Life Sciences Commons^™

Microscopic Analysis Of Dna And Dna-Protein Assembly By Transmission Electron Microscopy, Scanning Tunneling Microscopy And Scanning Force Microscopy, T. Müller-Reichhert, H. Gross

Scanning Microscopy

To investigate DNA and DNA-protein assembly, nucleic acids were adsorbed to freshly cleaved mica in the presence of magnesium ions. The efficiency of DNA adhesion and the distribution of the molecules on the mica surface were checked by transmission electron microscopy. In addition, various kinds of DNA-protein interactions including DNA wrapping and DNA super-coiling were analyzed using electron microscopy. In parallel, this Mg²⁺/mica method can be applied (1) to analyze embedded DNA by scanning tunneling microscopy, (2) to visualize freeze-dried, metal coated DNA-protein complexes by tunneling microscopy, and (3) to image DNA or DNA-protein interaction in air or …

Imaging Soft Materials With Scanning Tunneling Microscopy, J. T. Woodward Iv, J. A. Zasadzinski

Scanning Microscopy

By modifying freeze-fracture replication, a standard electron microscopy fixation technique, for use with the scanning tunneling microscope (STM), a variety of soft, non-conductive biomaterials can be imaged at high resolution in three dimensions. Metal replicas make near ideal samples for STM in comparison to the original biological materials. Modifications include a 0.1 μm backing layer of silver and mounting the replicas on a fine-mesh silver filters to enhance the rigidity of the metal replica. This is required unless STM imaging is carried out in vacuum; otherwise, a liquid film of contamination physically connects the STM tip with the sample. This …

Photon Emission Induced By The Scanning Tunneling Microscope, Richard Berndt

Scanning Microscopy

By using the tip of a scanning tunneling microscope (STM) as a local source for electrons (or holes) light emission can be excited from metals, semiconductors and molecules. Using this technique, it is possible to combine the high spatial resolution of STM with optical techniques. We review results obtained using a variety of modes of measurements including fluorescence spectroscopy, isochromat spectroscopy and simultaneous mapping of photon emission and surface topography. In spatial maps of the photon emission, clear contrasts are observed with lateral resolutions below 1 nm which are related to the geometric and electronic structure of the sample and …

Tip-Induced Modifications In Scanning Tunneling Microscopy And Atomic Force Microscopy, K. Cho, J. D. Joannopoulos

Scanning Microscopy

Tip-induced modifications of microscopic processes in scanning tunneling microscopy (STM) and atomic force microscopy (AFM) of the Si(l00) surface are investigated with ab initio total energy pseudopotential calculations. The results of the calculations lead to a new understanding of the microscopic STM measurement process and the micro-mechanical changes (hysteresis and plastic deformation) in the AFM process. In particular, in the latter case, the results predict that the tip can be used to flip dimers on the surface, from one buckled configuration to the other, reversibly, and without inducing damage to either the intrinsic surface or the tip.

Scanning Tunneling Microscope-Induced Luminescence Spectroscopy On Semiconductor Heterostructures, M. Pfister, M. B. Johnson, U. Marti, S. F. Alvarado, H. W. M. Salemink, D. Martin, F. Morier-Genoud, F. K. Reinhart

Scanning Microscopy

Scanning tunneling microscope (STM)-induced luminescence is explored as a technique for the characterization of semiconductor quantum wells and quantum wire heterostructures. By injecting minority carriers into the cleaved cross section of these structures, luminescence excitation on a nanometer scale is demonstrated. Using spectrally resolved STM-induced luminescence for the tip placed at various positions across the cleaved heterostructure, it is possible to obtain local spectroscopic information on closely spaced quantum structures.

