Statistics of DNA Capture by a Solid-State Nanopore

A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8-nm-wide nanopore reveals a strong bias favoring the capture of molecules near their ends. A theoretical model shows that bias to be a consequence of configurational entropy rather than a search by the polymer for an energetically favorable configuration. We also quantified the fluctuations and length dependence of the speed of simultaneously translocating polymer segments from our study of folded DNA configurations.

Figure 1

(a) A nanopore captures DNA from solution and initiates electrophoretic translocation by forming a hairpin. Segments of length $L_l$ and $L_s$ extend from the capture location. (Detail) TEM image of the 8-nm-wide nanopore used. (b) Ionic current traces from translocation events of types 1, 2-1, and 2 indicate the capture locations. (c) The ionic current trace of a folded DNA molecule shows $t_2$, $t_{\mathrm{tot}}$, and ECD.

Figure 2

(a) Overlaid ECD distributions for translocations of type 1 (dark grey), 2-1 (white), and 2 (medium grey) with $t_{\mathrm{tot}}>0.3\mathrm{ms}$. Events with $\mathrm{ECD}<0.27\mathrm{pC}$ and six with $\mathrm{ECD}>3\mathrm{pC}$ were dropped from subsequent analyses in order to exclude fragmented and stuck DNA molecules, respectively. Only $0\mathrm{pC}\le \mathrm{ECD}\le 1\mathrm{pC}$ is plotted for clarity. (b) Distribution of capture locations. The stacked histogram bars indicate the number of events of each type in a bin. Data points indicate the total number of events of all types and their mean $x$ in a bin. Error bars indicate the square root of the total events. The solid line shows the distribution predicted by Eq. (3) using ${\gamma }_1^S=0.703$ and ${\gamma }_2^S=0.203$ from [12].

Figure 3

Dependence of $⟨t_{\mathrm{tot}}⟩$ on $⟨t_2⟩$. Error bars indicate the standard deviation of the mean in a $80\mathrm{\text{−}}\mu \mathrm{s}$ bin. Bins with $⟨t_2⟩>1\mathrm{ms}$ contain an insignificant number of events ($\le 2$). The solid line shows the predictions of the dynamical model that includes velocity fluctuations and is described in the text. The dashed line accounts for the length dependence of the translocation speed of each segment with $t\propto L^{\alpha }$. The scaling exponent $\alpha =1.19\pm 0.04$ was obtained from a weighted least squares fit to the data in the range $⟨t_2⟩<0.7\mathrm{ms}$.