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Sample records for chemically modified oligonucleotides

  1. Characterization of chemically modified oligonucleotides targeting a pathogenic mutation in human mitochondrial DNA.

    PubMed

    Tonin, Yann; Heckel, Anne-Marie; Dovydenko, Ilya; Meschaninova, Mariya; Comte, Caroline; Venyaminova, Alya; Pyshnyi, Dmitrii; Tarassov, Ivan; Entelis, Nina

    2014-05-01

    Defects in mitochondrial genome can cause a wide range of clinical disorders, mainly neuromuscular diseases. Most of the deleterious mitochondrial mutations are heteroplasmic, meaning that wild type and mutated forms of mtDNA coexist in the same cell. Therefore, a shift in the proportion between mutant and wild type molecules could restore mitochondrial functions. The anti-replicative strategy aims to induce such a shift in heteroplasmy by mitochondrial targeting specifically designed molecules in order to inhibit replication of mutant mtDNA. Recently, we developed mitochondrial RNA vectors that can be used to address anti-replicative oligoribonucleotides into human mitochondria and impact heteroplasmy level, however, the effect was mainly transient, probably due to a rapid degradation of RNA molecules. In the present study, we introduced various chemically modified oligonucleotides in anti-replicative RNAs. We show that the most important increase of anti-replicative molecules' lifetime can be achieved by using synthetic RNA-DNA chimerical molecules or by ribose 2'-O-methylation in nuclease-sensitive sites. The presence of inverted thymidine at 3' terminus and modifications of 2'-OH ribose group did not prevent the mitochondrial uptake of the recombinant molecules. All the modified oligonucleotides were able to anneal specifically with the mutant mtDNA fragment, but not with the wild-type one. Nevertheless, the modified oligonucleotides did not cause a significant effect on the heteroplasmy level in transfected transmitochondrial cybrid cells bearing a pathogenic mtDNA deletion, proving to be less efficient than non-modified RNA molecules.

  2. 2'-modified nucleosides for site-specific labeling of oligonucleotides

    NASA Technical Reports Server (NTRS)

    Krider, Elizabeth S.; Miller, Jeremiah E.; Meade, Thomas J.

    2002-01-01

    We report the synthesis of 2'-modified nucleosides designed specifically for incorporating labels into oligonucleotides. Conversion of these nucleosides to phosphoramidite and solid support-bound derivatives proceeds in good yield. Large-scale synthesis of 11-mer oligonucleotides possessing the 2'-modified nucleosides is achieved using these derivatives. Thermal denaturation studies indicate that the presence of 2'-modified nucleosides in 11-mer duplexes has minimal destabilizing effects on the duplex structure when the nucleosides are placed at the duplex termini. The powerful combination of phosphoramidite and support-bound derivatives of 2'-modified nucleosides affords the large-scale preparation of an entirely new class of oligonucleotides. The ability to synthesize oligonucleotides containing label attachment sites at 3', intervening, and 5' locations of a duplex is a significant advance in the development of oligonucleotide conjugates.

  3. Monitoring integrity and localization of modified single-stranded RNA oligonucleotides using ultrasensitive fluorescence methods

    PubMed Central

    Hadwiger, Philipp; Wagner, Ernst; Lamb, Don C.

    2017-01-01

    Short single-stranded oligonucleotides represent a class of promising therapeutics with diverse application areas. Antisense oligonucleotides, for example, can interfere with various processes involved in mRNA processing through complementary base pairing. Also RNA interference can be regulated by antagomirs, single-stranded siRNA and single-stranded microRNA mimics. The increased susceptibility to nucleolytic degradation of unpaired RNAs can be counteracted by chemical modification of the sugar phosphate backbone. In order to understand the dynamics of such single-stranded RNAs, we investigated their fate after exposure to cellular environment by several fluorescence spectroscopy techniques. First, we elucidated the degradation of four differently modified, dual-dye labeled short RNA oligonucleotides in HeLa cell extracts by fluorescence correlation spectroscopy, fluorescence cross-correlation spectroscopy and Förster resonance energy transfer. We observed that the integrity of the oligonucleotide sequence correlates with the extent of chemical modifications. Furthermore, the data showed that nucleolytic degradation can only be distinguished from unspecific effects like aggregation, association with cellular proteins, or intramolecular dynamics when considering multiple measurement and analysis approaches. We also investigated the localization and integrity of the four modified oligonucleotides in cultured HeLa cells using fluorescence lifetime imaging microscopy. No intracellular accumulation could be observed for unmodified oligonucleotides, while completely stabilized oligonucleotides showed strong accumulation within HeLa cells with no changes in fluorescence lifetime over 24 h. The integrity and accumulation of partly modified oligonucleotides was in accordance with their extent of modification. In highly fluorescent cells, the oligonucleotides were transported to the nucleus. The lifetime of the RNA in the cells could be explained by a balance between

  4. Synthesis of 3'-, or 5'-, or internal methacrylamido-modified oligonucleotides

    DOEpatents

    Golova, Julia B.; Chernov, Boris K.

    2010-04-27

    New modifiers were synthesized for incorporation of a methacrylic function in 3'-, 5'- and internal positions of oligonucleotides during solid phase synthesis. A modifier was used for synthesis of 5'-methacrylated oligonucleotides for preparation of microarrays by a co-polymerization method.

  5. Drop drying on surfaces determines chemical reactivity - the specific case of immobilization of oligonucleotides on microarrays

    PubMed Central

    2013-01-01

    Background Drop drying is a key factor in a wide range of technical applications, including spotted microarrays. The applied nL liquid volume provides specific reaction conditions for the immobilization of probe molecules to a chemically modified surface. Results We investigated the influence of nL and μL liquid drop volumes on the process of probe immobilization and compare the results obtained to the situation in liquid solution. In our data, we observe a strong relationship between drop drying effects on immobilization and surface chemistry. In this work, we present results on the immobilization of dye labeled 20mer oligonucleotides with and without an activating 5′-aminoheptyl linker onto a 2D epoxysilane and a 3D NHS activated hydrogel surface. Conclusions Our experiments identified two basic processes determining immobilization. First, the rate of drop drying that depends on the drop volume and the ambient relative humidity. Oligonucleotides in a dried spot react unspecifically with the surface and long reaction times are needed. 3D hydrogel surfaces allow for immobilization in a liquid environment under diffusive conditions. Here, oligonucleotide immobilization is much faster and a specific reaction with the reactive linker group is observed. Second, the effect of increasing probe concentration as a result of drop drying. On a 3D hydrogel, the increasing concentration of probe molecules in nL spotting volumes accelerates immobilization dramatically. In case of μL volumes, immobilization depends on whether the drop is allowed to dry completely. At non-drying conditions, very limited immobilization is observed due to the low oligonucleotide concentration used in microarray spotting solutions. The results of our study provide a general guideline for microarray assay development. They allow for the initial definition and further optimization of reaction conditions for the immobilization of oligonucleotides and other probe molecule classes to different

  6. Effect of 2′-O-methyl/thiophosphonoacetate-modified antisense oligonucleotides on huntingtin expression in patient-derived cells

    PubMed Central

    Matsui, Masayuki; Threlfall, Richard N; Caruthers, Marvin H; Corey, David R

    2014-01-01

    ABSTRACT Optimizing oligonucleotides as therapeutics will require exploring how chemistry can be used to enhance their effects inside cells. To achieve this goal it will be necessary to fully explore chemical space around the native DNA/RNA framework to define the potential of diverse chemical modifications. In this report we examine the potential of thiophosphonoacetate (thioPACE)-modified 2′-O-methyl oligoribonucleotides as inhibitors of human huntingtin (HTT) expression. Inhibition occurred, but was less than with analogous locked nucleic acid (LNA)-substituted oligomers lacking the thioPACE modification. These data suggest that thioPACE oligonucleotides have the potential to control gene expression inside cells. However, advantages relative to other modifications were not demonstrated. Additional modifications are likely to be necessary to fully explore any potential advantages of thioPACE substitutions. PMID:26865404

  7. Inhibition Of Molecular And Biological Processes Using Modified Oligonucleotides

    DOEpatents

    Kozyavkin, Sergei A.; Malykh, Andrei G.; Polouchine, Nikolai N.; Slesarev, Alexei I.

    2003-04-15

    A method of inhibiting at least one molecular process in a sample, comprising administering to the sample an oligonucleotide or polynucleotide containing at least one monomeric unit having formula (I): wherein A is an organic moiety, n is at least 1, and each X is independently selected from the group consisting of --NRCOCONu, --NHCOCR.sub.2 CR.sub.2 CONu, --NHCOCR.dbd.CRCONu, and --NHCOSSCONu, wherein each R independently represents H or a substituted or unsubstituted alkyl group, and Nu represents a nucleophile, or a salt of the compound.

  8. 2-O-[2-(Methylthio)ethyl]-Modified Oligonucleotide: An Analog of 2-O-[2-(Methoxy)ethyl]-Modified Oligonucleotide with Improved Protein Binding Properties and High Binding Affinity to Target RNA

    SciTech Connect

    Prakash, T.P.; Manoharan, M.; Fraser, A.S.; Kawasaki, A.M.; Lesnik, E.; Sioufi, N.; Leeds, J.M.; Teplova, M.; Egli, M.

    2010-03-08

    A novel 2'-modification, 2'-O-[2-(methylthio)ethyl] or 2'-O-MTE, has been incorporated into oligonucleotides and evaluated for properties relevant to antisense activity. The results were compared with the previously characterized 2'-O-[2-(methoxy)ethyl] 2'-O-MOE modification. As expected, the 2'-O-MTE modified oligonucleotides exhibited improved binding to human serum albumin compared to the 2'-O-MOE modified oligonucleotides. The 2'-O-MTE oligonucleotides maintained high binding affinity to target RNA. Nuclease digestion of 2'-O-MTE oligonucleotides showed that they have limited resistance to exonuclease degradation. We analyzed the crystal structure of a decamer DNA duplex containing the 2'-O-MTE modifcation. Analysis of the crystal structure provides insight into the improved RNA binding affinity, protein binding affinity and limited resistance of 2'-O-MTE modified oligonucleotides to exonuclease degradation.

  9. Ribonuclease H1-dependent hepatotoxicity caused by locked nucleic acid-modified gapmer antisense oligonucleotides

    PubMed Central

    Kasuya, Takeshi; Hori, Shin-ichiro; Watanabe, Ayahisa; Nakajima, Mado; Gahara, Yoshinari; Rokushima, Masatomo; Yanagimoto, Toru; Kugimiya, Akira

    2016-01-01

    Gapmer antisense oligonucleotides cleave target RNA effectively in vivo, and is considered as promising therapeutics. Especially, gapmers modified with locked nucleic acid (LNA) shows potent knockdown activity; however, they also cause hepatotoxic side effects. For developing safe and effective gapmer drugs, a deeper understanding of the mechanisms of hepatotoxicity is required. Here, we investigated the cause of hepatotoxicity derived from LNA-modified gapmers. Chemical modification of gapmer’s gap region completely suppressed both knockdown activity and hepatotoxicity, indicating that the root cause of hepatotoxicity is related to intracellular gapmer activity. Gene silencing of hepatic ribonuclease H1 (RNaseH1), which catalyses gapmer-mediated RNA knockdown, strongly supressed hepatotoxic effects. Small interfering RNA (siRNA)-mediated knockdown of a target mRNA did not result in any hepatotoxic effects, while the gapmer targeting the same position on mRNA as does the siRNA showed acute toxicity. Microarray analysis revealed that several pre-mRNAs containing a sequence similar to the gapmer target were also knocked down. These results suggest that hepatotoxicity of LNA gapmer is caused by RNAseH1 activity, presumably because of off-target cleavage of RNAs inside nuclei. PMID:27461380

  10. Sequence selective naked-eye detection of DNA harnessing extension of oligonucleotide-modified nucleotides.

    PubMed

    Verga, Daniela; Welter, Moritz; Marx, Andreas

    2016-02-01

    DNA polymerases can efficiently and sequence selectively incorporate oligonucleotide (ODN)-modified nucleotides and the incorporated oligonucleotide strand can be employed as primer in rolling circle amplification (RCA). The effective amplification of the DNA primer by Φ29 DNA polymerase allows the sequence-selective hybridisation of the amplified strand with a G-quadruplex DNA sequence that has horse radish peroxidase-like activity. Based on these findings we develop a system that allows DNA detection with single-base resolution by naked eye.

  11. Extracellular delivery of modified oligonucleotide and superparamagnetic iron oxide nanoparticles from a degradable hydrogel triggered by tumor acidosis.

    PubMed

    Lin, Ching-Wen; Tseng, S-Ja; Kempson, Ivan M; Yang, Shuenn-Chen; Hong, Tse-Ming; Yang, Pan-Chyr

    2013-06-01

    Chemically modified antisense RNA oligonucleotides (antagomir) offer promise for cancer therapies but suffer from poor therapeutic effect after systemic administration. Chemical modification or loading in degradable hydrogels can offer improvements in the accuracy and efficacy for sustained delivery at specific sites. In our approach, antagomir were entrapped with degradable poly(ethylene glycol) (PEG)-based hydrogels, with and without incorporation of imidazole. Superparamagnetic iron oxide nanoparticles (SPION) were simultaneously loaded with intent for magnetic resonance imaging (MRI). The incorporation of imidazole into the PEG hydrogels led to a tunable-pH-response that dictated hydrogel swelling ratio and release rate of antagomir and SPION. As a result, the PEG-imidazole hydrogel swelling ratio and degradation over a 5 week period changed up to 734% and 149% as the pH dropped from 7.4 to 6.7, respectively. The swelling ratio of PEG-imidazole hydrogels was completely reversible over repeatable cycles of pH change. The stimuli-responsive behavior of PEG-imidazole hydrogels was used for the release of antagomir and SPION under conditions consistent with tumor acidosis. This manuscript demonstrates feasibility in designing tunable-pH-responsive hydrogels for loading multimodality therapeutic and contrast agents to enhance the bioactivity of chemically modified antisense RNA oligonucleotide and SPION for acidosis-related tumor therapy and MRI imaging applications.

  12. A High-Fidelity Codon Set for the T4 DNA Ligase-Catalyzed Polymerization of Modified Oligonucleotides.

    PubMed

    Lei, Yi; Kong, Dehui; Hili, Ryan

    2015-12-14

    In vitro selection of nucleic acid polymers can readily deliver highly specific receptors and catalysts for a variety of applications; however, it is suspected that the functional group deficit of nucleic acids has limited their potential with respect to proteinogenic polymers. This has stimulated research toward expanding their chemical diversity to bridge the functional gap between nucleic acids and proteins to develop a superior biopolymer. In this study, we investigate the effect of codon library size and composition on the sequence specificity of T4 DNA ligase in the DNA-templated polymerization of both unmodified and modified oligonucleotides. Using high-throughput DNA sequencing of duplex pairs, we have uncovered a 256-membered codon set that yields sequence-defined modified ssDNA polymers in high yield and with high fidelity.

  13. The Role of Fluorinated Alcohols as Mobile Phase Modifiers for LC-MS Analysis of Oligonucleotides

    NASA Astrophysics Data System (ADS)

    Basiri, Babak; van Hattum, Hilde; van Dongen, William D.; Murph, Mandi M.; Bartlett, Michael G.

    2017-01-01

    Hexafluoroisopropanol (HFIP) has been widely used as an acidic modifier for mobile phases for liquid chromatography-mass spectrometry (LC-MS) analysis of oligonucleotides ever since the first report of its use for this purpose. This is not surprising, considering the exceptional performance of HFIP compared with carboxylic acids, which cause significant MS signal suppression in electrospray ionization. However, we have found that other fluorinated alcohols can also be utilized for mobile phase preparation and the choice of optimal fluorinated alcohol is determined by the ion-pairing (IP) agent. Although HFIP is a very good choice to be used alongside less hydrophobic IP agents, other fluorinated alcohols such as 1,1,1,3,3,3-hexafluoro-2-methyl-2-propanol (HFMIP) can significantly outperform HFIP when used with more hydrophobic IP agents. We also found that more acidic fluorinated alcohols assist with the transfer of oligonucleotides with secondary structure (e.g., folded strands and hairpins) into the gas phase.

  14. De novo sequencing of highly modified therapeutic oligonucleotides by hydrophobic tag sequencing coupled with LC-MS.

    PubMed

    Goto, R; Miyakawa, S; Inomata, E; Takami, T; Yamaura, J; Nakamura, Y

    2017-02-01

    Correct sequences are prerequisite for quality control of therapeutic oligonucleotides. However, there is no definitive method available for determining sequences of highly modified therapeutic RNAs, and thereby, most of the oligonucleotides have been used clinically without direct sequence determination. In this study, we developed a novel sequencing method called 'hydrophobic tag sequencing'. Highly modified oligonucleotides are sequenced by partially digesting oligonucleotides conjugated with a 5'-hydrophobic tag, followed by liquid chromatography-mass spectrometry analysis. 5'-Hydrophobic tag-printed fragments (5'-tag degradates) can be separated in order of their molecular masses from tag-free oligonucleotides by reversed-phase liquid chromatography. As models for the sequencing, the anti-VEGF aptamer (Macugen) and the highly modified 38-mer RNA sequences were analyzed under blind conditions. Most nucleotides were identified from the molecular weight of hydrophobic 5'-tag degradates calculated from monoisotopic mass in simple full mass data. When monoisotopic mass could not be assigned, the nucleotide was estimated using the molecular weight of the most abundant mass. The sequences of Macugen and 38-mer RNA perfectly matched the theoretical sequences. The hydrophobic tag sequencing worked well to obtain simple full mass data, resulting in accurate and clear sequencing. The present study provides for the first time a de novo sequencing technology for highly modified RNAs and contributes to quality control of therapeutic oligonucleotides. Copyright © 2016 John Wiley & Sons, Ltd.

  15. Oligonucleotide-templated chemical reactions: pushing the boundaries of a nature-inspired process.

    PubMed

    Percivalle, Claudia; Bartolo, Jean-François; Ladame, Sylvain

    2013-01-07

    Widespread in nature, oligonucleotide-templated reactions of phosphodiester bond formation have inspired chemists who are now applying this elegant strategy to the catalysis of a broad range of otherwise inefficient reactions. This review highlights the increasing diversity of chemical reactions that can be efficiently catalysed by an oligonucleotide template, using Watson-Crick base-pairing to bring both reagents in close enough proximity to react, thus increasing significantly their effective molarity. The applications of this elegant concept for nucleic acid sensing and controlled organic synthesis will also be discussed.

  16. Automated synthesis of new ferrocenyl-modified oligonucleotides: study of their properties in solution

    PubMed Central

    Navarro, Aude-Emmanuelle; Spinelli, Nicolas; Moustrou, Corinne; Chaix, Carole; Mandrand, Bernard; Brisset, Hugues

    2004-01-01

    We have developed new ferrocenyl-modified oligonucleotide (ODN) probes for electrochemical DNA sensors. A monofunctional ferrocene containing phosphoramidite group has been prepared, and a new bisfunctional ferrocene containing phosphoramidite and dimethoxytrityl (DMT) groups has been developed. These ferrocenyl-phosphoramidites have been directly employed in an automated solid-phase DNA synthesizer using phosphoramidite chemistry. The advantages of this method are that it allows a non-specialist in nucleotide chemistry to access labeled ODNs and that it has demonstrated good results. ODNs modified at the 3′ and/or 5′ extremities have been prepared, with the incorporation of the ferrocenyl group into the chain. The 5′ position appears to be more important due to its particular behavior. The thermal stability and electrochemical properties of these new ODN ferrocenes were analyzed before and after hybridization with different ODNs. The feasibility of using these new ferrocenyl-labeled ODNs in DNA sensors has been demonstrated. PMID:15466597

  17. Synthesis and Biophysical Investigations of Oligonucleotides Containing Galactose-Modified DNA, LNA, and 2'-Amino-LNA Monomers.

    PubMed

    Ries, Annika; Kumar, Rajesh; Lou, Chenguang; Kosbar, Tamer; Vengut-Climent, Empar; Jørgensen, Per T; Morales, Juan C; Wengel, Jesper

    2016-11-18

    Galactose-modified thymidine, LNA-T, and 2'-amino-LNA-T nucleosides were synthesized, converted into the corresponding phosphoramidite derivatives and introduced into short oligonucleotides. Compared to the unmodified control strands, the galactose-modified oligonucleotides in general, and the N2'-functionalized 2'-amino-LNA derivatives in particular, showed improved duplex thermal stability against DNA and RNA complements and increased ability to discriminate mismatches. In addition, the 2'-amino-LNA-T derivatives induced remarkable 3'-exonuclease resistance. These results were further investigated using molecular modeling studies.

  18. Lipid-modified G4-decoy oligonucleotide anchored to nanoparticles: delivery and bioactivity in pancreatic cancer cells

    PubMed Central

    Cogoi, S.; Jakobsen, U.; Pedersen, E. B.; Vogel, S.; Xodo, L. E.

    2016-01-01

    KRAS is mutated in >90% of pancreatic ductal adenocarcinomas. As its inactivation leads to tumour regression, mutant KRAS is considered an attractive target for anticancer drugs. In this study we report a new delivery strategy for a G4-decoy oligonucleotide that sequesters MAZ, a transcription factor essential for KRAS transcription. It is based on the use of palmitoyl-oleyl-phosphatidylcholine (POPC) liposomes functionalized with lipid-modified G4-decoy oligonucleotides and a lipid-modified cell penetrating TAT peptide. The potency of the strategy in pancreatic cancer cells is demonstrated by cell cytometry, confocal microscopy, clonogenic and qRT-PCR assays. PMID:27929127

  19. Lipid-modified oligonucleotide conjugates: Insights into gene silencing, interaction with model membranes and cellular uptake mechanisms.

    PubMed

    Ugarte-Uribe, Begoña; Grijalvo, Santiago; Pertíñez, Samuel Núñez; Busto, Jon V; Martín, César; Alagia, Adele; Goñi, Félix M; Eritja, Ramón; Alkorta, Itziar

    2017-01-01

    The ability of oligonucleotides to silence specific genes or inhibit the biological activity of specific proteins has generated great interest in their use as research tools and therapeutic agents. Unfortunately, their biological applications meet the limitation of their poor cellular accessibility. Developing an appropriate delivery system for oligonucleotides is essential to achieve their efficient cellular uptake. In the present work a series of phosphorothioate lipid-oligonucleotide hybrids were synthesized introducing covalently single or double lipid tails at both 3'- and 5'-termini of an antisense oligonucleotide. Gene transfections in cultured cells showed antisense luciferase inhibition without the use of a transfecting agent for conjugates modified with the double-lipid tail at 5'-termini. The effect of the double lipid-tailed modification was further studied in detail in several model membrane systems as well as in cellular uptake experiments. During these studies the spontaneous formation of self-assembled microstructures is clearly observed. Lipidation allowed the efficient incorporation of the oligonucleotide in HeLa cells by a macropinocytosis mechanism without causing cytotoxicity in cells or altering the binding properties of the oligonucleotide conjugates. In addition, both single- and double-tailed compounds showed a similar behavior in lipid model membranes, making them useful in nucleotide-based technologies.

  20. Improved Genome Editing Efficiency and Flexibility Using Modified Oligonucleotides with TALEN and CRISPR-Cas9 Nucleases.

    PubMed

    Renaud, Jean-Baptiste; Boix, Charlotte; Charpentier, Marine; De Cian, Anne; Cochennec, Julien; Duvernois-Berthet, Evelyne; Perrouault, Loïc; Tesson, Laurent; Edouard, Joanne; Thinard, Reynald; Cherifi, Yacine; Menoret, Séverine; Fontanière, Sandra; de Crozé, Noémie; Fraichard, Alexandre; Sohm, Frédéric; Anegon, Ignacio; Concordet, Jean-Paul; Giovannangeli, Carine

    2016-03-08

    Genome editing has now been reported in many systems using TALEN and CRISPR-Cas9 nucleases. Precise mutations can be introduced during homology-directed repair with donor DNA carrying the wanted sequence edit, but efficiency is usually lower than for gene knockout and optimal strategies have not been extensively investigated. Here, we show that using phosphorothioate-modified oligonucleotides strongly enhances genome editing efficiency of single-stranded oligonucleotide donors in cultured cells. In addition, it provides better design flexibility, allowing insertions more than 100 bp long. Despite previous reports of phosphorothioate-modified oligonucleotide toxicity, clones of edited cells are readily isolated and targeted sequence insertions are achieved in rats and mice with very high frequency, allowing for homozygous loxP site insertion at the mouse ROSA locus in particular. Finally, when detected, imprecise knockin events exhibit indels that are asymmetrically positioned, consistent with genome editing taking place by two steps of single-strand annealing.

  1. DETECTING LOW-LEVEL SYNTHESIS IMPURITIES IN MODIFIED PHOSPHOROTHIOATE OLIGONUCLEOTIDES USING LIQUID CHROMATOGRAPHY – HIGH RESOLUTION MASS SPECTROMETRY

    PubMed Central

    Nikcevic, Irena; Wyrzykiewicz, Tadeusz K.; Limbach, Patrick A.

    2010-01-01

    Summary An LC-MS method based on the use of high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS) for profiling oligonucleotides synthesis impurities is described. Oligonucleotide phosphorothioatediesters (phosphorothioate oligonucleotides), in which one of the non-bridging oxygen atoms at each phosphorus center is replaced by a sulfur atom, are now one of the most popular oligonucleotide modifications due to their ease of chemical synthesis and advantageous pharmacokinetic properties. Despite significant progress in the solid-phase oligomerization chemistry used in the manufacturing of these oligonucleotides, multiple classes of low-level impurities always accompany synthetic oligonucleotides. Liquid chromatography-mass spectrometry has emerged as a powerful technique for the identification of these synthesis impurities. However, impurity profiling, where the entire complement of low-level synthetic impurities is identified in a single analysis, is more challenging. Here we present an LC-MS method based the use of high resolution-mass spectrometry, specifically Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS or FTMS). The optimal LC-FTMS conditions, including the stationary phase and mobile phases for the separation and identification of phosphorothioate oligonucleotides, were found. The characteristics of FTMS enable charge state determination from single m/z values of low-level impurities. Charge state information then enables more accurate modeling of the detected isotopic distribution for identification of the chemical composition of the detected impurity. Using this approach, a number of phosphorothioate impurities can be detected by LC-FTMS including failure sequences carrying 3′-terminal phosphate monoester and 3′-terminal phosphorothioate monoester, incomplete backbone sulfurization and desulfurization products, high molecular weight impurities, and chloral, isobutyryl, and N3 (2-cyanoethyl) adducts

  2. Development of a Novel Oligonucleotide Array for Genomic Screening of Chemical Warfare Agent Exposure in Guinea Pigs and Swine

    DTIC Science & Technology

    2004-04-01

    respectively. To address this gap in research tools, we have developed an oligonucleotide microarray that contains representative genes from guinea pig...To address this gap in research tools, we have developed an oligonucleotide microarray that contains representative genes from guinea pig...toxicogenomics. Toxicogenomics is focused on identifying changes in gene expression in response to a toxic chemical and then using that information to

  3. [Identification of genetically modified vegetable sources in food and feed using hydrogel oligonucleotide microchip].

    PubMed

    Griadunov, D A; Getman, I A; Chizhova, S I; Mikhaĭlovich, V M; Zasedatelev, A S; Romanov, G A

    2011-01-01

    A method of multiplex polymerase chain reaction (PCR) followed by the hybridization on a hydrogel oligonucleotide biochip was developed for simultaneous identification of ten different transgenic elements of plant DNA in feed and food products. The biochip contained 22 immobilized probes intended for (i) detection of plant DNA; (ii) plant species determination (soybean, maize, potato, rice); (iii) identification of transgenic elements, including 35S CaMV, 35S FMV, rice actine gene promoters, nos, 35S CaMV, ocs, pea rbcS1 gene terminators, and bar, gus, nptII marker genes. The limit of detection was 0.5% of genetically modified (GM) soybean and maize in analyzed samples. Identification of transgenic DNA in food and feed products using either the developed approach or real-time PCR led to virtually identical results. The assay can be used for selection of GM samples by screening food and feed products for subsequent quantitative determination of the GM component based on the identified transgene.

  4. Chemically Modified Electrodes for Electrocatalysis.

    DTIC Science & Technology

    1981-09-08

    TECHNICAL REPORT NO. 18 CHEMICALLY MODIFIED ELECTRODES FOR ELECTROCATALYSIS BY Royce W. Murray Prepared for Publication in the Philosophical Transactions of...Report) 0~. SUPPLEMENTARY NOTF.3 13. KEY WORDS (Continue, on favors. side 11 neceasey sad Idenifi by block nsumber) electrocatalysis , redox polymer...electrocataWlytic behavior of monomolecular and multimolecular layers are discussed; electrocatalysi * in the latter circumstance can include reaction rate elements

  5. Oligonucleotide-modified screen-printed gold electrodes for enzyme-amplified sensing of nucleic acids.

    PubMed

    Carpini, Guido; Lucarelli, Fausto; Marrazza, Giovanna; Mascini, Marco

    2004-09-15

    An electrochemical genosensor for the detection of specific sequences of DNA has been developed using disposable screen-printed gold electrodes. Screen-printed gold electrodes were firstly modified with a mixed monolayer of a 25-mer thiol-tethered DNA probe and a spacer thiol, 6-mercapto-1-hexanol (MCH). The DNA probe sequence was internal to the sequence of the 35S promoter, which sequence is inserted in the genome of GMOs regulating the transgene expression. An enzyme-amplified detection scheme, based on the coupling of a streptavidin-alkaline phosphatase conjugate and biotinylated target sequences was then applied. The enzyme catalysed the hydrolysis of the electroinactive alpha-naphthyl phosphate to alpha-naphthol; this product is electroactive and has been detected by means of differential pulse voltammetry. The assay was, firstly, characterised using synthetic oligonucleotides. Relevant parameters, such as the probe concentration and the immobilisation time, the use of the MCH and different enzymatic conjugates, were investigated and optimised. The genosensor response was found to be linearly related to the target concentration between 0 and 25 nmol/L; the detection limit was 0.25 nmol/L. The analytical procedure was then applied for the detection of the 35S promoter sequence, which was amplified from the pBI121 plasmid by polymerase chain reaction (PCR). Hybridisation conditions (i.e., hybridisation buffer and hybridisation time) were further optimised. The selectivity of the assay was confirmed using biotinylated non-complementary amplicons and PCR blanks. The results showed that the genosensor enabled sensitive (detection limit: 1 nmol/L) and specific detection of GMO-related sequences, thus providing a useful tool for the screening analysis of bioengineered food samples.

  6. Simultaneous rapid chemical synthesis of over one hundred oligonucleotides on a microscale

    PubMed Central

    Matthes, Hans W.D.; Zenke, W. Martin; Grundström, Thomas; Staub, Adrien; Wintzerith, Marguerite; Chambon, Pierre

    1984-01-01

    An inexpensive, extremely rapid manual method for simultaneous synthesis of large numbers of oligodeoxyribonucleotides on 50 or 150 nanomole scale is described. The oligonucleotides are assembled in parallel by the phosphotriester method on small cellulose paper disks in a simple gas pressure-controlled continuous-flow system. For each addition of a nucleotide the disks are sorted into four sets which are placed in four columns for addition of A, C, G and T, respectively. During one 2-week period, three rounds of synthesis by this method yielded 254 oligomers (8- to 22-mers), many of which were also purified during this time. Using 50 nanomole scale reactions the yields for 17-mers, for example, were in the range of 0.5 O.D.260 units (˜5 nmol, i.e., ˜10% yield), an amount sufficient for most purposes. The equipment required is relatively inexpensive and for the most part usually already available in molecular biology laboratories. All chemicals are commercially available and the current reagent cost per oligonucleotide (25 μg, average length 17-mer) is ˜3 US dollars. ImagesFig. 1.Fig. 3.Fig. 4.Fig. 5. PMID:16453516

  7. Detection of genetically modified canola using multiplex PCR coupled with oligonucleotide microarray hybridization.

    PubMed

    Schmidt, Anna-Mary; Sahota, Robert; Pope, Derek S; Lawrence, Tracy S; Belton, Mark P; Rott, Michael E

    2008-08-27

    A rapid method was developed for concurrent screening of transgenic elements in GM canola. This method utilizes a single multiplex PCR coupled with an oligonucleotide DNA array capable of simultaneously detecting the 12 approved GM canola lines in Canada. The assay includes construct-specific elements for identification of approved lines, common elements (e.g., CaMV 35S promoter, Agrobacterium tumefaciens nos terminator, or nptII gene) for screening of approved or unapproved lines, a canola-specific endogenous gene, and endogenous genes from heterologous crops to serve as additional controls. Oligonucleotide probes were validated individually for functionality and specificity by amplification of specific transgene sequences from appropriate GM canola lines corresponding to each probe sequence, and hybridization of amplicons to the array. Each target sequence hybridized to its corresponding oligonucleotide probe and no significant cross-hybridization was observed. The limit of detection was examined for the GM lines GT73, T45, and MS8/RF3, and was determined to be 0.1%, 0.1%, and 0.5%, respectively, well within the European food and feed labeling threshold level of 0.9% for approved GM product. Practically, the method was demonstrated to be effective for the detection of GM canola in several types of animal feed, as well as in commercial canola meal.

  8. Photouncaged Sequence-specific Interstrand DNA Cross-Linking with Photolabile 4-oxo-enal-modified Oligonucleotides

    NASA Astrophysics Data System (ADS)

    Sun, Jingjing; Tang, Xinjing

    2015-05-01

    DNA cross-linking technology is an attractive tool for the detection, regulation, and manipulation of genes. In this study, a series of photolabile 4-oxo-enal-modified oligonucleotides functionalized with photosensitive ο-nitrobenzyl derivatives were rationally designed as a new kind of photocaged cross-linking agents. A comprehensive evaluation of cross-linking reactions for different nucleobases in complementary strands under different conditions suggested that the modified DNA oligonucleotides tended to form interstrand cross-linking to nucleobases with the potential of thymidine > guanosine » cytidine ~ adenosine. Different from previous literature reports that cytidine and adenosine were preferential cross-linked nucleobases with 4-oxo-enal moieties, our study represents the first example of DNA cross-linking for T and G selectivity using 4-oxo-enal moiety. The cross-linked adducts were identified and their cross-linking mechanism was also illustrated. This greatly expands the applications of 4-oxo-enal derivatives in the studies of DNA damage and RNA structure

  9. Synthesis, hybridization characteristics, and fluorescence properties of oligonucleotides modified with nucleobase-functionalized locked nucleic acid adenosine and cytidine monomers.

    PubMed

    Kaura, Mamta; Kumar, Pawan; Hrdlicka, Patrick J

    2014-07-03

    Conformationally restricted nucleotides such as locked nucleic acid (LNA) are very popular as affinity-, specificity-, and stability-enhancing modifications in oligonucleotide chemistry to produce probes for nucleic acid targeting applications in molecular biology, biotechnology, and medicinal chemistry. Considerable efforts have been devoted in recent years to optimize the biophysical properties of LNA through additional modification of the sugar skeleton. We recently introduced C5-functionalization of LNA uridines as an alternative and synthetically more straightforward approach to improve the biophysical properties of LNA. In the present work, we set out to test the generality of this concept by studying the characteristics of oligonucleotides modified with four different C5-functionalized LNA cytidine and C8-functionalized LNA adenosine monomers. The results strongly suggest that C5-functionalization of LNA pyrimidines is indeed a viable approach for improving the binding affinity, target specificity, and/or enzymatic stability of LNA-modified ONs, whereas C8-functionalization of LNA adenosines is detrimental to binding affinity and specificity. These insights will impact the future design of conformationally restricted nucleotides for nucleic acid targeting applications.

  10. Synthetic oligonucleotide antigens modified with locked nucleic acids detect disease specific antibodies

    NASA Astrophysics Data System (ADS)

    Samuelsen, Simone V.; Solov’Yov, Ilia A.; Balboni, Imelda M.; Mellins, Elizabeth; Nielsen, Christoffer Tandrup; Heegaard, Niels H. H.; Astakhova, Kira

    2016-10-01

    New techniques to detect and quantify antibodies to nucleic acids would provide a significant advance over current methods, which often lack specificity. We investigate the potential of novel antigens containing locked nucleic acids (LNAs) as targets for antibodies. Particularly, employing molecular dynamics we predict optimal nucleotide composition for targeting DNA-binding antibodies. As a proof of concept, we address a problem of detecting anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We test the best oligonucleotide binders in surface plasmon resonance studies to analyze binding and kinetic aspects of interactions between antigens and target DNA. These DNA and LNA/DNA sequences showed improved binding in enzyme-linked immunosorbent assay using human samples of pediatric lupus patients. Our results suggest that the novel method is a promising tool to create antigens for research and point-of-care monitoring of anti-DNA antibodies.

  11. Synthetic oligonucleotide antigens modified with locked nucleic acids detect disease specific antibodies

    PubMed Central

    Samuelsen, Simone V.; Solov’yov, Ilia A.; Balboni, Imelda M.; Mellins, Elizabeth; Nielsen, Christoffer Tandrup; Heegaard, Niels H. H.; Astakhova, Kira

    2016-01-01

    New techniques to detect and quantify antibodies to nucleic acids would provide a significant advance over current methods, which often lack specificity. We investigate the potential of novel antigens containing locked nucleic acids (LNAs) as targets for antibodies. Particularly, employing molecular dynamics we predict optimal nucleotide composition for targeting DNA-binding antibodies. As a proof of concept, we address a problem of detecting anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We test the best oligonucleotide binders in surface plasmon resonance studies to analyze binding and kinetic aspects of interactions between antigens and target DNA. These DNA and LNA/DNA sequences showed improved binding in enzyme-linked immunosorbent assay using human samples of pediatric lupus patients. Our results suggest that the novel method is a promising tool to create antigens for research and point-of-care monitoring of anti-DNA antibodies. PMID:27775006

  12. Gene knockdown by morpholino-modified oligonucleotides in the zebrafish (Danio rerio) model: applications for developmental toxicology.

    PubMed

    Timme-Laragy, Alicia R; Karchner, Sibel I; Hahn, Mark E

    2012-01-01

    The zebrafish (Danio rerio) has long been used as a model for developmental biology, making it an excellent model to use also in developmental toxicology. The many advantages of zebrafish include their small size, prolific spawning, rapid development, and transparent embryos. They can be easily manipulated genetically through the use of transgenic technology and gene knockdown via morpholino-modified antisense oligonucleotides (MOs). Knocking down specific genes to assess their role in the response to toxicant exposure provides a way to further our knowledge of how developmental toxicants work on a molecular and mechanistic level while establishing a relationship between these molecular events and morphological, behavioral, and/or physiological effects (i.e., phenotypic anchoring). In this chapter, we address important considerations for using MOs to study developmental toxicology in zebrafish embryos and provide a protocol for their use.

  13. Chemically modified graphite for electrochemical cells

    DOEpatents

    Greinke, Ronald Alfred; Lewis, Irwin Charles

    1998-01-01

    This invention relates to chemically modified graphite particles: (a) that are useful in alkali metal-containing electrode of a electrochemical cell comprising: (i) the electrode, (ii) a non-aqueous electrolytic solution comprising an organic aprotic solvent which solvent tends to decompose when the electrochemical cell is in use, and an electrically conductive salt of an alkali metal, and (iii) a counterelectrode; and (b) that are chemically modified with fluorine, chlorine, iodine or phosphorus to reduce such decomposition. This invention also relates to electrodes comprising such chemically modified graphite and a binder and to electrochemical cells containing such electrodes.

  14. Chemically modified graphite for electrochemical cells

    DOEpatents

    Greinke, R.A.; Lewis, I.C.

    1998-05-26

    This invention relates to chemically modified graphite particles: (a) that are useful in alkali metal-containing electrode of a electrochemical cell comprising: (1) the electrode, (2) a non-aqueous electrolytic solution comprising an organic aprotic solvent which solvent tends to decompose when the electrochemical cell is in use, and an electrically conductive salt of an alkali metal, and (3) a counter electrode; and (b) that are chemically modified with fluorine, chlorine, iodine or phosphorus to reduce such decomposition. This invention also relates to electrodes comprising such chemically modified graphite and a binder and to electrochemical cells containing such electrodes. 3 figs.

  15. Universal strategies for the DNA-encoding of libraries of small molecules using the chemical ligation of oligonucleotide tags.

    PubMed

    Litovchick, Alexander; Clark, Matthew A; Keefe, Anthony D

    2014-01-01

    The affinity-mediated selection of large libraries of DNA-encoded small molecules is increasingly being used to initiate drug discovery programs. We present universal methods for the encoding of such libraries using the chemical ligation of oligonucleotides. These methods may be used to record the chemical history of individual library members during combinatorial synthesis processes. We demonstrate three different chemical ligation methods as examples of information recording processes (writing) for such libraries and two different cDNA-generation methods as examples of information retrieval processes (reading) from such libraries. The example writing methods include uncatalyzed and Cu(I)-catalyzed alkyne-azide cycloadditions and a novel photochemical thymidine-psoralen cycloaddition. The first reading method "relay primer-dependent bypass" utilizes a relay primer that hybridizes across a chemical ligation junction embedded in a fixed-sequence and is extended at its 3'-terminus prior to ligation to adjacent oligonucleotides. The second reading method "repeat-dependent bypass" utilizes chemical ligation junctions that are flanked by repeated sequences. The upstream repeat is copied prior to a rearrangement event during which the 3'-terminus of the cDNA hybridizes to the downstream repeat and polymerization continues. In principle these reading methods may be used with any ligation chemistry and offer universal strategies for the encoding (writing) and interpretation (reading) of DNA-encoded chemical libraries.

  16. Universal strategies for the DNA-encoding of libraries of small molecules using the chemical ligation of oligonucleotide tags

    PubMed Central

    Litovchick, Alexander; Clark, Matthew A; Keefe, Anthony D

    2014-01-01

    The affinity-mediated selection of large libraries of DNA-encoded small molecules is increasingly being used to initiate drug discovery programs. We present universal methods for the encoding of such libraries using the chemical ligation of oligonucleotides. These methods may be used to record the chemical history of individual library members during combinatorial synthesis processes. We demonstrate three different chemical ligation methods as examples of information recording processes (writing) for such libraries and two different cDNA-generation methods as examples of information retrieval processes (reading) from such libraries. The example writing methods include uncatalyzed and Cu(I)-catalyzed alkyne-azide cycloadditions and a novel photochemical thymidine-psoralen cycloaddition. The first reading method “relay primer-dependent bypass” utilizes a relay primer that hybridizes across a chemical ligation junction embedded in a fixed-sequence and is extended at its 3′-terminus prior to ligation to adjacent oligonucleotides. The second reading method “repeat-dependent bypass” utilizes chemical ligation junctions that are flanked by repeated sequences. The upstream repeat is copied prior to a rearrangement event during which the 3′-terminus of the cDNA hybridizes to the downstream repeat and polymerization continues. In principle these reading methods may be used with any ligation chemistry and offer universal strategies for the encoding (writing) and interpretation (reading) of DNA-encoded chemical libraries. PMID:25483841

  17. Position-dependent effects on stability in tricyclo-DNA modified oligonucleotide duplexes

    PubMed Central

    Ittig, Damian; Gerber, Anna-Barbara; Leumann, Christian J.

    2011-01-01

    A series of oligodeoxyribonucleotides and oligoribonucleotides containing single and multiple tricyclo(tc)-nucleosides in various arrangements were prepared and the thermal and thermodynamic transition profiles of duplexes with complementary DNA and RNA evaluated. Tc-residues aligned in a non-continuous fashion in an RNA strand significantly decrease affinity to complementary RNA and DNA, mostly as a consequence of a loss of pairing enthalpy ΔH. Arranging the tc-residues in a continuous fashion rescues Tm and leads to higher DNA and RNA affinity. Substitution of oligodeoxyribonucleotides in the same way causes much less differences in Tm when paired to complementary DNA and leads to substantial increases in Tm when paired to complementary RNA. CD-spectroscopic investigations in combination with molecular dynamics simulations of duplexes with single modifications show that tc-residues in the RNA backbone distinctly influence the conformation of the neighboring nucleotides forcing them into higher energy conformations, while tc-residues in the DNA backbone seem to have negligible influence on the nearest neighbor conformations. These results rationalize the observed affinity differences and are of relevance for the design of tc-DNA containing oligonucleotides for applications in antisense or RNAi therapy. PMID:20719742

  18. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: a powerful tool for the mass and sequence analysis of natural and modified oligonucleotides.

    PubMed Central

    Pieles, U; Zürcher, W; Schär, M; Moser, H E

    1993-01-01

    We report the analysis and characterization of natural and modified oligonucleotides by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). The present technology was highly improved for this class of compounds by using a new matrix, 2,4,6-trihydroxy acetophenone, together with di- and triammonium salts of organic or inorganic acids to suppress peak broadening due to multiple ion adducts. This methodology can be used in combination with time dependent degradation of oligonucleotides by exonucleases as powerful tool to determine sequence compositions. PMID:8341593

  19. Electrochemical biosensors for detection of point mutation based on surface ligation reaction and oligonucleotides modified gold nanoparticles.

    PubMed

    Wang, Qing; Yang, Lijuan; Yang, Xiaohai; Wang, Kemin; He, Leiliang; Zhu, Jinqing

    2011-03-04

    An electrochemical method for point mutation detection based on surface ligation reaction and oligonucleotides (ODNs) modified gold nanoparticles (AuNPs) was demonstrated. Point mutation identification was achieved using Escherichia coli DNA ligase. This system for point mutation detection relied on a sandwich assay comprising capture ODN immobilized on Au electrodes, target ODN and ligation ODN. Because of the sequence-specific surface reactions of E. coli DNA ligase, the ligation ODN covalently linked to the capture ODN only in the presence of a perfectly complementary target ODN. The presence of ligation products on Au electrode was detected using chronocoulometry through hybridization with reporter ODN modified AuNPs. The use of AuNPs improved the sensitivity of chronocoulometry in this approach, a detection limit of 0.9 pM complementary ODN was obtained. For single base mismatched ODN (smODN), a negligible signal was observed. Even if the concentration ratio of complementary ODN to smODN was decreased to 1:1000, a detectable signal was observed. This work may provide a specific, sensitive and cost-efficient approach for point mutant detection.

  20. Systematic evaluation and optimization of modification reactions of oligonucleotides with amines and carboxylic acids for the synthesis of DNA-encoded chemical libraries.

    PubMed

    Franzini, Raphael M; Samain, Florent; Abd Elrahman, Maaly; Mikutis, Gediminas; Nauer, Angela; Zimmermann, Mauro; Scheuermann, Jörg; Hall, Jonathan; Neri, Dario

    2014-08-20

    DNA-encoded chemical libraries are collections of small molecules, attached to DNA fragments serving as identification barcodes, which can be screened against multiple protein targets, thus facilitating the drug discovery process. The preparation of large DNA-encoded chemical libraries crucially depends on the availability of robust synthetic methods, which enable the efficient conjugation to oligonucleotides of structurally diverse building blocks, sharing a common reactive group. Reactions of DNA derivatives with amines and/or carboxylic acids are particularly attractive for the synthesis of encoded libraries, in view of the very large number of building blocks that are commercially available. However, systematic studies on these reactions in the presence of DNA have not been reported so far. We first investigated conditions for the coupling of primary amines to oligonucleotides, using either a nucleophilic attack on chloroacetamide derivatives or a reductive amination on aldehyde-modified DNA. While both methods could be used for the production of secondary amines, the reductive amination approach was generally associated with higher yields and better purity. In a second endeavor, we optimized conditions for the coupling of a diverse set of 501 carboxylic acids to DNA derivatives, carrying primary and secondary amine functions. The coupling efficiency was generally higher for primary amines, compared to secondary amine substituents, but varied considerably depending on the structure of the acids and on the synthetic methods used. Optimal reaction conditions could be found for certain sets of compounds (with conversions >80%), but multiple reaction schemes are needed when assembling large libraries with highly diverse building blocks. The reactions and experimental conditions presented in this article should facilitate the synthesis of future DNA-encoded chemical libraries, while outlining the synthetic challenges that remain to be overcome.

  1. Probing the microenvironments in the grooves of Z-DNA using dan-modified oligonucleotides.

    PubMed

    Kimura, Takumi; Kawai, Kiyohiko; Majima, Tetsuro

    2006-04-14

    The environment-sensitive fluorophore dan (6-dimethylamino-2-acyl-naphthalene)- modified dC or dG bases were introduced into the Z-DNA forming sequence. It was demonstrated that both grooves of Z-DNA are more hydrated than those of B-DNA. Dan will be useful for probing the microenvironments in the grooves among the DNA polymorphs.

  2. Binding specificity and stability of duplexes formed by modified oligonucleotides with a 4096-hexanucleotide microarray

    PubMed Central

    Timofeev, Edward; Mirzabekov, Andrei

    2001-01-01

    The binding of oligodeoxynucleotides modified with adenine 2′-O-methyl riboside, 2,6-diaminopurine 2′-O-methyl riboside, cytosine 2′-O-methyl riboside, 2,6-diaminopurine deoxyriboside or 5-bromodeoxyuridine was studied with a microarray containing all possible (4096) polyacrylamide-bound hexadeoxynucleotides (a generic microchip). The generic microchip was manufactured by using reductive immobilization of aminooligonucleotides in the activated copolymer of acrylamide, bis-acrylamide and N-(2,2-dimethoxyethyl) acrylamide. The binding of the fluorescently labeled modified octanucleotides to the array was analyzed with the use of both melting profiles and the fluorescence distribution at selected temperatures. Up to three substitutions of adenosines in the octamer sequence by adenine 2′-O-methyl ribosides (Am), 2,6-diaminopurine 2′-O-methyl ribosides (Dm) or 2,6-diaminopurine deoxyribosides (D) resulted in increased mismatch discrimination measured at the melting temperature of the corresponding perfect duplex. The stability of complexes formed by 2′-O-methyl-adenosine-modified oligodeoxynucleotides was slightly decreased with every additional substitution, yielding ∼4°C of total loss in melting temperature for three modifications, as followed from microchip thermal denaturation experiments. 2,6-Diaminopurine 2′-O-methyl riboside modifications led to considerable duplex stabilization. The cytosine 2′-O-methyl riboside and 5-bromodeoxyuridine modifications generally did not change either duplex stability or mismatch resolution. Denaturation experiments conducted with selected perfect duplexes on microchips and in solution showed similar results on thermal stabilities. Some hybridization artifacts were observed that might indicate the formation of parallel DNA. PMID:11410672

  3. Interplay of Structure, Hydration and Thermal Stability in Formacetal Modified Oligonucleotides: RNA May Tolerate Nonionic Modifications Better than DNA

    SciTech Connect

    Kolarovic, A.; Schweizer, E; Greene, E; Gironda, M; Pallan, P; Egli, M; Rozners, E

    2009-01-01

    DNA and RNA oligonucleotides having formacetal internucleoside linkages between uridine and adenosine nucleosides have been prepared and studied using UV thermal melting, osmotic stress, and X-ray crystallography. Formacetal modifications have remarkably different effects on double helical RNA and DNAethe formacetal stabilizes the RNA helix by +0.7 C but destabilizes the DNA helix by -1.6 C per modification. The apparently hydrophobic formacetal has little effect on hydration of RNA but decreases the hydration of DNA, which suggests that at least part of the difference in thermal stability may be related to differences in hydration. A crystal structure of modified DNA shows that two isolated formacetal linkages fit almost perfectly in an A-type helix (decamer). Taken together, the data suggest that RNA may tolerate nonionic backbone modifications better than DNA. Overall, formacetal appears to be an excellent mimic of phosphate linkage in RNA and an interesting modification for potential applications in fundamental studies and RNA-based gene control strategies, such as RNA interference.

  4. Molecular beacon modified sensor chips for oligonucleotide detection with optical readout.

    PubMed

    Su, Qiang; Wesner, Daniel; Schönherr, Holger; Nöll, Gilbert

    2014-12-02

    Three different surface bound molecular beacons (MBs) were investigated using surface plasmon fluorescence spectroscopy (SPFS) as an optical readout technique. While MB1 and MB2, both consisting of 36 bases, differed only in the length of the linker for surface attachment, the significantly longer MB3, consisting of 56 bases, comprised an entirely different sequence. For sensor chip preparation, the MBs were chemisorbed on gold via thiol anchors together with different thiol spacers. The influence of important parameters, such as the length of the MBs, the length of the linker between the MBs and the gold surface, the length and nature of the thiol spacers, and the ratio between the MBs and the thiol spacers was studied. After hybridization with the target, the fluorophore of the longer MB3 was oriented close to the surface, and the shorter MBs were standing more or less upright, leading to a larger increase in fluorescence intensity. Fluorescence microscopy revealed a homogeneous distribution of the MBs on the surface. The sensor chips could be used for simple and fast detection of target molecules with a limit of detection in the larger picomolar range. The response time was between 5 and 20 min. Furthermore, it was possible to distinguish between fully complementary and singly mismatched targets. While rinsing with buffer solution after hybridization with target did not result in any signal decrease, complete dehybridization could be carried out by intense rinsing with pure water. The MB modified sensor chips could be prepared in a repeatable manner and reused many times without significant decrease in performance.

  5. The mechanism of the chemical synthesis of oligonucleotides and its synthetic consequences.

    PubMed Central

    Knorre, D G; Zarytova, V F

    1976-01-01

    The data obtained mainly by pulsed NMR spectroscopy on phosphorus nuclei on the mechanism of the internucleotide phosphodiester (PDE) group formation are summarised. With arylsulphonyl chloride as condensing reagent monomeric nucleotide derivative B (nucleoside metaphosphate or its pyridinium adduct) is the highly reactive intermediate. In the presence of PDE groups in nucleoside or nucleotide component the significantly less reactive derivatives with trisubstituted pyrophosphoryl residues are formed both with arylsulphonyl chloride and dicyclohexylcarbodiimide (DCC). The reactive B form of nucleotide component may be obtained using greater excess of arylsulphonyl chloride with simultaneous convertion of PDE groups to tetrasubstituted pyrophosphates amenable to side reactions. The convertion of PDE groups to easily hydrolysable dicyclohexylurea derivatives by reaction with DCC is proposed to reversible blocking of PDE groups of nucleoside component. The B type derivatives of mononucleotides or oligonucleotides with blocked PDE groups seems to be the best nucleotide components. PMID:186762

  6. Polycationic ligands of different chemical classes stimulate DNA strand displacement between short oligonucleotides in a protein-free system.

    PubMed

    Volodin, Alexander A; Bocharova, Tatiana N; Smirnova, Elena A

    2016-09-01

    The ability of polycationic ligands to stimulate DNA strand displacement between short oligonucleotides in a protein-free system is demonstrated. We show that two ligands, tetracationic aliphatic amine (spermine) and a dicationic intercalating drug (chloroquine), promote strand displacement in a concentration-dependent manner. At low concentrations both ligands decelerate spontaneous strand displacement because of their impact on the stability of the DNA duplex. At elevated concentrations they accelerate strand displacement via formation of intermediate structures containing three DNA strands. The rate of the last process does not correlate with the thermal dissociation rate of the entire DNA duplex. It indicates that, possibly, the action of these agents cannot be explained by their influence on the stability of the DNA duplex. In general, our results suggest that the ability to stimulate DNA strand displacement appears to be a common feature of polycations of different chemical and structural classes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 633-641, 2016.

  7. Discrimination of oligonucleotides of different lengths with a wild-type aerolysin nanopore

    NASA Astrophysics Data System (ADS)

    Cao, Chan; Ying, Yi-Lun; Hu, Zheng-Li; Liao, Dong-Fang; Tian, He; Long, Yi-Tao

    2016-08-01

    Protein nanopores offer an inexpensive, label-free method of analysing single oligonucleotides. The sensitivity of the approach is largely determined by the characteristics of the pore-forming protein employed, and typically relies on nanopores that have been chemically modified or incorporate molecular motors. Effective, high-resolution discrimination of oligonucleotides using wild-type biological nanopores remains difficult to achieve. Here, we show that a wild-type aerolysin nanopore can resolve individual short oligonucleotides that are 2 to 10 bases long. The sensing capabilities are attributed to the geometry of aerolysin and the electrostatic interactions between the nanopore and the oligonucleotides. We also show that the wild-type aerolysin nanopores can distinguish individual oligonucleotides from mixtures and can monitor the stepwise cleavage of oligonucleotides by exonuclease I.

  8. Functionalization of silicon oxide using supercritical fluid deposition of 3,4-epoxybutyltrimethoxysilane for the immobilization of amino-modified oligonucleotide

    NASA Astrophysics Data System (ADS)

    Rull, Jordi; Nonglaton, Guillaume; Costa, Guillaume; Fontelaye, Caroline; Marchi-Delapierre, Caroline; Ménage, Stéphane; Marchand, Gilles

    2015-11-01

    The functionalization of silicon oxide based substrates using silanes is generally performed through liquid phase methodologies. These processes involve a huge quantity of potentially toxic solvents and present some important disadvantages for the functionalization of microdevices or porous materials, for example the low diffusion. To overcome this drawback, solvent-free methodologies like molecular vapor deposition (MVD) or supercritical fluid deposition (SFD) have been developed. In this paper, the deposition process of 3,4-epoxybutyltrimethoxysilane (EBTMOS) on silicon oxide using supercritical carbon dioxide (scCO2) as a solvent is studied for the first time. The oxirane ring of epoxy silanes readily reacts with amine group and is of particular interest for the grafting of amino-modified oligonucleotides or antibodies for diagnostic application. Then the ability of this specific EBTMOS layer to react with amine functions has been evaluated using the immobilization of amino-modified oligonucleotide probes. The presence of the probes is revealed by fluorescence using hybridization with a fluorescent target oligonucleotide. The performances of SFD of EBTMOS have been optimized and then compared with the dip coating and molecular vapor deposition methods, evidencing a better grafting efficiency and homogeneity, a lower reaction time in addition to the eco-friendly properties of the supercritical carbon dioxide. The epoxysilane layers have been characterized by surface enhanced ellipsometric contrast optical technique, atomic force microscopy, multiple internal reflection infrared spectroscopy and X-ray photoelectron spectroscopy. The shelf life of the 3,4-epoxybutyltrimethoxysilane coating layer has also been studied. Finally, two different strategies of NH2-oligonucleotide grafting on EBTMOS coating layer have been compared, i.e. reductive amination and nucleophilic substitution, SN2. This EBTMOS based coating layer can be used for a wide range of applications

  9. Quality of chemically modified hemp fibers.

    PubMed

    Kostic, Mirjana; Pejic, Biljana; Skundric, Petar

    2008-01-01

    Hemp fibers are very interesting natural material for textile and technical applications now. Applying hemp fibers to the apparel sector requires improved quality fibers. In this paper, hemp fibers were modified with sodium hydroxide solutions (5% and 18% w/v), at room and boiling temperature, for different periods of time, and both under tension and slack, in order to partially extract noncellulosic substances, and separate the fiber bundles. The quality of hemp fibers was characterised by determining their chemical composition, fineness, mechanical and sorption properties. The modified hemp fibers were finer, with lower content of lignin, increased flexibility, and in some cases tensile properties were improved. An original method for evaluation of tensile properties of hemp fibers was developed.

  10. In vitro evolution of chemically-modified nucleic acid aptamers: Pros and cons, and comprehensive selection strategies.

    PubMed

    Lipi, Farhana; Chen, Suxiang; Chakravarthy, Madhuri; Rakesh, Shilpa; Veedu, Rakesh N

    2016-12-01

    Nucleic acid aptamers are single-stranded DNA or RNA oligonucleotide sequences that bind to a specific target molecule with high affinity and specificity through their ability to adopt 3-dimensional structure in solution. Aptamers have huge potential as targeted therapeutics, diagnostics, delivery agents and as biosensors. However, aptamers composed of natural nucleotide monomers are quickly degraded in vivo and show poor pharmacodynamic properties. To overcome this, chemically-modified nucleic acid aptamers are developed by incorporating modified nucleotides after or during the selection process by Systematic Evolution of Ligands by EXponential enrichment (SELEX). This review will discuss the development of chemically-modified aptamers and provide the pros and cons, and new insights on in vitro aptamer selection strategies by using chemically-modified nucleic acid libraries.

  11. In vitro evolution of chemically-modified nucleic acid aptamers: Pros and cons, and comprehensive selection strategies

    PubMed Central

    Chen, Suxiang; Chakravarthy, Madhuri; Rakesh, Shilpa; Veedu, Rakesh N.

    2016-01-01

    ABSTRACT Nucleic acid aptamers are single-stranded DNA or RNA oligonucleotide sequences that bind to a specific target molecule with high affinity and specificity through their ability to adopt 3-dimensional structure in solution. Aptamers have huge potential as targeted therapeutics, diagnostics, delivery agents and as biosensors. However, aptamers composed of natural nucleotide monomers are quickly degraded in vivo and show poor pharmacodynamic properties. To overcome this, chemically-modified nucleic acid aptamers are developed by incorporating modified nucleotides after or during the selection process by Systematic Evolution of Ligands by EXponential enrichment (SELEX). This review will discuss the development of chemically-modified aptamers and provide the pros and cons, and new insights on in vitro aptamer selection strategies by using chemically-modified nucleic acid libraries. PMID:27715478

  12. Encoded libraries of chemically modified peptides.

    PubMed

    Heinis, Christian; Winter, Greg

    2015-06-01

    The use of powerful technologies for generating and screening DNA-encoded protein libraries has helped drive the development of proteins as pharmaceutical ligands. However the development of peptides as pharmaceutical ligands has been more limited. Although encoded peptide libraries are typically several orders of magnitude larger than classical chemical libraries, can be more readily screened, and can give rise to higher affinity ligands, their use as pharmaceutical ligands is limited by their intrinsic properties. Two of the intrinsic limitations include the rotational flexibility of the peptide backbone and the limited number (20) of natural amino acids. However these limitations can be overcome by use of chemical modification. For example, the libraries can be modified to introduce topological constraints such as cyclization linkers, or to introduce new chemical entities such as small molecule ligands, fluorophores and photo-switchable compounds. This article reviews the chemistry involved, the properties of the peptide ligands, and the new opportunities offered by chemical modification of DNA-encoded peptide libraries.

  13. Chemically modified carbonic anhydrases useful in carbon capture systems

    DOEpatents

    Novick, Scott J; Alvizo, Oscar

    2013-10-29

    The present disclosure relates to chemically modified carbonic anhydrase polypeptides and soluble compositions, homogenous liquid formulations comprising them. The chemically modified carbonic anhydrase polypeptides have improved properties relative to the same carbonic anhydrase polypeptide that is not chemically modified including the improved properties of increased activity and/or stability in the presence of amine compounds, ammonia, or carbonate ion. The present disclosure also provides methods of preparing the chemically modified polypeptides and methods of using the chemically modified polypeptides for accelerating the absorption of carbon dioxide from a gas stream into a solution as well as for the release of the absorbed carbon dioxide for further treatment and/or sequestering.

  14. Chemically modified carbonic anhydrases useful in carbon capture systems

    DOEpatents

    Novick, Scott; Alvizo, Oscar

    2013-01-15

    The present disclosure relates to chemically modified carbonic anhydrase polypeptides and soluble compositions, homogenous liquid formulations comprising them. The chemically modified carbonic anhydrase polypeptides have improved properties relative to the same carbonic anhydrase polypeptide that is not chemically modified including the improved properties of increased activity and/or stability in the presence of amine compounds, ammonia, or carbonate ion. The present disclosure also provides methods of preparing the chemically modified polypeptides and methods of using the chemically modified polypeptides for accelerating the absorption of carbon dioxide from a gas stream into a solution as well as for the release of the absorbed carbon dioxide for further treatment and/or sequestering.

  15. Pentopyranosyl Oligonucleotide Systems

    NASA Technical Reports Server (NTRS)

    Reck, Folkert; Kudick, Rene; Krishnamurthy, Ramanarayanan; Eschenmoser, Albert; Wippo, Harald

    2001-01-01

    To determine whether the remarkable chemical properties of the pyranosyl isomer of RNA as an informational Watson-Crick base-pairing system are unique to the pentopyranosyl-(4 + 2)-oligonucleotide isomer derived from the RNA-building block D-ribose, studies on the entire family of diastereoisomeric pyranosyL(4 - Z)-oligonucleotide systems deriving from D-ribose. L-lyxose. D-xylose, and L-arabinose were carried out. The result of these extended studies is unambiguous: not only pyranosyl-RNA, but all members of the pentopyranosyl(4 + 2)-oligonucleotide family are highly efficient Watson-Crick base-pairing systems. Their synthesis and pairing properties will be described in a series of publications in this journal.

  16. Renal uptake and tolerability of a 2'-O-methoxyethyl modified antisense oligonucleotide (ISIS 113715) in monkey.

    PubMed

    Henry, Scott P; Johnson, Mark; Zanardi, Thomas A; Fey, Robert; Auyeung, Diana; Lappin, Patrick B; Levin, Arthur A

    2012-11-15

    The primary target organ for uptake of systemically administered phosphorothioate oligonucleotides is the kidney cortex and the proximal tubular epithelium in particular. To determine the effect of oligonucleotide uptake on renal function, a detailed renal physiology study was performed in cynomolgus monkeys treated with 10-40 mg/kg/week ISIS 113715 for 4 weeks. The concentrations of oligonucleotide in the kidney cortex ranged from 1400 to 2600 μg/g. These concentrations were associated with histologic changes in proximal tubular epithelial cells that ranged from the appearance of cytoplasmic basophilic granules to atrophic and degenerative changes at higher concentrations. However, there were no renal functional abnormalities as determined by the typical measurements of blood urea nitrogen, serum creatinine, creatinine clearance, or urine specific gravity. Nor were there changes in glomerular filtration rate, or renal blood flow. Specific urinary markers of tubular epithelial cell damage, such as N-acetyl-glucosaminidase, and α-glutathione-s-transferase were not affected. Tubular function was further evaluated by monitoring the urinary excretion of amino acids, β(2)-microglobulin, or glucose. Renal function was challenged by administering a glucose load and by examining concentrating ability after a 4-h water deprivation. Neither challenge produced any evidence of change in renal function. The only change observed was a low incidence of increased urine protein/creatinine ratio in monkeys treated with ≥40 mg/kg/week which was rapidly reversible. Collectively, these data indicate that ISIS 113715-uptake by the proximal tubular epithelium has little or no effect on renal function at concentrations of 2600 μg/g.

  17. Double-stranded DNA-templated cleavage of oligonucleotides containing a P3'->N5' linkage triggered by triplex formation: the effects of chemical modifications and remarkable enhancement in reactivity.

    PubMed

    Ito, Kosuke Ramon; Kodama, Tetsuya; Tomizu, Masaharu; Negoro, Yoshinori; Orita, Ayako; Osaki, Tomohisa; Hosoki, Noritsugu; Tanaka, Takaya; Imanishi, Takeshi; Obika, Satoshi

    2010-11-01

    We recently reported double-stranded DNA-templated cleavage of oligonucleotides as a sequence-specific DNA-detecting method. In this method, triplex-forming oligonucleotides (TFOs) modified with 5'-amino-2',4'-BNA were used as a DNA-detecting probe. This modification introduced a P3'→N5' linkage (P-N linkage) in the backbone of the TFO, which was quickly cleaved under acidic conditions when it formed a triplex. The prompt fission of the P-N linkage was assumed to be driven by a conformational strain placed on the linkage upon triplex formation. Therefore, chemical modifications around the P-N linkage should change the reactivity by altering the microenvironment. We synthesized 5'-aminomethyl type nucleic acids, and incorporated them into TFOs instead of 5'-amino-2',4'-BNA to investigate the effect of 5'-elongation. In addition, 2',4'-BNA/LNA or 2',5'-linked DNA were introduced at the 3'- and/or 5'-neighboring residues of 5'-amino-2',4'-BNA to reveal neighboring residual effects. We evaluated the triplex stability and reaction properties of these TFOs, and found out that chemical modifications around the P-N linkage greatly affected their reaction properties. Notably, 2',5'-linked DNA at the 3' position flanking 5'-amino-2',4'-BNA brought significantly higher reactivity, and we succeeded in indicating that a TFO with this modification is promising as a DNA analysis tool.

  18. New Concepts of Fluorescent Probes for Specific Detection of DNA Sequences: Bis-Modified Oligonucleotides in Excimer and Exciplex Detection

    PubMed Central

    Gbaj, A; Bichenkova, EV; Walsh, L; Savage, HE; Sardarian, AR; Etchells, LL; Gulati, A; Hawisa, S; Douglas, KT

    2009-01-01

    The detection of single base mismatches in DNA is important for diagnostics, treatment of genetic diseases, and identification of single nucleotide polymorphisms. Highly sensitive, specific assays are needed to investigate genetic samples from patients. The use of a simple fluorescent nucleoside analogue in detection of DNA sequence and point mutations by hybridisation in solution is described in this study. The 5′-bispyrene and 3′-naphthalene oligonucleotide probes form an exciplex on hybridisation to target in water and the 5′-bispyrene oligonucleotide alone is an adequate probe to determine concentration of target present. It was also indicated that this system has a potential to identify mismatches and insertions. The aim of this work was to investigate experimental structures and conditions that permit strong exciplex emission for nucleic acid detectors, and show how such exciplexes can register the presence of mismatches as required in SNP analysis. This study revealed that the hybridisation of 5′-bispyrenyl fluorophore to a DNA target results in formation of a fluorescent probe with high signal intensity change and specificity for detecting a complementary target in a homogeneous system. Detection of SNP mutations using this split-probe system is a highly specific, simple, and accessible method to meet the rigorous requirements of pharmacogenomic studies. Thus, it is possible for the system to act as SNP detectors and it shows promise for future applications in genetic testing. PMID:21483539

  19. Synthesis, Improved Antisense Activity and Structural Rationale for the Divergent RNA Affinities of 3′-Fluoro Hexitol Nucleic Acid (FHNA and Ara-FHNA) Modified Oligonucleotides

    PubMed Central

    Egli, Martin; Pallan, Pradeep S.; Allerson, Charles R.; Prakash, Thazha P.; Berdeja, Andres; Yu, Jinghua; Lee, Sam; Watt, Andrew; Gaus, Hans; Bhat, Balkrishen; Swayze, Eric E.; Seth, Punit P.

    2011-01-01

    The synthesis, biophysical, structural and biological properties of both isomers of 3′-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides are reported. Synthesis of the FHNA and Ara-FHNA thymine phosphoramidites was efficiently accomplished starting from known sugar precursors. Optimal RNA affinities were observed with 3′-fluorine atom and nucleobase in a trans-diaxial orientation. The Ara-FHNA analog with an equatorial fluorine was found to be destabilizing. However, the magnitude of destabilization was sequence-dependent. Thus, the loss of stability is sharply reduced when Ara-FHNA residues were inserted at pyrimidine-purine (Py-Pu) steps compared to placement within a stretch of pyrimidines (Py-Py). Crystal structures of A-type DNA duplexes modified with either monomer, provide a rationalization for the opposing stability effects and point to a steric origin of the destabilization caused by the Ara-FHNA analog. The sequence dependent effect can be explained by the formation of an inter-nucleotide C-F…H-C pseudo hydrogen bond between F3′ of Ara-FHNA and C8-H of the nucleobase from the 3′-adjacent adenosine that is absent at Py-Py steps. In animal experiments, FHNA-modified antisense oligonucleotides formulated in saline showed potent downregulation of gene expression in liver tissue without producing hepatotoxicity. Our data establish FHNA as a useful modification for antisense therapeutics and also confirm the stabilizing influence of F(Py)…H-C(Pu) pseudo hydrogen bonds in nucleic acid structures. PMID:21919455

  20. Synthesis, Improved Antisense Activity and Structural Rationale for the Divergent RNA Affinities of 3;#8242;-Fluoro Hexitol Nucleic Acid (FHNA and Ara-FHNA) Modified Oligonucleotides

    SciTech Connect

    Egli, Martin; Pallan, Pradeep S.; Allerson, Charles R.; Prakash, Thazha P.; Berdeja, Andres; Yu, Jinghua; Lee, Sam; Watt, Andrew; Gaus, Hans; Bhat, Balkrishen; Swayze, Eric E.; Seth, Punit P.

    2012-03-16

    The synthesis, biophysical, structural, and biological properties of both isomers of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides are reported. Synthesis of the FHNA and Ara-FHNA thymine phosphoramidites was efficiently accomplished starting from known sugar precursors. Optimal RNA affinities were observed with a 3'-fluorine atom and nucleobase in a trans-diaxial orientation. The Ara-FHNA analog with an equatorial fluorine was found to be destabilizing. However, the magnitude of destabilization was sequence-dependent. Thus, the loss of stability is sharply reduced when Ara-FHNA residues were inserted at pyrimidine-purine (Py-Pu) steps compared to placement within a stretch of pyrimidines (Py-Py). Crystal structures of A-type DNA duplexes modified with either monomer provide a rationalization for the opposing stability effects and point to a steric origin of the destabilization caused by the Ara-FHNA analog. The sequence dependent effect can be explained by the formation of an internucleotide C-F {hor_ellipsis} H-C pseudo hydrogen bond between F3' of Ara-FHNA and C8-H of the nucleobase from the 3'-adjacent adenosine that is absent at Py-Py steps. In animal experiments, FHNA-modified antisense oligonucleotides formulated in saline showed a potent downregulation of gene expression in liver tissue without producing hepatotoxicity. Our data establish FHNA as a useful modification for antisense therapeutics and also confirm the stabilizing influence of F(Py) {hor_ellipsis} H-C(Pu) pseudo hydrogen bonds in nucleic acid structures.

  1. Versatile functionalization of nanoelectrodes by oligonucleotides via pyrrole electrochemistry.

    PubMed

    Descamps, Emeline; Nguyen, Khoa; Bouchain-Gautier, Christelle; Filoramo, Arianna; Goux-Capes, Laurence; Goffman, Marcello; Bourgoin, Jean-Philippe; Mailley, Pascal; Livache, Thierry

    2010-11-15

    Surface modification at the nanometer scale is a challenge for the future of molecular electronics. In particular, the precise anchoring and electrical addressing of biological scaffolds such as complex DNA nanonetworks is of importance for generating bio-directed assemblies of nano-objects for nanocircuit purposes. Herein, we consider the individual modification of nanoelectrodes with different oligonucleotide sequences by an electrochemically driven co-polymerization process of pyrrole and modified oligonucleotide sequences bearing pyrrole monomers. We demonstrate that this one-step technique presents the advantages of simplicity, localization of surface modification, mechanical, biological and chemical stability of the coatings, and high lateral resolution.

  2. A temperature-tolerant multiplex elements and genes screening system for genetically modified organisms based on dual priming oligonucleotide primers and capillary electrophoresis.

