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Sample records for chemically modified oligonucleotides

  1. Automated parallel synthesis of 5'-triphosphate oligonucleotides and preparation of chemically modified 5'-triphosphate small interfering RNA.

    PubMed

    Zlatev, Ivan; Lackey, Jeremy G; Zhang, Ligang; Dell, Amy; McRae, Kathy; Shaikh, Sarfraz; Duncan, Richard G; Rajeev, Kallanthottathil G; Manoharan, Muthiah

    2013-02-01

    A fully automated chemical method for the parallel and high-throughput solid-phase synthesis of 5'-triphosphate and 5'-diphosphate oligonucleotides is described. The desired full-length oligonucleotides were first constructed using standard automated DNA/RNA solid-phase synthesis procedures. Then, on the same column and instrument, efficient implementation of an uninterrupted sequential cycle afforded the corresponding unmodified or chemically modified 5'-triphosphates and 5'-diphosphates. The method was readily translated into a scalable and high-throughput synthesis protocol compatible with the current DNA/RNA synthesizers yielding a large variety of unique 5'-polyphosphorylated oligonucleotides. Using this approach, we accomplished the synthesis of chemically modified 5'-triphosphate oligonucleotides that were annealed to form small-interfering RNAs (ppp-siRNAs), a potentially interesting class of novel RNAi therapeutic tools. The attachment of the 5'-triphosphate group to the passenger strand of a siRNA construct did not induce a significant improvement in the in vitro RNAi-mediated gene silencing activity nor a strong specific in vitro RIG-I activation. The reported method will enable the screening of many chemically modified ppp-siRNAs, resulting in a novel bi-functional RNAi therapeutic platform. PMID:23260577

  2. Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides

    PubMed Central

    Zhou, Yuan; Kierzek, Elzbieta; Loo, Zi Ping; Antonio, Meraldo; Yau, Yin Hoe; Chuah, York Wieo; Geifman-Shochat, Susana; Kierzek, Ryszard; Chen, Gang

    2013-01-01

    Triplex is emerging as an important RNA tertiary structure motif, in which consecutive non-canonical base pairs form between a duplex and a third strand. RNA duplex region is also often functionally important site for protein binding. Thus, triplex-forming oligonucleotides (TFOs) may be developed to regulate various biological functions involving RNA, such as viral ribosomal frameshifting and reverse transcription. How chemical modification in TFOs affects RNA triplex stability, however, is not well understood. Here, we incorporated locked nucleic acid, 2-thio U- and 2′-O methyl-modified residues in a series of all pyrimidine RNA TFOs, and we studied the binding to two RNA hairpin structures. The 12-base-triple major-groove pyrimidine–purine–pyrimidine triplex structures form between the duplex regions of RNA/DNA hairpins and the complementary RNA TFOs. Ultraviolet-absorbance-detected thermal melting studies reveal that the locked nucleic acid and 2-thio U modifications in TFOs strongly enhance triplex formation with both parental RNA and DNA duplex regions. In addition, we found that incorporation of 2′-O methyl-modified residues in a TFO destabilizes and stabilizes triplex formation with RNA and DNA duplex regions, respectively. The (de)stabilization of RNA triplex formation may be facilitated through modulation of van der Waals contact, base stacking, hydrogen bonding, backbone pre-organization, geometric compatibility and/or dehydration energy. Better understanding of the molecular determinants of RNA triplex structure stability lays the foundation for designing and discovering novel sequence-specific duplex-binding ligands as diagnostic and therapeutic agents targeting RNA. PMID:23658228

  3. Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides.

    PubMed

    Zhou, Yuan; Kierzek, Elzbieta; Loo, Zi Ping; Antonio, Meraldo; Yau, Yin Hoe; Chuah, York Wieo; Geifman-Shochat, Susana; Kierzek, Ryszard; Chen, Gang

    2013-07-01

    Triplex is emerging as an important RNA tertiary structure motif, in which consecutive non-canonical base pairs form between a duplex and a third strand. RNA duplex region is also often functionally important site for protein binding. Thus, triplex-forming oligonucleotides (TFOs) may be developed to regulate various biological functions involving RNA, such as viral ribosomal frameshifting and reverse transcription. How chemical modification in TFOs affects RNA triplex stability, however, is not well understood. Here, we incorporated locked nucleic acid, 2-thio U- and 2'-O methyl-modified residues in a series of all pyrimidine RNA TFOs, and we studied the binding to two RNA hairpin structures. The 12-base-triple major-groove pyrimidine-purine-pyrimidine triplex structures form between the duplex regions of RNA/DNA hairpins and the complementary RNA TFOs. Ultraviolet-absorbance-detected thermal melting studies reveal that the locked nucleic acid and 2-thio U modifications in TFOs strongly enhance triplex formation with both parental RNA and DNA duplex regions. In addition, we found that incorporation of 2'-O methyl-modified residues in a TFO destabilizes and stabilizes triplex formation with RNA and DNA duplex regions, respectively. The (de)stabilization of RNA triplex formation may be facilitated through modulation of van der Waals contact, base stacking, hydrogen bonding, backbone pre-organization, geometric compatibility and/or dehydration energy. Better understanding of the molecular determinants of RNA triplex structure stability lays the foundation for designing and discovering novel sequence-specific duplex-binding ligands as diagnostic and therapeutic agents targeting RNA. PMID:23658228

  4. A status update of modified oligonucleotides for chemotherapeutics applications.

    PubMed

    Sanghvi, Yogesh S

    2011-09-01

    This unit presents an update of recent developments and clinical progress in chemically modified oliogonucleotides useful for therapeutic applications. During the last decade, the number of therapeutic oligonucleotides in clinical trials has nearly tripled. This is primarily due to advances in the synthesis protocols, better understanding of the biology, improved delivery, and better formulation technologies. Currently, over 100 clinical trials with oligonucleotide-based drugs are ongoing in the United States for potential treatment of a variety of life-threatening diseases. Among various oligonucleotides, antisense technology has been at the forefront, with one product on the market. Antisense technologies represent about half of the active clinical trials. Similarly, siRNA, aptamers, spiegelmers microRNA, shRNA, IMO, and CpG have been other active classes of oligonucleotides that are also undergoing clinical trials. This review attempts to summarize the current status of synthesis, chemical modifications, purification, and analysis in light of the rapid progress with multitude of oligonucleotides pursued as therapeutic modality. PMID:21901670

  5. Inhibition of dengue virus by novel, modified antisense oligonucleotides.

    PubMed Central

    Raviprakash, K; Liu, K; Matteucci, M; Wagner, R; Riffenburgh, R; Carl, M

    1995-01-01

    Five different target regions along the length of the dengue virus type 2 genome were compared for inhibition of the virus following intracellular injection of the cognate antisense oligonucleotides and their analogs. Unmodified phosphodiester oligonucleotides as well as the corresponding phosphorothioate oligonucleotides were ineffective in bringing about a significant inhibition of the virus. Novel modified phosphorothioate oligonucleotides in which the C-5 atoms of uridines and cytidines were replaced by propynyl groups caused a significant inhibition of the virus. Antisense oligonucleotide directed against the target region near the translation initiation site of dengue virus RNA was the most effective, followed by antisense oligonucleotide directed against a target in the 3' untranslated region of the virus RNA. It is suggested that the inhibitory effect of these novel modified oligonucleotides is due to their increased affinity for the target sequences and that they probably function via an RNase H cleavage of the oligonucleotide:RNA heteroduplex. PMID:7983769

  6. 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.

  7. 2′-Fluoro-modified phosphorothioate oligonucleotide can cause rapid degradation of P54nrb and PSF

    PubMed Central

    Shen, Wen; Liang, Xue-hai; Sun, Hong; Crooke, Stanley T.

    2015-01-01

    Synthetic oligonucleotides are used to regulate gene expression through different mechanisms. Chemical modifications of the backbone of the nucleic acid and/or of the 2′ moiety of the ribose can increase nuclease stability and/or binding affinity of oligonucleotides to target molecules. Here we report that transfection of 2′-F-modified phosphorothioate oligonucleotides into cells can reduce the levels of P54nrb and PSF proteins through proteasome-mediated degradation. Such deleterious effects of 2′-F-modified oligonucleotides were observed in different cell types from different species, and were independent of oligonucleotide sequence, positions of the 2′-F-modified nucleotides in the oligonucleotides, method of delivery or mechanism of action of the oligonucleotides. Four 2′-F-modified nucleotides were sufficient to cause the protein reduction. P54nrb and PSF belong to Drosophila behavior/human splicing (DBHS) family. The third member of the family, PSPC1, was also reduced by the 2′-F-modified oligonucleotides. Preferential association of 2′-F-modified oligonucleotides with P54nrb was observed, which is partially responsible for the protein reduction. Consistent with the role of DBHS proteins in double-strand DNA break (DSB) repair, elevated DSBs were observed in cells treated with 2′-F-modified oligonucleotides, which contributed to severe impairment in cell proliferation. These results suggest that oligonucleotides with 2′-F modifications can cause non-specific loss of cellular protein(s). PMID:25855809

  8. Use of a chemically modified antisense oligonucleotide library to identify and validate Eg5 (kinesin-like 1) as a target for antineoplastic drug development.

    PubMed

    Koller, Erich; Propp, Stephanie; Zhang, Hong; Zhao, Chenguang; Xiao, Xiaokun; Chang, MingYi; Hirsch, Scott A; Shepard, Peter J; Koo, Seongjoon; Murphy, Cain; Glazer, Robert I; Dean, Nicholas M

    2006-02-15

    A library of 2'-methoxyethyl-modified antisense oligonucleotides (2'MOE ASO) targeting 1,510 different genes has been developed, validated, and used to identify cell cycle regulatory genes. The most effective molecular target identified was Eg5 (kinesin-like-1), which when inhibited gave the largest increase in 4N DNA in various tumor cells. The Eg5 ASO reduced Eg5 levels, inhibited proliferation, increased apoptosis, and altered the expression of other cell cycle proteins, including survivin and Aurora-A. To examine the therapeutic utility of the Eg5 ASO, the compound was also evaluated in xenograft models. Treatment with Eg5 ASO produced a statistically significant reduction of tumor growth, reduction in Eg5 expression in the tumors, and changes in histone phosphorylation, consistent with a loss of Eg5 protein expression. These data show, for the first time, the utility of a 2'MOE ASO library for high-throughput cell culture-based functional assays and suggest that an Eg5 ASO also has potential in a therapeutic strategy. PMID:16489005

  9. Secondary binding sites for heavily modified triplex forming oligonucleotides

    PubMed Central

    Cardew, Antonia S.; Brown, Tom; Fox, Keith R.

    2012-01-01

    In order to enhance DNA triple helix stability synthetic oligonucleotides have been developed that bear amino groups on the sugar or base. One of the most effective of these is bis-amino-U (B), which possesses 5-propargylamino and 2′-aminoethoxy modifications. Inclusion of this modified nucleotide not only greatly enhances triplex stability, but also increases the affinity for related sequences. We have used a restriction enzyme protection, selection and amplification assay (REPSA) to isolate sequences that are bound by the heavily modified 9-mer triplex-forming oligonucleotide B6CBT. The isolated sequences contain An tracts (n = 6), suggesting that the 5′-end of this TFO was responsible for successful triplex formation. DNase I footprinting with these sequences confirmed triple helix formation at these secondary targets and demonstrated no interaction with similar oligonucleotides containing T or 5-propargylamino-dU. PMID:22180535

  10. 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.

  11. Correlating In Vitro Splice Switching Activity With Systemic In Vivo Delivery Using Novel ZEN-modified Oligonucleotides

    PubMed Central

    Hammond, Suzan M; McClorey, Graham; Nordin, Joel Z; Godfrey, Caroline; Stenler, Sofia; Lennox, Kim A; Smith, CI Edvard; Jacobi, Ashley M; Varela, Miguel A; Lee, Yi; Behlke, Mark A; Wood, Matthew J A; Andaloussi, Samir E L

    2014-01-01

    Splice switching oligonucleotides (SSOs) induce alternative splicing of pre-mRNA and typically employ chemical modifications to increase nuclease resistance and binding affinity to target pre-mRNA. Here we describe a new SSO non-base modifier (a naphthyl-azo group, “ZEN™”) to direct exon exclusion in mutant dystrophin pre-mRNA to generate functional dystrophin protein. The ZEN modifier is placed near the ends of a 2′-O-methyl (2′OMe) oligonucleotide, increasing melting temperature and potency over unmodified 2′OMe oligonucleotides. In cultured H2K cells, a ZEN-modified 2′OMe phosphorothioate (PS) oligonucleotide delivered by lipid transfection greatly enhanced dystrophin exon skipping over the same 2′OMePS SSO lacking ZEN. However, when tested using free gymnotic uptake in vitro and following systemic delivery in vivo in dystrophin deficient mdx mice, the same ZEN-modified SSO failed to enhance potency. Importantly, we show for the first time that in vivo activity of anionic SSOs is modelled in vitro only when using gymnotic delivery. ZEN is thus a novel modifier that enhances activity of SSOs in vitro but will require improved delivery methods before its in vivo clinical potential can be realized. PMID:25423116

  12. 2'-O-[2-(guanidinium)ethyl]-modified oligonucleotides: stabilizing effect on duplex and triplex structures

    SciTech Connect

    Prakash, T.P.; Puschl, A.; Lesnik, E.; Mohan, V.; Tereshko, V.; Egli, M.; Manoharan, M.

    2010-03-08

    Oligonucleotides with a novel 2'-O-[2-(guanidinium)ethyl] (2'-O-GE) modification have been synthesized using a novel protecting group strategy for the guanidinium group. This modification enhances the binding affinity of oligonucleotides to RNA as well as duplex DNA ({Delta}T{sub m} 3.2 C per modification). The 2'-O-GE modified oligonucleotides exhibited exceptional resistance to nuclease degradation. The crystal structure of a palindromic duplex formed by a DNA oligonucleotide with a single 2'-O-GE modification was solved at 1.16 {angstrom} resolution.

