Ion-beam sculpting at nanometre length scales

The 'right' size in nanobiotechnology

The biological and physical sciences share a common interest in small structures (the definition of 'small' depends on the application, but can range from 1 nm to 1 mm). A vigorous trade across the borders of these areas of science is developing around new materials and tools (largely from the physical sciences) and new phenomena (largely from the biological sciences). The physical sciences offer tools for synthesis and fabrication of devices for measuring the characteristics of cells and sub-cellular components, and of materials useful in cell and molecular biology; biology offers a window into the most sophisticated collection of functional nanostructures that exists.

Sputtering: survey of observations and derived principles

We review the most salient observations and physical principles of knock-on and electronic sputtering and the role of sputtering in several astrophysical settings and applications in research and technology. In addition, we emphasize some unsolved problems, propose experiments and provide guides to representative literature reviews and significant recent publications.

DNA molecules and configurations in a solid-state nanopore microscope

A nanometre-scale pore in a solid-state membrane provides a new way of electronically probing the structure of single linear polymers, including those of biological interest in their native environments. Previous work with biological protein pores wide enough to let through and sense single-stranded DNA molecules demonstrates the power of using nanopores, but many future tasks and applications call for a robust solid-state pore whose nanometre-scale dimensions and properties may be selected, as one selects the lenses of a microscope. Here we demonstrate a solid-state nanopore microscope capable of observing individual molecules of double-stranded DNA and their folding behaviour. We discuss extensions of the nanopore microscope concept to alternative probing mechanisms and applications, including the study of molecular structure and sequencing.

Fabrication of solid-state nanopores with single-nanometre precision

Single nanometre-sized pores (nanopores) embedded in an insulating membrane are an exciting new class of nanosensors for rapid electrical detection and characterization of biomolecules. Notable examples include alpha-hemolysin protein nanopores in lipid membranes and solid-state nanopores in Si3N4. Here we report a new technique for fabricating silicon oxide nanopores with single-nanometre precision and direct visual feedback, using state-of-the-art silicon technology and transmission electron microscopy. First, a pore of 20 nm is opened in a silicon membrane by using electron-beam lithography and anisotropic etching. After thermal oxidation, the pore can be reduced to a single-nanometre when it is exposed to a high-energy electron beam. This fluidizes the silicon oxide leading to a shrinking of the small hole due to surface tension. When the electron beam is switched off, the material quenches and retains its shape. This technique dramatically increases the level of control in the fabrication of a wide range of nanodevices.

Unzipping kinetics of double-stranded DNA in a nanopore

We studied the unzipping of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. Polymerase chain reaction analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip each molecule was inferred from the ionic current signature of DNA traversal. The distribution of times to unzip under various experimental conditions fit a simple kinetic model. Using this model, we estimated the enthalpy barriers to unzipping and the effective charge of a nucleotide in the pore, which was considerably smaller than previously assumed.

Scaling relations for implantation of size-selected Au, Ag, and Si clusters into graphite

The deposition of size-selected clusters represents a new route to the fabrication of truly nanometer-scale surface architectures, e.g., nanopores. We report a systematic experimental study, coupled with molecular dynamics simulations, of the implantation depths of size-selected Au7, Ag7, and Si7 clusters in the model graphite substrate. For impact energies between 1.0 and 5.5 keV, we find that the implantation depth scales linearly with the momentum of the clusters for all three types of cluster. This "universal" behavior is consistent with a (viscous) retarding force proportional to the velocity of the cluster, akin to Stokes's law.

Direct detection of antibody-antigen binding using an on-chip artificial pore

We demonstrate a rapid and highly sensitive all-electronic technique based on the resistive pulse method of particle sizing with a pore to detect the binding of unlabeled antibodies to the surface of latex colloids. Here, we use an on-chip pore to sense colloids derivatized with streptavidin and measure accurately their diameter increase on specific binding to several different types of antibodies. We show the sensitivity of this technique to the concentration of free antibody and that it can be used to perform immunoassays in both inhibition and sandwich configurations. Overall, our technique does not require labeling of the reactants and is performed rapidly by using very little solution, and the pore itself is fabricated quickly and inexpensively by using soft lithography. Finally, because this method relies only on the volume of bound ligand, it can be generally applied to detecting a wide range of ligand-receptor binding reactions.

Ion-beam sculpting time scales

A study of ion sculpting dynamics in SiO2 and SiN using periodically pulsed ion beams reveals material transport that depends strongly on the time structure of the pulsed beams. It is found that significant nanoscale matter transport can occur over second long time scales after the ion beam has been extinguished. A simple phenomenological model described the dynamics of ion beam sculpting in terms of two material time scales. The model accounts for the surprising observation of enhanced matter transport affected by pulsed ion beams over continuous ion beam exposure.

Biosensors for DNA sequence detection

DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

Whole cell patch clamp recording performed on a planar glass chip

The state of the art technology for the study of ion channels is the patch clamp technique. Ion channels mediate electrical current flow, have crucial roles in cellular physiology, and are important drug targets. The most popular (whole cell) variant of the technique detects the ensemble current over the entire cell membrane. Patch clamping is still a laborious process, requiring a skilled experimenter to micromanipulate a glass pipette under a microscope to record from one cell at a time. Here we report on a planar, microstructured quartz chip for whole cell patch clamp measurements without micromanipulation or visual control. A quartz substrate of 200 microm thickness is perforated by wet etching techniques resulting in apertures with diameters of approximately 1 microm. The apertures replace the tip of glass pipettes commonly used for patch clamp recording. Cells are positioned onto the apertures from suspension by application of suction. Whole cell recordings from different cell types (CHO, N1E-115 neuroblastoma) are performed with microstructured chips studying K(+) channels and voltage gated Ca(2+) channels.

Stochastic sensors inspired by biology

Sensory systems use a variety of membrane-bound receptors, including responsive ion channels, to discriminate between a multitude of stimuli. Here we describe how engineered membrane pores can be used to make rapid and sensitive biosensors with potential applications that range from the detection of biological warfare agents to pharmaceutical screening. Notably, use of the engineered pores in stochastic sensing, a single-molecule detection technology, reveals the identity of an analyte as well as its concentration.