    PubMed

    Fu, Wei; Wei, Shuang; Wang, Chenguang; Du, Zhixin; Zhu, Pengyu; Wu, Xiyang; Wu, Gang; Zhu, Shuifang

    2017-08-15

    High throughput screening systems are the preferred solution to meet the urgent requirement of increasing number of genetically modified organisms (GMOs). In this study, we have successfully developed a multiplex GMO element screening system with dual priming oligonucleotide (DPO) primers. This system can detect the cauliflower mosaic virus 35S (CaMV 35S), terminator of nopaline synthase gene (NOS), figwort mosaic virus 35S (FMV 35S) promoter, neomycin phosphotransferaseII (NPTII), Bt Cry 1Ab, phosphinothricin acetyltransferase genes (bar) and Streptomyces viridochromogenes (pat) simultaneously, which covers more than 90% of all authorized GMO species worldwide. This system exhibits a high tolerance to annealing temperatures, high specificity and a limit of detection equal to conventional PCR. A total of 214 samples from markets, national entry-exit agencies, the Institute for Reference Materials and Measurement (IRMM) and the American Oil Chemists' Society (AOCS) were also tested for applicability. This screening system is therefore suitable for GMO screening.

  3. Phase I trial of ISIS 104838, a 2'-methoxyethyl modified antisense oligonucleotide targeting tumor necrosis factor-alpha.

    PubMed

    Sewell, K Lea; Geary, Richard S; Baker, Brenda F; Glover, Josephine M; Mant, Timothy G K; Yu, Rosie Z; Tami, Joseph A; Dorr, F Andrew

    2002-12-01

    ISIS 104838 is a 20-mer phosphorothioate antisense oligonucleotide (ASO) that binds tumor necrosis factor-alpha (TNF-alpha) mRNA. It carries a 2'-methoxyethyl modification on the five 3' and 5' nucleotide sugars, with 10 central unmodified deoxynucleotides. ISIS 104838 was identified from a 264 ASO screen in phorbol myristate acetate-activated keratinocytes, and the dose response was assessed in lipopolysaccharide (LPS)-activated monocytes. Healthy males received multiple intravenous (i.v.) ISIS 104838 infusions in a placebo-controlled dose escalation trial (0.1-6 mg/kg). Additional volunteers received single or multiple subcutaneous (s.c.) injections. ISIS 104838 suppressed TNF-alpha protein by 85% in stimulated keratinocytes. The IC50 for TNF-alpha mRNA inhibition in stimulated monocytes was <1 microM. For i.v., C(max) occurred at the end of infusion. The effective plasma half-life was 15 to 45 min at 0.1 to 0.5 mg/kg and 1 to 1.8 h for higher doses. The apparent terminal plasma elimination half-life approximated 25 days. Obese subjects had higher plasma levels following equivalent mg/kg doses. For s.c. injections, C(max) occurred at 2 to 4 h and was lower than with equivalent i.v. dosing. Plasma bioavailability compared with i.v. was 82% following a 200 mg/ml s.c. injection. Transient activated partial thromboplastin time prolongation occurred after i.v. infusions and minimally after s.c. injections. Two subjects experienced rash, one a reversible platelet decrease, and mild injection site tenderness was noted. TNF-alpha production by peripheral blood leukocytes, induced ex vivo by LPS, was decreased by ISIS 104838 (p < 0.01). ISIS 104838, a second-generation antisense oligonucleotide, was generally well tolerated intravenously and subcutaneously. The pharmacokinetics support an infrequent dosing interval. Inhibition of TNF-alpha production ex vivo was demonstrated.

  4. In vitro correction of a pseudoexon-generating deep intronic mutation in LGMD2A by antisense oligonucleotides and modified small nuclear RNAs.

    PubMed

    Blázquez, Lorea; Aiastui, Ana; Goicoechea, Maria; Martins de Araujo, Mafalda; Avril, Aurélie; Beley, Cyriaque; García, Luis; Valcárcel, Juan; Fortes, Puri; López de Munain, Adolfo

    2013-10-01

    Limb-girdle muscular dystrophy type 2A (LGMD2A) is the most frequent autosomal recessive muscular dystrophy. It is caused by mutations in the calpain-3 (CAPN3) gene. The majority of the mutations described to date are located in the coding sequence of the gene. However, it is estimated that 25% of the mutations are present at exon-intron boundaries and modify the pre-mRNA splicing of the CAPN3 transcript. We have previously described the first deep intronic mutation in the CAPN3 gene: c.1782+1072G>C mutation. This mutation causes the pseudoexonization of an intronic sequence of the CAPN3 gene in the mature mRNA. In the present work, we show that the point mutation generates the inclusion of the pseudoexon in the mRNA using a minigene assay. In search of a treatment that restores normal splicing, splicing modulation was induced by RNA-based strategies, which included antisense oligonucleotides and modified small-nuclear RNAs. The best effect was observed with antisense sequences, which induced pseudoexon skipping in both HeLa cells cotransfected with mutant minigene and in fibroblasts from patients. Finally, transfection of antisense sequences and siRNA downregulation of serine/arginine-rich splicing factor 1 (SRSF1) indicate that binding of this factor to splicing enhancer sequences is involved in pseudoexon activation.

  5. Chemical and semisynthesis of modified histones.

    PubMed

    Maity, Suman Kumar; Jbara, Muhammad; Brik, Ashraf

    2016-05-01

    Post-translational modifications (PTMs) of histones play critical roles in the epigenetic regulation of eukaryotic genome by directly altering the biophysical properties of chromatin or by recruiting effector proteins. The large number of PTMs and the inherent complexity in their population and signaling processes make it highly challenging to understand epigenetics-related processes. To address these challenges, accesses to homogeneously modified histones are obligatory. Over the last decade, synthetic protein chemists have been devising novel synthetic tools and applying state-of-the-art chemoselective ligation strategies to prepare precious materials useful in answering fundamental questions in this area. In this short review, we cover some of the recent breakthroughs in these directions in particular the synthesis and semi-synthesis of modified histones and their use to unravel the mysteries of epigenetics. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

  6. Structural Transformations in Chemically Modified Graphene

    DTIC Science & Technology

    2012-07-16

    nanomaterials (CNMs), there remains interest in randomly assembled CNM films for commer- cial development and fundamental research. For example, in 2003...produce a material that is highly conducting or insulating , transparent or opaque, or very stiff or soft. We attempt to exploit this flexible carbon...on- insulator (SOI) substrates using a modified spin-casting technique (Fig. 1a) [9]. The thinnest con- tinuous films are approximately 1–4 monolayers

  7. Photoacoustic Spectroscopy of Chemically Modified Surfaces.

    DTIC Science & Technology

    1981-08-01

    silica gel (Baker column chromotography grade, 60-200 mesh) was dried overnight at 1100C in an evacuated oven. The surface area 105 of the silica gel was...modified silica gel in the proportion of 5 mL of solution per gram of silica gel . The silica gel was recovered by filtration , washed with methanol and air...25.0 mL aliquots of the copper (II) solutions. After separation of the silica gel by filtration , the silica gel was air dried. The copper loading was

  8. Chemically modified opals as thin permselective nanoporous membranes.

    PubMed

    Newton, Michael R; Bohaty, Andrew K; White, Henry S; Zharov, Ilya

    2005-05-25

    Thin-film opals comprising three layers of 440 nm diameter SiO2 spheres were assembled on Pt electrodes and modified with amino groups on the silica surface. Diffusion of anionic, cationic, and neutral redox species through the opals was studied by cyclic voltammetry. The chemically modified opal membranes demonstrate high molecular throughput and, at low pH, selectively block transport of a cationic redox species relative to that of anionic and neutral redox species. This permselective behavior is attributed to the electrostatic interactions that are enhanced by the tortuous pathway within the opal and by the high surface area of the chemically modified spheres.

  9. Antimicrobial activity of chemically modified dextran derivatives.

    PubMed

    Tuchilus, Cristina G; Nichifor, Marieta; Mocanu, Georgeta; Stanciu, Magdalena C

    2017-04-01

    Cationic amphiphilic dextran derivatives with a long alkyl group attached to the reductive end of the polysaccharide chain and quaternary ammonium groups attached as pendent groups to the main dextran backbone were synthesized and tested for their antimicrobial properties against several bacteria and fungi strains. Dependence of antimicrobial activity on both polymer chemical composition (dextran molar mass, length of end alkyl group and chemical structure of ammonium groups) and type of microbes was highlighted by disc-diffusion method (diameter of inhibition zone) and broth microdilution method (minimum inhibitory concentrations). Polymers had antimicrobial activity for all strains studied, except for Pseudomonas aeruginosa ATCC 27853. The best activity against Staphylococcus aureus (Minimun Inhibitory Concentration 60μg/mL) was provided by polymers obtained from dextran with lower molecular mass (Mn=4500), C12H25 or C18H37 end groups, and N,N-dimethyl-N-benzylammonium pendent groups.

  10. Stabilin-1 and Stabilin-2 are specific receptors for the cellular internalization of phosphorothioate-modified antisense oligonucleotides (ASOs) in the liver

    PubMed Central

    Miller, Colton M.; Donner, Aaron J.; Blank, Emma E.; Egger, Andrew W.; Kellar, Brianna M.; Østergaard, Michael E.; Seth, Punit P.; Harris, Edward N.

    2016-01-01

    Phosphorothioate (PS)-modified antisense oligonucleotides (ASOs) have been extensively investigated over the past three decades as pharmacological and therapeutic agents. One second generation ASO, Kynamro™, was recently approved by the FDA for the treatment of homozygous familial hypercholesterolemia and over 35 second generation PS ASOs are at various stages of clinical development. In this report, we show that the Stabilin class of scavenger receptors, which were not previously thought to bind DNA, do bind and internalize PS ASOs. With the use of primary cells from mouse and rat livers and recombinant cell lines each expressing Stabilin-1 and each isoform of Stabilin-2 (315-HARE and 190-HARE), we have determined that PS ASOs bind with high affinity and these receptors are responsible for bulk, clathrin-mediated endocytosis within the cell. Binding is primarily dependent on salt-bridge formation and correct folding of the intact protein receptor. Increased internalization rates also enhanced ASO potency for reducing expression of the non-coding RNA Malat-1, in Stabilin-expressing cell lines. A more thorough understanding of mechanisms by which ASOs are internalized in cells and their intracellular trafficking pathways will aid in the design of next generation antisense agents with improved therapeutic properties. PMID:26908652

  11. Chemically modified diamondoids as biosensors for DNA

    NASA Astrophysics Data System (ADS)

    Sivaraman, Ganesh; Fyta, Maria

    2014-03-01

    Understanding the interaction of biological molecules with materials is essential in view of the novel potential applications arising when these two are combined. To this end, we investigate the interaction of DNA with diamondoids, a broad family of tiny hydrogen-terminated diamond clusters with high technological potential. We model this interaction through quantum-mechanical computer simulations and focus on the hydrogen bonding possibilities of the different DNA nucleobases to the lower amine-modified diamondoids with respect to their relative distance and orientation. Our aim is to promote the binding between these two units, and probe this through the association energy, the electronic structure of the nucleobase-diamondoid system, and the specific role of their frontier orbitals. We discuss the relevance of our results in view of biosensing applications and specifically nanopore sequencing of DNA.

  12. Chemically modified graphene based supercapacitors for flexible and miniature devices

    NASA Astrophysics Data System (ADS)

    Ghosh, Debasis; Kim, Sang Ouk

    2015-09-01

    Rapid progress in the portable and flexible electronic devises has stimulated supercapacitor research towards the design and fabrication of high performance flexible devices. Recent research efforts for flexible supercapacitor electrode materials are highly focusing on graphene and chemically modified graphene owing to the unique properties, including large surface area, high electrical and thermal conductivity, excellent mechanical flexibility, and outstanding chemical stability. This invited review article highlights current status of the flexible electrode material research based on chemically modified graphene for supercapacitor application. A variety of electrode architectures prepared from chemically modified graphene are summarized in terms of their structural dimensions. Novel prototypes for the supercapacitor aiming at flexible miniature devices, i.e. microsupercapacitor with high energy and power density are highlighted. Future challenges relevant to graphene-based flexible supercapacitors are also suggested. [Figure not available: see fulltext.

  13. Nature of the chemical reaction for furfural modified asphalt

    SciTech Connect

    Memon, G.M.; Chollar, B.H.

    1994-12-31

    Three of the most serious problems of asphalt pavements today are rutting, cracking, and susceptibility to moisture damage (stripping). Asphalt manufacturers have been mixing asphalts with polymers to produce polymer-modified asphalts with improved rheological properties. However, the costs for these improved polymer-modified asphalts are almost double that of regular asphalts. FHWA researchers have found that asphalt modified by the chemical, furfural (which is prepared by simple elimination reaction of aldopentoses obtained from oat hulls), exhibited better stripping properties and was less temperature susceptible than the virgin asphalt while costing less than polymer-modified asphalts. This paper discusses the possible structure of the furfural-modified asphalt, data for the virgin and furfural-modified asphalts and their Corbett fractions, data from a model reaction between phenol and furfural, and a possible explanation of this structure based on these data.

  14. [Adsorption of phenol chemicals by surfactant-modified zeolites].

    PubMed

    Xie, Jie; Wang, Zhe; Wu, De-Yi; Li, Chun-Jie

    2012-12-01

    Two kinds of zeolites were prepared from fly ash and modified by surfactant subsequently. Surfactant-modified zeolites were studied for adsorption of phenol chemicals (phenol, p-chlorphenol, bisphenol A). It showed that the adsorption affinity of zeolite to phenol chemicals was significantly improved after surfactant modification. The adsorption isotherms of phenol chemicals were well fitted by the Langmuir isotherm. For the two surfactant-surfactant modified zeolites, the maximum adsorption amounts of phenol, p-chlorphenol, and bisphenol A calculated from the Langmuir equation were 37.7, 52.36, 90.9 mg x g(-1) and 10.7, 22.83, 56.8 mg x g(-1), respectively. When pH values of solutions were higher than the pK(a) values of phenol chemicals, the removal efficiencies were getting higher with the increase of pH values. The octanol/water partition coefficient (K(ow)) was also found to be an important factor affecting adsorption of phenol chemicals by the modified zeolites. Higher K(ow) value, which means the greater hydrophobicity of the chemicals, resulted in a higher removal.

  15. Lubricants from chemically modified vegetable oils.

    PubMed

    Campanella, Alejandrina; Rustoy, Eduardo; Baldessari, Alicia; Baltanás, Miguel A

    2010-01-01

    This work reports laboratory results obtained from the production of polyols with branched ether and ester compounds from epoxidized vegetable oils pertaining to annual, temperate climate crops (soybean, sunflower and high-oleic sunflower oils), focusing on their possible use as components of lubricant base stocks. To this end, two different opening reactions of the epoxide ring were studied. The first caused by the attack with glacial acetic acid (exclusively in a single organic phase) and the second using short-chain aliphatic alcohols, methanol and ethanol, in acid media. Both reactions proceed under mild conditions: low synthesis temperature and short reaction times and with conversions above 99%. Spectroscopic (NMR), thermal (DSC) and rheological techniques were used to characterize the oils, their epoxides and polyols, to assess the impact of the nature of the vegetable oil and the chemical modifications introduced, including long-term storage conditions. Several correlations were employed to predict the viscosity of the vegetable oils with temperature, and good agreement with the experimental data was obtained.

  16. Chemically-modified cellulose paper as a microstructured catalytic reactor.

    PubMed

    Koga, Hirotaka; Kitaoka, Takuya; Isogai, Akira

    2015-01-15

    We discuss the successful use of chemically-modified cellulose paper as a microstructured catalytic reactor for the production of useful chemicals. The chemical modification of cellulose paper was achieved using a silane-coupling technique. Amine-modified paper was directly used as a base catalyst for the Knoevenagel condensation reaction. Methacrylate-modified paper was used for the immobilization of lipase and then in nonaqueous transesterification processes. These catalytic paper materials offer high reaction efficiencies and have excellent practical properties. We suggest that the paper-specific interconnected microstructure with pulp fiber networks provides fast mixing of the reactants and efficient transport of the reactants to the catalytically-active sites. This concept is expected to be a promising route to green and sustainable chemistry.

  17. Thermoreversible gelation in aqueous binary solvents of chemically modified agarose.

    PubMed

    Dahmani, Mohammed; Ramzi, Mohamed; Rochas, Cyrille; Guenet, Jean-Michel

    2003-01-15

    The thermoreversible gelation of chemically modified agarose has been studied in aqueous binary solvents (dimethyl sulfoxide and a series of formamide) by differential calorimetry, mechanical testing, and small-angle neutron scattering. The temperature-composition phase diagrams have been established. It is concluded that gelation is promoted by the formation of ternary complexes modified agarose/water/cosolvent, wherein the cosolvent mediates the interaction between chains through the formation of electrostatic interactions.

  18. Visualized detection of single-base difference in multiplexed loop-mediated isothermal amplification amplicons by invasive reaction coupled with oligonucleotide probe-modified gold nanoparticles.

    PubMed

    Lu, Yan; Ma, Xueping; Wang, Jianping; Sheng, Nan; Dong, Tianhui; Song, Qinxin; Rui, Jianzhong; Zou, Bingjie; Zhou, Guohua

    2017-04-15

    Loop-mediated isothermal amplification (LAMP) is a well-developed DNA amplification method with an ultra-high sensitivity, but it is difficult to recognize a single-base difference (like genotyping) in target-specific amplicons by conventional detection ways, such as the intercalation of dyes into dsDNA amplicons or the increase of solution turbidity along with the polymerization process. To allow genotyping based on LAMP suitable for POCT (point-of-care testing) or on-site testing, here we proposed a highly specific and cost-effective method for detecting a single-base difference in LAMP amplicons. The method includes three key steps, sequence amplifier to amplify multiple fragments containing the single nucleotide polymorphisms (SNPs) of interest, allele identifier to recognize a targeted base in the amplicons by invasive reaction, and signal generator to yield signals by hybridization-induced assembly of oligonucleotide probe-modified gold nanoparticles. Because the allele identifier is sensitive to one base difference, it is possible to use multiplexed LAMP (mLAMP) to generate amplicon mixtures for multiple SNP typing. Genotyping of 3 different SNPs (CYP2C19*2, CYP2C19*3 and MDR1-C3435T) for guiding the dosage of clopidogrel is successfully carried out in a 3-plex LAMP on real clinical samples. As our method relies on the naked-eye detection and constant-temperature reaction, no expensive instrument is required for both target amplification and sequence identification, thus much suitable for inexpensive gene-guided personalized medicine in source-limited regions.

  19. Modified NASA-Lewis chemical equilibrium code for MHD applications

    NASA Technical Reports Server (NTRS)

    Sacks, R. A.; Geyer, H. K.; Grammel, S. J.; Doss, E. D.

    1979-01-01

    A substantially modified version of the NASA-Lewis Chemical Equilibrium Code was recently developed. The modifications were designed to extend the power and convenience of the Code as a tool for performing combustor analysis for MHD systems studies. The effect of the programming details is described from a user point of view.

  20. Pentopyranosyl Oligonucleotide Systems

    NASA Technical Reports Server (NTRS)

    Wagner, Thomas; Huyuh, Hoan K.; Krishnamurthy, Ramanarayanan; Eschenmoser, Albert

    2002-01-01

    Beta-D-Xylopyranosyl-(4 - 2 )-oligonucleotides containing adenine and thymine as nucleohases were synthesized as a part of a systematic study of the pairing properties of pentopyranosyl oligonucleotides. Contrary to earlier expectations based on qualitative conformational criteria, Beta-D-xylopyranosyl(4 - 2 )- oligonucleotides show Watson-Crick pairing comparable in strength to that shown by pyranosyl-RNA.

  1. Synthesis, thermal stability and reactivity towards 9-aminoellipticine of double-stranded oligonucleotides containing a true abasic site.

    PubMed Central

    Bertrand, J R; Vasseur, J J; Rayner, B; Imbach, J L; Paoletti, J; Paoletti, C; Malvy, C

    1989-01-01

    A 13 mers abasic oligonucleotide was synthetized. It was therefore possible to compare thermal stability and reactivity of duplex oligonucleotides either with an apurinic/apyrimidinic site or without any lesion. An important decrease in the melting temperature appeared for duplexes with an abasic site. The chemical reaction of these modified oligonucleotides with the intercalating agent 9-aminoellipticine was studied by gel electrophoresis and by fluorescence. The formation of a Schiff base between 9-aminoellipticine and abasic sites was rapid and complete with duplexes at 11 degrees C. Schiff base related fluorescence and beta-elimination cleavage were more important with the apyrimidinic sites than with the apurinic ones. When compared to previous results obtained with the model d(TprpT) some unexpected behaviours appeared with longer and duplex oligonucleotides. For instance only partial beta-elimination cleavage was observed. It is likely that stacking parameters in the double helix play a great role in the studied reaction. Images PMID:2602153

  2. Gene silencing by chemically modified siRNAs.

    PubMed

    Engels, Joachim W

    2013-03-25

    RNA interference (RNAi) has not only already risen as a gold standard for validating gene function in basic science studies, but also holds great promise as a new therapeutic paradigm. Advantages of RNAi-based therapeutics include relatively fast initial screening and the ability to target proteins not yet addressable by traditional drug design strategies. In this review we describe the development of chemically modified small inhibiting siRNAs and their application as potential therapeutics during the past decade. Focus is on proper siRNA design, choice of chemical modification and how to circumvent immunogenicity as well as off-target effects.

  3. ZnS nanoflakes deposition by modified chemical method

    SciTech Connect

    Desai, Mangesh A. Sartale, S. D.

    2014-04-24

    We report deposition of zinc sulfide nanoflakes on glass substrates by modified chemical method. The modified chemical method involves adsorption of zinc–thiourea complex on the substrate and its dissociation in presence of hydroxide ions to release sulfur ions from thiourea which react with zinc ions present in the complex to form zinc sulfide nanoflakes at room temperature. Influence of zinc salt and thiourea concentrations ratios on the morphology of the films was investigated by scanning electron microscope (SEM). The ratio of zinc and thiourea in the zinc–thiourea complex significantly affect the size of the zinc sulfide nanoflakes, especially width and density of the nanoflakes. The X-ray diffraction analysis exhibits polycrystalline nature of the zinc sulfide nanoflakes with hexagonal phase.

  4. Chemically Modified Metal Oxide Nanostructure for Photoelectrochemical Water Splitting

    NASA Astrophysics Data System (ADS)

    Wang, Gongming

    Hydrogen gas is chemical fuel with high energy density, and represents a clean, renewable and carbon-free burning fuel, which has the potential to solve the more and more urgent energy crisis in today's society. Inspired by natural photosynthesis, artificial photosynthesis to generate hydrogen energy has attracted a lot of attentions in the field of chemistry, physics and material. Photoelectrochemical water splitting based on semiconductors represents a green and low cost method to generate hydrogen fuel. However, the current overall efficiency of solar to hydrogen is quite low, due to some intrinsic limitations such as bandgap, diffusion distance, carrier lifetime and photostability of semiconductors. Although nanostructured semiconductors can improve their photoelectrochemical water splitting performance to some extent, by increasing electrolyte accessible area and shortening minority carrier diffusion distance, nanostructure engineering cannot change their intrinsic electronic properties. Recent development in chemically modified nanostructures such as surface catalyst decoration, element doping, plasmonic modification and interfacial hetero-junction design have led to significant advancement in the photoelectrochemical water splitting, by improving surface reaction kinetics and charge separation, transportation and collection efficiency. In this thesis, I will give a detailed discussion on the chemically modified metal oxide nanostructures for photoelectrocemical hydrogen generation, with a focus on the element doping, hydrogen treatment and catalyst modification. I have demonstrated nitrogen doping on ZnO and Ti doping on hematite can improve their photoelectrochemical performance. In addition, we found hydrogen treatment is a general and effective method to improve the photocatalytic performance, by increasing their carrier desities. Hydrogen treatment has been demonstrated on TiO2, WO3 and BiVO4. In the end, we also used electrochemical catalyt to modify

  5. Immobilization of urease onto chemically modified acrylonitrile copolymer membranes.

    PubMed

    Godjevargova, T; Gabrovska, K

    2003-06-26

    Poly (acrylonitrile-methylmethacrylate-sodium vinylsulfonate) membranes were subjected to seven different chemical modifications. The amounts of new groups incorporated in the membranes with the modifications were determined. Urease was covalently immobilized on the modified membranes. Both the amount of bound protein and relative activity of immobilized urease were measured. The highest activity was found for urease bound to membranes modified with hydroxylammonium sulfate (68%) and hydrazinium sulfate (67%). Optimum pH of free urease was determined to be 5.8. For positively charged membranes, pH optimum was shifted to higher values, while for negatively charged membranes-to lower pH. The charge of the matrix affected also the rate of the enzyme reaction. The highest rate was measured with urease immobilized on membranes modified with hydroxylammonium sulfate and hydrazinium sulfate. The major part of the immobilized enzyme on different modified membranes remained stable-only ca. 20% of enzyme activity was lost for 4 h at 70 degrees C while the free enzyme was totally inactivated.

  6. Adhesive and morphological characteristics of surface chemically modified polytetrafluoroethylene films

    NASA Astrophysics Data System (ADS)

    Hopp, B.; Kresz, N.; Kokavecz, J.; Smausz, T.; Schieferdecker, H.; Döring, A.; Marti, O.; Bor, Z.

    2004-01-01

    In the present paper, we report an experimental determination of adhesive and topographic characteristics of chemically modified surface of polytetrafluoroethylene (PTFE) films. The surface chemistry was modified by ArF excimer laser irradiation in presence of triethylene-tetramine photoreagent. The applied laser fluence was varied in the range of 0.4-9 mJ/cm 2, and the number of laser pulses incident on the same area was 1500. To detect the changes in the adhesive features of the treated Teflon samples, we measured receding contact angle for distilled water and adhesion strength, respectively. It was found that the receding contact angle decreased from 96° to 30-37° and the adhesion strength of two-component epoxy glue to the treated sample surface increased from 0.03 to 9 MPa in the applied laser fluence range. Additionally, it was demonstrated that the adhesion of human cells to the modified Teflon samples is far better than to the untreated ones. The contact mode and pulsed force mode atomic force microscopic investigations of the treated samples demonstrated that the measured effective contact area of the irradiated films does not differ significantly from that of the original films, but the derived adhesion force is stronger on the modified samples than on the untreated ones. Hence, the increased adhesion of the treated Teflon films is caused by the higher surface energy.

  7. Chemically modified cellulose paper as a thin film microextraction phase.

    PubMed

    Saraji, Mohammad; Farajmand, Bahman

    2013-11-01

    In this paper, chemically modified cellulose paper was introduced as a novel extracting phase for thin film microextraction (TFME). Different reagents (Octadecyltrichlorosilane, diphenyldichlorosilane, cyclohexyl isocyanate and phenyl isocyanate) were used to modify the cellulose papers. The modified papers were evaluated as a sorbent for the extraction of some synthetic and natural estrogenic hormones (17α-ethynylestradiol, estriol and estradiol) from aqueous samples. Liquid chromatography-fluorescence detection was used for the quantification of the extracted compounds. The cellulose paper modified with phenyl isocyanate showed the best affinity to the target compounds. TEME parameters such as desorption condition, shaking rate, sample ionic strength and extraction time were investigated and optimized. Limit of detections were between 0.05 and 0.23μgL(-1) and relative standard deviations were less than 11.1% under the optimized condition. The calibration curves were obtained in the range of 0.2-100μgL(-1) with a good linearity (r(2)>0.9935). Wastewater, human urine, pool and river water samples were studied as real samples for the evaluation of the method. Relative recoveries were found to be between 75% and 101%.

  8. The oral and craniofacial relevance of chemically modified RNA therapeutics.

    PubMed

    Elangovan, Satheesh; Kormann, Michael S D; Khorsand, Behnoush; Salem, Aliasger K

    2016-01-01

    Several tissue engineering strategies in the form of protein therapy, gene therapy, cell therapy, and their combinations are currently being explored for oral and craniofacial regeneration and repair. Though each of these approaches has advantages, they all have common inherent drawbacks of being expensive and raising safety concerns. Using RNA (encoding therapeutic protein) has several advantages that have the potential to overcome these limitations. Chemically modifying the RNA improves its stability and mitigates immunogenicity allowing for the potential of RNA to become an alternative to protein and gene based therapies. This brief review article focuses on the potential of RNA therapeutics in the treatment of disorders in the oral and craniofacial regions.

  9. Detecting Chemically Modified DNA Bases Using Surface Enhanced Raman Spectroscopy.

    PubMed

    Barhoumi, Aoune; Halas, Naomi J

    2011-12-15

    Post-translational modifications of DNA- changes in the chemical structure of individual bases that occur without changes in the DNA sequence- are known to alter gene expression. They are believed to result in frequently deleterious phenotypic changes, such as cancer. Methylation of adenine, methylation and hydroxymethylation of cytosine, and guanine oxidation are the primary DNA base modifications identified to date. Here we show it is possible to use surface enhanced Raman spectroscopy (SERS) to detect these primary DNA base modifications. SERS detection of modified DNA bases is label-free and requires minimal additional sample preparation, reducing the possibility of additional chemical modifications induced prior to measurement. This approach shows the feasibility of DNA base modification assessment as a potentially routine analysis that may be further developed for clinical diagnostics.

  10. G-Quadruplex Forming Oligonucleotides as Anti-HIV Agents.

    PubMed

    Musumeci, Domenica; Riccardi, Claudia; Montesarchio, Daniela

    2015-09-22

    Though a variety of different non-canonical nucleic acids conformations have been recognized, G-quadruplex structures are probably the structural motifs most commonly found within known oligonucleotide-based aptamers. This could be ascribed to several factors, as their large conformational diversity, marked responsiveness of their folding/unfolding processes to external stimuli, high structural compactness and chemo-enzymatic and thermodynamic stability. A number of G-quadruplex-forming oligonucleotides having relevant in vitro anti-HIV activity have been discovered in the last two decades through either SELEX or rational design approaches. Improved aptamers have been obtained by chemical modifications of natural oligonucleotides, as terminal conjugations with large hydrophobic groups, replacement of phosphodiester linkages with phosphorothioate bonds or other surrogates, insertion of base-modified monomers, etc. In turn, detailed structural studies have elucidated the peculiar architectures adopted by many G-quadruplex-based aptamers and provided insight into their mechanism of action. An overview of the state-of-the-art knowledge of the relevance of putative G-quadruplex forming sequences within the viral genome and of the most studied G-quadruplex-forming aptamers, selectively targeting HIV proteins, is here presented.

  11. Modified chemical route for deposition of molybdenum disulphide thin films

    SciTech Connect

    Vyas, Akshay N. Sartale, S. D.

    2014-04-24

    Molybdenum disulphide (MoS{sub 2}) thin films were deposited on quartz substrates using a modified chemical route. Sodium molybdate and sodium sulphide were used as precursors for molybdenum and sulphur respectively. The route involves formation of tetrathiomolybdate ions (MoS{sub 4}{sup 2−}) and further reduction by sodium borohydride to form MoS{sub 2}. The deposition was performed at room temperature. The deposited films were annealed in argon atmosphere at 1073 K for 1 hour to improve its crystallinity. The deposited films were characterized using scanning electron microscopy (SEM) for morphology, UV-Vis absorption spectroscopy for optical studies and X-ray diffraction (XRD) for structure determination.

  12. Engineering chemically modified viruses for prostate cancer cell recognition.

    PubMed

    Mohan, K; Weiss, G A

    2015-12-01

    Specific detection of circulating tumor cells and characterization of their aggressiveness could improve cancer diagnostics and treatment. Metastasis results from such tumor cells, and causes the majority of cancer deaths. Chemically modified viruses could provide an inexpensive and efficient approach to detect tumor cells and quantitate their cell surface biomarkers. However, non-specific adhesion between the cell surface receptors and the virus surface presents a challenge. This report describes wrapping the virus surface with different PEG architectures, including as fusions to oligolysine, linkers, spacers and scaffolded ligands. The reported PEG wrappers can reduce by >75% the non-specific adhesion of phage to cell surfaces. Dynamic light scattering verified the non-covalent attachment by the reported wrappers as increased sizes of the virus particles. Further modifications resulted in specific detection of prostate cancer cells expressing PSMA, a key prostate cancer biomarker. The approach allowed quantification of PSMA levels on the cell surface, and could distinguish more aggressive forms of the disease.

  13. The Oral and Craniofacial Relevance of Chemically Modified RNA Therapeutics

    PubMed Central

    Kormann, Michael S.D.; Khorsand, Behnoush

    2016-01-01

    Several tissue engineering strategies in the form of protein therapy, gene therapy, cell therapy and its combinations are currently being explored for oral and cranio-facial regeneration and repair. Though each of these approaches has advantages, they all have common inherent drawbacks of being expensive and raising safety concerns. Using RNA (encoding therapeutic protein) has several advantages that have the potential to overcome these limitations. Chemically modifying the RNA improves its stability and mitigates immunogenicity allowing for the potential of RNA to become an alternative to protein and gene based therapies. This brief review article focuses on the potential of RNA therapeutics in the treatment of disorders in the oral and craniofacial regions. PMID:26896600

  14. Impedimetric immunoglobulin G immunosensor based on chemically modified graphenes

    NASA Astrophysics Data System (ADS)

    Loo, Adeline Huiling; Bonanni, Alessandra; Ambrosi, Adriano; Poh, Hwee Ling; Pumera, Martin

    2012-01-01

    Immunosensors which display high sensitivity and selectivity are of utmost importance to the biomedical field. Graphene is a material which has immense potential for the fabrication of immunosensors. For the first time, we evaluate the immunosensing capabilities of various graphene surfaces in this work. We propose a simple and label-free electrochemical impedimetric immunosensor for immunoglobulin G (IgG) based on chemically modified graphene (CMG) surfaces such as graphite oxide, graphene oxide, thermally reduced graphene oxide and electrochemically reduced graphene oxide. Disposable electrochemical printed electrodes were first modified with CMG materials before anti-immunoglobulin G (anti-IgG), which is specific to IgG, was immobilized. The principle of detection lies in the changes in impedance spectra of the redox probe after the attachment of IgG to the immobilized anti-IgG. It was found that thermally reduced graphene oxide has the best performance when compared to the other CMG materials. In addition, the optimal concentration of anti-IgG to be deposited onto the modified electrode surface is 10 μg ml-1 and the linear range of detection of the immunosensor is from 0.3 μg ml-1 to 7 μg ml-1. Finally, the fabricated immunosensor also displays selectivity for IgG.Immunosensors which display high sensitivity and selectivity are of utmost importance to the biomedical field. Graphene is a material which has immense potential for the fabrication of immunosensors. For the first time, we evaluate the immunosensing capabilities of various graphene surfaces in this work. We propose a simple and label-free electrochemical impedimetric immunosensor for immunoglobulin G (IgG) based on chemically modified graphene (CMG) surfaces such as graphite oxide, graphene oxide, thermally reduced graphene oxide and electrochemically reduced graphene oxide. Disposable electrochemical printed electrodes were first modified with CMG materials before anti-immunoglobulin G (anti

  15. Highly efficient adsorption of chlorophenols onto chemically modified chitosan

    NASA Astrophysics Data System (ADS)

    Zhou, Liang-Chun; Meng, Xiang-Guang; Fu, Jing-Wei; Yang, Yu-Chong; Yang, Peng; Mi, Chun

    2014-02-01

    A novel chemically modified chitosan CS-SA-CD with phenol and β-cyclodextrin groups was prepared. The adsorptions of phenol, 2-chlorophenol (2-CP), 4-chlorophenol (4-CP), 2,4-dichlorophenol (DCP) and 2,4,6-trichlorophenol (TCP) on the functional chitosan from aqueous solution were investigated. CS-SA-CD exhibited excellent adsorption ability for chlorophenols especially for DCP and TCP. The maximum adsorption capacities of phenol, 2-CP, 4-CP, DCP and TCP on CS-SA-CD were 59.74, 70.52, 96.43, 315.46 and 375.94 mg/g, respectively. The scanning electron microscope and Brunauer-Emmett-Teller analyses revealed that the introduction of phenol group changed the surface morphology and surface properties of chitosan. The modified chitosan CS-SA-CD possesses larger surface areas (4.72 m2/g), pore volume (7.29 × 10-3 mL/g) and average pore diameter (59.99 Å) as compared to those of chitosan 3.27 m2/g, 2.00 × 10-3 mL/g and 15.95 Å, respectively. The enhanced adsorption of chlorophenols was also attributed to the interaction of hydrogen bond between Cl atom and sbnd OH group. The adsorption of chlorophenols on CS-SA-CD followed the pseudo-second-order kinetic model. Adsorbent could be regenerated easily and the regenerated CS-SA-CD remained 80-91% adsorption efficiency.

  16. P-chiral oligonucleotides in biological recognition processes.

    PubMed

    Guga, Piotr

    2007-01-01

    Internucleotide phosphodiester linkages in non-modified oligonucleotides are quickly degraded by nucleolytic enzymes present in the cells and this feature practically eliminates natural DNA and RNA molecules from medical applications and from many structural and mechanistic studies. P-chiral oligonucleotide analogs, in which one of the non-bridging phosphate oxygen atoms is substituted with another heteroatom (e.g. S, Se) or a chemical group (e.g. CH3, BH3(-)), have significantly greater nuclease resistance and also offer important possibilities for detailed studies of interactions with other biomolecules at the molecular level. Notably, these substitutions do not disrupt hydrogen bonding between nucleobases and affect the overall geometry of the oligomers to only low or moderate extent, although important changes of hydration patterns and changes of interactions with metal ions are observed. Such the probes, including isotopomeric species labeled with a heavy oxygen isotope, possessing phosphorus atoms of selected absolute configurations, have been used for elucidation of the mode of action of many enzymes (nucleases, transferases, kinases), ribozymes and DNA-zymes, as well as for investigations on thermodynamic stability of nucleic acids complexes (duplexes, triplexes, i-motif) and for studies on a mechanism of conformational changes of B-Z type. They are also useful tools for analysis of interactions of the phosphoryl oxygen atoms in natural precursors with functional groups of proteins. The synthetic routes to stereodefined forms of selected types of P-chiral oligonucleotides are presented, as well as recently developed methods for their configurational analysis at micromolar concentration. Selected examples of application of diastereomerically pure P-chiral oligonucleotides for structural, biochemical and biological experiments are discussed.

  17. Ratiometric detection of oligonucleotide stoichiometry on multifunctional gold nanoparticles by whispering gallery mode biosensing.

    PubMed

    Wu, F C; Wu, Y; Niu, Z; Vollmer, F

    2015-05-07

    A label-free method is developed to ratiometrically determine the stoichiometry of oligonucleotides attached to the surface of gold nanoparticle (GNP) by whispering gallery mode biosensing. Utilizing this scheme, it is furthermore shown that the stoichiometric ratio of GNP attached oligonucleotide species can be controlled by varying the concentration ratio of thiolated oligonucleotides that are used to modify the GNP.

  18. Synthesis of triazole-linked oligonucleotides with high affinity to DNA complements and an analysis of their compatibility with biosystems.

    PubMed

    Varizhuk, Anna M; Kaluzhny, Dmitry N; Novikov, Roman A; Chizhov, Alexandr O; Smirnov, Igor P; Chuvilin, Andrey N; Tatarinova, Olga N; Fisunov, Gleb Y; Pozmogova, Galina E; Florentiev, Vladimir L

    2013-06-21

    New oligonucleotide analogues with triazole internucleotide linkages were synthesized, and their hybridization properties were studied. The analogues demonstrated DNA binding affinities similar to those of unmodified oligonucleotides. The modification was shown to protect the oligonucleotides from nuclease hydrolysis. The modified oligonucleotides were tested as PCR primers. Modifications remote from the 3'-terminus were tolerated by polymerases. Our results suggest that these new oligonucleotide analogues are among the most promising triazole DNA mimics characterized to date.

  19. Oligonucleotide conjugates - Candidates for gene silencing therapeutics.

    PubMed

    Gooding, Matt; Malhotra, Meenakshi; Evans, James C; Darcy, Raphael; O'Driscoll, Caitriona M

    2016-10-01

    The potential therapeutic and diagnostic applications of oligonucleotides (ONs) have attracted great attention in recent years. The capability of ONs to selectively inhibit target genes through antisense and RNA interference mechanisms, without causing un-intended sideeffects has led them to be investigated for various biomedical applications, especially for the treatment of viral diseases and cancer. In recent years, many researchers have focused on enhancing the stability and target specificity of ONs by encapsulating/complexing them with polymers or lipid chains to formulate nanoparticles/nanocomplexes/micelles. Also, chemical modification of nucleic acids has emerged as an alternative to impart stability to ONs against nucleases and other degrading enzymes and proteins found in blood. In addition to chemically modifying the nucleic acids directly, another strategy that has emerged, involves conjugating polymers/peptide/aptamers/antibodies/proteins, preferably to the sense strand (3'end) of siRNAs. Conjugation to the siRNA not only enhances the stability and targeting specificity of the siRNA, but also allows for the development of self-administering siRNA formulations, with a much smaller size than what is usually observed for nanoparticle (∼200nm). This review concentrates mainly on approaches and studies involving ON-conjugates for biomedical applications.

  20. Magnetorheological finishing of chemical-vapor deposited zinc sulfide via chemically and mechanically modified fluids

    DOE PAGES

    Salzman, Sivan; Romanofsky, Henry J.; Giannechini, Lucca J.; ...

    2016-02-19

    In this study, we describe the anisotropy in the material removal rate (MRR) of the polycrystalline, chemical-vapor deposited zinc sulfide (ZnS).We define the polycrystalline anisotropy via microhardness and chemical erosion tests for four crystallographic orientations of ZnS: (100), (110), (111), and (311). Anisotropy in the MRR was studied under magnetorheological finishing (MRF) conditions. Three chemically and mechanically modified magnetorheological (MR) fluids at pH values of 4, 5, and 6 were used to test the MRR variations among the four single-crystal planes. When polishing the single-crystal planes and the polycrystalline with pH 5 and pH 6MR fluids, variations were found inmore » the MRR among the four single-crystal planes and surface artifacts were observed on the polycrystalline material. When polishing the single-crystal planes and the polycrystalline with the modified MR fluid at pH 4, however, minimal variation was observed in the MRR among the four orientations and a reduction in surface artifacts was achieved on the polycrystalline material.« less

  1. Magnetorheological finishing of chemical-vapor deposited zinc sulfide via chemically and mechanically modified fluids

    SciTech Connect

    Salzman, Sivan; Romanofsky, Henry J.; Giannechini, Lucca J.; Jacobs, Stephen D.; Lambropoulos, John C.

    2016-02-19

    In this study, we describe the anisotropy in the material removal rate (MRR) of the polycrystalline, chemical-vapor deposited zinc sulfide (ZnS).We define the polycrystalline anisotropy via microhardness and chemical erosion tests for four crystallographic orientations of ZnS: (100), (110), (111), and (311). Anisotropy in the MRR was studied under magnetorheological finishing (MRF) conditions. Three chemically and mechanically modified magnetorheological (MR) fluids at pH values of 4, 5, and 6 were used to test the MRR variations among the four single-crystal planes. When polishing the single-crystal planes and the polycrystalline with pH 5 and pH 6MR fluids, variations were found in the MRR among the four single-crystal planes and surface artifacts were observed on the polycrystalline material. When polishing the single-crystal planes and the polycrystalline with the modified MR fluid at pH 4, however, minimal variation was observed in the MRR among the four orientations and a reduction in surface artifacts was achieved on the polycrystalline material.

  2. Synthesis and anti-HIV activity of thiocholesteryl-coupled phosphodiester antisense oligonucleotides incorporated into immunoliposomes.

    PubMed

    Zelphati, O; Wagner, E; Leserman, L

    1994-09-01

    Encapsulation of oligonucleotides in antibody-targeted liposomes (immunoliposomes) which bind to target cells permits intracellular delivery of the oligonucleotides. This approach circumvents problems of extracellular degradation by nucleases and poor membrane permeability which free phosphodiester oligonucleotides are subject to, but leaves unresolved the inefficiency of encapsulation of oligonucleotides in liposomes. We have coupled oligonucleotides to cholesterol via a reversible disulfide bond. This modification of oligonucleotides improved their association with immunoliposomes by a factor of about 10 in comparison to unmodified oligonucleotides. The presence of cholesteryl-modified oligonucleotides incorporated in the bilayer of liposomes did not interfere with the coupling of the targeting protein to the liposome surface. Free or cholesterol coupled oligonucleotides associated with liposomes and directed against the tat gene of HIV-1 were tested for inhibition of HIV-1 proliferation in acutely infected cells. We demonstrate that the cholesteryl-modified as well as unmodified oligonucleotides acquire the target specificity of the antibody on the liposome. Their antiviral activity when delivered into cells is sequence-specific. The activity of these modified or unmodified oligonucleotides to inhibit the replication of HIV was the same on an equimolar basis (EC50 around 0.1 microM). Cholesterol coupled oligonucleotides thus offer increased liposome association without loss of antiviral activity.

  3. Chemically modified RNA activated matrices enhance bone regeneration.

    PubMed

    Elangovan, Satheesh; Khorsand, Behnoush; Do, Anh-Vu; Hong, Liu; Dewerth, Alexander; Kormann, Michael; Ross, Ryan D; Sumner, D Rick; Allamargot, Chantal; Salem, Aliasger K

    2015-11-28

    There exists a dire need for improved therapeutics to achieve predictable bone regeneration. Gene therapy using non-viral vectors that are safe and efficient at transfecting target cells is a promising approach to overcoming the drawbacks of protein delivery of growth factors. Here, we investigated the transfection efficiency, cytotoxicity, osteogenic potential and in vivo bone regenerative capacity of chemically modified ribonucleic acid (cmRNA) (encoding BMP-2) complexed with polyethylenimine (PEI) and made comparisons with PEI complexed with conventional plasmid DNA (encoding BMP-2). The polyplexes were fabricated at an amine (N) to phosphate (P) ratio of 10 and characterized for transfection efficiency using human bone marrow stromal cells (BMSCs). The osteogenic potential of BMSCs treated with these polyplexes was validated by determining the expression of bone-specific genes, osteocalcin and alkaline phosphatase as well as through the detection of bone matrix deposition. Using a calvarial bone defect model in rats, it was shown that PEI-cmRNA (encoding BMP-2)-activated matrices promoted significantly enhanced bone regeneration compared to PEI-plasmid DNA (BMP-2)-activated matrices. Our proof of concept study suggests that scaffolds loaded with non-viral vectors harboring cmRNA encoding osteogenic proteins may be a powerful tool for stimulating bone regeneration with significant potential for clinical translation.

  4. Deformability Calculation for Estimation of the Relative Stability of Chemically Modified RNA Duplexes.

    PubMed

    Masaki, Yoshiaki; Sekine, Mitsuo; Seio, Kohji

    2017-03-02

    Chemical modification of RNA duplexes alters their stability. We have attempted to develop a computational approach to estimate the thermal stability of chemically modified duplexes. These studies revealed that the deformability of chemically modified RNA duplexes, calculated from molecular dynamics simulations, could be used as a good indicator for estimating the effect of chemical modification on duplex thermal stability. This unit describes how deformability calculation can be applied to estimate the relative stability of chemically modified RNA duplexes. © 2017 by John Wiley & Sons, Inc.

  5. Why Carba-LNA-modified oligonucleotides show considerably improved 3'-exonuclease stability compared to that of the LNA modified or the native counterparts: A Michaelis-Menten kinetic analysis.

    PubMed

    Zhou, Chuanzheng; Chattopadhyaya, Jyoti

    2010-04-02

    In this study, 12 different native or LNA, carba-LNA-modified dinucleoside phosphates were designed as simple chemical models to study how carba-LNA modifications improve the 3'-exonuclease (SVPDE in this study) resistance of internucleotidic phosphate compared to those exhibited by LNA-modified and the native counterparts. Michaelis-Menten kinetic studies for dimers 3 - 7, in which the LNA or carba-LNA modifications are located at the 5'-end, showed that (i) increased 3'-exonuclease resistance of (5')[LNA-T](p)T (3) compared to the native (5')T(p)T (1) was mainly attributed to steric hindrance imposed by the LNA modification that retards the nuclease binding (K(M)) and (ii) digestion of (5')[carba-LNA-dT](p)T (4) and (5')[LNA-T](p)T (3), however, exhibit similar K(M)s, whereas the former shows a 100x decrease in K(cat) and is hence more stable than the latter. By studying the correlation between log k(cat) and pK(a) of the departing 3'(or 6')-OHs for 3-7, we found the pK(a) of 3'-OH of carba-LNA-T was 1.4 pK(a) units higher than that of LNA-T, and this relatively less acidic character of the 3'-OH in the former leads to the 100x decrease in the catalytic efficiency for the digestion of (5')[carba-LNA-T](p)T (4). In contrast, Michaelis-Menten kinetic studies for dimers 9-12, with the LNA or carba-LNA modifications at the 3'-end, showed that the digestion of (5')T(p)[LNA-T] (9) exhibited similar K(M) but k(cat) decreased around 40 times compared to that of the native (5')T(p)T (1). Similar k(cat) values have been observed for digestion of (5')T(p)[carba-LNA-T] (10) and (5')T(p)[LNA-T] (9). The higher stability of carba-LNA modified dimer 10 compared with LNA modified dimer 9 comes solely from the increased K(M).

  6. The delivery of therapeutic oligonucleotides

    PubMed Central

    Juliano, Rudolph L.

    2016-01-01

    The oligonucleotide therapeutics field has seen remarkable progress over the last few years with the approval of the first antisense drug and with promising developments in late stage clinical trials using siRNA or splice switching oligonucleotides. However, effective delivery of oligonucleotides to their intracellular sites of action remains a major issue. This review will describe the biological basis of oligonucleotide delivery including the nature of various tissue barriers and the mechanisms of cellular uptake and intracellular trafficking of oligonucleotides. It will then examine a variety of current approaches for enhancing the delivery of oligonucleotides. This includes molecular scale targeted ligand-oligonucleotide conjugates, lipid- and polymer-based nanoparticles, antibody conjugates and small molecules that improve oligonucleotide delivery. The merits and liabilities of these approaches will be discussed in the context of the underlying basic biology. PMID:27084936

  7. Noncoding oligonucleotides: the belle of the ball in gene therapy.

    PubMed

    Shum, Ka-To; Rossi, John J

    2015-01-01

    Gene therapy carries the promise of cures for many diseases based on manipulating the expression of a person's genes toward the therapeutic goal. The relevance of noncoding oligonucleotides to human disease is attracting widespread attention. Noncoding oligonucleotides are not only involved in gene regulation, but can also be modified into therapeutic tools. There are many strategies that leverage noncoding oligonucleotides for gene therapy, including small interfering RNAs, antisense oligonucleotides, aptamers, ribozymes, decoys, and bacteriophage phi 29 RNAs. In this chapter, we will provide a broad, comprehensive overview of gene therapies that use noncoding oligonucleotides for disease treatment. The mechanism and development of each therapeutic will be described, with a particular focus on its clinical development. Finally, we will discuss the challenges associated with developing nucleic acid therapeutics and the prospects for future success.

  8. Bromodeoxyuridine-labeled oligonucleotides as tools for oligonucleotide uptake studies.

    PubMed

    Maszewska, Maria; Kobylańska, Anna; Gendaszewska-Darmach, Edyta; Koziołkiewicz, Maria

    2002-12-01

    The mechanisms by which various oligonucleotides (ODNs) and their analogs enter cells are not fully understood. A common technique used in studies on cellular uptake of ODNs is their conjugation with fluorochromes. However, fluorescently labeled ODNs may vary from the parent compounds in charge and hydrophilicity, and they may interact differently with some components of cellular membranes. In this report, we present an alternative method based on the immunofluorescent detection of ODNs with incorporated 5-bromo-2'-deoxyuridine (BrdUrd). Localization of BrdUrd-modified ODNs has been achieved using FITC-labeled anti-BrdUrd antibodies. This technique allowed determination of the differences in cellular uptake of phosphodiester (PO) and phosphorothioate (PS) ODNs and their derivatives conjugated with cholesterol and menthol. The immunocytochemical method also has shown that the cellular uptake of some ODNs may be influenced by specific sequences that are responsible for the formation of higher-order structures.

  9. Comparison of small molecules and oligonucleotides that target a toxic, non-coding RNA.

    PubMed

    Costales, Matthew G; Rzuczek, Suzanne G; Disney, Matthew D

    2016-06-01

    Potential RNA targets for chemical probes and therapeutic modalities are pervasive in the transcriptome. Oligonucleotide-based therapeutics are commonly used to target RNA sequence. Small molecules are emerging as a modality to target RNA structures selectively, but their development is still in its infancy. In this work, we compare the activity of oligonucleotides and several classes of small molecules that target the non-coding r(CCUG) repeat expansion (r(CCUG)(exp)) that causes myotonic dystrophy type 2 (DM2), an incurable disease that is the second-most common cause of adult onset muscular dystrophy. Small molecule types investigated include monomers, dimers, and multivalent compounds synthesized on-site by using RNA-templated click chemistry. Oligonucleotides investigated include phosphorothioates that cleave their target and vivo-morpholinos that modulate target RNA activity via binding. We show that compounds assembled on-site that recognize structure have the highest potencies amongst small molecules and are similar in potency to a vivo-morpholino modified oligonucleotide that targets sequence. These studies are likely to impact the design of therapeutic modalities targeting other repeats expansions that cause fragile X syndrome and amyotrophic lateral sclerosis, for example.

  10. Evaluation of the effects of chemically different linkers on hepatic accumulations, cell tropism and gene silencing ability of cholesterol-conjugated antisense oligonucleotides.

    PubMed

    Wada, Shunsuke; Yasuhara, Hidenori; Wada, Fumito; Sawamura, Motoki; Waki, Reiko; Yamamoto, Tsuyoshi; Harada-Shiba, Mariko; Obika, Satoshi

    2016-03-28

    Cholesterol conjugation of oligonucleotides is an attractive way to deliver the oligonucleotides specifically to the liver. However cholesterol-conjugated antisense oligonucleotides (ASOs) mainly accumulate in non-parenchymal cells (NPCs) such as Kupffer cells. In this study, to increase the hepatic accumulation of cholesterol-conjugated ASOs, we prepared a variety of linkers for cholesterol conjugation to anti-Pcsk9 ASOs and examined their effects on pharmacological parameters. Hepatic accumulation of ASO was dramatically increased with cholesterol conjugation. The increase in hepatic accumulation depended largely on the linker chemistry of each cholesterol-conjugated ASO. In addition to hepatic accumulation, the cell tropism of each cholesterol-conjugated ASO tended to depend on their linker. Although a linker bearing a disulfide bond accumulated mainly in NPCs, hexamethylene succinimide linker accumulated mainly in hepatocytes. To estimate the benefits of releasing ASO from the conjugated cholesterol in hepatocyte, we designed another linker based on hexamethylene succinimide, which has a phosphodiester bond between the linker and the ASO. The cholesterol-conjugated ASO bearing such a phosphodiester bond showed a significantly improved Pcsk9 mRNA inhibitory effect compared to its counterpart, cholesterol-conjugated ASO with a phosphorothioate bond, while the hepatic accumulation of both cholesterol-conjugated ASOs was comparable, indicating the effectiveness of removing the conjugated cholesterol for ASO activity. In toxicity analysis, some of the linkers induced lethal toxicities when they were injected at high concentrations (>600μM). These toxicities were attributed to decreased platelet levels in the blood, suggesting an interaction between cholesterol-conjugated ASO and platelets. Our findings may provide a guideline for the design of molecule-conjugated ASOs.

  11. Synthesis of DNA oligonucleotides containing C5-ethynylbenzenesulfonamide-modified nucleotides (EBNA) by polymerases towards the construction of base functionalized nucleic acids.

    PubMed

    Goubet, Astrid; Chardon, Antoine; Kumar, Pawan; Sharma, Pawan K; Veedu, Rakesh N

    2013-02-01

    C5-Ethynylbenzenesulfonamide-modified nucleotide (EBNA) was investigated as substrate of various DNA polymerases. The experiments revealed that KOD, Phusion and Klenow DNA polymerases successfully accepted EBNA-T nucleotide as a substrate and yielded the fully extended DNA. KOD DNA polymerase was found to be the most efficient enzyme to furnish EBNA-T containing DNA in good yields. Phusion DNA polymerase efficiently amplified the template containing EBNA-T nucleotides by PCR.

  12. Chemically Modified Graphene for Sensing and Nanomechanical Applications

    DTIC Science & Technology

    2009-01-01

    chemical vapors at parts-per-billion concentrations,5 although these sensors require somewhat sophisticated electronics to realize their full...chemically (e.g., with hydrazine , N2H4) or thermally (e.g., by annealing in H2), providing a knob with which to tune the sensor response. These devices are...and mechanical devices. CMG can be fine-tuned to its specific application and has been used to produce sensors of extraordinary sensitivity

  13. Enhancement of gene silencing potency and nuclease stability by chemically modified duplex RNA.

    PubMed

    Kubo, Takanori; Zhelev, Zhivko; Bakalova, Rumiana; Ohba, Hideki

    2007-01-01

    In this study, we describe a development of chemically modified dsRNAs with improved biological properties. These dsRNAs possess an enhanced RNAi activity and a dramatically increased stability in cell cultured medium (containing 10% serum) in comparison with widely used 21nt siRNA. The chemically modified dsRNAs manifested a high longterm gene suppression after one week post-transfection, whereas 21nt siRNA showed a high RNAi activity only after 48 h cell transfection.

  14. a Novel Method to Synthesize N-DOPED CNTs Arrays via Chemical Modifying Porous Alumina Membrane

    NASA Astrophysics Data System (ADS)

    Li, Chengyong; He, Lei

    2014-01-01

    N-doped carbon nanotubes (CNTs) arrays were fabricated via simply chemical modifying porous alumina membrane (PAM) with dopamine. The diameter of N-doped CNTs is about 60-70 nm. The N/C atomic ratio is calculated to be 0.05 and the main functionality is pyridone/pyrrole N. This chemical modifying method can be used to fabricate mass of N-doped CNTs arrays in one step with single raw material.

  15. A facile method for the construction of oligonucleotide microarrays.

    PubMed

    Sethi, Dalip; Kumar, A; Gupta, K C; Kumar, P

    2008-11-19

    In recent years, the oligonucleotide-based microarray technique has emerged as a powerful and promising tool for various molecular biological studies. Here, a facile protocol for the construction of an oligonucleotide microarray is demonstrated that involves immobilization of oligonucleotide-trimethoxysilyl conjugates onto virgin glass microslides. The projected immobilization strategy reflects high immobilization efficiency ( approximately 36-40%) and signal-to-noise ratio ( approximately 98), and hybridization efficiency ( approximately 32-35%). Using the proposed protocol, aminoalkyl, mercaptoalkyl, and phosphorylated oligonucleotides were immobilized onto virgin glass microslides. Briefly, modified oligonucleotides were reacted first with 3-glycidyloxypropyltriethoxysilane (GOPTS), and subsequently, the resultant conjugates were directly immobilized onto the virgin glass surface by making use of silanization chemistry. The constructed microarrays were then used for discrimination of base mismatches. On subjecting to different pH and thermal conditions, the microarray showed sufficient stability. Application of this chemistry to manufacture oligonucleotide probe-based microarrays for detection of bacterial meningitis is demonstrated. Single-step reaction for the formation of conjugates with the commercially available reagent (GOPTS), omission of capping step and surface modification, and efficient immobilization of oligonucleotides onto the virgin glass surface are the key features of the proposed strategy.

  16. Design and analysis of mismatch probes for long oligonucleotide microarrays

    SciTech Connect

    Deng, Ye; He, Zhili; Van Nostrand, Joy D.; Zhou, Jizhong

    2008-08-15

    Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. Conclusions: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.

  17. Chemical reactivity of twin-modified copper nanowire surfaces

    NASA Astrophysics Data System (ADS)

    Huang, Chun-Lung; Liao, Chien-Neng

    2015-07-01

    Effect of twin boundary (TB) spacing on atomic surface structure and chemical reactivity of nanotwinned Cu nanowires (NWs) is investigated. Post-etching surface structure and wire diameter of Cu NWs were examined by transmission electron microscopy. When TB spacing is less than 10 nm, the Cu NWs remain almost intact after chemical attack and show faceted surface structures with low atomic step density. A mechanism based on surface tension torque acting on TB/surface triple junctions is proposed to explain the faceted structure formation and enhanced corrosion resistance of nanotwinned Cu NWs.

  18. Use of Specific Chemical Reagents for Detection of Modified Nucleotides in RNA

    PubMed Central

    Behm-Ansmant, Isabelle; Helm, Mark; Motorin, Yuri

    2011-01-01

    Naturally occurring cellular RNAs contain an impressive number of chemically distinct modified residues which appear posttranscriptionally, as a result of specific action of the corresponding RNA modification enzymes. Over 100 different chemical modifications have been identified and characterized up to now. Identification of the chemical nature and exact position of these modifications is typically based on 2D-TLC analysis of nucleotide digests, on HPLC coupled with mass spectrometry, or on the use of primer extension by reverse transcriptase. However, many modified nucleotides are silent in reverse transcription, since the presence of additional chemical groups frequently does not change base-pairing properties. In this paper, we give a summary of various chemical approaches exploiting the specific reactivity of modified nucleotides in RNA for their detection. PMID:21716696

  19. Antisense oligonucleotides in therapy for neurodegenerative disorders.

    PubMed

    Evers, Melvin M; Toonen, Lodewijk J A; van Roon-Mom, Willeke M C

    2015-06-29

    Antisense oligonucleotides are synthetic single stranded strings of nucleic acids that bind to RNA and thereby alter or reduce expression of the target RNA. They can not only reduce expression of mutant proteins by breakdown of the targeted transcript, but also restore protein expression or modify proteins through interference with pre-mRNA splicing. There has been a recent revival of interest in the use of antisense oligonucleotides to treat several neurodegenerative disorders using different approaches to prevent disease onset or halt disease progression and the first clinical trials for spinal muscular atrophy and amyotrophic lateral sclerosis showing promising results. For these trials, intrathecal delivery is being used but direct infusion into the brain ventricles and several methods of passing the blood brain barrier after peripheral administration are also under investigation.

  20. Sequence-dependent theory of oligonucleotide hybridization kinetics

    SciTech Connect

    Marimuthu, Karthikeyan; Chakrabarti, Raj E-mail: rajc@andrew.cmu.edu

    2014-05-07

    A theoretical approach to the prediction of the sequence and temperature-dependent rate constants for oligonucleotide hybridization reactions has been developed based on the theory of relaxation kinetics. One-sided and two-sided melting reaction mechanisms for oligonucleotide hybridization reactions have been considered, analyzed, modified, and compared to select a physically consistent as well as robust model for prediction of the relaxation times of DNA hybridization reactions that agrees with the experimental evidence. The temperature- and sequence-dependent parameters of the proposed model have been estimated using available experimental data. The relaxation time model that we developed has been combined with the nearest neighbor model of hybridization thermodynamics to estimate the temperature- and sequence-dependent rate constants of an oligonucleotide hybridization reaction. The model-predicted rate constants are compared to experimentally determined rate constants for the same oligonucleotide hybridization reactions. Finally, we consider a few important applications of kinetically controlled DNA hybridization reactions.

  1. Tritium labeling of antisense oligonucleotides by exchange with tritiated water.

    PubMed Central

    Graham, M J; Freier, S M; Crooke, R M; Ecker, D J; Maslova, R N; Lesnik, E A

    1993-01-01

    We describe a simple, efficient, procedure for labeling oligonucleotides to high specific activity (< 1 x 10(8) cpm/mumol) by hydrogen exchange with tritiated water at the C8 positions of purines in the presence of beta-mercaptoethanol, an effective radical scavenger. Approximately 90% of the starting material is recovered as intact, labeled oligonucleotide. The radiolabeled compounds are stable in biological systems; greater than 90% of the specific activity is retained after 72 hr incubation at 37 degrees C in serum-containing media. Data obtained from in vitro cellular uptake experiments using oligonucleotides labeled by this method are similar to those obtained using 35S or 14C-labeled compounds. Because this protocol is solely dependent upon the existence of purine residues, it should be useful for radiolabeling modified as well as unmodified phosphodiester oligonucleotides. Images PMID:8367289

  2. 40 CFR 372.20 - Process for modifying covered chemicals and facilities.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... chemicals and facilities. 372.20 Section 372.20 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SUPERFUND, EMERGENCY PLANNING, AND COMMUNITY RIGHT-TO-KNOW PROGRAMS TOXIC CHEMICAL RELEASE REPORTING: COMMUNITY RIGHT-TO-KNOW Reporting Requirements § 372.20 Process for modifying covered...

  3. Multifunctional Pristine Chemically Modified Graphene Films as Strong as Stainless Steel.

    PubMed

    Zhang, Miao; Wang, Yanlei; Huang, Liang; Xu, Zhiping; Li, Chun; Shi, Gaoquan

    2015-11-01

    Pristine chemically modified graphene films with light weights and excellent mechanical properties can be prepared by chemically engineering the structure of the graphene oxide sheets and the microstructures of the films. Particularly, these reduced graphene oxide films are as strong as stainless steel, ultra-tough, and have high electrical and thermal conductivities.

  4. Chemically modified IR-transparent fibers and their application as chemical sensors

    SciTech Connect

    Kellner, R.A.

    1993-12-31

    With the advent of chalcogenide- (As-Se-Te), Silverhalide- (AgBrCl) and TeXAs-fibers, the optical window available for analytical chemistry was significantly extended into the MID- and FAR-IR range (2 to 20 {mu}m) recently. These fibers have been chemically modified in our laboratory at 10 cm-distances of their surfaces (A) by covering them with 10-100 {mu}m thick layers of a suitable polymer such as LDPE ({open_quotes}Thickfilm-Sensor{close_quotes}) and (B) by immobilizing specifically reacting enzyme-layers such as GOx ({open_quotes}Thinfilm-Sensor{close_quotes}). In the first case, where the penetration depth of the IR-beam is smaller than the thickness of the polymer layer, a sensor for the simultaneous in situ-determination of chlorinated hydrocarbon traces in water down to 500 ppb could be developed and tested. In the second case, a system for the determination of glucose in complex aqueous solutions was developed, based on the catalytic oxidation of glucose to gluconic acid and hydrogen peroxide by the immobilized enzyme glucose oxidase (GOx) in the physiological range. The GOx-density at the fibers could be significantly enlarged by using S-Layers instead of silanes for immobilization. Secondly, a flow injection-approach was developed recently, which allowed for an even further increase of the enzyme density by separating the reaction- and detection-part of our sensor, using controlled pore glass as carrier for the GOx and tapered chalcogenide fibers for detection. With this system, which works perfectly linear in the physiological range also for urea (with urease) a practical (multi)enzyme-based IR-sensor system is presented for the first time.

  5. Iodine derivatives of chemically modified gum Arabic microspheres.

    PubMed

    Ganie, Showkat A; Ali, Akbar; Mazumdar, Nasreen

    2015-09-20

    Acetylated gum Arabic (AGA) derivatives with different degrees of substitution (DS 0.97-2.74) were synthesized using acetyl chloride and a base under varying reaction conditions. The AGA derivatives were obtained in the form of microspheres and thereafter stable iodine products were prepared by doping the microspheres with an iodinating agent, iodine monochloride (ICl). The reaction between electrophilic iodine and polar carbonyl groups was studied by FT-IR, (1)H-NMR, and UV-VIS spectroscopies. The products were also characterized by DSC, TGA and SEM studies. The incorporated iodine was released in aqueous medium as iodide ions (I(-)). A reaction scheme has been proposed for the iodination and de-iodination of the gum derivatives. This work suggests that the iodine derivatives of modified gum Arabic could be used as a source of iodide ions which is the nutritional form of iodine.

  6. Interfacial characterization and analytical applications of chemically-modified surfaces

    SciTech Connect

    Wang, Jianhong

    1998-02-23

    The goal of this work is to explore several new strategies and approaches to the surface modification and the microscopic characterization of interfaces in the areas mainly targeting sensor technologies that are of interest to environmental control or monitoring, and scanning probe microscopies techniques that can monitor interfacial chemical reactions in real time. Centered on the main theme, four specific topics are presented as four chapters in this dissertation following the general introduction. Chapter 1 describes the development of two immobilization schemes for covalently immobilizing fluoresceinamine at cellulose acetate and its application as a pH sensing film. Chapter 2 investigates the applicability of SFM to following the base-hydrolysis of a dithio-bis(succinimidylundecanoate) monolayer at gold in situ. Chapter 3 studies the mechanism for the accelerated rate of hydrolysis of the dithio-bis(succinimidylundecanoate) monolayer at Au(111) surface. Chapter 4 focuses on the development of an electrochemical approach to the elimination of chloride interference in Chemical Oxygen Demand (COD) analysis of waste water. The procedures, results and conclusions are described in each chapter. This report contains the introduction, references, and general conclusions. Chapters have been processed separately for inclusion on the data base. 95 refs.

  7. Gold Binding by Native and Chemically Modified Hops Biomasses

    DOE PAGES

    López, M. Laura; Gardea-Torresdey, J. L.; Peralta-Videa, J. R.; ...

    2005-01-01

    Heavy metals from mining, smelting operations and other industrial processing facilities pollute wastewaters worldwide. Extraction of metals from industrial effluents has been widely studied due to the economic advantages and the relative ease of technical implementation. Consequently, the search for new and improved methodologies for the recovery of gold has increased. In this particular research, the use of cone hops biomass ( Humulus lupulus ) was investigated as a new option for gold recovery. The results showed that the gold binding to native hops biomass was pH dependent from pH 2 to pH 6, with a maximum percentage bindingmore » at pH 3. Time dependency studies demonstrated that Au(III) binding to native and modified cone hops biomasses was found to be time independent at pH 2 while at pH 5, it was time dependent. Capacity experiments demonstrated that at pH 2, esterified hops biomass bound 33.4 mg Au/g of biomass, while native and hydrolyzed hops biomasses bound 28.2 and 12.0 mg Au/g of biomass, respectively. However, at pH 5 the binding capacities were 38.9, 37.8 and 11.4 mg of Au per gram of native, esterified and hydrolyzed hops biomasses, respectively.« less

  8. CO2 adsorption on chemically modified activated carbon.

    PubMed

    Caglayan, Burcu Selen; Aksoylu, A Erhan

    2013-05-15

    CO2 adsorption capacity of a commercial activated carbon was improved by using HNO3 oxidation, air oxidation, alkali impregnation and heat treatment under helium gas atmosphere. The surface functional groups produced were investigated by diffuse reflectance infrared Fourier transform spectrometer (DRIFTS). CO2 adsorption capacities of the samples were determined by gravimetric analyses for 25-200°C temperature range. DRIFTS studies revealed the formation of carboxylic acid groups on the HNO3 oxidized adsorbents. Increased aromatization and uniform distribution of the Na particles were observed on the samples prepared by Na2CO3 impregnation onto HNO3 oxidized AC support. The adsorption capacities of the nonimpregnated samples were increased by high temperature helium treatments or by increasing the adsorption temperature; both leading to decomposition of surface oxygen groups, forming sites that can easily adsorb CO2. The adsorption capacity loss due to cyclic adsorption/desorption procedures was overcome with further surface stabilization of Na2CO3 modified samples with high temperature He treatments. With Na2CO3 impregnation the mass uptakes of the adsorbents at 20 bars and 25 °C were improved by 8 and 7 folds and at 1 bar were increased 15 and 16 folds, on the average, compared to their air oxidized and nitric acid oxidized supports, respectively.

  9. Mechanical and chemical properties of cysteine-modified kinesin molecules.

    PubMed

    Iwatani, S; Iwane, A H; Higuchi, H; Ishii, Y; Yanagida, T

    1999-08-10

    To probe the structural changes within kinesin molecules, we made the mutants of motor domains of two-headed kinesin (4-411 aa) in which either all the five cysteines or all except Cys45 were mutated. A residual cysteine (Cys45) of the kinesin mutant was labeled with an environment-sensitive fluorescent probe, acrylodan. ATPase activity, mechanical properties, and fluorescence intensity of the mutants were measured. Upon acrylodan-labeled kinesin binding to microtubules in the presence of 1 mM AMPPNP, the peak intensity was enhanced by 3.4-fold, indicating the structural change of the kinesin head by the binding. Substitution of cysteines decreased both the maximum microtubule-activated ATPase and the sliding velocity to the same extent. However, the maximum force and the step size were not affected; the force produced by a single molecule was 6-6.5 pN, and a step size due to the hydrolysis of one ATP molecule by kinesin molecules was about 10 nm for all kinesins. This step size was close to a unitary step size of 8 nm. Thus, the mechanical events of kinesin are tightly coupled with the chemical events.

  10. Diels-Alder cycloadditions in water for the straightforward preparation of peptide–oligonucleotide conjugates

    PubMed Central

    Marchán, Vicente; Ortega, Samuel; Pulido, Daniel; Pedroso, Enrique; Grandas, Anna

    2006-01-01

    The Diels-Alder reaction between diene-modified oligonucleotides and maleimide-derivatized peptides afforded peptide–oligonucleotide conjugates with high purity and yield. Synthesis of the reagents was easily accomplished by on-column derivatization of the corresponding peptides and oligonucleotides. The cycloaddition reaction was carried out in mild conditions, in aqueous solution at 37°C. The speed of the reaction was found to vary depending on the size of the reagents, but it can be completed in 8–10 h by reacting the diene-oligonucleotide with a small excess of maleimide-peptide. PMID:16478710

  11. Correlation between dynamic wetting behavior and chemical components of thermally modified wood

    NASA Astrophysics Data System (ADS)

    Wang, Wang; Zhu, Yuan; Cao, Jinzhen; Sun, Wenjing

    2015-01-01

    In order to investigate the dynamic wetting behavior of thermally modified wood, Cathay poplar (Populus cathayana Rehd.) and Scots pine (Pinus sylvestris L.) samples were thermally modified in an oven at 160, 180, 200, 220 or 240 °C for 4 h in this study. The dynamic contact angles and droplet volumes of water droplets on modified and unmodified wood surfaces were measured by sessile drop method, and their changing rates (expression index: K value and wetting slope) calculated by wetting models were illustrated for mapping the dynamic wetting process. The surface chemical components were also measured by X-ray photoelectron spectroscopy analysis (XPS), thus the relationship between dynamic wetting behavior and chemical components of thermally modified wood were determined. The results indicated that thermal modification was capable of decreasing the dynamic wettability of wood, expressed in lowing spread and penetration speed of water droplets on wood surfaces. This change was more obvious with the increased heating temperature. The K values varied linearly with the chemical components parameter (mass loss, O/C ratio, and C1/C2 ratio), indicating a strong correlation between dynamic wetting behavior and chemical components of thermally modified wood.

  12. Applicability of chemically modified capillaries in chiral capillary electrophoresis for methamphetamine profiling.

    PubMed

    Iwata, Yuko T; Mikuma, Toshiyasu; Kuwayama, Kenji; Tsujikawa, Kenji; Miyaguchi, Hajime; Kanamori, Tatsuyuki; Inoue, Hiroyuki

    2013-03-10

    We examined the applicability of chemically modified capillaries on the chiral capillary electrophoresis of essential compounds for methamphetamine (MA) profiling (MA, amphetamine, ephedrine, pseudoephedrine, norephedrine, and norpseudoephedrine) using highly sulfated γ-cyclodextrin as a chiral selector. Four types of chemically modified capillaries, namely, FunCap-CE/Type D (possessing diol groups), Type A (amino groups), Type C (carboxyl groups), and Type S (sulfate groups), were evaluated. Repeatability, speed, and good chiral resolution sufficient for routine MA profiling were achieved with the Type S capillary.

