Electrical docking of microtubules for kinesin-driven motility in nanostructures

We demonstrate localized electrical control of the docking of microtubules onto engineered kinesin-coated structures. After applying a voltage to a gold electrode, we observe an enhanced transport of microtubules from solution toward the surface and a subsequent increase of the amount of moving microtubule shuttles. Switching off the voltage leads to a partial detachment of microtubules from the surface. The surface coverage of microtubules, during both the docking and undocking events, follows an exponential time dependence. We provide a simple kinetic model, incorporating the equilibrium between free and surface-bound microtubules, that explains these data.     

Nanofluidic channels fabrication and manipulation of DNA molecules

Nanofluidic channel arrays, which have a width of about 40 nm, depth of 60 nm and length of 50 mum, were created using a focused-ion-beam milling instrument on a silicon nitride film swiftly and exactly, as is necessary. Stained -DNA molecules were put inside these sub-100 nm conduits by capillary force and they were stretched and transferred along these conduits, which were dealt with activating reagent Brij aqueous solution in advance. The movements of DNA molecules in these channels were discussed. These nano-structure channels may be useful in the study and analysis of the statics as well as the dynamics of single biomolecules.     

Single DNA molecules as probes of chromatographic surfaces

YOYO-I-labeled lambda-DNA was employed as a nanoprobe for different functionalized surfaces to elucidate adsorption in chromatography. While the negatively charged backbone is not adsorbed, the 12-base unpaired ends of this DNA provide exposed purine and pyrimidine groups for adsorption. Self-assembled monolayers (SAMs) formed on gold substrate provide a wide range of choices of surface with well-defined and well-organized functional groups. Patterns of amino-terminated, carboxylic acid-terminated, and hydroxyl-terminated SAMs are generated by lithography. Patterns of metal oxides are generated spontaneously after deposition of metals. By recording the real-time dynamic motion of DNA molecules at the SAMs/aqueous interface, one can study the various parameters governing the retentivity of an analyte during chromatographic separation. Even subtle differences among adsorptive forces can be revealed.     

Spin doping of individual molecules by using single-atom manipulation

Being able to control the spin of magnetic molecules at the single-molecule level will make it possible to develop new spin-based nanotechnologies. Gate-field effects and electron and photon excitations have been used to achieve spin switching in molecules. Here, we show that atomic doping of molecules can be used to change the molecular spin. Furthermore, a scanning tunneling microscope was used to place or remove the atomic dopant on the molecule, allowing us to change the molecular spin in a controlled way. Bis(phthalocyaninato)yttrium (YPc(2)) molecules deposited on an Au (111) surface keep their spin-1/2 magnetic moment due to the small molecule-substrate interaction. However, when Cs atoms were carefully placed onto YPc(2) molecules, the spin of the molecule vanished as shown by our conductance measurements and corroborated by the results of density functional theory calculations.     

Quantitative detection of individual cleaved DNA molecules on surfaces using gold nanoparticles and scanning electron microscope imaging

Single-nucleotide polymorphisms (SNPs) are the most frequent type of human genetic variation. Recent work has shown that it is possible to directly analyze SNPs in unamplified human genomic DNA samples using the surface-invasive cleavage reaction followed by rolling circle amplification (RCA) labeling of the cleavage products. The individual RCA amplicon molecules were counted on the surface using fluorescence microscopy. Two principal limitations of such single-molecule counting are the variability in the amplicon size, which results in a large variation in fluorescence signal intensity from the dye-labeled DNA molecules, and a high level of background fluorescence. It is shown here that an excellent alternative to RCA labeling is tagging with gold nanoparticles followed by imaging with a scanning electron microscope. Gold nanoparticles have a uniform diameter (15 +/- 0.5 nm) and provide excellent contrast against the background of the silicon substrate employed. Individual gold nanoparticles are readily counted using publicly available software. The results demonstrate that the labeling efficiency is improved by as much as approximately 15-fold, and the signal-to-noise ratio is improved by approximately 4-fold. Detection of individual cleaved DNA molecules following surface-invasive cleavage was linear and quantitative over 3 orders of magnitude in amount of target DNA (10(-18)-10(-15) mol).     

