Detection of Hydrofluoric Acid by a SiO2 Sol-Gel Coating Fiber-Optic Probe Based on Reflection-Based Localized Surface Plasmon Resonance

PubMed Central

Chen, I-Cherng; Lin, Shiu-Shiung; Lin, Tsao-Jen; Du, Je-Kang

2011-01-01

A novel fiber-optic probe based on reflection-based localized surface plasmon resonance (LSPR) was developed to quantify the concentration of hydrofluoric acid (HF) in aqueous solutions. The LSPR sensor was constructed with a gold nanoparticle-modified PMMA fiber, integrated with a SiO2 sol-gel coating. This fiber-sensor was utilized to assess the relationship between HF concentration and SiO2 sol-gel layer etching reduction. The results demonstrated the LSPR sensor was capable of detecting HF-related erosion of hydrofluoric acid solutions of concentrations ranging from 1% to 5% using Relative RI Change Rates. The development of the LSPR sensor constitutes the basis of a detector with significant sensitivity for practical use in monitoring HF solution concentrations. PMID:22319388

Optical fiber nanoprobe preparation for near-field optical microscopy by chemical etching under surface tension and capillary action.

PubMed

Mondal, Samir K; Mitra, Anupam; Singh, Nahar; Sarkar, S N; Kapur, Pawan

2009-10-26

We propose a technique of chemical etching for fabrication of near perfect optical fiber nanoprobe (NNP). It uses photosensitive single mode optical fiber to etch in hydro fluoric (HF) acid solution. The difference in etching rate for cladding and photosensitive core in HF acid solution creates capillary ring along core-cladding boundary under a given condition. The capillary ring is filled with acid solution due to surface tension and capillary action. Finally it creates near perfect symmetric tip at the apex of the fiber as the height of the acid level in capillary ring decreases while width of the ring increases with continuous etching. Typical tip features are short taper length (approximately 4 microm), large cone angle (approximately 38 degrees ), and small probe tip dimension (<100 nm). A finite difference time domain (FDTD) analysis is also presented to compare near field optics of the NNP with conventional nanoprobe (CNP). The probe may be ideal for near field optical imaging and sensor applications.

Surface potential measurement of n-type organic semiconductor thin films by mist deposition via Kelvin probe microscopy

NASA Astrophysics Data System (ADS)

Odaka, Akihiro; Satoh, Nobuo; Katori, Shigetaka

2017-08-01

We partially deposited fullerene (C60) and phenyl-C61-butyric acid methyl ester thin films that are typical n-type semiconductor materials on indium-tin oxide by mist deposition at various substrate temperatures. The topographic and surface potential images were observed via dynamic force microscopy/Kelvin probe force microscopy with the frequency modulation detection method. We proved that the area where a thin film is deposited depends on the substrate temperature during deposition from the topographic images. It was also found that the surface potential depends on the substrate temperature from the surface potential images.

Site-specific protein labeling with PRIME and chelation-assisted Click chemistry

PubMed Central

Uttamapinant, Chayasith; Sanchez, Mateo I.; Liu, Daniel S.; Yao, Jennifer Z.; White, Katharine A.; Grecian, Scott; Clarke, Scott; Gee, Kyle R.; Ting, Alice Y.

2016-01-01

This protocol describes an efficient method to site-specifically label cell-surface or purified proteins with chemical probes in two steps: PRobe Incorporation Mediated by Enzymes (PRIME) followed by chelation-assisted copper-catalyzed azide-alkyne cycloaddition (CuAAC). In the PRIME step, Escherichia coli lipoic acid ligase site-specifically attaches a picolyl azide derivative to a 13-amino acid recognition sequence that has been genetically fused onto the protein of interest. Proteins bearing picolyl azide are chemoselectively derivatized with an alkyne-probe conjugate by chelation-assisted CuAAC in the second step. We describe herein the optimized protocols to synthesize picolyl azide, perform PRIME labeling, and achieve CuAAC derivatization of picolyl azide on live cells, fixed cells, and purified proteins. Reagent preparations, including synthesis of picolyl azide probes and expression of lipoic acid ligase, take 12 d, while the procedure to perform site-specific picolyl azide ligation and CuAAC on cells or on purified proteins takes 40 min-3 h. PMID:23887180

Gene quantification by the NanoGene assay is resistant to inhibition by humic acids.

PubMed

Kim, Gha-Young; Wang, Xiaofang; Ahn, Hosang; Son, Ahjeong

2011-10-15

NanoGene assay is a magnetic bead and quantum dot nanoparticles based gene quantification assay. It relies on a set of probe and signaling probe DNAs to capture the target DNA via hybridization. We have demonstrated the inhibition resistance of the NanoGene assay using humic acids laden genomic DNA (gDNA). At 1 μg of humic acid per mL, quantitiative PCR (qPCR) was inhibited to 0% of its quantification capability whereas NanoGene assay was able to maintain more than 60% of its quantification capability. To further increase the inhibition resistance of NanoGene assay at high concentration of humic acids, we have identified the specific mechanisms that are responsible for the inhibition. We examined five potential mechanisms with which the humic acids can partially inhibit our NanoGene assay. The mechanisms examined were (1) adsorption of humic acids on the particle surface; (2) particle aggregation induced by humic acids; (3) fluorescence quenching of quantum dots by humic acids during hybridization; (4) humic acids mimicking of target DNA; and (5) nonspecific binding between humic acids and target gDNA. The investigation showed that no adsorption of humic acids onto the particles' surface was observed for the humic acids' concentration. Particle aggregation and fluorescence quenching were also negligible. Humic acids also did not mimic the target gDNA except 1000 μg of humic acids per mL and hence should not contribute to the partial inhibition. Four of the above mechanisms were not related to the inhibition effect of humic acids particularly at the environmentally relevant concentrations (<100 μg/mL). However, a substantial amount of nonspecific binding was observed between the humic acids and target gDNA. This possibly results in lesser amount of target gDNA being captured by the probe and signaling DNA.

Mediated Electron Transfer at Vertically Aligned Single-Walled Carbon Nanotube Electrodes During Detection of DNA Hybridization.

PubMed

Wallen, Rachel; Gokarn, Nirmal; Bercea, Priscila; Grzincic, Elissa; Bandyopadhyay, Krisanu

2015-12-01

Vertically aligned single-walled carbon nanotube (VASWCNT) assemblies are generated on cysteamine and 2-mercaptoethanol (2-ME)-functionalized gold surfaces through amide bond formation between carboxylic groups generated at the end of acid-shortened single-walled carbon nanotubes (SWCNTs) and amine groups present on the gold surfaces. Atomic force microscopy (AFM) imaging confirms the vertical alignment mode of SWCNT attachment through significant changes in surface roughness compared to bare gold surfaces and the lack of any horizontally aligned SWCNTs present. These SWCNT assemblies are further modified with an amine-terminated single-stranded probe-DNA. Subsequent hybridization of the surface-bound probe-DNA in the presence of complementary strands in solution is followed using impedance measurements in the presence of Fe(CN)6 (3-/4-) as the redox probe in solution, which show changes in the interfacial electrochemical properties, specifically the charge-transfer resistance, due to hybridization. In addition, hybridization of the probe-DNA is also compared when it is attached directly to the gold surfaces without any intermediary SWCNTs. Contrary to our expectations, impedance measurements show a decrease in charge-transfer resistance with time due to hybridization with 300 nM complementary DNA in solution with the probe-DNA attached to SWCNTs. In contrast, an increase in charge-transfer resistance is observed with time during hybridization when the probe-DNA is attached directly to the gold surfaces. The decrease in charge-transfer resistance during hybridization in the presence of VASWCNTs indicates an enhancement in the electron transfer process of the redox probe at the VASWCNT-modified electrode. The results suggest that VASWCNTs are acting as mediators of electron transfer, which facilitate the charge transfer of the redox probe at the electrode-solution interface.

Mediated Electron Transfer at Vertically Aligned Single-Walled Carbon Nanotube Electrodes During Detection of DNA Hybridization

NASA Astrophysics Data System (ADS)

Wallen, Rachel; Gokarn, Nirmal; Bercea, Priscila; Grzincic, Elissa; Bandyopadhyay, Krisanu

2015-06-01

Vertically aligned single-walled carbon nanotube (VASWCNT) assemblies are generated on cysteamine and 2-mercaptoethanol (2-ME)-functionalized gold surfaces through amide bond formation between carboxylic groups generated at the end of acid-shortened single-walled carbon nanotubes (SWCNTs) and amine groups present on the gold surfaces. Atomic force microscopy (AFM) imaging confirms the vertical alignment mode of SWCNT attachment through significant changes in surface roughness compared to bare gold surfaces and the lack of any horizontally aligned SWCNTs present. These SWCNT assemblies are further modified with an amine-terminated single-stranded probe-DNA. Subsequent hybridization of the surface-bound probe-DNA in the presence of complementary strands in solution is followed using impedance measurements in the presence of Fe(CN)6 3-/4- as the redox probe in solution, which show changes in the interfacial electrochemical properties, specifically the charge-transfer resistance, due to hybridization. In addition, hybridization of the probe-DNA is also compared when it is attached directly to the gold surfaces without any intermediary SWCNTs. Contrary to our expectations, impedance measurements show a decrease in charge-transfer resistance with time due to hybridization with 300 nM complementary DNA in solution with the probe-DNA attached to SWCNTs. In contrast, an increase in charge-transfer resistance is observed with time during hybridization when the probe-DNA is attached directly to the gold surfaces. The decrease in charge-transfer resistance during hybridization in the presence of VASWCNTs indicates an enhancement in the electron transfer process of the redox probe at the VASWCNT-modified electrode. The results suggest that VASWCNTs are acting as mediators of electron transfer, which facilitate the charge transfer of the redox probe at the electrode-solution interface.

Space and time-resolved probing of heterogeneous catalysis reactions using lab-on-a-chip

NASA Astrophysics Data System (ADS)

Navin, Chelliah V.; Krishna, Katla Sai; Theegala, Chandra S.; Kumar, Challa S. S. R.

2016-03-01

Probing catalytic reactions on a catalyst surface in real time is a major challenge. Herein, we demonstrate the utility of a continuous flow millifluidic chip reactor coated with a nanostructured gold catalyst as an effective platform for in situ investigation of the kinetics of catalytic reactions by taking 5-(hydroxymethyl)furfural (HMF) to 2,5-furandicarboxylic acid (FDCA) conversion as a model reaction. The idea conceptualized in this paper can not only dramatically change the ability to probe the time-resolved kinetics of heterogeneous catalysis reactions but also used for investigating other chemical and biological catalytic processes, thereby making this a broad platform for probing reactions as they occur within continuous flow reactors.Probing catalytic reactions on a catalyst surface in real time is a major challenge. Herein, we demonstrate the utility of a continuous flow millifluidic chip reactor coated with a nanostructured gold catalyst as an effective platform for in situ investigation of the kinetics of catalytic reactions by taking 5-(hydroxymethyl)furfural (HMF) to 2,5-furandicarboxylic acid (FDCA) conversion as a model reaction. The idea conceptualized in this paper can not only dramatically change the ability to probe the time-resolved kinetics of heterogeneous catalysis reactions but also used for investigating other chemical and biological catalytic processes, thereby making this a broad platform for probing reactions as they occur within continuous flow reactors. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06752a

Structure and composition of insulin fibril surfaces probed by TERS

PubMed Central

Kurouski, Dmitry; Deckert-Gaudig, Tanja; Deckert, Volker; Lednev, Igor K.

2012-01-01

Amyloid fibrils associated with many neurodegenerative diseases are the most intriguing targets of modern structural biology. Significant knowledge has been accumulated about the morphology and fibril-core structure recently. However, no conventional methods could probe the fibril surface despite its significant role in the biological activity. Tip-enhanced Raman spectroscopy (TERS) offers a unique opportunity to characterize the surface structure of an individual fibril due to a high depth and lateral spatial resolution of the method in the nanometer range. Here, TERS is utilized for characterizing the secondary structure and amino acid residue composition of the surface of insulin fibrils. It was found that the surface is strongly heterogeneous and consists of clusters with various protein conformations. More than 30% of the fibril surface is dominated by β-sheet secondary structure, further developing Dobson’s model of amyloid fibrils (Jimenez et al. Proc. Natl. Acad. Sci. USA 2002). The propensity of various amino acids on the fibril surface and specific surface secondary structure elements were evaluated. β-sheet areas are rich in cysteine and aromatic amino acids, such as phenylalanine and tyrosine, whereas proline was found only in α-helical and unordered protein clusters. In addition, we showed that carboxyl, amino and imino groups are nearly equally distributed over β-sheet and α-helix/unordered regions. Overall, this study provides valuable new information about the structure and composition of the insulin fibril surface and demonstrates the power of TERS for fibril characterization. PMID:22813355

Shape Effect Undermined by Surface Reconstruction: Ethanol Dehydrogenation over Shape-Controlled SrTiO 3 Nanocrystals

DOE PAGES

Foo, Guo Shiou; Hood, Zachary D.; Wu, Zili

2017-12-05

For this research, to gain an in-depth understanding of the surface properties relevant for catalysis using ternary oxides, we report the acid–base pair reactivity of shape-controlled SrTiO 3 (STO) nanocrystals for the dehydrogenation of ethanol. Cubes, truncated cubes, dodecahedra, and etched cubes of STO with varying ratios of (001) and (110) crystal facets were synthesized using a hydrothermal method. Low-energy ion scattering (LEIS) analysis revealed that the (001) surface on cubes of STO is enriched with SrO due to surface reconstruction, resulting in a high ratio of strong base sites. Chemical treatment with dilute nitric acid to form etched cubesmore » of STO resulted in a surface enriched with Ti cations and strong acidity. Furthermore, the strength and distribution of surface acidic sites increase with the ratio of (110) facet from cubes to truncated cubes to dodecahedra for STO. Kinetic, isotopic, and spectroscopy methods show that the dehydrogenation of ethanol proceeds through the facile dissociation of the alcohol group, followed by the cleavage of the C α–H bond, which is the rate-determining step. Co-feeding of various probe molecules during catalysis, such as NH 3, 2,6-di-tert-butylpyridine, CO 2, and SO 2, reveals that a pair of Lewis acid site and basic surface oxygen atom is involved in the dehydrogenation reaction. The surface density of acid–base site pairs was measured using acetic acid as a probe molecule, allowing initial acetaldehyde formation turnover rates to be obtained. Comparison among various catalysts reveals no simple correlation between ethanol turnover rate and the percentage of either surface facet ((001) or (110)) of the STO nanocrystals. Instead, the reaction rate is found to increase with the strength of acid sites but reversely with the strength of base sites. The acid–base property is directly related to the surface composition as a result from different surface reconstruction behaviors of the shaped STO nanocrystals. Lastly, the finding in this work underscores the importance of characterizing the top surface compositions and sites properties when assessing the catalytic performance of shape-controlled complex oxides such as perovskites.« less

Shape Effect Undermined by Surface Reconstruction: Ethanol Dehydrogenation over Shape-Controlled SrTiO 3 Nanocrystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foo, Guo Shiou; Hood, Zachary D.; Wu, Zili

For this research, to gain an in-depth understanding of the surface properties relevant for catalysis using ternary oxides, we report the acid–base pair reactivity of shape-controlled SrTiO 3 (STO) nanocrystals for the dehydrogenation of ethanol. Cubes, truncated cubes, dodecahedra, and etched cubes of STO with varying ratios of (001) and (110) crystal facets were synthesized using a hydrothermal method. Low-energy ion scattering (LEIS) analysis revealed that the (001) surface on cubes of STO is enriched with SrO due to surface reconstruction, resulting in a high ratio of strong base sites. Chemical treatment with dilute nitric acid to form etched cubesmore » of STO resulted in a surface enriched with Ti cations and strong acidity. Furthermore, the strength and distribution of surface acidic sites increase with the ratio of (110) facet from cubes to truncated cubes to dodecahedra for STO. Kinetic, isotopic, and spectroscopy methods show that the dehydrogenation of ethanol proceeds through the facile dissociation of the alcohol group, followed by the cleavage of the C α–H bond, which is the rate-determining step. Co-feeding of various probe molecules during catalysis, such as NH 3, 2,6-di-tert-butylpyridine, CO 2, and SO 2, reveals that a pair of Lewis acid site and basic surface oxygen atom is involved in the dehydrogenation reaction. The surface density of acid–base site pairs was measured using acetic acid as a probe molecule, allowing initial acetaldehyde formation turnover rates to be obtained. Comparison among various catalysts reveals no simple correlation between ethanol turnover rate and the percentage of either surface facet ((001) or (110)) of the STO nanocrystals. Instead, the reaction rate is found to increase with the strength of acid sites but reversely with the strength of base sites. The acid–base property is directly related to the surface composition as a result from different surface reconstruction behaviors of the shaped STO nanocrystals. Lastly, the finding in this work underscores the importance of characterizing the top surface compositions and sites properties when assessing the catalytic performance of shape-controlled complex oxides such as perovskites.« less

Capillary electrophoresis, a method for the determination of nucleic acid ligands covalently attached to quantum dots representing a donor of Förster resonance energy transfer.

PubMed

Datinská, Vladimíra; Klepárník, Karel; Belšánová, Barbora; Minárik, Marek; Foret, František

2018-05-09

The synthesis and determination of the structure of a Förster resonance energy transfer probe intended for the detection of specific nucleic acid sequences are described here. The probe is based on the hybridization of oligonucleotide modified quantum dots with a fluorescently labeled nucleic acid sample resulting in changes of the fluorescence emission due to the energy transfer effect. The stoichiometry distribution of oligonucleotides conjugated to quantum dots was determined by capillary electrophoresis separation. The results indicate that one to four molecules of oligonucleotide are conjugated to the surface of a single nanoparticle. This conclusion is confirmed by the course of the dependence of Förster resonance energy transfer efficiency on the concentration of fluorescently labeled complementary single-stranded nucleic acid, showing saturation. While the energy transfer efficiency of the probe hybridized with complementary nucleic acid strands was 30%, negligible efficiency was observed with a non-complementary strands. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Lewis acid properties of alumina based catalysts: study by paramagnetic complexes of probe molecules

NASA Astrophysics Data System (ADS)

Fionov, Alexander V.

2002-06-01

Lewis acid properties of LiAl 5O 8/Al 2O 3 (2 wt.% Li) and MgAl 2O 4/Al 2O 3 (3 wt.% Mg) catalysts were studied by EPR of adsorbed probe molecules--anthraquinone and 2,2,6,6-tetramethylpiperidine- N-oxyl (TEMPO). The lesser (in comparison with γ-Al 2O 3) concentration and the strength of Lewis acid sites (LAS) formed on the surface of aluminate layer has been shown. The stability of this layer plays important role in the change of Lewis acid properties during the calcination of modified alumina. The lithium aluminate layer was stable at used calcination temperature, 773 K, meanwhile magnesium aluminate layer observed only at calcination temperature below 723 K. The increase of the calcination temperature to 773 K caused the segregation of MgAl 2O 4 on the surface resulted in the release of alumina surface and recovery of the Lewis acid properties. The differences in the LAS manifestations towards TEMPO and anthraquinone was discussed. The mechanism of the formation of anthraquinone paramagnetic complexes with LAS--three-coordinated aluminum ions--was proposed. This mechanism includes the formation of anthrasemiquinone, and then--anthrasemiquinone ion pair or triple ion. Fragments like -O-Al +-O- play the role of cations in these ion pairs and triple ions. Proposed mechanism can also be applied for the consideration of similar anthraquinone paramagnetic complexes on the surface of gallium oxide containing systems.

A rapid microwave synthesis of nitrogen-sulfur co-doped carbon nanodots as highly sensitive and selective fluorescence probes for ascorbic acid.

PubMed

Duan, Junxia; Yu, Jie; Feng, Suling; Su, Li

2016-06-01

A ultrafast one-step microwave-assisted method was developed for the synthesis of nitrogen-sulfur co-doped carbon nanodots (N,S-CDs) by using ethylenediamine as the carbon source and sulfamic acid as the surface passivation reagent. The morphology and the properties of N,S-CDs were explored by a series of techniques, such as high-resolution transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, UV-vis absorption and fluorescence spectroscopy. The prepared N,S-CDs exhibit bright blue photoluminescence with a high fluorescence quantum yield (FLQY) up to 28%, and high stability and excellent water solubility. A N,S-CDs-based fluorescent probe was developed for sensitive detection ascorbic acid (AA) in the presence of Cu(2+), based on the mechanism that AA reduces Cu(2+) to Cu(+), then Cu(+) quenches the fluorescence of N,S-CDs through electron or energy transfer due to the interaction between Cu(+) and thiol ligand on the N,S-CDs surface. The observed linear response concentration range was from 0.057 to 4.0μM to AA with a detection limit as low as 18nM. The probe exhibited a highly selective response toward AA even in the presence of possible interfering substances, such as uric acid and citric acid. Moreover, these promising features made the sensing system used for the analysis of human serum and urine samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Polyvinylpyrrolidone- (PVP-) coated silver aggregates for high performance surface-enhanced Raman scattering in living cells.

PubMed

Tan, Xuebin; Wang, Zhuyuan; Yang, Jing; Song, Chunyuan; Zhang, Ruohu; Cui, Yiping

2009-11-04

A biocompatible and stable surface-enhanced Raman scattering (SERS) probe has been successfully synthesized through a simple route with silver aggregates. Polyvinylpyrrolidone (PVP), a biocompatible polymer, was utilized to control the aggregation process and improve the chemical stability of the aggregates. Extinction spectroscopy and TEM results show the aggregation degree and core-shell structure of the probe. It is found that when we employ 4-mercaptobenzoic acid (4MBA), crystal violet (CV), Rhodamine 6G (R6G) or 4,4'-bipyridine molecules as Raman reporters, the SERS signal from the proposed probe can remain at a high level under aggressive chemical environments, even after being incorporated into living cells. In comparison with the traditional probes without the PVP shell, the new ones exhibit strong surface-enhanced effects and low toxicity towards living cells. We demonstrate that the PVP-coated silver aggregates are highly SERS effective, for which the fabrication protocol is advantageous in its simplicity and reproducibility.

Assessment of surface acidity in mesoporous materials containing aluminum and titanium

NASA Astrophysics Data System (ADS)

Araújo, Rinaldo S.; Maia, Débora A. S.; Azevedo, Diana C. S.; Cavalcante, Célio L., Jr.; Rodríguez-Castellón, E.; Jimenez-Lopez, A.

2009-04-01

The surface acidity of mesoporous molecular sieves of aluminum and titanium was evaluated using four different techniques: n-butylamine volumetry, cyclohexylamine thermodesorption, temperature-programmed desorption of ammonia and adsorption of pyridine. The nature, strength and concentration of the acid sites were determined and correlated to the results of a probe reaction of anthracene oxidation to 9,10-anthraquinone (in liquid phase). In general, the surface acidity was highly influenced by the nature, location and coordination of the metal species (Al and Ti) in the mesoporous samples. Moderate to strong Brönsted acid sites were identified for the Al-MCM-41 sample in a large temperature range. For mesoporous materials containing Ti, the acidity was represented by a combination of weak to moderate Brönsted and Lewis acid sites. The Ti-HMS sample exhibits a higher acidity of moderate strength together with a well-balanced concentration of Brönsted and Lewis acid sites, which enhanced both conversion and selectivity in the oxidation reaction of anthracene.

One-step synthesis of nitrogen, boron co-doped fluorescent carbon nanoparticles for glucose detection.

PubMed

Liang, Meijuan; Ren, Yi; Zhang, Haijuan; Ma, Yunxia; Niu, Xiaoying; Chen, Xingguo

2017-09-01

Heteroatom-doped carbon nanoparticles (CNPs) have attracted considerable attention due to an effective improvement in their intrinsic properties. Here, a facile and simple synthesis of nitrogen, boron co-doped carbon nanoparticles (NB-CNPs) from a sole precursor, 3-aminophenylboronic acid, was performed via a one-step solid-phase approach. Because of the presence of boronic acid, NB-CNPs can be used directly as a fluorescent probe for glucose. Based on a boronic acid-triggered specific reaction, we developed a simple NB-CNP probe without surface modification for the detection of glucose. When glucose was introduced, the fluorescence of NB-CNPs was suppressed through a surface-quenching states mechanism. Obvious fluorescence quenching allowed the highly sensitive determination of glucose with a limit of detection of 1.8 μM. Moreover, the proposed method has been successfully used to detect glucose in urine from people with diabetes, suggesting potential application in sensing glucose. Copyright © 2017 John Wiley & Sons, Ltd.

Poly-adenine-mediated fluorescent spherical nucleic acid probes for live-cell imaging of endogenous tumor-related mRNA.

PubMed

Zhu, Dan; Zhao, Dongxia; Huang, Jiaxuan; Zhu, Yu; Chao, Jie; Su, Shao; Li, Jiang; Wang, Lihua; Shi, Jiye; Zuo, Xiaolei; Weng, Lixing; Li, Qian; Wang, Lianhui

2018-05-16

Identification of tumor-related mRNA in living cells hold great promise for early cancer diagnosis and pathological research. Herein, we present poly-adenine (polyA)-mediated fluorescent spherical nucleic acid (FSNA) probes for intracellular mRNA detection with regulable sensitivities by programmably adjusting the loading density of DNA on gold nano-interface. Gold nanoparticles (AuNPs) functionalized with polyA-tailed recognition sequences were hybridized to fluorescent "reporter" strands to fabricate fluorescence-quenched FSNA probes. While exposed to target gene, the "reporter" strands were released from FSNA through strand displacement and fluorescence was recovered. With polyA20 tail as the attaching block, the detection limit of FSNA probes was calculated to be 0.31 nM, which is ~55 fold lower than that of thiolated probes without surface density regulation. Quantitative intracellular mRNA detection and imaging could be achieved with polyA-mediated FSNA probes within 2 hours, indicating their application potential in rapid and sensitive intracellular target imaging. Copyright © 2018. Published by Elsevier Inc.

Influence of polymorphism on the surface energetics of salmeterol xinafoate crystallized from supercritical fluids.

PubMed

Tong, Henry H Y; Shekunov, Boris Yu; York, Peter; Chow, Albert H L

2002-05-01

To characterize the surface thermodynamic properties of two polymorphic forms (I and II) of salmeterol xinafoate (SX) prepared from supercritical fluids and a commercial micronized SX (form 1) sample (MSX). Inverse gas chromatographic analysis was conducted on the SX samples at 30, 40, 50, and 60 degrees C using the following probes at infinite dilution: nonpolar probes (NPs; alkane C5-C9 series); and polar probes (PPs; i.e., dichloromethane, chloroform, acetone, ethyl acetate, diethyl ether, and tetrahydrofuran). Surface thermodynamic parameters of adsorption and Hansen solubility parameters were calculated from the retention times of the probes. The free energies of adsorption (- deltaG(A)) of the three samples obtained at various temperatures follow this order: SX-II > MSX approximately/= SX-I for the NPs; and SX-II > MSX > SX-I for the PPs. For both NPs and PPs, SX-II exhibits a less negative enthalpy of adsorption (deltaH(A)) and a much less negative entropy of adsorption (ASA) than MSX and SX-I, suggesting that the high -AGA of SX-II is contributed by a considerably reduced entropy loss. The dispersive component of surface free energy (gammas(D)) is the highest for MSX but the lowest for SX-II at all temperatures studied, whereas the specific component of surface free energy of adsorption (-deltaG(A)SP) is higher for SX-II than for SX-I. That SX-II displays the highest -deltaG(A) for the NP but the lowest gammasD of all the SX samples may be explained by the additional -AGA change associated with an increased mobility of the probe molecules on the less stable and more disordered SX-II surface. The acid and base parameters, K(A) and K(D) that were derived from deltaH(A)SP reveal significant differences in the relative acid and base properties among the samples. The calculated Hansen solubility parameters (deltaD, deltap, and deltaH) indicate that the surface of SX-II is the most polar and most energetic of all the three samples in terms of specific interactions (mostly hydrogen bonding). The metastable SX-II polymorph possesses a higher surface free energy, higher surface entropy, and a more polar surface than the stable SX-I polymorph.

A review of the different techniques for solid surface acid-base characterization.

PubMed

Sun, Chenhang; Berg, John C

2003-09-18

In this work, various techniques for solid surface acid-base (AB) characterization are reviewed. Different techniques employ different scales to rank acid-base properties. Based on the results from literature and the authors' own investigations for mineral oxides, these scales are compared. The comparison shows that Isoelectric Point (IEP), the most commonly used AB scale, is not a description of the absolute basicity or acidity of a surface, but a description of their relative strength. That is, a high IEP surface shows more basic functionality comparing with its acidic functionality, whereas a low IEP surface shows less basic functionality comparing with its acidic functionality. The choice of technique and scale for AB characterization depends on the specific application. For the cases in which the overall AB property is of interest, IEP (by electrokinetic titration) and H(0,max) (by indicator dye adsorption) are appropriate. For the cases in which the absolute AB property is of interest such as in the study of adhesion, it is more pertinent to use chemical shift (by XPS) and the heat of adsorption of probe gases (by calorimetry or IGC).

Investigating the photostability of carboxylic acids exposed to Mars surface ultraviolet radiation conditions.

PubMed

Stalport, F; Coll, P; Szopa, C; Cottin, H; Raulin, F

2009-01-01

The detection and identification of organic molecules on Mars are of primary importance to establish the existence of a possible ancient prebiotic chemistry or even biological activity. The harsh environmental conditions at the surface of Mars could explain why the Viking probes-the only efforts, to date, to search for organics on Mars-detected no organic matter. To investigate the nature, abundance, and stability of organic molecules that could survive such environmental conditions, we developed a series of experiments that simulate martian surface environmental conditions. Here, we present results with regard to the impact of solar UV radiation on various carboxylic acids, such as mellitic acid, which are of astrobiological interest to the study of Mars. Our results show that at least one carboxylic acid, mellitic acid, could produce a resistant compound-benzenehexacarboxylic acid-trianhydride (C(12)O(9))-when exposed to martian surface radiation conditions. The formation of such products could contribute to the presence of organic matter in the martian regolith, which should be considered a primary target for in situ molecular analyses during future surface missions.

Isotopic Probe Illuminates the Role of the Electrode Surface in Proton Coupled Hydride Transfer Electrochemical Reduction of Pyridinium on Pt(111)

DOE PAGES

Zeitler, Elizabeth L.; Ertem, Mehmed Z.; Pander, III, James E.; ...

2015-10-21

A recently proposed mechanism for electrochemical CO 2 reduction on Pt (111) catalyzed by aqueous acidic pyridine solutions suggests that the observed redox potential of ca. -600 mV vs. SCE is due to the one-electron reduction of pyridinium through proton coupled electron transfer (PCET) to form H atoms adsorbed on the Pt surface (H ads). The initial pyridinium reduction was probed isotopically via deuterium substitution. A combined experimental and theoretical analysis found equilibrium isotope effects (EIE) due to deuterium substitution at the acidic pyridinium site. A shift in the cathodic cyclic voltammetric half wave potential of -25 mV was observed,more » consistent with the theoretical prediction of -40 mV based on the recently proposed reaction mechanism where pyridinium is essential to establish a high concentration of Bronsted acid in contact with the substrate CO 2 and with the Pt surface. A prefeature in the cyclic voltammogram was examined under isotopic substitution and indicated an H-ads intermediate in pyridinium reduction. In conclusion, the theoretical prediction and observation of an BM supported the assignment of the cathodic wave to the proposed reduction of pyridinium through PCET forming H ads and eventually H 2 on the Pt surface.« less

Electrospun Nanofibers Made of Silver Nanoparticles, Cellulose Nanocrystals, and Polyacrylonitrile as Substrates for Surface-Enhanced Raman Scattering

PubMed Central

Ren, Suxia; Dong, Lili; Zhang, Xiuqiang; Lei, Tingzhou; Ehrenhauser, Franz; Song, Kunlin; Li, Meichun; Sun, Xiuxuan; Wu, Qinglin

2017-01-01

Nanofibers with excellent activities in surface-enhanced Raman scattering (SERS) were developed through electrospinning precursor suspensions consisting of polyacrylonitrile (PAN), silver nanoparticles (AgNPs), silicon nanoparticles (SiNPs), and cellulose nanocrystals (CNCs). Rheology of the precursor suspensions, and morphology, thermal properties, chemical structures, and SERS sensitivity of the nanofibers were investigated. The electrospun nanofibers showed uniform diameters with a smooth surface. Hydrofluoric (HF) acid treatment of the PAN/CNC/Ag composite nanofibers (defined as p-PAN/CNC/Ag) led to rougher fiber surfaces with certain pores and increased mean fiber diameters. X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) results confirmed the existence of AgNPs that were formed during heat and HF acid treatment processes. In addition, thermal stability of the electrospun nanofibers increased due to the incorporation of CNCs and AgNPs. The p-PAN/CNC/Ag nanofibers were used as a SERS substrate to detect p-aminothiophenol (p-ATP) probe molecule. The results show that this substrate exhibited high sensitivity for the p-ATP probe detection. PMID:28772428

Combined use of atomic force microscopy, X-ray photoelectron spectroscopy, and secondary ion mass spectrometry for cell surface analysis.

PubMed

Dague, Etienne; Delcorte, Arnaud; Latgé, Jean-Paul; Dufrêne, Yves F

2008-04-01

Understanding the surface properties of microbial cells is a major challenge of current microbiological research and a key to efficiently exploit them in biotechnology. Here, we used three advanced surface analysis techniques with different sensitivity, probing depth, and lateral resolution, that is, in situ atomic force microscopy, X-ray photoelectron spectroscopy, and secondary ion mass spectrometry, to gain insight into the surface properties of the conidia of the human fungal pathogen Aspergillus fumigatus. We show that the native ultrastructure, surface protein and polysaccharide concentrations, and amino acid composition of three mutants affected in hydrophobin production are markedly different from those of the wild-type, thereby providing novel insight into the cell wall architecture of A. fumigatus. The results demonstrate the power of using multiple complementary techniques for probing microbial cell surfaces.

Self-assembled monolayers of mercaptobenzoic acid and magnetite nanoparticles as an efficient support for development of tuberculosis genosensor.

PubMed

Costa, Maurilia P; Andrade, Cesar A S; Montenegro, Rosana A; Melo, Fabio L; Oliveira, Maria D L

2014-11-01

In this work, a genosensor for the electrochemical detection of genomic DNA from Mycobacterium tuberculosis was developed. The biosensor is based on self-assembled monolayers of mercaptobenzoic acid (MBA) and magnetite nanoparticles (Fe3O4Nps) on bare gold electrode for immobilization of DNA probe. The aim of this work was the development of a platform based on cysteine-coated magnetic Fe3O4Nps linked via the carboxylate group from MBA to the work electrode surface and subsequently to the DNA probe. The probe-genome interaction was evaluated using a [Fe(CN)6](4-)/[Fe(CN)6](3-) redox pair. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were used to evaluate the bioelectrochemical behavior of the sensor. Atomic force microscopy images showed Fe3O4Nps immobilized across the electrode surface. The interaction of the sensor with different genome DNA concentrations resulted in changes in the charge transfer resistance, indicating a possible use for tuberculosis detection at low concentrations (detection limit of 6ngμL(-1)). Copyright © 2014 Elsevier Inc. All rights reserved.

Competitive Reporter Monitored Amplification (CMA) - Quantification of Molecular Targets by Real Time Monitoring of Competitive Reporter Hybridization

PubMed Central

Ullrich, Thomas; Ermantraut, Eugen; Schulz, Torsten; Steinmetzer, Katrin

2012-01-01

Background State of the art molecular diagnostic tests are based on the sensitive detection and quantification of nucleic acids. However, currently established diagnostic tests are characterized by elaborate and expensive technical solutions hindering the development of simple, affordable and compact point-of-care molecular tests. Methodology and Principal Findings The described competitive reporter monitored amplification allows the simultaneous amplification and quantification of multiple nucleic acid targets by polymerase chain reaction. Target quantification is accomplished by real-time detection of amplified nucleic acids utilizing a capture probe array and specific reporter probes. The reporter probes are fluorescently labeled oligonucleotides that are complementary to the respective capture probes on the array and to the respective sites of the target nucleic acids in solution. Capture probes and amplified target compete for reporter probes. Increasing amplicon concentration leads to decreased fluorescence signal at the respective capture probe position on the array which is measured after each cycle of amplification. In order to observe reporter probe hybridization in real-time without any additional washing steps, we have developed a mechanical fluorescence background displacement technique. Conclusions and Significance The system presented in this paper enables simultaneous detection and quantification of multiple targets. Moreover, the presented fluorescence background displacement technique provides a generic solution for real time monitoring of binding events of fluorescently labelled ligands to surface immobilized probes. With the model assay for the detection of human immunodeficiency virus type 1 and 2 (HIV 1/2), we have been able to observe the amplification kinetics of five targets simultaneously and accommodate two additional hybridization controls with a simple instrument set-up. The ability to accommodate multiple controls and targets into a single assay and to perform the assay on simple and robust instrumentation is a prerequisite for the development of novel molecular point of care tests. PMID:22539973

Electroactive chitosan nanoparticles for the detection of single-nucleotide polymorphisms using peptide nucleic acids.

PubMed

Kerman, Kagan; Saito, Masato; Tamiya, Eiichi

2008-08-01

Here we report an electrochemical biosensor that would allow for simple and rapid analysis of nucleic acids in combination with nuclease activity on nucleic acids and electroactive bionanoparticles. The detection of single-nucleotide polymorphisms (SNPs) using PNA probes takes advantage of the significant structural and physicochemical differences between the full hybrids and SNPs in PNA/DNA and DNA/DNA duplexes. Ferrocene-conjugated chitosan nanoparticles (Chi-Fc) were used as the electroactive indicator of hybridization. Chi-Fc had no affinity towards the neutral PNA probe immobilized on a gold electrode (AuE) surface. When the PNA probe on the electrode surface hybridized with a full-complementary target DNA, Chi-Fc electrostatically attached to the negatively-charged phosphate backbone of DNA on the surface and gave rise to a high electrochemical oxidation signal from ferrocene at approximately 0.30 V. Exposing the surface to a single-stranded DNA specific nuclease, Nuclease S1, was found to be very effective for removing the nonspecifically adsorbed SNP DNA. An SNP in the target DNA to PNA made it susceptible to the enzymatic digestion. After the enzymatic digestion and subsequent exposure to Chi-Fc, the presence of SNPs was determined by monitoring the changes in the electrical current response of Chi-Fc. The method provided a detection limit of 1 fM (S/N = 3) for the target DNA oligonucleotide. Additionally, asymmetric PCR was employed to detect the presence of genetically modified organism (GMO) in standard Roundup Ready soybean samples. PNA-mediated PCR amplification of real DNA samples was performed to detect SNPs related to alcohol dehydrogenase (ALDH). Chitosan nanoparticles are promising biomaterials for various analytical and pharmaceutical applications.

Molecular-level Design of Heterogeneous Chiral Catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilfred T. Tysoe

2007-04-25

It has been shown previously that the adsorption of a chiral 2-butanol template on Pd(111) leads to enantioselective adsorption of chiral propylene oxide probe molecules. Enantioselectivity is expressed over a narrow coverage range where the maximum value of enantioselectivity ratio (ER defined as Θ(R-propylene oxide)/Θ(S-propylene oxide), where Θ is the coverage) reaches ~2. Probe coverages in this case were measured using either reflection-absorption infrared spectroscopy (RAIRS) or temperature-programmed desorption (TPD) [1,2]. The enantioselectivity disappears when the 2-butanol-covered surface was heated to ~200 K since the adsorbed butoxy species decomposes by a β-hydride elimination reaction to yield a non-chiral ketone. Montemore » Carlo calculations of the effect of chiral modifiers have yielded results that are consistent with these experimental observations [3,4]. Similar experiments using 2-methyl butanoic acid as a template, where the chiral center is identical to that in 2-butanol but is now anchored by a carboxylate group rather than by an alkoxide, shows no enantioselectivity. In this case, propylene oxide coverages were measured using the King and Wells method. RAIRS experiments and density functional calculations suggest that the 2-butyl group of the 2-butoxy species is oriented parallel to the surface. A possible origin for the lack of enantioselectivity of a 2-methyl butanoic acid-covered surface may be that the 2-butyl group is farther from the surface, allowing it to rotate more freely, averaging out any asymmetry, resulting in a loss of chirality. In order to test this idea, the alkyl group on the carboxylic acid was functionalized with an amine to anchor the chiral center to the surface. Using the amino-acids alanine and 2-amino butanoic acid as templates restored the enantioselectivity and yielded ER values of 2.0 ± 0.2 and 1.75 ± 0.15 respectively. These results suggest that a two-point attachment of the chiral template is required, one for surface adsorption and the other to allow the enantioselectivity to be expressed. Low-energy electron diffraction (LEED) intensity versus energy (I/E) measurements are used to measure the structure of templates and probes on the Pd(111) surface, where these results will be compared with calculations carried out by the Sholl group. Since the aminoacids are relatively large, initial experiments were carried out to determine the structure of carboxylates on the surface to determine the carboxylate group anchoring site. Since carboxylates do not form ordered structures on Pd(111), we have exploited a method recently developed in collaboration with Professor Saldin to measure structures of disordered overlayers [5]. Results show that the formate OCO plane is oriented perpendicular to the surface with the oxygen atoms located across a short bridge on the (111) surface. The effect of the size of the functional group on the amino acid template (RCH(NH2)COOH) was also investigated where the maximum ER values obtained using propylene oxide were 2.0 ± 0.2 (R=CH3), 1.75 ± 0.15 (R=C2H5), 1.65 ± 0.15 (R=C3H6) and 1.30 ± 0.15 (R=CH2CH(CH3)2) thus showing a decreasing trend with increasing size of the side chain. The enantioselectivity of S-(1-naphthyl) ethylamine-covered surfaces have been explored using propylene oxide as a probe, but these systems showed no enantioselectivity. However, using 2-butanol as a probe lead to enantioselective chemisorption implying that one-to-one modification requires a direct hydrogen-bonding interaction between the probe and modifier. 1. Enantioselective Chemisorption on a Chirally Patterned Surface in Ultrahigh Vacuum: Adsorption of Propylene Oxide on 2-butoxy-Covered Pd(111), D. Stacchiola, L. Burkholder and W.T. Tysoe, J. Am. Chem. Soc., 124, 8984 (2002) 2. Enantioselective Chemisorption on a Chirally Modified Surface in Ultrahigh Vacuum: Adsorption of Propylene Oxide on 2-butoxide-Covered Pd(111), Darío Stacchiola, Luke Burkholder and Wilfred T. Tysoe, J. Mol. Catal A: Chemical, 216, 215 (2004) 3. Theoretical Analysis of the Coverage Dependence of Enantioselective Chemisorption on a Chirally Patterned Surface, F. Roma, D. Stacchiola, G. Zgrablich and W. T. Tysoe, Journal of Chemical Physics, 118, 6030 (2003) 4. Lattice-gas Modeling of Enantioselective Adsorption by Template Chiral Substrates, F. Romá, D. Stacchiola, W.T. Tysoe and G. Zgrablich, Physica A., 338, 493 (2004) 5. Structure Determination of Disordered Organic Molecules on Surfaces from the Bragg Spots of Low Energy Electron Diffraction and Total Energy Calculations, H. C. Poon, M. Weinert, D. K. Saldin, D. Stacchiola, T. Zheng and W. T. Tysoe, Phys. Rev. B., 69, 35401 (2004)« less

α- and β-Proteobacteria Control the Consumption and Release of Amino Acids on Lake Snow Aggregates

PubMed Central

Schweitzer, Bernhard; Huber, Ingrid; Amann, Rudolf; Ludwig, Wolfgang; Simon, Meinhard

2001-01-01

We analyzed the composition of aggregate (lake snow)-associated bacterial communities in Lake Constance from 1994 until 1996 between a depth of 25 m and the sediment surface at 110 m by fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes of various specificity. In addition, we experimentally examined the turnover of dissolved amino acids and carbohydrates together with the microbial colonization of aggregates formed in rolling tanks in the lab. Generally, between 40 and more than 80% of the microbes enumerated by DAPI staining (4′,6′-diamidino-2-phenylindole) were detected as Bacteria by the probe EUB338. At a depth of 25 m, 10.5% ± 7.9% and 14.2% ± 10.2% of the DAPI cell counts were detected by probes specific for α- and β-Proteobacteria. These proportions increased to 12.0% ± 3.3% and 54.0% ± 5.9% at a depth of 50 m but decreased again at the sediment surface at 110 m to 2.7% ± 1.4% and 41.1% ± 8.4%, indicating a clear dominance of β-Proteobacteria at depths of 50 and 110 m, where aggregates have an age of 3 to 5 and 8 to 11 days, respectively. From 50 m to the sediment surface, cells detected by a Cytophaga/Flavobacteria-specific probe (CF319a) comprised increasing proportions up to 18% of the DAPI cell counts. γ-Proteobacteria always comprised minor proportions of the aggregate-associated bacterial community. Using only two probes highly specific for clusters of bacteria closely related to Sphingomonas species and Brevundimonas diminuta, we identified between 16 and 60% of the α-Proteobacteria. In addition, with three probes highly specific for close relatives of the β-Proteobacteria Duganella zoogloeoides (formerly Zoogloea ramigera), Acidovorax facilis, and Hydrogenophaga palleroni, bacteria common in activated sludge, 42 to 70% of the β-Proteobacteria were identified. In the early phase (<20 h) of 11 of the 15 experimental incubations of aggregates, dissolved amino acids were consumed by the aggregate-associated bacteria from the surrounding water. This stage was followed by a period of 1 to 3 days during which dissolved amino acids were released into the surrounding water, paralleled by an increasing dominance of β-Proteobacteria. Hence, our results show that lake snow aggregates are inhabited by a community dominated by a limited number of α- and β-Proteobacteria, which undergo a distinct succession. They successively decompose the amino acids bound in the aggregates and release substantial amounts into the surrounding water during aging and sinking. PMID:11157226

Adsorption, Mobility and Organisation of Organic Molecules at Clay Surfaces Probed by Photophysics and Photochemistry

DTIC Science & Technology

1989-06-15

and refluxed at 100 0 C during 24 hours. This basic hydrolysis results in the formation of polymethacrylic acid , which is soluble in basic media. The...from the supernatant solution by adding 3M HC The I.R.spectrum of the obtained polymer is identical to the I.R. spectrum of the polymethacrylic acid (8

Surface-functionalized nanoparticles for biosensing and imaging-guided therapeutics

NASA Astrophysics Data System (ADS)

Jiang, Shan; Win, Khin Yin; Liu, Shuhua; Teng, Choon Peng; Zheng, Yuangang; Han, Ming-Yong

2013-03-01

In this article, the very recent progress of various functional inorganic nanomaterials is reviewed including their unique properties, surface functionalization strategies, and applications in biosensing and imaging-guided therapeutics. The proper surface functionalization renders them with stability, biocompatibility and functionality in physiological environments, and further enables their targeted use in bioapplications after bioconjugation via selective and specific recognition. The surface-functionalized nanoprobes using the most actively studied nanoparticles (i.e., gold nanoparticles, quantum dots, upconversion nanoparticles, and magnetic nanoparticles) make them an excellent platform for a wide range of bioapplications. With more efforts in recent years, they have been widely developed as labeling probes to detect various biological species such as proteins, nucleic acids and ions, and extensively employed as imaging probes to guide therapeutics such as drug/gene delivery and photothermal/photodynamic therapy.

Size-Dependent Affinity of Glycine and Its Short Oligomers to Pyrite Surface: A Model for Prebiotic Accumulation of Amino Acid Oligomers on a Mineral Surface

PubMed Central

Afrin, Rehana; Ganbaatar, Narangerel; Aono, Masashi; Cleaves, H. James; Yano, Taka-aki; Hara, Masahiko

2018-01-01

The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, and penta-Gly, with a natural pyrite surface was directly measured using the force mode of an atomic force microscope (AFM). In recent years, selective activation of abiotically formed amino acids on mineral surfaces, especially that of pyrite, has been proposed as an important step in many origins of life scenarios. To investigate such notions, we used AFM-based force measurements to probe possible non-covalent interactions between pyrite and amino acids, starting from the simplest amino acid, Gly. Although Gly itself interacted with the pyrite surface only weakly, progressively larger unbinding forces and binding frequencies were obtained using oligomers from di-Gly to penta-Gly. In addition to an expected increase of the configurational entropy and size-dependent van der Waals force, the increasing number of polar peptide bonds, among others, may be responsible for this observation. The effect of chain length was also investigated by performing similar experiments using l-lysine vs. poly-l-lysine (PLL), and l-glutamic acid vs. poly-l-glutamic acid. The results suggest that longer oligomers/polymers of amino acids can be preferentially adsorbed on pyrite surfaces. PMID:29370126

Surface force analysis of glycine adsorption on different crystal surfaces of titanium dioxide (TiO2).

PubMed

Ganbaatar, Narangerel; Imai, Kanae; Yano, Taka-Aki; Hara, Masahiko

2017-01-01

Surface force analysis with atomic force microscope (AFM) in which a single amino acid residue was mounted on the tip apex of AFM probe was carried out for the first time at the molecular level on titanium dioxide (TiO 2 ) as a representative mineral surface for prebiotic chemical evolution reactions. The force analyses on surfaces with three different crystal orientations revealed that the TiO 2 (110) surface has unique characteristics for adsorbing glycine molecules showing different features compared to those on TiO 2 (001) and (100). To examine this difference, we investigated thermal desorption spectroscopy (TDS) and the interaction between the PEG cross-linker and the three TiO 2 surfaces. Our data suggest that the different single crystal surfaces would provide different chemical evolution field for amino acid molecules.

Redox polymer and probe DNA tethered to gold electrodes for enzyme-amplified amperometric detection of DNA hybridization.

PubMed

Kavanagh, Paul; Leech, Dónal

2006-04-15

The detection of nucleic acids based upon recognition surfaces formed by co-immobilization of a redox polymer mediator and DNA probe sequences on gold electrodes is described. The recognition surface consists of a redox polymer, [Os(2,2'-bipyridine)2(polyvinylimidazole)(10)Cl](+/2+), and a model single DNA strand cross-linked and tethered to a gold electrode via an anchoring self-assembled monolayer (SAM) of cysteamine. Hybridization between the immobilized probe DNA of the recognition surface and a biotin-conjugated target DNA sequence (designed from the ssrA gene of Listeria monocytogenes), followed by addition of an enzyme (glucose oxidase)-avidin conjugate, results in electrical contact between the enzyme and the mediating redox polymer. In the presence of glucose, the current generated due to the catalytic oxidation of glucose to gluconolactone is measured, and a response is obtained that is binding-dependent. The tethering of the probe DNA and redox polymer to the SAM improves the stability of the surface to assay conditions of rigorous washing and high salt concentration (1 M). These conditions eliminate nonspecific interaction of both the target DNA and the enzyme-avidin conjugate with the recognition surfaces. The sensor response increases linearly with increasing concentration of target DNA in the range of 1 x 10(-9) to 2 x 10(-6) M. The detection limit is approximately 1.4 fmol, (corresponding to 0.2 nM of target DNA). Regeneration of the recognition surface is possible by treatment with 0.25 M NaOH solution. After rehybridization of the regenerated surface with the target DNA sequence, >95% of the current is recovered, indicating that the redox polymer and probe DNA are strongly bound to the surface. These results demonstrate the utility of the proposed approach.

Factors determining electrostatic fields in molecular dynamics simulations of the Ras/effector interface.

PubMed

Ensign, Daniel L; Webb, Lauren J

2011-12-01

Using molecular dynamics simulations, we explore geometric and physical factors contributing to calculated electrostatic fields at the binding surface of the GTPase Ras with a spectroscopically labeled variant of a downstream effector, the Ras-binding domain of Ral guanine nucleotide dissociation stimulator (RalGDS). A related system (differing by mutation of one amino acid) has been studied in our group using vibrational Stark effect spectroscopy, a technique sensitive to electrostatic fields. Electrostatic fields were computed using the AMBER 2003 force field and averaged over snapshots from molecular dynamics simulation. We investigate geometric factors by exploring how the orientation of the spectroscopic probe changes on Ras-effector binding. In addition, we explore the physical origin of electrostatic fields at our spectroscopic probe by comparing contributions to the field from discrete components of the system, such as explicit solvent, residues on the Ras surface, and residues on the RalGDS surface. These models support our experimental hypothesis that vibrational Stark shifts are caused by Ras binding to its effector and not the structural rearrangements of the effector surface or probe reorientation on Ras-effector binding, for at least some of our experimental probes. These calculations provide physical insight into the origin, magnitude, and importance of electrostatic fields in protein-protein interactions and suggest new experiments to probe the field's role in protein docking. Copyright © 2011 Wiley-Liss, Inc.

Liquid microjunction surface sampling probe fluid dynamics: Characterization and application of an analyte plug formation operational mode

DOE Office of Scientific and Technical Information (OSTI.GOV)

ElNaggar, Mariam S.; Van Berkel, Gary J.

2011-08-10

The recently discovered sample plug formation and injection operational mode of a continuous flow, coaxial tube geometry, liquid microjunction surface sampling probe (LMJ-SSP) (J. Am. Soc. Mass Spectrom, 2011) was further characterized and applied for concentration and mixing of analyte extracted from multiple areas on a surface and for nanoliter-scale chemical reactions of sampled material. A transparent LMJ-SSP was constructed and colored analytes were used so that the surface sampling process, plug formation, and the chemical reactions could be visually monitored at the sampling end of the probe before being analyzed by mass spectrometry of the injected sample plug. Injectionmore » plug peak widths were consistent for plug hold times as long as the 8 minute maximum attempted (RSD below 1.5%). Furthermore, integrated injection peak signals were not significantly different for the range of hold times investigated. The ability to extract and completely mix individual samples within a fixed volume at the sampling end of the probe was demonstrated and a linear mass spectral response to the number of equivalent analyte spots sampled was observed. Lastly, using the color and mass changing chemical reduction of the redox dye 2,6-dichlorophenol-indophenol with ascorbic acid, the ability to sample, concentrate, and efficiently run reactions within the same plug volume within the probe was demonstrated.« less

In-plane conductance of thin films as a probe of surface chemical environment: Adsorbate effects on film electronic properties of indium tin oxide and gold

NASA Astrophysics Data System (ADS)

Swint, Amy Lynn

Changes in the in-plane conductance of conductive thin films are observed as a result of chemical adsorption at the surface. Reaction of the indium tin oxide (ITO) surface with Bronsted acids (bases) leads to increases (decreases) in its in-plane conductance as measured by a four-point probe configuration. The conductance varies monotonically with pH suggesting that the degree of surface protonation or hydroxylation controls the surface charge density, which in turn affects the width of the n-type depletion layer, and ultimately the in-plane conductance. Measurements at constant pH with a series of tetraalkylammonium hydroxide species of varying cation size indicate that surface dipoles also affect ITO conductance by modulating the magnitude of the surface polarization. Modulating the double layer with varying aqueous salt solutions also affects ITO conductance, though not to the same degree as strong Bronsted acids and bases. Solvents of varying dielectric constant and proton donating ability (ethanol, dimethylformamide) decrease ITO conductance relative to H2O. In addition, changing solvent gives rise to thermally-derived conductance transients, which result from exothermic solvent mixing. The self-assembly of alkanethiols at the surface increases the conductance of ITO films, most likely through carrier population effects. In all cases examined the combined effects of surface charge, adsorbed dipole layer magnitude and carrier injection are responsible for altering the ITO conductance. Besides being directly applicable to the control of electronic properties, these results also point to the use of four-point probe resistance measurements in condensed phase sensing applications. Ultrasensitive conductance-based gas phase sensing of organothiol adsorption to gold nanowires is accomplished with a limit of detection in the 105 molecule range. Further refinement of the inherently low noise resistance measurement may lead to observation of single adsorption events at the gold surface.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morales, Noppawan Phumala; Charlermchoung, Chalermkhwan; Luechapudiporn, Rataya

Atherosclerosis-related vascular complications in {beta}-thalassemia/hemoglobin E ({beta}-thal/Hb E) patients may result from iron induced oxidation of lipoproteins. To identify the specific site of oxidative damage, changes in lipid fluidity at different regions in LDL and HDL particle were investigated using two fluorescence probes and two ESR spin probes. The magnitude of increased lipid fluidity in thalassemic lipoproteins was dependent on the location of the probes. In hydrophobic region, the rotational correlation times for 16-doxyl stearic acid and DPH anisotropy were markedly changed in LDL and HDL of the patients. In the surface region, there was only a slight change inmore » the order parameter (S) for 5-doxyl stearic acid and TMA-DPH anisotropy. Lipid fluidity at the core of LDL and HDL showed good correlation with oxidative stress markers, the ratio of CL/CO, and the level of {alpha}-tocopherol, suggesting that hydrophobic region of thalassemic lipoprotein was a target site for oxidative damage.« less

Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.

PubMed

Steger, Doris; Berry, David; Haider, Susanne; Horn, Matthias; Wagner, Michael; Stocker, Roman; Loy, Alexander

2011-01-01

The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained. This study identifies and rationalizes a systematic spatial bias in the intensity of surface hybridization, characterized by markedly increased signal intensity of spots located at the boundaries of the spotted areas of the microarray slide. Combining observations from a simplified single-probe block array format with predictions from a mathematical model, the mechanism responsible for this bias is found to be a position-dependent variation in lateral diffusion of target molecules. Numerical simulations reveal a strong influence of microarray well geometry on the spatial bias. Reciprocal adjustment of the size of the microarray hybridization chamber to the area of surface-bound probes is a simple and effective measure to minimize or eliminate the diffusion-based bias, resulting in increased uniformity and accuracy of quantitative DNA microarray hybridization.

Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion

PubMed Central

Haider, Susanne; Horn, Matthias; Wagner, Michael; Stocker, Roman; Loy, Alexander

2011-01-01

Background The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained. Methodology/Principal Findings This study identifies and rationalizes a systematic spatial bias in the intensity of surface hybridization, characterized by markedly increased signal intensity of spots located at the boundaries of the spotted areas of the microarray slide. Combining observations from a simplified single-probe block array format with predictions from a mathematical model, the mechanism responsible for this bias is found to be a position-dependent variation in lateral diffusion of target molecules. Numerical simulations reveal a strong influence of microarray well geometry on the spatial bias. Conclusions Reciprocal adjustment of the size of the microarray hybridization chamber to the area of surface-bound probes is a simple and effective measure to minimize or eliminate the diffusion-based bias, resulting in increased uniformity and accuracy of quantitative DNA microarray hybridization. PMID:21858215

Determining the folding and unfolding rate constants of nucleic acids by biosensor. Application to telomere G-quadruplex.

PubMed

Zhao, Yong; Kan, Zhong-yuan; Zeng, Zhi-xiong; Hao, Yu-hua; Chen, Hua; Tan, Zheng

2004-10-20

Nucleic acid molecules may fold into secondary structures, and the formation of such structures is involved in many biological processes and technical applications. The folding and unfolding rate constants define the kinetics of conformation interconversion and the stability of these structures and is important in realizing their functions. We developed a method to determine these kinetic parameters using an optical biosensor based on surface plasmon resonance. The folding and unfolding of a nucleic acid is coupled with a hybridization reaction by immobilization of the target nucleic acid on a sensor chip surface and injection of a complementary probe nucleic acid over the sensor chip surface. By monitoring the time course of duplex formation, both the folding and unfolding rate constants for the target nucleic acid and the association and dissociation rate constants for the target-probe duplex can all be derived from the same measurement. We applied this method to determine the folding and unfolding rate constants of the G-quadruplex of human telomere sequence (TTAGGG)(4) and its association and dissociation rate constants with the complementary strand (CCCTAA)(4). The results show that both the folding and unfolding occur on the time scale of minutes at physiological concentration of K(+). We speculate that this property might be important for telomere elongation. A complete set of the kinetic parameters for both of the structures allows us to study the competition between the formation of the quadruplex and the duplex. Calculations indicate that the formation of both the quadruplex and the duplex is strand concentration-dependent, and the quadruplex can be efficiently formed at low strand concentration. This property may provide the basis for the formation of the quadruplex in vivo in the presence of a complementary strand.

Microscopic contour changes of tribological surfaces by chemical and mechanical action

NASA Technical Reports Server (NTRS)

Lauer, J. L.; Fung, S. S.

1982-01-01

An electronic optical laser interferometer capable of resolving depth differences of as low as 30 A and planar displacements of 6000 A was constructed for the examination of surface profiles of bearing surfaces without physical contact. This instrument was used to determine topological chemical reactivity by applying a drop of dilute alcoholic hydrochloric acid and measuring the profile of the solid surface before and after application of this probe. It was found that scuffed bearing surfaces reacted much faster than virgin ones but that bearing surfaces exposed to lubricants containing an organic chloride reacted much more slowly. In a separate series of experiments, a number of stainless steel plates were heated in a nitrogen atmosphere to different temperatures and their reactivity examined later at ambient temperature. The change of surface contour as a result of the probe reaction was found to follow an Arrhenius-type relation with respect to heat treatment temperature. This result could have implications on the scuffing mechanism.

Controls on the surface chemical reactivity of volcanic ash investigated with probe gases

NASA Astrophysics Data System (ADS)

Maters, Elena C.; Delmelle, Pierre; Rossi, Michel J.; Ayris, Paul M.; Bernard, Alain

2016-09-01

Increasing recognition that volcanic ash emissions can have significant impacts on the natural and human environment calls for a better understanding of ash chemical reactivity as mediated by its surface characteristics. However, previous studies of ash surface properties have relied on techniques that lack the sensitivity required to adequately investigate them. Here we characterise at the molecular monolayer scale the surfaces of ash erupted from Eyjafjallajökull, Tungurahua, Pinatubo and Chaitén volcanoes. Interrogation of the ash with four probe gases, trimethylamine (TMA; N(CH3)3), trifluoroacetic acid (TFA; CF3COOH), hydroxylamine (HA; NH2OH) and ozone (O3), reveals the abundances of acid-base and redox sites on ash surfaces. Measurements on aluminosilicate glass powders, as compositional proxies for the primary constituent of volcanic ash, are also conducted. We attribute the greater proportion of acidic and oxidised sites on ash relative to glass surfaces, evidenced by comparison of TMA/TFA and HA/O3 uptake ratios, in part to ash interaction with volcanic gases and condensates (e.g., H2O, SO2, H2SO4, HCl, HF) during the eruption. The strong influence of ash surface processing in the eruption plume and/or cloud is further supported by particular abundances of oxidised and reduced sites on the ash samples resulting from specific characteristics of their eruptions of origin. Intense interaction with water vapour may result in a higher fraction of oxidised sites on ash produced by phreatomagmatic than by magmatic activity. This study constitutes the first quantification of ash chemical properties at the molecular monolayer scale, and is an important step towards better understanding the factors that govern the role of ash as a chemical agent within atmospheric, terrestrial, aquatic or biotic systems.

High-Resolution Ambient MS Imaging of Negative Ions in Positive Ion Mode: Using Dicationic Reagents with the Single-Probe

NASA Astrophysics Data System (ADS)

Rao, Wei; Pan, Ning; Tian, Xiang; Yang, Zhibo

2016-01-01

We have used the Single-probe, a miniaturized sampling device utilizing in-situ surface microextraction for ambient mass spectrometry (MS) analysis, for the high resolution MS imaging (MSI) of negatively charged species in the positive ionization mode. Two dicationic compounds, 1,5-pentanediyl-bis(1-butylpyrrolidinium) difluoride [C5(bpyr)2F2] and 1,3-propanediyl-bis(tripropylphosphonium) difluoride [C3(triprp)2F2], were added into the sampling solvent to form 1+ charged adducts with the negatively charged species extracted from tissues. We were able to detect 526 and 322 negatively charged species this way using [C5(bpyr)2F2] and [C3(triprp)2F2], respectively, including oleic acid, arachidonic acid, and several species of phosphatidic acid, phosphoethanolamine, phosphatidylserine, phosphatidylglycerol, phosphatidylinositol, and others. In conjunction with the identification of the non-adduct cations, we have tentatively identified a total number of 1200 and 828 metabolites from mouse brain sections using [C5(bpyr)2F2] and [C3(triprp)2F2], respectively, through high mass accuracy measurements (mass error <5 ppm); MS/MS analyses were also performed to verify the identity of selected species. In addition to the high mass accuracy measurement, we were able to generate high spatial resolution (~17 μm) MS images of mouse brain sections. Our study demonstrated that utilization of dicationic compounds in the surface microextraction with the Single-probe device can perform high mass and spatial resolution ambient MSI measurements of broader types of compounds in tissues. Other reagents can be potentially used with the Single-probe device for a variety of reactive MSI studies to enable the analysis of species that are previously intractable.

A molecular rotor based ratiometric sensor for basic amino acids

NASA Astrophysics Data System (ADS)

Pettiwala, Aafrin M.; Singh, Prabhat K.

2018-01-01

The inevitable importance of basic amino acids, arginine and lysine, in human health and metabolism demands construction of efficient sensor systems for them. However, there are only limited reports on the 'ratiometric' detection of basic amino acids which is further restricted by the use of chemically complex sensor molecules, which impedes their prospect for practical applications. Herein, we report a ratiometric sensor system build on simple mechanism of disassociation of novel emissive Thioflavin-T H-aggregates from heparin surface, when subjected to interaction with basic amino acids. The strong and selective electrostatic and hydrogen bonding interaction of basic amino acids with heparin leads to large alteration in photophysical attributes of heparin bound Thioflavin-T, which forms a highly sensitive sensor platform for detection of basic amino acids in aqueous solution. These selective interactions between basic amino acids and heparin allow our sensor system to discriminate arginine and lysine from other amino acids. This unique mechanism of dissociation of Thioflavin-T aggregates from heparin surface provides ratiometric response on both fluorimetric and colorimetric outputs for detection of arginine and lysine, and thus it holds a significant advantage over other developed sensor systems which are restricted to single wavelength detection. Apart from the sensitivity and selectivity, our system also provides the advantage of simplicity, dual mode of sensing, and more importantly, it employs an inexpensive commercially available probe molecule, which is a significant advantage over other developed sensor systems that uses tedious synthesis protocol for the employed probe in the detection scheme, an impediment for practical applications. Additionally, our sensor system also shows response in complex biological media of serum samples.

Biomimetic nanochannels based biosensor for ultrasensitive and label-free detection of nucleic acids.

PubMed

Sun, Zhongyue; Liao, Tangbin; Zhang, Yulin; Shu, Jing; Zhang, Hong; Zhang, Guo-Jun

2016-12-15

A very simple sensing device based on biomimetic nanochannels has been developed for label-free, ultrasensitive and highly sequence-specific detection of DNA. Probe DNA was modified on the inner wall of the nanochannel surface by layer-by-layer (LBL) assembly. After probe DNA immobilization, DNA detection was realized by monitoring the rectified ion current when hybridization occurred. Due to three dimensional (3D) nanoscale environment of the nanochannel, this special geometry dramatically increased the surface area of the nanochannel for immobilization of probe molecules on the inner-surface and enlarged contact area between probes and target-molecules. Thus, the unique sensor reached a reliable detection limit of 10 fM for target DNA. In addition, this DNA sensor could discriminate complementary DNA (c-DNA) from non-complementary DNA (nc-DNA), two-base mismatched DNA (2bm-DNA) and one-base mismatched DNA (1bm-DNA) with high specificity. Moreover, the nanochannel-based biosensor was also able to detect target DNA even in an interfering environment and serum samples. This approach will provide a novel biosensing platform for detection and discrimination of disease-related molecular targets and unknown sequence DNA. Copyright © 2016 Elsevier B.V. All rights reserved.

Toward the Atomic-Level Mass Analysis of Biomolecules by the Scanning Atom Probe.

PubMed

Nishikawa, Osamu; Taniguchi, Masahiro

2017-04-01

In 1994, a new type of atom probe instrument, named the scanning atom probe (SAP), was proposed. The unique feature of the SAP is the introduction of a small extraction electrode, which scans over a specimen surface and confines the high field, required for field evaporation of surface atoms in a small space, between the specimen and the electrode. Thus, the SAP does not require a sharp specimen tip. This indicates that the SAP can mass analyze the specimens which are difficult to form in a sharp tip, such as organic materials and biomolecules. Clean single wall carbon nanotubes (CNT), made by high-pressure carbon monoxide process are found to be the best substrates for biomolecules. Various amino acids and dipeptide biomolecules were successfully mass analyzed, revealing characteristic clusters formed by strongly bound atoms in the specimens. The mass analysis indicates that SAP analysis of biomolecules is not only qualitative, but also quantitative.

A carbon dot-based "off-on" fluorescent probe for highly selective and sensitive detection of phytic acid.

PubMed

Gao, Zhao; Wang, Libing; Su, Rongxin; Huang, Renliang; Qi, Wei; He, Zhimin

2015-08-15

We herein report a facile, one-step pyrolysis synthesis of photoluminescent carbon dots (CDs) using citric acid as the carbon source and lysine as the surface passivation reagent. The as-prepared CDs show narrow size distribution, excellent blue fluorescence and good photo-stability and water dispersivity. The fluorescence of the CDs was found to be effectively quenched by ferric (Fe(III)) ions with high selectivity via a photo-induced electron transfer (PET) process. Upon addition of phytic acid (PA) to the CDs/Fe(III) complex dispersion, the fluorescence of the CDs was significantly recovered, arising from the release of Fe(III) ions from the CDs/Fe(III) complex because PA has a higher affinity for Fe(III) ions compared to CDs. Furthermore, we developed an "off-on" fluorescence assay method for the detection of phytic acid using CDs/Fe(III) as a fluorescent probe. This probe enables the selective detection of PA with a linear range of 0.68-18.69 μM and a limit of detection (signal-to-noise ratio is 3) of 0.36 μM. The assay method demonstrates high selectivity, repeatability, stability and recovery ratio in the detection of the standard and real PA samples. We believe that the facile operation, low-cost, high sensitivity and selectivity render this CD-based "off-on" fluorescent probe an ideal sensing platform for the detection of PA. Copyright © 2015 Elsevier B.V. All rights reserved.

Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

PubMed Central

Nicolau Jr., Dan V.; Paszek, Ewa; Fulga, Florin; Nicolau, Dan V.

2014-01-01

A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 Å, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced “leopard skin”-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions, can capture processes that are otherwise obscured to the amino acid-based formalism. PMID:25462574

Hybridization behavior of mixed DNA/alkylthiol monolayers on gold: characterization by surface plasmon resonance and 32P radiometric assay.

PubMed

Gong, Ping; Lee, Chi-Ying; Gamble, Lara J; Castner, David G; Grainger, David W

2006-05-15

Nucleic acid assay from a complex biological milieu is attractive but currently difficult and far from routine. In this study, DNA hybridization from serum dilutions into mixed DNA/mercaptoundecanol (MCU) adlayers on gold was monitored by surface plasmon resonance (SPR). Immobilized DNA probe and hybridized target densities on these surfaces were quantified using 32P-radiometric assays as a function of MCU diluent exposure. SPR surface capture results correlated with radiometric analysis for hybridization performance, demonstrating a maximum DNA hybridization on DNA/MCU mixed adlayers. The maximum target surface capture produced by MCU addition to the DNA probe layer correlates with structural and conformational data on identical mixed DNA/MCU adlayers on gold derived from XPS, NEXAFS, and fluorescence intensity measurements reported in a related study (Lee, C.-Y.; Gong, P.; Harbers, G. M.; Grainger, D. W.; Castner, D. G.; Gamble, L. J. Anal. Chem. 2006, 78, 3316-3325.). MCU addition into the DNA adlayer on gold also improved surface resistance to both nonspecific DNA and serum protein adsorption. Target DNA hybridization from serum dilutions was monitored with SPR on the optimally mixed DNA/MCU adlayers. Both hybridization kinetics and efficiency were strongly affected by nonspecific protein adsorption from a complex milieu even at a minimal serum concentration (e.g., 1%). No target hybridization was detected in SPR assays from serum concentrations above 30%, indicating nonspecific protein adsorption interference of DNA capture and hybridization from complex milieu. Removal of nonsignal proteins from nucleic acid targets prior to assay represents a significant issue for direct sample-to-assay nucleic acid diagnostics from food, blood, tissue, PCR mixtures, and many other biologically complex sample formats.

Detection and isolation of nucleic acid sequences using competitive hybridization probes

DOEpatents

Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

1997-01-01

A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided.

Detection and isolation of nucleic acid sequences using competitive hybridization probes

DOEpatents

Lucas, J.N.; Straume, T.; Bogen, K.T.

1997-04-01

A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided. 7 figs.

Sensitive and fast detection of fructose in complex media via symmetry breaking and signal amplification using surface-enhanced Raman spectroscopy.