  13. Insights into the electrocatalysis of nitrobenzene using chemically-modified carbon nanotube electrodes

    PubMed Central

    Sang, Yutao; Wang, Baoyan; Wang, Qinchao; Zhao, George; Guo, Peizhi

    2014-01-01

    The electrochemical behavior of nitrobenzene and its derivatives at chemically-functionalized multi-wall carbon nanotubes (MWNTs) modified electrodes was studied. Experimental results showed that hydroxyl-containing MWNTs exhibited the highest electrocatalytic activity among the used MWNTs because of its weak capacitive features and oxygen-containing functional groups. The cycle voltammetrys of nitrobenzene derivatives on the MWNTs modified electrodes can be easily tuned by changing the substituted groups of nitrobenzene. Based on the experimental data, the electrochemical reaction mechanisms of nitrobenzene and its derivatives on the MWNTs modified electrodes have been discussed and analyzed. PMID:25204889

  14. Evaluating Zeolite-Modified Sensors: towards a faster set of chemical sensors

    NASA Astrophysics Data System (ADS)

    Berna, A. Z.; Vergara, A.; Trincavelli, M.; Huerta, R.; Afonja, A.; Parkin, I. P.; Binions, R.; Trowell, S.

    2011-09-01

    The responses of zeolite-modified sensors, prepared by screen printing layers of chromium titanium oxide (CTO), were compared to unmodified tin oxide sensors using amplitude and transient responses. For transient responses we used a family of features, derived from the exponential moving average (EMA), to characterize chemo-resistive responses. All sensors were tested simultaneously against 20 individual volatile compounds from four chemical groups. The responses of the two types of sensors showed some independence. The zeolite-modified CTO sensors discriminated compounds better using either amplitude response or EMA features and CTO-modified sensors also responded three times faster.

  15. Modified clay minerals efficiency against chemical and biological warfare agents for civil human protection.

    PubMed

    Plachá, Daniela; Rosenbergová, Kateřina; Slabotínský, Jiří; Kutláková, Kateřina Mamulová; Studentová, Soňa; Martynková, Gražyna Simha

    2014-04-30

    Sorption efficiencies of modified montmorillonite and vermiculite of their mono ionic Na and organic HDTMA and HDP forms were studied against chemical and biological warfare agents such as yperite and selected bacterial strains. Yperite interactions with modified clay minerals were observed through its capture in low-density polyethylene foil-modified clay composites by measuring yperite gas permeation with using chemical indication and gas chromatography methods. The antibacterial activities of synthetized organoclays were tested against selected Gram-positive and Gram-negative bacterial species in minimum inhibitory concentration tests. The obtained results showed a positive influence of modified clay minerals on the significant yperite breakthrough-time increase. The most effective material was the polyethylene-Na form montmorillonite, while the polyethylene-Na form vermiculite showed the lowest efficiency. With increasing organic cations loading in the interlayer space the montmorillonite efficiency decreased, and in the case of vermiculite an opposite effect was observed. Generally the modified montmorillonites were more effective than modified vermiculites. The HDP cations seem to be more effective compare to the HDTMA. The antibacterial activity tests confirmed efficiency of all organically modified clay minerals against Gram-positive bacteria. The confirmation of antibacterial activity against Y. pestis, plague bacteria, is the most interesting result of this part of the study.

  16. Expanding the chemical toolbox for the synthesis of large and uniquely modified proteins

    NASA Astrophysics Data System (ADS)

    Bondalapati, Somasekhar; Jbara, Muhammad; Brik, Ashraf

    2016-05-01

    Methods to prepare proteins that include a specific modification at a desired position are essential for understanding their cellular functions and physical properties in living systems. Chemical protein synthesis, which relies on the chemoselective ligation of unprotected peptides, enables the preparation of modified proteins that are not easily fabricated by other methods. In contrast to recombinant approaches, chemical synthesis can be used to prepare protein analogues such as D-proteins, which are useful in protein structure determination and the discovery of novel therapeutics. Post-translationally modifying proteins is another example where chemical protein synthesis proved itself as a powerful approach for preparing samples with high homogeneity and in workable quantities. In this Review, we discuss the basic principles of the field, focusing on novel chemoselective peptide ligation approaches such as native chemical ligation and the recent advances based on this method with a proven record of success in the synthesis of highly important protein targets.

  17. Chemical treatment of the intra-canal dentin surface: a new approach to modify dentin hydrophobicity

    PubMed Central

    GAITAN-FONSECA, Cesar; COLLART-DUTILLEUL, Pierre-Yves; SEMETEY, Vincent; ROMIEU, Olivier; CRUZ, Roel; FLORES, Hector; CUISINIER, Frédéric; PÉREZ, Elías; POZOS-GUILLEN, Amaury

    2013-01-01

    Objective: This study evaluated the hydrophobicity of dentin surfaces that were modified through chemical silanization with octadecyltrichlorosilane (OTS). Material and Methods: An in vitro experimental study was performed using 40 human permanent incisors that were divided into the following two groups: non-silanized and silanized. The specimens were pretreated and chemically modified with OTS. After the chemical modification, the dentin hydrophobicity was examined using a water contact angle measurement (WCA). The effectiveness of the modification of hydrophobicity was verified by the fluid permeability test (FPT). Results and Conclusions: Statistically significant differences were found in the values of WCA and FPT between the two groups. After silanization, the hydrophobic intraradicular dentin surface exhibited in vitro properties that limit fluid penetration into the sealed root canal. This chemical treatment is a new approach for improving the sealing of the root canal system. PMID:23559114

  18. Chemical Genetic Screens for TDP-43 Modifiers and ALS Drug Discovery

    DTIC Science & Technology

    2013-10-01

    AD_________________ Award Number: W81XWH-11-1-0573 TITLE: Chemical Genetic Screens for TDP-43...15 Sept. 2012 – 14 Sept. 2013 4. TITLE AND SUBTITLE Chemical Genetic Screens for TDP-43 Modifiers and ALS Drug Discovery 5a. CONTRACT NUMBER...phenotypes in three unique in vivo genetic models of ALS that we have recently generated. Our new, functionally validated models are worms (C

  19. DNA damage response pathway and replication fork stress during oligonucleotide directed gene editing.

    PubMed

    Bonner, Melissa; Strouse, Bryan; Applegate, Mindy; Livingston, Paula; Kmiec, Eric B

    2012-04-03

    Single-stranded DNA oligonucleotides (ODNs) can be used to direct the exchange of nucleotides in the genome of mammalian cells in a process known as gene editing. Once refined, gene editing should become a viable option for gene therapy and molecular medicine. Gene editing is regulated by a number of DNA recombination and repair pathways whose natural activities often lead to single- and double-stranded DNA breaks. It has been previously shown that introduction of a phosphorotioated ODN, designed to direct a gene-editing event, into cells results in the activation of γH2AX, a well-recognized protein biomarker for double-stranded DNA breakage. Using a single copy, integrated mutant enhanced green fluorescent protein (eGFP) gene as our target, we now demonstrate that several types of ODNs, capable of directing gene editing, also activate the DNA damage response and the post-translational modification of proliferating cell nuclear antigen (PCNA), a signature modification of replication stress. We find that the gene editing reaction itself leads to transient DNA breakage, perhaps through replication fork collapse. Unmodified specific ODNs elicit a lesser degree of replication stress than their chemically modified counterparts, but are also less active in gene editing. Modified phosphothioate oligonucleotides (PTOs) are detrimental irrespective of the DNA sequence. Such collateral damage may prove problematic for proliferation of human cells genetically modified by gene editing.

  20. Near-infrared silver cluster optically signaling oligonucleotide hybridization and assembling two DNA hosts.

    PubMed

    Petty, Jeffrey T; Nicholson, David A; Sergev, Orlin O; Graham, Stuart K

    2014-09-16

    Silver clusters with ~10 atoms form within DNA strands, and the conjugates are chemical sensors. The DNA host hybridizes with short oligonucleotides, and the cluster moieties optically respond to these analytes. Our studies focus on how the cluster adducts perturb the structure of their DNA hosts. Our sensor is comprised of an oligonucleotide with two components: a 5'-cluster domain that complexes silver clusters and a 3'-recognition site that hybridizes with a target oligonucleotide. The single-stranded sensor encapsulates an ~11 silver atom cluster with violet absorption at 400 nm and with minimal emission. The recognition site hybridizes with complementary oligonucleotides, and the violet cluster converts to an emissive near-infrared cluster with absorption at 730 nm. Our key finding is that the near-infrared cluster coordinates two of its hybridized hosts. The resulting tertiary structure was investigated using intermolecular and intramolecular variants of the same dimer. The intermolecular dimer assembles in concentrated (~5 μM) DNA solutions. Strand stoichiometries and orientations were chromatographically determined using thymine-modified complements that increase the overall conjugate size. The intramolecular dimer develops within a DNA scaffold that is founded on three linked duplexes. The high local cluster concentrations and relative strand arrangements again favor the antiparallel dimer for the near-infrared cluster. When the two monomeric DNA/violet cluster conjugates transform to one dimeric DNA/near-infrared conjugate, the DNA strands accumulate silver. We propose that these correlated changes in DNA structure and silver stoichiometry underlie the violet to near-infrared cluster transformation.

  1. Chemical and Biological Tools for the Preparation of Modified Histone Proteins

    PubMed Central

    Howard, Cecil J.; Yu, Ruixuan R.; Gardner, Miranda L.; Shimko, John C.; Ottesen, Jennifer J.

    2016-01-01

    Eukaryotic chromatin is a complex and dynamic system in which the DNA double helix is organized and protected by interactions with histone proteins. This system is regulated through, a large network of dynamic post-translational modifications (PTMs) exists to ensure proper gene transcription, DNA repair, and other processes involving DNA. Homogenous protein samples with precisely characterized modification sites are necessary to better understand the functions of modified histone proteins. Here, we discuss sets of chemical and biological tools that have been developed for the preparation of modified histones, with a focus on the appropriate choice of tool for a given target. We start with genetic approaches for the creation of modified histones, including the incorporation of genetic mimics of histone modifications, chemical installation of modification analogs, and the use of the expanded genetic code to incorporate modified amino acids. Additionally, we will cover the chemical ligation techniques that have been invaluable in the generation of complex modified histones that are indistinguishable from the natural counterparts. Finally, we will end with a prospectus on future directions of synthetic chromatin in living systems. PMID:25863817

  2. Polyamine-oligonucleotide conjugates: a promising direction for nucleic acid tools and therapeutics.

    PubMed

    Menzi, Mirjam; Lightfoot, Helen L; Hall, Jonathan

    2015-01-01

    Chemical modification and/or the conjugation of small functional molecules to oligonucleotides have significantly improved their biological and biophysical properties, addressing issues such as poor cell penetration, stability to nucleases and low affinity for their targets. Here, the authors review the literature reporting on the biophysical, biochemical and biological properties of one particular class of modification - polyamine-oligonucleotide conjugates. Naturally derived and synthetic polyamines have been grafted onto a variety of oligonucleotide formats, including antisense oligonucleotides and siRNAs. In many cases this has had beneficial effects on their properties such as target hybridization, nuclease resistance, cellular uptake and activity. Polyamine-oligonucleotide conjugation, therefore, represents a promising direction for the further development of oligonucleotide-based therapeutics and tools.

  3. Modified Nucleoside Triphosphates for In-vitro Selection Techniques.

    PubMed

    Dellafiore, María A; Montserrat, Javier M; Iribarren, Adolfo M

    2016-01-01

    The development of SELEX (Selective Enhancement of Ligands by Exponential Enrichment) provides a powerful tool for the search of functional oligonucleotides with the ability to bind ligands with high affinity and selectivity (aptamers) and for the discovery of nucleic acid sequences with diverse enzymatic activities (ribozymes and DNAzymes). This technique has been extensively applied to the selection of natural DNA or RNA molecules but, in order to improve chemical and structural diversity as well as for particular applications where further chemical or biological stability is necessary, the extension of this strategy to modified oligonucleotides is desirable. Taking into account these needs, this review intends to collect the research carried out during the past years, focusing mainly on the use of modified nucleotides in SELEX and the development of mutant enzymes for broadening nucleoside triphosphates acceptance. In addition, comments regarding the synthesis of modified nucleoside triphosphate will be briefly discussed.

  4. Modified Nucleoside Triphosphates for In-vitro Selection Techniques

    PubMed Central

    Dellafiore, María A.; Montserrat, Javier M.; Iribarren, Adolfo M.

    2016-01-01

    The development of SELEX (Selective Enhancement of Ligands by Exponential Enrichment) provides a powerful tool for the search of functional oligonucleotides with the ability to bind ligands with high affinity and selectivity (aptamers) and for the discovery of nucleic acid sequences with diverse enzymatic activities (ribozymes and DNAzymes). This technique has been extensively applied to the selection of natural DNA or RNA molecules but, in order to improve chemical and structural diversity as well as for particular applications where further chemical or biological stability is necessary, the extension of this strategy to modified oligonucleotides is desirable. Taking into account these needs, this review intends to collect the research carried out during the past years, focusing mainly on the use of modified nucleotides in SELEX and the development of mutant enzymes for broadening nucleoside triphosphates acceptance. In addition, comments regarding the synthesis of modified nucleoside triphosphate will be briefly discussed. PMID:27200340

  5. Modified Nucleoside Triphosphates for in-vitro Selection Techniques

    NASA Astrophysics Data System (ADS)

    Iribarren, Adolfo; Dellafiore, María; Montserrat, Javier

    2016-05-01

    The development of SELEX (Selective Enhancement of Ligands by Exponential Enrichment) provides a powerful tool for the search of functional oligonucleotides with the ability to bind ligands with high affinity and selectivity (aptamers) and for the discovery of nucleic acid sequences with diverse enzymatic activities (ribozymes and DNAzymes). This technique has been extensively applied to the selection of natural DNA or RNA molecules but, in order to improve chemical and structural diversity as well as for particular applications where further chemical or biological stability is necessary, the extension of this strategy to modified oligonucleotides is desirable. Taking into account these needs, this review intends to collect the research carried out during the past years, focusing mainly on the use of modified nucleotides in SELEX and the development of mutant enzymes for broadening nucleoside triphosphates acceptance. In addition, comments regarding the synthesis of modified nucleoside triphosphate will be briefly discussed.

  6. Properties of amphiphilic oligonucleotide films at the air/water interface and after film transfer.

    PubMed

    Keller, R; Kwak, M; de Vries, J W; Sawaryn, C; Wang, J; Anaya, M; Müllen, K; Butt, H-J; Herrmann, A; Berger, R

    2013-11-01

    The self-assembly of amphiphilic hybrid materials containing an oligonucleotide sequence at the air/water interface was investigated by means of pressure-molecular area (Π-A) isotherms. In addition, films were transferred onto solid substrates and imaged using scanning force microscopy. We used oligonucleotide molecules with lipid tails, which consisted of a single stranded oligonucleotide 11 mer containing two hydrophobically modified 5-(dodec-1-ynyl)uracil nucleobases (dU11) at the 5'-end of the oligonucleotide sequence. The air/water interface was used as confinement for the self-assembling process of dU11. Scanning force microscopy of films transferred via Langmuir-Blodgett technique revealed mono-, bi- (Π ≥ 2 mN/m) and multilayer formation (Π ≥ 30 mN/m). The first layer was 1.6 ± 0.1 nm thick. It was oriented with the hydrophilic oligonucleotide moiety facing the hydrophilic substrate while the hydrophobic alkyl chains faced air. In the second layer the oligonucleotide moiety was found to face the air. The second layer was found to cover up to 95% of the sample area. Our measurements indicated that the rearrangement of the molecules into bi- and multiple bilayers happened already at the air/water interface. Similar results were obtained with a second type of oligonucleotide amphiphile, an oligonucleotide block copolymer, which was composed of an oligonucleotide 11 mer covalently attached at the terminus to polypropyleneoxide (PPO).

  7. The 5' binding MID domain of human Argonaute2 tolerates chemically modified nucleotide analogues.

    PubMed

    Deleavey, Glen F; Frank, Filipp; Hassler, Matthew; Wisnovsky, Simon; Nagar, Bhushan; Damha, Masad J

    2013-02-01

    Small interfering RNAs (siRNAs) can trigger potent gene silencing through the RNA interference (RNAi) pathway. The RNA-induced silencing complex (RISC) is key to this targeted mRNA degradation, and the human Argonaute2 (hAGO2) endonuclease component of RISC is responsible for the actual mRNA cleavage event. During RNAi, hAGO2 becomes loaded with the siRNA guide strand, making several key nucleic acid-enzyme interactions. Chemically modified siRNAs are now widely used in place of natural double-stranded RNAs, and understanding the effects chemical modifications have on guide strand-hAGO2 interactions has become particularly important. Here, interactions between the 5' nucleotide binding domain of hAGO2, MID, and chemically modified nucleotide analogues are investigated. Measured dissociation constants reveal that hAGO2 does not discriminate between nucleotide analogues during binding, regardless of the preferred sugar conformation of the nucleotide analogues. These results correlate well with cell-based gene silencing results employing siRNAs with 5'-modified guide strands. Additionally, chemical modification with 2'-deoxy-2'-fluoroarabino nucleic acid (2'F-ANA) and 2'-deoxy-2'-fluororibonucleic acid (2'F-RNA) at the passenger strand cleavage site of siRNAs has been shown to prevent hAGO2-mediated strand cleavage, an observation that appears to have little impact on overall gene silencing potency.

  8. Process for preparing chemically modified micas for removal of cesium salts from aqueous solution

    DOEpatents

    Yates, Stephen Frederic; DeFilippi, Irene; Gaita, Romulus; Clearfield, Abraham; Bortun, Lyudmila; Bortun, Anatoly

    2000-09-05

    A chemically modified mica composite formed by heating a trioctahedral mica in an aqueous solution of sodium chloride having a concentration of at least 1 mole/liter at a temperature greater than 180 degrees Centigrade for at least 20 hours, thereby replacing exchangeable ions in the mica with sodium. Formation is accomplished at temperatures and pressures which are easily accessed by industrial equipment. The reagent employed is inexpensive and non-hazardous, and generates a precipitate which is readily separated from the modified mica.

  9. Predicting oligonucleotide-directed mutagenesis failures in protein engineering

    PubMed Central

    Wassman, Christopher D.; Tam, Phillip Y.; Lathrop, Richard H.; Weiss, Gregory A.

    2004-01-01

    Protein engineering uses oligonucleotide-directed mutagenesis to modify DNA sequences through a two-step process of hybridization and enzymatic synthesis. Inefficient reactions confound attempts to introduce mutations, especially for the construction of vast combinatorial protein libraries. This paper applied computational approaches to the problem of inefficient mutagenesis. Several results implicated oligonucleotide annealing to non-target sites, termed ‘cross-hybridization’, as a significant contributor to mutagenesis reaction failures. Test oligonucleotides demonstrated control over reaction outcomes. A novel cross-hybridization score, quickly computable for any plasmid and oligonucleotide mixture, directly correlated with yields of deleterious mutagenesis side products. Cross-hybridization was confirmed conclusively by partial incorporation of an oligonucleotide at a predicted cross-hybridization site, and by modification of putative template secondary structure to control cross-hybridization. Even in low concentrations, cross-hybridizing species in mixtures poisoned reactions. These results provide a basis for improved mutagenesis efficiencies and increased diversities of cognate protein libraries. PMID:15585664

  10. Biominetic High Density Lipoproteins for the Delivery of Therapeutic Oligonucleotides

    NASA Astrophysics Data System (ADS)

    Tripathy, Sushant

    Advances in nanotechnology have brought about novel inorganic and hybrid nanoparticles with unique physico-chemical properties that make them suitable for a broad range of applications---from nano-circuitry to drug delivery. A significant part of those advancements have led to ground-breaking discoveries that have changed the approaches to formulation of therapeutics against diseases, such as cancer. Now-a-days the focus does not lie solely on finding a candidate small-molecule therapeutic with minimal adverse effects, but researchers are looking up to nanoparticles to improve biodistribution and biocompatibility profile of clinically proven therapeutics. The plethora of conjugation chemistries offered by currently extant inorganic nanoparticles have, in recent years, led to great leaps in the field of biomimicry---a modality that promises high biocompatibility. Further, in the pursuit of highly specific therapeutic molecules, researchers have turned to silencing oligonucleotides and some have already brought together the strengths of nanoparticles and silencing oligonucleotides in search of an efficacious therapy for cancer with minimal adverse effects. This dissertation work focuses on such a biomimetic platform---a gold nanoparticle based high density lipoprotein biomimetic (HDL NP), for the delivery of therapeutic oligonucleotides. The first chapter of this body of work introduces the molecular target of the silencing oligonucleotides---VEGFR2, and its role in the progression of solid tumor cancers. The background information also covers important aspects of natural high density lipoproteins (HDL), especially their innate capacity to bind and deliver exogenous and endogenous silencing oligonucleotides to tissues that express their high affinity receptor SRB1. We subsequently describe the synthesis of the biomimetic HDL NP and its oligonucleotide conjugates, and establish their biocompatibility. Further on, experimental data demonstrate the efficacy of silencing

  11. Oligonucleotide conjugates for therapeutic applications

    PubMed Central

    Winkler, Johannes

    2013-01-01

    Insufficient pharmacokinetic properties and poor cellular uptake are the main hurdles for successful therapeutic development of oligonucleotide agents. The covalent attachment of various ligands designed to influence the biodistribution and cellular uptake or for targeting specific tissues is an attractive possibility to advance therapeutic applications and to expand development options. In contrast to advanced formulations, which often consist of multiple reagents and are sensitive to a variety of preparation conditions, oligonucleotide conjugates are defined molecules, enabling structure-based analytics and quality control techniques. This review gives an overview of current developments of oligonucleotide conjugates for therapeutic applications. Attached ligands comprise peptides, proteins, carbohydrates, aptamers and small molecules, including cholesterol, tocopherol and folic acid. Important linkage types and conjugation methods are summarized. The distinct ligands directly influence biochemical parameters, uptake machanisms and pharmacokinetic properties. PMID:23883124

  12. Oligonucleotide conjugates for therapeutic applications.

    PubMed

    Winkler, Johannes

    2013-07-01

    Insufficient pharmacokinetic properties and poor cellular uptake are the main hurdles for successful therapeutic development of oligonucleotide agents. The covalent attachment of various ligands designed to influence the biodistribution and cellular uptake or for targeting specific tissues is an attractive possibility to advance therapeutic applications and to expand development options. In contrast to advanced formulations, which often consist of multiple reagents and are sensitive to a variety of preparation conditions, oligonucleotide conjugates are defined molecules, enabling structure-based analytics and quality control techniques. This review gives an overview of current developments of oligonucleotide conjugates for therapeutic applications. Attached ligands comprise peptides, proteins, carbohydrates, aptamers and small molecules, including cholesterol, tocopherol and folic acid. Important linkage types and conjugation methods are summarized. The distinct ligands directly influence biochemical parameters, uptake mechanisms and pharmacokinetic properties.

  13. Radiation-grafted, chemically modified membranes part I - Synthesis of a selective aluminum material

    NASA Astrophysics Data System (ADS)

    Bazante-Yamaguishi, Renata; Moura, Eduardo; Manzoli, José E.; Geraldo, Aurea B. C.

    2014-01-01

    Polymeric membranes were styrene grafted by irradiation methods and the obtained material was chemically modified to become aluminum selective. For this purpose, polymeric substrates of PVC (polyvinyl chloride) and PP (polypropylene) were styrene grafted mutually by gamma and electron beam irradiation. The modification process includes three basic reaction paths: Friedel-Crafts acylation, 2-methylanisole coupling and a final oxidation to achieve aluminum selectivity. Although this specific chemical modification in derivatives of polystyrene is not new, the new challenge is to obtain a selective material where original membrane characteristics (physical shape and mechanical resistance) are minimally conserved after such an aggressive treatment.

  14. Research on the chemical mechanism in the polyacrylate latex modified cement system

    SciTech Connect

    Wang, Min; Wang, Rumin; Zheng, Shuirong; Farhan, Shameel; Yao, Hao; Jiang, Hao

    2015-10-15

    In this paper, the chemical mechanism in the polyacrylate latex modified cement system was investigated by Fourier transform infrared spectra (FT-IR), X-ray photoelectron spectroscopy (XPS), gel permeation chromatography (GPC) and compact pH meter. All results have shown that the chemical reactions in the polyacrylate modified system can be divided into three stages. The hydration reactions of cement can produce large amounts of Ca(OH){sub 2} (calcium hydroxide) and lead the whole system to be alkali-rich and exothermic at the first stage. Subsequently, this environment can do great contributions to the hydrolysis of ester groups in the polyacrylate chains, resulting in the formation of carboxyl groups at the second stage. At the third stage, the final crosslinked network structure of the product was obtained by the reaction between the carboxyl groups in the polyacrylate latex chains and Ca(OH){sub 2}.

  15. Modified lignosulfonates as additives in oil recovery processes involving chemical recovery agents

    SciTech Connect

    Kalfoglou, G.

    1982-08-17

    A process for producing petroleum from subterranean formations is disclosed wherein production from the formation is obtained by driving a fluid from an injection well to a production well. The process involves injecting via the injection well into the formation an aqueous solution of modified lignosulfonate salt as a sacrificial agent to inhibit the deposition of surfactant and/or polymer on the reservoir matrix. The process may best be carried out by injecting the modified lignosulfonates into the formation through the injection well mixed with either a polymer, a surfactant solution and/or a micellar dispersion. This mixture would then be followed by a drive fluid such as water to push the chemicals to the production well. The lignosulfonates may be modified by any combination of any two or more of: reaction with chloroacetic acid, reaction with carbon dioxide, addition of the methylene sulfonate radical to the lignosulfonate molecule and oxidation with oxygen.

  16. Development of combinations of chemically modified vegetable oils as pork backfat substitutes in sausages formulation.

    PubMed

    Ospina-E, Juan Camilo; Cruz-S, Adriana; Pérez-Alvarez, José Angel; Fernández-López, Juana

    2010-03-01

    Today's consumers look for foods which provide nutrition and pleasure, while safeguarding their health, the result of which is that they increasingly avoid foods containing cholesterol and saturated and trans fatty acids. Chemically modified vegetable oils can help tailor meat products to meet this growing need and at the same time fulfil the technological needs of the meat processing industry. In this study, 16 backfat samples were characterised for their solid fat content (SFC) and melting point and these characteristics were used to design a mixture of chemically modified vegetable oils for use as a pork fat substitute for elaborating sausages. The mixtures were prepared with different vegetable oils bearing in mind with stearic acid content due to its close correlation with the SFC. The backfat was characterised as a function of its SFC and some modified vegetable oil mixtures were proposed, which led to a 10-20% diminution in saturated fatty acids and with a melting point similar to those observed in the backfat. The fatty acid profile pointed to a polyunsaturated/saturated fatty acids ratio higher than 0.4, and an n-6/n-3 fatty acid ratio of less than 4 in both modified vegetable oil mixtures proposed.

  17. Effect of chemical heterogeneity on photoluminescence of graphite oxide treated with S-/N-containing modifiers

    NASA Astrophysics Data System (ADS)

    Ebrahim, Amani M.; Rodríguez-Castellón, Enrique; Montenegro, José María; Bandosz, Teresa J.

    2015-03-01

    Graphite oxide (GO) obtained using Hummers method was modified by hydrothermal treatment either with sulfanilic acid or polystyrene (3-ammonium) sulfonate at 100 °C or 85 °C, respectively. Both modifiers contain sulfur in the oxidized forms and nitrogen in the reduced forms. The materials were characterized using FTIR, XPS, thermal analysis, potentiometric titration and SEM. Their photoluminescent properties and their alteration with an addition of Ag+ were also measured. As a result of these modifications nitrogen was introduced to the graphene layers as amines, imides, amides, and sulfur as sulfones and sulfonic acids. Moreover, the presence of polyaniline was detected. This significantly affected the polarity, acid-base character, and conductivity of the materials. Apparently carboxylic groups of GO were involved in the surface reactions. The modified GOs lost their layered structure and the modifications resulted in the high degree of structural and chemical heterogeneity. Photoluminescence in visible light was recorded and linked to the presence of heteroatoms. For the polystyrene (3-ammonium) sulfonate modified sample addition of Ag+ quenched the photoluminescence at low wavelength showing sensitivity as a possible optical detector. No apparent effect was found for the sulfanilic acid modified sample.

  18. Chemically modified Si(111) surfaces simultaneously demonstrating hydrophilicity, resistance against oxidation, and low trap state densities

    NASA Astrophysics Data System (ADS)

    Brown, Elizabeth S.; Hlynchuk, Sofiya; Maldonado, Stephen

    2016-03-01

    Chemically modified Si(111) surfaces have been prepared through a series of wet chemical surface treatments that simultaneously show resistance towards surface oxidation, selective reactivity towards chemical reagents, and areal defect densities comparable to unannealed thermal oxides. Specifically, grazing angle attenuated total reflectance infrared and X-ray photoelectron (XP) spectroscopies were used to characterize allyl-, 3,4-methylenedioxybenzene-, or 4-[bis(trimethylsilyl)amino]phenyl-terminated surfaces and the subsequently hydroxylated surfaces. Hydroxylated surfaces were confirmed through reaction with 4-(trifluoromethyl)benzyl bromide and quantified by XP spectroscopy. Contact angle measurements indicated all surfaces remained hydrophilic, even after secondary backfilling with CH3sbnd groups. Surface recombination velocity measurements by way of microwave photoconductivity transients showed the relative defect-character of as-prepared and aged surfaces. The relative merits for each investigated surface type are discussed.

  19. Prompt activation of telomerase by chemical carcinogens in rats detected with a modified TRAP assay.

    PubMed

    Miura, M; Karasaki, Y; Abe, T; Higashi, K; Ikemura, K; Gotoh, S

    1998-05-08

    The maintenance of telomere length is crucial for survival of cells. Telomerase is an RNA-containing reverse transcriptase, which is responsible for elongation of shortened telomeres. Telomerase reactivation has been suggested to be involved in malignant progressions. To study on the involvement of telomerase activation in in vivo carcinogenesis, we first modified the original TRAP assay by changing the primer designs and the labeling method of PCR products to an end-labeling method. Second, we investigated the activation of telomerase in different organs after treatments of rats with various chemical carcinogens. Very early after the beginning of the treatment, telomerase activity in the liver, kidney, and lung was increased. In most cases, telomerase activation occurred in the primary or favorite target organs. The present results suggest that telomerase activation occurs promptly when animals are exposed to chemical carcinogens, which may contribute to in vivo chemical carcinogenesis.

  20. Thermodynamics of Oligonucleotide Duplex Melting

    NASA Astrophysics Data System (ADS)

    Schreiber-Gosche, Sherrie; Edwards, Robert A.

    2009-05-01

    Melting temperatures of oligonucleotides are useful for a number of molecular biology applications, such as the polymerase chain reaction (PCR). Although melting temperatures are often calculated with simplistic empirical equations, application of thermodynamics provides more accurate melting temperatures and an opportunity for students to apply rigorous thermodynamic analysis to an important biochemical problem. Because the stacking of base pairs on top of one another is a significant factor in the energetics of oligonucleotide melting, several investigators have applied van't Hoff analysis to melting temperature data using a nearest-neighbor model and have obtained entropies and enthalpies for the stacking of bases. The present article explains how the equilibrium constant for the dissociation of strands from double-stranded oligonucleotides can be expressed in terms of the total strand concentration and thus how the total strand concentration influences the melting temperature. It also presents a simplified analysis based on the entropies and enthalpies of stacking that is manually tractable so that students can work examples to help them understand the thermodynamics of oligonucleotide melting.

  1. Thermodynamics of Oligonucleotide Duplex Melting

    ERIC Educational Resources Information Center

    Schreiber-Gosche, Sherrie; Edwards, Robert A.

    2009-01-01

    Melting temperatures of oligonucleotides are useful for a number of molecular biology applications, such as the polymerase chain reaction (PCR). Although melting temperatures are often calculated with simplistic empirical equations, application of thermodynamics provides more accurate melting temperatures and an opportunity for students to apply…

  2. A modified Lagrangian-volumes method to simulate chemical transport in heterogeneous porous media

    NASA Astrophysics Data System (ADS)

    de Dreuzy, J.; Davy, P.

    2008-12-01

    Transport in subsurface environments is conditioned by physical and chemical processes in interaction, the most common being advection and dispersion for the physical processes and sorption for chemical reactions. Several numerical approaches have been developed to solve the complex set of equations governing this type of solute transport. These methods become time consuming in highly heterogeneous porous media having a broad-range velocity distribution. In this paper; we discuss a new efficient Lagrangian method. This method, modified from the Lagrangian-volumes approach, consists in dividing the aqueous phase in elementary volumes moved with the flow and interacting with the solid phase. Like in continuous time random walk algorithms, rather than keeping a constant time step, the time is adapted to the mesh velocity and computed so that an elementary volume crosses a mesh in a single numerical step. The modified Lagrangian-volume approach remains thus efficient whatever the velocity field. This approach is also highly flexible as it achieves a decoupling of the physical and chemical processes at the elementary volume scale, i.e. at the lowest considered scale, giving way to model virtually all possible chemical reactions. The modified Lagrangian volume approach can model both reactions between species in solution and sorption reactions. Reactions in solution are modeled by exchanges of solutes between Lagrangian volumes. For sorption reactions, the surface-to-volume ratio variability, a key parameter of sorption reactions, is accounted for by deforming the shape of the elementary volume. We implement and validate the algorithm on the specific case of the nonlinear Freundlich kinetic sorption in highly heterogeneous lognormal and multifractal permeability fields.

  3. [Oligonucleotide analogues bearing an acyclonucleoside linked by an internucleotide amide bond].

    PubMed

    Kochetkova, S V; Fillipova, E A; Kolganova, N A; Timofeev, E N; Florent'ev, V L

    2008-01-01

    Oligonucleotide analogues bearing an acyclocytidine linked to thymidine by an amide (3'-O-CH2-CO-N-5') bond were synthesized. Melting curves of duplexes formed by modified oligonucleotides and complementary natural oligomers were obtained and thermodynamic parameters of their formation were measured. Replacement of dCpT by a modified dinucleotide only moderately decreased the melting temperature of these modified duplexes in comparison with unmodified duplexes containing complementary natural bases. CD spectra of modified duplexes were studied, and the duplex spatial structures are discussed. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2008, vol. 34, no. 2; see also http://www.maik.ru.

  4. Stabilisation of silver and copper nanoparticles in a chemically modified chitosan matrix.

    PubMed

    Tiwari, Anand D; Mishra, Ajay K; Mishra, Shivani B; Kuvarega, Alex T; Mamba, Bhekie B

    2013-02-15

    This work describes the stabilisation of silver and copper nanoparticles in chemically modified chitosan colloidal solution. Chitosan-N-2-methylidene-hydroxy-pyridine-6-methylidene hydroxy thiocarbohydrazide (CSPTH) was used as a stabilising and reducing agent for silver and copper nanoparticles. The modified chitosan derivatives and the synthesised nanoparticles were characterised by Fourier transform infrared (FT-IR) spectroscopy, Ultraviolet-visible (UV-Vis) spectroscopy and X-ray diffraction (XRD). Particle size, morphology and segregation of the nanoparticles were determined by transmission electron microscopy (TEM). The size of the nanoparticles was found to be less than 20 nm and 50 nm for silver and copper nanoparticles, respectively. These nanoparticles were stabilised in a chemically modified chitosan solution and their properties were studied using fluorescence spectroscopy, photoluminescence spectroscopy and surface-enhanced Raman scattering (SERS). The optical properties of silver nanoparticles in surface plasmon band (SPB) were enhanced at 407 nm compared to those of copper nanoparticles. Fluorescence (400 nm and 756 nm), photoluminescence (450 and 504 nm) and Raman scattering (1382 and 1581 cm(-1)) properties for the copper nanoparticles were superior to those of the silver nanoparticles.

  5. Deposition of carbon nanotubes onto aramid fibers using as-received and chemically modified fibers

    NASA Astrophysics Data System (ADS)

    Rodríguez-Uicab, O.; Avilés, F.; Gonzalez-Chi, P. I.; Canché-Escamilla, G.; Duarte-Aranda, S.; Yazdani-Pedram, M.; Toro, P.; Gamboa, F.; Mazo, M. A.; Nistal, A.; Rubio, J.

    2016-11-01

    Multiwall carbon nanotubes (MWCNTs) oxidized by an acid treatment were deposited on the surface of as-received commercial aramid fibers containing a surface coating ("sizing"), and fibers modified by either a chlorosulfonic treatment or a mixture of nitric and sulfuric acids. The surface of the aramid fiber activated by the chemical treatments presents increasing density of CO, COOH and OH functional groups. However, these chemical treatments reduced the tensile mechanical properties of the fibers, especially when the nitric and sulfuric acid mixture was used. Characterization of the MWCNTs deposited on the fiber surface was conducted by scanning electron microscopy, Raman spectroscopy mapping and X-ray photoelectron spectroscopy. These characterizations showed higher areal concentration and more homogeneous distribution of MWCNTs over the aramid fibers for as-received fibers and for those modified with chlorosulfonic acid, suggesting the existence of interaction between the oxidized MWCNTs and the fiber coating. The electrical resistance of the MWCNT-modified aramid yarns comprising ∼1000 individual fibers was in the order of MΩ/cm, which renders multifunctional properties.

  6. Conjugation of fluorescent proteins with DNA oligonucleotides.

    PubMed

    Lapiene, Vidmantas; Kukolka, Florian; Kiko, Kathrin; Arndt, Andreas; Niemeyer, Christof M

    2010-05-19

    This work describes the synthesis of covalent ssDNA conjugates of six fluorescent proteins, ECFP, EGFP, E(2)GFP, mDsRed, Dronpa, and mCherry, which were cloned with an accessible C-terminal cystein residue to enable site-selective coupling using a heterobispecific cross-linker. The resulting conjugates revealed similar fluorescence emission intensity to the unconjugated proteins, and the functionality of the tethered oligonucleotide was proven by specific Watson-Crick base pairing to cDNA-modified gold nanoparticles. Fluorescence spectroscopy analysis indicated that the fluorescence of the FP is quenched by the gold particle, and the extent of quenching varied with the intrinsic spectroscopic properties of FP as well as with the configuration of surface attachment. Since this study demonstrates that biological fluorophores can be selectively incorporated into and optically coupled with nanoparticle-based devices, applications in DNA-based nanofabrication can be foreseen.

  7. Adsorption of anionic dyes from aqueous solutions using chemically modified straw.

    PubMed

    Zhang, Wenxuan; Li, Haijiang; Kan, Xiaowei; Dong, Lei; Yan, Han; Jiang, Ziwen; Yang, Hu; Li, Aimin; Cheng, Rongshi

    2012-08-01

    The effective disposal of redundant straw is a significant work for environmental protection and full utilization of resource. In this work, the wheat straw has been modified by etherification to prepare a kind of quaternary ammonium straw adsorbents. The adsorption behaviors of the modified straw for methyl orange (MO) and acid green 25(AG25) were studied in both batch and column systems. The adsorption capacity of the straw for both dyes improved evidently after modification. The maximal MO and AG25 uptakes were more than 300 and 950 mg g(-1), respectively. Furthermore, the adsorption equilibrium, kinetics and column studies all indicated that the adsorption behavior was a monolayer chemical adsorption with an ion-exchange process. In addition, after adsorption of anionic dyes, the used adsorbents were successfully applied to adsorb a cationic dye directly at suitable conditions in the secondary adsorption. This was due to the altered surface structures of the used adsorbents.

  8. A modified method for estimation of chemical oxygen demand for samples having high suspended solids.

    PubMed

    Yadvika; Yadav, Asheesh Kumar; Sreekrishnan, T R; Satya, Santosh; Kohli, Sangeeta

    2006-03-01

    Determination of chemical oxygen demand (COD) of samples having high suspended solids concentration such as cattle dung slurry with open reflux method of APHA-AWWA-WPCF did not give consistent results. This study presents a modification of the open reflux method (APHA-AWWA-WPCF) to make it suitable for samples with high percentage of suspended solids. The new method is based on a different technique of sample preparation, modified quantities of reagents and higher reflux time as compared to the existing open reflux method. For samples having solids contents of 14.0 g/l or higher, the modified method was found to give higher value of COD with much higher consistency and accuracy as compared to the existing open reflux method.

  9. The Use of Aryl Hydrazide Linkers for the Solid Phase Synthesis of Chemically Modified Peptides

    SciTech Connect

    Woo, Y; Mitchell, A R; Camarero, J A

    2006-11-03

    Since Merrifield introduced the concept of solid phase synthesis in 1963 for the rapid preparation of peptides, a large variety of different supports and resin-linkers have been developed that improve the efficiency of peptide assembly and expand the myriad of synthetically feasible peptides. The aryl hydrazide is one of the most useful resin-linkers for the synthesis of chemically modified peptides. This linker is completely stable during Boc- and Fmoc-based solid phase synthesis and yet it can be cleaved under very mild oxidative conditions. The present article reviews the use of this valuable linker for the rapid and efficient synthesis of C-terminal modified peptides, head-to-tail cyclic peptides and lipidated peptides.

  10. Functionalization of PVC membrane with ss oligonucleotides for a potentiometric biosensor.

    PubMed

    Shishkanova, T V; Volf, R; Krondak, M; Král, V

    2007-05-15

    A novel application of a single stranded (ss) oligonucleotide as an active component of polymeric membrane in an ion-selective electrode (ISE) is described. The original oligonucleotides, oligo(dA)(15), modified by cholesterol, triphenylmethyl and hexadecyl derivatives, were immobilized into poly(vinyl chloride) (PVC) membrane using extraction protocol. In parallel, the adsorption protocol was used to immobilize unmodified oligo(dA)(15) on the PVC membrane based on tridodecylmethyammonium chloride (TDDMA(+)Cl(-)). Immobilization of ss oligonucleotide probe through spacer was more effective for the potentiometric detection of the hybridization between complementary oligonucleotides. It was found that cholesterol-oligo(dA)(15) modified membranes were sensitive toward complementary oligo(dT)(15) in the concentration range 2-80 nM at pH 7. An explanation for the detection mechanism is proposed.

  11. Adsorption characteristics of metal ions on chitosan chemically modified by D-galactose

    SciTech Connect

    Kondo, Kazuo; Sumi, Hisaharu; Matsumoto, Michiaki

    1996-07-01

    The adsorption characteristics of metal ions on chitosan chemically modified by D-galactose were examined. The pH dependency on the distribution ratio was found to be affected by the valency of the metal ion, and the apparent adsorption equilibrium constants of the metal ions were determined. The order of adsorption of the metal ions is Ga > In > Nd > Eu for the trivalent metal ions and Cu > Ni > Co for the divalent metal ions. It is believed that amino and hydroxyl groups in the chitosan act as a chelating ligand.

  12. Sorption of nickel (II) from aqueous system by chemically modified pungan (pongamia pinnata) seedpod carbon

    NASA Astrophysics Data System (ADS)

    Senthil, M.; Arulanantham, A.

    2013-06-01

    The adsorption of Ni (II) on chemically modified bicarbonate impregnated sulphuric acid treated pungan (pongamia pinnata) seedpod carbon (BSPAC) was investigated as a function of equilibrium time, solution pH and carbon dosage. The adsorption of nickel (II) was also studied by using Freundlich, Langmuir and Temkin isotherm models. Kinetic studies were conducted using reversible-first-order, pseudo-first-order and pseudo-second-order kinetic equations. The results obtained were compared with commercially available activated carbon (CAC) of same 20-50 ASTM mesh size.

  13. Retention of Proteins and Metalloproteins in Open Tubular Capillary Electrochromatography with Etched Chemically Modified Columns

    PubMed Central

    Pesek, Joseph J.; Matyska, Maria T.; Salgotra, Vasudha

    2010-01-01

    Etched chemically modified capillaries with two different bonded groups (pentyl and octadecyl) are compared for their migration behavior of several common proteins and metalloproteins as well as metalloproteinases. Migration times, efficiency and peak shape are evaluated over the pH range of 2.1 to 8.1 to determine any effects of the bonded group on the electrochromatographic behavior of these compounds. One goal was to determine if the relative hydrophobicity of the stationary phase has a significant effect on proteins in the open tubular format of capillary electrochromatography as it does in HPLC. Reproducibility of the migration times is also investigated. PMID:18850653

  14. Size-dependent mobility of gold nano-clusters during growth on chemically modified graphene

    NASA Astrophysics Data System (ADS)

    Bell, Gavin R.; Dawson, Peter M.; Pandey, Priyanka A.; Wilson, Neil R.; Mulheran, Paul A.

    2014-01-01

    Gold nano-clusters were grown on chemically modified graphene by direct sputter deposition. Transmission electron microscopy of the nano-clusters on these electron-transparent substrates reveals an unusual bimodal island size distribution (ISD). A kinetic Monte Carlo model of growth incorporating a size-dependent cluster mobility rule uniquely reproduces the bimodal ISD, providing strong evidence for the mobility of large clusters during surface growth. The cluster mobility exponent of -5/3 is consistent with cluster motion via one-dimensional diffusion of gold atoms around the edges of the nano-clusters.

  15. Size-dependent mobility of gold nano-clusters during growth on chemically modified graphene

    SciTech Connect

    Bell, Gavin R. Dawson, Peter M.; Pandey, Priyanka A.; Wilson, Neil R.; Mulheran, Paul A.

    2014-01-01

    Gold nano-clusters were grown on chemically modified graphene by direct sputter deposition. Transmission electron microscopy of the nano-clusters on these electron-transparent substrates reveals an unusual bimodal island size distribution (ISD). A kinetic Monte Carlo model of growth incorporating a size-dependent cluster mobility rule uniquely reproduces the bimodal ISD, providing strong evidence for the mobility of large clusters during surface growth. The cluster mobility exponent of −5/3 is consistent with cluster motion via one-dimensional diffusion of gold atoms around the edges of the nano-clusters.

  16. Peroxide-modified titanium dioxide: a chemical analog of putative Martian soil oxidants

    NASA Technical Reports Server (NTRS)

    Quinn, R. C.; Zent, A. P.

    1999-01-01

    Hydrogen peroxide chemisorbed on titanium dioxide (peroxide-modified titanium dioxide) is investigated as a chemical analog to the putative soil oxidants responsible for the chemical reactivity seen in the Viking biology experiments. When peroxide-modified titanium dioxide (anatase) was exposed to a solution similar to the Viking labeled release (LR) experiment organic medium, CO2 gas was released into the sample cell headspace. Storage of these samples at 10 degrees C for 48 hr prior to exposure to organics resulted in a positive response while storage for 7 days did not. In the Viking LR experiment, storage of the Martian surface samples for 2 sols (approximately 49 hr) resulted in a positive response while storage for 141 sols essentially eliminated the initial rapid release of CO2. Heating the peroxide-modified titanium dioxide to 50 degrees C prior to exposure to organics resulted in a negative response. This is similar to, but not identical to, the Viking samples where heating to approximately 46 degrees C diminished the response by 54-80% and heating to 51.5 apparently eliminated the response. When exposed to water vapor, the peroxide-modified titanium dioxide samples release O2 in a manner similar to the release seen in the Viking gas exchange experiment (GEx). Reactivity is retained upon heating at 50 degrees C for three hours, distinguishing this active agent from the one responsible for the release of CO2 from aqueous organics. The release of CO2 by the peroxide-modified titanium dioxide is attributed to the decomposition of organics by outer-sphere peroxide complexes associated with surface hydroxyl groups, while the release of O2 upon humidification is attributed to more stable inner-sphere peroxide complexes associated with Ti4+ cations. Heating the peroxide-modified titanium dioxide to 145 degrees C inhibited the release of O2, while in the Viking experiments heating to this temperature diminished but did not eliminated the response. Although the

  17. Peroxide-modified titanium dioxide: a chemical analog of putative Martian soil oxidants.

    PubMed

    Quinn, R C; Zent, A P

    1999-01-01

    Hydrogen peroxide chemisorbed on titanium dioxide (peroxide-modified titanium dioxide) is investigated as a chemical analog to the putative soil oxidants responsible for the chemical reactivity seen in the Viking biology experiments. When peroxide-modified titanium dioxide (anatase) was exposed to a solution similar to the Viking labeled release (LR) experiment organic medium, CO2 gas was released into the sample cell headspace. Storage of these samples at 10 degrees C for 48 hr prior to exposure to organics resulted in a positive response while storage for 7 days did not. In the Viking LR experiment, storage of the Martian surface samples for 2 sols (approximately 49 hr) resulted in a positive response while storage for 141 sols essentially eliminated the initial rapid release of CO2. Heating the peroxide-modified titanium dioxide to 50 degrees C prior to exposure to organics resulted in a negative response. This is similar to, but not identical to, the Viking samples where heating to approximately 46 degrees C diminished the response by 54-80% and heating to 51.5 apparently eliminated the response. When exposed to water vapor, the peroxide-modified titanium dioxide samples release O2 in a manner similar to the release seen in the Viking gas exchange experiment (GEx). Reactivity is retained upon heating at 50 degrees C for three hours, distinguishing this active agent from the one responsible for the release of CO2 from aqueous organics. The release of CO2 by the peroxide-modified titanium dioxide is attributed to the decomposition of organics by outer-sphere peroxide complexes associated with surface hydroxyl groups, while the release of O2 upon humidification is attributed to more stable inner-sphere peroxide complexes associated with Ti4+ cations. Heating the peroxide-modified titanium dioxide to 145 degrees C inhibited the release of O2, while in the Viking experiments heating to this temperature diminished but did not eliminated the response. Although the

  18. A Mechanistic Study of Chemically Modified Inorganic Membranes for Gas and Liquid Separations

    SciTech Connect

    Way, J Douglas

    2011-01-21

    This final report will summarize the progress made during the period August 1, 1993 - October 31, 2010 with support from DOE grant number DE-FG03-93ER14363. The objectives of the research have been to investigate the transport mechanisms in micro- and mesoporous, metal oxide membranes and to examine the relationship between the microstructure of the membrane, the membrane surface chemistry, and the separation performance of the membrane. Examples of the membrane materials under investigation are the microporous silica hollow fiber membrane manufactured by PPG Industries, chemically modified mesoporous oxide membranes, and polymer membranes containing microporous oxides (mixed matrix membranes). Analytical techniques such as NMR, FTIR and Raman spectroscopy, thermal analysis, and gas adsorption were used to investigate membrane microstructure and to probe the chemical interactions occurring at the gas-membrane interface.

  19. Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells

    PubMed Central

    Clark, Joseph T; Kennedy, Andrew B; Ryan, Daniel E; Roy, Subhadeep; Steinfeld, Israel; Lunstad, Benjamin D; Kaiser, Robert J; Wilkens, Alec B; Bacchetta, Rosa; Tsalenko, Anya; Dellinger, Douglas; Bruhn, Laurakay; Porteus, Matthew H

    2016-01-01

    CRISPR-Cas-mediated genome editing relies on guide RNAs that direct site-specific DNA cleavage facilitated by the Cas endonuclease. Here we report that chemical alterations to synthesized single guide RNAs (sgRNAs) enhance genome editing efficiency in human primary T cells and CD34+ hematopoietic stem and progenitor cells. Co-delivering chemically modified sgRNAs with Cas9 mRNA or protein is an efficient RNA- or ribonucleoprotein (RNP)-based delivery method for the CRISPR-Cas system, without the toxicity associated with DNA delivery. This approach is a simple and effective way to streamline the development of genome editing with the potential to accelerate a wide array of biotechnological and therapeutic applications of the CRISPR-Cas technology. PMID:26121415

  20. A factorial analysis of silanization conditions for the immobilization of oligonucleotides on glass surfaces.

    PubMed

    Halliwell, C M; Cass, A E

    2001-06-01

    The modification of glass surfaces with (3-mercaptopropyl)trimethoxysilane and the application of this to DNA chip technology are described. A range of factors influencing the silanization method, and hence the number of surface-bound, chemically active thiol groups, were investigated using a design of experiment approach based on analysis of variance. The number of thiol groups introduced on glass substrates were measured directly using a specific radiolabel, [14C]cysteamine hydrochloride. For liquid-phase silanization, the number of surface-bound thiol groups was found to be dependent on both postsilanization thermal curing and silanization time and relatively independent of silane concentration, reaction temperature, and sample pretreatment. Depending on the conditions used in liquid-phase silanization, (1.3-9.0) x 10(12) thiol groups/cm2 on the glass samples were bound. The reliability and repeatability of liquid- and vacuum-phase silanization were also investigated. Eighteen-base oligonucleotide probes were covalently attached to the modified surfaces via a 3'-amino modification on the DNA and subsequent reaction with the cross-linking reagent N-(gamma-maleimidobutyryloxy) succinimide ester (GMBS). The resulting probe levels were determined and found to be stoichiometric with that of the introduced thiol groups. These results demonstrate that silanization of glass surfaces under specific conditions, prior to probe attachment, is of great importance in the development of DNA chips that use the simple concept of the covalent attachment of presynthesized oligonucleotides to silicon oxide surfaces.

  1. Oligonucleotide-based antiviral strategies.

    PubMed

    Schubert, S; Kurreck, J

    2006-01-01

    In the age of extensive global traffic systems, the close neighborhood of man and livestock in some regions of the world, as well as inadequate prevention measures and medical care in poorer countries, greatly facilitates the emergence and dissemination of new virus strains. The appearance of avian influenza viruses that can infect humans, the spread of the severe acute respiratory syndrome (SARS) virus, and the unprecedented raging of human immunodeficiency virus (HIV) illustrate the threat of a global virus pandemic. In addition, viruses like hepatitis B and C claim more than one million lives every year for want of efficient therapy. Thus, new approaches to prevent virus propagation are urgently needed. Antisense strategies are considered a very attractive means of inhibiting viral replication, as oligonucleotides can be designed to interact with any viral RNA, provided its sequence is known. The ensuing targeted destruction of viral RNA should interfere with viral replication without entailing negative effects on ongoing cellular processes. In this review, we will give some examples of the employment of antisense oligonucleotides, ribozymes, and RNA interference strategies for antiviral purposes. Currently, in spite of encouraging results in preclinical studies, only a few antisense oligonucleotides and ribozymes have turned out to be efficient antiviral compounds in clinical trials. The advent of RNA interference now seems to be refueling hopes for decisive progress in the field of therapeutic employment of antisense strategies.

  2. Determination of bisphenol A in food-simulating liquids using LCED with a chemically modified electrode.

    PubMed

    D'Antuono, A; Dall'Orto, V C; Lo Balbo, A; Sobral, S; Rezzano, I

    2001-03-01

    Liquid chromatography with electrochemical detector (LC-ED), using a chemically modified electrode coated with a metalloporphyrin film, is reported for determination of bisphenol A (BPA) migration from polycarbonate baby bottles. The extraction process of the samples was performed according to regulations of the Southern Common Market (MERCOSUR), where certain food-simulating liquids [(A) distilled water, (B) acetic acid 3% V/V in distilled water, and (C) ethanol 15% V/V in distilled water] are defined along with controlled time and temperature conditions. The baseline obtained using the naked electrode showed a considerable drift which increased the detection limit. This effect was suppressed with the chemically modified electrode. A linear range up to 450 ppb along with a detection limit of 20 ppb for the amperometric detection technique was observed. The procedure described herein allowed lowering the detection limit of the method to 0.2 ppb. The value found for BPA in the food-simulating liquid is 1.2 ppb, which is below the tolerance limit for specific migration (4.8 ppm).

  3. Chemically modified inulin microparticles serving dual function as a protein antigen delivery vehicle and immunostimulatory adjuvant.

    PubMed

    Gallovic, Matthew D; Montjoy, Douglas G; Collier, Michael A; Do, Clement; Wyslouzil, Barbara E; Bachelder, Eric M; Ainslie, Kristy M

    2016-03-01

    To develop a new subunit vaccine adjuvant, we chemically modified a naturally-occurring, immunostimulatory inulin polysaccharide to produce an acid-sensitive biopolymer (acetalated inulin, Ace-IN). Various hydrophobic Ace-IN polymers were formed into microparticles (MPs) by oil-in-water emulsions followed by solvent evaporation These Ace-IN MPs possessed tunable degradation characteristics that, unlike polyesters used in FDA-approved microparticulate formulations, had only pH-neutral hydrolytic byproducts. Macrophages were passively targeted with cytocompatible Ace-IN MPs. TNF-α production by macrophages treated with Ace-IN MPs could be altered by adjusting the polymers' chemistry. Mice immunized with Ace-IN MPs encapsulating a model ovalbumin (OVA) antigen showed higher production of anti-OVA IgG antibody levels relative to soluble antigen. The antibody titers were also comparable to an alum-based formulation. This proof-of-concept establishes the potential for chemically-modified inulin MPs to simultaneously enable dual functionality as a stimuli-controlled antigen delivery vehicle and immunostimulatory adjuvant.

  4. Pharmacological profiling of zebrafish behavior using chemical and genetic classification of sleep-wake modifiers

    PubMed Central

    Nishimura, Yuhei; Okabe, Shiko; Sasagawa, Shota; Murakami, Soichiro; Ashikawa, Yoshifumi; Yuge, Mizuki; Kawaguchi, Koki; Kawase, Reiko; Tanaka, Toshio

    2015-01-01

    Sleep-wake states are impaired in various neurological disorders. Impairment of sleep-wake states can be an early condition that exacerbates these disorders. Therefore, treating sleep-wake dysfunction may prevent or slow the development of these diseases. Although many gene products are likely to be involved in the sleep-wake disturbance, hypnotics and psychostimulants clinically used are limited in terms of their mode of action and are not without side effects. Therefore, there is a growing demand for developing new hypnotics and psychostimulants with high efficacy and few side effects. Toward this end, animal models are indispensable for use in genetic and chemical screens to identify sleep-wake modifiers. As a proof-of-concept study, we performed behavioral profiling of zebrafish treated with chemical and genetic sleep-wake modifiers. We were able to demonstrate that behavioral profiling of zebrafish treated with hypnotics or psychostimulants from 9 to 10 days post-fertilization was sufficient to identify drugs with specific modes of action. We were also able to identify behavioral endpoints distinguishing GABA-A modulators and hypocretin (hcrt) receptor antagonists and between sympathomimetic and non-sympathomimetic psychostimulants. This behavioral profiling can serve to identify genes related to sleep-wake disturbance associated with various neuropsychiatric diseases and novel therapeutic compounds for insomnia and excessive daytime sleep with fewer adverse side effects. PMID:26578964

  5. Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment.

    PubMed

    Kusano, Miyako; Redestig, Henning; Hirai, Tadayoshi; Oikawa, Akira; Matsuda, Fumio; Fukushima, Atsushi; Arita, Masanori; Watanabe, Shin; Yano, Megumu; Hiwasa-Tanase, Kyoko; Ezura, Hiroshi; Saito, Kazuki

    2011-02-16

    As metabolomics can provide a biochemical snapshot of an organism's phenotype it is a promising approach for charting the unintended effects of genetic modification. A critical obstacle for this application is the inherently limited metabolomic coverage of any single analytical platform. We propose using multiple analytical platforms for the direct acquisition of an interpretable data set of estimable chemical diversity. As an example, we report an application of our multi-platform approach that assesses the substantial equivalence of tomatoes over-expressing the taste-modifying protein miraculin. In combination, the chosen platforms detected compounds that represent 86% of the estimated chemical diversity of the metabolites listed in the LycoCyc database. Following a proof-of-safety approach, we show that % had an acceptable range of variation while simultaneously indicating a reproducible transformation-related metabolic signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms.

  6. Covering Chemical Diversity of Genetically-Modified Tomatoes Using Metabolomics for Objective Substantial Equivalence Assessment

    PubMed Central

    Hirai, Tadayoshi; Oikawa, Akira; Matsuda, Fumio; Fukushima, Atsushi; Arita, Masanori; Watanabe, Shin; Yano, Megumu; Hiwasa-Tanase, Kyoko; Ezura, Hiroshi; Saito, Kazuki

    2011-01-01

    As metabolomics can provide a biochemical snapshot of an organism's phenotype it is a promising approach for charting the unintended effects of genetic modification. A critical obstacle for this application is the inherently limited metabolomic coverage of any single analytical platform. We propose using multiple analytical platforms for the direct acquisition of an interpretable data set of estimable chemical diversity. As an example, we report an application of our multi-platform approach that assesses the substantial equivalence of tomatoes over-expressing the taste-modifying protein miraculin. In combination, the chosen platforms detected compounds that represent 86% of the estimated chemical diversity of the metabolites listed in the LycoCyc database. Following a proof-of-safety approach, we show that % had an acceptable range of variation while simultaneously indicating a reproducible transformation-related metabolic signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms. PMID:21359231

  7. Aqueous dispersions of few-layer-thick chemically modified magnesium diboride nanosheets by ultrasonication assisted exfoliation.

    PubMed

    Das, Saroj Kumar; Bedar, Amita; Kannan, Aadithya; Jasuja, Kabeer

    2015-06-04

    The discovery of graphene has led to a rising interest in seeking quasi two-dimensional allotropes of several elements and inorganic compounds. Boron, carbon's neighbour in the periodic table, presents a curious case in its ability to be structured as graphene. Although it cannot independently constitute a honeycomb planar structure, it forms a graphenic arrangement in association with electron-donor elements. This is exemplified in magnesium diboride (MgB2): an inorganic layered compound comprising boron honeycomb planes alternated by Mg atoms. Till date, MgB2 has been primarily researched for its superconducting properties; it hasn't been explored for the possibility of its exfoliation. Here we show that ultrasonication of MgB2 in water results in its exfoliation to yield few-layer-thick Mg-deficient hydroxyl-functionalized nanosheets. The hydroxyl groups enable an electrostatically stabilized aqueous dispersion and create a heterogeneity leading to an excitation wavelength dependent photoluminescence. These chemically modified MgB2 nanosheets exhibit an extremely small absorption coefficient of 2.9 ml mg(-1) cm(-1) compared to graphene and its analogs. This ability to exfoliate MgB2 to yield nanosheets with a chemically modified lattice and properties distinct from the parent material presents a fundamentally new perspective to the science of MgB2 and forms a first foundational step towards exfoliating metal borides.

  8. Efficient photochemical water splitting by a chemically modified n-TiO2.

    PubMed

    Khan, Shahed U M; Al-Shahry, Mofareh; Ingler, William B

    2002-09-27

    Although n-type titanium dioxide (TiO2) is a promising substrate for photogeneration of hydrogen from water, most attempts at doping this material so that it absorbs light in the visible region of the solar spectrum have met with limited success. We synthesized a chemically modified n-type TiO2 by controlled combustion of Ti metal in a natural gas flame. This material, in which carbon substitutes for some of the lattice oxygen atoms, absorbs light at wavelengths below 535 nanometers and has a lower band-gap energy than rutile (2.32 versus 3.00 electron volts). At an applied potential of 0.3 volt, chemically modified n-type TiO2 performs water splitting with a total conversion efficiency of 11% and a maximum photoconversion efficiency of 8.35% when illuminated at 40 milliwatts per square centimeter. The latter value compares favorably with a maximum photoconversion efficiency of 1% for n-type TiO2 biased at 0.6 volt.

  9. Aqueous dispersions of few-layer-thick chemically modified magnesium diboride nanosheets by ultrasonication assisted exfoliation

    PubMed Central

    Das, Saroj Kumar; Bedar, Amita; Kannan, Aadithya; Jasuja, Kabeer

    2015-01-01

    The discovery of graphene has led to a rising interest in seeking quasi two-dimensional allotropes of several elements and inorganic compounds. Boron, carbon’s neighbour in the periodic table, presents a curious case in its ability to be structured as graphene. Although it cannot independently constitute a honeycomb planar structure, it forms a graphenic arrangement in association with electron-donor elements. This is exemplified in magnesium diboride (MgB2): an inorganic layered compound comprising boron honeycomb planes alternated by Mg atoms. Till date, MgB2 has been primarily researched for its superconducting properties; it hasn’t been explored for the possibility of its exfoliation. Here we show that ultrasonication of MgB2 in water results in its exfoliation to yield few-layer-thick Mg-deficient hydroxyl-functionalized nanosheets. The hydroxyl groups enable an electrostatically stabilized aqueous dispersion and create a heterogeneity leading to an excitation wavelength dependent photoluminescence. These chemically modified MgB2 nanosheets exhibit an extremely small absorption coefficient of 2.9 ml mg−1 cm−1 compared to graphene and its analogs. This ability to exfoliate MgB2 to yield nanosheets with a chemically modified lattice and properties distinct from the parent material presents a fundamentally new perspective to the science of MgB2 and forms a first foundational step towards exfoliating metal borides. PMID:26041686

  10. [Oligonucleotide derivatives in the nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insert].

    PubMed

    Kupriushkin, M S; Pyshnyĭ, D V

    2012-01-01

    Non-nucleotide phosporamidites were synthetized, having branched backbone with different position of functional groups. Obtained phosphoramidite monomers contain intercalator moiety--6-chloro-2-methoxyacridine, and additional hydroxyl residue protected with dimethoxytrityl group or with tert-butyldimethylsilyl group for post-synthetic modification. Synthesized oligothymidilates contain one or more modified units in different positions of sequence. Melting temperature and thermodynamic parameters of formation of complementary duplexes formed by modified oligonucleotides was defined (change in enthalpy and entropy). The introduction of intercalating residue causes a significant stabilization of DNA duplexes. It is shown that the efficiency of the fluorescence of acridine residue in the oligonucleotide conjugate significantly changes upon hybridization with DNA.

  11. Voltammetric determination of 4-nitrophenol at a sodium montmorillonite-anthraquinone chemically modified glassy carbon electrode.

    PubMed

    Hu, S; Xu, C; Wang, G; Cui, D

    2001-03-30

    A new method for the determination of 4-nitrophenol(4-NP) by differential pulse voltammetry (DPV) based on adsorptive stripping technique was described. Cyclic voltammetry (CV) and linear scan voltammetry (LSV) were used in a comparative investigation into the electrochemical reduction of 4-NP at a Na-montmorillonite(SWy-2) and anthraquione (AQ) modified glassy carbon electrode. With this chemically modified electrode, 4-NP was first irreversibly reduced from phiNO(2) to phiNHOH at -0.78 V. A couple of well-defined redox peaks at +0.22 V (vs. SCE) were responsible for a two-electron redox peak between phiNHOH and phiNO. Studies on the effect of pH on the peak height and peak potential were carried out over the pH range 2.0-9.0 with the phosphate buffer solution. A pH of 3.4 was chosen as the optimum pH. The other experimental parameters, such as film thickness, accumulation time and potential etc. were optimized. Anodic peak currents were found to be linearly related to concentration of 4-NP over the range 0.3-45 mg l(-1), with a detection limit of 0.02 mg l(-1). The interference of organic and inorganic species on the voltammetric response have been studied. This modified electrode can be used to the determination of 4-NP in water samples.

  12. Chemical etching mechanism and properties of microstructures in sapphire modified by femtosecond laser

    NASA Astrophysics Data System (ADS)

    Liu, Manyu; Hu, Youwang; Sun, Xiaoyan; Wang, Cong; Zhou, Jianying; Dong, Xinran; Yin, Kai; Chu, Dongkai; Duan, Ji'an

    2017-01-01

    Sapphire, with extremely high hardness, high-temperature stability and wear resistance, often corroded in molten KOH at 300 °C after processing. The fabrication of microstructures on sapphire substrate performed by femtosecond laser irradiation combined with KOH solution chemical etching at room temperature is presented. It is found that this method reduces the harsh requirements of sapphire corrosion. After femtosecond irradiation, the sapphire has a high corrosion speed at room temperature. Through the analysis of Raman spectrum and XRD spectrum, a novel insight of femtosecond laser interaction with sapphire (α-Al2O3) is proposed. Results indicated that grooves on sapphire surface were formed by the lasers ablation removal, and the groove surface was modified in a certain depth. The modified area of the groove surface was changed from α-Al2O3 to γ-Al2O3. In addition, the impacts of three experimental parameters, laser power, scanning velocities and etching time, on the width and depth of microstructures are investigated, respectively. The modified area dimension is about 2 μm within limits power and speed. This work could fabricate high-quality arbitrary microstructures and enhance the performance of sapphire processing.

  13. Geographical and geological origin of natural graphite heavily influence the electrical and electrochemical properties of chemically modified graphenes.

    PubMed

    Wong, Colin Hong An; Sofer, Zdeněk; Pumera, Martin

    2015-06-01

    Natural graphite is an important precursor for the production of chemically modified graphenes in bulk quantities for electrochemical applications. These natural graphites have varying fundamental properties due to the different geological processes and environments at their points of origin, which are expected to affect their chemical reactivity and hence the properties of the derived graphene materials. Four different natural graphites with known geographical and geological origins were exposed to a modified Hummers oxidation method and the resulting graphite oxides were studied. The graphite oxides were shown to have different extents of oxidation and types of oxygen groups, which directly influenced their electrochemical properties. These differences were propagated further in the subsequent chemical reduction of the graphite oxides, and the reduced graphene oxides exhibited significantly different reduction efficiencies and electrical conductivities. These findings show that the choice of natural graphite of known origin is important to synthesize chemically modified graphenes with a desired set of properties.

  14. Fabrication and long-wavelength characterization of neat and chemically modified graphene

    SciTech Connect

    Kalugin, Nikolai G.

    2014-03-31

    Graphene, a single- or several layer-thick carbon, attracts significant research activity because of its exceptional material properties. Graphene is a promising material for optoelectronic applications. Neat graphene demonstrates potential as a material for long wavelength photodetectors working at elevated temperatures. Chemical modification of graphene opens up many new applications of this material in electronics, in new composite materials, and in new catalysts for different chemical processes. Chemical vapor deposition-grown large-area graphene can be successfully modified with the creation of benzyne attachments. The investigation of microwave properties is an important part of graphene research. Two variants of near-field long wavelength microscopy were found efficient with graphene. Measurements with a probe formed by an electrically open end of a 4 GHz half-lambda parallel-strip transmission line resonator allow the implementation of an electrodynamic model of graphene microwave impedance. The results of near-field scanning superconducting quantum interference device (SQUID) RF microscopy of graphite and graphene at 200 MHz shed light on mechanisms of AC graphene response: screening currents induced in graphene by an external RF magnetic field tend to localize near structural defects.

  15. A real-time polymerase chain reaction assay for rapid, sensitive, and specific quantification of the JAK2V617F mutation using a locked nucleic acid-modified oligonucleotide.

    PubMed

    Denys, Barbara; El Housni, Hakim; Nollet, Friedel; Verhasselt, Bruno; Philippé, Jan

    2010-07-01

    The JAK2V617F mutation has emerged as an essential molecular determinant of myeloproliferative neoplasms (MPNs). The aim of this study was to evaluate the analytical and clinical performances of a real-time PCR (qPCR) assay using a combination of hydrolysis probes and a wild-type blocking oligonucleotide, all containing locked nucleic acid (LNA) bases. Moreover, we validated a procedure for precise quantification of the JAK2V617F allele burden. We used DNA samples from patients suspected to suffer from MPN and dilutions of HEL cells, carrying the mutation, to compare the LNA-qPCR assay to two previously published methods. All assays detected the same 36 JAK2V617F positive patients of 116 suspected MPN diagnostic samples. No amplification of normal donor DNA was observed in the LNA-qPCR, and the assay was able to detect and reproducibly quantify as few as 0.4% of the JAK2V617F allele in wild-type alleles. Quantification of the JAK2V617F allele burden showed similar proportion levels among the different MPN entities as described by other groups. In conclusion, the LNA-qPCR is a rapid, robust, sensitive, and highly specific assay for quantitative JAK2V617F determination that can be easily implemented in clinical molecular diagnostic laboratories. Moreover, precise quantification allows determination of JAK2V617F burden at diagnosis as well as the evaluation of response to JAK2 inhibitors.

  16. The prebiotic synthesis of oligonucleotides

    NASA Technical Reports Server (NTRS)

    Oro, J.; Stephen-Sherwood, E.

    1974-01-01

    This paper is primarily a review of recent developments in the abiotic synthesis of nucleotides, short chain oligonucleotides, and their mode of replication in solution. It also presents preliminary results from this laboratory on the prebiotic synthesis of thymidine oligodeoxynucleotides. A discussion, based on the physicochemical properties of RNA and DNA oligomers, relevant to the molecular evolution of these compounds leads to the tentative hypothesis that oligodeoxyribonucleotides of about 12 units may have been of sufficient length to initiate a self replicating coding system. Two models are suggested to account for the synthesis of high molecular weight oligomers using short chain templates and primers.

  17. Covalent incorporation of non-chemically modified gelatin into degradable PVA-tyramine hydrogels.

    PubMed

    Lim, Khoon S; Alves, Marie H; Poole-Warren, Laura A; Martens, Penny J

    2013-09-01

    Development of tissue engineering solutions for biomedical applications has driven the need for integration of biological signals into synthetic materials. Approaches to achieve this typically require chemical modification of the biological molecules. Examples include chemical grafting of synthetic polymers onto protein backbones and covalent modification of proteins using crosslinkable functional groups. However, such chemical modification processes can cause protein degradation, denaturation or loss of biological activity due to side chain disruption. This study exploited the observation that native tyrosine rich proteins could be crosslinked via radical initiated bi-phenol bond formation without any chemical modification of the protein. A new, tyramine functionalised poly(vinyl alcohol) (PVA) polymer was synthesised and characterised. The tyramine modified PVA (PVA-Tyr) was fabricated into hydrogels using a visible light initiated crosslinking system. Mass loss studies showed that PVA-Tyr hydrogels were completely degraded within 19 days most likely via degradation of ester linkages in the network. Protein incorporation to form a biosynthetic hydrogel was achieved using unmodified gelatin, a protein derived from collagen and results showed that 75% of gelatin was retained in the gel post-polymerisation. Incorporation of gelatin did not alter the sol fraction, swelling ratio and degradation profile of the hydrogels, but did significantly improve the cellular interactions. Moreover, incorporation of as little as 0.01 wt% gelatin was sufficient to facilitate fibroblast adhesion onto PVA-Tyr/gelatin hydrogels. Overall, this study details the synthesis of a new functionalised PVA macromer and demonstrates that tyrosine containing proteins can be covalently incorporated into synthetic hydrogels using this innovative PVA-Tyr system. The resultant degradable biosynthetic hydrogels hold great promise as matrices for tissue engineering applications.