  13. Enzymatic synthesis of modified oligonucleotides by PEAR using Phusion and KOD DNA polymerases.

    PubMed

    Wang, Xuxiang; Zhang, Jianye; Li, Yingjia; Chen, Gang; Wang, Xiaolong

    2015-02-01

    Antisense synthetic oligonucleotides have been developed as potential gene-targeted therapeutics. We previously reported polymerase-endonuclease amplification reaction (PEAR) for amplification of natural and 5'-O-(1-thiotriphosphate) (S)-modified oligonucleotides. Here, we extended the PEAR technique for enzymatic preparation of 2'-deoxy-2'-fluoro-(2'-F) and 2'-F/S double-modified oligonucleotides. The result showed that KOD and Phusion DNA polymerase could synthesize oligonucleotides with one or two modified nucleotides, and KOD DNA polymerase is more suitable than Phusion DNA polymerase for PEAR amplification of 2'-F and 2'-F/S double modified oligonucleotides. The composition of PEAR products were analyzed by electrospray ionization liquid chromatography mass spectrometry (ESI/LC/MS) detection and showed that the sequence of the PEAR products are maintained at an extremely high accuracy (>99.9%), and after digestion the area percent of full-length modified oligonucleotides reaches 89.24%. PEAR is suitable for synthesis of modified oligonucleotides efficiently and with high purity. PMID:25517220

  14. A convenient and efficient purification method for chemically labeled oligonucleotides.

    PubMed

    Hwang, Jihee; Kang, Junhee; Kim, Seong Keun; Kim, Younggyu

    2013-05-01

    We developed an efficient, cost-effective, and rapid purification method for chemically-labeled oligonucleotides that requires less time than conventional procedures such as ethanol precipitation or size-exclusion chromatography. Based on the hydrophilic and hydrophobic properties of DNA and amine-reactive fluorophores, we show that n-butanol saturated with distilled water may be used to remove unreacted fluorophores by sequestering them in the organic phase, while labeled DNA remains in the aqueous phase. This phase extraction method is simple, fast, and allows for processing multiple samples simultaneously, a necessity for high-throughput labeling strategies. PMID:23662899

  15. 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

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

    PubMed

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

    2014-12-15

    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

  17. Modified nucleotides in T1 RNase oligonucleotides of 18S ribosomal RNA of the Novikoff hepatoma.

    PubMed

    Choi, Y C; Busch, H

    1978-06-27

    The primary structure of 18S rRNA of the Novikoff hepatoma cells was investigated. Regardless of whether the primary sequence of 18S rRNA is finally determined by RNA sequencing methods or DNA sequencing methods, it is important to identify numbers and types of the modified nucleotides and accordingly the present study was designed to localize the modified regions in T1 RNase derived oligonucleotide. Modified nucleotides found in 66 different oligonucleotide sequences included 2 m62A, 1 m6A, 1 m7G, 1m1cap3psi, 7 Cm, 13 Am, 9 Gm, 11 Um, and 38 psi residues. A number of these modified nucleotides are now placed in defined sequences of T1 RNase oligonucleotides which are now being searched for in larger fragments derived from partial T1 RNase digests of 18S rRNA. Improved homochromatography fingerprinting (Choi et al. (1976) Cancer Res. 36, 4301) of T1 RNase derived oligonucleotides provided a distinctive pattern for 18S rRNA of Novikoff hepatoma ascites cells. The 116 spots obtained by homochromatography contain 176 oligonucleotide sequences. PMID:209819

  18. 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.

  19. 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.

  20. Approach to the synthesis of natural and modified oligonucleotides by the phosphotriester method using O-nucleophilic intramolecular catalysis.

    PubMed

    Efimov, Vladimir A; Molchanova, Natalia S; Chakhmakhcheva, Oksana G

    2007-01-01

    An approach to the solid phase synthesis of natural and modified oligonucleotides using phosphotriester technique has been developed. Particularly, this method allows the synthesis of ribo- and deoxyribo-oligonucleotides containing various 2'-modified mononucleotides as well as stereodefined nucleotide phosphorothioate analogues. PMID:18058542

  1. 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

  2. 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. PMID:26774580

  3. Potent triple helix stabilization by 5',3'-modified triplex-forming oligonucleotides.

    PubMed

    Ben Gaied, Nouha; Zhao, Zhengyun; Gerrard, Simon R; Fox, Keith R; Brown, Tom

    2009-07-20

    Anthraquinone and pyrene analogues attached to the 3' and/or 5' termini of triplex-forming oligonucleotides (TFOs) by various linkers increased the stability of parallel triple helices. The modifications are simple to synthesize and can be introduced during standard solid-phase oligonucleotide synthesis. Potent triplex stability was achieved by using doubly modified TFOs, which in the most favourable cases gave an increase in melting temperature of 30 degrees C over the unmodified counterparts and maintained their selectivity for the correct target duplex. Such TFOs can produce triplexes with melting temperatures of 40 degrees C at pH 7 even though they do not contain any triplex-stabilizing base analogues. These studies have implications for the design of triplex-forming oligonucleotides for use in biology and nanotechnology. PMID:19554592

  4. Terminally L-modified oligonucleotides: pairing, stability and biological properties.

    PubMed

    Tondelli, L; Garbesi, A; Morelli, S; Calastretti, A; Copreni, E; Gong, L; Nicolin, A

    1996-02-01

    An oligodeoxynucleotide (ODN), capable of reducing the growth of human B lymphocytes carrying the t(14;18) chromosome translocation, was prepared in different 'chemical versions': unmodified phosphodiester, phosphorothioate and phosphodiester capped with L-2'-deoxycytidine. Their binding affinity to the complementary synthetic target was studied by the melting point assay. The ODNs, administered to DOHH2 cells, were compared for stability in the culture medium, cellular uptake, time course of the intact sequence concentration within the cell and ability to inhibit cell growth. The 5', 3'-L-capped derivative and the phosphorothioate had comparable potency, superior to that of the unmodified ODN, in agreement with the concentration of undegraded ODNs within the cell. PMID:8740724

  5. N-Branched acyclic nucleoside phosphonates as monomers for the synthesis of modified oligonucleotides.

    PubMed

    Hocková, Dana; Rosenbergová, Šárka; Ménová, Petra; Páv, Ondřej; Pohl, Radek; Novák, Pavel; Rosenberg, Ivan

    2015-04-21

    Protected N-branched nucleoside phosphonates containing adenine and thymine bases were prepared as the monomers for the introduction of aza-acyclic nucleotide units into modified oligonucleotides. The phosphotriester and phosphoramidite methods were used for the incorporation of modified and natural units, respectively. The solid phase synthesis of a series of nonamers containing one central modified unit was successfully performed in both 3'→5' and 5'→3' directions. Hybridization properties of the prepared oligoribonucleotides and oligodeoxyribonucleotides were evaluated. The measurement of thermal characteristics of the complexes of modified nonamers with the complementary strand revealed a considerable destabilizing effect of the introduced units. We also examined the substrate/inhibitory properties of aza-acyclic nucleoside phosphono-diphosphate derivatives (analogues of nucleoside triphosphates) but neither inhibition of human and bacterial DNA polymerases nor polymerase-mediated incorporation of these triphosphate analogues into short DNA was observed. PMID:25766752

  6. Structure Activity Relationships of α-L-LNA Modified Phosphorothioate Gapmer Antisense Oligonucleotides in Animals.

    PubMed

    Seth, Punit P; Jazayeri, Ali; Yu, Jeff; Allerson, Charles R; Bhat, Balkrishen; Swayze, Eric E

    2012-01-01

    We report the structure activity relationships of short 14-mer phosphorothioate gapmer antisense oligonucleotides (ASOs) modified with α-L-locked nucleic acid (LNA) and related modifications targeting phosphatase and tensin homologue (PTEN) messenger RNA in mice. α-L-LNA represents the α-anomer of enantio-LNA and modified oligonucleotides show LNA like binding affinity for complementary RNA. In contrast to sequence matched LNA gapmer ASOs which showed elevations in plasma alanine aminotransferase (ALT) levels indicative of hepatotoxicity, gapmer ASOs modified with α-L-LNA and related analogs in the flanks showed potent downregulation of PTEN messenger RNA in liver tissue without producing elevations in plasma ALT levels. However, the α-L-LNA ASO showed a moderate dose-dependent increase in liver and spleen weights suggesting a higher propensity for immune stimulation. Interestingly, replacing α-L-LNA nucleotides in the 3'- and 5'-flanks with R-5'-Me-α-L-LNA but not R-6'-Me- or 3'-Me-α-L-LNA nucleotides, reversed the drug induced increase in organ weights. Examination of structural models of dinucleotide units suggested that the 5'-Me group increases steric bulk in close proximity to the phosphorothioate backbone or produces subtle changes in the backbone conformation which could interfere with recognition of the ASO by putative immune receptors. Our data suggests that introducing steric bulk at the 5'-position of the sugar-phosphate backbone could be a general strategy to mitigate the immunostimulatory profile of oligonucleotide drugs. In a clinical setting, proinflammatory effects manifest themselves as injection site reactions and flu-like symptoms. Thus, a mitigation of these effects could increase patient comfort and compliance when treated with ASOs.Molecular Therapy - Nucleic Acids (2012) 1, e47; doi:10.1038/mtna.2012.34; published online 18 September 2012. PMID:23344239

  7. Achieving successful delivery of oligonucleotides--From physico-chemical characterization to in vivo evaluation.

    PubMed

    Scomparin, Anna; Polyak, Dina; Krivitsky, Adva; Satchi-Fainaro, Ronit

    2015-11-01

    RNA interference is one of the most promising fields in modern medicine to treat several diseases, ranging from cancer to cardiac diseases, passing through viral infections and metabolic pathologies. Since the discovery of the potential therapeutic properties of non-self oligonucleotides, it was clear that it is important to develop delivery systems that are able to increase plasma stability and bestow membrane-crossing abilities to the oligonucleotides in order to reach their cytoplasmic targets. Polymer therapeutics, among other systems, are widely investigated as delivery systems for therapeutic agents, such as oligonucleotides. Physico-chemical characterization of the supramolecular polyplexes obtained upon charge interaction or covalent conjugation between the polymeric carrier and the oligonucleotides is critical. Appropriate characterization is fundamental in order to predict and understand the in vivo silencing efficacy and to avoid undesired side effects and toxicity profile. Shedding light on the physico-chemical and in vitro requirements of a polyplex leads to an efficient in vivo delivery system for RNAi therapeutics. In this review, we will present the most common techniques for characterization of obtained polymer/oligonucleotide polyplexes and an up-to-date state of the art in vivo preclinical and clinical studies. This is the first review to deal with the difficulties in appropriate characterization of small interfering RNA (siRNA) or microRNA (miRNA) polyplexes and conjugates which limit the clinical translation of this promising technology. PMID:25916823

  8. Targeting DNA with triplex-forming oligonucleotides to modify gene sequence.

    PubMed

    Simon, Philippe; Cannata, Fabio; Concordet, Jean-Paul; Giovannangeli, Carine

    2008-08-01

    Molecules that interact with DNA in a sequence-specific manner are attractive tools for manipulating gene sequence and expression. For example, triplex-forming oligonucleotides (TFOs), which bind to oligopyrimidine.oligopurine sequences via Hoogsteen hydrogen bonds, have been used to inhibit gene expression at the DNA level as well as to induce targeted mutagenesis in model systems. Recent advances in using oligonucleotides and analogs to target DNA in a sequence-specific manner will be discussed. In particular, chemical modification of TFOs has been used to improve binding to chromosomal target sequences in living cells. Various oligonucleotide analogs have also been found to expand the range of sequences amenable to manipulation, including so-called "Zorro" locked nucleic acids (LNAs) and pseudo-complementary peptide nucleic acids (pcPNAs). Finally, we will examine the potential of TFOs for directing targeted gene sequence modification and propose that synthetic nucleases, based on conjugation of sequence-specific DNA ligands to DNA damaging molecules, are a promising alternative to protein-based endonucleases for targeted gene sequence modification. PMID:18460344

  9. Chemically modified polypyrrole

    SciTech Connect

    Inagaki, T.; Skotheim, T.A.; Lee, H.S.; Okamoto, Y.; Samuelson, L.; Tripathy, S.

    1988-01-01

    Polypyrrole (PPy) films have been systematically modified with electroactive groups in the ..beta..-position to design electrode materials with specific electrochemical and surface active properties. Electrochemical copolymerization of pyrrole and 3-(6-ferrocenyl,6-hydroxyhexyl)pyrrole (P-6-Fc) yields a ferrocene functionalized polypyrrole with a controlled amount to ferrocene functionalization. And also, copolymers of pyrrole and 3-(4-(2,5- dimethoxyphenyl)butyl)pyrrole (P-MP) can be made by electrochemical polymerization and converted to the copolymers containing pH dependent electroactive hydroquinone moieties. Derivatized pyrroles have also been incorporated into Langmuir-Blodgett film structures. The surface pressure-area isotherms of 3-(13-ferrocenyl,13-hydroxytridecy)pyrrole (P-13-Fc) and the mixed monolayer of P-13-Fc and 3-n-hexadecylpyrrole (HDP) are shown. 17 refs., 4 figs.

  10. Assembly of hybrid oligonucleotide modified gold (Au) and alloy nanoparticles building blocks.

    PubMed

    Kuo, Yu-Ching; Jen, Chun-Ping; Chen, Yu-Hung; Su, Chia-Hao; Tsai, Shu-Hui; Yeh, Chen-Sheng

    2006-01-01

    The alloy-based hybrid materials with macroscopic network arrays were developed by AuAg/Au and AuAgPd/Au nanoparticle composites through oligonucleotides hybridization. AuAg/Au and AuAgPd/Au exhibited distinct organization. The morphology of AuAg/Au conjugation assembled mainly as compact aggregates while AuAgPd/Au hybrid conjugated into the loosen network assemblies. The dehybridization temperatures were studied as a function of molar ratio of alloy/Au. It was found that higher alloy/gold molar ratio led to stronger hybridization for alloy/gold composite, accompanied with increased melting temperature. These results could be interpreted in terms of more alloy nanoparticles bound to a Au particle when the molar ratio of alloy/gold increased. The thermal analysis also showed that AuAg/Au exhibited higher dehybridization temperature. A modified model describing the dehybridization probability of an intact Au/alloy aggregate was performed to support the dehybridization temperature increased with increasing alloy/Au molar ratio. As to more oligonucleotides carried by AuAg (4.9 +/- 1.9 nm) than by AuAgPd (4.4 +/- 1.5 nm) due to larger size in AuAg, the efficient hybridization could result in higher dehybridization temperature in AuAg/Au. PMID:16573077

  11. Synthesis of chemically modified DNA.

    PubMed

    Shivalingam, Arun; Brown, Tom

    2016-06-15

    Naturally occurring DNA is encoded by the four nucleobases adenine, cytosine, guanine and thymine. Yet minor chemical modifications to these bases, such as methylation, can significantly alter DNA function, and more drastic changes, such as replacement with unnatural base pairs, could expand its function. In order to realize the full potential of DNA in therapeutic and synthetic biology applications, our ability to 'write' long modified DNA in a controlled manner must be improved. This review highlights methods currently used for the synthesis of moderately long chemically modified nucleic acids (up to 1000 bp), their limitations and areas for future expansion. PMID:27284032

  12. NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A–T phosphoramidite building blocks

    PubMed Central

    Schmidtgall, Boris; Höbartner, Claudia

    2015-01-01

    Summary Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T–T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X–T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A–T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues. PMID:25670992

  13. NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A-T phosphoramidite building blocks.

    PubMed

    Schmidtgall, Boris; Höbartner, Claudia; Ducho, Christian

    2015-01-01

    Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T-T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X-T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A-T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues. PMID:25670992

  14. Aptamer-modified PLGA nanoparticle delivery of triplex forming oligonucleotide for targeted prostate cancer therapy.

    PubMed

    Jiao, J; Zou, Q; Zou, M H; Guo, R M; Zhu, S; Zhang, Y

    2016-01-01

    Presented study aimed to prepare A10 aptamer-modified poly (D,L-lactic-co-glycolic acid) (PLGA) nanoparticles loaded with triplex forming oligonucleotides(TFO) for targeted prostate cancer therapy. We first synthesized a PLGA-PEG-Apt copolymer. The PLGA-PEG-Apt nanoparticles (NP-Apt) were loaded with TFO using double emulsion solvent evaporation method. Carboxy-fluorescein labeled TFO-NP-Apt, TFO-NP and TFO were prepared for cellular uptake experiments. Cell counting kit-8 (CCK-8) test was used to determine the ability of TFO-NP-Apt to inhibit LNCaP cell proliferation. RT-PCR and Western blot was conducted to analyze AR gene expressing. Then, a mouse model of prostate cancer was used to evaluate the anti-cancer effect of TFO-NP-Apt in vivo. We confirmed that the PLGA-PEG-Apt conjugation was successful. The TFO encapsulation efficiency and drug loading percentage were 46.1± 3.6% and 40.8±5.3%, respectively. TFO-NP-Apt showed a more efficient cellular uptake than TFO-NP or TFO in LNCaP cells. TFO-NP-Apt was significantly more cytotoxic than TFO-NP and TFO in the CCK-8 test (p<0.001). TFO-NP-Apt silenced the AR gene better than unconjugated Apt, naked TFO, NP or saline. TFO-NP-Apt were more effective than TFO-NP, naked TFO, NP and saline at inhibiting prostate cancer growth in vivo (p<0.05). Aptamer-modified TFO-loaded PLGA nanoparticles may prove useful in targeted therapy for advanced prostate cancer. PMID:27268920

  15. Monitoring of microenvironmental changes in the major and minor grooves of DNA by dan-modified oligonucleotides.

    PubMed

    Kimura, Takumi; Kawai, Kiyohiko; Majima, Tetsuro

    2005-12-22

    [graph: see text] We describe the synthesis of new environmentally sensitive fluorescence probes to elucidate DNA structures. DNA oligonucleotides containing fluorophore dan (6-(dimethylamino)-2-acylnaphthalene)-modified dC or dG were able to monitor the microenvironmental changes in both the major and minor grooves of DNA with a B- to A-DNA conformational transition and RNA hybridization. PMID:16354077

  16. 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. PMID:15308218

  17. 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

    2016-03-01

    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. PMID:26923600

  18. Sensitive detection of glucose in human serum with oligonucleotide modified gold nanoparticles by using dynamic light scattering technique.

