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The DNA origami method allows the folding of long, single-stranded DNA sequences into arbitrary two-dimensional structures by a set of designed oligonucleotides. The method has revealed an unexpected strength and efficiency for programmed self-assembly of molecular nanostructures and makes it possible to produce fully addressable nanostructures with wide-reaching application potential within the emerging area of nanoscience. Here we present a user-friendly software package for designing DNA origami structures ( http://www.cdna.dk/origami ) and demonstrate its use by the design of a dolphin-like DNA origami structure that was imaged by high-resolution AFM in liquid. The software package provides automatic generation of DNA origami structures, manual editing, interactive overviews, atomic models, tracks the design history, and has a fully extendable toolbox. From the AFM images, it was demonstrated that different designs of the dolphin tail region provided various levels of flexibility in a predictable fashion. Finally, we show that the addition of specific attachment sites promotes dimerization between two independently self-assembled dolphin structures, and that these interactions stabilize the flexible tail.
ACS Nano 2008 Jun
PMID:DNA origami design of dolphin-shaped structures with flexible tails. 1920 39

We investigated hydroxyalkylphosphonate monolayers as a novel platform for the biofunctionalization of silicon-based field effect sensor devices. This included a detailed study of the thin film properties of organophosphonate films on Si substrates using several surface analysis techniques, including AFM, ellipsometry, contact angle, X-ray photoelectron spectroscopy (XPS), X-ray reflectivity, and current-voltage characteristics in electrolyte solution. Our results indicate the formation of a dense monolayer on the native silicon oxide that has excellent passivation properties. The monolayer was biofunctionalized with 12 mer peptide nucleic acid (PNA) receptor molecules in a two-step procedure using the heterobifunctional linker, 3-maleimidopropionic-acid-N-hydroxysuccinimidester. Successful surface modification with the probe PNA was verified by XPS and contact angle measurements, and hybridization with DNA was determined by fluorescence measurements. Finally, the PNA functionalization protocol was translated to 2 microm long, 100 nm wide Si nanowire field effect devices, which were successfully used for label-free DNA/PNA hybridization detection.
ACS Nano 2008 Aug
PMID:Organophosphonate-based PNA-functionalization of silicon nanowires for label-free DNA detection. 1920 69

Various methods for the patterned assembly of metal nanoparticles have been developed in order to harness their unique electrical and optical properties for device applications. This paper discusses a method for direct writing of Au nanoparticles at nanoscale resolution using dip-pen nanolithography. First, a procedure was developed for increasing the loading of Au nanoparticles onto AFM tips to prolong patterning life. AFM tips were subsequently imaged by scanning electron microscopy to determine ink coverage and to gain insight into the deposition process. Next, surface interactions, relative humidity, and writing speed were controlled to determine an optimal range of conditions for deposition. Various ink-substrate combinations were studied to elucidate the dependence of deposition on interactions between Au nanoparticles and the substrate surface; inks consisted of positively and negatively charged particles, and substrates were SiO(2) surfaces modified as hydrophilic or hydrophobic and interacted electrostatically or covalently with Au nanoparticles. Results indicate that a highly hydrophilic surface is required for Au nanoparticle deposition, unless covalent binding can occur between the Au and substrate surface. The optimal range of relative humidity for patterning was found to be 40-60%, and Au nanoparticle deposition was not sensitive to writing speeds ranging from 0.01 to 2 microm/s.
ACS Nano 2008 Oct 28
PMID:Direct patterning of gold nanoparticles using dip-pen nanolithography. 1920 60