Controlling surfaces and interfaces of semiconductors using organic molecules

Control over semiconductor surface energetics can be achieved using different chemisorbed organic molecules with diverse electronic properties. We find evidence of such control over CdTe upon adsorption of dicarboxylic acid derivatives with different substituted phenyl rings. FT-IR measurements show that the dicarboxylic acid derivatives bind as carboxylates to form approximately one monolayer. Such chemisorption modifies both the band bending and the electron affinity (up to 500 and 700 mV, respectively), as measured by contact potential difference WPM Changes in band bending result from a coupling between molecular orbitals and surface states close to the valence band and depend on the withdrawing character of the phenyl substituent. A model is presented to interpret and explain the data.     

Characteristics of subcooled water boiling on structured surfaces

Characteristics of the process and heat transfer of subcooled water boiling on mesostructured surfaces obtained by microarc oxidation of titanium foil with formation of a TiO₂ layer and deposition of Al₂O₃ particles from boiling nanofluid have been experimentally investigated. The experiments have been carried out in the forced flow of deaerated water in a vertical rectangular channel, 21 × 5 mm in size. The ranges of regime parameters are as follows: water mass velocity is up to 650 kg/(m2 s), subcooling is 30–75°C, pressure is ~10⁵ Pa, and heat flux rate is 0.7–5.0 MW/m². It is established that the number of active nucleation sites is (70–80) × 105 1/(m² s) at the heat flux of 1.5–2.0 MW/m². Significant subcooling of the liquid and good wettability of the structured surface provide intense deactivation and lead to random spatial distribution of the nucleation sites. The characteristic size of vapor bubbles is about 200–250 μm and the bubble lifetime is 200–500 μs. Application of the coating prepared by microarc oxidation enhances heat transfer by 20–30%. At high subcoolings of liquid, the characteristics of boiling on smooth surfaces and surfaces with the coating were fairly close.     

STM manipulation of molecular moulds on metal surfaces

Molecular Landers are a class of compounds containing an aromatic board as well as bulky side groups which upon adsorption of the molecule on a surface may lift the molecular board away from the substrate. Different molecular Landers have extensively been studied as model systems for nanomachines and the formation of molecular wires, as well as for their function as “molecular moulds”, i.e., acting as templates by accommodating metal atoms underneath their aromatic board. Here, we investigate the adsorption of a novel Lander molecule 1,4-bis(4-(2,4-diaminotriazine)phenyl)-2,3,5,6-tetrakis(4-tert-butylphenyl)benzene (DAT, C₆₄H₆₈N₁₀) on Cu(110) and Au(111) surfaces under ultrahigh vacuum (UHV) conditions. By means of scanning tunneling microscopy (STM) imaging and manipulation, we characterize the morphology and binding geometries of DAT molecules at terraces and step edges. On the Cu(110) surface, various contact configurations of individual DAT Landers were formed at the step edges in a controlled manner, steered by STM manipulation, including lateral translation, rotation, and pushing molecules to an upper terrace. The diffusion barrier of single DAT molecules on Au(111) is considerably smaller than on Cu(110). The DAT Lander is specially designed with diamino-triazine side groups making it suitable for future studies of molecular self-assembly by hydrogen-bonding interactions. The results presented here are an important guide to the choice of substrate for future studies using this compound. This article is published with open access at Springerlink.com These authors contributed equally to this work     

Probing the conformation of physisorbed molecules at the atomic scale using STM manipulation

We use scanning tunneling microscope (STM) manipulation and density functional theory calculation to investigate the structural properties of individual sexiphenyl molecules physisorbed on a Ag(111) surface at 6 K. The molecule-surface atomic registry is precisely determined by using atomic markers and a sexiphenyl functionalized tip. The calculations confirm the alternating twist of the sexiphenyl pi-rings on Ag(111). The pi-ring torsional angle, 11.4 degrees, is directly determined from the geometry of STM manipulation. This innovative experiment opens up a novel application of STM manipulation to probe the properties of "physisorbed" species on surfaces at the atomic level.     

