High-resolution STM imaging of novel single G4-DNA molecules

The molecular morphology of long G4-DNA wires made by a novel synthetic method was, for the first time, characterized by high-resolution scanning tunneling microscopy (STM). The STM images reveal a periodic structure seen as repeating "bulbs" along the molecules. These bulbs reflect the helix morphology of the wires. The STM measurements were supported by a statistical morphology analysis of the DNA pitch length and apparent height relative to the surface. In the absence of X-ray and NMR data for these wires, the STM measurements provide a unique alternative to characterize the helix morphology.     

Simultaneous time- and wavelength-resolved fluorescence microscopy of single molecules

Single fluorophores and single-pair fluorescence resonance energy transfer were studied with a new confocal fluorescence microscope that allows, for the first time, the wavelength and emission time of each detected photon to be simultaneously measured with single molecule sensitivity. In this apparatus, the photons collected from the sample are imaged through a dispersive optical system onto a time and position sensitive photon detector. For each detected photon the detection system records its wavelength, its emission time relative to the excitation pulse, and its absolute emission time. A histogram over many photons can generate a full fluorescence spectrum and correlated decay plot for a single molecule for any time interval. At the single molecule level, this approach makes possible entirely new types of temporal and spectral correlation spectroscopies. This paper presents our initial results on simultaneous time- and wavelength-resolved fluorescence measurements of single rhodamine 6G (R6G), tetramethylrhodamine (TMR), and Cy3 molecules embedded in thin films of poly(methyl methacrylate) (PMMA), and of single-pair fluorescence resonance energy transfer between two Alexa fluorophores spaced apart by a short polyproline peptide.     

Spectral imaging of single molecules by transmission grating-based epi-fluorescence microscopy

A spectral imaging method of single protein molecules labeled with a single fluorophore is presented. The method is based on a transmission grating and a routine fluorescence microscope. The bovine serum alubmin (BSA) and antiBSA molecules labeled with Alexa Fluor 488 and Alexa Fluor 594, respectively, are used as the model proteins. The fluorescence of single molecules is dispersed into zeroth-order spectrum and first-order spectrum by the transmission grating. Results show that the fluorescence emission spectrum of single molecule converted from the first-order spectral imaging is in good agreement with the bulk fluorescence spectrum. The spectral resolution of 2.4 nm/pixel is obtained, which is sufficient for identifying the molecular species in a multicomponent system.     

Observation of single dinuclear metal-complex molecules using scanning tunneling microscopy

We report a scanning tunneling microscopy (STM) investigation of a dinuclear organometallic molecule, trans-[Cl(dppe)2Ru(C[triple bond]C)6Ru(dppe)2Cl] (Ru2), absorbed on a Au(111) surface; this molecule is a potential candidate for use in molecular quantum-dot cellular automata (QCA) devices. Isolated Ru2 molecules were observed under ultra-high-vacuum conditions. Submolecular structure was clearly discernible in the STM images, with a bright feature corresponding to each of the two Ru-ligand complexes within the Ru2 molecule. Rotation and translation of the Ru2 molecules were observed to be induced by the STM tip under some tunneling conditions.     

High-resolution imaging of catalytic activity of a single graphene sheet using electrochemiluminescence microscopy

Here, the electrocatalytic activity of a single graphene sheet is mapped using electrochemiluminescence (ECL) microscopy with a nanometer resolution. The achievement of this high-spatial imaging relies on the varied adsorption of hydrogen peroxide at different sites on the graphene surface, leading to unsynchronized ECL emission. By shortening the exposure time to 0.2 ms, scattered ECL spots are observed in the ECL image that are not overlaid with the spots in the consecutive images. Accordingly, after stacking all the images into a graph, the ECL intensity of each pixel could be used to reflect the electrocatalytic features of the graphene surface with a resolution of 400 nm. This novel ECL method efficiently avoids the long-standing problem of classic ECL microscopy regarding the overlap of ECL emissions from adjacent regions and enables the nanometer spatial resolution of ECL microscopy for the first time.

High spatial electrochemiluminescence microscopy is established to map the electrocatalytic activity of a single graphene sheet with a nanometer resolution.     

Direct imaging of o-carborane molecules within single walled carbon nanotubes

Ortho-carborane molecules have been inserted into single walled carbon nanotubes (SWNTs) and imaged directly by high resolution transmission electron microscopy (HRTEM); both discrete molecules and 'zig-zag' 1D chains of o-carborane 'petit pois' were observed to pack into the tubule capillaries.     

High-resolution transmission electron microscopy using negative spherical aberration.

