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: 13.03). 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.

  • [Show abstract] [Hide abstract]
    ABSTRACT: This paper describes a fundamental study of the effect of electrostatic interactions on the resistive pulse waveshape associated with translocation of charged nanoparticles through a conical-shaped, charged glass nanopore. In contrast to single-peak resistive pulses normally associated with resistive-pulse methods, biphasic pulses, in which the normal current decrease is preceded by a current increase, were observed in the current–time recordings when a high negative potential (lower than −0.4 V) is applied between the pore interior and the external solution. The biphasic pulse is a consequence of the offsetting effects of an increased ion conductivity induced by the surface charge of the translocating particle and the current decrease due to the volume exclusion of electrolyte solution by the particle. Finite-element simulations based on the coupled Poisson–Nernst–Planck equations and a particle trajectory calculation successfully capture the evolution of the waveshape from a single resistive pulse to a biphasic response as the applied voltage is varied. The simulation results demonstrate that the surface charges of the nanopore and the particle are responsible for the voltage-dependent shape evolution. Additionally, the use of high ionic strength solution or high pressures to drive particle translocation was found to eliminate the biphasic response. The former is due to the screening of the electrical double layer, while the latter results from the solution flow preventing formation of an equilibrium double layer ion distribution within the nanopore, similar to the previously reported elimination of ion current rectification when solution flows through a nanopore.
    The Journal of Physical Chemistry C 01/2014; 118(5):2726–2734. · 4.84 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: We have simulated the transport properties of a uniformly charged flexible polymer chain and its counterions confined inside cylindrical nanopores under an external electric field. The hydrodynamic interaction is treated by describing the solvent molecules explicitly with the multiparticle collision dynamics method. The chain consisting of charged monomers and the counterions interact electrostatically with themselves and with the external electric field. We find rich behavior of the counterions around the polymer under confinement in the presence of the external electric field. The mobility of the counterions is heterogeneous depending on their location relative to the polymer. The adsorption isotherm of the counterions on the polymer depends nonlinearly on the electric field. As a result, the effective charge of the polymer exhibits a sigmoidal dependence on the electric field. This in turn leads to a nascent nonlinearity in the chain stretching and electrophoretic mobility of the polymer in terms of their dependence on the electric field. The product of the electric field and the effective polymer charge is found to be the key variable to unify our simulation data for various polymer lengths. Chain extension and the electrophoretic mobility show sigmoidal dependence on the electric field, with crossovers from the linear response regime to the nonlinear regime and then to the saturation regime. The mobility of adsorbed counterions is nonmonotonic with the electric field. For weaker and moderate fields, the adsorbed counterions move with the polymer and at higher fields they move opposite to the polymer's direction. We find that the effective charge and the mobility of the polymer decrease with a decrease in the pore radius.
    The Journal of Chemical Physics 09/2014; 141(11):114901. · 3.12 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. · 3.71 Impact Factor