Directed deposition of single molecules on surfaces

Scanning probe microscopy-based techniques can address and manipulate individual molecules. This makes it possible to use them for building nanostructures by assembling single molecules. Recently the formation of surface structures by positioning single molecules with the Atomic Force Microscope (AFM) was demonstrated on an irreversible delivery process. This inherits the drawback, that the transfer has to occur between differently functionalized surfaces and allows no proofreading of the built structures. Here we demonstrate a procedure for directed deposition of single DNA molecules, which intrinsically allows a reversible positioning. This method uses specific interactions between complementary DNA oligonucleotides for symmetric coupling of the transport molecules to the support and AFM tip, respectively. Thus, it allows for a simple "drag-and-drop" procedure, which relies on the statistical breakage of the molecular interaction under a force load. In addition, the delivery of the transport molecules was observed in real-time by single-molecule fluorescence microscopy.     

Dielectrophoretic manipulation of DNA

The characterisation and spatial manipulation of cells by AC electrokinetic methods such as dielectrophoresis and electrorotation is well established. However, applications to submicroscopical objects like viruses and molecules have been rare. Only recently has the number of such studies risen more quickly due to the availability of suitable electrodes and a growing need for single molecule techniques. Of special interest is the spatial control of single DNA molecules for genetic investigations as well as for the building of well defined structures with nanometre resolution. Here a review is given of dielectrophoretic studies dealing with single and double stranded DNA emphasising single molecule aspects.     

Controlled lateral manipulation of molecules on insulating films by STM

On metallic and semiconductor surfaces functional nanostructures can be built with atomic scale precision using the tip of an atomic force microscope/scanning tunneling microscope. In contrast, controlled lateral manipulation on insulators has not been reported. The traditional pushing and pulling based manipulation methods cannot be used for molecules adsorbed on insulating films because of the unfavorable ratio between diffusion barrier and desorption energy. Here, we demonstrate that molecules adsorbed on insulating films can be laterally manipulated in a controlled way by injecting inelastically tunneling electrons at well-defined positions in a molecule. The technique was successfully applied to several different molecules.     

Organic molecules reconstruct nanostructures on ionic surfaces

Modification and functionalization of the atomic-scale structure of insulating surfaces is fundamental to catalysis, self-assembly, and single-molecule technologies. Specially designed syn-5,10,15-tris(4-cyanophenylmethyl)truxene molecules can reshape features on an ionic KBr (001) surface. Atomic force microscopy images demonstrate that both KBr monolayer islands and pits can reshape from rectangular to round structures, a process which is directly facilitated by molecular adsorption. Simulations reveal that the mechanism of the surface reconstruction consists of collective atomic hops of ions on the step edges of the islands and pits, which correlate with molecular motion. The energy barriers for individual processes are reduced by the presence of the adsorbed molecules, which cause surface structural changes. These results show how appropriately designed organic molecules can modify surface morphology on insulating surfaces. Such strongly adsorbed molecules can also serve as anchoring sites for building new nanostructures on inert insulating surfaces.     

Comparative study of adatom manipulation on several fcc metal surfaces

For a set of fcc metals, our total energy calculations based on many body potentials show that activation barriers for lateral manipulation of an adatom at a step edge depend on the tip/substrate composition. Of the six homogeneous systems studied, manipulation on stepped Ag(111) showed the lowest energy barrier for adatom hopping toward the tip, although the relative probability for this process was largest on Cu(111). For a representative Cu/Pt heterogeneous system, we find lateral manipulation of a Pt adatom along a step on Pt(111) by a Cu(100) tip to be energetically much less favorable than the reverse case of a Cu adatom manipulated by a Pt(100) tip. In the case of vertical manipulation, atomic relaxations of the tip and its neighboring atoms are found to be prominent and tip-induced changes in the bonding of the adatom to its low coordinated surroundings help explain the relative ease with which an adatom next to a step edge or a kink site may be pulled as compared to that on a flat surface.     

