Collapse of DNA under alternating electric fields

Recent studies have shown that double-stranded DNA can collapse in the presence of a strong electric field. Here we provide an in-depth study of the collapse of DNA under weak confinement in microchannels as a function of buffer strength, driving frequency, applied electric-field strength, and molecule size. We find that the critical electric field at which DNA molecules collapse (tens of kV/m) is strongly dependent on driving frequency (100–800 Hz) and molecular size (20–160 kbp), and weakly dependent on the ionic strength (8–60 mM). We argue that an apparent stretching at very high electric fields is an artifact of the finite frame time of video microscopy.

Figure 1

Images of $\lambda$-DNA in alternating electric fields at 300 Hz in $1\times \text{TBE}$. (a) 0 kV/m, (b) 24 kV/m, (c) 66 kV/m, and (d) 122 kV/m. The scale bar is 5 microns.

Figure 2

(a) Radius of gyration changes with electric-field strength in $2\times \text{TBE}$ and 300 Hz electric field. Each black square at constant electric-field strength represents a molecule. (b) Anisotropy as function of strength in $2\times \text{TBE}$ and 300 Hz electric field. Each black triangle at constant electric-field strength represents a molecule.

Figure 3

Radius of gyration of $\lambda$-DNA as function of salt strength and frequency. We show the experimentally measured radius of gyration $R_{g,\mathrm{expt}}$ in panels (a)–(d) [(a) $0.25\times \text{TBE}$, (b) $0.5\times \text{TBE}$, (c) $1\times \text{TBE}$, and (d) $2\times \text{TBE}$]. The physical radius of gyration $R_{g,\mathrm{phys}}$ recovered after correction of motion during each video frame is shown in panels (e) and (f) [(e) $0.25\times \text{TBE}$, (f) $0.5\times \text{TBE}$, (g) $1\times \text{TBE}$, and (h) $2\times \text{TBE}$]. Curves for different frequencies are separated by a 0.3 $\mu \text{m}$ offset (purple $\times$, 100 Hz; yellow $*$, 200 Hz; green $◯$, 300 Hz; blue $\square$, 450 Hz; red $△$, 675 Hz; black $\diamond$, 800 Hz).

Figure 4

Image pattern due to center-of-mass motion. Panel (a) is a typical image in experiments ($\lambda$-DNA in $2\times \text{TBE}$ and 146.82 kV/m, 100 Hz driving). Panel (b) is a simulation of a molecule under sinusoidal motion and extended illumination.

Figure 5

(a) Correction factor $\gamma$ as function of driving frequency. (Green $◯$, $2\times \text{TBE}$; red $△$, $0.5\times \text{TBE}$.) No error bars given as fit was performed manually. (b) Critical electric-field strength vs electric-field frequencies (same color coding).

Figure 6

Critical electric-field strength vs electric-field frequencies for $\lambda$-DNA in nanochannels [14]. The solid square curve is the result from $225\times 325{\text{nm}}^2$ channels. The empty square curve is the result from $80\times 100{\text{nm}}^2$ channels.

Figure 7

Radius of gyration of T4-DNA multimers and fragments as function of electric-field strength in $2\times \text{TBE}$ at 300 Hz driving frequency. Probable length assignment: black $\diamond$, double T4 ($\sim 320\mathrm{kbp}$); red $△$, single T4 ($\sim 160\mathrm{kbp}$); blue $\square$, half T4 ($\sim 80\mathrm{bp}$); green $◯$, quarter T4 ($\sim 40\mathrm{kbp}$). (b) Radius of gyration of T4-DNA multimers and fragments as function of electric-field strength in $2\times \text{TBE}$ at 300 Hz driving frequency, after correction for the center-of-mass motion. (c) Normalized relative radius of gyration of T4-DNA in $2\times \text{TBE}$ (see text for definition).