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...

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Topoisomerases relieve the torsional strain in DNA that is built up during replication and transcription. They are vital for cell proliferation and are a target for poisoning by anti-cancer drugs. Type IB topoisomerase (TopIB) forms a protein clamp around the DNA duplex and creates a transient nick that permits removal of supercoils. Using real-time single-molecule observation, we show that TopIB releases supercoils by a swivel mechanism that involves friction between the rotating DNA and the enzyme cavity: that is, the DNA does not freely rotate. Unlike a nicking enzyme, TopIB does not release all the supercoils at once, but it typically does so in multiple steps. The number of supercoils removed per step follows an exponential distribution. The enzyme is found to be torque-sensitive, as the mean number of supercoils per step increases with the torque stored in the DNA. We propose a model for topoisomerization in which the torque drives the DNA rotation over a rugged periodic energy landscape in which the topoisomerase has a small but quantifiable probability to religate the DNA once per turn.

We introduce magnetic torque tweezers, which enable direct single-molecule measurements of torque. Our measurements of the effective torsional stiffness C of dsDNA indicated a substantial force dependence, with C = approximately 40 nm at low forces up to C = approximately 100 nm at high forces. The initial torsional stiffness of RecA filaments was nearly twofold larger than that for dsDNA, yet at moderate torques further build-up of torsional strain was prevented.

The RelA-mediated stringent response is at the heart of bacterial adaptation to starvation and stress, playing a major role in the bacterial cell cycle and virulence. RelA integrates several environmental cues and synthesizes the alarmone ppGpp, which globally reprograms transcription, translation, and replication. We have developed and implemented novel single-molecule tracking methodology to characterize the intracellular catalytic cycle of RelA. Our single-molecule experiments show that RelA is on the ribosome under nonstarved conditions and that the individual enzyme molecule stays off the ribosome for an extended period of time after activation. This suggests that the catalytically active part of the RelA cycle is performed off, rather than on, the ribosome, and that rebinding to the ribosome is not necessary to trigger each ppGpp synthesis event. Furthermore, we find fast activation of RelA in response to heat stress followed by RelA rapidly being reset to its inactive state, which makes the system sensitive to new environmental cues and hints at an underlying excitable response mechanism. cytosolic diffusion | single particle tracking | photoactivated localization microscopy | stroboscopic illumination

In this paper we review the biophysics revealed by stretching single biopolymers. During the last decade various techniques have emerged allowing micromanipulation of single molecules and simultaneous measurements of their elasticity. Using such techniques, it has been possible to investigate some of the interactions playing a role in biology. We shall first review the simplest case of a non-interacting polymer and then present the structural transitions in DNA, RNA and proteins that have been studied by single-molecule techniques. We shall explain how these techniques permit a new approach to the protein folding/unfolding transition.