    PubMed

    Miao, Xiangmin; Ling, Liansheng; Shuai, Xintao

    2013-03-15

    Dynamic light scattering based sensor for glucose was developed with oligonucleotide functionalized gold nanoparticles (Oligo-AuNPs). Oligonucleotide 5'-SH-(A)(12)-AGACAAGAGAGG-3' (Oligo 1) modified AuNPs and oligonucleotide 5'-CAACAGAGAACG-(A)(12)-HS-3' (Oligo 2) modified AuNPs could hybridize with oligonulceotide 5'-CGTTCTCTGTTGCCTCTCTTGTCT-3' (Oligo 3), which resulted in the aggregation of Oligo-AuNPs probes, and triggered the increase of their average diameter. However, Oligo 3 could be cleaved into DNA fragments by the mixture of glucose, glucose oxidase (GOD) and Fe(2+), and the DNA fragments could not hybridize with Oligo-AuNPs probes. Under the conditions of 3.7 nM Oligo 1-AuNPs, 3.7 nM Oligo 2-AuNPs, 8.0 μg/mL GOD, 100 nM Oligo 3 and 900 nM Fe(2+), the average diameter of Oligo-AuNPs probes decreased linearly with the increasing concentration of glucose over the range from 50 pmol/L to 5.0 nmol/L, with a detection limit of 38 pmol/L (3σ/slope). Moreover, five sugars had no effect on the average diameter of mixture of Oligo-AuNPs probes, GOD and Fe(2+), which demonstrated the good selectivity of the assay. PMID:23084753

  19. 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

  20. Crystallographic Studies of Chemically Modified Nucleic Acids: A Backward Glance

    PubMed Central

    Egli, Martin; Pallan, Pradeep S.

    2010-01-01

    Chemically modified nucleic acids (CNAs) are widely explored as antisense oligonucleotide or small interfering RNA (siRNA) candidates for therapeutic applications. CNAs are also of interest in diagnostics, high-throughput genomics and target validation, nanotechnology and as model systems in investigations directed at a better understanding of the etiology of nucleic acid structure as well as the physical-chemical and pairing properties of DNA and RNA and for probing protein-nucleic acid interactions. In this article we review research conducted by our laboratory over the past two decades with a focus on crystal structure analyses of CNAs and artificial pairing systems. We highlight key insights into issues ranging from conformational distortions as a consequence of modification to the modulation of pairing strength and RNA affinity by stereoelectronic effects and hydration. Although crystal structures have only been determined for a subset of the large number of modifications that were synthesized and analyzed in the oligonucleotide context to date, they have yielded guiding principles for the design of new analogs with tailormade properties, including pairing specificity, nuclease resistance and cellular uptake. And, perhaps less obviously, crystallographic studies of CNAs and synthetic pairing systems have shed light on fundamental aspects of DNA and RNA structure and function that would not have been disclosed by investigations solely focused on the natural nucleic acids. PMID:20087997

  1. Event-specific detection of seven genetically modified soybean and maizes using multiplex-PCR coupled with oligonucleotide microarray.

    PubMed

    Xu, Jia; Zhu, Shuifang; Miao, Haizhen; Huang, Wensheng; Qiu, Minyan; Huang, Yan; Fu, Xuping; Li, Yao

    2007-07-11

    With the increasing development of genetically modified organism (GMO) detection techniques, the polymerase chain reaction (PCR) technique has been the mainstay for GMO detection. An oligonucleotide microarray is a glass chip to the surface of which an array of oligonucleotides was fixed as spots, each containing numerous copies of a sequence-specific probe that is complementary to a gene of interest. So it is used to detect ten or more targets synchronously. In this research, an event-specific detection strategy based on the unique and specific integration junction sequences between the host plant genome DNA and the integrated gene is being developed for its high specificity using multiplex-PCR together with oligonucleotide microarray. A commercial GM soybean (GTS 40-3-2) and six GM maize events (MON810, MON863, Bt176, Bt11, GA21, and T25) were detected by this method. The results indicate that it is a suitable method for the identification of these GM soybean and maizes. PMID:17559227

  2. 2'-O-[2-[2-(N,N-Dimethylamino)ethoxy]ethyl] Modified Antisense Oligonucleotides: Symbiosis of Charge Interaction Factors and Stereoelectronic Effects

    SciTech Connect

    Prhavc, M.; Prakash, T.P.; Minasov, G.; Egli, M.; Manoharan, M.

    2010-03-08

    Oligonucleotides with a novel, 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] (2'-O-DMAEOE) modification have been synthesized. This modification, a cationic analogue of the 2'-O-(2-methoxyethyl) (2'-O-MOE) modification, exhibits high binding affinity to target RNA (but not to DNA) and exceptional resistance to nuclease degradation. Analysis of the crystal structure of a self-complementary oligonucleotide containing a single 2'-O-DMAEOE modification explains the importance of charge factors and gauche effects on the observed antisense properties. 2'-O-DMAEOE modified oligonucleotides are ideal candidates for antisense drugs.

  3. Effect of dose and plasma concentration on liver uptake and pharmacologic activity of a 2'-methoxyethyl modified chimeric antisense oligonucleotide targeting PTEN.

    PubMed

    Geary, Richard S; Wancewicz, Ed; Matson, John; Pearce, Megan; Siwkowski, Andrew; Swayze, Eric; Bennett, Frank

    2009-08-01

    The role of dose and plasma concentration on liver tissue uptake and resulting antisense pharmacology using a chemically modified antisense oligonucleotide (ASO) targeting PTEN was assessed in mice. A single bolus s.c. dose of 60 mg/kg in mice showed a time-dependent reduction in liver PTEN mRNA that was maximal at 48-72 h and returned to near control levels by 20 days after administration. These pharmacodynamics are in good agreement with liver concentrations of ASO and are consistent with slow elimination (t(1/2)=8 days) of the PTEN ASO from Balb/C mouse liver. As expected, highest ASO concentrations in liver resulted from the s.c. slow infusion at all doses tested. Unexpectedly, the liver EC(50) for the 24-h s.c. slow infusion was approximately twofold higher than the two bolus routes of administration. Based on plasma concentration analysis it appears that 1-2 microg/mL ASO plasma concentration is a threshold that, if exceeded, results in robust antisense effects and below which there is reduced or complete loss of antisense pharmacology in liver even though bulk uptake in the organ is improved. Co-administration of a nonsense ASO competed for liver uptake, but unexpectedly increased pharmacodynamic response for the active oligonucleotide (ISIS 116847) supporting inhibition of a nonproductive bulk uptake pathway while simultaneously improving productive uptake (pharmacodynamics). This competition effect was similar whether the nonsense oligonucleotide was co-administered with ASO or administered up to 24 h prior to active ASO injection. PMID:19393225

  4. In vitro optimization of 2′-OMe-4′-thioribonucleoside–modified anti-microRNA oligonucleotides and its targeting delivery to mouse liver using a liposomal nanoparticle

    PubMed Central

    Takahashi, Mayumi; Yamada, Naoki; Hatakeyama, Hiroto; Murata, Manami; Sato, Yusuke; Minakawa, Noriaki; Harashima, Hideyoshi; Matsuda, Akira

    2013-01-01

    MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally. Previous studies, which characterized miRNA function, revealed their involvement in fundamental biological processes. Importantly, miRNA expression is deregulated in many human diseases. Specific inhibition of miRNAs using chemically modified anti-miRNA oligonucleotides (AMOs) can be a potential therapeutic strategy for diseases in which a specific miRNA is overexpressed. 2′-O-Methyl (2′-OMe)-4′-thioRNA is a hybrid type of chemically modified oligonucleotide, exhibiting high binding affinity to complementary RNAs and high resistance to nuclease degradation. Here, we evaluate 2′-OMe-4′-thioribonucleosides for chemical modification on AMOs. Optimization of the modification pattern using a variety of chemically modified AMOs that are perfectly complementary to mature miR-21 revealed that the uniformly 2′-OMe-4′-thioribonucleoside–modified AMO was most potent. Further investigation showed that phosphorothioate modification contributed to long-term miR-122 inhibition by the 2′-OMe-4′-thioribonucleoside–modified AMO. Moreover, systemically administrated AMOs to mouse using a liposomal delivery system, YSK05-MEND, showed delivery to the liver and efficient inhibition of miR-122 activity at a low dose in vivo. PMID:24030710

  5. Quartz crystal microbalance with dissipation monitoring and spectroscopic ellipsometry measurements of the phospholipid bilayer anchoring stability and kinetics of hydrophobically modified DNA oligonucleotides.

    PubMed

    van der Meulen, Stef A J; Dubacheva, Galina V; Dogterom, Marileen; Richter, Ralf P; Leunissen, Mirjam E

    2014-06-10

    Decorating lipid bilayers with oligonucleotides has great potential for both fundamental studies and applications, taking advantage of the membrane properties and the specific Watson-Crick base pairing. Here, we systematically studied the binding of DNA oligonucleotides with the frequently used hydrophobic anchors cholesterol, stearyl, and distearyl to supported lipid bilayers made of dioleoylphosphatidylcholine (DOPC) by quartz crystal microbalance with dissipation monitoring and spectroscopic ellipsometry (SE). All three anchors were found to incorporate well into DOPC lipid membranes, yet only the distearyl-based anchor remained stable in the bilayer when it was rinsed. The unstable anchoring of the cholesterol- and stearyl-based oligonucleotides can, however, be stabilized by hybridization of the oligonucleotides to complementary DNA modified with a second hydrophobic anchor of the same type. In all cases, the incorporation into the lipid bilayer was found to be limited by mass transport, although micelle formation likely reduced the effective concentration of available oligonucleotides in some samples, leading to substantial differences in binding rates. Using a viscoelastic model to determine the thickness of the DNA layer and elucidating the surface coverage by SE, we found that at equal bulk concentrations double-stranded DNA constructs attached to the lipid bilayer establish a layer that is thicker than that of single-stranded oligonucleotides, whereas the DNA surface densities are similar. Shortening the length of the oligonucleotides, on the other hand, does alter both the thickness and surface density of the DNA layer. This indicates that at the bulk oligonucleotide concentrations employed in our experiments, the packing of the oligonucleotides is not affected by the anchor type, but rather by the length of the DNA. The results are useful for material and biomedical applications that require efficient linking of oligonucleotides to lipid membranes. PMID

  6. Chemical modification of triplex-forming oligonucleotide to promote pyrimidine motif triplex formation at physiological pH.

    PubMed

    Torigoe, Hidetaka; Nakagawa, Osamu; Imanishi, Takeshi; Obika, Satoshi; Sasaki, Kiyomi

    2012-04-01

    Extreme instability of pyrimidine motif triplex DNA at physiological pH severely limits its use in wide variety of potential applications, such as artificial regulation of gene expression, mapping of genomic DNA, and gene-targeted mutagenesis in vivo. Stabilization of pyrimidine motif triplex at physiological pH is, therefore, crucial for improving its potential in various triplex-formation-based strategies in vivo. To this end, we investigated the effect of 3'-amino-2'-O,4'-C-methylene bridged nucleic acid modification of triplex-forming oligonucleotide (TFO), in which 2'-O and 4'-C of the sugar moiety were bridged with the methylene chain and 3'-O was replaced by 3'-NH, on pyrimidine motif triplex formation at physiological pH. The modification not only significantly increased the thermal stability of the triplex but also increased the binding constant of triplex formation about 15-fold. The increased magnitude of the binding constant was not significantly changed when the number and position of the modification in TFO changed. The consideration of the observed thermodynamic parameters suggested that the increased rigidity of the modified TFO in the free state resulting from the bridging of different positions of the sugar moiety with an alkyl chain and the increased hydration of the modified TFO in the free state caused by the introduction of polar nitrogen atoms may significantly increase the binding constant at physiological pH. The study on the TFO viability in human serum showed that the modification significantly increased the resistance of TFO against nuclease degradation. This study presents an effective approach for designing novel chemically modified TFOs with higher binding affinity of triplex formation at physiological pH and higher nuclease resistance under physiological condition, which may eventually lead to progress in various triplex-formation-based strategies in vivo. PMID:22245184

  7. Efficient Targeting of Fatty-Acid Modified Oligonucleotides to Live Cell Membranes through Stepwise Assembly

    PubMed Central

    2014-01-01

    Lipid modifications provide efficient targeting of oligonucleotides to live cell membranes in a range of applications. Targeting efficiency is a function of the rate of lipid DNA insertion into the cell surface and its persistence over time. Here we show that increasing lipid hydrophobicity increases membrane persistence, but decreases the rate of membrane insertion due to the formation of nonproductive aggregates in solution. To ameliorate this effect, we split the net hydrophobicity of the membrane anchor between two complementary oligonucleotides. When prehybridized in solution, doubly anchored molecules also aggregate due to their elevated hydrophobicity. However, when added sequentially to cells, aggregation does not occur so membrane insertion is efficient. Hybridization between the two strands locks the complexes at the cell surface by increasing net hydrophobicity, increasing their total concentration and lifetime, and dramatically improving their utility in a variety of biomedical applications. PMID:25325667

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

    PubMed Central

    Sun, Jingjing; Tang, Xinjing

    2015-01-01

    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 PMID:26020694

  9. 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

  10. 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.

  11. 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.

  12. Invader Assisted Enzyme-Linked Immunosorbent Assay for Colorimetric Detection of Disease Biomarkers Using Oligonucleotide Probe-Modified Gold Nanoparticles.