PubMed

Sun, Fang; Bai, Tao; Zhang, Lei; Ella-Menye, Jean-Rene; Liu, Sijun; Nowinski, Ann K; Jiang, Shaoyi; Yu, Qiuming

2014-03-04

A new strategy is proposed to sensitively and rapidly detect analytes with weak Raman signals in complex media using surface-enhanced Raman spectroscopy (SERS) via detecting the SERS signal changes of the immobilized probe molecules on SERS-active substrates upon binding of the analytes. In this work, 4-mercaptophenylboronic acid (4-MPBA) was selected as the probe molecule which was immobilized on the gold surface of a quasi-three-dimensional plasmonic nanostructure array (Q3D-PNA) SERS substrate to detect fructose. The molecule of 4-MPBA possesses three key functions: molecule recognition and reversible binding of the analyte via the boronic acid group, amplification of SERS signals by the phenyl group and thus shielding of the background noise of complex media, and immobilization on the surface of SERS-active substrates via the thiol group. Most importantly, the symmetry breaking of the 4-MPBA molecule upon fructose binding leads to the change of area ratio between totally symmetric 8a ring mode and nontotally symmetric 8b ring mode, which enables the detection. The detection curves were obtained in phosphate-buffered saline (PBS) and in undiluted artificial urine at clinically relevant concentrations, and the limit of detection of 0.05 mM was achieved.

In situ SERS spectroelectrochemical analysis of antioxidants deposited on copper substrates: What is the effect of applied potential on sorption behavior?

NASA Astrophysics Data System (ADS)

Dendisova-Vyskovska, Marcela; Broncova, Gabriela; Clupek, Martin; Prokopec, Vadym; Matejka, Pavel

2012-12-01

The detection of p-coumaric acid and ferulic acid using a combined in situ electrochemical and surface-enhanced Raman scattering spectroscopic technique in specially made electrode cell is described. New in situ spectroelectrochemical cell was designed as the three-electrode arrangement connected via positioning device to fiber-optic probe of Raman spectrometer Dimension P2 (excitation wavelength 785 nm). In situ SERS spectra of p-coumaric acid and ferulic acid were recorded at varying applied negative potentials to copper substrates. The spectral intensities and shapes of bands as well as spatial orientation of molecules on the surface depend significantly on varying values of the applied electrode potential. The change of electrode potential influences analyte adsorption/desorption behavior on the surface of copper substrates, affecting the reversibility of the whole process and overall spectral enhancement level. Principal component analysis is used to distinguish several stages of spectral variations on potential changes.

Kit for detecting nucleic acid sequences using competitive hybridization probes

DOEpatents

Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

2001-01-01

A kit is provided for detecting a target nucleic acid sequence in a sample, the kit comprising: a first hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the first hybridization probe including a first complexing agent for forming a binding pair with a second complexing agent; and a second hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the first hybridization probe does not selectively hybridize, the second hybridization probe including a detectable marker; a third hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the third hybridization probe including the same detectable marker as the second hybridization probe; and a fourth hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the third hybridization probe does not selectively hybridize, the fourth hybridization probe including the first complexing agent for forming a binding pair with the second complexing agent; wherein the first and second hybridization probes are capable of simultaneously hybridizing to the target sequence and the third and fourth hybridization probes are capable of simultaneously hybridizing to the target sequence, the detectable marker is not present on the first or fourth hybridization probes and the first, second, third, and fourth hybridization probes each include a competitive nucleic acid sequence which is sufficiently complementary to a third portion of the target sequence that the competitive sequences of the first, second, third, and fourth hybridization probes compete with each other to hybridize to the third portion of the target sequence.

Characterization of the surface tension and solubility parameter of epoxy resin by using inverse gas chromatography.

PubMed

Shi, Fenghui; Dai, Zhishuang; Zhang, Baoyan

2010-07-01

Inverse gas chromatography (IGC) was used to measure the surface tension and solubility parameter of E51 epoxy resin in this work. By using the Schultz method, decane, nonane, octane and heptane were chosen as the neutral probes to calculate the dispersive surface tensions (gamma(D)). Based on the Good-van Oss equation, the specific surface tension (gamma(SP)) of E51 epoxy resin was calculated with the acidic probe of dichloromethane and the basic probe of toluene. The results showed that the gamma(D) and gamma(SP) of the E51 resin decreased linearly with the increase of temperature. According to the Flory-Huggins parameters (chi) between the resin and a series of probes, the solubility parameters (delta) of E51 resin at different temperatures were estimated using the method developed by DiPaola-Baranyi and Guillet. It was found that the values of delta of the E51 resin were 11.78, 11.57, 11.48 and 11.14 MPa1/2 at 30, 40, 50 and 60 degrees C, respectively. The dispersive component (delta(D)) and the specific component (delta(SP)) of solubility parameter at different temperatures of the E51 resin were investigated according to the relationships between surface tension, cohesion energy and solubility parameter. The results showed that the values of delta(D) were higher than those of delta(SP) for the epoxy resin, and both of them decreased with the increase of temperature.

Probing size-dependent electrokinetics of hematite aggregates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kedra-Królik, Karolina; Rosso, Kevin M.; Zarzycki, Piotr

Aqueous particle suspensions of many kinds are stabilized by the electrostatic potential developed at their surfaces from reaction with water and ions. An important and less well understood aspect of this stabilization is the dependence of the electrostatic surface potential on particle size. Surface electrostatics are typically probed by measuring particle electrophoretic mobilities and quantified in the electrokinetic potential (f), using commercially available Zeta Potential Analyzers (ZPA). Even though ZPAs provide frequency-spectra (histograms) of electrophoretic mobility and hydrodynamic diameter, typically only the maximal-intensity values are reported, despite the information in the remainder of the spectra. Here we propose a mappingmore » procedure that inter-correlates these histograms to extract additional insight, in this case to probe particle size-dependent electrokinetics. Our method is illustrated for a suspension of prototypical iron (III) oxide (hematite, a-Fe2O3). We found that the electrophoretic mobility and f-potential are a linear function of the aggregate size. By analyzing the distribution of surface site types as a function of aggregate size we show that site coordination increases with increasing aggregate diameter. This observation explains why the acidity of the iron oxide particles decreases with increasing particle size.« less

A molecular rotor based ratiometric sensor for basic amino acids.

PubMed

Pettiwala, Aafrin M; Singh, Prabhat K

2018-01-05

The inevitable importance of basic amino acids, arginine and lysine, in human health and metabolism demands construction of efficient sensor systems for them. However, there are only limited reports on the 'ratiometric' detection of basic amino acids which is further restricted by the use of chemically complex sensor molecules, which impedes their prospect for practical applications. Herein, we report a ratiometric sensor system build on simple mechanism of disassociation of novel emissive Thioflavin-T H-aggregates from heparin surface, when subjected to interaction with basic amino acids. The strong and selective electrostatic and hydrogen bonding interaction of basic amino acids with heparin leads to large alteration in photophysical attributes of heparin bound Thioflavin-T, which forms a highly sensitive sensor platform for detection of basic amino acids in aqueous solution. These selective interactions between basic amino acids and heparin allow our sensor system to discriminate arginine and lysine from other amino acids. This unique mechanism of dissociation of Thioflavin-T aggregates from heparin surface provides ratiometric response on both fluorimetric and colorimetric outputs for detection of arginine and lysine, and thus it holds a significant advantage over other developed sensor systems which are restricted to single wavelength detection. Apart from the sensitivity and selectivity, our system also provides the advantage of simplicity, dual mode of sensing, and more importantly, it employs an inexpensive commercially available probe molecule, which is a significant advantage over other developed sensor systems that uses tedious synthesis protocol for the employed probe in the detection scheme, an impediment for practical applications. Additionally, our sensor system also shows response in complex biological media of serum samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Silica surface characterization as a function of formation and surface treatment using traditional methods and proteins as surface probes

NASA Astrophysics Data System (ADS)

Korwin-Edson, Michelle Lynn

Previous works have shown that cells proliferate differently depending on the chemistry of the glass on which they are growing. Since proteins form the bonds between cells and glass, the hypothesis of this study is that proteins can distinguish between surface chemical variations of glass. This theory was examined through the use of various silica forms, a few select proteins, four surface treatment procedures, and a variety of characterization techniques. The silica forms include amorphous slides, cane, fiber, microspheres, fumed silica and quartz crystal terminals. The proteins selected were human serum albumin, mouse Immunoglobulin G, streptavidin, antimouse IgG, and biotin. The surface treatments utilized to bring about chemical variation on the silica surface were HF acid etching, ethanol cleaning, water plasma treatments, and 1000°C heat treatments. The characterization techniques encompassed both traditional material techniques and biological methods. The techniques studied were atomic force microscopy (AFM), chemical force microscopy (CFM), glancing incidence X-ray analysis (GIXA), fluorescence spectrometry, polyacrylamide gel electrophoresis (SDS-PAGE), and bicinchoninic acid (BCA) assay. It was the main goal of this project to determine the feasibility of these techniques in utilizing proteins as glass surface probes. Proteins were adsorbed to all of the various forms and the binding ability was studied by either stripping off the protein and quantifying them, or by deductive reasoning through the use of "depleted" protein solutions. Fluorimetry and BCA assay both utilized the depleted solutions, but the high error associated with this protocol was prohibitive. SDS-PAGE with streptavidin was very difficult due to staining problems, however the IgG proteins were able to be quantified with some success. GIXA showed that the protein layer thickness is monolayer in nature, which agrees well with the AFM fluid tapping data on protein height, but in addition showed features on the order of ten protein agglomerations. CFM is by far the most promising technique for utilizing proteins as surface probes. Functionalized tips of -COOH, streptavidin and -CH3 are able to discern between surface treatments, but not forms. A general conclusion is that adhesion forces are greatest for -COOH, then streptavidin, and least for -CH3.

Nanostar probes for tip-enhanced spectroscopy

NASA Astrophysics Data System (ADS)

Kim, Woong; Kim, Nara; Park, Joon Won; Kim, Zee Hwan

2015-12-01

To overcome the current limit of tip-enhanced spectroscopy that is based on metallic nano-probes, we developed a new scanning probe with a metallic nanostar, a nanoparticle with sharp spikes. A Au nanoparticle of 5 nm was first attached to the end of a tip through DNA-DNA hybridization and mechanical pick-up. The nanoparticle was converted to a nanostar with a core diameter of ~70 nm and spike lengths between 50 nm and 80 nm through the reduction of Au3+ with ascorbic acid in the presence of Ag+. Fabrication yields of such tips exceeded 60%, and more than 80% of such tips showed a mechanical durability sufficient for use in scanning microscopy. Effectiveness of the new probes for tip-enhanced Raman scattering (TERS) and tip-enhanced fluorescence (TEF) was confirmed. The probes exhibited the necessary enhancement for TEF, and the tip-on and tip-off ratios varied between 5 and 100. This large tip-to-tip variability may arise from the uncontrolled orientation of the apexes of the spike with respect to the sample surface, which calls for further fabrication improvement. The result overall supports a new fabrication approach for the probe that is effective for tip-enhanced spectroscopy.To overcome the current limit of tip-enhanced spectroscopy that is based on metallic nano-probes, we developed a new scanning probe with a metallic nanostar, a nanoparticle with sharp spikes. A Au nanoparticle of 5 nm was first attached to the end of a tip through DNA-DNA hybridization and mechanical pick-up. The nanoparticle was converted to a nanostar with a core diameter of ~70 nm and spike lengths between 50 nm and 80 nm through the reduction of Au3+ with ascorbic acid in the presence of Ag+. Fabrication yields of such tips exceeded 60%, and more than 80% of such tips showed a mechanical durability sufficient for use in scanning microscopy. Effectiveness of the new probes for tip-enhanced Raman scattering (TERS) and tip-enhanced fluorescence (TEF) was confirmed. The probes exhibited the necessary enhancement for TEF, and the tip-on and tip-off ratios varied between 5 and 100. This large tip-to-tip variability may arise from the uncontrolled orientation of the apexes of the spike with respect to the sample surface, which calls for further fabrication improvement. The result overall supports a new fabrication approach for the probe that is effective for tip-enhanced spectroscopy. Electronic supplementary information (ESI) available: Illustrations of TERS and TEF experiments, information about the TEM images, scheme of surface preparation and peak assignments of TERS spectra. See DOI: 10.1039/c5nr06657c

High-sensitive electrochemical detection of point mutation based on polymerization-induced enzymatic amplification.

PubMed

Feng, Kejun; Zhao, Jingjin; Wu, Zai-Sheng; Jiang, Jianhui; Shen, Guoli; Yu, Ruqin

2011-03-15

Here a highly sensitive electrochemical method is described for the detection of point mutation in DNA. Polymerization extension reaction is applied to specifically initiate enzymatic electrochemical amplification to improve the sensitivity and enhance the performance of point mutation detection. In this work, 5'-thiolated DNA probe sequences complementary to the wild target DNA are assembled on the gold electrode. In the presence of wild target DNA, the probe is extended by DNA polymerase over the free segment of target as the template. After washing with NaOH solution, the target DNA is removed while the elongated probe sequence remains on the sensing surface. Via hybridizing to the designed biotin-labeled detection probe, the extended sequence is capable of capturing detection probe. After introducing streptavidin-conjugated alkaline phosphatase (SA-ALP), the specific binding between streptavidin and biotin mediates a catalytic reaction of ascorbic acid 2-phosphate (AA-P) substrate to produce a reducing agent ascorbic acid (AA). Then the silver ions in solution are reduced by AA, leading to the deposition of silver metal onto the electrode surface. The amount of deposited silver which is determined by the amount of wild target can be quantified by the linear sweep voltammetry (LSV). The present approach proved to be capable of detecting the wild target DNA down to a detection limit of 1.0×10(-14) M in a wide target concentration range and identifying -28 site (A to G) of the β-thalassemia gene, demonstrating that this scheme offers a highly sensitive and specific approach for point mutation detection. Copyright © 2010 Elsevier B.V. All rights reserved.

Fluorescence in vivo imaging of live tumor cells with pH-activatable targeted probes via receptor-mediated endocytosis

NASA Astrophysics Data System (ADS)

Asanuma, Daisuke; Urano, Yasuteru; Nagano, Tetsuo; Hama, Yukihiro; Koyama, Yoshinori; Kobayashi, Hisataka

2009-02-01

One goal of molecular imaging is to establish a widely applicable technique for specific detection of tumors with minimal background. Here, we achieve specific in vivo tumor visualization with a newly-designed "activatable" targeted fluorescence probe. This agent is activated after cellular internalization by sensing the pH change in the lysosome. Novel acidic pH-activatable probes based on the BODIPY fluorophore were synthesized, and then conjugated to a cancer-targeting monoclonal antibody, Trastuzumab, or galactosyl serum albumin (GSA). As proof of concept, ex and in vivo imaging of two different tumor mouse models was performed: HER2-overexpressed lung metastasis tumor with Trastuzumab-pH probe conjugates and lectin-overexpressed i.p. disseminated tumor with GSA-pH probe conjugates. These pH-activatable targeted probes were highly specific for tumors with minimal background signal. Because the acidic pH in lysosomes is maintained by the energy-consuming proton pump, only viable cancer cells were successfully visualized. Furthermore, this strategy was also applied to fluorescence endoscopy in tumor mouse models, resulting in specific visualization of tumors as small as submillimeter in size that could hardly detected by naked eyes because of their poor contrast against normal tissues. The design concept can be widely adapted to cancer-specific cell-surface-targeting molecules that result in cellular internalization.

Fluorescent probes for understanding soil water repellency: the novel application of a chemist's tool to soil science

NASA Astrophysics Data System (ADS)

Balshaw, Helen M.; Davies, Matthew L.; Doerr, Stefan H.; Douglas, Peter

2015-04-01

Food security and production is one of the key global issues faced by society. It has become essential to work the land efficiently, through better soil management and agronomy whilst protecting the environment from air and water pollution. The failure of soil to absorb water - soil water repellency can lead to major environmental problems such as increased overland flow and soil erosion, poor uptake of agricultural chemicals, and increased risk of groundwater pollution due to the rapid transfer of contaminants and nutrient leaching through uneven wetting and preferential flow pathways. Understanding the causes of soil hydrophobicity is essential for the development of effective methods for its amelioration, supporting environmental stability and food security. Organic compounds deposited on soil mineral or aggregate surfaces have long been recognised as a major factor in causing soil water repellency. It is widely accepted that the main groups of compounds responsible are long-chain acids, alkanes and other organic compounds with hydrophobic properties. However, when reapplied to sands and soils, the degree of water repellency induced by these compounds and mixtures varied widely with compound type, amount, and mixture, in a seemingly unpredictable way. Fluorescent and phosphorescent probes are widely used in chemistry and biochemistry due to their sensitive response to their physical and chemical environment, such as polarity, and viscosity. However, they have to-date not been used to study soil water repellency. Here we present preliminary work on the evaluation of fluorescent probes as tools to study two poorly understood features that determine the degree of wettability for water repellent soils: (i) the distribution of organics on soils; (ii) the changes in polarity at soil surfaces required for water drops to infiltrate. In our initial work we have examined probes adsorbed onto model soils, prepared by adsorption of specific organics onto acid washed sand. Studies using steady-state and μs time-resolved emission spectroscopy, together with fluorescence microscopy and image analysis, of probe lifetime, spectra, and spatial distribution have been used to 'map' the emission characteristics of probes when adsorbed, and also to examine how the distribution of hydrophobic compounds changes during contact with materials used for treating hydrophobic soils (e.g. clays, biochar). Furthermore, while it has been suggested that during soil wetting the water droplet induces changes in conformation, orientation and arrangement of a hydrophobic layer of organics adsorbed to the soil surfaces, there is little direct evidence for this, and so we are also exploring the use of fluorescent/phosphorescent probes adsorbed on the soil surface to determine any changes in environment polarity, viscosity or hydrophobicity at the soil surface during the wetting process.

Transmission X-ray scattering as a probe for complex liquid-surface structures

DOE PAGES

Fukuto, Masafumi; Yang, Lin; Nykypanchuk, Dmytro; ...

2016-01-28

The need for functional materials calls for increasing complexity in self-assembly systems. As a result, the ability to probe both local structure and heterogeneities, such as phase-coexistence and domain morphologies, has become increasingly important to controlling self-assembly processes, including those at liquid surfaces. The traditional X-ray scattering methods for liquid surfaces, such as specular reflectivity and grazing-incidence diffraction, are not well suited to spatially resolving lateral heterogeneities due to large illuminated footprint. A possible alternative approach is to use scanning transmission X-ray scattering to simultaneously probe local intermolecular structures and heterogeneous domain morphologies on liquid surfaces. To test the feasibilitymore » of this approach, transmission small- and wide-angle X-ray scattering (TSAXS/TWAXS) studies of Langmuir films formed on water meniscus against a vertically immersed hydrophilic Si substrate were recently carried out. First-order diffraction rings were observed in TSAXS patterns from a monolayer of hexagonally packed gold nanoparticles and in TWAXS patterns from a monolayer of fluorinated fatty acids, both as a Langmuir monolayer on water meniscus and as a Langmuir–Blodgett monolayer on the substrate. The patterns taken at multiple spots have been analyzed to extract the shape of the meniscus surface and the ordered-monolayer coverage as a function of spot position. These results, together with continual improvement in the brightness and spot size of X-ray beams available at synchrotron facilities, support the possibility of using scanning-probe TSAXS/TWAXS to characterize heterogeneous structures at liquid surfaces.« less

Use of a Novel Rover-mounted Fluorescence Imager and Fluorescent Probes to Detect Biological Material in the Atacama Desert in Daylight

NASA Technical Reports Server (NTRS)

Weinstein, S.; Pane, D.; Warren-Rhodes, K.; Cockell, C.; Ernst, L. A.; Minkley, E.; Fisher, G.; Emani, S.; Wettergreen, D. S.; Wagner, M.

2005-01-01

We have developed an imaging system, the Fluorescence Imager (FI), for detecting fluorescence signals from sparse microorganisms and biofilms during autonomous rover exploration. The fluorescence signals arise both from naturally occurring chromophores, such as chlorophyll of cyanobacteria and lichens, and from fluorescent probes applied to soil and rocks. Daylight imaging has been accomplished by a novel use of a high-powered flashlamp synchronized to a CCD camera. The fluorescent probes are cell permanent stains that have extremely low intrinsic fluorescence (quantum yields less than 0.01) and a large fluorescence enhancement (quantum yields greater than 0.4) when bound to the target. Each probe specifically targets either carbohydrates, proteins, nucleic acids or membrane lipids, the four classes of macromolecules found in terrestrial life. The intent of the probes is to interrogate the environment for surface and endolithic life forms.

An Environmentally Sensitive Fluorescent Dye as a Multidimensional Probe of Amyloid Formation

PubMed Central

2016-01-01

We have explored amyloid formation using poly(amino acid) model systems in which differences in peptide secondary structure and hydrophobicity can be introduced in a controlled manner. We show that an environmentally sensitive fluorescent dye, dapoxyl, is able to identify β-sheet structure and hydrophobic surfaces, structural features likely to be related to toxicity, as a result of changes in its excitation and emission profiles and its relative quantum yield. These results show that dapoxyl is a multidimensional probe of the time dependence of amyloid aggregation, which provides information about the presence and nature of metastable aggregation intermediates that is inaccessible to the conventional probes that rely on changes in quantum yield alone. PMID:26865546

Solid phase sequencing of double-stranded nucleic acids

DOEpatents

Fu, Dong-Jing; Cantor, Charles R.; Koster, Hubert; Smith, Cassandra L.

2002-01-01

This invention relates to methods for detecting and sequencing of target double-stranded nucleic acid sequences, to nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probe comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include nucleic acids in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated determination of molecular weights and identification of the target sequence.

Poly(o-phenylenediamine) colloid-quenched fluorescent oligonucleotide as a probe for fluorescence-enhanced nucleic acid detection.

PubMed

Tian, Jingqi; Li, Hailong; Luo, Yonglan; Wang, Lei; Zhang, Yingwei; Sun, Xuping

2011-02-01

In this Letter, we demonstrate that chemical oxidation polymerization of o-phenylenediamine (OPD) by potassium bichromate at room temperature results in the formation of submicrometer-scale poly(o-phenylenediamine) (POPD) colloids. Such colloids can absorb and quench dye-labeled single-stranded DNA (ssDNA) very effectively. In the presence of a target, a hybridization event occurs, which produces a double-stranded DNA (dsDNA) that detaches from the POPD surface, leading to recovery of dye fluorescence. With the use of an oligonucleotide (OND) sequence associated with human immunodeficiency virus (HIV) as a model system, we demonstrate the proof of concept that POPD colloid-quenched fluorescent OND can be used as a probe for fluorescence-enhanced nucleic acid detection with selectivity down to single-base mismatch.

Solid phase sequencing of biopolymers

DOEpatents

Cantor, Charles; Koster, Hubert

2010-09-28

This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

Inclusion of Ti and Zr species on clay surfaces and their effect on the interaction with organic molecules

NASA Astrophysics Data System (ADS)

Rangel-Rivera, Pedro; Bachiller-Baeza, María Belén; Galindo-Esquivel, Ignacio; Rangel-Porras, Gustavo

2018-07-01

The interactions between the clay surface and the organic molecules play an important role in the efficient of these materials in adsorption and catalytic processes. These materials are often modified with the inclusion of other catalytic particles for the purpose of enhancing the activity. In this study, commercial clay K10 was modified with the particles inclusion of titanium and zirconium. The solid surfaces were examined by infrared spectroscopy, scanning electron microscopy (SEM) coupled to an energy-dispersive X-ray spectroscopy device (EDS), and X-ray photoelectron spectroscopy (XPS). Temperature programmed desorption of ammonia (TPD-NH3) and propan-2-ol decomposition test reaction were performed to probe the acid properties. The adsorption of acetic acid, ethanol, and propan-2-ol on the surface of each solid and their thermal stability were studied by diffuse reflectance infrared Fourier transform spectroscopy (DRIFT). Finally, these materials were used in the esterification of acetic acid with penta-1-ol. The real effect over the incorporation of titanium species and zirconium species on clay surface for interacting with the organic molecules was discussed.

Quantifying Functional Group Interactions that Determine Urea Effects on Nucleic Acid Helix Formation

PubMed Central

Guinn, Emily J.; Schwinefus, Jeffrey J.; Cha, Hyo Keun; McDevitt, Joseph L.; Merker, Wolf E.; Ritzer, Ryan; Muth, Gregory W.; Engelsgjerd, Samuel W.; Mangold, Kathryn E.; Thompson, Perry J.; Kerins, Michael J.; Record, Thomas

2013-01-01

Urea destabilizes helical and folded conformations of nucleic acids and proteins, as well as protein-nucleic acid complexes. To understand these effects, extend previous characterizations of interactions of urea with protein functional groups, and thereby develop urea as a probe of conformational changes in protein and nucleic acid processes, we obtain chemical potential derivatives (μ23 = dμ2/dm3) quantifying interactions of urea (component 3) with nucleic acid bases, base analogs, nucleosides and nucleotide monophosphates (component 2) using osmometry and hexanol-water distribution assays. Dissection of these μ23 yields interaction potentials quantifying interactions of urea with unit surface areas of nucleic acid functional groups (heterocyclic aromatic ring, ring methyl, carbonyl and phosphate O, amino N, sugar (C,O)); urea interacts favorably with all these groups, relative to interactions with water. Interactions of urea with heterocyclic aromatic rings and attached methyl groups (as on thymine) are particularly favorable, as previously observed for urea-homocyclic aromatic ring interactions. Urea m-values determined for double helix formation by DNA dodecamers near 25°C are in the range 0.72 to 0.85 kcal mol−1 m−1 and exhibit little systematic dependence on nucleobase composition (17–42% GC). Interpretation of these results using the urea interaction potentials indicates that extensive (60–90%) stacking of nucleobases in the separated strands in the transition region is required to explain the m-value. Results for RNA and DNA dodecamers obtained at higher temperatures, and literature data, are consistent with this conclusion. This demonstrates the utility of urea as a quantitative probe of changes in surface area (ΔASA) in nucleic acid processes. PMID:23510511

Simultaneous Nanoscale Surface Charge and Topographical Mapping.

PubMed

Perry, David; Al Botros, Rehab; Momotenko, Dmitry; Kinnear, Sophie L; Unwin, Patrick R

2015-07-28

Nanopipettes are playing an increasingly prominent role in nanoscience, for sizing, sequencing, delivery, detection, and mapping interfacial properties. Herein, the question of how to best resolve topography and surface charge effects when using a nanopipette as a probe for mapping in scanning ion conductance microscopy (SICM) is addressed. It is shown that, when a bias modulated (BM) SICM scheme is used, it is possible to map the topography faithfully, while also allowing surface charge to be estimated. This is achieved by applying zero net bias between the electrode in the SICM tip and the one in bulk solution for topographical mapping, with just a small harmonic perturbation of the potential to create an AC current for tip positioning. Then, a net bias is applied, whereupon the ion conductance current becomes sensitive to surface charge. Practically this is optimally implemented in a hopping-cyclic voltammetry mode where the probe is approached at zero net bias at a series of pixels across the surface to reach a defined separation, and then a triangular potential waveform is applied and the current response is recorded. Underpinned with theoretical analysis, including finite element modeling of the DC and AC components of the ionic current flowing through the nanopipette tip, the powerful capabilities of this approach are demonstrated with the probing of interfacial acid-base equilibria and high resolution imaging of surface charge heterogeneities, simultaneously with topography, on modified substrates.

Aqueous or solvent based surface modification: The influence of the combination solvent - organic functional group on the surface characteristics of titanium dioxide grafted with organophosphonic acids

NASA Astrophysics Data System (ADS)

Roevens, Annelore; Van Dijck, Jeroen G.; Geldof, Davy; Blockhuys, Frank; Prelot, Benedicte; Zajac, Jerzy; Meynen, Vera

2017-09-01

To alter the versatility of interactions at its surface, TiO2 is modified with organophosphonic acids (PA). A thorough understanding of the role of all synthesis conditions is necessary to achieve controlled functionalization. This study reports on the effect of using water, toluene and their mixtures when performing the modification of TiO2 with PA. Sorption and calorimetry measurements of surface interactions with various probing species clearly indicate that, by grafting PA in water, clear differences appear in the distribution of organic groups on the surface. Also the functional group of the PA determines the impact of using water as solvent. Modification in toluene results in a higher modification degree for propylphosphonic acid (3PA), as the solvent-solute interaction may hinder the grafting with phenylphosphonic acid (PhPA) in toluene. Water is preferred as solvent for PhPA modification as stabilizing π-OH interactions enhance surface grafting overcoming the competitive interaction of water at the surface as observed with 3PA. By using water in toluene mixtures for the functionalization of TiO2 with 3PA, the degree of functionalization is higher than when only water or toluene is used. Furthermore, adding small amounts of water leads to the formation of titanium propylphosphonates, next to surface grafting.

Venus Interior Probe Using In-Situ Power and Propulsion (VIP-INSPR)

NASA Technical Reports Server (NTRS)

Bugga, Ratnakumar V.

2016-01-01

Venus, despite being our closest neighboring planet, is under-explored due to its hostile and extreme environment, with a 92 bar pressure and 467 C temperature at the surface. The temperature decreases at higher altitudes, almost at the rate of 7.9 C/km, reaching the Earth surface conditions at 65 km. Due to the less extreme conditions, balloon missions could survive as long as 46 h at an altitude of 54 km. However, because of the opacity of the Venus atmosphere filled with clouds of sulfuric acid and CO2, orbiter or balloon missions are not as revealing and informative in characterizing the surface, as similar missions on Moon and Mars. To understand the evolutionary paths of Venus in relation to Earth, it is imperative to gather basic information on the crust, mantle, core, atmosphere/exosphere and bulk composition of Venus, through in-situ investigations using landers, probes and variable altitude areal platforms.

Doping Level of Boron-Doped Diamond Electrodes Controls the Grafting Density of Functional Groups for DNA Assays.

PubMed

Švorc, Ĺubomír; Jambrec, Daliborka; Vojs, Marian; Barwe, Stefan; Clausmeyer, Jan; Michniak, Pavol; Marton, Marián; Schuhmann, Wolfgang

2015-09-02

The impact of different doping levels of boron-doped diamond on the surface functionalization was investigated by means of electrochemical reduction of aryldiazonium salts. The grafting efficiency of 4-nitrophenyl groups increased with the boron levels (B/C ratio from 0 to 20,000 ppm). Controlled grafting of nitrophenyldiazonium was used to adjust the amount of immobilized single-stranded DNA strands at the surface and further on the hybridization yield in dependence on the boron doping level. The grafted nitro functions were electrochemically reduced to the amine moieties. Subsequent functionalization with a succinic acid introduced carboxyl groups for subsequent binding of an amino-terminated DNA probe. DNA hybridization significantly depends on the probe density which is in turn dependent on the boron doping level. The proposed approach opens new insights for the design and control of doped diamond surface functionalization for the construction of DNA hybridization assays.

Virus-based surface patterning of biological molecules, probes, and inorganic materials.

PubMed

Ahn, Suji; Jeon, Seongho; Kwak, Eun-A; Kim, Jong-Man; Jaworski, Justyn

2014-10-01

An essential requirement for continued technological advancement in many areas of biology, physics, chemistry, and materials science is the growing need to generate custom patterned materials. Building from recent achievements in the site-specific modification of virus for covalent surface tethering, we show in this work that stable 2D virus patterns can be generated in custom geometries over large area glass surfaces to yield templates of biological, biochemical, and inorganic materials in high density. As a nanomaterial building block, filamentous viruses have been extensively used in recent years to produce materials with interesting properties, owing to their ease of genetic and chemical modification. By utilizing un-natural amino acids generated at specific locations on the filamentous fd bacteriophage protein coat, surface immobilization is carried out on APTES patterned glass resulting in precise geometries of covalently linked virus material. This technique facilitated the surface display of a high density of virus that were labeled with biomolecules, fluorescent probes, and gold nanoparticles, thereby opening the possibility of integrating virus as functional components for surface engineering. Copyright © 2014 Elsevier B.V. All rights reserved.

Manipulating fatty acid biosynthesis in microalgae for biofuel through protein-protein interactions.

PubMed

Blatti, Jillian L; Beld, Joris; Behnke, Craig A; Mendez, Michael; Mayfield, Stephen P; Burkart, Michael D

2012-01-01

Microalgae are a promising feedstock for renewable fuels, and algal metabolic engineering can lead to crop improvement, thus accelerating the development of commercially viable biodiesel production from algae biomass. We demonstrate that protein-protein interactions between the fatty acid acyl carrier protein (ACP) and thioesterase (TE) govern fatty acid hydrolysis within the algal chloroplast. Using green microalga Chlamydomonas reinhardtii (Cr) as a model, a structural simulation of docking CrACP to CrTE identifies a protein-protein recognition surface between the two domains. A virtual screen reveals plant TEs with similar in silico binding to CrACP. Employing an activity-based crosslinking probe designed to selectively trap transient protein-protein interactions between the TE and ACP, we demonstrate in vitro that CrTE must functionally interact with CrACP to release fatty acids, while TEs of vascular plants show no mechanistic crosslinking to CrACP. This is recapitulated in vivo, where overproduction of the endogenous CrTE increased levels of short-chain fatty acids and engineering plant TEs into the C. reinhardtii chloroplast did not alter the fatty acid profile. These findings highlight the critical role of protein-protein interactions in manipulating fatty acid biosynthesis for algae biofuel engineering as illuminated by activity-based probes.

Manipulating Fatty Acid Biosynthesis in Microalgae for Biofuel through Protein-Protein Interactions

PubMed Central

Blatti, Jillian L.; Beld, Joris; Behnke, Craig A.; Mendez, Michael; Mayfield, Stephen P.; Burkart, Michael D.

2012-01-01

Microalgae are a promising feedstock for renewable fuels, and algal metabolic engineering can lead to crop improvement, thus accelerating the development of commercially viable biodiesel production from algae biomass. We demonstrate that protein-protein interactions between the fatty acid acyl carrier protein (ACP) and thioesterase (TE) govern fatty acid hydrolysis within the algal chloroplast. Using green microalga Chlamydomonas reinhardtii (Cr) as a model, a structural simulation of docking CrACP to CrTE identifies a protein-protein recognition surface between the two domains. A virtual screen reveals plant TEs with similar in silico binding to CrACP. Employing an activity-based crosslinking probe designed to selectively trap transient protein-protein interactions between the TE and ACP, we demonstrate in vitro that CrTE must functionally interact with CrACP to release fatty acids, while TEs of vascular plants show no mechanistic crosslinking to CrACP. This is recapitulated in vivo, where overproduction of the endogenous CrTE increased levels of short-chain fatty acids and engineering plant TEs into the C. reinhardtii chloroplast did not alter the fatty acid profile. These findings highlight the critical role of protein-protein interactions in manipulating fatty acid biosynthesis for algae biofuel engineering as illuminated by activity-based probes. PMID:23028438

Surface Organometallic Chemistry of Supported Iridium(III) as a Probe for Organotransition Metal–Support Interactions in C–H Activation

DOE PAGES

Kaphan, David M.; Klet, Rachel C.; Perras, Frederic A.; ...

2018-05-11

Systematic study of the interactions between organometallic catalysts and metal oxide support materials is essential for the realization of rational design in heterogeneous catalysis. Herein we describe the stoichiometric and catalytic chemistry of a [Cp*(PMe 3)Ir(III)] complex chemisorbed on a variety of acidic metal oxides as a multifaceted probe for stereoelectronic communication between the support and organometallic center. Electrophilic bond activation was explored in the context of stoichiometric hydrogenolysis as well as catalytic H/D exchange. Further information was obtained from the observation of processes related to dynamic exchange between grafted organometallic species and those in solution. The supported organometallic speciesmore » were characterized by a variety of spectroscopic techniques including dynamic nuclear polarization-enhanced solid-state NMR spectroscopy, diffuse reflectance infrared Fourier transform spectroscopy, and X-ray absorption spectroscopy. Finally, strongly acidic modified metal oxides such as sulfated zirconia engender high levels of activity toward electrophilic bond activation of both sp 2 and sp 3 C–H bonds, including the rapid deuteration of methane at room temperature; however, the global trend for the supports studied here does not suggest a direct correlation between activity and surface Brønsted acidity.« less

Surface Organometallic Chemistry of Supported Iridium(III) as a Probe for Organotransition Metal–Support Interactions in C–H Activation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaphan, David M.; Klet, Rachel C.; Perras, Frederic A.

Systematic study of the interactions between organometallic catalysts and metal oxide support materials is essential for the realization of rational design in heterogeneous catalysis. Herein we describe the stoichiometric and catalytic chemistry of a [Cp*(PMe 3)Ir(III)] complex chemisorbed on a variety of acidic metal oxides as a multifaceted probe for stereoelectronic communication between the support and organometallic center. Electrophilic bond activation was explored in the context of stoichiometric hydrogenolysis as well as catalytic H/D exchange. Further information was obtained from the observation of processes related to dynamic exchange between grafted organometallic species and those in solution. The supported organometallic speciesmore » were characterized by a variety of spectroscopic techniques including dynamic nuclear polarization-enhanced solid-state NMR spectroscopy, diffuse reflectance infrared Fourier transform spectroscopy, and X-ray absorption spectroscopy. Finally, strongly acidic modified metal oxides such as sulfated zirconia engender high levels of activity toward electrophilic bond activation of both sp 2 and sp 3 C–H bonds, including the rapid deuteration of methane at room temperature; however, the global trend for the supports studied here does not suggest a direct correlation between activity and surface Brønsted acidity.« less

The effect of charge on the release kinetics from polysaccharide-nanoclay composites

NASA Astrophysics Data System (ADS)

Del Buffa, Stefano; Grifoni, Emanuele; Ridi, Francesca; Baglioni, Piero

2015-03-01

The objective of this study was to integrate inorganic halloysite nanotubes (HNT) with chitosan and hyaluronic acid to obtain hybrid nanocomposites with opposing charges and to investigate their potential in the controlled release of drug model probes. Two oppositely charged polysaccharides, chitosan and hyaluronic acid, were selected for their biocompatibility and their importance in biomedical applications. The high surface area and the hollow nanometric-sized lumen of HNT allowed for the efficient loading of rhodamine 110 and carboxyfluorescein, used as models for oppositely charged drugs. In the case of chitosan, the preparation of the nanocomposite was carried out exploiting the electrostatic interaction between the polymer and HNT in water, while with hyaluronic acid, a covalent functionalization strategy was employed to couple the polymer with the clay. Nanocomposites were characterized with thermal, microscopic, and spectroscopic techniques, and the release kinetics of the model compounds was assessed by fluorescence measurements. The release curves were fitted with a model able to account for the desorption process from the external and the internal halloysite surfaces. The results show that both polymeric coatings alter the release of the probes, indicating a key role of both charge and coating composition on the initial and final amount of released dye, as well as on the rate of the desorption process.

Array-Based Rational Design of Short Peptide Probe-Derived from an Anti-TNT Monoclonal Antibody.

PubMed

Okochi, Mina; Muto, Masaki; Yanai, Kentaro; Tanaka, Masayoshi; Onodera, Takeshi; Wang, Jin; Ueda, Hiroshi; Toko, Kiyoshi

2017-10-09

Complementarity-determining regions (CDRs) are sites on the variable chains of antibodies responsible for binding to specific antigens. In this study, a short peptide probe for recognition of 2,4,6-trinitrotoluene (TNT), was identified by testing sequences derived from the CDRs of an anti-TNT monoclonal antibody. The major TNT-binding site in this antibody was identified in the heavy chain CDR3 by antigen docking simulation and confirmed by an immunoassay using a spot-synthesis based peptide array comprising amino acid sequences of six CDRs in the variable region. A peptide derived from heavy chain CDR3 (RGYSSFIYWF) bound to TNT with a dissociation constant of 1.3 μM measured by surface plasmon resonance. Substitution of selected amino acids with basic residues increased TNT binding while substitution with acidic amino acids decreased affinity, an isoleucine to arginine change showed the greatest improvement of 1.8-fold. The ability to create simple peptide binders of volatile organic compounds from sequence information provided by the immune system in the creation of an immune response will be beneficial for sensor developments in the future.

U-bent plastic optical fiber based plasmonic biosensor for nucleic acid detection

NASA Astrophysics Data System (ADS)

Gowri, A.; Sai, V. V. R.

2017-05-01

This study presents the development of low cost, rapid and highly sensitive plasmonic sandwich DNA biosensor using U-bent plastic optical fiber (POF) probes with high evanescent wave absorbance sensitivity and gold nanoparticles (AuNP) as labels. Plastic optical fiber (PMMA core and fluorinated polymer as cladding) offer ease in machinability and handling due to which optimum U-bent geometry (with fiber and bend diameter of 0.5 and 1.5 mm respectively) for high sensitivity could be achieved. A sensitive fiber optic DNA biosensor is realized by (i) modifying the PMMA surface using ethylenediamine (EDA) in order to maximize the immobilization of capture oligonucleotides (ONs) and (ii) conjugating probe ONs to AuNP labels of optimum size ( 35 nm) with high extinction coefficient and optimal ON surface density. The sandwich hybridization assay on U-bent POF probes results in increase in optical absorbance through the probe with increase in target ON concentration due to the presence of increased number of AuNPs. The absorbance of light passing through the U-bent probe due to the presence of AuNP labels on its surface as result of sandwich DNA hybridization is measured using a halogen lamp and a fiber optic spectrometer. A picomolar limit of detection of target ON (0.2 pM or 1 pg/ml or 5 attomol in 25 μL) is achieved with this biosensing scheme, indicating its potential for the development of a highly sensitive DNA biosensor.

In situ analysis of plant tissue underivatized carbohydrates and on-probe enzymatic degraded starch by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry by using carbon nanotubes as matrix.

PubMed

Gholipour, Yousef; Nonami, Hiroshi; Erra-Balsells, Rosa

2008-12-15

Underivatized carbohydrates of tulip bulb and leaf tissues were characterized in situ by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) by using carbon nanotubes (CNTs) as matrix. Two sample preparation methods--(i) depositing CNTs on the fresh tissue slices placed on the probe and (ii) locating semitransparent tissues on a dried layer of CNTs on the probe--were examined. Furthermore, practicability of in situ starch analysis by MALDI-TOF MS was examined by detection of glucose originated from on-probe amyloglucosidase-catalyzed degradation of starch on the tissue surface. Besides, CNTs could efficiently desorb/ionize natural mono-, di-, and oligosaccharides extracted from tulip bulb tissues as well as glucose resulting from starch enzymatic degradation in vitro. These results were compared with those obtained by in situ MALDI-TOF MS analysis of similar tissues. Positive ion mode showed superior signal reproducibility. CNTs deposited under semitransparent tissue could also desorb/ionize neutral carbohydrates, leading to nearly complete elimination of matrix cluster signals but with an increase in tissue-originated signals. Furthermore, several experiments were carried out to compare the efficiency of 2,5-dihydroxybenzoic acid, nor-harmane, alpha-cyano-4-hydroxycinnamic acid, and CNTs as matrices for MALDI of neutral carbohydrates from the intact plant tissue surface and for enzymatic tissue starch degradation; these results are discussed in brief. Among matrices studied, the lowest laser power was needed to acquire carbohydrate signals with high signal-to-noise ratio and resolution when CNTs were used.

BODIPY-Based Fluorescent Probes for Sensing Protein Surface-Hydrophobicity.

PubMed

Dorh, Nethaniah; Zhu, Shilei; Dhungana, Kamal B; Pati, Ranjit; Luo, Fen-Tair; Liu, Haiying; Tiwari, Ashutosh

2015-12-18

Mapping surface hydrophobic interactions in proteins is key to understanding molecular recognition, biological functions, and is central to many protein misfolding diseases. Herein, we report synthesis and application of new BODIPY-based hydrophobic sensors (HPsensors) that are stable and highly fluorescent for pH values ranging from 7.0 to 9.0. Surface hydrophobic measurements of proteins (BSA, apomyoglobin, and myoglobin) by these HPsensors display much stronger signal compared to 8-anilino-1-naphthalene sulfonic acid (ANS), a commonly used hydrophobic probe; HPsensors show a 10- to 60-fold increase in signal strength for the BSA protein with affinity in the nanomolar range. This suggests that these HPsensors can be used as a sensitive indicator of protein surface hydrophobicity. A first principle approach is used to identify the molecular level mechanism for the substantial increase in the fluorescence signal strength. Our results show that conformational change and increased molecular rigidity of the dye due to its hydrophobic interaction with protein lead to fluorescence enhancement.

Nucleic Acid Detection Methods

DOEpatents

Smith, Cassandra L.; Yaar, Ron; Szafranski, Przemyslaw; Cantor, Charles R.

1998-05-19

The invention relates to methods for rapidly determining the sequence and/or length a target sequence. The target sequence may be a series of known or unknown repeat sequences which are hybridized to an array of probes. The hybridized array is digested with a single-strand nuclease and free 3'-hydroxyl groups extended with a nucleic acid polymerase. Nuclease cleaved heteroduplexes can be easily distinguish from nuclease uncleaved heteroduplexes by differential labeling. Probes and target can be differentially labeled with detectable labels. Matched target can be detected by cleaving resulting loops from the hybridized target and creating free 3-hydroxyl groups. These groups are recognized and extended by polymerases added into the reaction system which also adds or releases one label into solution. Analysis of the resulting products using either solid phase or solution. These methods can be used to detect characteristic nucleic acid sequences, to determine target sequence and to screen for genetic defects and disorders. Assays can be conducted on solid surfaces allowing for multiple reactions to be conducted in parallel and, if desired, automated.

Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes.

PubMed

Marras, Salvatore A E; Tyagi, Sanjay; Kramer, Fred Russell

2006-01-01

A number of formats for nucleic acid hybridization have been developed to identify DNA and RNA sequences that are involved in cellular processes and that aid in the diagnosis of genetic and infectious diseases. The introduction of hybridization probes with interactive fluorophore pairs has enabled the development of homogeneous hybridization assays for the direct identification of nucleic acids. A change in the fluorescence of these probes indicates the presence of a target nucleic acid, and there is no need to separate unbound probes from hybridized probes. The advantages of homogeneous hybridization assays are their speed and simplicity. In addition, homogeneous assays can be combined with nucleic acid amplification, enabling the detection of rare target nucleic acids. These assays can be followed in real time, providing quantitative determination of target nucleic acids over a broad range of concentrations.

Development of a DNA Sensor Based on Nanoporous Pt-Rich Electrodes

NASA Astrophysics Data System (ADS)

Van Hao, Pham; Thanh, Pham Duc; Xuan, Chu Thi; Hai, Nguyen Hoang; Tuan, Mai Anh

2017-06-01

Nanoporous Pt-rich electrodes with 72 at.% Pt composition were fabricated by sputtering a Pt-Ag alloy, followed by an electrochemical dealloying process to selectively etch away Ag atoms. The surface properties of nanoporous membranes were investigated by energy-dispersive x-ray spectroscopy (EDS), scanning electron microscopy (SEM), atomic force microscopy (AFM), a documentation system, and a gel image system (Gel Doc Imager). A single strand of probe deoxyribonucleic acid (DNA) was immobilized onto the electrode surface by physical adsorption. The DNA probe and target hybridization were measured using a lock-in amplifier and an electrochemical impedance spectroscope (EIS). The nanoporous Pt-rich electrode-based DNA sensor offers a fast response time of 3.7 s, with a limit of detection (LOD) of 4.35 × 10-10 M of DNA target.

Wide angle near-field optical probes by reverse tube etching.

PubMed

Patanè, S; Cefalì, E; Arena, A; Gucciardi, P G; Allegrini, M

2006-04-01

We present a simple modification of the tube etching process for the fabrication of fiber probes for near-field optical microscopy. It increases the taper angle of the probe by a factor of two. The novelty is that the fiber is immersed in hydrofluoric acid and chemically etched in an upside-down geometry. The tip formation occurs inside the micrometer tube cavity formed by the polymeric jacket. By applying this approach, called reverse tube etching, to multimode fibers with 200/250 microm core/cladding diameter, we have fabricated tapered regions featuring high surface smoothness and average cone angles of approximately 30 degrees . A simple model based on the crucial role of the gravity in removing the etching products, explains the tip formation process.

Decomposition of total solvation energy into core, side-chains and water contributions: Role of cross correlations and protein conformational fluctuations in dynamics of hydration layer

NASA Astrophysics Data System (ADS)

Mondal, Sayantan; Mukherjee, Saumyak; Bagchi, Biman

2017-09-01

Dynamical coupling between water and amino acid side-chain residues in solvation dynamics is investigated by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on protein surface. Such differently placed residues are found to exhibit different timescales of relaxation. The total solvation response measured by the probe is decomposed in terms of its interactions with (i) protein core, (ii) side-chain and (iii) water. Significant anti cross-correlation among these contributions are observed. When the motion of the protein side-chains is quenched, solvation either becomes faster or slower depending on the location of the probe.

Influence of short chain organic acids and bases on the wetting properties and surface energy of submicrometer ceramic powders.

PubMed

Neirinck, Bram; Soccol, Dimitri; Fransaer, Jan; Van der Biest, Omer; Vleugels, Jef

2010-08-15

The effect of short chained organic acids and bases on the surface energy and wetting properties of submicrometer alumina powder was assessed. The surface chemistry of treated powders was determined by means of Diffuse Reflectance Infrared Fourier Transform spectroscopy and compared to untreated powder. The wetting of powders was measured using a modified Washburn method, based on the use of precompacted powder samples. The geometric factor needed to calculate the contact angle was derived from measurements of the porous properties of the powder compacts. Contact angle measurements with several probe liquids before and after modification allowed a theoretical estimation of the surface energy based on the surface tension component theory. Trends in the surface energy components were linked to observations in infrared spectra. The results showed that the hydrophobic character of the precompacted powder depends on both the chain length and polar group of the modifying agent. Copyright 2010 Elsevier Inc. All rights reserved.

Water evaporation from substrate tooth surface during dentin treatments.

PubMed

Kusunoki, Mizuho; Itoh, Kazuo; Gokan, Yuka; Nagai, Yoshitaka; Tani, Chihiro; Hisamitsu, Hisashi

2011-01-01

The purpose of this study was to evaluate changes in the quantity of water evaporation from tooth surfaces. The amount of water evaporation was measured using Multi probe adapter MPA5 and Tewameter TM300 (Courage+Khazaka Electric GmbH, Köln, Germany) after acid etching and GM priming of enamel; and after EDTA conditioning and GM priming of dentin. The results indicated that the amount of water evaporation from the enamel surface was significantly less than that from the dentin. Acid etching did not affect the water evaporation from enamel, though GM priming significantly decreased the evaporation (83.48 ± 15.14% of that before priming). The evaporation from dentin was significantly increased by EDTA conditioning (131.38 ± 42.08% of that before conditioning) and significantly reduced by GM priming (80.26 ± 7.43% of that before priming). It was concluded that dentin priming reduced water evaporation from the dentin surface.

Selection of fluorophore and quencher pairs for fluorescent nucleic acid hybridization probes.

PubMed

Marras, Salvatore A E

2006-01-01

With the introduction of simple and relatively inexpensive methods for labeling nucleic acids with nonradioactive labels, doors have been opened that enable nucleic acid hybridization probes to be used for research and development, as well as for clinical diagnostic applications. The use of fluorescent hybridization probes that generate a fluorescence signal only when they bind to their target enables real-time monitoring of nucleic acid amplification assays. The use of hybridization probes that bind to the amplification products in real-time markedly improves the ability to obtain quantitative results. Furthermore, real-time nucleic acid amplification assays can be carried out in sealed tubes, eliminating carryover contamination. Because fluorescent hybridization probes are available in a wide range of colors, multiple hybridization probes, each designed for the detection of a different nucleic acid sequence and each labeled with a differently colored fluorophore, can be added to the same nucleic acid amplification reaction, enabling the development of high-throughput multiplex assays. It is therefore important to carefully select the labels of hybridization probes, based on the type of hybridization probe used in the assay, the number of targets to be detected, and the type of apparatus available to perform the assay. This chapter outlines different aspects of choosing appropriate labels for the different types of fluorescent hybridization probes used with different types of spectrofluorometric thermal cyclers.

Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

DOEpatents

Ramsey, J. Michael; Foote, Robert S.

2003-12-09

A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

DOEpatents

Ramsey, J. Michael; Foote, Robert S.

2002-01-01

A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

Lateral diffusion and retrograde movements of individual cell surface components on single motile cells observed with Nanovid microscopy

PubMed Central

1991-01-01

A recently introduced extension of video-enhanced light microscopy, called Nanovid microscopy, documents the dynamic reorganization of individual cell surface components on living cells. 40-microns colloidal gold probes coupled to different types of poly-L-lysine label negative cell surface components of PTK2 cells. Evidence is provided that they bind to negative sialic acid residues of glycoproteins, probably through nonspecific electrostatic interactions. The gold probes, coupled to short poly-L-lysine molecules (4 kD) displayed Brownian motion, with a diffusion coefficient in the range 0.1-0.2 micron2/s. A diffusion coefficient in the 0.1 micron2/s range was also observed with 40-nm gold probes coupled to an antibody against the lipid-linked Thy-1 antigen on 3T3 fibroblasts. Diffusion of these probes is largely confined to apparent microdomains of 1-2 microns in size. On the other hand, the gold probes, coupled to long poly-L-lysine molecules (240 kD) molecules and bound to the leading lamella, were driven rearward, toward the boundary between lamelloplasm and perinuclear cytoplasm at a velocity of 0.5-1 micron/min by a directed ATP-dependent mechanism. This uniform motion was inhibited by cytochalasin, suggesting actin microfilament involvement. A similar behavior on MO cells was observed when the antibody-labeled gold served as a marker for the PGP-1 (GP-80) antigen. These results show that Nanovid microscopy, offering the possibility to observe the motion of individual specific cell surface components, provides a new and powerful tool to study the dynamic reorganization of the cell membrane during locomotion and in other biological contexts as well. PMID:1670778

Role of auxin and protons in plant shoot gravitropism

NASA Technical Reports Server (NTRS)

Rayle, D. L.; Migliaccio, F.; Watson, E.

1982-01-01

Experiments designed to probe the relationship between asymmetric acid efflux and auxin redistribution during gravitropism are reported. Gravistimulation of sunflower hypocotyls results in the retardation of growth on the upper surface and the acceleration of growth on the lower surface relative to a vertically oriented control. Auxin and H(+) both elicit growth over a similarly broad region of the hypocotyl. The correspondence between auxin, H(+), and gravisensitive tissues is consistent with the notion that auxin redistribution may initiate asymmetric acid efflux during gravistimulation. Data are presented showing a redistribution of C-14-IAA and H-3-IAA occurs within 20-30 minutes of gravistimulation. Data on the effects of selected inhibitors of shoot gravitropism are also presented. Taken together, the data suggest that lateral transport of auxin initiates asymmetric acid efflux in gravitropically stimulated shoots.

Arrays of nucleic acid probes on biological chips

DOEpatents

Chee, Mark; Cronin, Maureen T.; Fodor, Stephen P. A.; Huang, Xiaohua X.; Hubbell, Earl A.; Lipshutz, Robert J.; Lobban, Peter E.; Morris, MacDonald S.; Sheldon, Edward L.

1998-11-17

DNA chips containing arrays of oligonucleotide probes can be used to determine whether a target nucleic acid has a nucleotide sequence identical to or different from a specific reference sequence. The array of probes comprises probes exactly complementary to the reference sequence, as well as probes that differ by one or more bases from the exactly complementary probes.

Interactive fluorophore and quencher pairs for labeling fluorescent nucleic acid hybridization probes.

PubMed

Marras, Salvatore A E

2008-03-01

The use of fluorescent nucleic acid hybridization probes that generate a fluorescence signal only when they bind to their target enables real-time monitoring of nucleic acid amplification assays. Real-time nucleic acid amplification assays markedly improves the ability to obtain qualitative and quantitative results. Furthermore, these assays can be carried out in sealed tubes, eliminating carryover contamination. Fluorescent nucleic acid hybridization probes are available in a wide range of different fluorophore and quencher pairs. Multiple hybridization probes, each designed for the detection of a different nucleic acid sequence and each labeled with a differently colored fluorophore, can be added to the same nucleic acid amplification reaction, enabling the development of high-throughput multiplex assays. In order to develop robust, highly sensitive and specific real-time nucleic acid amplification assays it is important to carefully select the fluorophore and quencher labels of hybridization probes. Selection criteria are based on the type of hybridization probe used in the assay, the number of targets to be detected, and the type of apparatus available to perform the assay. This article provides an overview of different aspects of choosing appropriate labels for the different types of fluorescent hybridization probes used with different types of spectrofluorometric thermal cyclers currently available.

A rapid method for detection of genetically modified organisms based on magnetic separation and surface-enhanced Raman scattering.

PubMed

Guven, Burcu; Boyacı, İsmail Hakkı; Tamer, Ugur; Çalık, Pınar

2012-01-07

In this study, a new method combining magnetic separation (MS) and surface-enhanced Raman scattering (SERS) was developed to detect genetically modified organisms (GMOs). An oligonucleotide probe which is specific for 35 S DNA target was immobilized onto gold coated magnetic nanospheres to form oligonucleotide-coated nanoparticles. A self assembled monolayer was formed on gold nanorods using 5,5'-dithiobis (2-nitrobenzoic acid) (DTNB) and the second probe of the 35 S DNA target was immobilized on the activated nanorod surfaces. Probes on the nanoparticles were hybridized with the target oligonucleotide. Optimization parameters for hybridization were investigated by high performance liquid chromatography. Optimum hybridization parameters were determined as: 4 μM probe concentration, 20 min immobilization time, 30 min hybridization time, 55 °C hybridization temperature, 750 mM buffer salt concentration and pH: 7.4. Quantification of the target concentration was performed via SERS spectra of DTNB on the nanorods. The correlation between the target concentration and the SERS signal was found to be linear within the range of 25-100 nM. The analyses were performed with only one hybridization step in 40 min. Real sample analysis was conducted using Bt-176 maize sample. The results showed that the developed MS-SERS assay is capable of detecting GMOs in a rapid and selective manner. This journal is © The Royal Society of Chemistry 2012

Spaser as a biological probe

NASA Astrophysics Data System (ADS)

Galanzha, Ekaterina I.; Weingold, Robert; Nedosekin, Dmitry A.; Sarimollaoglu, Mustafa; Nolan, Jacqueline; Harrington, Walter; Kuchyanov, Alexander S.; Parkhomenko, Roman G.; Watanabe, Fumiya; Nima, Zeid; Biris, Alexandru S.; Plekhanov, Alexander I.; Stockman, Mark I.; Zharov, Vladimir P.

2017-06-01

Understanding cell biology greatly benefits from the development of advanced diagnostic probes. Here we introduce a 22-nm spaser (plasmonic nanolaser) with the ability to serve as a super-bright, water-soluble, biocompatible probe capable of generating stimulated emission directly inside living cells and animal tissues. We have demonstrated a lasing regime associated with the formation of a dynamic vapour nanobubble around the spaser that leads to giant spasing with emission intensity and spectral width >100 times brighter and 30-fold narrower, respectively, than for quantum dots. The absorption losses in the spaser enhance its multifunctionality, allowing for nanobubble-amplified photothermal and photoacoustic imaging and therapy. Furthermore, the silica spaser surface has been covalently functionalized with folic acid for molecular targeting of cancer cells. All these properties make a nanobubble spaser a promising multimodal, super-contrast, ultrafast cellular probe with a single-pulse nanosecond excitation for a variety of in vitro and in vivo biomedical applications.

Compositions and methods for detecting single nucleotide polymorphisms

DOEpatents

Yeh, Hsin-Chih; Werner, James; Martinez, Jennifer S.

2016-11-22

Described herein are nucleic acid based probes and methods for discriminating and detecting single nucleotide variants in nucleic acid molecules (e.g., DNA). The methods include use of a pair of probes can be used to detect and identify polymorphisms, for example single nucleotide polymorphism in DNA. The pair of probes emit a different fluorescent wavelength of light depending on the association and alignment of the probes when hybridized to a target nucleic acid molecule. Each pair of probes is capable of discriminating at least two different nucleic acid molecules that differ by at least a single nucleotide difference. The methods can probes can be used, for example, for detection of DNA polymorphisms that are indicative of a particular disease or condition.

A single pH fluorescent probe for biosensing and imaging of extreme acidity and extreme alkalinity.

PubMed

Chao, Jian-Bin; Wang, Hui-Juan; Zhang, Yong-Bin; Li, Zhi-Qing; Liu, Yu-Hong; Huo, Fang-Jun; Yin, Cai-Xia; Shi, Ya-Wei; Wang, Juan-Juan

2017-07-04

A simple tailor-made pH fluorescent probe 2-benzothiazole (N-ethylcarbazole-3-yl) hydrazone (Probe) is facilely synthesized by the condensation reaction of 2-hydrazinobenzothiazole with N-ethylcarbazole-3-formaldehyde, which is a useful fluorescent probe for monitoring extremely acidic and alkaline pH, quantitatively. The pH titrations indicate that Probe displays a remarkable emission enhancement with a pK a of 2.73 and responds linearly to minor pH fluctuations within the extremely acidic range of 2.21-3.30. Interestingly, Probe also exhibits strong pH-dependent characteristics with pK a 11.28 and linear response to extreme-alkalinity range of 10.41-12.43. In addition, Probe shows a large Stokes shift of 84 nm under extremely acidic and alkaline conditions, high selectivity, excellent sensitivity, good water-solubility and fine stability, all of which are favorable for intracellular pH imaging. The probe is further successfully applied to image extremely acidic and alkaline pH values fluctuations in E. coli cells. Copyright © 2017 Elsevier B.V. All rights reserved.

Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes

PubMed Central

Junager, Nina P. L.; Kongsted, Jacob; Astakhova, Kira

2016-01-01

Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells. PMID:27472344

A ω-mercaptoundecylphosphonic acid chemically modified gold electrode for uranium determination in waters in presence of organic matter.

PubMed

Merli, Daniele; Protti, Stefano; Labò, Matteo; Pesavento, Maria; Profumo, Antonella

2016-05-01

A chemically modified electrode (CME) on a gold surface assembled with a ω-phosphonic acid terminated thiol was investigated for its capability to complex uranyl ions. The electrode, characterized by electrochemical techniques, demonstrated to be effective for the determination of uranyl at sub-μgL(-1) level by differential pulse adsorptive stripping voltammetry (DPAdSV) in environmental waters, also in presence of humic matter and other potential chelating agents. The accuracy of the measurements was investigated employing as model probes ligands of different complexing capability (humic acids and EDTA). Copyright © 2016 Elsevier B.V. All rights reserved.

Highlighting cancer cells with macromolecular probes

NASA Astrophysics Data System (ADS)

Tang, Sicheng; Zhang, Yang; Thapaliya, Ek Raj; Brown, Adrienne S.; Wilson, James N.; Raymo, Françisco M.

2017-02-01

Conventional fluorophore-ligand constructs for the detection of cancer cells generally produce relatively weak signals with modest contrast. The inherently low brightness accessible per biding event with the pairing of a single organic fluorophore to a single ligand as well as the contribution of unbound probes to background fluorescence are mainly responsible for these limitations. Our laboratories identified a viable structural design to improve both brightness and contrast. It is based on the integration of activatable fluorophores and targeting ligands within the same macromolecular construct. The chromophoric components are engineered to emit bright fluorescence exclusively in acidic environments. The targeting agents are designed to bind complementary receptors overexpressed on the surface of cancer cells and allow internalization of the macromolecules into acidic organelles. As a result of these properties, our macromolecular probes switch their intense emission on exclusively in the intracellular space of target cells with minimal background fluorescence from the extracellular matrix. In fact, these operating principles translate into a 170-fold enhancement in brightness, relative to equivalent but isolated chromophoric components, and a 3-fold increase in contrast, relative to model but non-activatable fluorophores. Thus, our macromolecular probes might ultimately evolve into valuable analytical tools to highlight cancer cells with optimal signal-to-noise ratios in a diversity of biomedical applications.

Quantitative Investigation of Protein-Nucleic Acid Interactions by Biosensor Surface Plasmon Resonance.

PubMed

Wang, Shuo; Poon, Gregory M K; Wilson, W David

2015-01-01

Biosensor-surface plasmon resonance (SPR) technology has emerged as a powerful label-free approach for the study of nucleic acid interactions in real time. The method provides simultaneous equilibrium and kinetic characterization for biomolecular interactions with low sample requirements and without the need for external probes. A detailed and practical guide for protein-DNA interaction analyses using biosensor-SPR methods is presented. Details of SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips and samples, experimental design, quantitative and qualitative data analyses and presentation. A specific example of the interaction of a transcription factor with DNA is provided with results evaluated by both kinetic and steady-state SPR methods.

A PDDA/poly(2,6-pyridinedicarboxylic acid)-CNTs composite film DNA electrochemical sensor and its application for the detection of specific sequences related to PAT gene and NOS gene.

PubMed

Yang, Tao; Zhang, Wei; Du, Meng; Jiao, Kui

2008-05-30

2,6-Pyridinedicarboxylic acid (PDC) was electropolymerized on the glassy carbon electrode (GCE) surface combined with carboxylic group-functionalized single-walled carbon nanotubes (SWNTs) by cyclic voltammetry (CV) to form PDC-SWNTs composite film, which was rich in negatively charged carboxylic group. Then, poly(diallyldimethyl ammonium chloride) (PDDA), a linear cationic polyelectrolyte, was electrostatically adsorbed on the PDC-SWNTs/GCE surface. DNA probes with negatively charged phosphate group at the 5' end were immobilized on the PDDA/PDC-SWNTs/GCE due to the strong electrostatic attraction between PDDA and phosphate group of DNA. It has been found that modification of the electrode with PDC-SWNTs film has enhanced the effective electrode surface area and electron-transfer ability, in addition to providing negatively charged groups for the electrostatic assembly of cationic polyelectrolyte. PDDA plays a key role in the attachment of DNA probes to the PDC-SWNTs composite film and acts as a bridge to connect DNA with PDC-SWNTs film. The cathodic peak current of methylene blue (MB), an electroactive label, decreased obviously after the hybridization of DNA probe (ssDNA) with the complementary DNA (cDNA). This peak current change was used to monitor the recognition of the specific sequences related to PAT gene in the transgenic corn and the polymerase chain reaction (PCR) amplification of NOS gene from the sample of transgenic soybean with satisfactory results. Under optimal conditions, the dynamic detection range of the sensor to PAT gene target sequence was from 1.0x10(-11) to 1.0x10(-6) mol/L with the detection limit of 2.6x10(-12) mol/L.

Exciton-controlled fluorescence: application to hybridization-sensitive fluorescent DNA probe.

PubMed

Okamoto, Akimitsu; Ikeda, Shuji; Kubota, Takeshi; Yuki, Mizue; Yanagisawa, Hiroyuki

2009-01-01

A hybridization-sensitive fluorescent probe has been designed for nucleic acid detection, using the concept of fluorescence quenching caused by the intramolecular excitonic interaction of fluorescence dyes. We synthesized a doubly thiazole orange-labeled nucleotide showing high fluorescence intensity for a hybrid with the target nucleic acid and effective quenching for the single-stranded state. This exciton-controlled fluorescent probe was applied to living HeLa cells using microinjection to visualize intracellular mRNA localization. Immediately after injection of the probe into the cell, fluorescence was observed from the probe hybridizing with the target RNA. This fluorescence rapidly decreased upon addition of a competitor DNA. Multicoloring of this probe resulted in the simple simultaneous detection of plural target nucleic acid sequences. This probe realized a large, rapid, reversible change in fluorescence intensity in sensitive response to the amount of target nucleic acid, and facilitated spatiotemporal monitoring of the behavior of intracellular RNA.

Chemical Synthesis and Evaluation of a Disialic Acid-Containing Dextran Polymer as an Inhibitor for the Interaction between Siglec 7 and Its Ligand.

PubMed

Yamaguchi, Sho; Yoshimura, Atsushi; Yasuda, Yu; Mori, Airi; Tanaka, Hiroshi; Takahashi, Takashi; Kitajima, Ken; Sato, Chihiro

2017-07-04

A new sialic acid (Sia)-containing glycopolymer-a fluorescent probe with high-density disialic acid (diSia) on the surface of polysaccharide dextran (diSia-Dex)-was synthesized as a key molecule to regulate the Sia recognition lectins, Siglecs, that are involved in the immune system. According to our original methods, diSia was synthesized by α-selective sialylation, and a dextran template possessing terminal acetylenes and amino groups was prepared. A diSia and a fluorescent molecule were subsequently introduced to surface-modified dextran by Hüisgen reaction and amidation, respectively. The modulatory activity of Siglec7 was evaluated by using synthetic probes. DiSia-Dex showed high binding avidity toward Siglec7, with a K D value of 5.87×10 -10  m, and a high inhibitory activity for the interaction between Siglec7 and a ligand (GD3), with a IC 50 value of 1.0 nm. Notably, diSia-Dex was able to release Siglec7 from the pre-existing Siglec7-GD3 complex, possibly due to its unique properties of a slow dissociation rate and a high association rate. Together, these data show that diSia-Dex can be widely applicable as a modulator of Siglec7 functions. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Magnetic purification of curcumin from Curcuma longa rhizome by novel naked maghemite nanoparticles.

PubMed

Magro, Massimiliano; Campos, Rene; Baratella, Davide; Ferreira, Maria Izabela; Bonaiuto, Emanuela; Corraducci, Vittorino; Uliana, Maíra Rodrigues; Lima, Giuseppina Pace Pereira; Santagata, Silvia; Sambo, Paolo; Vianello, Fabio

2015-01-28

Naked maghemite nanoparticles, namely, surface active maghemite nanoparticles (SAMNs), characterized by a diameter of about 10 nm, possessing peculiar colloidal stability, surface chemistry, and superparamagnetism, present fundamental requisites for the development of effective magnetic purification processes for biomolecules in complex matrices. Polyphenolic molecules presenting functionalities with different proclivities toward iron chelation were studied as probes for testing SAMN suitability for magnetic purification. Thus, the binding efficiency and reversibility on SAMNs of phenolic compounds of interest in the pharmaceutical and food industries, namely, catechin, tyrosine, hydroxytyrosine, ferulic acid, coumaric acid, rosmarinic acid, naringenin, curcumin, and cyanidin-3-glucoside, were evaluated. Curcumin emerged as an elective compound, suitable for magnetic purification by SAMNs from complex matrices. A combination of curcumin, demethoxycurcumin, and bis-demethoxycurcumin was recovered by a single magnetic purification step from extracts of Curcuma longa rhizomes, with a purity >98% and a purification yield of 45%, curcumin being >80% of the total purified curcuminoids.

Understanding Thermal Transport in Graded, Layered and Hybrid Materials

DTIC Science & Technology

2014-04-01

interfacial chemistries, including metallic and carbide layers, and; (iv) mimic the observed interface structure on a TDTR specimen by manipulating the...surface carbides , which were extracted from several different composites via acid dissolution of Cu, continued throughout the last 12 months of the...effort. The previously-reported electron probe microanalysis (EPMA) based techniques were employed to estimate the interfacial carbide layer thickness

A new class of homogeneous nucleic acid probes based on specific displacement hybridization

PubMed Central

Li, Qingge; Luan, Guoyan; Guo, Qiuping; Liang, Jixuan

2002-01-01

We have developed a new class of probes for homogeneous nucleic acid detection based on the proposed displacement hybridization. Our probes consist of two complementary oligodeoxyribonucleotides of different length labeled with a fluorophore and a quencher in close proximity in the duplex. The probes on their own are quenched, but they become fluorescent upon displacement hybridization with the target. These probes display complete discrimination between a perfectly matched target and single nucleotide mismatch targets. A comparison of double-stranded probes with corresponding linear probes confirms that the presence of the complementary strand significantly enhances their specificity. Using four such probes labeled with different color fluorophores, each designed to recognize a different target, we have demonstrated that multiple targets can be distinguished in the same solution, even if they differ from one another by as little as a single nucleotide. Double-stranded probes were used in real-time nucleic acid amplifications as either probes or as primers. In addition to its extreme specificity and flexibility, the new class of probes is simple to design and synthesize, has low cost and high sensitivity and is accessible to a wide range of labels. This class of probes should find applications in a variety of areas wherever high specificity of nucleic acid hybridization is relevant. PMID:11788731

A novel acidic pH fluorescent probe based on a benzothiazole derivative

NASA Astrophysics Data System (ADS)

Ma, Qiujuan; Li, Xian; Feng, Suxiang; Liang, Beibei; Zhou, Tiqiang; Xu, Min; Ma, Zhuoyi

2017-04-01

A novel acidic pH fluorescent probe 1 based on a benzothiazole derivative has been designed, synthesized and developed. The linear response range covers the acidic pH range from 3.44 to 6.46, which is valuable for pH researches in acidic environment. The evaluated pKa value of the probe 1 is 4.23. The fluorescence enhancement of the studied probe 1 with an increase in hydrogen ions concentration is based on the hindering of enhanced photo-induced electron transfer (PET) process. Moreover, the pH sensor possesses a highly selective response to H+ in the presence of metal ions, anions and other bioactive small molecules which would be interfere with its fluorescent pH response. Furthermore, the probe 1 responds to acidic pH with short response time that was less than 1 min. The probe 1 has been successfully applied to confocal fluorescence imaging in live HeLa cells and can selectively stain lysosomes. All of such good properties prove it can be used to monitoring pH fluctuations in acidic environment with high sensitivity, pH dependence and short response time.