Principles Of Semiconductor Surface Reconstruction, C. B. Duke

Scanning Microscopy

Semiconductor surfaces are known to reconstruct, i.e., their surface atomic geometries differ from those of the corresponding surface planes in the bulk material. For clean tetrahedrally coordinated semiconductors, these reconstructed geometries are shown to be predicted by five simple principles. These principles are illustrated by the specific examples of Si(100)-(2x1), Si(111)-(2x1), GaAs(100)-c(2x8), GaAs(111)-(2x2), and relaxed zincblende (110) surfaces. The concept of universal (i.e., material independent) semiconductor surface structures is introduced and shown to be characteristic of the cleavage surfaces of tetrahedrally coordinated compound semiconductors. The role of scanning tunneling microscopy in identifying and validating these principles is highlighted.

Light Scattering And Electron Microscopy Study Of The Surface Morphology Of Gaas Films Grown By Molecular Beam Epitaxy, M. K. Nissen, C. Lavoie, S. Eisebitt, T. Pinnington, T. Tiedje

Scanning Microscopy

The surface morphology of thermally quenched GaAs films grown by molecular beam epitaxy on GaAs substrates has been studied by elastic light scattering, by scanning electron microscopy and by scanning tunneling microscopy (STM) in air. STM shows that the oxide-desorbed surface of GaAs is pitted, but smooths after deposition of a few hundred nanometers of material. Light scattering shows that, after the surface has smoothed, the power spectral density of the surface approaches a q^-2 dependence on spatial frequency over the spatial frequency range 0.2 μm^-1 < q < 20 μm^-1 that is accessible to the light scattering measurements at 488 nm. …

Boron Reconstructed Si(111) Surfaces Produced By B2o3 Decomposition, J. Nogami, S. Yoshikawa, J. C. Glueckstein, P. Pianetta

Scanning Microscopy

Scanning tunneling microscopy has been used to study the growth of boron on the Si(111) surface. Boron was deposited in the form of B₂O₃ which was decomposed by heating the substrate. With this technique, it is possible to control the B coverage, and also to produce the well known √3 x √3 reconstruction at annealing temperatures as low as 600°C. The optimal conditions for the formation of the √3 x √3 surface by B₂O₃ decomposition are given. In addition, the nature of the √3 x √3 surface over …

Molecular Imaging Of Petroleum Asphaltenes By Scanning Tunneling Microscopy: Verification Of Structure From 13c And Proton Nuclear Magnetic Resonance Data, G. W. Zajac, N. K. Sethi, J. T. Joseph

Scanning Microscopy

Scanning tunneling microscopy (STM) was used to verify the molecular structure of Maya asphaltene which had been derived from combined ¹³C and proton nuclear magnetic resonance (NMR) experiments. Petroleum asphaltenes are known to contain large polynuclear aromatic centers with aliphatic sidechains. Average molecular models of Maya asphaltenes were derived using studies which included combined proton and ¹³C NMR data to determine total aromatic carbon content and the ratio of peripheral to internal aromatic ring carbons. These parameters permitted estimating the average number of aromatic rings per condensed cluster.

These Maya asphaltenes were imaged by scanning tunneling microscopy (STM) …

Electron Spectroscopy And Atomic Force Microscopy Studies Of Dna Adsorption On Mica, Carol E. Rabke, Lisa A. Wenzler, Thomas P. Beebe Jr.

Scanning Microscopy

Various methods for the deposition of deoxyribonucleic acid (DNA) molecules on mica are investigated to determine their reproducibility, and to quantify their ability to bind DNA. The use of these deposition methods for sample preparation for biological scanning tunneling microscopy (STM) and atomic force microscopy (AFM) studies is discussed. Auger electron spectroscopy (AES) and electron spectroscopy for chemical analysis (ESCA) were used to investigate the quantity of DNA adsorbed. AFM images of DNA deposited using the methods investigated are presented. The combination of AFM results with AES and ESCA results provides a basic understanding of the deposition techniques studied and …

Superstructures Of Graphite Intercalation Compound Formed By Sodium-Hydroxide Solution Studied By Scanning Tunneling Microscopy, Koji Miyake, Aiso Yoshiaki, Makoto Komiyama, Hidemi Shigekawa

Scanning Microscopy

Highly oriented pyrolytic graphite (HOPG) treated with sodium hydroxide solution was found to show an X-ray diffraction pattern characteristic of a stage-8 intercalation compound. Superstructures such as 2 X 2, √3 X √3 and noble orthorhombic lattices were observed on the NaOH-treated graphite surfaces by scanning tunneling microscopy, as was previously observed on stage-1 alkali-metal graphite intercalation compound (GIC) surfaces formed by Li, K, Rb and Cs intercalates. The orthorhombic phase has a periodic structure formed by four bright and two dark rows, which were explained by the intercalant arrangement occupying two different sites, in the GIC.