Cancer and many other diseases are characterized by changes in cell morphology, motion, and mechanical rigidity. However, in live cell cytology, stimulus-induced morphologic changes typically take 10-30 min to detect. Here, we employ live-cell interferometry (LCI) to visualize the rapid response of a whole cell to mechanical stimulation, on a time scale of seconds, and we detect cytoskeletal remodeling behavior within 200 s. This behavior involved small, rapid changes in cell content and miniscule changes in shape; it would be difficult to detect with conventional or phase contrast microscopy alone and is beyond the dynamic capability of AFM. We demonstrate that LCI provides a rapid, quantitative reconstruction of the cell body with no labeling. This is an advantage over traditional microscopy and flow cytometry, which require cell surface tagging and/or destructive cell fixation for labeling.
ACS Nano 2008 May
PMID:Live cell interferometry reveals cellular dynamism during force propagation. 1920 80

The development of novel molecular and biomolecular devices relies on the understanding of charge transport across molecule-substrate interfaces. However, different strategies adopted so far for fabricating and studying transport through metal-molecule-metal junctions yield values for the transport coefficients that differ by up to orders of magnitude even for the same junction. Conductive tip atomic force microscopy (CT-AFM) allows for the simultaneous measurement of transport and morphological properties of molecular assemblies, but absolute transport measurements depend on the nature of the AFM tip-molecule contact. In this work we present a differential approach to the study of metal-molecule-metal junctions based on the combination of AFM-driven nanolithography and CT-AFM. We nanograft patches of alkanethiol molecules in a self-assembled monolayer of alkanethiol molecules of different chain length and measure by CT-AFM the morphology and the transport properties of the nanopatches and of the reference layer. The method allows for the determination of the differential resistance between the two molecular layers and is thus independent of environmental factors. The validity of this approach is demonstrated by measuring the tunneling decay constant of alkanethiols as a function of their length.
ACS Nano 2008 Mar
PMID:Electron transfer mediating properties of hydrocarbons as a function of chain length: a differential scanning conductive tip atomic force microscopy investigation. 1920 77

The patterning of biologically active materials has been accomplished by the use of imprint lithography of functional photopolymer resins to create controlled nanoscale patterns of a cross-linked photopolymer containing embedded initiator groups. Functionalized polymer brushes consisting of polystyrene and poly(N,N-dimethylacrylamide) were grown from these patterned layers by nitroxide-mediated polymerization. Chain-end functionalization of the brush layer was accomplished by nitroxide radical exchange during the polymerization. Accordingly, brush layers terminated by pyrene and biotin functional groups were obtained by exchange with the appropriate alkoxyamines. The presence of pyrene functionality at the chain ends of the brushes was confirmed by fluorescent emission measurements. Fluorescently labeled streptavidin protein was selectively attached with high selectivity to the patterned biotinylated brush layer through biotin-streptavidin interactions. The functionalized polymer grafted surfaces and nanopatterns have been successfully characterized using a fluorescence spectrophotometer, AFM, SEM, confocal microscopy, and water contact angle measurements.
ACS Nano 2008 Apr
PMID:Chain-end functionalized nanopatterned polymer brushes grown via in situ nitroxide free radical exchange. 1920 3

Self-assembled monolayers (SAMs) of oligo(ethylene glycol) (OEG)-tethered molecules on gold are important for various biorelevant applications ranging from biomaterials to bioanalytical devices, where surface resistance to nonspecific protein adsorption is needed. Incorporation of a stimuli-responsive character to the OEG SAMs enables the creation of nonfouling surfaces with switchable functionality. Here we present an OEG-derived structure that is highly responsive to temperature changes in the vicinity of the physiological temperature, 37 degrees C. The temperature-responsive solution behavior of this new compound was demonstrated by UV-vis and nuclear magnetic resonance spectroscopy. Its chemisorption onto gold(111), and the retention of responsive behavior after chemisorption have been demonstrated by surface plasmon resonance (SPR), X-ray photoelectron spectroscopy (XPS), and atomic force and scanning tunneling microscopy. The OEG-derived SAMs have been shown to reversibly switch the wettability of the surface, as determined by contact angle measurements. More importantly, SPR and AFM studies showed that the OEG SAMs can be utilized to control the affinity binding of streptavidin to the biotin-tethered surface in a temperature-dependent manner while still offering the nonspecific protein-resistance to the surface.
ACS Nano 2008 Apr
PMID:Temperature-responsive self-assembled monolayers of oligo(ethylene glycol): control of biomolecular recognition. 1920 8