    PubMed

    Song, Qinxin; Qi, Xiemin; Jia, Huning; He, Liang; Kumar, Shalen; Pitman, Janet L; Zou, Bingjie; Zhou, Guohua

    2016-04-01

    We successfully developed an invader assisted ELISA assay (iaELISA) for sensitive detection of disease biomarkers. The method includes three key steps as follows; biotinylated detection antibody was at first used to capture targeted antigen by sandwich ELISA. The biotinylated oligonucleotide was then attached to detection antibody via streptavidin. Finally, the cascade invader reactions were employed to amplify the biotinylated oligonucleotide specific to the antigen so that detection of the antigen was transformed into signal amplification of the antigen-specific DNA. To achieve colorimetric detection, oligonucleotide probe and modified gold nanoparticles (AuNPs) were coupled with the invader assay. Utilization of the hairpin probes in the invader reaction brought about free AuNPs, resulting in the positive read-out (red color). On the other hand, aggregation of the AuNPs occurred when the hairpin probes were not utilized in the reaction. This method was successfully used to detect as low as 2.4 x 10(-11) g/mL of HBsAg by both naked eye and spectrophotometer. This sensitivity was about 100 times higher than that of conventional ELISA method. The method was also used to assay 16 serum specimens from HBV-infected patients and 8 serum specimens from HBV-negative donors and results were in good agreement with those obtained from the conventional ELISA. As the invader assay is sensitive to one base sequence, a good specificity was also obtained by detecting other antigens like hepatitis A virus (HAV) and BSA. The method has therefore much potential for ultrasensitive and cost-effective detection of targeted proteins that have clinical importance. PMID:27301208

  13. Improved bioactivity of G-rich triplex-forming oligonucleotides containing modified guanine bases.

    PubMed

    Rogers, Faye A; Lloyd, Janice A; Tiwari, Meetu Kaushik

    2014-01-01

    Triplex structures generated by sequence-specific triplex-forming oligonucleotides (TFOs) have proven to be promising tools for gene targeting strategies. In addition, triplex technology has been highly utilized to study the molecular mechanisms of DNA repair, recombination and mutagenesis. However, triplex formation utilizing guanine-rich oligonucleotides as third strands can be inhibited by potassium-induced self-association resulting in G-quadruplex formation. We report here that guanine-rich TFOs partially substituted with 8-aza-7-deaza-guanine (PPG) have improved target site binding in potassium compared with TFOs containing the natural guanine base. We designed PPG-substituted TFOs to bind to a polypurine sequence in the supFG1 reporter gene. The binding efficiency of PPG-substituted TFOs to the target sequence was analyzed using electrophoresis mobility gel shift assays. We have determined that in the presence of potassium, the non-substituted TFO, AG30 did not bind to its target sequence, however binding was observed with the PPG-substituted AG30 under conditions with up to 140 mM KCl. The PPG-TFOs were able to maintain their ability to induce genomic modifications as measured by an assay for gene-targeted mutagenesis. In addition, these compounds were capable of triplex-induced DNA double strand breaks, which resulted in activation of apoptosis. PMID:25483840

  14. Improved bioactivity of G-rich triplex-forming oligonucleotides containing modified guanine bases

    PubMed Central

    Rogers, Faye A; Lloyd, Janice A; Tiwari, Meetu Kaushik

    2014-01-01

    Triplex structures generated by sequence-specific triplex-forming oligonucleotides (TFOs) have proven to be promising tools for gene targeting strategies. In addition, triplex technology has been highly utilized to study the molecular mechanisms of DNA repair, recombination and mutagenesis. However, triplex formation utilizing guanine-rich oligonucleotides as third strands can be inhibited by potassium-induced self-association resulting in G-quadruplex formation. We report here that guanine-rich TFOs partially substituted with 8-aza-7-deaza-guanine (PPG) have improved target site binding in potassium compared with TFOs containing the natural guanine base. We designed PPG-substituted TFOs to bind to a polypurine sequence in the supFG1 reporter gene. The binding efficiency of PPG-substituted TFOs to the target sequence was analyzed using electrophoresis mobility gel shift assays. We have determined that in the presence of potassium, the non-substituted TFO, AG30 did not bind to its target sequence, however binding was observed with the PPG-substituted AG30 under conditions with up to 140 mM KCl. The PPG-TFOs were able to maintain their ability to induce genomic modifications as measured by an assay for gene-targeted mutagenesis. In addition, these compounds were capable of triplex-induced DNA double strand breaks, which resulted in activation of apoptosis. PMID:25483840

  15. Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides.

    PubMed

    Kel'in, Alexander V; Zlatev, Ivan; Harp, Joel; Jayaraman, Muthusamy; Bisbe, Anna; O'Shea, Jonathan; Taneja, Nate; Manoharan, Rajar M; Khan, Saeed; Charisse, Klaus; Maier, Martin A; Egli, Martin; Rajeev, Kallanthottathil G; Manoharan, Muthiah

    2016-03-18

    Although judicious use of chemical modifications has contributed to the success of nucleic acid therapeutics, poor systemic stability remains a major hurdle. The introduction of functional groups around the phosphate backbone can enhance the nuclease resistance of oligonucleotides (ONs). Here, we report the synthesis of enantiomerically pure (R)- and (S)-5'-C-methyl (C5'-Me) substituted nucleosides and their incorporation into ONs. These modifications generally resulted in a decrease in thermal stability of oligonucleotide (ON) duplexes in a manner dependent on the stereoconfiguration at C5' with greater destabilization characteristic of (R)-epimers. Enhanced stability against snake venom phosphodiesterase resulted from modification of the 3'-end of an ON with either (R)- or (S)-C5'-Me nucleotides. The (S)-isomers with different 2'-substituents provided greater resistance against 3'-exonucleases than the corresponding (R)-isomers. Crystal structure analyses of RNA octamers with (R)- or (S)-5'-C-methyl-2'-deoxy-2'-fluorouridine [(R)- or (S)-C5'-Me-2'-FU, respectively] revealed that the stereochemical orientation of the C5'-Me and the steric effects that emanate from the alkyl substitution are the dominant determinants of thermal stability and are likely molecular origins of resistance against nucleases. X-ray and NMR structural analyses showed that the (S)-C5'-Me epimers are spatially and structurally more similar to their natural 5' nonmethylated counterparts than the corresponding (R)-epimers. PMID:26940174

  16. Microenvironmental Effect of 2'-O-(1-Pyrenylmethyl)uridine Modified Fluorescent Oligonucleotide Probes on Sensitive and Selective Detection of Target RNA.

    PubMed

    Imincan, Gülnur; Pei, Fen; Yu, Lijia; Jin, Hongwei; Zhang, Liangren; Yang, Xiaoda; Zhang, Lihe; Tang, XinJing

    2016-04-19

    2'-O-(1-Pyrenylmethyl)uridine modified oligoribonucleotides provide highly sensitive pyrene fluorescent probes for detecting specific nucleotide mutation of RNA targets. To develop more stable and cost-effective oligonucleotide probes, we investigated the local microenvironmental effects of nearby nucleobases on pyrene fluorescence in duplexes of RNAs and 2'-O-(1-pyrenylmethyl)uridine modified oligonucleotides. By incorporation of deoxyribonucleotides, ribonucleotides, 2'-MeO-nucleotides and 2'-F-nucleotides at both sides of 2'-O-(1-pyrenylmethyl)uridine (Up) in oligodeoxynucleotide probes, we synthesized a series of pyrene modified oligonucleotide probes. Their pyrene fluorescence emission spectra indicated that only two proximal nucleotides have a substantial effect on the pyrene fluorescence properties of these oligonucleotide probes hybridized with target RNA with an order of fluorescence sensitivity of 2'-F-nucleotides > 2'-MeO-nucleotides > ribonucleotides ≫ deoxyribonucleotides. While based on circular dichroism spectra, overall helix conformations (either A- or B-form) of the duplexes have marginal effects on the sensitivity of the probes. Instead, the local substitution reflected the propensity of the nucleotide sugar ring to adopt North type conformation and, accordingly, shifted their helix geometry toward a more A-type like conformation in local microenvironments. Thus, higher enhancement of pyrene fluorescence emission favored local A-type helix structures and more polar and hydrophobic environments (F > MeO > OH at 2' substitution) of duplex minor grooves of probes with the target RNA. Further dynamic simulation revealed that local microenvironmental effect of 2'-F-nucleotides or ribonucleotides was enough for pyrene moiety to move out of nucleobases to the minor groove of duplexes; in addition, 2'-F-nucleotide had less effect on π-stack of pyrene-modified uridine with upstream and downstream nucleobases. The present oligonucleotide probes

  17. Synthesis of selenomethylene-locked nucleic acid (SeLNA)-modified oligonucleotides by polymerases.

    PubMed

    Wheeler, Megan; Chardon, Antoine; Goubet, Astrid; Morihiro, Kunihiko; Tsan, Sze Yee; Edwards, Stacey L; Kodama, Tetsuya; Obika, Satoshi; Veedu, Rakesh N

    2012-11-18

    Enzymatic recognition of SeLNA nucleotides was investigated. KOD XL DNA polymerase was found to be an efficient enzyme in primer extension reactions. Polymerase chain reaction (PCR) amplification of SeLNA-modified DNA templates was also efficiently achieved by Phusion and KOD XL DNA polymerases. PMID:23042489

  18. Cross-linking to an interrupted polypurine sequence with a platinum-modified triplex-forming oligonucleotide.

    PubMed

    Campbell, Meghan A; Miller, Paul S

    2009-08-01

    Triplex-forming oligonucleotides (TFOs) can bind specifically to polypurine sequences in double-stranded DNA. A single interruption of this polypurine tract can greatly destabilize triplex formation. The stability of triplexes can be significantly enhanced by covalently linking the TFO to its DNA target with reactive functional groups conjugated to the TFO. Covalently cross-linked TFOs are effective inhibitors of transcription of the target DNA sequence. We have designed a TFO with a platinum-modified base that can interact with and cross-link to a cytosine interruption in the polypurine tract of a target DNA duplex. The TFO contains an N(4)-(aminoalkyl)cytosine derivatized with cis-diamminediaquaplatinum(II) or trans-diamminediaquaplatinum(II). When bound to its target, the tethered platinum of the TFO can reach across the major groove and form an adduct with the guanine N7 of the interrupting C.G base pair. The optimal tether length is five methylene groups, and cross-linking is most efficient when the tether is modified with trans-diamminediaquaplatinum(II). Cross-linking requires that the TFO is bound to its designated DNA target. Addition of cyanide to the cross-linked TFO product reversed the cross-link, behavior that is consistent with the presence of a platinum-guanine adduct. The kinetics of the cross-linking reaction were studied and the half-life of the cross-linking reaction was approximately 3 h. Our results demonstrate that platinum-conjugated TFOs can be designed to cross-link with DNA targets that contain a single pyrimidine interruption. Modifications of this type may prove useful for expanding the DNA sequences that can be targeted by TFOs and increasing the stability of the resulting triplexes. PMID:19350290

  19. Chemically modified electrodes and related solution studies

    SciTech Connect

    Elliott, C.M.

    1990-01-01

    This report briefly discusses work done in the following areas of chemically modified electrodes: Spectroscopic studies of the modes of interactions of pyridine containing ligands with metal surfaces; attempted synthesis of gem-dihalide containing polymers for attachment of Mo{sub 2}S{sub 4} clusters; Synthesis of oxo-ruthenium dimer complexes as catalysts for H{sub 2} oxidation; and, studies of porphyrin based polymers which catalyze the oxidation (oxygenation) of olefins and benzylic carbons. (JDL)

  20. Immobilization of oligonucleotides onto zirconia-modified filter paper and specific molecular recognition.

    PubMed

    Xiao, Wei; Huang, Jianguo

    2011-10-18

    A morphologically complex cellulosic substance (e.g., commercial filter paper) was employed as a substrate for DNA immobilization and successive recognition. A uniform ultrathin zirconia gel film was first deposited on each cellulose nanofiber in bulk filter paper by a facile sol-gel process. Relying on the large surface area of filter paper and the strong affinity of zirconia for the phosphate group, terminal-phosphate probe DNA was abundantly immobilized on the zirconia-modified filter paper so as to convert the composite to a biofunctional material for the sensitive and repetitive recognition of the corresponding complementary target DNA on the nanomolar level. By contrast, in spite of the viability of the immobilization of the probe DNA and the recognition of target DNA on the quartz plate, the amount of captured probe DNA or recognized target DNA on such a flat substrate was much less than that captured or recognized on filter paper, resulting in a relatively insensitive recognition event. Moreover, control experiments on bare filter paper (without a zirconia nanocoating) suggested that the zirconia gel film was essential to probe DNA immobilization and subsequent target DNA recognition. PMID:21905718

  1. Effects of Repeated Complement Activation Associated with Chronic Treatment of Cynomolgus Monkeys with 2'-O-Methoxyethyl Modified Antisense Oligonucleotide.

    PubMed

    Shen, Lijiang; Engelhardt, Jeffrey A; Hung, Gene; Yee, Jenna; Kikkawa, Rie; Matson, John; Tayefeh, Bryan; Machemer, Todd; Giclas, Patricia C; Henry, Scott P

    2016-08-01

    The effects of repeated complement activation in cynomolgus monkeys after chronic antisense oligonucleotide (ASO) treatment were evaluated by using ISIS 104838, a representative 2'-O-methoxyethyl (2'-MOE) modified ASO. The treatment was up to 9 months with a total weekly dose of 30 mg/kg, given either as daily [4.3 mg/kg/day, subcutaneous (s.c.) injection] or once weekly [30 mg/kg, either as s.c. injection or 30-min intravenous (i.v.) infusion]. Acute elevations of complement split products (Bb and C3a) and a transient decrease in C3 occurred after the first dose and were drug plasma concentration dependent. However, with repeated complement activation after chronic ASO treatment, there were progressive increases in basal (predose) levels of Bb and C3a, and a sustained C3 reduction in all treated groups. There was also a progressive increase in C3d-bound circulating immune complex (CIC) that was considered secondary to the C3 depletion. Evidence of vascular inflammation was observed, mostly in the liver, kidney, and heart, and correlated with severe C3 depletion and increases in plasma IgG and IgM. Vascular inflammation was accompanied by increased C3 and IgM immunereactivity in the affected vasculatures and endothelial activation markers in serum. In summary, repeated complement activations in monkeys lead to a sustained decrease in circulating C3 over time. The concomitantly increased inflammatory signals and decreased CIC clearance due to impairment of complement function may lead to vascular inflammation after chronic ASO treatment in monkeys. However, based on the known sensitivity of monkeys to ASO-induced complement activation, these findings have limited relevance to humans. PMID:27140858

  2. 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.

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

    PubMed

    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. PMID:27111839

  4. 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

  5. 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. PMID:27106951

  6. Stability measurements of antisense oligonucleotides by capillary gel electrophoresis.

    PubMed

    Bruin, G J; Börnsen, K O; Hüsken, D; Gassmann, E; Widmer, H M; Paulus, A

    1995-08-11

    The approach of using antisense oligonucleotides as potential drugs is based on hybridization of a short chemically-modified oligonucleotide with complementary cellular DNA or RNA sequences. A critical question is the stability of chemically modified antisense oligonucleotides in cellular environments. In a model system, resistance against various nucleases was evaluated by capillary gel electrophoresis (CGE). For some of the samples, matrix assisted laser desorption and ionization mass spectrometry (MALDI-MS) was used as an additional analytical tool to perform stability measurements. Using CGE, the enzymatic degradation of single nucleotides from the oligomer can be followed after different incubation times. 10% T polyacrylamide gels give baseline resolution for oligonucleotides ranging between 5 and 30 bases in length. The kinetic influence of a specific nuclease concentration and the antisense oligonucleotide structure on the cleavage reaction are discussed. Also, a simple desalting method to improve the injection efficiency and sensitivity of the method are described. Examples of measurements of chemically modified antisense 19-mers are presented. PMID:7581844

  7. Chemically modified carbonic anhydrases useful in carbon capture systems

    SciTech Connect

    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.

