We report experimental measurements of the salt dependence of ion transport and DNA translocation through solid-state nanopores. The ionic conductance shows a three-order-of-magnitude decrease with decreasing salt concentrations from 1 M to 1 muM, strongly deviating from bulk linear behavior. The data are described by a model that accounts for a salt-dependent surface charge of the pore. Subsequently, we measure translocation of 16.5-mum-long dsDNA for 50 mM to 1 M salt concentrations. DNA translocation is shown to result in either a decrease ([KCl] > 0.4 M) or increase of the ionic current ([KCl] < 0.4 M). The data are described by a model where current decreases result from the partial blocking of the pore and current increases are attributed to motion of the counterions that screen the charge of the DNA backbone. We demonstrate that the two competing effects cancel at a KCl concentration of 370 +/- 40 mM.

A mong the variety of roles for nanopores in biology, an important one is enabling polymer transport, for example in gene transfer between bacteria 1 and transport of RNA through the nuclear membrane 2 . Recently, this has inspired the use of protein 3-5 and solid-state 6-10 nanopores as single-molecule sensors for the detection and structural analysis of DNA and RNA by voltage-driven translocation. The magnitude of the force involved is of fundamental importance in understanding and exploiting this translocation mechanism, yet so far it has remained unknown. Here, we demonstrate the first measurements of the force on a single DNA molecule in a solid-state nanopore by combining optical tweezers 11 with ionic-current detection. The opposing force exerted by the optical tweezers can be used to slow down and even arrest the translocation of the DNA molecules. We obtain a value of 0.24 ± 0.02 pN mV −1 for the force on a single DNA molecule, independent of salt concentration from 0.02 to 1 M KCl. This force corresponds to an effective charge of 0.50 ± 0.05 electrons per base pair equivalent to a 75% reduction of the bare DNA charge.It is possible to manipulate DNA molecules using electric fields because DNA is negatively charged in solution. Confining an electrical field to a nanopore enables the study of voltagedriven DNA translocation where the force is only applied to the few monomers that are inserted in the nanopore. We can calculate the electrical force F el on the DNA in the nanopore as F el = (q eff (z)/a)E(z)dz, where q eff is the effective charge of a DNA base pair, E(z) is the position-dependent electrical field in our system, a is the distance between two base pairs, and the integral is taken along the DNA contour. Assuming that q eff is identical for every base pair leads to F el = (q eff /a) E(z)dz = q eff V /a, with V the applied potential across the nanopore. The simplicity of this formula stems from the translational invariance of our system, in which the contour length of the DNA exceeds the length of the nanopore.

We study ionic current fluctuations in solid-state nanopores over a wide frequency range and present a complete description of the noise characteristics. At low frequencies ( f Շ 100 Hz) we observe 1/f-type of noise. We analyze this low-frequency noise at different salt concentrations and find that the noise power remarkably scales linearly with the inverse number of charge carriers, in agreement with Hooge's relation. We find a Hooge parameter ␣ ‫؍‬ (1.1 ؎ 0.1) ؋ 10 ؊4 . In the high-frequency regime ( f տ 1 kHz), we can model the increase in current power spectral density with frequency through a calculation of the Johnson noise. Finally, we use these results to compute the signal-to-noise ratio for DNA translocation for different salt concentrations and nanopore diameters, yielding the parameters for optimal detection efficiency. Nanometer-sized pores can be used as versatile sensors for single biomolecules such as DNA, RNA, or proteins. The charged molecules are electrophoretically driven through the nanopore, resulting in temporal changes of the ionic current. The technique was first demonstrated by measuring the passage of DNA and RNA through the protein pore ␣-hemolysin (1). More recently, solid-state nanopores were developed and used to measure the traversal of polynucleotides (2). These translocation experiments have already addressed a wide range of interesting properties of nucleic acids (3). Fabricated solid-state nanopores have obvious advantages over their biological counterparts, such as high stability, adjustable geometry, and surface properties, and the potential of integration into devices. However, to date, they have been accompanied by a large variability in low-frequency noise, which limits their sensitivity and reliability (4, 5). Studies of the ionic current noise can provide detailed information on dynamic processes occuring in the nanoscale volume of a single nanopore, and can help to improve and optimize nanopore characteristics. In protein pores, the protonation of ionization sites (6), the transport of sugars (7-10), ATP (11), and antibiotic molecules (12), and the conformational dynamics of protein pores (13) were all detected by studying ionic current fluctuations. On fabricated nanopores, only a few noise studies were performed so far, which related an increased low-frequency noise to the motion of polymeric subunits constituting the channel walls (14), and to the presence of nanometer-sized bubbles (nanobubbles) inside the nanopore (5).In this article, we present a complete picture of the current noise of fabricated solid-state nanopores by addressing both the low-and high-frequency regimes. We first give a brief overview of the general characteristics of our nanopores, showing a linear current-voltage (I-V) relation with resistance values that can vary significantly from pore-to-pore. We compare current-time traces and power spectra of illustrative nanopores of similar diameter but substantially different resistance, and we find that, whereas the high-frequency noise is of compara...

From conductance and noise studies, we infer that nanometer-sized gaseous bubbles (nanobubbles) are the dominant noise source in solid-state nanopores. We study the ionic conductance through solid-state nanopores as they are moved through the focus of an infrared laser beam. The resulting conductance profiles show strong variations in both the magnitude of the conductance and in the low-frequency noise when a single nanopore is measured multiple times. Differences up to 5 orders of magnitude are found in the current power spectral density. In addition, we measure an unexpected double-peak ionic conductance profile. A simple model of a cylindrical nanopore that contains a nanobubble explains the measured profile and accounts for the observed variations in the magnitude of the conductance.

We report translocation of double-stranded DNA (dsDNA) molecules that are coated with RecA protein through solid-state nanopores. Translocation measurements show current-blockade events with a wide variety in time duration (10-4-10-1 s) and conductance blockade values (3-14 nS). Large blockades (11.4+/-0.7 nS) are identified as being caused by translocations of RecA-dsDNA filaments. We confirm these results through a variety of methods, including changing molecular length and using an optical tweezer system to deliver bead-functionalized molecules to the nanopore. We further distinguish two different regimes of translocation: a low-voltage regime (<150 mV) in which the event rate increases exponentially with voltage, and a high-voltage regime in which it remains constant. Our results open possibilities for a variety of future experiments with (partly) protein-coated DNA molecules, which is interesting for both fundamental science and genomic screening applications.