A novel imaging mode for high-resolution transmission electron microscopy is described. It is based on the adjustment of a negative value of the spherical aberration C S of the objective lens of a transmission electron microscope equipped with a multipole aberration corrector system. Negative spherical aberration applied together with an overfocus yields high-resolution images with bright-atom contrast. Compared to all kinds of images taken in conventional transmission electron microscopes, where the then unavoidable positive spherical aberration is combined with an underfocus, the contrast is dramatically increased. This effect can only be understood on the basis of a full nonlinear imaging theory. Calculations show that the nonlinear contrast contributions diminish the image contrast relative to the linear image for a positive-C S setting whereas they reinforce the image contrast relative to the linear image for a negative-C S setting. The application of the new mode to the imaging of oxygen in SrTiO3 and YBa2Cu3O7 demonstrates the benefit to materials science investigations. It allows us to image directly, without further image processing, strongly scattering heavy-atom columns together with weakly scattering light-atom columns.     

High-resolution nonlinear raman spectroscopy of small molecules

After a review of recent progress in nonlinear coherent Raman spectroscopy of gaseous small molecules we report on measurement by the techniques of intra- cavity cw CARS in Munich and inverse Raman spectroscopy in forward and backward scattering configuations in Dijon.     

Visualisation of an ultrafiltration membrane by non-contact atomic force microscopy at single pore resolution

Non-contact atomic force microscopy (AFM) has been used to investigate the furface pore structure of a polyethersulfone ultrafitration membrane of specified molecular weight cut off (MWCO) 25 000 (ES625, PCI Membrane Systems). Excellent images at up to single pore resolution were obtained. This is the first time that AFM images of a membrane at such high resolution have been presented. Analysis of the images gave a mean pore size of 5.1 nm with a standard deviation of 1.1 nm. The results have been compared to previously published studies of membranes of comparable MWCO using contact AFM and electron microscopy. Non-contact AFM is a powerful means of studying the surface pore characteristics of ultrafiltration membranes.     

Controllable distribution of single molecules and peptides within oligomer template investigated by STM

This communication provides a facile method for distributing and dispersing molecules within a molecular template. Using the self-assembled template of oligo(phenylene-ethynylene) (OPE), organic molecules such as coronene (COR) and biomolecules such as tripeptide are controllably distributed and dispersed within this molecular template on highly oriented pyrolytic graphite (HOPG) surfaces. COR molecules were controllably distributed into various regular arrays by simply adjusting the molecular molar ratio, while tripeptide molecules were uniformly positioned at the vacancies of the OPE template.     

High-resolution transmission electron microscopy: the ultimate nanoanalytical technique

To be able to determine the elemental composition and morphology of individual nanoparticles consisting of no more than a dozen or so atoms that weigh a few zeptograms (10(-21) g) is but one of the attainments of modern electron microscopy. With slightly larger specimens (embracing a few unit cells of the structure) their symmetry, crystallographic phase, unit-cell dimension, chemical composition and often the valence state (from parallel electron spectroscopic measurements) of the constituent atoms may also be determined using a scanning beam of electrons of ca. 0.5 nm diameter. Nowadays electron crystallography, which treats the digital data of electron diffraction (ED) and high-resolution transmission electron microscope (HRTEM) images of minute (ca. 10(-18)g) specimens in a quantitatively rigorous manner, solves hitherto unknown structures just as X-ray diffraction does with bulk single crystals. In addition, electron tomography (see cover photograph and its animation) enables a three-dimensional picture of the internal structure of minute objects, such as nanocatalysts in a single pore, as well as structural faults such as micro-fissures, to be constructed with a resolution of 1 nm from an angular series of two-dimensional (projected) images. Very recently (since this article was first written) a new meaning has been given to electron crystallography as a result of the spatio-temporal resolution of surface phenomena achieved on a femtosecond timescale.     

Magnetic field dependence of the diffusion of single dextran molecules within a hydrogel containing magnetite nanoparticles

We consider the effect of applied magnetic fields on the diffusion of single dextran molecules labeled with fluorescein isothiocyanate within a ferrogel [a composite of magnetite nanoparticles in a poly(methacrylic acid) hydrogel] using fluorescence correlation spectroscopy. We show that the mesh size of the ferrogel is controlled by the applied magnetic field, B, and scales as exp(-(4)√ξ(3)B(2)/2μ(0)k(B)T), where ξ is a correlation length, μ(0) the magnetic constant, k(B) the Boltzmann constant, and T is the absolute temperature. The diffusion coefficient of the dextran can be modeled with a simple Stokes-Einstein law, containing the same scaling behavior with magnetic field as the swelling of the hydrogel. Furthermore, the magnetic field-dependent release of dextran from the hydrogel is also controlled by the same relationship. The samples were characterized by small angle x-ray scattering (SAXS) and magnetometry experiments. Magnetic hysteresis loops from these ferrogels and zero field cooled∕field cooled measurements reveal single domain ferromagnetic behavior at room temperature with a similar coercivity for both as-prepared and fully swollen ferrogels, and for increasing magnetic nanoparticle concentration. SAXS experiments, such as the hysteresis loops, show that magnetite does not aggregate in these gels.     