  8. Antitumor activity of chemical modified natural compounds.

    PubMed

    de Oliveira, M M

    1991-01-01

    Search of new activity substances starting from chemotherapeutic agents, continuously appears in international literature. Perhaps this search has been done more frequently in the field of antitumor chemotherapy on account of the unsuccess in saving advanced stage patients. The new point in this matter during the last decade was computer aid in planning more rational drugs. In near future "the accessibility of super computers and emergence of computer net systems, will open new avenues to rational drug design" (Portoghese, P. S., J. Med. Chem. 1989, 32, 1). Unknown pharmacological active compounds synthetized by plants can be found even without this electronic devices, as traditional medicine has pointed out in many countries, and give rise to a new drug. These compounds used as found in nature or after chemical modifications have produced successful experimental medicaments as FAA, "flavone acetic acid" with good results as inhibitors of slow growing animal tumors currently in preclinical evaluation for human treatment. In this lecture some international contributions in the field of chemical modified compounds as antineoplastic drugs will be examined, particularly those done by Brazilian researches. PMID:1842015

  9. Fluorescent oligonucleotides can serve as suitable alternatives to radiolabeled oligonucleotides.

    PubMed

    Ballal, Rahul; Cheema, Amrita; Ahmad, Waaqar; Rosen, Eliot M; Saha, Tapas

    2009-09-01

    Prolonged exposure to radiation from radionuclei used in medical research can cause DNA damage and mutation, which lead to several diseases including cancer. Radioactivity-based experiments are expensive and associated with specialized training, dedication of instruments, approvals, and cleanup with potential hazardous waste. The objective of this study was to find an alternative to the use of radioactivity in medical research using nucleic acid chemistry. FITC-labeled oligonucleotides that contain wild-type (wt) and modified base (8-oxo-G) at the same position and their complementary unlabeled strand were synthesized. Purified DNA repair enzyme, OGG1, and nuclear lysates from MCF-7 breast cancer cells were incubated with double-stranded FITC-labeled wt and 8-oxo-G oligonucleotide to demonstrate the OGG1 incision assay. We found that FITC-coupled oligonucleotides do not impose a steric hindrance during duplex formation, and the fluorescence intensity of the oligonucleotide is comparable with the intensity of the radioactive oligonucleotide. Moreover, we have seen that the OGG1 incision assay can be performed using these fluorescence oligonucleotides, replacing conventional use of radiolabeled oligonucleotides in the assay. Although the use of fluorescent-labeled oligonucleotides was described in detail for incision assays, the technique can be applied to replace a broad range of experiments, where radioactive oligonucleotides are used, eliminating the hazardous consequences of radiation. PMID:19721820

  10. Chemically modified flexible strips as electrochemical biosensors.

    PubMed

    Thota, Raju; Ganesh, V

    2014-09-21

    A flexible and disposable strip sensor for non-enzymatic glucose detection is demonstrated in this work. The strips are prepared by using chemical modification processes followed by a simple electroless deposition of copper. Essentially, polyester overhead projector (OHP) transparent films are modified with a monolayer of 3-aminopropyltrimethoxysilane (APTMS) and polyaniline (PANI) conducting polymer. Later, nanostructured copper is deposited onto this modified film. Scanning electron microscope (SEM) and X-ray diffraction (XRD) studies are used for the structural, morphological and crystallinity characterization of the modified films. Electrochemical techniques, namely cyclic voltammetry (CV) and chronoamperometry (CA), are employed for the non-enzymatic detection of glucose. These studies clearly reveal the formation of homogeneous, close-packed spherical Cu particles converged into uniform film that exhibits a good catalytic activity towards the oxidation of glucose. The Cu/PANI/APTMS/OHP sensor displays a remarkable enhancement in the oxidation current density, a very high sensitivity value of 2.8456 mA cm(-2) per mM, and a linear concentration range from 100 μM to 6.5 mM associated with glucose detection. Detection limit is estimated to be 5 μM and the response time of the sensor is determined to be less than 5 s. For comparison, similar studies are performed without PANI, namely Cu/APTMS/OHP films for glucose detection. In this case, a sensitivity value of 2.4457 mA cm(-2) per mM and a linear concentration range of 100 μM-3 mM are estimated. The higher performance characteristics observed in the case of Cu/PANI/APTMS/OHP are attributed to the synergistic effects of the conducting polymer acting as an electron facilitator and the nanostructured Cu films. These disposable, flexible and low-cost strip sensors have also been applied to the detection of glucose in clinical blood serum samples and the results obtained agree very well with the actual glucose

  11. 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. PMID:20615902

  12. 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.

  13. 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.

  14. 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

    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

    2011-10-19

    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···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)···H-C(Pu) pseudo hydrogen bonds in nucleic acid structures. PMID:21919455

  15. 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

  16. Chemically Modifying Viruses for Diverse Applications.

    PubMed

    Mohan, Kritika; Weiss, Gregory A

    2016-05-20

    Long fascinating to biologists, viruses offer nanometer-scale benchtops for building molecular-scale devices and materials. Viruses tolerate a wide range of chemical modifications including reaction conditions, pH values, and temperatures. Recent examples of nongenetic manipulation of viral surfaces have extended viruses into applications ranging from biomedical imaging, drug delivery, tissue regeneration, and biosensors to materials for catalysis and energy generation. Chemical reactions on the phage surface include both covalent and noncovalent modifications, including some applied in conjunction with genetic modifications. Here, we survey viruses chemically augmented with capabilities limited only by imagination. PMID:26930417

  17. 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. PMID:26778211

  18. Development of a Method for Profiling Protein Interactions with LNA-Modified Antisense Oligonucleotides Using Protein Microarrays.

    PubMed

    Kakiuchi-Kiyota, Satoko; Whiteley, Lawrence O; Ryan, Anne M; Mathialagan, Nagappan

    2016-04-01

    Development of locked nucleic acid (LNA) gapmers, antisense oligonucleotides used for efficient inhibition of target RNA expression, is limited by nontarget-mediated hepatotoxicity. Increased binding of hepatocellular proteins to toxic LNA gapmers may be one of the mechanisms contributing to LNA gapmer-induced hepatotoxicity in vivo. In the present study, we investigated the protein binding propensity of nontoxic sequence-1 (NTS-1), toxic sequence-2 (TS-2), and severely highly toxic sequence-3 (HTS-3) LNA gapmers using human protein microarrays. We previously demonstrated by the transcription profiling analysis of liver RNA isolated from mice that TS-2 and HTS-3 gapmers modulate different transcriptional pathways in mice leading to hepatotoxicity. Our protein array profiling demonstrated that a greater number of proteins, including ones associated with hepatotoxicity, hepatic system disorder, and cell functions, were bound by TS-2 and HTS-3 compared with NTS-1. However, the profiles of proteins bound by TS-2 and HTS-3 were similar and did not distinguish proteins contributing to severe in vivo toxicity. These results, together with the previous transcription profiling analysis, indicate that the combination of sequence-dependent transcription modulation and increased protein binding of toxic LNA gapmers contributes to hepatotoxicity. PMID:26643897

  19. Cytokines and therapeutic oligonucleotides.

    PubMed

    Hartmann, G; Bidlingmaier, M; Eigler, A; Hacker, U; Endres, S

    1997-12-01

    Therapeutic oligonucleotides - short strands of synthetic nucleic acids - encompass antisense and aptamer oligonucleotides. Antisense oligonucleotides are designed to bind to target RNA by complementary base pairing and to inhibit translation of the target protein. Antisense oligonucleotides enable specific inhibition of cytokine synthesis. In contrast, aptamer oligonucleotides are able to bind directly to specific proteins. This binding depends on the sequence of the oligonucleotide. Aptamer oligonucleotides with CpG motifs can exert strong immunostimulatory effects. Both kinds of therapeutic oligonucleotides - antisense and aptamer oligonucleotides - provide promising tools to modulate immunological functions. Recently, therapeutic oligonucleotides have moved towards clinical application. An antisense oligonucleotide directed against the proinflammatory intercellular adhesion molecule 1 (ICAM-1) is currently being tested in clinical trials for therapy of inflammatory disease. Immunostimulatory aptamer oligonucleotides are in preclinical development for immunotherapy. In the present review we summarize the application of therapeutic oligonucleotides to modulate immunological functions. We include technological aspects as well as current therapeutic concepts and clinical studies. PMID:9740353

  20. Chemically modified primers for improved multiplex PCR

    PubMed Central

    Shum, Jonathan; Paul, Natasha

    2009-01-01

    Multiplexed PCR, the amplification of multiple targets in a single reaction, presents a new set of challenges that further complicate more traditional PCR set-ups. These complications include a greater probability for non-specific amplicon formation and for imbalanced amplification of different targets, each of which can compromise quantification and detection of multiple targets. Despite these difficulties, multiplex PCR is frequently used in such applications as pathogen detection, RNA quantification, mutation analysis and now, next generation DNA sequencing. Herein, we investigate the utility of primers with one or two thermolabile 4-oxo-1-pentyl phosphotriester modifications in improving multiplex PCR performance. Initial endpoint and real-time analyses reveal a decrease in off-target amplification and subsequent increase in amplicon yield. Furthermore, the use of modified primers in multiplex set-ups revealed a greater limit of detection and more uniform amplification of each target as compared to unmodified primers. Overall, the thermolabile modified primers present a novel and exciting avenue in improving multiplex PCR performance. PMID:19258004

  1. Biopolymer synthesis on polypropylene supports. I. Oligonucleotides.

    PubMed

    Matson, R S; Rampal, J B; Coassin, P J

    1994-03-01

    We have modified polypropylene to serve as a new solid-phase support for oligonucleotide synthesis. The plastic is first surface aminated by exposure to an ammonia plasma generated by radiofrequency plasma discharge. The aminated polypropylene has been found to be useful as a support for the in situ synthesis of oligonucleotides from monomers. Furthermore, oligonucleotides synthesized on the surface of the plastic remain attached following deprotection and can be used directly for hybridization. PMID:8203760

  2. Effects of Chemically Modified Messenger RNA on Protein Expression.

    PubMed

    Li, Bin; Luo, Xiao; Dong, Yizhou

    2016-03-16

    Chemically modified nucleotides play significant roles in the effectiveness of mRNA translation. Here, we describe the synthesis of two sets of chemically modified mRNAs [encoding firefly Luciferase (FLuc) and enhanced green fluorescent protein (eGFP), respectively], evaluation of protein expression, and correlation analysis of expression level under various conditions. The results indicate that chemical modifications of mRNAs are able to significantly improve protein expression, which is dependent on cell types and coding sequences. Moreover, eGFP mRNAs with N1-methylpseudouridine (me(1)ψ), 5-methoxyuridine (5moU), and pseudouridine (ψ) modifications ranked top three in cell lines tested. Interestingly, 5moU-modified eGFP mRNA was more stable than other eGFP mRNAs. Consequently, me(1)ψ, 5moU, and ψ are promising nucleotides for chemical modification of mRNAs. PMID:26906521

  3. Bifunctional phosphoramidite reagents for the introduction of histidyl and dihistidyl residues into oligonucleotides.

    PubMed

    Smith, T H; LaTour, J V; Bochkariov, D; Chaga, G; Nelson, P S

    1999-01-01

    The synthesis and characterization of reagents for the incorporation of histidyl residues into oligonucleotides by automated chemical synthesis is described. Automated oligonucleotide synthesis utilizing a bifunctional reagent for the incorporation of a dihistidyl residue into oligonucleotides is described. Oligonucleotides incorporating one to three dihistidyl residues were prepared and characterized. The interaction of these oligonucleotides with a metal chelating IMAC matrix was explored. PMID:10411463

  4. 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.

  5. Identification and characterization of modified antisense oligonucleotides targeting DMPK in mice and nonhuman primates for the treatment of myotonic dystrophy type 1.

    PubMed

    Pandey, Sanjay K; Wheeler, Thurman M; Justice, Samantha L; Kim, Aneeza; Younis, Husam S; Gattis, Danielle; Jauvin, Dominic; Puymirat, Jack; Swayze, Eric E; Freier, Susan M; Bennett, C Frank; Thornton, Charles A; MacLeod, A Robert

    2015-11-01

    Myotonic dystrophy type 1 (DM1) is the most common form of muscular dystrophy in adults. DM1 is caused by an expanded CTG repeat in the 3'-untranslated region of DMPK, the gene encoding dystrophia myotonica protein kinase (DMPK). Antisense oligonucleotides (ASOs) containing 2',4'-constrained ethyl-modified (cEt) residues exhibit a significantly increased RNA binding affinity and in vivo potency relative to those modified with other 2'-chemistries, which we speculated could translate to enhanced activity in extrahepatic tissues, such as muscle. Here, we describe the design and characterization of a cEt gapmer DMPK ASO (ISIS 486178), with potent activity in vitro and in vivo against mouse, monkey, and human DMPK. Systemic delivery of unformulated ISIS 486718 to wild-type mice decreased DMPK mRNA levels by up to 90% in liver and skeletal muscle. Similarly, treatment of either human DMPK transgenic mice or cynomolgus monkeys with ISIS 486178 led to up to 70% inhibition of DMPK in multiple skeletal muscles and ∼50% in cardiac muscle in both species. Importantly, inhibition of DMPK was well tolerated and was not associated with any skeletal muscle or cardiac toxicity. Also interesting was the demonstration that the inhibition of DMPK mRNA levels in muscle was maintained for up to 16 and 13 weeks post-treatment in mice and monkeys, respectively. These results demonstrate that cEt-modified ASOs show potent activity in skeletal muscle, and that this attractive therapeutic approach warrants further clinical investigation to inhibit the gain-of-function toxic RNA underlying the pathogenesis of DM1. PMID:26330536

  6. 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 Central

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

    2010-01-01

    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. PMID:20615902

  7. 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

  8. Molecular Dynamics Investigations of the Local Structural Characteristics of DNA Oligonucleotides: Studies of Helical Axis Deformations, Conformational Sequence Dependence and Modified Nucleoside Perturbations.

