Molecular-basis of single-walled carbon nanotube recognition by single-stranded DNA

Hybrids of biological molecules and single-walled carbon nanotubes (SWCNT) have proven useful for SWCNT sorting and are enabling several biomedical applications in sensing, imaging, and drug delivery. In the DNA-SWCNT system, certain short (10-20mer) sequences of single-stranded DNA recognize specific SWCNT, allowing the latter to be sorted from a chirality diverse mixture. (1) However, little is known about the DNA secondary structures that underlie their recognition of SWCNTs. Using replica exchange molecular dynamics (REMD) of multiple strands on a single SWCNT, we report that DNA forms ordered structures on SWCNTs that are strongly DNA sequence and SWCNT dependent. DNA sequence (TAT)(4) on its recognition partner, the (6,5) SWCNT, (1) forms an ordered right-handed helically wrapped barrel, stabilized by intrastrand, self-stitching hydrogen bonds and interstrand hydrogen bonding. The same sequence on the larger diameter (8,7)-SWCNT forms a different and less-stable structure, demonstrating SWCNT selectivity. In contrast, homopolymer (T)(12), with weaker tendency for intrastrand hydrogen bonding, forms a distinctly left-handed wrap on the (6,5)-SWCNT, demonstrating DNA sequence specificity. Experimental measurements show that (TAT)(4) selectively disperses smaller diameter SWCNTs more efficiently than (T)(12), establishing a relationship between recognition motifs and binding strength. The developing understanding of DNA secondary structure on nanomaterials can shed light on a number of issues involving hybrids of nanomaterials and biological molecules, including nanomedicine, health-effects of nanomaterials, and nanomaterial processing.     

Conductivity of a single DNA duplex bridging a carbon nanotube gap

We describe a general method to integrate DNA strands between single-walled carbon nanotube electrodes and to measure their electrical properties. We modified DNA sequences with amines on either the 5' terminus or both the 3' and 5' termini and coupled these to the single-walled carbon nanotube electrodes through amide linkages, enabling the electrical properties of complementary and mismatched strands to be measured. Well-matched duplex DNA in the gap between the electrodes exhibits a resistance on the order of 1 M(Omega). A single GT or CA mismatch in a DNA 15-mer increases the resistance of the duplex approximately 300-fold relative to a well-matched one. Certain DNA sequences oriented within this gap are substrates for Alu I, a blunt end restriction enzyme. This enzyme cuts the DNA and eliminates the conductive path, supporting the supposition that the DNA is in its native conformation when bridging the ends of the single-walled carbon nanotubes.     

Single-walled carbon nanotube based SERS substrate with single molecule sensitivity

In single molecule study,surface-enhanced Raman scattering(SERS)has the advantage of specifically providing structural information of the molecules targeted.The main challenge in single molecule SERS is developing reusable plasmonic substrates that ensures single molecule sensitivity and acquires intrinsic information of molecules.Here,we proposed a strategy to utilize single-walled carbon nanotubes(SWNTs)to construct SERS substrates.Employing ultrasonic spray pyrolysis,we prepared in situ polyhedral gold nanocrystals closely spaced and attached to nanotubes,ensuring valid hot spots formed along the tube-walls.With such SERS substrates,we proved the single molecule detection by the statistical analysis based on the natural abundance of isotopes.Since SWNTs provide non-chemical bonding adsorption sites,our SERS substrates are easily reusable and have a unique advantage of preserving the intrinsic property of the molecules detected.Using SWNTs to build SERS substrates may become a powerful general strategy in various static and dynamic studies of single molecules.     