Direct Observation By Scanning Tunneling Microscopy Of The Two-Dimensional Lattice Structure Of The S-Layer Sheath Of The Archaeobacterium Methanospirillum Hungatei Gp1, B. L. Blackford, W. Xu, M. H. Jericho, P. J. Mulhern, M. Firtel, T. J. Beveridge

Scanning Microscopy

Observation of the two-dimensional (2-D) 3 nm x 3 nm lattice structure of the S-layer sheath of the archaeobacterium Methanospirillum hungatei is reported for the first time by scanning tunneling microscopy. The samples consisted of sheath fragments deposited on a TaSe₂ substrate and coated with a Pt/Ir film. In addition to confirming the 2-D structure, the images reveal some new information about the nano-scale details of the sheath structure. A lateral resolution of 1 nm was achieved, suggesting that the grain size of the Pt/Ir films was much less than for similar films deposited on a smooth metal surface.

New Methods For Depositing And Imaging Molecules In Scanning Tunneling Microscopy, Victor N. Morozov, Nadrian C. Seeman, Neville R. Kallenbach

Scanning Microscopy

Methods and apparatus are described to deposit and image molecules by scanning tunneling microscopy (STM) under an inert atmosphere. Three methods of applying molecules have been evaluated: equilibrium adsorption from the vapor phase, sublimation, and electrospraying. Using these methods, a variety of organic and biopolymer molecules have been deposited and imaged on graphite and on gold (111), grown epitaxially on mica. Compared with alternatives, such as the use of high vacuum apparatus or glove boxes, these procedures offer some important advantages: they are inexpensive, convenient, and more rapid. Mercaptoethanol, ethanolamine, ethanol, acetic acid, and water produce two-dimensional crystalline adlayers on …

Scanning Tunneling Microscopy: A Chemical Perspective, C. Julian Chen

Scanning Microscopy

In this review article, scanning tunneling microscopy (STM) is presented in a chemical perspective. The typical distance from the nucleus of the apex atom of the tip to the top-layer nuclei of the sample is 4-6 Å, where a strong attractive atomic force, i.e., a partial covalent bond, arises between the tip and the sample. The origin of the covalent bond is the back-and-forth transfer of electrons between two atoms, which Pauling has called resonance. While a bias voltage is applied between them, a net electron current in a specific direction arises. This tunneling current is a result of …

A Scanning Tunneling Microscopy Study Of Vanadium Oxide, Takanori Oshio, Yoshiyuki Sakai, Tohru Moriya, Shaw Ehara

Scanning Microscopy

Atomic resolution images of the (010) surface of a divanadiun pentoxide (V₂O₅) single crystal were successfully obtained by the use of a scanning tunneling microscope (STM).

The images of the filled states at sample bias voltage, Vs = -2 V and the empty states at Vs = +2 V correspond to oxygen and vanadium ions, respectively.

As for the vanadium ion sites, an additional peak of the electronic states at the conduction band edge due to the defects of vanadyl oxygen ions was found in the normalized conductance spectrum through the tunneling spectroscopy (TS) measurement.

