Measurement of the Docking Time of a DNA Molecule onto a Solid-State Nanopore

Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands.
Nano Letters (Impact Factor: 13.59). 07/2012; 12(8):4159-63. DOI: 10.1021/nl301719a
Source: PubMed


We present measurements of the change in ionic conductance due to double-stranded (ds) DNA translocation through small (6 nm diameter) nanopores at low salt (100 mM KCl). At both low (<200 mV) and high (>600 mV) voltages we observe a current enhancement during DNA translocation, similar to earlier reports. Intriguingly, however, in the intermediate voltage range, we observe a new type of composite events, where within each single event the current first decreases and then increases. From the voltage dependence of the magnitude and timing of these current changes, we conclude that the current decrease is caused by the docking of the DNA random coil onto the nanopore. Unexpectedly, we find that the docking time is exponentially dependent on voltage (t ∝ e(-V/V(0))). We discuss a physical picture where the docking time is set by the time that a DNA end needs to move from a random location within the DNA coil to the nanopore. Upon entrance of the pore, the current subsequently increases due to enhanced flow of counterions along the DNA. Interestingly, these composite events thus allow to independently measure the actual translocation time as well as the docking time before translocation.

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    • "The stronger interaction of the ions with the DNA thus creates a much stronger drag because the movements of the ions and the DNA occur in the opposite directions (Kowalczyk et al., 2012). "
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    Frontiers in Chemistry 02/2014; 2:5. DOI:10.3389/fchem.2014.00005
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    • "In this contribution we deal with the mass and charge transport in a solid state nanopore of diameter D = 6nm and length L = 20nm. The size is selected in order to resemble the typical size of solid state nanopores that are commonly drilled using FIB or TEM [10] [11] in 20 nm wide silicon nitride (SiN ) membranes. In particular we analyze via numerical simulation the effect of a charge distribution at the pore entrance on the mass and charge fluxes across the pore, as a preliminary investigation of the current alteration due to the presence of charged macromolecule, in particular the negatively charged DNA molecule, stuck in front of the pore on the way of translocating. "
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