High density single-molecule-bead arrays for parallel single molecule force spectroscopy

The assembly of a highly parallel force spectroscopy tool requires careful placement of single-molecule targets on the substrate and the deliberate manipulation of a multitude of force probes. Since the probe must approach the target biomolecule for covalent attachment, while avoiding irreversible adhesion to the substrate, the use of polymer microspheres as force probes to create the tethered bead array poses a problem. Therefore, the interactions between the force probe and the surface must be repulsive at very short distances (<5 nm) and attractive at long distances. To achieve this balance, the chemistry of the substrate, force probe, and solution must be tailored to control the probe-surface interactions. In addition to an appropriately designed chemistry, it is necessary to control the surface density of the target molecule in order to ensure that only one molecule is interrogated by a single force probe. We used gold-thiol chemistry to control both the substrate's surface chemistry and the spacing of the studied molecules, through binding of the thiol-terminated DNA and an inert thiol forming a blocking layer. For our single molecule array, we modeled the forces between the probe and the substrate using DLVO theory and measured their magnitude and direction with colloidal probe microscopy. The practicality of each system was tested using a probe binding assay to evaluate the proportion of the beads remaining adhered to the surface after application of force. We have translated the results specific for our system to general guiding principles for preparation of tethered bead arrays and demonstrated the ability of this system to produce a high yield of active force spectroscopy probes in a microwell substrate. This study outlines the characteristics of the chemistry needed to create such a force spectroscopy array.     

Encapsulation of a benzene molecule into a carbon nanotube

Aromatic hydrocarbon molecules encapsulated in carbon nanotubes have been proposed for applications as semiconductors. They can be formed by exploiting the van der Waals interaction as a simple method to incorporate molecules into carbon nanotubes. However, the existence of energy barriers near the open ends of carbon nanotubes may be an obstacle for molecules entering carbon nanotubes. In this paper, we investigate the encapsulation mechanism of a typical aromatic hydrocarbon, namely a benzene molecule, into a carbon nanotube in order to determine the dependence on radius of the tube. A continuous approach which assumes that the molecular interactions can be approximated using average atomic densities together with the semi-empirical Lennard–Jones potential function is adopted, and an analytical expression for the interaction energy is obtained which may be readily evaluated by algebraic computer packages. In particular, we determine the threshold radius of the carbon nanotube for which the benzene molecule will enter the carbon nanotube. The analytical approach adopted here provides a computationally rapid procedure for the determination of critical numerical values.     

Electrochemical impedance-based DNA sensor using a modified single walled carbon nanotube electrode

Carbon nanotubes have become promising functional materials for the development of advanced electrochemical biosensors with novel features which could promote electron-transfer with various redox active biomolecules. This paper presents the detection of Salmonella enterica serovar Typhimurium using chemically modified single walled carbon nanotubes (SWNTs) with single stranded DNA (ssDNA) on a polished glassy carbon electrode. Hybridization with the corresponding complementary ssDNA has shown a shift in the impedance studies due to a higher charge transfer in ssDNA. The developed biosensor has revealed an excellent specificity for the appropriate targeted DNA strand. The methodologies to prepare and functionalize the electrode could be adopted in the development of DNA hybridization biosensor.     

Confined dynamics of a single DNA molecule

The effect of a slit-like confinement on the relaxation dynamics of DNA is studied via a mesoscale model in which a bead and spring model for the polymer is coupled to a particle-based Navier-Stokes solver (multi-particle collision dynamics). The confinement is found to affect the equilibrium stretch of the chain when the bulk gyration radius is comparable to or smaller than the channel height and our data are in agreement with the (R(g,bulk)/h)(1/4) scaling of the polymer extension in the wall tangential direction. Relaxation simulation at different confinements indicates that, while the overall behaviour of the relaxation dynamics is similar for low and strong confinements, a small, but significant, slowing of the far-equilibrium relaxation is found as the confinement increases.     

