Improved Visualization of DNA in Aqueous Buffer with the Atomic Force Microscope

An improved method has been developed for imaging deoxyribonucleic acid (DNA) in aqueous buffer with the atomic force microscope (AFM). DNA on untreated mica can be imaged in aqueous buffer with the AFM if the DNA is deposited onto the mica in a buffer with HEPES and MgCl2, if the sample is rinsed thoroughly with high water pressure, and if the imaging is done with an electron beam-deposited (EBD) tip that has been deposited in the scanning electron microscope (SEM). The water rinse removes DNA that is otherwise easily scraped off the substrate. There is evidence that sharper tips may be more damaging to DNA when imaged in aqueous buffer especially when the DNA is bound tightly to the mica. The ability to image DNA in nearly biological conditions has potential applications for imaging biomolecular processes with the AFM

Scanning Tunneling Microscopy and Fabrication of Nanometer Scale Structures at the Liquid-Gold Interface

The Scanning Tunneling Microscope (STM) can image gold surfaces covered with a variety of liquids. This paper reviews the results obtained using the STM to image gold surfaces covered with liquid. These results include the creation of 10 nm structures, images of the electrochemical process of electroplating, and the production of atomically flat Au (111) surfaces. We conclude that in the future STM will find further application in the area of nanostructure fabrication and electrochemistry. The trend in the field is toward greater control of the electrochemical environment

Molecular mechanistic origin of the toughness of natural adhesives, fibres and composites

Natural materials are renowned for their strength and toughness(1-5). Spider dragline silk has a breakage energy per unit weight two orders of magnitude greater than high tensile steel(1,6), and is representative of many other strong natural fibres(3,7,8). The abalone shell, a composite of calcium carbonate plates sandwiched between organic material, is 3,000 times more fracture resistant than a single crystal of the pure mineral(4,5). The organic component, comprising just a few per cent of the composite by weight(9), is thought to hold the key to nacre's fracture toughness(10,11). Ceramics laminated with organic material are more fracture resistant than non-laminated ceramics(11,12), but synthetic materials made of interlocking ceramic tablets bound by a few weight per cent of ordinary adhesives do not have a toughness comparable to nacre(13). We believe that the key to nacre's fracture resistance resides in the polymer adhesive, and here we reveal the properties of this adhesive by using the atomic force microscope(14) to stretch the organic molecules exposed on the surface of freshly cleaved nacre. The adhesive fibres elongate in a stepwise manner as folded domains or loops are pulled open. The elongation events occur for forces of a few hundred piconewtons, which are smaller than the forces of over a nanonewton required to break the polymer backbone in the threads. We suggest that this 'modular' elongation mechanism might prove to be quite general for conveying toughness to natural fibres and adhesives, and we predict that it might be found also in dragline silk

Theory of a Scanning Tunneling Microscope with a Two-Protrusion Tip

We consider a scanning tunneling microscope (STM) such that tunneling occurs through two atomically sharp protrusions on its tip. When the two protrusions are separated by at least several atomic spacings, the differential conductance of this STM depends on the electronic transport in the sample between the protrusions. Furthermore two-protrusion tips commonly occur during STM tip preparation. We explore possible applications to probing dynamical impurity potentials on a metallic surface and local transport in an anisotropic superconductor.Comment: revtex, 11 pages, 6 figures upon reques

Autoregulation of the Escherichia coli melR promoter: repression involves four molecules of MelR

The Escherichia coli MelR protein is a transcription activator that autoregulates its own promoter by repressing transcription initiation. Optimal repression requires MelR binding to a site that overlaps the melR transcription start point and to upstream sites. In this work, we have investigated the different determinants needed for optimal repression and their spatial requirements. We show that repression requires a complex involving four DNA-bound MelR molecules, and that the global CRP regulator plays little or no role