Detection of abasic sites on individual DNA molecules using atomic force microscopy

We have developed an atomic force microscopy-based method for detecting abasic sites (AP sites) on individual DNA molecules. By using uracil and uracil DNA glycosylase, we first prepared a 250-bp DNA template consisting of two AP sites at specific locations. We then detected the AP sites by marking them with biotinylated aldehyde-reactive probes and monomeric avidin. We demonstrate here that (i) the location of monomeric avidin bound on a single DNA molecule was detectable by atomic force microscopy; (ii) the observed location of avidin was in good agreement to the predicted AP sites at a few nanometer resolution; and (iii) by end-labeling the 5'-terminus of one DNA strand, the AP sites were determined without directional ambiguity. The technique described here will provide a sensitive way of locating AP sites and contribute to screen DNA damages from individual molecules.     

Parallel optical trap assisted nanopatterning on rough surfaces

There exist many optical lithography techniques for generating nanostructures on hard, flat surfaces over large areas. However, few techniques are able to create such patterns on soft materials or surfaces with pre-existing structure. To address this need, we demonstrate the use of parallel optical trap assisted nanopatterning (OTAN) to provide an efficient and robust direct-write method of producing nanoscale features without the need for focal plane adjustment. Parallel patterning on model surfaces of polyimide with vertical steps greater than 1.5?μm shows a feature size uncertainty better than 4% across the step and lateral positional accuracy of 25?nm. A Brownian motion model is used to describe the positional accuracy enabling one to predict how variation in system parameters will affect the nanopatterning results. These combined results suggest that OTAN is a viable technique for massively parallel direct-write nanolithography on non-traditional surfaces.     

Electrostretching DNA molecules using polymer-enhanced media within microfabricated devices

In this paper, we demonstrate immobilization and stretching of single lambda-phage DNA molecules within microfluidic systems using ac fields. We present a novel "thiol-on-gold"-based immobilization technique for fixing one specific end (3' end) of a DNA molecule onto a gold electrode. A polymer-enhanced medium (approximately 3.75 wt % linear polyacrylamide in Tris-HCl) is used to obtain fully stretched configurations (21 microm) of fluorescently stained lambda-DNA molecules. We also present an optimized microelectrode design with pointed electrodes and an electrode spacing of 20 microm for stretching DNA molecules with an ac field (1 MHz, 3 x 10(5) V/m). Finally, using these techniques, we immobilize a single DNA molecule at one electrode edge, stretch the molecule, and fix the other end at an adjacent electrode edge, forming a bridge between two electrodes within a microfabricated device.     

Dielectrophoretic manipulation of surface-bound DNA

Dielectrophoretic manipulation enables the positioning and orientation of DNA molecules for nanometer-scale applications. However, the dependence of the dielectrophoretic force and torque on the electric field magnitude and frequency has to be well characterised to realise fully the potential of this technique. DNA in solution is attracted to the strongest electric field gradient (i.e. the electrode edge) as a result of the dielectrophoretic force, while the dielectrophoretic torque aligns the DNA with its longest axis parallel to the electric field. In this work, the authors attached -DNA fragments (48 and 25 kilobases) to an array of gold microelectrodes via a terminal thiol bond and characterised the orientation and elongation as a function of electric field magnitude (0.1-0.8 MVm) and frequency (0.08-1.1 MHz). Maximum elongation was observed between 200 and 500 kHz for the attached DNA. Dielectrophoresis is limited by thermal randomisation at electric fields below 0.1 MVm and by electrothermal effects above 0.7 MVm. The authors conclude that dielectrophoresis can be used to manipulate surface-immobilised DNA reproducibly.