Charge trapping in carbon nanotube loops demonstrated by electrostatic force microscopy

Electronic devices made from carbon nanotubes (CNTs) can be greatly affected by substrate charges, which, for instance, induce strong hysteresis in CNT field effect transistors. In this work, electrostatic force microscopy (EFM) is employed to investigate single-walled nanotubes grown by chemical vapor deposition on SiO2 substrates. We demonstrate the use of this technique to gain quantitative information on the substrate charges. It is found that charge pools with densities around 10(-8) C/cm2 can be trapped inside nanotube loops for extended periods of time, showing that nanotubes can act as confining barriers for substrate charges. The trapped charges can be removed by scanning probe manipulation.     

Launching propagating surface plasmon polaritons by a single carbon nanotube dipolar emitter

We report on the excitation of propagating surface plasmon polaritons in thin metal films by a single emitter. Upon excitation in the visible regime, individual semiconducting single-walled carbon nanotubes are shown to act as directional near-infrared point dipole sources launching propagating surface plasmons mainly along the direction of the nanotube axis. Plasmon excitation and propagation is monitored in Fourier and real space by leakage radiation microscopy and is modeled by rigorous theoretical calculations. Coupling to plasmons almost completely reshapes the emission of nanotubes both spatially and with respect to polarization as compared to photoluminescence on a dielectric substrate.     

Photolithographic fabrication of gated self-aligned parallel electron beam emitters with a single-stranded carbon nanotube

In this paper we report on the development of a photolithographic process to fabricate a gated-emitter array with single-stranded carbon nanotubes (CNTs) self-aligned to the center of the emitter gate using plasma-enhanced chemical vapor deposition (PECVD). Si tips are formed on a silicon wafer by anisotropic etching of Si using SiO(2) as a mask. Deposition of a SiO(2) insulating layer and Cr-W electrode layers creates protrusions above the Si tips. This wafer is polished, and the Cr-W on the tips is removed. Etching of the SiO(2) using hydrofluoric acid is performed to expose the gated Si tip. Incorporation of a novel diffusion process produces single-stranded CNTs by depositing a thin Ni layer on the Si tips and thermally diffusing the Ni layer to yield a catalyst particle for single-stranded CNT growth. The large surface to volume ratio at the apex of the Si tip allows a Ni particle to remain to act as a catalyst to grow a single-stranded CNT for fabricating the CNT based emitter structure. Diffusion of the Ni is carried out in situ during the heating phase of the PECVD CNT growth process at 600?°C. The diameters of the observed CNTs are on the order of 20?nm. The field emission characteristics of the gated field emitters are evaluated. The measured turn-on voltage of the gated emitter is 5?V.     

Analysing one isolated single walled carbon nanotube in the near-field domain with selective nanovolume Raman spectroscopy

In this paper, we describe a new method to the selective nanovolume analysing of one isolated single walled carbon nanotube (SWNT). This concept is based on actually available imaging micro-spectrometry systems for working in near-field domain combined with a stigmatic solid immersion lens. This combination of different analytical methods, and modified and configured equipment entitles us to expand the functionality toward a three-dimensional (3D) nanovolume Raman mapping and photoluminescence intensity with a possible discrimination in polarization, as well as photoluminescence decaytime constant mapping with their unique combination. Subsequently, selective spectra can be acquired from the same location on the samples. By spectrally selecting a SWNT, we registered the spatial distribution of the emitted photons in x, y, z vectors to determine the position of a SWNT in the near-field domain. For the SWNTs that are localized with an accuracy better than 18 nm in the x, y and <1 nm in the z directions, we demonstrate an analytical sensitivity close to a single nanotube with unity throughput. This near-field capability is applied to resolve local variations unambiguously in the Raman spectrum along one single SWNT. Finally, in this paper, we report what we believe to be the first evidence of Raman mapping and 3D real optical imaging of carbon nanotubes with near-field resolution.     