High-resolution transmission electron microscopy study of nanostructured hydroxyapatite

Crystalline properties of synthetic nanostructured hydroxyapatite (n-HA) were studied using high-resolution transmission electron microscopy. The focal-series-restoration technique, obtaining exit-plane wavefunction and spherical aberration-corrected images, was successfully applied for the first time in this electron-beam-susceptible material. Multislice simulations and energy dispersive X-ray spectroscopy were also employed to determine unequivocally that n-HA particles of different size preserve stoichiometric HA-like crystal structure. n-HA particles with sizes of twice the HA lattice parameter were found. These results can be used to optimize n-HA sinterization parameters to improve bioactivity.     

Determining charge transport pathways through single porphyrin molecules using scanning tunneling microscopy break junctions

Charge transport in a porphyrin with four identical pyridyl substituents, 5,10,15,20-tetra(4-pyridyl)-21H,23H-porphine (TPyP), was investigated using the scanning tunneling microscopy break junction method. To determine the dominant pathway, we studied two structurally similar porphyrins, o-DPyP and p-DPyP. Our experiments reveal that charge transport through TPyP in a break junction configuration does not follow the traditional assumption, i.e., the shortest path between the neighboring side groups. Instead, the charge transport pathway was dominated by the farthest anchoring groups. Furthermore, these single molecule experiments can distinguish between the two structural isomers, which is important in molecular discrimination, porphyrin chemistry, and molecular electronics.     

Power-law blinking in the fluorescence of single organic molecules.

The blinking behavior of perylene diïmide molecules is investigated at the single‐molecule level. We observe long‐time scale blinking of individual multi‐chromophoric complexes embedded in a poly(methylmethacrylate) matrix, as well as for the monomeric dye absorbed on a glass substrate at ambient conditions. In both these different systems, the blinking of single molecules is found to obey analogous power‐law statistics for both the on and off periods. The observed range for single‐molecular power‐law blinking extends over the full experimental time window, covering four orders of magnitude in time and six orders of magnitude in probability density. From molecule to molecule, we observe a large spread in off‐time power‐law exponents. The distributions of off‐exponents in both systems are markedly different whereas both on‐exponent distributions appear similar. Our results are consistent with models that ascribe the power‐law behavior to charge separation and (environment‐dependent) recombination by electron tunneling to a dynamic distribution of charge acceptors. As a consequence of power‐law statistics, single molecule properties like the total number of emitted photons display non‐ergodicity.     

Super-resolution morphological dissemination of intercalating dye in single DNA molecules via binding activated localization microscopy

Super-localization of intercalating dye YOYO-1 in single λ-DNA at super-resolution by binding activation localization microscopy (BALM).     

Motion of single DNA molecules at a liquid-solid interface as revealed by variable-angle evanescent-field microscopy

A variable-angle total-internal-reflection fluorescence microscope (VATIRFM) capable of providing a large range of incident angles was constructed for imaging single DNA molecule dynamics at a solid/liquid interface. An algorithm using a public-domain image-processing program, ImageJ, was developed for single-molecule counting. The experimental counts at various incident angles with different evanescent-field layer (EFL) thicknesses are affected by molecular diffusion. The dynamics of molecules near the surface and the observed counts in the VATIRFM are elucidated using a limited one-dimensional random-walk diffusion model. The simulation fits well with the experimental counting results. Further analysis using the simulation reveals the details of single-molecule motion. One implication is that the measured intensities cannot be used directly to determine the distances of molecules from the surface, though the majority of fluorescence does come from the EFL. Another implication is that rather than providing molecular concentrations within EFL the experimental counting results depict the distance-dependent dynamics of molecules near the surface. Thus, the VATIRFM could be a powerful technique to study the surface repulsion/attraction of molecules within a few hundred nanometers of the surface. Further studies show that molecules at low ionic strengths experience electrostatic repulsion at distances much further away from the surface than the calculated thickness of the electrical double layer.