Morphology Studies Of Iron-Manganese Thin Films, G. Mathew, K. -W. Ng, A. R. Sethuraman, J. M. Stencel

Scanning Microscopy

Fe-based catalysts are known to be effective for Fischer-Tropsch synthesis from coal but are sensitive to sulfur poisoning. Addition of manganese to these catalysts has been proposed in an effort to combat this catalyst deactivation. To investigate the fundamental physical aspects of Mn incorporation into Fe, different compositions of model thin films of Fe-Mn, ranging from 100% Fe to 100% Mn were studied for the very first time, using scanning tunneling microscopy (STM), atomic force microscopy (AFM) and scanning electron microscopy. Our preliminary results indicate that the grain size of iron varied from 50 nm to 150 nm using the …

A Review Of Graphite And Gold Surface Studies For Use As Substrates In Biological Scanning Tunneling Microscopy Studies, Carol R. Clemmer, Thomas P. Beebe Jr.

Scanning Microscopy

The current status of biological Scanning Tunneling Microscopy (STM) investigations and the importance of using a well-characterized substrate are discussed. The findings of over two years of experiments and over 1,000 images obtained on gold substrates prepared by a variety of different methods are statistically summarized and compared to a very flat reference substrate, highly oriented pyrolytic graphite (HOPG). In an effort to begin to corroborate STM results with those obtained from other more established techniques, the results of Auger Electron Spectroscopy (AES) and Electron Spectroscopy for Chemical Analysis (ESCA) of biomolecular STM samples are presented.

The Scanning Probe Microscope, J. Jahanmir, B. G. Haggar, J. B. Hayes

Scanning Microscopy

Scanning probe microscopy bas evolved into a powerful tool since its inception in 1982. The scanning probe microscope bas found applications in metrology, spectroscopy, and lithography. We will review the background of the technology, discuss the different types of scanning probe microscopes including the scanning tunneling microscope and the scanning force microscope, and present many of the applications for the instrument.

Scanning Tunneling Microscopy Of Biological Macromolecular Structures Coated With A Conducting Film, M. Amrein, H. Gross

Scanning Microscopy

We have studied the capability of scanning tunneling microscopy (STM) to reveal the three-dimensional structure of biological macromolecular structures that have been rendered conductive by metal-coating. The sample preparation used has been derived from a well established method in transmission electron microscopy (TEM). It includes adsorption, freezing and dehydration by vacuum-sublimation, followed by metal-shadowing of the specimen. As an alternative to adsorption and coating, fluid biomaterials can be replaced by conductive freeze-fracture replica.

We give an introduction into the sample preparation of metal-coated specimens and discuss how each step can affect the structural preservation and thereby the quality of the …

The Stability Of Adsorbates Imaged With A Scanning Tunneling Microscope Using Hopping Versus Constant Current Scanning, Terje G. Vold

Scanning Microscopy

We have studied the stability of various adsorbates, including gold, a platinum-iridium alloy, and DNA, on monoatomically flat gold imaged with a scanning tunneling microscope. We find that adsorbates are generally more stable, sometimes dramatically so, if imaged with a hopping trajectory of the tip rather than with the conventional constant-current scanning technique. Gold pits and associated debris formed on flat gold surfaces under saline solution by mechanical impact of the tip with the surface are always much more stable when imaged with hopping. Samples of thin, sub-monoatomic layers (0.1 nm and 0.2 nm thick) of a platinum-iridium alloy evaporated …

The Application Of Multispectral Techniques To Analytical Electron Microscopy, P. G. Kenny, M. Prutton, R. H. Roberts, I. R. Barkshire, J. C. Greenwood, M. J. Hadley, S. P. Tear

Scanning Microscopy

The York multispectral analytical electron microscope (MULSAM) was the first instrument specifically designed to acquire and process multiple Auger, X-ray, backscattered electron, elastically scattered electron, scanning electron microscopy (SEM) and specimen absorption current images simultaneously. Analyzing combinations of these signals with multispectral correlation techniques yields more information than would normally be obtained by treating each image separately. This paper reports some of the multispectral methods we have investigated at York which may be of use to other workers. Included are (1) a method that corrects for beam current fluctuations during long acquisition runs which is based on the anti-correlation between …

Scanning Tunneling Microscope Images Of Adenine And Thymine At Atomic Resolution, M. J. Allen, M. Balooch, S. Subbiah, R. J. Tench, W. Siekhaus, R. Balhorn