Drying induced upright sliding and reorganization of carbon nanotube arrays

Driven by capillary force, wet carbon nanotube (CNT) arrays have been found to reorganize into cellular structures upon drying. During the reorganization process, individual CNTs are firmly attached to the substrate and have to lie down on the substrate at cell bottoms, forming closed cells. Here we demonstrate that by modifying catalyst structures, the adhesion of CNTs to the substrate can be weakened. Upon drying such CNT arrays, CNTs may slide away from their original sites on the surface and self-assemble into cellular patterns with bottoms open. It is also found that the sliding distance of CNTs increases with array height, and drying millimetre tall arrays leads to the sliding of CNTs over a few hundred micrometres and the eventual self-assembly into discrete islands. By introducing regular vacancies in CNT arrays, CNTs may be manipulated into different patterns.     

The effect of environmental factors on the electrical conductivity of a single oligo-DNA molecule measured using single-walled carbon nanotube nanoelectrodes

We present an electrical conductivity study on a double-stranded DNA molecule bridging a single-walled carbon nanotube (SWNT) gap. The amine terminated DNA molecule was trapped between carboxyl functionalized SWNT electrodes by dielectrophoresis. The conductivity of DNA was measured while under the influence of various environmental factors, including salt concentration, counterion variation, pH and temperature. Typically, a current of tens of picoamperes at 1?V was observed at ambient conditions, with a decrease in conductance of about 33% in high vacuum conditions. The counterion variation was analyzed by changing the buffer from sodium acetate to tris(hydroxymethyl) aminomethane, which resulted in a two orders of magnitude increase in the conductivity of the DNA. A reversible shift in the current signal was observed for pH variation. An increase in conductivity of the DNA was also observed at high salt concentrations.     

Self-assembly of single-stranded RNA on carbon nanotube: polyadenylic acid to form a duplex structure

All messenger-RNA (mRNA) molecules in eukaryotic cells have a polyadenylic acid [poly(rA)] tail at the 3'-end and human poly(rA) polymerase (PAP) has been considered as a tumor-specific target. A ligand that is capable of recognizing and binding to the poly(rA) tail of mRNA might interfere with the full processing of mRNA by PAP and can be a potential therapeutic agent. We report here for the first time that single-walled carbon nanotubes (SWNTs) can cause single-stranded poly(rA) to self-structure and form a duplex structure, which is studied by UV melting, atomic force microscopy, circular dichroism spectroscopy, and NMR spectrometry. SWNTs have shown potential applications that range from nanodevices, gene therapy, and drug delivery to membrane separations. Our studies may provide new insights into the application of SWNTs under physiological conditions, possibly being used as probes that target specific gene sequences.     

Microwave impedance spectroscopy of dense carbon nanotube bundles

We have performed impedance spectroscopy of dense carbon nanotube (CNT) bundles in the broad frequency range from 10 MHz to 67 GHz. Dense CNT bundles were formed on sharp tips from aqueous suspension by ac dielectrophoresis and incorporated into on-wafer test structures. The frequency response of the bundles can be fit to a model with frequency-independent elements in the entire frequency range up to 67 GHz strongly suggesting that CNT properties do not depend on the frequency throughout the whole frequency range. The measurements at microwave frequencies allowed separate characterization of the bundle/metal electrode contacts and the bundle bulk. Effects of different CNT fabrication and suspension processing routes on bundle characteristics were identified. We have also made a preliminary estimation of the average inductance per current carrying shell in the bundles. For good quality nanotube bundles, the inductance has been found to fall within the range from approximately 3.5 to 40 nH/microm. With decreasing nanotube quality, the implemented estimation procedure yields higher values with a large uncertainty. Systematic measurements of devices with individual nanotubes are required to provide more accurate data.     

Excited state spectroscopy in carbon nanotube double quantum dots

We report on low-temperature measurements in a fully tunable carbon nanotube double quantum dot. A new fabrication technique has been used for the top-gates in order to avoid covering the whole nanotube with an oxide layer as in previous experiments. The top-gates allow us to form single dots and control the coupling between them, and we observe 4-fold shell filling. We perform inelastic transport spectroscopy via the excited states in the double quantum dot, a necessary step toward the implementation of new microwave-based experiments.     

