Recapturing and trapping single molecules with a solid-state nanopore

Original entry: Tamas Szalay (APPHY225 2012)

"Recapturing and trapping single molecules with a solid-state nanopore"

Marc Gershow & J. A. Golovchenko

Nature Nanotechnology 2, 775 - 779 (2007)

Summary

In this experiment, the authors build upon previous nanopore experiments by Golovchenko et al, feeding DNA through a solid-state nanopore and then attempting to subsequently pull it back through in the other direction. The DNA is initially fed through a 5-nm pore ("translocated") using a driving voltage set up across the pore. Once the translocation completes, the setup waits a specified delay time (2-32 ms) before reversing the bias voltage, attempting to pull the DNA back through the pore, at which point the DNA is either recaptured and detected, or it diffuses away into the bulk. The fraction of molecules captured yields insights as to the particular polymer relaxation and diffusion processes.

Soft matter keywords

DNA, diffusion, single molecule capture, nanopores

DNA Recapture Theory

In the paper, the effects of diffusion and electrophoretically directed motion (drift) are compared. The diffusive motion is considered by calculating the expected velocity of the molecule as it moves away from the pore, which is shown to be $v_D=\frac{D}{r}$ where D is the diffusion constant and r is the distance from the pore. The electrophoretic velocity, given some simplifying assumptions, was shown to be $v_e=\frac{\mu I}{2\pi r^2 \sigma}$

and as a result, the characteristic capture distance is

$L = \frac{|\mu I|}{2\pi \sigma D}$

Outside of this distance, diffusion is more likely, and inside it, capture (provided that this is where the molecule is when the capture voltage is turned on).

The entire time-dependent capture process was also be described using the drift-diffusion equation, which was numerically solved to produce the theoretical curves shown below.

Experimental Results

The results of the experiment are shown below. The left-hand panel shows the instantaneous translocation rate a given amount of time after the bias voltage is flipped, for both forward and reverse translocations. The solid lines are the theoretical predictions for forward translocations, and the dashed lines are theoretical predictions for reverse translocations (the recapture events). The forward translocation curve is calculated from knowing the concentration of DNA in the initial chamber to calculate the expected translocation time.

The right-hand panel shows the recapture probability as a function of delay, and can also be seen to agree well with the experimental data. In all of the fits, the only free parameter was a difference in the overall recapture rate, a scaling of 70%, which the authors attribute to some of the charge and electric field related assumptions in their model.

In the following figure, the time-dependent capture probability is plotted for each particular value of recapture delay. Note especially the increased probability at extremely short times for short delays - this can be attributed to the polymer not having relaxed completely, as suggested by the authors, and later probed in other experiments ("Molecular Ping-Pong").