    NASA Astrophysics Data System (ADS)

    Louise-May, Shirley

    The present DNA studies investigate the local structure of DNA oligonucleotides in order to characterize helical axis deformations, sequence dependent fine structure and modified nucleoside perturbations of selected oligonucleotide sequences. The molecular dynamics method is used to generate an ensemble of energetically feasible DNA conformations which can then be analyzed for dynamical conformational properties, some of which can be compared to experimentally derived values. A theory and graphical presentation for the analysis of helical deformations of DNA based on the configurational statistics of polymers, called "Persistence Analysis", was designed. The results of the analysis on prototype forms, static crystal structures and two solvated MD simulations of the sequence d(CGCGAATTCGCG) indicate that all of the expected features of bending can be sensitively and systematically identified by this approach. Comparison of the relative performance of three molecular dynamics potential functions commonly used for dynamical modeling of biological macromolecules; CHARMm, AMBER and GROMOS was investigated via in vacuo MD simulations on the dodecamer sequence d(CGCGAATTCGCG)_2 with respect to the conformational properties of each dynamical model and their ability to support A and B families of DNA. Vacuum molecular dynamics simulations using the CHARMm force field carried out on simple homo- and heteropolymers of DNA led to the conclusion that sequence dependent fine structure appears to be well defined for adenine-thymine rich sequences both at the base pair and base step level whereas much of the the fine structure found in cytosine -guanine rich sequences appears to be context dependent. The local conformational properties of the homopolymer poly (dA) -poly (dT) revealed one dynamical model which was found in general agreement with fiber models currently available. Investigation of the relative structural static and dynamical effect of the misincorporation of

  9. Modified H5 real-time reverse transcriptase-PCR oligonucleotides for detection of divergent avian influenza H5N1 viruses in Egypt.

    PubMed

    Abdelwhab, E M; Abdelwhab, El-Sayed M; Arafa, Abdel-Satar; Erfan, Ahmed M; Aly, Mona M; Hafez, Hafez M

    2010-12-01

    The efforts exerted to prevent circulation of highly pathogenic avian influenza (HPAI) H5N1 virus in birds are the best way to prevent the emergence of a new virus subtype with pandemic potential. Despite the blanket vaccination strategy against HPAI H5N1 in Egypt, continuous circulation of the virus in poultry has increased since late 2007 as a result of the presence of genetic and antigenic distinct variant strains that have escaped during the immune response of vaccinated birds. Although the suspected poultry flocks have had signs and lesions commonly seen in HPAI H5N1-infected birds, escape of variant strains from detection by real-time reverse transcriptase-PCR (RRT-PCR) was observed. Sequence analysis of these variants revealed multiple single nucleotide substitutions in the primers and probe target sequences of the H5 gene by real-time RT-PCR. This study describes the results of RRT-PCR, modified from an existing protocol with regard to the detection of the partial H5 gene segment of the Egyptian H5N1 divergent viruses and applied to nationwide surveillance. The modified RRT-PCR assay was more sensitive than the original one in the detection of Egyptian isolates, with 104% amplification efficiency. Sixty-one field samples were found to be positive in our assay, but only 51 samples tested positive by the original protocol and were more sensitive than matrix gene RRT-PCR detection assay. A detection limit of 10 mean embryo infective dose (EID50) with the updated oligonucleotides primers and probe set was found. For the foreseeable future, mutation of H5N1 viruses and the endemic situation in developing countries require continuous improvement of current diagnostics to aid in the containment of the H5N1 virus in poultry sectors and to lower the threat of influenza virus spread. PMID:21313854

  10. Styrene oxide DNA adducts: in vitro reaction and sensitive detection of modified oligonucleotides using capillary zone electrophoresis interfaced to electrospray mass spectrometry.

    PubMed

    Schrader, W; Linscheid, M

    1997-01-01

    Styrene is one of the most important synthetic chemicals in the world and is subject to investigations concerning carcinogenicity and mutagenicity due to the active metabolite, styrene-7,8-oxide. This epoxide shows a tendency to react, among others, with DNA and DNA constituents. The in vitro reaction of styrene oxide with DNA was investigated by cleaving incubated calf thymus DNA with two different enzymes, namely Benzonase and alkaline phosphatase, to obtain oligonucleotides of the type n-nucleotide-(n-1)-phosphate with chain length from 2 to 8 bases. Alkylated and nonalkylated nucleotides were separated in groups according to their chain length using capillary zone electrophoresis and were detected with electrospray mass spectrometry. This improvement in sensitivity made it possible to obtain new information about the reaction of styrene oxide with DNA, especially to detect unknown reaction products. The results indicate that primarily purine bases were alkylated by styrene oxide before pyrimidine bases, which react with higher concentrations of styrene oxide. This means that in addition to the already reported adducts in DNA at the N-7-, O6- and N2-position of guanine also adducts at the nucleophilic sites of adenine can be found using mass spectrometry. We anticipate for the future this procedure will allow us to investigate base sequence specific reactions as well as interactions from xenobiotics and cytostatic drugs, since reaction products would directly be detectable. PMID:9285042

  11. 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.

  12. A new general approach for the simultaneous chemical synthesis of large numbers of oligonucleotides: segmental solid supports.

    PubMed Central

    Frank, R; Heikens, W; Heisterberg-Moutsis, G; Blöcker, H

    1983-01-01

    A new approach is described which will allow the simultaneous synthesis of large numbers of pre-defined oligonucleotide chains. No machine aid is needed. The simultaneous syntheses can be performed by one person and do not require much more time than is currently needed for the synthesis of just one oligonucleotide in existing strategies. The general idea is the following: One uses noninterchangeable polymeric entities from each of which enough OD units can be isolated after completion of the syntheses. Whenever growing chains on different entities have to be elongated with the same building block these entities are gathered in the same reaction vessel. After such a common reaction cycle the entities are separated and now combined according to the next common building blocks etc. The practicability of this approach is demonstrated by the synthesis of d(T-A-A-T-A-T-T-A) and d(T-A-G-T-A-C-T-A) on cellulose filter disks following the phosphotriester approach. Images PMID:6306587

  13. Lubricant base stock potential of chemically modified vegetable oils.

    PubMed

    Erhan, Sevim Z; Sharma, Brajendra K; Liu, Zengshe; Adhvaryu, Atanu

    2008-10-01

    The environment must be protected against pollution caused by lubricants based on petroleum oils. The pollution problem is so severe that approximately 50% of all lubricants sold worldwide end up in the environment via volatility, spills, or total loss applications. This threat to the environment can be avoided by either preventing undesirable losses, reclaiming and recycling mineral oil lubricants, or using environmentally friendly lubricants. Vegetable oils are recognized as rapidly biodegradable and are thus promising candidates as base fluids in environment friendly lubricants. Lubricants based on vegetable oils display excellent tribological properties, high viscosity indices, and flash points. To compete with mineral-oil-based lubricants, some of their inherent disadvantages, such as poor oxidation and low-temperature stability, must be corrected. One way to address these problems is chemical modification of vegetable oils at the sites of unsaturation. After a one-step chemical modification, the chemically modified soybean oil derivatives were studied for thermo-oxidative stability using pressurized differential scanning calorimetry and a thin-film micro-oxidation test, low-temperature fluid properties using pour-point measurements, and friction-wear properties using four-ball and ball-on-disk configurations. The lubricants formulated with chemically modified soybean oil derivatives exhibit superior low-temperature flow properties, improved thermo-oxidative stability, and better friction and wear properties. The chemically modified soybean oil derivatives having diester substitution at the sites of unsaturation have potential in the formulation of industrial lubricants. PMID:18783238

  14. Polymer materials as modified optical fiber cladding for chemical sensors

    NASA Astrophysics Data System (ADS)

    Yuan, Jianming

    An intrinsic fiber optic chemical sensor has been designed and developed by using a polymer material as a modified fiber cladding. The sensor is constructed by replacing a certain portion of the original cladding with a chemically sensitive material, specifically, polyaniline or polypyrrole. Both the light absorption coefficient and the refractive index of the polymers change upon the exposure to different chemical vapors. These changes induce the optical intensity modulation of the fiber optic sensor. Polyaniline or polypyrrole is coated as the modified cladding by either spin-cast or in-situ deposition method for sensing HCl, NH3, H 2O2, and H4N2 vapors. All sensors show rapid and strong response to the chemical vapors. Thus, these sensors demonstrate that polyaniline and polypyrrole are viable candidate materials for the detection of volatile toxic gases. Sensors exhibit better performance when correct parameters, such as modification area, in-situ deposition time, and spin-rate, are used in the cladding modification process. The reversibility of the sensor depends on the reaction between the modified cladding material and the chemical vapors. Polyaniline cladding has better reversibility than polypyrrole. The optimized sensor response and sensitivity can be achieved by selecting an incident light with suitable wavelength, power, and incident angle.

  15. Intercalator conjugates of pyrimidine locked nucleic acid-modified triplex-forming oligonucleotides: improving DNA binding properties and reaching cellular activities

    PubMed Central

    Brunet, Erika; Corgnali, Maddalena; Perrouault, Loïc; Roig, Victoria; Asseline, Ulysse; Sørensen, Mads D.; Babu, B. Ravindra; Wengel, Jesper; Giovannangeli, Carine

    2005-01-01

    Triplex-forming oligonucleotides (TFOs) are powerful tools to interfere sequence-specifically with DNA-associated biological functions. (A/T,G)-containing TFOs are more commonly used in cells than (T,C)-containing TFOs, especially C-rich sequences; indeed the low intracellular stability of the non-covalent pyrimidine triplexes make the latter less active. In this work we studied the possibility to enhance DNA binding of (T,C)-containing TFOs, aiming to reach cellular activities; to this end, we used locked nucleic acid-modified TFOs (TFO/LNAs) in association with 5′-conjugation of an intercalating agent, an acridine derivative. In vitro a stable triplex was formed with the TFO-acridine conjugate: by SPR measurements at 37°C and neutral pH, the dissociation equilibrium constant was found in the nanomolar range and the triplex half-life ∼10 h (50-fold longer compared with the unconjugated TFO/LNA). Moreover to further understand DNA binding of (T,C)-containing TFO/LNAs, hybridization studies were performed at different pH values: triplex stabilization associated with pH decrease was mainly due to a slower dissociation process. Finally, biological activity of pyrimidine TFO/LNAs was evaluated in a cellular context: it occurred at concentrations ∼0.1 μM for acridine-conjugated TFO/LNA (or ∼2 μM for the unconjugated TFO/LNA) whereas the corresponding phosphodiester TFO was inactive, and it was demonstrated to be triplex-mediated. PMID:16049028

  16. Furan-modified oligonucleotides for fast, high-yielding and site-selective DNA inter-strand cross-linking with non-modified complements†

    PubMed Central

    Stevens, Kristof; Madder, Annemieke

    2009-01-01

    Among the various types of DNA damage, inter-strand cross-links (ICL) represent one of the most cytotoxic lesions. Processes such as transcription and replication can be fully blocked by ICLs, as shown by the mechanism of action of some anticancer drugs. However, repair of ICLs can be a possible cause of resistance. To study the mechanisms of cross-link repair stable, site-specifically cross-linked duplexes are needed. We here report on the synthesis of site-specifically cross-linked DNA using an acyclic furan containing nucleoside. Selective in situ oxidation of the incorporated furan moiety generates a highly reactive oxo-enal that instantly reacts with the complementary base in a non-modified strand, yielding one specific stable cross-linked duplex species. Varying sequence context showed that a strong selectivity for cross-linking to either complementary A or complementary C is operating, without formation of cross-links to neighboring or distant bases. Reaction times are very short and high isolated yields are obtained using only one equivalent of modified strand. The formed covalent link is stable and the isolated cross-linked duplexes can be stored for several months without degradation. Structural characterization of the obtained ICL was possible by comparison to the natural mutagenic adducts of cis-2-butene-1,4-dial, a metabolite of furan primarily responsible for furan carcinogenicity. PMID:19151089

  17. Design and Application of an Easy to Use Oligonucleotide Mass Calculation Program

    NASA Astrophysics Data System (ADS)

    Yang, Jiong; Leopold, Peter; Helmy, Roy; Parish, Craig; Arvary, Becky; Mao, Bing; Meng, Fanyu

    2013-08-01

    With the development of new synthesis procedures, an ever increasing number of chemical modifications can now be incorporated into synthetic oligonucleotides, representing new challenges for analytical chemists to efficiently identify and characterize such molecules. While conventional mass spectrometry (MS) has proven to be a powerful tool to study nucleic acids, new and improved methods and software are now needed to address this emerging challenge. In this report, we describe a simple yet powerful program that affords great flexibility in the calculation of theoretical masses for conventional as well as modified oligonucleotide molecules. This easy to use program can accept input oligonucleotide sequences and then calculate the theoretical mass values for full length products, process impurities, potential metabolites, and gas phase fragments. We intentionally designed this software so that modified nucleotide residues can be incorporated into oligonucleotide sequences, and corresponding mass values can be rapidly calculated. To test the utility of this program, two oligonucleotides that contain a large number of chemical modifications were synthesized. We have analyzed these samples using a Q-TOF mass spectrometer and compared the calculated masses to the observed ones. We found that all of the data matched very well with less than 30 ppm mass errors, well within the expectation for our instrument operated in its current mode. These data confirmed the validity of calculations performed with this new software.

  18. In vitro binding of the purified hormone-binding subunit of the estrogen receptor to oligonucleotides containing natural or modified sequences of an estrogen-responsive element.

    PubMed

    Medici, N; Nigro, V; Abbondanza, C; Moncharmont, B; Molinari, A M; Puca, G A

    1991-04-01

    Estrogen receptor (ER) was purified from calf uterus by immunoaffinity chromatography in the absence of the ligand. The purified ER consists of a mixture of monomer and homodimer forms of 67-kDa hormone-binding subunit (no 90-kDa heat shock protein is present). The purified ER was incubated with a 32P-labeled 61-basepair oligonucleotide containing the sequence of the estrogen response element (ERE) of the Xenopus laevis A2 vitellogenin gene. DNA mobility shift assays showed formation of specific complexes of the ERE containing oligonucleotide with ER, formation which did not require and was not affected by estradiol or antiestrogenic molecules. Both the monomer and the dimer were equally able to interact with the ERE-containing oligonucleotide. Sucrose gradient experiments showed that only the ER monomer is able to interact with an oligonucleotide in which a single mutation destroyed the dyad symmetry of ERE. Multiple symmetric mutations which did not alter the dyad symmetry of ERE nevertheless totally destroyed the ability of the oligonucleotide to form complexes with either the monomeric or dimeric form of ER. These results suggest that ER is able to bind to ERE independently of the presence of estradiol or other proteins and, therefore, that estradiol does not act by modulating the ability of ER to bind to ERE on DNA. PMID:1922088

  19. Supersensitive fingerprinting of explosives by chemically modified nanosensors arrays

    NASA Astrophysics Data System (ADS)

    Lichtenstein, Amir; Havivi, Ehud; Shacham, Ronen; Hahamy, Ehud; Leibovich, Ronit; Pevzner, Alexander; Krivitsky, Vadim; Davivi, Guy; Presman, Igor; Elnathan, Roey; Engel, Yoni; Flaxer, Eli; Patolsky, Fernando

    2014-06-01

    The capability to detect traces of explosives sensitively, selectively and rapidly could be of great benefit for applications relating to civilian national security and military needs. Here, we show that, when chemically modified in a multiplexed mode, nanoelectrical devices arrays enable the supersensitive discriminative detection of explosive species. The fingerprinting of explosives is achieved by pattern recognizing the inherent kinetics, and thermodynamics, of interaction between the chemically modified nanosensors array and the molecular analytes under test. This platform allows for the rapid detection of explosives, from air collected samples, down to the parts-per-quadrillion concentration range, and represents the first nanotechnology-inspired demonstration on the selective supersensitive detection of explosives, including the nitro- and peroxide-derivatives, on a single electronic platform. Furthermore, the ultrahigh sensitivity displayed by our platform may allow the remote detection of various explosives, a task unachieved by existing detection technologies.

