Atomic resolution imaging of a carbon nanotube from diffraction intensities.

Atomic imaging of three-dimensional structures has required a crystal in diffraction or a lens in electron imaging. Whereas diffraction achieves very high resolution by averaging over many cells, imaging gives localized structural information, such as the position of a single dopant atom. However, lens aberrations limit electron imaging resolution to about 1 angstrom. Resolution is reduced further by low contrast from weakscattering or from the limitations on electron dose for radiation-sensitive molecules. We show that both high resolution and high contrast can be achieved by imaging from diffraction with a nanometer-sized coherent electron beam. The phase problem is solved by oversampling and iterative phase retrieval. We apply this technique to image a double-wall carbon nanotube at 1-angstrom resolution, revealing the structure of two tubes of different helicities. Because the only requirement for imaging is a diffraction pattern sampled below the Nyquist frequency, our technique has the potential to image nonperiodic nanostructures, including biological macromolecules, at diffraction intensity-limited resolutions.

Molecular adsorption onto metallic quantum wires.

We have studied the adsorption of mercaptopropionic acid, 2,2'-bipyridine, and dopamine onto electrochemically fabricated Cu nanowires. The nanowires are atomically thin with conductance quantized near integer multiples of 2e(2)/h. Upon molecular adsorption, the quantized conductance decreases to a fractional value, due to the scattering of the conduction electrons by the adsorbates. The decrease is as high as 50% for the thinnest nanowires whose conductance is at the lowest quantum step, and smaller for thicker nanowires with conductance at higher quantum steps. The adsorbate-induced conductance changes depend on the binding strengths of the molecules to the nanowires, which are in the order of mercaptopropionic acid, 2,2'-bipyridine, and dopamine, from strongest to weakest. The sensitive dependence of the quantized conductance on molecular adsorption may be used for molecular detection.

Electrochemical deposition of molecular adsorbates for in situ scanning probe microscopy.

We have studied gold and graphite electrodes in an electrochemistry cell under various solutions using the scanning tunneling microscope (STM). The gold (111) surface yields quite reproducible images and cyclic voltammograms. In situ voltammograms show that, under certain conditions, nanomolar quantities of DNA fragments can suppress the adsorption of a buffer salt of millimolar concentration. When the DNA concentration is reduced below that required for a monolayer coverage, the salt adsorption is restored. We show images of bare gold, gold covered with an adsorbate produced by the buffer salt, and gold prepared with a concentration of DNA fragments close to that required for monolayer coverage added to the buffer. Under these conditions, the surface is found to be uniformly covered with a characteristic structure.

STM and AFM images of nucleosome DNA under water.

We have imaged DNA from the calf thymus nucleosome using a scanning tunneling microscope (STM) operated in water. The fragments are deposited onto the interface between a buffer solution and an epitaxially grown gold surface using an electrochemical tecnique. Most of the fragments are fairly straight, and when individual polymers can be identified, their length is consistent with the expected 146 basepairs (approximately 500 A). The resolution is often adequate to show signs of the 36 A helical pitch. Some images show a structure which appears to have abrupt kinks of the sort predicted by Crick and Klug (Nature 255, 530-533, 1975). In order to check that this shape is not a consequence of binding to underlying structure on the gold substrate, we have also made images of kinked structures using an atomic force microscope (AFM) with the DNA bound to glass.

Sequence, packing and nanometer scale structure in STM images of nucleic acids under water.

Scanning tunneling microscope (STM) images of random-sequence nucleic acid polymers under water show internal structure which depends strongly on the packing density of the polymer. Images of dense aggregates have a semicrystalline order with the individual polymers adopting simple periodic structures. Loose aggregates (or isolated molecules) show structural variability with considerable local bending and curving on a nanometer scale. It is not clear to what extent this structure is induced by the operation of the microscope. In order to investigate the possibility that the structure is sequence directed, we have imaged various DNA and RNA polymers at low packing densities. We present results here for random sequence DNA, poly(dAT).poly(dAT), poly(dA).poly(dT), poly(dCG).poly(dCG) and for random sequence RNA and poly(U). In contrast to loose aggregates of the random sequence material, the homopolymers show few sharp bends. Furthermore, the homopolymers appear to yield characteristic backbone patterns, usually at resolutions in excess of that obtained with random sequence polymers. The random sequence polymers show much more evidence of image distortion due to tip-molecule interactions, suggesting that they are, on average, mechanically less stable in the STM tunnel-gap than the homopolymers. Thus, while some of the structure observed in STM images is a consequence of tip-molecule interactions, it is related to sequence-directed properties of the polymer.