Nanoscopic Tunneling Contacts on Mesoscopic Multiprobe Conductors

We derive Bardeen-like expressions for the transmission probabilities between two multi-probe mesoscopic conductors coupled by a weak tunneling contact. We emphasize especially the dual role of a weak coupling contact as a current source and sink and analyze the magnetic field symmetry. In the limit of a point-like tunneling contact the transmission probability becomes a product of local, partial density of states of the two mesoscopic conductors. We present expressions for the partial density of states in terms of functional derivatives of the scattering matrix with respect to the local potential and in terms of wave functions. We discuss voltage measurements and resistance measurements in the transport state of conductors. We illustrate the theory for the simple case of a scatterer in an otherwise perfect wire. In particular, we investigate the development of the Hall-resistance as measured with weak coupling probes.Comment: 10 pages, 5 figures, revte

Tuning the translational freedom of DNA for high speed AFM

Direct observation is arguably the preferred way to investigate the interactions between two molecular complexes. With the development of high speed atomic force microscopy it is becoming possible to observe directly DNA protein interactions with relevant spatial and temporal resolutions. These interactions are of central importance to biology, bio-nanotechnology but also functional biologically inspired materials. Critically, sample preparation plays a central role in all microscopy studies and minimal perturbation of the sample is desired. Here, we demonstrate the ability to tune the interactions of DNA molecules with the surface such that an association strong enough to enable high resolution AFM imaging while providing sufficient translational freedom to allow the relevant protein DNA interactions to take place, can be maintained. Furthermore, we describe a quantitative method for measuring the DNA mobility, which also allows the dissection of the different contributions to the overall movement of the DNA molecules. We find that for weak surface association, a significant contribution to the movement arises from the interaction of the AFM tip with the DNA. In combination, these methods enable the tuning of the surface translational freedom of DNA molecules to allow the direct study of a wide range of nucleo-protein interactions by high speed atomic force microscopy

Radio-frequency Bloch-transistor electrometer

A quantum-limited electrometer based on charge modulation of the Josephson supercurrent in the Bloch transistor inserted into a superconducting ring is proposed. As this ring is inductive coupled to a high-Q resonance tank circuit, the variations of the charge on the transistor island (input signal) are converted into variations of amplitude and phase of radio-frequency oscillations in the tank. These variations are amplified and then detected. The output noise, the back-action fluctuations and their cross-correlation are computed. It is shown that our device enables measurements of the charge with a sensitivity which is determined by the energy resolution of its amplifier, that can be reduced down to the standard quantum limit of \hbar/2. On the basis of this setup a "back-action-evading" scheme of the charge measurements is proposed.Comment: 5 pages incl. 2 figure

Dual-barrel conductance micropipet as a new approach to the study of ionic crystal dissolution kinetics

A new approach to the study of ionic crystal dissolution kinetics is described, based on the use of a dual-barrel theta conductance micropipet. The solution in the pipet is undersaturated with respect to the crystal of interest, and when the meniscus at the end of the micropipet makes contact with a selected region of the crystal surface, dissolution occurs causing the solution composition to change. This is observed, with better than 1 ms time resolution, as a change in the ion conductance current, measured across a potential bias between an electrode in each barrel of the pipet. Key attributes of this new technique are: (i) dissolution can be targeted at a single crystal surface; (ii) multiple measurements can be made quickly and easily by moving the pipet to a new location on the surface; (iii) materials with a wide range of kinetics and solubilities are open to study because the duration of dissolution is controlled by the meniscus contact time; (iv) fast kinetics are readily amenable to study because of the intrinsically high mass transport rates within tapered micropipets; (v) the experimental geometry is well-defined, permitting finite element method modeling to allow quantitative analysis of experimental data. Herein, we study the dissolution of NaCl as an example system, with dissolution induced for just a few milliseconds, and estimate a first-order heterogeneous rate constant of 7.5 (±2.5) × 10–5 cm s–1 (equivalent surface dissolution flux ca. 0.5 μmol cm–2 s–1 into a completely undersaturated solution). Ionic crystals form a huge class of materials whose dissolution properties are of considerable interest, and we thus anticipate that this new localized microscale surface approach will have considerable applicability in the future