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: 12.94). 07/2012; 12(8):4159-63. DOI: 10.1021/nl301719a
Source: PubMed

ABSTRACT 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.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: We investigated the biphasic resistive pulses during particle translocation through cylindrical nanopores at low salt concentration by simulation, and the effects of electrolyte concentration, surface charge, electric potential, and pore geometry were systematically discussed. The formation of positive peaks in the pulses is ascribed to the surface charge on the particle and the pore. The peak current enhancement/decline ratio increases linearly with the particle surface charge density but decreases with the salt concentration increase. We find that there is an optimum electric potential for the peak current enhancement ratio to reach the maximum value. When a negatively charged particle is at the orifice of the pore on the low/high potential side, the ion concentration inside and around the pore is significantly depleted/enriched, while inverse electric potential or inverse surface charge has an opposite effect. The extent of such ion modulation is larger with a longer pore. The peak current enhancement/ decline ratio is quantitatively linked to the percent of ion concentration enrichment/depletion inside and around the pore, by considering particle occupied volume and concentration change.
    The Journal of Physical Chemistry C 03/2015; DOI:10.1021/acs.jpcc.5b00047 · 4.84 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: We describe a number of techniques for the analysis of solid-state nanopore ionic current traces and introduce a new package of Matlab analysis scripts with GUI front ends. We discuss methods for the detection of the local baseline and propose a new detection algorithm that bypasses some of the classical weaknesses of moving-average detection. Our new approach removes detected events and re-creates an ideal event-free baseline subsequently used to recalculate the local baseline. Iterative operation of this algorithm causes both the moving average of the baseline current and its standard deviation to converge to their correct values. We explain different approaches to selecting events and building event populations, and we show the value of keeping track of the changes in parameters, such as the event rate and the pore resistance, throughout the course of the experiment. Finally, we introduce a new technique for separating unfolded events and detecting current spikes present within translocation events. This open source software package is available online at:
    Nanotechnology 02/2015; 26(8):084003. DOI:10.1088/0957-4484/26/8/084003 · 3.67 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Recent experimental studies showed that the access resistance (AR) of a nanopore with a low thickness-to-diameter aspect ratio plays an important role in particle translocation. The existing theories usually only consider the AR without the presence of particles in the pore systems. Based on the continuum model, we systematically investigate the current change caused by nanoparticle translocation in different nanopore configurations. From numerical results, an analytical model is proposed to estimate the influence of the AR on the resistive-pulse amplitude, i.e., the ratio of the AR to the pore resistance. The current change is first predicted by our model for nanoparticles and nanopores with a wide range of sizes at the neutral surface charge. Subsequently, the effect of surface charges is studied. The results show that resistive-pulse amplitude decreases with the increasing surface charge of the nanoparticle or the nanopore. We also find that the shape of the position-dependent resistive-pulse might be distorted significantly at low bulk concentration due to concentration polarization. This study provides a deep insight into the AR in particle-pore systems and could be useful in designing nanopore-based detection devices.
    RSC Advances 01/2014; 4(15):7601. DOI:10.1039/c3ra46032k · 3.71 Impact Factor