DNA-templated self-assembly of protein and nanoparticle linear arrays

Self-assembling DNA tiling lattices represent a versatile system for nanoscale construction. Self-assembled DNA arrays provide an excellent template for spatially positioning other molecules with increased relative precision and programmability. Here we report an experiment using a linear array of DNA triple crossover tiles to controllably template the self-assembly of single-layer or double-layer linear arrays of streptavidin molecules and streptavidin-conjugated nanogold particles through biotin-streptavidin interaction. The organization of streptavidin and its conjugated gold nanoparticles into periodic arrays was visualized by atomic force microscopy and scanning electron microscopy.     

Curve crossing and negative refraction in simulations of near-field coupled metallic nanoparticle arrays

We extend our previous results [R. Baer et al., J. Chem. Phys. 126, 014705 (2007).] to develop a simple theory of localized surface plasmon-polariton (LSPP) dispersion on regular arrays of metal nanoparticles in the weak-field and weak-damping limits. This theory describes the energy-momentum as well as the polarization-momentum properties of LSPP waves, both of which are crucial to plasmonic device design. We then explicitly compute the dispersion relation for isotropic and anisotropic two-dimensional square lattices, and show curve crossings between all three levels as well as negative refraction where the phase and group velocities (refractive indices), or at least their projection along the main axis, have different signs. The curve crossing implies that scattering between the different polarizations, and therefore different velocities, is easy at the curve crossing momenta, so that a quick change in wave packet direction can be achieved. Time-resolved wave packet dynamics simulations demonstrate negative refraction and the easy scattering over nanometer length scales. This paper also gives some computational schemes for future applications, such as a way to include source terms and how to efficiently treat dissipative effects.     

A self-assembling protein template for constrained synthesis and patterning of nanoparticle arrays

Self-assembling biomolecules that form highly ordered structures have attracted interest as potential alternatives to conventional lithographic processes for patterning materials. Here, we introduce a general technique for patterning nanoparticle arrays using two-dimensional crystals of genetically modified hollow protein structures called chaperonins. Constrained chemical synthesis of transition metal nanoparticles is initiated using templates functionalized with polyhistidine sequences. These nanoparticles are ordered into arrays because the template-driven synthesis is constrained by the nanoscale structure of the crystallized protein. We anticipate that this system may be used to pattern different classes of nanoparticles based on the growing library of sequences shown to specifically bind or direct the growth of materials.     

Preparation of alumina-pillared layered tetratitanates with different interlayer spacings

The synthesis of pillared clays have led to the development of new materialswith suitable pore size and sufficient stability to be used as shape-selective catalystsand molecular sieves. There are numerous layered inorganic oxides which havethe potential to undergo ion-exchange reactions analogous to those observed withclays, but the nonswelling nature of most ionic layered oxides generally prevents     

Combustion analysis of biodiesel blends with different piston geometries

Journal of Thermal Analysis and Calorimetry - Shallow reentrant piston (SRP) and deep cylindrical piston (DCP) geometries were designed by modifying the compression ratio of an engine with baseline...     

Chemically bound gold nanoparticle arrays on silicon: assembly, properties and SERS study of protein interactions

A highly reproducible and facile method for formation of ordered 2 dimensional arrays of CTAB protected 50 nm gold nanoparticles bonded to silicon wafers is described. The silicon wafers have been chemically modified with long-chain silanes terminated with thiol that penetrate the CTAB bilayer and chemically bind to the underlying gold nanoparticle. The silicon wafer provides a reproducibly smooth, chemically functionalizable and non-fluorescent substrate with a silicon phonon mode which may provide a convenient internal frequency and intensity calibration for vibrational spectroscopy. The CTAB bilayer provides a potentially biomimetic environment for analyte, yet allows a sufficiently small nanoparticle separation to achieve a significant electric field enhancement. The arrays have been characterized using SEM and Raman spectroscopy. These studies reveal that the reproducibility of the arrays is excellent both between batches (<10% RSD) and across a single batch (<5% RSD). The arrays also exhibit good stability, and the effect of temperature on the arrays was also investigated. The interaction of protein and amino acid with the nanoparticle arrays was investigated using Raman microscopy to investigate their potential in bio-SERS spectroscopy. Raman of phenylalanine and the protein bovine pancreatic trypsin inhibitor, BPTI were studied using 785 nm excitation, coincident with the surface plasmon absorbance of the array. The arrays exhibit SERS enhancements of the order of 2.6 x 10(4) for phenylalanine, the standard deviation on the relative intensity of the 1555 cm(-1) mode of phenylalanine is less than 10% for 100 randomly distributed locations across a single substrate and less than 20% between different substrates. Significantly, comparisons of the Raman spectra of the protein and phenylalanine in solution and immobilized on the nanoparticle arrays indicates that the protein is non-randomly orientated on the arrays. Selective SERS enhancements suggest that aromatic residues penetrate through the bilayer inducing conformational changes in the protein.     