Variations in collagen fibrils network structure and surface dehydration of acid demineralized intertubular dentin: effect of dentin depth and air-exposure time.

PubMed

Fawzy, Amr S

2010-01-01

The aim was to characterize the variations in the structure and surface dehydration of acid demineralized intertubular dentin collagen network with the variations in dentin depth and time of air-exposure (3, 6, 9 and 12 min). In addition, to study the effect of these variations on the tensile bond strength (TBS) to dentin. Phosphoric acid demineralized superficial and deep dentin specimens were prepared. The structure of the dentin collagen network was characterized by AFM. The surface dehydration was characterized by probing the nano-scale adhesion force (F(ad)) between AFM tip and intertubular dentin surface as a new experimental approach. The TBS to dentin was evaluated using an alcohol-based dentin self-priming adhesive. AFM images revealed a demineralized open collagen network structure in both of superficial and deep dentin at 3 and 6 min of air-exposure. However, at 9 min, superficial dentin showed more collapsed network structure compared to deep dentin that partially preserved the open network structure. Total collapsed structure was found at 12 min for both of superficial and deep dentin. The value of the F(ad) is decreased with increasing the time of air-exposure and is increased with dentin depth at the same time of air-exposure. The TBS was higher for superficial dentin at 3 and 6 min, however, no difference was found at 9 and 12 min. The ability of the demineralized dentin collagen network to resist air-dehydration and to preserve the integrity of open network structure with the increase in air-exposure time is increased with dentin depth. Although superficial dentin achieves higher bond strength values, the difference in the bond strength is decreased by increasing the time of air-exposure. The AFM probed F(ad) showed to be sensitive approach to characterize surface dehydration, however, further researches are recommended regarding the validity of such approach.

The use of the ion probe mass spectrometer in the measurement of hydrogen concentration gradients in Monel K 500

NASA Technical Reports Server (NTRS)

Truhan, J. J., Jr.; Hehemann, R. F.

1974-01-01

The ion probe mass spectrometer was used to measure hydrogen concentration gradients in cathodically charged Monel K 500. Initial work with the ion probe involved the calibration of the instrument and the establishment of a suitable experimental procedure for this application. Samples of Monel K 500 were cathodically charged in a weak sulfuric acid solution. By varying the current density, different levels of hydrogen were introduced into the samples. Hydrogen concentration gradients were taken by ion sputtering on the surface of these samples and monitoring the behavior of the hydrogen mass peak as a function of time. An attempt was made to determine the relative amounts of hydrogen in the bulk and grain boundaries by analyzing a fresh fracture surface with a higher proportion of grain boundary area. It was found that substantially more hydrogen was detected in the grain boundaries than in the bulk, confirming the predictions of previous workers. A sputter rate determination was made in order to establish the rate of erosion.

Phthalic acid chemical probes synthesized for protein-protein interaction analysis.

PubMed

Liang, Shih-Shin; Liao, Wei-Ting; Kuo, Chao-Jen; Chou, Chi-Hsien; Wu, Chin-Jen; Wang, Hui-Min

2013-06-24

Plasticizers are additives that are used to increase the flexibility of plastic during manufacturing. However, in injection molding processes, plasticizers cannot be generated with monomers because they can peel off from the plastics into the surrounding environment, water, or food, or become attached to skin. Among the various plasticizers that are used, 1,2-benzenedicarboxylic acid (phthalic acid) is a typical precursor to generate phthalates. In addition, phthalic acid is a metabolite of diethylhexyl phthalate (DEHP). According to Gene_Ontology gene/protein database, phthalates can cause genital diseases, cardiotoxicity, hepatotoxicity, nephrotoxicity, etc. In this study, a silanized linker (3-aminopropyl triethoxyslane, APTES) was deposited on silicon dioxides (SiO2) particles and phthalate chemical probes were manufactured from phthalic acid and APTES-SiO2. These probes could be used for detecting proteins that targeted phthalic acid and for protein-protein interactions. The phthalic acid chemical probes we produced were incubated with epithelioid cell lysates of normal rat kidney (NRK-52E cells) to detect the interactions between phthalic acid and NRK-52E extracted proteins. These chemical probes interacted with a number of chaperones such as protein disulfide-isomerase A6, heat shock proteins, and Serpin H1. Ingenuity Pathways Analysis (IPA) software showed that these chemical probes were a practical technique for protein-protein interaction analysis.

Lipoteichoic acids are embedded in cell walls during logarithmic phase, but exposed on membrane vesicles in Lactobacillus gasseri JCM 1131T.

PubMed

Shiraishi, T; Yokota, S; Sato, Y; Ito, T; Fukiya, S; Yamamoto, S; Sato, T; Yokota, A

2018-06-15

Lipoteichoic acid (LTA) is a cell surface molecule specific to Gram-positive bacteria. How LTA localises on the cell surface is a fundamental issue in view of recognition and immunomodulation in hosts. In the present study, we examined LTA localisation using strain JCM 1131T of Lactobacillus gasseri, which is a human intestinal lactic acid bacterium, during various growth phases by immunoelectron microscopy. We first evaluated the specificity of anti-LTA monoclonal antibody clone 55 used as a probe. The glycerophosphate backbone comprising almost intact size (20 to 30 repeating units) of LTA was required for binding. The antibody did not bind to other cellular components, including wall-teichoic acid. Immunoelectron microscopy indicated that LTA was embedded in the cell wall during the logarithmic phase, and was therefore not exposed on the cell surface. Similar results were observed for Lactobacillus fermentum ATCC 9338 and Lactobacillus rhamnosus ATCC 7469T. By contrast, membrane vesicles were observed in the logarithmic phase of L. gasseri with LTA exposed on their surface. In the stationary and death phases, LTA was exposed on cell wall-free cell membrane generated by autolysis. The dramatic alternation of localisation in different growth phases and exposure on the surface of membrane vesicles should relate with complicated interaction between bacteria and host.

Construction of a novel peptide nucleic acid piezoelectric gene sensor microarray detection system.

PubMed

Chen, Ming; Liu, Minghua; Yu, Lili; Cai, Guoru; Chen, Qinghai; Wu, Rong; Wang, Feng; Zhang, Bo; Jiang, Tianlun; Fu, Welling

2005-08-01

A novel 2 x 5 clamped style piezoelectric gene sensor microarray has been successfully constructed. Every crystal unit of the fabricated gene sensor can oscillate independently without interfering with each other. The bis-peptide nucleic acid (bis-PNA) probe, which can combine with target DNA or RNA sequences more effectively and specifically than a DNA probe, was designed and immobilized on the surface of the gene sensor microarray to substitute the conventional DNA probe for direct detection of the hepatitis B virus (HBV) genomic DNA. Detection conditions were then explored and optimized. Results showed that PBS buffer of pH 6.8, an ion concentration of 20 mmol/liter, and a probe concentration of 1.5 micromol/liter were optimal for the detection system. Under such optimized experimental conditions, the specificity of bis-PNA was proved much higher than that of DNA probe. The relationship between quantity of target and decrease of frequency showed a typical saturation curve when concentrations of target HBV DNA varied from 10 pg/liter to 100 microg/liter, and 10 microg/liter was the watershed, with a statistic linear regression equation of I gC = -2.7455 + 0.0691 deltaF and the correlating coefficient of 0.9923. Fortunately, this is exactly the most ordinary variant range of the HBV virus concentration in clinical hepatitis samples. So, a good technical platform is successfully constructed and it will be applied to detect HBV quantitatively in clinical samples.

Nucleic acid detection methods

DOEpatents

Smith, C.L.; Yaar, R.; Szafranski, P.; Cantor, C.R.

1998-05-19

The invention relates to methods for rapidly determining the sequence and/or length a target sequence. The target sequence may be a series of known or unknown repeat sequences which are hybridized to an array of probes. The hybridized array is digested with a single-strand nuclease and free 3{prime}-hydroxyl groups extended with a nucleic acid polymerase. Nuclease cleaved heteroduplexes can be easily distinguish from nuclease uncleaved heteroduplexes by differential labeling. Probes and target can be differentially labeled with detectable labels. Matched target can be detected by cleaving resulting loops from the hybridized target and creating free 3-hydroxyl groups. These groups are recognized and extended by polymerases added into the reaction system which also adds or releases one label into solution. Analysis of the resulting products using either solid phase or solution. These methods can be used to detect characteristic nucleic acid sequences, to determine target sequence and to screen for genetic defects and disorders. Assays can be conducted on solid surfaces allowing for multiple reactions to be conducted in parallel and, if desired, automated. 18 figs.

Crystallographic Fragment Based Drug Discovery: Use of a Brominated Fragment Library Targeting HIV Protease

PubMed Central

Tiefenbrunn, Theresa; Forli, Stefano; Happer, Meaghan; Gonzalez, Ana; Tsai, Yingssu; Soltis, Michael; Elder, John H.; Olson, Arthur J.; Stout, C. David

2013-01-01

A library of 68 brominated fragments was screened against a new crystal form of inhibited HIV-1 protease in order to probe surface sites in soaking experiments. Often fragments are weak binders with partial occupancy, resulting in weak, difficult-to-fit electron density. The use of a brominated fragment library addresses this challenge, as bromine can be located unequivocally via anomalous scattering. Data collection was carried out in an automated fashion using AutoDrug at SSRL. Novel hits were identified in the known surface sites: 3-bromo-2,6-dimethoxybenzoic acid (Br6) in the flap site, and 1-bromo-2-naphthoic acid (Br27) in the exosite, expanding the chemistry of known fragments for development of higher affinity potential allosteric inhibitors. At the same time, mapping the binding sites of a number of weaker binding Br-fragments provides further insight into the nature of these surface pockets. PMID:23998903

Structural Characterization of Polymer-Clay Nanocomposites Prepared by Co-Precipitation Using EPR Techniques

PubMed Central

Kielmann, Udo; Jeschke, Gunnar; García-Rubio, Inés

2014-01-01

Polymer-clay nanocomposites (PCNCs) containing either a rubber or an acrylate polymer were prepared by drying or co-precipitating polymer latex and nanolayered clay (synthetic and natural) suspensions. The interface between the polymer and the clay nanoparticles was studied by electron paramagnetic resonance (EPR) techniques by selectively addressing spin probes either to the surfactant layer (labeled stearic acid) or the clay surface (labeled catamine). Continuous-wave (CW) EPR studies of the surfactant dynamics allow to define a transition temperature T* which was tentatively assigned to the order-disorder transition of the surfactant layer. CW EPR studies of PCNC showed that completely exfoliated nanoparticles coexist with agglomerates. HYSCORE spectroscopy in PCNCs showed couplings within the probe −assigned with DFT computations− and couplings with nuclei of the environment, 1H and 23Na for the surfactant layer probe, and 29Si, 7Li, 19F and 23Na for the clay surface probe. Analysis of these couplings indicates that the integrity of the surfactant layer is conserved and that there are sizeable ionic regions containing sodium ions directly beyond the surfactant layer. Simulations of the very weak couplings demonstrated that the HYSCORE spectra are sensitive to the composition of the clay and whether or not clay platelets stack. PMID:28788520

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

PubMed Central

Munir, Ahsan; Waseem, Hassan; Williams, Maggie R.; Stedtfeld, Robert D.; Gulari, Erdogan; Tiedje, James M.; Hashsham, Syed A.

2017-01-01

Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131). PMID:28555058

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB.

PubMed

Munir, Ahsan; Waseem, Hassan; Williams, Maggie R; Stedtfeld, Robert D; Gulari, Erdogan; Tiedje, James M; Hashsham, Syed A

2017-05-29

Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R² = 0.8131).

The interaction of amino acids with macrocyclic pH probes of pseudopeptidic nature.

PubMed

Izquierdo, M Angeles; Wadhavane, Prashant D; Vigara, Laura; Burguete, M Isabel; Galindo, Francisco; Luis, Santiago V

2017-08-09

The fluorescence quenching, by a series of amino acids, of pseudopeptidic compounds acting as probes for cellular acidity has been investigated. It has been found that amino acids containing electron-rich aromatic side chains like Trp or Tyr, as well as Met quench the emission of the probes mainly via a collisional mechanism, with Stern-Volmer constants in the 7-43 M -1 range, while other amino acids such as His, Val or Phe did not cause deactivation of the fluorescence. Only a minor contribution of a static quenching due to the formation of ground-state complexes has been found for Trp and Tyr, with association constants in the 9-24 M -1 range. For these ground-state complexes, a comparison between the macrocyclic probes and an open chain analogue reveals the existence of a moderate macrocyclic effect due to the preorganization of the probes in the more rigid structure.

Site-specific incorporation of probes into RNA polymerase by unnatural-amino-acid mutagenesis and Staudinger-Bertozzi ligation

PubMed Central

Chakraborty, Anirban; Mazumder, Abhishek; Lin, Miaoxin; Hasemeyer, Adam; Xu, Qumiao; Wang, Dongye; Ebright, Yon W.; Ebright, Richard H.

2015-01-01

Summary A three-step procedure comprising (i) unnatural-amino-acid mutagenesis with 4-azido-phenylalanine, (ii) Staudinger-Bertozzi ligation with a probe-phosphine derivative, and (iii) in vitro reconstitution of RNA polymerase (RNAP) enables the efficient site-specific incorporation of a fluorescent probe, a spin label, a crosslinking agent, a cleaving agent, an affinity tag, or any other biochemical or biophysical probe, at any site of interest in RNAP. Straightforward extensions of the procedure enable the efficient site-specific incorporation of two or more different probes in two or more different subunits of RNAP. We present protocols for synthesis of probe-phosphine derivatives, preparation of RNAP subunits and the transcription initiation factor σ, unnatural amino acid mutagenesis of RNAP subunits and σ, Staudinger ligation with unnatural-amino-acid-containing RNAP subunits and σ, quantitation of labelling efficiency and labelling specificity, and reconstitution of RNAP. PMID:25665560

Facilitation of NADH Electrooxidation at Treated Carbon Nanotubes

PubMed Central

Wooten, Marilyn; Gorski, Waldemar

2010-01-01

The relationship between the state of the surface of carbon nanotubes (CNT) and their electrochemical activity was investigated using the enzyme cofactor dihydronicotinamide adenine dinucleotide (NADH) as a redox probe. The boiling of CNT in water, while nondestructive, activated them toward the oxidation of NADH as indicated by a shift in the anodic peak potential of NADH (ENADH) from 0.4 to 0.0 V. The shift in ENADH was due to the redox mediation of NADH oxidation by traces of quinone species that were formed on the surface of treated CNT. The harsher treatment that comprised of microwaving of CNT in concentrated nitric acid had a similar effect on the ENADH and, additionally, it increased the anodic peak current of NADH. The latter correlated with the formation of defects on the surface of acid-microwaved CNT as indicated by their Raman spectra. The increase in current was discussed considering a role of surface mediators on the buckled graphene sheets of acid-microwaved CNT. The other carbon allotropes including the edge plane pyrolytic graphite, graphite powder, and glassy carbon did not display a comparable activation toward the oxidation of NADH. PMID:20088562

Thermally induced anchoring of a zinc-carboxyphenylporphyrin on rutile TiO2 (110)

NASA Astrophysics Data System (ADS)

Jöhr, Res; Hinaut, Antoine; Pawlak, Rémy; Zajac, Łukasz; Olszowski, Piotr; Such, Bartosz; Glatzel, Thilo; Zhang, Jun; Muntwiler, Matthias; Bergkamp, Jesse J.; Mateo, Luis-Manuel; Decurtins, Silvio; Liu, Shi-Xia; Meyer, Ernst

2017-05-01

Functionalization of surfaces has become of high interest for a wealth of applications such as sensors, hybrid photovoltaics, catalysis, and molecular electronics. Thereby molecule-surface interactions are of crucial importance for the understanding of interface properties. An especially relevant point is the anchoring of molecules to surfaces. In this work, we analyze this process for a zinc-porphyrin equipped with carboxylic acid anchoring groups on rutile TiO2 (110) using scanning probe microscopy. After evaporation, the porphyrins are not covalently bound to the surface. Upon annealing, the carboxylic acid anchors undergo deprotonation and bind to surface titanium atoms. The formation of covalent bonds is evident from the changed stability of the molecule on the surface as well as the adsorption configuration. Annealed porphyrins are rotated by 45° and adopt another adsorption site. The influence of binding on electronic coupling with the surface is investigated using photoelectron spectroscopy. The observed shifts of Zn 2p and N 1s levels to higher binding energies indicate charging of the porphyrin core, which is accompanied by a deformation of the macrocycle due to a strong interaction with the surface.

Method for identifying and quantifying nucleic acid sequence aberrations

DOEpatents

Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

1998-01-01

A method for detecting nucleic acid sequence aberrations by detecting nucleic acid sequences having both a first and a second nucleic acid sequence type, the presence of the first and second sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. The method uses a first hybridization probe which includes a nucleic acid sequence that is complementary to a first sequence type and a first complexing agent capable of attaching to a second complexing agent and a second hybridization probe which includes a nucleic acid sequence that selectively hybridizes to the second nucleic acid sequence type over the first sequence type and includes a detectable marker for detecting the second hybridization probe.

Method for identifying and quantifying nucleic acid sequence aberrations

DOEpatents

Lucas, J.N.; Straume, T.; Bogen, K.T.

1998-07-21

A method is disclosed for detecting nucleic acid sequence aberrations by detecting nucleic acid sequences having both a first and a second nucleic acid sequence type, the presence of the first and second sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. The method uses a first hybridization probe which includes a nucleic acid sequence that is complementary to a first sequence type and a first complexing agent capable of attaching to a second complexing agent and a second hybridization probe which includes a nucleic acid sequence that selectively hybridizes to the second nucleic acid sequence type over the first sequence type and includes a detectable marker for detecting the second hybridization probe. 11 figs.

Synthesis and catalytic activity of polysaccharide templated nanocrystalline sulfated zirconia

NASA Astrophysics Data System (ADS)

Sherly, K. B.; Rakesh, K.

2014-01-01

Nanoscaled materials are of great interest due to their unique enhanced optical, electrical and magnetic properties. Sulfate-promoted zirconia has been shown to exhibit super acidic behavior and high activity for acid catalyzed reactions. Nanocrystalline zirconia was prepared in the presence of polysaccharide template by interaction between ZrOCl2ṡ8H2O and chitosan template. The interaction was carried out in aqueous phase, followed by the removal of templates by calcination at optimum temperature and sulfation. The structural and textural features were characterized by powder XRD, TG, SEM and TEM. XRD patterns showed the peaks of the diffractogram were in agreement with the theoretical data of zirconia with the catalytically active tetragonal phase and average crystalline size of the particles was found to be 9 nm, which was confirmed by TEM. TPD using ammonia as probe, FTIR and BET surface area analysis were used for analyzing surface features like acidity and porosity. The BET surface area analysis showed the sample had moderately high surface area. FTIR was used to find the type species attached to the surface of zirconia. UV-DRS found the band gap of the zirconia was found to be 2.8 eV. The benzylation of o-xylene was carried out batchwise in atmospheric pressure and 433K temperature using sulfated zirconia as catalyst.

PNA-PEG modified silicon platforms as functional bio-interfaces for applications in DNA microarrays and biosensors.

PubMed

Cattani-Scholz, Anna; Pedone, Daniel; Blobner, Florian; Abstreiter, Gerhard; Schwartz, Jeffrey; Tornow, Marc; Andruzzi, Luisa

2009-03-09

The synthesis and characterization of two types of silicon-based biofunctional interfaces are reported; each interface bonds a dense layer of poly(ethylene glycol) (PEG(n)) and peptide nucleic acid (PNA) probes. Phosphonate self-assembled monolayers were derivatized with PNA using a maleimido-terminated PEG(45). Similarly, siloxane monolayers were functionalized with PNA using a maleimido-terminated PEG(45) spacer and were subsequently modified with a shorter methoxy-terminated PEG(12) ("back-filling"). The long PEG(45) spacer was used to distance the PNA probe from the surface and to minimize undesirable nonspecific adsorption of DNA analyte. The short PEG(12) "back-filler" was used to provide additional passivation of the surface against nonspecific DNA adsorption. X-ray photoelectron spectroscopic (XPS) analysis near the C 1s and N 1s ionization edges was done to characterize chemical groups formed in the near-surface region, which confirmed binding of PEG and PNA to the phosphonate and silane films. XPS also indicated that additional PEG chains were tethered to the surface during the back-filling process. Fluorescence hybridization experiments were carried out with complementary and noncDNA strands; both phosphonate and siloxane biofunctional surfaces were effective for hybridization of cDNA strands and significantly reduced nonspecific adsorption of the analyte. Spatial patterns were prepared by polydimethylsiloxane (PDMS) micromolding on the PNA-functionalized surfaces; selective hybridization of fluorescently labeled DNA was shown at the PNA functionalized regions, and physisorption at the probe-less PEG-functionalized regions was dramatically reduced. These results show that PNA-PEG derivatized phosphonate monolayers hold promise for the smooth integration of device surface chemistry with semiconductor technology for the fabrication of DNA biosensors. In addition, our results confirm that PNA-PEG derivatized self-assembled carboxyalkylsiloxane films are promising substrates for DNA microarray applications.

Brønsted acid sites based on penta-coordinated aluminum species

NASA Astrophysics Data System (ADS)

Wang, Zichun; Jiang, Yijiao; Lafon, Olivier; Trébosc, Julien; Duk Kim, Kyung; Stampfl, Catherine; Baiker, Alfons; Amoureux, Jean-Paul; Huang, Jun

2016-12-01

Zeolites and amorphous silica-alumina (ASA), which both provide Brønsted acid sites (BASs), are the most extensively used solid acid catalysts in the chemical industry. It is widely believed that BASs consist only of tetra-coordinated aluminum sites (AlIV) with bridging OH groups in zeolites or nearby silanols on ASA surfaces. Here we report the direct observation in ASA of a new type of BAS based on penta-coordinated aluminum species (AlV) by 27Al-{1H} dipolar-mediated correlation two-dimensional NMR experiments at high magnetic field under magic-angle spinning. Both BAS-AlIV and -AlV show a similar acidity to protonate probe molecular ammonia. The quantitative evaluation of 1H and 27Al sites demonstrates that BAS-AlV co-exists with BAS-AlIV rather than replaces it, which opens new avenues for strongly enhancing the acidity of these popular solid acids.

Experimental study of the evanescent-wave photonic sensors response in presence of molecular beacon conformational changes.

PubMed

Ruiz-Tórtola, Ángela; Prats-Quílez, Francisco; Gónzalez-Lucas, Daniel; Bañuls, María-José; Maquieira, Ángel; Wheeler, Guy; Dalmay, Tamas; Griol, Amadeu; Hurtado, Juan; Bohlmann, Helge; Götzen, Reiner; García-Rupérez, Jaime

2018-04-17

An experimental study of the influence of the conformational change suffered by molecular beacon (MB) probes -upon the biorecognition of nucleic acid target oligonucleotides over evanescent wave photonic sensors- is reported. To this end, high sensitivity photonic sensors based on silicon photonic bandgap (PBG) structures were used, where the MB probes were immobilized via their 5' termination. Those MBs incorporate a biotin moiety close to their 3' termination in order to selectively bind a streptavidin molecule to them. The different photonic sensing responses obtained towards the target oligonucleotide detection, when the streptavidin molecule was bound to the MB probes or not, demonstrate the conformational change suffered by the MB upon hybridization, which promotes the displacement of the streptavidin molecule away from the surface of the photonic sensing structure. Schematic diagram of the PBG sensing structure on which the streptavidin-labeled MB probes were immobilized. This article is protected by copyright. All rights reserved.

Studies of Heterogenous Palladium and Related Catalysts for Aerobic Oxidation of Primary Alcohols

NASA Astrophysics Data System (ADS)

Ahmed, Maaz S.

Development of aerobic oxidation methods is of critical importance for the advancement of green chemistry, where the only byproduct produced is water. Recent work by our lab has produced an efficient Pd based heterogenous catalyst capable of preforming the aerobic oxidation of a wide spectrum of alcohols to either carboxylic acid or methyl ester. The well-defined catalyst PdBi 0.35Te0.23/C (PBT/C) catalyst has been shown to can perform the aerobic oxidation of alcohols to carboxylic acids in basic conditions. Additionally, we explored this catalyst for a wide range of alcohols and probed the nature of the selectivity of PBT/C for methyl esterification over other side products. Finally, means by which the catalyst operates with respect to oxidation states of the three components, Pd, Bi, and Te, was probed. Carboxylic acids are an important functional group due to their prevalence in various pharmaceutically active agents, agrochemicals, and commodity scale chemicals. The well-defined catalyst PBT/C catalyst was discovered to be effective for the oxidation of a wide spectrum of alcohols to carboxylic acid. The demonstrated substrate scope and functional group tolerance are the widest reported for an aerobic heterogeneous catalyst. Additionally, the catalyst has been implemented in a packed bed reactor with quantitative yield of benzoic acid maintained throughout a two-day run. Biomass derived 5-(hydroxymethyl)furfural (HMF) is also oxidized to 2,5-furandicarboxylic acid (FDCA) in high yield. Exploration of PBT/C for the oxidative methyl esterification was found to exhibit exquisite selectivity for the initial oxidation of primary alcohol instead of methanol, which is the bulk solvent. We explored this selectivity and conclude that it results from various substrate-surface interactions, which are not attainable by methanol. The primary alcohol can outcompete the methanol for binding on the catalyst surface through various interactions between the side chain of the alcohol solvent and the surface of the catalyst: (listed in order of strength) lone pair-surface (heterocyclic primary alcohols) > pi-surface (aryl primary alcohols) > van der Waals-surface (alkyl primary alcohols). These interactions were previously underappreciated in condensed phase heterogeneously catalyzed aerobic oxidations. Bi and Te serve as synergistic promoters that enhance both the rate and yield of the reactions relative to reactions employing Pd alone or Pd in combination with Bi or with Te as the sole promoter. We report X-ray absorption spectroscopic studies of the heterogenous catalyst. These methods show that the promoters undergo oxidation in preference to Pd, maintaining the Pd surface in the active metallic state and preventing inhibition by surface Pd-oxide formation. The data also suggest formation of a Pd-Te alloy phase that modifies the electronic properties of the Pd catalyst. Collectively, these results provide valuable insights into the synergistic benefits of multiple promoters in heterogeneous catalytic oxidation reactions.

3D hierarchical Ag nanostructures formed on poly(acrylic acid) brushes grafted graphene oxide as promising SERS substrates

NASA Astrophysics Data System (ADS)

Xing, Guoke; Wang, Ke; Li, Ping; Wang, Wenqin; Chen, Tao

2018-03-01

In this study, in situ generation of Ag nanostructures with various morphology on poly(acrylic acid) (PAA) brushes grafted onto graphene oxide (GO), for use as substrates for surface-enhanced Raman scattering (SERS), is demonstrated. The overall synthetic strategy involves the loading of Ag precursor ions ((Ag+ and [Ag(NH3)2]+) onto PAA brush-grafted GO, followed by their in situ reduction to Ag nanostructures of various morphology using a reducing agent (NaBH4 or ascorbic acid). Novel 3D hierarchical flowerlike Ag nanostructures were obtained by using AgNO3 as precursor and ascorbic acid as reducing agent. Using 4-aminothiophenol as probe molecules, the as-prepared hierarchical Ag nanostructures exhibited excellent SERS performance, providing enhancement factors of ˜107.

Morpholine Derivative-Functionalized Carbon Dots-Based Fluorescent Probe for Highly Selective Lysosomal Imaging in Living Cells.

PubMed

Wu, Luling; Li, Xiaolin; Ling, Yifei; Huang, Chusen; Jia, Nengqin

2017-08-30

The development of a suitable fluorescent probe for the specific labeling and imaging of lysosomes through the direct visual fluorescent signal is extremely important for understanding the dysfunction of lysosomes, which might induce various pathologies, including neurodegenerative diseases, cancer, and Alzheimer's disease. Herein, a new carbon dot-based fluorescent probe (CDs-PEI-ML) was designed and synthesized for highly selective imaging of lysosomes in live cells. In this probe, PEI (polyethylenimine) is introduced to improve water solubility and provide abundant amine groups for the as-prepared CDs-PEI, and the morpholine group (ML) serves as a targeting unit for lysosomes. More importantly, passivation with PEI could dramatically increase the fluorescence quantum yield of CDs-PEI-ML as well as their stability in fluorescence emission under different excitation wavelength. Consequently, experimental data demonstrated that the target probe CDs-PEI-ML has low cytotoxicity and excellent photostability. Additionally, further live cell imaging experiment indicated that CDs-PEI-ML is a highly selective fluorescent probe for lysosomes. We speculate the mechanism for selective staining of lysosomes that CDs-PEI-ML was initially taken up by lysosomes through the endocytic pathway and then accumulated in acidic lysosomes. It is notable that there was less diffusion of CDs-PEI-ML into cytoplasm, which could be ascribed to the presence of lysosome target group morpholine on surface of CDs-PEI-ML. The blue emission wavelength combined with the high photo stability and ability of long-lasting cell imaging makes CDs-PEI-ML become an alternative fluorescent probe for multicolor labeling and long-term tracking of lysosomes in live cells and the potential application in super-resolution imaging. To best of our knowledge, there are still limited carbon dots-based fluorescent probes that have been studied for specific lysosomal imaging in live cells. The concept of surface functionality of carbon dots will also pave a new avenue for developing carbon dots-based fluorescent probes for subcellular labeling.

Aspheric surface measurement using capacitive probes

NASA Astrophysics Data System (ADS)

Tao, Xin; Yuan, Daocheng; Li, Shaobo

2017-02-01

With the application of aspheres in optical fields, high precision and high efficiency aspheric surface metrology becomes a hot research topic. We describe a novel method of non-contact measurement of aspheric surface with capacitive probe. Taking an eccentric spherical surface as the object of study, the averaging effect of capacitive probe measurement and the influence of tilting the capacitive probe on the measurement results are investigated. By comparing measurement results from simultaneous measurement of the capacitive probe and contact probe of roundness instrument, this paper indicates the feasibility of using capacitive probes to test aspheric surface and proposes the compensation method of measurement error caused by averaging effect and the tilting of the capacitive probe.

The Role of Structural Enthalpy in Spherical Nucleic Acid Hybridization.

PubMed

Fong, Lam-Kiu; Wang, Ziwei; Schatz, George C; Luijten, Erik; Mirkin, Chad A

2018-05-23

DNA hybridization onto DNA-functionalized nanoparticle surfaces (e.g., in the form of a spherical nucleic acid (SNA)) is known to be enhanced relative to hybridization free in solution. Surprisingly, via isothermal titration calorimetry, we reveal that this enhancement is enthalpically, as opposed to entropically, dominated by ∼20 kcal/mol. Coarse-grained molecular dynamics simulations suggest that the observed enthalpic enhancement results from structurally confining the DNA on the nanoparticle surface and preventing it from adopting enthalpically unfavorable conformations like those observed in the solution case. The idea that structural confinement leads to the formation of energetically more stable duplexes is evaluated by decreasing the degree of confinement a duplex experiences on the nanoparticle surface. Both experiment and simulation confirm that when the surface-bound duplex is less confined, i.e., at lower DNA surface density or at greater distance from the nanoparticle surface, its enthalpy of formation approaches the less favorable enthalpy of duplex formation for the linear strand in solution. This work provides insight into one of the most important and enabling properties of SNAs and will inform the design of materials that rely on the thermodynamics of hybridization onto DNA-functionalized surfaces, including diagnostic probes and therapeutic agents.

Molecular basis of crystal morphology-dependent adhesion behavior of mefenamic acid during tableting.

PubMed

Waknis, Vrushali; Chu, Elza; Schlam, Roxana; Sidorenko, Alexander; Badawy, Sherif; Yin, Shawn; Narang, Ajit S

2014-01-01

The molecular basis of crystal surface adhesion leading to sticking was investigated by exploring the correlation of crystal adhesion to oxidized iron coated atomic force microscope (AFM) tips and bulk powder sticking behavior during tableting of two morphologically different crystals of a model drug, mefenamic acid (MA), to differences in their surface functional group orientation and energy. MA was recrystallized into two morphologies (plates and needles) of the same crystalline form. Crystal adhesion to oxidized iron coated AFM tips and bulk powder sticking to tablet punches was assessed using a direct compression formulation. Surface functional group orientation and energies on crystal faces were modeled using Accelrys Material Studio software. Needle-shaped morphology showed higher sticking tendency than plates despite similar particle size. This correlated with higher crystal surface adhesion of needle-shaped morphology to oxidized iron coated AFM probe tips, and greater surface energy and exposure of polar functional groups. Higher surface exposure of polar functional groups correlates with higher tendency to stick to metal surfaces and AFM tips, indicating involvement of specific polar interactions in the adhesion behavior. In addition, an AFM method is identified to prospectively assess the risk of sticking during the early stages of drug development.

A Phagostimulant Blend for the Asian Citrus Psyllid.

PubMed

Lapointe, Stephen L; Hall, David G; George, Justin

2016-09-01

Chemical cues that elicit orientation by the Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae), are of interest because it is the primary vector of the causal pathogen of citrus greening disease. Non-pesticidal control methods for D. citri remain a high priority for the citrus industry. While searching for semiochemicals that may be involved in orientation to host plants, we previously identified a blend of formic and acetic acids that stimulated substrate probing by D. citri. Here, we applied geometric mixture designs and response surface modeling to identify and optimize a 3-component blend that further increased the number of salivary sheaths produced by D. citri on a wax substrate containing a 3.5:1.6:1 blend of formic acid, acetic acid, and p-cymene, respectively. No evidence was found for remote orientation by D. citri adults through olfaction to the phagostimulant blends. Increased probing in response to the presence of phagostimulants in the wax matrix occurred after contact with the substrate. Yellow wax beads always attracted more D. citri adults and received more probes compared with white wax beads. Yellow beads containing the 3-component blend of phagostimulants were probed by D. citri 2 to 3 times more often compared with yellow beads alone. The phagostimulant effect also was tested by covering wax beads containing the 3-component blend with a plastic film to minimize olfaction or contact chemoreception by antennation. The plastic film did not affect the probing response, thus suggesting that chemosensation was associated with mouthparts and not olfactory receptors. Salivary sheaths produced in wax beads containing the phagostimulant blend were 4.5 times longer than sheaths produced in beads without tastants. This phenomenon might be used to improve a trap, design an attract-and-kill product, or enhance other means of managing D. citri and citrus greening disease.

Nucleic acid probes in diagnostic medicine

NASA Technical Reports Server (NTRS)

Oberry, Phillip A.

1991-01-01

The need for improved diagnostic procedures is outlined and variations in probe technology are briefly reviewed. A discussion of the application of probe technology to the diagnosis of disease in animals and humans is presented. A comparison of probe versus nonprobe diagnostics and isotopic versus nonisotopic probes is made and the current state of sequence amplification is described. The current market status of nucleic acid probes is reviewed with respect to their diagnostic application in human and veterinary medicine. Representative product examples are described and information on probes being developed that offer promise as future products is discussed.

Exceptionally crystalline and conducting acid doped polyaniline films by level surface assisted solution casting approach

NASA Astrophysics Data System (ADS)

Puthirath, Anand B.; Methattel Raman, Shijeesh; Varma, Sreekanth J.; Jayalekshmi, S.

2016-04-01

Emeraldine salt form of polyaniline (PANI) was synthesized by chemical oxidative polymerisation method using ammonium persulfate as oxidant. Resultant emeraldine salt form of PANI was dedoped using ammonia solution and then re-doped with camphor sulphonic acid (CSA), naphthaline sulphonic acid (NSA), hydrochloric acid (HCl), and m-cresol. Thin films of these doped PANI samples were deposited on glass substrates using solution casting method with m-cresol as solvent. A level surface was employed to get homogeneous thin films of uniform thickness. Detailed X-ray diffraction studies have shown that the films are exceptionally crystalline. The crystalline peaks observed in the XRD spectra can be indexed to simple monoclinic structure. FTIR and Raman spectroscopy studies provide convincing explanation for the exceptional crystallinity observed in these polymer films. FESEM and AFM images give better details of surface morphology of doped PANI films. The DC electrical conductivity of the samples was measured using four point probe technique. It is seen that the samples also exhibit quite high DC electrical conductivity, about 287 S/cm for CSA doped PANI, 67 S/cm for NSA doped PANI 65 S/cm for HCl doped PANI, and just below 1 S/cm for m-cresol doped PANI. Effect of using the level surface for solution casting is studied and correlated with the observed crystallinity.

Exceptionally crystalline and conducting acid doped polyaniline films by level surface assisted solution casting approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Puthirath, Anand B.; Varma, Sreekanth J.; Jayalekshmi, S., E-mail: jayalekshmi@cusat.ac.in

2016-04-18

Emeraldine salt form of polyaniline (PANI) was synthesized by chemical oxidative polymerisation method using ammonium persulfate as oxidant. Resultant emeraldine salt form of PANI was dedoped using ammonia solution and then re-doped with camphor sulphonic acid (CSA), naphthaline sulphonic acid (NSA), hydrochloric acid (HCl), and m-cresol. Thin films of these doped PANI samples were deposited on glass substrates using solution casting method with m-cresol as solvent. A level surface was employed to get homogeneous thin films of uniform thickness. Detailed X-ray diffraction studies have shown that the films are exceptionally crystalline. The crystalline peaks observed in the XRD spectra canmore » be indexed to simple monoclinic structure. FTIR and Raman spectroscopy studies provide convincing explanation for the exceptional crystallinity observed in these polymer films. FESEM and AFM images give better details of surface morphology of doped PANI films. The DC electrical conductivity of the samples was measured using four point probe technique. It is seen that the samples also exhibit quite high DC electrical conductivity, about 287 S/cm for CSA doped PANI, 67 S/cm for NSA doped PANI 65 S/cm for HCl doped PANI, and just below 1 S/cm for m-cresol doped PANI. Effect of using the level surface for solution casting is studied and correlated with the observed crystallinity.« less

Rapid amplification/detection of nucleic acid targets utilizing a HDA/thin film biosensor.

PubMed

Jenison, Robert; Jaeckel, Heidi; Klonoski, Joshua; Latorra, David; Wiens, Jacinta

2014-08-07

Thin film biosensors exploit a flat, optically coated silicon-based surface whereupon formation of nucleic acid hybrids are enzymatically transduced in a molecular thin film that can be detected by the unaided human eye under white light. While the limit of sensitivity for detection of nucleic acid targets is at sub-attomole levels (60 000 copies) many clinical specimens containing bacterial pathogens have much lower levels of analyte present. Herein, we describe a platform, termed HDA/thin film biosensor, which performs helicase-dependant nucleic acid amplification on a thin film biosensor surface to improve the limit of sensitivity to 10 copies of the mecA gene present in methicillin-resistant strains of Staphylococcus. As double-stranded DNA is unwound by helicase it was either bound by solution-phase DNA primers to be copied by DNA polymerase or hybridized to surface immobilized probe on the thin film biosensor surface to be detected. Herein, we show that amplification reactions on the thin film biosensor are equivalent to in standard thin wall tubes, with detection at the limit of sensitivity of the assay occurring after 30 minutes of incubation time. Further we validate the approach by detecting the presence of the mecA gene in methicillin-resistant Staphylococcus aureus (MRSA) from positive blood culture aliquots with high specificity (signal/noise ratio of 105).

Probing hydrogen and halogen-oxo interactions in uranyl coordination polymers: a combined crystallographic and computational study

DOE PAGES

Carter, Korey P.; Kalaj, Mark; Kerridge, Andrew; ...

2018-01-01

Four uranyl compounds containing either benzoic acid ( 1 ), m -chlorobenzoic acid ( 2 ), m -bromobenzoic acid ( 3 ), or m -iodobenzoic acid ( 4 ) are described, and the latter two compounds are used to probe non-covalent interaction strengths via structural, vibrational, and computational means.

Visualization of nucleic acids with synthetic exciton-controlled fluorescent oligonucleotide probes.

PubMed

Wang, Dan Ohtan; Okamoto, Akimitsu

2015-01-01

Engineered probes to adapt new photochemical properties upon recognition of target nucleic acids offer powerful tools to DNA and RNA visualization technologies. Herein, we describe a rapid and effective visualization method of nucleic acids in both fixed and living cells with hybridization-sensitive fluorescent oligonucleotide probes. These probes are efficiently quenched in an aqueous environment due to the homodimeric, excitonic interactions between fluorophores but become highly fluorescent upon hybridization to DNA or RNA with complementary sequences. The fast hybridization kinetics and quick fluorescence activation of the new probes allow applications to simplify the conventional fluorescent in situ hybridization protocols and reduce the amount of time to process the samples. Furthermore, hybridization-sensitive fluorescence emission of the probes allows monitoring dynamic behaviors of RNA in living cells.

Perceiving the vertical distances of surfaces by means of a hand-held probe.

PubMed

Chan, T C; Turvey, M T

1991-05-01

Nine experiments were conducted on the haptic capacity of people to perceive the distances of horizontal surfaces solely on the basis of mechanical stimulation resulting from contacting the surfaces with a vertically held rod. Participants touched target surfaces with rods inside a wooden cabinet and reported the perceived surface location with an indicator outside the cabinet. The target surface, rod, and the participant's hand were occluded, and the sound produced in exploration was muffled. Properties of the probe (length, mass, moment of inertia, center of mass, and shape) were manipulated, along with surface distance and the method and angle of probing. Results suggest that for the most common method of probing, namely, tapping, perceived vertical distance is specific to a particular relation among the rotational inertia of the probe, the distance of the point of contact with the surface from the probe's center of percussion, and the inclination at contact of the probe to the surface. They also suggest that the probe length and the distance probed are independently perceivable. The results were discussed in terms of information specificity versus percept-percept coupling and parallels between selective attention in haptic and visual perception.

An ultrasensitive universal detector based on neutralizer displacement

NASA Astrophysics Data System (ADS)

Das, Jagotamoy; Cederquist, Kristin B.; Zaragoza, Alexandre A.; Lee, Paul E.; Sargent, Edward H.; Kelley, Shana O.

2012-08-01

Diagnostic technologies that can provide the simultaneous detection of nucleic acids for gene expression, proteins for host response and small molecules for profiling the human metabolome will have a significant advantage in providing comprehensive patient monitoring. Molecular sensors that report changes in the electrostatics of a sensor's surface on analyte binding have shown unprecedented sensitivity in the detection of charged biomolecules, but do not lend themselves to the detection of small molecules, which do not carry significant charge. Here, we introduce the neutralizer displacement assay that allows charge-based sensing to be applied to any class of molecule irrespective of the analyte charge. The neutralizer displacement assay starts with an aptamer probe bound to a neutralizer. When analyte binding occurs the neutralizer is displaced, which results in a dramatic change in the surface charge for all types of analytes. We have tested the sensitivity, speed and specificity of this system in the detection of a panel of molecules: (deoxy)ribonucleic acid, ribonucleic acid, cocaine, adenosine triphosphate and thrombin.

A Mesopore-Dependent Catalytic Cracking of n-Hexane Over Mesoporous Nanostructured ZSM-5.

PubMed

Qamar, M; Ahmed, M I; Qamaruddin, M; Asif, M; Sanhoob, M; Muraza, O; Khan, M Y

2018-08-01

Herein, pore size, crystalinity, and Si/Al ratio of mesoporous ZSM-5 (MFI) nanocrystals was controlled by synthesis parameters, such as surfactant concentration ([3-(trimethoxysilyl)propyl] hexa-decyl dimethyl ammonium chloride), sodium hydroxide concentrations, synthesis temperature and time. The morphology, surface structure and composition of the MFI particles was systematically investigated. More notably, the mesopore-dependent catalytic activity of ZSM-5 was evaluated by studying the cracking of n-hexane. The findings suggest the porosity has pronounced impact on the catalytic activity, selectivity and stability of ZSM-5 nanocrystals. Critical surface attributes such as nature of acid sites (Brønsted and Lewis), concentration, and strength are obtained by the infrared study of adsorbed probe molecules (pyridine) and the temperature programmed desorption. In spite of being weaker in Si/Al ratio or acidic strength, mesoporous catalysts showed more stable and efficient cracking of n-hexane suggesting that acidity seems not the predominant factor operative in the activity, selectivity and stability.

Nanometer-scale water- and proton-diffusion heterogeneities across water channels in polymer electrolyte membranes.

PubMed

Song, Jinsuk; Han, Oc Hee; Han, Songi

2015-03-16

Nafion, the most widely used polymer for electrolyte membranes (PEMs) in fuel cells, consists of a fluorocarbon backbone and acidic groups that, upon hydration, swell to form percolated channels through which water and ions diffuse. Although the effects of the channel structures and the acidic groups on water/ion transport have been studied before, the surface chemistry or the spatially heterogeneous diffusivity across water channels has never been shown to directly influence water/ion transport. By the use of molecular spin probes that are selectively partitioned into heterogeneous regions of the PEM and Overhauser dynamic nuclear polarization relaxometry, this study reveals that both water and proton diffusivity are significantly faster near the fluorocarbon and the acidic groups lining the water channels than within the water channels. The concept that surface chemistry at the (sub)nanometer scale dictates water and proton diffusivity invokes a new design principle for PEMs. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spin label studies of micellar and pre-micellar aggregates.

PubMed

Ernades, J R; Schreier, S; Chaimovich, H

1976-02-01

Micelles of hexadecyl trimethyl ammonium bromide (CTABr) have been investigated with the use of a faty acid spin label and its methyl ester derivative. The esr * spectra provided information about the degree of motion of the probes in the micelles as evaluated from calculation of rotational correlation times. Evidence is presented for the formation of pre-micellar aggregates at concentrations below the cmc. The effect of addition of thiophenoxide on the structure of CTABr micelles was to decrease the rate of motion of the spin probes, probably due to a tighter packing of the hydrophobic core as a consequence of charge neutralization at the micelle surface by the substrate. Decreasing values of the isotropic hyperfine splitting of the spin probe with increasing concentration of thiophenoxide were taken as indicating that the latter causes a decrease of the degree of hydration of the polar head region of the detergent.

Folate receptor targeting silica nanoparticle probe for two-photon fluorescence bioimaging

PubMed Central

Wang, Xuhua; Yao, Sheng; Ahn, Hyo-Yang; Zhang, Yuanwei; Bondar, Mykhailo V.; Torres, Joseph A.; Belfield, Kevin D.

2010-01-01

Narrow dispersity organically modified silica nanoparticles (SiNPs), diameter ~30 nm, entrapping a hydrophobic two-photon absorbing fluorenyl dye, were synthesized by hydrolysis of triethoxyvinylsilane and (3-aminopropyl)triethoxysilane in the nonpolar core of Aerosol-OT micelles. The surface of the SiNPs were functionalized with folic acid, to specifically deliver the probe to folate receptor (FR) over-expressing Hela cells, making these folate two-photon dye-doped SiNPs potential candidates as probes for two-photon fluorescence microscopy (2PFM) bioimaging. In vitro studies using FR over-expressing Hela cells and low FR expressing MG63 cells demonstrated specific cellular uptake of the functionalized nanoparticles. One-photon fluorescence microscopy (1PFM) imaging, 2PFM imaging, and two-photon fluorescence lifetime microscopy (2P-FLIM) imaging of Hela cells incubated with folate-modified two-photon dye-doped SiNPs were demonstrated. PMID:21258480

Surface acidity and solid-state compatibility of excipients with an acid-sensitive API: case study of atorvastatin calcium.

PubMed

Govindarajan, Ramprakash; Landis, Margaret; Hancock, Bruno; Gatlin, Larry A; Suryanarayanan, Raj; Shalaev, Evgenyi Y

2015-04-01

The objectives of this study were to measure the apparent surface acidity of common excipients and to correlate the acidity with the chemical stability of an acid-sensitive active pharmaceutical ingredient (API) in binary API-excipient powder mixtures. The acidity of 26 solid excipients was determined by two methods, (i) by measuring the pH of their suspensions or solutions and (ii) the pH equivalent (pHeq) measured via ionization of probe molecules deposited on the surface of the excipients. The chemical stability of an API, atorvastatin calcium (AC), in mixtures with the excipients was evaluated by monitoring the appearance of an acid-induced degradant, atorvastatin lactone, under accelerated storage conditions. The extent of lactone formation in AC-excipient mixtures was presented as a function of either solution/suspension pH or pHeq. No lactone formation was observed in mixtures with excipients having pHeq > 6, while the lactone levels were pronounced (> 0.6% after 6 weeks at 50°C/20% RH) with excipients exhibiting pHeq < 3. The three pHeq regions (> 6, 3-6, and < 3) were consistent with the reported solution pH-stability profile of AC. In contrast to the pHeq scale, lactone formation did not show any clear trend when plotted as a function of the suspension/solution pH. Two mechanisms to explain the discrepancy between the suspension/solution pH and the chemical stability data were discussed. Acidic excipients, which are expected to be incompatible with an acid-sensitive API, were identified based on pHeq measurements. The incompatibility prediction was confirmed in the chemical stability tests using AC as an example of an acid-sensitive API.

Fluorescence lifetime imaging with time-gated detection of hyaluronidase using a long lifetime azadioxatriangulenium (ADOTA) fluorophore

NASA Astrophysics Data System (ADS)

Chib, Rahul; Requena, Sebastian; Mummert, Mark; Strzhemechny, Yuri M.; Gryczynski, Ignacy; Borejdo, Julian; Gryczynski, Zygmunt; Fudala, Rafal

2016-12-01

A fluorescence lifetime imaging probe with a long lifetime was used in combination with time-gating for the detection of hyaluronidase using hyaluronic acid as the probe template. This probe was developed by heavily labeling hyaluronic acid with long lifetime azadioxatriangulenium fluorophores (ADOTA). We used this probe to image hyaluronidase produced by DU-145 prostate cancer cells.

Implications of contamination and surface area ratios for Langmuir probe diagnostics on CubeSats

NASA Astrophysics Data System (ADS)

Suresh, P.; Swenson, C.

2009-12-01

Theories describing the current collected by a biased probe under various conditions are necessary for such observation to be used to accurately determine plasma properties. Langmuir probes are routinely used on spacecraft to measure plasma parameters such as density, temperature, and vehicle charging. The collected current is a function of the potential between the surrounding plasma and probe surface. There have been both observations of and concepts for unaccounted variations of this potential which limit the application of Langmuir probe theory for determining plasma properties. These variations occur due to spatial variations of the work function across the probe surface due to non-uniformity of the crystalline surface properties and surface contamination of the probe. Currently we do not have theoretical expressions which consider these factors as first principles in their derivation. In the event of these surface potential variations, the analysis of the plasma using the currently available theories of the Langmuir probe yield erroneous results. We present a theory which models the current as a function of the surface potential variations. Another consideration for Langmuir probes on CubeSats is the ratio of the probe area to the return current collection area. If the area ratio is unfavorable this can also lead to erroneous results in the interpretation of observations. A mathematical formulation of the current collected by the probe for contaminated surfaces is presented and compared with data from a Langmuir probe flown on a sounding rocket mission. The implications of using Langmuir probes on CubeSats given the engineering limitations of probe cleanliness and area ratios are reviewed.

Surface-induced effects in fluctuation-based measurements of single-polymer elasticity: A direct probe of the radius of gyration

NASA Astrophysics Data System (ADS)

Innes-Gold, Sarah N.; Morgan, Ian L.; Saleh, Omar A.

2018-03-01

Single-molecule measurements of polymer elasticity are powerful, direct probes of both biomolecular structure and principles of polymer physics. Recent work has revealed low-force regimes in which biopolymer elasticity is understood through blob-based scaling models. However, the small tensions required to observe these regimes have the potential to create measurement biases, particularly due to the increased interactions of the polymer chain with tethering surfaces. Here, we examine one experimentally observed bias, in which fluctuation-based estimates of elasticity report an unexpectedly low chain compliance. We show that the effect is in good agreement with predictions based on quantifying the exclusion effect of the surface through an image-method calculation of available polymer configurations. The analysis indicates that the effect occurs at an external tension inversely proportional to the polymer's zero-tension radius of gyration. We exploit this to demonstrate a self-consistent scheme for estimating the radius of gyration of the tethered polymer. This is shown in measurements of both hyaluronic acid and poly(ethylene glycol) chains.

Mechanistic Study of the Validity of Using Hydroxyl Radical Probes To Characterize Electrochemical Advanced Oxidation Processes.

PubMed

Jing, Yin; Chaplin, Brian P

2017-02-21

The detection of hydroxyl radicals (OH • ) is typically accomplished by using reactive probe molecules, but prior studies have not thoroughly investigated the suitability of these probes for use in electrochemical advanced oxidation processes (EAOPs), due to the neglect of alternative reaction mechanisms. In this study, we investigated the suitability of four OH • probes (coumarin, p-chlorobenzoic acid, terephthalic acid, and p-benzoquinone) for use in EAOPs. Experimental results indicated that both coumarin and p-chlorobenzoic acid are oxidized via direct electron transfer reactions, while p-benzoquinone and terephthalic acid are not. Coumarin oxidation to form the OH • adduct product 7-hydroxycoumarin was found at anodic potentials lower than that necessary for OH • formation. Density functional theory (DFT) simulations found a thermodynamically favorable and non-OH • mediated pathway for 7-hydroxycoumarin formation, which is activationless at anodic potentials > 2.10 V/SHE. DFT simulations also provided estimates of E° values for a series of OH • probe compounds, which agreed with voltammetry results. Results from this study indicated that terephthalic acid is the most appropriate OH • probe compound for the characterization of electrochemical and catalytic systems.

Methods of staining target chromosomal DNA employing high complexity nucleic acid probes

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Ol'li-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

2006-10-03

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Evanescent wave cavity ring-down spectroscopy (EW-CRDS) as a probe of macromolecule adsorption kinetics at functionalized interfaces.

PubMed

O'Connell, Michael A; de Cuendias, Anne; Gayet, Florence; Shirley, Ian M; Mackenzie, Stuart R; Haddleton, David M; Unwin, Patrick R

2012-05-01

Evanescent wave cavity ring-down spectroscopy (EW-CRDS) has been employed to study the interfacial adsorption kinetics of coumarin-tagged macromolecules onto a range of functionalized planar surfaces. Such studies are valuable in designing polymers for complex systems where the degree of interaction between the polymer and surface needs to be tailored. Three tagged synthetic polymers with different functionalities are examined: poly(acrylic acid) (PAA), poly(3-sulfopropyl methacrylate, potassium salt) (PSPMA), and a mannose-modified glycopolymer. Adsorption transients at the silica/water interface are found to be characteristic for each polymer, and kinetics are deduced from the initial rates. The chemistry of the adsorption interfaces has been varied by, first, manipulation of silica surface chemistry via the bulk pH, followed by surfaces modified by poly(L-glutamic acid) (PGA) and cellulose, giving five chemically different surfaces. Complementary atomic force microscopy (AFM) imaging has been used for additional surface characterization of adsorbed layers and functionalized interfaces to allow adsorption rates to be interpreted more fully. Adsorption rates for PSPMA and the glycopolymer are seen to be highly surface sensitive, with significantly higher rates on cellulose-modified surfaces, whereas PAA shows a much smaller rate dependence on the nature of the adsorption surface.

Anionic magnetite nanoparticle conjugated with pyrrolidinyl peptide nucleic acid for DNA base discrimination

NASA Astrophysics Data System (ADS)

Khadsai, Sudarat; Rutnakornpituk, Boonjira; Vilaivan, Tirayut; Nakkuntod, Maliwan; Rutnakornpituk, Metha

2016-09-01

Magnetite nanoparticles (MNPs) were surface modified with anionic poly( N-acryloyl glycine) (PNAG) and streptavidin for specific interaction with biotin-conjugated pyrrolidinyl peptide nucleic acid (PNA). Hydrodynamic size ( D h) of PNAG-grafted MNPs varied from 334 to 496 nm depending on the loading ratio of the MNP to NAG in the reaction. UV-visible and fluorescence spectrophotometries were used to confirm the successful immobilization of streptavidin and PNA on the MNPs. About 291 pmol of the PNA/mg MNP was immobilized on the particle surface. The PNA-functionalized MNPs were effectively used as solid supports to differentiate between fully complementary and non-complementary/single-base mismatch DNA using the PNA probe. These novel anionic MNPs can be efficiently applicable for use as a magnetically guidable support for DNA base discrimination.

Method for nucleic acid hybridization using single-stranded DNA binding protein

DOEpatents

Tabor, Stanley; Richardson, Charles C.

1996-01-01

Method of nucleic acid hybridization for detecting the presence of a specific nucleic acid sequence in a population of different nucleic acid sequences using a nucleic acid probe. The nucleic acid probe hybridizes with the specific nucleic acid sequence but not with other nucleic acid sequences in the population. The method includes contacting a sample (potentially including the nucleic acid sequence) with the nucleic acid probe under hybridizing conditions in the presence of a single-stranded DNA binding protein provided in an amount which stimulates renaturation of a dilute solution (i.e., one in which the t.sub.1/2 of renaturation is longer than 3 weeks) of single-stranded DNA greater than 500 fold (i.e., to a t.sub.1/2 less than 60 min, preferably less than 5 min, and most preferably about 1 min.) in the absence of nucleotide triphosphates.

UHV AFM based colloidal probe studies of adhesive properties of VAlN hard coatings

NASA Astrophysics Data System (ADS)

Wiesing, M.; de los Arcos, T.; Grundmeier, G.

2018-01-01

The adhesion of polystyrene (PS) on V0.27Al0.29N0.44 and the related influence of the oxidation states of both surfaces was investigated using X-Ray Photoelectron Spectroscopy (XPS) and Colloidal Force Spectroscopy (CFS) in Ultra-High Vacuum (UHV). Complementary, the intimate relation between the adhesion force, the chemical structure and surface polarizability was investigated by XPS valence band spectroscopy and the calculation of non-retarded Hamaker coefficients using Lifshitz theory based on optical data as derived from Reflection Electron Energy Loss Spectroscopy (REELS) spectra. The combined electron and force spectroscopic analysis of the interaction forces disclosed quantitatively the separation of the adhesion force in van der Waals and Lewis acid-base contributions. Further, the surface polarizability of VAlN was shown to be unaffected by oxygen incorporation due to the formation of an only gradually oxidized surface comprising a range of vanadium oxidation states. In contrast, the adhesion force analysis revealed additional Lewis acid-base interactions between the oxidized and non-oxidized VAlN surfaces and carboxyl groups present in the surface of PS after an oxidative oxygen beam treatment.

The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization

PubMed Central

2013-01-01

Background Hybridization based assays and capture systems depend on the specificity of hybridization between a probe and its intended target. A common guideline in the construction of DNA microarrays, for instance, is that avoiding complementary stretches of more than 15 nucleic acids in a 50 or 60-mer probe will eliminate sequence specific cross-hybridization reactions. Here we present a study of the behavior of partially matched oligonucleotide pairs with complementary stretches starting well below this threshold complementarity length – in silico, in solution, and at the microarray surface. The modeled behavior of pairs of oligonucleotide probes and their targets suggests that even a complementary stretch of sequence 12 nt in length would give rise to specific cross-hybridization. We designed a set of binding partners to a 50-mer oligonucleotide containing complementary stretches from 6 nt to 21 nt in length. Results Solution melting experiments demonstrate that stable partial duplexes can form when only 12 bp of complementary sequence are present; surface hybridization experiments confirm that a signal close in magnitude to full-strength signal can be obtained from hybridization of a 12 bp duplex within a 50mer oligonucleotide. Conclusions Microarray and other molecular capture strategies that rely on a 15 nt lower complementarity bound for eliminating specific cross-hybridization may not be sufficiently conservative. PMID:23445545

Effect of pH value of probe molecule on the graphene oxide-based surface enhanced Raman scattering

NASA Astrophysics Data System (ADS)

Cui, Shao-li; Du, Xiao-qing; Zeng, Chao; Li, Lu; Bao, Jun

2017-06-01

The dependence of graphene oxide (GO)-based surface enhanced Raman scattering (SERS) on the pH value of probe molecule was investigated. Water-soluble copper phthalocyanine (TSCuPc) was used as probe molecule and its pH value was adjusted with HCl and NaOH solution. The Raman spectra of TSCuPc with pH equaling 3, 8, and 11 on GO base were tested, respectively. The results show that both Raman enhanced intensity and full width at half maximum (FWHM) of characteristic peaks vary with the pH value of TSCuPc. It is shown that there is no obvious spectral widening of TSCuPc characteristic peaks when TSCuPc is neutral or acidic, and the chemical enhancement intensity of neutral TSCuPc on GO is biggest. In contrast, when TSCuPc is alkaline, the characteristic Raman peaks between 1350 and 1600 cm-1 of TSCuPc on GO are much wider and the intensities of characteristic peaks decrease considerably. The reasons for the pH dependence of GO-based Raman spectra were explored by comparing the wettability of molecule droplet on GO and the absorbance of different pH-adjusted TSCuPc films. It is found that the effect of molecule's pH value on SERS can be contributed to the differences of concentration and distributions on GO surface for varied pH-treated molecule.

Nonlinear optical probe of biopolymer adsorption on colloidal particle surface: poly-L-lysine on polystyrene sulfate microspheres.

PubMed

Eckenrode, Heather M; Dai, Hai-Lung

2004-10-12

A nonlinear optical technique--second harmonic generation (SHG)--has been applied to characterize the adsorption of poly-L-lysine on micrometer size polystyrene particles, whose surface is covered with negatively charged sulfonate groups, in aqueous solutions. Adsorption behavior of the biopolymer with two chain lengths (14 and 75 amino acid units; PL14 and PL75) has been examined. Centrifugation experiments were also performed to support the adsorption measurements made using SHG. The adsorption free energies of the two polymers PL75 and PL14 are determined as -16.57 and -14.40 kcal/mol, respectively. The small difference in the adsorption free energies of the two chain lengths, however, leads to dramatic difference in the concentration needed for saturated surface coverage: nearly 50 times higher concentration is needed for the smaller polymer. Under acidic colloidal conditions, polylysine is found to adsorb in a relatively flat conformation on the surface. The surface area that each polylysine molecule occupies is nearly 1 order of magnitude larger than the size of the molecule in its extended form. The low adsorption density is likely a result from Coulombic repulsion between the positive charges on the amino acid units of PL. The measurements demonstrate the utility of SHG as an efficient and sensitive experimental approach for measuring adsorption characteristics of bio/macromolecules on colloidal particles and define surface and colloidal conditions for achieving maximum surface coverage of a widely used biopolymer. Copyright 2004 American Chemical Society

A highly sensitive nanoscale pH-sensor using Au nanoparticles linked by a multifunctional Raman-active reporter molecule

NASA Astrophysics Data System (ADS)

Lawson, Latevi S.; Chan, James W.; Huser, Thomas

2014-06-01

Chemical sensing on the nanoscale has been breaking new ground since the discovery of surface enhanced Raman scattering (SERS). For nanoparticles, controlled particle aggregation is necessary to achieve the largest SERS enhancements. Therefore, aggregating agents such as salts or linker molecules are used in conjunction with chemically sensitive reporters in order to develop robust environmentally sensitive SERS probes. While salt-induced colloidal nanosphere aggregates have produced robust SERS signals, their variability in aggregate size contributes significantly to poor SERS signal reproducibility, which can complicate their use in in vitro cellular studies. Such systems often also lack reproducibility in spectral measurements between different nanoparticle clusters. Preaggregation of colloids via linkers followed by surface functionalization with reporter molecules results in the linker occupying valuable SERS hotspot volume which could otherwise be utilized by additional reporter molecules. Ideally, both functionalities should be obtained from a single molecule. Here, we report the use of 3,5-dimercaptobenzoic acid, a single multifunctional molecule that creates SERS hotspots via the controlled aggregation of nanoparticles, and also reports pH values. We show that 3,5-dimercaptobenzoic acid bound to Au nanospheres results in an excellent pH nanoprobe, producing very robust, and highly reproducible SERS signals that can report pH across the entire physiological range with excellent pH resolution. To demonstrate the efficacy of our novel pH reporters, these probes were also used to image both the particle and pH distribution in the cytoplasm of human induced pluripotent stem cells (hiPSCs).Chemical sensing on the nanoscale has been breaking new ground since the discovery of surface enhanced Raman scattering (SERS). For nanoparticles, controlled particle aggregation is necessary to achieve the largest SERS enhancements. Therefore, aggregating agents such as salts or linker molecules are used in conjunction with chemically sensitive reporters in order to develop robust environmentally sensitive SERS probes. While salt-induced colloidal nanosphere aggregates have produced robust SERS signals, their variability in aggregate size contributes significantly to poor SERS signal reproducibility, which can complicate their use in in vitro cellular studies. Such systems often also lack reproducibility in spectral measurements between different nanoparticle clusters. Preaggregation of colloids via linkers followed by surface functionalization with reporter molecules results in the linker occupying valuable SERS hotspot volume which could otherwise be utilized by additional reporter molecules. Ideally, both functionalities should be obtained from a single molecule. Here, we report the use of 3,5-dimercaptobenzoic acid, a single multifunctional molecule that creates SERS hotspots via the controlled aggregation of nanoparticles, and also reports pH values. We show that 3,5-dimercaptobenzoic acid bound to Au nanospheres results in an excellent pH nanoprobe, producing very robust, and highly reproducible SERS signals that can report pH across the entire physiological range with excellent pH resolution. To demonstrate the efficacy of our novel pH reporters, these probes were also used to image both the particle and pH distribution in the cytoplasm of human induced pluripotent stem cells (hiPSCs). Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr06277e

Methods for making nucleotide probes for sequencing and synthesis

DOEpatents

Church, George M; Zhang, Kun; Chou, Joseph

2014-07-08

Compositions and methods for making a plurality of probes for analyzing a plurality of nucleic acid samples are provided. Compositions and methods for analyzing a plurality of nucleic acid samples to obtain sequence information in each nucleic acid sample are also provided.

Defined surface immobilization of glycosaminoglycan molecules for probing and modulation of cell-material interactions.

PubMed

Wang, Kai; Luo, Ying

2013-07-08

As one important category of biological molecules on the cell surface and in the extracellular matrix (ECM), glycosaminoglycans (GAGs) have been widely studied for biomedical applications. With the understanding that the biological functions of GAGs are driven by the complex dynamics of physiological and pathological processes, methodologies are desired to allow the elucidation of cell-GAG interactions with molecular level precision. In this study, a microtiter plate-based system was devised through a new surface modification strategy involving polydopamine (PDA) and GAG molecules functionalized with hydrazide chemical groups. A small library of GAGs including hyaluronic acid (with different molecular weights), heparin, and chondroitin sulfate was successfully immobilized via defined binding sites onto the microtiter plate surface under facile aqueous conditions. The methodology then allowed parallel studies of the GAG-modified surfaces in a high-throughput format. The results show that immobilized GAGs possess distinct properties to mediate protein adsorption, cell adhesion, and inflammatory responses, with each property showing dependence on the type and molecular weight of specific GAG molecules. The PDA-assisted immobilization of hydrazide-functionalized GAGs allows biomimetic attachment of GAG molecules and retains their bioactivity, providing a new methodology to systematically probe fundamental cell-GAG interactions to modulate the bioactivity and biocompatibility of biomaterials.

Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations.

PubMed

Lathe, R

1985-05-05

Synthetic probes deduced from amino acid sequence data are widely used to detect cognate coding sequences in libraries of cloned DNA segments. The redundancy of the genetic code dictates that a choice must be made between (1) a mixture of probes reflecting all codon combinations, and (2) a single longer "optimal" probe. The second strategy is examined in detail. The frequency of sequences matching a given probe by chance alone can be determined and also the frequency of sequences closely resembling the probe and contributing to the hybridization background. Gene banks cannot be treated as random associations of the four nucleotides, and probe sequences deduced from amino acid sequence data occur more often than predicted by chance alone. Probe lengths must be increased to confer the necessary specificity. Examination of hybrids formed between unique homologous probes and their cognate targets reveals that short stretches of perfect homology occurring by chance make a significant contribution to the hybridization background. Statistical methods for improving homology are examined, taking human coding sequences as an example, and considerations of codon utilization and dinucleotide frequencies yield an overall homology of greater than 82%. Recommendations for probe design and hybridization are presented, and the choice between using multiple probes reflecting all codon possibilities and a unique optimal probe is discussed.

Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices

NASA Astrophysics Data System (ADS)

Justino, Licínia L. G.; Reva, Igor; Fausto, Rui

2016-07-01

Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N2, Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.

Combinatorial localized dissolution analysis: Application to acid-induced dissolution of dental enamel and the effect of surface treatments.

PubMed

Parker, Alexander S; Al Botros, Rehab; Kinnear, Sophie L; Snowden, Michael E; McKelvey, Kim; Ashcroft, Alexander T; Carvell, Mel; Joiner, Andrew; Peruffo, Massimo; Philpotts, Carol; Unwin, Patrick R

2016-08-15

A combination of scanning electrochemical cell microscopy (SECCM) and atomic force microscopy (AFM) is used to quantitatively study the acid-induced dissolution of dental enamel. A micron-scale liquid meniscus formed at the end of a dual barrelled pipette, which constitutes the SECCM probe, is brought into contact with the enamel surface for a defined period. Dissolution occurs at the interface of the meniscus and the enamel surface, under conditions of well-defined mass transport, creating etch pits that are then analysed via AFM. This technique is applied to bovine dental enamel, and the effect of various treatments of the enamel surface on acid dissolution (1mM HNO3) is studied. The treatments investigated are zinc ions, fluoride ions and the two combined. A finite element method (FEM) simulation of SECCM mass transport and interfacial reactivity, allows the intrinsic rate constant for acid-induced dissolution to be quantitatively determined. The dissolution of enamel, in terms of Ca(2+) flux ( [Formula: see text] ), is first order with respect to the interfacial proton concentration and given by the following rate law: [Formula: see text] , with k0=0.099±0.008cms(-1). Treating the enamel with either fluoride or zinc ions slows the dissolution rate, although in this model system the partly protective barrier only extends around 10-20nm into the enamel surface, so that after a period of a few seconds dissolution of modified surfaces tends towards that of native enamel. A combination of both treatments exhibits the greatest protection to the enamel surface, but the effect is again transient. Copyright © 2016 Elsevier Inc. All rights reserved.

Robust forests of vertically aligned carbon nanotubes chemically assembled on carbon substrates.

PubMed

Garrett, David J; Flavel, Benjamin S; Shapter, Joseph G; Baronian, Keith H R; Downard, Alison J

2010-02-02

Forests of vertically aligned carbon nanotubes (VACNTs) have been chemically assembled on carbon surfaces. The structures show excellent stability over a wide potential range and are resistant to degradation from sonication in acid, base, and organic solvent. Acid-treated single-walled carbon nanotubes (SWCNTs) were assembled on amine-terminated tether layers covalently attached to pyrolyzed photoresist films. Tether layers were electrografted to the carbon substrate by reduction of the p-aminobenzenediazonium cation and oxidation of ethylenediamine. The amine-modified surfaces were incubated with cut SWCNTs in the presence of N,N'-dicyclohexylcarbodiimide (DCC), giving forests of vertically aligned carbon nanotubes (VACNTs). The SWCNT assemblies were characterized by scanning electron microscopy, atomic force microscopy, and electrochemistry. Under conditions where the tether layers slow electron transfer between solution-based redox probes and the underlying electrode, the assembly of VACNTs on the tether layer dramatically increases the electron-transfer rate at the surface. The grafting procedure, and hence the preparation of VACNTs, is applicable to a wide range of materials including metals and semiconductors.

Crystallographic fragment-based drug discovery: use of a brominated fragment library targeting HIV protease.

PubMed

Tiefenbrunn, Theresa; Forli, Stefano; Happer, Meaghan; Gonzalez, Ana; Tsai, Yingssu; Soltis, Michael; Elder, John H; Olson, Arthur J; Stout, Charles D

2014-02-01

A library of 68 brominated fragments was screened against a new crystal form of inhibited HIV-1 protease in order to probe surface sites in soaking experiments. Often, fragments are weak binders with partial occupancy, resulting in weak, difficult-to-fit electron density. The use of a brominated fragment library addresses this challenge, as bromine can be located unequivocally via anomalous scattering. Data collection was carried out in an automated fashion using AutoDrug at SSRL. Novel hits were identified in the known surface sites: 3-bromo-2,6-dimethoxybenzoic acid (Br6) in the flap site and 1-bromo-2-naphthoic acid (Br27) in the exosite, expanding the chemistry of known fragments for development of higher affinity potential allosteric inhibitors. At the same time, mapping the binding sites of a number of weaker binding Br-fragments provides further insight into the nature of these surface pockets. © 2013 John Wiley & Sons A/S.

Identification of N-acetylneuraminic acid and its 9-O-acetylated derivative on the cell surface of Cryptococcus neoformans: influence on fungal phagocytosis.