Scanning Microscopy

The scanning tunneling microscope has been used to obtain images of DNA that reveal its major and minor grooves and the direction of helical coiling, but sufficient resolution has not yet been achieved to identify its bases. To determine if this technology is capable of identifying individual DNA bases, we have examined the molecular arrangements of adenine and thymine attached to the basal plane of highly oriented pyrolytic graphite. Both molecules form highly organized lattices following deposition on heated graphite. Lattice dimensions, structural periodicities, and the epitaxy of adenine and thymine molecules with respect to the basal plane of graphite …

High-Resolution, Real-Space Imaging Of Conformational Structures Of Poly-L-Proline Helixes, N. J. Zheng, G. Rau, C. F. Hazlewood, C. Rau

Scanning Microscopy

In 1954, Edsall postulated that the imino-acid proline, which is a frequently found constituent of protein molecules, is a key determinant to the three-dimensional architecture of proteins. It not only should play a fundamental role in stabilizing helical structures of polypeptides, it should allow for sharp bends and even for a complete reversal of the direction of a helix looping back on itself. No direct evidence has yet been published to prove this prediction. Using scanning tunneling microscopy, we have presented high-resolution, real-space images of two conformations of poly-L-proline, where one structure clearly exhibits the predicted 180° back-folding behavior. The …

Scanning Tunneling Microscopy Imaging Of Synthetic Oligonucleotides And Oligonucleotide-Metal Complexes, Yun Kim, Charles M. Lieber

Scanning Microscopy

Scanning tunneling microscopy (STM) has been used to image 12-and 24-base pair (bp) synthetic oligonucleotide duplexes alone or with intercalatively-bound metal complexes with submolecular resolution. The sizes of the 12-and 24-bp oligonucleotides determined from STM images are close to expected values, and images of isolated duplexes resolve the two nucleotide strands of these molecules. The variation of duplex size in our images demonstrates that these features are not due to surface artifacts. In addition, images of the 12-bp duplex in the presence of bis(9, 10-phenanthrenequinone diimine)(2, 2'-bipyridyl) rhodium(III) exhibit a new structural feature at 14 ± 2 Å from the …

Scanning Tunneling Microscopy And Spectroscopy Of Plasmid Dna, D. P. Allison, J. R. Thompson, K. Bruce Jacobson, R. J. Warmack, T. L. Ferrell

Scanning Microscopy

We present scanning tunneling microscope (STM) images of uncoated deoxyribonucleic acid (DNA) electrochemically mounted on highly-oriented pyrolytic graphite (HOPG) and imaged in air. Images of linear abnormalities inherent to HOPG surfaces that can be confused with DNA are also presented. Scanning tunneling spectroscopic (STS) images generated by superimposing a small, high frequency ac bias onto the de tunnel bias and recording the ac current signal were taken simultaneously with the topographic images. These spectroscopic images reveal contrast due to local conductivity variations and can be used to differentiate DNA molecules from graphite artifacts.

Scanning Tunneling Microscopy And Fabrication Of Nanometer Scale Structures At The Liquid-Gold Interface, J. Schneir, H. H. Harary, J. A. Dagata, P. K. Hansma, R. Sonnenfeld

Scanning Microscopy

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.

Scanning Tunneling Microscopy Of Proteins On Graphite Surfaces, L. Feng, J. D. Andrade, C. Z. Hu

Scanning Microscopy

We applied scanning tunneling microscopy (STM) to the observation of amino acids and proteins deposited and/or adsorbed on highly oriented pyrolytic graphite (HOPG).

Although many questions remain, it is demonstrated that relatively high resolution images of uncoated proteins can often be obtained in air. We present images of five amino acids (glycine, leucine, lysine, methionine and tryptophan) and three proteins (lysozyme, albumin and fibrinogen) under various conditions of deposition and adsorption. We discuss the role of affinity of the amino acids and proteins to the substrate, their adsorbed states and distribution, and STM tip-induced deformation and/or destruction.

STM studies of …