  18. Efficient ex vivo delivery of chemically modified messenger RNA using lipofection and magnetofection.

    PubMed

    Badieyan, Zohreh Sadat; Pasewald, Tamara; Mykhaylyk, Olga; Rudolph, Carsten; Plank, Christian

    2017-01-22

    Recently, chemically modified mRNA (cmRNA) therapeutics have been the subject of extensive application-oriented research in both academia and industry as a safer alternative for gene and recombinant protein therapies. However, the lack of an efficient delivery system hinders widespread application. Here we used ∼100-nm lipoplexes and magnetic lipoplexes that can protect cmRNA from RNases and efficiently deliver it into muscle and fat tissues as well as to the endothelium of the carotid artery. Establishing magnetofection for ex vivo cmRNA delivery for the first time, we suggest this method for potential enhanced and targeted delivery of cmRNA. This study introduces optimal cmRNA complexes with high ex vivo efficiency as good candidates for further in vivo cmRNA delivery.

  19. Impedance based detection of chemical warfare agent mimics using ferrocene-lysine modified carbon nanotubes.

    PubMed

    Diakowski, Piotr M; Xiao, Yizhi; Petryk, Michael W P; Kraatz, Heinz-Bernhard

    2010-04-15

    A recognition layer formed by multiwalled carbon nanotubes (MWCNTs) covalently modified with a ferrocene-lysine conjugate deposited on the indium tin oxide (ITO) was investigated as a sensor for chemical warfare agent (CWA) mimics. Electrochemical impedance spectroscopy measurements showed that upon addition of CWA mimic dramatic changes occurred in the electrical properties of the recognition layer. These changes allowed the detection of nerve agent analogues at the micromolar level, and a limited sensitivity was observed toward a sulfur mustard mimic. Experimental parameters were optimized so as to allow the detection of CWAs at single frequency, thereby significantly reducing acquisition time and simplifying data treatment. A proposed method of detection represents a significant step toward the design of an affordable and "fieldable" electrochemical CWA sensor.

  20. Genome mining expands the chemical diversity of the cyanobactin family to include highly modified linear peptides.

    PubMed

    Leikoski, Niina; Liu, Liwei; Jokela, Jouni; Wahlsten, Matti; Gugger, Muriel; Calteau, Alexandra; Permi, Perttu; Kerfeld, Cheryl A; Sivonen, Kaarina; Fewer, David P

    2013-08-22

    Ribosomal peptides are produced through the posttranslational modification of short precursor peptides. Cyanobactins are a growing family of cyclic ribosomal peptides produced by cyanobacteria. However, a broad systematic survey of the genetic capacity to produce cyanobactins is lacking. Here we report the identification of 31 cyanobactin gene clusters from 126 genomes of cyanobacteria. Genome mining suggested a complex evolutionary history defined by horizontal gene transfer and rapid diversification of precursor genes. Extensive chemical analyses demonstrated that some cyanobacteria produce short linear cyanobactins with a chain length ranging from three to five amino acids. The linear peptides were N-prenylated and O-methylated on the N and C termini, respectively, and named aeruginosamide and viridisamide. These findings broaden the structural diversity of the cyanobactin family to include highly modified linear peptides with rare posttranslational modifications.

  1. Chemically Modified Graphene: The Influence of Structural Properties on the Assessment of Antioxidant Capacity.

    PubMed

    Hui, Kai Hwee; Pumera, Martin; Bonanni, Alessandra

    2015-08-10

    Graphene materials obtained by different synthetic routes possess dissimilar amount of defects and surface functionalities, which can influence their electrochemical performance towards the detection of electroactive probes. Oxygen-containing groups can be either detrimental to the heterogeneous charge transfer or promote favorable interactions between the graphene surface and the analyte of interest, depending on the structure of the latter. Here, we compared three chemically modified graphenes, obtained by various procedures and carrying different amounts of oxygen functionalities, for the detection of standard gallic acid, a compound commonly used as an index of the antioxidant capacity of food and beverages. We found that electrochemically reduced graphene provided the best electrochemical performance in terms of calibration sensitivity, selectivity, and linearity of response. Our findings are important in order to understand the suitability of graphene platforms for the assessment of food quality.

  2. [The isolation and characteristics of a chemically modified allergen (allergoid) from Dermatophagoides pteronyssinus mites].

    PubMed

    Petrunov, B; Nikolov, G; Konstantinova, D; Antonova, T; Iankova, R

    1996-01-01

    Chemically modified allergens (allergoids) were obtained from house dust mites (Dermatophagoides pteronyssinus). The allergenicity of allergoids in comparison with commercial mite allergen was determined by the skin prick test and by the in vitro test of degranulation of passively sensitized rat mast cells. Changes in allergoid molecules were determined with the use of gel filtration in a column packed with Sephadex G-75, isoelectric focusing in polyacrylamide gel, the determination of the concentration of end amino groups and the enzymatic activity of preparations, as well as HPLC. The possibility of using these methods for controlling the process of modification was studied. The results confirmed the fact that the modification on the allergenic preparation really occurred and the allergenic activity of allergoids was low.

  3. Palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides.

    PubMed

    Shaughnessy, Kevin H

    2015-05-22

    Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides.

  4. Structural resistance of chemically modified 1-D nanostructured titanates in inorganic acid environment

    SciTech Connect

    Marinkovic, Bojan A.; Fredholm, Yann C.; Morgado, Edisson

    2010-10-15

    Sodium containing one-dimensional nanostructured layered titanates (1-D NSLT) were produced both from commercial anatase powder and Brazilian natural rutile mineral sands by alkali hydrothermal process. The 1-D NSLT were chemically modified with proton, cobalt or iron via ionic exchange and all products were additionally submitted to intensive inorganic acid aging (pH = 0.5) for 28 days. The morphology and crystal structure transformations of chemically modified 1-D NSLT were followed by transmission electron microscopy, powder X-ray diffraction, selected area electron diffraction and energy dispersive spectroscopy. It was found that the original sodium rich 1-D NSLT and cobalt substituted 1-D NSLT were completely converted to rutile nanoparticles, while the protonated form was transformed in a 70%-30% (by weight) anatase-rutile nanoparticles mixture, very similar to that of the well-known TiO{sub 2}-photocatalyst P25 (Degussa). The iron substituted 1-D NSLT presented better acid resistance as 13% of the original structure and morphology remained, the rest being converted in rutile. A significant amount of remaining 1-D NSLT was also observed after the acid treatment of the product obtained from rutile sand. The results showed that phase transformation of NSLT into titanium dioxide polymorph in inorganic acid conditions were controllable by varying the exchanged cations. Finally, the possibility to transform, through acid aging, 1-D NSLT obtained from Brazilian natural rutile sand into TiO{sub 2}-polymorphs was demonstrated for the first time to the best of authors' knowledge, opening path for producing TiO{sub 2}-nanoproducts with different morphologies through a simple process and from a low cost precursor.

  5. Synthesis of Geranyl-2-Thiouridine-Modified RNA.

    PubMed

    Wang, Rui; Haruehanroengra, Phensinee; Sheng, Jia

    2017-03-02

    This unit describes the chemical synthesis of the S-geranyl-2-thiouridine (ges(2) U) phosphoramidite and its incorporation into RNA oligonucleotides through solid-phase synthesis. Starting from the 2-thiouracil nucleobase and the protected ribose, the 2-thiouridine is synthesized and the geranyl functionality is introduced into the 2-thio position by using geranyl bromide as the geranylating reagent before the conversion of this modified nucleoside into a phosphoramidite building block. The modified phosphoramidite is used to make the geranyl-RNA oligonucleotides with a solid-phase DNA synthesizer. These RNA strands are then purified by ion-exchange HPLC before further structural and functional studies, such as base pairing and enzyme recognition, can be done. © 2017 by John Wiley & Sons, Inc.

  6. Single and mixed chemically modified carbon paste ion-selective electrodes for determination of ketotifen fumarate.

    PubMed

    Khater, M M; Issa, Y M; Mohamed, S H

    2013-02-01

    New modified carbon paste electrodes for determination of ketotifen fumarate in its pure and pharmaceutical preparations were constructed. The used modifiers are ketotifen phosphotungestate (Keto(3) PT), and ketotifen tetraphenylborate (Keto-TPB). Single and mixed ion-associate electrodes were prepared. Both Keto-TPB and mixed (Keto-TPB and Keto(3) PT) electrodes have a linearity range of 1.00 × 10(-5) -1.00 × 10(-2) mol L(-1) . The slopes were 58.30 and 54.20 mV/decade for Keto-TPB and mixed chemically modified carbon paste electrodes (CMCPE), respectively. The limits of detection were 1.42 × 10(-6) and 1.00 × 10(-5) mol L(-1) for Keto-TPB and mixed CMCPEs, respectively. The potential variation due to pH change is considered acceptable in the pH ranges 4.44-9.11 and 2.50-9.00 for Keto-TPB and mixed ion-exchanger CMCPE, respectively. The response time was ≤10 s for both electrodes. Selectivity coefficients values towards different inorganic cations, sugars, and amino acids reflect high selectivity of the prepared electrodes. Potentiometric titrations and standard addition methods were applied for the determination of ketotifen ion in its pure samples and pharmaceutical formulations (Zaditen tablet and syrup) using proposed electrodes. The electrodes were also tested in flow injection analysis (FIA). The results obtained from both methods were statistically treated by F- and t-tests. The carbon paste electrodes have the advantages of being more easily prepared and longer life span compared to the plastic membrane electrodes previously reported.

  7. Synchrotron Infrared Confocal Microspectroscopical Detection of Heterogeneity Within Chemically Modified Single Starch Granules

    SciTech Connect

    Wetzel, D.; Shi, Y; Reffner, J

    2010-01-01

    This reports the first detection of chemical heterogeneity in octenyl succinic anhydride modified single starch granules using a Fourier transform infrared (FT-IR) microspectroscopical technique that combines diffraction-limited infrared microspectroscopy with a step size that is less than the mask projected spot size focused on the plane of the sample. The high spatial resolution was achieved with the combination of the application of a synchrotron infrared source and the confocal image plane masking system of the double-pass single-mask Continuum{reg_sign} infrared microscope. Starch from grains such as corn and wheat exists in granules. The size of the granules depends on the plant producing the starch. Granules used in this study typically had a median size of 15 {micro}m. In the production of modified starch, an acid anhydride typically is reacted with OH groups of the starch polymer. The resulting esterification adds the ester carbonyl (1723 cm{sup -1}) organic functional group to the polymer and the hydrocarbon chain of the ester contributes to the CH{sub 2} stretching vibration to enhance the intensity of the 2927 cm{sup -1} band. Detection of the relative modifying population on a single granule was accomplished by ratioing the baseline adjusted peak area of the carbonyl functional group to that of a carbohydrate band. By stepping a confocally defined infrared beam as small as 5 {micro}m x 5 {micro}m across a starch granule 1 {micro}m at a time in both the x and y directions, the heterogeneity is detected with the highest possible spatial resolution.

  8. Development of improved nanosilver-based antibacterial textiles via synthesis of versatile chemically modified cotton fabrics.

    PubMed

    Hebeish, A; El-Shafei, A; Sharaf, S; Zaghloul, S

    2014-11-26

    Cationization of cotton fabric form was effected by reacting the cellulose with 3-chloro-2 hydroxypropyl trimethyl ammonium chloride in presence of sodium hydroxide as per the pad dry cure method. Thus obtained cationized cotton cellulose was reacted with a reactive copolymer, namely, reactive β-cyclodextrin grafted with polyacrylic acid (MCT-βCD-g-PAA).Bridging of another copolymer, namely, β-cyclodextrin grafted with polyacrylic acid (βCD-g-PAA) to the cationized fabric using epichlorohydrin crosslinker was also performed. Inclusion of Ag nanoparticles in these three cotton substrates via treatment of the latter with colloid of Ag nanoparticles or through in situ formation of the former was exercised. Characterization of cotton fabric before and after being chemically modified was carried out using FTIR, XRD and SEM. Bacterial examination of the cationized cotton containing either (MCT-βCD-g-PAA) or (βCD-g-PAA) incorporated with Ag nanoparticles showed these substrates function against G+ve and G-ve bacteria. Ability of (MCT-βCD-g-PAA) modified cotton to include hydrophobic molecules was examined.

  9. Chemically Modified Plastic Tube for High Volume Removal and Collection of Circulating Tumor Cells

    PubMed Central

    Gaitas, Angelo; Kim, Gwangseong

    2015-01-01

    In this preliminary effort, we use a commercially available and chemically modified tube to selectively capture circulating tumor cells (CTCs) from the blood stream by immobilizing human anti-EpCAM antibodies on the tube's interior surface. We describe the requisite and critical steps required to modify a tube into a cancer cell-capturing device. Using these simple modifications, we were able to capture or entrap about 85% of cancer cells from suspension and 44% of cancer cells from spiked whole blood. We also found that the percentage of cells captured was dependent on the tube's length and also the number of cancer cells present. It is our strong belief that with the utilization of appropriate tube lengths and procedures, we can ensure capture and removal of nearly the entire CTC population in whole blood. Importantly after a patient’s entire blood volume has circulated through the tube, the tube can then be trypsinized to release the captured live CTCs for further analysis and testing. PMID:26176235

  10. Influence of ionizing radiation on physical properties of native and chemically modified starches

    NASA Astrophysics Data System (ADS)

    Henry, F.; Costa, L. C.; Aymes-Chodur, C.

    2010-01-01

    Cationic and anionic starches (chemically modified) and native starch (non-modified) were exposed to electron-beam irradiation at doses of 25, 75 and 150 kGy. The increasing solubility in water, due to chain scission and creation of polar groups as already mentioned in the literature, has been confirmed using several physical methodologies. Impedance Spectroscopy (IS) on water solutions was carried out in order to calculate the relaxation parameters of the Cole-Cole model and α and β parameters of the Jones-Dole equation, which show the influence of radiation dose on increasing polarity, decreasing of molecular mass and increasing of electrostatic attraction between chains. Infra-red spectroscopy (FTIR) and Differential Scanning Calorimetry (DSC) confirm the formation of polar groups that retain water. The aim of this work was to confirm that the control of chain scission and functionalization of starches with irradiation could then be used in a future work to create nanoparticles by complex coacervation in an aqueous base.

  11. Mutational analysis using oligonucleotide microarrays

    PubMed Central

    Hacia, J.; Collins, F.

    1999-01-01

    The development of inexpensive high throughput methods to identify individual DNA sequence differences is important to the future growth of medical genetics. This has become increasingly apparent as epidemiologists, pathologists, and clinical geneticists focus more attention on the molecular basis of complex multifactorial diseases. Such undertakings will rely upon genetic maps based upon newly discovered, common, single nucleotide polymorphisms. Furthermore, candidate gene approaches used in identifying disease associated genes necessitate screening large sequence blocks for changes tracking with the disease state. Even after such genes are isolated, large scale mutational analyses will often be needed for risk assessment studies to define the likely medical consequences of carrying a mutated gene.
This review concentrates on the use of oligonucleotide arrays for hybridisation based comparative sequence analysis. Technological advances within the past decade have made it possible to apply this technology to many different aspects of medical genetics. These applications range from the detection and scoring of single nucleotide polymorphisms to mutational analysis of large genes. Although we discuss published scientific reports, unpublished work from the private sector12 could also significantly affect the future of this technology.


Keywords: mutational analysis; oligonucleotide microarrays; DNA chips PMID:10528850

  12. Oligonucleotide therapeutics for human leukaemia.

    PubMed

    Gewirtz, A M

    1997-01-01

    The concept of antisense oligonucleotide 'therapeutics' has generated a great deal of controversy. Questions abound regarding the mechanism of action of these compounds, their reliability and their ultimate utility. These problems are compounded by the 'hype', which has attended their development, and the inability of workers in this area to meet the expectations raised by its most zealous proponents. Nevertheless, it is worth pointing out that there have been some notable gene disruption successes with this technique that have stood up to rigorous scrutiny. Our own work with c-myb as a target is perhaps a reasonable example. Though much remains to be accomplished before antisense drugs are commonly, and usefully, employed in the clinic, it is important to remember what motivates their development. Gene-targeted drugs have the promise of exquisite specificity and the potential to do much good with little toxicity. Accordingly, antisense oligonucleotides can serve as a paradigm of rational drug development. For all these reasons then, we believe that efforts should be increased to decipher the mechanism of action of antisense oligodeoxynucleotides, and to learn how they may be successfully employed in the clinic.

  13. Study of permeability changes induced by external stimuli on chemically modified electrodes

    NASA Astrophysics Data System (ADS)

    Perera, Dingiri Mudiyanselage Neluni T.

    This research was focused on understanding how external stimuli affect the permeability of the chemically modified electrodes, and how the materials used in modifying the working electrodes respond to the changes in the surface charge. We adopted a voltammetric type electrochemical sensor to investigate the permeability effects induced by pH and organic solvents. The working electrodes used in this research were chemically modified with thioctic acid self assembled monolayer (TA SAM), track etched polycarbonate membranes (TEPCM) and PS-b-PMMA nanoporous films (polystyrene-block-polymethylmethacrylate). We studied the permeability behavior of each of the material upon application of external stimuli. In chapter 3, the permeability changes induced by change in surface charge of thioctic acid SAM was investigated. The surface charge of the monolayer was tuned by changing pH of the medium, which resulted in decrease of redox current of a negatively charged marker due to deprotonation of the surface --COOH groups of TA SAM. Decrease in redox current reflected a decrease in the reaction rate, and by using closed form equations the effective rate constants at several pKa values were extracted. In chapter 4, permeability changes induced by pH in TEPCM were investigated. We assessed the surface charge of these membranes via cyclic voltammetry generated for neutral and charged redox molecules. Limiting current of charged markers were affected by the surface charge induced by pH, where as the redox current for the neutral marker was not affected. Experimental redox currents were larger than the theoretical current, indicating that redox molecules preferentially distributed in a surface layer on the nanopore. Organic solvent induced permeability changes of PS-b-PMMA nanoporous films were investigated via electrochemical impedance spectroscopy and AFM. Higher response of pore resistance in the presence of organic solvents indicated either swelling of the nanoporous film or

  14. Chemical composition and resistance-modifying effect of the essential oil of Lantana camara Linn

    PubMed Central

    Sousa, Erlânio O.; Silva, Natálya F.; Rodrigues, Fabiola F. G.; Campos, Adriana R.; Lima, Sidney G.; Costa, José Galberto M.

    2010-01-01

    In this work, the chemical constituents, antibacterial and modulatory activities of the essential oil of Lantana camara Linn were studied. The essential oil was extracted from the leaves of L. camara by hydrodistillation method using Clevenger's apparatus and its chemical constituents were separated and identified by GC-MS, and the relative content of each constituent was determined by area normalization. Among the 25 identified components, bicyclogermacrene (19.42%), isocaryophyllene (16.70%), valecene (12.94%) and germacrene D (12.34%) were the main constituents. The oil was examined to antibacterial and modulatory activities against the multiresistant strains of Escherichia coli and Staphylococcus aureus by microdilution test. The results show an inhibitory activity to E. coli (MIC 512 μg/ml) and S. aureus (MIC 256 μg/ml). The synergism of the essential oil and aminoglycosides was verified too, with significant reduction of MICs (7 ×, 1250-5 μg/ml) against E. coli. It is suggested that the essential oil of Lantana camara Linn could be used as a source of plant-derived natural products with resistance-modifying activity. PMID:20668570

  15. Chemical composition and resistance-modifying effect of the essential oil of Lantana camara Linn.

    PubMed

    Sousa, Erlânio O; Silva, Natálya F; Rodrigues, Fabiola F G; Campos, Adriana R; Lima, Sidney G; Costa, José Galberto M

    2010-04-01

    In this work, the chemical constituents, antibacterial and modulatory activities of the essential oil of Lantana camara Linn were studied. The essential oil was extracted from the leaves of L. camara by hydrodistillation method using Clevenger's apparatus and its chemical constituents were separated and identified by GC-MS, and the relative content of each constituent was determined by area normalization. Among the 25 identified components, bicyclogermacrene (19.42%), isocaryophyllene (16.70%), valecene (12.94%) and germacrene D (12.34%) were the main constituents. The oil was examined to antibacterial and modulatory activities against the multiresistant strains of Escherichia coli and Staphylococcus aureus by microdilution test. The results show an inhibitory activity to E. coli (MIC 512 mug/ml) and S. aureus (MIC 256 mug/ml). The synergism of the essential oil and aminoglycosides was verified too, with significant reduction of MICs (7 x, 1250-5 mug/ml) against E. coli. It is suggested that the essential oil of Lantana camara Linn could be used as a source of plant-derived natural products with resistance-modifying activity.

  16. Photolithographic strategy for patterning preformed, chemically modified, porous silicon photonic crystal using click chemistry.

    PubMed

    Zhu, Ying; Gupta, Bakul; Guan, Bin; Ciampi, Simone; Reece, Peter J; Gooding, J Justin

    2013-07-24

    Porous silicon (PSi) is an ideal platform for label-free biosensing, and the development of porous silicon patterning will open a pathway to the development of highly parallel PSi biochips for detecting multiple analytes. The optical response of PSi photonic crystal is determined by the changes in the effective bulk refractive index resulting from reactions/events occurring within the internal pore space. Therefore, introducing precise chemical functionalities in the pores of PSi is essential to ensure device selectivity. Here we describe the fabrication of PSi patterns that possess discrete chemical functionalities that are restricted to precise locations. The key difference to previous patterning protocols for PSi is that the entire porous material is first modified with a self-assembled monolayer of a α,ω-diyne adsorbate prior to patterning using a microfabricated titanium mask. The distal alkyne moieties in the monolayer are then amenable to further selective modification by the archetypal "click" reaction, the copper catalyzed alkyne-azide cycloaddition (CuAAC), using the titanium mask as a resist. This type of patterning is suitable for further immobilization of biological recognition elements, and presents a new platform for highly parallel PSi biosensor for multiple detections.

  17. The effects of space radiation on a chemically modified graphite-epoxy composite material

    NASA Technical Reports Server (NTRS)

    Reed, S. M.; Herakovich, C. T.; Sykes, G. F.

    1986-01-01

    The effects of the space environment on the engineering properties and chemistry of a chemically modified T300/934 graphite-epoxy composite system are characterized. The material was subjected to 1.0 x 10 to the 10th power rads of 1.0 MeV electron irradiation under vacuum to simulate 30 years in geosynchronous earth orbit. Monotonic tension tests were performed at room temperature (75 F/24 C) and elevated temperature (250 F/121 C) on 4-ply unidirectional laminates. From these tests, inplane engineering and strength properties (E sub 1, E sub 2, Nu sub 12, G sub 12, X sub T, Y sub T) were determined. Cyclic tests were also performed to characterize energy dissipation changes due to irradiation and elevated temperature. Large diameter graphite fibers were tested to determine the effects of radiation on their stiffness and strength. No significant changes were observed. Dynamic-mechanical analysis demonstrated that the glass transition temperature was reduced by 50 F(28 C) after irradiation. Thermomechanical analysis showed the occurrence of volatile products generated upon heating of the irradiated material. The chemical modification of the epoxy did not aid in producing a material which was more radiation resistant than the standard T300/934 graphite-epoxy system. Irradiation was found to cause crosslinking and chain scission in the polymer. The latter produced low molecular weight products which plasticize the material at elevated temperatures and cause apparent material stiffening at low stresses at room temperature.

  18. Sequential extraction study of stability of adsorbed mercury in chemically modified activated carbons.

    PubMed

    Tong, Shitang; Fan, Mingxia; Mao, Lei; Jia, Charles Q

    2011-09-01

    Activated carbons chemically modified with sulfur and bromine are known for their greater effectiveness in capturing vapor Hg from coal combustion and other industrial flue gases. The stability of captured Hg in spent activated carbons determines the final fate of Hg and is critical to devising Hg control strategy. However, it remains a subject that is largely unknown, particularly for Br-treated activated carbons. Using a six-step sequential extraction procedure, this work evaluated the leaching potential of Hg captured with four activated carbons, one lignite-derived activated carbon, and three chemically treated with Br(2), KClO(3), and SO(2). The results demonstrated clearly the positive effect of Br- and SO(2)-treatment on the stability of captured Hg. The Hg captured with brominated activated carbon was very stable and likely in the form of mercurous bromide complex. Sulfur added at high temperature with SO(2) was able to stabilize a majority of Hg by forming sulfide and possibly sulfonate chelate. The presence of sulfate however made a small fraction of captured Hg (<10%) labile under mild conditions. Treating activated carbon with KClO(3) lowered the overall stability of captured Hg. A positive dependence of Hg stability on Hg loading temperature was observed for the first time.

  19. Efficiency of modified chemical remediation techniques for soil contaminated by organochlorine pesticides

    NASA Astrophysics Data System (ADS)

    Correa-Torres, S. N.; Kopytko, M.; Avila, S.

    2016-07-01

    This study reports the optimization of innovation chemical techniques in order to improve the remediation of soils contaminated with organochloride pesticides. The techniques used for remediation were dehalogenation and chemical oxidation in soil contaminated by pesticides. These techniques were applied sequentially and combined to evaluate the design optimize the concentration and contact time variables. The soil of this study was collect in cotton crop zone in Agustin Codazzi municipality, Colombia, and its physical properties was measure. The modified dehalogenation technique of EPA was applied on the contaminated soil by adding Sodium Bicarbonate solution at different concentrations and rates during 4, 7 and 14 days, subsequently oxidation technique was implemented by applying a solution of KMnO4 at different concentration and reaction times. Organochlorine were detected by Gas Chromatography analysis coupled Mass Spectrometry and its removals were between 85.4- 90.0% of compounds such as 4, 4’-DDT, 4,4’-DDD, 4,4-DDE, trans-Clordane y Endrin. These results demonstrate that the technique of dehalogenation with oxidation chemistry can be used for remediation soils contaminated by organochloride pesticides.

  20. On the structure and topography of free-standing chemically modified graphene

    NASA Astrophysics Data System (ADS)

    Wilson, N. R.; Pandey, P. A.; Beanland, R.; Rourke, J. P.; Lupo, U.; Rowlands, G.; Römer, R. A.

    2010-12-01

    The mechanical, electrical and chemical properties of chemically modified graphene (CMG) are intrinsically linked to its structure. Here, we report on our study of the topographic structure of free-standing CMG using atomic force microscopy (AFM) and electron diffraction. We find that, unlike graphene, suspended sheets of CMG are corrugated and distorted on nanometre length scales. AFM reveals not only long-range (100 nm) distortions induced by the support, as previously observed for graphene, but also short-range corrugations with length scales down to the resolution limit of 10 nm. These corrugations are static not dynamic, and are significantly diminished on CMG supported on atomically smooth substrates. Evidence for even shorter-range distortions, down to a few nanometres or less, is found by electron diffraction of suspended CMG. Comparison of the experimental data with simulations reveals that the mean atomic displacement from the nominal lattice position is of order 10% of the carbon-carbon bond length. Taken together, these results suggest a complex structure for CMG where heterogeneous functionalization creates local strain and distortion.

  1. In vitro and in vivo evaluation of chemically modified degradable starch microspheres for topical haemostasis.

    PubMed

    Björses, Katarina; Faxälv, Lars; Montan, Carl; Wildt-Persson, Katarina; Fyhr, Peter; Holst, Jan; Lindahl, Tomas L

    2011-06-01

    Degradable starch microspheres (DSMs) are starch chains cross-linked with epichlorhydrin, forming glycerol-ether links. DSMs have been used for many years for temporary vascular occlusion and drug delivery in treatment of malignancies. They are also approved and used for topical haemostasis by absorbing excess fluid from the blood and concentrating endogenous coagulation factors, thereby facilitating haemostasis. This mechanism of action is not sufficient for larger bleedings in current chemical formulations of DSMs, and modification of DSMs to trigger activation of platelets or coagulation would be required for use in such applications. Chemical modifications of DSMs with N-octenyl succinic anhydride, chloroacetic acid, acetic anhydride, diethylaminoethyl chloride and ellagic acid were performed and evaluated in vitro with thrombin generation and platelet adhesion tests, and in vivo using an experimental renal bleeding model in rat. DSMs modified to activate platelets in vitro were superior in haemostatic capacity in vivo. Further studies with non-toxic substances are warranted to confirm these results and develop the DSM as a more effective topical haemostatic agent.

  2. Chemically and biologically modified activated carbon sorbents for the removal of lead ions from aqueous media.

    PubMed

    Mahmoud, Mohamed E; Abdel-Fattah, Tarek M; Osman, Maher M; Ahmed, Somia B

    2012-01-01

    A method is described for hybridization of the adsorption and biosorption characteristics of chemically treated commercial activated carbon and baker's yeast, respectively, for the formation of environmental friendly multifunctional sorbents. Activated carbon was loaded with baker's yeast after acid-base treatment. Scanning Electron Microscopy (SEM) and Fourier Transform Infrared (FTIR) Spectroscopy were used to characterize these sorbents. Moreover, the sorption capabilities for lead (II) ions were evaluated. A value of 90 μmol g(-1) was identified as the maximum sorption capacity of activated carbon. Acid-base treatment of activated carbon was found to double the sorption capacity (140-180 μmol g(-1)). Immobilization of baker's yeast on the surface of activated carbon sorbents was found to further improve the sorption capacity efficiency of lead to 360, 510 and 560 μmol g(-1), respectively. Several important factors such as pH, contact time, sorbent dose, lead concentration and interfering ions were examined. Lead sorption process was studied and evaluated by several adsorption isotherms and found to follow the Langmuir and BET models. The potential applications of various chemically and biologically modified sorbents and biosorbents for removal of lead from real water matrices were also investigated via multistage micro-column technique and the results referred to excellent recovery values of lead (95.0-99.0 ± 3.0-5.0 %).

  3. Cellular Uptake and Intracellular Trafficking of Oligonucleotides: Implications for Oligonucleotide Pharmacology

    PubMed Central

    Ming, Xin; Carver, Kyle; Laing, Brian

    2014-01-01

    One of the major constraints on the therapeutic use of oligonucleotides is inefficient delivery to their sites of action in the cytosol or nucleus. Recently it has become evident that the pathways of cellular uptake and intracellular trafficking of oligonucleotides can strongly influence their pharmacological actions. Here we provide background information on the basic processes of endocytosis and trafficking and then review recent literature on targeted delivery and subcellular trafficking of oligonucleotides in that context. A variety of approaches including molecular scale ligand-oligonucleotide conjugates, ligand-targeted nanocarriers, and the use of small molecules to enhance oligonucleotide effects are discussed. PMID:24383421

  4. Adhesion force interactions between cyclopentane hydrate and physically and chemically modified surfaces.

    PubMed

    Aman, Zachary M; Sloan, E Dendy; Sum, Amadeu K; Koh, Carolyn A

    2014-12-07

    Interfacial interactions between liquid-solid and solid-solid phases/surfaces are of fundamental importance to the formation of hydrate deposits in oil and gas pipelines. This work establishes the effect of five categories of physical and chemical modification to steel on clathrate hydrate adhesive force: oleamide, graphite, citric acid ester, nonanedithiol, and Rain-X anti-wetting agent. Hydrate adhesive forces were measured using a micromechanical force apparatus, under both dry and water-wet surface conditions. The results show that the graphite coating reduced hydrate-steel adhesion force by 79%, due to an increase in the water wetting angle from 42 ± 8° to 154 ± 7°. Two chemical surface coatings (nonanedithiol and the citric acid ester) induced rapid hydrate growth in the hydrate particles; nonanedithiol increased hydrate adhesive force by 49% from the baseline, while the citric acid ester coating reduced hydrate adhesion force by 98%. This result suggests that crystal growth may enable a strong adhesive pathway between hydrate and other crystalline structures, however this effect may be negated in cases where water-hydrocarbon interfacial tension is minimised. When a liquid water droplet was placed on the modified steel surfaces, the graphite and citric acid ester became less effective at reducing adhesive force. In pipelines containing a free water phase wetting the steel surface, chemical or physical surface modifications alone may be insufficient to eliminate hydrate deposition risk. In further tests, the citric acid ester reduced hydrate cohesive forces by 50%, suggesting mild activity as a hybrid anti-agglomerant suppressing both hydrate deposition and particle agglomeration. These results demonstrate a new capability to develop polyfunctional surfactants, which simultaneously limit the capability for hydrate particles to aggregate and deposit on the pipeline wall.

  5. Complementary addressed modification and cleavage of a single stranded DNA fragment with alkylating oligonucleotide derivatives.

    PubMed Central

    Vlassov, V V; Zarytova, V F; Kutiavin, I V; Mamaev, S V; Podyminogin, M A

    1986-01-01

    A single stranded DNA fragment was modified with alkylating derivatives of oligonucleotides complementary to a certain nucleotide sequences in the fragment. The derivatives carried aromatic 2-chloroethylamino groups at their 3'- or 5'-terminal nucleotide residues. Some of the derivatives carried both alkylating group and intercalating phenazine group which stabilized complementary complexes. It was found that these oligonucleotide derivatives modify the DNA fragment in a specific way near the target complementary nucleotide sequences, and the DNA fragment can be cleaved at the alkylated nucleotides positions. Alkylating derivatives carrying phenazine groups were found to be the most efficient in reaction with the DNA fragment. Images PMID:3714471

  6. The Fidelity of Template-Directed Oligonucleotide Ligation and the Inevitability of Polymerase Function

    NASA Astrophysics Data System (ADS)

    James, Kenneth D.; Ellington, Andrew D.

    1999-08-01

    The first living systems may have employed template-directed oligonucleotide ligation for replication. The utility of oligonucleotide ligation as a mechanism for the origin and evolution of life is in part dependent on its fidelity. We have devised a method for evaluating ligation fidelity in which ligation substrates are selected from random sequence libraries. The fidelities of chemical and enzymatic ligation are compared under a variety of conditions. While reaction conditions can be found that promote high fidelity copying, departure from these conditions leads to error-prone copying. In particular, ligation reactions with shorter oligonucleotide substrates are less efficient but more faithful. These results support a model for origins in which there was selective pressure for template-directed oligonucleotide ligation to be gradually supplanted by mononucleotide polymerization.

  7. Oligonucleotide-based biosensors for in vitro diagnostics and environmental hazard detection.

    PubMed

    Jung, Il Young; Lee, Eun Hee; Suh, Ah Young; Lee, Seung Jin; Lee, Hyukjin

    2016-04-01

    Oligonucleotide-based biosensors have drawn much attention because of their broad applications in in vitro diagnostics and environmental hazard detection. They are particularly of interest to many researchers because of their high specificity as well as excellent sensitivity. Recently, oligonucleotide-based biosensors have been used to achieve not only genetic detection of targets but also the detection of small molecules, peptides, and proteins. This has further broadened the applications of these sensors in the medical and health care industry. In this review, we highlight various examples of oligonucleotide-based biosensors for the detection of diseases, drugs, and environmentally hazardous chemicals. Each example is provided with detailed schematics of the detection mechanism in addition to the supporting experimental results. Furthermore, future perspectives and new challenges in oligonucleotide-based biosensors are discussed.

  8. Atmospheric pressure MALDI-FTMS of normal and chemically modified RNA.

    PubMed

    Kellersberger, Katherine A; Yu, Eizadora T; Merenbloom, Samuel I; Fabris, Daniele

    2005-02-01

    Atmospheric pressure (AP) MALDI has been combined with Fourier transform mass spectrometry (FTMS) to obtain the unambiguous characterization of RNA samples modified by solvent accessibility reagents used in structural studies of RNA and protein-RNA complexes. The formation of cation adducts typical of MS analysis of nucleic acids was effectively reduced by extensive washing of the anionic analytes retained onto the probe surface by strong interactions with a cationic layer of poly(diallyldimethylammonium chloride) (PADMAC). This rapid desalting procedure allowed for the detection of DNA and RNA samples in high femtomole quantities distributed over a 4 x 4 mm sample well. AP MALDI-FTMS was shown to provide high-resolution spectra for analytes as large as approximately 6.4 kDa with little or no evidence of metastable decomposition. The absence of significant metastable decay observed for precursor ions selected for tandem experiments offered a further measure of the low energy content typical of ions generated by AP MALDI. This feature proved to be very beneficial in the characterization of chemically modified RNA samples, which become particularly prone to base losses upon alkylation. The high resolution offered by FTMS enabled the application of a data-reduction algorithm capable of rejecting any signal devoid of plausible isotopic distribution, thus facilitating the analysis of complex analyte mixtures produced by nuclease treatment of RNA substrates. Proper selection of nucleases and digestion conditions can ensure the production of hydrolytic fragments of manageable size, which could extend the range of applicability of this bottom-up strategy to the structural investigation of very large RNA and protein-RNA complexes.

  9. Oligonucleotide-Functionalized Anisotropic Gold Nanoparticles

    NASA Astrophysics Data System (ADS)

    Jones, Matthew Robert

    In this thesis, we describe the properties of oligonucleotide-functionalized gold colloids under the unique set of conditions where the particles are geometrically anisotropic and have nanometer-scale dimensions. While nearly two decades of previous work elucidated numerous unexpected and emergent phenomena arising from the combination of inorganic nanoparticles with surface-bound DNA strands, virtually nothing was known about how these properties are altered when the shape of the nanoparticle core is chosen to be non-spherical. In particular, we are interested in understanding, and ultimately controlling, the ways in which these DNA-conjugated anisotropic nanostructures interact when their attraction is governed by programmable DNA hybridization events. Chapter 1 introduces the field of DNA-based materials assembly by discussing how nanoscale building blocks which present rigid, directional interactions can be thought of as possessing artificial versions of the familiar chemical principles of "bonds" and "valency". In chapter 2 we explore the fundamental interparticle binding thermodynamics of DNA-functionalized spherical and anisotropic nanoparticles, which reveals enormous preferences for collective ligand interactions occurring between flat surfaces over those that occur between curved surfaces. Using these insights, chapter 3 demonstrates that when syntheses produce mixtures of different nanoparticle shapes, the tailorable nature of DNA-mediated interparticle association can be used to selectively crystallize and purify the desired anisotropic nanostructure products, leaving spherical impurity particles behind. Chapter 4 leverages the principle that the flat facets of anisotropic particles generate directional DNA-based hybridization interactions to assemble a variety of tailorable nanoparticle superlattices whose symmetry and dimensionality are a direct consequence of the shape of the nanoparticle building block used in their construction. Chapter 5 explores

  10. Adaptive resolution simulation of oligonucleotides

    NASA Astrophysics Data System (ADS)

    Netz, Paulo A.; Potestio, Raffaello; Kremer, Kurt

    2016-12-01

    Nucleic acids are characterized by a complex hierarchical structure and a variety of interaction mechanisms with other molecules. These features suggest the need of multiscale simulation methods in order to grasp the relevant physical properties of deoxyribonucleic acid (DNA) and RNA using in silico experiments. Here we report an implementation of a dual-resolution modeling of a DNA oligonucleotide in physiological conditions; in the presented setup only the nucleotide molecule and the solvent and ions in its proximity are described at the atomistic level; in contrast, the water molecules and ions far from the DNA are represented as computationally less expensive coarse-grained particles. Through the analysis of several structural and dynamical parameters, we show that this setup reliably reproduces the physical properties of the DNA molecule as observed in reference atomistic simulations. These results represent a first step towards a realistic multiscale modeling of nucleic acids and provide a quantitatively solid ground for their simulation using dual-resolution methods.

  11. Adaptive resolution simulation of oligonucleotides.

    PubMed

    Netz, Paulo A; Potestio, Raffaello; Kremer, Kurt

    2016-12-21

    Nucleic acids are characterized by a complex hierarchical structure and a variety of interaction mechanisms with other molecules. These features suggest the need of multiscale simulation methods in order to grasp the relevant physical properties of deoxyribonucleic acid (DNA) and RNA using in silico experiments. Here we report an implementation of a dual-resolution modeling of a DNA oligonucleotide in physiological conditions; in the presented setup only the nucleotide molecule and the solvent and ions in its proximity are described at the atomistic level; in contrast, the water molecules and ions far from the DNA are represented as computationally less expensive coarse-grained particles. Through the analysis of several structural and dynamical parameters, we show that this setup reliably reproduces the physical properties of the DNA molecule as observed in reference atomistic simulations. These results represent a first step towards a realistic multiscale modeling of nucleic acids and provide a quantitatively solid ground for their simulation using dual-resolution methods.

  12. Antisense oligonucleotide therapeutics for human leukemia.

    PubMed

    Gewirtz, A M

    1998-01-01

    The development of reliable gene disruption strategies, and their application in living cells, has proven to be an extraordinary important advance for cell and molecular biologists. Using the various available approaches, the specific functions of any given gene may now be investigated directly in the relevant cell type. Application of similar experimental tools in a clinical setting might prove to be equally valuable and could well form the basis of a monumental advance in the practice of clinical medicine. This seems particularly true at the present time because much progress has been made in understanding the molecular pathogenesis of many diseases, including cancer. For these reasons a tremendous amount of interest has been generated in the use of oligodeoxynucleotides to modify gene expression. However, in spite of some notable successes which are detailed in this review, oligonucleotides have generated controversy in regard to their mechanism of action, reliability, and ultimate therapeutic utility. Nevertheless, the potential power of the "antisense" approach remains undisputed, and its ultimate therapeutic utility is far reaching. Accordingly, the problems associated with the use of these compounds are clearly worth solving. It remains the hope of many laboratories that the day will soon come when these techniques will make an important contribution to the management of chronic myelogenous leukemia and other neoplastic disorders.

  13. Antisense oligonucleotide therapeutics for human leukemia.

    PubMed

    Gewirtz, A M

    1997-01-01

    The development of reliable gene disruption strategies, and their application in living cells, has proven to be an extraordinarily important advance for cell and molecular biologists. Using the various available approaches, the specific functions of any given gene may now be investigated directly in the relevant cell type. Application of similar experimental tools in a clinical setting might prove to be equally valuable and could well form the basis of a monumental advance in the practice of clinical medicine. This seems particularly true at the present time since much progress has been made in understanding the molecular pathogenesis of many diseases, including cancer. For these reasons a tremendous amount of interest has been generated in the use of oligodeoxynucleotides to modify gene expression. However, in spite of some notable successes which are detailed in this review, oligonucleotides have generated controversy in regards to their mechanism of action, reliability, and ultimate therapeutic utility. Nevertheless, the potential power of the "antisense" approach remains undisputed, and its ultimate therapeutic utility is far reaching. Accordingly, the problems associated with the use of these compounds are clearly worth solving. It remains the hope of many laboratories that the day will soon come when these techniques will make an important contribution to the management of CML and other neoplastic disorders.

  14. Chemical Sensors Based on IR Spectroscopy and Surface-Modified Waveguides

    NASA Technical Reports Server (NTRS)

    Lopez, Gabriel P.; Niemczyk, Thomas

    1999-01-01

    Sol-gel processing techniques have been used to apply thin porous films to the surfaces of planar infrared (IR) waveguides to produce widely useful chemical sensors. The thin- film coating serves to diminish the concentration of water and increase the concentration of the analyte in the region probed by the evanescent IR wave. These porous films are composed of silica, and therefore, conventional silica surface modification techniques can be used to give the surface a specific functional character. The sol-gel film was surface-modified to make the film highly hydrophobic. These sensors were shown to be capable of detecting non-polar organic analytes, such as benzonitrile, in aqueous solution with detection limits in the ppb range. Further, these porous sol-gel structures allow the analytes to diffuse into and out of the films rapidly, thus reaching equilibrium in less than ten seconds. These sensors are unique because of the fact that their operation is based on the measurement of an IR absorption spectrum. Thus, these sensors are able to identify the analytes as well as measure concentration with high sensitivity. These developments have been documented in previous reports and publications. Recently, we have also targeted detection of the polar organic molecules acetone and isopropanol in aqueous solution. Polar organics are widely used in industrial and chemical processes, hence it is of interest to monitor their presence in effluents or decontamination process flows. Although large improvements in detection limits were expected with non-polar organic molecules in aqueous solutions using very hydrophobic porous sol-gel films on silicon attenuated total reflectance (Si ATR) waveguides, it was not as clear what the detection enhancements might be for polar organic molecules. This report describes the use of modified sol-gel-coated Si ATR sensors for trace detection and quantitation of small polar organic molecules in aqueous solutions. The detection of both acetone

  15. A modified parallel artificial membrane permeability assay for evaluating the bioconcentration of highly hydrophobic chemicals in fish.

    PubMed

    Kwon, Jung-Hwan; Escher, Beate I

    2008-03-01

    Low cost in vitro tools are needed at the screening stage of assessment of bioaccumulation potential of new and existing chemicals because the number of chemical substances that needs to be tested highly exceeds the capacity of in vivo bioconcentration tests. Thus, the parallel artificial membrane permeability assay (PAMPA) system was modified to predict passive uptake/ elimination rate in fish. To overcome the difficulties associated with low aqueous solubility and high membrane affinity of highly hydrophobic chemicals, we measured the rate of permeation from the donor poly(dimethylsiloxane)(PDMS) disk to the acceptor PDMS disk through aqueous and PDMS membrane boundary layers and term the modified PAMPA system "PDMS-PAMPA". Twenty chemicals were selected for validation of PDMS-PAMPA. The measured permeability is proportional to the passive elimination rate constant in fish and was used to predict the "minimum" in vivo elimination rate constant. The in vivo data were very close to predicted values except for a few polar chemicals and metabolically active chemicals, such as pyrene and benzo[a]pyrene. Thus, PDMS-PAMPA can be an appropriate in vitro system for nonmetabolizable chemicals. Combination with metabolic clearance rates using a battery of metabolic degradation assays would enhance the applicability for metabolizable chemicals.

  16. The chemical and catalytic properties of nanocrystalline metal oxides prepared through modified sol-gel synthesis

    NASA Astrophysics Data System (ADS)

    Carnes, Corrie Leigh

    The goal of this research was to synthesize, characterize and study the chemical properties of nanocrystalline metal oxides. Nanocrystalline (NC) ZnO, CuO, NiO, Al2O3, and the binary Al2O 3/MgO and ZnO/CuO were prepared through modified sol gel methods. These NC metal oxides were studied in comparison to the commercial (CM) metal oxides. The samples were characterized by XRD, TGA, FTIR, BET, and TEM. The NC samples were all accompanied by a significant increase in surface area and decrease in crystallite size. Several chemical reactions were studied to compare the NC samples to the CM samples. One of the reactions involved a high temperature reaction between carbon tetrachloride and the oxide to form carbon dioxide and the corresponding metal chloride. A similar high temperature reaction was conducted between the metal oxide and hydrogen sulfide to form water and the corresponding metal sulfide. A room temperature gas phase adsorption was studied where SO2 was adsorbed onto the oxide. A liquid phase adsorption conducted at room temperature was the destructive adsorption of paraoxon (a toxic insecticide). In all reactions the NC samples exhibited greater activity, destroying or adsorbing a larger amount of the toxins compared to the CM samples. To better study surface area effects catalytic reactions were also studied. The catalysis of methanol was studied over the nanocrystalline ZnO, CuO, NiO, and ZnO/CuO samples in comparison to their commercial counterparts. In most cases the NC samples proved to be more active catalysts, having higher percent conversions and turnover numbers. A second catalytic reaction was also studied, this reaction was investigated to look at the support effects. The catalysis of cyclopropane to propane was studied over Pt and Co catalysts. These catalysts were supported onto NC and CM alumina by impregnation. By observing differences in the catalytic behavior, support effects have become apparent.

  17. Chemical ligation methods for the tagging of DNA-encoded chemical libraries.

    PubMed

    Keefe, Anthony D; Clark, Matthew A; Hupp, Christopher D; Litovchick, Alexander; Zhang, Ying

    2015-06-01

    The generation of DNA-encoded chemical libraries requires the unimolecular association of multiple encoding oligonucleotides with encoded chemical entities during combinatorial synthesis processes. This has traditionally been achieved using enzymatic ligation. We discuss a range of chemical ligation methods that provide alternatives to enzymatic ligation. These chemical ligation methods include the generation of modified internucleotide linkages that support polymerase translocation and other modified linkages that while not supporting the translocation of polymerases can also be used to generate individual cDNA molecules containing encoded chemical information specifying individual library members. We also describe which of these approaches have been successfully utilized for the preparation of DNA-encoded chemical libraries and those that were subsequently used for the discovery of inhibitors.

  18. Tailoring the selectivity and stability of chemically modified platinum nanocatalysts to design highly durable anodes for PEM fuel cells.

    SciTech Connect

    Genorio, B.; Subbaraman, R.; Strmcnik, D.; Tripkovic, D.; Stamenkovic, V. R.; Markovic, N. M.

    2011-06-06

    Chemically modifying platinum with calix[4]arene yields a highly stable anode catalyst that effectively suppresses the oxidation reduction reaction without altering the maximum activity for the hydrogen oxidation reaction (see picture, Pt blue, C gray, O red, S yellow). This behavior extends from long-range-ordered stepped single-crystal surfaces to nanocatalysts.

  19. Sex determination of bovine preimplantation embryos by oligonucleotide microarray.

    PubMed

    Yang, Hua; Zhong, Fagang; Yang, Yonglin; Wang, Xinhua; Liu, Shouren; Zhu, Bin

    2013-06-01

    The aim has been to set up a rapid and accurate microarray assay using sandwich mode for sex determination of bovine preimplantation embryos. Twelve sequence-specific oligonucleotide capture probes used to discriminate 12 samples were spotted onto the aldehyde-modified glass slides by Arrayer. The 2 recognition probes used to identify coding regions of the sex-determining region of the Y chromosome gene (SRY) and β-casein (CSN2) reference gene were coupled with biotin. The assay was optimized by using genomic DNA extracted from blood samples of known sex individuals. Polymerase chain reaction (PCR) was used to amplify the fragments in the HMG box region of SRY gene and CSN2 gene with sequence-specific primers. The sex of samples was identified by detecting both the SRY and CSN2 genes simultaneously in 2 reaction cells of microarrays, with the male having SRY and CSN2 signals and the female only CSN2. The sex of 20 bovine preimplantation embryos was determined by oligonucleotide microarray. The protocol was run with a blind test that showed a 100% (82/82) specificity and accuracy in sexing of leukocytes. The bovine embryos were transferred into 20 bovine recipients, with a pregnant rate of 40% (8/20). Three calves were born at term, and 5 fetuses were miscarried. Their sexes were fully in accordance with the embryonic sex predetermination predicted by oligonucleotide microarray. This suggests that the oligonucleotide microarray method of SRY gene analysis can be used in early sex prediction of bovine embryos in breeding programs.

  20. Determination of bismuth in environmental samples by slurry sampling graphite furnace atomic absorption spectrometry using combined chemical modifiers.

    PubMed

    Dobrowolski, Ryszard; Dobrzyńska, Joanna; Gawrońska, Barbara

    2015-01-01

    Slurry sampling graphite furnace atomic absorption spectrometry technique was applied for the determination of Bi in environmental samples. The study focused on the effect of Zr, Ti, Nb and W carbides, as permanent modifiers, on the Bi signal. Because of its highest thermal and chemical stability and ability to substantially increase Bi signal, NbC was chosen as the most effective modifier. The temperature programme applied for Bi determination was optimized based on the pyrolysis and atomization curves obtained for slurries prepared from certified reference materials (CRMs) of the soil and sediments. To overcome interferences caused by sulfur compounds, Ba(NO₃)₂ was used as a chemical modifier. Calibration was performed using the aqueous standard solutions. The analysis of the CRMs confirmed the reliability of the proposed analytical method. The characteristic mass for Bi was determined to be 16 pg with the detection limit of 50 ng/g for the optimized procedure at the 5% (w/v) slurry concentration.

  1. Effects of Zn Content on Crystal Structure, Cytocompatibility, Antibacterial Activity, and Chemical Stability in Zn-Modified Calcium Silicate Coatings

    NASA Astrophysics Data System (ADS)

    Li, Kai; Yu, Jiangming; Xie, Youtao; Huang, Liping; Ye, Xiaojian; Zheng, Xuebin

    2013-08-01

    In our previous study, Zn-modified calcium silicate coatings possess not only excellent chemical stability but also well antibacterial activity. Still, effects of zinc content on these properties and cytocompatibility remain unclear. In this paper, two kinds of Zn-modified calcium silicate coatings (ZC0.3, ZC0.5) were fabricated on Ti-6Al-4V substrates via plasma spraying technology. X-ray diffraction results and transmission electron microscopy observations showed that the ZC0.5 coating was composed of pure hardystonite (Ca2ZnSi2O7) phase, while, besides Ca2ZnSi2O7 phase, the amorphous CaSiO3 phase was also detected in the ZC0.3 coating. Chemical stability in Tris-HCl buffer solution and antibacterial activity of the Zn-modified calcium silicate coatings increased with an increase in zinc content. In vitro cytocompatibility evaluation demonstrated that the proliferation and alkaline phosphatase activity and collagen type I (COLI) secretion of osteoblast-like MC3T3-E1 cells on Zn-modified coatings were significantly enhanced compared to the Zn-free coating and Ti-6Al-4V control, and no cytotoxicity appeared on Zn-modified coatings. The better antibacterial activity and the enhanced capability to promote MC3T3-E1 cells differentiation of Zn-modified coatings should be attributed to the slow and constant Zn2+ releasing from the coatings.

  2. Streptavidin-coated gold nanoparticles: critical role of oligonucleotides on stability and fractal aggregation

    PubMed Central

    D'Agata, Roberta; Palladino, Pasquale

    2017-01-01

    Gold nanoparticles (AuNPs) exhibit unique properties that can be modulated through a tailored surface functionalization, enabling their targeted use in biochemical sensing and medical diagnostics. In particular, streptavidin-modified AuNPs are increasingly used for biosensing purposes. We report here a study of AuNPs surface-functionalized with streptavidin-biotinylated oligonucleotide, focussing on the role played by the oligonucleotide probes in the stabilization/destabilization of the functionalized nanoparticle dispersion. The behaviour of the modified AuNP dispersion as a consequence of the competitive displacement of the biotinylated oligonucleotide has been investigated and the critical role of displaced oligonucletides in triggering the quasi one-dimensional aggregation of nanoparticles is demonstrated for the first time. The thorough understanding of the fundamental properties of bioconjugated AuNPs is of great importance for the design of highly sensitive and reliable functionalized AuNP-based assays. PMID:28144559

  3. Soot-overcladding process for enlarging modified chemical vapor deposition preforms

    NASA Astrophysics Data System (ADS)

    Ihalainen, Heikki; Kurki, Jouko

    1995-09-01

    The equipment and the process for soot sleeving of optical fiber preforms made by the modified chemical vapor deposition (MCVD) method has been developed. The equipment consists of a soot-sleeving lathe that is used for deposition of soot glass particles onto the surface of an MCVD core preform and a separate furnace that is used for drying and sintering the deposited porous glass layer. An outline of the equipment is presented. This equipment has then been used to study the basic parameters of flame hydrolysis deposition as well as sintering of the porous layer. The raw material and the fuel gas flow as well as the substrate diameter proved to be the most important parameters affecting the process. The basic knowledge achieved is used to optimize the process for three different preform sizes. In the soot-sleeving process for 80-km optical fiber preforms, an average deposition rate of 5.2 g/min is achieved with a double burner. The overall quality of the drawn fiber proved to be good. The typical attenuations were 0.330 and 0.215 dB/km at 1310- and 1550-nm wavelengths, respectively. The geometry of the drawn fibers was found to be very good.

  4. Removal of methylene blue from aqueous solutions by chemically modified bamboo.

    PubMed

    Guo, Jian-Zhong; Li, Bing; Liu, Li; Lv, Kangle

    2014-09-01

    Chemically modified bamboo (CMB) was utilized for removing methylene blue (MB) from aqueous media in the present study. The adsorbent was characterized by Fourier transform infrared (FTIR) spectra and elemental analysis, which confirms that carboxyl groups and diethylenetriamine were successfully introduced into the surface of bamboo. The effects of initial MB concentration (100-900mgL(-1)), contact time (15-315min), the pH of the solution (3-10), temperature (298-318K), adsorbent dosage (0.4-2.6gL(-1)) and salt concentration on the adsorption efficiency of CMB towards MB were investigated. It was found that the adsorption of MB in CMB fits Langmuir mode well, and the maximum adsorption capacity of CMB achieved 606mgg(-1) at 298K, which is much higher than those obtained from previously investigated bioadsorbents. The adsorption kinetics can be described by pseudo-second-order kinetic model, and the adsorption of MB on CMB was an exothermic process. The results of the present study suggest that CMB is an effective biosorbent for removal of organic pollutants from aqueous solutions.

  5. Chemically modified graphene films for high-performance optical NO2 sensors.

    PubMed

    Xing, Fei; Zhang, Shan; Yang, Yong; Jiang, Wenshuai; Liu, Zhibo; Zhu, Siwei; Yuan, Xiaocong

    2016-08-07

    Various graphene-based gas sensors that operate based on the electrical properties of graphene have been developed for accurate detection of gas components. However, electronic graphene-based gas sensors are unsafe under explosive atmospheres and sensitive to electromagnetic interference. Here, a novel optical graphene-based gas sensor for NO2 detection is established based on surface chemical modification of high-temperature-reduced graphene oxide (h-rGO) films with sulfo groups. Sulfo group-modified h-rGO (S-h-rGO) films with a thickness of several nanometers exhibit excellent performance in NO2 detection at room temperature and atmospheric pressure based on the polarization absorption effect of graphene. Initial slope analysis of the S-h-rGO sensor indicates that it has a limit of detection of 0.28 ppm and a response time of 300 s for NO2 gas sensing. Furthermore, the S-h-rGO sensor also possesses the advantages of good linearity, reversibility, selectivity, non-contact operation, low cost and safety. This novel optical gas sensor has the potential to serve as a general platform for the selective detection of a variety of gases with high performance.

  6. Removal of lead from aqueous solution with native and chemically modified corncobs.

    PubMed

    Tan, Guangqun; Yuan, Hongyan; Liu, Yong; Xiao, Dan

    2010-02-15

    In this study, corncobs biomass was utilized as an adsorbent to remove Pb(II) from aqueous solution. The adsorption behavior of Pb(II) was studied under different conditions, including solution pH, contact time and metal concentration. Ground corncobs were modified with CH(3)OH and NaOH to investigate the effect of chemical modification on Pb(II) binding capacity. Results showed that Pb(II) binding on the biomass is pH-dependent and the kinetics can be well described by the Lagergren-second-order model. The maximum Pb(II) binding capacity q(max) calculated from Langmuir isotherm was 0.0783 mmol/g. After base hydrolysis of the biomass, Pb(II) binding capacity increased from 0.0783 to 0.2095 mmol/g (about 43.4 mg Pb/g). However, Pb(II) binding capacity on the esterified corncobs decreased greatly from 0.0783 to 0.0381 mmol/g. Fourier transform infrared spectroscopy (FTIR) analysis showed that hydroxyl and carboxylic (COO(-)) groups on the biomass play an important role in Pb(II) binding process. The X-ray photoelectron spectroscopy (XPS) data further indicated that lead is adsorbed as Pb(2+) and is attached to oxide groups on the biomass.

  7. Changes in the Chemical Composition and Decay Resistance of Thermally-Modified Hevea brasiliensis Wood

    PubMed Central

    2016-01-01

    In this study the effect of thermal treatment on the equilibrium moisture content, chemical composition and biological resistance to decay fungi of juvenile and mature Hevea brasiliensis wood (rubber wood) was evaluated. Samples were taken from a 53-year-old rubber wood plantation located in Tabapuã, Sao Paulo, Brazil. The samples were thermally-modified at 180°C, 200°C and 220°C. Results indicate that the thermal modification caused: (1) a significant increase in the extractive content and proportional increase in the lignin content at 220°C; (2) a significant decrease in the equilibrium moisture content, holocelluloses, arabinose, galactose and xylose content, but no change in glucose content; and (3) a significant increase in wood decay resistance against both Pycnoporus sanguineus (L.) Murrill and Gloeophyllum trabeum (Pers.) Murrill decay fungi. The greatest decay resistance was achieved from treatment at 220°C which resulted in a change in wood decay resistance class from moderately resistant to resistant. Finally, this study also demonstrated that the influence of thermal treatment in mature wood was lower than in juvenile wood. PMID:26986200

  8. Laminating of chemically modified silan based nanosols for advanced functionalization of cotton textiles.

    PubMed

    Mohamed, Amina L; El-Naggar, Mehrez E; Shaheen, Th I; Hassabo, Ahmed G

    2017-02-01

    As per to silver nanoparticles/silicon dioxide nanoparticles (SiO2@AgNPs) properties (e.g., conductivity, reactant, adsorption, detachment and antimicrobial), many researchers were focused on its preparation technique. A core/shell of silicon dioxide and silver nanoparticles (SiO2@AgNPs) has been prepared by facile route. The as synthesized core/shell nanoparticles were chemically modified with two different silan compounds, nominated, vinyltriethoxysilan (VTEOS) and (3-aminopropyl)trimethoxysilan (APTEOS). World class facilities such as XRD, FT-IR, TEM, Particle size, DLS, SEM techniques were utilized for the nanoparticles characterization. The nanoparticulate system comprises SiO2@AgNPs, SiO2@AgNPs/APTEOS were applied to cotton fabric using butantetracarboxylic acid (BTCA) as across-linking agent. While UV irradiation by photo initiator was used as crosslinking agent for SiO2@AgNPs/VTEOS on cotton fabrics. The Treated cotton fabrics were evaluated for their surface morphology and heat transfer ability as well as antibacterial activity. The obtained data prove that the core/shell was successfully prepared, with AgNPs in core. In addition, both silan compounds (APTEOS, VTEOS) were successfully reacted with the outer shell SiO2. The results declared also that the treated fabrics exhibit a good antibacterial activity as well as good thermal properties.

  9. Specificities of a chemically modified laccase from Trametes hirsuta on soluble and cellulose-bound substrates.

    PubMed

    Schroeder, M; Heumann, S; Silva, C J S M; Cavaco-Paulo, A; Guebitz, G M

    2006-05-01

    Laccases could prevent fabrics and garments from re-deposition of dyes during washing and finishing processes by degrading the solubilized dye. However, laccase action must be restricted to solubilized dye molecules thereby avoiding decolorization of fabrics. Chemical modification of enzymes can provide a powerful tool to change the adsorption behaviour of enzymes on water insoluble polymers. Polyethylene glycol (PEG) was covalently attached onto a laccase from Trametes hirsuta. Different molecular weights of the synthetic polymer were tested in terms of adsorption behaviour and retained laccase activity. Covalent attachment of PEG onto the laccase resulted in enhanced enzyme stability while with increasing molecular weight of attached PEG the substrate affinity for the laccase conjugate decreased. The activity of the modified laccases on fibre bound dye was drastically reduced decreasing the adsorption of the enzyme on various fabrics. Compared to the 5 kDa PEG laccase conjugate (K/S value 47.60) the K/S value decreased much more (47.96-46.35) after the treatment of dyed cotton fabrics with native laccase.

  10. Adhesion-dependent negative friction coefficient on chemically modified graphite at the nanoscale.

    PubMed

    Deng, Zhao; Smolyanitsky, Alex; Li, Qunyang; Feng, Xi-Qiao; Cannara, Rachel J

    2012-12-01

    From the early tribological studies of Leonardo da Vinci to Amontons' law, friction has been shown to increase with increasing normal load. This trend continues to hold at the nanoscale, where friction can vary nonlinearly with normal load. Here we present nanoscale friction force microscopy (FFM) experiments for a nanoscale probe tip sliding on a chemically modified graphite surface in an atomic force microscope (AFM). Our results demonstrate that, when adhesion between the AFM tip and surface is enhanced relative to the exfoliation energy of graphite, friction can increase as the load decreases under tip retraction. This leads to the emergence of an effectively negative coefficient of friction in the low-load regime. We show that the magnitude of this coefficient depends on the ratio of tip-sample adhesion to the exfoliation energy of graphite. Through both atomistic- and continuum-based simulations, we attribute this unusual phenomenon to a reversible partial delamination of the topmost atomic layers, which then mimic few- to single-layer graphene. Lifting of these layers with the AFM tip leads to greater deformability of the surface with decreasing applied load. This discovery suggests that the lamellar nature of graphite yields nanoscale tribological properties outside the predictive capacity of existing continuum mechanical models.

  11. Progress in chemical treatment of LEU targets by the modified Cintichem process

    SciTech Connect

    Wu, D.; Landsberger, S.; Vandegrift, G.F.

    1996-12-31

    Presented here are recent experimental results on tests of a modified Cintichem process for producing {sup 99}Mo from low enriched uranium (LEU). Studies were focused in three areas: (1) testing the effects on {sup 99}Mo recovery and purity of dissolving LEU foil in nitric acid alone, rather than in the sulfuric/nitric acid mixture currently used, (2) measuring decontamination factors for radionuclide impurities in each purification step, and (3) testing the effects on processing of adding barrier materials to the LEU metal-foil target. The experimental results show that switching from dissolving the target in the sulfuric/nitric mixture to using nitric acid alone should cause no significant difference in {sup 99}Mo product yield or purity. Further, the results show that overall decontamination factors for gamma emitters in the LEU-target processing are high enough to meet the purity requirements for the {sup 99}Mo product. The results also show that the selected barrier materials, Cu, Fe, and Ni, do not interfere with {sup 99}Mo recovery and can be removed during chemical processing of the LEU target.

  12. Optimizing the lanthanum adsorption process onto chemically modified biomaterials using factorial and response surface design.

    PubMed

    Gabor, Andreea; Davidescu, Corneliu Mircea; Negrea, Adina; Ciopec, Mihaela; Grozav, Ion; Negrea, Petru; Duteanu, Narcis

    2017-01-29

    The rare metals' potential to pollute air, water, soil, and especially groundwater has received lot of attention recently. One of the most common rare earth group elements, lanthanum, is used in many industrial branches, and due to its toxicity, it needs to be eliminated from all residual aqueous solutions. The goal of this study was to evaluate the control of the adsorption process for lanthanum removal from aqueous solutions, using cellulose, a known biomaterial with high adsorbent properties, cheap, and environment friendly. The cellulose was chemically modified by functionalization with sodium β-glycerophosphate. The experimental results obtained after factorial design indicate optimum adsorption parameters as pH 6, contact time 60 min, and temperature 298 K, when the equilibrium concentration of lanthanum was 250 mg L(-1), and the experimental adsorption capacity obtained was 31.58 mg g(-1). Further refinement of the optimization of the adsorption process by response surface design indicates that at pH 6 and the initial concentration of 256 mg L(-1), the adsorption capacity has maximum values between 30.87 and 36.73 mg g(-1).

  13. Changes in the Chemical Composition and Decay Resistance of Thermally-Modified Hevea brasiliensis Wood.

    PubMed

    Severo, Elias Taylor Durgante; Calonego, Fred Willians; Sansígolo, Cláudio Angeli; Bond, Brian

    2016-01-01

    In this study the effect of thermal treatment on the equilibrium moisture content, chemical composition and biological resistance to decay fungi of juvenile and mature Hevea brasiliensis wood (rubber wood) was evaluated. Samples were taken from a 53-year-old rubber wood plantation located in Tabapuã, Sao Paulo, Brazil. The samples were thermally-modified at 180°C, 200°C and 220°C. Results indicate that the thermal modification caused: (1) a significant increase in the extractive content and proportional increase in the lignin content at 220°C; (2) a significant decrease in the equilibrium moisture content, holocelluloses, arabinose, galactose and xylose content, but no change in glucose content; and (3) a significant increase in wood decay resistance against both Pycnoporus sanguineus (L.) Murrill and Gloeophyllum trabeum (Pers.) Murrill decay fungi. The greatest decay resistance was achieved from treatment at 220°C which resulted in a change in wood decay resistance class from moderately resistant to resistant. Finally, this study also demonstrated that the influence of thermal treatment in mature wood was lower than in juvenile wood.

  14. Adhesion-dependent negative friction coefficient on chemically modified graphite at the nanoscale

    NASA Astrophysics Data System (ADS)

    Deng, Zhao; Smolyanitsky, Alex; Li, Qunyang; Feng, Xi-Qiao; Cannara, Rachel J.

    2012-12-01

    From the early tribological studies of Leonardo da Vinci to Amontons’ law, friction has been shown to increase with increasing normal load. This trend continues to hold at the nanoscale, where friction can vary nonlinearly with normal load. Here we present nanoscale friction force microscopy (FFM) experiments for a nanoscale probe tip sliding on a chemically modified graphite surface in an atomic force microscope (AFM). Our results demonstrate that, when adhesion between the AFM tip and surface is enhanced relative to the exfoliation energy of graphite, friction can increase as the load decreases under tip retraction. This leads to the emergence of an effectively negative coefficient of friction in the low-load regime. We show that the magnitude of this coefficient depends on the ratio of tip-sample adhesion to the exfoliation energy of graphite. Through both atomistic- and continuum-based simulations, we attribute this unusual phenomenon to a reversible partial delamination of the topmost atomic layers, which then mimic few- to single-layer graphene. Lifting of these layers with the AFM tip leads to greater deformability of the surface with decreasing applied load. This discovery suggests that the lamellar nature of graphite yields nanoscale tribological properties outside the predictive capacity of existing continuum mechanical models.

  15. Inhibitory impacts of chemically modified tetracycline-3 and underlying mechanism in human cervical cancer cells.

    PubMed

    Zhao, Lin; Xu, Jiaying; Yang, Yang; Chong, Yu; Liu, Chang; Jiao, Yang; Fan, Saijun

    2013-09-01

    Chemically modified tetracyclines (CMTs) have been rationally designed from tetracyclines. The CMTs that show the antimicrobial properties are eliminated, whereas matrix metalloproteinase inhibitory properties are retained. Interestingly, CMT-3 (COL-3, by eliminating the dimethylamino, methyl, and hydroxyl functionalities on the basic tetracycline structure), one of the CMTs, has shown strong anticancer activity. In this study, we found that CMT-3 showed dose-dependent and time-dependent cytotoxicity in HeLa and Siha cells, two human cervical cancer cell lines. HeLa cells were more sensitive to CMT-3 compared with Siha cells. The antiproliferation potential of CMT-3 was associated with the mitochondrial apoptosis pathway, increasing reactive oxygen species level, and proapoptosis protein (e.g. caspase-3) expression, but decreasing antiapoptosis protein expression (e.g. Bcl-2). N-acetylcysteine (a reactive oxygen species inhibitor) and Z-LEHD-FMK significantly reduced or blocked the apoptosis event resulting from cytotoxic effect of CMT-3. CMT-3 also induced G0/G1 phase arrest with the reduction of cell cycle regulatory protein cyclin E and the translocation of NF-κB from the cytoplasm to the nucleus. Our findings provide the important foundation for further investigation of the underlying mechanism for the anticancer activity of CMT-3 and the potential application of CMT-3 as a new therapeutic candidate for clinical cervical cancer therapy.

  16. Chemically-modified graphenes for oxidation of DNA bases: analytical parameters.

    PubMed

    Goh, Madeline Shuhua; Bonanni, Alessandra; Ambrosi, Adriano; Sofer, Zdeněk; Pumera, Martin

    2011-11-21

    We studied the electroanalytical performances of chemically-modified graphenes (CMGs) containing different defect densities and amounts of oxygen-containing groups, namely graphite oxide (GPO), graphene oxide (GO), thermally reduced graphene oxide (TR-GO) and electrochemically reduced graphene oxide (ER-GO) by comparing the sensitivity, selectivity, linearity and repeatability towards the oxidation of DNA bases. We have observed that for differential pulse voltammetric (DPV) detection of adenine and cytosine, all CMGs showed enhanced sensitivity to oxidation, while for guanine and thymine, ER-GO and TR-GO exhibited much improved sensitivity over bare glassy carbon (GC) as well as over GPO and GO. There is also significant selectivity enhancement when using GPO for adenine and TR-GO for thymine. Our results have uncovered that the differences in surface functionalities, structure and defects of various CMGs largely influence their electrochemical behaviour in detecting the oxidation of DNA bases. The findings in this report will provide a useful guide for the future development of label-free electrochemical devices for DNA analysis.

  17. Photoelectrocatalytic reduction of CO2 into chemicals using Pt-modified reduced graphene oxide combined with Pt-modified TiO2 nanotubes.

    PubMed

    Cheng, Jun; Zhang, Meng; Wu, Gai; Wang, Xin; Zhou, Junhu; Cen, Kefa

    2014-06-17

    The photoelectrocatalytic (PEC) reduction of CO2 into high-value chemicals is beneficial in alleviating global warming and advancing a low-carbon economy. In this work, Pt-modified reduced graphene oxide (Pt-RGO) and Pt-modified TiO2 nanotubes (Pt-TNT) were combined as cathode and photoanode catalysts, respectively, to form a PEC reactor for converting CO2 into valuable chemicals. XRD, XPS, TEM, AFM, and SEM were employed to characterize the microstructures of the Pt-RGO and Pt-TNT catalysts. Reduction products, such as C2H5OH and CH3COOH, were obtained from CO2 under band gap illumination and biased voltage. A combined liquid product generation rate (CH3OH, C2H5OH, HCOOH, and CH3COOH) of approximately 600 nmol/(h·cm(2)) was observed. Carbon atom conversion rate reached 1,130 nmol/(h·cm(2)), which were much higher than those achieved using Pt-modified carbon nanotubes and platinum carbon as cathode catalysts.

  18. Detection of Aeromonas hydrophila DNA oligonucleotide sequence using a biosensor design based on Ceria nanoparticles decorated reduced graphene oxide and Fast Fourier transform square wave voltammetry.

    PubMed

    Jafari, Safiye; Faridbod, Farnoush; Norouzi, Parviz; Dezfuli, Amin Shiralizadeh; Ajloo, Davood; Mohammadipanah, Fatemeh; Ganjali, Mohammad Reza

    2015-10-01

    A new strategy was introduced for ssDNA immobilization on a modified glassy carbon electrode. The electrode surface was modified using polyaniline and chemically reduced graphene oxide decorated cerium oxide nanoparticles (CeO2NPs-RGO). A single-stranded DNA (ssDNA) probe was immobilized on the modified electrode surface. Fast Fourier transform square wave voltammetry (FFT-SWV) was applied as detection technique and [Ru(bpy)3](2+/3+) redox signal was used as electrochemical marker. The hybridization of ssDNA with its complementary target caused a dramatic decrease in [Ru(bpy)3](2+/3+) FFT-SW signal. The proposed electrochemical biosensor was able to detect Aeromonas hydrophila DNA oligonucleotide sequence encoding aerolysin protein. Under optimal conditions, the biosensor showed excellent selectivity toward complementary sequence in comparison with noncomplementary and two-base mismatch sequences. The dynamic linear range of this electrochemical DNA biosensor for detecting 20-mer oligonucleotide sequence of A. hydrophila was from 1 × 10(-15) to 1 × 10(-8) mol L(-1). The proposed biosensor was successfully applied for the detection of DNA extracted from A. hydrophila in fish pond water up to 0.01 μg mL(-1) with RSD of 5%. Besides, molecular docking was applied to consider the [Ru(bpy)3](2+/3+) interaction with ssDNA before and after hybridization.

  19. In vitro characterization of two novel biodegradable vectors for the delivery of radiolabeled antisense oligonucleotides.

