Measurement of the Docking Time of a DNA Molecule onto a Solid-State Nanopore
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.
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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). "
ABSTRACT: Owing to the potential use for real personalized genome sequencing, DNA sequencing with solid-state nanopores has been investigated intensively in recent time. However, the area still confronts problems and challenges. In this work, we present a brief overview of computational studies of key issues in DNA sequencing with solid-state nanopores by addressing the progress made in the last few years. We also highlight future challenges and prospects for DNA sequencing using this technology.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   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. "
ABSTRACT: . Nanofluidics, thanks to the recent progress in the fabrication of micro and nanode-vices, has become an intense research field. Confined fluids in nanoscale geometries exhibit physical behaviors that, in several cases, largely differ from macroscale dynamics. The crucial differences are: i) in nanoscale systems the usual mathematical description for continuum fluid dynamics (Navier-Stokes equation), often fails to reproduce the correct fluid dynamics behavior and ii) in a number of crucial applications the focus is on the motion of a single macromolecule. These occurrences natu-rally call for an atomistic description of the whole system, which however remains currently limited to relatively small systems (tens of nm simulated for hundreds of ns). The simulation of the fluid mo-tion at nanoscale is here addressed via a recent developed mesoscale approach. In particular the flow of an electrolyte through a nano channel is analyzed. The system represent an experimentally well characterized solid-state nanopore employed for DNA and protein translocation. The simulations are aimed at estimating the effect of DNA translocation on mass and charge flow rate potentially shedding light on the molecular mechanism behind recent experimental observations. 1 INTRODUCTION Nanopore-based protocols for macromolecule detection and characterization are a promising technology for the development of sensors and devices able to operate at single-molecule level. Their working principle is, in essence, very simple. A nanopore connects two reservoirs containing an electrolyte solution and an applied voltage across the chambers generates a net ion current. When one of the macromolecules dispersed in the solution engages the pore, the ion flux is altered and a change in the current is measured. The intensity, the sign and the duration of the current drop depend on the physico-chemical properties of the passing molecule. Hence the current track can, in principle, provide precise information on a single-molecule level. In the past decade significant
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ABSTRACT: A novel polyelectrolyte (PE)-modified nanopore, comprising a solid-state nanopore functionalized by a nonregulated PE brush layer connecting two large reservoirs, is proposed to regulate the electrokinetic translocation of a soft nanoparticle (NP), comprising a rigid core covered by a pH-regulated, zwitterionic, soft layer, through it. The type of NP considered mimics bionanoparticles such as proteins and biomolecules. We find that a significant enrichment of H(+) occurs near the inlet of a charged solid-state nanopore, appreciably reducing the charge density of the NP as it approaches there, thereby lowering the NP translocation velocity and making it harder to thread the nanopore. This difficulty can be resolved by the proposed PE-modified nanopore, which raises effectively both the capture rate and the capture velocity of the soft NP and simultaneously reduces its translocation velocity through the nanopore so that both the sensing efficiency and the resolution are enhanced. The results gathered provide a conceptual framework for the interpretation of relevant experimental data and for the design of nanopore-based devices used in single biomolecules sensing and DNA sequencing.Analytical Chemistry 10/2012; 84(21). DOI:10.1021/ac302429d · 5.83 Impact Factor