Scanning tunneling microscope images of adenine and thymine at atomic resolution (original) (raw)
Related papers
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.
Molecular orbital interpretation of thymine/graphite nc-AFM images
Surface and Interface Analysis, 2001
Recent non-contact atomic force microscopy (nc-AFM) images of a deoxyribonucleic acid (DNA) base thymine (2,4-dioxy-5-methylpyrimidine) vacuum-deposited on a highly oriented pyrolytic graphite (HOPG) surface are interpreted by means of theoretical adsorption simulations, and the molecular geometry and the energetics of the adsorption system are estimated. The lowest-energy dimer configuration was found to be the one in which the respective hydrogen on N1 and the oxygen on C6 of two thymine molecules hydrogen bond to each other. A surface unit cell structure was reproduced. Adsorption energy for the thymine pair on HOPG is rather small, amounting to only ∼1 kcal mol −1 , with small variations depending on the molecular orientation with respect to the substrate surface. The possibility of having a mirrored adsorption configuration in adjacent domains also is suggested.
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.
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.
Imaging of oligonucleotide-metal complexes by scanning tunneling microscopy
Langmuir, 1992
Scanning tunneling microscopy (STM) has been used to image synthetic oligonucleotide duplexes alone or with an intercalatively bound metal complex with submolecular resolution. The sizes of 12 and 24 base pair (bp) oligonucleotides determined from STM images are in agreement with expected values, and images of isolated duplexes resolve the two nucleotide strands of these molecules. In addition, images of the 12-bp duplex in the presence of bis(9,lO-phenanthrenequinone diimine) (2,2'-bipyridyl)rhodium(III) exhibit a new structural feature a t 14 A from the 12-bp duplex end. This new feature corresponds well to the metal binding sites determined from DNA cleavage and molecular modeling studies. These results indicate that STM can be used to image directly transition-metal complexes bound to DNA and thus suggest that metal complexes bound specifically to biological and other macromolecules could serve as useful labels in STM structural studies.
STM Structure Determination of Adenine Bilayers by Moir� Interpretation
physica status solidi (a), 2001
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.
Scanning Tunneling Spectroscopy of Single DNA Molecules
2009
ABSTRACT We briefly present the results of recent experiments of transverse scanning tunneling spectroscopy of homogeneous poly (dG)-poly (dC) DNA molecules and discuss them in the light of theoretical investigation. A semiempirical theoretical model is adopted to describe the transverse tunneling current across a DNA molecule placed between a metallic gold substrate and a metallic STM tip.
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.