PubMed Central

Rodrigues, M L; Rozental, S; Couceiro, J N; Angluster, J; Alviano, C S; Travassos, L R

1997-01-01

Sialic acids from sialoglycoconjugates present at the cell surface of Cryptococcus neoformans yeast forms were analyzed by high-performance thin-layer chromatography, binding of influenza A and C virus strains, enzymatic treatment, and flow cytofluorimetry with fluorescein isothiocyanate-labeled lectins. C. neoformans yeast forms grown in a chemically defined medium contain N-acetylneuraminic acid and its 9-O-acetylated derivative. A density of 3 x 10(6) residues of sialic acid per cell was found in C. neoformans. Sialic acids in cryptococcal cells are glycosidically linked to galactopyranosyl units as inferred from the increased reactivity of neuraminidase-treated yeasts with peanut agglutinin. N-Acetylneuraminic acids are alpha-2,6 and alpha-2,3 linked, as indicated by using virus strains M1/5 and M1/5 HS8, respectively, as agglutination probes. The alpha-2,6 linkage markedly predominated. These findings were essentially confirmed by the interaction of cryptococcal cells with the lectins Sambucus nigra agglutinin and Maackia amurensis agglutinin. We also investigated whether the sialyl residues present in C. neoformans are involved in the fungal interaction with a cationic solid-phase substrate and with mouse resident macrophages. Adhesion of yeast cells to poly-L-lysine was mediated, in part, by sialic acid residues, since the number of adherent cells was markedly reduced after treatment with bacterial neuraminidase. The enzymatic removal of sialic acids also made C. neoformans yeast cells more susceptible to endocytosis by macrophages. The results show that sialic acids are components of the cryptococcal cell surface that contribute to its negative charge and protect yeast forms against phagocytosis. PMID:9393779

pH at the micellar interface: synthesis of pH probes derived from salicylic acid, acid-base dissociation in sodium dodecyl sulfate micelles, and Poisson-Boltzmann simulation.

PubMed

Souza, T P; Zanette, D; Kawanami, A E; de Rezende, L; Ishiki, H M; do Amaral, A T; Chaimovich, H; Agostinho-Neto, A; Cuccovia, I M

2006-05-01

The study of the H+ concentration at the micellar interface is a convenient system for modeling the distribution of H+ at interfaces. We have synthesized salicylic acid derivatives to analyze the proton dissociation of both the carboxylic and phenol groups of the probes, determining spectrophotometrically the apparent pK(a)'s (pK(ap)) in sodium dodecyl sulfate, SDS, micelles with and without added salt. The synthesized probes were 2-hydroxy-5-(2-trimethylammoniumacetyl)benzoate; 2-hydroxy-5-(2-dimethylhexadecylammoniumacetyl)benzoate; 2-hydroxy-5-(2-dimethylhexadecylammoniumhexanoyl)benzoate; 2-hydroxy-5-(2-dimethylhexadecylammoniumundecanoyl)benzoate; 2-hydroxy-5-acetylbenzoic acid; and 2-hydroxy-5-dodecanoylbenzoic acid. Upon incorporation into SDS micelles the pK(ap)'s of both carboxylic and phenol groups increased by ca. 3 pH units and NaCl addition caused a decrease in the probe-incorporated pK(ap). The experimental results were fitted with a cell model Poisson-Boltzmann (P-B) equation taking in consideration the effect of salt on the aggregation number of SDS and using the distance of the dissociating group as a parameter. The conformations of the probes were analyzed theoretically using two dielectric constants, e.g., 2 and 78. Both the P-B analysis and conformation calculations can be interpreted by assuming that the acid groups dissociate very close to, or at, the interface. Our results are consistent with the assumption that the intrinsic pK(a)'s of both carboxylic and phenol groups of the salicylic acid probes used here can be taken as those in water. Using this assumption the micellar and salt effects on the pK(ap)'s of the (trialkylammonium)benzoate probes were described accurately using a cell model P-B analysis.

Surface chemistry of a hydrogenated mesoporous p-type silicon

NASA Astrophysics Data System (ADS)

Media, El-Mahdi; Outemzabet, Ratiba

2017-02-01

The finality of this work is devoted to the grafting of organic molecules on hydrogen passivated mesoporous silicon surfaces. The study would aid in the development for the formation of organic monolayers on silicon surface to be exploited for different applications such as the realisation of biosensors and medical devices. The basic material is silicon which has been first investigated by FTIR at atomistic plane during the anodic forward and backward polarization (i.e. "go" and "return"). For this study, we applied a numerical program based on least squares method to infrared absorbance spectra obtained by an in situ attenuated total reflection on p-type silicon in diluted HF electrolyte. Our numerical treatment is based on the fitting of the different bands of IR absorbance into Gaussians corresponding to the different modes of vibration of molecular groups such as siloxanes and hydrides. An adjustment of these absorbance bands is done systematically. The areas under the fitted bands permit one to follow the intensity of the different modes of vibration that exist during the anodic forward and backward polarization in order to compare the reversibility of the phenomenon of the anodic dissolution of silicon. It permits also to follow the evolution between the hydrogen silicon termination at forward and backward scanning applied potential. Finally a comparison between the states of the initial and final surface was carried out. We confirm the presence of clearly four and three distinct vibration modes of siloxanes/hydroxide, SiOx, and hydrides, SiHx, respectively. The results show clearly that the adsorbed species found in the final stage after an electrochemical treatment consist of surface hydrogen and they show also that the surface morphology is different compared to the starting one, which is considered as reference. It is clear that the H-terminated of porous silicon surface is hydrophobic in nature. The hydrophobic character of this surface makes difficult the grafting of a probe which serves to get other molecules; where from the necessity of the presence of a hydrophilic surface on the porous silicon surface. This will facilitate the penetration and the grafting of the molecules probes. So to improve the penetration and the grafting of the organic molecules or the immobilization of the probes on the hydrogenated mesoporous silicon surfaces under wet chemical conditions an intermediate step is required. In this second study, we use the following procedure. After the porosification of the silicon by electrochemical anodisation, the porous SiH layer returns a hydrophobic surface. This stage is a starting point of multistep scheme for the surface modification. The next step is the thermal hydrosilylation in order to have an acidic surface. The acidic surface was then modified by the chains of Poly(ethylene glycol) (PEG) which is a highly investigated polymer for the covalent modification of biological macromolecules and surfaces. The grafting of PEG returns a hydrophilic surface confirmed by the IR results.

Direct measurements of intermolecular forces by chemical force microscopy

NASA Astrophysics Data System (ADS)

Vezenov, Dmitri Vitalievich

1999-12-01

Detailed description of intermolecular forces is key to understanding a wide range of phenomena from molecular recognition to materials failure. The unique features of atomic force microscopy (AFM) to make point contact force measurements with ultra high sensitivity and to generate spatial maps of surface topography and forces have been extended to include measurements between well-defined organic molecular groups. Chemical modification of AFM probes with self-assembled monolayers (SAMs) was used to make them sensitive to specific molecular interactions. This novel chemical force microscopy (CFM) technique was used to probe forces between different molecular groups in a range of environments (vacuum, organic liquids and aqueous solutions); measure surface energetics on a nanometer scale; determine pK values of the surface acid and base groups; measure forces to stretch and unbind a short synthetic DNA duplex and map the spatial distribution of specific functional groups and their ionization state. Studies of adhesion forces demonstrated the important contribution of hydrogen bonding to interactions between simple organic functionalities. The chemical identity of the tip and substrate surfaces as well as the medium had a dramatic effect on adhesion between model monolayers. A direct correlation between surface free energy and adhesion forces was established. The adhesion between epoxy polymer and model mixed SAMs varied with the amount of hydrogen bonding component in the monolayers. A consistent interpretation of CFM measurements in polar solvents was provided by contact mechanics models and intermolecular force components theory. Forces between tips and surfaces functionalized with SAMs terminating in acid or base groups depended on their ionization state. A novel method of force titration was introduced for highly local characterization of the pK's of surface functional groups. The pH-dependent changes in friction forces were exploited to map spatially the changes in ionization state on SAM surfaces. The phase contrast in tapping mode AFM between chemically distinct monolayer regions and corresponding adhesion forces were found to be directly correlated. Thus, both friction and intermittent contact CFM images could be interpreted in terms of the strength of intermolecular interactions. CFM was also used to probe biomolecular interactions. Separation forces between complementary oligonucleotide strands were significantly larger than the forces measured between noncomplementary strands and were consistent with the unbinding of a single DNA duplex. CFM data provided a direct measure of the forces required to elastically deform, structurally-transform and separate well-defined, synthetic duplexes into single strand oligonucleotides.

Detection and isolation of nucleic acid sequences using a bifunctional hybridization probe

DOEpatents

Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

2000-01-01

A method for detecting and isolating a target sequence in a sample of nucleic acids is provided using a bifunctional hybridization probe capable of hybridizing to the target sequence that includes a detectable marker and a first complexing agent capable of forming a binding pair with a second complexing agent. A kit is also provided for detecting a target sequence in a sample of nucleic acids using a bifunctional hybridization probe according to this method.

Synthesis and catalytic activity of polysaccharide templated nanocrystalline sulfated zirconia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sherly, K. B.; Rakesh, K.

Nanoscaled materials are of great interest due to their unique enhanced optical, electrical and magnetic properties. Sulfate-promoted zirconia has been shown to exhibit super acidic behavior and high activity for acid catalyzed reactions. Nanocrystalline zirconia was prepared in the presence of polysaccharide template by interaction between ZrOCl{sub 2}⋅8H{sub 2}O and chitosan template. The interaction was carried out in aqueous phase, followed by the removal of templates by calcination at optimum temperature and sulfation. The structural and textural features were characterized by powder XRD, TG, SEM and TEM. XRD patterns showed the peaks of the diffractogram were in agreement with themore » theoretical data of zirconia with the catalytically active tetragonal phase and average crystalline size of the particles was found to be 9 nm, which was confirmed by TEM. TPD using ammonia as probe, FTIR and BET surface area analysis were used for analyzing surface features like acidity and porosity. The BET surface area analysis showed the sample had moderately high surface area. FTIR was used to find the type species attached to the surface of zirconia. UV-DRS found the band gap of the zirconia was found to be 2.8 eV. The benzylation of o-xylene was carried out batchwise in atmospheric pressure and 433K temperature using sulfated zirconia as catalyst.« less

Direct ultrasensitive electrochemical biosensing of pathogenic DNA using homogeneous target-initiated transcription amplification

PubMed Central

Yan, Yurong; Ding, Shijia; Zhao, Dan; Yuan, Rui; Zhang, Yuhong; Cheng, Wei

2016-01-01

Sensitive and specific methodologies for detection of pathogenic gene at the point-of-care are still urgent demands in rapid diagnosis of infectious diseases. This work develops a simple and pragmatic electrochemical biosensing strategy for ultrasensitive and specific detection of pathogenic nucleic acids directly by integrating homogeneous target-initiated transcription amplification (HTITA) with interfacial sensing process in single analysis system. The homogeneous recognition and specific binding of target DNA with the designed hairpin probe triggered circular primer extension reaction to form DNA double-strands which contained T7 RNA polymerase promoter and served as templates for in vitro transcription amplification. The HTITA protocol resulted in numerous single-stranded RNA products which could synchronously hybridized with the detection probes and immobilized capture probes for enzyme-amplified electrochemical detection on the biosensor surface. The proposed electrochemical biosensing strategy showed very high sensitivity and selectivity for target DNA with a dynamic response range from 1 fM to 100 pM. Using salmonella as a model, the established strategy was successfully applied to directly detect invA gene from genomic DNA extract. This proposed strategy presented a simple, pragmatic platform toward ultrasensitive nucleic acids detection and would become a versatile and powerful tool for point-of-care pathogen identification. PMID:26729209

Direct ultrasensitive electrochemical biosensing of pathogenic DNA using homogeneous target-initiated transcription amplification

NASA Astrophysics Data System (ADS)

Yan, Yurong; Ding, Shijia; Zhao, Dan; Yuan, Rui; Zhang, Yuhong; Cheng, Wei

2016-01-01

Sensitive and specific methodologies for detection of pathogenic gene at the point-of-care are still urgent demands in rapid diagnosis of infectious diseases. This work develops a simple and pragmatic electrochemical biosensing strategy for ultrasensitive and specific detection of pathogenic nucleic acids directly by integrating homogeneous target-initiated transcription amplification (HTITA) with interfacial sensing process in single analysis system. The homogeneous recognition and specific binding of target DNA with the designed hairpin probe triggered circular primer extension reaction to form DNA double-strands which contained T7 RNA polymerase promoter and served as templates for in vitro transcription amplification. The HTITA protocol resulted in numerous single-stranded RNA products which could synchronously hybridized with the detection probes and immobilized capture probes for enzyme-amplified electrochemical detection on the biosensor surface. The proposed electrochemical biosensing strategy showed very high sensitivity and selectivity for target DNA with a dynamic response range from 1 fM to 100 pM. Using salmonella as a model, the established strategy was successfully applied to directly detect invA gene from genomic DNA extract. This proposed strategy presented a simple, pragmatic platform toward ultrasensitive nucleic acids detection and would become a versatile and powerful tool for point-of-care pathogen identification.

Direct ultrasensitive electrochemical biosensing of pathogenic DNA using homogeneous target-initiated transcription amplification.

PubMed

Yan, Yurong; Ding, Shijia; Zhao, Dan; Yuan, Rui; Zhang, Yuhong; Cheng, Wei

2016-01-05

Sensitive and specific methodologies for detection of pathogenic gene at the point-of-care are still urgent demands in rapid diagnosis of infectious diseases. This work develops a simple and pragmatic electrochemical biosensing strategy for ultrasensitive and specific detection of pathogenic nucleic acids directly by integrating homogeneous target-initiated transcription amplification (HTITA) with interfacial sensing process in single analysis system. The homogeneous recognition and specific binding of target DNA with the designed hairpin probe triggered circular primer extension reaction to form DNA double-strands which contained T7 RNA polymerase promoter and served as templates for in vitro transcription amplification. The HTITA protocol resulted in numerous single-stranded RNA products which could synchronously hybridized with the detection probes and immobilized capture probes for enzyme-amplified electrochemical detection on the biosensor surface. The proposed electrochemical biosensing strategy showed very high sensitivity and selectivity for target DNA with a dynamic response range from 1 fM to 100 pM. Using salmonella as a model, the established strategy was successfully applied to directly detect invA gene from genomic DNA extract. This proposed strategy presented a simple, pragmatic platform toward ultrasensitive nucleic acids detection and would become a versatile and powerful tool for point-of-care pathogen identification.

FABRICATION AND OPTOELECTRONIC PROPERTIES OF MgxZn1-xO ULTRATHIN FILMS BY LANGMUIR-BLODGETT TECHNOLOGY

NASA Astrophysics Data System (ADS)

Tang, Dongyan; Feng, Qian; Jiang, Enying; He, Baozhu

2012-08-01

By transferring MgxZn1-xO sol and stearic acid onto a hydrophilic silicon wafer or glass plate, the Langmuir-Blodgett (LB) multilayers of MgxZn1-xO (x:0, 0.2, 0.4) were deposited. After calcinations at 350°C for 0.5 h and at 500°C for 3 h, MgxZn1-xO ultrathin films were fabricated. The optimized parameters for monolayer formation and multilayer deposition were determined by the surface pressure-surface (Π-A) area and the transfer coefficient, respectively. The expended areas of stearic acid with MgxZn1-xO sols under Π-A isotherms inferred the interaction of stearic acid with MgxZn1-xO sols during the formation of monolayer at air-water interface. X-ray diffraction (XRD) was used to determine the crystal structures of MgxZn1-xO nanoparticles and ultrathin films. The surface morphologies of MgxZn1-xO ultrathin films were observed by scanning probe microscopy (AFM). And the optoelectronic properties of MgxZn1-xO were detected and discussed based on photoluminescence (PL) spectra.

Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

DOEpatents

Lucas, J.N.; Straume, T.; Bogen, K.T.

1998-03-24

A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration. 14 figs.

Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

DOEpatents

Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

1998-01-01

A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration.

Controlling Reaction Selectivity through the Surface Termination of Perovskite Catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polo-Garzon, Felipe; Yang, Shi-Ze; Fung, Victor

2017-07-19

Although perovskites have been widely used in catalysis, tuning their surface terminations to control reaction selectivities has not been well established. In this work, we employ multiple surface sensitive techniques to characterize the surface termination (one aspect of surface reconstruction) of SrTiO 3 (STO) after thermal pretreatment (Sr-enrichment) and chemical etching (Ti-enrichment). We show, using the conversion of 2-propanol as a probe reaction, that the surface termination of STO can be controlled to greatly tune catalytic acid/base properties and consequently the reaction selectivities in a wide range, which are inaccessible using single metal oxides, either SrO or TiO 2. Densitymore » functional theory (DFT) calculations well explain the selectivity tuning and reaction mechanism on different surface terminations of STO. Similar catalytic tunability is also observed on BaZrO 3, highlighting the generality of the finding from this work.« less

Mapping Protein Surface Accessibility via an Electron Transfer Dissociation Selectively Cleavable Hydrazone Probe*

PubMed Central

Vasicek, Lisa; O'Brien, John P.; Browning, Karen S.; Tao, Zhihua; Liu, Hung-Wen; Brodbelt, Jennifer S.

2012-01-01

A protein's surface influences its role in protein-protein interactions and protein-ligand binding. Mass spectrometry can be used to give low resolution structural information about protein surfaces and conformations when used in combination with derivatization methods that target surface accessible amino acid residues. However, pinpointing the resulting modified peptides upon enzymatic digestion of the surface-modified protein is challenging because of the complexity of the peptide mixture and low abundance of modified peptides. Here a novel hydrazone reagent (NN) is presented that allows facile identification of all modified surface residues through a preferential cleavage upon activation by electron transfer dissociation coupled with a collision activation scan to pinpoint the modified residue in the peptide sequence. Using this approach, the correlation between percent reactivity and surface accessibility is demonstrated for two biologically active proteins, wheat eIF4E and PARP-1 Domain C. PMID:22393264

Charge separation in photoredox reactions. Technical progress report, May 1, 1981-May 1, 1984. [N,N,N',N'-tetramethylbenzidine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kevan, L.

1984-05-01

The structural aspects controlling charge separation in molecular photoionization reactions in organized molecular assemblies involving micelles and vesicles are being studied by optical and electron magnetic resonance techniques including the time domain technique of electron spin echo modulation (ESEM). Photoionization of N,N,N',N'-tetramethylbenzidine (TMB) to give the cation radical has been carried out in both liquid and frozen micellar and vesicular solutions. Cation-water interactions have been detected by ESEM analysis and indicate that the cation is localized asymmetrically within these organized molecular assemblies. x-Doxylstearic acid spin probes have been used to determine that the neutral TMB molecule before photoionization is alsomore » localized asymmetrically within such organized molecular assemblies. Electron spin echo detection of laser photogenerated TMB cation in liquid micellar solutions gives a direct measurement of the phase memory magnetic relaxation time which gives additional structural information. The photoionization efficiency has been related to cation-water interactions measured by ESEM. The photoionization efficiency is also dependent on surface charge and is about twofold greater in cationic micelles and vesicles compared to anionic micelles and vesicles. TMB is in a less polar environment in vesicles compared to micelles consistent with ESEM results. The preferential adsorption of metal species at micellar surfaces has been detected by ESEM. Modifications in the micelle surface have been effected by added salts and varying counterions which have been related to cation-water interactions and to the TMB photoionization efficiency. Corresponding changes in the surface and internal micellar structure have been investigated by x-doxylstearic acid spin probes and specifically deuterated surfactants. The decay kinetics of TMB cations in micelles have been interpreted in terms of a time dependent rate constant.« less

Design and synthesis of a novel lanthanide fluorescent probe (TbIII-dtpa-bis(2,6-diaminopurine)) and its application to the detection of uric acid in urine sample.

PubMed

Yang, Fan; Yu, Zhiyue; Li, Xinyi; Ren, Peipei; Liu, Guanhong; Song, Youtao; Wang, Jun

2018-06-03

In this study, a novel fluorescent probe, Tb III -dtpa-bis(2,6-diaminopurine) (Tb-dtpa-bdap), is designed based on the principle of complementary base pairing and synthesized for uric acid detection. The synthesized fluorescent probe is characterized by 1 H NMR, 13 C NMR, infra-red (IR) spectrum and ultraviolet-visible (UV-vis) spectra. It is found that the fluorescence of Tb-dtpa-bdap solution can be quenched obviously in the presence of uric acid. The affecting factors, including solution acidity, uric acid concentration and interfering substances, on the detection of uric acid using this probe are examined. Under optimized conditions, the fluorescence intensities of Tb-dtpa-bdap solution towards different uric acid concentrations show a linear response in the range from 1.00 × 10 -5  mol·L -1 to 5.00 × 10 -5  mol·L -1 with a linear correlation coefficient (R 2 ) of 0.9877. And the obtained limit of detection (LOD) is about 5.80 × 10 -6  mol·L -1 , which is lower than the level of uric acid in actual urine. The mechanism on the detection of uric acid by using Tb-dtpa-bdap is inferred from the experimental results. The facts demonstrate that the proposed fluorescent probe can be successfully applied for the determination of uric acid in human urine samples. Copyright © 2018 Elsevier B.V. All rights reserved.

AFM fluid delivery/liquid extraction surface sampling/electrostatic spray cantilever probe

DOEpatents

Van Berkel, Gary J.

2015-06-23

An electrospray system comprises a liquid extraction surface sampling probe. The probe comprises a probe body having a liquid inlet and a liquid outlet, and having a liquid extraction tip. A solvent delivery conduit is provided for receiving solvent liquid from the liquid inlet and delivering the solvent liquid to the liquid extraction tip. An open liquid extraction channel extends across an exterior surface of the probe body from the liquid extraction tip to the liquid outlet. An electrospray emitter tip is in liquid communication with the liquid outlet of the liquid extraction surface sampling probe. A system for analyzing samples, a liquid junction surface sampling system, and a method of analyzing samples are also disclosed.

Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets.

PubMed

Rant, Ulrich; Arinaga, Kenji; Scherer, Simon; Pringsheim, Erika; Fujita, Shozo; Yokoyama, Naoki; Tornow, Marc; Abstreiter, Gerhard

2007-10-30

We report a method to detect label-free oligonucleotide targets. The conformation of surface-tethered probe nucleic acids is modulated by alternating electric fields, which cause the molecules to extend away from or fold onto the biased surface. Binding (hybridization) of targets to the single-stranded probes results in a pronounced enhancement of the layer-height modulation amplitude, monitored optically in real time. The method features an exceptional detection limit of <3 x 10(8) bound targets per cm(2) sensor area. Single base-pair mismatches in the sequences of DNA complements may readily be identified; moreover, binding kinetics and binding affinities can be determined with high accuracy. When driving the DNA to oscillate at frequencies in the kHz regime, distinct switching kinetics are revealed for single- and double-stranded DNA. Molecular dynamics are used to identify the binding state of molecules according to their characteristic kinetic fingerprints by using a chip-compatible detection format.

Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets

PubMed Central

Rant, Ulrich; Arinaga, Kenji; Scherer, Simon; Pringsheim, Erika; Fujita, Shozo; Yokoyama, Naoki; Tornow, Marc; Abstreiter, Gerhard

2007-01-01

We report a method to detect label-free oligonucleotide targets. The conformation of surface-tethered probe nucleic acids is modulated by alternating electric fields, which cause the molecules to extend away from or fold onto the biased surface. Binding (hybridization) of targets to the single-stranded probes results in a pronounced enhancement of the layer-height modulation amplitude, monitored optically in real time. The method features an exceptional detection limit of <3 × 108 bound targets per cm2 sensor area. Single base-pair mismatches in the sequences of DNA complements may readily be identified; moreover, binding kinetics and binding affinities can be determined with high accuracy. When driving the DNA to oscillate at frequencies in the kHz regime, distinct switching kinetics are revealed for single- and double-stranded DNA. Molecular dynamics are used to identify the binding state of molecules according to their characteristic kinetic fingerprints by using a chip-compatible detection format. PMID:17951434

SPM for functional identification of individual biomolecules

NASA Astrophysics Data System (ADS)

Ros, Robert; Schwesinger, Falk; Padeste, Celestino; Plueckthun, Andreas; Anselmetti, Dario; Guentherodt, Hans-Joachim; Tiefenauer, Louis

1999-06-01

The identification of specific binding molecules is of increasing interest in the context of drug development based on combinatorial libraries. Scanning Probe Microscopy (SPM) is the method of choice to image and probe individual biomolecules on a surface. Functional identification of biomolecules is a first step towards screening on a single molecule level. As a model system we use recombinant single- chain Fv fragment (scFv) antibody molecules directed against the antigen fluorescein. The scFv's are covalently immobilized on a flat gold surface via the C-terminal cysteine, resulting in a high accessibility of the binding site. The antigen is immobilized covalently via a long hydrophilic spacer to the silicon nitride SPM-tip. This arrangement allows a direct measurement of binding forces. Thus, closely related antibody molecules differing in only one amino acid at their binding site could be distinguished. A novel SPM-software has been developed which combines imaging, force spectroscopic modes, and online analysis. This is a major prerequisite for future screening methods.

Mechanistic Insights into the Catalytic Oxidation of Carboxylic Acids on Au/TiO 2: Partial Oxidation of Propionic and Butyric Acid to Gold Ketenylidene through Unsaturated Acids

DOE Office of Scientific and Technical Information (OSTI.GOV)

McEntee, Monica; Tang, Wenjie; Neurock, Matthew

Here, the partial oxidation of model C 2–C 4 (acetic, propionic, and butyric) carboxylic acids on Au/TiO 2 catalysts consisting of Au particles ~3 nm in size was investigated using transmission infrared spectroscopy and density functional theory. All three acids readily undergo oxidative dehydrogenation on Au/TiO 2. Propionic and butyric acid dehydrogenate at the C2–C3 positions, whereas acetic acid dehydrogenates at the C1–C2 position. The resulting acrylate and crotonate intermediates are subsequently oxidized to form β-keto acids that decarboxylate. All three acids form a gold ketenylidene intermediate, Au 2C=C=O, along the way to their full oxidation to form CO 2.more » Infrared measurements of Au 2C=C=O formation as a function of time provides a surface spectroscopic probe of the kinetics for the activation and oxidative dehydrogenation of the alkyl groups in the carboxylate intermediates that form.« less

Mechanistic Insights into the Catalytic Oxidation of Carboxylic Acids on Au/TiO 2: Partial Oxidation of Propionic and Butyric Acid to Gold Ketenylidene through Unsaturated Acids

DOE PAGES

McEntee, Monica; Tang, Wenjie; Neurock, Matthew; ...

2014-12-12

Here, the partial oxidation of model C 2–C 4 (acetic, propionic, and butyric) carboxylic acids on Au/TiO 2 catalysts consisting of Au particles ~3 nm in size was investigated using transmission infrared spectroscopy and density functional theory. All three acids readily undergo oxidative dehydrogenation on Au/TiO 2. Propionic and butyric acid dehydrogenate at the C2–C3 positions, whereas acetic acid dehydrogenates at the C1–C2 position. The resulting acrylate and crotonate intermediates are subsequently oxidized to form β-keto acids that decarboxylate. All three acids form a gold ketenylidene intermediate, Au 2C=C=O, along the way to their full oxidation to form CO 2.more » Infrared measurements of Au 2C=C=O formation as a function of time provides a surface spectroscopic probe of the kinetics for the activation and oxidative dehydrogenation of the alkyl groups in the carboxylate intermediates that form.« less

Frictional response of fatty acids on steel.

PubMed

Sahoo, Rashmi R; Biswas, S K

2009-05-15

Self-assembled monolayers of fatty acids were formed on stainless steel by room-temperature solution deposition. The acids are covalently bound to the surface as carboxylate in a bidentate manner. To explore the effect of saturation in the carbon backbone on friction in sliding tribology, we study the response of saturated stearic acid (SA) and unsaturated linoleic acid (LA) as self-assembled monolayers using lateral force microscopy and nanotribometry and when the molecules are dispersed in hexadecane, using pin-on-disc tribometry. Over a very wide range (10 MPa-2.5 GPa) of contact pressures it is consistently demonstrated that the unsaturated linoleic acid molecules yield friction which is significantly lower than that of the saturated stearic acid. It is argued, using density functional theory predictions and XPS of slid track, that when the molecular backbone of unsaturated fatty acids are tilted and pressed strongly by a probe, in tribological contact, the high charge density of the double bond region of the backbone allows coupling with the steel substrate. The interaction yields a low friction carboxylate soap film on the substrate. The saturated fatty acid does not show this effect.

Asymmetric Cationic Porphyrin as a New G-Quadruplex Probe with Wash-Free Cancer-Targeted Imaging Ability Under Acidic Microenvironments.

PubMed

Zhang, Ran; Cheng, Meng; Zhang, Li-Ming; Zhu, Li-Na; Kong, De-Ming

2018-04-25

Porphyrins are promising candidates for nucleic acid G-quadruplex-specific optical recognition. We previously demonstrated that G-quadruplex recognition specificity of porphyrins could be improved by introducing bulky side arm substituents, but the enhanced protonation tendency limits their applications in some cases, such as under acidic conditions. Here, we demonstrated that the protonation tendency of porphyrin derivatives could be efficiently overcome by increasing molecular asymmetry. To validate this, an asymmetric, water-soluble, cationic porphyrin FA-TMPipEOPP (5-{4-[2-[[(2 E)-3-[3-methoxy-4-[2-(1-methyl-1-piperidinyl)ethoxy]phenyl]-1-oxo-2-propenyl]oxy]ethoxy]phenyl},10,15,20-tri{4-[2-(1-methyl-1-piperidinyl)ethoxy]-phenyl}porphyrin) was synthesized by introducing a ferulic acid (FA) unit at one side arm, and its structure was well-characterized. Unlike its symmetric counterpart TMPipEOPP that has a tendency to protonate under acidic conditions, FA-TMPipEOPP remained in the unprotonated monomeric form under the pH range of 2.0-8.0. Correspondingly, FA-TMPipEOPP showed better G-quadruplex recognition specificity than TMPipEOPP and thus might be used as a specific optical probe for colorimetric and fluorescent recognition of G-quadruplexes under acidic conditions. The feasibility was demonstrated by two proof-of-concept studies: probing structural competition between G-quadruplexes and duplexes and label-free and wash-free cancer cell-targeted bioimaging under an acidic tumor microenvironment. As G-quadruplex optical probes, FA-TMPipEOPP works well under acidic conditions, whereas TMPipEOPP works well under neutral conditions. This finding provides useful information for G-quadruplex probe research. That is, porphyrin-based G-quadruplex probes suitable for different pH conditions might be obtained by adjusting the molecular symmetry.

Single Probe for Imaging and Biosensing of pH, Cu(2+) Ions, and pH/Cu(2+) in Live Cells with Ratiometric Fluorescence Signals.

PubMed

Han, Yingying; Ding, Changqin; Zhou, Jie; Tian, Yang

2015-01-01

It is very essential to disentangle the complicated inter-relationship between pH and Cu in the signal transduction and homeostasis. To this end, reporters that can display distinct signals to pH and Cu are highly valuable. Unfortunately, there is still no report on the development of biosensors that can simultaneously respond to pH and Cu(2+), to the best of our knowledge. In this work, we developed a single fluorescent probe, AuNC@FITC@DEAC (AuNC, gold cluster; FITC, fluorescein isothiocyanate; DEAC, 7-diethylaminocoumarin-3-carboxylic acid), for biosensing of pH, Cu(2+), and pH/Cu(2+) with different ratiometric fluorescent signals. First, 2,2',2″-(2,2',2″-nitrilotris(ethane-2,1-diyl)tris((pyridin-2-yl-methyl)azanediyl))triethanethiol (TPAASH) was designed for specific recognition of Cu(2+), as well as for organic ligand to synthesize fluorescent AuNCs. Then, pH-sensitive molecule, FITC emitting at 518 nm, and inner reference molecule, DEAC with emission peak at 472 nm, were simultaneously conjugated on the surface of AuNCs emitting at 722 nm, thus, constructing a single fluorescent probe, AuNC@FITC@DEAC, to sensing pH, Cu(2+), and pH/Cu(2+) excited by 405 nm light. The developed probe exhibited high selectivity and accuracy for independent determination of pH and Cu(2+) against reactive oxygen species (ROS), other metal ions, amino acids, and even copper-containing proteins. The AuNC-based inorganic-organic probe with good cell-permeability and high biocompatibility was eventually applied in monitoring both pH and Cu(2+) and in understanding the interplaying roles of Cu(2+) and pH in live cells by ratiometric multicolor fluorescent imaging.

Optimization of peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria: The effect of pH, dextran sulfate and probe concentration.

PubMed

Rocha, Rui; Santos, Rita S; Madureira, Pedro; Almeida, Carina; Azevedo, Nuno F

2016-05-20

Fluorescence in situ hybridization (FISH) is a molecular technique widely used for the detection and characterization of microbial populations. FISH is affected by a wide variety of abiotic and biotic variables and the way they interact with each other. This is translated into a wide variability of FISH procedures found in the literature. The aim of this work is to systematically study the effects of pH, dextran sulfate and probe concentration in the FISH protocol, using a general peptide nucleic acid (PNA) probe for the Eubacteria domain. For this, response surface methodology was used to optimize these 3 PNA-FISH parameters for Gram-negative (Escherichia coli and Pseudomonas fluorescens) and Gram-positive species (Listeria innocua, Staphylococcus epidermidis and Bacillus cereus). The obtained results show that a probe concentration higher than 300nM is favorable for both groups. Interestingly, a clear distinction between the two groups regarding the optimal pH and dextran sulfate concentration was found: a high pH (approx. 10), combined with lower dextran sulfate concentration (approx. 2% [w/v]) for Gram-negative species and near-neutral pH (approx. 8), together with higher dextran sulfate concentrations (approx. 10% [w/v]) for Gram-positive species. This behavior seems to result from an interplay between pH and dextran sulfate and their ability to influence probe concentration and diffusion towards the rRNA target. This study shows that, for an optimum hybridization protocol, dextran sulfate and pH should be adjusted according to the target bacteria. Copyright © 2016 Elsevier B.V. All rights reserved.

Translational and rotational diffusion of flexible PEG and rigid dendrimer probes in sodium caseinate dispersions and acid gels.

PubMed

Salami, Souad; Rondeau-Mouro, Corinne; Barhoum, Myriam; van Duynhoven, John; Mariette, François

2014-09-01

The dynamics of rigid dendrimer and flexible PEG probes in sodium caseinate dispersions and acid gels, including both translational diffusion and rotational diffusion, were studied by NMR. Above the onset of the close-packing limit (C ∼ 10 g/100 g H2 O), translational diffusion of the probe depended on its flexibility and on the fluctuations of the matrix chains. The PEG probe diffused more rapidly than the spherical dendrimer probe of corresponding hydrodynamic radius. The greater conformational flexibility of PEG facilitated its motion through the crowded casein matrix. Rotational diffusion was, however, substantially less hindered than the translational diffusion and depended on the local protein-probe friction which became high when the casein concentration increased. The coagulation of the matrix led to the formation of large voids, which resulted in an increase in the translational diffusion of the probes, whereas the rotational diffusion of the probes was retarded in the gel, which could be attributed to the immobilized environment surrounding the probe. Quantitative information from PFG-NMR and SEM micrographs have been combined for characterizing microstructural details in SC acid gels. © 2014 Wiley Periodicals, Inc.

Sum frequency generation and solid-state NMR study of the structure, orientation, and dynamics of polystyrene-adsorbed peptides

PubMed Central

Weidner, Tobias; Breen, Nicholas F.; Li, Kun; Drobny, Gary P.; Castner, David G.

2010-01-01

The power of combining sum frequency generation (SFG) vibrational spectroscopy and solid-state nuclear magnetic resonance (ssNMR) spectroscopy to quantify, with site specificity and atomic resolution, the orientation and dynamics of side chains in synthetic model peptides adsorbed onto polystyrene (PS) surfaces is demonstrated in this study. Although isotopic labeling has long been used in ssNMR studies to site-specifically probe the structure and dynamics of biomolecules, the potential of SFG to probe side chain orientation in isotopically labeled surface-adsorbed peptides and proteins remains largely unexplored. The 14 amino acid leucine-lysine peptide studied in this work is known to form an α-helical secondary structure at liquid-solid interfaces. Selective, individual deuteration of the isopropyl group in each leucine residue was used to probe the orientation and dynamics of each individual leucine side chain of LKα14 adsorbed onto PS. The selective isotopic labeling methods allowed SFG analysis to determine the orientations of individual side chains in adsorbed peptides. Side chain dynamics were obtained by fitting the deuterium ssNMR line shape to specific motional models. Through the combined use of SFG and ssNMR, the dynamic trends observed for individual side chains by ssNMR have been correlated with side chain orientation relative to the PS surface as determined by SFG. This combination provides a more complete and quantitative picture of the structure, orientation, and dynamics of these surface-adsorbed peptides than could be obtained if either technique were used separately. PMID:20628016

Probing functional groups at the gas-aerosol interface using heterogeneous titration reactions: a tool for predicting aerosol health effects?

PubMed

Setyan, Ari; Sauvain, Jean-Jacques; Guillemin, Michel; Riediker, Michael; Demirdjian, Benjamin; Rossi, Michel J

2010-12-17

The complex chemical and physical nature of combustion and secondary organic aerosols (SOAs) in general precludes the complete characterization of both bulk and interfacial components. The bulk composition reveals the history of the growth process and therefore the source region, whereas the interface controls--to a large extent--the interaction with gases, biological membranes, and solid supports. We summarize the development of a soft interrogation technique, using heterogeneous chemistry, for the interfacial functional groups of selected probe gases [N(CH(3))(3), NH(2)OH, CF(3)COOH, HCl, O(3), NO(2)] of different reactivity. The technique reveals the identity and density of surface functional groups. Examples include acidic and basic sites, olefinic and polycyclic aromatic hydrocarbon (PAH) sites, and partially and completely oxidized surface sites. We report on the surface composition and oxidation states of laboratory-generated aerosols and of aerosols sampled in several bus depots. In the latter case, the biomarker 8-hydroxy-2'-deoxyguanosine, signaling oxidative stress caused by aerosol exposure, was isolated. The increase in biomarker levels over a working day is correlated with the surface density N(i)(O3) of olefinic and/or PAH sites obtained from O(3) uptakes as well as with the initial uptake coefficient, γ(0), of five probe gases used in the field. This correlation with γ(0) suggests the idea of competing pathways occurring at the interface of the aerosol particles between the generation of reactive oxygen species (ROS) responsible for oxidative stress and cellular antioxidants.

Glowing locked nucleic acids: brightly fluorescent probes for detection of nucleic acids in cells.

PubMed

Østergaard, Michael E; Cheguru, Pallavi; Papasani, Madhusudhan R; Hill, Rodney A; Hrdlicka, Patrick J

2010-10-13

Fluorophore-modified oligonucleotides have found widespread use in genomics and enable detection of single-nucleotide polymorphisms, real-time monitoring of PCR, and imaging of mRNA in living cells. Hybridization probes modified with polarity-sensitive fluorophores and molecular beacons (MBs) are among the most popular approaches to produce hybridization-induced increases in fluorescence intensity for nucleic acid detection. In the present study, we demonstrate that the 2'-N-(pyren-1-yl)carbonyl-2'-amino locked nucleic acid (LNA) monomer X is a highly versatile building block for generation of efficient hybridization probes and quencher-free MBs. The hybridization and fluorescence properties of these Glowing LNA probes are efficiently modulated and optimized by changes in probe backbone chemistry and architecture. Correctly designed probes are shown to exhibit (a) high affinity toward RNA targets, (b) excellent mismatch discrimination, (c) high biostability, and (d) pronounced hybridization-induced increases in fluorescence intensity leading to formation of brightly fluorescent duplexes with unprecedented emission quantum yields (Φ(F) = 0.45-0.89) among pyrene-labeled oligonucleotides. Finally, specific binding between messenger RNA and multilabeled quencher-free MBs based on Glowing LNA monomers is demonstrated (a) using in vitro transcription assays and (b) by quantitative fluorometric assays and direct microscopic observation of probes bound to mRNA in its native form. These features render Glowing LNA as promising diagnostic probes for biomedical applications.

Measurement of molecular length of self-assembled monolayer probed by localized surface plasmon resonance

NASA Astrophysics Data System (ADS)

Ito, Juri; Kajikawa, Kotaro

2016-02-01

We propose a method to measure the variation of the molecular length of self-assembled monolayers (SAMs) when it is exposed to solutions at different pH conditions. The surface immobilized gold nanospheres (SIGNs) shows strong absorption peak at the wavelengths of 600-800 nm when p-polarized light is illuminated. The peak wavelength depends on the length of the gap distance between the SIGNs and the substrate. The gap is supported by the SAM molecules. According to the analytical calculation based on multiple expansion, the relation between the peak wavelength of the SIGN structures and the gap distance is calculated, to evaluate the molecular length of the SAM through the optical absorption spectroscopy for the SIGN structures. The molecular length of the SIGN structure was measured in air, water, acidic, and basic solutions. It was found that the molecular lengths are longer in acidic solutions.

Vertically aligned carbon nanotube probes for monitoring blood cholesterol

NASA Astrophysics Data System (ADS)

Roy, Somenath; Vedala, Harindra; Choi, Wonbong

2006-02-01

Detection of blood cholesterol is of great clinical significance. The amperometric detection technique was used for the enzymatic assay of total cholesterol. Multiwall carbon nanotubes (MWNTs), vertically aligned on a silicon platform, promote heterogeneous electron transfer between the enzyme and the working electrode. Surface modification of the MWNT with a biocompatible polymer, polyvinyl alcohol (PVA), converted the hydrophobic nanotube surface into a highly hydrophilic one, which facilitates efficient attachment of biomolecules. The fabricated working electrodes showed a linear relationship between cholesterol concentration and the output signal. The efficacy of the multiwall carbon nanotubes in promoting heterogeneous electron transfer was evident by distinct electrochemical peaks and higher signal-to-noise ratio as compared to the Au electrode with identical enzyme immobilization protocol. The selectivity of the cholesterol sensor in the presence of common interferents present in human blood, e.g. uric acid, ascorbic acid and glucose, is also reported.

Oligonucleotide probes functionalization of nanogap electrodes.

PubMed

Zaffino, Rosa Letizia; Mir, Mònica; Samitier, Josep

2017-11-01

Nanogap electrodes have attracted a lot of consideration as promising platform for molecular electronic and biomolecules detection. This is mainly for their higher aspect ratio, and because their electrical properties are easily accessed by current-voltage measurements. Nevertheless, application of standard current-voltages measurements used to characterize nanogap response, and/or to modify specific nanogap electrodes properties, represents an issue. Since the strength of electrical fields in nanoscaled devices can reach high values, even at low voltages. Here, we analyzed the effects induced by different methods of surface modification of nanogap electrodes, in test-voltage application, employed for the electrical detection of a desoxyribonucleic acid (DNA) target. Nanogap electrodes were functionalized with two antisymmetric oligo-probes designed to have 20 terminal bases complementary to the edges of the target, which after hybridization bridges the nanogap, closing the electrical circuit. Two methods of functionalization were studied for this purpose; a random self-assembling of a mixture of the two oligo-probes (OPs) used in the platform, and a selective method that controls the position of each OP at selected side of nanogap electrodes. We used for this aim, the electrophoretic effect induced on negatively charged probes by the application of an external direct current voltage. The results obtained with both functionalization methods where characterized and compared in terms of electrode surface covering, calculated by using voltammetry analysis. Moreover, we contrasted the electrical detection of a DNA target in the nanogap platform either in site-selective and in randomly assembled nanogap. According to our results, a denser, although not selective surface functionalization, is advantageous for such kind of applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Compatibility of Hepatocytes with Chemically Modified Porous Silicon with Reference to In Vitro Biosensors

PubMed Central

Alvarez, Sara D.; Derfus, Austin M.; Schwartz, Michael P.; Bhatia, Sangeeta N.; Sailor, Michael J.

2008-01-01

Porous Si is a nanostructured material that is of interest for molecular and cell-based biosensing, drug delivery, and tissue engineering applications. Surface chemistry is an important factor determining the stability of porous Si in aqueous media, its affinity for various biomolecular species, and its compatibility with tissues. In this study, the attachment and viability of a primary cell type to porous Si samples containing various surface chemistries is reported, and the ability of the porous Si films to retain their optical reflectivity properties relevant to molecular biosensing is assessed. Four chemical species grafted to the porous Si surface are studied: silicon oxide (via ozone oxidation), dodecyl (via hydrosilylation with dodecene), undecanoic acid (via hydrosilylation with undecylenic acid), and oligo(ethylene) glycol (via hydrosilylation with undecylenic acid followed by an oligo(ethylene) glycol coupling reaction). Fourier Transform Infrared (FTIR) spectroscopy and contact angle measurements are used to characterize the surface. Adhesion and short-term viability of primary rat hepatocytes on these surfaces, with and without pre-adsorption of collagen type I, are assessed using vital dyes (calcein-AM and ethidium homodimer I). Cell viability on undecanoic acid-terminated porous Si, oxide-terminated porous Si, and oxide-terminated flat (non-porous) Si are monitored by quantification of albumin production over the course of 8 days. The stability of porous Si thin films after 8 days in cell culture is probed by measuring the optical interferometric reflectance spectra. Results show that hepatocytes adhere better to surfaces coated with collagen, and that chemical modification does not exert a deleterious effect on primary rat hepatocytes. The hydrosilylation chemistry greatly improves the stability of porous Si in contact with cultured primary cells while allowing cell coverage levels comparable to standard culture preparations on tissue culture polystyrene. PMID:18845334

Accessible reactive surface area and abiotic redox reactivity of iron oxyhydroxides in acidic brines

NASA Astrophysics Data System (ADS)

Strehlau, Jennifer H.; Toner, Brandy M.; Arnold, William A.; Penn, R. Lee

2017-01-01

The reactivity of iron oxyhydroxide nanoparticles in low pH and high ionic strength solutions was quantified to assess abiotic contributions to oxidation-reduction chemistry in acidic brine environments, such as mine groundwater seepage, lakes in Western Australia, and acid mine drainage settings, which are of global interest for their environmental impacts and unique geomicrobiology. Factors expected to influence accessible and reactive surface area, including Fe(II) adsorption and aggregate size, were measured as a function of pH and CaCl2 concentration and related to the kinetics of redox reactions in aqueous suspensions of synthetic goethite (α-FeOOH), akaganeite (β-FeOOH), and ferrihydrite (Fe10O14(OH)2) nanoparticles. Aqueous conditions and iron oxyhydroxides were chosen based on characterization of natural iron-rich mine microbial mats located in Soudan Underground Mine State Park, Minnesota, USA. Quinone species were used as redox sensors because they are well-defined probes and are present in natural organic matter. Fe(II) adsorption to the iron oxyhydroxide mineral surfaces from aqueous solution was measurable only at pH values above 4 and either decreased or was not affected by CaCl2 concentration. Concentrations at or above 0.020 M CaCl2 in acetate buffer (pH 4.5) induced particle aggregation. Assessment of Fe(II) adsorption and particle aggregation in acidic brine suggested that accessible reactive surface area may be limited in acidic brines. This was supported by observations of decreasing benzoquinone reduction rate by adsorbed Fe(II) at high CaCl2 concentration. In contrast, the hydroquinone oxidation rate increased at high CaCl2 concentrations, which may be due to suppressed adsorption of Fe(II) generated by the reaction. Results suggest that iron geochemical cycling in acidic brine environments will be substantially different than for iron oxyhydroxides in low-saline waters with circumneutral pH. These findings have implications for acidic brine lakes and acid mine drainage locations that contain precipitated iron oxyhydroxides.

Controlling Reaction Selectivity through the Surface Termination of Perovskite Catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polo-Garzon, Felipe; Yang, Shi-Ze; Fung, Victor

2017-07-19

Although well known in the material science field, surface reconstruction of perovskites has not been implemented in heterogeneous catalysis. In this work, we employ multiple surface sensitive techniques to characterize the surface reconstruction of SrTiO3 (STO) after thermal pretreatment (Sr-enrichment) and chemical etching (Ti-enrichment). We show, using the conversion of 2-propanol as a probe reaction, that the surface reconstruction of STO can be controlled to greatly tune catalytic acid/base properties and consequently the reaction selectivities in a wide range, which are inaccessible using single metal oxides, either SrO or TiO2. Density functional theory (DFT) calculations well explain the selectivity tuningmore » and reaction mechanism on differently reconstructed surfaces of STO. Similar catalytic tunability is also observed on BaZrO3, highlighting the generality of the finding from this work.« less

Principles of Chemical Biology: From Sexy Fatty Acids and EBV probes to Anti-Acid Antibiotic via Post-Biotics and Host-Microbe Metabolic Complementarity.

PubMed

2017-06-22

This month: The role of fatty acids in sex determination; a probe to monitor and inhibit EBNA1 at the same time; a biological role for post-biotics; what happens when you mix microbes, hosts, and drugs; and an antibiotic that cross-protects with acid. Copyright © 2017. Published by Elsevier Ltd.

Diffusion of uncharged probe reveals structural changes in polyacids initiated by their neutralization: poly(acrylic acids).

PubMed

Hyk, Wojciech; Masiak, Michal; Stojek, Zbigniew; Ciszkowska, Malgorzata

2005-03-17

The diffusion studies of the uncharged probe (1,1'-ferrocenedimethanol) have been successfully applied for the evaluation of the changes in the three-dimensional structure of poly(acrylic acids) of various molecular weights (ranging from 2000 to 4,000,000 g/mol) during their neutralization with a strong base. The qualitative picture of the macromolecule arrangement during the titration of the polyacids has been obtained from the conductometric measurements. The characteristic changes in the poly(acrylic acid) conductivity are practically the same for all polyacids examined and are in a very good agreement with the predictions of our theoretical model of the polyelectrolyte conductance. The transformation of the polyelectrolyte solution into the gel-like or gel phase has been investigated more quantitatively by tracing the changes in the diffusion coefficient of the uncharged probe redox system. The probe diffusivities, D, were determined using steady-state voltammetry at microelectrodes for a wide range of neutralization degree, alpha, of the polyacids tested. The dependencies of D versus alpha are of similar shape for all poly(acrylic acids). The first parts of the dependencies reflect a rapid increase in D (up to neutralization degree of either 45% for the lowest molecular-weight poly(acrylic acid) or 75-80% for other polyacids). They are followed by the parts of a slight drop in the diffusion coefficient. The changes in the probe diffusivity become stronger as the molecular weight of poly(acrylic acid) increases. The maximum probe diffusion coefficients are greater than the initial values in the pure polyacid solutions by 14, 24, 19, 30, and 28% for poly(acrylic acid) of molecular weights of 2000, 450,000, 1,250,000, 3,000,000, and 4,000,000 g/mol, respectively. The variation in the probe diffusion coefficient qualitatively follows the line of the changes in the macroscopic viscosity of the polyelectrolyte system. This is in contrast to the predictions of the Stokes-Einstein relation and, therefore, suggests that the changes in the probe diffusion rate are mainly due to the structural changes in the polyacrylate medium and the macromolecular rearrangements induced by the chemical, acid-base reaction. By adapting the obstruction model for diffusion in homogeneous gels, the transport characteristics of the probe were converted into the structural characteristics of the polyelectrolytic systems. It has been found that the most ordered structure of the polyelectrolyte, or in other words the most permeable structure, is obtained when poly(acrylic acid) is neutralized at 75-80%.

Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Justino, Licínia L. G., E-mail: liciniaj@ci.uc.pt; Reva, Igor; Fausto, Rui

2016-07-07

Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N{sub 2},more » Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.« less

A benzothiazole-based fluorescent probe for hypochlorous acid detection and imaging in living cells

NASA Astrophysics Data System (ADS)

Nguyen, Khac Hong; Hao, Yuanqiang; Zeng, Ke; Fan, Shengnan; Li, Fen; Yuan, Suke; Ding, Xuejing; Xu, Maotian; Liu, You-Nian

2018-06-01

A benzothiazole-based turn-on fluorescent probe with a large Stokes shift (190 nm) has been developed for hypochlorous acid detection. The probe displays prompt fluorescence response for HClO with excellent selectivity over other reactive oxygen species as well as a low detection limit of 0.08 μM. The sensing mechanism involves the HClO-induced specific oxidation of oxime moiety of the probe to nitrile oxide, which was confirmed by HPLC-MS technique. Furthermore, imaging studies demonstrated that the probe is cell permeable and can be applied to detect HClO in living cells.

Probing protein surface with a solvent mimetic carbene coupled to detection by mass spectrometry.

PubMed

Gómez, Gabriela E; Mundo, Mariana R; Craig, Patricio O; Delfino, José M

2012-01-01

Much knowledge into protein folding, ligand binding, and complex formation can be derived from the examination of the nature and size of the accessible surface area (SASA) of the polypeptide chain, a key parameter in protein science not directly measurable in an experimental fashion. To this end, an ideal chemical approach should aim at exerting solvent mimicry and achieving minimal selectivity to probe the protein surface regardless of its chemical nature. The choice of the photoreagent diazirine to fulfill these goals arises from its size comparable to water and from being a convenient source of the extremely reactive methylene carbene (:CH(2)). The ensuing methylation depends primarily on the solvent accessibility of the polypeptide chain, turning it into a valuable signal to address experimentally the measurement of SASA in proteins. The superb sensitivity and high resolution of modern mass spectrometry techniques allows us to derive a quantitative signal proportional to the extent of modification (EM) of the sample. Thus, diazirine labeling coupled to electrospray mass spectrometry (ESI-MS) detection can shed light on conformational features of the native as well as non-native states, not easily addressable by other methods. Enzymatic fragmentation of the polypeptide chain at the level of small peptides allows us to locate the covalent tag along the amino acid sequence, therefore enabling the construction of a map of solvent accessibility. Moreover, by subsequent MS/MS analysis of peptides, we demonstrate here the feasibility of attaining amino acid resolution in defining the target sites. © American Society for Mass Spectrometry, 2011

Nonenzymatic catalytic signal amplification for nucleic acid hybridization assays

NASA Technical Reports Server (NTRS)

Fan, Wenhong (Inventor); Han, Jie (Inventor); Cassell, Alan M. (Inventor)

2006-01-01

Devices, methods, and kits for amplifying the signal from hybridization reactions between nucleic acid probes and their cognate targets are presented. The devices provide partially-duplexed, immobilized probe complexes, spatially separate from and separately addressable from immobilized docking strands. Cognate target acts catalytically to transfer probe from the site of probe complex immobilization to the site of immobilized docking strand, generating a detectable signal. The methods and kits of the present invention may be used to identify the presence of cognate target in a fluid sample.

SERS diagnostic platforms, methods and systems microarrays, biosensors and biochips

DOEpatents

Vo-Dinh, Tuan [Knoxville, TN

2007-09-11

A Raman integrated sensor system for the detection of targets including biotargets includes at least one sampling platform, at least one receptor probe disposed on the sampling platform, and an integrated circuit detector system communicably connected to the receptor. The sampling platform is preferably a Raman active surface-enhanced scattering (SERS) platform, wherein the Raman sensor is a SERS sensor. The receptors can include at least one protein receptor and at least one nucleic acid receptor.

Interfacial Shear Strength and Adhesive Behavior of Silk Ionomer Surfaces.

PubMed

Kim, Sunghan; Geryak, Ren D; Zhang, Shuaidi; Ma, Ruilong; Calabrese, Rossella; Kaplan, David L; Tsukruk, Vladimir V

2017-09-11

The interfacial shear strength between different layers in multilayered structures of layer-by-layer (LbL) microcapsules is a crucial mechanical property to ensure their robustness. In this work, we investigated the interfacial shear strength of modified silk fibroin ionomers utilized in LbL shells, an ionic-cationic pair with complementary ionic pairing, (SF)-poly-l-glutamic acid (Glu) and SF-poly-l-lysine (Lys), and a complementary pair with partially screened Coulombic interactions due to the presence of poly(ethylene glycol) (PEG) segments and SF-Glu/SF-Lys[PEG] pair. Shearing and adhesive behavior between these silk ionomer surfaces in the swollen state were probed at different spatial scales and pressure ranges by using functionalized atomic force microscopy (AFM) tips as well as functionalized colloidal probes. The results show that both approaches were consistent in analyzing the interfacial shear strength of LbL silk ionomers at different spatial scales from a nanoscale to a fraction of a micron. Surprisingly, the interfacial shear strength between SF-Glu and SF-Lys[PEG] pair with partially screened ionic pairing was greater than the interfacial shear strength of the SF-Glu and SF-Lys pair with a high density of complementary ionic groups. The difference in interfacial shear strength and adhesive strength is suggested to be predominantly facilitated by the interlayer hydrogen bonding of complementary amino acids and overlap of highly swollen PEG segments.

Guanine oxidation signal enhancement in DNA via a polyacrylonitrile nanofiber-coated and cyclic voltammetry-treated pencil graphite electrode

NASA Astrophysics Data System (ADS)

Aladag Tanik, Nilay; Demirkan, Elif; Aykut, Yakup

2018-07-01

This study investigated the electrochemical detection of specific nucleic acid hybridization sequences using a nanofiber-coated pencil graphite biosensor. The biosensor was developed to detect Val66Met single point mutations in the brain-derived neurotrophic factor gene, which is frequently observed in neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and bipolar disorder. The oxidation signal of the most electroactive and stable DNA base, i.e., guanine, was used at approximately +1.0 V. Pencil graphite electrode (PGE) surfaces were coated with polyacrylonitrile nanofibers by electrospinning. Cyclic voltammetry was applied to the nanofiber-coated PGE to pretreat its surfaces. The application of cyclic voltammetry to the nanofiber-coated PGE surfaces before attaching the probe yielded a four fold increase in the oxidation signal for guanine compared with that using the untreated and uncoated PGE surface. The signal reductions were 70% for hybridization, 10% for non-complementary binding, and 14% for a single mismatch compared with the probe. The differences in full match, non-complementary, and mismatch binding indicated that the biosensor selectively detected the target, and that it was possible to determine hybridization in about 65 min. The detection limit was 0.19 μg/ml at a target concentration of 10 ppm.

A multi-parametric assessment of decontamination protocols for the subglacial Lake Ellsworth probe.

PubMed

Magiopoulos, I; McQuillan, J S; Burd, C L; Mowlem, M; Tsaloglou, M-N

2016-04-01

Direct measurement and sampling of pristine environments, such as subglacial lakes, without introducing contaminating microorganisms and biomolecules from the surface, represents a significant engineering and microbiological challenge. In this study, we compare methods for decontamination of titanium grade 5 surfaces, the material extensively used to construct a custom-made probe for reaching, measuring and sampling subglacial Lake Ellsworth in West Antarctica. Coupons of titanium were artificially contaminated with Pseudomonas fluorescens bacteria and then exposed to a number of decontamination procedures. The most effective sterilants were (i) hydrogen peroxide vapour, and (ii) Biocleanse™, a commercially available, detergent-based biocidal solution. After each decontamination procedure the bacteria were incapable of proliferation, and showed no evidence of metabolic activity based on the generation of adenosine triphosphate (ATP). The use of ultraviolet irradiation or ethyl alcohol solution was comparatively ineffective for sterilisation. Hydrogen peroxide vapour and ultraviolet irradiation, which directly damage nucleic acids, were the most effective methods for removing detectable DNA, which was measured using 16S rRNA gene copy number and fluorescence-based total DNA quantification. Our results have not only been used to tailor the Ellsworth probe decontamination process, but also hold value for subsequent engineering projects, where high standards of decontamination are required. Copyright © 2016 Elsevier B.V. All rights reserved.

Enhanced solid-phase recombinase polymerase amplification and electrochemical detection.

PubMed

Del Río, Jonathan Sabaté; Lobato, Ivan Magriñà; Mayboroda, Olena; Katakis, Ioanis; O'Sullivan, Ciara K

2017-05-01

Recombinase polymerase amplification (RPA) is an elegant method for the rapid, isothermal amplification of nucleic acids. Here, we elucidate the optimal surface chemistry for rapid and efficient solid-phase RPA, which was fine-tuned in order to obtain a maximum signal-to-noise ratio, defining the optimal DNA probe density, probe-to-lateral spacer ratio (1:0, 1:1, 1:10 and 1:100) and length of a vertical spacer of the probe as well as investigating the effect of different types of lateral spacers. The use of different labelling strategies was also examined in order to reduce the number of steps required for the analysis, using biotin or horseradish peroxidase-labelled reverse primers. Optimisation of the amplification temperature used and the use of surface blocking agents were also pursued. The combination of these changes facilitated a significantly more rapid amplification and detection protocol, with a lowered limit of detection (LOD) of 1 · 10 -15 M. The optimised protocol was applied to the detection of Francisella tularensis in real samples from hares and a clear correlation with PCR and qPCR results observed and the solid-phase RPA demonstrated to be capable of detecting 500 fM target DNA in real samples. Graphical abstract Relative size of thiolated lateral spacers tested versus the primer and the uvsx recombinase protein.

Glucose oxidase probe as a surface-enhanced Raman scattering sensor for glucose.

PubMed

Qi, Guohua; Wang, Yi; Zhang, Biying; Sun, Dan; Fu, Cuicui; Xu, Weiqing; Xu, Shuping

2016-10-01

Glucose oxidase (GOx) possessing a Raman-active chromophore (flavin adenine dinucleotide) is used as a signal reporter for constructing a highly specific "turn off" surface-enhanced Raman scattering (SERS) sensor for glucose. This sensing chip is made by the electrostatic assembly of GOx over silver nanoparticle (Ag NP)-functionalized SERS substrate through a positively charged polyelectrolyte linker under the pH of 6.86. To trace glucose in blood serum, owing to the reduced pH value caused by the production of gluconic acid in the GOx-catalyzed oxidation reaction, the bonding force between GOx and polyelectrolyte weakens, making GOx drop off from the sensing chip. As a result, the SERS intensity of GOx on the chip decreases along with the concentration of glucose. This glucose SERS sensor exhibits excellent selectivity based on the specific GOx/glucose catalysis reaction and high sensitivity to 1.0 μM. The linear sensing range is 2.0-14.0 mM, which also meets the requirement on the working range of the human blood glucose detection. Using GOx as a probe shows superiority over other organic probes because GOx almost has no toxicity to the biological system. This sensing mechanism can be applied for intracellular in vivo SERS monitoring of glucose in the future. Graphical abstract Glucose oxidase is used as a Raman signal reporter for constructing a highly specific glucose surface-enhanced Raman scattering (SERS) sensor.

An off-on fluorescence probe targeting mitochondria based on oxidation-reduction response for tumor cell and tissue imaging

NASA Astrophysics Data System (ADS)

Yao, Hanchun; Cao, Li; Zhao, Weiwei; Zhang, Suge; Zeng, Man; Du, Bin

2017-10-01

In this study, a tumor-targeting poly( d, l-lactic-co-glycolic acid) (PLGA) loaded "off-on" fluorescent probe nanoparticle (PFN) delivery system was developed to evaluate the region of tumor by off-on fluorescence. The biodegradability of the nanosize PFN delivery system readily released the probe under tumor acidic conditions. The probe with good biocompatibility was used to monitor the intracellular glutathione (GSH) of cancer cells and selectively localize to mitochondria for tumor imaging. The incorporated tumor-targeting probe was based on the molecular photoinduced electron transfer (PET) mechanism preventing fluorescence ("off" state) and could be easily released under tumor acidic conditions. However, the released tumor-targeting fluorescence probe molecule was selective towards GSH with high selectivity and an ultra-sensitivity for the mitochondria of cancer cells and tissues significantly increasing the probe molecule fluorescence signal ("on" state). The tumor-targeting fluorescence probe showed sensitivity to GSH avoiding interference from cysteine and homocysteine. The PFNs could enable fluorescence-guided cancer imaging during cancer therapy. This work may expand the biological applications of PFNs as a diagnostic reagent, which will be beneficial for fundamental research in tumor imaging. [Figure not available: see fulltext.

Origin of the selectivity in the gold-mediated oxidation of benzyl alcohol

NASA Astrophysics Data System (ADS)

Rodríguez-Reyes, Juan Carlos F.; Friend, Cynthia M.; Madix, Robert J.

2012-08-01

Benzyl alcohol has received substantial attention as a probe molecule to test the selectivity and efficiency of novel metallic gold catalysts. Herein, the mechanisms of benzyl alcohol oxidation on a gold surface covered with atomic oxygen are elucidated; the results show direct correspondence to the reaction on gold-based catalysts. The selective, partial oxidation of benzyl alcohol to benzaldehyde is achieved with low oxygen surface concentrations and takes place through dehydrogenation of the alcohol to form benzaldehyde via a benzyloxy (C6H5-CH2O) intermediate. While in this case atomic oxygen plays solely a dehydrogenating role, at higher concentrations it leads to the formation of intermediates from benzaldehyde, producing benzoic acid and CO2. Facile ester (benzyl benzoate) formation also occurs at low oxygen concentrations, which indicates that benzoic acid is not a precursor of further oxidation of the ester; instead, the ester is produced by the coupling of adsorbed benzyloxy and benzaldehyde. Key to the high selectivity seen at low oxygen concentrations is the fact that the production of the aldehyde (and esters) is kinetically favored over the production of benzoic acid.

Direct visualization of clay microfabric signatures driving organic matter preservation in fine-grained sediment

NASA Astrophysics Data System (ADS)

Curry, Kenneth J.; Bennett, Richard H.; Mayer, Lawrence M.; Curry, Ann; Abril, Maritza; Biesiot, Patricia M.; Hulbert, Matthew H.

2007-04-01

We employed direct visualization of organic matter (OM) sequestered by microfabric signatures in organo-clay systems to study mechanisms of OM protection. We studied polysaccharides, an abundant class of OM in marine sediments, associated with the nano- and microfabric of clay sediment using a novel application of transmission electron microscopy, histochemical staining (periodic acid-thiosemicarbazide-silver proteinate), and enzymatic digestion techniques. We used two experimental organo-clay sediment environments. First, laboratory-consolidated sediment with 10% chitin (w/w) added was probed for chitin before and after digestion with chitinase. Second, fecal pellets from the polychaete Heteromastus filiformis were used as a natural environment rich in clay and polysaccharides. Sections of this material were probed with silver proteinate for polysaccharides before and after digestion with a mixture of enzymes (amylase, cellulase, chitinase, dextranase, and pectinase). In both environments, chitin or other polysaccharides were found within pores, bridging clay domains, and attached to clay surfaces in undigested samples. Digested samples showed chitin or polysaccharides more closely associated with clay surfaces and in small pores. Our results imply protective roles for both sorption to clay surfaces and encapsulation within clay microfabric signatures.

Fluorescence turn-on detection of iodide, iodate and total iodine using fluorescein-5-isothiocyanate-modified gold nanoparticles.

PubMed

Chen, Yi-Ming; Cheng, Tian-Lu; Tseng, Wei-Lung

2009-10-01

Selective turn-on fluorescence detection of I(-) was accomplished using fluorescein isothiocyanate-decorated gold nanoparticles (FITC-AuNPs). FITC molecules, which fluoresce strongly in an alkaline solution, were severely quenched when they were attached to the surface of AuNPs through their isothiocyanate group. Upon the addition of I(-), FITC molecules were detached because of I(-) adsorption on the surface of AuNPs. As a result, released FITC molecules were restored to their original fluorescence intensity. Because I(-) has a higher binding affinity to the surface of Au than do Br(-), Cl(-), or F(-), the FITC-AuNPs obviously have a higher selectivity toward I(-) than toward these other anions. Meanwhile, after IO(3)(-) was reduced to I(-) with ascorbic acid, the detection of IO(3)(-) was successfully achieved using the FITC-AuNPs. Under an optimum pH and AuNP concentration, the lowest detectable concentrations of I(-) and IO(3)(-) using this probe were 10.0 and 50.0 nM, respectively. The FITC-AuNPs provide a number of advantages, including easy preparation, selectivity, sensitivity, and low cost. This unique probe was applied to an analysis of the total iodine in edible salt and seawater.

Optimizing the specificity of nucleic acid hybridization.

PubMed

Zhang, David Yu; Chen, Sherry Xi; Yin, Peng

2012-01-22

The specific hybridization of complementary sequences is an essential property of nucleic acids, enabling diverse biological and biotechnological reactions and functions. However, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature. Here, we analytically derived the thermodynamic properties of a hybridization probe that would enable near-optimal single-base discrimination and perform robustly across diverse temperature, salt and concentration conditions. We rationally designed 'toehold exchange' probes that approximate these properties, and comprehensively tested them against five different DNA targets and 55 spurious analogues with energetically representative single-base changes (replacements, deletions and insertions). These probes produced discrimination factors between 3 and 100+ (median, 26). Without retuning, our probes function robustly from 10 °C to 37 °C, from 1 mM Mg(2+) to 47 mM Mg(2+), and with nucleic acid concentrations from 1 nM to 5 µM. Experiments with RNA also showed effective single-base change discrimination.

Culturable Facultative Methylotrophic Bacteria from the Cactus Neobuxbaumia macrocephala Possess the Locus xoxF and Consume Methanol in the Presence of Ce3+ and Ca2+

PubMed Central

del Rocío Bustillos-Cristales, María; Corona-Gutierrez, Ivan; Castañeda-Lucio, Miguel; Águila-Zempoaltécatl, Carolina; Seynos-García, Eduardo; Hernández-Lucas, Ismael; Muñoz-Rojas, Jesús; Medina-Aparicio, Liliana; Fuentes-Ramírez, Luis Ernesto

2017-01-01

Methanol-consuming culturable bacteria were isolated from the plant surface, rhizosphere, and inside the stem of Neobuxbaumia macrocephala. All 38 isolates were facultative methylotrophic microorganisms. Their classification included the Classes Actinobacteria, Sphingobacteriia, Alpha-, Beta-, and Gammaproteobacteria. The deduced amino acid sequences of methanol dehydrogenase obtained by PCR belonging to Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria showed high similarity to rare-earth element (REE)-dependent XoxF methanol dehydrogenases, particularly the group XoxF5. The sequences included Asp301, the REE-coordinating amino acid, present in all known XoxF dehydrogenases and absent in MxaF methanol dehydrogenases. The quantity of the isolates showed positive hybridization with a xoxF probe, but not with a mxaF probe. Isolates of all taxonomic groups showed methylotrophic growth in the presence of Ce3+ or Ca2+. The presence of xoxF-like sequences in methylotrophic bacteria from N. macrocephala and its potential relationship with their adaptability to xerophytic plants are discussed. PMID:28855445

Characterisation of embroidered 3D electrodes by use of anthraquinone-1,5-disulfonic acid as probe system

NASA Astrophysics Data System (ADS)

Aguiló-Aguayo, Noemí; Bechtold, Thomas

2014-05-01

New electrode designs are required for electrochemical applications such as batteries or fuel cells. Embroidered 3D Cu porous electrodes with a geometric surface of 100 cm2 are presented and characterised by means of the anthraquinone-1,5-disfulfonic acid (AQDS2-) redox system in alkaline solution. The electrochemical behaviour of the 3D electrode is established by the comparison of cyclic voltammetry responses using a micro cell and a 100 cm2 plane Cu-plate electrode. Dependencies of the peak currents and peak-to-peak potential separation on scan rate and AQDS2- concentration are studied. The AQDS2- characterisation is also performed by means of spectroelectrochemical experiments.

Method for making a hot wire anemometer and product thereof

NASA Technical Reports Server (NTRS)

Milkulla, V. (Inventor)

1977-01-01

A hot wire anemometer probe is described that includes a ceramic body supporting two conductive rods parallel to each other. The body has a narrow edge surface from which the rods protrude. A probe wire is welded to the rods and extends along the edge surface. A ceramic adhesive is used to secure the probe wire to the surface so that the probe wire is rigid. A method for fabricating the probe is also described in which the body is molded and precisely shaped by machining techniques before the probe wires are installed.

A novel and sensitive fluorescence sensor for glutathione detection by controlling the surface passivation degree of carbon quantum dots.

PubMed

Pan, Jiahong; Zheng, Zengyao; Yang, Jianying; Wu, Yaoyu; Lu, Fushen; Chen, Yaowen; Gao, Wenhua

2017-05-01

A novel fluorescence sensor based on controlling the surface passivation degree of carbon quantum dots (CQDs) was developed for glutathione (GSH) detection. First, we found that the fluorescence intensity of the CQDs which was obtained by directly pyrolyzing citric acid would increased largely after the surface passivation treatment by 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC). In the light of this phenomenon, we designed a simple, rapid and selective fluorescence sensor based on the surface passivated CQDs. A certain and excess amount of EDC were mixed with GSH, part of EDC would form a stable complex with GSH owing to the exposed sulfhydryl group of GSH. As the synthesized CQDs were added into the above mixture solution, the fluorescence intensity of the (EDC/GSH)/CQDs mixture solution could be directly related to the amount of GSH. Compared to other fluorescence analytical methods, the fluorescence sensor we design is neither the traditional fluorescent "turn on" probes nor "turn off" probes. It is a new fluorescence analytical method that target object indirectly control the surface passivation degree of CQDs so that it can realize the detection of the target object. Moreover, the proposed method manifested great advantages including short analysis time, low cost and ease of operation. Copyright © 2017 Elsevier B.V. All rights reserved.