  20. Supersensitive fingerprinting of explosives by chemically modified nanosensors arrays.

    PubMed

    Lichtenstein, Amir; Havivi, Ehud; Shacham, Ronen; Hahamy, Ehud; Leibovich, Ronit; Pevzner, Alexander; Krivitsky, Vadim; Davivi, Guy; Presman, Igor; Elnathan, Roey; Engel, Yoni; Flaxer, Eli; Patolsky, Fernando

    2014-01-01

    The capability to detect traces of explosives sensitively, selectively and rapidly could be of great benefit for applications relating to civilian national security and military needs. Here, we show that, when chemically modified in a multiplexed mode, nanoelectrical devices arrays enable the supersensitive discriminative detection of explosive species. The fingerprinting of explosives is achieved by pattern recognizing the inherent kinetics, and thermodynamics, of interaction between the chemically modified nanosensors array and the molecular analytes under test. This platform allows for the rapid detection of explosives, from air collected samples, down to the parts-per-quadrillion concentration range, and represents the first nanotechnology-inspired demonstration on the selective supersensitive detection of explosives, including the nitro- and peroxide-derivatives, on a single electronic platform. Furthermore, the ultrahigh sensitivity displayed by our platform may allow the remote detection of various explosives, a task unachieved by existing detection technologies. PMID:24960270

  1. Biocatalytic transformation of petroporphyrins by chemical modified cytochrome C.

    PubMed

    García-Arellano, Humberto; Buenrostro-Gonzalez, Eduardo; Vazquez-Duhalt, Rafael

    2004-03-30

    A semi-synthetic biocatalyst was prepared by a double chemical modification of cytochrome c. Free amino groups were modified with poly(ethylene glycol) while free carboxylic groups were alkylated to form methyl esters. The double chemically modified protein, PEG-Cyt-Met, oxidized synthetic porphyrins in a ternary solvent mixture composed by methylene chloride, methanol, and phosphate buffer. The highest activity was found in the ternary systems with low water content (5%). The use of relatively hydrophobic peroxides, such as tert-butyl and cumene hydroperoxides, extended the operational life of the biocatalyst, which, in turn, resulted in an extended oxidation of the substrates tested. PEG-Cyt-Met is able to transform asphaltenes, a highly recalcitrant petroleum fraction. The huge energetic resource found as asphaltene-rich deposits is the driving force to investigate and to innovate upgrading technologies, including biotechnological strategies. PMID:14991657

  2. 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.

  3. Cationic nanoemulsion as a delivery system for oligonucleotides targeting malarial topoisomerase II.

    PubMed

    Bruxel, F; Cojean, S; Bochot, A; Teixeira, H; Bories, C; Loiseau, P-M; Fattal, E

    2011-09-20

    A promising strategy based on the antisense oligonucleotides against the Plasmodium falciparum topoisomerase II has been considered using cationic nanoemulsion as oligonucleotide delivery system. Phosphodiester and chemically modified phosphorothioate oligonucleotides bearing negative charges were adsorbed on positively charged emulsion composed of medium chain triglycerides, egg lecithin, 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), and water, at different +/- charge ratios (positive charges from cationic lipid/negative charges from oligonucleotide): +0.5/-, +2/-, +4/- and +6/-. The physicochemical properties of the complexes were determined, as well as their stability in culture medium. Their interaction with erythrocytes through hemolysis, binding experiments and confocal microscopy were also evaluated. Finally, the in vitro evaluation of parasite growth and reinfection capacity was performed. The overall results showed that antisense oligonucleotides against P. falciparum topoisomerase II gene can be efficiently adsorbed onto a cationic nanoemulsion forming complexes. Whereas unloaded nanoemulsion displayed an hemolytic effect due to the presence of the cationic lipid, this was not the case of loaded nanoemulsion at low +/- ratios. Oligonucleotide-loaded nanoemulsions were found to be located inside the infected erythrocytes, inhibiting efficiently parasite growth (until 80%) and causing a delay in P. falciparum life cycle. PMID:21291974

  4. 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

  5. Film forming capacity of chemically modified corn starches.

    PubMed

    López, Olivia V; García, María A; Zaritzky, Noemí E

    2008-09-01

    Native starch can be chemically modified to improve its functionality and to expand its uses. Modified starches were characterized and the rheological behavior of filmogenic suspensions was analyzed. The film forming capacity of different chemical modified corn starches was evaluated. Acetylated starch was selected by the characteristics of the resulted films; its optimum concentration was 5% w/w since their films exhibited the lowest water vapor permeability (WVP, 1.26×10(-10)g/msPa). The effect of glycerol as plasticizer on film properties depend on its concentration, being 1.5% w/w those that allows to obtain the lowest WVP value (1.64×10(-11)g/msPa), low film solubility in water and a more compact structure than those of unplasticized films. Mechanical behavior of plasticized acetylated starch films depends on glycerol concentration, being rigid and brittle the unplasticized ones, ductile those containing 1.5% w/w of glycerol and very flexible those with a higher plasticizer content. PMID:26048223

  6. Recovery of palladium using chemically modified cedar wood powder.

    PubMed

    Parajuli, Durga; Hirota, Koichi

    2009-10-15

    Japanese cedar wood powder (CWP) was chemically modified to a tertiary-amine-type adsorbent and studied for the selective recovery of Pd(II) from various industrial waters. Batch adsorption tests performed from 0.1 M to 5 M HCl and HNO3 systems reveal stable performance with better results in HNO3 medium. The maximum loading capacity for Pd(II) was studied in HCl as well as in HNO3. A continuous-flow experiment taking a real industrial solution revealed the feasibility of using modified CWP for the selective uptake and preconcentration of traces of palladium contained in acidic effluents. In addition, stable adsorption performance even on long exposure to gamma-irradiation and selective recovery of palladium from simulated high-level liquid waste (HLW) are important outcomes of the study. PMID:19640546

  7. Chemically modified tetracyclines: The novel host modulating agents

    PubMed Central

    Swamy, Devulapalli Narasimha; Sanivarapu, Sahitya; Moogla, Srinivas; Kapalavai, Vasavi

    2015-01-01

    Periodontal pathogens and destructive host responses are involved in the initiation and progression of periodontitis. The emergence of host response modulation as a treatment concept has resulted from our improved understanding of the pathogenesis of periodontal disease. A variety of drugs have been evaluated as host modulation agents (HMA), including Non Steroidal Anti Inflammatory Drugs (NSAIDS), bisphosphonates, tetracyclines, enamel matrix proteins and bone morphogenetic proteins. Chemically modified tetracyclines (CMTs) are one such group of drugs which have been viewed as potential host modulating agents by their anticollagenolytic property. The CMTs are designed to be more potent inhibitors of pro inflammatory mediators and can increase the levels of anti inflammatory mediators. PMID:26392682

  8. Chemically modified tetracyclines: The novel host modulating agents.

    PubMed

    Swamy, Devulapalli Narasimha; Sanivarapu, Sahitya; Moogla, Srinivas; Kapalavai, Vasavi

    2015-01-01

    Periodontal pathogens and destructive host responses are involved in the initiation and progression of periodontitis. The emergence of host response modulation as a treatment concept has resulted from our improved understanding of the pathogenesis of periodontal disease. A variety of drugs have been evaluated as host modulation agents (HMA), including Non Steroidal Anti Inflammatory Drugs (NSAIDS), bisphosphonates, tetracyclines, enamel matrix proteins and bone morphogenetic proteins. Chemically modified tetracyclines (CMTs) are one such group of drugs which have been viewed as potential host modulating agents by their anticollagenolytic property. The CMTs are designed to be more potent inhibitors of pro inflammatory mediators and can increase the levels of anti inflammatory mediators. PMID:26392682

  9. One-pot synthesis of chemically modified vegetable oils.

    PubMed

    Sharma, Brajendra K; Liu, Zengshe; Adhvaryu, Atanu; Erhan, Sevim Z

    2008-05-14

    Vegetable oils are promising candidates as substitutes for petroleum base oils in lubricant applications, such as total loss lubrication, military applications, and outdoor activities. Although vegetable oils have some advantages, they also have poor oxidation and low temperature stability. One of the ways to address these issues is chemical modification of fatty acid chain of triglyceride. We report a one-pot synthesis of a novel class of chemically modified vegetable oils from epoxidized triacylglycerols and various anhydrides. In an anhydrous solvent, boron trifluoride etherate is used as catalyst to simultaneously open the oxirane ring and activate the anhydride. The reaction was monitored and products confirmed by NMR, FTIR, GPC, and TGA analysis. Experimental conditions were optimized for research quantity and laboratory scale-up (up to 4 lbs). The resultant acyl derivatives of vegetable oil, having diester substitution at the sites of unsaturation, have potential in formulation of industrial fluids such as hydraulic fluids, lubricants, and metal working fluids. PMID:18399638

  10. Probing Chromatin-modifying Enzymes with Chemical Tools.

    PubMed

    Fischle, Wolfgang; Schwarzer, Dirk

    2016-03-18

    Chromatin is the universal template of genetic information in all eukaryotic organisms. Chemical modifications of the DNA-packaging histone proteins and the DNA bases are crucial signaling events in directing the use and readout of eukaryotic genomes. The enzymes that install and remove these chromatin modifications as well as the proteins that bind these marks govern information that goes beyond the sequence of DNA. Therefore, these so-called epigenetic regulators are intensively studied and represent promising drug targets in modern medicine. We summarize and discuss recent advances in the field of chemical biology that have provided chromatin research with sophisticated tools for investigating the composition, activity, and target sites of chromatin modifying enzymes and reader proteins. PMID:26845102

  11. Reduced chemically modified graphene oxide for supercapacitor electrode

    PubMed Central

    2014-01-01

    An efficient active material for supercapacitor electrodes is prepared by reacting potassium hydroxide (KOH) with graphene oxide followed by chemical reduction with hydrazine. The electrochemical performance of KOH treated graphene oxide reduced for 24 h (reduced chemically modified graphene oxide, RCMGO-24) exhibits a specific capacitance of 253 F g-1 at 0.2 A g-1 in 2 M H2SO4 compared to a value of 141 F g-1 for graphene oxide reduced for 24 h (RGO-24), and good cyclic stability up to 3,000 cycles. Interestingly, RCMGO-24 demonstrated a higher specific capacitance and excellent cycle stability due to its residual oxygen functional groups that accelerate the faradaic reactions and aid in faster wetting. This non-annealed strategy offers the potential for simple and cost-effective preparation of an active material for a supercapacitor electrode. PMID:25298756

  12. Novel aerobic tetracycline resistance gene that chemically modifies tetracycline.

    PubMed Central

    Speer, B S; Salyers, A A

    1989-01-01

    A tetracycline resistance gene that was found originally on the Bacteroides plasmid pBF4 confers resistance on Escherichia coli but only when cells are growing aerobically. When E. coli EM24 carrying this aerobic tetracycline resistance (*Tcr) gene is grown in medium containing tetracycline, the resulting spent medium is no longer toxic to tetracycline-sensitive (Tcs) E. coli EM24 (B.S. Speer and A.A. Salyers, J. Bacteriol. 170: 1423-1429, 1988). To determine whether the *Tcr gene product modified tetracycline, we characterized the material resulting from incubation of E. coli (*Tcr) with tetracycline. When [7-3H(N)]tetracycline was added to cultures of E. coli (*Tcr), at least 90% of the label was recovered in the extracellular fluid. Therefore, tetracycline was not being sequestered by the cells. The labeled material behaved similarly to tetracycline with respect to solubility in various organic solvents. However, the UV-visible light spectrum had a single peak at 258 nm, whereas the tetracycline spectrum had a peak at 364 nm. The labeled material also had a faster migration rate than did tetracycline on thin-layer plates in a solvent system of butanol-methanol-10% citric acid (4:1:2, vol/vol/vol) and was separable from tetracycline by reverse-phase high-pressure liquid chromatography, using an acetronitrile-0.1% trifluoroacetic acid solvent system. These results demonstrate that the *Tcr gene product chemically modifies tetracycline. The *Tcr gene is the first example of a chemically modifying tetracycline resistance mechanism. PMID:2644186

  13. Gene Assembly from Chip-Synthesized Oligonucleotides

    PubMed Central

    Eroshenko, Nikolai; Kosuri, Sriram; Marblestone, Adam H; Conway, Nicholas; Church, George M.

    2012-01-01

    De novo synthesis of long double-stranded DNA constructs has a myriad of applications in biology and biological engineering. However, its widespread adoption has been hindered by high costs. Cost can be significantly reduced by using oligonucleotides synthesized on high-density DNA chips. However, most methods for using off-chip DNA for gene synthesis have failed to scale due to the high error rates, low yields, and high chemical complexity of the chip-synthesized oligonucleotides. We have recently demonstrated that some commercial DNA chip manufacturers have improved error rates, and that the issues of chemical complexity and low yields can be solved by using barcoded primers to accurately and efficiently amplify subpools of oligonucleotides. This article includes protocols for computationally designing the DNA chip, amplifying the oligonucleotide subpools, and assembling 500-800 basepair (bp) constructs. PMID:25077042

  14. Maltodextrins from chemically modified starches. Selected physicochemical properties.

    PubMed

    Pycia, Karolina; Juszczak, Lesław; Gałkowska, Dorota; Witczak, Mariusz; Jaworska, Grażyna

    2016-08-01

    The aim of this work was to evaluate the effect of chemical modification of starch (cross-linking and/or stabilisation) on selected rheological and functional properties of maltodextrins of dextrose equivalent of 6, 11 and 16. It was found that values of glass transition temperatures were decreasing with dextrose equivalent of maltodextrin. The highest values of glass transition temperature (TG) were determined for maltodextrin of DE 6-obtained from distarch phosphate and acetylated distarch phosphate. Increase in DE value of maltodextrin was also accompanied by decrease and increase in values of intrinsic viscosity and the critical concentration, respectively; however, there was no significant effect of kind of chemical modification of starch on the values of these parameters. Maltodextrin solutions at concentrations of from 10 to 70 % exhibited Newtonian flow behaviour. In the case of 50% solutions of maltodextrins of DE 6 the highest viscosity was produced by maltodextrin from native potato starch, while the lowest one by maltodextrin from acetylated starch. On the other hand, among the maltodextrin of DE 11 this one produced from acetylated starch showed the highest viscosity. All the maltodextrins exhibited surfactant properties in a water-air system, with the strongest effect observed for maltodextrins produced from double chemically modified starches and from acetylated starch. The surface activity was increasing with increasing of the DE value of maltodextrin. Moreover, values of surface tension were decreasing with increasing in maltodextrin concentration in the system. PMID:27112878

  15. Oxidized SWCNT chemically attached to a modified copper substrate

    NASA Astrophysics Data System (ADS)

    Hernandez, Dionne; Cabrera, Carlos R.; Mendez, Laura; Diaz-Serrano, Madeline; Vega, Omar; Weiner, Brad R.; Rosa, Luis G.