    PubMed

    von Guggenberg, Elisabeth; Shahhosseini, Soraya; Koslowsky, Ingrid; Lavasanifar, Afsaneh; Murray, David; Mercer, John

    2010-12-01

    The development of antisense oligonucleotides suitable for tumor targeting applications is hindered by low stability and bioavailability of oligonucleotides in vivo and by the absence of efficient and safe vectors for oligonucleotide delivery. Stabilization in vivo has been achieved through chemical modification of oligonucleotides by various means, but effective approaches to enhance their intracellular delivery are lacking. This study reports on the characterization in vitro of a fully phosphorothioated 20-mer oligonucleotide, complementary to p21 mRNA, radiolabeled with fluorine-18 using a thiol reactive prosthetic group. The potential of two novel synthetic block copolymers containing grafted polyamines on their hydrophobic blocks for vector-assisted cell delivery was studied in vitro. Extensive cellular uptake studies were performed in human colon carcinoma cell lines with enhanced or deficient p21 expression to evaluate and compare the uptake mechanism of naked and vectorized radiolabeled formulations. Uptake studies with the two novel biodegradable vectors showed a moderate increase in cell uptake of the radiofluorinated antisense oligonucleotide. The two vectors show, however, promising advantages over conventional lipidic vectors regarding their biocompatibility and subcellular distribution.

  20. Complex DNA nanostructures from oligonucleotide ensembles.

    PubMed

    Mathur, Divita; Henderson, Eric R

    2013-04-19

    The first synthetic DNA nanostructures were created by self-assembly of a small number of oligonucleotides. Introduction of the DNA origami method provided a new paradigm for designing and creating two- and three-dimensional DNA nanostructures by folding a large single-stranded DNA and 'stapling' it together with a library of oligonucleotides. Despite its power and wide-ranging implementation, the DNA origami technique suffers from some limitations. Foremost among these is the limited number of useful single-stranded scaffolds of biological origin. This report describes a new approach to creating large DNA nanostructures exclusively from synthetic oligonucleotides. The essence of this approach is to replace the single-stranded scaffold in DNA origami with a library of oligonucleotides termed "scaples" (scaffold staples). Scaples eliminate the need for scaffolds of biological origin and create new opportunities for producing larger and more diverse DNA nanostructures as well as simultaneous assembly of distinct structures in a "single-pot" reaction.

  1. DNA-binding and oxidative properties of cationic phthalocyanines and their dimeric complexes with anionic phthalocyanines covalently linked to oligonucleotides.

    PubMed

    Kuznetsova, A A; Lukyanets, E A; Solovyeva, L I; Knorre, D G; Fedorova, O S

    2008-12-01

    Design of chemically modified oligonucleotides for regulation of gene expression has attracted considerable attention over the past decades. One actively pursued approach involves antisense or antigene oligonucleotide constructs carrying reactive groups, many of these based on transition metal complexes. The complexes of Fe(II) and Co(II) with phthalocyanines are extremely good catalysts of oxidation of organic compounds with molecular oxygen and hydrogen peroxide. The binding of positively charged Fe(II) and Co(II) phthalocyanines with single- and double-stranded DNA was investigated. It was shown that these phthalocyanines interact with nucleic acids through an outside binding mode. The site-directed modification of single-stranded DNA by O2 and H2O2 in the presence of dimeric complexes of negatively and positively charged Fe(II) and Co(II) phthalocyanines was investigated. These complexes were formed directly on single-stranded DNA through interaction between negatively charged phthalocyanine in conjugate and positively charged phthalocyanine in solution. The resulting oppositely charged phthalocyanine complexes showed significant increase of catalytic activity compared with monomeric forms of phthalocyanines Fe(II) and Co(II). These complexes catalyzed the DNA oxidation with high efficacy and led to direct DNA strand cleavage. It was determined that oxidation of DNA by molecular oxygen catalyzed by complex of Fe(II)-phthalocyanines proceeds with higher rate than in the case of Co(II)-phthalocyanines but the latter led to a greater extent of target DNA modification.

  2. Adsorptive separation of rhodium(III) using Fe(III)-templated oxine type of chemically modified chitosan

    SciTech Connect

    Alam, M.S.; Inoue, Katsutoshi; Yoshizuka, Kazuharu; Ishibashi, Hideaki

    1998-03-01

    The oxine type of chemically modified chitosan was prepared by the template crosslinking method using Fe(III) as a template ion. Batchwise adsorption of rhodium(III) on this chemically modified chitosan was examined from chloride media in the absence and presence of a large amount of tin(II). It was observed that the Fe(III)-templated oxine type of chemically modified chitosan shows better performance for rhodium adsorption than that of the original chitosan. When Sn(II) is absent from the solution, Rh(III) is hardly adsorbed on the modified chitosan and the order of selectivity of the adsorption of Rh(III), Pt(IV), and Cu(II) was found to be Pt(IV) > Cu(II) {approx} Rh(III). On the other hand, adsorption of rhodium is significantly increased in the presence of Sn(II) and the selectivity order of the adsorption was drastically changed to Rh(III) > Pt(IV) {much_gt} Cu(II), which ensures selective separation of Rh(III) from their mixture. Adsorption of Rh(III) increases with an increase in the concentration of Sn(II) in the aqueous solution, and maximum adsorption is achieved at a molar ratio, [Sn]/[Rh], of >6. The adsorption of Rh(III) decreases at a high concentration of hydrochloric acid. The maximum adsorption capacity was evaluated to be 0.92 mol/kg-dry adsorbent. Stripping tests of rhodium from the loaded chemically modified chitosan were carried out using different kinds of stripping agents containing some oxidizing agent. The maximum stripping of rhodium under these experimental conditions was found to be 72.5% by a single contact with 0.5 M HCl + 8 M HNO{sub 3}.

  3. Antisense oligonucleotides as therapeutics for malignant diseases.

    PubMed

    Ho, P T; Parkinson, D R

    1997-04-01

    The continued progress in our understanding of the biology of neoplasia and in the identification, cloning, and sequencing of genes critical to tumor cell function permits the exploitation of this information to develop specific agents that may directly modulate the function of these genes or their protein products. Antisense oligonucleotides are being investigated as a potential therapeutic modality that takes direct advantage of molecular sequencing. The antisense approach uses short oligonucleotides designed to hybridize to a target mRNA transcript through Watson-Crick base pairing. The formation of this oligonucleotide: RNA heteroduplex results in mRNA inactivation and consequent inhibition of synthesis of the protein product. A fundamental attraction of the antisense approach is that this method potentially may be applied to any gene product, in theory, for the treatment of malignant and non-malignant diseases. However, this simple and attractive model has proven to be much more complex in practice. A number of important challenges in the preclinical development of antisense oligonucleotides have been identified, including stability, sequence length, cellular uptake, target sequence selection, appropriate negative controls, oligonucleotide: protein interactions, and cost of manufacture. Although the biological activity of an oligonucleotide against its molecular target is theoretically sequence-dependent, the animal pharmacokinetics and toxicology of phosphorothioate analogues directed against vastly disparate gene products appear relatively non-sequence-specific. In oncology, a number of clinical trials have been initiated with antisense oligonucleotides directed against molecular targets including: p53; bcl-2; raf kinase; protein kinase C-alpha; c-myb. The experience gained from these early clinical trials will be applicable to the next generation of antisense agents in development. These may include molecules with novel backbones or other structural

  4. Chemically and compositionally modified solid solution disordered multiphase nickel hydroxide positive electrode for alkaline rechargeable electrochemical cells

    DOEpatents

    Ovshinsky, Stanford R.; Corrigan, Dennis; Venkatesan, Srini; Young, Rosa; Fierro, Christian; Fetcenko, Michael A.

    1994-01-01

    A high capacity, long cycle life positive electrode for use in an alkaline rechargeable electrochemical cell comprising: a solid solution nickel hydroxide material having a multiphase structure that comprises at least one polycrystalline .gamma.-phase including a polycrystalline .gamma.-phase unit cell comprising spacedly disposed plates with at least one chemical modifier incorporated around the plates, the plates having a range of stable intersheet distances corresponding to a 2.sup.+ oxidation state and a 3.5.sup.+, or greater, oxidation state; and at least one compositional modifier incorporated into the solid solution nickel hydroxide material to promote the multiphase structure.

  5. In vivo site-directed mutagenesis using oligonucleotides.

    PubMed

    Storici, F; Lewis, L K; Resnick, M A

    2001-08-01

    Functional characterization of the genes of higher eukaryotes has been aided by their expression in model organisms and by analyzing site-specific changes in homologous genes in model systems such as the yeast Saccharomyces cerevisiae. Modifying sequences in yeast or other organisms such that no heterologous material is retained requires in vitro mutagenesis together with subcloning. PCR-based procedures that do not involve cloning are inefficient or require multistep reactions that increase the risk of additional mutations. An alternative approach, demonstrated in yeast, relies on transformation with an oligonucleotide, but the method is restricted to the generation of mutants with a selectable phenotype. Oligonucleotides, when combined with gap repair, have also been used to modify plasmids in yeast; however, this approach is limited by restriction-site availability. We have developed a mutagenesis approach in yeast based on transformation by unpurified oligonucleotides that allows the rapid creation of site-specific DNA mutations in vivo. A two-step, cloning-free process, referred to as delitto perfetto, generates products having only the desired mutation, such as a single or multiple base change, an insertion, a small or a large deletion, or even random mutations. The system provides for multiple rounds of mutation in a window up to 200 base pairs. The process is RAD52 dependent, is not constrained by the distribution of naturally occurring restriction sites, and requires minimal DNA sequencing. Because yeast is commonly used for random and selective cloning of genomic DNA from higher eukaryotes such as yeast artificial chromosomes, the delitto perfetto strategy also provides an efficient way to create precise changes in mammalian or other DNA sequences.

  6. Quantum chemical characterization of zwitterionic structures: Supramolecular complexes for modifying the wettability of oil-water-limestone system.

    PubMed

    Lopez-Chavez, Ernesto; Garcia-Quiroz, Alberto; Gonzalez-Garcia, Gerardo; Orozco-Duran, Gabriela E; Zamudio-Rivera, Luis S; Martinez-Magadan, José M; Buenrostro-Gonzalez, Eduardo; Hernandez-Altamirano, Raul

    2014-06-01

    In this work, we present a quantum chemical study pertaining to some supramolecular complexes acting as wettability modifiers of oil-water-limestone system. The complexes studied are derived from zwitterionic liquids of the types N'-alkyl-bis, N-alquenil, N-cycloalkyl, N-amyl-bis-beta amino acid or salts acting as sparkling agents. We studied two molecules of zwitterionic liquids (ZL10 and ZL13), HOMO and LUMO levels, and the energy gap between them, were calculated, as well as the electron affinity (EA) and ionization potential (IP), chemical potential, chemical hardness, chemical electrophilicity index and selectivity descriptors such Fukui indices. In this work, electrochemical comparison was realized with cocamidopropyl betaine (CPB), which is a structure zwitterionic liquid type, nowadays widely applied in enhanced recovery processes.

  7. Nanogels for Oligonucleotide Delivery to the Brain

    PubMed Central

    Vinogradov, Serguei V.; Batrakova, Elena V.; Kabanov, Alexander V.

    2009-01-01

    Systemic delivery of oligonucleotides (ODN) to the central nervous system is needed for development of therapeutic and diagnostic modalities for treatment of neurodegenerative disorders. Macromolecules injected in blood are poorly transported across the blood–brain barrier (BBB) and rapidly cleared from circulation. In this work we propose a novel system for ODN delivery to the brain based on nanoscale network of cross-linked poly(ethylene glycol) and polyethylenimine (“nanogel”). The methods of synthesis of nanogel and its modification with specific targeting molecules are described. Nanogels can bind and encapsulate spontaneously negatively charged ODN, resulting in formation of stable aqueous dispersion of polyelectrolyte complex with particle sizes less than 100 nm. Using polarized monolayers of bovine brain microvessel endothelial cells as an in vitro model this study demonstrates that ODN incorporated in nanogel formulations can be effectively transported across the BBB. The transport efficacy is further increased when the surface of the nanogel is modified with transferrin or insulin. Importantly the ODN is transported across the brain microvessel cells through the transcellular pathway; after transport, ODN remains mostly incorporated in the nanogel and ODN displays little degradation compared to the free ODN. Using mouse model for biodistribution studies in vivo, this work demonstrated that as a result of incorporation into nanogel 1 h after intravenous injection the accumulation of a phosphorothioate ODN in the brain increases by over 15 fold while in liver and spleen decreases by 2-fold compared to the free ODN. Overall, this study suggests that nanogel is a promising system for delivery of ODN to the brain. PMID:14733583

  8. Investigation of chemical modifiers for phosphorus in a graphite furnace using high-resolution continuum source atomic absorption spectrometry

    NASA Astrophysics Data System (ADS)

    Lepri, Fábio G.; Dessuy, Morgana B.; Vale, Maria Goreti R.; Borges, Daniel L. G.; Welz, Bernhard; Heitmann, Uwe

    2006-08-01

    Phosphorus is not one of the elements that are typically determined by atomic absorption spectrometry, but this technique nevertheless offers several advantages that make it attractive, such as the relatively great freedom from interferences. As the main resonance lines for phosphorus are in the vacuum-ultraviolet, inaccessible by conventional atomic absorption spectrometry equipment, Ĺvov and Khartsyzov proposed to use the non-resonance doublet at 213.5 / 213.6 nm. Later it turned out that with conventional equipment it is necessary to use a chemical modifier in order to get reasonable sensitivity, and lanthanum was the first one suggested for that purpose. In the following years more than 30 modifiers have been proposed for the determination of this element, and there is no consensus about the best one. In this work high-resolution continuum source atomic absorption spectrometry has been used to investigate the determination of phosphorus without a modifier and with the addition of selected modifiers of very different nature, including the originally recommended lanthanum modifier, several palladium-based modifiers and sodium fluoride. As high-resolution continuum source atomic absorption spectrometry is revealing the spectral environment of the analytical line at high resolution, it became obvious that without the addition of a modifier essentially no atomic phosphorus is formed, even at 2700 °C. The absorption measured with line source atomic absorption spectrometry in this case is due to the PO molecule, the spectrum of which is overlapping with the atomic line. Palladium, with or without the addition of calcium or ascorbic acid, was found to be the only modifier to produce almost exclusively atomic phosphorus. Lanthanum and particularly sodium fluoride produced a mixture of P and PO, depending on the atomization temperature. This fact can explain at least some of the discrepancies found in the literature and some of the phenomena observed in the

  9. Direct determination of bismuth, indium and lead in sea water by Zeeman ETAAS using molybdenum containing chemical modifiers.

    PubMed

    Acar, O; Türker, A R; Kılıç, Z

    1999-06-01

    Direct determination of Bi, In and Pb in sea water samples has been carried out by ETAAS with Zeeman background correction using molybdenum containing chemical modifiers and tartaric acid as a reducing agent. Maximum pyrolysis temperatures and the effect of mass ratios of the mixed modifier components on analytes have been investigated. Mo+Pd+TA or Mo+Pt+TA mixture was found to be powerful for the determination of 50 mug l(-1) of Bi, In and Pb spiked into synthetic and real sea waters. The accuracy and precision of the determination were thereby enhanced. The recoveries of analytes spiked were 94-103% with Mo+Pd+TA or Mo+Pt+TA and they are only 49-61% without modifier.

  10. GenoMass software: a tool based on electrospray ionization tandem mass spectrometry for characterization and sequencing of oligonucleotide adducts

    PubMed Central

    Sharma, Vaneet K; Glick, James; Liao, Qing; Shen, Chang; Vouros, Paul

    2012-01-01

    The analysis of DNA adducts is of importance in understanding DNA damage, and in the last few years mass spectrometry (MS) has emerged as the most comprehensive and versatile tool for routine characterization of modified oligonucleotides. The structural analysis of modified oligonucleotides, although routinely analyzed using mass spectrometry, is followed by a large amount of data, and a significant challenge is to locate the exact position of the adduct by computational spectral interpretation, which still is a bottleneck. In this report, we present an additional feature of the in-house developed GenoMass software, which determines the exact location of an adduct in modified oligonucleotides by connecting tandem mass spectrometry (MS/MS) to a combinatorial isomer library generated in silico for nucleic acids. The performance of this MS/MS approach using GenoMass software was evaluated by MS/MS data interpretation for an unadducted and its corresponding N-acetylaminofluorene (AAF) adducted 17-mer (5′OH-CCT ACC CCT TCC TTG TA-3′OH) oligonucleotide. Further computational screening of this AAF adducted 17-mer oligonucleotide (5′OH-CCT ACC CCT TCC TTG TA-3′OH) from a complex oligonucleotide mixture was performed using GenoMass. Finally, GenoMass was also used to identify the positional isomers of the AAF adducted 15-mer oligonucleotide (5′OH-ATGAACCGGAGGCCC-3′OH). GenoMass is a simple, fast, data interpretation software that uses an in silico constructed library to relate the MS/MS sequencing approach to identify the exact location of adduct on oligonucleotides. PMID:22689626

  11. Chemically modified, non-anticoagulant heparin derivatives are potent galectin-3 binding inhibitors and inhibit circulating galectin-3-promoted metastasis.

    PubMed

    Duckworth, Carrie A; Guimond, Scott E; Sindrewicz, Paulina; Hughes, Ashley J; French, Neil S; Lian, Lu-Yun; Yates, Edwin A; Pritchard, D Mark; Rhodes, Jonathan M; Turnbull, Jeremy E; Yu, Lu-Gang

    2015-09-15

    Concentrations of circulating galectin-3, a metastasis promoter, are greatly increased in cancer patients. Here we show that 2- or 6-de-O-sulfated, N-acetylated heparin derivatives are galectin-3 binding inhibitors. These chemically modified heparin derivatives inhibited galectin-3-ligand binding and abolished galectin-3-mediated cancer cell-endothelial adhesion and angiogenesis. Unlike standard heparin, these modified heparin derivatives and their ultra-low molecular weight sub-fractions had neither anticoagulant activity nor effects on E-, L- or P-selectin binding to their ligands nor detectable cytotoxicity. Intravenous injection of such heparin derivatives (with cancer cells pre-treated with galectin-3 followed by 3 subcutaneous injections of the derivatives) abolished the circulating galectin-3-mediated increase in lung metastasis of human melanoma and colon cancer cells in nude mice. Structural analysis using nuclear magnetic resonance and synchrotron radiation circular dichroism spectroscopies showed that the modified heparin derivatives bind to the galectin-3 carbohydrate-recognition domain. Thus, these chemically modified, non-anticoagulant, low-sulfated heparin derivatives are potent galectin-3 binding inhibitors with substantial potential as anti-metastasis/cancer drugs.

  12. Biosorption of Cr(VI) from aqueous solution by chemically modified potato starch: equilibrium and kinetic studies.

    PubMed

    Pillai, Saumya S; Mullassery, Manohar D; Fernandez, Noeline B; Girija, N; Geetha, P; Koshy, Mathew

    2013-06-01

    The biosorption capacity of chemically modified potato starch (CPS) for Cr(VI) from aqueous solution was investigated. The materials derived from carbohydrates are biodegradable and are generally regarded as safe and environmentally acceptable. The hydroxyl, carboxyl and carbonyl groups are responsible for the biosorption process. In the present study, the influence of various important parameters such as pH, time, biosorbent dose and initial Cr(VI) concentration on the biosorption capacity were investigated. The isotherms such as Langmuir, Freundlich and Tempkin were studied. The Freundlich and the Redlich-Peterson isotherms had been well fitted the biosorption of Cr(VI) with chemically modified potato starch. The kinetics of Cr(VI) removal using chemically modified potato starch was well explained by second-order kinetic model. The thermodynamic parameters were also evaluated from the biosorption measurements. Among the various desorbing agents tested, 98.2 percent chromium recovery was achieved with 0.1molL(-1) NaOH.

  13. Study of the adsorption and electroadsorption process of Cu (II) ions within thermally and chemically modified activated carbon.

    PubMed

    Macías-García, A; Gómez Corzo, M; Alfaro Domínguez, M; Alexandre Franco, M; Martínez Naharro, J

    2017-04-15

    The aim of this work is to modify the porous texture and superficial groups of a commercial activated carbon through chemical and thermal treatment and subsequently study the kinetics of adsorption and electroadsorption of Cu (II) ion for these carbons. Samples of three activated carbons were used. These were a commercial activated carbon, commercial activated carbon modified thermically (C-N2-900) and finally commercial activated carbon modified chemically C-SO2-H2S-200. The activated carbons were characterized chemically and texturally and the electrical conductivity of them determined. Different kinetic models were applied. The kinetics of the adsorption and electroadsorption process of the Cu (II) ion fits a pseudo second order model and the most likely mechanism takes place in two stages. A first step through transfer of the metal mass through the boundary layer of the adsorbent and distribution of the Cu (II) on the external surface of the activated carbon and a second step that represents intraparticle diffusion and joining of the Cu (II) with the active centres of the activated carbon. Finally, the kinetics of the adsorption process are faster than the kinetics of the electroadsorption but the percentage of the Cu (II) ion retained is much higher in the electroadsorption process.

  14. Cell and tissue distribution of synthetic oligonucleotides in healthy and tumor-bearing nude mice. An autoradiographic, immunohistological, and direct fluorescence microscopy study.

    PubMed Central

    Plenat, F.; Klein-Monhoven, N.; Marie, B.; Vignaud, J. M.; Duprez, A.

    1995-01-01

    Antisense oligonucleotides have the ability to inhibit individual gene expression in the potential treatment of cancer and viral diseases. However, the way parenterally administered oligonucleotides distribute themselves into healthy tissues or tumors is poorly understood. In this study, the cell and tissue distribution of two modified or unmodified phosphodiester pentadeca-beta-oligonucleotides intravenously administered to healthy or tumor-bearing nude mice was assessed by autoradiography as well as by direct fluorescence and immunoenzymatic histological methods. Resistance of oligonucleotides to degradation by nuclease activity was previously studied in vitro. Using these methods we were able to show the following: 1) within minutes, oligonucleotides permeate all cells and tissues with the exceptions of erythrocytes and intervertebral discs; 2) cell and tissue distribution does not depend on the sequence of the given oligonucleotide; 3) concentration of oligonucleotides is higher within the connective tissue cells than in the interstitial matrix; 4) after uptake, oligomers partition throughout all of the cellular compartments, including at the highest intracellular concentrations in the nuclei; 5) oligonucleotides penetrate easily the tumor cell compartments, oligonucleotide diffusion being unimpeded by the extracellular matrix. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 Figure 12 PMID:7604874

  15. Repair of Thalassemic Human β -globin mRNA in Mammalian Cells by Antisense Oligonucleotides

    NASA Astrophysics Data System (ADS)

    Sierakowska, Halina; Sambade, Maria J.; Agrawal, Sudhir; Kole, Ryszard

    1996-11-01

    In one form of β -thalassemia, a genetic blood disorder, a mutation in intron 2 of the β -globin gene (IVS2-654) causes aberrant splicing of β -globin pre-mRNA and, consequently, β -globin deficiency. Treatment of mammalian cells stably expressing the IVS2-654 human β -globin gene with antisense oligonucleotides targeted at the aberrant splice sites restored correct splicing in a dose-dependent fashion, generating correct human β -globin mRNA and polypeptide. Both products persisted for up to 72 hr posttreatment. The oligonucleotides modified splicing by a true antisense mechanism without overt unspecific effects on cell growth and splicing of other pre-mRNAs. This novel approach in which antisense oligonucleotides are used to restore rather than to down-regulate the activity of the target gene is applicable to other splicing mutants and is of potential clinical interest.

  16. Binding of Co(II) and Cu(II) cations to chemically modified wool fibres: an IR investigation

    NASA Astrophysics Data System (ADS)

    Taddei, Paola; Monti, Patrizia; Freddi, Giuliano; Arai, Takayuki; Tsukada, Masuhiro

    2003-05-01

    Wool fibres were modified by treatment with tannic acid (TA) solution or by acylation with ethylenediaminetetraacetic (EDTA) dianhydride. The unmodified and modified fibres were subsequently treated with Cu 2+ and Co 2+ solutions, at alkaline pH, and analysed by Attenuated Total Reflectance, ATR/IR spectroscopy to evaluate the changes induced in the structure of the fibre by metal binding. The spectral changes were correlated to metal adsorption results obtained by Inductive Coupled Plasma-Atomic Emission Spectrometry (ICP-AES). The IR results were discussed in relation to our previous findings on the metal binding mode of Bombyx mori and Tussah silk fibres; the changes observed in the spectra were explained by considering the different affinity of the fibres for the modifying reagent and the amount of the metal absorbed. More relevant spectral changes were observed upon Cu 2+ complexation rather than Co 2+ complexation, according to the metal absorption results. The most relevant changes were observed for the EDTA-modified wool sample treated with Cu 2+, according to the higher affinity of wool for EDTA. The IR spectra were quantitatively evaluated by the intensity ratio between the Amide I and Amide II bands (I AmideI/I AmideII) and its trend as a function of metal absorption was reported. The present investigation demonstrated that the interaction between fibre and metal and the subsequent fibre modification depend on the chemical nature of the fibre, the metal cation and the modifying reagent.

  17. Chemical modifiers for direct determination of cobalt in coal combustion residues by ultrasonic slurry-sampling-ETAAS.

    PubMed

    Felipe-Sotelo, M; Carlosena, A; Fernández, E; López-Mahía, P; Muniategui, S; Prada, D

    2001-12-01

    Five modifiers were tested for the direct determination of cobalt in coal fly ash and slag by ultrasonic slurry-sampling electrothermal atomic absorption spectrometry (USS-ETAAS). The furnace temperature programs and the appropriate amount for each modifier were optimized to get the highest signal and the best separation between the atomic and background signals. Nitric acid (0.5% v/v) was the most adequate chemical modifier for cobalt determination, selecting 1,450 degrees C and 2,100 degrees C as pyrolysis and atomization temperatures, respectively. This modifier also acts as liquid medium for the slurry simplifying the procedure. The remaining modifiers enhanced the background signal, totally overlapped with cobalt peak. The method optimized gave a limit of detection of 0.36 microg g(-1), a characteristic mass of 13 +/- 1 pg and an overall-method precision which is highly satisfactory (<7%, RSD). The method was validated by analyzing two certified coal fly ash materials, and satisfactory recoveries were obtained (83-90%) and no statistical differences were observed between the experimental and the certified cobalt concentrations. Additionally, certified sediment, soil and urban particulate matter were assayed; again good results were obtained. The developed methodology was used to determine cobalt in several coal combustion residues from five Spanish power plants.

  18. An oligonucleotide hybridization approach to DNA sequencing.

    PubMed

    Khrapko, K R; Lysov YuP; Khorlyn, A A; Shick, V V; Florentiev, V L; Mirzabekov, A D

    1989-10-09

    We have proposed a DNA sequencing method based on hybridization of a DNA fragment to be sequenced with the complete set of fixed-length oligonucleotides (e.g., 4(8) = 65,536 possible 8-mers) immobilized individually as dots of a 2-D matrix [(1989) Dokl. Akad. Nauk SSSR 303, 1508-1511]. It was shown that the list of hybridizing octanucleotides is sufficient for the computer-assisted reconstruction of the structures for 80% of random-sequence fragments up to 200 bases long, based on the analysis of the octanucleotide overlapping. Here a refinement of the method and some experimental data are presented. We have performed hybridizations with oligonucleotides immobilized on a glass plate, and obtained their dissociation curves down to heptanucleotides. Other approaches, e.g., an additional hybridization of short oligonucleotides which continuously extend duplexes formed between the fragment and immobilized oligonucleotides, should considerably increase either the probability of unambiguous reconstruction, or the length of reconstructed sequences, or decrease the size of immobilized oligonucleotides.

  19. Surface modification of plasmonic nanostructured materials with thiolated oligonucleotides in 10 seconds using selective microwave heating

    PubMed Central

    Abel, Biebele; Aslan, Kadir

    2013-01-01

    This study demonstrates the proof-of-principle of rapid surface modification of plasmonic nanostructured materials with oligonucleotides using low power microwave heating. Due to their interesting optical and electronic properties, silver nanoparticle films (SNFs, 2 nm thick) deposited onto glass slides were used as the model plasmonic nanostructured materials. Rapid surface modification of SNFs with oligonucleotides was carried out using two strategies (1) Strategy 1: for ss-oligonucleotides, surface hybridization and (2) Strategy 2: for ds-oligonucleotides, solution hybridization), where the samples were exposed to 10, 15, 30 and 60 seconds microwave heating. To assess the efficacy of our new rapid surface modification technique, identical experiments carried out without the microwave heating (i.e., conventional method), which requires 24 hours for the completion of the identical steps. It was found that SNFs can be modified with ss- and ds-oligonucleotides in 10 seconds, which typically requires several hours of incubation time for the chemisorption of thiol groups on to the planar metal surface using conventional techniques. PMID:23645933

  20. Combined in vitro transcription and reverse transcription to amplify and label complex synthetic oligonucleotide probe libraries.

    PubMed

    Murgha, Yusuf; Beliveau, Brian; Semrau, Kassandra; Schwartz, Donald; Wu, Chao-Ting; Gulari, Erdogan; Rouillard, Jean-Marie

    2015-06-01

    Oligonucleotide microarrays allow the production of complex custom oligonucleotide libraries for nucleic acid detection-based applications such as fluorescence in situ hybridization (FISH). We have developed a PCR-free method to make single-stranded DNA (ssDNA) fluorescent probes through an intermediate RNA library. A double-stranded oligonucleotide library is amplified by transcription to create an RNA library. Next, dye- or hapten-conjugate primers are used to reverse transcribe the RNA to produce a dye-labeled cDNA library. Finally the RNA is hydrolyzed under alkaline conditions to obtain the single-stranded fluorescent probes library. Starting from unique oligonucleotide library constructs, we present two methods to produce single-stranded probe libraries. The two methods differ in the type of reverse transcription (RT) primer, the incorporation of fluorescent dye, and the purification of fluorescent probes. The first method employs dye-labeled reverse transcription primers to produce multiple differentially single-labeled probe subsets from one microarray library. The fluorescent probes are purified from excess primers by oligonucleotide-bead capture. The second method uses an RNA:DNA chimeric primer and amino-modified nucleotides to produce amino-allyl probes. The excess primers and RNA are hydrolyzed under alkaline conditions, followed by probe purification and labeling with amino-reactive dyes. The fluorescent probes created by the combination of transcription and reverse transcription can be used for FISH and to detect any RNA and DNA targets via hybridization.

  1. Simple Method To Prepare Oligonucleotide-Conjugated Antibodies and Its Application in Multiplex Protein Detection in Single Cells.

    PubMed

    Gong, Haibiao; Holcomb, Ilona; Ooi, Aik; Wang, Xiaohui; Majonis, Daniel; Unger, Marc A; Ramakrishnan, Ramesh

    2016-01-20

    The diversity of nucleic acid sequences enables genomics studies in a highly multiplexed format. Since multiplex protein detection is still a challenge, it would be useful to use genomics tools for this purpose. This can be accomplished by conjugating specific oligonucleotides to antibodies. Upon binding of the oligonucleotide-conjugated antibodies to their targets, the protein levels can be converted to oligonucleotide levels. In this report we describe a simple method for preparing oligonucleotide-conjugated antibodies and discuss this method's application in oligonucleotide extension reaction (OER) for multiplex protein detection. Conjugation is based on strain-promoted alkyne-azide cycloaddition (the Cu-free click reaction), in which the antibody is activated with a dibenzocyclooctyne (DBCO) moiety and subsequently linked covalently with an azide-modified oligonucleotide. In the functional test, the reaction conditions and purification processes were optimized to achieve maximum yield and best performance. The OER assay employs a pair of antibody binders (two antibodies, each conjugated with its own oligonucleotide) developed for each protein target. The two oligonucleotides contain unique six-base complementary regions at their 3' prime ends to allow annealing and extension by DNA synthesis enzymes to form a DNA template. Following preamplification, the DNA template is detected by qPCR. Distinct oligonucleotide sequences are assigned to different antibody binders to enable multiplex protein detection. When tested using recombinant proteins, some antibody binders, such as those specific to CSTB, MET, EpCAM, and CASP3, had dynamic ranges of 5-6 logs. The antibody binders were also used in a multiplexed format in OER assays, and the binders successfully detected their protein targets in cell lysates, and in single cells in combination with the C1 system. This click reaction-based antibody conjugation procedure is cost-effective, needs minimal hands-on time, and

  2. Oligonucleotide Aptamers: New Tools for Targeted Cancer Therapy

    PubMed Central

    Sun, Hongguang; Zhu, Xun; Lu, Patrick Y; Rosato, Roberto R; Tan, Wen; Zu, Youli

    2014-01-01

    Aptamers are a class of small nucleic acid ligands that are composed of RNA or single-stranded DNA oligonucleotides and have high specificity and affinity for their targets. Similar to antibodies, aptamers interact with their targets by recognizing a specific three-dimensional structure and are thus termed “chemical antibodies.” In contrast to protein antibodies, aptamers offer unique chemical and biological characteristics based on their oligonucleotide properties. Hence, they are more suitable for the development of novel clinical applications. Aptamer technology has been widely investigated in various biomedical fields for biomarker discovery, in vitro diagnosis, in vivo imaging, and targeted therapy. This review will discuss the potential applications of aptamer technology as a new tool for targeted cancer therapy with emphasis on the development of aptamers that are able to specifically target cell surface biomarkers. Additionally, we will describe several approaches for the use of aptamers in targeted therapeutics, including aptamer-drug conjugation, aptamer-nanoparticle conjugation, aptamer-mediated targeted gene therapy, aptamer-mediated immunotherapy, and aptamer-mediated biotherapy. PMID:25093706

  3. Cr(VI) adsorption from electroplating plating wastewater by chemically modified coir pith.

    PubMed

    Suksabye, Parinda; Thiravetyan, Paitip

    2012-07-15

    Coir pith samples were chemically modified by grafting with acrylic acid for the removal of Cr(VI) from electroplating wastewater. The presence of acrylic acid on the coir pith surface was verified by a scanning electron microscope with an electron dispersive x-ray spectrometer (SEM/EDX), Fourier transform infrared spectroscopy (FTIR) and thermogravimetry (TG). The carbonyl groups (C==O) from the carboxylic acids (COOH) increased on the coir pith surface after grafting with acrylic acid. In addition, the thermal stability of the acrylic acid-grafted coir pith also improved. The optimum conditions for grafting the acrylic acid on the coir pith consisted of 2 M acrylic acid and 0.00125 M ceric ammonium nitrate (CAN, as an initiator). The maximum Cr(VI) removal (99.99 ± 0.07%) was obtained with the following conditions: a 1.3% (w/v) dosage of acrylic acid-grafted coir pith, a system pH of 2, a contact time of 22 h, a temperature of 30 °C, a particle size of <150 μm and an initial Cr(VI) of 1,171 mg l(-1). At system pH of 2, Cr(VI) in the HCrO(4)(-) form can be adsorbed with acrylic acid-grafted coir pith via an electrostatic attraction. The adsorption isotherm of 2 M acrylic acid-grafted coir pith exhibited a good fit with the Langmuir isotherm. The maximum Cr(VI) adsorption capacity of the 2 M acrylic acid-grafted coir pith was 196.00 mg Cr(VI) g(-1) adsorbent, whereas for coir pith without grafting, the maximum Cr(VI) removal was 165.00 mg Cr(VI) g(-1) adsorbent. The adsorption capacity of the acrylic acid-grafted coir pith for Cr(VI) was higher compared to the original coir pith. This result was due to the enhancement of the carbonyl groups on the coir pith surface that may have involved the mechanism of chromium adsorption. The X-ray absorption near edged structure (XANES) and desorption studies suggested that most of the Cr(III) that presented on the acrylic acid-grafted coir pith was due to the Cr(VI) being reduced to Cr(III) on the adsorbent surface. FTIR

  4. Oligonucleotide-based therapy for neurodegenerative diseases.

    PubMed

    Magen, Iddo; Hornstein, Eran

    2014-10-10

    Molecular genetics insight into the pathogenesis of several neurodegenerative diseases, such as Alzheimer׳s disease, Parkinson׳s disease, Huntington׳s disease and amyotrophic lateral sclerosis, encourages direct interference with the activity of neurotoxic genes or the molecular activation of neuroprotective pathways. Oligonucleotide-based therapies are recently emerging as an efficient strategy for drug development and these can be employed as new treatments of neurodegenerative states. Here we review advances in this field in recent years which suggest an encouraging assessment that oligonucleotide technologies for targeting of RNAs will enable the development of new therapies and will contribute to preservation of brain integrity.

  5. Magnetorheological finishing with chemically modified fluids for studying material removal of single-crystal ZnS

    NASA Astrophysics Data System (ADS)

    Salzman, S.; Romanofsky, H. J.; Clara, Y. I.; Giannechini, L. J.; West, Garrett J.; Lambropoulos, J. C.; Jacobs, S. D.

    2013-09-01

    Magnetorheological finishing (MRF) of polycrystalline, chemical-vapor-deposited (CVD) zinc sulfide (ZnS) and zinc selenide (ZnSe) can leave millimeter-size artifacts on the part surface. These pebble-like features come from the anisotropic mechanical and chemical properties of the ceramic material and from the CVD growth process itself. The resulting surface texture limits the use of MRF for polishing aspheric and other complex shapes using these important infrared (IR) ceramics. An investigation of the individual contributions of chemistry and mechanics to polishing of other polycrystalline ceramics has been employed in the past to overcome similar material anisotropy problems. The approach taken was to study the removal process for the different single-crystal orientations that comprise the ceramic, making adjustments to mechanics (polishing abrasive type and concentration) and polishing slurry chemistry (primarily pH) to equalize the removal rate for all crystal orientations. Polishing with the modified slurry was shown to prevent the development of surface texture. Here we present mechanical (microhardness testing) and chemical (acid etching) studies performed on the four single-crystal orientations of ZnS: 100, 110, 111, and 311. We found that the (111) plane is 35% to 55% harder and 30% to 40% more resistant to chemical etching than the other three planes. This relatively high degree of variation in these properties can help to explain the surface texture developed from MRF of the polycrystalline material. Theoretical calculations of microhardness, planar, and bond densities are presented and compared with the experimental data. Here surface characterization of these single-crystal orientations of ZnS for material removal and roughness with chemically modified MR fluids at various pH levels between pH 4 and pH 6 are presented for the first time.

  6. DOTAP/UDCA vesicles: novel approach in oligonucleotide delivery.

    PubMed

    Ruozi, Barbara; Battini, Renata; Montanari, Monica; Mucci, Adele; Tosi, Giovanni; Forni, Flavio; Vandelli, Maria Angela

    2007-03-01

    The relatively hydrophilic bile acid, ursodeoxycholic acid (UDCA), was used as an additive to DOTAP cationic liposomes to evaluate the effect on the cellular uptake of an oligonucleotide. Nuclear magnetic resonance studies were applied to estimate the relative amount of incorporated UDCA into the lipidic bilayers. DOTAP or DOTAP-UDCA vesicles (MixVes; DOTAP/UDCA molar ratios 1:0.25, 1:0.5, 1:1, and 1:2) formed complexes with 5'-fluorescein conjugated 29-mer phosphorothioate oligonucleotides (PS-ODNs) and studied using gel electrophoresis. In addition, the complexes were tested after transfection to assess the cellular uptake and the localization of the oligo in a HaCaT cell line by the use of cytofluorimetric and confocal microscopic analysis. DOTAP lipid formulated in the presence of a defined amount of UDCA forms more stable, flexible, and active MixVes. In particular, the MixVes at 1:0.25 and 1:0.5 molar ratios increase and modify the cellular uptake of PS-ODNs if compared with DOTAP liposomes 3 hours after the transfection studies. Moreover, the in vitro data suggest that these new formulations are not toxic.

  7. Gas-phase Dissociation of homo-DNA Oligonucleotides

    NASA Astrophysics Data System (ADS)

    Stucki, Silvan R.; Désiron, Camille; Nyakas, Adrien; Marti, Simon; Leumann, Christian J.; Schürch, Stefan

    2013-12-01

    Synthetic modified oligonucleotides are of interest for diagnostic and therapeutic applications, as their biological stability, pairing selectivity, and binding strength can be considerably increased by the incorporation of unnatural structural elements. Homo-DNA is an oligonucleotide homologue based on dideoxy-hexopyranosyl sugar moieties, which follows the Watson-Crick A-T and G-C base pairing system, but does not hybridize with complementary natural DNA and RNA. Homo-DNA has found application as a bioorthogonal element in templated chemistry applications. The gas-phase dissociation of homo-DNA has been investigated by ESI-MS/MS and MALDI-MS/MS, and mechanistic aspects of its gas-phase dissociation are discussed. Experiments revealed a charge state dependent preference for the loss of nucleobases, which are released either as neutrals or as anions. In contrast to DNA, nucleobase loss from homo-DNA was found to be decoupled from backbone cleavage, thus resulting in stable products. This renders an additional stage of ion activation necessary in order to generate sequence-defining fragment ions. Upon MS3 of the primary base-loss ion, homo-DNA was found to exhibit unspecific backbone dissociation resulting in a balanced distribution of all fragment ion series.

  8. Chemical force mapping of phosphate and carbon on acid-modified tapioca starch surface.

    PubMed

    Wuttisela, Karntarat; Triampo, Wannapong; Triampo, Darapond

    2009-01-01

    Surface chemical microstructure of hydrochloric acid hydrolyzed tapioca starch producing different amylose:amylopectin (Am:Ap) ratios were studied with scanning chemical force microscopy (CFM). The chemical force probes were functionalized of two types with -OH (phosphate specific) and -CH3 (carbon specific). Lateral force trace-minus-retrace (TMR) images from -OH and -CH3 probes revealed changes in the phosphate domains and the carbon backbone for the varying acid hydrolyzed tapioca starch compared to that of the native tapioca starch. Scanning electron micrographs (SEM) showed different degree of the granule surface disruption before and after hydrolysis. The exterior structures of the acid hydrolyzed starch granules were chemically investigated with CFM to study the relationships of the surface molecular structures and the Am:Ap ratios.

  9. Recent Methods for Purification and Structure Determination of Oligonucleotides

    PubMed Central

    Zhang, Qiulong; Lv, Huanhuan; Wang, Lili; Chen, Man; Li, Fangfei; Liang, Chao; Yu, Yuanyuan; Jiang, Feng; Lu, Aiping; Zhang, Ge

    2016-01-01

    Aptamers are single-stranded DNA or RNA oligonucleotides that can interact with target molecules through specific three-dimensional structures. The excellent features, such as high specificity and affinity for target proteins, small size, chemical stability, low immunogenicity, facile chemical synthesis, versatility in structural design and engineering, and accessible for site-specific modifications with functional moieties, make aptamers attractive molecules in the fields of clinical diagnostics and biopharmaceutical therapeutics. However, difficulties in purification and structural identification of aptamers remain a major impediment to their broad clinical application. In this mini-review, we present the recently attractive developments regarding the purification and identification of aptamers. We also discuss the advantages, limitations, and prospects for the major methods applied in purifying and identifying aptamers, which could facilitate the application of aptamers. PMID:27999357

  10. Oligonucleotide recombination in gram negative bacteria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This report describes several key aspects of a novel form of RecA-independent homologous recombination. We found that synthetic single stranded DNA oligonucleotides (oligos) introduced into bacteria by transformation can site-specifically recombine with bacterial chromosomes in the absence of any a...

  11. Liver as a target for oligonucleotide therapeutics.

    PubMed

    Sehgal, Alfica; Vaishnaw, Akshay; Fitzgerald, Kevin

    2013-12-01

    Oligonucleotide-based therapeutics are an emerging class of drugs that hold the promise for silencing "un-druggable" targets,thus creating unique opportunities for innovative medicines. As opposed to gene therapy, oligonucleotides are considered to be more akin to small molecule therapeutics because they are small,completely synthetic in origin, do not integrate into the host genome,and have a defined duration of therapeutic activity after which effects recover to baseline. They offer a high degree of specificity at the genetic level, thereby reducing off-target effects.At the same time, they provide a strategy for targeting any gene in the genome, including transcripts that produce mutated proteins.Oligonucleotide-based therapeutics include short interfering RNA (siRNA), that degrade target mRNA through RISC mediated RNAi; anti-miRs, that target miRNAs; miRNA mimics, that regulate target mRNA; antisense oligonucleotides, that may be working through RNAseH mediated mRNA decay; mRNA upregulation,by targeting long non-coding RNAs; and oligonucleotides induced alternative splicing [1]. All these approaches require some minimal degree of homology at the nucleic acid sequence level for them to be functional. The different mechanisms of action and their relevant activity are outlined in Fig. 1. Besides homology,RNA secondary structure has also been exploited in the case of ribozymes and aptamers, which act by binding to nucleic acids or proteins, respectively. While there have been many reports of gene knockdown and gene modulation in cell lines and mice with all these methods, very few have advanced to clinical stages.The main obstacle to date has been the safe and effective intracellular delivery of these compounds in higher species, including humans. Indeed, their action requires direct interaction with DNA/RNA within the target cell so even when one solves the issues of tissue and cellular access, intracellular/intranuclear location represents yet another barrier to

  12. Salicylhydroxamic acid functionalized affinity membranes for specific immobilization of proteins and oligonucleotides.

    PubMed

    Springer, Amy L; Gall, Anna S; Hughes, Karin A; Kaiser, Robert J; Li, Guisheng; Lund, Kevin P

    2003-09-01

    Immobilization of proteins and other biological macromolecules on solid supports is a method suitable for purification or screening applications in life science research. Prolinx, Inc. has developed a novel chemical affinity system that can be used for specific immobilization of proteins and other macromolecules via interaction of two small synthetic molecules, phenyldiboronic acid (PDBA) and salicylhydroxamic acid (SHA). This report describes immobilization applications of activated microporous membranes that have been functionalized with SHA derivatives. These SHA-membranes exhibit high capacity and specificity for binding of PDBA-labeled nucleic acids and proteins. Conjugation of active protein with PDBA is performed in solution independent of the immobilization step on SHA membranes. The resulting PDBA-protein conjugate is immobilized directly without purification and retains biological activity. PDBA conjugates may also be released from these SHA-affinity membranes in a controlled manner. Capture and release of PBA-modified oligonucleotides is also demonstrated. SHA-membranes can be used as surfaces for microarrays, and are therefore compatible with high-throughput analyses. These properties make them useful for development of numerous preparative or screening applications.

  13. Application of pervaporation and vapor permeation processes to separate aqueous ethanol solution through chemically modified Nylon 4 membranes

    SciTech Connect

    Wang, Y.H.; Teng, M.Y.; Lee, K.R.; Wang, D.M.; Lai, J.Y.

    1998-08-01

    The pervaporation performance of a Nylon 4 membrane, chemically grafted by N,N-dimethylaminoethyl methacrylate (DMAEM), DMAEM-g-N4, was studied by measurement of the permeation ratio and the pervaporation separation index. It was found that the water permselectivity and permeation rate for the chemically modified Nylon 4 membrane were higher than those of the unmodified Nylon 4 membrane. Optimum pervaporation results, a separation factor of 28.3, and a permeation rate of 439 g/m{sup 2}{center_dot}h, were obtained when the degree of grafting was 12.7%. It was also found that all the permeation ratios at low temperature were less than unity. In addition, compared with pervaporation, vapor permeation effectively increases the permselectivity of water.

  14. Mechanism of enhanced Sb(V) removal from aqueous solution using chemically modified aerobic granules.

    PubMed

    Wang, Li; Wan, Chun-li; Zhang, Yi; Lee, Duu-Jong; Liu, Xiang; Chen, Xiao-feng; Tay, Joo-Hwa

    2015-03-02

    Sb(V) removal using Fe-modified aerobic granules was investigated. Increasing the biomass dosage improved the Sb(V) removal rate, but lowered the adsorption quantity; the optimal biomass concentration was 20 g/L (wet basis). Adsorption equilibrium was obtained at 2h at 175 rpm; the adsorption quantity was 36.6 mg/g. NaCl and other salts inhibited Sb(V) adsorption on Fe-modified granules, and the mechanism possibly lied more with the anions. The adsorption isotherms were evaluated using the Langmuir, Freundlich, and Temkin models. The Langmuir model best described the adsorption process, and gave a maximum monolayer adsorption quantity of 125 mg/g. The ΔH value for adsorption was 16.1 kJ/mol, indicating endothermicity, and the negative ΔG values at various temperatures suggested spontaneous adsorption. Outer-sphere and inner-sphere complexations were involved in Sb(V) adsorption.

  15. Improved removal of malachite green from aqueous solution using chemically modified cellulose by anhydride.

    PubMed

    Zhou, Yanmei; Min, Yinghao; Qiao, Han; Huang, Qi; Wang, Enze; Ma, Tongsen

    2015-03-01

    Cellulose modified with maleic (M) and phthalic (P) anhydride, to be named CMA and CPA, were tested as feasible adsorbents for the removal of malachite green from aqueous solution. At the same time, the uptake ability of natural cellulose was also studied for comparison. The structure of material was characterized by FT-IR and XRD. The effects of solution pH, initial dye concentration, contact time and temperature were investigated in detail by batch adsorption experiments. The kinetic and isotherm studies suggested that the adsorption followed the pseudo-second-order model and Langmuir isotherm. The maximum adsorption capacity on CMA and CPA were 370 mg g(-1) and 111 mg g(-1), respectively. Furthermore, the thermodynamics studies indicated the spontaneous nature of adsorption of malachite green on adsorbents. All the studied results showed that the modified cellulose could be used as effective adsorption material for the removal of malachite green from aqueous solutions.

  16. Synthesis and Functionalization of Gold Nanoparticles Using Chemically Modified ssDNA

    NASA Astrophysics Data System (ADS)

    Calabrese, P. G.

    In the first part of this thesis, methods for functionalizing spherical gold nanoparticles with nucleic acid binding ligands (aptamers) that target the VEGF receptor complex were developed. In order to provide a multiplexed labeling strategy for imaging the VEGF receptor complex in electron microscopy, gold nanoparticles of distinct sizes were conjugated to modified ssDNA aptamers that target the VEGF-A cytokine, the VEGFR-2 RTK receptor and a membrane associated co-receptor, Nrp-1. The modified ssDNA gold nanoparticle conjugates were applied to a human lung carcinoma cell line (A549) which has been shown to express each of these proteins and used as a model system for VEGF signaling. Binding constants for the modified aptamers were also determined using a fluorescence polarization anisotropy assay to determine KD and KOFF for the aptamers with their respective proteins. In the latter part of this thesis, a modied ssDNA SELEX protocol was also developed in order to evolve imidazole modied ssDNA sequences that assemble gold nanoparticles from Au3+ precursor ions in aqueous solution. Active sequences bound to nanoparticles were partitioned from inactive sequences based on density via ultracentrifugation through a discontinuous sucrose gradient. Colloidal gold solutions produced by the evolved pool had a distinct absorbance spectra and produced nanoparticles with a narrower distribution of sizes compared to colloidal gold solutions produced by the starting randomized pool of imidazole modified ssDNA. Sequencing data from the evolved pool shows that conserved 5 and 6 nt motifs were shared amongst many of the isolates, which indicates that these motifs could serve as chelation sites for gold atoms or help stabilize colloidal gold solutions in a base specific manner.

  17. Fabrication of BaTiO3 Thin Films Using Modified Chemical Solutions and Sintering Method

    NASA Astrophysics Data System (ADS)

    Tanaka, Kiyotaka; Suzuki, Kazuyuki; Kato, Kazumi

    2008-09-01

    BaTiO3 thin films were fabricated at 650 °C by single sintering using additive-free and diethanolamine (DEA)-modified alkoxide solutions. The BaTiO3 thin films derived from the DEA-modified solution had a flat surface and an rms roughness below 2.5 nm. The grain size on Pt/Ti/SiO2/Si substrates single-sintered at 650 °C for 100 min was estimated to be about 34 to 43 nm. We succeeded in obtaining the electric properties of Pt/BaTiO3/Pt capacitors by single sintering at 650 °C for 1 min. The dielectric constant ɛr and dielectric loss tan δ at 1 MHz were 110 and 0.05, respectively. On the other hand, the grain size on SiO2/Si substrates single-sintered at 650 °C for 100 min reached about 55 to 62 nm. For the thickness and Fourier-transform infrared (FT-IR) spectra of the gel films, it was found that the thickness of the gel films at around 200 °C derived from the DEA-modified solution became abnormally thick and that the intermediate compounds generated during the decomposition of DEA remained in the gel films.

  18. Influence of pyrolysis temperature on lead immobilization by chemically modified coconut fiber-derived biochars in aqueous environments.

    PubMed

    Wu, Weidong; Li, Jianhong; Niazi, Nabeel Khan; Müller, Karin; Chu, Yingchao; Zhang, Lingling; Yuan, Guodong; Lu, Kouping; Song, Zhaoliang; Wang, Hailong

    2016-11-01

    Biochar has received widespread attention as an eco-friendly and efficient material for immobilization of toxic heavy metals in aqueous environments. In the present study, three types of coconut fiber-derived biochars were obtained by pyrolyzing at three temperatures, i.e., 300, 500, and 700 °C. In addition, nine types of biochars were prepared by chemical modification with ammonia, hydrogen peroxide, and nitric acid, respectively, which were used to investigate changes in physico-chemical properties by inter alia, Fourier transformation infrared spectrophotometry (FTIR), scanning electron microscope (SEM), and BET specific surface area analysis. Batch sorption experiments were carried out to determine the sorption capacity of the biochars for lead (Pb) in aqueous solutions. Results showed that the cation exchange capacity of biochar pyrolyzed at 300 °C and modified with nitric acid increased threefold compared to the control. Loosely corrugated carbon surface and uneven carbon surface of the biochar pyrolyzed at 300 °C were produced during ammonia and nitric acid modifications. Removal rate of Pb by the coconut biochar pyrolyzed at 300 °C and modified with ammonia was increased from 71.8 to 99.6 % compared to the untreated biochar in aqueous solutions containing 100 mg L(-1) Pb. However, chemical modification did not enhance adsorption of Pb of the biochars pyrolyzed at higher temperatures (e.g., 500 or 700 °C), indicating that resistance of biochars to chemical treatment increased with pyrolysis temperature.

  19. Light-generated oligonucleotide arrays for rapid DNA sequence analysis.

    PubMed Central

    Pease, A C; Solas, D; Sullivan, E J; Cronin, M T; Holmes, C P; Fodor, S P

    1994-01-01

    In many areas of molecular biology there is a need to rapidly extract and analyze genetic information; however, current technologies for DNA sequence analysis are slow and labor intensive. We report here how modern photolithographic techniques can be used to facilitate sequence analysis by generating miniaturized arrays of densely packed oligonucleotide probes. These probe arrays, or DNA chips, can then be applied to parallel DNA hybridization analysis, directly yielding sequence information. In a preliminary experiment, a 1.28 x 1.28 cm array of 256 different octanucleotides was produced in 16 chemical reaction cycles, requiring 4 hr to complete. The hybridization pattern of fluorescently labeled oligonucleotide targets was then detected by epifluorescence microscopy. The fluorescence signals from complementary probes were 5-35 times stronger than those with single or double base-pair hybridization mismatches, demonstrating specificity in the identification of complementary sequences. This method should prove to be a powerful tool for rapid investigations in human genetics and diagnostics, pathogen detection, and DNA molecular recognition. Images PMID:8197176

  20. Chemically modified fatty acid methyl esters: their potential for use as lubrication fluids and surfactants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A review of recent developments in the synthesis and characterization of lubrication fluids and surfactants from methyl oleate. The synthesis of materials made using an epoxidation route is the focus. This versatile method of chemical modification of fatty acid methyl esters improves their oxidati...

  1. Chemical and physical properties of Paulownia elongata biochar modified with oxidants for horticultural applications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Treatment of biochar with oxidants such as acids and hydrogen peroxide has been shown to alter porosity, increase adsorption of chemicals, and introduce functional groups on the biochar surfaces, all of which are desirable for their use in horticultural applications. Biochar was produced from the py...

  2. Hsp90 protein interacts with phosphorothioate oligonucleotides containing hydrophobic 2'-modifications and enhances antisense activity.

    PubMed

    Liang, Xue-Hai; Shen, Wen; Sun, Hong; Kinberger, Garth A; Prakash, Thazha P; Nichols, Joshua G; Crooke, Stanley T

    2016-05-05

    RNase H1-dependent antisense oligonucleotides (ASOs) are chemically modified to enhance pharmacological properties. Major modifications include phosphorothioate (PS) backbone and different 2'-modifications in 2-5 nucleotides at each end (wing) of an ASO. Chemical modifications can affect protein binding and understanding ASO-protein interactions is important for better drug design. Recently we identified many intracellular ASO-binding proteins and found that protein binding could affect ASO potency. Here, we analyzed the structure-activity-relationships of ASO-protein interactions and found 2'-modifications significantly affected protein binding, including La, P54nrb and NPM. PS-ASOs containing more hydrophobic 2'-modifications exhibit higher affinity for proteins in general, although certain proteins, e.g. Ku70/Ku80 and TCP1, are less affected by 2'-modifications. We found that Hsp90 protein binds PS-ASOs containing locked-nucleic-acid (LNA) or constrained-ethyl-bicyclic-nucleic-acid ((S)-cEt) modifications much more avidly than 2'-O-methoxyethyl (MOE). ASOs bind the mid-domain of Hsp90 protein. Hsp90 interacts with more hydrophobic 2' modifications, e.g. (S)-cEt or LNA, in the 5'-wing of the ASO. Reduction of Hsp90 protein decreased activity of PS-ASOs with 5'-LNA or 5'-cEt wings, but not with 5'-MOE wing. Together, our results indicate Hsp90 protein enhances the activity of PS/LNA or PS/(S)-cEt ASOs, and imply that altering protein binding of ASOs using different chemical modifications can improve therapeutic performance of PS-ASOs.

  3. Targeted gene correction with 5' acridine-oligonucleotide conjugates.

    PubMed

    de Piédoue, G; Andrieu-Soler, C; Concordet, J P; Maurisse, R; Sun, J-S; Lopez, B; Kuzniak, I; Leboulch, P; Feugeas, J-P

    2007-01-01

    Single-stranded oligonucleotides (SSOs) mediate gene repair of punctual chromosomal mutations at a low frequency. We hypothesized that enhancement of DNA binding affinity of SSOs by intercalating agents may increase the number of corrected cells. Several biochemical modifications of SSOs were tested for their capability to correct a chromosomally integrated and mutated GFP reporter gene in human 293 cells. SSOs of 25 nucleotide length conjugated with acridine at their 5' end increased the efficiency of gene correction up to 10-fold compared to nonmodified SSOs. Acridine and psoralen conjugates were both evaluated, and acridine-modified SSOs were the most effective. Conjugation with acridine at the 3' end of the SSO inhibited gene correction, whereas flanking the SSO by acridine on both sides provided an intermediate level of correction. These results suggest that increasing the stability of hybridization between SSO and its target without hampering a 3' extension improves gene targeting, in agreement with the "annealing-integration" model of DNA repair.

  4. Calorimetric and Spectroscopic Analysis of the Thermal Stability of Short Duplex DNA-Containing Sugar and Base-Modified Nucleotides.

    PubMed

    Fakhfakh, Kareem; Hughesman, Curtis B; Louise Creagh, A; Kao, Vincent; Haynes, Charles

    2016-01-01

    Base- and sugar-modified analogs of DNA and RNA are finding ever expanding use in medicine and biotechnology as tools to better tailor structured oligonucleotides by altering their thermal stability, nuclease resistance, base-pairing specificity, antisense activity, or cellular uptake. Proper deployment of these chemical modifications generally requires knowledge of how each affects base-pairing properties and thermal stabilities. Here, we describe in detail how differential scanning calorimetry and UV spectroscopy may be used to quantify the melting thermodynamics of short dsDNA containing chemically modified nucleosides in one or both strands. Insights are provided into why and how the presence of highly stable base pairs containing modified nucleosides can alter the nature of calorimetry or melting spectroscopy data, and how each experiment must therefore be conducted to ensure high-quality melting thermodynamics data are obtained. Strengths and weaknesses of the two methods when applied to chemically modified duplexes are also addressed.

  5. Adsorption of hexavalent chromium from synthetic and electroplating effluent on chemically modified Swietenia mahagoni shell in a packed bed column.

    PubMed

    Rangabhashiyam, S; Nandagopal, M S Giri; Nakkeeran, E; Selvaraju, N

    2016-07-01

    Packed bed column studies were carried out to evaluate the performance of chemically modified adsorbents for the sequestration of hexavalent chromium from synthetic and electroplating industrial effluent. The effects of parameters such as bed height (3-9 cm), inlet flow rate (5-15 mL/min), and influent Cr(VI) concentration (50-200 mg/L) on the percentage removal of Cr(VI) and the adsorption capacity of the adsorbents in a packed bed column were investigated. The breakthrough time increased with increasing bed height and decreased with the increase of inlet flow rate and influent Cr(VI) concentration. The adsorption column models such as Thomas, Adams-Bohart, Yoon-Nelson, and bed depth service time (BDST) were successfully correlated with the experimental data. The Yoon-Nelson and BDST model showed good agreement with the experimental data for all the studied parameter conditions. Results of the present study indicated that the chemically modified Swietenia mahagoni shell can be used as an adsorbent for the removal of Cr(VI) from industrial wastewater in a packed bed column.

  6. Crystal engineering of energetic materials: co-crystals of Ethylenedinitramine (EDNA) with modified performance and improved chemical stability.

    PubMed

    Aakeröy, Christer B; Wijethunga, Tharanga K; Desper, John

    2015-07-27

    In the area of energetic materials, co-crystallization is emerging as a new technology for modifying or enhancing the properties of existing energetic substances. Ethylenedinitramine (EDNA) is a known energetic material which requires attention partly due to its chemical instability originating with its two highly acidic protons. In order to stabilize EDNA, a co-crystallization approach targeting the acidic protons using a series of co-crystallizing agents with suitable hydrogen-bond acceptors was employed. Fifteen attempted co-crystallizations resulted in eight successful outcomes and six of these were crystallographically characterized and all showed evidence of hydrogen bonds to the intended protons. Calculated detonation properties and experimental thermal and impact data for the co-crystals were obtained and compared with those of pure EDNA. The co-crystal of EDNA and 1,2-bis(4-pyridyl)ethylene was recognized as a more thermally stable alternative to EDNA while the co-crystal of EDNA and pyrazine N,N'-dioxide showed comparable detonation strengths (and much improved chemical stability) compared with that of EDNA. The co-crystals EDNA:4,4'-bipyridine and EDNA:pyrazine N,N'-dioxide were found to be about 50 % less impact sensitive than EDNA, all of which illustrate how co-crystallizations can be utilized for successfully modifying specific aspects of energetic materials.

  7. Thermogravimetric Analysis of Modified Hematite by Methane (CH{sub 4}) for Chemical-Looping Combustion: A Global Kinetics Mechanism

    SciTech Connect

    Monazam, Esmail R; Breault, Ronald W; Siriwardane, Ranjani; Miller, Duane D

    2013-10-01

    Iron oxide (Fe{sub 2}O{sub 3}) or in its natural form (hematite) is a potential material to capture CO{sub 2} through the chemical-looping combustion (CLC) process. It is known that magnesium (Mg) is an effective methyl cleaving catalyst and as such it has been combined with hematite to assess any possible enhancement to the kinetic rate for the reduction of Fe{sub 2}O{sub 3} with methane. Therefore, in order to evaluate its effectiveness as a hematite additive, the behaviors of Mg-modified hematite samples (hematite –5% Mg(OH){sub 2}) have been analyzed with regard to assessing any enhancement to the kinetic rate process. The Mg-modified hematite was prepared by hydrothermal synthesis. The reactivity experiments were conducted in a thermogravimetric analyzer (TGA) using continuous stream of CH{sub 4} (5, 10, and 20%) at temperatures ranging from 700 to 825 {degrees}C over ten reduction cycles. The mass spectroscopy analysis of product gas indicated the presence of CO{sub 2}, H{sub 2}O, H{sub 2} and CO in the gaseous product. The kinetic data at reduction step obtained by isothermal experiments could be well fitted by two parallel rate equations. The modified hematite samples showed higher reactivity as compared to unmodified hematite samples during reduction at all investigated temperatures.

  8. Enhancing adsorption capacity of toxic malachite green dye through chemically modified breadnut peel: equilibrium, thermodynamics, kinetics and regeneration studies.

    PubMed

    Chieng, Hei Ing; Lim, Linda B L; Priyantha, Namal

    2015-01-01

    Breadnut skin, in both its unmodified (KS) and base-modified (BM-KS) forms, was investigated for its potential use as a low-cost adsorbent for the removal of toxic dye, malachite green (MG). Characterization of the adsorbents was carried out using scanning electron microscope, X-ray fluorescence and Fourier transform infra-red spectroscopy. Batch adsorption experiments, carried out under optimized conditions, for the adsorption of MG were fitted using five isotherm models (Langmuir, Freundlich, Dubinin-Radushkevich, Temkin and Sips) and six error functions to determine the best-fit model. The adsorption capacity was greatly enhanced when breadnut skin was chemically modified with NaOH, leading to an adsorption capacity of 353.0 mg g(-1), that was far superior to most reported adsorbents for the removal of MG. Thermodynamics studies indicated that the adsorption of MG was spontaneous on KS and BM-KS, and the reactions were endothermic and exothermic, respectively. Kinetics studies showed that both followed the pseudo-second order. Regeneration experiments on BM-KS indicated that its adsorption capacity was still maintained at>90% even after five cycles. It can be concluded that NaOH-modified breadfruit skin has great potential to be utilized in real-life application as a low-cost adsorbent for the removal of MG in wastewater treatment.

  9. Site-specifically modified oligodeoxynucleotides as probes for the structural and biological effect of DNA-damaging agents

    SciTech Connect

    Basu, A.K.; Essigmann, J.M.

    1988-01-01

    This review critically analyzes the state of knowledge on the preparation, characterization, and uses of site-specifically modified DNA segments. Although these substrates have begun to have an impact upon several fields, the review focuses upon their applications in site-directed mutagenesis studies and for defining the effect of chemical damage upon DNA structure. Oligonucleotides have been synthesized containing alkylated DNA bases, aromatic amine adducts, base oxidation products, cyclic nucleic acid adducts, model apurinic/apyrimidinic sites, UV and psoralen photoadducts, and several antitumor drug-DNA covalent complexes. Below, the authors shall describe the progress to date on synthesis of site-specifically modified DNA segments and how these oligonucleotides have been used to further their understanding of the roles of individual DNA adducts in toxicology. The structures of the DNA adducts and adduct-derived products discussed in this review are presented. 168 references.

  10. Discrimination of base differences in oligonucleotides using mid-infrared spectroscopy and multivariate analysis.

    PubMed

    Kelly, Jemma G; Martin-Hirsch, Pierre L; Martin, Francis L

    2009-07-01

    Attenuated total reflection Fourier transform-infrared (ATR-FTIR) spectroscopy was employed to interrogate a panel of simple oligonucleotides designed to contain various base differences; combined with subsequent multivariate analysis, we set out to determine whether the specificity of this approach would point to a novel means for mutation detection. Oligonucleotides were designed that were 15 bases in length and contained various combinations of purines (adenine, guanine) or pyrimidines (cytosine, thymine). These were applied to 1 cm x 1 cm low-E reflective glass slides, and triplicate samples were interrogated using ATR-FTIR spectroscopy. Per oligonucleotide sample, 10 independent spectral acquisitions were obtained. Prior to multivariate analysis, infrared spectra were baseline-corrected and vector normalized over the 1750-760 cm(-1) region specific to the chemical bonds of organic molecules. Spectral categories were then analyzed using principal component analysis (PCA) followed by linear discriminant analysis (LDA). Scores plots revealed that PCA-LDA clearly segregated different oligonucleotide sequences, even in the presence of a single base difference. Loadings plots confirmed the chemical entities associated with distinguishing base differences. These results suggest that mid-IR spectroscopy might have future roles in interrogating polymorphic forms of a DNA template.

  11. The optimal one dimensional periodic table: a modified Pettifor chemical scale from data mining

    NASA Astrophysics Data System (ADS)

    Glawe, Henning; Sanna, Antonio; Gross, E. K. U.; Marques, Miguel A. L.

    2016-09-01

    Starting from the experimental data contained in the inorganic crystal structure database, we use a statistical analysis to determine the likelihood that a chemical element A can be replaced by another B in a given structure. This information can be used to construct a matrix where each entry (A,B) is a measure of this likelihood. By ordering the rows and columns of this matrix in order to reduce its bandwidth, we construct a one-dimension ordering of the chemical elements, analogous to the famous Pettifor scale. The new scale shows large similarities with the one of Pettifor, but also striking differences, especially in what comes to the ordering of the non-metals.

  12. Comparative repellent properties of certain chemicals against mosquitoes, house flies and cockroaches using modified techniques.

    PubMed

    Vartak, P H; Tungikar, V B; Sharma, R N

    1994-09-01

    Several terpenoids were assessed for their repellent/toxic properties against mosquitoes (Aedes aegypti), house flies (Musca domestica) and cockroaches (Periplaneta americana). Impregnated wide mesh netting was used in the case of the Dipterans, while treated filtered paper was employed for the bioassays with cockroaches. Persistence of the repellent chemicals was studied. Doses ranged from 5-20 gm/M2 for the Dipterans and 25-100 mg per 4 x 4 cm filter paper for the cockroaches. Dimethyl phthalate (DMP) offered the maximum protection of the chemicals tested against mosquitoes but was not so effective against house flies and cockroaches. Citral and Eugenol were effective against all the three test insects. Other test compounds afforded varying degrees of protection. Application strategy and utility of the findings are discussed.

  13. Biosorption of heavy metals from aqueous solutions by chemically modified orange peel.

    PubMed

    Feng, Ningchuan; Guo, Xueyi; Liang, Sha; Zhu, Yanshu; Liu, Jianping

    2011-01-15

    Equilibrium, thermodynamic and kinetic studies were carried out for the biosorption of Pb(2+), Cd(2+) and Ni(2+) ions from aqueous solution using the grafted copolymerization-modified orange peel (OPAA). Langmuir and Freundlich isotherm models were applied to describe the biosorption of the metal ions onto OPAA. The influences of pH and contact time of solution on the biosorption were studied. Langmuir model fitted the equilibrium data better than the Freundlich isotherm. According to the Langmuir equation, the maximum uptake capacities for Pb(2+), Cd(2+) and Ni(2+) ions were 476.1, 293.3 and 162.6 mg g(-1), respectively. Compared with the unmodified orange peel, the biosorption capacity of the modified biomass increased 4.2-, 4.6- and 16.5-fold for Pb(2+), Cd(2+) and Ni(2+), respectively. The kinetics for Pb(2+), Cd(2+) and Ni(2+) ions biosorption followed the pseudo-second-order kinetics. The free energy changes (ΔG°) for Pb(2+), Cd(2+) and Ni(2+) ions biosorption process were found to be -3.77, -4.99 and -4.22 kJ mol(-1), respectively, which indicates the spontaneous nature of biosorption process. FTIR demonstrated that carboxyl and hydroxyl groups were involved in the biosorption of the metal ions. Desorption of Pb(2+), Cd(2+) and Ni(2+) ions from the biosorbent was effectively achieved in a 0.05 mol L(-1) HCl solution.

  14. Treatment of swine wastewater using chemically modified zeolite and bioflocculant from activated sludge.

    PubMed

    Guo, Junyuan; Yang, Chunping; Zeng, Guangming

    2013-09-01

    Sterilization, alkaline-thermal and acid-thermal treatments were applied to activated sludge and the pre-treated sludge was used as raw material for Rhodococcus R3 to produce polymeric substances. After 60 h of fermentation, bioflocculant of 2.7 and 4.2 g L(-1) were produced in sterilized and alkaline-thermal treated sludge as compared to that of 0.9 g L(-1) in acid-thermal treated sludge. Response surface methodology (RSM) was employed to optimize the treatment process of swine wastewater using the composite of bioflocculant and zeolite modified by calcining with MgO. The optimal flocculating conditions were bioflocculant of 24 mg L(-1), modified zeolite of 12 g L(-1), CaCl2 of 16 mg L(-1), pH of 8.3 and contact time of 55 min, and the corresponding removal rates of COD, ammonium and turbidity were 87.9%, 86.9%, and 94.8%. The use of the composite by RSM provides a feasible way to improve the pollutant removal efficiencies and recycle high-level of ammonium from wastewater.

  15. Physico-chemical properties of corn starch modified with cyclodextrin glycosyltransferase.

    PubMed

    Dura, Angela; Rosell, Cristina M

    2016-06-01

    Cyclodextrin glycosyltransferase (CGTase) has been used to produce cyclodextrins (CDs) from starches, but their ability to modify starches has been barely explored. The effect of CGTase on corn starch at sub-gelatinization temperature (50°C) and at different pH conditions, pH 4.0 and pH 6.0, was evaluated. Biochemical features, thermal and structural analysis, oligosaccharides and CDs content were studied. Microscopic analysis of the granules confirmed the enzymatic modification of the starches obtaining structures with irregular surface and small pinholes. The extent of the starch modification was largely dependent on the pHs, being higher at pH 6.0. This was also confirmed by the low viscosity of the resulting pastes during a heating and cooling cycle. Thermal parameters were not affected due to enzymatic treatment. Modified starches were less susceptible to undergo α-amylase hydrolysis. CDs released were higher for samples treated at pH 4.0. Therefore, CGTase modification of corn starches at sub-gelatinization temperature offers an attractive alternative for obtaining porous starches with different properties depending on the pH conditions.

  16. Unconventional assembly of bimetallic Au-Ni janus nanoparticles on chemically modified silica spheres.

    PubMed

    Jia, Lei; Pei, Xiaowei; Zhou, Feng; Liu, Weimin

    2014-02-10

    This paper reports that Janus Au-Ni nanoparticles (JANNPs) can self-assemble onto silica spheres in a novel way, which is different from that of single-component isotropic nanoparticles. JANNPs modified with octadecylamine (ODA) assemble onto catechol-modified silica spheres (SiO2-OH) to form a very special core-loop complex structure and finally the core-loop assemblies link each other to form large assemblies through capillary force and the hydrophobic interaction of the alkyl chains of ODA. The nanocomposites disassemble in the presence of vanillin and oleic acid because of the breakage of the catechol-metal link. Vanillin-induced disassembly enables the JANNPs to reassemble into a core-loop structure upon ODA addition. The assembly of SiO2-OH and isotropic Ni or Fe3O4 particles generates traditional core-satellite structures. This unconventional self-assembly can be attributed to the synergistic effect of Janus specificity and capillary force, which is also confirmed by the assembly of thiol-terminated silica spheres (SH-SiO2) with anisotropic JANNPs, isotropic Au, and Ni nanoparticles. These results can guide the development of novel composite materials using Janus nanoparticles as the primary building blocks.