A single synthetic small molecule that generates force against a load

Some biomolecules are able to generate directional forces by rectifying random thermal motions. This allows these molecular machines to perform mechanical tasks such as intracellular cargo transport or muscle contraction in plants and animals. Although some artificial molecular machines have been synthesized and used collectively to perform mechanical tasks, so far there have been no direct measurements of mechanical processes at the single-molecule level. Here we report measurements of the mechanical work performed by a synthetic molecule less than 5?nm long. We show that biased Brownian motion of the sub-molecular components in a hydrogen-bonded [2]rotaxane-a molecular ring threaded onto a molecular axle-can be harnessed to generate significant directional forces. We used the cantilever of an atomic force microscope to apply a mechanical load to the ring during single-molecule pulling-relaxing cycles. The ring was pulled along the axle, away from the thermodynamically favoured binding site, and was then found to travel back to this site against an external load of 30?pN. Using fluctuation theorems, we were able to relate measurements of the work done at the level of individual rotaxane molecules to the free-energy change as previously determined from ensemble measurements. The results show that individual rotaxanes can generate directional forces of similar magnitude to those generated by natural molecular machines.     

Sharp burnout failure observed in high current-carrying double-walled carbon nanotube fibers

We report on the current-carrying capability and the high-current-induced thermal burnout failure modes of 5-20 μm diameter double-walled carbon nanotube (DWNT) fibers made by an improved dry-spinning method. It is found that the electrical conductivity and maximum current-carrying capability for these DWNT fibers can reach up to 5.9 × 10(5) S m(-1) and over 1 × 10(5) A cm(-2) in air. In comparison, we observed that standard carbon fiber tended to be oxidized and burnt out into cheese-like morphology when the maximum current was reached, while DWNT fiber showed a much slower breakdown behavior due to the gradual burnout in individual nanotubes. The electron microscopy observations further confirmed that the failure process of DWNT fibers occurs at localized positions, and while the individual nanotubes burn they also get aligned due to local high temperature and electrostatic field. In addition a finite element model was constructed to gain better understanding of the failure behavior of DWNT fibers.     

Hydrodynamic flow profiling in microchannel structures by single molecule fluorescence correlation spectroscopy

In this paper we demonstrate high spatial resolution hydrodynamic flow profiling in silicon wafer based microchannels using single molecule fluorescence correlation spectroscopy (FCS). We have used confocal fluorescence microscopy to detect single tetramethylrhodamine (TMR-4-dUTP) biomolecules traversing a approximately 1 fL volume element defined by an argon laser beam focus. By elevating a (approximately 10(-10) M) reservoir of diluted analyte, a continuous hydrodynamic flow through the microstructure could be accomplished. The microchannel was then scanned with a diffraction-limited focus in approximately 1-microm steps in both the vertical and the horizontal directions to determine the flow profile across a 50 x 50 microm2 channel. The flow profile measured was parabolic in both dimensions, thereby showing a Poiseuille laminar flow profile. Future microstructures can hereby be nondestructively investigated with the use of high spatial resolution confocal correlation microscopy.     

Two-dimensional dopant profiling by electrostatic force microscopy using carbon nanotube modified cantilevers

A two-dimensional (2D) dopant profiling technique is demonstrated in this work. We apply a unique cantilever probe in electrostatic force microscopy (EFM) modified by the attachment of a multiwalled carbon nanotube (MWNT). Furthermore, the tip apex of the MWNT was trimmed to the sharpness of a single-walled carbon nanotube (SWNT). This ultra-sharp MWNT tip helps us to resolve dopant features to within 10?nm in air, which approaches the resolution achieved by ultra-high vacuum scanning tunnelling microscopy (UHV STM). In this study, the CNT-probed EFM is used to profile 2D buried dopant distribution under a nano-scale device structure and shows the feasibility of device characterization for sub-45?nm complementary metal-oxide-semiconductor (CMOS) field-effect transistors.