Radio-frequency scanning tunnelling microscopy

The scanning tunnelling microscope (STM) relies on localized electron tunnelling between a sharp probe tip and a conducting sample to attain atomic-scale spatial resolution. In the 25-year period since its invention, the STM has helped uncover a wealth of phenomena in diverse physical systems--ranging from semiconductors to superconductors to atomic and molecular nanosystems. A severe limitation in scanning tunnelling microscopy is the low temporal resolution, originating from the diminished high-frequency response of the tunnel current readout circuitry. Here we overcome this limitation by measuring the reflection from a resonant inductor-capacitor circuit in which the tunnel junction is embedded, and demonstrate electronic bandwidths as high as 10 MHz. This approximately 100-fold bandwidth improvement on the state of the art translates into fast surface topography as well as delicate measurements in mesoscopic electronics and mechanics. Broadband noise measurements across the tunnel junction using this radio-frequency STM have allowed us to perform thermometry at the nanometre scale. Furthermore, we have detected high-frequency mechanical motion with a sensitivity approaching approximately 15 fm Hz(-1/2). This sensitivity is on par with the highest available from nanoscale optical and electrical displacement detection techniques, and the radio-frequency STM is expected to be capable of quantum-limited position measurements.     

Atomic-scale imaging of insulating diamond through resonant electron injection

The electronic properties of insulators such as diamond are of interest not only for their passive dielectric capabilities for use in electronic devices, but also for their strong electron confinement on atomic scales. However, the inherent lack of electrical conductivity in insulators usually prevents the investigation of their surfaces by atomic-scale characterization techniques such as scanning tunnelling microscopy (STM). And although atomic force microscopy could in principle be used, imaging diamond surfaces has not yet been possible. Here, we demonstrate that STM can be used in an unconventional resonant electron injection mode to image insulating diamond surfaces and to probe their electronic properties at the atomic scale. Our results reveal striking electronic features in high-purity diamond single crystals, such as the existence of one-dimensional fully delocalized electronic states and a very long diffusion length for conduction-band electrons. We expect that our method can be applied to investigate the electronic properties of other insulating materials and so help in the design of atomic-scale electronic devices.     

Images of single-stranded nucleic acids by scanning tunnelling microscopy

The scanning tunnelling microscope has the potential to resolve the structure of biological molecules with atomic detail. Progress has been made in the imaging of dried, unshadowed double helices of DNA4-7 and in recording images of DNA under water. Also, images of unshadowed complexes of DNA with the RecA protein from Escherichia coli indicate that this technique may not be restricted to thin biological samples. Here we present images of polydeoxyadenylate molecules aligned in parallel, with their bases lying flat on a surface of highly oriented pyrolytic graphite and with their charged phosphodiester backbones protruding upwards. Based on these images, a molecular model has been built which suggests the presence of a hydrogen bond that could stabilize the parallel alignment. Our micrographs demonstrate the potential application of scanning tunnelling microscopy in structural studies of nucleic acids and provide evidence that it could be used to sequence DNA.     

Determination of surface topography of biological specimens at high resolution by scanning tunnelling microscopy

Although techniques are available for the determination of the three-dimensional structure of biological specimens, for example scanning electron microscopy, they all have some serious drawback, such as low resolution, the requirement for crystals or for the sample to be analysed in a high vacuum. In an attempt to develop a technique for high-resolution three-dimensional structure analysis of non-crystalline biological material, we have tested the applicability of scanning tunnelling microscopy (STM), a method that has been used successfully in the analysis of metal and semiconductor surface structures. We report here that scanning tunnelling electron microscopy can be used to determine the surface topography of biological specimens at atmospheric pressure and room temperature, giving a vertical resolution of the order of 1 A. Our results show that quantum mechanical tunnelling of electrons through biological material is possible provided that the specimen is deposited on a conducting surface.     

The three-dimensional structure of a DNA duplex containing looped-out bases

Unpaired bases in DNA have been assigned a possible role in the mechanism of frameshift mutagenesis in sequences with repeated base pairs. They also occur in quasipalindromic DNA sequences, which have been implicated in mutagenesis where there are no repeated base pairs, through the formation of single-stranded hairpin loops. The conformation of unpaired bases in DNA has been the subject of numerous thermodynamic as well as high resolution NMR (nuclear magnetic resonance) studies (reviewed in ref. 4). The NMR studies in solution have shown that the duplex of the tridecamer DNA fragment d(CGCAGAATTCGCG) remains intact, and that the unpaired adenosines are stacked into the duplex. Having crystallized this oligonucleotide and determined its structure, we find its conformation in the crystal is close to that of a B-DNA duplex, with the two additional adenosines looped out from the double helix and causing little disruption of the rest of the structure.     