Photoacoustic spectrometry for trace gas analysis and leak detection using different cell geometries

A photoacoustic (PA) spectrometer with high selectivity and sensitivity has been developed for trace gas analysis and for the detection of gas leak at part per trillion by volume (pptV) level. This PA system comprises of a resonant photoacoustic cell, a pulsed line tunable CO₂ laser as an excitation source and a sensitive electret microphone as a photoacoustic detector with an option to trigger the safety alarm system for early warning of gas leaks. In this work, three resonant PA cells with various geometries have been developed at our laboratory for the detection of photoacoustic signal using pulsed laser system and their comparative performance have been studied. As a special application of this PA system, the detection of sulfur hexa fluoride (SF₆) gas using these three cells has been carried out for optimizing the sensitivity. Besides this, our PA system can very well be applied for pollution monitoring and detection of hazardous gases in a noisy environment.     

Thin film processing using S-layer proteins: biotemplated assembly of colloidal gold etch masks for fabrication of silicon nanopillar arrays

We explored the bionanofabrication of silicon nanopillar structures using ordered gold nanoparticle arrays generated from microbial surface layer (S-layer) protein templates. The S-layer template used for these thin film processing experiments was isolated from the Gram-positive bacterium Deinococcus radiodurans. In this preliminary work, S-layers preimmobilized onto chemically modified silicon substrates were initially used to template the fabrication of a nanolithographic hard mask pattern comprised of a hexagonally ordered array of 5-nm gold nanoparticles (lattice constant = 18 nm). Significantly, the use of the biotemplated gold nanoparticle mask patterns in an inductively coupled plasma (ICP) etching process successfully yielded silicon nanopillar structures. However, it was found that the resultant nanopillars (8–13 nm wide at the tip, 15–20 nm wide at half-height, 20–30 nm wide at the base, and 60–90 nm tall) appeared to lack any significant degree of translational ordering. The results suggest that further studies are needed in order to elucidate the optimal plasma processing parameters that will lead to the generation of long-range ordered arrays of silicon-based nanostructures using S-layer protein templates.     

Electrochemically superfilling of n-type ZnO nanorod arrays with p-type CuSCN semiconductor

The primary problem for constructing three-dimensional (3D) heterojunctions lies in poor pore filling and interface contact quality. An electrochemical superfilling technique is developed to construct well-organized heterojunctions based on a bottom-up filling mechanism. Morphology observation shows that ZnO nanorod arrays are completely filled with CuSCN and intimate interface contact is formed between ZnO and CuSCN. Electrical test confirms that as-fabricated 3D heterojunction has high diode current density and high rectification ratio of 154. This superfilling technique has promising applications in other 3D heterojunctions.     

Large-area and high-density gold nanoparticle arrays with sub-10 nm gaps

Electrochemical techniques are widely used for the fabrication of nanostructured materials, yet a desired high-density nanoparticle arrays remains a challenge. Here large-area and high-density gold nanoparticle arrays with sub-10 nm gaps have been, for the first time, synthesized on Si(1 0 0) substrate within an electrochemical deposition system via the application of an unusually high over-potential. The extremely high over-potential contributes to the relatively small critical island size and high nucleation rate. It is believed that this method can be extended to the electrochemical fabrication nanoparticle arrays of other materials.     

Inkjet-printed gold nanoparticle electrochemical arrays on plastic. Application to immunodetection of a cancer biomarker protein

Electrochemical detection combined with nanostructured sensor surfaces offers potentially low-cost, high-throughput solutions for detection of clinically significant proteins. Inkjet printing offers an inexpensive non-contact fabrication method for microelectronics that is easily adapted for incorporating into protein immunosensor devices. Herein we report the first direct fabrication of inkjet-printed gold nanoparticle arrays, and apply them to electrochemical detection of the cancer biomarker interleukin-6 (IL-6) in serum. The gold nanoparticle ink was printed on a flexible, heat resistant polyimide Kapton substrate and subsequently sintered to create eight-electrode arrays costing <0.2 euro per array. The inkjet-printed working electrodes had reproducible surface areas with RSD <3%. Capture antibodies for IL-6 were linked onto the eight-electrode array, and used in sandwich immunoassays. A biotinylated secondary antibody with 16-18 horseradish peroxidase labels was used, and detection was achieved by hydroquinone-mediated amperometry. The arrays provided a clinically relevant detection limit of 20 pg mL(-1) in calf serum, sensitivity of 11.4 nA pg(-1) cm(-2), and a linear dynamic range of 20-400 pg mL(-1).     