  17. Removal of Pb2+ from aqueous solution by adsorption on chemically modified muskmelon peel.

    PubMed

    Huang, Kai; Zhu, Hongmin

    2013-07-01

    A cost-effective biosorbent was prepared by a green chemical modification process from muskmelon peel by saponification with alkaline solution of Ca(OH)2. Its adsorption behavior for lead ions was investigated and found to exhibit excellent adsorption properties. Results showed that the optimal equilibrium pH range for 100% adsorption is from 4 up to 6.4. Adsorption equilibrium was attained within 10 min. The adsorption process can be described well by Langmuir model and pseudo-second-order kinetics equation, respectively. The maximum adsorption capacity for lead ions was found to be 0.81 mol/kg. Pectic acid contained in the muskmelon peel is the main factor responsible for the uptake of lead ions onto the gel, and the chemical modification process presented in this study can be assumed effective to prepare other similar biomaterials. The large adsorption capacity and the fast adsorption rate indicated that chemically saponified muskmelon peel gel in present study has great potential to be used as a cost-effective adsorbent for the removal of lead ions from the water.

  18. Effect of modified atmospheric packaging on chemical and microbial changes in dietetic rabri during storage.

    PubMed

    Ghayal, Gajanan; Jha, Alok; Kumar, Arvind; Gautam, Anuj Kumar; Rasane, Prasad

    2015-03-01

    Rabri is a dairy based sweet popular in the Indian subcontinent. The high sugar and fat content impose restrictions on its consumption due to health reasons. Dietetic rabri was prepared by the replacement of sugar with aspartame. Inulin was added to partially replace the milk fat and to improve the consistency of rabri. The rabri samples were packed in the polyethylene bags filled with different gaseous compositions (Air, 50 % CO2:50 % N2 and 100 % N2) and stored at 10 °C. The shelf life was evaluated on the basis of changes in the chemical quality parameters such as HMF, TBA and FFA and microbial content such as total plate count, yeast and molds and coliform counts. The chemical parameters and microbial spoilage increased in all the samples with the progression of storage period. The samples packed with air showed significantly higher chemical deterioration and microbial spoilage as compared to the other two combinations. The samples packed with 100 % N2 were more shelf stable than with air and 50 % CO2:50 % N2 combinations.

  19. Drug targeting: synthesis and endocytosis of oligonucleotide-neoglycoprotein conjugates.

    PubMed Central

    Bonfils, E; Depierreux, C; Midoux, P; Thuong, N T; Monsigny, M; Roche, A C

    1992-01-01

    Inhibition of gene expression by antisense oligonucleotides is limited by their low ability to enter cells. Knowing that sugar binding receptors, also called membrane lectins, efficiently internalize neoglycoproteins bearing the relevant sugar, 6-phosphomannose, for instance, oligonucleotides--substituted on their 5'-end with either a fluorescent probe or a radioactive label on the one hand, and bearing a thiol function on their 3'-end, on the other hand,--were coupled onto 6-phosphomannosylated proteins via a disulfide bridge. The oligonucleotide bound to 6-phosphomannosylated serum albumin is much more efficiently internalized roughly 20 times than the free oligonucleotide. Although most of the oligonucleotides are associated with vesicular compartments, oligonucleotides after releasing from the carrier by reduction of the disulfide bridge may find their way to reach the cytosol and then lead to an increase in the efficiency of the oligonucleotides. Images PMID:1408764

  20. Nickel release behavior and surface characteristics of porous NiTi shape memory alloy modified by different chemical processes.

    PubMed

    Wu, Shuilin; Liu, Xiangmei; Chan, Y L; Chu, Paul K; Chung, C Y; Chu, Chenglin; Yeung, Kelvin W K; Lu, W W; Cheung, Kenneth M C; Luk, K D K

    2009-05-01

    As a non-line-of-sight surface modification technique, chemical treatment is an effective method to treat porous NiTi with complex surface morphologies and large exposed areas due to its liquidity and low temperature. In the work described here, three different chemical processes are used to treat porous NiTi alloys. Our results show that H(2)O(2) treatment, NaOH treatment, and H(2)O(2) pre-treatment plus subsequent NaOH treatment can mitigate leaching of nickel from the alloy. The porous NiTi samples modified by the two latter processes favor deposition of a layer composed of Ca and P due to the formation of bioactive Na(2)TiO(3) on the surface. Among the three processes, H(2)O(2) pre-treatment plus subsequent NaOH modification is the most effective in suppressing nickel release. Small area X-ray photoelectron spectroscopy reveals that the surfaces treated by different chemical processes have different structures and compositions. The sample modified by the H(2)O(2) treatment is composed of rough TiO(2) on the outer surface and an oxide transition layer underneath whereas the sample treated by NaOH comprises a surface layer of titanium oxide and Na(2)TiO(3) together with a transition layer. The sample processed by the H(2)O(2) and NaOH treatment has a pure Na(2)TiO(3) layer on the surface and a transition layer underneath. These results help to elucidate the different nickel release behavior and bioactivity of porous NiTi alloys processed by different methods.

  1. Purification and physico-chemical characterisation of genetically modified phytases expressed in Aspergillus awamori.

    PubMed

    Martin, Judith A; Murphy, Richard A; Power, Ronan F G

    2006-09-01

    Two heterologous phytases from Aspergillus awamori and Aspergillus fumigatus obtained from submerged cultures of genetically modified fungal strains in addition to two commercially available phytase preparations (Allzyme and Natuphos phytases) were purified to homogeneity using a combination of ultrafiltration, gel filtration and ion exchange. The purified preparations were used in subsequent characterisation studies, in which Western Immunoblot analysis, pH and temperature optima, thermal stability and substrate specificity were assessed. A. fumigatus phyA phytase expressed in A. awamori exhibited activity over a broad pH range together with an increased temperature optimum, and slightly enhanced thermal stability compared to the other phytases tested, and is thus a promising candidate for animal feed applications. This particular phytase retains activity over a wide range of pH values characteristic of the digestive tract and could conceivably be more suited to the increasingly higher feed processing temperatures being utilised today, than the corresponding phytases from Aspergillus niger.

  2. Wrapping of a single bacterium with Functionalized - Chemically Modified Graphene (FCMG) sheets via highly specific protein-cell wall interaction

    NASA Astrophysics Data System (ADS)

    Mohanty, Nihar; Berry, Vikas

    2009-03-01

    Graphene has recently generated a lot of interest due to its unique structural and electrical properties. It's micro-scale area and sub-nano-scale thickness coupled with ballistic electronic transport at room temperature, low Johnston noise and low charge scattering, have made it a gold mine for novel applications. Since its discovery in 2004, there have been a plethora of studies on characterizing its unique physical, chemical and electrical properties of graphene as well as on integrating it with various physical/chemical systems to utilize these properties. But there have been limited or no studies on the integration of graphene with living microorganisms or mammalian cells. Here we describe the novel wrapping of a single live bacterium (Bacillus cereus) with a chemically modified graphene sheet functionalized with the protein Concanavalin-A (Con-A) via the highly specific Con-A - Teichoic acid interaction. We are investigating the structural and the electrical properties of these novel bacteria-FCMG ensembles. Further, we are also interested in characterizing this wrapping process in detail by studying the kinetics and the mechanism of action of bacterial-wrapping via 3D modelling. This is a first step towards the live-bio-nano-integration of graphene which would open up avenues for applications as diverse as bio-batteries using the Geobacter to recombinant enzyme compartmentalization.

  3. Detection of Ligand-Induced Conformational Changes in Oligonucleotides by Second-Harmonic Generation at a Supported Lipid Bilayer Interface.

    PubMed

    Butko, Margaret T; Moree, Ben; Mortensen, Richard B; Salafsky, Joshua

    2016-11-01

    There is a high demand for characterizing oligonucleotide structural changes associated with binding interactions as well as identifying novel binders that modulate their structure and function. In this study, second-harmonic generation (SHG) was used to study RNA and DNA oligonucleotide conformational changes associated with ligand binding. For this purpose, we developed an avidin-based biotin capture surface based on a supported lipid bilayer membrane. The technique was applied to two well-characterized aptamers, both of which undergo conformational changes upon binding either a protein or a small molecule ligand. In both cases, SHG was able to resolve conformational changes in these oligonucleotides sensitively and specifically, in solution and in real time, using nanogram amounts of material. In addition, we developed a competition assay for the oligonucleotides between the specific ligands and known, nonspecific binders, and we demonstrated that intercalators and minor groove binders affect the conformation of the DNA and RNA oligonucleotides in different ways upon binding and subsequently block specific ligand binding in all cases. Our work demonstrates the broad potential of SHG for studying oligonucleotides and their conformational changes upon interaction with ligands. As SHG offers a powerful, high-throughput screening approach, our results here also open an important new avenue for identifying novel chemical probes or sequence-targeted drugs that disrupt or modulate DNA or RNA structure and function.

  4. Oligonucleotide and Parylene Surface Coating of Polystyrene and ePTFE for Improved Endothelial Cell Attachment and Hemocompatibility

    PubMed Central

    Schleicher, Martina; Hansmann, Jan; Elkin, Bentsian; Kluger, Petra J.; Liebscher, Simone; Huber, Agnes J. T.; Fritze, Olaf; Schille, Christine; Müller, Michaela; Schenke-Layland, Katja; Seifert, Martina; Walles, Heike; Wendel, Hans-Peter; Stock, Ulrich A.

    2012-01-01

    In vivo self-endothelialization by endothelial cell adhesion on cardiovascular implants is highly desirable. DNA-oligonucleotides are an intriguing coating material with nonimmunogenic characteristics and the feasibility of easy and rapid chemical fabrication. The objective of this study was the creation of cell adhesive DNA-oligonucleotide coatings on vascular implant surfaces. DNA-oligonucleotides immobilized by adsorption on parylene (poly(monoaminomethyl-para-xylene)) coated polystyrene and ePTFE were resistant to high shear stress (9.5 N/m2) and human blood serum for up to 96 h. Adhesion of murine endothelial progenitor cells, HUVECs and endothelial cells from human adult saphenous veins as well as viability over a period of 14 days of HUVECs on oligonucleotide coated samples under dynamic culture conditions was significantly enhanced (P < 0.05). Oligonucleotide-coated surfaces revealed low thrombogenicity and excellent hemocompatibility after incubation with human blood. These properties suggest the suitability of immobilization of DNA-oligonucleotides for biofunctionalization of blood vessel substitutes for improved in vivo endothelialization. PMID:22481939

  5. Clean Transformation of Ethanol to Useful Chemicals. The Behavior of a Gold-Modified Silicalite Catalyst.

    PubMed

    Falletta, Ermelinda; Rossi, Michele; Teles, Joaquim Henrique; Della Pina, Cristina

    2016-03-19

    Upon addition of gold to silicalite-1 pellets (a MFI-type zeolite), the vapor phase oxidation of ethanol could be addressed to acetaldehyde or acetic acid formation. By optimizing the catalyst composition and reaction conditions, the conversion of ethanol could be tuned to acetaldehyde with 97% selectivity at 71% conversion or to acetic acid with 78% selectivity at total conversion. Considering that unloaded silicalite-1 was found to catalyze the dehydration of ethanol to diethylether or ethene, a green approach for the integrated production of four important chemicals is herein presented. This is based on renewable ethanol as a reagent and a modular catalytic process.

  6. [Bio-based pharmaceutical polymers, possibility of their chemical modification and the applicability of modified polymers].

    PubMed

    Sebe, István; Szabó, Barnabás; Zelkó, Romána

    2012-01-01

    Different types of polymers are widely used in biomedical, pharmaceutical and cosmetic purposes. Their applications are curbed, if the polymers can not break down by the body or if the polymer itself is harmful or decompose to harmful material. Authors provide an overview of different types of pharmaceutical polymers of various sources, of the structural characterization and possibilities of their chemical modification and of the classical and instrumental analytical examination methods. The paper deals with the limitations of the use of biopolymers, as well.

  7. Modifying culture conditions in chemical library screening identifies alternative inhibitors of mycobacteria.

    PubMed

    Miller, Christopher H; Nisa, Shahista; Dempsey, Sandi; Jack, Cameron; O'Toole, Ronan

    2009-12-01

    In this study, application of a dual absorbance/fluorescence assay to a chemical library screen identified several previously unknown inhibitors of mycobacteria. In addition, growth conditions had a significant effect on the activity profile of the library. Some inhibitors such as Se-methylselenocysteine were detected only when screening was performed under nutrient-limited culture conditions as opposed to nutrient-rich culture conditions. We propose that multiple culture condition library screening is required for complete inhibitory profiling and for maximal antimycobacterial compound detection.

  8. The prebiotic synthesis of deoxythymidine oligonucleotides

    NASA Technical Reports Server (NTRS)

    Stephen-Sherwood, E.; Odom, D. G.; Oro, J.

    1974-01-01

    Deoxythymidine 5 prime-triphosphate in the presence of deoxythymidine 5 prime-phosphate, cyanamide and 4-amino-5-imidazole carboxamide polymerizes under drying conditions at moderate temperatures (60 to 90 C) to yield oligonucleotides of up to four units in length. Enzymatic analysis indicated that the majority of these oligomers contained natural 3 prime-5 prime phosphodiester bonds. This reaction offers a possible method for the formation of deoxyoligonucleotides under primitive earth conditions.

  9. Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta1

    PubMed Central

    Jordon-Thaden, Ingrid E.; Chanderbali, Andre S.; Gitzendanner, Matthew A.; Soltis, Douglas E.

    2015-01-01

    Premise of the study: Here we present a series of protocols for RNA extraction across a diverse array of plants; we focus on woody, aromatic, aquatic, and other chemically complex taxa. Methods and Results: Ninety-one taxa were subjected to RNA extraction with three methods presented here: (1) TRIzol/TURBO DNA-free kits using the manufacturer’s protocol with the addition of sarkosyl; (2) a combination method using cetyltrimethylammonium bromide (CTAB) and TRIzol/sarkosyl/TURBO DNA-free; and (3) a combination of CTAB and QIAGEN RNeasy Plant Mini Kit. Bench-ready protocols are given. Conclusions: After an iterative process of working with chemically complex taxa, we conclude that the use of TRIzol supplemented with sarkosyl and the TURBO DNA-free kit is an effective, efficient, and robust method for obtaining RNA from 100 mg of leaf tissue of land plant species (Embryophyta) examined. Our protocols can be used to provide RNA of suitable stability, quantity, and quality for transcriptome sequencing. PMID:25995975

  10. Evaluation of alkyne-modified isoprenoids as chemical reporters of protein prenylation.

    PubMed

    DeGraw, Amanda J; Palsuledesai, Charuta; Ochocki, Joshua D; Dozier, Jonathan K; Lenevich, Stepan; Rashidian, Mohammad; Distefano, Mark D

    2010-12-01

    Protein prenyltransferases catalyze the attachment of C15 (farnesyl) and C20 (geranylgeranyl) groups to proteins at specific sequences localized at or near the C-termini of specific proteins. Determination of the specific protein prenyltransferase substrates affected by the inhibition of these enzymes is critical for enhancing knowledge of the mechanism of such potential drugs. Here, we investigate the utility of alkyne-containing isoprenoid analogs for chemical proteomics experiments by showing that these compounds readily penetrate mammalian cells in culture and become incorporated into proteins that are normally prenylated. Derivatization via Cu(I) catalyzed click reaction with a fluorescent azide reagent allows the proteins to be visualized and their relative levels to be analyzed. Simultaneous treatment of cells with these probes and inhibitors of prenylation reveals decreases in the levels of some but not all of the labeled proteins. Two-dimensional electrophoretic separation of these labeled proteins followed by mass spectrometric analysis allowed several labeled proteins to be unambiguously identified. Docking experiments and density functional theory calculations suggest that the substrate specificity of protein farnesyl transferase may vary depending on whether azide- or alkyne-based isoprenoid analogs is employed. These results demonstrate the utility of alkyne-containing analogs for chemical proteomic applications.

  11. Evaluation of alkyne-modified isoprenoids as chemical reporters of protein prenylation

    PubMed Central

    DeGraw, Amanda J.; Palsuledesai, Charuta; Ochocki, Joshua D.; Dozier, Jonathan K.; Lenevich, Stepan; Rashidian, Mohammad; Distefano, Mark D.

    2010-01-01

    Protein prenyltransferases catalyze the attachment of C15 (farnesyl) and C20 (geranylgeranyl) groups to proteins at specific sequences localized at or near the C-termini of specific proteins. Determination of the specific protein prenyltransferase substrates affected by the inhibition of these enzymes is critical for enhancing knowledge of the mechanism of such potential drugs. Here we investigate the utility of alkyne-containing isoprenoid analogues for chemical proteomics experiments by showing that these compounds readily penetrate mammalian cells in culture and become incorporated into proteins that are normally prenylated. Derivatization via Cu(I) catalyzed Click reaction with a fluorescent azide reagent allows the proteins to be visualized and their relative levels to be analyzed. Simultaneous treatment of cells with these probes and inhibitors of prenylation reveals decreases in the levels of some but not all of the labeled proteins. Two-dimensional electrophoretic separation of these labeled proteins followed by mass spectrometric analysis allowed several labeled proteins to be unambiguously identified. Docking experiments and DFT calculations suggest that the substrate specificity of PFTase may vary depending on whether azide- or alkyne-based isoprenoid analogues are employed. These results demonstrate the utility of alkyne-containing analogues for chemical proteomic applications. PMID:21040496

  12. Improved actuation strain of PDMS-based DEA materials chemically modified with softening agents

    NASA Astrophysics Data System (ADS)

    Biedermann, Miriam; Blümke, Martin; Wegener, Michael; Krüger, Hartmut

    2015-04-01

    Dielectric elastomer actuators (DEAs) are smart materials that gained much in interest particularly in recent years. One active field of research is the improvement of their properties by modification of their structural framework. The object of this work is to improve the actuation properties of polydimethylsiloxane (PDMS)-based DEAs by covalent incorporation of mono-vinyl-terminated low-molecular PDMS chains into the PDMS network. These low-molecular units act as a kind of softener within the PDMS network. The loose chain ends interfere with the network formation and lower the network's density. PDMS films with up to 50wt% of low-molecular PDMS additives were manufactured and the chemical, mechanical, electrical, and electromechanical properties of these novel materials were investigated.

  13. Facile synthesis of graphene oxide-modified lithium hydroxide for low-temperature chemical heat storage

    NASA Astrophysics Data System (ADS)

    Yang, Xixian; Huang, Hongyu; Wang, Zhihui; Kubota, Mitsuhiro; He, Zhaohong; Kobayashi, Noriyuki

    2016-01-01

    LiOH·H2O nanoparticles supported on graphene oxide (GO) were facilely synthesized by a hydrothermal process. The mean diameter of nanoparticles on the integrated graphene sheet was about 5⿿10 nm showed by SEM and TEM results. XRD results suggested that the nanoparticles are in good agreement with the data of LiOH·H2O. The as-prepared sample showed a greatly enhanced thermal energy storage density and exhibit higher rate of heat release than pure lithium hydroxide, and thermal conductivity of composites increased due to the introduction of nano carbon. LiOH·H2O/GO nanocomposites are novel chemical heat storage materials for potential highly efficient energy system.

  14. Chemically Modified Interleukin-6 Aptamer Inhibits Development of Collagen-Induced Arthritis in Cynomolgus Monkeys

    PubMed Central

    Murakami, Ikuo; Ishikawa, Yuichi; Suzuki, Tomoki; Sumida, Shun-ichiro; Ibaragi, Shigeru; Kasai, Hayato; Horai, Naoto; Drolet, Daniel W.; Gupta, Shashi; Janjic, Nebojsa

    2016-01-01

    Interleukin-6 (IL-6) is a potent mediator of inflammatory and immune responses, and a validated target for therapeutic intervention of inflammatory diseases. Previous studies have shown that SL1026, a slow off-rate modified aptamer (SOMAmer) antagonist of IL-6, neutralizes IL-6 signaling in vitro. In the present study, we show that SL1026 delays the onset and reduces the severity of rheumatoid symptoms in a collagen-induced arthritis model in cynomolgus monkeys. SL1026 (1 and 10 mg/kg), administered q.i.d., delayed the progression of arthritis and the concomitant increase in serum IL-6 levels compared to the untreated control group. Furthermore, SL1026 inhibited IL-6-induced STAT3 phosphorylation ex vivo in T lymphocytes from human blood and IL-6-induced C-reactive protein and serum amyloid A production in human primary hepatocytes. Importantly, SOMAmer treatment did not elicit an immune response, as evidenced by the absence of anti-SOMAmer antibodies in plasma of treated monkeys. These results demonstrate that SOMAmer antagonists of IL-6 may be attractive agents for the treatment of IL-6-mediated diseases, including rheumatoid arthritis. PMID:26579954

  15. Ingestion and digestion studies in Tetrahymena pyriformis based on chemically modified microparticles.

    PubMed

    Dürichen, Hendrike; Siegmund, Lisa; Burmester, Anke; Fischer, Martin S; Wöstemeyer, Johannes

    2016-02-01

    Recognition of food and, in consequence, ingestion of digestible particles is a prerequisite for energy metabolism in Tetrahymena pyriformis. Understanding why some particles are ingested and digested, whereas others are not, is important for many fields of research, e.g. survival of pathogens in single-celled organisms or establishment of endosymbiotic relationships. We offered T. pyriformis synthetical bovine-serum-albumin (BSA)-methacrylate microparticles of approximately 5.5 μm diameter and studied the ciliates' ingestion and digestion behaviour. Different staining techniques as well as co-feeding with a transformant strain of Escherichia coli revealed that T. pyriformis considers these particles as natural food source and shows no feeding preference. Further, they are ingested at normal rates and may serve as sole food source. A pivotal advantage of these particles is the convenient modification of their surface by binding different ligands resulting in defined surface properties. Ingestion rate of modified microparticles either increased (additional BSA, enzymes) or decreased (amino acids). Furthermore, we investigated glycosylation patterns by lectin binding. By binding different substances to the surface in combination with various staining techniques, we provide a versatile experimental tool for elucidating details on food recognition and digestion that may allow to study evading digestion by pathogens or potential endosymbionts, too.

  16. NOx Direct Decomposition: Potentially Enhanced Thermodynamics and Kinetics on Chemically Modified Ferroelectric Surfaces

    NASA Astrophysics Data System (ADS)

    Kakekhani, Arvin; Ismail-Beigi, Sohrab

    2014-03-01

    NOx are regulated pollutants produced during automotive combustion. As part of an effort to design catalysts for NOx decomposition that operate in oxygen rich environment and permit greater fuel efficiency, we study chemistry of NOx on (001) ferroelectric surfaces. Changing the polarization at such surfaces modifies electronic properties and leads to switchable surface chemistry. Using first principles theory, our previous work has shown that addition of catalytic RuO2 monolayer on ferroelectric PbTiO3 surface makes direct decomposition of NO thermodynamically favorable for one polarization. Furthermore, the usual problem of blockage of catalytic sites by strong oxygen binding is overcome by flipping polarization that helps desorb the oxygen. We describe a thermodynamic cycle for direct NO decomposition followed by desorption of N2 and O2. We provide energy barriers and transition states for key steps of the cycle as well as describing their dependence on polarization direction. We end by pointing out how a switchable order parameter of substrate,in this case ferroelectric polarization, allows us to break away from some standard compromises for catalyst design(e.g. the Sabatier principle). This enlarges the set of potentially catalytic metals. Primary support from Toyota Motor Engineering and Manufacturing, North America, Inc.

  17. Chemical, Physical, and Mechanical Characterization of Isocyanate Cross-linked Amine-Modified Silica Aerogels

    NASA Technical Reports Server (NTRS)

    Katti, Atul; Shimpi, Nilesh; Roy, Samit; Lu, Hongbing; Fabrizio, Eve F.; Dass, Amala; Capadona, Lynn A.; Leventis, Nicholas

    2006-01-01

    We describe a new mechanically strong lightweight porous composite material obtained by encapsulating the skeletal framework of amine-modified silica aerogels with polyurea. The conformal polymer coating preserves the mesoporous structure of the underlying silica framework and the thermal conductivity remains low at 0.041 plus or minus 0.001 W m(sup -1 K(sup -1). The potential of the new cross-linked silica aerogels for load-carrying applications was determined through characterization of their mechanical behavior under compression, three-point bending, and dynamic mechanical analysis (DMA). A primary glass transition temperature of 130 C was identified through DMA. At room temperature, results indicate a hyperfoam behavior where in compression cross-linked aerogels are linearly elastic under small strains (less than 4%) and then exhibit yield behavior (until 40% strain), followed by densification and inelastic hardening. At room temperature the compressive Young's modulus and the Poisson's ratio were determined to be 129 plus or minus 8 MPa and 0.18, respectively, while the strain at ultimate failure is 77% and the average specific compressive stress at ultimate failure is 3.89 x 10(exp 5) N m kg(sup -1). The specific flexural strength is 2.16 x 10(exp 4) N m kg(sup -1). Effects on the compressive behavior of strain rate and low temperature were also evaluated.

  18. Using the Photolysis of Chemically Modified Gel Films Preparing ITO Fine Patterned Thin Films

    NASA Astrophysics Data System (ADS)

    Li, Ying; Zhao, Gaoyang; Zhang, Weihua; Chen, Yuanqing

    2006-06-01

    A novel technique for the fabrication of tin-doped indium oxide (ITO) fine patterning in sol-gel technology is presented in this paper. The fabricated ITO fine patterning could be obtained through a process which combines film fabrication with film etching. ITO films have good comprehensive property of visible transmittance and electrical conductivity, consequently they have been extensively used as coating electrodes. Indium nitrate (In(NO3)3.4.5H2O) and stannic chloride (SnCl4.5H2O) were used as starting materials which were modified with benzytone (BzAcH). The chelate complexes containing indium ions were produced during the process which of forming photosensitive ITO/BzAcH gel films through sol-gel technique. It was found that the gel films are sensitive to both the ultraviolet (UV) light irradiation and their solubility on solvents as well. For example, ethanol was reduced remarkably while the UV absorption peak disappeared with the dissociation of the chelate complexes correspondingly by means of UV-vis and IR spectrophotometers. Utilizing these characteristics, a fine pattern was obtained by irradiation of UV light on the ITO/BzAcH gel films through a pattern mask. of the fine patterned ITO films were heat treated at 500 °C for 15 min, the optical, electrical properties and the surface element components were examined by X-ray photoelectron spectroscopy (XPS) spectra in this work.

  19. 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

  20. Chemically modified cellulose strips with pyridoxal conjugated red fluorescent gold nanoclusters for nanomolar detection of mercuric ions.

    PubMed

    Bothra, Shilpa; Upadhyay, Yachana; Kumar, Rajender; Ashok Kumar, S K; Sahoo, Suban K

    2017-04-15

    One-pot approach was adopted for the synthesis of highly luminescent near-infrared (NIR)-emitting gold nanoclusters (AuNCs) using bovine serum albumin (BSA) as a protecting agent. The vitamin B6 cofactor pyridoxal was conjugated with the luminescent BSA-AuNCs through the free amines of BSA and then employed for the nanomolar detection of Hg(2+) in aqueous medium via selective fluorescence quenching of AuNCs. This nano-assembly was successfully applied for the real sample analysis of Hg(2+) in fish, tap water and river water. The study also presents chemically-modified cellulosic paper strips with the pyridoxal conjugated BSA-AuNCs for detecting Hg(2+) ion up to 1nM.

  1. The application of solid sorbents for the purification of aluminum contaminated chemicals used as modifiers in electrothermal atomic absorption spectrometry.

    PubMed

    Bulska, E; Pyrzyńska, K

    1996-06-01

    Various microcolumns with solid sorbents (ion exchange resins, functionalised cellulose sorbents, chelating resins) have been tested with respect to their ability for the purification of aluminum contaminated chemicals used as modifiers in electrothermal atomic absorption spectrometry. The purification of NaNO(3), Mg(NO(3))(2), K(2)SO(4) and (NH(4))(2)HPO(4) has been the most effective with an almost 100% efficiency, when Spheron-Oxine was used as chelating resin. The sorption of aluminum from KOH solution has been found to be very high (around 90%) for all investigated sorbents. However, the best results have been obtained with anion-exchange resins. It has been difficult to purify concentrated mineral acids (HCl, H(2)SO(4)). A retention of aluminum above 80% has been achieved only when Cellex P, Chelex 100 or Amberlite XAD-2 have been used.

  2. Chemically modified amino porphyrin/TiO2 for the degradation of Acid Black 1 under day light illumination.

    PubMed

    Krishnakumar, Balu; Balakrishna, Avula; Arranja, Cláudia T; Dias, Carlos M F; Sobral, Abilio J F N

    2017-04-05

    In this paper, for the first time, chemically modified 5,10,15,20-meso-tetra-(para-amino)-phenyl-porphyrin/TiO2 (TPAPP/TiO2) was prepared and used for the degradation of an azo dye Acid Black 1 (AB 1) under direct sunlight. Initially, TiO2 was prepared by sol-gel method. Before making a TPAPP/TiO2 composite, the surface modification of TiO2 was carried out with glycidoxypropyltrimethoxy silane (GPTMS) which acts as a coupling agent. This is an epoxy terminated silane and could easily bond to the amino group of TPAPP through epoxy cleavage. The formation of TPAPP/TiO2 was confirmed by different characterization techniques such as FT-IR, XRD, SEM and DRS. The photocatalytic activity of TiO2 was highly influenced by TPAPP. A mechanism was proposed for AB 1 degradation by TPAPP/TiO2 under sun light.

  3. A modified method for the determination of chemical oxygen demand (COD) for samples with high salinity and low organics.

    PubMed

    Vyrides, I; Stuckey, D C

    2009-01-01

    This study proposes a modification to the standard method for the determination of the chemical oxygen demand of samples with a salinity up to 40 g NaCl/L and low organic concentrations (20-230 mg COD/L). The masking of chloride by the use of a HgSO(4):Cl ratio of 20:1 prior to digestion, and the use of 3g K(2)Cr(2)O(7)/L in the digestion solution resulted in an error of less than 10% and 12% for samples containing 40 g NaCl/L at 20-190 mg COD/L and 230 mg COD/L, respectively. Comparison of the standard method with the new proposed method using a synthetic sewage highlights the large errors (50-85%) of the standard method in contrast to an error of less than 10% for the proposed modified method.

  4. Raman spectra investigation of the defects of chemical vapor deposited multilayer graphene and modified by oxygen plasma treatment

    NASA Astrophysics Data System (ADS)

    Li, Zongyao; Xu, Yu; Cao, Bing; Qi, Lin; He, Shunyu; Wang, Chinhua; Zhang, Jicai; Wang, Jianfeng; Xu, Ke

    2016-11-01

    Graphene, a two dimensional material, can be modified its properties by defects engineering. Here, we present Raman spectra studies of the multilayer graphene (MLG) fabricated by low-pressure chemical vapor deposition over copper foil, and report that the defects of MLG can be controlled by adjusting methane concentration. Moreover, MLG can be changed from metallic to semiconductoring properties by using oxygen plasma treatment, and we investigate the defects evolution of the graphene after exposing to oxygen plasma by Raman spectra. Our results indicate that the amount of defects in graphene can be changed by regulating the methane concentration and oxygen plasma exposure times, but the primary type of defect in MLG is still boundary-like defect. It is valuable for understanding the physics of defects evolution through artificially generated defects, and such defect engineering will greatly open up the future application of the novel material.

  5. Chemically modified amino porphyrin/TiO2 for the degradation of Acid Black 1 under day light illumination

    NASA Astrophysics Data System (ADS)

    Krishnakumar, Balu; Balakrishna, Avula; Arranja, Cláudia T.; Dias, Carlos M. F.; Sobral, Abilio J. F. N.

    2017-04-01

    In this paper, for the first time, chemically modified 5,10,15,20-meso-tetra-(para-amino)-phenyl-porphyrin/TiO2 (TPAPP/TiO2) was prepared and used for the degradation of an azo dye Acid Black 1 (AB 1) under direct sunlight. Initially, TiO2 was prepared by sol-gel method. Before making a TPAPP/TiO2 composite, the surface modification of TiO2 was carried out with glycidoxypropyltrimethoxy silane (GPTMS) which acts as a coupling agent. This is an epoxy terminated silane and could easily bond to the amino group of TPAPP through epoxy cleavage. The formation of TPAPP/TiO2 was confirmed by different characterization techniques such as FT-IR, XRD, SEM and DRS. The photocatalytic activity of TiO2 was highly influenced by TPAPP. A mechanism was proposed for AB 1 degradation by TPAPP/TiO2 under sun light.

  6. Glassy carbon electrode modified with a graphene oxide/poly(o-phenylenediamine) composite for the chemical detection of hydrogen peroxide.

    PubMed

    Nguyen, Van Hoa; Tran, Trung Hieu; Shim, Jae-Jin

    2014-11-01

    Conducting poly(o-phenylenediamine) (POPD)/graphene oxide (GO) composites were prepared using a facile and efficient method involving the in-situ polymerization of OPD in the presence of GO in an aqueous medium. Copper sulfate was used as an oxidative initiator for the polymerization of OPD. Scanning electron microscopy and transmission electron microscopy images showed that POPD microfibrils were formed and distributed relatively uniformly with GO sheets in the obtained composites. X-ray diffraction results revealed the highly crystal structure of POPD. This composite exhibited good catalytic activity and stability. These results highlight the potential applications of POPD/GO composites as excellent electrochemical sensors. The composites were used to modify glass carbon electrodes for the chemical detection of hydrogen peroxide in aqueous media.

  7. Dye-sensitized solar cells with modified TiO2 surface chemical states: The role of Ti3+

    NASA Astrophysics Data System (ADS)

    Yu, Yang; Wu, Kunjie; Wang, Deliang

    2011-11-01

    Dye-sensitized solar cells (DSSCs) with TiO2 electrodes, which were modified to have different surface chemical states, were fabricated. The DSSCs had an ultra-flat TiO2 electrode, on which only a mono-layer dye was attached. The cell I-V measurement showed that Ti3+ ion had a dramatic effect on cell performance. The efficiency of a DSSC was shown to have a strong correlation with the concentration of the Ti3+ surface state, it decreased almost linearly with increased Ti3+ concentration. The oxygen vacancy-Ti3+ defect served as electron recombination center and decreased both the open-circuit voltage and the fill factor.

  8. Applicability of Vacuum Impregnation to Modify Physico-Chemical, Sensory and Nutritive Characteristics of Plant Origin Products—A Review

    PubMed Central

    Radziejewska-Kubzdela, Elżbieta; Biegańska-Marecik, Róża; Kidoń, Marcin

    2014-01-01

    Vacuum impregnation is a non-destructive method of introducing a solution with a specific composition to the porous matrices of fruit and vegetables. Mass transfer in this process is a result of mechanically induced differences in pressure. Vacuum impregnation makes it possible to fill large volumes of intercellular spaces in tissues of fruit and vegetables, thus modifying physico-chemical properties and sensory attributes of products. This method may be used, e.g., to reduce pH and water activity of the product, change its thermal properties, improve texture, color, taste and aroma. Additionally, bioactive compounds may be introduced together with impregnating solutions, thus improving health-promoting properties of the product or facilitating production of functional food. PMID:25244012

  9. Adsorption of sulfur dioxide on natural clinoptilolite chemically modified with salt solutions.

    PubMed

    Ivanova, Emilia; Koumanova, Bogdana

    2009-08-15

    Various ion exchange forms of preliminary partly decationised zeolite (hydrogen forms) were obtained by indirect modification with metal salt solutions, as well as by direct treatment of natural clinoptilolite taken from Bulgarian deposits. Direct modification leads to a higher extent of samples enrichment with corresponding ion. Independently of the conditions, the alkaline and alkaline earth metal ions (especially sodium and calcium) were inserted at a greater extent, while the transitional metals-at a comparatively lower extent. The cationic forms of clinoptilolite were used for adsorption and desorption experiments. The breakthrough adsorption curves and the concentration curves at temperature-programmed desorption were obtained and compared. The breakthrough and saturation times, the adsorption capacity, the distribution coefficient, the adsorbed SO(2), the portions desorbed as SO(2) and SO(3), respectively, as well as the not desorbed portion of SO(2), were determined using these curves. It was established that a definite quantity of undesorbed SO(2) has remained in the zeolite forms modified with transitional metal cations. This statement was proved not only by the comparison between the adsorbed and desorbed quantities, but also by three-cycle adsorption-desorption experiments for the Cu(2+)-form. The results demonstrate a decrease in the capacity for each following cycle in an extent similar to the undesorbed SO(2) quantity. It was not observed a visible difference in the values of the distribution coefficients for adsorption on identical cation forms, directly or indirectly obtained. However, the breakthrough time of the samples obtained by ion exchange of the hydrogen form was longer in all cases. Definite quantities of desorbed SO(3) were registered for all forms, except for the natural clinoptilolite and the samples enriched with alkaline and alkaline earth metal cations.

  10. Surface Charge, Electroosmotic Flow and DNA Extension in Chemically Modified Thermoplastic Nanoslits and Nanochannels

    PubMed Central

    Uba, Franklin I.; Pullagurla, Swathi R.; Sirasunthorn, Nichanun; Wu, Jiahao; Park, Sunggook; Chantiwas, Rattikan; Cho, Yoonkyoung; Shin, Heungjoo; Soper, Steven A.

    2014-01-01

    Thermoplastics have become attractive alternatives to glass/quartz for microfluidics, but the realization of thermoplastic nanofluidic devices has been slow in spite of the rather simple fabrication techniques that can be used to produce these devices. This slow transition has in part been attributed to insufficient understanding of surface charge effects on the transport properties of single molecules through thermoplastic nanochannels. We report the surface modification of thermoplastic nanochannels and an assessment of the associated surface charge density, zeta potential and electroosmotic flow (EOF). Mixed-scale fluidic networks were fabricated in poly(methylmethacrylate), PMMA. Oxygen plasma was used to generate surface-confined carboxylic acids with devices assembled using low temperature fusion bonding. Amination of the carboxylated surfaces using ethylenediamine (EDA) was accomplished via EDC coupling. XPS and ATR-FTIR revealed the presence of carboxyl and amine groups on the appropriately prepared surfaces. A modified conductance equation for nanochannels was developed to determine their surface conductance and was found to be in good agreement with our experimental results. The measured surface charge density and zeta potential of these devices were lower than glass nanofluidic devices and dependent on the surface modification adopted, as well as the size of the channel. This property, coupled to an apparent increase in fluid viscosity due to nanoconfinement, contributed to the suppression of the EOF in PMMA nanofluidic devices by an order of magnitude compared to the micro-scale devices. Carboxylated PMMA nanochannels were efficient for the transport and elongation of λ-DNA while these same DNA molecules were unable to translocate through aminated nanochannels. PMID:25369728

  11. Development of Green Solvent Modified Zeolite (GSMZ) for the Removal of Chemical Contaminants and Pathogens from Water

    NASA Astrophysics Data System (ADS)

    Li, Z.; Stapleton, E. R.; Xu, S.

    2012-12-01

    Sorption represents an important strategy in the remediation of groundwater contamination. As a naturally-occurring mineral with large cation exchange capacity, zeolite is negatively charged and has been widely used as an inexpensive and effective sorbent for the removal of positively charged contaminants such as heavy metals from water. The negative charges of zeolite, however, make it generally ineffective in the sorption of anionic contaminants such as chromate and arsenate as well as many pathogens. In this research, we used the imidazolium group of chemicals, which are considered as "green solvents" and differ from the surfactants used in previous studies, to modify zeolite. Both batch and column experiments were performed to evaluate the effectiveness of GSMZ in the removal of representative anionic pollutant (i.e., Cr) and bacterium (i.e., Eschericha coli) under various water chemistry conditions. Our experimental results showed that the adsorption of Cr on GSMZ was fast (equilibrium was reached within ~5 min) and the capacity of GSMZ to remove chromate (>1000 mg/kg) was ~100% higher than surfactant modified zeolite (SMZ). GSMZ was also found to be very effective in the removal of E. coli. As pH was found to have minimal effects on the adsorption of chromium on GSMZ, higher ionic strength could lower the adsorption capacity of chromium by GSMZ.

  12. Efficient acetone-butanol-ethanol production (ABE) by Clostridium acetobutylicum XY16 immobilized on chemically modified sugarcane bagasse.

    PubMed

    Kong, Xiangping; He, Aiyong; Zhao, Jie; Wu, Hao; Jiang, Min

    2015-07-01

    Sugarcane bagasse was chemically modified by polyethylenimine (PEI) and glutaraldehyde (GA) and then used as a support to immobilize Clostridium acetobutylicum XY16 in the process of butanol production. Compared with batch fermentation using unmodified sugarcane bagasse, 22.3 g/L total solvents were produced by cells immobilized on 4 g/L PEI treated sugarcane bagasse with high solvent productivity of 0.62 g/(L h) and glucose consumption rate of 1.67 g/(L h). Improvement of 14, 43, and 37 % in total solvent titer, solvent productivity and glucose consumption rate was observed, respectively. Enhanced solvent production of 25.14 g/L was obtained when using a high concentration of glucose of 80 g/L. Continuous fermentation was studied using PEI/GA modified sugarcane bagasse as immobilization support with a range of dilution which rates from 0.2 to 2.5 to find an optimal condition. The maximum solvent productivity of 11.32 g/(L h) was obtained at a high dilution rate of 2.0 h(-1).

  13. Factors affecting protein transfer into surfactant-isooctane solution: a case study of extraction behavior of chemically modified cytochrome c.

    PubMed

    Ono, T; Goto, M

    1998-01-01

    The extraction mechanism of proteins by surfactant molecules in an organic solvent has been investigated using a chemically modified protein. We conducted guanidylation on lysine residues of cytochrome c by replacing their amino groups with homoarginine to enhance the protein-surfactant interaction. Results have shown that guanidylated cytochrome c readily forms a hydrophobic complex with dioleyl phosphoric acid (DOLPA) through hydrogen bonding between the phosphate moiety and the guanidinium groups. Although improved protein-surfactant interaction activated the formation of a hydrophobic complex at the interface, it could not improve the protein transfer in isooctane. It has been established that the protein extraction mechanism using surfactant molecules is mainly governed by two processes: formation of an interfacial complex at the oil-water interface and the subsequent solubilization of the complex into the organic phase. In addition, a kinetic study demonstrated that guanidylation of lysine accelerated the initial extraction rate of cytochrome c. This fact implies that the protein transferability from aqueous phase into organic phase depends on the protein-surfactant interaction which can be modified by protein surface engineering.

  14. The chemical synthesis of α-conotoxins and structurally modified analogs with enhanced biological stability.

    PubMed

    Banerjee, Jayati; Gyanda, Reena; Chang, Yi-Pin; Armishaw, Christopher J

    2013-01-01

    α-Conotoxins are peptide neurotoxins isolated from the venom ducts of carnivorous marine cone snails that exhibit exquisite pharmacological potency and selectivity for various nicotinic acetylcholine receptor subtypes. As such, they are important research tools and drug leads for treating various diseases of the central nervous system, including pain and tobacco addiction. Despite their therapeutic potential, the chemical synthesis of α-conotoxins for use in structure-activity relationship studies is complicated by the possibility of three disulfide bond isomers, where inefficient folding methods can lead to a poor recovery of the pharmacologically active isomer. In order to achieve higher yields of the native isomer, especially in high-throughput syntheses it is necessary to select appropriate oxidative folding conditions. Moreover, the poor biochemical stability exhibited by α-conotoxins limits their general therapeutic applicability in vivo. Numerous strategies to enhance their stability including the substitution of disulfide bond with diselenide bond and N-to-C cyclization via an oligopeptide spacer have successfully overcome these limitations. This chapter describes methods for performing both selective and nonselective disulfide bond oxidation strategies for controlling the yields and formation of α-conotoxin disulfide bond isomers, as well as methods for the production of highly stable diselenide-containing and N-to-C cyclized conotoxin analogs.

  15. Enhanced triboelectric nanogenerators and triboelectric nanosensor using chemically modified TiO2 nanomaterials.

    PubMed

    Lin, Zong-Hong; Xie, Yannan; Yang, Ya; Wang, Sihong; Zhu, Guang; Wang, Zhong Lin

    2013-05-28

    Mechanical energy harvesting based on triboelectric effect has been proven to be a simple, cost-effective, and robust method for electricity generation. In this study, we developed a rationally designed triboelectric nanogenerator (TENG) by utilizing the contact electrification between a polytetrafluoroethylene (PTFE) thin film and a layer of TiO2 nanomaterial (nanowire and nanosheet) array. The as-developed TENG was systematically studied and demonstrated as a self-powered nanosensor toward catechin detection. The high sensitivity (detection limit of 5 μM) and selectivity are achieved through a strong interaction between Ti atoms of TiO2 nanomaterial and enediol group of catechin. The output voltage and current density were increased by a factor of 5.0 and 2.9, respectively, when adsorbed with catechin of a saturated concentration, because of the charge transfer from catechin to TiO2. This study demonstrates the possibility of improving the electrical output of TENG through chemical modification.

  16. Physisorption of DNA molecules on chemically modified single-walled carbon nanotubes with and without sonication.

    PubMed

    Umemura, Kazuo; Ishibashi, Yu; Oura, Shusuke

    2016-09-01

    We investigated the physisorption phenomenon of single-stranded DNA (ssDNA) molecules onto two types of commercially available chemically functionalized single-walled carbon nanotubes (SWNTs) by atomic force microscopy (AFM) and agarose gel electrophoresis. We found that DNA molecules can adsorb on the water-soluble SWNT surfaces without sonication, although sonication treatment has been used for hybridization of DNA and SWNTs in many previous studies. Using our method, damage of DNA molecules by sonication can be avoided. On the other hand, the amount of DNA molecules adsorbed on SWNT surfaces increased when the samples were sonicated. This fact suggests that the sonication is effective not only at debundling of SWNTs, but also at assisting DNA adsorption. Furthermore, DNA adsorption was affected by the types of functionalized SWNTs. In the case of SWNTs functionalized with polyethylene glycol (PEG-SWNT), physisorption of ssDNA molecules was confirmed only by agarose-gel electrophoresis. In contrast, amino-terminated SWNTs (NH2-SWNTs) showed a change in the height distribution profile based on AFM observations. These results suggest that DNA molecules tended to adsorb to NH2-SWNT surfaces, although DNA molecules can also adsorb on PEG-SWNT surfaces. Our results revealed fundamental information for developing nanobiodevices using hybrids of DNA and SWNTs.

  17. Chemically modified diamond-like carbon (DLC) for protein enrichment and profiling by MALDI-MS.

    PubMed

    Najam-ul-Haq, M; Rainer, M; Huck, C W; Ashiq, M N; Bonn, G K

    2012-08-01

    The development of new high throughput methods based on different materials with chemical modifications for protein profiling of complex mixtures leads towards biomarkers; used particularly for early diagnosis of a disease. In this work, diamond-like carbon (DLC) is developed and optimized for serum protein profiling by matrix-assisted laser/desorption ionization mass spectrometry (MALDI-MS). This study is carried out in connection with a material-based approach, termed as material-enhanced laser desorption ionization mass spectrometry. DLC is selected as carrier surface which provides large surface to volume ratio and offers high sensitivity. DLC has a dual role of working as MALDI target while acting as an interface for protein profiling by specifically binding peptides and proteins out of serum samples. Serum constituents are bound through immobilized metal ion affinity chromatography (IMAC) functionality, created through glycidyl methacrylate polymerization under ultraviolet light followed by further derivatization with iminodiacetic acid and copper ion loading. Scanning electron microscopy highlights the morphological characteristics of DLC surface. It could be demonstrated that IMAC functionalized DLC coatings represent a powerful material in trapping biomolecules for their further analysis by MALDI-MS resulting in improved sensitivity, specificity and capacity in comparison to other protein-profiling methods.

  18. Chemically modified nylons as supports for enzyme immobilization. Polyisonitrile-nylon

    PubMed Central

    Goldstein, Leon; Freeman, Amihay; Sokolovsky, Mordechai

    1974-01-01

    Four-component condensations between amine, carboxyl, isocyanide and aldehyde lead to the formation of N-substituted amides (Ugi, 1962). The present paper describes the use of such condensations for the introduction of chemically reactive groups on to the polyamide backbone of nylon. Polyisonitrile-nylon was synthesized by partial hydrolysis of nylon-6 powder, followed by resealing of the newly formed −CO2... NH2− pairs via a four-component condensation, by using acetaldehyde and 1,6-di-isocyanohexane. Polyisonitrile-nylon could also be converted into a diazotizable arylamino derivative, polyaminoaryl-nylon, by a four-component condensation by using a bifunctional amine, pp′-diaminodiphenylmethane, in the presence of an aldehyde and a carboxylate compound. The versatility of four-component condensations involving the isocyanide functional group of polyisonitrile-nylon allowed coupling of proteins, in an aqueous medium at neutral pH, through either their amino or carboxyl groups. Trypsin and papain were bound to polyisonitrile-nylon through their amino groups by a four-component condensation by using acetaldehyde and acetate; conversely, succinyl-(3-carboxypropionyl-)trypsin, pepsin and papain were coupled through their carboxyl groups in the presence of acetaldehyde and an amine (Tris). Diazotized polyaminoaryl-nylon could be utilized for the immobilization of papain, via the tyrosine residues of the enzyme. PMID:4618475

  19. Growth of aligned ZnO nanowires via modified atmospheric pressure chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Zhao, Yuping; Li, Chengchen; Chen, Mingming; Yu, Xiao; Chang, Yunwei; Chen, Anqi; Zhu, Hai; Tang, Zikang

    2016-12-01

    In this work, we report the growth of high-quality aligned ZnO nanowires via a facile atmospheric pressure chemical vapor deposition (CVD) method. The CVD reactor chamber used was more complicated than a conventional one due to the quartz boats loaded with sources (ZnO/C) and substrates being inserted into a semi-open quartz tube, and then placed inside the CVD reactor. The semi-open quartz tube played a very important role in growing the ZnO nanowires, and demonstrated that the transportation properties of Zn and O vapor differ from those in the conventional CVD reactor chamber. Aligned ZnO nanowires were successfully obtained, though they were only found at substrates located upstream. The very high crystalline quality of the obtained ZnO nanowires was demonstrated by high-resolution transmission electron microscopy and room temperature photoluminescence investigations. Such ZnO nanowires with high crystalline quality may provide opportunities for the fabrication of ZnO-based nano-devices in future.

  20. Epithelial cell morphology and adhesion on diamond films deposited and chemically modified by plasma processes.

    PubMed

    Rezek, Bohuslav; Ukraintsev, Egor; Krátká, Marie; Taylor, Andrew; Fendrych, Frantisek; Mandys, Vaclav

    2014-09-01

    The authors show that nanocrystalline diamond (NCD) thin films prepared by microwave plasma enhanced chemical vapor deposition apparatus with a linear antenna delivery system are well compatible with epithelial cells (5637 human bladder carcinoma) and significantly improve the cell adhesion compared to reference glass substrates. This is attributed to better adhesion of adsorbed layers to diamond as observed by atomic force microscopy (AFM) beneath the cells. Moreover, the cell morphology can be adjusted by appropriate surface treatment of diamond by using hydrogen and oxygen plasma. Cell bodies, cytoplasmic rims, and filopodia were characterized by Peakforce AFM. Oxidized NCD films perform better than other substrates under all conditions (96% of cells adhered well). A thin adsorbed layer formed from culture medium and supplemented with fetal bovine serum (FBS) covered the diamond surface and played an important role in the cell adhesion. Nevertheless, 50-100 nm large aggregates formed from the RPMI medium without FBS facilitated cell adhesion also on hydrophobic hydrogenated NCD (increase from 23% to 61%). The authors discuss applicability for biomedical uses.

  1. A 3D Chemically Modified Graphene Hydrogel for Fast, Highly Sensitive, and Selective Gas Sensor

    PubMed Central

    Wu, Jin; Tao, Kai; Guo, Yuanyuan; Li, Zhong; Wang, Xiaotian; Luo, Zhongzhen; Du, Chunlei; Chen, Di; Norford, Leslie K.

    2016-01-01

    Reduced graphene oxide (RGO) has proved to be a promising candidate in high‐performance gas sensing in ambient conditions. However, trace detection of different kinds of gases with simultaneously high sensitivity and selectivity is challenging. Here, a chemiresistor‐type sensor based on 3D sulfonated RGO hydrogel (S‐RGOH) is reported, which can detect a variety of important gases with high sensitivity, boosted selectivity, fast response, and good reversibility. The NaHSO3 functionalized RGOH displays remarkable 118.6 and 58.9 times higher responses to NO2 and NH3, respectively, compared with its unmodified RGOH counterpart. In addition, the S‐RGOH sensor is highly responsive to volatile organic compounds. More importantly, the characteristic patterns on the linearly fitted response–temperature curves are employed to distinguish various gases for the first time. The temperature of the sensor is elevated rapidly by an imbedded microheater with little power consumption. The 3D S‐RGOH is characterized and the sensing mechanisms are proposed. This work gains new insights into boosting the sensitivity of detecting various gases by combining chemical modification and 3D structural engineering of RGO, and improving the selectivity of gas sensing by employing temperature dependent response characteristics of RGO for different gases. PMID:28331786

  2. Chemically modified carbon nanostructures for electrospun thin film polymer-nanocomposites

    NASA Astrophysics Data System (ADS)

    Behler, Kristopher

    Various nano-structured carbon materials, most notably carbon nanotubes (CNTs) and nanodiamonds (NDs), are used in preparing polymer-nanocomposites. Surface-modified NDs, multi-walled (MWCNT), double-walled (DWCNT) and triple-walled (TWCNT) have been incorporated into polymer matrix systems. Treatments include vacuum annealing, thermal oxidation in air and acid treatments (nitric and sulfuric acids for the CNTs and hydrochloric acid for NDs). Acid treatments have led to carboxylic group formation on the surface of CNTs and NDs, promoting improved dispersion. As-received, thermal and acid treated MWCNTs have been incorporated into polyvinylidene fluoride and polyamide-11 and -12 electrospun nanofibers with little improvements in the electrical conductivity. To improve the electrical properties of CNT-polyamide composites, negatively charged CNTs were self-assembled on the nanofiber's surface. At a 2 wt% loading, the electrical resistance of the nanofibers decreased two orders of magnitude (to 154 O/sq) by increasing the number of MWCNT self-assembly depositions and then another three orders of magnitude by using DWCNTs (700 O/sq). Further heat treatments were used to fuse (110°C) and completely remove the nanofibers (450°C) to produce ˜150 nm coatings with improved transparency, ˜96% transmission, in the visible spectrum. HCl-purified NDs have also been successfully incorporated in polyamide 11 and polyacrylonitrile nanofibers leading to improvements in the mechanical properties of the fibers. Extremely high loadings of up to 90 wt% ND in the polymer have also been achieved. The Young's modulus of the ND-polyamide-11 composites increased by a factor of four, the hardness doubled and the scratch resistance was improved such that a load three times larger than used on the pure polymer was required to generate a scratch of the identical depth in the composite material. The ND-polymer films have shown about a 50% decrease in transmission in the UV-range, making

  3. Phase Stability of Ce-Modified La2Zr2O7 Coatings and Chemical Compatibility with YSZ

    NASA Astrophysics Data System (ADS)

    Wu, Qiong; Ji, Xiaojuan; Peng, Haoran; Ren, Xianjing; Yu, Yueguang

    2016-04-01

    Ce-modified La2Zr2O7 powders, i.e., La2Zr2O7 (LZ), La2(Zr0.7Ce0.3)2O7 (LZ7C3), and La2(Zr0.3Ce0.7)2O7 (LZ3C7), were used to produce thermal barrier coatings by atmospheric plasma spray process. The chemical compatibility of the CeO2-doped La2Zr2O7 with the traditional YSZ was investigated in LZ-YSZ powder mixtures and LZ-YSZ bilayer coatings by x-ray diffraction and scanning electron microscope. The powder mixtures and coatings were aged at 1200 and 1300 °C for 100 h. The results showed that LZ and LZ7C3 presented single pyrochlore structure after the heat treatments at both 1200 and 1300 °C. For LZ3C7, however, fluorite structure was observed at 1300 °C, indicating a poor phase stability of LZ3C7 at the elevated temperature. The results further showed that La2(Zr0.3Ce0.7)2O7 reacted with YSZ in the bilayer ceramic coatings due to the diffusion of cerium, zirconium, and yttrium. While for La2Zr2O7(LZ) and La2(Zr0.7Ce0.3)2O7, a better chemical compatibility with YSZ was shown.

  4. Development of pH Sensitive Nanoparticles for Intestinal Drug Delivery Using Chemically Modified Guar Gum Co-Polymer

    PubMed Central

    Varma, Vegesna Naga Sravan Kumar; Shivakumar, Hosakote Gurumalappa; Balamuralidhara, Veerna; Navya, Manne; Hani, Umme

    2016-01-01

    The aim of the research work was to chemically modify guargum (GG) as a pH sensitive co-polymer and formulating intestinal targeting ESO nanoparticles (NPs) using the synthesized co-polymer. Poly acrylamide-grafted-guar gum (PAAm-g-GG) co-polymer was synthesized by free radical polymerization. Chemical modification of PAAm-g-GG by alkaline hydrolysis results in formation of a pH-sensitive co-polymer. The effect of GG and acryl amide (AAm) on grafting was studied. Esomeprazole magnesium (ESO) loaded pH sensitive NPs were prepared by nano-emulsification polymer crosslinking method and characterized. Sixteen formulations were prepared and the concentration of process variables wasvaried to obtain nanoparticles of 200-600 nm. The NPs were found to be homogenous in size distribution. The encapsulation efficiency and drug loading ranged from 33.2% to 50.1% and 12.2% to 17.2% respectively. Particle size, encapsulation efficiency and drug loading increasedalong with co-polymer concentration. In-vitro release studies at pH 1.2 for 2 h, followed by pH 6.8 showed that environment pH significantly affected the drug release. SEM has shown that NPsare spherical with smooth surface. The pH sensitive PAAm-g-GGNPs resisted the initial release of the drug from the drug loaded NPs in acidic pH and delayed the release process to a longer period in alkaline environment. PMID:27610149

  5. A chemically modified [alpha]-amylase with a molten-globule state has entropically driven enhanced thermal stability

    SciTech Connect

    Siddiqui, Khawar Sohail; Poljak, Anne; De Francisci, Davide; Guerriero, Gea; Pilak, Oliver; Burg, Dominic; Raftery, Mark J.; Parkin, Don M.; Trewhella, Jill; Cavicchioli, Ricardo

    2010-11-15

    The thermostability properties of TAA were investigated by chemically modifying carboxyl groups on the surface of the enzyme with AMEs. The TAA{sub MOD} exhibited a 200% improvement in starch-hydrolyzing productivity at 60 C. By studying the kinetic, thermodynamic and biophysical properties, we found that TAA{sub MOD} had formed a thermostable, MG state, in which the unfolding of the tertiary structure preceded that of the secondary structure by at least 20 C. The X-ray crystal structure of TAA{sub MOD} revealed no new permanent interactions (electrostatic or other) resulting from the modification. By deriving thermodynamic activation parameters of TAA{sub MOD}, we rationalised that thermostabilisation have been caused by a decrease in the entropy of the transition state, rather than being enthalpically driven. Far-UV CD shows that the origin of decreased entropy may have arisen from a higher helical content of TAA{sub MOD}. This study provides new insight into the intriguing properties of an MG state resulting from the chemical modification of TAA.

  6. Enhanced compatibility of chemically modified titanium surface with periodontal ligament cells

    NASA Astrophysics Data System (ADS)

    Kado, T.; Hidaka, T.; Aita, H.; Endo, K.; Furuichi, Y.

    2012-12-01

    A simple chemical modification method was developed to immobilize cell-adhesive molecules on a titanium surface to improve its compatibility with human periodontal ligament cells (HPDLCs).The polished titanium disk was immersed in 1% (v/v) p-vinylbenzoic acid solution for 2 h to introduce carboxyl groups onto the surface. After rinsing with distilled deionized water, the titanium disk was dipped into 1.47% 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide solution containing 0.1 mg/ml Gly-Arg-Gly-Asp-Ser (GRGDS), human plasma fibronectin (pFN), or type I collagen from calf skin (Col) to covalently immobilize the cell-adhesive molecules on the titanium surface via formation of peptide bonds. X-ray photoelectron spectroscopy analyses revealed that cell-adhesive molecules were successfully immobilized on the titanium surfaces. The Col-immobilized titanium surface revealed higher values regarding nano rough characteristics than the as-polished titanium surface under scanning probe microscopy. The number of HPDLCs attached to both the pFN- and Col-immobilized titanium surfaces was twice that attached to the as-polished titanium surfaces. The cells were larger with the cellular processes that stretched to a greater extent on the pFN- and Col-immobilized titanium surfaces than on the as-polished titanium surface (p < 0.05). HPDLCs on the Col-immobilized titanium surfaces showed more extensive expression of vinculin at the tips of cell projections and more contiguously along the cell outline than on the as-polished, GRGDS-immobilized and pFN-immobilized titanium surfaces. It was concluded that cell-adhesive molecules successfully immobilized on the titanium surface and improved the compatibility of the surface with HPDLCs. The Col-immobilized titanium surface could be used for forming ligament-like tissues around titanium dental implants.

  7. The effect of chemically modified alginates on macrophage phenotype and biomolecule transport.

    PubMed

    Bygd, Hannah C; Bratlie, Kaitlin M

    2016-07-01

    Macrophage (MΦ) reprogramming has received significant attention in applications such as cancer therapeutics and tissue engineering where the host immune response to biomaterials is crucial in determining the success or failure of an implanted device. Polymeric systems can potentially be used to redirect infiltrating M1 MΦs toward a proangiogenic phenotype. This work exploits the concept of MΦ reprogramming in the engineering of materials for improving the longevity of tissue engineering scaffolds. We have investigated the effect of 13 different chemical modifications of alginate on MΦ phenotype. Markers of the M1 response-tumor necrosis factor-α (TNF-α) and inducible nitric oxide synthase-and the M2 response-arginase-were measured and used to determine the ability of the materials to alter MΦ phenotype. It was found that some modifications were able to reduce the pro-inflammatory response of M1 MΦs, others appeared to amplify the M2 phenotype, and the results for two materials suggested they were able to reprogram a MΦ population from M1 to M2. These findings were supplemented by studies done to examine the permselectivity of the materials. Diffusion of TNF-α was completely prevented through some of these materials, while up to 84% was found to diffuse through others. The diffusion of insulin through the materials was statistically consistent. These results suggest that the modification of these materials might alter mass transport in beneficial ways. The ability to control polarization of MΦ phenotypes with immunoprotective materials has the potential to augment the success of tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1707-1719, 2016.

  8. Template-Directed Ligation of Peptides to Oligonucleotides

    NASA Technical Reports Server (NTRS)

    Bruick, Richard K.; Dawson, Philip E.; Kent, Stephen BH; Usman, Nassim; Joyce, Gerald F.

    1996-01-01

    Synthetic oligonucleotides and peptides have enjoyed a wide range of applications in both biology and chemistry. As a consequence, oligonucleotide-peptide conjugates have received considerable attention, most notably in the development of antisense constructs with improved pharmacological properties. In addition, oligonucleotide-peptide conjugates have been used as molecular tags, in the assembly of supramolecular arrays and in the construction of encoded combinatorial libraries. To make these chimeric molecules more accessible for a broad range of investigations, we sought to develop a facile method for joining fully deprotected oligonucleotides and peptides through a stable amide bond linkage. Furthermore, we wished to make this ligation reaction addressable, enabling one to direct the ligation of specific oligonucleotide and peptide components.To confer specificity and accelerate the rate of the reaction, the ligation process was designed to be dependent on the presence of a complementary oligonucleotide template.

  9. Electron Transfer Reactivity Patterns at Chemically Modified Electrodes: Fundamentals and Application to the Optimization of Redox Recycling Amplification Systems

    SciTech Connect

    Bergren, Adam Johan

    2006-01-01

    Electroanalytical chemistry is often utilized in chemical analysis and Fundamental studies. Important advances have been made in these areas since the advent of chemically modified electrodes: the coating of an electrode with a chemical film in order to impart desirable, and ideally, predictable properties. These procedures enable the exploitation of unique reactivity patterns. This dissertation presents studies that investigate novel reaction mechanisms at self-assembled monolayers on gold. In particular, a unique electrochemical current amplification scheme is detailed that relies on a selective electrode to enable a reactivity pattern that results in regeneration of the analyte (redox recycling). This regenerating reaction can occur up to 250 times for each analyte molecule, leading to a notable enhancement in the observed current. The requirements of electrode selectivity and the resulting amplification and detection limit improvements are described with respect to the heterogeneous and homogeneous electron transfer rates that characterize the system. These studies revealed that the heterogeneous electrolysis of the analyte should ideally be electrochemically reversible, while that for the regenerating agent should be held to a low level. Moreover, the homogeneous reaction that recycles the analyte should occur at a rapid rate. The physical selectivity mechanism is also detailed with respect to the properties of the electrode and redox probes utilized. It is shown that partitioning of the analyte into/onto the adlayer leads to the extraordinary selectivity of the alkanethiolate monolayer modified electrode. Collectively, these studies enable a thorough understanding of the complex electrode mechanism required for successful redox recycling amplification systems, Finally, in a separate (but related) study, the effect of the akyl chain length on the heterogeneous electron transfer behavior of solution-based redox probes is reported, where an odd-even oscillation

  10. Fragmentation and reactivity in collisions of protonated diglycine with chemically modified perfluorinated alkylthiolate-self-assembled monolayer surfaces

    SciTech Connect

    Barnes, George L.; Yang Li; Hase, William L.; Young, Kelsey

    2011-03-07

    Direct dynamics simulations are reported for quantum mechanical (QM)/molecular mechanical (MM) trajectories of N-protonated diglycine (gly{sub 2}-H{sup +}) colliding with chemically modified perfluorinated octanethiolate self-assembled monolayer (SAM) surfaces. The RM1 semiempirical theory is used for the QM component of the trajectories. RM1 activation and reaction energies were compared with those determined from higher-level ab initio theories. Two chemical modifications are considered in which a head group (-COCl or -CHO) is substituted on the terminal carbon of a single chain of the SAM. These surfaces are designated as the COCl-SAM and CHO-SAM, respectively. Fragmentation, peptide reaction with the SAM, and covalent linkage of the peptide or its fragments with the SAM surface are observed. Peptide fragmentation via concerted CH{sub 2}-CO bond breakage is the dominant pathway for both surfaces. HCl formation is the dominant species produced by reaction with the COCl-SAM, while for the CHO-SAM a concerted H-atom transfer from the CHO-SAM to the peptide combined with either a H-atom or radical transfer from the peptide to the surface to form singlet reaction products is the dominant pathway. A strong collision energy dependence is found for the probability of peptide fragmentation, its reactivity, and linkage with the SAM. Surface deposition, i.e., covalent linkage between the surface and the peptide, is compared to recent experimental observations of such bonding by Laskin and co-workers [Phys. Chem. Chem. Phys. 10, 1512 (2008)]. Qualitative differences in reactivity are seen between the COCl-SAM and CHO-SAM showing that chemical identity is important for surface reactivity. The probability of reactive surface deposition, which is most closely analogous to experimental observables, peaks at a value of around 20% for a collision energy of 50 eV.

  11. Biolubricant basestocks from chemically modified plant oils: ricinoleic acid based-tetraesters

    PubMed Central

    2013-01-01

    Background Plant oils have been investigated as a potential source of environmentally favorable biolubricants because of their biodegradability, renewability and excellent lubrication performance. Low oxidation and thermal stability, poor low-temperature properties and a narrow range of available viscosities, however, limit their potential application as industrial lubricants. The inherent problems of plant oils can be improved by attaching functional groups at the sites of unsaturation through chemical modifications. In this article, we will demonstrate how functionalization helps overcome these disadvantages. Results In this work, mono-, tri- and tetra-esters have been synthesized, including 10,12-dihydroxy-9-(stearoyloxy)octadecanoic acid 3; 9,10,12-tris(stearoyloxy)octadecanoic acid 4; and 18-(4-ethylhexyloxy)-18-oxooctadecane-7,9,10-triyl tristearate 5. Pour-point and cloud-point measurements have shown that these derivatives have improved low-temperature properties as compared to the precursor. The tetra ester compound, 18-(4-ethylhexyloxy)-18-oxooctadecane-7,9,10-triyl tristearate 5, had the lowest pour point (PP) (−44.37°C) and the lowest cloud point (CP) (−41.25°C). This derivatization also improved the compound’s thermo-oxidative stability, measured using pressurized differential scanning calorimetry (PDSC) and thin-film micro-oxidation (TFMO) testing. 18-(4-Ethylhexyloxy)-18-oxooctadecane-7,9,10-triyl tristearate 5 also had the highest onset temperature (OT) (282.10°C) and the lowest volatile loss and insoluble deposit (37.39% and 50.87%, respectively). Furthermore, the compounds’ tribological behaviors were evaluated using the four-ball method. 18-(4-Ethylhexyloxy)-18-oxooctadecane-7,9,10-triyl tristearate 5 also had the lowest coefficient of friction (μ) (0.44). Conclusions The results showed that, in general, these derivatives have good anti-wear and friction-reducing properties at relatively low concentrations under all of the test loads

  12. Detection of SPO11-oligonucleotide complexes from mouse testes.

    PubMed

    Pan, Jing; Keeney, Scott

    2009-01-01

    The SPO11 protein generates programmed DNA double-strand breaks (DSBs) that initiate meiotic recombination. Endonucleolytic cleavage 3' to the DSB sites releases SPO11 from DNA, leaving SPO11 covalently associated with an oligonucleotide. This chapter describes detection of the release product, SPO11-oligonucleotide complexes, from mouse testis lysates. The method for determining the size of SPO11-associated oligonucleotides is also provided.

  13. DNA-modified nanocrystalline diamond thin-films as stable, biologically active substrates

    NASA Astrophysics Data System (ADS)

    Yang, Wensha; Auciello, Orlando; Butler, James E.; Cai, Wei; Carlisle, John A.; Gerbi, Jennifer E.; Gruen, Dieter M.; Knickerbocker, Tanya; Lasseter, Tami L.; Russell, John N.; Smith, Lloyd M.; Hamers, Robert J.

    2002-12-01

    Diamond, because of its electrical and chemical properties, may be a suitable material for integrated sensing and signal processing. But methods to control chemical or biological modifications on diamond surfaces have not been established. Here, we show that nanocrystalline diamond thin-films covalently modified with DNA oligonucleotides provide an extremely stable, highly selective platform in subsequent surface hybridization processes. We used a photochemical modification scheme to chemically modify clean, H-terminated nanocrystalline diamond surfaces grown on silicon substrates, producing a homogeneous layer of amine groups that serve as sites for DNA attachment. After linking DNA to the amine groups, hybridization reactions with fluorescently tagged complementary and non-complementary oligonucleotides showed no detectable non-specific adsorption, with extremely good selectivity between matched and mismatched sequences. Comparison of DNA-modified ultra-nanocrystalline diamond films with other commonly used surfaces for biological modification, such as gold, silicon, glass and glassy carbon, showed that diamond is unique in its ability to achieve very high stability and sensitivity while also being compatible with microelectronics processing technologies. These results suggest that diamond thin-films may be a nearly ideal substrate for integration of microelectronics with biological modification and sensing.

  14. Synthesis of the tellurium-derivatized phosphoramidites and their incorporation into DNA oligonucleotides.

    PubMed

    Jiang, Sibo; Sheng, Jia; Huang, Zhen

    2011-12-01

    In this unit, an efficient method for the synthesis of 2'-tellerium-modified phosphoramidite and its incorporation into oligonucleotide are presented. We choose 5'-O-DMTr-2,2'-anhydro-uridine and -thymidine nucleosides (S.1, S.2) as starting materials due to their easy preparation. The 5'-O-DMTr-2,2'-anhydro-uridine and -thymidine can be converted to the corresponding 2'-tellerium-derivatized nucleosides by treating with the telluride nucleophiles. Subsequently, the 2'-Te-nucleosides can be transformed into 3'-phosphoramidites, which are the building blocks for DNA/RNA synthesis. The DNA synthesis, purification, and applications of oligonucleotides containing 2'-Te-U or 2'-Te-T are described in the protocol.

  15. Synthesis of the first tellurium-derivatized oligonucleotides for structural and functional studies.

    PubMed

    Sheng, Jia; Hassan, Abdalla E A; Huang, Zhen

    2009-10-05

    We report here the first synthesis of Te-nucleoside phosphoramidites and Te-modified oligonucleotides. We protected the 2'-tellurium functionality by alkylation and found that the Te functionality is compatible with solid-phase synthesis and that the Te oligonucleotides are stable during deprotection and purification. In addition, the redox properties of the Te functionalities have been explored. We found that the telluride and telluoxide DNAs are interchangeable by redox reactions. At elevated temperature, the Te-DNA can also be site-specifically fragmented oxidatively or reductively when 2'-TePh functionality is present, whereas elimination of the nucleobase is observed in the presence of 2'-TeMe. Moreover, the stability of the DNA duplexes derivatized with the Te functionalities has been investigated. Our Te derivatization of nucleic acids provides a novel approach for investigating DNA damage as well as for structure and function studies of nucleic acids and their protein complexes.

  16. In situ oligonucleotide synthesis on carbon materials: stable substrates for microarray fabrication

    PubMed Central

    Phillips, Margaret F.; Lockett, Matthew R.; Rodesch, Matthew J.; Shortreed, Michael R.; Cerrina, Franco; Smith, Lloyd M.

    2008-01-01

    Glass has become the standard substrate for the preparation of DNA arrays. Typically, glass is modified using silane chemistries to provide an appropriate functional group for nucleic acid synthesis or oligonucleotide immobilization. We have found substantial issues with the stability of these surfaces as manifested in the unwanted release of oligomers from the surface when incubated in aqueous buffers at moderate temperatures. To address this issue, we have explored the use of carbon-based substrates. Here, we demonstrate in situ synthesis of oligonucleotide probes on carbon-based substrates using light-directed photolithographic phosphoramidite chemistry and evaluate the stabilities of the resultant DNA arrays compared to those fabricated on silanized glass slides. DNA arrays on carbon-based substrates are substantially more stable than arrays prepared on glass. This superior stability enables the use of high-density DNA arrays for applications involving high temperatures, basic conditions, or where serial hybridization and dehybridization is desired. PMID:18084027

  17. Template switching between PNA and RNA oligonucleotides

    NASA Technical Reports Server (NTRS)

    Bohler, C.; Nielsen, P. E.; Orgel, L. E.; Miller, S. L. (Principal Investigator)

    1995-01-01

    The origin of the RNA world is not easily understood, as effective prebiotic syntheses of the components of RNA, the beta-ribofuranoside-5'-phosphates, are hard to envisage. Recognition of this difficulty has led to the proposal that other genetic systems, the components of which are more easily formed, may have preceded RNA. This raises the question of how transitions between one genetic system and another could occur. Peptide nucleic acid (PNA) resembles RNA in its ability to form double-helical complexes stabilized by Watson-Crick hydrogen bonding between adenine and thymine and between cytosine and guanine, but has a backbone that is held together by amide rather than by phosphodiester bonds. Oligonucleotides bases on RNA are known to act as templates that catalyse the non-enzymatic synthesis of their complements from activated mononucleotides, we now show that RNA oligonucleotides facilitate the synthesis of complementary PNA strands and vice versa. This suggests that a transition between different genetic systems can occur without loss of information.