Conducting electrospun fibres with polyanionic grafts as highly selective, label-free, electrochemical biosensor with a low detection limit for non-Hodgkin lymphoma gene.

PubMed

Kerr-Phillips, Thomas E; Aydemir, Nihan; Chan, Eddie Wai Chi; Barker, David; Malmström, Jenny; Plesse, Cedric; Travas-Sejdic, Jadranka

2018-02-15

A highly selective, label-free sensor for the non-Hodgkin lymphoma gene, with an aM detection limit, utilizing electrochemical impedance spectroscopy (EIS) is presented. The sensor consists of a conducting electrospun fibre mat, surface-grafted with poly(acrylic acid) (PAA) brushes and a conducting polymer sensing element with covalently attached oligonucleotide probes. The sensor was fabricated from electrospun NBR rubber, embedded with poly(3,4-ethylenedioxythiophene) (PEDOT), followed by grafting poly(acrylic acid) brushes and then electrochemically polymerizing a conducting polymer monomer with ssDNA probe sequence pre-attached. The resulting non-Hodgkin lymphoma gene sensor showed a detection limit of 1aM (1 × 10 -18 mol/L), more than 400 folds lower compared to a thin-film analogue. The sensor presented extraordinary selectivity, with only 1%, 2.7% and 4.6% of the signal recorded for the fully non-complimentary, T-A and G-C base mismatch oligonucleotide sequences, respectively. We suggest that such greatly enhanced selectivity is due to the presence of negatively charged carboxylic acid moieties from PAA grafts that electrostatically repel the non-complementary and mismatch DNA sequences, overcoming the non-specific binding. Copyright © 2017 Elsevier B.V. All rights reserved.

Preparation and characterization of zinc oxide nanoparticles and their sensor applications for electrochemical monitoring of nucleic acid hybridization.

PubMed

Yumak, Tugrul; Kuralay, Filiz; Muti, Mihrican; Sinag, Ali; Erdem, Arzum; Abaci, Serdar

2011-09-01

In this study, ZnO nanoparticles (ZNP) of approximately 30 nm in size were synthesized by the hydrothermal method and characterized by X-ray diffraction (XRD), Braun-Emmet-Teller (BET) N2 adsorption analysis and transmission electron microscopy (TEM). ZnO nanoparticles enriched with poly(vinylferrocenium) (PVF+) modified single-use graphite electrodes were then developed for the electrochemical monitoring of nucleic acid hybridization related to the Hepatitis B Virus (HBV). Firstly, the surfaces of polymer modified and polymer-ZnO nanoparticle modified single-use pencil graphite electrodes (PGEs) were characterized using scanning electron microscopy (SEM). The electrochemical behavior of these electrodes was also investigated using differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). Subsequently, the polymer-ZnO nanoparticle modified PGEs were evaluated for the electrochemical detection of DNA based on the changes at the guanine oxidation signals. Various modifications in DNA oligonucleotides and probe concentrations were examined in order to optimize the electrochemical signals that were generated by means of nucleic acid hybridization. After the optimization studies, the sequence-selective DNA hybridization was investigated in the case of a complementary amino linked probe (target), or noncomplementary (NC) sequences, or target and mismatch (MM) mixture in the ratio of (1:1). Copyright © 2011 Elsevier B.V. All rights reserved.

Quantum dot-based microfluidic biosensor for cancer detection

NASA Astrophysics Data System (ADS)

Ghrera, Aditya Sharma; Pandey, Chandra Mouli; Ali, Md. Azahar; Malhotra, Bansi Dhar

2015-05-01

We report results of the studies relating to fabrication of an impedimetric microfluidic-based nucleic acid sensor for quantification of DNA sequences specific to chronic myelogenous leukemia (CML). The sensor chip is prepared by patterning an indium-tin-oxide (ITO) coated glass substrate via wet chemical etching method followed by sealing with polydimethylsiloxane (PDMS) microchannel for fluid control. The fabricated microfluidic chip comprising of a patterned ITO substrate is modified by depositing cadmium selenide quantum dots (QCdSe) via Langmuir-Blodgett technique. Further, the QCdSe surface has been functionalized with specific DNA probe for CML detection. The probe DNA functionalized QCdSe integrated miniaturized system has been used to monitor target complementary DNA concentration by measuring the interfacial charge transfer resistance via hybridization. The presence of complementary DNA in buffer solution significantly results in decreased electro-conductivity of the interface due to presence of a charge barrier for transport of the redox probe ions. The microfluidic DNA biosensor exhibits improved linearity in the concentration range of 10-15 M to 10-11 M.

The detection of HBV DNA with gold-coated iron oxide nanoparticle gene probes

NASA Astrophysics Data System (ADS)

Xi, Dong; Luo, XiaoPing; Lu, QiangHua; Yao, KaiLun; Liu, ZuLi; Ning, Qin

2008-03-01

Gold-coated iron oxide nanoparticle Hepatitis B virus (HBV) DNA probes were prepared, and their application for HBV DNA measurement was studied. Gold-coated iron oxide nanoparticles were prepared by the citrate reduction of tetra-chloroauric acid in the presence of iron oxide nanoparticles which were added as seeds. With a fluorescence-based method, the maximal surface coverage of hexaethiol 30-mer oligonucleotides and the maximal percentage of hybridization strands on gold-coated iron oxide nanoparticles were (120 ± 8) oligonucleotides per nanoparticle, and (14 ± 2%), respectively, which were comparable with those of (132 ± 10) and (22 ± 3%) in Au nanoparticle groups. Large network aggregates were formed when gold-coated iron oxide nanoparticle HBV DNA gene probe was applied to detect HBV DNA molecules as evidenced by transmission electron microscopy and the high specificity was verified by blot hybridization. Our results further suggested that detecting DNA with iron oxide nanoparticles and magnetic separator was feasible and might be an alternative effective method.

Method and apparatus for staining immobilized nucleic acids

DOEpatents

Ramsey, J. Michael; Foote, Robert S.; Jacobson, Stephen C.

2000-01-01

A method for staining immobilized nucleic acids includes the steps of affixing DNA probes to a solid substrate, moving target DNA material into proximity with the DNA probes, whereby the target DNA hybridized with specific ones of the DNA probes, and moving a fluorescent dye into proximity with the hybridized target DNA, whereby the fluorescent dye binds to the hybridized DNA to enable subsequent detection of fluorescence.

Characterizing monoclonal antibody structure by carboxyl group footprinting

PubMed Central

Kaur, Parminder; Tomechko, Sara E; Kiselar, Janna; Shi, Wuxian; Deperalta, Galahad; Wecksler, Aaron T; Gokulrangan, Giridharan; Ling, Victor; Chance, Mark R

2015-01-01

Structural characterization of proteins and their antigen complexes is essential to the development of new biologic-based medicines. Amino acid-specific covalent labeling (CL) is well suited to probe such structures, especially for cases that are difficult to examine by alternative means due to size, complexity, or instability. We present here a detailed account of carboxyl group labeling (with glycine ethyl ester (GEE) tagging) applied to a glycosylated monoclonal antibody therapeutic (mAb). The experiments were optimized to preserve the structural integrity of the mAb, and experimental conditions were varied and replicated to establish the reproducibility of the technique. Homology-based models were generated and used to compare the solvent accessibility of the labeled residues, which include aspartic acid (D), glutamic acid (E), and the C-terminus (i.e., the target probes), with the experimental data in order to understand the accuracy of the approach. Data from the mAb were compared to reactivity measures of several model peptides to explain observed variations in reactivity. Attenuation of reactivity in otherwise solvent accessible probes is documented as arising from the effects of positive charge or bond formation between adjacent amine and carboxyl groups, the latter accompanied by observed water loss. A comparison of results with previously published data by Deperalta et al using hydroxyl radical footprinting showed that 55% (32/58) of target residues were GEE labeled in this study whereas the previous study reported 21% of the targets were labeled. Although the number of target residues in GEE labeling is fewer, the two approaches provide complementary information. The results highlight advantages of this approach, such as the ease of use at the bench top, the linearity of the dose response plots at high levels of labeling, reproducibility of replicate experiments (<2% variation in modification extent), the similar reactivity of the three target probes, and significant correlation of reactivity and solvent accessible surface area. PMID:25933350

Development and Application of Small-Subunit rRNA Probes for Assessment of Selected Thiobacillus Species and Members of the Genus Acidiphilium

PubMed Central

Peccia, Jordan; Marchand, Eric A.; Silverstein, Joann; Hernandez, Mark

2000-01-01

Culture-dependent studies have implicated sulfur-oxidizing bacteria as the causative agents of acid mine drainage and concrete corrosion in sewers. Thiobacillus species are considered the major representatives of the acid-producing bacteria in these environments. Small-subunit rRNA genes from all of the Thiobacillus and Acidiphilium species catalogued by the Ribosomal Database Project were identified and used to design oligonucleotide DNA probes. Two oligonucleotide probes were synthesized to complement variable regions of 16S rRNA in the following acidophilic bacteria: Thiobacillus ferrooxidans and T. thiooxidans (probe Thio820) and members of the genus Acidiphilium (probe Acdp821). Using 32P radiolabels, probe specificity was characterized by hybridization dissociation temperature (Td) with membrane-immobilized RNA extracted from a suite of 21 strains representing three groups of bacteria. Fluorochrome-conjugated probes were evaluated for use with fluorescent in situ hybridization (FISH) at the experimentally determined Tds. FISH was used to identify and enumerate bacteria in laboratory reactors and environmental samples. Probing of laboratory reactors inoculated with a mixed culture of acidophilic bacteria validated the ability of the oligonucleotide probes to track specific cell numbers with time. Additionally, probing of sediments from an active acid mine drainage site in Colorado demonstrated the ability to identify numbers of active bacteria in natural environments that contain high concentrations of metals, associated precipitates, and other mineral debris. PMID:10877807

A novel universal real-time PCR system using the attached universal duplex probes for quantitative analysis of nucleic acids.

PubMed

Yang, Litao; Liang, Wanqi; Jiang, Lingxi; Li, Wenquan; Cao, Wei; Wilson, Zoe A; Zhang, Dabing

2008-06-04

Real-time PCR techniques are being widely used for nucleic acids analysis, but one limitation of current frequently employed real-time PCR is the high cost of the labeled probe for each target molecule. We describe a real-time PCR technique employing attached universal duplex probes (AUDP), which has the advantage of generating fluorescence by probe hydrolysis and strand displacement over current real-time PCR methods. AUDP involves one set of universal duplex probes in which the 5' end of the fluorescent probe (FP) and a complementary quenching probe (QP) lie in close proximity so that fluorescence can be quenched. The PCR primer pair with attached universal template (UT) and the FP are identical to the UT sequence. We have shown that the AUDP technique can be used for detecting multiple target DNA sequences in both simplex and duplex real-time PCR assays for gene expression analysis, genotype identification, and genetically modified organism (GMO) quantification with comparable sensitivity, reproducibility, and repeatability with other real-time PCR methods. The results from GMO quantification, gene expression analysis, genotype identification, and GMO quantification using AUDP real-time PCR assays indicate that the AUDP real-time PCR technique has been successfully applied in nucleic acids analysis, and the developed AUDP real-time PCR technique will offer an alternative way for nucleic acid analysis with high efficiency, reliability, and flexibility at low cost.

Deoxyribonucleic Acid Probes Analyses for the Detection of Periodontal Pathogens.

PubMed

Al Yahfoufi, Zoubeida; Hadchiti, Wahib; Berberi, Antoine

2015-09-01

In clinical microbiology several techniques have been used to identify bacteria. Recently, Deoxyribonucleic acid (DNA)-based techniques have been introduced to detect human microbial pathogens in periodontal diseases. Deoxyribonucleic acid probes can detect bacteria at a very low level if we compared with the culture methods. These probes have shown rapid and cost-effective microbial diagnosis, good sensitivity and specificity for some periodontal pathogens in cases of severe periodontitis. Eighty-five patients were recruited for the study. Twenty-one subjects ranging between 22 and 48 years of age fulfilled the inclusion and exclusion criteria. Seventy-eight samples became available for DNA probe analysis from the deepest pockets in each quadrant. All 21 patients showed positive results for Prevotella intermedia; also, Prevotella gingivalis was identified in 19 subjects, Aggregatibacter actinomycetemcomitans in 6 subjects. P. intermedia was diagnosed positive in 82% of the subgingival samples taken, 79% for P. gingivalis, and 23% for A. actinomycetemcomitans. This study shows a high frequency of putative periodontal pathogens by using DNA probe technology, which is semi-quantitative in this study. Deoxyribonucleic acid probes can detect bacteria at very low level about 10(3) which is below the detection level of culture methods. The detection threshold of cultural methods. The three types of bacteria can be detected rapidly with high sensitivity by using the DNA probe by general practitioners, and thus can help in the diagnosis process and the treatment.

Highly specific and reversible fluoride sensor based on an organic semiconductor.

PubMed

Aboubakr, Hecham; Brisset, Hugues; Siri, Olivier; Raimundo, Jean-Manuel

2013-10-15

A novel sulfonamide-conjugated benzo-[2,1-b:3,4-b']bithiophene semiconductor has been designed and synthetized in order to develop a probe for specific detection of anions both in the homogeneous (solution) and heterogeneous phase. Its photophysical and electrochemical data were reported in this study. On the basis of the optical and NMR titrations analysis, the chelator was found to be highly selective for fluoride compared to others anions (Ka = 1.6 × 10(4) M(-1) in dimethyl sulfoxide (DMSO)). In addition, from an intricate sample, the novel chelator shows exceptional specificity toward fluoride and reveals a complete reversibility after addition of trifluoroacetic acid (TFA). Sensing films were obtained by electrochemical polymerization of the probe on an electrode surface, which clearly show effective detection of fluoride.

Art By Don Davis Artist's concept of one of the probes on the hot surface of Venus. Although the

NASA Technical Reports Server (NTRS)

1977-01-01

Art By Don Davis Artist's concept of one of the probes on the hot surface of Venus. Although the probes were not designed to withstand impact, there was a chance that one might survive and transmit some data from the surface. A small probe did survive and transmitted data for 67 minutes.

Simultaneous surface and depth neural activity recording with graphene transistor-based dual-modality probes.

PubMed

Du, Mingde; Xu, Xianchen; Yang, Long; Guo, Yichuan; Guan, Shouliang; Shi, Jidong; Wang, Jinfen; Fang, Ying

2018-05-15

Subdural surface and penetrating depth probes are widely applied to record neural activities from the cortical surface and intracortical locations of the brain, respectively. Simultaneous surface and depth neural activity recording is essential to understand the linkage between the two modalities. Here, we develop flexible dual-modality neural probes based on graphene transistors. The neural probes exhibit stable electrical performance even under 90° bending because of the excellent mechanical properties of graphene, and thus allow multi-site recording from the subdural surface of rat cortex. In addition, finite element analysis was carried out to investigate the mechanical interactions between probe and cortex tissue during intracortical implantation. Based on the simulation results, a sharp tip angle of π/6 was chosen to facilitate tissue penetration of the neural probes. Accordingly, the graphene transistor-based dual-modality neural probes have been successfully applied for simultaneous surface and depth recording of epileptiform activity of rat brain in vivo. Our results show that graphene transistor-based dual-modality neural probes can serve as a facile and versatile tool to study tempo-spatial patterns of neural activities. Copyright © 2018 Elsevier B.V. All rights reserved.

Eddy-Current Inspection of Ball Bearings

NASA Technical Reports Server (NTRS)

Bankston, B.

1985-01-01

Custom eddy-current probe locates surface anomalies. Low friction air cushion within cone allows ball to roll easily. Eddy current probe reliably detects surface and near-surface cracks, voids, and material anomalies in bearing balls or other spherical objects. Defects in ball surface detected by probe displayed on CRT and recorded on strip-chart recorder.

Rapid detection of IHNV by molecular padlock recognition and surface-associated isothermal amplification

NASA Astrophysics Data System (ADS)

McCarthy, Erik L.; Egeler, Teressa J.; Bickerstaff, Lee E.; Pereira da Cunha, Mauricio; Millard, Paul J.

2005-11-01

RNA sequences derived from infectious hematopoeitic necrosis virus (IHNV) could be detected using a combination of surface-associated molecular padlock DNA probes (MPP) and rolling circle amplification (RCA) in microcapillary tubes. DNA oligonucleotides with base sequences identical to RNA obtained from IHNV were recognized by MPP. Circularized MPP were then captured on the inner surface of glass microcapillary tubes by immobilized DNA oligonucleotide primers. Extension of the immobilized primers by isothermal RCA gave rise to DNA concatamers, which were in turn bound by the fluorescent reporter SYBR Green II nucleic acid stain, and measured by microfluorimetry. Surface-associated molecular padlock technology, combined with isothermal RCA, exhibited high selectivity and sensitivity without thermal cycling. This technology is applicable to direct RNA and DNA detection, permitting detection of a variety of viral or bacterial pathogens.

The surface chemical reactivity of particles and its impact on human health

NASA Astrophysics Data System (ADS)

Setyan, A.; Sauvain, J. J.; Riediker, M.; Guillemin, M.; Rossi, M. J.

2017-12-01

The chemical composition of the particle-air interface is the gateway to chemical reactions of gases with condensed phase particles. It is of prime importance to understand the reactivity of particles and their interaction with surrounding gases, biological membranes, and solid supports. We used a Knudsen flow reactor to quantify functional groups on the surface of a few selected particle types. This technique is based on a heterogeneous titration reaction between a probe gas and a specific functional group on the particle surface. Six probe gases have been selected for the identification and quantification of important functional groups: N(CH3)3 for the titration of acidic sites, NH2OH for the detection of carbonyl functions (aldehydes and ketones) and/or oxidized sites owing to its strong reducing properties, CF3COOH and HCl for basic sites of different strength, O3 and NO2 for oxidizable groups. We also studied the kinetics of the reactions between particles and probe gases (uptake coefficient γ0). We tested the surface chemical composition and oxidation states of laboratory-generated aerosols (3 amorphous carbons, 2 flame soots, 2 Diesel particles, 2 secondary organic aerosols [SOA], 4 multiwall carbon nanotubes [MWCNT], 3 TiO2, and 2 metal salts) and of aerosols sampled in several bus depots. The sampling of particles in the bus depots was accompanied by the collection of urine samples of mechanics working full-time in these bus depots, and the quantification of 8-hydroxy-2'-deoxyguanosine, a biomarker of oxidative stress. The increase in oxidative stress biomarker levels over a working day was correlated (p<0.05) with the number of olefinic and/or PAH sites on the surface of particles sampled at the bus depots, obtained from O3 uptakes, as well as with the initial uptake coefficient (γ0) of five probe gases used in the field. This correlation with γ0 suggests the idea of competing pathways occurring at the interface of the aerosol particles between the generation of reactive oxygen species (ROS) responsible for oxidative stress and cellular antioxidants.

Synthesis and characterization of 64SiO2-26CaO-5P2O5-5CuO bioactive composition for the growth of hydroxyapatite layer by XRD, Raman and pH studies

NASA Astrophysics Data System (ADS)

Kaur, Pardeep; Singh, K. J.

2016-05-01

Bioactive sample with the nominal composition of 64SiO2-26CaO-5P2O5-5CuO has been prepared in the laboratory by using the sol-gel technique. The bioactivity of the prepared sample has been analyzed by using the Tris Simulated Body Fluid which has also been prepared in the laboratory. XRD and Raman techniques have been employedto probe the formation of hydroxyapatite layer. pH studies has also been undertaken to check the acidic/non-acidic behavior of sample. Growth of hydroxyapatite layer has been observed after one day on the surface of the sample. Moreover, sample has been observed to be non-acidic in nature.

Carbon Nanotube Tip Probes: Stability and Lateral Resolution in Scanning Probe Microscopy and Application to Surface Science to Semiconductors

NASA Technical Reports Server (NTRS)

Nguyen, Cattien V.; Chao, Kuo-Jen; Stevens, Ramsey M. D.; Delzeit, Lance; Cassell, Alan; Han, Jie; Meyyappan, M.; Arnold, James (Technical Monitor)

2001-01-01

In this paper we present results on the stability and lateral resolution capability of carbon nanotube (CNT) scanning probes as applied to atomic force microscopy (AFM). Surface topography images of ultra-thin films (2-5 nm thickness) obtained with AFM are used to illustrate the lateral resolution capability of single-walled carbon nanotube probes. Images of metal films prepared by ion beam sputtering exhibit grain sizes ranging from greater than 10 nm to as small as approximately 2 nm for gold and iridium respectively. In addition, imaging stability and lifetime of multi-walled carbon nanotube scanning probes are studied on a relatively hard surface of silicon nitride (Si3N4). AFM images Of Si3N4 surface collected after more than 15 hrs of continuous scanning show no detectable degradation in lateral resolution. These results indicate the general feasibility of CNT tips and scanning probe microscopy for examining nanometer-scale surface features of deposited metals as well as non-conductive thin films. AFM coupled with CNT tips offers a simple and nondestructive technique for probing a variety of surfaces, and has immense potential as a surface characterization tool in integrated circuit manufacturing.

Examining Model Atmospheric Particles Inside and Out

NASA Astrophysics Data System (ADS)

Wingen, L. M.; Zhao, Y.; Fairhurst, M. C.; Perraud, V. M.; Ezell, M. J.; Finlayson-Pitts, B. J.

2017-12-01

Atmospheric particles scatter incoming solar radiation and act as cloud condensation nuclei (CCN), thereby directly and indirectly affecting the earth's radiative balance and reducing visibility. These atmospheric particles may not be uniform in composition. Differences in the composition of a particle's outer surface from its core can arise during particle growth, (photo)chemical aging, and exchange of species with the gas phase. The nature of the surface on a molecular level is expected to impact growth mechanisms as well as their ability to act as CCN. Model laboratory particle systems are explored using direct analysis in real time-mass spectrometry (DART-MS), which is sensitive to surface composition, and contrasted with average composition measurements using high resolution, time-of-flight aerosol mass spectrometry (HR-ToF-AMS). Results include studies of the heterogeneous reactions of amines with solid dicarboxylic acid particles, which are shown to generate aminium dicarboxylate salts at the particle surface, leaving an unreacted core. Combination of both mass spectrometric techniques reveals a trend in reactivity of C3-C7 dicarboxylic acids with amines and allows calculation of the DART probe depth into the particles. The results of studies on additional model systems that are currently being explored will also be reported.

Probing the Interaction of Dielectric Nanoparticles with Supported Lipid Membrane Coatings on Nanoplasmonic Arrays

PubMed Central

Ferhan, Abdul Rahim; Ma, Gamaliel Junren; Jackman, Joshua A.; Sut, Tun Naw; Park, Jae Hyeon; Cho, Nam-Joon

2017-01-01

The integration of supported lipid membranes with surface-based nanoplasmonic arrays provides a powerful sensing approach to investigate biointerfacial phenomena at membrane interfaces. While a growing number of lipid vesicles, protein, and nucleic acid systems have been explored with nanoplasmonic sensors, there has been only very limited investigation of the interactions between solution-phase nanomaterials and supported lipid membranes. Herein, we established a surface-based localized surface plasmon resonance (LSPR) sensing platform for probing the interaction of dielectric nanoparticles with supported lipid bilayer (SLB)-coated, plasmonic nanodisk arrays. A key emphasis was placed on controlling membrane functionality by tuning the membrane surface charge vis-à-vis lipid composition. The optical sensing properties of the bare and SLB-coated sensor surfaces were quantitatively compared, and provided an experimental approach to evaluate nanoparticle–membrane interactions across different SLB platforms. While the interaction of negatively-charged silica nanoparticles (SiNPs) with a zwitterionic SLB resulted in monotonic adsorption, a stronger interaction with a positively-charged SLB resulted in adsorption and lipid transfer from the SLB to the SiNP surface, in turn influencing the LSPR measurement responses based on the changing spatial proximity of transferred lipids relative to the sensor surface. Precoating SiNPs with bovine serum albumin (BSA) suppressed lipid transfer, resulting in monotonic adsorption onto both zwitterionic and positively-charged SLBs. Collectively, our findings contribute a quantitative understanding of how supported lipid membrane coatings influence the sensing performance of nanoplasmonic arrays, and demonstrate how the high surface sensitivity of nanoplasmonic sensors is well-suited for detecting the complex interactions between nanoparticles and lipid membranes. PMID:28644423

Highly Sensitive Detection of Target Biomolecules on Cell Surface Using Gold Nanoparticle Conjugated with Aptamer Probe

NASA Astrophysics Data System (ADS)

Kim, Hyonchol; Terazono, Hideyuki; Hayashi, Masahito; Takei, Hiroyuki; Yasuda, Kenji

2012-06-01

A method of gold nanoparticle (Au NP) labeling with backscattered electron (BE) imaging of field emission scanning electron microscopy (FE-SEM) was applied for specific detection of target biomolecules on a cell surface. A single-stranded DNA aptamer, which specifically binds to the target molecule on a human acute lymphoblastic leukemia cell, was conjugated with a 20 nm Au NP and used as a probe to label its target molecule on the cell. The Au NP probe was incubated with the cell, and the interaction was confirmed using BE imaging of FE-SEM through direct counting of the number of Au NPs attached on the target cell surface. Specific Au NP-aptamer probes were observed on a single cell surface and their spatial distributions including submicron-order localizations were also clearly visualized, whereas the nonspecific aptamer probes were not observed on it. The aptamer probe can be potentially dislodged from the cell surface with treatment of nucleases, indicating that Au NP-conjugated aptamer probes can be used as sensitive and reversible probes to label target biomolecules on cells.

Kinetics and efficiency of the hydrated electron-induced dehalogenation by the sulfite/UV process.

PubMed

Li, Xuchun; Fang, Jingyun; Liu, Guifang; Zhang, Shujuan; Pan, Bingcai; Ma, Jun

2014-10-01

Hydrated electron (e(aq)(-)), which is listed among the most reactive reducing species, has great potential for removal and detoxification of recalcitrant contaminants. Here we provided quantitative insight into the availability and conversion of e(aq)(-) in a newly developed sulfite/UV process. Using monochloroacetic acid as a simple e(aq)(-)-probe, the e(aq)(-)-induced dehalogenation kinetics in synthetic and surface water was well predicted by the developed models. The models interpreted the complex roles of pH and S(IV), and also revealed the positive effects of UV intensity and temperature quantitatively. Impacts of humic acid, ferrous ion, carbonate/bicarbonate, and surface water matrix were also examined. Despite the retardation of dehalogenation by electron scavengers, the process was effective even in surface water. Efficiency of the process was discussed, and the optimization approaches were proposed. This study is believed to better understand the e(aq)(-)-induced dehalogenation by the sulfite/UV process in a quantitative manner, which is very important for its potential application in water treatment. Copyright © 2014 Elsevier Ltd. All rights reserved.

Unraveling the Nature of Active Sites in Ethanol Electro-oxidation by Site-Specific Marking of a Pt Catalyst with Isotope-Labeled 13CO.

PubMed

Farias, Manuel J S; Cheuquepán, William; Tanaka, Auro A; Feliu, Juan M

2018-03-15

This works deals with the identification of preferential site-specific activation at a model Pt surface during a multiproduct reaction. The (110)-type steps of a Pt(332) surface were selectively marked by attaching isotope-labeled 13 CO molecules to them, and ethanol oxidation was probed by in situ Foureir transfrom infrared spectroscopy in order to precisely determine the specific sites at which CO 2 , acetic acid, and acetaldehyde were preferentially formed. The (110) steps were active for splitting the C-C bond, but unexpectedly, we provide evidence that the pathway of CO 2 formation was preferentially activated at (111) terraces, rather than at (110) steps. Acetaldehyde was formed at (111) terraces at potentials comparable to those for CO 2 formation also at (111) terraces, while the acetic acid formation pathway became active only when the (110) steps were released by the oxidation of adsorbed 13 CO, at potentials higher than for the formation of CO 2 at (111) terraces of the stepped surface.

Experimental and computational investigation of acetic acid deoxygenation over oxophilic molybdenum carbide: Surface chemistry and active site identity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaidle, Joshua A.; Blackburn, Jeffrey; Farberow, Carrie A.

Ex situ catalytic fast pyrolysis (CFP) is a promising route for producing fungible biofuels; however, this process requires bifunctional catalysts that favor C–O bond cleavage, activate hydrogen at near atmospheric pressure and high temperature (350–500 °C), and are stable under high-steam, low hydrogen-to-carbon environments. Recently, early transition-metal carbides have been reported to selectively cleave C–O bonds of alcohols, aldehydes, and oxygenated aromatics, yet there is limited understanding of the metal carbide surface chemistry under reaction conditions and the identity of the active sites for deoxygenation. In this study, we evaluated molybdenum carbide (Mo 2C) for the deoxygenation of acetic acid,more » an abundant component of biomass pyrolysis vapors, under ex situ CFP conditions, and we probed the Mo 2C surface chemistry, identity of the active sites, and deoxygenation pathways using in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations.« less

Experimental and computational investigation of acetic acid deoxygenation over oxophilic molybdenum carbide: Surface chemistry and active site identity

DOE PAGES

Schaidle, Joshua A.; Blackburn, Jeffrey; Farberow, Carrie A.; ...

2016-01-21

Ex situ catalytic fast pyrolysis (CFP) is a promising route for producing fungible biofuels; however, this process requires bifunctional catalysts that favor C–O bond cleavage, activate hydrogen at near atmospheric pressure and high temperature (350–500 °C), and are stable under high-steam, low hydrogen-to-carbon environments. Recently, early transition-metal carbides have been reported to selectively cleave C–O bonds of alcohols, aldehydes, and oxygenated aromatics, yet there is limited understanding of the metal carbide surface chemistry under reaction conditions and the identity of the active sites for deoxygenation. In this study, we evaluated molybdenum carbide (Mo 2C) for the deoxygenation of acetic acid,more » an abundant component of biomass pyrolysis vapors, under ex situ CFP conditions, and we probed the Mo 2C surface chemistry, identity of the active sites, and deoxygenation pathways using in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations.« less

Fluorogenic PNA probes

PubMed Central

2018-01-01

Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years. PMID:29507634

Synergistic Combination of Unquenching and Plasmonic Fluorescence Enhancement in Fluorogenic Nucleic Acid Hybridization Probes.

PubMed

Vietz, Carolin; Lalkens, Birka; Acuna, Guillermo P; Tinnefeld, Philip

2017-10-11

Fluorogenic nucleic acid hybridization probes are widely used for detecting and quantifying nucleic acids. The achieved sensitivity strongly depends on the contrast between a quenched closed form and an unquenched opened form with liberated fluorescence. So far, this contrast was improved by improving the quenching efficiency of the closed form. In this study, we modularly combine these probes with optical antennas used for plasmonic fluorescence enhancement and study the effect of the nanophotonic structure on the fluorescence of the quenched and the opened form. As quenched fluorescent dyes are usually enhanced more by fluorescence enhancement, a detrimental reduction of the contrast between closed and opened form was anticipated. In contrast, we could achieve a surprising increase of the contrast with full additivity of quenching of the dark form and fluorescence enhancement of the bright form. Using single-molecule experiments, we demonstrate that the additivity of the two mechanisms depends on the perfect quenching in the quenched form, and we delineate the rules for new nucleic acid probes for enhanced contrast and absolute brightness. Fluorogenic hybridization probes optimized not only for quenching but also for the brightness of the open form might find application in nucleic acid assays with PCR avoiding detection schemes.

Electro-Optic Surface Field Imaging System

DTIC Science & Technology

1989-06-01

ELECTRO - OPTIC SURFACE FIELD IMAGING SYSTEM L. E. Kingsley and W. R. Donaldson LABORATORY FOR LASER ENERGETICS University of Rochester 250 East...surface electric fields present during switch operation. The electro - optic , or Pockel’s effect, provides an extremely useful probe of surface electric...fields. Using the electro - optic effect, surface fields can be measured with an optical probe. This paper describes an electro - optic probe which is

Surface-enhanced Raman scattering (SERS) dosimeter and probe

DOEpatents

Vo-Dinh, Tuan

1995-01-01

A dosimeter and probe for measuring exposure to chemical and biological compounds is disclosed. The dosimeter or probe includes a collector which may be analyzed by surface-enhanced Raman spectroscopy. The collector comprises a surface-enhanced Raman scattering-active material having a coating applied thereto to improve the adsorption properties of the collector. The collector may also be used in automated sequential devises, in probe array devices.

Structure analysis of the single-domain Si(111)4 × 1-In surface by μ-probe Auger electron diffraction and μ-probe reflection high energy electron diffraction

NASA Astrophysics Data System (ADS)

Nakamura, N.; Anno, K.; Kono, S.

1991-10-01

A single-domain Si(111)4 × 1-In surface has been studied by μ-probe reflection high-energy electron diffraction (RHEED) to elucidate the symmetry of the 4 × 1 surface. Azimuthal diffraction patterns of In MNN Auger electron have been obtained by a μ-probe Auger electron diffraction (AED) apparatus from the single-domain Si(111)4 × 1-In surface. On the basis of information from scanning tunneling microscopy [J. Microsc. 152 (1988) 727] and under the assumption that the 4 × 1 surface is composed of In-overlayers, the μ-probe AED patterns were kinematically analyzed to reach a concrete model of indium arrangement.

Far-red fluorescent probes for canonical and non-canonical nucleic acid structures: current progress and future implications.

PubMed

Suseela, Y V; Narayanaswamy, Nagarjun; Pratihar, Sumon; Govindaraju, Thimmaiah

2018-02-05

The structural diversity and functional relevance of nucleic acids (NAs), mainly deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are indispensable for almost all living organisms, with minute aberrations in their structure and function becoming causative factors in numerous human diseases. The standard structures of NAs, termed canonical structures, are supported by Watson-Crick hydrogen bonding. Under special physiological conditions, NAs adopt distinct spatial organisations, giving rise to non-canonical conformations supported by hydrogen bonding other than the Watson-Crick type; such non-canonical structures have a definite function in controlling gene expression and are considered as novel diagnostic and therapeutic targets. Development of molecular probes for these canonical and non-canonical DNA/RNA structures has been an active field of research. Among the numerous probes studied, probes with turn-on fluorescence in the far-red (600-750 nm) region are highly sought-after due to minimal autofluorescence and cellular damage. Far-red fluorescent probes are vital for real-time imaging of NAs in live cells as they provide good resolution and minimal perturbation of the cell under investigation. In this review, we present recent advances in the area of far-red fluorescent probes of DNA/RNA and non-canonical G-quadruplex structures. For the sake of continuity and completeness, we provide a brief overview of visible fluorescent probes. Utmost importance is given to design criteria, characteristic properties and biological applications, including in cellulo imaging, apart from critical discussion on limitations of the far-red fluorescent probes. Finally, we offer current and future prospects in targeting canonical and non-canonical NAs specific to cellular organelles, through sequence- and conformation-specific far-red fluorescent probes. We also cover their implications in chemical and molecular biology, with particular focus on decoding various disease mechanisms involving NAs.

Eddy current probe response to open and closed surface flaws

NASA Technical Reports Server (NTRS)

Auld, B. A.; Muennemann, F.; Winslow, D. K.

1981-01-01

A general analysis of eddy current response to certain types of open and closed surface flaws is presented for both standard low-frequency and ferromagnetic-resonance (FMR) probes. It is shown analytically that for two-dimensional and three-dimensional surface flaws interrogated by a uniform probe field, the crack opening sensitivity increases with the operating frequency of the probe, this behavior being due to the Faraday induction effect. Experiments with low-frequency probes operating at or below 1 MHz and with the FMR probe operating at approximately 1000 MHz confirm this increase of the crack mouth opening displacement for practical situations where the probe field is not uniform in the vicinity of the flaw.

The role of probe oxide in local surface conductivity measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barnett, C. J.; Kryvchenkova, O.; Wilson, L. S. J.

2015-05-07

Local probe methods can be used to measure nanoscale surface conductivity, but some techniques including nanoscale four point probe rely on at least two of the probes forming the same low resistivity non-rectifying contact to the sample. Here, the role of probe shank oxide has been examined by carrying out contact and non-contact I V measurements on GaAs when the probe oxide has been controllably reduced, both experimentally and in simulation. In contact, the barrier height is pinned but the barrier shape changes with probe shank oxide dimensions. In non-contact measurements, the oxide modifies the electrostatic interaction inducing a quantummore » dot that alters the tunneling behavior. For both, the contact resistance change is dependent on polarity, which violates the assumption required for four point probe to remove probe contact resistance from the measured conductivity. This has implications for all nanoscale surface probe measurements and macroscopic four point probe, both in air and vacuum, where the role of probe oxide contamination is not well understood.« less

Dual-probe near-field fiber head with gap servo control for data storage applications.

PubMed

Fang, Jen-Yu; Tien, Chung-Hao; Shieh, Han-Ping D

2007-10-29

We present a novel fiber-based near-field optical head consisting of a straw-shaped writing probe and a flat gap sensing probe. The straw-shaped probe with a C-aperture on the end face exhibits enhanced transmission by a factor of 3 orders of magnitude over a conventional fiber probe due to a hybrid effect that excites both propagation modes and surface plasmon waves. In the gap sensing probe, the spacing between the probe and the disk surface functions as an external cavity. The high sensitivity of the output power to the change in the gap width is used as a feedback control signal. We characterize and design the straw-shaped writing probe and the flat gap sensing probe. The dual-probe system is installed on a conventional biaxial actuator to demonstrate the capability of flying over a disk surface with nanometer position precision.

An intramolecular charge transfer process based fluorescent probe for monitoring subtle pH fluctuation in living cells.

PubMed

Sun, Mingtai; Du, Libo; Yu, Huan; Zhang, Kui; Liu, Yang; Wang, Suhua

2017-01-01

It is crucial to monitor intracellular pH values and their fluctuation since the organelles of cells have different pH distribution. Herein we construct a new small molecule fluorescent probe HBT-O for monitoring the subtle pH values within the scope of neutral to acid in living cells. The probe exhibited good water solubility, a marked turquoise to olivine emission color change in response to pH, and tremendous fluorescence hypochromatic shift of ∼50nm (1718cm -1 ) as well as the increased fluorescence intensity when the pH value changed from neutral to acid. Thus, the probe HBT-O can distinguish the subtle changes in the range of normal pH values from neutral to acid with significant fluorescence changes. These properties can be attributed to the intramolecular charge transfer (ICT) process of the probe upon protonation in buffer solutions at varied pH values. Moreover, the probe was reversible and nearly non-toxic for living cells. Then the probe was successfully used to detect pH fluctuation in living cells by exhibiting different fluorescence colors and intensity. These findings demonstrate that the probe will find useful applications in biology and biomedical research. Copyright © 2016 Elsevier B.V. All rights reserved.

Detection and prevention of mycoplasma hominis infection

DOEpatents

DelVecchio, Vito G.; Gallia, Gary L.; McCleskey, Ferne K.

1997-01-21

The present invention is directed to a rapid and sensitive method for detecting Mycoplasma hominis using M. hominis-specific probes, oligonucleotides or antibodies. In particular a target sequence can be amplified by in vitro nucleic acid amplification techniques, detected by nucleic acid hybridization using the subject probes and oligonucleotides or detected by immunoassay using M. hominis-specific antibodies. M. hominis-specific nucleic acids which do not recognize or hybridize to genomic nucleic acid of other Mycoplasma species are also provided.

Four-probe measurements with a three-probe scanning tunneling microscope.

PubMed

Salomons, Mark; Martins, Bruno V C; Zikovsky, Janik; Wolkow, Robert A

2014-04-01

We present an ultrahigh vacuum (UHV) three-probe scanning tunneling microscope in which each probe is capable of atomic resolution. A UHV JEOL scanning electron microscope aids in the placement of the probes on the sample. The machine also has a field ion microscope to clean, atomically image, and shape the probe tips. The machine uses bare conductive samples and tips with a homebuilt set of pliers for heating and loading. Automated feedback controlled tip-surface contacts allow for electrical stability and reproducibility while also greatly reducing tip and surface damage due to contact formation. The ability to register inter-tip position by imaging of a single surface feature by multiple tips is demonstrated. Four-probe material characterization is achieved by deploying two tips as fixed current probes and the third tip as a movable voltage probe.

An in vitro bacterial adhesion assessment of surface-modified medical-grade PVC.

PubMed

Asadinezhad, Ahmad; Novák, Igor; Lehocký, Marián; Sedlarík, Vladimir; Vesel, Alenka; Junkar, Ita; Sáha, Petr; Chodák, Ivan

2010-06-01

Medical-grade polyvinyl chloride was surface modified by a multistep physicochemical approach to improve bacterial adhesion prevention properties. This was fulfilled via surface activation by diffuse coplanar surface barrier discharge plasma followed by radical graft copolymerization of acrylic acid through surface-initiated pathway to render a structured high density brush. Three known antibacterial agents, bronopol, benzalkonium chloride, and chlorhexidine, were then individually coated onto functionalized surface to induce biological properties. Various modern surface probe techniques were employed to explore the effects of the modification steps. In vitro bacterial adhesion and biofilm formation assay was performed. Escherichia coli strain was found to be more susceptible to modifications rather than Staphylococcus aureus as up to 85% reduction in adherence degree of the former was observed upon treating with above antibacterial agents, while only chlorhexidine could retard the adhesion of the latter by 50%. Also, plasma treated and graft copolymerized samples were remarkably effective to diminish the adherence of E. coli. Copyright 2010 Elsevier B.V. All rights reserved.

A novel single fluorophore-labeled double-stranded oligonucleotide probe for fluorescence-enhanced nucleic acid detection based on the inherent quenching ability of deoxyguanosine bases and competitive strand-displacement reaction.

PubMed

Zhang, Yingwei; Tian, Jingqi; Li, Hailong; Wang, Lei; Sun, Xuping

2012-01-01

We develop a novel single fluorophore-labeled double-stranded oligonucleotide (OND) probe for rapid, nanostructure-free, fluorescence-enhanced nucleic acid detection for the first time. We further demonstrate such probe is able to well discriminate single-base mutation in nucleic acid. The design takes advantage of an inherent quenching ability of guanine bases. The short strand of the probe is designed with an end-labeled fluorophore that is placed adjacent to two guanines as the quencher located on the long opposite strand, resulting in great quenching of dye fluorescence. In the presence of a target complementary to the long strand of the probe, a competitive strand-displacement reaction occurs and the long strand forms a more stable duplex with the target, resulting in the two strands of the probe being separated from each other. As a consequence of this displacement, the fluorophore and the quencher are no longer in close proximity and dye fluorescence increases, signaling the presence of target.

Surface-enhanced Raman scattering (SERS) dosimeter and probe

DOEpatents

Vo-Dinh, T.

1995-03-21

A dosimeter and probe for measuring exposure to chemical and biological compounds is disclosed. The dosimeter or probe includes a collector which may be analyzed by surface-enhanced Raman spectroscopy. The collector comprises a surface-enhanced Raman scattering-active material having a coating applied thereto to improve the adsorption properties of the collector. The collector may also be used in automated sequential devices, in probe array devices. 10 figures.

Surface-enhanced Raman scattering based nonfluorescent probe for multiplex DNA detection.

PubMed

Sun, Lan; Yu, Chenxu; Irudayaraj, Joseph

2007-06-01

To provide rapid and accurate detection of DNA markers in a straightforward, inexpensive, and multiplex format, an alternative surface-enhanced Raman scattering based probe was designed and fabricated to covalently attach both DNA probing sequence and nonfluorescent Raman tags to the surface of gold nanoparticles (DNA-AuP-RTag). The intensity of Raman signal of the probes could be controlled through the surface coverage of the nonfluorescent Raman tags (RTags). Detection sensitivity of these probes could be optimized by fine-tuning the amount of DNA molecules and RTags on the probes. Long-term stability of the DNA-AuP-RTag probes was found to be good (over 3 months). Excellent multiplexing capability of the DNA-AuP-RTag scheme was demonstrated by simultaneous identification of up to eight probes in a mixture. Detection of hybridization of single-stranded DNA to its complementary targets was successfully accomplished with a long-term goal to use nonfluorescent RTags in a Raman-based DNA microarray platform.

Surface-Enhanced Raman Scattering Based Nonfluorescent Probe for Multiplex DNA Detection

PubMed Central

Sun, Lan; Yu, Chenxu; Irudayaraj, Joseph

2008-01-01

To provide rapid and accurate detection of DNA markers in a straightforward, inexpensive and multiplex format, an alternative surface enhanced Raman scattering (SERS) based probe was designed and fabricated to covalently attach both DNA probing sequence and non-fluorescent Raman tags to the surface of gold nanoparticles (DNA-AuP-RTag). The intensity of Raman signal of the probes could be controlled through the surface coverage of the non-fluorescent Raman tags (RTags). Detection sensitivity of these probes could be optimized by fine-tuning the amount of DNA molecules and RTags on the probes. Long-term stability of the DNA-AuP-RTag probes was found to be good (over 3 months). Excellent multiplexing capability of the DNA-AuP-RTag scheme was demonstrated by simultaneous identification of up to eight probes in a mixture. Detection of hybridization of single-stranded DNA (ssDNA) to its complementary targets was successfully accomplished with a long-term goal to use non-fluorescent RTags in a Raman-based DNA microarray platform. PMID:17465531

A water-soluble rhodamine B-derived fluorescent probe for pH monitoring and imaging in acidic regions

NASA Astrophysics Data System (ADS)

Cui, Peng; Jiang, Xuekai; Sun, Junyong; Zhang, Qiang; Gao, Feng

2017-06-01

A structurally simple, water-soluble rhodamine-derivatived fluorescent probe, which is responsive to acidic pH, was conveniently synthesized via a one-step condensation reaction of rhodamine B hydrazide and 4-formybenzene-1,3-disulfonate. As a stable and highly sensitive pH sensor, the probe displays an approximately 50-fold fluorescence enhancement over the pH range of 7.16-4.89 as the structure of probe changes from spirocyclic (weak fluorescent) to ring-open (strong fluorescent) with decreasing pH. The synthesized fluorescent probe is applied to the detection of pH changes in vitro and in vivo bioimaging of immortalized gastric cancer cells, with satisfactory results.

A novel universal real-time PCR system using the attached universal duplex probes for quantitative analysis of nucleic acids

PubMed Central

Yang, Litao; Liang, Wanqi; Jiang, Lingxi; Li, Wenquan; Cao, Wei; Wilson, Zoe A; Zhang, Dabing

2008-01-01

Background Real-time PCR techniques are being widely used for nucleic acids analysis, but one limitation of current frequently employed real-time PCR is the high cost of the labeled probe for each target molecule. Results We describe a real-time PCR technique employing attached universal duplex probes (AUDP), which has the advantage of generating fluorescence by probe hydrolysis and strand displacement over current real-time PCR methods. AUDP involves one set of universal duplex probes in which the 5' end of the fluorescent probe (FP) and a complementary quenching probe (QP) lie in close proximity so that fluorescence can be quenched. The PCR primer pair with attached universal template (UT) and the FP are identical to the UT sequence. We have shown that the AUDP technique can be used for detecting multiple target DNA sequences in both simplex and duplex real-time PCR assays for gene expression analysis, genotype identification, and genetically modified organism (GMO) quantification with comparable sensitivity, reproducibility, and repeatability with other real-time PCR methods. Conclusion The results from GMO quantification, gene expression analysis, genotype identification, and GMO quantification using AUDP real-time PCR assays indicate that the AUDP real-time PCR technique has been successfully applied in nucleic acids analysis, and the developed AUDP real-time PCR technique will offer an alternative way for nucleic acid analysis with high efficiency, reliability, and flexibility at low cost. PMID:18522756

Arrays of probes for positional sequencing by hybridization

DOEpatents

Cantor, Charles R [Boston, MA; Prezetakiewiczr, Marek [East Boston, MA; Smith, Cassandra L [Boston, MA; Sano, Takeshi [Waltham, MA

2008-01-15

This invention is directed to methods and reagents useful for sequencing nucleic acid targets utilizing sequencing by hybridization technology comprising probes, arrays of probes and methods whereby sequence information is obtained rapidly and efficiently in discrete packages. That information can be used for the detection, identification, purification and complete or partial sequencing of a particular target nucleic acid. When coupled with a ligation step, these methods can be performed under a single set of hybridization conditions. The invention also relates to the replication of probe arrays and methods for making and replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5'- and/or 3'-overhangs.

Molecular-level chemistry of model single-crystal oxide surfaces with model halogenated compounds

NASA Astrophysics Data System (ADS)

Adib, Kaveh

Synchrotron-based X-ray photoelectron spectroscopy (XPS), temperature-programmed desorption (TPD) and low energy electron diffraction (LEED) have been used to investigate, at a molecular level, the chemistry of different terminations of single crystal iron-oxide surfaces with probe molecules (CCl4 and D2O). Comparisons of the reactivity of these surfaces towards CCl4, indicate that the presence of an uncapped surface Fe cation (strong Lewis acid site) and an adjacent oxygen site capped by that cation can effect the C-Cl bond cleavage in CCl4, resulting in dissociatively adsorbed Cl-adatoms and carbon-containing fragments. If in addition to these sites, an uncapped surface oxygen (Lewis base) site is also available, the carbon-containing moiety can then move that site, coordinate itself with that uncapped oxygen, and stabilize itself. At a later step, the carbon-containing fragment may form a strong covalent bond with the uncapped oxygen and may even abstract that surface oxygen. On the other hand, if an uncapped oxygen is not available to stabilize the carbon-containing fragment, the surface coordination will not occur and upon the subsequent thermal annealing of the surface the Cl-adatoms and the carbon-containing fragments will recombine and desorb as CCl4. Finally, the presence of surface deuteroxyls blocking the strong Lewis acid and base sites of the reactive surface, passivates this surface. Such a deuteroxylated surface will be unreactive towards CCl 4. Such a molecular level understanding of the surface chemistry of metal-oxides will have applications in the areas of selective catalysis, including environmental catalysis, and chemical sensor technology.

Optimizing the specificity of nucleic acid hybridization

PubMed Central

Zhang, David Yu; Chen, Sherry Xi; Yin, Peng

2014-01-01

The specific hybridization of complementary sequences is an essential property of nucleic acids, enabling diverse biological and biotechnological reactions and functions. However, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature. Here, we analytically derived the thermodynamic properties of a hybridization probe that would enable near-optimal single-base discrimination and perform robustly across diverse temperature, salt and concentration conditions. We rationally designed ‘toehold exchange’ probes that approximate these properties, and comprehensively tested them against five different DNA targets and 55 spurious analogues with energetically representative single-base changes (replacements, deletions and insertions). These probes produced discrimination factors between 3 and 100+ (median, 26). Without retuning, our probes function robustly from 10 °C to 37 °C, from 1 mM Mg2+ to 47 mM Mg2+, and with nucleic acid concentrations from 1 nM to 5 μM. Experiments with RNA also showed effective single-base change discrimination. PMID:22354435

Ultrasensitive detection of nucleic acids and proteins using quartz crystal microbalance and surface plasmon resonance sensors based on target-triggering multiple signal amplification strategy.

PubMed

Sun, Wenbo; Song, Weiling; Guo, Xiaoyan; Wang, Zonghua

2017-07-25

In this study, quartz crystal microbalance (QCM) and surface plasmon resonance (SPR) sensors were combined with template enhanced hybridization processes (TEHP), rolling circle amplification (RCA) and biocatalytic precipitation (BCP) for ultrasensitive detection of DNA and protein. The DNA complementary to the aptamer was released by the specific binding of the aptamer to the target protein and then hybridized with the capture probe and the assistant DNA to form a ternary "Y" junction structure. The initiation chain was generated by the template-enhanced hybridization process which leaded to the rolling circle amplification reaction, and a large number of repeating unit sequences were formed. Hybridized with the enzyme-labeled probes, the biocatalytic precipitation reaction was further carried out, resulting in a large amount of insoluble precipitates and amplifying the detection signal. Under the optimum conditions, detection limits as low as 43 aM for target DNA and 53 aM for lysozyme were achieved. In addition, this method also showed good selectivity and sensitivity in human serum. Copyright © 2017 Elsevier B.V. All rights reserved.

PPV-Based Conjugated Polymer Nanoparticles as a Versatile Bioimaging Probe: A Closer Look at the Inherent Optical Properties and Nanoparticle-Cell Interactions.

PubMed

Peters, Martijn; Zaquen, Neomy; D'Olieslaeger, Lien; Bové, Hannelore; Vanderzande, Dirk; Hellings, Niels; Junkers, Thomas; Ethirajan, Anitha

2016-08-08

Conjugated polymers have attracted significant interest in the bioimaging field due to their excellent optical properties and biocompatibility. Tailor-made poly(p-phenylenevinylene) (PPV) conjugated polymer nanoparticles (NPs) are in here described. Two different nanoparticle systems using poly[2-methoxy-5-(3',7'-dimethoxyoctyloxy)-1,4-phenylenevinylene] (MDMO-PPV) and a functional statistical copolymer 2-(5'-methoxycarbonylpentyloxy)-5-methoxy-1,4-phenylenevinylene (CPM-MDMO-PPV), containing ester groups on the alkoxy side chains, were synthesized by combining miniemulsion and solvent evaporation processes. The hydrolysis of ester groups into carboxylic acid groups on the CPM-MDMO-PPV NPs surface allows for biomolecule conjugation. The NPs exhibited excellent optical properties with a high fluorescent brightness and photostability. The NPs were in vitro tested as potential fluorescent nanoprobes for studying cell populations within the central nervous system. The cell studies demonstrated biocompatibility and surface charge dependent cellular uptake of the NPs. This study highlights that PPV-derivative based particles are a promising bioimaging probe and can cater potential applications in the field of nanomedicine.

In situ, accurate, surface-enhanced Raman scattering detection of cancer cell nucleus with synchronous location by an alkyne-labeled biomolecular probe.

PubMed

Zhang, Jing; Liang, Lijia; Guan, Xin; Deng, Rong; Qu, Huixin; Huang, Dianshuai; Xu, Shuping; Liang, Chongyang; Xu, Weiqing

2018-01-01

A surface-enhanced Raman scattering (SERS) method for in situ detection and analysis of the intranuclear biomolecular information of a cell has been developed based on a small, biocompatible, nuclear-targeting alkyne-tagged deoxyribonucleic acid (DNA) probe (5-ethynyl-2'-deoxyuridine, EDU) that can specially accumulate in the cell nucleus during DNA replications to precisely locate the nuclear region without disturbance in cell biological activities and functions. Since the specific alkyne group shows a Raman peak in the Raman-silent region of cells, it is an interior label to visualize the nuclear location synchronously in real time when measuring the SERS spectra of a cell. Because no fluorescent-labeled dyes were used for locating cell nuclei, this method is simple, nondestructive, non- photobleaching, and valuable for the in situ exploration of vital physiological processes with DNA participation in cell organelles. Graphical abstract A universal strategy was developed to accurately locate the nuclear region and obtain precise molecular information of cell nuclei by SERS.

Zeolitic imidazolate framework-methacrylate composite monolith characterization by inverse gas chromatography.

PubMed

Yusuf, Kareem; Badjah-Hadj-Ahmed, Ahmed Yacine; Aqel, Ahmad; Aouak, Taieb; ALOthman, Zeid Abdullah

2016-04-22

Thermodynamic characterization of butyl methacrylate-co-ethylene dimethacrylate neat monolith and zeolitic imidazolate framework-8 incorporated with butyl methacrylate-co-ethylene dimethacrylate composite monolith were studied using inverse gas chromatography at infinite dilution under 1MPa column pressure and various column temperatures. The free energy of adsorption (ΔGA), enthalpy of adsorption (ΔHA) and entropy of adsorption (ΔSA) were determined using a series of n-alkanes. The dispersive component of surface energy (γS(D)) was estimated by Dorris-Gray and Schultz et al. The composite monolith showed a more energetic surface than the neat monolith. The acidic, KA, and basic, KD, parameters for both materials were estimated using a group of polar probes. A basic character was concluded with more basic behavior for the neat monolith. Flory-Huggins parameter, χ, was taken as a measure of miscibility between the probes with the low molecular weight and the high molecular weight monolith. Inverse gas chromatography provides a better understanding of the role of incorporated zeolitic imidazolate framework (ZIF-8) into the polymer matrix in its monolithic form. Copyright © 2016 Elsevier B.V. All rights reserved.

Europium-decorated graphene quantum dots as a fluorescent probe for label-free, rapid and sensitive detection of Cu(2+) and L-cysteine.

PubMed

Lin, Liping; Song, Xinhong; Chen, Yiying; Rong, Mingcong; Wang, Yiru; Zhao, Li; Zhao, Tingting; Chen, Xi

2015-09-03

In this work, europium-decorated graphene quantum dots (Eu-GQDs) were prepared by treating three-dimensional Eu-decorated graphene (3D Eu-graphene) via a strong acid treatment. Various characterizations revealed that Eu atoms were successfully complexed with the oxygen functional groups on the surface of graphene quantum dots (GQDs) with the atomic ratio of 2.54%. Compared with Eu free GQDs, the introduction of Eu atoms enhanced the electron density and improved the surface chemical activities of Eu-GQDs. Therefore, the obtained Eu-GQDs were used as a novel "off-on" fluorescent probe for the label-free determination of Cu(2+) and l-cysteine (L-Cys) with high sensitivity and selectivity. The fluorescence intensity of Eu-GQDs was quenched in the presence of Cu(2+) owing to the coordination reaction between Cu(2+) and carboxyl groups on the surface of the Eu-GQDs. The fluorescence intensity of Eu-GQDs recovered with the subsequent addition of L-Cys because of the strong affinity of Cu(2+) to L-Cys via the Cu-S bond. The experimental results showed that the fluorescence variation of the proposed approach had a good linear relationship in the range of 0.1-10 μM for Cu(2+) and 0.5-50 μM for L-Cys with corresponding detection limits of 0.056 μM for Cu(2+) and 0.31 μM for L-Cys. The current approach also displayed a special response to Cu(2+) and L-Cys over the other co-existing metal ions and amino acids, and the results obtained from buffer-diluted serum samples suggested its applicability in biological samples. Copyright © 2015 Elsevier B.V. All rights reserved.

STM, SECPM, AFM and Electrochemistry on Single Crystalline Surfaces

PubMed Central

Wolfschmidt, Holger; Baier, Claudia; Gsell, Stefan; Fischer, Martin; Schreck, Matthias; Stimming, Ulrich

2010-01-01

Scanning probe microscopy (SPM) techniques have had a great impact on research fields of surface science and nanotechnology during the last decades. They are used to investigate surfaces with scanning ranges between several 100 μm down to atomic resolution. Depending on experimental conditions, and the interaction forces between probe and sample, different SPM techniques allow mapping of different surface properties. In this work, scanning tunneling microscopy (STM) in air and under electrochemical conditions (EC-STM), atomic force microscopy (AFM) in air and scanning electrochemical potential microscopy (SECPM) under electrochemical conditions, were used to study different single crystalline surfaces in electrochemistry. Especially SECPM offers potentially new insights into the solid-liquid interface by providing the possibility to image the potential distribution of the surface, with a resolution that is comparable to STM. In electrocatalysis, nanostructured catalysts supported on different electrode materials often show behavior different from their bulk electrodes. This was experimentally and theoretically shown for several combinations and recently on Pt on Au(111) towards fuel cell relevant reactions. For these investigations single crystals often provide accurate and well defined reference and support systems. We will show heteroepitaxially grown Ru, Ir and Rh single crystalline surface films and bulk Au single crystals with different orientations under electrochemical conditions. Image studies from all three different SPM methods will be presented and compared to electrochemical data obtained by cyclic voltammetry in acidic media. The quality of the single crystalline supports will be verified by the SPM images and the cyclic voltammograms. Furthermore, an outlook will be presented on how such supports can be used in electrocatalytic studies. PMID:28883327

Curcumin-cysteine and curcumin-tryptophan conjugate as fluorescence turn on sensors for picric Acid in aqueous media.

PubMed

Gogoi, Bedanta; Sen Sarma, Neelotpal

2015-06-03

Rapid detection of picric acid in real sample is of outmost importance from the perspective of health, safety, and environment. In this study, a very simple and cost-effective detection of picric acid is accomplished by developing a couple of biobased conjugates curcumin-cysteine (CC) and curcumin-tryptophan (CT), which undergo efficient fluorescence turn on toward picric acid in aqueous media. Both the probes experience about 26.5-fold fluorescence enhancements at 70 nM concentration of the analyte. Here, the fluorescence turn on process is governed by the aggregation induced emission, which is induced from the electrostatic interaction between the conjugates with picric acid. The detection limit of CC and CT are about 13.51 and 13.54 nM of picric acid, respectively. Importantly, both the probes exhibit high selectivity and low interference of other analogues toward the detection of picric acid. In addition, the probes are highly photostable, show low response time and are practically applicable for sensing picric acid in real environmental samples, which is the ultimate goal of this work.

Systems and methods for laser assisted sample transfer to solution for chemical analysis

DOEpatents

Van Berkel, Gary J.; Kertesz, Vilmos; Ovchinnikova, Olga S.

2014-06-03

Systems and methods are described for laser ablation of an analyte from a specimen and capturing of the analyte in a dispensed solvent to form a testing solution. A solvent dispensing and extraction system can form a liquid microjunction with the specimen. The solvent dispensing and extraction system can include a surface sampling probe. The laser beam can be directed through the surface sampling probe. The surface sampling probe can also serve as an atomic force microscopy probe. The surface sampling probe can form a seal with the specimen. The testing solution including the analyte can then be analyzed using an analytical instrument or undergo further processing.

Systems and methods for laser assisted sample transfer to solution for chemical analysis

DOEpatents

Van Berkel, Gary J.; Kertesz, Vilmos; Ovchinnikova, Olga S.

2015-09-29

Systems and methods are described for laser ablation of an analyte from a specimen and capturing of the analyte in a dispensed solvent to form a testing solution. A solvent dispensing and extraction system can form a liquid microjunction with the specimen. The solvent dispensing and extraction system can include a surface sampling probe. The laser beam can be directed through the surface sampling probe. The surface sampling probe can also serve as an atomic force microscopy probe. The surface sampling probe can form a seal with the specimen. The testing solution including the analyte can then be analyzed using an analytical instrument or undergo further processing.

Systems and methods for laser assisted sample transfer to solution for chemical analysis

DOEpatents

Van Berkel, Gary J; Kertesz, Vilmos; Ovchinnikova, Olga S

2013-08-27

Systems and methods are described for laser ablation of an analyte from a specimen and capturing of the analyte in a dispensed solvent to form a testing solution. A solvent dispensing and extraction system can form a liquid microjunction with the specimen. The solvent dispensing and extraction system can include a surface sampling probe. The laser beam can be directed through the surface sampling probe. The surface sampling probe can also serve as an atomic force microscopy probe. The surface sampling probe can form a seal with the specimen. The testing solution including the analyte can then be analyzed using an analytical instrument or undergo further processing.

Protein-lipid interactions at the air/water interface.

PubMed

Lad, Mitaben D; Birembaut, Fabrice; Frazier, Richard A; Green, Rebecca J

2005-10-07

Surface pressure measurements and external reflection FTIR spectroscopy have been used to probe protein-lipid interactions at the air/water interface. Spread monomolecular layers of stearic acid and phosphocholine were prepared and held at different compressed phase states prior to the introduction of protein to the buffered subphase. Contrasting interfacial behaviour of the proteins, albumin and lysozyme, was observed and revealed the role of both electrostatic and hydrophobic interactions in protein adsorption. The rate of adsorption of lysozyme to the air/water interface increased dramatically in the presence of stearic acid, due to strong electrostatic interactions between the negatively charged stearic acid head group and lysozyme, whose net charge at pH 7 is positive. Introduction of albumin to the subphase resulted in solubilisation of the stearic acid via the formation of an albumin-stearic acid complex and subsequent adsorption of albumin. This observation held for both human and bovine serum albumin. Protein adsorption to a PC layer held at low surface pressure revealed adsorption rates similar to adsorption to the bare air/water interface and suggested very little interaction between the protein and the lipid. For PC layers in their compressed phase state some adsorption of protein occurred after long adsorption times. Structural changes of both lysozyme and albumin were observed during adsorption, but these were dramatically reduced in the presence of a lipid layer compared to that of adsorption to the pure air/water interface.

Four-probe measurements with a three-probe scanning tunneling microscope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salomons, Mark; Martins, Bruno V. C.; Zikovsky, Janik

2014-04-15

We present an ultrahigh vacuum (UHV) three-probe scanning tunneling microscope in which each probe is capable of atomic resolution. A UHV JEOL scanning electron microscope aids in the placement of the probes on the sample. The machine also has a field ion microscope to clean, atomically image, and shape the probe tips. The machine uses bare conductive samples and tips with a homebuilt set of pliers for heating and loading. Automated feedback controlled tip-surface contacts allow for electrical stability and reproducibility while also greatly reducing tip and surface damage due to contact formation. The ability to register inter-tip position bymore » imaging of a single surface feature by multiple tips is demonstrated. Four-probe material characterization is achieved by deploying two tips as fixed current probes and the third tip as a movable voltage probe.« less

A NBD-based simple but effective fluorescent pH probe for imaging of lysosomes in living cells.

PubMed

Cao, Xiang-Jian; Chen, Li-Na; Zhang, Xuan; Liu, Jin-Ting; Chen, Ming-Yu; Wu, Qiu-Rong; Miao, Jun-Ying; Zhao, Bao-Xiang

2016-05-12

NBDlyso with lysosome-locating morpholine moiety has been developed as a high selective and sensitive fluorescent pH probe. This probe can respond to acidic pH (2.0-7.0) in a short time (less than 1 min) and not almost change after continuously illuminated for an extended period by ultraviolet light. The fluorescence intensity of NBDlyso enhanced 100-fold in acidic solution, with very good linear relationship (R(2) = 0.996). The pKa of probe NBDlyso is 4.10. Therefore, NBDlyso was used to detect lysosomal pH changes successfully. Besides, X-ray crystallography was used to verify the structure of NBDlyso, and the recognition mechanism involving photo-induced electron transfer was interpreted theoretically by means of DFT and TDDFT calculations skillfully when NBDlyso comes into play under the acidic condition. This probe showed good ability to sense pH change in living cell image. Copyright © 2016 Elsevier B.V. All rights reserved.

Sensing Parts per Million Level Ammonia and Parts per Billion Level Acetic Acid in the Gas Phase by Common Black Film with a Fluorescent pH Probe.

PubMed

Fu, Jingni; Zhang, Luning

2018-01-16

Relying on the nanometer-thick water core and large surface area-to-volume ratio (∼2 × 10 8 m -1 ) of common black film (CBF), we are able to use a pH-sensitive dye (carboxy-seminaphthorhodafluor-1, SNARF-1) to detect ammonia and acetic acid gas adsorption into the CBF, with the limit of detection reaching 0.8 ppm for NH 3 gas and 3 ppb for CH 3 COOH gas in the air. Data analysis reveals that fluorescence signal change is linearly proportional to the gas concentration up to 15 ppm and 65 ppb for NH 3 and CH 3 COOH, respectively.

Surface plasmon resonance spectroscopy sensor and methods for using same

DOEpatents

Anderson, Brian Benjamin; Nave, Stanley Eugene

2002-01-01

A surface plasmon resonance ("SPR") probe with a detachable sensor head and system and methods for using the same in various applications is described. The SPR probe couples fiber optic cables directly to an SPR substrate that has a generally planar input surface and a generally curved reflecting surface, such as a substrate formed as a hemisphere. Forming the SPR probe in this manner allows the probe to be miniaturized and operate without the need for high precision, expensive and bulky collimating or focusing optics. Additionally, the curved reflecting surface of the substrate can be coated with one or multiple patches of sensing medium to allow the probe to detect for multiple analytes of interest or to provide multiple readings for comparison and higher precision. Specific applications for the probe are disclosed, including extremely high sensitive relative humidity and dewpoint detection for, e.g., moisture-sensitive environment such as volatile chemical reactions. The SPR probe disclosed operates with a large dynamic range and provides extremely high quality spectra despite being robust enough for field deployment and readily manufacturable.

Method of detecting genetic translocations identified with chromosomal abnormalities

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Tkachuk, Douglas

2001-01-01

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Chromosome-specific staining to detect genetic rearrangements

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Tkachuk, Douglas; Westbrook, Carol

2013-04-09

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Method of detecting genetic deletions identified with chromosomal abnormalities

DOEpatents

Gray, Joe W; Pinkel, Daniel; Tkachuk, Douglas

2013-11-26

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acids probes are typically of a complexity greater tha 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particlularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar ut genetically different diseases, and for many prognostic and diagnostic applications.

Probing inhibitory effects of nanocrystalline cellulose: inhibition versus surface charge

NASA Astrophysics Data System (ADS)

Male, Keith B.; Leung, Alfred C. W.; Montes, Johnny; Kamen, Amine; Luong, John H. T.

2012-02-01

NCC derived from different biomass sources was probed for its plausible cytotoxicity by electric cell-substrate impedance sensing (ECIS). Two different cell lines, Spodoptera frugiperda Sf9 insect cells and Chinese hamster lung fibroblast V79, were exposed to NCC and their spreading and viability were monitored and quantified by ECIS. Based on the 50%-inhibition concentration (ECIS50), none of the NCC produced was judged to have any significant cytotoxicity on these two cell lines. However, NCC derived from flax exhibited the most pronounced inhibition on Sf9 compared to hemp and cellulose powder. NCCs from flax and hemp pre-treated with pectate lyase were also less inhibitory than NCCs prepared from untreated flax and hemp. Results also suggested a correlation between the inhibitory effect and the carboxylic acid contents on the NCC.

Sampling probe for microarray read out using electrospray mass spectrometry

DOEpatents

Van Berkel, Gary J.

2004-10-12

An automated electrospray based sampling system and method for analysis obtains samples from surface array spots having analytes. The system includes at least one probe, the probe including an inlet for flowing at least one eluting solvent to respective ones of a plurality of spots and an outlet for directing the analyte away from the spots. An automatic positioning system is provided for translating the probe relative to the spots to permit sampling of any spot. An electrospray ion source having an input fluidicly connected to the probe receives the analyte and generates ions from the analyte. The ion source provides the generated ions to a structure for analysis to identify the analyte, preferably being a mass spectrometer. The probe can be a surface contact probe, where the probe forms an enclosing seal along the periphery of the array spot surface.

Organophosphonate-based PNA-functionalization of silicon nanowires for label-free DNA detection.

PubMed

Cattani-Scholz, Anna; Pedone, Daniel; Dubey, Manish; Neppl, Stefan; Nickel, Bert; Feulner, Peter; Schwartz, Jeffrey; Abstreiter, Gerhard; Tornow, Marc

2008-08-01

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.

Simple control of surface topography of gold nanoshells by a surfactant-less seeded-growth method.

PubMed

Topete, Antonio; Alatorre-Meda, Manuel; Villar-Álvarez, Eva M; Cambón, Adriana; Barbosa, Silvia; Taboada, Pablo; Mosquera, Víctor

2014-07-23

We report the synthesis of branched gold nanoshells (BGNS) through a seeded-growth surfactant-less method. This was achieved by decorating chitosan-Pluronic F127 stabilized poly(lactic-co-gycolic) acid nanoparticles (NPs) with Au seeds (NP-seed), using chitosan as an electrostatic self-assembling agent. Branched shells with different degrees of anisotropy and optical response were obtained by modulating the ratios of HAuCl4/K2CO3 growth solution, ascorbic acid (AA) and NP-seed precursor. Chitosan and AA were crucial in determining the BGNS size and structure, acting both as coreductants and structure directing growth agents. Preliminary cytotoxicity experiments point to the biocompatibility of the obtained BGNS, allowing their potential use in biomedical applications. In particular, these nanostructures with "hybrid" compositions, which combine the features of gold nanoshells and nanostars showed a better performance as surface enhanced Raman spectroscopy probes in detecting intracellular cell components than classical smoother nanoshells.

Development of Raman Spectroscopy as a Clinical Diagnostic Tool

NASA Astrophysics Data System (ADS)

Borel, Santa

Raman spectroscopy is the collection of inelastically scattered light in which the spectra contain biochemical information of the probed cells or tissue. This work presents both targeted and untargeted ways that the technique can be exploited in biological samples. First, surface enhanced Raman scattering (SERS) gold nanoparticles conjugated to targeting antibodies were shown to be successful for multiplexed detection of overexpressed surface antigens in lung cancer cell lines. Further work will need to optimize the conjugation technique to preserve the strong binding affinity of the antibodies. Second, untargeted Raman microspectroscopy combined with multivariate statistical analysis was able to successfully differentiate mouse ovarian surface epithelial (MOSE) cells and spontaneously transformed ovarian surface epithelial (STOSE) cells with high accuracy. The differences between the two groups were associated with increased nucleic acid content in the STOSE cells. This shows potential for single cell detection of ovarian cancer.

