of frequencies. Error bars are standard deviations of means. (B) Fractional extension in $225\mathrm{nm}\times 325\mathrm{nm}$ channels. 300 (○), 400 (■), 500 (×), and 600 Hz (△). (C) Fractional radius of gyration (ratio of $\mathit{R}g$ to equilibrium $\mathit{R}g$) in microfluidic channels. 100 (▲), 300 (■), and 675 Hz (○).

Figure 5

Model of collapses. (a) and (b) limiting geometries for “curvature condensation.” The electric field polarizes only highly curved DNA segment, which then interact. (c) Polarization of density fluctuations. The counterion (pink) and coion (not shown) clouds are displaced to yield a local polarization that is polyelectrolyte density dependent, thus leading to local, interacting charges.