Imaging and dynamics of light atoms and molecules on graphene

Observing the individual building blocks of matter is one of the primary goals of microscopy. The invention of the scanning tunnelling microscope revolutionized experimental surface science in that atomic-scale features on a solid-state surface could finally be readily imaged. However, scanning tunnelling microscopy has limited applicability due to restrictions in, for example, sample conductivity, cleanliness, and data acquisition rate. An older microscopy technique, that of transmission electron microscopy (TEM), has benefited tremendously in recent years from subtle instrumentation advances, and individual heavy (high-atomic-number) atoms can now be detected by TEM even when embedded within a semiconductor material. But detecting an individual low-atomic-number atom, for example carbon or even hydrogen, is still extremely challenging, if not impossible, via conventional TEM owing to the very low contrast of light elements. Here we demonstrate a means to observe, by conventional TEM, even the smallest atoms and molecules: on a clean single-layer graphene membrane, adsorbates such as atomic hydrogen and carbon can be seen as if they were suspended in free space. We directly image such individual adatoms, along with carbon chains and vacancies, and investigate their dynamics in real time. These techniques open a way to reveal dynamics of more complex chemical reactions or identify the atomic-scale structure of unknown adsorbates. In addition, the study of atomic-scale defects in graphene may provide insights for nanoelectronic applications of this interesting material.     

Scanning tunnelling microscopy of Z-DNA

Scanning tunnelling microscopy (STM) has been used to map the surface topography of inorganic materials at the atomic level, and is potentially one of the most powerful techniques for probing biomolecular structure. Recent STM studies of calf thymus DNA and poly(rA).poly(rU) have shown that the helical pitch and periodic alternation of major and minor grooves can be visualized and reliably measured. Here we present the first STM images of poly(dG-me5dC).poly(dG-me5dC) in the Z-form. Both the general appearance of the fibres and measurements of helical parameters are in good agreement with models derived from X-ray diffraction.     

对一种新型全有机复合薄膜的超高密度信息存储研究

用真空热壁法生长了一种新型全有机复合薄膜TTF/m-NBP(tetrathiofulvalene/m-nitrobenzylidene propanedinitrile)。用透射电子显微镜和傅立叶变换红外光谱对薄膜的表征结果证明,该制备方法能够生长出较大面积的化学结构完善的单晶薄膜。用原子力显微镜(AFM)和扫描隧道显微镜(STM)都观察到了TTF/m-NBP薄膜表面的原子级分辨像。通过STM针尖施加脉冲电压在TTF/m-NBP薄膜上实现了纳米级的信息存储,最小记录点直径约为1.2nm。扫描隧道谱分析表明TTF/m-NBP薄膜具有很好的电开关“记忆”特性。初步研究认为其电开关机制可能主要是脉冲电压诱发的TTF电子给体与m-NBP电子受体分子间的电荷转移的变化所致。     

DDME分子在石墨(HOPG)表面吸附

用扫描隧道显微镜(STM)研究了用真空沉积法在高定向有序石墨(HOPG)上制备的1, 1dicyano-2, 2-(4-dimethylaminophenyl) ethylene(DDME)薄膜。DDME在石墨表面形成十分平整的分子柱状堆积二维有序结构。还观察到了随覆盖度降低转变成为其他二维有序结构,并对其形成机理进行了研究。     

Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet.

A new Watson-Crick base pair, with a hydrogen bonding pattern different from that in the A.T and G.C base pairs, is incorporated into duplex DNA and RNA by DNA and RNA polymerases and expands the genetic alphabet from 4 to 6 letters. This expansion could lead to RNAs with greater diversity in functional groups and greater catalytic potential.     

An unusual DNA structure detected in a telomeric sequence under superhelical stress and at low pH

Telomeric sequences of DNA, which are found at the ends of linear chromosomes, have been attracting attention as potential sites for the formation of unusual DNA structures. They consist of (GnTm) or (GnATm) motifs (n greater than or equal to m) and, in the single-stranded state, form hairpins stabilized by non-canonical G.G pairs. In the duplex state and under superhelical stress they exhibit hypersensitivity to SI nuclease which by analogy with homopurine-homopyrimidine sequences may reflect the formation of an unusual structure. To determine whether this is the case we have inserted into a plasmid the Tetrahymena telomeric motif (G4T2).(A2C4) and probed it by two-dimensional gel electrophoresis, chemical modification and oligonucleotide binding. Our data demonstrate that, under superhelical stress and at low pH, the insert does indeed adopt a novel DNA conformation. We have concluded that in this structure the C-rich strand forms a hairpin stabilized by non-Watson-Crick base pairs C.C+ and A.A+, whereas the G-rich strand remains unstructured. We term this new DNA structure the (C,A)-hairpin.     

Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair

The Ku heterodimer (Ku70 and Ku80 subunits) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. The crystal structure of the human Ku heterodimer was determined both alone and bound to a 55-nucleotide DNA element at 2.7 and 2.5 A resolution, respectively. Ku70 and Ku80 share a common topology and form a dyad-symmetrical molecule with a preformed ring that encircles duplex DNA. The binding site can cradle two full turns of DNA while encircling only the central 3-4 base pairs (bp). Ku makes no contacts with DNA bases and few with the sugar-phosphate backbone, but it fits sterically to major and minor groove contours so as to position the DNA helix in a defined path through the protein ring. These features seem well designed to structurally support broken DNA ends and to bring the DNA helix into phase across the junction during end processing and ligation.     

