Imaging Single-Stranded DNA, Antigen-Antibody Reaction and Polymerized Langmuir-Blodgett Films with an Atomic Force Microscope

The combination of an (AFM) atomic force microscope together with microfabricated cantilevers that have integrated tips opens many possibilities for imaging systems of great importance in biology. We have imaged single-stranded 25mer DNA that was adsorbed on treated mica or that was covalently bound with a crosslinker to a polymerized Langmuir-Blodgett (LB) film, the top monolayer of a bilayer system. At low magnification the AFM shows cracks between solid domains, like in an image taken with a fluorescence microscope. At higher magnification, however, the AFM reveals much finer cracks and at still higher magnification it reveals rows of individual molecules in the polymerized LB film with a spacing of 0.45 nm. We have also imaged a LB film consisting of lipids in which 4% of the lipids had hapten molecules chemically bound to the lipid headgroups. Specific antibodies can then bind to these hapten molecules and be imaged with the AFM. This points to the possibility of using the AFM to monitor selective antibody binding

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

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

The flexibility of locally melted DNA

Protein-bound duplex DNA is often bent or kinked. Yet, quantification of intrinsic DNA bending that might lead to such protein interactions remains enigmatic. DNA cyclization experiments have indicated that DNA may form sharp bends more easily than predicted by the established worm-like chain (WLC) model. One proposed explanation suggests that local melting of a few base pairs introduces flexible hinges. We have expanded this model to incorporate sequence and temperature dependence of the local melting, and tested it for three sequences at temperatures from 23°C to 42°C. We find that small melted bubbles are significantly more flexible than double-stranded DNA and can alter DNA flexibility at physiological temperatures. However, these bubbles are not flexible enough to explain the recently observed very sharp bends in DNA

Force-Extension Relations for Polymers with Sliding Links

Topological entanglements in polymers are mimicked by sliding rings (slip-links) which enforce pair contacts between monomers. We study the force-extension curve for linear polymers in which slip-links create additional loops of variable size. For a single loop in a phantom chain, we obtain exact expressions for the average end-to-end separation: The linear response to a small force is related to the properties of the unstressed chain, while for a large force the polymer backbone can be treated as a sequence of Pincus--de Gennes blobs, the constraint effecting only a single blob. Generalizing this picture, scaling arguments are used to include self-avoiding effects.Comment: 4 pages, 5 figures; accepted to Phys. Rev. E (Brief Report

Fabrication and characterization of dual function nanoscale pH-scanning ion conductance microscopy (SICM) probes for high resolution pH mapping

The easy fabrication and use of nanoscale dual function pH-scanning ion conductance microscopy (SICM) probes is reported. These probes incorporate an iridium oxide coated carbon electrode for pH measurement and an SICM barrel for distance control, enabling simultaneous pH and topography mapping. These pH-SICM probes were fabricated rapidly from laser pulled theta quartz pipets, with the pH electrode prepared by in situ carbon filling of one of the barrels by the pyrolytic decomposition of butane, followed by electrodeposition of a thin layer of hydrous iridium oxide. The other barrel was filled with an electrolyte solution and Ag/AgCl electrode as part of a conductance cell for SICM. The fabricated probes, with pH and SICM sensing elements typically on the 100 nm scale, were characterized by scanning electron microscopy, energy-dispersive X-ray spectroscopy, and various electrochemical measurements. They showed a linear super-Nernstian pH response over a range of pH (pH 2–10). The capability of the pH-SICM probe was demonstrated by detecting both pH and topographical changes during the dissolution of a calcite microcrystal in aqueous solution. This system illustrates the quantitative nature of pH-SICM imaging, because the dissolution process changes the crystal height and interfacial pH (compared to bulk), and each is sensitive to the rate. Both measurements reveal similar dissolution rates, which are in agreement with previously reported literature values measured by classical bulk methods

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

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

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