STM Structure Determination of Adenine Bilayers by Moir� Interpretation (original) (raw)
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STM Structure Determination of Adenine Bilayers by MoireInterpretation
2000
Scanning tunnelling microscopy (STM) has been performed in air at room temperature on bilayers of the nucleic acid base adenine, adsorbed to a graphite surface following evaporation of saturated aqueous solutions. Our results indicate that the upper layer of the bilayer structure shows a structural change compared to the layer adsorbed directly to the graphite. The upper layer has a slightly larger unit cell, and is slightly sheared and rotated with respect to the layer directly adsorbed to the substrate. We can interpret these observations in terms of a model of rows of the adsorbate molecules stabilised by intermolecular hydrogen bonds.
Molecular mechanics study of hydrogen bonded self-assembled adenine monolayers on graphite
Surface Science, 1998
Molecular mechanics calculations using the Dreiding II force field were applied to self-assembled monolayer configurations of the nucleic acid base adenine adsorbed on graphite surfaces. Energy minimization calculations were used to refine the structures proposed by scanning tunneling microscopy (STM ) studies and low energy electron diffraction (LEED), and allowed discrimination between competing models on the basis of final configurations and local minima convergence. This allowed the relative position of the adenine molecules within the unit cell of p2gg symmetry to be inferred.
Ultramicroscopy, 1992
Analysis by AFM of adenine and thymine adsorbed onto a hot graphite surface shows that these molecules are adsorbed in patches typically 50 nm wide and 5 nm high, but does not provide any discernable atomic structure. In contrast, STM image scans that contain both parts of the graphite substrate and of the adsorbate would mislead one to believe that the adsorbates consist of just one ordered monolayer of either adenine of thymine (like alkylcyanobiphenyl on graphite [D.P.E. Smith et al., Nature 344 (1990) 641]). From these STM images the lattice dimensions, structural periodicities, and the epitaxy of the adsorbed molecules with respect to the basal plane of graphite can be determined. The aromatic regions are strongly detected with near-atomic resolution in both molecules, while the various sidegroups are not well resolved. Thus STM can discriminate between purines and pyrimidines -if they are held in thick patches.
Coexistence of Homochiral and Heterochiral Adenine Domains at the Liquid/Solid Interface
The Journal of Physical Chemistry B, 2007
In this work, the self-assembly of the DNA base molecule adenine (A) is imaged with high-resolution scanning tunneling microscopy (STM) at the liquid (1-octanol)/solid (HOPG) interface at room temperature. Rather surprisingly, the STM results reveal, for the first time, the spontaneous formation of two coexisting distinct (homo-and heterochiral) domains of adenine, which are formed at the liquid/solid interface without changing any experimental conditions. Ab initio density functional theory (DFT) calculations support our STM findings and suggest the existence of various A networks of nearly similar stability that all are constructed from the most stable A dimer.
Scanning tunneling microscope images of adenine and thymine at atomic resolution
Scanning microscopy, 1991
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 have been determined. Images of these molecules at atomic resolution reveal that the aromatic regions are strongly detected in both molecules while the various side-groups are not well-resolved. These studies provide the first evidence that tunneling microscopy can be used to discriminate between purines and pyramidines.
Structure of hydrated oligonucleotides studied by in situ scanning tunneling microscopy
Proceedings of the National Academy of Sciences, 1993
We have used the scanning tunneling microscope (STM) to image several synthetic oligonucleotides adsorbed onto a positively charged Au(111) electrode. The molecules were deposited and imaged in aqueous electrolyte under potential control, a procedure that eliminated the problem of the substrate artifacts that had limited some previous STM studies. Experiments were carried out with two types of single-stranded molecules (11 and 20 bases long) and three types of double-stranded molecules (20 and 61 base pairs and 31 bases with 25 bases paired and 6-base "sticky" ends). The molecules lie along symmetry directions on the reconstructed (23 x \/3-) gold surface, and length measurements indicate that they adopt simple base-stacked structures. The base stacking disances are, within experimental uncertainty, equal to the 0.33 nm measured for polymeric aggregates of stacked purines by direct imaging in identical conditions. The images show features consistent with helical structures. Double helices have a major-groove periodicity that is consistent with a 360 twist.
Scanning tunnelling microscopy observations of biomolecules on layered materials
Faraday Discussions, 1992
Scanning tunnelling microscopy (STM) has been performed on the reverse transcriptases of the human immunodeficiency virus (HIV-1) and the moloney murine leukaemia virus (MuLV). The biological molecules are adsorbed on n-type semiconducting MoTe2. The p66 (66 kD) subunit of the RT of HIV-1 is imaged by STM. Both STM and processed transmission electron microscopy (TEM) data show a spherical and horseshoe-like shape of external diameter ca. 65 A, depending on the angle of observation. The STM results show a larger diameter which is related to the curvature radius of the tip of the probing needle. The RTs of HIV-1 and MuLV exhibit a circular hole of ca. 20 A diameter in accordance with structure predictions and functioning considerations. The surface-molecule interaction is discussed in terms of the electronic properties of the semiconductor surface including the influence of small defect sites at the layered crystal surface.
Langmuir, 2013
The early stage of adsorption of adenine on Si(111)7×7 is studied by scanning tunneling microscopy (STM). Bright protrusions are observed in both empty-state and filled-state STM images, indicative of molecular adsorption of adenine through dative bonding. The majority of these bright protrusions appear as dimer pairs formed by hydrogen bonding at the initial adsorption stage. The formation of dative bonds between the substrate and adenine and the feasibility of the Hbond mediated dimers are supported by ab initio DFT/B3LYP/ 6-31G++(d,p) calculations, and are in excellent accord with our recent X-ray photoemission data. Remarkably, these dimers are found to undergo self-organization into aligned superstructures, evidently with common link arrangements, including straight, offset, and zigzag chains, square quartets, double quartets, and other multiple dimer structures. As the exposure of adenine increases, the populations of dimers as well as the self-organized double dimer and other higher-order structures also increase. The end-to-end dimer links are found to be most prominent in the growth of adenine molecular chains, most notably aligned along the Si dimer-wall or [−1 1 0] direction of the 7×7 unit cell. The self-aligned adenine dimer molecular chains offer a natural template for catch-and-release biosensing, lithography, and molecular electronic applications.