Carbon-Based Solid-State Calcium Ion-Selective Microelectrode and Scanning Electrochemical Microscopy: A Quantitative Study of pH-Dependent Release of Calcium Ions from Bioactive Glass.

PubMed

Ummadi, Jyothir Ganesh; Downs, Corey J; Joshi, Vrushali S; Ferracane, Jack L; Koley, Dipankar

2016-03-15

Solid-state ion-selective electrodes are used as scanning electrochemical microscope (SECM) probes because of their inherent fast response time and ease of miniaturization. In this study, we report the development of a solid-state, low-poly(vinyl chloride), carbon-based calcium ion-selective microelectrode (Ca(2+)-ISME), 25 μm in diameter, capable of performing an amperometric approach curve and serving as a potentiometric sensor. The Ca(2+)-ISME has a broad linear response range of 5 μM to 200 mM with a near Nernstian slope of 28 mV/log[a(Ca(2+))]. The calculated detection limit for Ca(2+)-ISME is 1 μM. The selectivity coefficients of this Ca(2+)-ISME are log K(Ca(2+),A) = -5.88, -5.54, and -6.31 for Mg(2+), Na(+), and K(+), respectively. We used this new type of Ca(2+)-ISME as an SECM probe to quantitatively map the chemical microenvironment produced by a model substrate, bioactive glass (BAG). In acidic conditions (pH 4.5), BAG was found to increase the calcium ion concentration from 0.7 mM ([Ca(2+)] in artificial saliva) to 1.4 mM at 20 μm above the surface. In addition, a solid-state dual SECM pH probe was used to correlate the release of calcium ions with the change in local pH. Three-dimensional pH and calcium ion distribution mapping were also obtained by using these solid-state probes. The quantitative mapping of pH and Ca(2+) above the BAG elucidates the effectiveness of BAG in neutralizing and releasing calcium ions in acidic conditions.

Maskless micro/nanofabrication on GaAs surface by friction-induced selective etching

PubMed Central

2014-01-01

In the present study, a friction-induced selective etching method was developed to produce nanostructures on GaAs surface. Without any resist mask, the nanofabrication can be achieved by scratching and post-etching in sulfuric acid solution. The effects of the applied normal load and etching period on the formation of the nanostructure were studied. Results showed that the height of the nanostructure increased with the normal load or the etching period. XPS and Raman detection demonstrated that residual compressive stress and lattice densification were probably the main reason for selective etching, which eventually led to the protrusive nanostructures from the scratched area on the GaAs surface. Through a homemade multi-probe instrument, the capability of this fabrication method was demonstrated by producing various nanostructures on the GaAs surface, such as linear array, intersecting parallel, surface mesas, and special letters. In summary, the proposed method provided a straightforward and more maneuverable micro/nanofabrication method on the GaAs surface. PMID:24495647

What Is a pH Probe Study?

MedlinePlus

What is a pH Probe Study ? What is pH a probe study? M easuring the pH in the esophagus helps determine whether or not acid is coming up from the stomach. A pH probe study is usually done in patients where ...

16 CFR 1505.51 - Hot surfaces.

Code of Federal Regulations, 2011 CFR

2011-01-01

... CHILDREN Policies and Interpretations § 1505.51 Hot surfaces. (a) Test probe. Section 1505.6(g)(2) defines... inches long. To test for accessibility using this test probe, it shall be inserted no more than 3 inches into any opening in the toy. Unless the probe contacts a surface within 3 inches of the plane of the...

16 CFR 1505.51 - Hot surfaces.

Code of Federal Regulations, 2014 CFR

2014-01-01

... CHILDREN Policies and Interpretations § 1505.51 Hot surfaces. (a) Test probe. Section 1505.6(g)(2) defines... inches long. To test for accessibility using this test probe, it shall be inserted no more than 3 inches into any opening in the toy. Unless the probe contacts a surface within 3 inches of the plane of the...

16 CFR 1505.51 - Hot surfaces.

Code of Federal Regulations, 2012 CFR

2012-01-01

... CHILDREN Policies and Interpretations § 1505.51 Hot surfaces. (a) Test probe. Section 1505.6(g)(2) defines... inches long. To test for accessibility using this test probe, it shall be inserted no more than 3 inches into any opening in the toy. Unless the probe contacts a surface within 3 inches of the plane of the...

Mastering fundamentals of supramolecular design with carboxylic acids. Common lessons from X-ray crystallography and scanning tunneling microscopy.

PubMed

Ivasenko, Oleksandr; Perepichka, Dmitrii F

2011-01-01

Hydrogen bonding is one of the most important non-covalent interactions in both biological (DNA, peptides, saccharides etc.) and artificial systems (various soft materials, host-guest architectures, molecular networks, etc.). Carboxylic acids are some of the most simple yet powerful hydrogen-bonding building blocks, that possess a particularly rich supramolecular chemistry. This tutorial review focuses on the structural diversity of supramolecular architectures accessible via hydrogen bonding of carboxylic acids, as observed both in single crystals using X-ray analysis and in monolayers on surfaces using scanning probe techniques. It provides a concise overview of the key concepts and principles of modern supramolecular design and is given in the form of case studies of finely selected literature examples, covering formation of macrocycles, chains, ladders, rotaxanes, catenanes, various 2D and 3D nets, host-guest systems and some applications thereof.

Ordered Structure Formed by Biologically Related Molecules

NASA Astrophysics Data System (ADS)

Hatta, Ichiro; Nishino, Junichiro; Sumi, Akinori; Hibino, Masahiro

1995-07-01

The two-dimensional arrangement of biologically related molecules was studied by means of scanning probe microscopy. For monolayers of fatty acid molecules with a saturated hydrocarbon chain adsorbed on a graphite substrate, in the scanning tunneling microscope image, the position associated with the carbon atoms was clearly distinguished. In addition, based on the image for fatty acid molecules with an unsaturated hydrocarbon chain, at the position of a double bond, local electrical conductance was found to increase. Based on the images, it was pointed out that not the position of each carbon but the interaction between a graphite substrate and an alkyl chain plays an important role in imaging. On the other hand, for the surface of Langmuir-Blodgett films composed of phosphatidic acids with cations, the scanning force microscope image shows, for the first time, evidence of the methyl ends in the arrangement of phospholipid molecules.

Structure Dependence of Long-Chain [18F]Fluorothia Fatty Acids as Myocardial Fatty Acid Oxidation Probes

PubMed Central

Pandey, Mukesh K.; Belanger, Anthony P.; Wang, Shuyan; DeGrado, Timothy R.

2012-01-01

In-vivo imaging of regional fatty acid oxidation (FAO) rates would have considerable potential for evaluation of mammalian diseases. We have synthe sized and evaluated 18F-labeled thia fatty acid analogues as metabolically trapped FAO probes to understand the effect of chain length, degree of unsaturation and placement of the thia-substituent on myocardial uptake and retention. 18-[18F]fluoro-4-thia-(9Z)-octadec-9-enoic acid (3) showed excellent heart:background radioactivity concentration ratios along with highest retention in heart and liver. Pretreatment of rats with the CPT-1 inhibitor, POCA, caused >80% reduction in myocardial uptake of 16-[18F]fluoro-4-thia-hexadecanoic acid (2), and 3 indicating high specificity for FAO. In contrast, 18-[18F]fluoro-4-thia-octadecanoic acid (4), showed dramatically reduced myocardial uptake and blunted response to POCA. 18-[18F]fluoro-6-thia-octadecanoic acid (5), showed moderate myocardial uptake and no sensitivity of myocardial uptake to POCA. The results demonstrate relationships between structures of 18F-labelled thia fatty acid and uptake, and their utility as FAO probes in various tissues. PMID:23153307

Label-free detection of DNA using a light-addressable potentiometric sensor modified with a positively charged polyelectrolyte layer

NASA Astrophysics Data System (ADS)

Wu, Chunsheng; Bronder, Thomas; Poghossian, Arshak; Werner, Carl Frederik; Schöning, Michael J.

2015-03-01

A multi-spot (16 spots) light-addressable potentiometric sensor (MLAPS) consisting of an Al-p-Si-SiO2 structure modified with a weak polyelectrolyte layer of PAH (poly(allylamine hydrochloride)) was applied for the label-free electrical detection of DNA (deoxyribonucleic acid) immobilization and hybridization by the intrinsic molecular charge for the first time. To achieve a preferentially flat orientation of DNA strands and thus, to reduce the distance between the DNA charge and MLAPS surface, the negatively charged probe single-stranded DNAs (ssDNA) were electrostatically adsorbed onto the positively charged PAH layer using a simple layer-by-layer (LbL) technique. In this way, more DNA charge can be positioned within the Debye length, yielding a higher sensor signal. The surface potential changes in each spot induced due to the surface modification steps (PAH adsorption, probe ssDNA immobilization, hybridization with complementary target DNA (cDNA), non-specific adsorption of mismatched ssDNA) were determined from the shifts of photocurrent-voltage curves along the voltage axis. A high sensor signal of 83 mV was registered after immobilization of probe ssDNA onto the PAH layer. The hybridization signal increases from 5 mV to 32 mV with increasing the concentration of cDNA from 0.1 nM to 5 μM. In contrast, a small signal of 5 mV was recorded in the case of non-specific adsorption of fully mismatched ssDNA (5 μM). The obtained results demonstrate the potential of the MLAPS in combination with the simple and rapid LbL immobilization technique as a promising platform for the future development of multi-spot light-addressable label-free DNA chips with direct electrical readout.A multi-spot (16 spots) light-addressable potentiometric sensor (MLAPS) consisting of an Al-p-Si-SiO2 structure modified with a weak polyelectrolyte layer of PAH (poly(allylamine hydrochloride)) was applied for the label-free electrical detection of DNA (deoxyribonucleic acid) immobilization and hybridization by the intrinsic molecular charge for the first time. To achieve a preferentially flat orientation of DNA strands and thus, to reduce the distance between the DNA charge and MLAPS surface, the negatively charged probe single-stranded DNAs (ssDNA) were electrostatically adsorbed onto the positively charged PAH layer using a simple layer-by-layer (LbL) technique. In this way, more DNA charge can be positioned within the Debye length, yielding a higher sensor signal. The surface potential changes in each spot induced due to the surface modification steps (PAH adsorption, probe ssDNA immobilization, hybridization with complementary target DNA (cDNA), non-specific adsorption of mismatched ssDNA) were determined from the shifts of photocurrent-voltage curves along the voltage axis. A high sensor signal of 83 mV was registered after immobilization of probe ssDNA onto the PAH layer. The hybridization signal increases from 5 mV to 32 mV with increasing the concentration of cDNA from 0.1 nM to 5 μM. In contrast, a small signal of 5 mV was recorded in the case of non-specific adsorption of fully mismatched ssDNA (5 μM). The obtained results demonstrate the potential of the MLAPS in combination with the simple and rapid LbL immobilization technique as a promising platform for the future development of multi-spot light-addressable label-free DNA chips with direct electrical readout. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07225a

Recognition of extended linear and cyclised polyketide mimics by a type II acyl carrier protein† †Electronic supplementary information (ESI) available: Detailed experimental procedures and characterisation data for all new compounds, additional spectra and structural statistics for derivatised ACP three-dimensional structures. See DOI: 10.1039/c5sc03864b Click here for additional data file.

PubMed Central

Dong, Xu; Bailey, Christopher D.; Williams, Christopher; Crosby, John; Simpson, Thomas J.

2016-01-01

Polyketides are secondary metabolites which display both valuable pharmaceutical and agrochemical properties. Biosynthesis is performed by polyketide synthases (PKSs), and the acyl carrier protein (ACP), a small acidic protein, that transports the growing polyketide chain and is essential for activity. Here we report the synthesis of two aromatic probes and a linear octaketide mimic that have been tethered to actinorhodin ACP. These experiments were aimed at probing the ACP's capacity to sequester a non-polar versus a phenolic aromatic ring (that more closely mimics a polyketide intermediate) as well as investigations with extended polyketide chain surrogates. The binding of these mimics has been assessed using high-resolution solution NMR studies and high-resolution structure determination. These results reveal that surprisingly a PKS ACP is able to bind and sequester a bulky non-polar substrate containing an aromatic ring in a fatty acid type binding mode, but the introduction of even a small degree of polarity favours a markedly different association at a surface site that is distinct from that employed by fatty acid ACPs. PMID:28936328

Near infrared fluorescent trypsin stabilized gold nanoclusters as surface plasmon enhanced energy transfer biosensor and in vivo cancer imaging bioprobe.

PubMed

Liu, Jing-Min; Chen, Jia-Tong; Yan, Xiu-Ping

2013-03-19

The simplicity of the green-synthesized routine and the availability of surface modification of diverse bioactive molecules make noble metal nanostructures highly suitable as multifunctional biomaterials for biological and biomedical application. Here, we report the preparation of trypsin stabilized gold nanoclusters (try-AuNCs) with near-infrared fluorescence for biosensing heparin based on surface plasmon enhanced energy transfer (SPEET) and folic acid (FA) modified try-AuNCs for in vivo cancer bioimaging. The SPEET/try-AuNCs fluorescence biosensor was designed via heparin mediated energy transfer between try-AuNCs and cysteamine modified gold nanoparticles (cyst-AuNPs). The developed SPEET/try-AuNCs fluorescence biosensor allowed sensitive and selective detection of heparin with a linear range of 0.1-4.0 μg mL(-1) and a detection limit (3s) of 0.05 μg mL(-1). The relative standard deviation for eleven replicate detections of 2.5 μg mL(-1) heparin was 1.1%, and the recoveries of the spiked heparin in human serum samples ranged from 97% to 100%. In addition, folic acid was immobilized on the surface of try-AuNCs to ameliorate the specific affinity of AuNCs for tumors, and the near-infrared fluorescent FA-try-AuNCs were applied for in vivo cancer imaging of high folate receptor (FR) expressing Hela tumor. In vivo study of the dynamic behavior and targeting ability of FA-try-AuNCs probe to Hela tumor bearing mice and normal nude mice validated the high specific affinity of FA-try-AuNCs probe to FR positive tumors. The results show that the prepared try-AuNCs have great potential as multifunctional biomaterials for biosensing biomolecules with SPEET mode and in vivo cancer imaging with high targeting ability.

A Multi-technique Characterization of Adsorbed Protein Films: Orientation and Structure by ToF-SIMS, NEXAFS, SFG, and XPS

NASA Astrophysics Data System (ADS)

Baio, Joseph E.

There are many techniques that allow surface scientists to study interfaces. However, few are routinely applied to probe biological surfaces. The work presented here demonstrates how detailed information about the conformation, orientation, chemical state, and molecular structure of biological molecules immobilized onto a surface can be assessed by electron spectroscopy, mass spectrometry, and nonlinear vibrational spectroscopy techniques. This investigation began with the development of simple model systems (small proteins, and peptides) and evolved into a study of more complex --- real world systems. Initially, two model systems based on the chemical and electrostatic immobilization of a small rigid protein (Protein G B1 domain, 6kDa) were built to develop the capabilities of time-of-flight secondary ion mass spectrometry (ToFSIMS), near edge X-ray absorption fine structure spectroscopy (NEXAFS) and sum frequency generation (SFG) spectroscopy as tools to probe the structure of surface immobilized proteins. X-ray photoelectron spectroscopy (XPS) was used to measure the amount of immobilized protein and ToF-SIMS sampled the amino acid composition of the exposed surface of the protein film. Within the ToF-SIMS spectra, an enrichment of secondary ions from amino acids located at opposite ends of the proteins were used to describe protein orientation. SFG spectral peaks characteristic of ordered alpha-helix and beta-sheet elements were observed for both systems and the phase of the peaks indicated a predominantly upright orientation for both the covalent and electrostatic configurations. Polarization dependence of the NEXAFS signal from the N 1s to pi* transition of the peptide bonds that make up the beta-sheets also indicated protein ordering at the surface. Building upon the Protein G B1 studies, the orientation and structure of a surface immobilized antibody (HuLys Fv: variant of humanized anti-lysozyme variable fragment, 26kDa) was characterized across two immobilization schemes. This protein contained both a hexahistidine tag and a cysteine residue, introduced at opposite ends of the HuLys Fv, for immobilization onto nitrilotriacetic acid (NTA) and maleimide oligo- (ethylene glycol) (MEG)-terminated substrates. The thiol group on the cysteine residue selectively binds to the MEG groups, while the his-tag selectively binds to the Ni-loaded NTA groups. XPS was used to monitor protein coverage on both surfaces by following the change in the nitrogen atomic %. The ToF-SIMS data provided a clear differentiation between the two samples due to the intensity differences of secondary ions originating from asymmetrically located amino acids in HuLys Fv. Indicating that the HuLys Fv fragment when adsorbed into the NTA and MEG substrates will be induced into two different orientations. On the NTA substrate the protein's binding site is accessible, while on the MEG substrate the binding site is oriented towards the surface. By taking advantage of the electron pathway through the heme group in cytochrome c (CytoC) electrochemists have built sensors based upon CytoC immobilized onto functionalized metal electrodes. When immobilized onto a charged surface, CytoC, with its distribution of lysine and glutamate residues around its surface, should orient and form a well-ordered protein film. Here a detailed examination of CytoC orientation when electrostatically immobilized onto both amine (NH 3+) and carboxyl (COO-) functionalized gold is presented. Again, protein coverage, on both surfaces, was monitored by the change in the atomic % N, as determined by XPS. ToF-SIMS data demonstrated a clear separation between the two samples based on the intensity differences of secondary ions stemming from amino acids located asymmetrically within CytoC, indicating opposite orientations of the protein on the two different surfaces. Spectral features within the in situ sum frequency generation vibrational spectra, acquired for the protein interacting with positively and negatively charged surfaces, indicates that these electrostatic interactions do induce the protein into a well ordered film.

Active radiometer for self-calibrated furnace temperature measurements

DOEpatents

Woskov, Paul P.; Cohn, Daniel R.; Titus, Charles H.; Wittle, J. Kenneth; Surma, Jeffrey E.

1996-01-01

Radiometer with a probe beam superimposed on its field-of-view for furnace temperature measurements. The radiometer includes a heterodyne millimeter/submillimeter-wave receiver including a millimeter/submillimeter-wave source for probing. The receiver is adapted to receive radiation from a surface whose temperature is to be measured. The radiation includes a surface emission portion and a surface reflection portion which includes the probe beam energy reflected from the surface. The surface emission portion is related to the surface temperature and the surface reflection portion is related to the emissivity of the surface. The simultaneous measurement of surface emissivity serves as a real time calibration of the temperature measurement.

Density functional theory based probe of the affinity interaction of saccharide ligands with extra-cellular sialic acid residues.

PubMed

Patel, Anjali; Tiwari, Sanjay; Jha, Prafulla K

2018-05-10

Changes in glycosylation pattern leads to malignant transformations among the cells. In combination with upregulated actions of sialyltransferases, it ultimately leads to differential expression of sialic acid (SA) at cell surface. Given its negative charge and localization to extracellular domain, SA has been exploited for the development of targeted theranostics using approaches, such as, cationization and appending recognition saccharides on carrier surface. In this study, we have performed quantum mechanical calculations based on density functional theory (DFT) to study the interaction of saccharides with extracellular SA. Gradient-corrected DFT with the three parameter function (B3) was utilized for the calculation of Lee-Yang-Parr (LYP) correlation function. Atomic charge, vibrational frequencies and energy of the optimized structures were calculated through B3LYP. Our calculations demonstrate a stronger galactose-sialic acid interaction at tumour-relevant low pH and hyperthermic condition. These results support the application of pH responsive delivery vehicles and targeted hyperthermic chemotherapy for eradicating solid tumour deposits. These studies, conducted a priori, can guide the formulation scientists over appropriate choice of ligands and their applications in the design of 'smart' theranostic tools.

Multifunctional Surface-Enhanced Raman Spectroscopy-Detectable Silver Nanoparticles Combined Photodynamic Therapy and pH-Triggered Chemotherapy.

PubMed

Srinivasan, Supriya; Bhardwaj, Vinay; Nagasetti, Abhignyan; Fernandez-Fernandez, Alicia; McGoron, Anthony J

2016-12-01

This research paper reports the development of a multifunctional anti-cancer prodrug system based on silver nanoparticles. This prodrug system is composed of 70-nm sized nanoparticles and features photodynamic therapeutic properties and active, pH-triggered drug release. The silver nanoparticles are decorated with a folic acid (FA) targeting ligand via an amide bond, and also conjugated to the chemotherapeutic drug doxorubicin (DOX) via an acid-cleavable hydrazone bond. Both FA and DOX are attached to the silver nanoparticles through a polyethylene glycol (PEG) spacer. This prodrug system can preferentially enter cells that over-express folic acid receptors, with subsequent intracellular drug release triggered by reduced intracellular pH. Moreover, the silver nanoparticle carrier system exhibits photodynamic therapeutic (PDT) activity, so that the cell viability of cancer cells that overexpress folate receptors can be further reduced upon light irradiation. The dual effects of pH-triggered drug release and PDT increase the therapeutic efficacy of this system. The multifunctional nanoparticles can be probed intracellularly through Surface-Enhanced Raman Spectroscopy (SERS) and fluorescence spectroscopy. The current report explores the applicability of this multifunctional silver nanoparticle-based system for cancer theranostics.

Probing the surface of γ-Al2O3 by oxygen-17 dynamic nuclear polarization enhanced solid-state NMR spectroscopy.

PubMed

Li, Wenzheng; Wang, Qiang; Xu, Jun; Aussenac, Fabien; Qi, Guodong; Zhao, Xingling; Gao, Pan; Wang, Chao; Deng, Feng

2018-06-14

γ-Al2O3 is an important catalyst and catalyst support of industrial interest. Its acid/base characteristics are correlated to the surface structure, which has always been an issue of concern. In this work, the complex (sub-)surface oxygen species on surface-selectively labelled γ-Al2O3 were probed by 17O dynamic nuclear polarization surface-enhanced NMR spectroscopy (DNP-SENS). Direct 17O MAS and indirect 1H-17O cross-polarization (CP)/MAS DNP experiments enable observation of the (sub-)surface bare oxygen species and hydroxyl groups. In particular, a two-dimensional (2D) 17O 3QMAS DNP spectrum was for the first time achieved for γ-Al2O3, in which two O(Al)4 and one O(Al)3 bare oxygen species were identified. The 17O isotropic chemical shifts (δcs) vary from 56.7 to 81.0 ppm and the quadrupolar coupling constants (CQ) range from 0.6 to 2.5 MHz for the three oxygen species. The coordinatively unsaturated O(Al)3 species is characterized by a higher field chemical shift (56.7 ppm) and the largest CQ value (2.5 MHz) among these oxygen sites. 2D 1H → 17O HETCOR DNP experiments allow us to discriminate three bridging (Aln)-μ2-OH and two terminal (Aln)-μ1-OH hydroxyl groups. The structural features of the bare oxygen species and hydroxyl groups are similar for the γ-Al2O3 samples isotopically labelled by 17O2 gas or H217O. The results presented here show that the combination of surface-selective labelling and DNP-SENS is an effective approach for characterizing oxides with complex surface species.

Linking interfacial chemistry of CO2 to surface structures of hydrated metal oxide nanoparticles: hematite.

PubMed

Chernyshova, Irina V; Ponnurangam, Sathish; Somasundaran, Ponisseril

2013-05-14

A better understanding of interaction with dissolved CO2 is required to rationally design and model the (photo)catalytic and sorption processes on metal (hydr)oxide nanoparticles (NPs) in aqueous media. Using in situ FTIR spectroscopy, we address this problem for rhombohedral 38 nm hematite (α-Fe2O3) nanoparticles as a model. We not only resolve the structures of the adsorbed carbonate species, but also specify their adsorption sites and their location on the nanoparticle surface. The spectral relationships obtained present a basis for a new method of characterizing the microscopic structural and acid-base properties (related to individual adsorption sites) of hydrated metal (hydr)oxide NPs using atmospherically derived CO2 as a probe. Specifically, we distinguish two carbonate species suggesting two principally different adsorption mechanisms. One species, which is more weakly adsorbed, has an inner-sphere mononuclear monodentate structure which is formed by a conventional ligand-exchange mechanism. At natural levels of dissolved carbonate and pH from 3 to 11, this species is attached to the most acidic/reactive surface cations (surface states) associated with ferrihydrite-like surface defects. The second species, which is more strongly adsorbed, presents a mixed C and O coordination of bent CO2. This species uniquely recognizes the stoichiometric rhombohedral {104} facets in the NP texture. Like in gas phase, it is formed through the surface coordination of molecular CO2. We address how the adsorption sites hosting these two carbonate species are affected by the annealing and acid etching of the NPs. These results support the nanosize-induced phase transformation of hematite towards ferrihydrite under hydrous conditions, and additionally show that the process starts from the roughened areas of the facet intersections.

Unraveling origins of the heterogeneous curvature dependence of polypeptide interactions with carbon nanostructures.

PubMed

Jana, Asis K; Tiwari, Mrityunjay K; Vanka, Kumar; Sengupta, Neelanjana

2016-02-17

Emerging nanotechnology has rapidly broadened interfacial prospects of biological molecules with carbon nanomaterials (CNs). A prerequisite for effectively harnessing such hybrid materials is a multi-faceted understanding of their complex interfacial interactions as functions of the physico-chemical characteristics and the surface topography of the individual components. In this article, we address the origins of the curvature dependence of polypeptide adsorption on CN surfaces (CNSs), a phenomenon bearing an acute influence upon the behavior and activity of CN-protein conjugates. Our benchmark molecular dynamics (MD) simulations with the amphiphilic full-length amyloid beta (Aβ) peptide demonstrate that protein adsorption is strongest on the concave (inner) CN surface, weakest on the convex (outer) surface, and intermediary on the planar surface, in agreement with recent experimental reports. The curvature effects, however, are found to manifest non-uniformly between the amino acid subtypes. To understand the underlying interplay of the chemical nature of the amino acids and surface topography of the CNs, we performed high-level quantum chemical (QM) calculations with amino acid analogs (AAA) representing their five prominent classes, and convex, concave and planar CN fragments. Molecular electrostatic potential maps reveal pronounced curvature dependence in the mixing of electron densities, and a resulting variance in the stabilization of the non-covalently bound molecular complexes. Interestingly, our study revealed that the interaction trends of the high-level QM calculations were captured well by the empirical force field. The findings in this study have important bearing upon the design of carbon based bio-nanomaterials, and additionally, provide valuable insights into the accuracy of various computational techniques for probing non-bonded interfacial interactions.

Differentiation of respiratory syncytial virus subgroups with cDNA probes in a nucleic acid hybridization assay.

PubMed Central

Sullender, W M; Anderson, L J; Anderson, K; Wertz, G W

1990-01-01

A new approach to respiratory syncytial (RS) virus subgroup determination was developed by using a simple nucleic acid filter hybridization technique. By this method, virus-infected cells are bound and fixed in a single step, and the viral RNA in the fixed-cell preparation is characterized directly by its ability to hybridize to cDNA probes specific for either the A or B subgroups of RS virus. The subgroup-specific probes were constructed from cDNA clones that corresponded to a portion of the extracellular domain of the RS virus G protein of either a subgroup B RS virus (8/60) or a subgroup A RS virus (A2). The cDNA probes were labeled with 32P and used to analyze RS virus isolates collected over a period of three decades. Replicate templates of infected cell preparations were hybridized with either the subgroup A or B probe. The subgroup assignments of 40 viruses tested by nucleic acid hybridization were in agreement with the results of subgroup determinations based on their reactivities with monoclonal antibodies, which previously has been the only method available for determining the subgroup classification of RS virus isolates. The nucleic acid hybridization assay has the advantage of providing broad-based discrimination of the two subgroups on the basis of nucleic acid homology, irrespective of minor antigenic differences that are detected in assays in which monoclonal antibodies are used. The nucleic acid hybridization technique provides a reliable method for RS virus subgroup characterization. Images PMID:2118548

Fluorescent hybridization probes for nucleic acid detection.

PubMed

Guo, Jia; Ju, Jingyue; Turro, Nicholas J

2012-04-01

Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical principles. These probes have shown particular applicability in a variety of studies, such as mRNA tracking, single nucleotide polymorphism (SNP) detection, polymerase chain reaction (PCR) monitoring, and microorganism identification. Molecular beacons are hairpin oligonucleotide probes that present distinctive fluorescent signatures in the presence and absence of their target. Binary probes consist of two fluorescently labeled oligonucleotide strands that can hybridize to adjacent regions of their target and generate distinctive fluorescence signals. These probes have been extensively studied and modified for different applications by modulating their structures or using various combinations of fluorophores, excimer-forming molecules, and metal complexes. This review describes the applicability and advantages of various hybridization probes that utilize novel and creative design to enhance their target detection sensitivity and specificity.

Coupling Molecular Beacons to Barcoded Metal Nanowires for Multiplexed, Sealed Chamber DNA Bioassays

PubMed Central

Stoermer, Rebecca L.; Cederquist, Kristin B.; McFarland, Sean K.; Sha, Michael Y.; Penn, Sharron G.

2010-01-01

We have combined molecular beacon (MB) probes with barcoded metal nanowires to enable no-wash, sealed chamber, multiplexed detection of nucleic acids. Probe design and experimental parameters important in nanowire-based MB assays are discussed. Loop regions of 24 bases and 5 base pair stem regions in the beacon probes gave optimal performance. Our results suggest that thermodynamic predictions for secondary structure stability of solution-phase MB can guide probe design for nanowire-based assays. Dengue virus-specific probes with predicted solution-phase ΔG of folding in 500 mM buffered NaCl of approximately −4 kcal/mol performed better than those with ΔG > −2 or < −6 kcal/mol. Buffered 300–500 mM NaCl was selected after comparison of several buffers previously reported for similar types of assays, and 200–500 mM NaCl was found to be the optimal ionic strength for the hybridization temperatures (25 and 50 °C) and probe designs used here. Target binding to the surface as a function of solution concentration fit a Sips isotherm with Kd = 1.7 ± 0.3 nM. The detection limit was ∼100 pM, limited by incomplete quenching. Single base mismatches could be discriminated from fully complementary targets. Oligonucleotide target sequences specific for human immunodeficiency, hepatitis C, and severe acute respiratory viruses were assayed simultaneously in a no-wash, sealed chamber, multiplexed experiment in which each of three probe sequences was attached to a different pattern of encoded nanowires. Finally, we demonstrated that probe-coated nanowires retain their selectivity and sensitivity in a triplexed assay after storage for over 3 months. PMID:17177440

The effect of probe choice and solution conditions on the apparent photoreactivity of dissolved organic matter.

PubMed

Maizel, Andrew C; Remucal, Christina K

2017-08-16

Excited triplet states of dissolved organic matter ( 3 DOM) are quantified directly with the species-specific probes trans,trans-hexadienoic acid (HDA) and 2,4,6-trimethylphenol (TMP), and indirectly with the singlet oxygen ( 1 O 2 ) probe furfuryl alcohol (FFA). Although previous work suggests that these probe compounds may be sensitive to solution conditions, including dissolved organic carbon concentration ([DOC]) and pH, and may quantify different 3 DOM subpopulations, the probes have not been systematically compared. Therefore, we quantify the apparent photoreactivity of diverse environmental waters using HDA, TMP, and FFA. By conducting experiments under ambient [DOC] and pH, with standardized [DOC] and pH, and with solid phase extraction isolates, we demonstrate that much of the apparent dissimilarity in photochemical measurements is attributable to solution conditions, rather than intrinsic differences in 3 DOM production. In general, apparent quantum yields (Φ 1 O 2 ≥ Φ 3 DOM,TMP ≫ Φ 3 DOM,HDA ) and pseudo-steady state concentrations ([ 1 O 2 ] ss > [ 3 DOM] ss,TMP > [ 3 DOM] ss,HDA ) show consistent relationships in all waters under standardized conditions. However, intrinsic differences in 3 DOM photoreactivity are apparent between DOM from diverse sources, as seen in the higher Φ 1 O 2 and lower Φ 3 DOM,TMP of wastewater effluents compared with oligotrophic lakes. Additionally, while conflicting trends in photoreactivity are observed under ambient conditions, all probes observe quantum yields increasing from surface wetlands to terrestrially influenced waters to oligotrophic lakes under standardized conditions. This work elucidates how probe selection and solution conditions influence the apparent photoreactivity of environmental waters and confirms that 3 DOM or 1 O 2 probes cannot be used interchangeably in waters that vary in [DOC], pH, or DOM source.

Enhanced biocompatibility of neural probes by integrating microstructures and delivering anti-inflammatory agents via microfluidic channels

NASA Astrophysics Data System (ADS)

Liu, Bin; Kim, Eric; Meggo, Anika; Gandhi, Sachin; Luo, Hao; Kallakuri, Srinivas; Xu, Yong; Zhang, Jinsheng

2017-04-01

Objective. Biocompatibility is a major issue for chronic neural implants, involving inflammatory and wound healing responses of neurons and glial cells. To enhance biocompatibility, we developed silicon-parylene hybrid neural probes with open architecture electrodes, microfluidic channels and a reservoir for drug delivery to suppress tissue responses. Approach. We chronically implanted our neural probes in the rat auditory cortex and investigated (1) whether open architecture electrode reduces inflammatory reaction by measuring glial responses; and (2) whether delivery of antibiotic minocycline reduces inflammatory and tissue reaction. Four weeks after implantation, immunostaining for glial fibrillary acid protein (astrocyte marker) and ionizing calcium-binding adaptor molecule 1 (macrophages/microglia cell marker) were conducted to identify immunoreactive astrocyte and microglial cells, and to determine the extent of astrocytes and microglial cell reaction/activation. A comparison was made between using traditional solid-surface electrodes and newly-designed electrodes with open architecture, as well as between deliveries of minocycline and artificial cerebral-spinal fluid diffused through microfluidic channels. Main results. The new probes with integrated micro-structures induced minimal tissue reaction compared to traditional electrodes at 4 weeks after implantation. Microcycline delivered through integrated microfluidic channels reduced tissue response as indicated by decreased microglial reaction around the neural probes implanted. Significance. The new design will help enhance the long-term stability of the implantable devices.

16 CFR § 1505.51 - Hot surfaces.

Code of Federal Regulations, 2013 CFR

2013-01-01

... CHILDREN Policies and Interpretations § 1505.51 Hot surfaces. (a) Test probe. Section 1505.6(g)(2) defines... inches long. To test for accessibility using this test probe, it shall be inserted no more than 3 inches into any opening in the toy. Unless the probe contacts a surface within 3 inches of the plane of the...

Protein organic chemistry and applications for labeling and engineering in live-cell systems.

PubMed

Takaoka, Yousuke; Ojida, Akio; Hamachi, Itaru

2013-04-08

The modification of proteins with synthetic probes is a powerful means of elucidating and engineering the functions of proteins both in vitro and in live cells or in vivo. Herein we review recent progress in chemistry-based protein modification methods and their application in protein engineering, with particular emphasis on the following four strategies: 1) the bioconjugation reactions of amino acids on the surfaces of natural proteins, mainly applied in test-tube settings; 2) the bioorthogonal reactions of proteins with non-natural functional groups; 3) the coupling of recognition and reactive sites using an enzyme or short peptide tag-probe pair for labeling natural amino acids; and 4) ligand-directed labeling chemistries for the selective labeling of endogenous proteins in living systems. Overall, these techniques represent a useful set of tools for application in chemical biology, with the methods 2-4 in particular being applicable to crude (living) habitats. Although still in its infancy, the use of organic chemistry for the manipulation of endogenous proteins, with subsequent applications in living systems, represents a worthy challenge for many chemists. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optic probe for semiconductor characterization

DOEpatents

Sopori, Bhushan L [Denver, CO; Hambarian, Artak [Yerevan, AM

2008-09-02

Described herein is an optical probe (120) for use in characterizing surface defects in wafers, such as semiconductor wafers. The optical probe (120) detects laser light reflected from the surface (124) of the wafer (106) within various ranges of angles. Characteristics of defects in the surface (124) of the wafer (106) are determined based on the amount of reflected laser light detected in each of the ranges of angles. Additionally, a wafer characterization system (100) is described that includes the described optical probe (120).

Modulated optical phase conjugation in rhodamine 110 doped boric acid glass saturable absorber thin films

NASA Astrophysics Data System (ADS)

Sharma, Ramesh C.; Waigh, Thomas A.; Singh, Jagdish P.

2008-03-01

The optical phase conjugation signal in nearly nondegenerate four wave mixing was studied using a rhodamine 110 doped boric acid glass saturable absorber nonlinear medium. We have demonstrated a narrow band optical filter (2.56±0.15Hz) using an optical phase conjugation signal in the frequency modulation of a weak probe beam in the presence of two strong counterpropagating pump beams in rhodamine 110 doped boric acid glass thin films (10-4m). Both the pump beams and the probe beam are at a wavelength of 488nm (continuous-wave Ar+ laser). The probe beam frequency was detuned with a ramp signal using a piezoelectric transducer mirror.

Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Olli-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

2002-01-01

Methods and compositions for staining based upon nucleic acid sequence that employ nudeic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Olli-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

2008-09-09

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

DOEpatents

Gray, Joe W [San Francisco, CA; Pinkel, Daniel [Lafayette, CA; Kallioniemi, Olli-Pekka [Turku, FI; Kallioniemi, Anne [Tampere, FI; Sakamoto, Masaru [Tokyo, JP

2009-10-06

Methods and compositions for staining based upon nucleic acid sequence that employ .[.nudeic.]. .Iadd.nucleic .Iaddend.acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Chromosome-Specific Staining To Detect Genetic Rearrangements Associated With Chromosome 3 And/Or Chromosone 17

DOEpatents

Gray; Joe W.; Pinkel; Daniel; Kallioniemi; Olli-Pekka; Kallioniemi; Anne; Sakamoto; Masaru

2002-02-05

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Probing the Orientation of Surface-Immobilized Protein G B1 Using ToF-SIMS Sum Frequency Generation and NEXAFS Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

L Baugh; T Weidner; J Baio

2011-12-31

The ability to orient active proteins on surfaces is a critical aspect of many medical technologies. An important related challenge is characterizing protein orientation in these surface films. This study uses a combination of time-of-flight secondary ion mass spectrometry (ToF-SIMS), sum frequency generation (SFG) vibrational spectroscopy, and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to characterize the orientation of surface-immobilized Protein G B1, a rigid 6 kDa domain that binds the Fc fragment of IgG. Two Protein G B1 variants with a single cysteine introduced at either end were immobilized via the cysteine thiol onto maleimide-oligo(ethylene glycol)-functionalized gold and baremore » gold substrates. X-ray photoelectron spectroscopy was used to measure the amount of immobilized protein, and ToF-SIMS was used to measure the amino acid composition of the exposed surface of the protein films and to confirm covalent attachment of protein thiol to the substrate maleimide groups. SFG and NEXAFS were used to characterize the ordering and orientation of peptide or side chain bonds. On both substrates and for both cysteine positions, ToF-SIMS data showed enrichment of mass peaks from amino acids located at the end of the protein opposite to the cysteine surface position as compared with nonspecifically immobilized protein, indicating end-on protein orientations. Orientation on the maleimide substrate was enhanced by increasing pH (7.0-9.5) and salt concentration (0-1.5 M NaCl). SFG spectral peaks characteristic of ordered {alpha}-helix and {beta}-sheet elements were observed for both variants but not for cysteine-free wild type protein on the maleimide surface. The phase of the {alpha}-helix and {beta}-sheet peaks indicated a predominantly upright orientation for both variants, consistent with an end-on protein binding configuration. Polarization dependence of the NEXAFS signal from the N 1s to {pi}* transition of {beta}-sheet peptide bonds also indicated protein ordering, with an estimated tilt angle of inner {beta}-strands of 40-50{sup o} for both variants (one variant more tilted than the other), consistent with SFG results. The combined results demonstrate the power of using complementary techniques to probe protein orientation on surfaces.« less

Method for replicating an array of nucleic acid probes

DOEpatents

Cantor, Charles R.; Przetakiewicz, Marek; Smith, Cassandra L.; Sano, Takeshi

1998-01-01

The invention relates to the replication of probe arrays and methods for replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5'- and/or 3'-overhangs.

Quantum dot-based microfluidic biosensor for cancer detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghrera, Aditya Sharma; School of Engineering and Technology, ITM University, Gurgaon-122017; Pandey, Chandra Mouli

2015-05-11

We report results of the studies relating to fabrication of an impedimetric microfluidic–based nucleic acid sensor for quantification of DNA sequences specific to chronic myelogenous leukemia (CML). The sensor chip is prepared by patterning an indium–tin–oxide (ITO) coated glass substrate via wet chemical etching method followed by sealing with polydimethylsiloxane (PDMS) microchannel for fluid control. The fabricated microfluidic chip comprising of a patterned ITO substrate is modified by depositing cadmium selenide quantum dots (QCdSe) via Langmuir–Blodgett technique. Further, the QCdSe surface has been functionalized with specific DNA probe for CML detection. The probe DNA functionalized QCdSe integrated miniaturized system hasmore » been used to monitor target complementary DNA concentration by measuring the interfacial charge transfer resistance via hybridization. The presence of complementary DNA in buffer solution significantly results in decreased electro-conductivity of the interface due to presence of a charge barrier for transport of the redox probe ions. The microfluidic DNA biosensor exhibits improved linearity in the concentration range of 10{sup −15} M to 10{sup −11} M.« less

Electrochemical biosensor based on enzyme substrate as a linker: Application for aldolase activity with pectin-thionine complex as recognization element and signal amplification probe.

PubMed

Wang, Xiaonan; Wang, Meiwen; Zhang, Yuanyuan; Miao, Xiaocao; Huang, Yuanyuan; Zhang, Juan; Sun, Lizhou

2016-09-15

A new strategy to fabricate electrochemical biosensor is reported based on the linkage of enzyme substrate, thereby an electrochemical method to detect aldolase activity is established using pectin-thionine complex (PTC) as recognization element and signal probe. The linkage effect of fructose-1,6-bisphosphate (FBP), the substrate of aldolase, can be achieved via its strong binding to magnetic nanoparticles (MNPs)/aminophenylboronic acid (APBA) and the formation of phosphoramidate bond derived from its reaction with p-phenylenediamine (PDA) on the surface of electrode. Aldolase can reversibly catalyze the substrates into the products which have no binding capacity with MNPs/APBA, resulting in the exposure of the corresponding binding sites and its subsequent recognization on signal probe. Meanwhile, signal amplification can be accomplished by using the firstly prepared PTC which can bind with MNPs/APBA, and accuracy can be strengthened through magnetic separation. With good precision and accuracy, the established sensor may be extended to other proteins with reversible catalyzed ability. Copyright © 2016 Elsevier B.V. All rights reserved.

Simultaneous determination of isoproterenol, acetaminophen, folic acid, propranolol and caffeine using a sensor platform based on carbon black, graphene oxide, copper nanoparticles and PEDOT:PSS.

PubMed

Wong, Ademar; Santos, Anderson Martin; Silva, Tiago Almeida; Fatibello-Filho, Orlando

2018-06-01

We explored the use of carbon black (CB), graphene oxide (GO), copper nanoparticles (CuNPs) and poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) as electrode materials for the simultaneous determination of isoproterenol, acetaminophen, folic acid, propranolol and caffeine. The designed nanostructured surface was widely characterized by scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), contact angle measurements and electrochemistry. From electrochemical characterization assays carried out towards the potassium ferricyanide redox probe, fast electron transfer kinetics and a considerably higher electroactive surface area were observed for the modified electrodic surface based on CB, GO, CuNPs and PEDOT:PSS film. Using square-wave voltammetry (SWV), well defined and resolved anodic peaks were detected for isoproterenol, acetaminophen, folic acid, propranolol and caffeine, with peak-to-peak potential separation not less than 170 mV. Then, the SWV technique was explored for the simultaneous determination of quinary mixtures of these analytes, resulting in analytical curves with linear ranges and limits of detection at micromolar concentration levels. The practical viability of the proposed voltammetric sensor was illustrated in the analysis of human body fluid samples. The proposed sensor showed good repeatability and a successful application using urine and serum matrices, with recoveries close to 100%. Copyright © 2018 Elsevier B.V. All rights reserved.

Chemical analysis of acoustically levitated drops by Raman spectroscopy.

PubMed

Tuckermann, Rudolf; Puskar, Ljiljana; Zavabeti, Mahta; Sekine, Ryo; McNaughton, Don

2009-07-01

An experimental apparatus combining Raman spectroscopy with acoustic levitation, Raman acoustic levitation spectroscopy (RALS), is investigated in the field of physical and chemical analytics. Whereas acoustic levitation enables the contactless handling of microsized samples, Raman spectroscopy offers the advantage of a noninvasive method without complex sample preparation. After carrying out some systematic tests to probe the sensitivity of the technique to drop size, shape, and position, RALS has been successfully applied in monitoring sample dilution and preconcentration, evaporation, crystallization, an acid-base reaction, and analytes in a surface-enhanced Raman spectroscopy colloidal suspension.

Couplings

NASA Astrophysics Data System (ADS)

Stošić, Dušan; Auroux, Aline

Basic principles of calorimetry coupled with other techniques are introduced. These methods are used in heterogeneous catalysis for characterization of acidic, basic and red-ox properties of solid catalysts. Estimation of these features is achieved by monitoring the interaction of various probe molecules with the surface of such materials. Overview of gas phase, as well as liquid phase techniques is given. Special attention is devoted to coupled calorimetry-volumetry method. Furthermore, the influence of different experimental parameters on the results of these techniques is discussed, since it is known that they can significantly influence the evaluation of catalytic properties of investigated materials.

A scanning probe mounted on a field-effect transistor: Characterization of ion damage in Si.

PubMed

Shin, Kumjae; Lee, Hoontaek; Sung, Min; Lee, Sang Hoon; Shin, Hyunjung; Moon, Wonkyu

2017-10-01

We have examined the capabilities of a Tip-On-Gate of Field-Effect Transistor (ToGoFET) probe for characterization of FIB-induced damage in Si surface. A ToGoFET probe is the SPM probe which the Field Effect Transistor(FET) is embedded at the end of a cantilever and a Pt tip was mounted at the gate of FET. The ToGoFET probe can detect the surface electrical properties by measuring source-drain current directly modulated by the charge on the tip. In this study, a Si specimen whose surface was processed with Ga+ ion beam was prepared. Irradiation and implantation with Ga+ ions induce highly localized modifications to the contact potential. The FET embedded on ToGoFET probe detected the surface electric field profile generated by schottky contact between the Pt tip and the sample surface. Experimentally, it was shown that significant differences of electric field due to the contact potential barrier in differently processed specimens were observed using ToGOFET probe. This result shows the potential that the local contact potential difference can be measured by simple working principle with high sensitivity. Copyright © 2017 Elsevier Ltd. All rights reserved.

ESTIMATION OF BACTERIAL CELL NUMBERS IN HUMIC ACID-RICH SALT MARSH SEDIMENTS WITH PROBES DIRECTED TO 16S RIBOSOMAL DNA

EPA Science Inventory

The feasibility of using probes directed towards ribosomal DNAs (rDNAs) as a quantitative approach to estimating cell numbers was examined and applied to study the structure of a bacterial community in humic acid-rich salt marsh sediments. Hybridizations were performed with membr...

DNA surface hybridization regimes

PubMed Central

Gong, Ping; Levicky, Rastislav

2008-01-01

Surface hybridization reactions, in which sequence-specific recognition occurs between immobilized and solution nucleic acids, are routinely carried out to quantify and interpret genomic information. Although hybridization is fairly well understood in bulk solution, the greater complexity of an interfacial environment presents new challenges to a fundamental understanding, and hence application, of these assays. At a surface, molecular interactions are amplified by the two-dimensional nature of the immobilized layer, which focuses the nucleic acid charge and concentration to levels not encountered in solution, and which impacts the hybridization behavior in unique ways. This study finds that, at low ionic strengths, an electrostatic balance between the concentration of immobilized oligonucleotide charge and solution ionic strength governs the onset of hybridization. As ionic strength increases, the importance of electrostatics diminishes and the hybridization behavior becomes more complex. Suppression of hybridization affinity constants relative to solution values, and their weakened dependence on the concentration of DNA counterions, indicate that the immobilized strands form complexes that compete with hybridization to analyte strands. Moreover, an unusual regime is observed in which the surface coverage of immobilized oligonucleotides does not significantly influence the hybridization behavior, despite physical closeness and hence compulsory interactions between sites. These results are interpreted and summarized in a diagram of hybridization regimes that maps specific behaviors to experimental ranges of ionic strength and probe coverage. PMID:18381819

Two Successive Reactions on a DNA Template: A Strategy for Improving Background and Specificity in Nucleic Acid Detection

PubMed Central

Franzini, Raphael M.

2015-01-01

We report a new strategy for template-mediated fluorogenic chemistry that results in enhanced performance for the fluorescence detection of nucleic acids. In this approach, two successive templated reactions are required to induce a fluorescence signal, rather than only one. These novel fluorescein-labeled oligonucleotide probes, termed 2-STAR probes, contain two quencher groups tethered by separate reductively cleavable linkers. When a 2-STAR quenched probe binds adjacent to either two successive mono triphenyl-phosphine (TPP)-DNAs or a dual TPP-DNA, the two quenchers are released, resulting in a fluorescence signal. Because of the requirement for two consecutive reactions, 2-STAR probes display an unprecedented level of sequence-specificity for template-mediated probe designs. At the same time, background emission generated by off-template reactions or incomplete quenching is among the lowest of any fluorogenic reactive probes for the detection of DNA or RNA. PMID:21294182

A highly selective fluorescent probe for the detection of hypochlorous acid in tap water and living cells.

PubMed

Wang, Xiao; Zhou, Yanmei; Xu, Chenggong; Song, Haohan; Li, Li; Zhang, Junli; Guo, Meixia

2018-06-03

A turn-on fluorescent probe (DAME) for sensing hypochlorous acid (HClO) with excellent selectivity was presented. The fluorescent probe was composed of coumarin derivative as the fluorophore and dimethylcarbamothioic chloride group with a sulfide moiety as modulator. Additionally, the sulfide moiety would be oxidized by HClO, and then free dye of coumarin derivate was released and exhibited significant fluorescence. In addition, the probe could respond to HClO in solutions within 60 s and the limit of detection was down to 34.75 nM. Moreover, the probe was used for the detection of HClO in tap water through the home-made test paper. And confocal images confirmed that probe DAME could be used for recognizing HClO in living cells. Copyright © 2017 Elsevier B.V. All rights reserved.

Nucleic acid probes as a diagnostic method for tick-borne hemoparasites of veterinary importance.

PubMed

Figueroa, J V; Buening, G M

1995-03-01

An increased number of articles on the use of nucleic acid-based hybridization techniques for diagnostic purposes have been recently published. This article reviews nucleic acid-based hybridization as an assay to detect hemoparasite infections of economic relevance in veterinary medicine. By using recombinant DNA techniques, selected clones containing inserts of Anaplasma, Babesia, Cowdria or Theileria genomic DNA sequences have been obtained, and they are now available to be utilized as specific, highly sensitive DNA or RNA probes to detect the presence of the hemoparasite DNA in an infected animal. Either in an isotopic or non-isotopic detection system, probes have allowed scientists to test for--originally in samples collected from experimentally infected animals and later in samples collected in the field--the presence of hemoparasites during the prepatent, patent, convalescent, and chronic periods of the infection in the host. Nucleic acid probes have given researchers the opportunity to carry out genomic analysis of parasite DNA to differentiate hemoparasite species and to identify genetically distinct populations among and within isolates, strains and clonal populations. Prevalence of parasite infection in the tick vector can now be accomplished more specifically with the nucleic acid probes. Lately, with the advent of the polymerase chain reaction technique, small numbers of hemoparasites can be positively identified in the vertebrate host and tick vector. These techniques can be used to assess the veterinary epidemiological situation in a particular geographical region for the planning of control measures.

A new fluorescent pH probe for imaging lysosomes in living cells.

PubMed

Lv, Hong-Shui; Huang, Shu-Ya; Xu, Yu; Dai, Xi; Miao, Jun-Ying; Zhao, Bao-Xiang

2014-01-15

A new rhodamine B-based pH fluorescent probe has been synthesized and characterized. The probe responds to acidic pH with short response time, high selectivity and sensitivity, and exhibits a more than 20-fold increase in fluorescence intensity within the pH range of 7.5-4.1 with the pKa value of 5.72, which is valuable to study acidic organelles in living cells. Also, it has been successfully applied to HeLa cells, for its low cytotoxicity, brilliant photostability, good membrane permeability and no 'alkalizing effect' on lysosomes. The results demonstrate that this probe is a lysosome-specific probe, which can selectively stain lysosomes and monitor lysosomal pH changes in living cells. Copyright © 2013 Elsevier Ltd. All rights reserved.

Liquid Microjunction Surface Sampling Probe Fluid Dynamics: Computational and Experimental Analysis of Coaxial Intercapillary Positioning Effects on Sample Manipulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

ElNaggar, Mariam S; Barbier, Charlotte N; Van Berkel, Gary J

A coaxial geometry liquid microjunction surface sampling probe (LMJ-SSP) enables direct extraction of analytes from surfaces for subsequent analysis by techniques like mass spectrometry. Solution dynamics at the probe-to-sample surface interface in the LMJ-SSP has been suspected to influence sampling efficiency and dispersion but has not been rigorously investigated. The effect on flow dynamics and analyte transport to the mass spectrometer caused by coaxial retraction of the inner and outer capillaries from each other and the surface during sampling with a LMJ-SSP was investigated using computational fluid dynamics and experimentation. A transparent LMJ-SSP was constructed to provide the means formore » visual observation of the dynamics of the surface sampling process. Visual observation, computational fluid dynamics (CFD) analysis, and experimental results revealed that inner capillary axial retraction from the flush position relative to the outer capillary transitioned the probe from a continuous sampling and injection mode through an intermediate regime to sample plug formationmode caused by eddy currents at the sampling end of the probe. The potential for analytical implementation of these newly discovered probe operational modes is discussed.« less

Active radiometer for self-calibrated furnace temperature measurements

DOEpatents

Woskov, P.P.; Cohn, D.R.; Titus, C.H.; Wittle, J.K.; Surma, J.E.

1996-11-12

A radiometer is described with a probe beam superimposed on its field-of-view for furnace temperature measurements. The radiometer includes a heterodyne millimeter/submillimeter-wave receiver including a millimeter/submillimeter-wave source for probing. The receiver is adapted to receive radiation from a surface whose temperature is to be measured. The radiation includes a surface emission portion and a surface reflection portion which includes the probe beam energy reflected from the surface. The surface emission portion is related to the surface temperature and the surface reflection portion is related to the emissivity of the surface. The simultaneous measurement of surface emissivity serves as a real time calibration of the temperature measurement. 5 figs.

Acid-Activatable Michael-Type Fluorescent Probes for Thiols and for Labeling Lysosomes in Live Cells.

PubMed

Dai, Chun-Guang; Du, Xiao-Jiao; Song, Qin-Hua

2015-12-18

A Michael addition is usually taken as a base-catalyzed reaction. Most fluorescent probes have been designed to detect thiols in slightly alkaline solutions (pH 7-9). The sensing reactions of almost all Michael-type fluorescent probes for thiols are faster in a high pH solution than in a low pH solution. In this work, we synthesized a series of 7-substituted 2-(quinolin-2-ylmethylene)malonic acids (QMAs, substituents: NEt2, OH, H, Cl, or NO2) and their ethyl esters (QMEs) as Michael-type fluorescent probes for thiols. The sensing reactions of QMAs and QMEs occur in distinct pH ranges, pH < 7 for QMAs and pH > 7 for QMEs. On the basis of experimental and theoretic studies, we have clarified the distinct pH effects on the sensing reactivity between QMAs and QMEs and demonstrated that two QMAs (NEt2, OH) are highly sensitive and selective fluorescent probes for thiols in acidic solutions (pH < 7) and promising dyes that can label lysosomes in live cells.

Utilizing Intrinsic Properties of Polyaniline to Detect Nucleic Acid Hybridization through UV-Enhanced Electrostatic Interaction.

PubMed

Sengupta, Partha Pratim; Gloria, Jared N; Amato, Dahlia N; Amato, Douglas V; Patton, Derek L; Murali, Beddhu; Flynt, Alex S

2015-10-12

Detection of specific RNA or DNA molecules by hybridization to "probe" nucleic acids via complementary base-pairing is a powerful method for analysis of biological systems. Here we describe a strategy for transducing hybridization events through modulating intrinsic properties of the electroconductive polymer polyaniline (PANI). When DNA-based probes electrostatically interact with PANI, its fluorescence properties are increased, a phenomenon that can be enhanced by UV irradiation. Hybridization of target nucleic acids results in dissociation of probes causing PANI fluorescence to return to basal levels. By monitoring restoration of base PANI fluorescence as little as 10(-11) M (10 pM) of target oligonucleotides could be detected within 15 min of hybridization. Detection of complementary oligos was specific, with introduction of a single mismatch failing to form a target-probe duplex that would dissociate from PANI. Furthermore, this approach is robust and is capable of detecting specific RNAs in extracts from animals. This sensor system improves on previously reported strategies by transducing highly specific probe dissociation events through intrinsic properties of a conducting polymer without the need for additional labels.

Exploring the recognized bio-mimicry materials for gas sensing.

PubMed

Wu, T Z; Lo, Y R; Chan, E C

2001-12-01

This study was undertaken to synthesize peptides that are partially similar to the binding sites of human olfactory receptor protein. First, a putative 3-D model structure of human olfactory receptor protein (P30953) was modeled using a molecular simulation method. The computer docking simulation was then performed to determine the most plausible binding sites between the model structure and target gases, trimethylamine, ammonia, acetic acid, and o-xylene. According to the simulation result, a series of polypeptide sequences, horp61 for TMA, horp103 for o-xylene, horp109 for ammonia, and horp193 for acetic acid as recognized molecules were designed for gas sensing purposes. Preparing these peptides as corresponding gas sensing probes, the results showed a high relative sensitivity response of 6.7 for TMA (probe horp61), 5.1 for o-xylene (probe horp103), 11 for ammonia (probe horp109), and 28 for acetic acid (probe horp193), respectively. These results indicate that peptide mimicking of binding domain on olfactory receptor opens a new window and offers a novel strategy for the further development of recognized materials for gas sensing.

EPR spin probe and spin label studies of some low molecular and polymer micelles

NASA Astrophysics Data System (ADS)

Wasserman, A. M.; Kasaikin, V. A.; Timofeev, V. P.

1998-12-01

The rotational mobility of spin probes of different shape and size in low molecular and polymer micelles has been studied. Several probes having nitroxide fragment localized either in the vicinity of micelle interface or in the hydrocarbon core have been used. Upon increasing the number of carbon atoms in hydrocarbon chain of detergent from 7 to 13 (sodium alkyl sulfate micelles) or from 12 to 16 (alkyltrimethylammonium bromide micelles) the rotational mobility of spin probes is decreased by the factor 1.5-2.0. The spin probe rotational mobility in polymer micelles (the complexes of alkyltrimethylammonium bromides and polymethacrylic or polyacrylic acids) is less than mobility in free micelles of the same surfactants. The study of EPR-spectra of spin labeled polymethacrylic acid (PMA) indicated that formation of water soluble complexes of polymer and alkyltrimethylammonium bromides in alkaline solutions (pH 9) does not affect the polymer segmental mobility. On the other hand, the polymer complexes formation in slightly acidic water solution (pH 6) breaks down the compact PMA conformation, thus increasing the polymer segmental mobility. Possible structures of polymer micelles are discussed.

Improved molecular fingerprint analysis employing multi-branched gold nanoparticles in conjunction with surface-enhanced Raman scattering.

PubMed

Johnston, Jencilin; Taylor, Erik N; Gilbert, Richard J; Webster, Thomas J

2016-01-01

Vibrational spectroscopy is a powerful analytical tool that assesses molecular properties based on spectroscopic signatures. In this study, the effect of gold nanoparticle morphology (spherical vs multi-branched) was assessed for the characterization of a Raman signal (ie, molecular fingerprint) that may be helpful for numerous medical applications. Multi-branched gold nanoparticles (MBAuNPs) were fabricated using a green chemistry method which employed the reduction of gold ion solute by 2-[4-(2-hydroxyethyl)-1-piperazyl] ethane sulfonic acid. Two types of reporter dyes, indocyanine (IR820 and IR792) and carbocyanine (DTTC [3,3'-diethylthiatricarbocyanine iodide] and DTDC [3,3'-diethylthiadicarbocyanine iodide]), were functionalized to the surface of the MBAuNPs and stabilized with denatured bovine serum albumin, thus forming the surface-enhanced Raman spectroscopy tag. Fluorescein isothiocyanate-conjugated anti-epidermal growth factor receptor to the surface-enhanced Raman spectroscopy tags and the properties of the resulting conjugates were assessed through determination of the Raman signal. Using the MBAuNP Raman probes synthesized in this manner, we demonstrated that MBAuNP provided significantly more surface-enhanced Raman scattering signal when compared with the associated spherical gold nanoparticle of similar size and concentration. MBAuNP enhancements were retained in the surface-enhanced Raman spectroscopy tags complexed to anti-epidermal growth factor receptor, providing evidence that this could be a useful biological probe for enhanced Raman molecular fingerprinting. Furthermore, while utilizing IR820 as a novel reporter dye linked with MBAuNP, superior Raman signal fingerprint results were obtained. Such results provide significant promise for the use of MBAuNP in the detection of numerous diseases for which biologically specific surface markers exist.

Improved molecular fingerprint analysis employing multi-branched gold nanoparticles in conjunction with surface-enhanced Raman scattering

PubMed Central

Johnston, Jencilin; Taylor, Erik N; Gilbert, Richard J; Webster, Thomas J

2016-01-01

Vibrational spectroscopy is a powerful analytical tool that assesses molecular properties based on spectroscopic signatures. In this study, the effect of gold nanoparticle morphology (spherical vs multi-branched) was assessed for the characterization of a Raman signal (ie, molecular fingerprint) that may be helpful for numerous medical applications. Multi-branched gold nanoparticles (MBAuNPs) were fabricated using a green chemistry method which employed the reduction of gold ion solute by 2-[4-(2-hydroxyethyl)-1-piperazyl] ethane sulfonic acid. Two types of reporter dyes, indocyanine (IR820 and IR792) and carbocyanine (DTTC [3,3′-diethylthiatricarbocyanine iodide] and DTDC [3,3′-diethylthiadicarbocyanine iodide]), were functionalized to the surface of the MBAuNPs and stabilized with denatured bovine serum albumin, thus forming the surface-enhanced Raman spectroscopy tag. Fluorescein isothiocyanate-conjugated anti-epidermal growth factor receptor to the surface-enhanced Raman spectroscopy tags and the properties of the resulting conjugates were assessed through determination of the Raman signal. Using the MBAuNP Raman probes synthesized in this manner, we demonstrated that MBAuNP provided significantly more surface-enhanced Raman scattering signal when compared with the associated spherical gold nanoparticle of similar size and concentration. MBAuNP enhancements were retained in the surface-enhanced Raman spectroscopy tags complexed to anti-epidermal growth factor receptor, providing evidence that this could be a useful biological probe for enhanced Raman molecular fingerprinting. Furthermore, while utilizing IR820 as a novel reporter dye linked with MBAuNP, superior Raman signal fingerprint results were obtained. Such results provide significant promise for the use of MBAuNP in the detection of numerous diseases for which biologically specific surface markers exist. PMID:26730189

Stretchable ultrasonic transducer arrays for three-dimensional imaging on complex surfaces

PubMed Central

Zhu, Xuan; Li, Xiaoshi; Chen, Zeyu; Chen, Yimu; Lei, Yusheng; Li, Yang; Nomoto, Akihiro; Zhou, Qifa; di Scalea, Francesco Lanza

2018-01-01

Ultrasonic imaging has been implemented as a powerful tool for noninvasive subsurface inspections of both structural and biological media. Current ultrasound probes are rigid and bulky and cannot readily image through nonplanar three-dimensional (3D) surfaces. However, imaging through these complicated surfaces is vital because stress concentrations at geometrical discontinuities render these surfaces highly prone to defects. This study reports a stretchable ultrasound probe that can conform to and detect nonplanar complex surfaces. The probe consists of a 10 × 10 array of piezoelectric transducers that exploit an “island-bridge” layout with multilayer electrodes, encapsulated by thin and compliant silicone elastomers. The stretchable probe shows excellent electromechanical coupling, minimal cross-talk, and more than 50% stretchability. Its performance is demonstrated by reconstructing defects in 3D space with high spatial resolution through flat, concave, and convex surfaces. The results hold great implications for applications of ultrasound that require imaging through complex surfaces. PMID:29740603

Laser-based ultrasonics by dual-probe interferometer detection and narrow-band ultrasound generation

NASA Astrophysics Data System (ADS)

Huang, Jin

1993-01-01

Despite the advantages of laser-based ultrasonic (LBU) systems, the overall sensitivity of LBU systems needs to be improved for practical applications. Progress is reported to achieve better LBU detection accuracy and sensitivity for applications with surface waves and Lamb waves. A novel dual-probe laser interferometer has been developed to measure the same signal at two points. The dual-probe interferometer is a modification of a conventional single-probe interferometer in that the reference beam is guided to a second detecting point on the specimen surface to form a differential measurement mode, which measure the difference of the displacements at the two points. This dual-probe interferometer is particularly useful for accurate measurements of the speed and attenuation of surface waves and Lamb waves. The dual-probe interferometer has been applied to obtain accurate measurements of the surface wave speed and attenuation on surfaces of increasing surface roughness. It has also been demonstrated that with an appropriate signal processing method, namely, the power cepstrum method, the dual-probe interferometer is applicable to measure the local surface wave speed even when the probe separation is so small that the two waveforms in the interferometer output signal overlap in the time domain. Narrow-band signal generation and detection improve the sensitivity of LBU systems. It is proposed to use a diffraction grating to form an array of illuminating strips which form a source of narrowband surface and Lamb waves. The line-array of thermoelastic sources generates narrow-band signals whose frequency and bandwidth can be easily controlled. The optimum line-array parameters, such as width, spacing and the number of lines in the array have been derived theoretically and verified experimentally. Narrow-band signal generation with optimum parameters has been demonstrated. The enhanced LBU system with dual-probe detection and narrowband signal generation has been successfully applied to the detection of cracks emanating from rivet holes in aircraft fuselage panel samples. A compact fiber-optic dual-probe interferometer has also been developed and applied to the above mentioned problem of crack detection. Results agree well with those obtained with a bulk LBU system.

Propagation of biochirality: crossovers and nonclassical crystallization kinetics of aspartic acid in water.

PubMed

Lee, Tu; Lin, Yu Kun; Tsai, Ya Chung; Lee, Hung Lin

2013-11-01

All experimental procedures discussed could be treated as a screening tool for probing the existence of molecular association among the chiral molecules and the solvent system. The molecular association phases of a racemic conglomerate solution (CS) and a racemic compound solution (RCS), and the templating effect of aspartic acid solid surface were observed to minimize the chance of redissolving racemic conglomerate and racemic compound aspartic acid in water and reforming an RCS in crossovers experiments. Only 1 %wt% of l-aspartic acid was adequate enough to induce a transformation from a racemic compound aspartic acid to a racemic conglomerate aspartic acid. This would make the propagation of biochirality more feasible and sound. However, tetrapeptide, (l-aspartic acid)4 , failed to induce enantioseparation as templates purely by crystallization. Nonclassical crystallization theory was needed to take into account the existence of a CS. Fundamental parameters of the crystallization kinetics such as the induction time, interfacial energy, Gibbs energetic barrier, nucleation rate, and critical size of stable nuclei of: (i) racemic compound aspartic acid, (ii) racemic compound aspartic acid seeded with 1 %wt% l-aspartic acid, (iii) racemic conglomerate aspartic acid, and (iv) l-aspartic acid were evaluated and compared with different initial supersaturation ratios. Morphological studies of crystals grown from the crystallization kinetics were also carried out. © 2013 Wiley Periodicals, Inc.

Method for replicating an array of nucleic acid probes

DOEpatents

Cantor, C.R.; Przetakiewicz, M.; Smith, C.L.; Sano, T.

1998-08-18

The invention relates to the replication of probe arrays and methods for replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5{prime}- and/or 3{prime}-overhangs. 16 figs.

Enzyme-enhanced fluorescence detection of DNA on etched optical fibers.

PubMed

Niu, Shu-yan; Li, Quan-yi; Ren, Rui; Zhang, Shu-sheng

2009-05-15

A novel DNA biosensor based on enzyme-enhanced fluorescence detection on etched optical fibers was developed. The hybridization complex of DNA probe and biotinylated target was formed on the etched optical fiber, and was then bound with streptavidin labeled horseradish peroxidase (streptavidin-HRP). The target DNA was quantified through the fluorescent detection of bi-p,p'-4-hydroxyphenylacetic acid (DBDA) generated from the substrate 4-hydroxyphenylacetic acid (p-HPA) under the catalysis of HRP, with a detection limit of 1 pM and a linear range from 1.69 pM to 169 pM. It is facile to regenerate this sensor through surface treatment with concentrated urea solution. It was discovered that the sensor can retain 70% of its original activity after three detection-regeneration cycles.

The Harp probe - An in situ Bragg scattering sensor

NASA Technical Reports Server (NTRS)

Mollo-Christensen, E.; Huang, N. E.; Long, S. R.; Bliven, L. F.

1984-01-01

A wave sensor, consisting of parallel, evenly spaced capacitance wires, whose output is the sum of the water surface deflections at the wires, has been built and tested in a wave tank. The probe output simulates Bragg scattering of electromagnetic waves from a water surface with waves; it can be used to simulate electromagnetic probing of the sea surface by radar. The study establishes that the wave probe, called the 'Harp' for short, will simulate Bragg scattering and that it can also be used to study nonlinear wave processes.

Electro-optical interfacial effects on a graphene/π-conjugated organic semiconductor hybrid system

PubMed Central

Araujo, Karolline A S; Cury, Luiz A; Matos, Matheus J S; Fernandes, Thales F D; Cançado, Luiz G

2018-01-01

The influence of graphene and retinoic acid (RA) – a π-conjugated organic semiconductor – interface on their hybrid system is investigated. The physical properties of the interface are assessed via scanning probe microscopy, optical spectroscopy (photoluminescence and Raman) and ab initio calculations. The graphene/RA interaction induces the formation of a well-organized π-conjugated self-assembled monolayer (SAM) at the interface. Such structural organization leads to the high optical emission efficiency of the RA SAM, even at room temperature. Additionally, photo-assisted electrical force microscopy, photo-assisted scanning Kelvin probe microscopy and Raman spectroscopy indicate a RA-induced graphene doping and photo-charge generation. Finally, the optical excitation of the RA monolayer generates surface potential changes on the hybrid system. In summary, interface-induced organized structures atop 2D materials may have an important impact on both design and operation of π-conjugated nanomaterial-based hybrid systems. PMID:29600157

‘Green’-synthesized near-infrared PbS quantum dots with silica-PEG dual-layer coating: ultrastable and biocompatible optical probes for in vivo animal imaging

NASA Astrophysics Data System (ADS)

Wang, D.; Qian, J.; Cai, F.; He, S.; Han, S.; Mu, Y.

2012-06-01

In this paper, PbS semiconductor quantum dots (QDs) with near-infrared (NIR) photoluminescence were synthesized in oleic acid and paraffin liquid mixture by using an easily handled and ‘green’ approach. Surface functionalization of the QDs was accomplished with a silica and polyethylene glycol (PEG) phospholipid dual-layer coating and the excellent chemical stability of the nanoparticles is demonstrated. We then successfully applied the ultrastable PbS QDs to in vivo sentinel lymph node (SLN) mapping of mice. Histological analyses were also carried out to ensure that the intravenously injected nanoparticles did not produce any toxicity to the organism of mice. These experimental results suggested that our ultrastable NIR PbS QDs can serve as biocompatible and efficient probes for in vivo optical bioimaging and has great potentials for disease diagnosis and clinical therapies in the future.

Identification of Dekkera bruxellensis (Brettanomyces) from Wine by Fluorescence In Situ Hybridization Using Peptide Nucleic Acid Probes

PubMed Central

Stender, Henrik; Kurtzman, Cletus; Hyldig-Nielsen, Jens J.; Sørensen, Ditte; Broomer, Adam; Oliveira, Kenneth; Perry-O'Keefe, Heather; Sage, Andrew; Young, Barbara; Coull, James

2001-01-01

A new fluorescence in situ hybridization method using peptide nucleic acid (PNA) probes for identification of Brettanomyces is described. The test is based on fluorescein-labeled PNA probes targeting a species-specific sequence of the rRNA of Dekkera bruxellensis. The PNA probes were applied to smears of colonies, and results were interpreted by fluorescence microscopy. The results obtained from testing 127 different yeast strains, including 78 Brettanomyces isolates from wine, show that the spoilage organism Brettanomyces belongs to the species D. bruxellensis and that the new method is able to identify Brettanomyces (D. bruxellensis) with 100% sensitivity and 100% specificity. PMID:11157265

Spiroguanidine rhodamines as fluorogenic probes for lysophosphatidic acid

PubMed Central

Wang, Lei; Sibrian-Vazquez, Martha; Escobedo, Jorge O.; Wang, Jialu; Moore, Richard G.