  18. BIOCONJUGATION OF OLIGONUCLEOTIDES FOR TREATING LIVER FIBROSIS

    PubMed Central

    Ye, Zhaoyang; Hajj Houssein, Houssam S.; Mahato, Ram I.

    2009-01-01

    Liver fibrosis results from chronic liver injury due to hepatitis B and C, excessive alcohol ingestion, and metal ion overload. Fibrosis culminates in cirrhosis and results in liver failure. Therefore, a potent antifibrotic therapy is in urgent need to reverse scarring and eliminate progression to cirrhosis. Although activated hepatic stellate cells (HSCs) remains the principle cell type responsible for liver fibrosis, perivascular fibroblasts of portal and central veins as well as periductular fibroblasts are other sources of fibrogenic cells. This review will critically discuss various treatment strategies for liver fibrosis, including prevention of liver injury, reduction of inflammation, inhibition of HSC activation, degradation of scar matrix, and inhibition of aberrant collagen synthesis. Oligonucleotides (ODNs) are short, single-stranded nucleic acids, which disrupt expression of target protein by binding to complementary mRNA or forming triplex with genomic DNA. Triplex forming oligonucleotides (TFOs) provide an attractive strategy for treating liver fibrosis. A series of TFOs have been developed for inhibiting the transcription of α1(I) collagen gene, which opens a new area for antifibrotic drugs. There will be in depth discussion on the use of TFOs and how different bioconjugation strategies can be utilized for their site-specific delivery to HSCs or hepatocytes for enhanced antifibrotic activities. Various insights developed in individual strategy and the need for multipronged approaches will also be discussed. PMID:18154454

  19. Detoxified Bacterial Endotoxins II. Preparation and Biological Properties of Chemically Modified Crude Endotoxins from Salmonella typhimurium1

    PubMed Central

    Martin, William J.; Marcus, Stanley

    1966-01-01

    Martin, William J. (University of Utah, Salt Lake City), and Stanley Marcus. Detoxified bacterial endotoxins. II. Preparation and biological properties of chemically modified crude endotoxins from Salmonella typhimurium. J. Bacteriol. 91:1750–1758. 1966.—Chemical modification of a crude endotoxin prepared by the Roschka-Edwards (RE) procedure from a strain of Salmonella typhimurium yielded products which were nontoxic for mice and had reduced fever effects in rabbits. A reduction in rabbit pyrogenicity of approximately 100 times was noted with a potassium periodate-treated RE preparation when compared with the parent RE preparation. Measured in a similar fashion, pyrogenicity of a potassium methylate-treated RE preparation was reduced by a factor of 10 while pyrogenicity of a boron trifluoride RE preparation was unchanged. All of these endotoxoids, including the parent RE preparation, showed little toxicity for mice. Immunogenicity was determined in mice by comparing Boivin, RE, and endotoxoid preparations with a heat-killed, phenol-preserved (HP) vaccine prepared from the same strain of S. typhimurium. Employing a 10 ld50 challenge, the protective immunogenicity of the respective vaccines was determined by active immunized mouse protection tests. Although two 100 μg immunizing doses of the Boivin, RE, and the respective endotoxoid preparations varied in mouse protection (potassium methylate RE > Boivin > RE > boron trifluoride RE > potassium periodate RE), it was evident that, with the exception of the potassium methylate preparation, the HP vaccine yielded greatest protection against the 10 ld50 challenge with S. typhimurium. Further mouse protection experiments suggested that the minimal immunogenic dose of the potassium methylate RE vaccine preparation was approximately 50 μg. These data indicated an approximate fivefold difference between the minimal pyrogenic dose (10 μg) and the minimal immunogenic dose (50 μg). These findings further suggest that

  20. The effect of different annealing temperatures on tin and cadmium telluride phases obtained by a modified chemical route

    SciTech Connect

    Mesquita, Anderson Fuzer; Porto, Arilza de Oliveira; Magela de Lima, Geraldo; Paniago, Roberto; Ardisson, José Domingos

    2012-11-15

    Graphical abstract: Display Omitted Highlights: ► Synthesis of cadmium and tin telluride. ► Chemical route to obtain pure crystalline cadmium and tin telluride. ► Effect of the annealing temperature on the crystalline phases. ► Removal of tin oxide as side product through thermal treatment. -- Abstract: In this work tin and cadmium telluride were prepared by a modification of a chemical route reported in the literature to obtain metallacycles formed by oxidative addition of tin-tellurium bonds to platinum (II). Through this procedure it was possible to obtain tin and cadmium telluride. X-ray diffraction and X-ray photoelectron spectroscopy were used to identify the crystalline phases obtained as well as the presence of side products. In the case of tin telluride it was identified potassium chloride, metallic tellurium and tin oxide as contaminants. The tin oxidation states were also monitored by {sup 119}Sn Mössbauer spectroscopy. The annealing in hydrogen atmosphere was chosen as a strategy to reduce the tin oxide and promote its reaction with the excess of tellurium present in the medium. The evolution of this tin oxide phase was studied through the annealing of the sample at different temperatures. Cadmium telluride was obtained with high degree of purity (98.5% relative weight fraction) according to the Rietveld refinement of X-ray diffraction data. The modified procedure showed to be very effective to obtain amorphous tin and cadmium telluride and the annealing at 450 °C has proven to be useful to reduce the amount of oxide produced as side product.

  1. Effects of modified atmosphere and vacuum packaging on microbiological and chemical properties of rainbow trout (Oncorynchus mykiss) fillets.

    PubMed

    Arashisar, Sükriye; Hisar, Olcay; Kaya, Mükerrem; Yanik, Telat

    2004-12-15

    Microbial (psychrotrophic, mesophilic aerobic bacteria and Enterobacteriacae counts), and chemical analysis [pH, total volatile bases nitrogen (TVB-N), lipid oxidation (Thiobarbituric acid reactive substance, TBARS)] of rainbow trout (Oncorynchus mykiss) fillets in air (control), vacuum and modified atmosphere packaging (MAP) with various gas mixtures conditions at 4+/-1 degrees C were determined. The gas mixtures evaluated were 100% CO2, 2.5% O2+7.5% N2+90% CO2 and 30% O2+30% N2+40% CO2. Psychrotrophic bacteria count was above 1 x 10(7) cfu/g on the 12th day in 100% CO2. However; mesophilic bacteria count was below 1 x 10(6) cfu/g at the end of the 14-day storage period. Enterobacteriaceae count was significantly lower in samples packaged with MAP. Lipid oxidation increased rapidly after 6 days of storage in the samples containing 30% O2. While minimum TBARS values were recorded in fillets containing 100% CO2 and vacuumed fillets, the lowest TVB-N values were obtained in fillets with 100% CO2.

  2. Chemically modified RNA induces osteogenesis of stem cells and human tissue explants as well as accelerates bone healing in rats.

    PubMed

    Balmayor, Elizabeth R; Geiger, Johannes P; Aneja, Manish K; Berezhanskyy, Taras; Utzinger, Maximilian; Mykhaylyk, Olga; Rudolph, Carsten; Plank, Christian

    2016-05-01

    Limitations associated to the use of growth factors represent a major hurdle to musculoskeletal regeneration. On the one hand, they are needed to induce neo-tissue formation for the substitution of a necrotic or missing tissue. On the other hand, these factors are used in supraphysiological concentrations, are short lived and expensive and result in many side effects. Here we develop a gene transfer strategy based on the use of chemically modified mRNA (cmRNA) coding for human bone morphogenetic protein 2 (hBMP-2) that is non-immunogenic and highly stable when compared to unmodified mRNA. Transfected stem cells secrete hBMP-2, show elevated alkaline phosphatase levels and upregulated expression of RunX2, ALP, Osterix, Osteocalcin, Osteopontin and Collagen Type I genes. Mineralization was induced as seen by positive Alizarin red staining. hBMP-2 cmRNA transfected human fat tissue also yielded an osteogenic response in vitro as indicated by expression of hBMP-2, RunX2, ALP and Collagen Type I. Delivering hBMP-2 cmRNA to a femur defect in a rat model results in new bone tissue formation as early as 2 weeks after application of very low doses. Overall, our studies demonstrate the feasibility and therapeutic potential of a new cmRNA-based gene therapy strategy that is safe and efficient. When applied clinically, this approach could overcome BMP-2 growth factor associated limitations in bone regeneration.

  3. Distribution of phosphorus and hydroxypropyl groups within granules of modified sweet potato starches as determined after chemical peeling.

    PubMed

    Zhao, Jianwei; Schols, Henk A; Chen, Zhenghong; Jin, Zhengyu; Buwalda, Piet; Gruppen, Harry

    2015-11-05

    The distributions of phosphorus and hydroxypropyl groups within granules of cross-linked and hydroxypropylated sweet potato starches were investigated. Chemical surface peeling of starch granules was performed after sieving of native and modified starches into large-size (diameter ≥ 20 μm) and small-size (diameter < 20 μm) fractions. Starch granules were surface gelatinized in a 4M calcium chloride solution at different levels. After the peeling step, the remaining starch granules were analysed for the content of phosphorus and hydroxypropyl groups. The phosphorus level of the parental starch gradually decreased from periphery to core of the granules. The increase in phosphorus content after cross-linking in periphery was higher than that in core. The subsequent hydroxypropylation reaction resulted in lower phosphate levels. Hydroxypropylation resulted in a gradient of hydroxypropyl group concentration from periphery to core. Cross-linking prior to the hydroxypropylation resulted in lower levels of hydroxypropyl groups and less pronounced differences between periphery and core.

  4. Large-Area Chemically Modified Graphene Films: Electrophoretic Deposition and Characterization by Soft X-ray Absorption Spectroscopy

    SciTech Connect

    Lee, V.; Whittaker, L; Jaye, C; Baroudi, K; Fischer, D; Banerjee, S

    2009-01-01

    A facile, rapid, and scalable electrophoretic deposition approach is developed for the fabrication of large-area chemically derived graphene films on conductive substrates based on the electrophoretic deposition of graphene oxide and reduced graphene oxide components. Two distinctive approaches for fabricating conformal graphene films are developed. In the first approach, graphene oxide sheets are electrophoretically deposited from an aqueous solution after the oxidation of graphite to graphite oxide and the subsequent exfoliation of graphite oxide to graphene oxide. Next, the graphene oxide films are reduced via dip-coating in an aqueous solution of hydrazine. In the second approach, graphene oxide is reduced to graphene nanosheets in a strongly alkaline solution and the reduced graphene sheets are directly electrophoretically deposited onto conductive substrates. The film thickness can be modified by the deposition time and the obtained films span several square millimeters in area. Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy is used to study the surface chemistry, electronic band structure, and degree of alignment of the electrophoretically deposited films. Polarized NEXAFS measurements verify the presence of epoxide surface functionalities on the graphene basal planes and indicate significant recovery of extended p-bonded networks upon defunctionalization by hydrazine treatment. These measurements further indicate significantly improved alignment of the graphene sheet components of the films parallel to the substrate surface when defunctionalization is performed prior to electrophoretic deposition.

  5. Multiple Soaking with Different Solution Concentration in Doped Silica Preform Fabrication Using Modified Chemical Vapor Deposition and Solution Doping

    NASA Astrophysics Data System (ADS)

    Aljamimi, S. M.; Khairul Anuar, M. S.; Muhamad-Yassin, S. Z.; Zulkifli, M. I.; Hanif, S.; Tamchek, N.; Yusoff, Z.; Abdul-Rashid, H. A.

    2014-01-01

    Incorporation of alumina (Al2O3) into a silica matrix by modified chemical vapor deposition and a solution doping technique is investigated in this study. Multiple soaking cycles were used to increase the aluminum content in the core layer. The effect of alumina retention in silica matrix soot is focused by multiple cycles of soaking with different solution concentrations, while the effect of the adsorption mechanism is fixed by maintaining the soot deposition process (such as temperature [1,800°C], precursor, total gas flow, and soaking time). The deposited soot is examined for porosity characteristics and effective surface area by a gas adsorption technique with Brunauer-Emett-Teller surface area analysis and the surface and cross-section morphology using scanning electron microscopy. Three different concentrations are used in this work (0.3, 0.7, and 1.2 M) with multiple cycles of soaking. Sintering and the collapsing process is controlled for each preform. The result shows that the alumina content is increased substantially as the number of soaking processes is increased, which may be due to the retention effect as only a small amount of adsorption process takes place as indicated by the slight decrease in the surface area of soot. The collapsed preforms are analyzed using a preform analyzer. Energy dispersive x-ray spectrometry is used to check aluminum content and distribution into the core layer.

  6. Optical properties of carbon nanostructures produced by laser irradiation on chemically modified multi-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Santiago, Enrique Vigueras; López, Susana Hernández; Camacho López, Marco A.; Contreras, Delfino Reyes; Farías-Mancilla, Rurik; Flores-Gallardo, Sergio G.; Hernández-Escobar, Claudia A.; Zaragoza-Contreras, E. Armando

    2016-10-01

    This research focused on the nanosecond (Nd: YAG-1064 nm) laser pulse effect on the optical and morphological properties of chemically modified multi-walled carbon nanotubes (MWCNT). Two suspensions of MWCNT in tetrahydrofuran (THF) were prepared, one was submitted to laser pulses for 10 min while the other (blank) was only mechanically homogenized during the same time. Following the laser irradiation, the suspension acquired a yellow-amber color, in contrast to the black translucent appearance of the blank. UV-vis spectroscopy confirmed this observation, showing the blank a higher absorption. Additionally, photoluminescence measurements exhibited a broad blue-green emission band both in the blank and irradiated suspension when excited at 369 nm, showing the blank a lower intensity. However, a modification in the excitation wavelength produced a violet to green tuning in the irradiated suspension, which did not occur in the blank. Lastly, the electron microscopy analysis of the treated nanotubes showed the abundant formation of amorphous carbon, nanocages, and nanotube unzipping, exhibiting the intense surface modification produced by the laser pulse. Nanotube surface modification and the coexistence with the new carbon nanostructures were considered as the conductive conditions for optical properties modification.

  7. Evaluating Kinase ATP Uptake and Tyrosine Phosphorylation using Multiplexed Quantification of Chemically Labeled and Post-Translationally Modified Peptides

    PubMed Central

    Fang, Bin; Hoffman, Melissa A.; Mirza, Abu-Sayeef; Mishall, Katie M.; Li, Jiannong; Peterman, Scott M.; Smalley, Keiran S. M.; Shain, Kenneth H.; Weinberger, Paul M.; Wu, Jie; Rix, Uwe; Haura, Eric B.; Koomen, John M.

    2015-01-01

    Cancer biologists and other healthcare researchers face an increasing challenge in addressing the molecular complexity of disease. Biomarker measurement tools and techniques now contribute to both basic science and translational research. In particular, liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM) for multiplexed measurements of protein biomarkers has emerged as a versatile tool for systems biology. Assays can be developed for specific peptides that report on protein expression, mutation, or post-translational modification; discovery proteomics data rapidly translated into multiplexed quantitative approaches. Complementary advances in affinity purification enrich classes of enzymes or peptides representing post-translationally modified or chemically labeled substrates. Here, we illustrate the process for the relative quantification of hundreds of peptides in a single LC-MRM experiment. Desthiobiotinylated peptides produced by activity-based protein profiling (ABPP) using ATP probes and tyrosine-phosphorylated peptides are used as examples. These targeted quantification panels can be applied to further understand the biology of human disease. PMID:25782629

  8. Cloned calves derived from somatic cell nuclear transfer embryos cultured in chemically defined medium or modified synthetic oviduct fluid.

    PubMed

    Jang, Goo; Hong, So Gun; Lee, Byeong Chun

    2011-03-01

    Somatic cell nuclear transfer (SCNT) is considered to be a critical tool for propagating valuable animals. To determine the productivity calves resulting from embryos derived with different culture media, enucleated oocytes matured in vitro were reconstructed with fetal fibroblasts, fused, and activated. The cloned embryos were cultured in modified synthetic oviduct fluid (mSOF) or a chemically defined medium (CDM) and developmental competence was monitored. After 7 days of culturing, the blastocysts were transferred into the uterine horn of estrus-synchronized recipients. SCNT embryos that were cultured in mSOF or CDM developed to the blastocysts stages at similar rates (26.6% vs. 22.5%, respectively). A total of 67 preimplantational stage embryos were transferred into 34 recipients and six cloned calves were born by caesarean section, or assisted or natural delivery. Survival of transferred blastocysts to live cloned calves in the mSOF and the CDM was 18.5% (to recipients), 9.6% (to blastocysts) and 42.9% (to recipients), 20.0% (to blastocysts), respectively. DNA analysis showed that all cloned calves were genetically identical to the donor cells. These results demonstrate that SCNT embryos cultured in CDM showed higher viability as judged by survival of the calves that came to term compared to blastocysts derived from mSOF cultures.

  9. Control of growth and squamous differentiation in normal human bronchial epithelial cells by chemical and biological modifiers and transferred genes.

    PubMed Central

    Pfeifer, A M; Lechner, J F; Masui, T; Reddel, R R; Mark, G E; Harris, C C

    1989-01-01

    The majority of human lung cancers arise from bronchial epithelial cells. The normal pseudostratified bronchial epithelium is composed of basal, mucous, and ciliated cells. This multi-differentiated epithelium usually responds to xenobiotics and physical injury by undergoing basal cell hyperplasia, mucous cell hyperplasia, and squamous metaplasia. One step of the multistage process of carcinogenesis is thought to involve aberrations in control of the squamous metaplastic processes. Decreased responsiveness to regulators of terminal squamous differentiation may confer a selective clonal expansion advantage to an initiated cell. We studied the effects of endogenous [e.g., transforming growth factor beta 1 (TGF-beta 1) and serum] and exogenous [e.g., 12-O-tetradecanoyl-13-phorbol-acetate (TPA), tobacco smoke condensate, and aldehydes] modifiers of normal human bronchial epithelial (NHBE) cell in a serum-free culture system. NHBE cells are growth inhibited by all of these compounds and induced to undergo squamous differentiation by TGF-beta 1 or TPA. In contrast, lung carcinoma cell lines are relatively resistant to inducers of terminal squamous differentiation which may provide them with a selective growth advantage. Chemical agents and activated protooncogenes (ras,raf,myc) altered the response to endogenous and exogenous inducers of squamous differentiation and caused extended cellular lifespan, aneuploidy, and/or tumorigenicity. The data suggest a close relationship between dysregulation of terminal differentiation pathways and neoplastic transformation of human bronchial epithelial cells. PMID:2538323

  10. Chemical composition and selected mechanical properties of Al-Zn alloy modified in plasma conditions by RF CVD

    NASA Astrophysics Data System (ADS)

    Kyzioł, Karol; Kluska, Stanisława; Januś, Marta; Środa, Marcin; Jastrzębski, Witold; Kaczmarek, Łukasz

    2014-08-01

    The paper reports results of the study of surface composition and selected functional properties of 7075 (Al-Zn) alloys modified in Ar, N2, SiH4 and CH4 atmosphere at reduced pressure. RF CVD (Radio Frequency Chemical Vapour Deposition) technique was used in the study. The type or weight percentage of carbon in each modification varied in the resultant SiN:H and SiCN:H coatings. Alloy samples were treated with Ar+ plasma etching and N+ ion implantation at reduced pressure. The tests proved the values of selected mechanical properties (hardness ca. 10.5 GPa, Young modulus ca. 95 GPa) and adhesion (delamination force ca. 11.5 mN) to be higher in the case of SiCN:H anti-wear coating (deposited in SiH4:CH4:N2 = 1:1:2 gas mixture) than the values of the respective parameters obtained in the remaining modifications. Further, carbon doped coatings (SiCN:H) exhibited significantly improved hardness (by about 50 to 70%) and nearly threefold increase in delamination force in comparison with SiCN:H coatings.

  11. Transient radiation responses of silica-based optical fibers: Influence of modified chemical-vapor deposition process parameters

    SciTech Connect

    Girard, S.; Ouerdane, Y.; Boukenter, A.; Meunier, J.-P.

    2006-01-15

    We characterized the behaviors of eight prototype single-mode optical fibers, made by the modified chemical-vapor deposition process, under pulsed x-ray ({approx}1 MeV) irradiation. For this purpose, we measured the time-dependent changes (10{sup -6}-10{sup 2} s) in the radiation-induced attenuation at 1.55 and 1.31 {mu}m after exposure to an x-ray pulse. By using a dedicated set of prototype germanosilicate fibers with carefully designed process parameters, we show the predominant impact on their vulnerability of the two codopants (germanium and phosphorus) incorporated in their claddings ({approx}0.3 Wt %). Compared to these influences on the radiation-induced loss levels and recovery kinetics, the impacts of the preform deposition temperature and of the fiber drawing tension on the fiber radiation sensitivity are less important. However, our results show that lowering the standard preform deposition temperature from 2000 to 1600 deg. C and the drawing tension from 140 to 20 g slightly decreases the induced losses at both wavelengths. We propose some hypotheses on the radiation-induced defects and physical mechanisms at the origin of these influences.

  12. Disulfide-linked oligonucleotide phosphorothioates - Novel analogues of nucleic acids

    NASA Technical Reports Server (NTRS)

    Wu, Taifeng; Orgel, Leslie E.

    1991-01-01

    The synthesis of phosphorothioate analogs of oligonucleotides by the oxidation of deoxyadenosine 3',5'-bisphosphorothioate (3) was attempted. Cyclization of 3 is much more efficient than oligomerization under all the conditions investigated. However, a preformed oligonucleotide carrying a 5'-terminal phosphorotioate group undergoes efficient chain-extension when oxidized in the presence of 3.

  13. Oligonucleotide therapies for disorders of the nervous system.

    PubMed

    Khorkova, Olga; Wahlestedt, Claes

    2017-03-01

    Oligonucleotide therapies are currently experiencing a resurgence driven by advances in backbone chemistry and discoveries of novel therapeutic pathways that can be uniquely and efficiently modulated by the oligonucleotide drugs. A quarter of a century has passed since oligonucleotides were first applied in living mammalian brain to modulate gene expression. Despite challenges in delivery to the brain, multiple oligonucleotide-based compounds are now being developed for treatment of human brain disorders by direct delivery inside the blood brain barrier (BBB). Notably, the first new central nervous system (CNS)-targeted oligonucleotide-based drug (nusinersen/Spinraza) was approved by US Food and Drug Administration (FDA) in late 2016 and several other compounds are in advanced clinical trials. Human testing of brain-targeted oligonucleotides has highlighted unusual pharmacokinetic and pharmacodynamic properties of these compounds, including complex active uptake mechanisms, low systemic exposure, extremely long half-lives, accumulation and gradual release from subcellular depots. Further work on oligonucleotide uptake, development of formulations for delivery across the BBB and relevant disease biology studies are required for further optimization of the oligonucleotide drug development process for brain applications.

  14. Voltage-gated calcium channel and antisense oligonucleotides thereto

    NASA Technical Reports Server (NTRS)

    Hruska, Keith A. (Inventor); Friedman, Peter A. (Inventor); Barry, Elizabeth L. R. (Inventor); Duncan, Randall L. (Inventor)

    1998-01-01

    An antisense oligonucleotide of 10 to 35 nucleotides in length that can hybridize with a region of the .alpha..sub.1 subunit of the SA-Cat channel gene DNA or mRNA is provided, together with pharmaceutical compositions containing and methods utilizing such antisense oligonucleotide.

  15. The spherulites™: a promising carrier for oligonucleotide delivery

    PubMed Central

    Mignet, Nathalie; Brun, Armelle; Degert, Corinne; Delord, Brigitte; Roux, Didier; Hélène, Claude; Laversanne, René; François, Jean-Christophe

    2000-01-01

    Concentric multilamellar microvesicles, named spherulites™, were evaluated as an oligonucleotide carrier. Up to 80% oligonucleotide was encapsulated in these vesicles. The study was carried out on two different spherulite™ formulations. The spherulite™ size and stability characteristics are presented. Delivery of encapsulated oligonucleotide was performed on a rat hepatocarcinoma and on a lymphoblastoid T cell line, both expressing the luciferase gene. We showed that spherulites™ were able to transfect both adherent and suspension cell lines and deliver the oligonucleotide to the nucleus. Moreover, 48–62% luciferase inhibition was obtained in the rat hepatocarcinoma cell line when the antisense oligonucleotide targeted to the luciferase coding region was encapsulated at 500 nM concentration in spherulites™ of different compositions. PMID:10931929

  16. Preparation and characterization of carboxyl functionalization of magnetite nanoparticles for oligonucleotide immobilization

    NASA Astrophysics Data System (ADS)

    Kim, Min-Jung; Jang, Dae-Hwan; Choa, Yong-Ho

    2010-05-01

    Fe3O4 nanoparticles prepared by the co-precipitation of Fe2+ and Fe3+ with NH4OH were simply modified by the carboxylic acid group of 3-thiopheneacetic acid (3TA) and meso-2,3-dimercaptosuccinic acid (DMSA). These functionalized Fe3O4 nanoparticles when coated with 3TA and DMSA have increased hydrophilic properties, thus causing them to be well dispersed in aqueous solutions. Then oligonucleotides (5'-AGC T-Amine-3') were immobilized on the carboxylic acid group-modified Fe3O4 nanoparticles. They were characterized by using FT-IR, XRD and TEM. The concentration of the oligonucleotide-modified Fe3O4 nanoparticles was investigated using a UV-vis spectrometer and compared to that of Fe3O4 nanoparticles without any surface modification. The Fe3O4 nanoparticles were spherical and the particle sizes were approximately 10 nm. The immobilizing efficiencies of the Fe3O4 nanoparticles modified with 3TA and DMSA were higher than those of the non-functionalized Fe3O4 nanoparticles.

  17. Heated oligonucleotide ligation assay (HOLA): an affordable single nucleotide polymorphism assay.

    PubMed

    Black, W C; Gorrochotegui-Escalante, N; Duteau, N M

    2006-03-01

    Most single nucleotide polymorphism (SNP) detection requires expensive equipment and reagents. The oligonucleotide ligation assay (OLA) is an inexpensive SNP assay that detects ligation between a biotinylated "allele-specific detector" and a 3' fluorescein-labeled "reporter" oligonucleotide. No ligation occurs unless the 3' detector nucleotide is complementary to the SNP nucleotide. The original OLA used chemical denaturation and neutralization. Heated OLA (HOLA) instead uses a thermal stable ligase and cycles of denaturing and hybridization for ligation and SNP detection. The cost per genotype is approximately US$1.25 with two-allele SNPs or approximately US$1.75 with three-allele SNPs. We illustrate the development of HOLA for SNP detection in the Early Trypsin and Abundant Trypsin loci in the mosquito Aedes aegypti (L.) and at the a-glycerophosphate dehydrogenase locus in the mosquito Anopheles gambiae s.s.

  18. The precursor strategy: terminus methoxyoxalamido modifiers for single and multiple functionalization of oligodeoxyribonucleotides

    PubMed Central

    Polushin, Nikolai N.

    2000-01-01

    Synthesis of new terminus modifiers, bearing, along with a phosphoramidite moiety, one, two or four methoxyoxalamido (MOX) precursor groups, is described. These modifiers are introduced onto the 5′-end of a synthetic oligodeoxyribonucleotide as the last step of an automated synthesis to form the MOX precursor oligonucleotide. The MOX groups are then post-synthetically derivatized with an appropriate primary amine to construct a 5′-modified oligonucleotide. The efficiency and simplicity of the novel modifying strategy were demonstrated in the synthesis of a number of 5′-functionalized oligonucleotides. PMID:10931928

  19. Abiotic formation of oligonucleotides on basalt surfaces

    NASA Astrophysics Data System (ADS)

    Otroshchenko, V. A.; Vasilyeva, N. V.; Kopilov, A. M.

    1985-06-01

    The complication and further evolution of abiotic syntheses products occurred under environmental influences at the prebiological stage. From this point of view, the influence of some types of irradiation on the organic molecules adsorbed on the surfaces of volcanic rocks, appeared to be of great importance. In this connection, the effect of gamma rays on the AMP molecules adsorbed on mineral surfaces such as cinders and ashes has been studied. It has been shown that they can polymerize with the formation of oligonucleotides. The treatment of oligomers obtained by venom phosphodiesterase has shown that a polymeric product has mainly 3' 5' and 2' 5' bonds between nucleotides. The results obtained have been discussed from the evolutionary aspect.

  20. Direct oligonucleotide-photosensitizer conjugates for photochemical delivery of antisense oligonucleotides.

    PubMed

    Yuan, Ahu; Laing, Brian; Hu, Yiqiao; Ming, Xin

    2015-04-18

    Activation of photosensitizers in endosomes enables release of therapeutic macromolecules into the cytosol of the target cells for pharmacological actions. In this study, we demonstrate that direct conjugation of photosensitizers to oligonucleotides (ONs) allows spatial and temporal co-localization of the two modalities in the target cells, and thus leads to superior functional delivery of ONs. Further, light-activated delivery of an anticancer ON caused cancer cell killing via modulation of an oncogene and photodynamic therapy.

  1. Kinetic Hairpin Oligonucleotide Blockers for Selective Amplification of Rare Mutations

    PubMed Central

    Jia, Yanwei; Sanchez, J. Aquiles; Wangh, Lawrence J.

    2014-01-01

    Detection of rare mutant alleles in an excess of wild type alleles is increasingly important in cancer diagnosis. Several methods for selective amplification of a mutant allele via the polymerase chain reaction (PCR) have been reported, but each of these methods has its own limitations. A common problem is that Taq DNA polymerase errors early during amplification generate false positive mutations which also accumulate exponentially. In this paper, we described a novel method using hairpin oligonucleotide blockers that can selectively inhibit the amplification of wild type DNA during LATE-PCR amplification. LATE-PCR generates double-stranded DNA exponentially followed by linear amplification of single-stranded DNA. The efficiency of the blocker is optimized by adjusting the LATE-PCR temperature cycling profile. We also demonstrate that it is possible to minimize false positive signals caused by Taq DNA polymerase errors by using a mismatched excess primer plus a modified PCR profile to preferentially enrich for mutant target sequences prior to the start of the exponential phase of LATE-PCR amplification. In combination these procedures permit amplification of specific KRAS mutations in the presence of more than 10,000 fold excess of wild type DNA without false positive signals. PMID:25082368

  2. Antineoplastic effect of decoy oligonucleotide derived from MGMT enhancer.

    PubMed

    Canello, Tamar; Ovadia, Haim; Refael, Miri; Zrihan, Daniel; Siegal, Tali; Lavon, Iris

    2014-01-01

    Silencing of O(6)-methylguanine-DNA-methyltransferase (MGMT) in tumors, mainly through promoter methylation, correlates with a better therapeutic response and with increased survival. Therefore, it is conceivable to consider MGMT as a potential therapeutic target for the treatment of cancers. Our previous results demonstrated the pivotal role of NF-kappaB in MGMT expression, mediated mainly through p65/NF-kappaB homodimers. Here we show that the non-canonical NF-KappaB motif (MGMT-kappaB1) within MGMT enhancer is probably the major inducer of MGMT expression following NF-kappaB activation. Thus, in an attempt to attenuate the transcription activity of MGMT in tumors we designed locked nucleic acids (LNA) modified decoy oligonucleotides corresponding to the specific sequence of MGMT-kappaB1 (MGMT-kB1-LODN). Following confirmation of the ability of MGMT-kB1-LODN to interfere with the binding of p65/NF-kappaB to the NF-KappaB motif within MGMT enhancer, the efficacy of the decoy was studied in-vitro and in-vivo. The results of these experiments show that the decoy MGMT-kB1-LODN have a substantial antineoplastic effect when used either in combination with temozolomide or as monotherapy. Our results suggest that MGMT-kB1-LODN may provide a novel strategy for cancer therapy.

  3. Splice-switching antisense oligonucleotides as therapeutic drugs

    PubMed Central

    Havens, Mallory A.; Hastings, Michelle L.

    2016-01-01

    Splice-switching oligonucleotides (SSOs) are short, synthetic, antisense, modified nucleic acids that base-pair with a pre-mRNA and disrupt the normal splicing repertoire of the transcript by blocking the RNA–RNA base-pairing or protein–RNA binding interactions that occur between components of the splicing machinery and the pre-mRNA. Splicing of pre-mRNA is required for the proper expression of the vast majority of protein-coding genes, and thus, targeting the process offers a means to manipulate protein production from a gene. Splicing modulation is particularly valuable in cases of disease caused by mutations that lead to disruption of normal splicing or when interfering with the normal splicing process of a gene transcript may be therapeutic. SSOs offer an effective and specific way to target and alter splicing in a therapeutic manner. Here, we discuss the different approaches used to target and alter pre-mRNA splicing with SSOs. We detail the modifications to the nucleic acids that make them promising therapeutics and discuss the challenges to creating effective SSO drugs. We highlight the development of SSOs designed to treat Duchenne muscular dystrophy and spinal muscular atrophy, which are currently being tested in clinical trials. PMID:27288447

  4. Preparation and application of triple helix forming oligonucleotides and single strand oligonucleotide donors for gene correction.

    PubMed

    Alam, Rowshon; Thazhathveetil, Arun Kalliat; Li, Hong; Seidman, Michael M

    2014-01-01

    Strategies for site-specific modulation of genomic sequences in mammalian cells require two components. One must be capable of recognizing and activating a specific target sequence in vivo, driving that site into an exploitable repair pathway. Information is transferred to the site via participation in the pathway by the second component, a donor nucleic acid, resulting in a permanent change in the target sequence. We have developed biologically active triple helix forming oligonucleotides (TFOs) as site-specific gene targeting reagents. These TFOs, linked to DNA reactive compounds (such as a cross-linking agent), activate pathways that can engage informational donors. We have used the combination of a psoralen-TFO and single strand oligonucleotide donors to generate novel cell lines with directed sequence changes at the target site. Here we describe the synthesis and purification of bioactive psoralen-linked TFOs, their co-introduction into mammalian cells with donor nucleic acids, and the identification of cells with sequence conversion of the target site. We have emphasized details in the synthesis and purification of the oligonucleotides that are essential for preparation of reagents with optimal activity.

  5. Targeting the r(CGG) Repeats That Cause FXTAS with Modularly Assembled Small Molecules and Oligonucleotides

    PubMed Central

    2015-01-01

    We designed small molecules that bind the structure of the RNA that causes fragile X-associated tremor ataxia syndrome (FXTAS), an incurable neuromuscular disease. FXTAS is caused by an expanded r(CGG) repeat (r(CGG)exp) that inactivates a protein regulator of alternative pre-mRNA splicing. Our designed compounds modulate r(CGG)exp toxicity in cellular models of FXTAS, and pull-down experiments confirm that they bind r(CGG)expin vivo. Importantly, compound binding does not affect translation of the downstream open reading frame (ORF). We compared molecular recognition properties of our optimal compound to oligonucleotides. Studies show that r(CGG)exp’s self-structure is a significant energetic barrier for oligonucleotide binding. A fully modified 2′-OMethyl phosphorothioate is incapable of completely reversing an FXTAS-associated splicing defect and inhibits translation of the downstream ORF, which could have deleterious effects. Taken together, these studies suggest that a small molecule that recognizes structure may be more well suited for targeting highly structured RNAs that require strand invasion by a complementary oligonucleotide. PMID:24506227

  6. Image-based detection of oligonucleotides--a low cost alternative to spectrophotometric or fluorometric methods.

    PubMed

    Ahirwar, Rajesh; Tanwar, Swati; Parween, Shahila; Kumar, Ashok; Nahar, Pradip

    2014-05-07

    Herein, we report a sensitive and low cost image-based (photocolorimetric) method for the detection of oligonucleotides on an activated polypropylene microtest plate (APPμTP). The assay was developed on the APPμTP by covalently immobilising 20-mer amino-modified oligonucleotides. Biotin-tagged complementary target sequences were then hybridised with the immobilised oligonucleotides. Colour was developed by streptavidin-HRP conjugate and the image of the coloured assay solution was taken by a desktop scanner and analysed using colour saturation. The developed method was analysed for its detection limit, accuracy, sensitivity and interference. The linearity range was found to be 1.7-170 ng mL(-1) while the lower limit of detection and limit of quantification were 1.7 and 5.6 ng mL(-1) respectively. The method showed comparable sensitivity to fluorometric methods, and was found to be correlated to fluorescence (R(2) = 0.8081, p-value < 0.0001) and absorbance (R(2) = 0.9394, p-value < 0.0001)-based quantification. It discriminates mismatched base sequences from perfectly matched sequences efficiently. Validation of the method was carried out by detecting por A DNA of Neisseria meningitidis in bacterial meningitis samples. The por A-specific probe having a 6-carbon spacer at its 5'-NH2 terminus was immobilised covalently to the APPμTP and hybridised with different samples of biotinylated single-stranded por A DNA.

  7. Detection of Glucose with Atomic Absorption Spectroscopy by Using Oligonucleotide Functionalized Gold Nanoparticle.

    PubMed

    Zhang, Hong; Yan, Honglian; Ling, Liansheng

    2016-06-01

    A novel method for the detection of glucose was established with atomic absorption spectroscopy by using the label of gold nanoparticle (AuNP). Silver-coated glass assembled with oligonucleotide 5'-SH-T12-AGA CAA GAG AGG-3' (Oligo 1) was acted as separation probe, oligonucleotide 5'-CAA CAG AGA ACG-T12-SH-3' modified gold nanoparticle (AuNP-Oligo 2) was acted as signal-reporting probe. Oligonucleotide 5'-CGT TCT CTG TTG CCT CTC TTG TCT-3' (Oligo 3) could hybridize with Oligo 1 on the surface of silver-coated glass and AuNP-Oligo 2, and free AuNP-Oligo 2 could be removed by rinsing with buffer. Hence the concentration of Oligo 3 was transformed into the concentration of gold element. In addition, Oligo 3 could be cleaved into DNA fragments by glucose, glucose oxidase and Fe(2+)-EDTA through Fenton reaction. Thereby the concentration of glucose could be transformed to the absorbance of gold element. Under the optimum conditions, the integrated absorbance decreased proportionally to the concentration of glucose over the range from 50.0 μM to 1.0 mM with a detection limit of 40.0 μM. Moreover, satisfactory result was obtained when the assay was used to determinate glucose in human serum.

  8. Targeting the r(CGG) repeats that cause FXTAS with modularly assembled small molecules and oligonucleotides.

    PubMed

    Tran, Tuan; Childs-Disney, Jessica L; Liu, Biao; Guan, Lirui; Rzuczek, Suzanne; Disney, Matthew D

    2014-04-18

    We designed small molecules that bind the structure of the RNA that causes fragile X-associated tremor ataxia syndrome (FXTAS), an incurable neuromuscular disease. FXTAS is caused by an expanded r(CGG) repeat (r(CGG)(exp)) that inactivates a protein regulator of alternative pre-mRNA splicing. Our designed compounds modulate r(CGG)(exp) toxicity in cellular models of FXTAS, and pull-down experiments confirm that they bind r(CGG)(exp) in vivo. Importantly, compound binding does not affect translation of the downstream open reading frame (ORF). We compared molecular recognition properties of our optimal compound to oligonucleotides. Studies show that r(CGG)(exp)'s self-structure is a significant energetic barrier for oligonucleotide binding. A fully modified 2'-OMethyl phosphorothioate is incapable of completely reversing an FXTAS-associated splicing defect and inhibits translation of the downstream ORF, which could have deleterious effects. Taken together, these studies suggest that a small molecule that recognizes structure may be more well suited for targeting highly structured RNAs that require strand invasion by a complementary oligonucleotide.

  9. Cationic derivatives of biocompatible hyaluronic acids for delivery of siRNA and antisense oligonucleotides.

    PubMed

    Han, Su-Eun; Kang, Hyungu; Shim, Ga Yong; Kim, Sun Jae; Choi, Han-Gon; Kim, Jiseok; Hahn, Sei Kwang; Oh, Yu-Kyoung

    2009-02-01

    In this study, we tested the use of cationic polymer derivatives of biocompatible hyaluronic acid (HA) as a delivery system of siRNA and antisense oligonucleotides. HA was modified with cationic polymer polyethylenimine (PEI). When compared with PEI alone, cationic PEI derivatives of HA (HA-PEI) provided increased cellular delivery of Small interfering RNA (siRNA) in B16F1, A549, HeLa, and Hep3B tumor cells. Indeed, more than 95% of the cells were positive for siRNA following its delivery with HA-PEI. A survivin-specific siRNA that was delivered using HA-PEI potently reduced the mRNA expression levels of the target gene in all of the cell lines. By contrast, survivin-specific siRNA delivered by PEI alone did not induce a significant reduction in mRNA levels. In green fluorescent protein (GFP)-expressing 293 T cells, a loss of GFP expression was evident in the cells that had been treated with GFP-specific siRNA and HA-PEI complex. The inhibition of target gene expression by antisense oligonucleotide G3139 was also enhanced after delivery with HA-PEI. Moreover, HA-PEI displayed lower cytotoxicity than PEI alone. These results suggest that HA-PEI could be further developed as biocompatible delivery systems of siRNA and antisense oligonucleotides for enhanced cellular uptake and inhibition of target gene expression.

  10. A Comparative Study of the Bone Regenerative Effect of Chemically Modified RNA Encoding BMP-2 or BMP-9.

    PubMed

    Khorsand, Behnoush; Elangovan, Satheesh; Hong, Liu; Dewerth, Alexander; Kormann, Michael S D; Salem, Aliasger K

    2017-03-01

    Employing cost-effective biomaterials to deliver chemically modified ribonucleic acid (cmRNA) in a controlled manner addresses the high cost, safety concerns, and lower transfection efficiency that exist with protein and gene therapeutic approaches. By eliminating the need for nuclear entry, cmRNA therapeutics can potentially overcome the lower transfection efficiencies associated with non-viral gene delivery systems. Here, we investigated the osteogenic potential of cmRNA-encoding BMP-9, in comparison to cmRNA-encoding BMP-2. Polyethylenimine (PEI) was used as a vector to increase in vitro transfection efficacy. Complexes of PEI-cmRNA (encoding BMP-2 or BMP-9) were fabricated at an amine (N) to phosphate (P) ratio of 10 and characterized for transfection efficacy in vitro using human bone marrow stromal cells (BMSCs). The osteogenic potential of BMSCs treated with these complexes was determined by evaluating the expression of bone-specific genes as well as through the detection of bone matrix deposition. It was found that alkaline phosphatase (ALP) expression 3 days post transfection in the group treated with BMP-9-cmRNA was significantly higher than that in the group that received BMP-2-cmRNA treatment. Alizarin red staining and atomic absorption spectroscopy demonstrated enhanced osteogenic differentiation as evidenced by increased bone matrix production by the BMSCs treated with BMP-9-cmRNA when compared to cells treated with BMP-2-cmRNA. In vivo studies showed increased bone formation in calvarial defects treated with the BMP-9-cmRNA and BMP-2-cmRNA collagen scaffolds when compared to empty defects. The connectivity density of the regenerated bone was higher (2-fold-higher) in the group that received BMP-9-cmRNA compared to BMP-2-cmRNA. Together, these findings suggest that cmRNA-activated matrix encoding osteogenic molecules can provide a powerful strategy for bone regeneration with significant clinical translational potential.

  11. Biosorption of cesium by native and chemically modified biomass of marine algae: introduce the new biosorbents for biotechnology applications.

    PubMed

    Jalali-Rad, R; Ghafourian, H; Asef, Y; Dalir, S T; Sahafipour, M H; Gharanjik, B M

    2004-12-10

    Biosorption batch experiments were conducted to determine the cesium binding ability of native biomass and chemically modified biosorbents derived from marine algae, namely ferrocyanide algal sorbents type 1 and type 2 (FASs1 and FASs2). The applicability of the Langmuir and Freundlich isotherms for representation of the experimental data was investigated. The cesium sorption performances of the various types of sorbents were compared using the maximum capacities (qmax values) obtained from fitting the Langmuir isotherm to the values calculated from the sorption experiments, which FASs type 1 and type 2 showed better sorption performances for cesium. FASs1 and FASs2 derived from formaldehyde and glutaraldehyde crosslinked Padina australis exhibited lower sorption capacities than those prepared from the non-crosslinked one. Most of the cesium ions were bound to FASs1, derived from Sargassum glaucescens and P. australis, in < 2 min and equilibrium reached within the first 30 min of contact. Biosorption of cesium by FASs1 derived from P. australis and Cystoseria indica was constantly occurred at a wide range of pH, between 1 and 10, and the highest removal took place at pH 4. The presence of sodium and potassium at 0.5 and 1mM did not inhibit cesium biosorption by algae biomass. The maximum cesium uptake was acquired using the large particles of FAS2 originated from S. glaucescens (2-4 mm). Desorption of cesium from the metal-laden FASs1 (from P. australis, S. glaucescens and Dictyota indica) was completely achieved applying 0.5 and 1 M NaOH and KOH, although the cesium sorption capacity of the biosorbents (from C. indica and S. glaucescens) decreased by 46-51% after 9 sorption-desorption cycles.

  12. A Standardized Chemically Modified Curcuma longa Extract Modulates IRAK-MAPK Signaling in Inflammation and Potentiates Cytotoxicity

    PubMed Central

    Rana, Minakshi; Maurya, Preeti; Reddy, Sukka S.; Singh, Vishal; Ahmad, Hafsa; Dwivedi, Anil K.; Dikshit, Madhu; Barthwal, Manoj K.

    2016-01-01

    The TLR/IL-1R pathway is a critical signaling module that is misregulated in pathologies like inflammation and cancer. Extracts from turmeric (Curcuma longa L.) enriched in curcumin and carbonyls like turmerones have been shown to exert potent anti-inflammatory effects. The present study evaluated the anti-inflammatory activity, cytotoxic effect and the underlying mechanism of a novel chemically modified, non-carbonyl compound enriched Curcuma longa L. (C. longa) extract (CMCE). CMCE (1 or 10 μg/mL; 14 h) significantly decreased LPS (50-100 ng/mL) induced TNF-α and IL-1β production in THP-1 cells, human, and mouse whole blood as measured by ELISA. LPS-induced IRAK1, MAPK activation, TLR4 expression, TLR4-MyD88 interaction, and IκBα degradation were significantly reduced in CMCE pre-treated THP-1 cells as assessed by Western blotting. CMCE (30, 100, and 300 mg/kg; 10 days p.o.) pre-treated and LPS (10 mg/kg) challenged Swiss mice exhibited attenuated plasma TNF-α, IL-1β, nitrite, aortic iNOS expression, and vascular dysfunction. In a PI permeability assay, cell lines derived from acute myeloid leukemia were most sensitive to the cytotoxic effects of CMCE. Analysis of Sub-G1 phase, Annexin V-PI positivity, loss of mitochondrial membrane potential, increased caspase-3, and PARP-1 activation confirmed CMCE induced apoptosis in HL-60 cells. IRAK inhibition also sensitized HL-60 cells to CMCE induced cytotoxicity. The present study defines the mechanism underlying the action of CMCE and suggests a therapeutic potential for its use in sepsis and leukemia. PMID:27504095

  13. A Standardized Chemically Modified Curcuma longa Extract Modulates IRAK-MAPK Signaling in Inflammation and Potentiates Cytotoxicity.

    PubMed

    Rana, Minakshi; Maurya, Preeti; Reddy, Sukka S; Singh, Vishal; Ahmad, Hafsa; Dwivedi, Anil K; Dikshit, Madhu; Barthwal, Manoj K

    2016-01-01

    The TLR/IL-1R pathway is a critical signaling module that is misregulated in pathologies like inflammation and cancer. Extracts from turmeric (Curcuma longa L.) enriched in curcumin and carbonyls like turmerones have been shown to exert potent anti-inflammatory effects. The present study evaluated the anti-inflammatory activity, cytotoxic effect and the underlying mechanism of a novel chemically modified, non-carbonyl compound enriched Curcuma longa L. (C. longa) extract (CMCE). CMCE (1 or 10 μg/mL; 14 h) significantly decreased LPS (50-100 ng/mL) induced TNF-α and IL-1β production in THP-1 cells, human, and mouse whole blood as measured by ELISA. LPS-induced IRAK1, MAPK activation, TLR4 expression, TLR4-MyD88 interaction, and IκBα degradation were significantly reduced in CMCE pre-treated THP-1 cells as assessed by Western blotting. CMCE (30, 100, and 300 mg/kg; 10 days p.o.) pre-treated and LPS (10 mg/kg) challenged Swiss mice exhibited attenuated plasma TNF-α, IL-1β, nitrite, aortic iNOS expression, and vascular dysfunction. In a PI permeability assay, cell lines derived from acute myeloid leukemia were most sensitive to the cytotoxic effects of CMCE. Analysis of Sub-G1 phase, Annexin V-PI positivity, loss of mitochondrial membrane potential, increased caspase-3, and PARP-1 activation confirmed CMCE induced apoptosis in HL-60 cells. IRAK inhibition also sensitized HL-60 cells to CMCE induced cytotoxicity. The present study defines the mechanism underlying the action of CMCE and suggests a therapeutic potential for its use in sepsis and leukemia.

  14. Minimizing DNA microarrays to a single molecule per spot: using zero-mode waveguide technology to obtain kinetic data for a large number of short oligonucleotide hybridization reactions

    NASA Astrophysics Data System (ADS)

    Sobek, Jens; Rehrauer, Hubert; Kuhn, Gerrit; Schlapbach, Ralph

    2016-03-01

    We have shown recently that the hybridization of short oligonucleotides can be studied in a zero-mode waveguide nanostructure (ZMW) chip using a modified DNA sequencer.[1] Here we present an extension of this method enabling the parallel measurement of kinetic constants of a large number of hybridization reactions on a single chip. This can be achieved by immobilization of a mixture of oligonucleotides, which leads to a statistical and random distribution of single molecules in the 150'000 ZMWs of a SMRT™ cell. This setup is comparable to a classical microarray with ZMWs in place of spots but unknown allocation of probes. The probe surface density is reduced by a factor of ~1010 allowing the study of hybridization in the absence of interactions with neighboring probes. Hybridization with a dye labelled oligonucleotide results in trains of fluorescence pulses from which interpulse durations (IPDs) and pulse widths (PWs) can be extracted. Since the identity of a probe in a ZMW is unknown, the immobilized oligonucleotide is sequenced in a subsequent step. After mapping the fluorescence traces to the sequence, the association and dissociation rate constant for each oligonucleotide can be calculated. By selecting suitable probes, the method can be used to determine rate constants of hybridization for a large number of mismatch oligonucleotides in a single measurement and at single-molecule level.

  15. Polypurine reverse-Hoogsteen (PPRH) oligonucleotides can form triplexes with their target sequences even under conditions where they fold into G-quadruplexes

    PubMed Central

    Solé, Anna; Delagoutte, Emmanuelle; Ciudad, Carlos J.; Noé, Véronique; Alberti, Patrizia

    2017-01-01

    Polypurine reverse-Hoogsteen (PPRH) oligonucleotides are non-modified DNA molecules composed of two mirror-symmetrical polypurine stretches linked by a five-thymidine loop. They can fold into reverse-Hoogsteen hairpins and bind to their polypyrimidine target sequence by Watson-Crick bonds forming a three-stranded structure. They have been successfully used to knockdown gene expression and to repair single-point mutations in cells. In this work, we provide an in vitro characterization (UV and fluorescence spectroscopy, gel electrophoresis and nuclease assays) of the structure and stability of two repair-PPRH oligonucleotides and of the complexes they form with their single-stranded targets. We show that one PPRH oligonucleotide forms a hairpin, while the other folds, in potassium, into a guanine-quadruplex (G4). However, the hairpin-prone oligonucleotide does not form a triplex with its single-stranded target, while the G4-prone oligonucleotide converts from a G4 into a reverse-Hoogsteen hairpin forming a triplex with its target sequence. Our work proves, in particular, that folding of a PPRH oligonucleotide into a G4 does not necessarily impair sequence-specific DNA recognition by triplex formation. It also illustrates an original example of DNA structural conversion of a G4 into a reverse-Hoogsteen hairpin driven by triplex formation; this kind of conversion might occur at particular loci of genomic DNA. PMID:28067256

  16. Empirical Calculations of {sup 29}Si NMR Chemical Shielding Tensors: A Partial Charge Model Investigation of Hydrolysis in Organically Modified Alkoxy Silanes

    SciTech Connect

    Alam, Todd M.; Henry, Marc

    1999-08-05

    Organically modified alkoxy silanes play an important role in tailoring different properties of silica produced by the sol-gel method. Changes in the size and functionality of the organic group allows control of both physical and chemical properties of the resulting gel, with the kinetics of the polymerization process playing an important role in the design of new siloxane materials. High resolution {sup 29}Si NMR has proven to be valuable tool for monitoring the polymerization reaction, and has been used to investigate a variety of organically modified alkoxy silane systems.

  17. Nucleic acid sequence detection using multiplexed oligonucleotide PCR

    DOEpatents

    Nolan, John P.; White, P. Scott

    2006-12-26

    Methods for rapidly detecting single or multiple sequence alleles in a sample nucleic acid are described. Provided are all of the oligonucleotide pairs capable of annealing specifically to a target allele and discriminating among possible sequences thereof, and ligating to each other to form an oligonucleotide complex when a particular sequence feature is present (or, alternatively, absent) in the sample nucleic acid. The design of each oligonucleotide pair permits the subsequent high-level PCR amplification of a specific amplicon when the oligonucleotide complex is formed, but not when the oligonucleotide complex is not formed. The presence or absence of the specific amplicon is used to detect the allele. Detection of the specific amplicon may be achieved using a variety of methods well known in the art, including without limitation, oligonucleotide capture onto DNA chips or microarrays, oligonucleotide capture onto beads or microspheres, electrophoresis, and mass spectrometry. Various labels and address-capture tags may be employed in the amplicon detection step of multiplexed assays, as further described herein.

  18. Carboranyl Nucleosides & Oligonucleotides for Neutron Capture Therapy Final Report

    SciTech Connect

    Schinazi, Raymond F.

    2004-12-01

    -methyl)phosphonate (CBMP) internucleotide group. Unmodified phosphodiester linkages were formed using a standard {beta}-cyanoethyl cycle and automated DNA synthesizer. Modified CBMP internucleotide linkage was produced using the phosphotriester method and 5'-O-monomethoxytritylthymidine 3'-O-[(o-carboran-1-yl-methyl)phosphonate] monomer. Several dodecathymidylic acids bearing modification at 3'- or 5'-end, or in the middle of oligonucleotide chain were synthesized. The resulting oligomers are being characterized by reverse phase high-pressure liquid chromatography (RP-HPLC), electrospray ionization mass spectrometry (ESIMS), ultraviolet spectroscopy (UV), and circular dichroism (CD). In collaboration with Cornell University, we employed a secondary ion mass spectrometry (SIMS) based subcellular isotopic imaging technique of ion microscopy for evaluating 4 carboranyl nucleosides. Nucleosides synthesized by our group, including CDU, HMCDU, CTU, and CFAU were tested for their boron delivery to the nuclear and cytoplasmic compartments of U251 human and F98 rat glioma cells. Quantitative SIMS analysis of boron was performed in cryogenically prepared cells. For all drugs, the cell cytoplasm revealed significantly higher boron than the nucleus. However, the boron partitioning between the cell nucleus and the nutrient medium indicated 6.4-10.6 times higher boron in the nucleus. The results suggested that these novel carboranyl nucleosides should provide efficient BNCT agents that accumulate in malignant cells and the need for further evaluations in vitro and in animal models.

  19. Method for the preparation of size marker for synthetic oligonucleotides

    SciTech Connect

    Jing, G.Z.; Liu, A.; Leung, W.C.

    1986-01-01

    Terminal deoxynucleotidyltransferase was used for the addition of (..cap alpha..-/sup 32/P)dCTP to the 3'-OH termini of oligo(dT)/sub 12-18/. A collection of oligonucleotides with chain lengths ranging continuously from 13-mer to over 100-mer was generated. The reaction mixture was then mixed with oligo(dT)/sub 12-18/ labeled with (..gamma..-/sup 32/P)ATP by T/sub 4/ polynucleotide kinase. A sequence ladder with the bottom base as 12-mer was then formed. These oligonucleotides served as size marker for the purification and identification of oligonucleotides on polyacrylamide gel.

  20. Retro-1 Analogues Differentially Affect Oligonucleotide Delivery and Toxin Trafficking.

    PubMed

    Yang, Bing; Ming, Xin; Abdelkafi, Hajer; Pons, Valerie; Michau, Aurelien; Gillet, Daniel; Cintrat, Jean-Christophe; Barbier, Julien; Juliano, Rudy

    2016-11-21

    Retro-1 is a small molecule that displays two important biological activities: First, it blocks the actions of certain toxins by altering their intracellular trafficking. Second, it enhances the activity of oligonucleotides by releasing them from entrapment in endosomes. This raises the question of whether the two actions involve the same cellular target. Herein we report the effects of several Retro-1 analogues on both toxins and oligonucleotides. We found analogues that affect toxins but not oligonucleotides and vice-versa, while Retro-1 is the only compound that affects both. This indicates that the molecular target(s) involved in the two processes are distinct.

  1. Therapeutic oligonucleotides and delivery technologies: Research topics in Japan.

    PubMed

    Murakami, Masahiro

    2016-01-01

    Oligonucleotides have been gaining considerable attention as promising and effective candidate therapeutics against various diseases. This special issue is aimed at providing a better understanding of the recent progress in the development of oligonucleotide-based therapeutics to encourage further research and innovation in this field to achieve these advancements. Several Japanese scientists have been invited to contribute to this issue by describing their recent findings, overviews, insights, or commentaries on rational designing of therapeutic oligonucleotide molecules and their novel delivery technologies, especially nanocarrier systems.

  2. Chemically-enzymatic synthesis of photosensitive DNA.

    PubMed

    Westphal, Kinga; Zdrowowicz, Magdalena; Zylicz-Stachula, Agnieszka; Rak, Janusz

    2017-02-01

    The sensitizing propensity of radio-/photosensitizing nucleoside depends on DNA sequence surrounding a sensitizer. Therefore, in order to compare sensitizers with regard to their ability to induce a DNA damage one has to study the sequence dependence of damage yield. However, chemical synthesis of oligonucleotides labeled with sensitizing nucleosides is hindered due to the fact that a limited number of such nucleoside phosphoramidites are accessible. Here, we report on a chemically-enzymatic method, employing a DNA polymerase and ligase, that enables a modified nucleoside, in the form of its 5'-triphosphate, to be incorporated into DNA fragment in a pre-determined site. Using such a protocol two double-stranded DNA fragments - a long one, 75 base pairs (bp), and a short one, 30bp in length - were pin-point labeled with 5-bromodeoxyuridine. Four DNA polymerases together with DHPLC for the inspection of reaction progress were used to optimize the process under consideration. As an ultimate test showing that the product possessing an assumed nucleotide sequence was actually obtained, we irradiated the synthesized oligonucleotide with UVB photons and analyzed its photoreactivity with the LC-MS method. Our results prove that a general approach enabling precise labeling of DNA with any nucleoside modification processed by DNA polymerase and ligase has been worked out.

  3. Use of sodium tungstate as a permanent chemical modifier for slurry sampling electrothermal atomic absorption spectrometric determination of indium in soils.

    PubMed

    López-García, Ignacio; Rivas, Ricardo E; Hernández-Córdoba, Manuel

    2008-06-01

    A number of chemical modifiers have been assessed for the direct determination of indium in soils using electrothermal atomic absorption spectrometry and slurry sampling. The best results were obtained when the graphite atomizer was impregnated with sodium tungstate, which acts as a permanent chemical modifier. Slurries were prepared by suspending 100 mg sample in a solution containing 1% (v/v) concentrated nitric acid and 10% (v/v) concentrated hydrofluoric acid and then 15-microL aliquots were directly introduced into the atomizer. Standard indium solutions prepared in the suspension medium in the range 4-80 microg L(-1) indium were used for calibration. The relative standard deviation for ten consecutive measurements of a 40 microg L(-1) indium solution was 2.8%. The limit of detection in soils was 0.1 microg g(-1). The reliability of the procedures was confirmed by analysing two standard reference materials and by using an alternative procedure.

  4. Intrinsically Labeled Fluorescent Oligonucleotide Probes on Quantum Dots for Transduction of Nucleic Acid Hybridization.

    PubMed

    Shahmuradyan, Anna; Krull, Ulrich J

    2016-03-15

    Quantum dots (QDs) have been widely used in chemical and biosensing due to their unique photoelectrical properties and are well suited as donors in fluorescence resonance energy transfer (FRET). Selective hybridization interactions of oligonucleotides on QDs have been determined by FRET. Typically, the QD-FRET constructs have made use of labeled targets or have implemented labeled sandwich format assays to introduce dyes in proximity to the QDs for the FRET process. The intention of this new work is to explore a method to incorporate the acceptor dye into the probe molecule. Thiazole orange (TO) derivatives are fluorescent intercalating dyes that have been used for detection of double-stranded nucleic acids. One such dye system has been reported in which single-stranded oligonucleotide probes were doubly labeled with adjacent thiazole orange derivatives. In the absence of the fully complementary (FC) oligonucleotide target, the dyes form an H-aggregate, which results in quenching of fluorescence emission due to excitonic interactions between the dyes. The hybridization of the FC target to the probe provides for dissociation of the aggregate as the dyes intercalate into the double stranded duplex, resulting in increased fluorescence. This work reports investigation of the dependence of the ratiometric signal on the type of linkage used to conjugate the dyes to the probe, the location of the dye along the length of the probe, and the distance between adjacent dye molecules. The limit of detection for 34mer and 90mer targets was found to be identical and was 10 nM (2 pmol), similar to analogous QD-FRET using labeled oligonucleotide target. The detection system could discriminate a one base pair mismatch (1BPM) target and was functional without substantial compromise of the signal in 75% serum. The 1BPM was found to reduce background signal, indicating that the structure of the mismatch affected the environment of the intercalating dyes.

  5. Polyphosphorylation and non-enzymatic template-directed ligation of oligonucleotides

    NASA Technical Reports Server (NTRS)

    Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    2000-01-01

    Oligonucleotide 5'-polyphosphates are formed under potentially prebiotic conditions from oligonucleotide 5'-phosphates and sodium trimetaphosphate. Oligonucleotides activated as polyphosphates undergo template-directed ligation. We believe that these reactions could have produced longer oligonucleotide products from shorter substrates under prebiotic conditions.

  6. Characterization of a chemically modified plant cell culture expressed human α-Galactosidase-A enzyme for treatment of Fabry disease.

    PubMed

    Kizhner, Tali; Azulay, Yaniv; Hainrichson, Mariana; Tekoah, Yoram; Arvatz, Gil; Shulman, Avidor; Ruderfer, Ilya; Aviezer, David; Shaaltiel, Yoseph

    2015-02-01

    Fabry disease is an X-linked recessive disorder caused by the loss of function of the lysosomal enzyme α-Galactosidase-A. Although two enzyme replacement therapies (ERTs) are commercially available, they may not effectively reverse some of the Fabry pathology. PRX-102 is a novel enzyme for the therapy of Fabry disease expressed in a BY2 Tobacco cell culture. PRX-102 is chemically modified, resulting in a cross-linked homo-dimer. We have characterized the in-vitro and in-vivo properties of PRX-102 and compared the results with the two commercially produced α-Galactosidase-A enzymes. Results show that PRX-102 has prolonged in-vitro stability in plasma, after 1h incubation it retains 30% activity compared with complete inactivation of the commercial enzymes. Under lysosomal-like conditions PRX-102 maintains over 80% activity following 10 days of incubation, while commercial enzymes become inactive after 2days. Pharmacokinetic profile of PRX-102 measured in male Fabry mice shows a 10 fold increase in t1/2 in mice (581min) compared to approved drugs. The enzyme has significantly different kinetic parameters to the alternative ERTs available (p-value<0.05, one way ANOVA), although these differences do not indicate any significant biochemical variations. PRX-102 is uptaken to primary human Fabry fibroblasts. The repeat administration of the enzyme to Fabry mice caused significant reduction (p-value<0.05) of Gb3 in various tissues (the measured residual content was 64% in kidney, liver was cleaned, 23% in heart, 5.7% in skin and 16.2% in spleen). PRX-102 has a relatively simple glycosylation pattern, characteristic to plants, having mainly tri-mannose structures with the addition of either α(1-3)-linked fucose or β(1-2)-linked xylose, or both, in addition to various high mannose structures, while agalsidase beta has a mixture of sialylated glycans in addition to high mannose structures. This study concludes that PRX-102 is equivalent in functionality to the current

  7. Effect of chemically modified Vulcan XC-72R on the performance of air-breathing cathode in a single-chamber microbial fuel cell.

    PubMed

    Duteanu, N; Erable, B; Senthil Kumar, S M; Ghangrekar, M M; Scott, K

    2010-07-01

    The catalytic activity of modified carbon powder (Vulcan XC-72R) for oxygen reduction reaction (ORR) in an air-breathing cathode of a microbial fuel cell (MFC) has been investigated. Chemical modification was carried out by using various chemicals, namely 5% nitric acid, 0.2N phosphoric acid, 0.2N potassium hydroxide and 10% hydrogen peroxide. Electrochemical study was performed for ORR of these modified carbon materials in the buffer solution pH range of 6-7.5 in the anodic compartment. Although, these treatments influenced the surface properties of the carbon material, as evident from the SEM-EDX analysis, treatment with H(2)PO(4), KOH, and H(2)O(2) did not show significant activity during the electrochemical test. The HNO(3) treated Vulcan demonstrated significant ORR activity and when used in the single-chamber MFC cathode, current densities (1115mA/m(2), at 5.6mV) greater than those for a Pt-supported un-treated carbon cathode were achieved. However, the power density for the latter was higher. Such chemically modified carbon material can be a cheaper alternative for expensive platinum catalyst used in MFC cathode construction.

  8. Micro- and nano-structure based oligonucleotide sensors.

    PubMed

    Ferrier, David C; Shaver, Michael P; Hands, Philip J W

    2015-06-15

    This paper presents a review of micro- and nano-structure based oligonucleotide detection and quantification techniques. The characteristics of such devices make them very attractive for Point-of-Care or On-Site-Testing biosensing applications. Their small scale means that they can be robust and portable, their compatibility with modern CMOS electronics means that they can easily be incorporated into hand-held devices and their suitability for mass production means that, out of the different approaches to oligonucleotide detection, they are the most suitable for commercialisation. This review discusses the advantages of micro- and nano-structure based sensors and covers the various oligonucleotide detection techniques that have been developed to date. These include: Bulk Acoustic Wave and Surface Acoustic Wave devices, micro- and nano-cantilever sensors, gene Field Effect Transistors, and nanowire and nanopore based sensors. Oligonucleotide immobilisation techniques are also discussed.

  9. PRACTICAL STRATEGIES FOR PROCESSING AND ANALYZING SPOTTED OLIGONUCLEOTIDE MICROARRAY DATA

    EPA Science Inventory

    Thoughtful data analysis is as important as experimental design, biological sample quality, and appropriate experimental procedures for making microarrays a useful supplement to traditional toxicology. In the present study, spotted oligonucleotide microarrays were used to profile...

  10. Methods to Characterize the Oligonucleotide Functionalization of Quantum Dots.

    PubMed

    Weichelt, Richard; Leubner, Susanne; Henning-Knechtel, Anja; Mertig, Michael; Gaponik, Nikolai; Schmidt, Thorsten-Lars; Eychmüller, Alexander

    2016-09-01

    Currently, DNA nanotechnology offers the most programmable, scalable, and accurate route for the self-assembly of matter with nanometer precision into 1, 2, or 3D structures. One example is DNA origami that is well suited to serve as a molecularly defined "breadboard", and thus, to organize various nanomaterials such as nanoparticles into hybrid systems. Since the controlled assembly of quantum dots (QDs) is of high interest in the field of photonics and other optoelectronic applications, a more detailed view on the functionalization of QDs with oligonucleotides shall be achieved. In this work, four different methods are presented to characterize the functionalization of thiol-capped cadmium telluride QDs with oligonucleotides and for the precise quantification of the number of oligonucleotides bound to the QD surface. This study enables applications requiring the self-assembly of semiconductor-oligonucleotide hybrid materials and proves the conjugation success in a simple and straightforward manner.

  11. SERS beacons for multiplexed oligonucleotide detection

    NASA Astrophysics Data System (ADS)

    Sun, Jian; Cullum, Brian M.

    2007-09-01

    Gold-based surface-enhanced Raman scattering (SERS) beacons have been developed, which represent a simple, biocompatible and rapid means of performing multiplexed DNA sequence detection in a non-arrayed format. These SERS beacons consist of a simple stem-loop oligonucleotide probe in its native form with one end attached to a SERS active dye molecule and the other to a gold nanoparticle, approximately 50 nm in diameter. The probe sequence is designed to achieve a stem-loop structure, with the loop portion complementary to the target sequence, similar to fluorescent molecular beacons. In the absence of the target DNA sequence, the SERS signal of the associated dye molecule is detected, representing the "ON" state of the probe. When the target sequence is hybridized to the probe, which results in an open conformation, its respective reporter dye is separated from the gold nanoparticle, producing diminished SERS signal. In this paper, the fabrication and characterization of these SERS beacons is described. We also demonstrate selective hybridization of a target sequence to one beacon in a mixture, revealing their potential for use in a multiplexed fashion.

  12. Photophysical deactivation pathways in adenine oligonucleotides.

    PubMed

    Spata, Vincent A; Matsika, Spiridoula

    2015-12-14

    In this work we study deactivation processes in adenine oligomers after absorption of UV radiation using Quantum Mechanics combined with Molecular Mechanics (QM/MM). Correlated electronic structure methods appropriate for describing the excited states are used to describe a π-stacked dimer of adenine bases incorporated into (dA)20(dT)20. The results of these calculations reveal three different types of excited state minima which play a role in deactivation processes. Within this set of minima there are minima where the excited state is localized on one adenine (monomer-like) as well as minima where the excited state is delocalized on two adenines, forming different types of excimers and bonded excimers of varying but inter-related character. The proximity of their energies reveals that the minima can decay into one another along a flat potential energy surface dependent on the interbase separation. Additionally, analysis of the emissive energies and other physical properties, including theoretical anisotropy calculations, and comparison with fluorescence experiments, provides evidence that excimers play an important role in long-lived signals in adenine oligonucleotides while the subpicosecond decay is attributed to monomer-like minima. The necessity for a close approach of the nucleobases reveals that the deactivation mechanism is tied to macro-molecular motion.

  13. Antisense Oligonucleotide Therapy for Inherited Retinal Dystrophies.

    PubMed

    Gerard, Xavier; Garanto, Alejandro; Rozet, Jean-Michel; Collin, Rob W J

    2016-01-01

    Inherited retinal dystrophies (IRDs) are an extremely heterogeneous group of genetic diseases for which currently no effective treatment strategies exist. Over the last decade, significant progress has been made utilizing gene augmentation therapy for a few genetic subtypes of IRD, although several technical challenges so far prevent a broad clinical application of this approach for other forms of IRD. Many of the mutations leading to these retinal diseases affect pre-mRNA splicing of the mutated genes . Antisense oligonucleotide (AON)-mediated splice modulation appears to be a powerful approach to correct the consequences of such mutations at the pre-mRNA level , as demonstrated by promising results in clinical trials for several inherited disorders like Duchenne muscular dystrophy, hypercholesterolemia and various types of cancer. In this mini-review, we summarize ongoing pre-clinical research on AON-based therapy for a few genetic subtypes of IRD , speculate on other potential therapeutic targets, and discuss the opportunities and challenges that lie ahead to translate splice modulation therapy for retinal disorders to the clinic.

  14. Diagnostic Oligonucleotide Microarray Fingerprinting of Bacillus Isolates

    SciTech Connect

    Chandler, Darrell P.; Alferov, Oleg; Chernov, Boris; Daly, Don S.; Golova, Julia; Perov, Alexander N.; Protic, Miroslava; Robison, Richard; Shipma, Matthew; White, Amanda M.; Willse, Alan R.

    2006-01-01

    A diagnostic, genome-independent microbial fingerprinting method using DNA oligonucleotide microarrays was used for high-resolution differentiation between closely related Bacillus strains, including two strains of Bacillus anthracis that are monomorphic (indistinguishable) via amplified fragment length polymorphism fingerprinting techniques. Replicated hybridizations on 391-probe nonamer arrays were used to construct a prototype fingerprint library for quantitative comparisons. Descriptive analysis of the fingerprints, including phylogenetic reconstruction, is consistent with previous taxonomic organization of the genus. Newly developed statistical analysis methods were used to quantitatively compare and objectively confirm apparent differences in microarray fingerprints with the statistical rigor required for microbial forensics and clinical diagnostics. These data suggest that a relatively simple fingerprinting microarray and statistical analysis method can differentiate between species in the Bacillus cereus complex, and between strains of B. anthracis. A synthetic DNA standard was used to understand underlying microarray and process-level variability, leading to specific recommendations for the development of a standard operating procedure and/or continued technology enhancements for microbial forensics and diagnostics.

  15. Syntheses of oligonucleotide derivatives with P(V) porphyrin and their properties.

    PubMed

    Shimidzu, T; Segawa, H; Kitamura, M; Nimura, A

    1992-01-01

    Two types of oligonucleotide derivatives which are substituted by P(V) porphyrin at the phosphorus atom of an internucleotidic linkage and at the 5'-terminal internucleotidic linkage via a spacer were synthesized (Fig. 1), and hybridization capabilities of them with complementary oligonucleotides were evaluated. A novel method for a sensing of oligonucleotide by the fluorescence quenching via photo-induced electron transfer between the P(V) porphyrin labeled oligonucleotide and pyrene-labeled one on the oligonucleotide template is reported.

  16. Targeted delivery of chemically modified anti-miR-221 to hepatocellular carcinoma with negatively charged liposomes.

    PubMed

    Zhang, Wendian; Peng, Fangqi; Zhou, Taotao; Huang, Yifei; Zhang, Li; Ye, Peng; Lu, Miao; Yang, Guang; Gai, Yongkang; Yang, Tan; Ma, Xiang; Xiang, Guangya

    2015-01-01

    Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death. Gene therapy was established as a new strategy for treating HCC. To explore the potential delivery system to support the gene therapy of HCC, negatively charged liposomal delivery system was used to deliver miR-221 antisense oligonucleotide (anti-miR-221) to the transferrin (Tf) receptor over expressed HepG2 cells. The liposome exhibited a mean particle size of 122.5 nm, zeta potential of -15.74 mV, anti-miR-221 encapsulation efficiency of 70%, and excellent colloidal stability at 4°C. Anti-miR-221-encapsulated Tf-targeted liposome demonstrated a 15-fold higher delivery efficiency compared to nontargeted liposome in HepG2 cells in vitro. Anti-miR-221 Tf-targeted liposome effectively delivered anti-miR-221 to HepG2 cells, upregulated miR-221 target genes PTEN, P27(kip1), and TIMP3, and exhibited greater silencing efficiency over nontargeted anti-miR-221 liposome. After intravenous injection into HepG2 tumor-bearing xenografted mice with Cy3-labeled anti-miR-221 Tf-targeted liposome, Cy3-anti-miR-221 was successfully delivered to the tumor site and increased the expressions of PTEN, P27(kip1), and TIMP3. Our results demonstrate that the Tf-targeted negatively charged liposome could be a potential therapeutic modality in the gene therapy of human HCC.