Subduction erosion along the Middle America convergent margin

'Subduction erosion' has been invoked to explain material missing from some continents along convergent margins. It has been suggested that this form of tectonic erosion removes continental material at the front of the margin or along the underside of the upper (continental) plate. Frontal erosion is interpreted from disrupted topography at the base of a slope and is most evident in the wake of subducting seamounts. In contrast, structures resulting from erosion at the base of a continental plate are seldom recognized in seismic reflection images because such images typically have poor resolution at distances greater than approximately 5 km from the trench axis. Basal erosion from seamounts and ridges has been inferred, but few large subducted bodies--let alone the eroded base of the upper plate--are imaged convincingly. From seismic images we identify here two mechanisms of basal erosion: erosion by seamount tunnelling and removal of large rock lenses of a distending upper plate. Seismic cross-sections from Costa Rica to Nicaragua indicate that erosion may extend along much of the Middle America convergent margin.     

碳纳米管的STM观测

本文利用隧道扫描显微镜（STM）在室温条件下，低真空环境中，在高定向裂解石墨（HOPG）表面，对单壁碳纳米管（SWCN）以及多壁碳纳米管（MWCN）进行了观测，效果良好。     

Local destabilisation of a DNA double helix by a T--T wobble pair.

Nuclear magnetic resonance is a technique which permits direct observation of the Waton--Click hydrogen-bonded ring imino protons (guanine N1H and thymine N3H). As the formation and disruption of hydrogen bonds of double-helical RNA and DNA structures are key events during various biological processes, NMR thus provides a useful tool for studying the fluctuational mobility of the individual base pairs. Indeed, several NMR studies of oligo- and polynucleotides have been carried out to probe the structure and dynamics of nucleic acids in solution (for a review see ref. 1). The present study constitutes the first part of our attempt to assess the influence of non-complementary base pairs on the stability of nucleic acid double helices. We report the spectral assignment and temperature-dependent NMR profiles of the hydrogen-bonded imino protons of the two DNA fragments shown in Fig. 1. The assignment is based solely on experimental grounds using the principle of chemical modification. It will be demonstrated that the introduction of a non-complementary (wobble) base pair in a DNA duplex introduces an extra melting site in addition to the sequential melting which starts with the terminal base pairs in the double helix structure.     

X-ray structure of a DNA hairpin molecule

We have solved the crystal structure of a synthetic DNA hexadecanucleotide of sequence: C-G-C-G-C-G-T-T-T-T-C-G-C-G-C-G, at 2.1 A resolution, and observed that it adopts a monomeric hairpin configuration with a Z-DNA hexamer stem. In the T4 loop the bases stack with one another and with neighbouring molecules of the crystal, and not with base pairs of their own hexamer stem. Two thymine T10 rings from different molecules stack between the C1-G16 ends of a third and a fourth hairpin helix, in a manner that suggests T-T base 'pairing' and simulates a long, 13-base-pair helix. Although such T-T interactions would not be present in solution, they illustrate a remarkable tendency of thymines for self-association. Purine-purine G-A base pairs are known to exist in the anti-anti conformation with an increase in local helix width; it may be that more serious consideration should be given to the possible existence of pyrimidine-pyrimidine C-T base pairs with decreased local helix width, particularly where several such base pairs occur sequentially.     

Two-electron dissociation of single molecules by atomic manipulation at room temperature

Using the tip of a scanning tunnelling microscope (STM) to mechanically manipulate individual atoms and molecules on a surface is now a well established procedure. Similarly, selective vibrational excitation of adsorbed molecules with an STM tip to induce motion or dissociation has been widely demonstrated. Such experiments are usually performed on weakly bound atoms that need to be stabilized by operating at cryogenic temperatures. Analogous experiments at room temperature are more difficult, because they require relatively strongly bound species that are not perturbed by random thermal fluctuations. But manipulation can still be achieved through electronic excitation of the atom or molecule by the electron current tunnelling between STM tip and surface at relatively high bias voltages, typically 1-5 V. Here we use this approach to selectively dissociate chlorine atoms from individual oriented chlorobenzene molecules adsorbed on a Si(111)-7 x 7 surface. We map out the final destination of the chlorine daughter atoms, finding that their radial and angular distributions depend on the tunnelling current and hence excitation rate. In our system, one tunnelling electron has nominally sufficient energy to induce dissociation, yet the process requires two electrons. We explain these observations by a two-electron mechanism that couples vibrational excitation and dissociative electron attachment steps.     

色氨酸分子在石墨表面吸附的扫描隧道显微镜研究

用扫描隧道显微镜(STM)研究了室温下色氨酸分子(L-Tryptophane)在石墨(HOPG)表面的吸附行为。实验发现,在室温下色氨酸分子可以在石墨表面形成均匀的吸附层,并形成二维条状结构和二维单斜晶格两种有序结构。针对这2种结构给出了可能的吸附模型。这2种有序结构的形成原因被认为与相邻色氨酸分子侧链之间的π堆积相互作用有关。