2015-01-01

Direct determination of total lysophosphatidic acid (LPA) was accomplished using newly developed spiroguanidines derived from rhodamine B as universal fluorogenic probes. Optimum conditions for the quantitative analysis of total LPA were investigated. The linear range for the determination of total LPA is up to 5 μM with a limit of detection of 0.512 μM. PMID:25516957

Sensitive detection of strong acidic condition by a novel rhodamine-based fluorescent pH chemosensor.

PubMed

Tan, Jia-Lian; Yang, Ting-Ting; Liu, Yu; Zhang, Xue; Cheng, Shu-Jin; Zuo, Hua; He, Huawei

2016-05-01

A novel rhodamine-based fluorescent pH probe responding to extremely low pH values has been synthesized and characterized. This probe showed an excellent photophysical response to pH on the basis that the colorless spirocyclic structure under basic conditions opened to a colored and highly fluorescent form under extreme acidity. The quantitative relationship between fluorescence intensity and pH value (1.75-2.62) was consistent with the equilibrium equation pH = pKa + log[(Imax - I)/(I - Imin)]. This sensitive pH probe was also characterized with good reversibility and no interaction with interfering metal ions, and was successfully applied to image Escherichia coli under strong acidity. Copyright © 2015 John Wiley & Sons, Ltd.

Estimation of the binding ability of main transport proteins of blood plasma with liver cirrhosis by the fluorescent probe method

NASA Astrophysics Data System (ADS)

Korolenko, E. A.; Korolik, E. V.; Korolik, A. K.; Kirkovskii, V. V.

2007-07-01

We present results from an investigation of the binding ability of the main transport proteins (albumin, lipoproteins, and α-1-acid glycoprotein) of blood plasma from patients at different stages of liver cirrhosis by the fluorescent probe method. We used the hydrophobic fluorescent probes anionic 8-anilinonaphthalene-1-sulfonate, which interacts in blood plasma mainly with albumin; cationic Quinaldine red, which interacts with α-1-acid glycoprotein; and neutral Nile red, which redistributes between lipoproteins and albumin in whole blood plasma. We show that the binding ability of albumin and α-1-acid glycoprotein to negatively charged and positively charged hydrophobic metabolites, respectively, increases in the compensation stage of liver cirrhosis. As the pathology process deepens and transitions into the decompensation stage, the transport abilities of albumin and α-1-acid glycoprotein decrease whereas the binding ability of lipoproteins remains high.

Fabrication of antibody microarrays by light-induced covalent and oriented immobilization.

PubMed

Adak, Avijit K; Li, Ben-Yuan; Huang, Li-De; Lin, Ting-Wei; Chang, Tsung-Che; Hwang, Kuo Chu; Lin, Chun-Cheng

2014-07-09

Antibody microarrays have important applications for the sensitive detection of biologically important target molecules and as biosensors for clinical applications. Microarrays produced by oriented immobilization of antibodies generally have higher antigen-binding capacities than those in which antibodies are immobilized with random orientations. Here, we present a UV photo-cross-linking approach that utilizes boronic acid to achieve oriented immobilization of an antibody on a surface while retaining the antigen-binding activity of the immobilized antibody. A photoactive boronic acid probe was designed and synthesized in which boronic acid provided good affinity and specificity for the recognition of glycan chains on the Fc region of the antibody, enabling covalent tethering to the antibody upon exposure to UV light. Once irradiated with optimal UV exposure (16 mW/cm(2)), significant antibody immobilization on a boronic acid-presenting surface with maximal antigen detection sensitivity in a single step was achieved, thus obviating the necessity of prior antibody modifications. The developed approach is highly modular, as demonstrated by its implementation in sensitive sandwich immunoassays for the protein analytes Ricinus communis agglutinin 120, human prostate-specific antigen, and interleukin-6 with limits of detection of 7.4, 29, and 16 pM, respectively. Furthermore, the present system enabled the detection of multiple analytes in samples without any noticeable cross-reactivities. Antibody coupling via the use of boronic acid and UV light represents a practical, oriented immobilization method with significant implications for the construction of a large array of immunosensors for diagnostic applications.

A dual-selective fluorescent probe for GSH and Cys detection: Emission and pH dependent selectivity.

PubMed

Tang, Yunqiang; Jin, Longyi; Yin, Bingzhu

2017-11-15

A novel fluorescent probe 1 based on acridine orange was developed for the selective detection and bioimaging of biothiols. The probe exhibits higher selectivity and turn-on fluorescence response to cysteine (Cys), homocysteine (Hcy), and glutathione (GSH) than to other amino acids. Importantly, the probe responds to GSH and Cys/Hcy with distinct fluorescence emissions in PBS buffer at pH of 7.4. The Cys/Hcy-triggered tandem S N Ar-rearrangement reaction and GSH-induced S N Ar reaction with the probe led to the corresponding amino-acridinium and thio-acridinium dyes, respectively, which can discriminate GSH from Cys/Hcy through different emission channels. Interestingly, Cys finishes the tandem reaction with the probe and subsequently forms amino-acridinium and Hcy/GSH induces S N Ar reaction with the probe to form thio-acridiniums at weakly acidic conditions (pH 6.0), enabling Cys to be discriminated from Hcy/GSH at different emissions. Finally, we demonstrated that probe 1 can selectively probe GSH over Cys and Hcy or Cys over GSH and Hcy in HeLa cells through multicolor imaging. Copyright © 2017 Elsevier B.V. All rights reserved.

Using tobacco mosaic virus to probe enhanced surface diffusion of molecular glasses.

PubMed

Zhang, Yue; Potter, Richard; Zhang, William; Fakhraai, Zahra

2016-11-09

Recent studies have shown that diffusion on the surface of organic glasses can be many orders of magnitude faster than bulk diffusion. Developing new probes that can readily measure surface diffusion can help study the effect of parameters such as chemical structure, intermolecular interaction, molecules' shape and size on the enhanced surface diffusion. In this study, we develop a novel probe that significantly simplifies these types of studies. Tobacco mosaic virus (TMV) is used as probe particle to measure surface diffusion coefficient of molecular glass N,N'-bis(3-methylphenyl)-N,N'-diphenylbenzidine (TPD). The evolution of the meniscus formed around TMV is probed as a function of time at various temperatures. TMV has a well-defined, mono-dispersed, cylindrical shape, with a large aspect-ratio (average diameter of 16.6 nm, length of 300 nm). As such, the shape of the meniscus around the center of TMV is semi-two dimensional, which compared to using a nanosphere as probe, increases the driving force for meniscus formation and simplifies the analysis of surface diffusion. We show that under these conditions, after a short transient time the shape of the meniscus is self-similar, allowing accurate determination of the surface diffusion coefficient. Measurements at various temperatures are then performed to investigate the temperature dependence of the surface diffusion coefficient. It is found that surface diffusion is greatly enhanced in TPD and has a lower activation barrier compared to the bulk counterpart. These observations are consistent with previous studies of surface diffusion on molecular glasses, demonstrating the accuracy of this method.

Pump-probe Kelvin-probe force microscopy: Principle of operation and resolution limits

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murawski, J.; Graupner, T.; Milde, P., E-mail: peter.milde@tu-dresden.de

Knowledge on surface potential dynamics is crucial for understanding the performance of modern-type nanoscale devices. We describe an electrical pump-probe approach in Kelvin-probe force microscopy that enables a quantitative measurement of dynamic surface potentials at nanosecond-time and nanometer-length scales. Also, we investigate the performance of pump-probe Kelvin-probe force microscopy with respect to the relevant experimental parameters. We exemplify a measurement on an organic field effect transistor that verifies the undisturbed functionality of our pump-probe approach in terms of simultaneous and quantitative mapping of topographic and electronic information at a high lateral and temporal resolution.

Advancements in non-contact metrology of asphere and diffractive optics

NASA Astrophysics Data System (ADS)

DeFisher, Scott

2017-11-01

Advancements in optical manufacturing technology allow optical designers to implement steep aspheric or high departure surfaces into their systems. Measuring these surfaces with profilometers or CMMs can be difficult due to large surface slopes or sharp steps in the surface. OptiPro has developed UltraSurf to qualify the form and figure of steep aspheric and diffractive optics. UltraSurf is a computer controlled, non-contact coordinate measuring machine. It incorporates five air-bearing axes, linear motors, high-resolution feedback, and a non-contact probe. The measuring probe is scanned over the optical surface while maintaining perpendicularity and a constant focal offset. Multiple probe technologies are available on UltraSurf. Each probe has strengths and weaknesses relative to the material properties, surface finish, and figure error of an optical component. The measuring probes utilize absolute distance to resolve step heights and diffractive surface patterns. The non-contact scanning method avoids common pitfalls with stylus contact instruments. Advancements in measuring speed and precision has enabled fast and accurate non-contact metrology of diffractive and steep aspheric surfaces. The benefits of data sampling with twodimensional profiles and three-dimensional topography maps will be presented. In addition, accuracy, repeatability, and machine qualification will be discussed with regards to aspheres and diffractive surfaces.

Luminescence Probe Studies of Ionomers. I. Steady-State Measurements from Nafion Membrane.

DTIC Science & Technology

1985-02-03

Bu4N+ was monitored by titrating the released protons with NaOH. Bu4N+ uptake by Na+ membranes was assumed to be the same as uptake by acidic form...spaced excited states (21). Because of their solvent sensitivity, 1,5-DNS derivatives may also be used as polarity probes (20). The acid -base... acid . The basic (unprotonated) form of the DNS derivative used here (DA+ ) shows *absorption maxima at ca. 325 and 245 nm (aqueous solution, pH 6.8

Eddy current probe with foil sensor mounted on flexible probe tip and method of use

DOEpatents

Viertl, John R. M.; Lee, Martin K.

2001-01-01

A pair of copper coils are embedded in the foil strip. A first coil of the pair generates an electromagnetic field that induces eddy currents on the surface, and the second coil carries a current influenced by the eddy currents on the surface. The currents in the second coil are analyzed to obtain information on the surface eddy currents. An eddy current probe has a metal housing having a tip that is covered by a flexible conductive foil strip. The foil strip is mounted on a deformable nose at the probe tip so that the strip and coils will conform to the surface to which they are applied.

Phosphorylation of hormone-sensitive lipase by protein kinase A in vitro promotes an increase in its hydrophobic surface area.

PubMed

Krintel, Christian; Mörgelin, Matthias; Logan, Derek T; Holm, Cecilia

2009-09-01

Hormone-sensitive lipase (EC 3.1.1.79; HSL) is a key enzyme in the mobilization of fatty acids from stored triacylglycerols. HSL activity is controlled by phosphorylation of at least four serines. In rat HSL, Ser563, Ser659 and Ser660 are phosphorylated by protein kinase A (PKA) in vitro as well as in vivo, and Ser660 and Ser659 have been shown to be the activity-controlling sites in vitro. The exact molecular events of PKA-mediated activation of HSL in vitro are yet to be determined, but increases in both Vmax and S0.5 seem to be involved, as recently shown for human HSL. In this study, the hydrophobic fluorescent probe 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) was found to inhibit the hydrolysis of triolein by purified recombinant rat adipocyte HSL, with a decrease in the effect of bis-ANS upon PKA phosphorylation of HSL. The interaction of HSL with bis-ANS was found to have a Kd of 1 microM in binding assays. Upon PKA phosphorylation, the interactions of HSL with both bis-ANS and the alternative probe SYPRO Orange were increased. By negative stain transmission electron microscopy, phosphorylated HSL was found to have a closer interaction with phospholipid vesicles than unphosphorylated HSL. Taken together, our results show that HSL increases its hydrophobic nature upon phosphorylation by PKA. This suggests that PKA phosphorylation induces a conformational change that increases the exposed hydrophobic surface and thereby facilitates binding of HSL to the lipid substrate.

A highly sensitive nanoscale pH-sensor using Au nanoparticles linked by a multifunctional Raman-active reporter molecule.

PubMed

Lawson, Latevi S; Chan, James W; Huser, Thomas

2014-07-21

Chemical sensing on the nanoscale has been breaking new ground since the discovery of surface enhanced Raman scattering (SERS). For nanoparticles, controlled particle aggregation is necessary to achieve the largest SERS enhancements. Therefore, aggregating agents such as salts or linker molecules are used in conjunction with chemically sensitive reporters in order to develop robust environmentally sensitive SERS probes. While salt-induced colloidal nanosphere aggregates have produced robust SERS signals, their variability in aggregate size contributes significantly to poor SERS signal reproducibility, which can complicate their use in in vitro cellular studies. Such systems often also lack reproducibility in spectral measurements between different nanoparticle clusters. Preaggregation of colloids via linkers followed by surface functionalization with reporter molecules results in the linker occupying valuable SERS hotspot volume which could otherwise be utilized by additional reporter molecules. Ideally, both functionalities should be obtained from a single molecule. Here, we report the use of 3,5-dimercaptobenzoic acid, a single multifunctional molecule that creates SERS hotspots via the controlled aggregation of nanoparticles, and also reports pH values. We show that 3,5-dimercaptobenzoic acid bound to Au nanospheres results in an excellent pH nanoprobe, producing very robust, and highly reproducible SERS signals that can report pH across the entire physiological range with excellent pH resolution. To demonstrate the efficacy of our novel pH reporters, these probes were also used to image both the particle and pH distribution in the cytoplasm of human induced pluripotent stem cells (hiPSCs).

Evaluation of folate conjugated superparamagnetic iron oxide nanoparticles for scintigraphic/magnetic resonance imaging.

PubMed

Chauhan, Ram Prakash; Mathur, Rashi; Singh, Gurjaspreet; Kaul, Ankur; Bag, Narmada; Singh, Sweta; Kumar, Hemanth; Patra, Manoj; Mishra, Anil K

2013-03-01

The physical and chemical properties of the nanoparticles influence their pharmacokinetics and ability to accumulate in tumors. In this paper we report a facile method to conjugate folic acid molecule to iron oxide nanoparticles to increase the specific uptake of these nanoparticles by the tumor, which will be useful in targeted imaging of the tumor. The iron oxide nanoparticles were synthesized by alkaline co precipitation method and were surface modified with dextranto make them stable. The folic acid is conjugated to the dextran modified iron oxide nanoparticles by reductive amination process after the oxidation of the dextran with periodate. The synthesized folic acid conjugated nanoparticles were characterized for size, phase, morphology and magnetization by using various physicochemical characterization techniques such as transmission electron microscopy, X-ray diffraction, fourier transform infrared spectroscopy, vibrating sample magnetometry, dynamic light scattering and zetasizer etc. The quantification of the generated carbonyl groups and folic acid conjugated to the surface of the magnetic nanoparticles was done by colorimetric estimations using UV-Visible spectroscopy. The in vitro MR studies were carried out over a range of concentrations and showed significant shortening of the transverse relaxation rate, showing the ability of the nanoconjugate to act as an efficient probe for MR imaging. The biodistribution studies and the scintigraphy done by radiolabeling the nanoconjugate with 99mTc show the enhanced uptake at the tumor site showing its enhanced specificity.

Laminar Boundary Layer Stability Measurements at Mach 7 Including Wall Temperature Effects

DTIC Science & Technology

1977-11-01

Diagnostics were done by a four-probe rake bearing a pitot tube, a To probe and two hot films - a boundary layer hot film probe (BLHF) and a freestream hot...tunnel. Inset shows hot film probe close to the surface with second probe positioned higher to sample simultaneously the frcestream turbulence ( pitot ... rake away from the surface by small increments and taking readings at each stop. The readings were simultaneously recorded and reduced by the Tunnel B

Test probe for surface mounted leadless chip carrier

DOEpatents

Meyer, Kerry L.; Topolewski, John

1989-05-23

A test probe for a surface mounted leadless chip carrier is disclosed. The probed includes specially designed connector pins which allow size reductions in the probe. A thermoplastic housing provides spring action to ensure good mechanical and electrical contact between the pins and the contact strips of a leadless chip carrier. Other features include flexible wires molded into the housing and two different types of pins alternately placed in the housing. These features allow fabrication of a smaller and simpler test probe.

Test probe for surface mounted leadless chip carrier

DOEpatents

Meyer, K.L.; Topolewski, J.

1987-10-02

A test probe for a surface mounted leadless chip carrier is disclosed. The probe includes specially designed connector pins which allow size reductions in the probe. A thermoplastic housing provides spring action to ensure good mechanical and electrical contact between the pins and the contact strips of a leadless chip carrier. Other features include flexible wires molded into the housing and two different types of pins alternately placed in the housing. These features allow fabrication of a smaller and simpler test probe. 1 fig.

Isotopic tracing for calculating the surface density of arginine-glycine-aspartic acid-containing peptide on allogeneic bone.

PubMed

Hou, Xiao-bin; Hu, Yong-cheng; He, Jin-quan

2013-02-01

To investigate the feasibility of determining the surface density of arginine-glycine-aspartic acid (RGD) peptides grafted onto allogeneic bone by an isotopic tracing method involving labeling these peptides with (125) I, evaluating the impact of the input concentration of RGD peptides on surface density and establishing the correlation between surface density and their input concentration. A synthetic RGD-containing polypeptide (EPRGDNYR) was labeled with (125) I and its specific radioactivity calculated. Reactive solutions of RGD peptide with radioactive (125) I-RGD as probe with input concentrations of 0.01 mg/mL, 0.10 mg/mL, 0.50 mg/mL, 1.00 mg/mL, 2.00 mg/mL and 4.00 mg/mL were prepared. Using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide as a cross-linking agent, reactions were induced by placing allogeneic bone fragments into reactive solutions of RGD peptide of different input concentrations. On completion of the reactions, the surface densities of RGD peptides grafted onto the allogeneic bone fragments were calculated by evaluating the radioactivity and surface areas of the bone fragments. The impact of input concentration of RGD peptides on surface density was measured and a curve constructed. Measurements by a radiodensity γ-counter showed that the RGD peptides had been labeled successfully with (125) I. The allogeneic bone fragments were radioactive after the reaction, demonstrating that the RGD peptides had been successfully grafted onto their surfaces. It was also found that with increasing input concentration, the surface density increased. It was concluded that the surface density of RGD peptides is quantitatively related to their input concentration. With increasing input concentration, the surface density gradually increases to saturation value. © 2013 Chinese Orthopaedic Association and Wiley Publishing Asia Pty Ltd.

Melting probes revisited - Ice penetration experiments under Mars surface pressure conditions

NASA Astrophysics Data System (ADS)

Kömle, Norbert I.; Tiefenbacher, Patrick; Weiss, Peter; Bendiukova, Anastasiia

2018-07-01

Melting probes as vehicles to explore terrestrial ice sheets have been designed and applied successfully since the early 1960's. Later on, in the 1990's, various proposals were made to apply such probes also as a means to explore ice sheets on other bodies of the solar system, e.g. Jupiter's icy satellite Europa or the ice caps of Mars. For this type of subsurface probes the name cryobot has become common. We review both early developments and more recent efforts to develop probes for application in planetary environments, i.e. under low pressures and low temperatures. The current state of art as well as the pros and cons of the different concepts hitherto considered are described. While many tests with various probes have been done in terrestrial environments, experiments under low surface pressure conditions are rare. Therefore, we report here on lab tests with a simple melting probe under the range of pressure and temperature conditions that would be encountered on the surface of Mars and compare them with corresponding tests under a much lower gas pressure, possibly representative for icy satellites. The contribution of evaporation during the melting and its variation with surface pressure is also considered. All surface pressure measurements that have been performed on Mars up to now indicate a surface pressure above the water triple point pressure (612 Pa). This means that water ice always transforms into the liquid phase when warmed up to 0°C, before it evaporates into the ambient atmosphere. The temporary existence of the liquid phase around the heated tip of the cryobot allows good thermal conductance between probe and surrounding ice, which is an important pre-requisite for efficient melt penetration. Our experiments indicate that under all possible Mars surface pressures the liquid phase is present when the probe is heated up. This finding confirms experimentally that a probe as it was proposed by Paige (1992) for in situ exploration of the Mars north polar layers would work in the expected way, although the penetration velocity must be expected be lower than under Earth pressure conditions. A test with the same probe, but under an almost two orders of magnitude lower gas pressure than on Mars, still indicates the temporary existence of the liquid phase in the contact region between the probe and the surrounding ice.

Rapid Screening of Carboxylic Acids from Waste and Surface Waters by ESI-MS/MS Using Barium Ion Chemistry and On-Line Membrane Sampling.

PubMed

Duncan, Kyle D; Volmer, Dietrich A; Gill, Chris G; Krogh, Erik T

2016-03-01

Negative ion tandem mass spectrometric analysis of aliphatic carboxylic acids often yields only non-diagnostic ([M - H](-)) ions with limited selective fragmentation. However, carboxylates cationized with Ba(2+) have demonstrated efficient dissociation in positive ion mode, providing structurally diagnostic product ions. We report the application of barium adducts followed by collision induced dissociation (CID), to improve selectivity for rapid screening of carboxylic acids in complex aqueous samples. The quantitative MS/MS method presented utilizes common product ions of [M - H + Ba](+) precursor ions. The mechanism of product ion formation is investigated using isotopically labeled standards and a series of structurally related carboxylic acids. The results suggest that hydrogen atoms in the β and γ positions yield common product ions ([BaH](+) and [BaOH](+)). Furthermore, the diagnostic product ion at m/z 196 serves as a qualifying ion for carboxylate species. This methodology has been successfully used in conjunction with condensed phase membrane introduction mass spectrometry (CP-MIMS), with barium acetate added directly to the methanol acceptor phase. The combination enables rapid screening of carboxylic acids directly from acidified water samples (wastewater effluent, spiked natural waters) using a capillary hollow fiber PDMS membrane immersion probe. We have applied this technique for the direct analysis of complex naphthenic acid mixtures spiked into natural surface waters using CP-MIMS. Selectivity at the ionization and tandem mass spectrometry level eliminate isobaric interferences from hydroxylated species present within the samples, which have been observed in negative electrospray ionization.

Conjugation of arginine-glycine-aspartic acid peptides to poly(ethylene oxide)-b-poly(epsilon-caprolactone) micelles for enhanced intracellular drug delivery to metastatic tumor cells.

PubMed

Xiong, Xiao-Bing; Mahmud, Abdullah; Uludağ, Hasan; Lavasanifar, Afsaneh

2007-03-01

An arginine-glycine-aspartic acid (RGD) containing model peptide was conjugated to the surface of poly(ethylene oxide)-block-poly(epsilon-caprolactone) (PEO-b-PCL) micelles as a ligand that can recognize adhesion molecules overexpressed on the surface of metastatic cancer cells, that is, integrins, and that can enhance the micellar delivery of encapsulated hydrophobic drug into a tumor cell. Toward this goal, PEO-b-PCL copolymers bearing acetal groups on the PEO end were synthesized, characterized, and assembled to polymeric micelles. The acetal group on the surface of the PEO-b-PCL micelles was converted to reactive aldehyde under acidic condition at room temperature. An RGD-containing linear peptide, GRGDS, was conjugated on the surface of the aldehyde-decorated PEO-b-PCL micelles by incubation at room temperature. A hydrophobic fluorescent probe, that is, DiI, was physically loaded in prepared polymeric micelles to imitate hydrophobic drugs loaded in micellar carrier. The cellular uptake of DiI loaded GRGDS-modified micelles by melanoma B16-F10 cells was investigated at 4 and 37 degrees C by fluorescent spectroscopy and confocal microscopy techniques and was compared to the uptake of DiI loaded valine-PEO-b-PCL micelles (as the irrelevant ligand decorated micelles) and free DiI. GRGDS conjugation to polymeric micelles significantly facilitated the cellular uptake of encapsulated hydrophobic DiI most probably by intergrin-mediated cell attachment and endocytosis. The results indicate that acetal-terminated PEO-b-PCL micelles are amenable for introducing targeting moieties on the surface of polymeric micelles and that RGD-peptide conjugated PEO-b-PCL micelles are promising ligand-targeted carriers for enhanced drug delivery to metastatic tumor cells.

Tribological behavior of micro/nano-patterned surfaces in contact with AFM colloidal probe

NASA Astrophysics Data System (ADS)

Zhang, Xiaoliang; Wang, Xiu; Kong, Wen; Yi, Gewen; Jia, Junhong

2011-10-01

In effort to investigate the influence of the micro/nano-patterning or surface texturing on the nanotribological properties of patterned surfaces, the patterned polydimethylsiloxane (PDMS) surfaces with pillars were fabricated by replica molding technique. The surface morphologies of patterned PDMS surfaces with varying pillar sizes and spacing between pillars were characterized by atomic force microscope (AFM) and scanning electron microscope (SEM). The AFM/FFM was used to acquire the friction force images of micro/nano-patterned surfaces using a colloidal probe. A difference in friction force produced a contrast on the friction force images when the colloidal probe slid over different regions of the patterned polymer surfaces. The average friction force of patterned surface was related to the spacing between the pillars and their size. It decreased with the decreasing of spacing between the pillars and the increasing of pillar size. A reduction in friction force was attributed to the reduced area of contact between patterned surface and colloidal probe. Additionally, the average friction force increased with increasing applied load and sliding velocity.

DNA biosensors implemented on PNA-functionalized microstructured optical fibers Bragg gratings

NASA Astrophysics Data System (ADS)

Candiani, A.; Giannetti, S.; Cucinotta, A.; Bertucci, A.; Manicardi, A.; Konstantaki, M.; Margulis, W.; Pissadakis, S.; Corradini, R.; Selleri, S.

2013-05-01

A novel DNA sensing platform based on a Peptide Nucleic Acid - functionalized Microstructured Optical Fibers gratings has been demonstrated. The inner surface of different MOFs has been functionalized using PNA probes, OligoNucleotides mimic that are well suited for specific DNA target sequences detection. The hybrid sensing systems were tested for optical DNA detection of targets of relevance in biomedical application, using the cystic fibrosis gene mutation, and food-analysis, using the genomic DNA from genetic modified organism soy flour. After the solutions of DNA molecules has been infiltrated inside the fibers capillaries and hybridization has occurred, oligonucleotidefunctionalized gold nanoparticles were infiltrated and used to form a sandwich-like system to achieve signal amplification. Spectral measurements of the reflected signal reveal a clear wavelength shift of the reflected modes when the infiltrated complementary DNA matches with the PNA probes placed on the inner fiber surface. Measurements have also been made using the mismatched DNA solution for the c, containing a single nucleotide polymorphism, showing no significant changes in the reflected spectrum. Several experiments have been carried out demonstrating the reproducibility of the results and the high selectivity of the sensors, showing the simplicity and the potential of this approach.

Excitation and emission wavelength ratiometric cyanide-sensitive probes for physiological sensing.

PubMed

Badugu, Ramachandram; Lakowicz, Joseph R; Geddes, Chris D

2004-04-01

We characterize three new fluorescent probes that show both spectral shifts and intensity changes in the presence of aqueous cyanide, allowing for both excitation and fluorescence emission wavelength ratiometric and colorimetric sensing. The relatively high binding constants of the probes for cyanide enables a distinct colorimetric change to be visually observed with as little as 10 microM cyanide. The response of the new probes is based on the ability of the boronic acid group to interact with the CN(-) anion, changing from the neutral form of the boronic acid group R-B(OH)(2) to the anionic R-B(-)(OH)3 form, which is an electron-donating group. The presence of an electron-deficient quaternary heterocyclic nitrogen center and a strong electron-donating amino group in the 6 position on the quinolinium backbone provides for the spectral changes observed upon CN(-) complexation. We have determined the binding constants for the ortho-, meta-, and para-boronic acid probes to be 0.12, 0.17, and 0.14 microM(-3). In addition we have synthesized a control compound that does not contain the boronic acid moiety, allowing for structural comparisons and a rationale for the sensing mechanism to be made. Finally we show that the affinity for monosaccharides, such as glucose or fructose, is relatively low as compared to that for cyanide, enabling the potential detection of cyanide in physiologies up to lethal levels.

Hybrid catadioptric system for advanced optical cavity velocimetry

DOEpatents

Frayer, Daniel K.

2018-02-06

A probe including reflector is disclosed to measure the velocity distribution of a moving surface along many lines of sight. Laser light, directed to the surface by the probe and then reflected back from the surface, is Doppler shifted by the moving surface, collected into probe, and then directed to detection equipment through optic fibers. The received light is mixed with reference laser light and using photonic Doppler velocimetry, a continuous time record of the surface movement is obtained. An array of single-mode optical fibers provides an optic signal to one or more lens groups and a reflector, such as a parabolic reflector having a mirrored interior surface.

Design of ultrasensitive bisphenol A-aptamer based on platinum nanoparticles loading to polyethyleneimine-functionalized carbon nanotubes.

PubMed

Derikvandi, Zeinab; Abbasi, Amir Reza; Roushani, Mahmoud; Derikvand, Zohreh; Azadbakht, Azadeh

2016-11-01

Here, a highly sensitive electrochemical aptasensor based on a novel signal amplification strategy for the determination of bisphenol A (BPA) was developed. Construction of the aptasensor began with the deposition of highly dispersed platinum nanoparticles (PtNPs)/acid-oxidized carbon nanotubes (CNTs-COOH) functionalized with polyethyleneimine (PEI) at the surface of glassy carbon (PtNPs/PEI/CNTs-COOH/GC) electrode. After immobilizing the amine-capped capture probe (ssDNA1) through the covalent amide bonds formed by the carboxyl groups on the nanotubes and the amino groups on the oligonucleotides, we employed a designed complementary BPA-aptamer (ssDNA2) as a detection probe to hybridize with the ssDNA1. By adding BPA as a target, the aptamer specifically bound to BPA and its end folded into a BPA-binding junction. Because of steric/conformational restrictions caused by aptamer-BPA complex formation at the surface of modified electrode, the interfacial electron transfer of [Fe(CN)6](3-/4-) as a probe was blocked. Sensitive quantitative detection of BPA was carried out by monitoring the decrease of differential pulse voltammetric responses of [Fe(CN)6](3-/4-) peak current with increasing BPA concentrations. The newly developed aptasensor embraced a number of attractive features such as ease of fabrication, low detection limit, excellent selectivity, good stability and a wide linear range with respect to BPA. Copyright © 2016 Elsevier Inc. All rights reserved.

An Electrochemical Genosensing Assay Based on Magnetic Beads and Gold Nanoparticle-Loaded Latex Microspheres for Vibrio cholerae Detection.

PubMed

Low, Kim-Fatt; Rijiravanich, Patsamon; Singh, Kirnpal Kaur Banga; Surareungchai, Werasak; Yean, Chan Yean

2015-04-01

An ultrasensitive electrochemical genosensing assay was developed for the sequence-specific detection of Vibrio cholerae DNA using magnetic beads as the biorecognition surface and gold nanoparticle-loaded latex microspheres (latex-AuNPs) as a signal-amplified hybridization tag. This biorecognition surface was prepared by immobilizing specific biotinylated capturing probes onto the streptavidin-coupled magnetic beads. Fabricating a hybridization tag capable of amplifying the electrochemical signal involved loading multiple AuNPs onto polyelectrolyte multilayer film-coated poly(styrene-co-acrylic acid) latex microspheres as carrier particles. The detection targets, single-stranded 224-bp asymmetric PCR amplicons of the V. cholerae lolB gene, were sandwich-hybridized to magnetic bead-functionalized capturing probes and fluorescein-labeled detection probes and tagged with latex-AuNPs. The subsequent electrochemical stripping analysis of chemically dissolved AuNPs loaded onto the latex microspheres allowed for the quantification of the target amplicons. The high-loading capacity of the AuNPs on the latex microspheres for sandwich-type dual-hybridization genosensing provided eminent signal amplification. The genosensing variables were optimized, and the assay specificity was demonstrated. The clinical applicability of the assay was evaluated using spiked stool specimens. The current signal responded linearly to the different V. cholerae concentrations spiked into stool specimens with a detection limit of 2 colony-forming units (CFU)/ml. The proposed latex-AuNP-based magnetogenosensing platform is promising, exhibits an effective amplification performance, and offers new opportunities for the ultrasensitive detection of other microbial pathogens.

Reversible electrochemical modification of the surface of a semiconductor by an atomic-force microscope probe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kozhukhov, A. S., E-mail: antonkozhukhov@yandex.ru; Sheglov, D. V.; Latyshev, A. V.

A technique for reversible surface modification with an atomic-force-microscope (AFM) probe is suggested. In this method, no significant mechanical or topographic changes occur upon a local variation in the surface potential of a sample under the AFM probe. The method allows a controlled relative change in the ohmic resistance of a channel in a Hall bridge within the range 20–25%.

Eliminating Size-Associated Diffusion Constraints for Rapid On-Surface Bioassays with Nanoparticle Probes.

PubMed

Li, Junwei; Zrazhevskiy, Pavel; Gao, Xiaohu

2016-02-24

Nanoparticle probes enable implementation of advanced on-surface assay formats, but impose often underappreciated size-associated constraints, in particular on assay kinetics and sensitivity. The present study highlights substantially slower diffusion-limited assay kinetics due to the rapid development of a nanoprobe depletion layer next to the surface, which static incubation and mixing of bulk solution employed in conventional assay setups often fail to disrupt. In contrast, cyclic solution draining and replenishing yields reaction-limited assay kinetics irrespective of the probe size. Using common surface bioassays, enzyme-linked immunosorbent assays and immunofluorescence, this study shows that this conceptually distinct approach effectively "erases" size-dependent diffusion constraints, providing a straightforward route to rapid on-surface bioassays employing bulky probes and procedures involving multiple labeling cycles, such as multicycle single-cell molecular profiling. For proof-of-concept, the study demonstrates that the assay time can be shortened from hours to minutes with the same probe concentration and, at a typical incubation time, comparable target labeling can be achieved with up to eight times lower nanoprobe concentration. The findings are expected to enable realization of novel assay formats and stimulate development of rapid on-surface bioassays with nanoparticle probes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification

PubMed Central

Schouten, Jan P.; McElgunn, Cathal J.; Waaijer, Raymond; Zwijnenburg, Danny; Diepvens, Filip; Pals, Gerard

2002-01-01

We describe a new method for relative quantification of 40 different DNA sequences in an easy to perform reaction requiring only 20 ng of human DNA. Applications shown of this multiplex ligation-dependent probe amplification (MLPA) technique include the detection of exon deletions and duplications in the human BRCA1, MSH2 and MLH1 genes, detection of trisomies such as Down’s syndrome, characterisation of chromosomal aberrations in cell lines and tumour samples and SNP/mutation detection. Relative quantification of mRNAs by MLPA will be described elsewhere. In MLPA, not sample nucleic acids but probes added to the samples are amplified and quantified. Amplification of probes by PCR depends on the presence of probe target sequences in the sample. Each probe consists of two oligonucleotides, one synthetic and one M13 derived, that hybridise to adjacent sites of the target sequence. Such hybridised probe oligonucleotides are ligated, permitting subsequent amplification. All ligated probes have identical end sequences, permitting simultaneous PCR amplification using only one primer pair. Each probe gives rise to an amplification product of unique size between 130 and 480 bp. Probe target sequences are small (50–70 nt). The prerequisite of a ligation reaction provides the opportunity to discriminate single nucleotide differences. PMID:12060695

Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification.

PubMed

Schouten, Jan P; McElgunn, Cathal J; Waaijer, Raymond; Zwijnenburg, Danny; Diepvens, Filip; Pals, Gerard

2002-06-15

We describe a new method for relative quantification of 40 different DNA sequences in an easy to perform reaction requiring only 20 ng of human DNA. Applications shown of this multiplex ligation-dependent probe amplification (MLPA) technique include the detection of exon deletions and duplications in the human BRCA1, MSH2 and MLH1 genes, detection of trisomies such as Down's syndrome, characterisation of chromosomal aberrations in cell lines and tumour samples and SNP/mutation detection. Relative quantification of mRNAs by MLPA will be described elsewhere. In MLPA, not sample nucleic acids but probes added to the samples are amplified and quantified. Amplification of probes by PCR depends on the presence of probe target sequences in the sample. Each probe consists of two oligonucleotides, one synthetic and one M13 derived, that hybridise to adjacent sites of the target sequence. Such hybridised probe oligonucleotides are ligated, permitting subsequent amplification. All ligated probes have identical end sequences, permitting simultaneous PCR amplification using only one primer pair. Each probe gives rise to an amplification product of unique size between 130 and 480 bp. Probe target sequences are small (50-70 nt). The prerequisite of a ligation reaction provides the opportunity to discriminate single nucleotide differences.

A Single Molecular Beacon Probe Is Sufficient for the Analysis of Multiple Nucleic Acid Sequences

PubMed Central

Gerasimova, Yulia V.; Hayson, Aaron; Ballantyne, Jack; Kolpashchikov, Dmitry M.

2010-01-01

Molecular beacon (MB) probes are dual-labeled hairpin-shaped oligodeoxyribonucleotides that are extensively used for real-time detection of specific RNA/DNA analytes. In the MB probe, the loop fragment is complementary to the analyte: therefore, a unique probe is required for the analysis of each new analyte sequence. The conjugation of an oligonucleotide with two dyes and subsequent purification procedures add to the cost of MB probes, thus reducing their application in multiplex formats. Here we demonstrate how one MB probe can be used for the analysis of an arbitrary nucleic acid. The approach takes advantage of two oligonucleotide adaptor strands, each of which contains a fragment complementary to the analyte and a fragment complementary to an MB probe. The presence of the analyte leads to association of MB probe and the two DNA strands in quadripartite complex. The MB probe fluorescently reports the formation of this complex. In this design, the MB does not bind the analyte directly; therefore, the MB sequence is independent of the analyte. In this study one universal MB probe was used to genotype three human polymorphic sites. This approach promises to reduce the cost of multiplex real-time assays and improve the accuracy of single-nucleotide polymorphism genotyping. PMID:20665615

Surface enhanced Raman gene probe and methods thereof

DOEpatents

Vo-Dinh, T.

1998-09-29

The subject invention disclosed herein is a new gene probe biosensor and methods based on surface enhanced Raman scattering (SERS) label detection. The SER gene probe biosensor comprises a support means, a SER gene probe having at least one oligonucleotide strand labeled with at least one SERS label, and a SERS active substrate disposed on the support means and having at least one of the SER gene probes adsorbed thereon. Biotargets such as bacterial and viral DNA, RNA and PNA are detected using a SER gene probe via hybridization to oligonucleotide strands complementary to the SER gene probe. The support means supporting the SERS active substrate includes a fiberoptic probe, an array of fiberoptic probes for performance of multiple assays and a waveguide microsensor array with charge-coupled devices or photodiode arrays. 18 figs.

Surface enhanced Raman gene probe and methods thereof

DOEpatents

Vo-Dinh, Tuan

1998-01-01

The subject invention disclosed herein is a new gene probe biosensor and methods thereof based on surface enhanced Raman scattering (SERS) label detection. The SER gene probe biosensor comprises a support means, a SER gene probe having at least one oligonucleotide strand labeled with at least one SERS label, and a SERS active substrate disposed on the support means and having at least one of the SER gene probes adsorbed thereon. Biotargets such as bacterial and viral DNA, RNA and PNA are detected using a SER gene probe via hybridization to oligonucleotide strands complementary to the SER gene probe. The support means supporting the SERS active substrate includes a fiberoptic probe, an array of fiberoptic probes for performance of multiple assays and a waveguide microsensor array with charge-coupled devices or photodiode arrays.

Surface enhanced Raman gene probe and methods thereof

DOEpatents

Vo-Dinh, T.

1998-02-24

The subject invention disclosed is a new gene probe biosensor and methods based on surface enhanced Raman scattering (SERS) label detection. The SER gene probe biosensor comprises a support means, a SER gene probe having at least one oligonucleotide strand labeled with at least one SERS label, and a SERS active substrate disposed on the support means and having at least one of the SER gene probes adsorbed thereon. Biotargets such as bacterial and viral DNA, RNA and PNA are detected using a SER gene probe via hybridization to oligonucleotide strands complementary to the SER gene probe. The support means includes a fiberoptic probe, an array of fiberoptic probes for performance of multiple assays and a waveguide microsensor array with charge-coupled devices or photodiode arrays. 18 figs.

Surface enhanced Raman gene probe and methods thereof

DOEpatents

Vo-Dinh, T.

1998-07-21

The subject invention disclosed is a new gene probe biosensor and methods based on surface enhanced Raman scattering (SERS) label detection. The SER gene probe biosensor comprises a support means, a SER gene probe having at least one oligonucleotide strand labeled with at least one SERS label, and a SERS active substrate disposed on the support means and having at least one of the SER gene probes adsorbed. Biotargets such as bacterial and viral DNA, RNA and PNA are detected using a SER gene probe via hybridization to oligonucleotide strands complementary to the SER gene probe. The support means supporting the SERS active substrate includes a fiberoptic probe, an array of fiberoptic probes for performance of multiple assays and a waveguide microsensor array with charge-coupled devices or photodiode arrays. 18 figs.

Definition of the specific roles of lysolecithin and palmitic acid in altering the susceptibility of dipalmitoylphosphatidylcholine bilayers to phospholipase A2.

PubMed

Henshaw, J B; Olsen, C A; Farnbach, A R; Nielson, K H; Bell, J D

1998-07-28

Bilayers composed of phosphatidylcholine initially resist catalysis by phospholipase A2. However, after a latency period, they become susceptible when sufficient reaction products (lysolecithin and fatty acid) accumulate in the membrane. Temperature near the main bilayer phase transition and calcium concentration modulate the effectiveness of the reaction products. The purpose of this study was to examine the individual contributions of lysolecithin and palmitic acid to the susceptibility of dipalmitoylphosphatidylcholine vesicles and to rationalize the effects of temperature and calcium. Various fluorescent probes (Prodan, Laurdan, pyrene-labeled fatty acid, and dansyl-labeled phospholipid) were used to assess changes in the ability of the reaction products to perturb the bilayer and to affect the interactions with the enzyme. Un-ionized palmitic acid decreased bilayer polarity and perturbed the membrane surface exposing some of the Prodan to bulk water. Lysolecithin increased bilayer polarity and the rate of dipolar relaxation in response to the excited states of Laurdan and Prodan. A combination of the individual contributions of each product was observed when palmitic acid and lysolecithin were present together at low calcium, and the effects of lysolecithin dominated at high calcium. Palmitic acid, but not lysolecithin, promoted the binding of phospholipase A2 to the bilayer surface in the absence of calcium. Lysolecithin reduced the ability of fatty acid to enhance binding apparently by altering the structure of fatty acid domains in the membrane. Furthermore, increased temperature and ionization of the fatty acid tended to cause segregation of bound phospholipase A2 into domains poor in phospholipid content which presumably impeded bilayer hydrolysis. In contrast, un-ionized palmitic acid and lysolecithin promoted hydrolysis by augmenting a step distal to the adsorption of enzyme to the bilayer. This kinetic response to lysolecithin was calcium-dependent. A model accounting for these varied influences of the reaction products is presented.

A Novel Method for Rapid Hybridization of DNA to a Solid Support

PubMed Central

Pettersson, Erik; Ahmadian, Afshin; Ståhl, Patrik L.

2013-01-01

Here we present a novel approach entitled Magnetic Forced Hybridization (MFH) that provides the means for efficient and direct hybridization of target nucleic acids to complementary probes immobilized on a glass surface in less than 15 seconds at ambient temperature. In addition, detection is carried out instantly since the beads become visible on the surface. The concept of MFH was tested for quality control of array manufacturing, and was combined with a multiplex competitive hybridization (MUCH) approach for typing of Human Papilloma Virus (HPV). Magnetic Forced Hybridization of bead-DNA constructs to a surface achieves a significant reduction in diagnostic testing time. In addition, readout of results by visual inspection of the unassisted eye eliminates the need for additional expensive instrumentation. The method uses the same set of beads throughout the whole process of manipulating and washing DNA constructs prior to detection, as in the actual detection step itself. PMID:23950946

Shallow Heavily Doped n++ Germanium by Organo-Antimony Monolayer Doping.

PubMed

Alphazan, Thibault; Díaz Álvarez, Adrian; Martin, François; Grampeix, Helen; Enyedi, Virginie; Martinez, Eugénie; Rochat, Névine; Veillerot, Marc; Dewitte, Marc; Nys, Jean-Philippe; Berthe, Maxime; Stiévenard, Didier; Thieuleux, Chloé; Grandidier, Bruno

2017-06-14

Functionalization of Ge surfaces with the aim of incorporating specific dopant atoms to form high-quality junctions is of particular importance for the development of solid-state devices. In this study, we report the shallow doping of Ge wafers with a monolayer doping strategy that is based on the controlled grafting of Sb precursors and the subsequent diffusion of Sb into the wafer upon annealing. We also highlight the key role of citric acid in passivating the surface before its reaction with the Sb precursors and the benefit of a protective SiO 2 overlayer that enables an efficient incorporation of Sb dopants with a concentration higher than 10 20 cm -3 . Microscopic four-point probe measurements and photoconductivity experiments show the full electrical activation of the Sb dopants, giving rise to the formation of an n++ Sb-doped layer and an enhanced local field-effect passivation at the surface of the Ge wafer.

Locked Nucleic Acid Probe-Based Real-Time PCR Assay for the Rapid Detection of Rifampin-Resistant Mycobacterium tuberculosis

PubMed Central

Sun, Chongyun; Li, Chao; Wang, Xiaochen; Liu, Haican; Zhang, Pingping; Zhao, Xiuqin; Wang, Xinrui; Jiang, Yi; Yang, Ruifu; Wan, Kanglin; Zhou, Lei

2015-01-01

Drug-resistant Mycobacterium tuberculosis can be rapidly diagnosed through nucleic acid amplification techniques by analyzing the variations in the associated gene sequences. In the present study, a locked nucleic acid (LNA) probe-based real-time PCR assay was developed to identify the mutations in the rpoB gene associated with rifampin (RFP) resistance in M. tuberculosis. Six LNA probes with the discrimination capability of one-base mismatch were designed to monitor the 23 most frequent rpoB mutations. The target mutations were identified using the probes in a “probe dropout” manner (quantification cycle = 0); thus, the proposed technique exhibited superiority in mutation detection. The LNA probe-based real-time PCR assay was developed in a two-tube format with three LNA probes and one internal amplification control probe in each tube. The assay showed excellent specificity to M. tuberculosis with or without RFP resistance by evaluating 12 strains of common non-tuberculosis mycobacteria. The limit of detection of M. tuberculosis was 10 genomic equivalents (GE)/reaction by further introducing a nested PCR method. In a blind validation of 154 clinical mycobacterium isolates, 142/142 (100%) were correctly detected through the assay. Of these isolates, 88/88 (100%) were determined as RFP susceptible and 52/54 (96.3%) were characterized as RFP resistant. Two unrecognized RFP-resistant strains were sequenced and were found to contain mutations outside the range of the 23 mutation targets. In conclusion, this study established a sensitive, accurate, and low-cost LNA probe-based assay suitable for a four-multiplexing real-time PCR instrument. The proposed method can be used to diagnose RFP-resistant tuberculosis in clinical laboratories. PMID:26599667

Methods of and apparatus for levitating an eddy current probe

DOEpatents

Stone, William J.

1988-05-03

An eddy current probe is supported against the force of gravity with an air earing while being urged horizontally toward the specimen being examined by a spring and displaced horizontally against the force of the spring pneumatically. The pneumatic displacement is accomplished by flowing air between a plenum chamber fixed with respect to the probe and the surface of the specimen. In this way, the surface of the specimen can be examined without making mechanical contact therewith while precisely controlling the distance at which the probe stands-off from the surface of the specimen.

Association of a cucumber mosaic virus strain with mosaic disease of banana, Musa paradisiaca--an evidence using immuno/nucleic acid probe.

PubMed

Srivastava, A; Raj, S K; Haq, Q M; Srivastava, K M; Singh, B P; Sane, P V

1995-12-01

Virus causing severe chlorosis/mosaic disease of banana was identified as a strain of cucumber mosaic virus (CMV). Association of CMV with the disease was established by Western immunoblot using polyclonal antibodies to CMV-T and slot blot hybridization with nucleic acid probe of CMV-P genome.

Surface topography acquisition method for double-sided near-right-angle structured surfaces based on dual-probe wavelength scanning interferometry.

PubMed

Zhang, Tao; Gao, Feng; Jiang, Xiangqian

2017-10-02

This paper proposes an approach to measure double-sided near-right-angle structured surfaces based on dual-probe wavelength scanning interferometry (DPWSI). The principle and mathematical model is discussed and the measurement system is calibrated with a combination of standard step-height samples for both probes vertical calibrations and a specially designed calibration artefact for building up the space coordinate relationship of the dual-probe measurement system. The topography of the specially designed artefact is acquired by combining the measurement results with white light scanning interferometer (WLSI) and scanning electron microscope (SEM) for reference. The relative location of the two probes is then determined with 3D registration algorithm. Experimental validation of the approach is provided and the results show that the method is able to measure double-sided near-right-angle structured surfaces with nanometer vertical resolution and micrometer lateral resolution.

Probing phospholipase a(2) with fluorescent phospholipid substrates.

PubMed

Wichmann, Oliver; Gelb, Michael H; Schultz, Carsten

2007-09-03

The Foerster resonance energy transfer-based sensor, PENN, measures intracellular phospholipase A(2) (PLA(2)) activity in living cells and small organisms. In an attempt to modify the probe for the detection of particular isoforms, we altered the sn-2 fatty acid in such a way that either one or three of the Z double bonds in arachidonic acid were present in the sensor molecule. Arachidonic-acid-mimicking fatty acids were prepared by copper-mediated coupling reactions. Probes with a single double bond in the 5-position exhibited favorable substrate properties for secretory PLA(2)s. In vitro experiments with the novel unsaturated doubly labeled phosphatidylethanolamine derivatives showed preferred cleavage of the sensor PENN2 (one double bond) by the physiologically important group V sPLA(2), while the O-methyl-derivative PMNN2 was accepted best by the isoform from hog pancreas. For experiments in living cells, we demonstrated that bioactivation via S-acetylthioethyl (SATE) groups is essential for probe performance. Surprisingly, membrane-permeant versions of the new sensors that contained double bonds, PENN2 and PENN3, were only cleaved to a minor extent in HeLa cells while the saturated form, PENN, was well accepted.

Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

PubMed Central

2011-01-01

Background The purpose of this study was to design and evaluate fluorescent in situ hybridization (FISH) probes for the single-cell detection and enumeration of lactic acid bacteria, in particular organisms belonging to the major phylogenetic groups and species of oral lactobacilli and to Abiotrophia/Granulicatella. Results As lactobacilli are known for notorious resistance to probe penetration, probe-specific assay protocols were experimentally developed to provide maximum cell wall permeability, probe accessibility, hybridization stringency, and fluorescence intensity. The new assays were then applied in a pilot study to three biofilm samples harvested from variably demineralized bovine enamel discs that had been carried in situ for 10 days by different volunteers. Best probe penetration and fluorescent labeling of reference strains were obtained after combined lysozyme and achromopeptidase treatment followed by exposure to lipase. Hybridization stringency had to be established strictly for each probe. Thereafter all probes showed the expected specificity with reference strains and labeled the anticipated morphotypes in dental plaques. Applied to in situ grown biofilms the set of probes detected only Lactobacillus fermentum and bacteria of the Lactobacillus casei group. The most cariogenic biofilm contained two orders of magnitude higher L. fermentum cell numbers than the other biofilms. Abiotrophia/Granulicatella and streptococci from the mitis group were found in all samples at high levels, whereas Streptococcus mutans was detected in only one sample in very low numbers. Conclusions Application of these new group- and species-specific FISH probes to oral biofilm-forming lactic acid bacteria will allow a clearer understanding of the supragingival biome, its spatial architecture and of structure-function relationships implicated during plaque homeostasis and caries development. The probes should prove of value far beyond the field of oral microbiology, as many of them detect non-oral species and phylogenetic groups of importance in a variety of medical conditions and the food industry. PMID:21247450

Lectin histochemistry reveals SNA as a prognostic carbohydrate-dependent probe for invasive ductal carcinoma of the breast: a clinicopathological and immunohistochemical auxiliary tool

PubMed Central

dos-Santos, Petra B; Zanetti, Juliana S; Vieira-de-Mello, Gabriela S; Rêgo, Moacyr BM; A, Alfredo Ribeiro-Silva; Beltrão, Eduardo Isidoro Carneiro

2014-01-01

Increased sialylation and β1,6-branched oligosaccharides has been associated with a variety of structural changes in cell surface carbohydrates, most notably in tumorigenesis. Lectins are defined as proteins that preferentially recognize and bind carbohydrate complexes protruding from glycolipids and glycoproteins. This interaction with carbohydrates can be as specific as the interaction between antigen and antibody. Due to this type of interaction lectins have been used as experimental auxiliary tools in histopathological diagnosis of cancer. This study was designed to evaluate the differential expression of sialic acids and β1,6-N-acetylglucosaminyltransferase V (MGAT5) in invasive (IDC) and in situ (DCIS) ductal carcinoma of the breast and its possible application as prognostic biomarkers. A possible transition between pre-malign and malign lesions was evaluated using DCIS samples. Biopsies were analyzed regarding the expression of MUC1, p53, Ki-67, estrogen receptor, progesterone receptor, HER-2 and MGAT5. α2,6-linked sialic acids residues recognized by SNA lectin was overexpressed in 33.3% of IDC samples and it was related with Ki-67 (p=0.042), PR (p=0.029), lymphnodes status (p=0.017) and death (p=0.011). Regarding survival analysis SNA was the only lectin able to correlate with specific-disease survival and disease-free survival (p=0.024 and p=0.041, respectively), besides, it presents itself as an independent variable by Cox Regression analysis (p= 0.004). Comparing IDC and DCIS cases, only SNA showed different staining pattern (p=0.034). The presence of sialic acids on tumor cell surface can be an indicative of poor prognosis and our study provides further evidence that SNA lectin can be used as a prognostic probe in IDC and DCIS patients. PMID:24966944

Miniaturized multiplex label-free electronic chip for rapid nucleic acid analysis based on carbon nanotube nanoelectrode arrays

NASA Technical Reports Server (NTRS)

Koehne, Jessica E.; Chen, Hua; Cassell, Alan M.; Ye, Qi; Han, Jie; Meyyappan, Meyya; Li, Jun

2004-01-01

BACKGROUND: Reducing cost and time is the major concern in clinical diagnostics, particularly in molecular diagnostics. Miniaturization technologies have been recognized as promising solutions to provide low-cost microchips for diagnostics. With the recent advancement in nanotechnologies, it is possible to further improve detection sensitivity and simplify sample preparation by incorporating nanoscale elements in diagnostics devices. A fusion of micro- and nanotechnologies with biology has great potential for the development of low-cost disposable chips for rapid molecular analysis that can be carried out with simple handheld devices. APPROACH: Vertically aligned multiwalled carbon nanotubes (MWNTs) are fabricated on predeposited microelectrode pads and encapsulated in SiO2 dielectrics with only the very end exposed at the surface to form an inlaid nanoelectrode array (NEA). The NEA is used to collect the electrochemical signal associated with the target molecules binding to the probe molecules, which are covalently attached to the end of the MWNTs. CONTENT: A 3 x 3 microelectrode array is presented to demonstrate the miniaturization and multiplexing capability. A randomly distributed MWNT NEA is fabricated on each microelectrode pad. Selective functionalization of the MWNT end with a specific oligonucleotide probe and passivation of the SiO2 surface with ethylene glycol moieties are discussed. Ru(bpy)2+ -mediator-amplified guanine oxidation is used to directly measure the electrochemical signal associated with target molecules. SUMMARY: The discussed MWNT NEAs have ultrahigh sensitivity in direct electrochemical detection of guanine bases in the nucleic acid target. Fewer than approximately 1000 target nucleic acid molecules can be measured with a single microelectrode pad of approximately 20 x 20 microm2, which approaches the detection limit of laser scanners in fluorescence-based DNA microarray techniques. MWNT NEAs can be easily integrated with microelectronic circuitry and microfluidics for development of a fully automated system for rapid molecular analysis with minimum cost.

Heated Surface Temperatures Measured by Infrared Detector in a Cascade Environment

NASA Technical Reports Server (NTRS)

Boyle, Robert J.

2002-01-01

Investigators have used infrared devices to accurately measure heated surface temperatures. Several of these applications have been for turbine heat transfer studies involving film cooling and surface roughness, typically, these measurements use an infrared camera positioned externally to the test section. In cascade studies, where several blades are used to ensure periodic flow, adjacent blades block the externally positioned camera's views of the test blade. To obtain a more complete mapping of the surface temperatures, researchers at the NASA Glenn Research Center fabricated a probe with an infrared detector to sense the blade temperatures. The probe size was kept small to minimize the flow disturbance. By traversing and rotating the probe, using the same approach as for total pressure surveys, one can find the blade surface temperatures. Probe mounted infrared detectors are appropriate for measuring surface temperatures where an externally positioned infrared camera is unable to completely view the test object. This probe consists of a 8-mm gallium arsenide (GaAs) lens mounted in front of a mercury-cadmium-zinc-tellurium (HgCdZnTe) detector. This type of photovoltaic detector was chosen because of its high sensitivity to temperature when the detector is uncooled. The particular application is for relatively low surface temperatures, typically ambient to 100 C. This requires a detector sensitive at long wavelengths. The detector is a commercial product enclosed in a 9-mm-diameter package. The GaAs lens material was chosen because of its glass-like hardness and its good long-wavelength transmission characteristics. When assembled, the 6.4-mm probe stem is held in the traversing actuator. Since the entire probe is above the measurement plane, the flow field disturbance in the measurement plane is minimized. This particular probe body is somewhat wider than necessary, because it was designed to have replaceable detectors and lenses. The signal for the detector is fed through the hollow probe body. The detector's signal goes to an externally mounted preamplifier. The detector assembly, along with a preamplifier, is calibrated as a function of the surface temperature for various detector temperatures. The output voltage is a function of both the detector and object temperatures.

A potentiometric non-enzymatic glucose sensor using a molecularly imprinted layer bonded on a conducting polymer.

PubMed

Kim, Dong-Min; Moon, Jong-Min; Lee, Won-Chul; Yoon, Jang-Hee; Choi, Cheol Soo; Shim, Yoon-Bo

2017-05-15

A non-enzymatic potentiometric glucose sensor for the determination of glucose in the micomolar level in saliva was developed based on a molecularly imprinted polymer (MIP) binding on a conducting polymer layer. A MIP containing acrylamide, and aminophenyl boronic acid, as a host molecule to glucose, was immobilized on benzoic acid-functionalized poly(terthiophene) (pTBA) by the amide bond formation onto a gold nanoparticles deposited-screen printed carbon electrode (pTBA/AuNPs/SPCE). Aromatic boronic acid was incorporated into the MIP layer to stably capture glucose and create a potentiometric signal through the changed pKa value of polymer film by the formation of boronate anion-glucose complex with generation of H + ions by the cis-diol reaction. Reversible binding and extraction of glucose on the sensor surface was observed using a quartz crystal microbalance. Each layer of the sensor probe was characterized by cyclic voltammetry, electrochemical impedance spectroscopy, X-ray photoelectron spectroscopy, and atomic force microscopy. The potentiometric response at the optimized conditions exhibited a wide linear dynamic range of 3.2×10 -7 to 1.0×10 -3 M, with a detection limit of 1.9 (±0.15)×10 -7 M. The sensor probe revealed an excellent selectivity and sensitivity for glucose compared to other saccharides. In addition, the reliability of the proposed glucose sensor was evaluated in physiological fluid samples of saliva and finger prick blood. Copyright © 2016 Elsevier B.V. All rights reserved.

Darkfield microspectroscopy of nanostructures on silver tip-enhanced Raman scattering probes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Itoh, Tamitake, E-mail: tamitake-itou@aist.go.jp; Yamamoto, Yuko S., E-mail: yamayulab@gmail.com; Department of Chemistry, School of Science and Technology, Kagawa University, Takamatsu, Kagawa 761-0396

2016-01-11

We report an evaluation method employing darkfield microspectroscopy for silver probes used in tip-enhanced Raman scattering (TERS). By adjusting the darkfield illumination, the diffracted light from the probe outlines disappears and the diffracted light from the surface nanostructures and tips of the probes appears as colorful spots. Scanning electron microscopy reveals that the spectral variations in these spots reflect the shapes of the surface nanostructures. The tip curvatures correlate to the spectral maxima of their spots. Temporal color changes in the spots indicate the deterioration due to the oxidation of the silver surfaces. These results show that the proposed methodmore » is useful for in situ evaluation of plasmonic properties of TERS probes.« less

Probe diffusion of labeled polymers inside polyacrylic acid solutions: A polyelectrolyte effect

NASA Astrophysics Data System (ADS)

Mishra, Banani; Mithra, K.; Khandai, Santripti; Jena, Sidhartha S.

2018-05-01

Probe diffusion of fluorescently labeled Dextran 40 inside polyelectrolyte solution of polyacrylic acid (PAA) was investigated using Fluorescence Recovery After Photobleaching technique. The crowding and interaction effects on probe diffusion were controlled by tuning background polymer and added external electrolyte concentration. For all the salt concentration, an overall decrease in diffusion coefficient is observed with rise in polymer concentration. The diffusion coefficient decreases with decrease in salt concentration whereas the solution viscosity increases, indicating a competition between viscous drag and electrostatic interaction. A large positive deviation from the ideal Stokes-Einstein relation is observed for high polymer and low salt concentration, which reduces markedly with addition of salt confirming polyelectrolyte effects, plays a major role in deciding the probe diffusion.

Red-emitting fluorescent probe for detecting hypochlorite acid in vitro and in vivo.

PubMed

Chen, Hong; Sun, Tao; Qiao, Xiao-Guang; Tang, Qian-Oian; Zhao, Shan-Chao; Zhou, Zhan

2018-06-12

Due to the importance of hypochlorous acid (HClO) in biological and industrial, development of fluorescent probes for HClO has been an active research area. Here, a new red-emitting ratiometric fluorescent probe (P) was synthesized and well defined characterization via NMR, HR-MS, and fluorescence spectrum, which serves as a selective and sensitive probe for ClO - group. The probe showed a ratiometric fluorescent response to hypochlorite at the emission intensities ratio (I 480 /I 612 ) increasing from 0.28 to 27.46. The emission intensities ratio (I 480 /I 612 ) was linearly enhanced (I 480 /I 612  = 0.064 X + 0.096) with the ClO - concentration range from 1 to 30 μM. The detection limitation for ClO - in aqueous solution is 0.47 μM. Moreover, this biocompatible red-emitting ratiometric fluorescent probe was utilized to the fluorescence imaging of ClO - in living cells and Zebrafish. Copyright © 2018. Published by Elsevier B.V.

High sensitive and direct fluorescence detection of single viral DNA sequences by integration of double strand probes onto microgels particles.

PubMed

Aliberti, A; Cusano, A M; Battista, E; Causa, F; Netti, P A

2016-02-21

A novel class of probes for fluorescence detection was developed and combined to microgel particles for a high sensitive fluorescence detection of nucleic acids. A double strand probe with an optimized fluorescent-quencher couple was designed for the detection of different lengths of nucleic acids (39 nt and 100 nt). Such probe proved efficient in target detection in different contests and specific even in presence of serum proteins. The conjugation of double strand probes onto polymeric microgels allows for a sensitive detection of DNA sequences from HIV, HCV and SARS corona viruses with a LOD of 1.4 fM, 3.7 fM and 1.4 fM, respectively, and with a dynamic range of 10(-9)-10(-15) M. Such combination enhances the sensitivity of the detection of almost five orders of magnitude when compared to the only probe. The proposed platform based on the integration of innovative double strand probe into microgels particles represents an attractive alternative to conventional sensitive DNA detection technologies that rely on amplifications methods.

Ligand-surface interactions and surface oxidation of colloidal PbSe quantum dots revealed by thin-film positron annihilation methods

NASA Astrophysics Data System (ADS)

Shi, Wenqin; Eijt, Stephan W. H.; Suchand Sandeep, C. S.; Siebbeles, Laurens D. A.; Houtepen, Arjan J.; Kinge, Sachin; Brück, Ekkes; Barbiellini, Bernardo; Bansil, Arun

2016-02-01

Positron Two Dimensional Angular Correlation of Annihilation Radiation (2D-ACAR) measurements reveal modifications of the electronic structure and composition at the surfaces of PbSe quantum dots (QDs), deposited as thin films, produced by various ligands containing either oxygen or nitrogen atoms. In particular, the 2D-ACAR measurements on thin films of colloidal PbSe QDs capped with oleic acid ligands yield an increased intensity in the electron momentum density (EMD) at high momenta compared to PbSe quantum dots capped with oleylamine. Moreover, the EMD of PbSe QDs is strongly affected by the small ethylenediamine ligands, since these molecules lead to small distances between QDs and favor neck formation between near neighbor QDs, inducing electronic coupling between neighboring QDs. The high sensitivity to the presence of oxygen atoms at the surface can be also exploited to monitor the surface oxidation of PbSe QDs upon exposure to air. Our study clearly demonstrates that positron annihilation spectroscopy applied to thin films can probe surface transformations of colloidal semiconductor QDs embedded in functional layers.

Docosahexaenoic acid conjugated near infrared flourescence probe for in vivo early tumor diagnosis

NASA Astrophysics Data System (ADS)

Li, Siwen; Cao, Jie; Qin, Jingyi; Zhang, Xin; Achilefu, Samuel; Qian, Zhiyu; Gu, Yueqing

2013-02-01

Docosahexaenoic acid(DHA) is an omega-3 C22 natural fatty acid with six cis double bonds and as a constituent of membranes used as a precursor for metabolic and biochemical path ways. In this manuscript,we describe the synthesis of near-infrared(NIR) flourescence ICG-Der-01 labeled DHA for in vitro and vivo tumor targeting.The structure of the probe was intensively characterized by UV and MS. The in vitro and vivo tumor targeting abilities of the DHA-based NIR probes were investigeted in MCF-7 cells and MCF-7 xenograft mice model differently by confocal microscopy and CCD camera. The cell cytotoxicity were tested in tumor cells MCF-7 .The results shows that the DHA-based NIR probes have high affinity with the tumor both in vitro and vivo.In addition ,we also found that the DHA-based NIR probes have the apparent cytotoxicity on MCF-7 cells .which demonstrated that DHA was conjugated with other antitumor drug could increase the abilities of antirumor efficacy .So DHA-ICG-Der-01 is a promising optical agent for diagnosis of tumors especially in their early stage.

Fluorescent probes for nucleic Acid visualization in fixed and live cells.

PubMed

Boutorine, Alexandre S; Novopashina, Darya S; Krasheninina, Olga A; Nozeret, Karine; Venyaminova, Alya G

2013-12-11

This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.

Evaluation of TaqMan qPCR System Integrating Two Identically Labelled Hydrolysis Probes in Single Assay

PubMed Central

Nagy, Alexander; Vitásková, Eliška; Černíková, Lenka; Křivda, Vlastimil; Jiřincová, Helena; Sedlák, Kamil; Horníčková, Jitka; Havlíčková, Martina

2017-01-01

Ongoing evolution of viral pathogens is a significant issue in diagnostic virology employing TaqMan qPCR/RT-qPCR. Specific concerns are related to false negativity due to probe binding failure. One option for compensating for such deficiency is to integrate a second identically labelled probe in the assay. However, how this alteration influences the reaction parameters has not been comprehensively demonstrated. In the present study, we evaluate a TaqMan protocol using two identically labelled hydrolysis probes (simple, LNA (locked-nucleic-acid)) and MGB (minor-groove-binder) modified probes and combinations thereof in a single assay. Our results based on a synthetic amplicon suggest that the second probe does not compromise the TaqMan qPCR/RT-qPCR parameters, which repeatedly and reproducibly remained comparable to those of the corresponding single-probe assays, irrespective of the relative probe orientation, whether opposite or tandem, and probe modifications or combinations thereof. On the other hand, the second probe additively contributed to the overall fluorescence signal. The utility of the dual-probe approach was demonstrated on practical examples by using field specimens. We hope that the present study might serve as a theoretical basis for the development or improvement of TaqMan qPCR/RT-qPCR assays for the detection of highly variable nucleic acid templates. PMID:28120891

Robotic end effector

DOEpatents

Minichan, Richard L.

1993-01-01

An end effector for use in probing a surface with a robotic arm. The end effector has a first portion that carries a gimbal with a probe, the gimbal holding the probe normal to the surface, and a second portion with a set of three shafts within a housing for urging the gimbal and probe against the surface. The second portion contains a potentiometer connected by another shaft to the first portion to measure the position of the first portion with respect to the second so that the second portion can be moved to place and maintain the shafts at the midpoint of their travel. Then, as irregularities in the surface are encountered, the first portion can respond by moving closer to or farther from the second portion.

Robotic end effector

DOEpatents

Minichan, R.L.

1993-10-05

An end effector is described for use in probing a surface with a robotic arm. The end effector has a first portion that carries a gimbal with a probe, the gimbal holding the probe normal to the surface, and a second portion with a set of three shafts within a housing for urging the gimbal and probe against the surface. The second portion contains a potentiometer connected by another shaft to the first portion to measure the position of the first portion with respect to the second so that the second portion can be moved to place and maintain the shafts at the midpoint of their travel. Then, as irregularities in the surface are encountered, the first portion can respond by moving closer to or farther from the second portion. 7 figures.

Effect of silicic acid on arsenate and arsenite retention mechanisms on 6-L ferrihydrite: A spectroscopic and batch adsorption approach

PubMed Central

Gao, Xiaodong; Root, Robert A.; Farrell, James; Ela, Wendell; Chorover, Jon

2014-01-01

The competitive adsorption of arsenate and arsenite with silicic acid at the ferrihydrite-water interface was investigated over a wide pH range using batch sorption experiments, attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, extended X-ray absorption fine structure (EXAFS) spectroscopy, and density functional theory (DFT) modeling. Batch sorption results indicate that the adsorption of arsenate and arsenite on the 6-L ferrihydrite surface exhibits a strong pH-dependence, and the effect of pH on arsenic sorption differs between arsenate and arsenite. Arsenate adsorption decreases consistently with increasing pH; whereas arsenite adsorption initially increases with pH to a sorption maximum at pH 7–9, where after sorption decreases with further increases in pH. Results indicate that competitive adsorption between silicic acid and arsenate is negligible under the experimental conditions; whereas strong competitive adsorption was observed between silicic acid and arsenite, particularly at low and high pH. In-situ, flow-through ATR-FTIR data reveal that in the absence of silicic acid, arsenate forms inner-sphere, binuclear bidentate, complexes at the ferrihydrite surface across the entire pH range. Silicic acid also forms inner-sphere complexes at ferrihydrite surfaces throughout the entire pH range probed by this study (pH 2.8 – 9.0). The ATR-FTIR data also reveal that silicic acid undergoes polymerization at the ferrihydrite surface under the environmentally-relevant concentrations studied (e.g., 1.0 mM). According to ATR-FTIR data, arsenate complexation mode was not affected by the presence of silicic acid. EXAFS analyses and DFT modeling confirmed that arsenate tetrahedra were bonded to Fe metal centers via binuclear bidentate complexation with average As(V)-Fe bond distance of 3.27 Å. The EXAFS data indicate that arsenite forms both mononuclear bidentate and binuclear bidentate complexes with 6-L ferrihydrite as indicated by two As(III)-Fe bond distances of ~2.92–2.94 and 3.41–3.44 Å, respectively. The As-Fe bond distances in both arsenate and arsenite EXAFS spectra remained unchanged in the presence of Si, suggesting that whereas Si diminishes arsenite adsorption preferentially, it has a negligible effect on As-Fe bonding mechanisms. PMID:25382933

Toward a Molecular Understanding of Protein Solubility: Increased Negative Surface Charge Correlates with Increased Solubility

PubMed Central

Kramer, Ryan M.; Shende, Varad R.; Motl, Nicole; Pace, C. Nick; Scholtz, J. Martin

2012-01-01

Protein solubility is a problem for many protein chemists, including structural biologists and developers of protein pharmaceuticals. Knowledge about how intrinsic factors influence solubility is limited due to the difficulty of obtaining quantitative solubility measurements. Solubility measurements in buffer alone are difficult to reproduce, because gels or supersaturated solutions often form, making it impossible to determine solubility values for many proteins. Protein precipitants can be used to obtain comparative solubility measurements and, in some cases, estimations of solubility in buffer alone. Protein precipitants fall into three broad classes: salts, long-chain polymers, and organic solvents. Here, we compare the use of representatives from two classes of precipitants, ammonium sulfate and polyethylene glycol 8000, by measuring the solubility of seven proteins. We find that increased negative surface charge correlates strongly with increased protein solubility and may be due to strong binding of water by the acidic amino acids. We also find that the solubility results obtained for the two different precipitants agree closely with each other, suggesting that the two precipitants probe similar properties that are relevant to solubility in buffer alone. PMID:22768947

The failure of poly (ether ether ketone) in high speed contacts

NASA Astrophysics Data System (ADS)

Briscoe, B. J.; Stuart, B. H.; Sebastian, S.; Tweedale, P. J.