Peptide and protein assays using customizable bio-affinity arrays combined with ambient ionization mass spectrometry

High-throughput identification and quantification of protein/peptide biomarkers from biofluids in a label-free manner is achieved by interfacing bio-affinity arrays (BAAs) with nano-electrospray desorption electrospray ionization mass spectrometry (nano-DESI-MS). A wide spectrum of proteins and peptides ranging from phosphopeptides to cis-diol biomolecules as well as thrombin can be rapidly extracted via arbitrarily predefined affinity interactions including coordination chemistry, covalent bonding, and biological recognition. An integrated MS platform allows continuous interrogation. Profiling and quantitation of dysregulated phosphopeptides from small-volume (∼5 μL) serum samples has been successfully demonstrated. As a front-end device adapted to any mass spectrometer, this MS platform might hold much promise in protein/peptide analysis in point-of-care (POC) diagnostics and clinical applications.

Customizable bio-affinity arrays were interfaced with ambient ionization mass spectrometry for high-throughput assays of protein/peptide biomarkers in biofluids.     

Evaluation of cell-free protein synthesis using PDMS-based microreactor arrays.

A living cell has numerous proteins, only a few thousand of which have been identified to date. Cell-free protein synthesis is a useful and promising technique to discover and produce various proteins that might be beneficial for biotechnological, pharmaceutical, and medical applications. For this study, we evaluated the performance and the general applicability of our previously developed microreactor array chip to cell-free protein synthesis by comparisons with a commercially available system. The microreactor array chip comprises a temperature control chip made of glass and a disposable reaction chamber chip made of polydimethylsiloxane (PDMS). For evaluation of the microreactor array chip, rat adipose-type fatty acid binding protein, glyceraldehyde-3-phosphate dehydrogenase, cyclophilin, and firefly luciferase were synthesized from their respective DNA templates using a cell-free extract prepared from Escherichia coli. All these proteins were synthesized in the microreactor array chip, and their respective amounts and yields were investigated quantitatively.     

Mapping of possible prion protein self-interaction domains using peptide arrays

Background  

The common event in transmissible spongiform encephalopathies (TSEs) or prion diseases is the conversion of host-encoded protease sensitive cellular prion protein (PrP^C) into strain dependent isoforms of scrapie associated protease resistant isoform (PrP^Sc) of prion protein (PrP). These processes are determined by similarities as well as strain dependent variations in the PrP structure. Selective self-interaction between PrP molecules is the most probable basis for initiation of these processes, potentially influenced by chaperone molecules, however the mechanisms behind these processes are far from understood. We previously determined that polymorphisms do not affect initial PrP^C to PrP^Sc binding but rather modulate a subsequent step in the conversion process. Determining possible sites of self-interaction could elucidate which amino acid(s) or amino acid sequences contribute to binding and further conversion into other isoforms. To this end, ovine – and bovine PrP peptide-arrays consisting of 15-mer overlapping peptides were probed with recombinant sheep PrP^C fused to maltose binding protein (MBP-PrP).     

Synthesis and characterization of axial heterojunction inorganic-organic semiconductor nanowire arrays

The end-to-end P-N heterojunction nanowire arrays combined organic (poly[1,4-bis(pyrrol-2-yl)benzene], BPB) and inorganic (CdS) molecules have been successfully designed and fabricated. The electrical properties of P-N heterojunctions of organic-inorganic nanowire arrays were investigated. The diode nature and rectifying feature of P-N heterojunction nanowire arrays were observed. The rectification ratio of the diode increased from 29.9 to 129.7 as the illumination intensity increased. The material exhibits a new property, which is an improvement in the integration of the physical and chemical properties of the two independent components.     

Electrochemically controlled assembly and logic gates operations of gold nanoparticle arrays

The reversible assembly of β-cyclodextrin-functionalized gold NPs (β-CD Au NPs) is studied on mixed self-assembled monolayer (SAM), formed by coadsorption of redox-active ferrocenylalkylthiols and n-alkanethiols on gold surfaces. The surface coverage and spatial distribution of the β-CD Au NPs monolayer on the gold substrate are tuned by the self-assembled monolayer composition. The binding and release of β-CD Au NPs to and from the SAMs modified surface are followed by surface plasmon resonance (SPR) spectroscopy. The redox state of the tethered ferrocene in binary SAMs controls the formation of the supramolecular interaction between ferrocene moieties and β-CD-capped Au NPs. As a result, the potential-induced uptake and release of β-CD Au NPs to and from the surface is accomplished. The competitive binding of β-CD Au NPs with guest molecules in solution shifted the equilibrium of the complexation-decomplexation process involving the supramolecular interaction with the Fc-functionalized surface. The dual controlled assembly of β-CD Au NPs on the surface enabled to use two stimuli as inputs for logic gate activation; the coupling between the localized surface plasmon, associated with the Au NP, and the surface plasmon wave, associated with the thin metal surface, is implemented as readout signal for "AND" logic gate operations.     

Characteristics of the electronic structure of transition metal oxides with metallic and semiconductor conductivity

Institute of Inorganic Chemistry, Siberian Branch, Academy of Sciences of the USSR. Translated from Zhurnal Strukturnoi Khimii, Vol. 31, No. 4, pp. 145–148, July–August, 1990.