  17. Environmental risks of chemicals and genetically modified organisms: a comparison. Part II: Sustainability and precaution in risk assessment and risk management.

    PubMed

    Steinhäuser, K G

    2001-01-01

    The principles of precaution and sustainability require more consideration in the assessment of environmental risks posed by chemicals and genetically modified organisms. Instead of applying risk reduction measures when there are serious indications for damage, full scientific certainty is often waited for before taking action. The precautionary principle particularly should be applied in those cases in which the extent and probability of damage are uncertain, e.g. in the case of persistent chemicals which are additionally bioaccumulative or highly mobile. Based on these principles, environmental action targets for risks associated with GMOs and chemicals can be developed. Risk management not only includes statutory measures but also instruments designed to influence behaviour indirectly are important to achieve the goals. Particularly for risks of GMOs which provoke fear, risk communication is important. Some rules to which attention should be paid in communication with the public are presented.

  18. The Identification and Role of Non-Chemical Stressors as Modifiers of Chemical Exposures that Lead to Changes in Health and Well-Being in Children

    EPA Science Inventory

    Describe the Sustainable and Health Communities (SHC) Research Program at the U.S. EPA Discuss non-chemical stressors found in the social environment, What are they? Why are they important? Summarize current and planned work

  19. Chemical analysis for optimal synthesis of ferrihydrite-modified diatomite using soft X-ray absorption near-edge structure spectroscopy

    NASA Astrophysics Data System (ADS)

    Xiong, Wenhui; Peng, Jian; Hu, Yongfeng

    2009-12-01

    Effects of process parameters such as concentrations of FeCl2, NaOH, and drying temperature on the formation mechanism and chemical characteristics of ferrihydrite-modified diatomite are studied by using X-ray absorption near-edge structure spectroscopy. The spectra were recorded in total electron yield mode and/or fluorescence yield mode to investigate the chemical nature of Fe and Si on the surface and/or in the bulk of ferrihydrite-modified diatomite, respectively. It was found that only the surface SiO2 was partially dissolved in the NaOH solution with stirring and heating, whereas the bulk of diatomite seemed to be preserved. The dissolved Si was incorporated into the structure of ferrihydrite to form the 2-line Si-containing ferrihydrite on the surface of diatomite. The crystalline degree of ferrihydrite increased with the increasing FeCl2 concentration and the Brunauer-Emmett-Teller specific surface area of ferrihydrite-modified diatomite decreased with the increasing FeCl2 concentration. The crystalline degree of ferrihydrite decreased with the increase of NaOH concentration. The high temperature calcination caused an energy shift in the Si L-edge spectra to the high energy side and a transformation of Si-containing ferrihydrite to crystallized hematite might occur when ferrihydrite-modified diatomite is calcined at 900°C. In this study, the optimal synthesis conditions for the ferrihydrite-modified diatomite with the least crystalline Si-containing ferrihydrite and the highest surface area were found to be as the follows: 0.5 M FeCl2 solution, 6 M NaOH solution and drying temperature of 50°C.

  20. [Effects of Different Modifier Concentrations on Lead-Zinc Tolerance, Subcellular Distribution and Chemical Forms for Four Kinds of Woody Plants].

    PubMed

    Chen, Yong-hua; Zhang, Fu-yun; Wu, Xiao-fu; Liang, Xi; Yuan, Si-wen

    2015-10-01

    Four kinds of lead-zinc tolerant woody plants: Nerium oleander, Koelreuteria paniculata, Paulownia and Boehmeria were used as materials to estimate their enrichment and transferable capacity of lead (Pb) and zinc (Zn) and analyze the subcellular distribution and chemical speciation of Zn and Ph in different parts of plants, under different modifier concentrations (CK group: 100% lead-zinc slag plus a small amount of phosphate fertilizer, improved one: 85% of lead-zinc slag ± 10% peat ± 5% bacterial manure plus a small amount of phosphate fertilizer, improved two: 75% lead-zinc slag ± 20% peat ± 5% bacterial manure ± a small amount of phosphate). Results showed that: (1) The content of Pb, Zn in matrix after planting four kinds of plants was lower than before, no significant difference between improved one and improved two of Nerium oleander and Boehmeria was found, but improved two was better than improved one of Paulownia, while improved one was better than improved two of Koelreuteria paniculata; Four plants had relatively low aboveground enrichment coefficient of Pb and Zn, but had a high transfer coefficient, showed that the appropriate modifier concentration was able to improve the Pb and Zn enrichment and transfer ability of plants. (2) In subcellular distribution, most of Pb and Zn were distributed in plant cell wall components and soluble components while the distribution in cell organelles such as mitochondria, chloroplasts and nucleus component were less. Compared with CK group, two improved group made soluble components of the cell walls of Pb fixation and retention of zinc role in the enhancement. (3) As for the chemical forms of Pb and Zn in plants, the main chemical forms of Pb were hydrochloric acid, sodium chloride and ethanol extractable forms, while other chemical form contents were few, the main chemical forms of Zn were different based on plant type. Compared with CK group, the proportion of the active Pb chemical form in different plant

  1. Preconcentration and determination of mercury(II) at a chemically modified electrode containing 3-(2-thioimidazolyl)propyl silica gel.

    PubMed

    Dias Filho, Newton L; do Carmo, Devaney R; Caetano, Laércio; Rosa, André H

    2005-11-01

    A mercury-sensitive chemically modified graphite paste electrode was constructed by incorporating modified silica gel into a conventional graphite paste electrode. The functional group attached to the (3-chloropropyl) silica gel surface was 2-mercaptoimidazole, giving a new product denoted by 3-(2-thioimidazolyl)propyl silica gel, which is able to complex mercury ions. Mercury was chemically adsorbed on the modified graphite paste electrode containing 3-(2-thioimidazolyl)propyl silica (TIPSG GPE) by immersion in a Hg(II) solution, and the resultant surface was characterized by cyclic and differential pulse anodic stripping voltammetry. One cathodic peak at 0.1 V and other anodic peak at 0.34 V were observed on scanning the potential from -0.1 to 0.8 V (0.01 M KNO3; v = 2.0 mV s(-1) vs. Ag/AgCl). The anodic peak at 0.34 V show an excellent sensitivity for Hg(II) ions in the presence of several foreign ions. A calibration graph covering the concentration range from 0.02 to 2 mg L(-1) was obtained. The detection limit was estimated to be 5 microg L(-1). The precision for six determinations of 0.05 and 0.26 mg L(-1) Hg(II) was 3.0 and 2.5% (relative standard deviation), respectively. The method can be used to determine the concentration of mercury(II) in natural waters contaminated by this metal.

  2. Investigation of chemical modifiers for sulfur determination in diesel fuel samples by high-resolution continuum source graphite furnace molecular absorption spectrometry using direct analysis

    NASA Astrophysics Data System (ADS)

    Huber, Charles S.; Vale, Maria Goreti R.; Welz, Bernhard; Andrade, Jailson B.; Dessuy, Morgana B.

    2015-06-01

    High-resolution continuum source graphite furnace molecular absorption spectrometry has been applied for sulfur determination in diesel fuel. The sharp rotational lines of the carbon monosulfide molecule (formed during the vaporization step) were used to measure the absorbance. The analytical line at 258.056 nm was monitored using the sum of three pixels. Different chemical modifiers were investigated and the mixture of palladium and magnesium was used as chemical modifier in combination with iridium as permanent modifier. L-Cysteine was chosen as sulfur standard and the calibration was done against aqueous standard solutions. The proposed method was applied for the analyses of four diesel samples: two S10 samples and two S500 samples. The trueness of the method was checked with a certified reference material (CRM) of sulfur in diesel fuel (NIST 2724b). Accurate results, for samples and CRM, were achieved after a dilution with propan-1-ol. The following figures of merit were obtained: characteristic mass of 17 ± 3 ng, limit of detection and limit of quantification of 1.4 mg kg- 1 and 4.7 mg kg- 1, respectively.

  3. A Human In Vitro Whole Blood Assay to Predict the Systemic Cytokine Response to Therapeutic Oligonucleotides Including siRNA

    PubMed Central

    Schwickart, Anna; Putschli, Bastian; Renn, Marcel; Höller, Tobias; Barchet, Winfried

    2013-01-01

    Therapeutic oligonucleotides including siRNA and immunostimulatory ligands of Toll-like receptors (TLR) or RIG-I like helicases (RLH) are a promising novel class of drugs. They are in clinical development for a broad spectrum of applications, e.g. as adjuvants in vaccines and for the immunotherapy of cancer. Species-specific immune activation leading to cytokine release is characteristic for therapeutic oligonucleotides either as an unwanted side effect or intended pharmacology. Reliable in vitro tests designed for therapeutic oligonucleotides are therefore urgently needed in order to predict clinical efficacy and to prevent unexpected harmful effects in clinical development. To serve this purpose, we here established a human whole blood assay (WBA) that is fast and easy to perform. Its response to synthetic TLR ligands (R848: TLR7/8, LPS: TLR4) was on a comparable threshold to the more time consuming peripheral blood mononuclear cell (PBMC) based assay. By contrast, the type I IFN profile provoked by intravenous CpG-DNA (TLR9 ligand) in humans in vivo was more precisely replicated in the WBA than in stimulated PBMC. Since Heparin and EDTA, but not Hirudin, displaced oligonucleotides from their delivery agent, only Hirudin qualified as the anticoagulant to be used in the WBA. The Hirudin WBA exhibited a similar capacity as the PBMC assay to distinguish between TLR7-activating and modified non-stimulatory siRNA sequences. RNA-based immunoactivating TLR7/8- and RIG-I-ligands induced substantial amounts of IFN-α in the Hirudin-WBA dependent on delivery agent used. In conclusion, we present a human Hirudin WBA to determine therapeutic oligonucleotide-induced cytokine release during preclinical development that can readily be performed and offers a close reflection of human cytokine response in vivo. PMID:23940691

  4. Identification of drug-binding sites on human serum albumin using affinity capillary electrophoresis and chemically modified proteins as buffer additives.

    PubMed

    Kim, Hee Seung; Austin, John; Hage, David S

    2002-03-01

    A technique based on affinity capillary electrophoresis (ACE) and chemically modified proteins was used to screen the binding sites of various drugs on human serum albumin (HSA). This involved using HSA as a buffer additive, following the site-selective modification of this protein at two residues (tryptophan 214 or tyrosine 411) located in its major binding regions. The migration times of four compounds (warfarin, ibuprofen, suprofen and flurbiprofen) were measured in the presence of normal or modified HSA. These times were then compared and the mobility shifts observed with the modified proteins were used to identify the binding regions of each injected solute on HSA. Items considered in optimizing this assay included the concentration of protein placed into the running buffer, the reagents used to modify HSA, and the use of dextran as a secondary additive to adjust protein mobility. The results of this method showed good agreement with those of previous reports. The advantages and disadvantages of this approach are examined, as well as its possible extension to other solutes.

  5. A STUDY COMPARING CHEMICAL PEELING USING MODIFIED JESSNER'S SOLUTION AND 15%TRICHLOROACETIC ACID VERSUS 15% TRICHLOROACETIC ACID IN THE TREATMENT OF MELASMA

    PubMed Central

    Safoury, Omar Soliman; Zaki, Nagla Mohamed; El Nabarawy, Eman Ahmad; Farag, Eman Abas

    2009-01-01

    Background: Melasma is a symmetric progressive hyperpigmentation of the facial skin that occurs in all races but has a predilection for darker skin phenotypes. Depigmenting agents, laser and chemical peeling as classic Jessner's solution, modified Jessner's solution and trichloroacetic acid have been used alone and in combination in the treatment of melasma. Objectives: The aim of the study was to compare the therapeutic effect of combined 15% Trichloroacetic acid (TCA) and modified Jessner's solution with 15% TCA on melasma. Materials and Methods: Twenty married females with melasma (epidermal type), with a mean age of 38.25 years, were included in this study. All were of skin type III or IV. Fifteen percent TCA was applied to the whole face, with the exception of the left malar area to which combined TCA 15% and modified Jessner's solution was applied. Results: Our results revealed statistically highly significant difference between MASI Score (Melasma Area and Severity Index) between the right malar area and the left malar area. Conclusion: Modified Jessner's solution proved to be useful as an adjuvant treatment with TCA in the treatment of melasma, improving the results and minimizing postinflammatory hyperpigmentation. PMID:20049268

  6. Comparison of Fe-Al-modified natural materials by an electrochemical method and chemical precipitation for the adsorption of F- and As(V).

    PubMed

    Vázquez Mejía, G; Martínez-Miranda, V; Fall, C; Linares-Hernández, I; Solache-Ríos, M

    2016-01-01

    The adsorption of fluoride and arsenic ions by modified natural materials may have an impact on the removal of F- and As(V) from waters. In this work, a zeolitic material and pozzolan (commonly known as pumicite) were modified with aluminium an iron by an electrochemical method and chemical precipitation, respectively. The adsorbents were characterized by X-ray diffraction, scanning electron microscopy with energy X-ray disperse spectroscopy analysis and the point of zero charge (pHzpc). F- and As(V) adsorption properties of both materials were investigated. Adsorption kinetic data were best fitted to pseudo-second-order model and equilibrium data to the Langmuir isotherm model. The highest F- and As(V) sorption capacities were obtained for modified zeolitic (0.866 mg/g) and pozzolan (3.35 mg/g) materials, respectively, with initial F- or As(V) concentrations of 10 mg/L. It was found that the unmodified materials did not show either adsorption of F- ions or As(V), which indicated that Al and Fe in the adsorbents are responsible for the adsorption of these ions. In general, both modified materials show similar capacities for the adsorption of F- and As(V).

  7. IR study on the binding mode of metal cations to chemically modified Bombyx mori and Tussah silk fibres

    NASA Astrophysics Data System (ADS)

    Taddei, Paola; Monti, Patrizia; Freddi, Giuliano; Arai, Takayuki; Tsukada, Masuhiro

    2003-06-01

    Bombyx mori ( B. mori) and Tussah ( Antheraea pernyi) silk fibres were modified by treatment with tannic acid (TA) or ethylenediaminetetraacetic (EDTA) dianhydride, subsequently treated with Cu 2+ and Co 2+ solutions, at alkaline pH, and analysed by attenuated total reflectance/infrared spectroscopy to evaluate the changes induced in their structure by metal binding. The spectral changes were correlated to metal binding results obtained by inductive coupled plasma-atomic emission spectrometry. Upon Co 2+ complexation, the spectra of all the B. mori and Tussah silk samples showed a decrease in intensity of the Amide I band with a trend related to the metal uptake. The most relevant changes in the whole spectra were observed for the EDTA- and TA-modified samples in the case of B. mori and Tussah silks, respectively. Upon Cu 2+ complexation, the decrease in intensity of the Amide I band follows the trend of the metal uptake only in the case of Tussah silk. Moreover, the most relevant changes with respect to the untreated sample were observed for the TA-modified B. mori silk sample. The spectral changes were explained by considering the different affinities of the fibres for the modifying reagent, the amount of the metal bound and the relative stability of the complexes formed.

  8. Chemically modified polymeric resins for separation of cations, organic acids, and small polar moleculea by high performance liquid chromatography

    SciTech Connect

    Morris, John B.

    1993-07-01

    This thesis is divided into 4 parts: a review, ion chromatography of metal cations on carboxylic resins, separation of hydrophilic organic acids and small polar compounds on macroporous resin columns, and use of eluent modifiers for liquid chromatographic separation of carboxylic acids using conductivity detection.

  9. Enzymatically hydrolysed, acetylated and dually modified corn starch: physico-chemical, rheological and nutritional properties and effects on cake quality.

    PubMed

    Sahnoun, Mouna; Ismail, Nouha; Kammoun, Radhouane

    2016-01-01

    Corn starch was treated by enzymatic hydrolysis with Aspergillus oryzae S2 α-amylase, acetylation with vinyl acetate, and dual modification. The dual modified starch displayed a higher substitution degree than the acetylated starch and lower reducing sugar content than the hydrolysed starch. The results revealed that the cooling viscosity and amylose content of those products decrease (P < 0.05). An increase in moisture, water, and oil absorption capacity was observed for the acetylated starch and, which was less pronounced for the enzymatically hydrolysed starch but more pronounced for the enzymatically hydrolysed acetylated product. The latter product underwent an increase in resistant starch content, which is induced by a rise in hydrolysis time to attain about 67 % after 1 h of reaction. The modified starch samples were added to cake formulations at 5 and 10 % concentrations on a wheat flour basis and compared to native starch. The results revealed that when applied at 5 % concentrations, the modified starches reduced the hardness, cohesion, adhesion and chewiness of baked cakes and enhanced their elasticity, volume, height, crust color, and appearance as compared to native starch. These effects were more pronounced for the cake incorporating the dually modified starch.

  10. Oligonucleotide-arrayed TFT photosensor applicable for DNA chip technology.

    PubMed

    Tanaka, Tsuyoshi; Hatakeyama, Keiichi; Sawaguchi, Masahiro; Iwadate, Akihito; Mizutani, Yasushi; Sasaki, Kazuhiro; Tateishi, Naofumi; Takeyama, Haruko; Matsunaga, Tadashi

    2006-09-05

    A thin film transistor (TFT) photosensor fabricated by semiconductor integrated circuit (IC) technology was applied to DNA chip technology. The surface of the TFT photosensor was coated with TiO2 using a vapor deposition technique for the fabrication of optical filters. The immobilization of thiolated oligonucleotide probes onto a TiO2-coated TFT photosensor using gamma-aminopropyltriethoxysilane (APTES) and N-(gamma-maleimidobutyloxy) sulfosuccinimide ester (GMBS) was optimized. The coverage value of immobilized oligonucleotides reached a plateau at 33.7 pmol/cm2, which was similar to a previous analysis using radioisotope-labeled oligonucleotides. The lowest detection limits were 0.05 pmol/cm2 for quantum dot and 2.1 pmol/cm2 for Alexa Fluor 350. Furthermore, single nucleotide polymorphism (SNP) detection was examined using the oligonucleotide-arrayed TFT photosensor. A SNP present in the aldehyde dehydrogenase 2 (ALDH2) gene was used as a target. The SNPs in ALDH2*1 and ALDH2*2 target DNA were detected successfully using the TFT photosensor. DNA hybridization in the presence of both ALDH2*1 and ALDH2*2 target DNA was observed using both ALDH2*1 and ALDH2*2 detection oligonucleotides-arrayed TFT photosensor. Use of the TFT photosensor will allow the development of a disposable photodetecting device for DNA chip systems.

  11. Target mRNA inhibition by oligonucleotide drugs in man

    PubMed Central

    Lightfoot, Helen L.; Hall, Jonathan

    2012-01-01

    Oligonucleotide delivery in vivo is commonly seen as the principal hurdle to the successful development of oligonucleotide drugs. In an analysis of 26 oligonucleotide drugs recently evaluated in late-stage clinical trials we found that to date at least half have demonstrated suppression of the target mRNA and/or protein levels in the relevant cell types in man, including those present in liver, muscle, bone marrow, lung, blood and solid tumors. Overall, this strongly implies that the drugs are being delivered to the appropriate disease tissues. Strikingly we also found that the majority of the drug targets of the oligonucleotides lie outside of the drugable genome and represent new mechanisms of action not previously investigated in a clinical setting. Despite the high risk of failure of novel mechanisms of action in the clinic, a subset of the targets has been validated by the drugs. While not wishing to downplay the technical challenges of oligonucleotide delivery in vivo, here we demonstrate that target selection and validation are of equal importance for the success of this field. PMID:22989709

  12. A novel setup for the determination of absolute cross sections for low-energy electron induced strand breaks in oligonucleotides - The effect of the radiosensitizer 5-fluorouracil*

    NASA Astrophysics Data System (ADS)

    Rackwitz, Jenny; Ranković, Miloš Lj.; Milosavljević, Aleksandar R.; Bald, Ilko

    2017-02-01

    Low-energy electrons (LEEs) play an important role in DNA radiation damage. Here we present a method to quantify LEE induced strand breakage in well-defined oligonucleotide single strands in terms of absolute cross sections. An LEE irradiation setup covering electron energies <500 eV is constructed and optimized to irradiate DNA origami triangles carrying well-defined oligonucleotide target strands. Measurements are presented for 10.0 and 5.5 eV for different oligonucleotide targets. The determination of absolute strand break cross sections is performed by atomic force microscopy analysis. An accurate fluence determination ensures small margins of error of the determined absolute single strand break cross sections σ SSB . In this way, the influence of sequence modification with the radiosensitive 5-Fluorouracil (5FU) is studied using an absolute and relative data analysis. We demonstrate an increase in the strand break yields of 5FU containing oligonucleotides by a factor of 1.5 to 1.6 compared with non-modified oligonucleotide sequences when irradiated with 10 eV electrons.

  13. Chemical Modification of Cyclodextrin and Amylose by Click Reaction and Its Application to the Synthesis of Poly-alkylamine-Modified Antibacterial Sugars.

    PubMed

    Yamamura, Hatsuo

    2017-01-01

    Cyclodextrin (CD) can be chemically modified into desired and sophisticated functional molecules. However, poly-modification often produces complicated mixtures, resulting in a low yield of the desired product. As the most promising procedure to solve such problems and to achieve poly-modification of the CD molecule, we present here the Huisgen 1,3-dipolar cycloaddition, known as a click reaction. This review will describe the results of our microwave-assisted click reaction for the poly-modification of CD and amylose molecules, and its application to the study of synthetic membrane active antibacterial derivatives.

  14. Ab-initio simulations of deformation potentials and electron mobility in chemically modified graphene and two-dimensional hexagonal boron-nitride

    NASA Astrophysics Data System (ADS)

    Bruzzone, Samantha; Fiori, Gianluca

    2011-11-01

    We present an ab-initio study of electron mobility and electron-phonon coupling in chemically modified graphene, considering fluorinated and hydrogenated graphene at different percentage coverage. Hexagonal boron carbon nitrogen is also investigated due the increased interest shown by the research community towards this material. In particular, the deformation potentials are computed by means of density functional theory, while the carrier mobility is obtained according to the Takagi model (S. Takagi, A. Toriumi, and H. Tango, IEEE Trans. Electron Devices 41, 2363 (1994)). We will show that graphene with a reduced degree of hydrogenation can compete, in terms of mobility, with silicon technology.

  15. Electrocatalysis of chloroacetic acids (mono-, di- and tri-) at a C60-[dimethyl-(beta-cyclodextrin)]2 and nafion chemically modified electrode.

    PubMed

    Wei, M; Li, M; Li, N; Gu, Z; Zhou, X

    2001-01-26

    The C(60)-[dimethyl-(beta-cyclodextrin)](2) and nafion chemically modified electrode (CME) exhibits one electroreduction peak and two electro-oxidation peaks in a mixed solvent of water and acetonitrile (3:2, v/v) containing tetra-butylammonium perchlorate. The reduction of chloroacetic acids (mono-, di- and tri-) can be electrocatalyzed at this electrode, indicating that C(60)-[dimethyl-(beta-cyclodextrin)](2) is capable of mediating the electron transfer to chloroacetic acids. Values of the apparent catalytic rate constant, k, were determined by using the rotating-disk electrode (RDE).

  16. One-pot chemical synthesis of small ubiquitin-like modifier protein-peptide conjugates using bis(2-sulfanylethyl)amido peptide latent thioester surrogates.

    PubMed

    Boll, Emmanuelle; Drobecq, Hervé; Ollivier, Nathalie; Blanpain, Annick; Raibaut, Laurent; Desmet, Rémi; Vicogne, Jérôme; Melnyk, Oleg

    2015-02-01

    Small ubiquitin-like modifier (SUMO) post-translational modification (PTM) of proteins has a crucial role in the regulation of important cellular processes. This protocol describes the chemical synthesis of functional SUMO-peptide conjugates. The two crucial stages of this protocol are the solid-phase synthesis of peptide segments derivatized by thioester or bis(2-sulfanylethyl)amido (SEA) latent thioester functionalities and the one-pot assembly of the SUMO-peptide conjugate by a sequential native chemical ligation (NCL)/SEA native peptide ligation reaction sequence. This protocol also enables the isolation of a SUMO SEA latent thioester, which can be attached to a target peptide or protein in a subsequent step. It is compatible with 9-fluorenylmethoxycarbonyl (Fmoc) chemistry, and it gives access to homogeneous, reversible and functional SUMO conjugates that are not easily produced using living systems. The synthesis of SUMO-peptide conjugates on a milligram scale takes 20 working days.

  17. Towards combined electrochemistry and surface-enhanced resonance Raman of heme proteins: Improvement of diffusion electrochemistry of cytochrome c at silver electrodes chemically modified with 4-mercaptopyridine.

    PubMed

    Millo, Diego; Ranieri, Antonio; Koot, Wynanda; Gooijer, Cees; van der Zwan, Gert

    2006-08-01

    To date, a successful combination of surface-enhanced resonance Raman spectroscopy (SERRS) and electrochemistry to study heme proteins is inhibited by the problems raised by the prerequisite to use silver as electrode metal. This paper indicates an approach to overcome these problems. It describes a quick and reproducible procedure to prepare silver electrodes chemically modified with 4-mercaptopyridine suitable to perform diffusion electrochemistry of cytochrome c (cyt c). The method involves the employment of a mechanical and a chemical treatment and avoids the use of alumina slurries and any electrochemical pretreatment. Cyclic voltammetry (CV) was used to test the electrochemical response of cyt c, and the CV signals were found identical with those obtained on gold electrodes under the same experimental conditions. Compared to previous literature, a significant improvement of the CV signal of cyt c at silver electrodes was achieved. Preliminary results show that this treatment can be also successfully employed for the preparation of SERRS-active electrodes.

  18. Structural and mechanical characteristics of film using modified corn starch by the same two chemical processes used in different sequences.

    PubMed

    Qiu, Liping; Hu, Fei; Peng, Yali

    2013-01-16

    Structure of dual modified starches, cross-linked esterified corn starch (CES) and esterified cross-linked corn starch (ECS), and product films (CEF and ECF) were characterized by Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction and scanning electron microscopy (SEM). The peak 1730cm(-1) of IR spectra confirmed the formation of ester carbonyl groups in starch matrix. The sequence of modification procedure had an impact on the final modification degree, resulting in structural differences of modified starches and starch films. Compared to native starch film (NF), CEF and ECF showed improved transparence (77.59% and 74.39% respectively) with compact structure, lower crystallinity (6.5% and 7.4% respectively). Results of mechanical test indicated that structure of ECF was more flexible than CEF, whereas tensile strength was higher in CEF. Accordingly, complex modification could be an effective method to adequate properties of starch films for specific processing requirements.

  19. Investigation of chemical modifiers for the determination of lead in fertilizers and limestone using graphite furnace atomic absorption spectrometry with Zeeman-effect background correction and slurry sampling

    NASA Astrophysics Data System (ADS)

    Borges, Aline R.; Becker, Emilene M.; Dessuy, Morgana B.; Vale, Maria Goreti R.; Welz, Bernhard

    2014-02-01

    In this work, chemical modifiers in solution (Pd/Mg, NH4H2PO4 and NH4NO3/Pd) were compared with permanent modifiers (Ir and Ru) for the determination of lead in fertilizer and limestone samples using slurry sampling and graphite furnace atomic absorption spectrometry with Zeeman-effect background correction. The analytical line at 283.3 nm was used due to some spectral interference observed at 217.0 nm. The NH4H2PO4 was abandoned due to severe spectral interference even at the 283.3-nm line. For Pd/Mg and NH4NO3/Pd the optimum pyrolysis and atomization temperatures were 900 °C and 1900 °C, respectively. For Ru and Ir, the integrated absorbance signal was stable up to pyrolysis temperatures of 700 °C and 900 °C, respectively, and up to atomization temperature of 1700 °C. The limit of detection (LOD) was 17 ng g- 1 using Pd/Mg and 29 ng g- 1 using NH4NO3/Pd. Among the permanent modifiers investigated, the LOD was 22 ng g- 1 Pb for Ir and 10 ng g- 1 Pb for Ru. The accuracy of the method was evaluated using the certified reference material NIST SRM 695. Although Ru provided lower LOD, which can be attributed to a lower blank signal, only the modifiers in solution showed concordant values of Pb concentration for the NIST SRM 695 and the most of analyzed samples. Moreover, the Pd/Mg modifier provided the highest sensitivity and for this reason it is more suitable for the determination of Pb in fertilizers samples in slurry; besides this it presented a better signal-to-noise ratio than NH4NO3/Pd.

  20. Development of a virus concentration method using lanthanum-based chemical flocculation coupled with modified membrane filtration procedures.

    PubMed

    Zhang, Yanyan; Riley, Lela K; Lin, Mengshi; Purdy, Gregory A; Hu, Zhiqiang

    2013-06-01

    Direct membrane filtration is often used to concentrate viruses in water but it may suffer from severe membrane fouling and clogging. Here, a lanthanum-based flocculation method coupled with modified membrane filtration procedures was developed and evaluated to detect viruses in large volume (40 L) water samples. The lanthanum-based flocculation method could easily reduce the water sample volume by a factor of 40. Additional volume reduction was achieved by a two-step membrane filtration approach. First, selected membrane filters (including 1MDS electropositive filters and nitrocellulose electronegative filters-Millipore HATF filters) were used to reduce water sample volume further and compare their efficiencies in virus recovery. The Mg²⁺-modified HATF membrane performed better on MS2 retention with an average virus recovery of 83.4% (±4.5% [standard deviation]). After HATF membrane filtration and elution, centrifugal ultrafiltration through a 30 kDa cut-off membrane resulted in an overall concentration factor of 20,000. Results from the infectivity assay showed that the MS2 recovery efficiencies from the NanoCeram- and 1MDS-based direct filtration and the lanthanum-based concentration coupled with the modified filtration procedure were 10.1% (±1.0%), 3.3% (±0.1%), and 17.5% (±1.1%), respectively. Results from the PCR analysis showed that the virus recoveries of the lanthanum-based method were 20.6% (±2.9%) and 19.5% (±3.4%) for MS2 and adenovirus, respectively, while no adenovirus could be detected through the NanoCeram- and 1MDS-based direct filtration. The lanthanum-based concentration method coupled with modified membrane filtration procedures is therefore a promising method for detecting waterborne viruses.

  1. Safety of antisense oligonucleotide and siRNA-based therapeutics.

    PubMed

    Chi, Xuan; Gatti, Philip; Papoian, Thomas

    2017-01-31

    Oligonucleotide-based therapy is an active area of drug development designed to treat a variety of gene-specific diseases. Two of the more promising platforms are the antisense oligonucleotides (ASOs) and short interfering RNAs (siRNAs), both of which are often directed against similar targets. In light of recent reports on clinical trials of severe thrombocytopenia with two different ASO drugs and increased peripheral neuropathy with an siRNA drug, we compared and contrasted the specific safety characteristics of these two classes of oligonucleotide therapeutic. The objectives were to assess factors that could contribute to the specific toxicities observed with these two classes of promising drugs, and get a better understanding of the potential mechanism(s) responsible for these rare, but serious, adverse events.

  2. Current progress on aptamer-targeted oligonucleotide therapeutics

    PubMed Central

    Dassie, Justin P; Giangrande, Paloma H

    2014-01-01

    Exploiting the power of the RNAi pathway through the use of therapeutic siRNA drugs has remarkable potential for treating a vast array of human disease conditions. However, difficulties in delivery of these and similar nucleic acid-based pharmacological agents to appropriate organs or tissues, remains a major impediment to their broad clinical application. Synthetic nucleic acid ligands (aptamers) have emerged as effective delivery vehicles for therapeutic oligonucleotides, including siRNAs. In this review, we summarize recent attractive developments in creatively employing cell-internalizing aptamers to deliver therapeutic oligonucleotides (e.g., siRNAs, miRNAs, anti-miRs and antisense oligos) to target cells. We also discuss advancements in aptamer-siRNA chimera technology, as well as, aptamer-functionalized nanoparticles for siRNA delivery. In addition, the challenges and future prospects of aptamer-targeted oligonucleotide drugs for clinical translation are further highlighted. PMID:24304250

  3. Non-radioactive detection of oligonucleotide probes by photochemical amplification of dioxetanes.

    PubMed Central

    Schubert, F; Knaf, A; Möller, U; Cech, D

    1995-01-01

    We describe a new method of non-radioactive labelling and detection of oligonucleotide probes. The approach is based on a simple chemical principle. Oligonucleotides labelled with methylene blue (a photosensitizer) are hybridized on a membrane to immobilized DNA target sequences. After hybridization and stringency washing 2(-)[3-(hydroxyphenyl)methoxymethylene] adamantane is added to the membrane and the membrane is irradiated with a tungsten lamp light source through a cut-off filter. Thermally stable dioxetanes are amplified during irradiation at the positions of the labelled probe. These amplified dioxetanes are detected using chemically triggered chemiluminescent decay. Signals are recorded on commercial X-ray film. Detection is possible immediately after the last washing step and a hard copy of the blot is obtained within 1 h. Dependent on the level of the target sequences, the sensitivity of the method allows detection of 0.3 pg single-stranded M13mp18(+) plasmid DNA in dot blots and 75 pg in Southern blots. Additional immunological reaction steps and washing steps with blocking reagents and buffers are avoided. Furthermore, expensive reagents and equipment for physical detection are not necessary. The method might be particularly useful for fast routine analysis in forensic and medical applications. The synthesis of the olefin, conditions of hybridization and the protocol of detection are described in detail. Images PMID:8524657

  4. Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications

    SciTech Connect

    Egli, Martin; Minasov, George; Tereshko, Valentina; Pallan, Pradeep S.; Teplova, Marianna; Inamati, Gopal B.; Lesnik, Elena A.; Owens, Steve R.; Ross, Bruce S.; Prakash, Thazha P.; Manoharan, Muthiah

    2010-03-05

    The syntheses of 10 new RNA 2'-O-modifications, their incorporation into oligonucleotides, and an evaluation of their properties such as RNA affinity and nuclease resistance relevant to antisense activity are presented. All modifications combined with the natural phosphate backbone lead to significant gains in terms of the stability of hybridization to RNA relative to the first-generation DNA phosphorothioates (PS-DNA). The nuclease resistance afforded in particular by the 2'-O-modifications carrying a positive charge surpasses that of PS-DNA. However, small electronegative 2'-O-substituents, while enhancing the RNA affinity, do not sufficiently protect against degradation by nucleases. Similarly, oligonucleotides containing 3'-terminal residues modified with the relatively large 2'-O-[2-(benzyloxy)ethyl] substituent are rapidly degraded by exonucleases, proving wrong the assumption that steric bulk will generally improve protection against nuclease digestion. To analyze the factors that contribute to the enhanced RNA affinity and nuclease resistance we determined crystal structures of self-complementary A-form DNA decamer duplexes containing single 2'-O-modified thymidines per strand. Conformational preorganization of substituents, favorable electrostatic interactions between substituent and sugar-phosphate backbone, and a stable water structure in the vicinity of the 2'-O-modification all appear to contribute to the improved RNA affinity. Close association of positively charged substituents and phosphate groups was observed in the structures with modifications that protect most effectively against nucleases. The promising properties exhibited by some of the analyzed 2'-O-modifications may warrant a more detailed evaluation of their potential for in vivo antisense applications. Chemical modification of RNA can also be expected to significantly improve the efficacy of small interfering RNAs (siRNA). Therefore, the 2'-O-modifications introduced here may benefit the

  5. Study of the roles of chemical modifiers in determining boron using graphite furnace atomic absorption spectrometry and optimization of the temperature profile during atomization.

    PubMed

    Yamamoto, Yuhei; Shirasaki, Toshihiro; Yonetani, Akira; Imai, Shoji

    2015-01-01

    The measurement conditions for determining boron using graphite furnace-atomic absorption spectrometry (GF-AAS) were investigated. Differences in the boron absorbance profiles were found using three different commercially available GF-AAS instruments when the graphite atomizers in them were not tuned. The boron absorbances found with and without adjusting the graphite atomizers suggested that achieving an adequate absorbance for the determination of boron requires a sharp temperature profile that overshoots the target temperature during the atomization process. Chemical modifiers that could improve the boron absorbance without the need for using coating agents were tested. Calcium carbonate improved the boron absorbance but did not suppress variability in the peak height. Improvement of boron absorbance was comparatively less using iron nitrate or copper nitrate than using calcium carbonate, but variability in the peak height was clearly suppressed using iron nitrate or copper nitrate. The limit of detection was 0.0026 mg L(-1) when iron nitrate was used. It appears that iron nitrate is a useful new chemical modifier for the quick and simple determination of boron using GF-AAS.

  6. Adsorption/desorption of Cd(II), Cu(II) and Pb(II) using chemically modified orange peel: Equilibrium and kinetic studies

    NASA Astrophysics Data System (ADS)

    Lasheen, Mohamed R.; Ammar, Nabila S.; Ibrahim, Hanan S.

    2012-02-01

    Waste materials from industries such as food processing may act as cost effective and efficient biosorbents to remove toxic contaminants from wastewater. This study aimed to establish an optimized condition and closed loop application of processed orange peel for metals removal. A comparative study of the adsorption capacity of the chemically modified orange peel was performed against environmentally problematic metal ions, namely, Cd 2+, Cu 2+ and Pb 2+, from aqueous solutions. Chemically modified orange peel (MOP) showed a significantly higher metal uptake capacity compared to original orange peel (OP). Fourier Transform Infrared (FTIR) Spectra of peel showed that the carboxylic group peak shifted from 1637 to 1644 cm -1 after Pb (II) ions binding, indicated the involvement of carboxyl groups in Pb(II) ions binding. The metals uptake by MOP was rapid and the equilibrium time was 30 min at constant temperature and pH. Sorption kinetics followed a second-order model. The mechanism of metal sorption by MOP gave good fits for Freundlich and Langmuir models. Desorption of metals and regeneration of the biosorbent was attained simultaneously by acid elution. Even after four cycles of adsorption-elution, the adsorption capacity was regained completely and adsorption efficiency of metal was maintained at around 90%.

  7. Chemical synthesis of long RNAs with terminal 5'-phosphate groups.

    PubMed

    Pradère, Ugo; Halloy, François; Hall, Jonathan

    2017-03-12

    Long structured RNAs are useful biochemical and biological tools. They are usually prepared enzymatically, but this precludes their site-specific modification with functional groups for chemical biology studies. One solution is to perform solid-phase synthesis of multiple RNAs loaded with 5'-terminal phosphate groups, so that RNAs can be concatenated using template ligation reactions. However, there are currently no readily available reagents suitable for the incorporation of the phosphate group into long RNAs by solid-phase synthesis. Here we describe an easy-to-prepare phosphoramidite reagent suitable for the chemical introduction of 5'-terminal phosphate groups into long RNAs. The phosphate is protected by a dinitrobenzhydryl group that serves as an essential lipophilic group for the separation of oligonucleotide by-products. The phosphate is unmasked quantitatively by brief UV irradiation. We demonstrate the value of this reagent in the preparation of a library of long structured RNAs that are site-specifically modified with functional groups.

  8. Significant temperature and pressure sensitivities of electrical properties in chemically modified multiwall carbon nanotube/methylvinyl silicone rubber nanocomposites

    NASA Astrophysics Data System (ADS)

    Jiang, Mei-Juan; Dang, Zhi-Min; Xu, Hai-Ping

    2006-10-01

    The effects of γ-aminopropyltriethoxy silane coupling agent on electrical properties in multiwall carbon nanotube/methylvinyl silicone rubber nanocomposites were studied. The results showed that the modified nanotubes could be dispersed homogeneously and that they had a tight bonding with the rubber matrix. The concentration of coupling agent played a crucial role in deciding the conductivity and the electrical properties of the nanocomposites exhibited strong dependences on temperature and pressure. Dependences of electrical properties on temperature and pressure were also improved by increasing the content of coupling agent.

  9. Selectivity of Enzymatic Conversion of Oligonucleotide Probes during Nucleotide Polymorphism Analysis of DNA

    PubMed Central

    Vinogradova, O.A.

    2010-01-01

    The analysis of DNA nucleotide polymorphisms is one of the main goals of DNA diagnostics. DNA–dependent enzymes (DNA polymerases and DNA ligases) are widely used to enhance the sensitivity and reliability of systems intended for the detection of point mutations in genetic material. In this article, we have summarized the data on the selectiveness of DNA–dependent enzymes and on the structural factors in enzymes and DNA which influence the effectiveness of mismatch discrimination during enzymatic conversion of oligonucleotide probes on a DNA template. The data presented characterize the sensitivity of a series of DNA–dependent enzymes that are widely used in the detection of noncomplementary base pairs in nucleic acid substrate complexes. We have analyzed the spatial properties of the enzyme–substrate complexes. These properties are vital for the enzymatic reaction and the recognition of perfect DNA–substrates. We also discuss relevant approaches to increasing the selectivity of enzyme–dependent reactions. These approaches involve the use of modified oligonucleotide probes which “disturb” the native structure of the DNA–substrate complexes. PMID:22649627

  10. Oligonucleotide-mediated gene modification and its promise for animal agriculture.

    PubMed

    Laible, Götz; Wagner, Stefan; Alderson, Jon

    2006-01-17

    One of the great aspirations in modern biology is the ability to utilise the expanding knowledge of the genetic basis of phenotypic diversity through the purposeful tailoring of the mammalian genome. A number of technologies are emerging which have the capacity to modify genes in their chromosomal context. Not surprisingly, the major thrust in this area has come from the evaluation of gene therapy applications to correct mutations implicated in human genetic diseases. The recent development of somatic cell nuclear transfer (SCNT) provides access to these technologies for the purposeful modification of livestock animals. The enormous phenotypic variety existent in contemporary livestock animals has in many cases been linked to quantitative trait loci (QTL) and their underlying point mutations, often referred to as single-nucleotide polymorphisms (SNPs). Thus, the ability for the targeted genetic modification of livestock animals constitutes an attractive opportunity for future agricultural applications. In this review, we will summarize attempts and approaches for oligonucleotide-mediated gene modification (OGM) strategies for the site-specific modification of the genome, with an emphasis on chimeric RNA-DNA oligonucleotides (RDOs) and single-stranded oligonucletides (ssODNs). The potential of this approach for the directed genetic improvement of livestock animals is illustrated through examples, outlining the effects of point mutations on important traits, including meat and milk production, reproductive performance, disease resistance and superior models of human diseases. Current technological hurdles and potential strategies that might remove these barriers in the future are discussed.

  11. Oligonucleotide labelling using a fluorogenic "click" reaction with a hemicarboxonium salt.

    PubMed

    Maether, Marie-Pierre; Lapin, Kristie; Muntean, Andreea; Payrastre, Corinne; Escudier, Jean-Marc

    2013-10-17

    Two fluorescent streptocyanine labelled oligonucleotides have been synthesized by a simple "click" reaction between a non-fluorescent hemicarboxonium salt and aminoalkyl functionalized thymidines within the oligonucleotide and their spectrophotometric properties have been studied.

  12. Chemical modification of poly(ethylene terephthalate) and immobilization of the selected enzymes on the modified film

    NASA Astrophysics Data System (ADS)

    Irena, Gancarz; Jolanta, Bryjak; Karolina, Zynek

    2009-07-01

    Poly(ethylene terephthalate) (PET) film was modified by reaction with hydrazine (HD), ethylenediamine (EDA), 1,2-diaminopropane (1,2-DAP) and 1,3-diaminopropane (1,3-DAP). The maximal amount of amine functionalities introduced in the chosen conditions on the surface was found as 0.07, 3.35, 0.76 and 1.99 nmol cm -2 for HD, EDA, 1,2-DAP and 1,3-DAP respectively. During the modification process etching of the sample and an increase of stiffness takes place. FTIR-ATR spectra prove that the surface chemistry after modification in amine solution is very complex. The lack of clear correlation between the surface tension and surface concentration of amine functionalities seems to confirm that. For immobilization purpose invertase, laccase and tyrosinase were used. The amount of covalently attached proteins at first increases with the increase of surface concentration of amine groups but after reaching a certain level of amine groups, decrease of the immobilization level was observed. All enzymes tested showed highest activity for a moderate level of aminolysis and this activity had the highest values for EDA-modified PET.

  13. Determination of nickel in saliva by electrothermal atomic absorption spectrometry using various chemical modifiers with Zeeman-effect background correction.

    PubMed

    Burguera, E; Sanchez de Briceño, A; Rondon, C E; Burguera, J L; Burguera, M; Carrero, P

    1998-07-01

    The profile of nickel signal using electrothermal atomic absorption spectrometry with deuterium and Zeeman-effect background correction is presented. The Zeeman effect system of background correction offered definitive advantages and therefore was used for the determination of nickel in saliva in the presence of various isomorphous metals. The highest nickel absorbance values corresponded at 200, 300, 300, 300, 600, and 200 ng of Tb, Mg, Sm, Lu, Tm, and Pd, respectively. On the other hand, the addition of Eu, Er, and Ho decreased the nickel signal. The presence on each modifier alone does not eliminate the matrix interference. However, the use of 200 ng of Pd in conjuction with 300 ng of Lu has a higher sensitivity, offers an advantage against interference from the background of saliva matrix and produces good recoveries (98 to 102% from unspiked and spiked saliva samples). The limit of detection was 0.11 micrograms/L for a characteristic mass of 16.6 pg of nickel using Pd-Lu as modifier. The within-batch precision varied between 0.8 and 1.5% relative standard deviations. The analysis of thirty samples of whole saliva gave an average of 0.81 +/- 0.30 of micrograms/L of Ni (range from 0.5 to 2.0 micrograms/L of Ni). The agreement between the observed and certified values obtained from a Seronorm Blood Serum Standard Reference Material was good.

  14. Improvement of the activation of lipase from Candida rugosa following physical and chemical immobilization on modified mesoporous silica.

    PubMed

    Wang, Chunfeng; Li, Yanjing; Zhou, Guowei; Jiang, Xiaojie; Xu, Yunqiang; Bu, Zhaosheng

    2014-12-01

    Lipase from Candida rugosa (CRL) was chemically and physically immobilized onto four types of rod-shaped mesoporous silica (RSMS). RSMS prepared using surfactant P123 and poly(ethylene glycol) as co-templates was functionalized with (3-aminopropyl)triethoxysilane (APTES) to obtain P-RSMS by post-synthesis grafting. Tetraethoxysilane was hydrothermally co-condensed with APTES to obtain C-RSMS. A two-step process using APTES and glutaraldehyde was also performed to obtain G-RSMS. The effects of modification methods (including post-synthesis grafting and co-condensation) and glutaraldehyde on the mesoscopic order, interplanar spacing d100, cell parameter a0, mesoporous structure, and wall thickness of RSMS were studied in detail. Results showed that all samples were mesoporous materials with 2D mesostructures (p6mm). Pore size and d100 decreased, whereas the wall thickness increased after different modifications. CRL was used as a model enzyme to determine the effect of physical and chemical adsorption on loading amount and enzymatic activity. The possible mechanism of CRL immobilization on G-RSMS by chemical adsorption was systematically investigated. The chemical immobilization of CRL on G-RSMS increased the loading amount, hydrolytic activity, thermal stability, and reusability. Moreover, immobilized CRL was employed to catalyze the resolution of 2-octanol by esterification with caprylic acid. The enantiomeric excess of 2-octanol was 45.8% when the reaction was catalyzed by G-RSMS-CRL and decreased to about 38%-39% using the physically immobilized CRL, after 48 h of reaction in hexane.

  15. Relative embryotoxicity of two classes of chemicals in a modified zebrafish embryotoxicity test and comparison with their in vivo potencies.

    PubMed

    Hermsen, Sanne A B; van den Brandhof, Evert-Jan; van der Ven, Leo T M; Piersma, Aldert H

    2011-04-01

    The zebrafish embryotoxicity test (ZET) is a fast and simple method to study chemical toxicity after exposure of the complete vertebrate embryo during embryogenesis in ovo. We developed a novel quantitative evaluation method to assess the development of the zebrafish embryo based on specific endpoints in time, the general morphology score (GMS) system. For teratogenic effects a separate scoring list was developed. The relative effects of eight glycol ethers and six 1,2,4-triazole anti-fungals were evaluated in this system and results were compared with in vivo developmental toxicity potencies. Methoxyacetic acid and ethoxyacetic acid appeared as the most potent glycol ether metabolites, inducing growth retardation and malformations. Other glycol ethers showed no developmental toxicity. Flusilazole appeared the most potent triazole, followed by hexaconazole, cyproconazole, triadimefon, myclobutanil and triticonazole, respectively. In general, the potency ranking of the compounds within their class in the ZET was comparable to their in vivo ranking. In conclusion, the ZET with the GMS system appears an efficient and useful test system for screening embryotoxic properties of chemicals within the classes of compounds tested. This alternative test method may also be useful for the detection of embryotoxic properties of other classes of chemicals.

  16. Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity.

    PubMed

    Jin, K; Sales, B C; Stocks, G M; Samolyuk, G D; Daene, M; Weber, W J; Zhang, Y; Bei, H

    2016-02-01

    Equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. In order to understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized, and their electrical, thermal, and magnetic properties are systematically investigated in the range of 4-300 K by combining experiments with ab initio Korring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased due to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. The temperature dependence of the electrical and thermal transport properties is further discussed, and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T.

  17. Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity

    SciTech Connect

    Jin, Ke; Sales, Brian C.; Stocks, George Malcolm; Samolyuk, German D.; Daene, Markus; Weber, William J.; Zhang, Yanwen; Bei, Hongbin

    2016-02-01

    We discovered that equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. To understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized, and their electrical, thermal, and magnetic properties are systematically investigated in the range of 4–300 K by combining experiments with ab initio Korring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased due to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. Moreover, the temperature dependence of the electrical and thermal transport properties is further discussed, and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T.

  18. Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity

    DOE PAGES

    Jin, Ke; Sales, Brian C.; Stocks, George Malcolm; ...

    2016-02-01

    We discovered that equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. To understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized, and their electrical, thermal, and magnetic properties are systematically investigated in the range of 4–300 K by combining experiments with ab initio Korring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased duemore » to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. Moreover, the temperature dependence of the electrical and thermal transport properties is further discussed, and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T.« less

  19. Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity

    NASA Astrophysics Data System (ADS)

    Jin, K.; Sales, B. C.; Stocks, G. M.; Samolyuk, G. D.; Daene, M.; Weber, W. J.; Zhang, Y.; Bei, H.

    2016-02-01

    Equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. In order to understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized, and their electrical, thermal, and magnetic properties are systematically investigated in the range of 4–300 K by combining experiments with ab initio Korring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased due to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. The temperature dependence of the electrical and thermal transport properties is further discussed, and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T.

  20. Validation of the Swine Protein-Annotated Oligonucleotide Microarray

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The specificity and utility of the Swine Protein-Annotated Oligonucleotide Microarray, or Pigoligoarray (www.pigoligoarray.org), has been evaluated by profiling the expression of transcripts from four porcine tissues. Tools for comparative analyses of expression on the Pigoligoarray were developed i...

  1. Gene expression profiling in peanut using oligonucleotide microarrays

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transcriptome expression analysis in peanut to date has been limited to a relatively small set of genes and only recently have a moderately significant number of ESTs been released into the public domain. Utilization of these ESTs for the oligonucleotide microarrays provides a means to investigate l...

  2. Oligonucleotide-directed mutagenesis for precision gene editing.

    PubMed

    Sauer, Noel J; Mozoruk, Jerry; Miller, Ryan B; Warburg, Zachary J; Walker, Keith A; Beetham, Peter R; Schöpke, Christian R; Gocal, Greg F W

    2016-02-01

    Differences in gene sequences, many of which are single nucleotide polymorphisms, underlie some of the most important traits in plants. With humanity facing significant challenges to increase global agricultural productivity, there is an urgent need to accelerate the development of these traits in plants. oligonucleotide-directed mutagenesis (ODM), one of the many tools of Cibus' Rapid Trait Development System (RTDS(™) ) technology, offers a rapid, precise and non-transgenic breeding alternative for trait improvement in agriculture to address this urgent need. This review explores the application of ODM as a precision genome editing technology, with emphasis on using oligonucleotides to make targeted edits in plasmid, episomal and chromosomal DNA of bacterial, fungal, mammalian and plant systems. The process of employing ODM by way of RTDS technology has been improved in many ways by utilizing a fluorescence conversion system wherein a blue fluorescent protein (BFP) can be changed to a green fluorescent protein (GFP) by editing a single nucleotide of the BFP gene (CAC→TAC; H66 to Y66). For example, dependent on oligonucleotide length, applying oligonucleotide-mediated technology to target the BFP transgene in Arabidopsis thaliana protoplasts resulted in up to 0.05% precisely edited GFP loci. Here, the development of traits in commercially relevant plant varieties to improve crop performance by genome editing technologies such as ODM, and by extension RTDS, is reviewed.

  3. Chromosome-specific painting in Cucumis species using bulked oligonucleotides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chromosome-specific painting is a powerful technique in molecular cytogenetic and genome research. We developed an oligonucleotide (oligo)-based chromosome painting technique in cucumber (Cucumis sativus) that will be applicable in any plant species with a sequenced genome. Oligos specific to a sing...

  4. Solid-phase-supported synthesis of morpholinoglycine oligonucleotide mimics

    PubMed Central

    Belov, Sergey S; Tarasenko, Yulia V; Silnikov, Vladimir N

    2014-01-01

    Summary An efficient solid-phase-supported peptide synthesis (SPPS) of morpholinoglycine oligonucleotide (MorGly) mimics has been developed. The proposed strategy includes a novel specially designed labile linker group containing the oxalyl residue and the 2-aminomethylmorpholino nucleoside analogues as first subunits. PMID:24991266

  5. Regioselective immobilization of short oligonucleotides to acrylic copolymer gels.

    PubMed Central

    Timofeev, E; Kochetkova, S V; Mirzabekov, A D; Florentiev, V L

    1996-01-01

    Four types of polyacrylamide or polydimethyl-acrylamide gels for regioselective (by immobilization at the 3' end) of short oligonucleotides have been designed for use in manufacturing oligonucleotide microchips. Two of these supports contain amino or aldehyde groups in the gel, allowing coupling with oligonucleotides bearing aldehyde or amino groups, respectively, in the presence of a reducing agent. The aldehyde gel support showed a higher immobilization efficiency relative to the amino gel. Of all reducing agents tested, the best results were obtained with a pyridine-borane complex. The other supports are based on an acrylamide gel activated with glutaraldehyde or a hydroxyalkyl-functionalized gel treated with mesyl chloride. The use of dimethylacrylamide instead of acrylamide allows subsequent gel modifications in organic solvents. All the immobilization methods are easy and simple to perform, give high and reproducible yields, allow long durations of storage of the activated support, and provide high stability of attachment and low non-specific binding. Although these gel supports have been developed for preparing oligonucleotide microchips, they may be used for other purposes as well. PMID:8774893

  6. Novel epoxy-silicone thermolytic transparent packaging adhesives chemical modified by ZnO nanowires for HB LEDs

    NASA Astrophysics Data System (ADS)

    He, Ying; Wang, Jun-An; Pei, Chang-Long; Song, Ji-Zhong; Zhu, Di; Chen, Jie

    2010-10-01

    A novel high transparent thermolytic epoxy-silicone for high-brightness light-emitting diode (HB-LED) is introduced, which was synthesized by polymerization using silicone matrix via diglycidyl ether bisphenol-A epoxy resin (DGEBA) as reinforcing agent, and filling ZnO nanowires to modify thermal conductivity and control refractive index of the hybrid material. The interactions of ZnO nanowires with polymers are mediated by the ligands attached to the nanoparticles. Thus, the ligands markedly influence the properties of ZnO nanowires/epoxy-silicone composites. The refractive indices of the prepared hybrid adhesives can be tuned by the ZnO nanowires from 1.4711 to 1.5605. Light transmittance can be increased by 20% from 80 to 95%. The thermal conductivity of the transparent packaging adhesives is 0.89-0.90 W/mK.

  7. Chemically modified polymeric resins for solid-phase extraction and group separation prior to analysis by liquid or gas chromatography

    SciTech Connect

    Schmidt, L.W.

    1993-07-01

    Polystyrene divinylbenzene was modified by acetyl, sulfonic acid, and quaternary ammonium groups. A resin functionalized with an acetyl group was impregnated in a PTFE membrane and used to extract and concentrate phenolic compounds from aqueous samples. The acetyl group created a surface easily wetted, making it an efficient adsorbent for polar compounds in water. The membrane stabilized the resin bed. Partially sulfonated high surface area resins are used to extract and group separate an aqueous mixture of neutral and basic organics; the bases are adsorbed electrostatically to the sulfonic acid groups, while the neutraons are adsorbed hydrophobically. A two-step elution is then used to separate the two fractions. A partially functionalized anion exchange resin is used to separate organic acids and phenols from neutrals in a similar way. Carboxylic acids are analyzed by HPLC and phenols by GC.

  8. Electrochemical anion sensing using electrodes chemically modified with Au(I)-Cu(I) heterotrimetallic alkynyl cluster complexes containing ferrocenyl groups.

    PubMed

    Doménech, Antonio; Koshevoy, Igor O; Montoya, Noemí; Pakkanen, Tapani A

    2010-07-01

    A novel family of electrochemical anion sensors operating in aqueous media, based on the heterometallic Au(I)-Cu(I) [{Au(3)Cu(2)(C(2)R)(6)}Au(3)(PPh(2)C(6)H(4)PPh(2))(3)](PF(6))(2) (L1, R = Fc; L2, R = C(6)H(4)Fc) alkynyl cluster complexes, is presented. Upon attachment to graphite and gold electrodes, these compounds exhibit a well-defined, essentially reversible, solid-state electrochemistry in contact with aqueous media, based on ferrocenyl-centered oxidation processes involving anion insertion, leading to distinctive pH-independent electrochemical responses for fluoride, chloride, bromide, perchlorate, bicarbonate, carbonate, phosphate, hydrogen phosphate, dihydrogen phosphate, and nitrate anions. Cluster-modified electrodes can be used as potentiometric sensors as a result of the reversible, diffusion-controlled electrochemistry obtained for the anion-assisted electrochemical oxidation of L1 and L2.

  9. Directly coupled high-performance liquid chromatography-accelerator mass spectrometry measurement of chemically modified protein and peptides.

    PubMed

    Thomas, Avi T; Stewart, Benjamin J; Ognibene, Ted J; Turteltaub, Kenneth W; Bench, Graham

    2013-04-02

    Quantitation of low-abundance protein modifications involves significant analytical challenges, especially in biologically important applications, such as studying the role of post-translational modifications in biology and measurement of the effects of reactive drug metabolites. (14)C labeling combined with accelerator mass spectrometry (AMS) provides exquisite sensitivity for such experiments. Here, we demonstrate real-time (14)C quantitation of high-performance liquid chromatography (HPLC) separations by liquid sample accelerator mass spectrometry (LS-AMS). By enabling direct HPLC-AMS coupling, LS-AMS overcomes several major limitations of conventional HPLC-AMS, where individual HPLC fractions must be collected and converted to graphite before measurement. To demonstrate LS-AMS and compare the new technology to traditional solid sample AMS (SS-AMS), reduced and native bovine serum albumin (BSA) was modified by (14)C-iodoacetamide, with and without glutathione present, producing adducts on the order of 1 modification in every 10(6) to 10(8) proteins. (14)C incorporated into modified BSA was measured by solid carbon AMS and LS-AMS. BSA peptides were generated by tryptic digestion. Analysis of HPLC-separated peptides was performed in parallel by LS-AMS, fraction collection combined with SS-AMS, and (for peptide identification) electrospray ionization and tandem mass spectrometry (ESI-MS/MS). LS-AMS enabled (14)C quantitation from ng sample sizes and was 100 times more sensitive to (14)C incorporated in HPLC-separated peptides than SS-AMS, resulting in a lower limit of quantitation of 50 zmol (14)C/peak. Additionally, LS-AMS turnaround times were minutes instead of days, and HPLC trace analyses required 1/6th the AMS instrument time required for analysis of graphite fractions by SS-AMS.

  10. Effects of fluid flow on the oligonucleotide folding in single-walled carbon nanotubes.

    PubMed

    Lim, M C G; Zhong, Z W

    2009-10-01

    This paper presents molecular-dynamics (MD) simulations of DNA oligonucleotide and water molecules translocating through carbon nanotube (CNT) channels. An induced pressure difference is applied to the system by pushing a layer of water molecules toward the flow direction to drive the oligonucleotide and other molecules. This MD simulation investigates the changes that occur in the conformation of the oligonucleotide due to water molecules in nanochannels while controlling the temperature and volume of the system in a canonical ensemble. The results show that the oligonucleotide in the (8,8)-(12,12) CNT channel forms a folded state at a lower pressure, whereas the oligonucleotide in the (10,10)-(14,14) CNT channel forms a folded state at a higher pressure instead. The van der Waals forces between the water molecules and the oligonucleotide suggest that the attraction between these two types of molecules results in the linear arrangements of the bases of the oligonucleotide. For a larger nanotube channel, the folding of the oligonucleotide is mainly dependent on the solvent (water molecules), whereas pressure, the size of the nanotube junction, and water molecules are the considering factors of the folding of the oligonucleotide at a smaller nanotube channel. For a folded oligonucleotide, the water distribution around the oligonucleotide is concentrated at a smaller range than that for the distribution around an unfolded oligonucleotide.

  11. Oligonucleotide-directed self-assembly of proteins: semisynthetic DNA--streptavidin hybrid molecules as connectors for the generation of macroscopic arrays and the construction of supramolecular bioconjugates.

    PubMed Central

    Niemeyer, C M; Sano, T; Smith, C L; Cantor, C R

    1994-01-01

    Modified biomolecules were used for the non-covalent assembly of novel bioconjugates. Hybrid molecules were synthesized from short single-stranded DNA and streptavidin by chemical methods using a heterobispecific crosslinker. The covalent attachment of an oligonucleotide moiety to streptavidin provides a specific recognition domain for a complementary nucleic acid sequence, in addition to the four native biotin-binding sites. These bispecific binding capabilities allow the hybrid molecules to serve as versatile connectors in a variety of applications. Bifunctional constructs have been prepared from two complementary hybrid molecules, each previously conjugated to biotinylated immunoglobulin G or alkaline phosphatase. The use of nucleic acid sequences as a template for the formation of an array of proteins is further demonstrated on two size scales. A macroscopic DNA array on a microtiter plate has been transformed into a comparable protein chip. A nano-scale array was made by hybridizing DNA-tagged proteins to specific positions along a RNA or DNA sequence. The generation of supramolecular bioconjugates was shown by quantitative measurements and gel-retardation assays. Images PMID:7530841

  12. Antisense Oligonucleotides Modulating Activation of a Nonsense-Mediated RNA Decay Switch Exon in the ATM Gene

    PubMed Central

    Kralovicova, Jana; Moreno, Pedro M.D.; Cross, Nicholas C.P.; Pêgo, Ana Paula

    2016-01-01

    ATM (ataxia-telangiectasia, mutated) is an important cancer susceptibility gene that encodes a key apical kinase in the DNA damage response pathway. ATM mutations in the germ line result in ataxia-telangiectasia (A-T), a rare genetic syndrome associated with hypersensitivity to double-strand DNA breaks and predisposition to lymphoid malignancies. ATM expression is limited by a tightly regulated nonsense-mediated RNA decay (NMD) switch exon (termed NSE) located in intron 28. In this study, we identify antisense oligonucleotides that modulate NSE inclusion in mature transcripts by systematically targeting the entire 3.1-kb-long intron. Their identification was assisted by a segmental deletion analysis of transposed elements, revealing NSE repression upon removal of a distant antisense Alu and NSE activation upon elimination of a long terminal repeat transposon MER51A. Efficient NSE repression was achieved by delivering optimized splice-switching oligonucleotides to embryonic and lymphoblastoid cells using chitosan-based nanoparticles. Together, these results provide a basis for possible sequence-specific radiosensitization of cancer cells, highlight the power of intronic antisense oligonucleotides to modify gene expression, and demonstrate transposon-mediated regulation of NSEs. PMID:27658045

  13. Anti-fouling characteristics of surface-confined oligonucleotide strands bioconjugated on streptavidin platforms in the presence of nanomaterials.

    PubMed

    Mir, Mònica; Cameron, Petra J; Zhong, Xinhua; Azzaroni, Omar; Alvarez, Marta; Knoll, Wolfgang

    2009-05-15

    This work describes our studies on the molecular design of interfacial architectures suitable for DNA sensing which could resist non-specific binding of nanomaterials commonly used as labels for amplifying biorecognition events. We observed that the non-specific binding of bio-nanomaterials to surface-confined oligonucleotide strands is highly dependent on the characteristics of the interfacial architecture. Thiolated double stranded oligonucleotide arrays assembled on Au surfaces evidence significant fouling in the presence of nanoparticles (NPs) at the nanomolar level. The non-specific interaction between the oligonucleotide strands and the nanomaterials can be sensitively minimized by introducing streptavidin (SAv) as an underlayer conjugated to the DNA arrays. The role of the SAv layer was attributed to the significant hydrophilic repulsion between the SAv-modified surface and the nanomaterials in close proximity to the interface, thus conferring outstanding anti-fouling characteristics to the interfacial architecture. These results provide a simple and straightforward strategy to overcome the limitations introduced by the non-specific binding of labels to achieve reliable detection of DNA-based biorecognition events.

  14. Glycoclusters on oligonucleotide and PNA scaffolds: synthesis and applications.

    PubMed

    Spinelli, Nicolas; Defrancq, Eric; Morvan, François

    2013-06-07

    Conjugation of oligonucleotides (ONs) to a variety of reporter groups has been the subject of intensive research during the last decade. Conjugation is indeed of great interest because it can be used not only to improve the existing ONs properties but also to impart new ones. In this context tremendous efforts have been made to conjugate carbohydrate moieties to ONs. Indeed carbohydrates play an important role in biological processes such as signal transduction and cell adhesion through the recognition with sugar-binding proteins (i.e. lectins) located on the surface of cells. For this reason, carbohydrate-oligonucleotide conjugates (COCs) have been first developed for improving the poor cellular uptake or tissue specific delivery of ONs through receptor-mediated endocytosis. Besides the targeted ONs delivery, carbohydrate-oligonucleotide conjugates (COCs) are also evaluated in the context of carbohydrate biochips in which surface coating with carbohydrates is achieved by using the DNA-directed immobilization strategy (DDI). Peptide nucleic acids (PNAs) have also been extensively investigated as a surrogate of DNA for diverse applications. Therefore attachment of carbohydrate moieties to this class of molecules has been studied. The aforementioned applications of COCs require mimicking of the natural processes, in which the weak individual protein-carbohydrate binding is overcome by using multivalent interactions. This tutorial review focuses on the recent advances in carbohydrate-oligonucleotide conjugates and describes the major synthetic approaches available. In addition, an overview of applications that have been developed using various scaffolds allowing multivalent interactions is provided. Finally recent results on the use of peptide nucleic acids as oligonucleotides surrogate are described.

  15. Copper(II) removal from aqueous solutions by adsorption on non-treated and chemically modified cactus fibres.

    PubMed

    Prodromou, M; Pashalidis, I

    2013-01-01

    The adsorption efficiency of a biomass by-product (cactus fibres) regarding the removal of copper(II) from aqueous solutions has been investigated before and after its chemical treatment. The chemical treatment of the biomass by-product included phosphorylation and MnO2-coating. The separation/removal efficiency has been studied as a function of pH, Cu(II) concentration, ionic strength, temperature and contact time. Evaluation of the experimental data shows that the MnO2-coated product presents the highest adsorption capacity, followed by the non-treated and phosphorylated material. Regarding the effect of ionic strength/salinity on the adsorption, in contrast to the removal efficiency of the phosphorylated product, which is significantly affected, the MnO2-coated and non-treated material don't show any effect, indicating the formation of inner-sphere surface complexes. The adsorption reaction is in all cases endothermic and relatively fast, particularly the adsorption on the MnO2-coated product. The results of the present study indicate that for the removal of bivalent metal-ions from contaminated waters the MnO2-coated material is expected to be the most effective adsorbent and an alternative to MnO2 resins for the treatment of environmentally relevant waters.

  16. A modified BAF system configuring synergistic denitrification and chemical phosphorus precipitation: Examination on pollutants removal and clogging development.

    PubMed

    Wang, Hongjie; Dong, Wengyi; Li, Ting; Liu, Tongzhou

    2015-01-01

    The performance of a BAF system configuring simultaneous chemical phosphorus precipitation in the pre-denitrification stage was examined using a continuously operated setup to treat real domestic wastewater. The effects of using no chemical, dosing sole Fe(2+), and dosing combined Fe(2+), PAM, and NaHCO3 in the pre-denitrification tank were assessed by monitoring COD, nitrogen, and phosphorus removal and hydraulic headloss development in the BAF column. Though dosing sole Fe(2+) significantly enhanced phosphorus removal, it would consume alkalinity through hydrolysis and form smaller-sized sludge flocs in the pre-denitrification tank, and hence resulted in affected NH4(+)-N, insoluble COD, and SS removal in the BAF. Dosing combined Fe(2+), PAM, and NaHCO3 can enhance sludge flocculation to form larger flocs and compensate alkalinity consumption. It exhibited sound performance on COD, nitrogen, and phosphorus removal, and led to less frequent BAF backwashing by slowing clogging development in the BAF filter layer.

  17. Pentopyranosyl Oligonucleotide Systems. Part 11: Systems with Shortened Backbones: D)-beta-Ribopyranosyl-(4 yields 3 )- and (L)-alpha - Lyxopyranosyl-(4 yields 3 )-oligonucleotides

    NASA Technical Reports Server (NTRS)

    Wippo, Harald; Reck, Folkert; Kudick, Rene; Ramaseshan, Mahesh; Ceulemans, Griet; Bolli, Martin; Krishnamurthy, Ramanarayanan; Eschenmoser, Albert

    2001-01-01

    The (L)-a-lyxopyranosyl-(4'yields 3')-oligonucleotide system-a member of a pentopyranosyl oligonucleotide family containing a shortened backbone-is capable of cooperative base-pairing and of cross-pairing with DNA and RNA. In contrast, corresponding (D)-beta-ribopyransoyl-(4' yields 3')-oligonucleotides do not show base-pairing under similar conditions. We conclude that oligonucleotide systems can violate the six-bonds-per-backbone-unit rule by having five bonds instead, if their vicinally bound phosphodiester bridges can assume an antiperiplanar conformation. An additional structural feature that seems relevant to the cross-pairing capability of the (L)-a-lyxopyranosyl-(4' yields 3')-oligonucleotide system is its (small) backbone/basepair axes inclination. An inclination which is similar to that in B-DNA seems to be a prerequisite for an oligonucleotide system s capability to cross-pair with DNA.

  18. Small antisense oligonucleotides against G-quadruplexes: specific mRNA translational switches

    PubMed Central

    Rouleau, Samuel G.; Beaudoin, Jean-Denis; Bisaillon, Martin; Perreault, Jean-Pierre

    2015-01-01

    G-quadruplexes (G4) are intricate RNA structures found throughout the transcriptome. Because they are associated with a variety of biological cellular mechanisms, these fascinating structural motifs are seen as potential therapeutic targets against many diseases. While screening of chemical compounds specific to G4 motifs has yielded interesting results, no single compound successfully discriminates between G4 motifs based on nucleotide sequences alone. This level of specificity is best attained using antisense oligonucleotides (ASO). Indeed, oligonucleotide-based strategies are already used to modulate DNA G4 folding in vitro. Here, we report that, in human cells, the use of short ASO to promote and inhibit RNA G4 folding affects the translation of specific mRNAs, including one from the 5′UTR of the H2AFY gene, a histone variant associated with cellular differentiation and cancer. These results suggest that the relatively high specificity of ASO-based strategies holds significant potential for applications aimed at modulating G4-motif folding. PMID:25510493

  19. Theoretical analysis of the kinetics of DNA hybridization with gel-immobilized oligonucleotides.

    PubMed Central

    Livshits, M A; Mirzabekov, A D

    1996-01-01

    A new method of DNA sequencing by hybridization using a microchip containing a set of immobilized oligonucleotides is being developed. A theoretical analysis is presented of the kinetics of DNA hybridization with deoxynucleotide molecules chemically tethered in a polyacrylamide gel layer. The analysis has shown that long-term evolution of the spatial distribution and of the amount of DNA bound in a hybridization cell is governed by "retarded diffusion," i.e., diffusion of the DNA interrupted by repeated association and dissociation with immobile oligonucleotide molecules. Retarded diffusion determines the characteristic time of establishing a final equilibrium state in a cell, i.e., the state with the maximum quantity and a uniform distribution of bound DNA. In the case of cells with the most stable, perfect duplexes, the characteristic time of retarded diffusion (which is proportional to the equilibrium binding constant and to the concentration of binding sites) can be longer than the duration of the real hybridization procedure. This conclusion is indirectly confirmed by the observation of nonuniform fluorescence of labeled DNA in perfect-match hybridization cells (brighter at the edges). For optimal discrimination of perfect duplexes from duplexes with mismatches the hybridization process should be brought to equilibrium under low-temperature nonsaturation conditions for all cells. The kinetic differences between perfect and nonperfect duplexes in the gel allow further improvement in the discrimination through additional washing at low temperature after hybridization. Images FIGURE 1 PMID:8913616

  20. Electrochemical Detection of a Dengue-related Oligonucleotide Sequence Using Ferrocenium as a Hybridization Indicator

    PubMed Central

    Ribeiro Teles, Fernando Rodrigues; França dos Prazeres, Duarte Miguel; de Lima-Filho, José Luiz

    2007-01-01

    A simple method for electrochemical detection of a synthetic 20-bp oligonucleotide sequence related with dengue virus genome was developed. A complimentary DNA probe sequence was electrostatically immobilized onto a glassy carbon electrode modified with chitosan. Electrochemical detection of hybridization between probe and target was performed by cyclic voltammetry, using ferrocene (Fc+) as a hybridization label. After hybridization, the peak current response of Fc+ oxidation increased around 26%. A higher voltammetric decay rate constant (kd) and a lower half-life period (t1/2) for the interaction of Fc+ with dsDNA compared to those with ssDNA quantitatively characterize the different strengths of interaction with both types of DNA. By combining the simplicity of DNA immobilization onto a chitosan film and suitable voltammetric detection of hybridization concomitant with ferrocene attachment, a good discrimination between ssDNA and dsDNA was obtained.