1993-04-01

The paper describes an experimental study, with an associated analysis incorporating supplementary data, of the anti-boundary lubricating action of an alkane-aliphatic carboxylic acid lubricant system in a poly (ether ether ketone)-mild steel contact. The experiments involve progressively increasing the load in a contact formed between a polymer plate and a rotating steel shaft and estimating the frictional work dissipated. Scuffing is identified when a rapid increase in frictional work is noted at a characteristic normal load. It is shown that the additive induces premature scuffing. Subsidiary data is provided using Raman spectroscopy and hardness probes, and confirms that certain additives such as decanoic acid and dodecylamine will induce surface plasticization in poly (ether ether ketone). The trends in the frictional data have been interpreted using the adhesive model of friction in conjunction with temperature-dependent interfacial theology and bulk mechanical property data. It is proposed that the scuffing process is induced prematurely as a consequence of excessive additive-induced subsurface plasticization. Restricted surface plasticization in this system provides an enhanced self-lubricating capacity.

PNA-COMBO-FISH: From combinatorial probe design in silico to vitality compatible, specific labelling of gene targets in cell nuclei.

PubMed

Müller, Patrick; Rößler, Jens; Schwarz-Finsterle, Jutta; Schmitt, Eberhard; Hausmann, Michael

2016-07-01

Recently, advantages concerning targeting specificity of PCR constructed oligonucleotide FISH probes in contrast to established FISH probes, e.g. BAC clones, have been demonstrated. These techniques, however, are still using labelling protocols with DNA denaturing steps applying harsh heat treatment with or without further denaturing chemical agents. COMBO-FISH (COMBinatorial Oligonucleotide FISH) allows the design of specific oligonucleotide probe combinations in silico. Thus, being independent from primer libraries or PCR laboratory conditions, the probe sequences extracted by computer sequence data base search can also be synthesized as single stranded PNA-probes (Peptide Nucleic Acid probes) or TINA-DNA (Twisted Intercalating Nucleic Acids). Gene targets can be specifically labelled with at least about 20 probes obtaining visibly background free specimens. By using appropriately designed triplex forming oligonucleotides, the denaturing procedures can completely be omitted. These results reveal a significant step towards oligonucleotide-FISH maintaining the 3d-nanostructure and even the viability of the cell target. The method is demonstrated with the detection of Her2/neu and GRB7 genes, which are indicators in breast cancer diagnosis and therapy. Copyright © 2016. Published by Elsevier Inc.

Continuously tunable nucleic acid hybridization probes.

PubMed

Wu, Lucia R; Wang, Juexiao Sherry; Fang, John Z; Evans, Emily R; Pinto, Alessandro; Pekker, Irena; Boykin, Richard; Ngouenet, Celine; Webster, Philippa J; Beechem, Joseph; Zhang, David Yu

2015-12-01

In silico-designed nucleic acid probes and primers often do not achieve favorable specificity and sensitivity tradeoffs on the first try, and iterative empirical sequence-based optimization is needed, particularly in multiplexed assays. We present a novel, on-the-fly method of tuning probe affinity and selectivity by adjusting the stoichiometry of auxiliary species, which allows for independent and decoupled adjustment of the hybridization yield for different probes in multiplexed assays. Using this method, we achieved near-continuous tuning of probe effective free energy. To demonstrate our approach, we enforced uniform capture efficiency of 31 DNA molecules (GC content, 0-100%), maximized the signal difference for 11 pairs of single-nucleotide variants and performed tunable hybrid capture of mRNA from total RNA. Using the Nanostring nCounter platform, we applied stoichiometric tuning to simultaneously adjust yields for a 24-plex assay, and we show multiplexed quantitation of RNA sequences and variants from formalin-fixed, paraffin-embedded samples.

Growth of carbon nanofibers on tipless cantilevers: process development and applications in scanning probe microscopy

NASA Astrophysics Data System (ADS)

Cui, Hongtao; Kalinin, Sergei; Yang, Xiaojing; Lowndes, Douglas

2005-03-01

Carbon nanofibers (CNFs) are grown on tipless cantilevers as probe tips for scanning probe microscopy. A catalyst dot pattern is formed on the surface of the tipless cantilever using electron beam lithography and CNF growth is performed in a direct-current plasma enhanced chemical vapor deposition reactor. Because the CNF is aligned with the electric field near the edge of the cantilever during growth, it is tilted with respect to the cantilever surface, which compensates partially for the probe tilt introduced when used in scanning probe microscopy. CNFs with different shapes and tip radii can be produced by variation of experimental conditions. The tip geometries of the CNF probes are defined by their catalyst particles, whose magnetic nature also imparts a capability for imaging magnetic samples. We have demonstrated their use in both atomic force and magnetic force surface imaging. These probe tips may provide information on magnetic phenomena at the nanometer scale in connection with the drive for ever-increasing storage density of magnetic hard disks.

In vitro performance of DIAGNOdent laser fluorescence device for dental calculus detection on human tooth root surfaces.

PubMed

Rams, Thomas E; Alwaqyan, Abdulaziz Y

2017-10-01

This study assessed the reproducibility of a red diode laser device, and its capability to detect dental calculus in vitro on human tooth root surfaces. On each of 50 extracted teeth, a calculus-positive and calculus-free root surface was evaluated by two independent examiners with a low-power indium gallium arsenide phosphide diode laser (DIAGNOdent) fitted with a periodontal probe-like sapphire tip and emitting visible red light at 655 nm wavelength. Laser autofluorescence intensity readings of examined root surfaces were scored on a 0-99 scale, with duplicate assessments performed using the laser probe tip directed both perpendicular and parallel to evaluated tooth root surfaces. Pearson correlation coefficients of untransformed measurements, and kappa analysis of data dichotomized with a >40 autofluorescence intensity threshold, were calculated to assess intra- and inter-examiner reproducibility of the laser device. Mean autofluorescence intensity scores of calculus-positive and calculus-free root surfaces were evaluated with the Student's t -test. Excellent intra- and inter-examiner reproducibility was found for DIAGNOdent laser autofluorescence intensity measurements, with Pearson correlation coefficients above 94%, and kappa values ranging between 0.96 and 1.0, for duplicate readings taken with both laser probe tip orientations. Significantly higher autofluorescence intensity values were measured when the laser probe tip was directed perpendicular, rather than parallel, to tooth root surfaces. However, calculus-positive roots, particularly with calculus in markedly-raised ledges, yielded significantly greater mean DIAGNOdent laser autofluorescence intensity scores than calculus-free surfaces, regardless of probe tip orientation. DIAGNOdent autofluorescence intensity values >40 exhibited a stronger association with calculus (36.6 odds ratio) then measurements of ≥5 (20.1 odds ratio) when the laser probe tip was advanced parallel to root surfaces. Excellent intra- and inter-examiner reproducibility of autofluorescence intensity measurements was obtained with the DIAGNOdent laser fluorescence device on human tooth roots. Calculus-positive root surfaces exhibited significantly greater DIAGNOdent laser autofluorescence than calculus-free tooth roots, even with the laser probe tip directed parallel to root surfaces. These findings provide further in vitro validation of the potential utility of a DIAGNOdent laser fluorescence device for identifying dental calculus on human tooth root surfaces.

Optimization of fluorimetric lipid membrane biosensor sensitivity through manipulation of membrane structure and nitrobenzoxadiazole dipalmitoylphosphatidylethanolamine concentration

NASA Astrophysics Data System (ADS)

Shrive, Jason D. A.; Krull, Ulrich J.

1995-01-01

In the work reported here, surface concentrations of 0.027 and 0.073 molecules nm-2 of the fluorescent membrane probe molecule nitrobenzoxadiazole dipalmitoylphosphatidylethanolamine (NBD-PE) were shown to yield optimum sensitivity for fluorimetric transduction of membrane structural perturbations for lipid membrane-based biosensor development. These optima were obtained through correlation of experimental data with theoretical predictions of optimum surface concentrations based on a model for NBD-PE self quenching previously published by our group. It was also determined that membrane structural heterogeneity improves the sensitivity of NBD-PE labeled membrane transducers. Together with fluorescence microscopy, observations of surface potential change upon compression or expansion of phosphatidylcholine (PC)/phosphatidic acid (PA) monolayers were used to qualitatively indicate the degree of structural heterogeneity in these membranes. It was determined that sub-microscopic domains must exist in microscopically homogeneous egg PC/egg PA membranes in order to facilitate the observed NBD-PE self-quenching responses upon alteration of bulk pH and therefore, membrane surface electrostatics and structure.

New Approaches Towards Recognition of Nucleic Acid Triple Helices

PubMed Central

Arya, Dev P.

2012-01-01

We show that groove recognition of nucleic acid triple helices can be achieved with aminosugars. Among these aminosugars, neomycin is the most effective aminoglycoside (groove binder) for stabilizing a DNA triple helix. It stabilizes both the T·A·T triplex and mixed-base DNA triplexes better than known DNA minor groove binders (which usually destabilize the triplex) and polyamines. Neomycin selectively stabilizes the triplex (T·A·T and mixed base) without any effect on the DNA duplex. The selectivity of neomycin likely originates from its potential and shape complementarity to the triplex Watson–Hoogsteen groove, making it the first molecule that selectively recognizes a triplex groove over a duplex groove. The groove recognition of aminoglycosides is not limited to DNA triplexes, but also extends to RNA and hybrid triple helical structures. Intercalator–neomycin conjugates are shown to simultaneously probe the base stacking and groove surface in the DNA triplex. Calorimetric and spectrosocopic studies allow the quantification of the effect of surface area of the intercalating moiety on binding to the triplex. These studies outline a novel approach to the recognition of DNA triplexes that incorporates the use of non-competing binding sites. These principles of dual recognition should be applicable to the design of ligands that can bind any given nucleic acid target with nanomolar affinities and with high selectivity. PMID:21073199

A selective glucose sensor based on direct oxidation on a bimetal catalyst with a molecular imprinted polymer.

PubMed

Cho, Seong Je; Noh, Hui-Bog; Won, Mi-Sook; Cho, Chul-Ho; Kim, Kwang Bok; Shim, Yoon-Bo

2018-01-15

A selective nonenzymatic glucose sensor was developed based on the direct oxidation of glucose on hierarchical CuCo bimetal-coated with a glucose-imprinted polymer (GIP). Glucose was introduced into the GIP composed of Nafion and polyurethane along with aminophenyl boronic acid (APBA), which was formed on the bimetal electrode formed on a screen-printed electrode. The extraction of glucose from the GIP allowed for the selective permeation of glucose into the bimetal electrode surface for oxidation. The GIP-coated bimetal sensor probe was characterized using electrochemical and surface analytical methods. The GIP layer coated on the NaOH pre-treated bimetal electrode exhibited a dynamic range between 1.0µM and 25.0mM with a detection limit of 0.65±0.10µM in phosphate buffer solution (pH 7.4). The anodic responses of uric acid, acetaminophen, dopamine, ascorbic acid, L-cysteine, and other saccharides (monosaccharides: galactose, mannose, fructose, and xylose; disaccharides: sucrose, lactose, and maltose) were not detected using the GIP-coated bimetal sensor. The reliability of the sensor was evaluated by the determination of glucose in artificial and whole blood samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Two-probe STM experiments at the atomic level.

PubMed

Kolmer, Marek; Olszowski, Piotr; Zuzak, Rafal; Godlewski, Szymon; Joachim, Christian; Szymonski, Marek

2017-11-08

Direct characterization of planar atomic or molecular scale devices and circuits on a supporting surface by multi-probe measurements requires unprecedented stability of single atom contacts and manipulation of scanning probes over large, nanometer scale area with atomic precision. In this work, we describe the full methodology behind atomically defined two-probe scanning tunneling microscopy (STM) experiments performed on a model system: dangling bond dimer wire supported on a hydrogenated germanium (0 0 1) surface. We show that 70 nm long atomic wire can be simultaneously approached by two independent STM scanners with exact probe to probe distance reaching down to 30 nm. This allows direct wire characterization by two-probe I-V characteristics at distances below 50 nm. Our technical results presented in this work open a new area for multi-probe research, which can be now performed with precision so far accessible only by single-probe scanning probe microscopy (SPM) experiments.

Imaging of acoustic waves induced by excimer laser ablation of the cornea

NASA Astrophysics Data System (ADS)

Rossi, Francesca; Pini, Roberto; Siano, Salvatore; Salimbeni, Renzo

1996-12-01

In this present study a pump-and-probe imaging set up was arranged to image and analyze the evolution of pressure waves induced by ArF ablation of the cornea, during their propagation into the eyeball. In vitro experiments simulating the effects of clinical PRK have been performed by using an artificial model of the human eyeball, composed of a cell filled with hyaluronic acid gel with a sample of freshly excised bovine cornea placed on the gel surface. LAser irradiation was provided at a fluence of 180 mJ/cm2. Irradiation spot diameters were varied in the range 2.0-5.0 mm. Images of the traveling acoustic waves evidenced diffraction effects, related to the diameter of laser spots on the corneal surface.

Three-dimensional nanoporous MoS2 framework decorated with Au nanoparticles for surface-enhanced Raman scattering

NASA Astrophysics Data System (ADS)

Sheng, Yingqiang; Jiang, Shouzhen; Yang, Cheng; Liu, Mei; Liu, Aihua; Zhang, Chao; Li, Zhen; Huo, Yanyan; Wang, Minghong; Man, Baoyuan

2017-08-01

The three-dimensional (3D) MoS2 decorated with Au nanoparticles (Au NPs) hybrids (3D MoS2-Au NPs) for surface-enhanced Raman scattering (SERS) sensing was demonstrated in this paper. SEM, Raman spectroscopy, TEM, SAED, EDX and XRD were performed to characterize 3D MoS2-Au NPs hybrids. Rhodamine 6G (R6G), fluorescein and gallic acid molecules were used as the probe for the SERS detection of the 3D MoS2-Au NPs hybrids. In addition, we modeled the enhancement of the electric field of MoS2-Au NPs hybrids using Finite-difference time-domain (FDTD) analysis, which can further give assistance to the mechanism understanding of the SERS activity.

Analysis of Protein–Protein Interactions in MCF-7 and MDA-MB-231 Cell Lines Using Phthalic Acid Chemical Probes

PubMed Central

Liang, Shih-Shin; Wang, Tsu-Nai; Tsai, Eing-Mei

2014-01-01

Phthalates are a class of plasticizers that have been characterized as endocrine disrupters, and are associated with genital diseases, cardiotoxicity, hepatotoxicity, and nephrotoxicity in the GeneOntology gene/protein database. In this study, we synthesized phthalic acid chemical probes and demonstrated differing protein–protein interactions between MCF-7 cells and MDA-MB-231 breast cancer cell lines. Phthalic acid chemical probes were synthesized using silicon dioxide particle carriers, which were modified using the silanized linker 3-aminopropyl triethoxyslane (APTES). Incubation with cell lysates from breast cancer cell lines revealed interactions between phthalic acid and cellular proteins in MCF-7 and MDA-MB-231 cells. Subsequent proteomics analyses indicated 22 phthalic acid-binding proteins in both cell types, including heat shock cognate 71-kDa protein, ATP synthase subunit beta, and heat shock protein HSP 90-beta. In addition, 21 MCF-7-specific and 32 MDA-MB-231 specific phthalic acid-binding proteins were identified, including related proteasome proteins, heat shock 70-kDa protein, and NADPH dehydrogenase and ribosomal correlated proteins, ras-related proteins, and members of the heat shock protein family, respectively. PMID:25402641

Profiling the decomposition odour at the grave surface before and after probing.

PubMed

Forbes, S L; Troobnikoff, A N; Ueland, M; Nizio, K D; Perrault, K A

2016-02-01

Human remains detection (HRD) dogs are recognised as a valuable and non-invasive search method for remains concealed in many different environments, including clandestine graves. However, the search for buried remains can be a challenging task as minimal odour may be available at the grave surface for detection by the dogs. Handlers often use a soil probe during these searches in an attempt to increase the amount of odour available for detection, but soil probing is considered an invasive search technique. The aim of this study was to determine whether the soil probe assists with increasing the abundance of volatile organic compounds (VOCs) available at the grave surface. A proof-of-concept method was developed using porcine remains to collect VOCs within the grave without disturbing the burial environment, and to compare their abundance at the grave surface before and after probing. Detection and identification of the VOC profiles required the use of comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-TOFMS) due to its superior sensitivity and selectivity for decomposition odour profiling. The abundance of decomposition VOCs was consistently higher within the grave environment compared to the grave surface, except when the grave surface had been disturbed, confirming the reduced availability of odour at the grave surface. Although probing appeared to increase the abundance of VOCs at the grave surface on many of the sampling days, there were no clear trends identified across the study and no direct relationships with the environmental variables measured. Typically, the decomposition VOCs that were most prevalent in the grave soil were the same VOCs detected at the grave surface, whereas the trace VOCs detected in these environments varied throughout the post-burial period. This study highlighted that probing the soil can assist with releasing decomposition VOCs but is likely correlated to environmental and burial variables which require further study. The use of a soil probe to assist HRD dogs should not be disregarded but should only follow the use of non-invasive methods if deemed appropriate. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Making the Venus Concept Watch 1.0

NASA Astrophysics Data System (ADS)

Balint, Tibor S.; Melchiorri, Julian P.

2014-08-01

Over the past year we have celebrated the 50th anniversary of planetary exploration, which started with the Venus flyby of Mariner-2; and the 35th anniversary of the Pioneer-Venus multi-probe mission where one large and three small probes descended to the surface of Venus, encountering extreme environmental conditions. At the surface of Venus the temperature is about 460 °C, and the pressure is 92 bar, with a highly corrosive super-critical CO2 atmosphere. At a Venusian altitude of 50 km the pressure and temperature conditions are near Earth-like, but the clouds carry sulfuric acid droplets. Deep probe missions to Jupiter and Saturn, targeting the 100 bar pressure depth encounter similar pressure and temperature conditions as the Pioneer-Venus probes did. Mitigating these environments is highly challenging and requires special considerations for designs and materials. While assessing such space mission concepts, we have found that there is an overlap between the extreme environments in planetary atmospheres and the environments experienced by deep-sea explorers back on Earth. Consequently, the mitigation approaches could be also similar between planetary probes and diver watches. For example, both need to tolerate about 100 bar of pressure-although high temperatures are not factors on Earth. Mitigating these environments, the potential materials are: titanium for the probe and the watch housing; sapphire for the window and glass; resin impregnated woven carbon fiber for the aeroshell's thermal protection system and for the face of the watch; and nylon ribbon for the parachute and for the watch band. Planetary probes also utilize precision watches; thus there is yet another crosscutting functionality with diver watches. Our team, from the Innovation Design Engineering Program of the Royal College of Art, has designed and built a concept watch to commemorate these historical events, while highlighting advances in manufacturing processes over the past three to five decades, relevant to both future planetary mission designs and can be used to produce deep diver watches. In this paper we describe our design considerations; give a brief overview of the extreme environments these components would experience on both Venus and Earth; the manufacturing techniques and materials we used to build the Venus Watch; and its outreach potential to bring a distant concept of planetary exploration closer to Earth. We will also address lessons learned from this project and new ideas forward, for the next generation of this concept design.

Atmospheric Probe Model: Construction and Wind Tunnel Tests

NASA Technical Reports Server (NTRS)

Vogel, Jerald M.

1998-01-01

The material contained in this document represents a summary of the results of a low speed wind tunnel test program to determine the performance of an atmospheric probe at low speed. The probe configuration tested consists of a 2/3 scale model constructed from a combination of hard maple wood and aluminum stock. The model design includes approximately 130 surface static pressure taps. Additional hardware incorporated in the baseline model provides a mechanism for simulating external and internal trailing edge split flaps for probe flow control. Test matrix parameters include probe side slip angle, external/internal split flap deflection angle, and trip strip applications. Test output database includes surface pressure distributions on both inner and outer annular wings and probe center line velocity distributions from forward probe to aft probe locations.

Intracellular delivery of peptide nucleic acid and organic molecules using zeolite-L nanocrystals.

PubMed

Bertucci, Alessandro; Lülf, Henning; Septiadi, Dedy; Manicardi, Alex; Corradini, Roberto; De Cola, Luisa

2014-11-01

The design and synthesis of smart nanomaterials can provide interesting potential applications for biomedical purposes from bioimaging to drug delivery. Manufacturing multifunctional systems in a way to carry bioactive molecules, like peptide nucleic acids able to recognize specific targets in living cells, represents an achievement towards the development of highly selective tools for both diagnosis and therapeutics. This work describes a very first example of the use of zeolite nanocrystals as multifunctional nanocarriers to deliver simultaneously PNA and organic molecules into living cells. Zeolite-L nanocrystals are functionalized by covalently attaching the PNA probes onto the surface, while the channel system is filled with fluorescent guest molecules. The cellular uptake of the PNA/Zeolite-L hybrid material is then significantly increased by coating the whole system with a thin layer of biodegradable poly-L-lysine. The delivery of DAPI as a model drug molecule, inserted into the zeolite pores, is also demonstrated to occur in the cells, proving the multifunctional ability of the system. Using this zeolite nanosystem carrying PNA probes designed to target specific RNA sequences of interest in living cells could open new possibilities for theranostic and gene therapy applications. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Improvement of arthroscopic cartilage stiffness probe using amorphous diamond coating.

PubMed

Töyräs, Juha; Korhonen, Rami K; Voutilainen, Tanja; Jurvelin, Jukka S; Lappalainen, Reijo

2005-04-01

During arthroscopic evaluation of articular cartilage unstable contact and even slipping of the measurement instrument on the tissue surface may degrade the reproducibility of the measurement. The main aim of the present study was to achieve more stable contact by controlling the friction between articular cartilage surface and the arthroscopic cartilage stiffness probe (Artscan 200, Artscan Oy, Helsinki, Finland) using amorphous diamond (AD) coating. In order to obtain surfaces with different average roughnesses (R(a)), polished stainless steel disks were coated with AD by using the filtered pulsed arc-discharge (FPAD) method. Dynamic coefficient of friction (mu) between the articular cartilage (n = 8) and the coated plates along one non-coated plate was then determined. The friction between AD and cartilage could be controlled over a wide range (mu = 0.027-0.728, p < 0.05, Wilcoxon test) by altering the roughness. Possible deterioration of cartilage was investigated by measuring surface roughness after friction tests and comparing it with the roughness of the adjacent, untested samples (n = 8). Importantly, even testing with the roughest AD (R(a) = 1250 nm) did not damage articular surface. On the basis of the friction measurements, a proper AD coating was selected for the stiffness probe. The performance of coated and non-coated probe was compared by measuring bovine osteochondral samples (n = 22) with both instruments. The reproducibility of the stiffness measurements was significantly better with the AD-coated probe (CV% = 4.7) than with the uncoated probe (CV% = 8.2). To conclude, AD coating can be used to safely control dynamic friction with articular surface. Sufficient friction between articular surface and reference plate of the arthroscopic probe improves significantly reproducibility of the stiffness measurements. (c) 2005 Wiley Periodicals, Inc.

Preassembled Fluorescent Multivalent Probes for the Imaging of Anionic Membranes.

PubMed

Roland, Felicia M; Peck, Evan M; Rice, Douglas R; Smith, Bradley D

2017-04-19

A new self-assembly process known as Synthavidin (synthetic avidin) technology was used to prepare targeted probes for near-infrared fluorescence imaging of anionic membranes and cell surfaces, a hallmark of many different types of disease. The probes were preassembled by threading a tetralactam macrocycle with six appended zinc-dipicolylamine (ZnDPA) targeting units onto a linear scaffold with one or two squaraine docking stations to produce hexavalent or dodecavalent fluorescent probes. A series of liposome titration experiments showed that multivalency promoted stronger membrane binding by the dodecavalent probe. In addition, the dodecavalent probe exhibited turn-on fluorescence due to probe unfolding during fluorescence microscopy at the membrane surface. However, the dodecavalent probe also had a higher tendency to self-aggregate after membrane binding, leading to probe self-quenching under certain conditions. This self-quenching effect was apparent during fluorescence microscopy experiments that recorded low fluorescence intensity from anionic dead and dying mammalian cells that were saturated with the dodecavalent probe. Conversely, probe self-quenching was not a factor with anionic microbial surfaces, where there was intense fluorescence staining by the dodecavalent probe. A successful set of rat tumor imaging experiments confirmed that the preassembled probes have sufficient mechanical stability for effective in vivo imaging. The results demonstrate the feasibility of this general class of preassembled fluorescent probes for multivalent targeting, but fluorescence imaging performance depends on the specific physical attributes of the biomarker target, such as the spatial distance between different copies of the biomarker and the propensity of the probe-biomarker complex to self-aggregate.

Double displacement: An improved bioorthogonal reaction strategy for templated nucleic acid detection.

PubMed

Kleinbaum, Daniel J; Miller, Gregory P; Kool, Eric T

2010-06-16

Quenched autoligation probes have been employed previously in a target-templated nonenzymatic ligation strategy for detecting nucleic acids in cells by fluorescence. A common source of background signal in such probes is the undesired reaction with water and other cellular nucleophiles. Here, we describe a new class of self-ligating probes, double displacement (DD) probes, that rely on two displacement reactions to fully unquench a nearby fluorophore. Three potential double displacement architectures, all possessing two fluorescence quencher/leaving groups (dabsylate groups), were synthesized and evaluated for templated reaction with nucleophile (phosphorothioate) probes both in vitro and in intact bacterial cells. All three DD probe designs provided substantially better initial quenching than a single-Dabsyl control. In isothermal templated reactions in vitro, double displacement probes yielded considerably lower background signal than previous single displacement probes; investigation into the mechanism revealed that one dabsylate acts as a sacrificial leaving group, reacting nonspecifically with water, but yielding little signal because another quencher group remains. Templated reaction with the specific nucleophile probe is required to activate a signal. The double displacement probes provided a ca. 80-fold turn-on signal and yielded a 2-4-fold improvement in signal/background over single Dabsyl probes. The best-performing probe architecture was demonstrated in a two-color, FRET-based two-allele discrimination system in vitro and was shown to be capable of discriminating between two closely related species of bacteria differing by a single nucleotide at an rRNA target site.

Interfacial transduction of nucleic acid hybridization using immobilized quantum dots as donors in fluorescence resonance energy transfer.

PubMed

Algar, W Russ; Krull, Ulrich J

2009-01-06

Fluorescence resonance energy transfer (FRET) using immobilized quantum dots (QDs) as energy donors was explored as a transduction method for the detection of nucleic acid hybridization at an interface. This research was motivated by the success of the QD-FRET-based transduction of nucleic acid hybridization in solution-phase assays. This new work represents a fundamental step toward the assembly of a biosensor, where immobilization of the selective chemistry on a surface is desired. After immobilizing QD-probe oligonucleotide conjugates on optical fibers, a demonstration of the retention of selectivity was achieved by the introduction of acceptor (Cy3)-labeled single-stranded target oligonucleotides. Hybridization generated the proximity required for FRET, and the resulting fluorescence spectra provided an analytical signal proportional to the amount of target. This research provides an important framework for the future development of nucleic acid biosensors based on QDs and FRET. The most important findings of this work are that (1) a QD-FRET solid-phase hybridization assay is viable and (2) a passivating layer of denatured bovine serum albumin alleviates nonspecific adsorption, ultimately resulting in (3) the potential for a reusable assay format and mismatch discrimination. In this, the first incarnation of a solid-phase QD-FRET hybridization assay, the limit of detection was found to be 5 nM, and the dynamic range was almost 2 orders of magnitude. Selective discrimination of the target was shown using a three-base-pairs mismatch from a fully complementary sequence. Despite a gradual loss of signal, reuse of the optical fibers over multiple cycles of hybridization and dehybridization was possible. Directions for further improvement of the analytical performance by optimizing the design of the QD-probe oligonucleotide interface are identified.

Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm

PubMed Central

Öhrmalm, Christina; Jobs, Magnus; Eriksson, Ronnie; Golbob, Sultan; Elfaitouri, Amal; Benachenhou, Farid; Strømme, Maria; Blomberg, Jonas

2010-01-01

One of the main problems in nucleic acid-based techniques for detection of infectious agents, such as influenza viruses, is that of nucleic acid sequence variation. DNA probes, 70-nt long, some including the nucleotide analog deoxyribose-Inosine (dInosine), were analyzed for hybridization tolerance to different amounts and distributions of mismatching bases, e.g. synonymous mutations, in target DNA. Microsphere-linked 70-mer probes were hybridized in 3M TMAC buffer to biotinylated single-stranded (ss) DNA for subsequent analysis in a Luminex® system. When mismatches interrupted contiguous matching stretches of 6 nt or longer, it had a strong impact on hybridization. Contiguous matching stretches are more important than the same number of matching nucleotides separated by mismatches into several regions. dInosine, but not 5-nitroindole, substitutions at mismatching positions stabilized hybridization remarkably well, comparable to N (4-fold) wobbles in the same positions. In contrast to shorter probes, 70-nt probes with judiciously placed dInosine substitutions and/or wobble positions were remarkably mismatch tolerant, with preserved specificity. An algorithm, NucZip, was constructed to model the nucleation and zipping phases of hybridization, integrating both local and distant binding contributions. It predicted hybridization more exactly than previous algorithms, and has the potential to guide the design of variation-tolerant yet specific probes. PMID:20864443

[Oligonucleotide derivatives in the nucleic acid hybridization analysis. I. Covalent immobilization of oligonucleotide probes onto the nylon].

PubMed

Dmitrienko, E V; Pyshnaia, I A; Pyshnyĭ, D V

2010-01-01

The features of UV-induced immobilization of oligonucleotides on a nylon membranes and the effectiveness of enzymatic labeling of immobilized probes at heterophase detection of nucleic acids are studied. Short terminal oligothymidilate (up to 10 nt) sequences are suggested to attach to the probe via a flexible ethylene glycol based linker. The presence of such fragment enhances the intensity of immobilization and reduces UV-dependent degradation of the targeted (sequence-specific) part of the probe by reducing the dose needed for the immobilization of DNA. The optimum dose of UV-irradiation is determined to be ~0.4 J/cm(2) at the wavelength 254 nm. This dose provides high level of hybridization signal for immobilized probes with various nucleotide composition of the sequence specific moiety. The amide groups of the polyamide are shown to play the key role in the photoinduced immobilization of nucleic acids, whereas the primary amino groups in the structure of PA is not the center responsible for the covalent binding of DNA by UV-irradiation, as previously believed. Various additives in the soaking solution during the membrane of UV-dependent immobilization of probes are shown to influence its effectiveness. The use of alternative to UV-irradiation system of radical generation are shown to provide the immobilization of oligonucleotides onto the nylon membrane.

Titan probe technology assessment and technology development plan study

NASA Technical Reports Server (NTRS)

Castro, A. J.

1980-01-01

The need for technology advances to accomplish the Titan probe mission was determined by defining mission conditions and requirements and evaluating the technology impact on the baseline probe configuration. Mission characteristics found to be technology drivers include (1) ten years dormant life in space vacuum; (2) unknown surface conditions, various sample materials, and a surface temperature; and (3) mission constraints of the Saturn Orbiter Dual Probe mission regarding weight allocation. The following areas were identified for further development: surface sample acquisition system; battery powered system; nonmetallic materials; magnetic bubble memory devices, and the landing system. Preentry science, reliability, and weight reduction and redundancy must also be considered.

Development progress of the Materials Analysis and Particle Probe

NASA Astrophysics Data System (ADS)

Lucia, M.; Kaita, R.; Majeski, R.; Bedoya, F.; Allain, J. P.; Boyle, D. P.; Schmitt, J. C.; Onge, D. A. St.

2014-11-01

The Materials Analysis and Particle Probe (MAPP) is a compact in vacuo surface science diagnostic, designed to provide in situ surface characterization of plasma facing components in a tokamak environment. MAPP has been implemented for operation on the Lithium Tokamak Experiment at Princeton Plasma Physics Laboratory (PPPL), where all control and analysis systems are currently under development for full remote operation. Control systems include vacuum management, instrument power, and translational/rotational probe drive. Analysis systems include onboard Langmuir probes and all components required for x-ray photoelectron spectroscopy, low-energy ion scattering spectroscopy, direct recoil spectroscopy, and thermal desorption spectroscopy surface analysis techniques.

Development progress of the Materials Analysis and Particle Probe.

PubMed

Lucia, M; Kaita, R; Majeski, R; Bedoya, F; Allain, J P; Boyle, D P; Schmitt, J C; Onge, D A St

2014-11-01

The Materials Analysis and Particle Probe (MAPP) is a compact in vacuo surface science diagnostic, designed to provide in situ surface characterization of plasma facing components in a tokamak environment. MAPP has been implemented for operation on the Lithium Tokamak Experiment at Princeton Plasma Physics Laboratory (PPPL), where all control and analysis systems are currently under development for full remote operation. Control systems include vacuum management, instrument power, and translational/rotational probe drive. Analysis systems include onboard Langmuir probes and all components required for x-ray photoelectron spectroscopy, low-energy ion scattering spectroscopy, direct recoil spectroscopy, and thermal desorption spectroscopy surface analysis techniques.

Thermophoretic melting curves quantify the conformation and stability of RNA and DNA

PubMed Central

Wienken, Christoph J.; Baaske, Philipp; Duhr, Stefan; Braun, Dieter

2011-01-01

Measuring parameters such as stability and conformation of biomolecules, especially of nucleic acids, is important in the field of biology, medical diagnostics and biotechnology. We present a thermophoretic method to analyse the conformation and thermal stability of nucleic acids. It relies on the directed movement of molecules in a temperature gradient that depends on surface characteristics of the molecule, such as size, charge and hydrophobicity. By measuring thermophoresis of nucleic acids over temperature, we find clear melting transitions and resolve intermediate conformational states. These intermediate states are indicated by an additional peak in the thermophoretic signal preceding most melting transitions. We analysed single nucleotide polymorphisms, DNA modifications, conformational states of DNA hairpins and microRNA duplexes. The method is validated successfully against calculated melting temperatures and UV absorbance measurements. Interestingly, the methylation of DNA is detected by the thermophoretic amplitude even if it does not affect the melting temperature. In the described setup, thermophoresis is measured all-optical in a simple setup using a reproducible capillary format with only 250 nl probe consumption. The thermophoretic analysis of nucleic acids shows the technique’s versatility for the investigation of nucleic acids relevant in cellular processes like RNA interference or gene silencing. PMID:21297115

Chirality, photochemistry and the detection of amino acids in interstellar ice analogues and comets.

PubMed

Evans, Amanda C; Meinert, Cornelia; Giri, Chaitanya; Goesmann, Fred; Meierhenrich, Uwe J

2012-08-21

The primordial appearance of chiral amino acids was an essential component of the asymmetric evolution of life on Earth. In this tutorial review we will explore the original life-generating, symmetry-breaking event and summarise recent thoughts on the origin of enantiomeric excess in the universe. We will then highlight the transfer of asymmetry from chiral photons to racemic amino acids and elucidate current experimental data on the photochemical synthesis of amino and diamino acid structures in simulated interstellar and circumstellar ice environments. The chirality inherent within actual interstellar (cometary) ice environments will be considered in this discussion: in 2014 the Rosetta Lander Philae onboard the Rosetta space probe is planned to detach from the orbiter and soft-land on the surface of the nucleus of comet 67P/Churyumov-Gerasimenko. It is equipped for the in situ enantioselective analysis of chiral prebiotic organic species in cometary ices. The scientific design of this mission will therefore be presented in the context of analysing the formation of amino acid structures within interstellar ice analogues as a means towards furthering understanding of the origin of asymmetric biological molecules.

Ternary Surface Monolayers for Ultrasensitive (Zeptomole) Amperometric Detection of Nucleic-Acid Hybridization without Signal Amplification

PubMed Central

Wu, Jie; Campuzano, Susana; Halford, Colin; Haake, David A.; Wang, Joseph

2010-01-01

A ternary surface monolayer, consisting of co-assembled thiolated capture probe (SHCP) mercaptohexanol (MCH) and dithiothreitol (DTT), is shown to offer dramatic improvements in the signal-to-noise characteristics of electrochemical DNA hybridization biosensors based on common self-assembled monolayers (SAMs). Remarkably low detection limits down to 40 zmole (in 4 μL samples) as well as only 1 CFU E. coli per sensor are thus obtained without any additional amplification step in connection to the commonly used horseradish peroxidase/3,3′,5,5′-tetramethylbenzidine (HRP/TMB) system. Such dramatic improvements in the detection limits (compared to common binary alkanethiol interfaces and to most electrochemical DNA sensing strategies without target or signal amplification) are attributed primarily to the remarkably higher resistance to non-specific adsorption. This reflects the highly compact layer (with lower pinhole density) produced by the coupling of the cyclic- and linear-configuration ‘backfillers’ that leads to a remarkably low background noise even in the presence of complex sample matrices. A wide range of surface compositions have been investigated and the ternary mixed monolayer has been systematically optimized. Detailed impedance spectroscopy and cyclic voltammetric studies shed useful insights into the surface coverage. The impressive sensitivity and high specificity of the simple developed methodology indicate great promise for a wide range of nucleic acid testing, including clinical diagnostics, biothreat detection, food safety and forensic analysis. PMID:20883023

Ternary surface monolayers for ultrasensitive (zeptomole) amperometric detection of nucleic acid hybridization without signal amplification.

PubMed

Wu, Jie; Campuzano, Susana; Halford, Colin; Haake, David A; Wang, Joseph

2010-11-01

A ternary surface monolayer, consisting of coassembled thiolated capture probe, mercaptohexanol and dithiothreitol, is shown to offer dramatic improvements in the signal-to-noise characteristics of electrochemical DNA hybridization biosensors based on common self-assembled monolayers. Remarkably low detection limits down to 40 zmol (in 4 μL samples) as well as only 1 CFU Escherichia coli per sensor are thus obtained without any additional amplification step in connection to the commonly used horseradish peroxidase/3,3',5,5'-tetramethylbenzidine system. Such dramatic improvements in the detection limits (compared to those of common binary alkanethiol interfaces and to those of most electrochemical DNA sensing strategies without target or signal amplification) are attributed primarily to the remarkably higher resistance to nonspecific adsorption. This reflects the highly compact layer (with lower pinhole density) produced by the coupling of the cyclic- and linear-configuration "backfillers" that leads to a remarkably low background noise even in the presence of complex sample matrixes. A wide range of surface compositions have been investigated, and the ternary mixed monolayer has been systematically optimized. Detailed impedance spectroscopy and cyclic voltammetric studies shed useful insights into the surface coverage. The impressive sensitivity and high specificity of the simple developed methodology indicate great promise for a wide range of nucleic acid testing, including clinical diagnostics, biothreat detection, food safety, and forensic analysis.

Ground Simulations of Near-Surface Plasma Field and Charging at the Lunar Terminator

NASA Astrophysics Data System (ADS)

Polansky, J.; Ding, N.; Wang, J.; Craven, P.; Schneider, T.; Vaughn, J.

2012-12-01

Charging in the lunar terminator region is the most complex and is still not well understood. In this region, the surface potential is sensitively influenced by both solar illumination and plasma flow. The combined effects from localized shadow generated by low sun elevation angles and localized wake generated by plasma flow over the rugged terrain can generate strongly differentially charged surfaces. Few models currently exist that can accurately resolve the combined effects of plasma flow and solar illumination over realistic lunar terminator topographies. This paper presents an experimental investigation of lunar surface charging at the terminator region in simulated plasma environments in a vacuum chamber. The solar wind plasma flow is simulated using an electron bombardment gridded Argon ion source. An electrostatic Langmuir probe, nude Faraday probes, a floating emissive probe, and retarding potential analyzer are used to quantify the plasma flow field. Surface potentials of both conducting and dielectric materials immersed in the plasma flow are measured with a Trek surface potential probe. The conducting material surface potential will simultaneously be measured with a high impedance voltmeter to calibrate the Trek probe. Measurement results will be presented for flat surfaces and objects-on-surface for various angles of attack of the plasma flow. The implications on the generation of localized plasma wake and surface charging at the lunar terminator will be discussed. (This research is supported by the NASA Lunar Advanced Science and Exploration Research program.)

Contoured Surface Eddy Current Inspection System

DOEpatents

Batzinger, Thomas James; Fulton, James Paul; Rose, Curtis Wayne; Perocchi, Lee Cranford

2003-04-08

Eddy current inspection of a contoured surface of a workpiece is performed by forming a backing piece of flexible, resiliently yieldable material with a contoured exterior surface conforming in shape to the workpiece contoured surface. The backing piece is preferably cast in place so as to conform to the workpiece contoured surface. A flexible eddy current array probe is attached to the contoured exterior surface of the backing piece such that the probe faces the contoured surface of the workpiece to be inspected when the backing piece is disposed adjacent to the workpiece. The backing piece is then expanded volumetrically by inserting at least one shim into a slot in the backing piece to provide sufficient contact pressure between the probe and the workpiece contoured surface to enable the inspection of the workpiece contoured surface to be performed.

In Cell Footprinting Coupled with Mass Spectrometry for the Structural Analysis of Proteins in Live Cells.

PubMed

Espino, Jessica A; Mali, Vishaal S; Jones, Lisa M

2015-08-04

Protein footprinting coupled with mass spectrometry has become a widely used tool for the study of protein-protein and protein-ligand interactions and protein conformational change. These methods provide residue-level analysis on protein interaction sites and have been successful in studying proteins in vitro. The extension of these methods for in cell footprinting would open an avenue to study proteins that are not amenable for in vitro studies and would probe proteins in their native environment. Here we describe the application of an oxidative-based footprinting approach inside cells in which hydroxyl radicals are used to oxidatively modify proteins. Mass spectrometry is used to detect modification sites and to calculate modification levels. The method is probing biologically relevant proteins in live cells, and proteins in various cellular compartments can be oxdiatively modified. Several different amino acid residues are modified making the method a general labeling strategy for the study of a variety of proteins. Further, comparison of the extent of oxidative modification with solvent accessible surface area reveals the method successfully probes solvent accessibility. This marks the first time protein footprinting has been performed in live cells.

Eddy Current Probe for Surface and Sub-Surface Inspection

NASA Technical Reports Server (NTRS)

Wincheski, Russell A. (Inventor); Simpson, John W. (Inventor)

2014-01-01

An eddy current probe includes an excitation coil for coupling to a low-frequency alternating current (AC) source. A magneto-resistive sensor is centrally disposed within and at one end of the excitation coil to thereby define a sensing end of the probe. A tubular flux-focusing lens is disposed between the excitation coil and the magneto-resistive sensor. An excitation wire is spaced apart from the magneto-resistive sensor in a plane that is perpendicular to the sensor's axis of sensitivity and such that, when the sensing end of the eddy current probe is positioned adjacent to the surface of a structure, the excitation wire is disposed between the magneto-resistive sensor and the surface of the structure. The excitation wire is coupled to a high-frequency AC source. The excitation coil and flux-focusing lens can be omitted when only surface inspection is required.

Effectiveness of adjunctive subgingival administration of amino acids and sodium hyaluronate gel on clinical and immunological parameters in the treatment of chronic periodontitis

PubMed Central

Bevilacqua, Lorenzo; Eriani, Jessica; Serroni, Ilde; Liani, Giuliana; Borelli, Violetta; Castronovo, Gaetano; Di Lenarda, Roberto

2012-01-01

Summary Aims The aim of this clinical trial was to compare clinical and biochemical healing outcomes following ultrasonic mechanical instrumentation versus ultrasonic mechanical instrumentation associated with topical subgingival application of amino acids and sodium hyaluronate gel. Methods Eleven systemically healthy subjects with moderate-severe chronic periodontitis, who had four sites with pocket probing depth and clinical attachment level greater than or equal to 5 mm were randomly assigned to two different types of treatment: two pockets were treated with ultrasonic debridement (Control Group) and two pockets with ultrasonic mechanical instrumentation associated with 0,5 ml of amino acids and sodium hyaluronate gel (Test Group). Probing depth, clinical attachment level, plaque index and bleeding on probing were recorded at baseline, 45 and 90 days. Levels of calprotectin and myeloperoxidase activity in gingival crevicular fluid were assessed at baseline and on day 7 and 45. Results Statistical significance was found between baseline and day 45 in relation to probing depth reduction and bleeding on probing between groups for both of the tested treatments. Significant reductions in μg/sample of calprotectin and myeloperoxidase were found after 1-week and an increase at 45 days in both groups. There were no statistically significant differences between other variables evaluated in this study. Conclusions These data suggest that subgingival application of hyaluronic acid following ultrasonic mechanical instrumentation is beneficial for improving periodontal parameters. PMID:23087790

Physical properties and application in the confined geometrical systems

NASA Astrophysics Data System (ADS)

Pak, Hunkyun

Surface viscoelasticity of a vitamin E modified polyethylene glycol (vitamin E-TPGS) monolayers at the air/water interface is deduced by the surface light scattering method and Wilhelmy plate method. It was found that the viscoelasticity of vitamin E-TPGS monolayer is similar to that of PEO monolayer at the surface pressure lower than the collapse pressure of the polyethylene oxide (PEO). However, at higher surface pressure than the collapse pressure of PEO, it deviates from the viscoelastic behavior of PEO. Lateral diffusion constants of a probe lipid (NBD-PC) in a binary monolayer of L-a-dilauroylphosphatidylcholine (DLPC) and poly-(di-isobutylene-alt-maleic acid) (PDIBMA) were determined by the fluorescence recovery after photobleaching (FRAP) method at the air/pH 7 buffer interface as a function of composition. The diffusion constant is found to retard down to less than one hundredth to that at pure DLPC monolayers as the mole fraction of PDIBMA increased. The free area model was used to interpret the probe diffusion retardation. Translational diffusion constants of a probe molecule, 4-octadecylamino-7-nitrobenzo-2-oxa-1,3-diazole (C18-NBD), in thin polyisoprene (PI) and polydimethyl siloxane (PDMS) films, spin coated on methylated and propylyaminated silicon wafers, are studied by the FRAP method as a function of film thickness. Reduction of the diffusion constant is observed as thickness of the films is decreased. Two empirical models, the two-layer model and the continuous layer model are proposed to account for the diffusion constant dependence on the film thickness vs. thickness. It was observed that the diffusion profiles in the films are dependet on the nature of the substrate surfaces. Self-assembled patterns of magnetic particles were made and fixed by applying magnetic field on the particles dispersed at the air/liquid interface, followed by gelling of the liquid subphase. With this method, the large patterns with controllable lattice constant can be made. The fixation of the subphase enhances the stability of the patterns. Further, three-dimensional self-assembled patterns can be made by this method when the fixation process is incorporated.

Application of a unique server-based oligonucleotide probe selection tool toward a novel biosensor for the detection of Streptococcus pyogenes.

PubMed

Nugen, Sam R; Leonard, Barbara; Baeumner, Antje J

2007-05-15

We developed a software program for the rapid selection of detection probes to be used in nucleic acid-based assays. In comparison to commercially available software packages, our program allows the addition of oligotags as required by nucleic acid sequence-based amplification (NASBA) as well as automatic BLAST searches for all probe/primer pairs. We then demonstrated the usefulness of the program by designing a novel lateral flow biosensor for Streptococcus pyogenes that does not rely on amplification methods such as the polymerase chain reaction (PCR) or NASBA to obtain low limits of detection, but instead uses multiple reporter and capture probes per target sequence and an instantaneous amplification via dye-encapsulating liposomes. These assays will decrease the detection time to just a 20 min hybridization reaction and avoid costly enzymatic gene amplification reactions. The lateral flow assay was developed quantifying the 16S rRNA from S. pyogenes by designing reporter and capture probes that specifically hybridize with the RNA and form a sandwich. DNA reporter probes were tagged with dye-encapsulating liposomes, biotinylated DNA oligonucleotides were used as capture probes. From the initial number of capture and reporter probes chosen, a combination of two capture and three reporter probes were found to provide optimal signal generation and significant enhancement over single capture/reporter probe combinations. The selectivity of the biosensor was proven by analyzing organisms closely related to S. pyogenes, such as other Streptococcus and Enterococcus species. All probes had been selected by the software program within minutes and no iterative optimization and re-design of the oligonucleotides was required which enabled a very rapid biosensor prototyping. While the sensitivity obtained with the biosensor was only 135 ng, future experiments will decrease this significantly by the addition of more reporter and capture probes for either the same rRNA or a different nucleic acid target molecule. This will lead to the possibility of detecting S. pyogenes with a rugged assay that does not require a cell culturing or gene amplification step and will therefore enable rapid, specific and sensitive onsite testing.

DNA microdevice for electrochemical detection of Escherichia coli 0157:H7 molecular markers.

PubMed

Berganza, J; Olabarria, G; García, R; Verdoy, D; Rebollo, A; Arana, S

2007-04-15

An electrochemical DNA sensor based on the hybridization recognition of a single-stranded DNA (ssDNA) probe immobilized onto a gold electrode to its complementary ssDNA is presented. The DNA probe is bound on gold surface electrode by using self-assembled monolayer (SAM) technology. An optimized mixed SAM with a blocking molecule preventing the nonspecific adsorption on the electrode surface has been prepared. In this paper, a DNA biosensor is designed by means of the immobilization of a single stranded DNA probe on an electrochemical transducer surface to recognize specifically Escherichia coli (E. coli) 0157:H7 complementary target DNA sequence via cyclic voltammetry experiments. The 21 mer DNA probe including a C6 alkanethiol group at the 5' phosphate end has been synthesized to form the SAM onto the gold surface through the gold sulfur bond. The goal of this paper has been to design, characterise and optimise an electrochemical DNA sensor. In order to investigate the oligonucleotide probe immobilization and the hybridization detection, experiments with different concentration of DNA and mismatch sequences have been performed. This microdevice has demonstrated the suitability of oligonucleotide Self-assembled monolayers (SAMs) on gold as immobilization method. The DNA probes deposited on gold surface have been functional and able to detect changes in bases sequence in a 21-mer oligonucleotide.

High quality-factor quartz tuning fork glass probe used in tapping mode atomic force microscopy for surface profile measurement

NASA Astrophysics Data System (ADS)

Chen, Yuan-Liu; Xu, Yanhao; Shimizu, Yuki; Matsukuma, Hiraku; Gao, Wei

2018-06-01

This paper presents a high quality-factor (Q-factor) quartz tuning fork (QTF) with a glass probe attached, used in frequency modulation tapping mode atomic force microscopy (AFM) for the surface profile metrology of micro and nanostructures. Unlike conventionally used QTFs, which have tungsten or platinum probes for tapping mode AFM, and suffer from a low Q-factor influenced by the relatively large mass of the probe, the glass probe, which has a lower density, increases the Q-factor of the QTF probe unit allowing it to obtain better measurement sensitivity. In addition, the process of attaching the probe to the QTF with epoxy resin, which is necessary for tapping mode AFM, is also optimized to further improve the Q-factor of the QTF glass probe. The Q-factor of the optimized QTF glass probe unit is demonstrated to be very close to that of a bare QTF without a probe attached. To verify the effectiveness and the advantages of the optimized QTF glass probe unit, the probe unit is integrated into a home-built tapping mode AFM for conducting surface profile measurements of micro and nanostructures. A blazed grating with fine tool marks of 100 nm, a microprism sheet with a vertical amplitude of 25 µm and a Fresnel lens with a steep slope of 90 degrees are used as measurement specimens. From the measurement results, it is demonstrated that the optimized QTF glass probe unit can achieve higher sensitivity as well as better stability than conventional probes in the measurement of micro and nanostructures.

Label-Free Electrochemical Detection of the Specific Oligonucleotide Sequence of Dengue Virus Type 1 on Pencil Graphite Electrodes

PubMed Central

Souza, Elaine; Nascimento, Gustavo; Santana, Nataly; Ferreira, Danielly; Lima, Manoel; Natividade, Edna; Martins, Danyelly; Lima-Filho, José

2011-01-01

A biosensor that relies on the adsorption immobilization of the 18-mer single-stranded nucleic acid related to dengue virus gene 1 on activated pencil graphite was developed. Hybridization between the probe and its complementary oligonucleotides (the target) was investigated by monitoring guanine oxidation by differential pulse voltammetry (DPV). The pencil graphite electrode was made of ordinary pencil lead (type 4B). The polished surface of the working electrode was activated by applying a potential of 1.8 V for 5 min. Afterward, the dengue oligonucleotides probe was immobilized on the activated electrode by applying 0.5 V to the electrode in 0.5 M acetate buffer (pH 5.0) for 5 min. The hybridization process was carried out by incubating at the annealing temperature of the oligonucleotides. A time of five minutes and concentration of 1 μM were found to be the optimal conditions for probe immobilization. The electrochemical detection of annealing between the DNA probe (TS-1P) immobilized on the modified electrode, and the target (TS-1T) was achieved. The target could be quantified in a range from 1 to 40 nM with good linearity and a detection limit of 0.92 nM. The specificity of the electrochemical biosensor was tested using non-complementary sequences of dengue virus 2 and 3. PMID:22163916

Synthesis and evaluation of a photoresponsive quencher for fluorescent hybridization probes.

PubMed

Kovaliov, Marina; Wachtel, Chaim; Yavin, Eylon; Fischer, Bilha

2014-10-21

Nowadays, most nucleic acid detections using fluorescent probes rely on quenching of fluorescence by energy transfer from one fluorophore to another or to a non-fluorescent molecule (quencher). The most widely used quencher in fluorescent probes is 4-((4-(dimethylamino)phenyl)azo)benzoic acid (DABCYL). We targeted a nucleoside-DABCYL analogue which could be incorporated anywhere in an oligonucleotide sequence and in any number, and used as a quencher in different hybridization sensitive probes. Specifically, we introduced a 5-(4-((dimethylamino)phenyl)azo)benzene)-2'-deoxy-uridine (dU(DAB)) quencher. The photoisomerization and dU(DAB)'s ability to quench fluorescein emission have been investigated. We incorporated dU(DAB) into a series of oligonucleotide (ON) probes including strand displacement probes, labeled with both fluorescein (FAM) and dU(DAB), and TaqMan probes bearing one or two dU(DAB) and a FAM fluorophore. We used these probes for the detection of a DNA target in real-time PCR (RT-PCR). All probes showed amplification of targeted DNA. A dU(DAB) modified TaqMan RT-PCR probe was more efficient as compared to a DABCYL bearing probe (93% vs. 87%, respectively). Furthermore, dU(DAB) had a stabilizing effect on the duplex, causing an increase in Tm up to 11 °C. In addition we showed the photoisomerisation of the azobenzene moiety of dU(DAB) and the dU(DAB) triply-labeled oligonucleotide upon irradiation. These findings suggest that dU(DAB) modified probes are promising probes for gene quantification in real-time PCR detection and as photoswitchable devices.

Method for nanoscale spatial registration of scanning probes with substrates and surfaces

NASA Technical Reports Server (NTRS)

Wade, Lawrence A. (Inventor)

2010-01-01

Embodiments in accordance with the present invention relate to methods and apparatuses for aligning a scanning probe used to pattern a substrate, by comparing the position of the probe to a reference location or spot on the substrate. A first light beam is focused on a surface of the substrate as a spatial reference point. A second light beam then illuminates the scanning probe being used for patterning. An optical microscope images both the focused light beam, and a diffraction pattern, shadow, or light backscattered by the illuminated scanning probe tip of a scanning probe microscope (SPM), which is typically the tip of the scanning probe on an atomic force microscope (AFM). Alignment of the scanning probe tip relative to the mark is then determined by visual observation of the microscope image. This alignment process may be repeated to allow for modification or changing of the scanning probe microscope tip.

Measuring Fluxes Of Heat To A Plasma-Arc Anode

NASA Technical Reports Server (NTRS)

Sankovic, John M.; Menart, James A.; Pfender, Emil; Heberlein, Joachim

1995-01-01

Three probes constructed to provide measurements indicative of conductive, convective, and radiative transfer of heat from free-burning plasma arc to water-cooled copper anode used in generating arc. Each probe consists mainly of copper body with two thermocouples embedded at locations 4 mm apart along length. Thermocouples provide measure of rate of conduction of heat along probe and transfers of heat from plasma to sensing surface at tip of probe. Probes identical except sensing surface of one uncoated and other two coated with different materials to make them sensitive to different components of overall flux of heat.

Scanning probe recognition microscopy investigation of tissue scaffold properties

PubMed Central

Fan, Yuan; Chen, Qian; Ayres, Virginia M; Baczewski, Andrew D; Udpa, Lalita; Kumar, Shiva

2007-01-01

Scanning probe recognition microscopy is a new scanning probe microscopy technique which enables selective scanning along individual nanofibers within a tissue scaffold. Statistically significant data for multiple properties can be collected by repetitively fine-scanning an identical region of interest. The results of a scanning probe recognition microscopy investigation of the surface roughness and elasticity of a series of tissue scaffolds are presented. Deconvolution and statistical methods were developed and used for data accuracy along curved nanofiber surfaces. Nanofiber features were also independently analyzed using transmission electron microscopy, with results that supported the scanning probe recognition microscopy-based analysis. PMID:18203431

Scanning probe recognition microscopy investigation of tissue scaffold properties.

PubMed

Fan, Yuan; Chen, Qian; Ayres, Virginia M; Baczewski, Andrew D; Udpa, Lalita; Kumar, Shiva

2007-01-01

Scanning probe recognition microscopy is a new scanning probe microscopy technique which enables selective scanning along individual nanofibers within a tissue scaffold. Statistically significant data for multiple properties can be collected by repetitively fine-scanning an identical region of interest. The results of a scanning probe recognition microscopy investigation of the surface roughness and elasticity of a series of tissue scaffolds are presented. Deconvolution and statistical methods were developed and used for data accuracy along curved nanofiber surfaces. Nanofiber features were also independently analyzed using transmission electron microscopy, with results that supported the scanning probe recognition microscopy-based analysis.

NMR Studies of Mass Transport in New Conducting Media for Fuel Cells

DTIC Science & Technology

2009-01-01

PEM films, for example those containing phosphoric acid and ionic liquids . Dynamical processes are probed at the short range by spin-lattice...structural environments of muticomponent PEM films, for example those containing phosphoric acid and ionic liquids . Dynamical processes are probed at the...correlation between water diffusivity and proton conductivity in the nanocomposites Transport properties of several ionic liquids (IL’s) and membranes

Deuterated fatty acids as Raman spectroscopic probes of membrane structure.

PubMed

Mendelsohn, R; Sunder, S; Bernstein, H J

1976-09-07

Raman spectra are reported for the C-D stretching region of stearic acid-d35 bound in egg lecithin multilayers. The temperature dependence of the spectra shows that the linewidth of the C-D stretching bands is a sensitive and non-perturbative probe of membrane hydrocarbon chain conformation. The utility of this approach for studying lipid conformation in membranes containing a significant fraction of non-lipid component is discussed.

Chemoselective ratiometric imaging of protein S-sulfenylation.

PubMed

Tom, Christopher T M B; Crellin, John E; Motiwala, Hashim F; Stone, Matthew B; Davda, Dahvid; Walker, William; Kuo, Yu-Hsuan; Hernandez, Jeannie L; Labby, Kristin J; Gomez-Rodriguez, Lyanne; Jenkins, Paul M; Veatch, Sarah L; Martin, Brent R

2017-06-29

Here we report a ratiometric fluorescent probe for chemoselective conjugation to sulfenic acids in living cells. Our approach couples an α-fluoro-substituted dimedone to an aminonaphthalene fluorophore (F-DiNap), which upon sulfenic acid conjugation is locked as the 1,3-diketone, changing the fluorophore excitation. F-DiNap reacts with S-sulfenylated proteins at equivalent rates to current probes, but the α-fluorine substitution blocks side-reactions with biological aldehydes.

Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes.

PubMed

Wang, Yongxiang; Li, Jishan; Wang, Hao; Jin, Jianyu; Liu, Jinhua; Wang, Kemin; Tan, Weihong; Yang, Ronghua

2010-08-01

Conformationally constraint nucleic acid probes were usually designed by forming an intramolecular duplex based on Watson-Crick hydrogen bonds. The disadvantages of these approaches are the inflexibility and instability in complex environment of the Watson-Crick-based duplex. We report that this hydrogen bonding pattern can be replaced by metal-ligation between specific metal ions and the natural bases. To demonstrate the feasibility of this principle, two linear oligonucleotides and silver ions were examined as models for DNA hybridization assay and adenosine triphosphate detection. The both nucleic acids contain target binding sequences in the middle and cytosine (C)-rich sequences at the lateral portions. The strong interaction between Ag(+) ions and cytosines forms stable C-Ag(+)-C structures, which promises the oligonucleotides to form conformationally constraint formations. In the presence of its target, interaction between the loop sequences and the target unfolds the C-Ag(+)-C structures, and the corresponding probes unfolding can be detected by a change in their fluorescence emission. We discuss the thermodynamic and kinetic opportunities that are provided by using Ag(+) ion complexes instead of traditional Watson-Crick-based duplex. In particular, the intrinsic feature of the metal-ligation motif facilitates the design of functional nucleic acids probes by independently varying the concentration of Ag(+) ions in the medium.

Is there evidence for man-made nanoparticles in the Dutch environment?

PubMed

Bäuerlein, Patrick S; Emke, Erik; Tromp, Peter; Hofman, Jan A M H; Carboni, Andrea; Schooneman, Ferry; de Voogt, Pim; van Wezel, Annemarie P

2017-01-15

Only very limited information is available on measured environmental concentrations of nanoparticles. In this study, several environmental compartments in The Netherlands were probed for the presence of nanoparticles. Different types of water were screened for the presence of inorganic (Ag, Au, TiO 2 ) and organic nanoparticles (C 60 , C 70 , [6,6]-phenyl-C 61 -butyric acid octyl ester, [6,6]-phenyl-C 61 -butyric acid butyl ester, [6,6]-phenyl-C 61 -butyric acid methyl ester, [6,6]-bis-phenyl-C 61 -butyric acid methyl ester, [6,6]-phenyl-C 71 -butyric acid methyl ester, [6,6]-thienyl-C 61 -butyric acid methyl ester). Air samples were analysed for the presence of nanoparticulate Mo, Ag, Ce, W, Pd, Pt, Rh, Zn, Ti, Si, B as well as Fe and Cu. ICP-MS, Orbitrap-HRMS, SEM and EDX were used for this survey. Water samples included dune and bank filtrates, surface waters and ground waters as well as influents, effluents and sludge of sewage treatment plants (STPs), and surface waters collected near airports and harbours. Air samples included both urban and rural samples. C 60 was detected in air, sewage treatment plants, influents, effluents and sludge, but in no other aqueous samples despite the low detection limit of 0.1ng/L. C 70 and functionalised fullerenes were not detected at all. In STP sludge and influent the occurrence of Ag and Au nanoparticles was verified by SEM/EDX and ICP-MS. In air up to about 25m% of certain metals was found in the nanosize fraction. Overall, between 1 and 6% of the total mass from metals in the air samples was found in the size fraction <100nm. Copyright © 2016 Elsevier B.V. All rights reserved.

Self-Nulling Eddy Current Probe for Surface and Subsurface Flaw Detection

NASA Technical Reports Server (NTRS)

Wincheski, B.; Fulton, J. P.; Nath, S.; Namkung, M.; Simpson, J. W.

1994-01-01

An eddy current probe which provides a null-signal in the presence of unflawed material without the need for any balancing circuitry has been developed at NASA Langley Research Center. Such a unique capability of the probe reduces set-up time, eliminates tester configuration errors, and decreases instrumentation requirements. The probe is highly sensitive to surface breaking fatigue cracks, and shows excellent resolution for the measurement of material thickness, including material loss due to corrosion damage. The presence of flaws in the material under test causes an increase in the extremely stable and reproducible output voltage of the probe. The design of the probe and some examples illustrating its flaw detection capabilities are presented.

Conserved electrostatic fields at the Ras-effector interface measured through vibrational Stark effect spectroscopy explain the difference in tilt angle in the Ras binding domains of Raf and RalGDS.

PubMed

Walker, David M; Wang, Ruifei; Webb, Lauren J

2014-10-07

Vibrational Stark effect (VSE) spectroscopy was used to measure the electrostatic fields present at the interface of the human guanosine triphosphatase (GTPase) Ras docked with the Ras binding domain (RBD) of the protein kinase Raf. Nine amino acids located on the surface of Raf were selected for labeling with a nitrile vibrational probe. Eight of the probe locations were situated along the interface of Ras and Raf, and one probe was 2 nm away on the opposite side of Raf. Vibrational frequencies of the nine Raf nitrile probes were compared both in the monomeric, solvated protein and when docked with wild-type (WT) Ras to construct a comprehensive VSE map of the Ras-Raf interface. Molecular dynamics (MD) simulations employing an umbrella sampling strategy were used to generate a Boltzmann-weighted ensemble of nitrile positions in both the monomeric and docked complexes to determine the effect that docking has on probe location and orientation and to aid in the interpretation of VSE results. These results were compared to an identical study that was previously conducted on nine nitrile probes on the RBD of Ral guanidine dissociation stimulator (RalGDS) to make comparisons between the docked complexes formed when either of the two effectors bind to WT Ras. This comparison finds that there are three regions of conserved electrostatic fields that are formed upon docking of WT Ras with both downstream effectors. Conservation of this pattern in the docked complex then results in different binding orientations observed in otherwise structurally similar proteins. This work supports an electrostatic cause of the known binding tilt angle between the Ras-Raf and Ras-RalGDS complexes.

Experimental study of the competitive adsorption of HNO3 and H2O on surfaces by using Brewster angle cavity ring-down spectroscopy in the 295-345 nm region.

PubMed

Du, Juan; Keesee, Robert G; Zhu, Lei

2014-09-18

The competitive adsorption of HNO3 and H2O from the gas phase onto fused silica surfaces is investigated. Brewster angle cavity ring-down spectroscopy is used to measure absorption of a laser probe beam by the HNO3/H2O coadsorbed on fused silica surfaces as a function of the mixture pressure. The laser absorption measurements were made in the 295-345 nm region. Langmuir adsorption constants for nitric acid and water were found to be 107 ± 17 and 562 ± 21 Torr(-1), respectively. A method has been developed for calculating absorption by HNO3 and H2O codeposited on the surface as a function of the HNO3/H2O mixture pressure using multicomponent Langmuir adsorption isotherms and absorption cross-sections at a given wavelength for surface-adsorbed HNO3 and H2O. The validity of this treatment has been evaluated both as a function of wavelength and as a function of mixing ratio.

Real time non invasive imaging of fatty acid uptake in vivo

PubMed Central

Henkin, Amy H.; Cohen, Allison S.; Dubikovskaya, Elena A.; Park, Hyo Min; Nikitin, Gennady F.; Auzias, Mathieu G.; Kazantzis, Melissa; Bertozzi, Carolyn R.; Stahl, Andreas

2012-01-01

Detection and quantification of fatty acid fluxes in animal model systems following physiological, pathological, or pharmacological challenges is key to our understanding of complex metabolic networks as these macronutrients also activate transcription factors and modulate signaling cascades including insulin-sensitivity. To enable non-invasive, real-time, spatiotemporal quantitative imaging of fatty acid fluxes in animals, we created a bioactivatable molecular imaging probe based on long-chain fatty acids conjugated to a reporter molecule (luciferin). We show that this probe faithfully recapitulates cellular fatty acid uptake and can be used in animal systems as a valuable tool to localize and quantitate in real-time lipid fluxes such as intestinal fatty acid absorption and brown adipose tissue activation. This imaging approach should further our understanding of basic metabolic processes and pathological alterations in multiple disease models. PMID:22928772

Toward a solid-phase nucleic acid hybridization assay within microfluidic channels using immobilized quantum dots as donors in fluorescence resonance energy transfer.

PubMed

Chen, Lu; Algar, W Russ; Tavares, Anthony J; Krull, Ulrich J

2011-01-01

The optical properties and surface area of quantum dots (QDs) have made them an attractive platform for the development of nucleic acid biosensors based on fluorescence resonance energy transfer (FRET). Solid-phase assays based on FRET using mixtures of immobilized QD-oligonucleotide conjugates (QD biosensors) have been developed. The typical challenges associated with solid-phase detection strategies include non-specific adsorption, slow kinetics of hybridization, and sample manipulation. The new work herein has considered the immobilization of QD biosensors onto the surfaces of microfluidic channels in order to address these challenges. Microfluidic flow can be used to dynamically control stringency by adjustment of the potential in an electrokinetic-based microfluidics environment. The shearing force, Joule heating, and the competition between electroosmotic and electrophoretic mobilities allow the optimization of hybridization conditions, convective delivery of target to the channel surface to speed hybridization, amelioration of adsorption, and regeneration of the sensing surface. Microfluidic flow can also be used to deliver (for immobilization) and remove QD biosensors. QDs that were conjugated with two different oligonucleotide sequences were used to demonstrate feasibility. One oligonucleotide sequence on the QD was available as a linker for immobilization via hybridization with complementary oligonucleotides located on a glass surface within a microfluidic channel. A second oligonucleotide sequence on the QD served as a probe to transduce hybridization with target nucleic acid in a sample solution. A Cy3 label on the target was excited by FRET using green-emitting CdSe/ZnS QD donors and provided an analytical signal to explore this detection strategy. The immobilized QDs could be removed under denaturing conditions by disrupting the duplex that was used as the surface linker and thus allowed a new layer of QD biosensors to be re-coated within the channel for re-use of the microfluidic chip.

Catalytic and electrocatalytic oxidation of ethanol over palladium-based nanoalloy catalysts.

PubMed

Yin, Jun; Shan, Shiyao; Ng, Mei Shan; Yang, Lefu; Mott, Derrick; Fang, Weiqin; Kang, Ning; Luo, Jin; Zhong, Chuan-Jian

2013-07-23

The control of the nanoscale composition and structure of alloy catalysts plays an important role in heterogeneous catalysis. This paper describes novel findings of an investigation for Pd-based nanoalloy catalysts (PdCo and PdCu) for ethanol oxidation reaction (EOR) in gas phase and alkaline electrolyte. Although the PdCo catalyst exhibits a mass activity similar to Pd, the PdCu catalyst is shown to display a much higher mass activity than Pd for the electrocatalytic EOR in alkaline electrolyte. This finding is consistent with the finding on the surface enrichment of Pd on the alloyed PdCu surface, in contrast to the surface enrichment of Co in the alloyed PdCo surface. The viability of C-C bond cleavage was also probed for the PdCu catalysts in both gas-phase and electrolyte-phase EOR. In the gas-phase reaction, although the catalytic conversion rate for CO2 product is higher over Pd than PdCu, the nanoalloy PdCu catalyst appears to suppress the formation of acetic acid, which is a significant portion of the product in the case of pure Pd catalyst. In the alkaline electrolyte, CO2 was detected from the gas phase above the electrolyte upon acid treatment following the electrolysis, along with traces of aldehyde and acetic acid. An analysis of the electrochemical properties indicates that the oxophilicity of the base metal alloyed with Pd, in addition to the surface enrichment of metals, may have played an important role in the observed difference of the catalytic and electrocatalytic activities. In comparison with Pd alloyed with Co, the results for Pd alloyed with Cu showed a more significant positive shift of the reduction potential of the oxygenated Pd species on the surface. These findings have important implications for further fine-tuning of the Pd nanoalloys in terms of base metal composition toward highly active and selective catalysts for EOR.

Molecularly imprinted polymer-matrix nanocomposite for enantioselective electrochemical sensing of D- and L-aspartic acid.

PubMed

Prasad, Bhim Bali; Srivastava, Amrita; Tiwari, Mahavir Prasad

2013-10-01

A new molecularly imprinted polymer-matrix (titanium dioxide nanoparticle/multiwalled carbon nanotubes) nanocomposite was developed for the modification of pencil graphite electrode as an enantioselective sensing probe for aspartic acid isomers, prevalent at ultra trace level in aqueous and real samples. The nanocomposite having many shape complementary cavities was synthesized adopting surface initiated-activators regenerated by electron transfer for atom transfer radical polymerization. The proposed sensor has high stability, nanocomposite uniformity, good reproducibility, and enhanced electrocatalytic activity to respond oxidative peak current of L-aspartic acid quantitatively by differential pulse anodic stripping voltammetry, without any cross-reactivity in real samples. Under the optimized operating conditions, the L-aspartic acid imprinted modified electrode showed a wide linear response for L-aspartic acid within the concentration range 9.98-532.72 ng mL(-1), with the minimum detection limit of 1.73-1.79 ng mL(-1) (S/N=3) in aqueous and real samples. Almost similar stringent limit (1.79 ng mL(-1)) was obtained with cerebrospinal fluid which is typical for the primitive diagnosis of neurological disorders, caused by an acute depletion of L-aspartic acid biomarker, in clinical settings. Copyright © 2013 Elsevier B.V. All rights reserved.