Solution processable methanofullerene-based solar cells are the most widely studied class of organic photovoltaics (OPVs). The evolution of the electronic properties with solvent vapor annealing (SVA) in polyfluorene-copolymer and [6,6]phenyl-C61-butyric acid methyl ester (PCBM) blended OPVs is studied using various scanning probe techniques: light beam induced current spectroscopy (LBIC), conductive atomic force microscopy (c-AFM), and photoconductive AFM (pc-AFM). We demonstrate that SVA improves the power conversion efficiency by 40% while forming mesoscopic PCBM crystallites and a approximately 3 nm copolymer-rich overlayer at the cathode interface. We find that the large crystallites created during annealing do not directly improve the local performance of the device, but instead attribute the performance improvement to the ripened blend morphology and an increase in the hole mobility of the copolymer in comparison to the unannealed blend. The PCBM-rich aggregates act as a sink for excess PCBM, although excess PCBM is initially required to form the appropriate structural features prior to the annealing process.
ACS Nano 2009 Mar 24
PMID:The role of mesoscopic PCBM crystallites in solvent vapor annealed copolymer solar cells. 1922 11

Vertically aligned ZnO-ZnS heterojunction nanowire (NW) arrays were synthesized by thermal evaporation in a tube furnace under controlled conditions. Both ZnO and ZnS are of wurtzite structure, and the axial heterojunctions are formed by epitaxial growth of ZnO on ZnS with an orientation relationship of [0001](ZnO)//[0001](ZnS). Vertical ZnS NW arrays have been obtained by selectively etching ZnO-ZnS NW arrays. Cathodoluminescence measurements of ZnO-ZnS NW arrays and ZnS NW arrays show emissions at 509 and 547 nm, respectively. Both types of aligned NW arrays have been applied to convert mechanical energy into electricity when they are deflected by a conductive AFM tip in contact mode. The received results are explained by the mechanism proposed for nanogenerator.
ACS Nano 2009 Feb 24
PMID:ZnO-ZnS heterojunction and ZnS nanowire arrays for electricity generation. 1923 72

This paper presents the first steps toward the development of a new type of high-resolution AFM-SECM microscopy which relies on the use of tip-attached redox-labeled polymer chains as mediators to probe the local electrochemical reactivity of a planar substrate at the nanoscale. Submicrometer-sized combined gold AFM-SECM probes were functionalized by linear, nanometer-sized, flexible, PEG3400 chains bearing a ferrocene (Fc) redox label at their free end. Analysis of the force and current approach curves recorded when such Fc-PEGylated probes (tips) were approached to a bare gold substrate allowed the presence of the Fc-PEG chains at the very tip end of the combined probes to be specifically demonstrated. It also allowed the chain coverage, configuration, and dynamics to be determined. When the Fc-PEGylated probe is positioned some approximately 5 nm above the substrate, only a few hundred chains are actually electrochemically contacting the surface, thus reducing the size of the tip-substrate interaction area to 20-40 nm. Most importantly, we have shown that the tip-borne PEG chains are flexible enough to allow their Fc heads to efficiently "sense" locally the electrochemical reactivity of the substrate, thus validating the working principle of the new AFM-SECM microscopy we propose. This innovative microscopy, we label Tarm (for tip-attached redox mediator)/AFM-SECM, should be particularly suitable for probing the activity of slowly functioning nanometer-sized active sites on surfaces, such as individual enzyme molecules, because it is, by design, free of the diffusional constraints which hamper the characterization of such nanosystems by classical SECM.
ACS Nano 2009 Apr 28
PMID:Electrochemical atomic-force microscopy using a tip-attached redox mediator. Proof-of-concept and perspectives for functional probing of nanosystems. 1928 Dec 24


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