    2015-08-01

    Oxidized single-wall carbon nanotubes were chemically attached to a modified copper substrate by means of a 4-aminothiophenol (4-ATP) self-assembly monolayer (SAM). This bottom up approach offers a low cost route to attach carbon nanotubes by using a condensation reaction. Here, the exposed amine from the 4-ATP SAM reacts with the carboxylic group (COOH) on the CNT. The reaction was followed using ATR-FTIR and the surface was characterized using SEM, XPS, and Raman. The analytical techniques used on this study suggest that the condensation reaction employed using a carbodiimide such as 1-Ethyl-3-[3-dimethylaminopropyl] carbodiimide hydrochloride (EDC) produced SWCNT attached to the copper substrate.

  16. Modelling Amperometric Biosensors Based on Chemically Modified Electrodes

    PubMed Central

    Baronas, Romas; Kulys, Juozas

    2008-01-01

    The response of an amperometric biosensor based on a chemically modified electrode was modelled numerically. A mathematical model of the biosensor is based on a system of non-linear reaction-diffusion equations. The modelling biosensor comprises two compartments: an enzyme layer and an outer diffusion layer. In order to define the main governing parameters the corresponding dimensionless mathematical model was derived. The digital simulation was carried out using the finite difference technique. The adequacy of the model was evaluated using analytical solutions known for very specific cases of the model parameters. By changing model parameters the output results were numerically analyzed at transition and steady state conditions. The influence of the substrate and mediator concentrations as well as of the thicknesses of the enzyme and diffusion layers on the biosensor response was investigated. Calculations showed complex kinetics of the biosensor response, especially when the biosensor acts under a mixed limitation of the diffusion and the enzyme interaction with the substrate.

  17. Mesoscale assembly of chemically modified graphene into complex cellular networks

    NASA Astrophysics Data System (ADS)

    Barg, Suelen; Perez, Felipe Macul; Ni, Na; Do Vale Pereira, Paula; Maher, Robert C.; Garcia-Tuñon, Esther; Eslava, Salvador; Agnoli, Stefano; Mattevi, Cecilia; Saiz, Eduardo

    2014-07-01

    The widespread technological introduction of graphene beyond electronics rests on our ability to assemble this two-dimensional building block into three-dimensional structures for practical devices. To achieve this goal we need fabrication approaches that are able to provide an accurate control of chemistry and architecture from nano to macroscopic levels. Here, we describe a versatile technique to build ultralight (density ≥1 mg cm-3) cellular networks based on the use of soft templates and the controlled segregation of chemically modified graphene to liquid interfaces. These novel structures can be tuned for excellent conductivity; versatile mechanical response (elastic-brittle to elastomeric, reversible deformation, high energy absorption) and organic absorption capabilities (above 600 g per gram of material). The approach can be used to uncover the basic principles that will guide the design of practical devices that by combining unique mechanical and functional performance will generate new technological opportunities.

  18. 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. PMID:26896600

  19. 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.

  20. Mesoscale assembly of chemically modified graphene into complex cellular networks

    PubMed Central

    Barg, Suelen; Perez, Felipe Macul; Ni, Na; do Vale Pereira, Paula; Maher, Robert C.; Garcia-Tuñon, Esther; Eslava, Salvador; Agnoli, Stefano; Mattevi, Cecilia; Saiz, Eduardo

    2014-01-01

    The widespread technological introduction of graphene beyond electronics rests on our ability to assemble this two-dimensional building block into three-dimensional structures for practical devices. To achieve this goal we need fabrication approaches that are able to provide an accurate control of chemistry and architecture from nano to macroscopic levels. Here, we describe a versatile technique to build ultralight (density ≥1 mg cm−3) cellular networks based on the use of soft templates and the controlled segregation of chemically modified graphene to liquid interfaces. These novel structures can be tuned for excellent conductivity; versatile mechanical response (elastic-brittle to elastomeric, reversible deformation, high energy absorption) and organic absorption capabilities (above 600 g per gram of material). The approach can be used to uncover the basic principles that will guide the design of practical devices that by combining unique mechanical and functional performance will generate new technological opportunities. PMID:24999766

  1. 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.

  2. Modifying steam generator corrosion behavior via chemical cleaning

    SciTech Connect

    Sweeney, K.; Neese, K.

    1994-12-31

    A steam generator chemical cleaning program was conducted in Palo Verde nuclear generating station (PVNGS) units 2 and 3 in 1994. This effort represented the first full-bundle chemical cleaning of a recirculating steam generator in the United States. The objectives of the process were: (1) to remove deposits in the upper bundle regions, which were identified by eddy-current analysis and linked to a free-span outside-diameter stress corrosion cracking (ODSCC) condition; (2) to remove tube scale deposits that interfere with heat transfer and may contain undesirable contaminants; (3) to remove deposits from the surface of the tube sheet and the flow distribution plate; and (4) to remove deposits from the drilled hole crevices in the FDP, which may be contributing to low recirculation ratios and upper bundle transition boiling. The Electric Power Research Institute/Steam Generator Owners` Group low-temperature process, modified to include {open_quotes}crevice cleaning{close_quotes} and {open_quotes}passivation{close_quotes} steps, was selected as the best method. Babock & Wilcox Nuclear Technologies was selected as the vendor.

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

    PubMed

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

    2016-02-20

    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 6 MR 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. PMID:26906603

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

    DOE PAGESBeta

    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 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

  5. 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. PMID:26463253

  6. Chemically modified nucleic acids as immunodetectable probes in hybridization experiments.

    PubMed Central

    Tchen, P; Fuchs, R P; Sage, E; Leng, M

    1984-01-01

    Guanine residues in nucleic acids can be modified by treatment with N-acetoxy-N-2-acetylaminofluorene and its 7-iodo derivative in an in vitro nonenzymatic reaction. The modified nucleic acids (ribo or deoxyribo, single or double stranded) are recognized by specific antibodies. They can be immunoprecipitated or used as probes in hybridization experiments and detected by immunochemical techniques. Images PMID:6374657

  7. Development of Therapeutic Splice-Switching Oligonucleotides

    PubMed Central

    Kryczka, Adrianna; Liu, Yuqi; Badi, Yusef E.; Wong, Jessie J.; Owen, James S.; Khoo, Bernard

    2014-01-01

    Abstract Synthetic splice-switching oligonucleotides (SSOs) target nuclear pre-mRNA molecules to change exon splicing and generate an alternative protein isoform. Clinical trials with two competitive SSO drugs are underway to treat Duchenne muscular dystrophy (DMD). Beyond DMD, many additional therapeutic applications are possible, with some in phase 1 clinical trials or advanced preclinical evaluation. Here, we present an overview of the central factors involved in developing therapeutic SSOs for the treatment of diseases. The selection of susceptible pre-mRNA target sequences, as well as the design and chemical modification of SSOs to increase SSO stability and effectiveness, are key initial considerations. Identification of effective SSO target sequences is still largely empirical and published guidelines are not a universal guarantee for success. Specifically, exon-targeted SSOs, which are successful in modifying dystrophin splicing, can be ineffective for splice-switching in other contexts. Chemical modifications, importantly, are associated with certain characteristic toxicities, which need to be addressed as target diseases require chronic treatment with SSOs. Moreover, SSO delivery in adequate quantities to the nucleus of target cells without toxicity can prove difficult. Last, the means by which these SSOs are administered needs to be acceptable to the patient. Engineering an efficient therapeutic SSO, therefore, necessarily entails a compromise between desirable qualities and effectiveness. Here, we describe how the application of optimal solutions may differ from case to case. PMID:24826963

  8. 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. PMID:27521696

  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. PMID:27117425

  10. Poly(oligonucleotide)

    PubMed Central

    2015-01-01

    Here we report the preparation of poly(oligonucleotide) brush polymers and amphiphilic brush copolymers from nucleic acid monomers via graft-through polymerization. We describe the polymerization of PNA-norbornyl monomers to yield poly-PNA (poly(peptide nucleic acid)) via ring-opening metathesis polymerization (ROMP) with the initiator, (IMesH2)(C5H5N)2(Cl)2RuCHPh.1 In addition, we present the preparation of poly-PNA nanoparticles from amphiphilic block copolymers and describe their hybridization to a complementary single-stranded DNA (ssDNA) oligonucleotide. PMID:25077676

  11. The delivery of therapeutic oligonucleotides.

    PubMed

    Juliano, Rudolph L

    2016-08-19

    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

  12. 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. PMID:23265899

  13. Safety evaluation of chemically modified beta-lactoglobulin administered intravaginally.

    PubMed

    Guo, Xuetao; Qiu, Lixia; Wang, Yonghong; Wang, Yue; Meng, Yuanguang; Zhu, Yun; Lu, Lu; Jiang, Shibo

    2016-06-01

    Currently, there is no specific antiviral therapy for treatment of HPV infection. Jiang and colleagues previously reported that anhydride-modified proteins have inhibitory activities against multiple viruses including HPV. Here, we evaluated the safety of 3-hydroxyphthalic anhydride-modified bovine beta-lactoglobulin, designated JB01, vaginally applied in women infected by high-risk HPV. After the vaginal application of JB01 in 38 women for 3 months, no serious adverse events were reported, and normalization of the vaginal micro-environment has been observed. It can be concluded that JB01-BD is safe for vaginal use in HPV-infected women, suggesting its potential application for the treatment of HPV infection. J. Med. Virol. 88:1098-1101, 2016. © 2015 Wiley Periodicals, Inc. PMID:26629967

  14. Chemical reactivity of twin-modified copper nanowire surfaces

    SciTech Connect

    Huang, Chun-Lung; Liao, Chien-Neng

    2015-07-13

    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.

  15. 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.

  16. Synthesis of 5'-Aldehyde Oligonucleotide.

    PubMed

    Lartia, Rémy

    2016-01-01

    Synthesis of oligonucleotide ending with an aldehyde functional group at their 5'-end (5'-AON) is possible for both DNA (5'-AODN) and RNA (5'-AORN) series irrespectively of the nature of the last nucleobase. The 5'-alcohol of on-support ODN is mildly oxidized under Moffat conditions. Transient protection of the resulting aldehyde by N,N'-diphenylethylenediamine derivatives allows cleavage, deprotection, and RP-HPLC purification of the protected 5'-AON. Finally, 5'-AON is deprotected by usual acetic acid treatment. In the aggregates, 5'-AON can be now synthesized and purified as routinely as non-modified ODNs, following procedures similar to the well-known "DMT-On" strategy. PMID:26967469

  17. Poly(dG) spacers lead to increased surface coverage of DNA probes: an XPS study of oligonucleotide binding to zirconium phosphonate modified surfaces.

    PubMed

    Lane, Sarah M; Monot, Julien; Petit, Marc; Tellier, Charles; Bujoli, Bruno; Talham, Daniel R

    2008-07-15

    A spacer is often employed between the surface linking group and the probe sequence to improve the performance of DNA microarrays. Previous work demonstrated that a consecutive stretch of guanines as a spacer increased target capture during hybridization relative to probes with either no spacer or a similar stretch of one of the other nucleotides. Using zirconium phosphonate modified surfaces with 5'-phosphorylated ssDNA probes, the present study compares the surface coverage of ssDNA probes containing either a poly(dG) spacer or a poly(dA) spacer. Surface coverages are quantified by XPS using a modified overlayer model. The results show that after treatment to mimic conditions of the passivation and hybridization steps the probe with the poly(dG) spacer has about twice the surface coverage as the probe with the poly(dA) spacer, indicating that increased target capture is due to higher probe coverage. When monitoring the surface coverage after each rinsing step, it is observed that the probe with the poly(dA) spacer is more susceptible to rinsing, suggesting the interaction with the surface is different for the two probes. It is suggested that the formation of G quadruplexes causes an increased avidity of the probe for the zirconium phosphonate surface. PMID:18547070

  18. A Highly Sensitive Oligonucleotide Hybridization Assay for Klebsiella pneumoniae Carbapenemase with the Probes on a Gold Nanoparticles Modified Glassy Carbon Electrode.

    PubMed

    Pan, Hong-zhi; Yu, Hong- Wei; Wang, Na; Zhang, Ze; Wan, Guang-Cai; Liu, Hao; Guan, Xue; Chang, Dong

    2015-01-01

    To develop a new electrochemical DNA biosensor for determination of Klebsiella pneumoniae carbapenemase, a highly sensitive and selective electrochemical biosensor for DNA detection was constructed based on a glassy carbon electrode (GCE) modified with gold nanoparticles (Au-nano). The Au-nano/GCE was characterized by scanning electromicroscopy, cyclic voltammetry, and electrochemical impedance spectroscopy. The hybridization detection was measured by differential pulse voltammetry using methylene blue as the hybridization indicator. The dynamic range of detection of the sensor for the target DNA sequences was from 1 × 10(-11) to 1 × 10(-8) M, with an LOD of 1 × 10(-12) M. The DNA biosensor had excellent specificity for distinguishing complementary DNA sequence in the presence of non-complementary and mismatched DNA sequence. The Au-nano/GCE showed significant improvement in electrochemical characteristics, and this biosensor was successfully applied for determination of K. pneumoniae. PMID:26651586

  19. 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...

  20. PERFORMANCE CHARACTERISTICS OF 65-MER OLIGONUCLEOTIDE MICROARRAYS

    PubMed Central

    Lee, Myoyong; Xiang, Charlie C.; Trent, Jeffrey M.; Bittner, Michael L.

    2009-01-01

    Microarray fabrication using pre-synthesized long oligonucleotide is becoming increasingly important, but a study of large-scale array productions is not published yet. We addressed the issue of fabricating oligonucleotide microarrays by spotting commercial, pre-synthesized 65-mers with 5′ amines representing 7500 murine genes. Amine-modified oligonucleotides were immobilized on glass slides having aldehyde groups via transient Schiff base formation followed by reduction to produce a covalent conjugate. When RNA derived from the same source was used for Cy3 and Cy5 labeling and hybridized to the same array, signal intensities spanning three orders of magnitude were observed, and the coefficient of variation between the two channels for all spots was 8–10%. To ascertain the reproducibility of ratio determination of these arrays, two triplicate hybridizations (with fluorochrome reversal) comparing RNAs from a fibroblast (NIH3T3) and a breast cancer (JC) cell line were carried out. The 95% confidence interval for all spots in the six hybridizations was 0.60 – 1.66. This level of reproducibility allows use of the full range of pattern finding and discriminant analysis typically applied to cDNA microarrays. Further comparative testing was carried out with oligonucleotide microarrays, cDNA microarrays and RT-PCR assays to examine the comparability of results across these different methodologies. PMID:17617369

  1. 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. PMID:26050909

  2. Mthfd1 is a modifier of chemically induced intestinal carcinogenesis

    PubMed Central

    MacFarlane, Amanda J.; Perry, Cheryll A.; McEntee, Michael F.; Lin, David M.; Stover, Patrick J.

    2011-01-01

    The causal metabolic pathways underlying associations between folate and risk for colorectal cancer (CRC) have yet to be established. Folate-mediated one-carbon metabolism is required for the de novo synthesis of purines, thymidylate and methionine. Methionine is converted to S-adenosylmethionine (AdoMet), the major one-carbon donor for cellular methylation reactions. Impairments in folate metabolism can modify DNA synthesis, genomic stability and gene expression, characteristics associated with tumorigenesis. The Mthfd1 gene product, C1-tetrahydrofolate synthase, is a trifunctional enzyme that generates one-carbon substituted tetrahydrofolate cofactors for one-carbon metabolism. In this study, we use Mthfd1gt/+ mice, which demonstrate a 50% reduction in C1-tetrahydrofolate synthase, to determine its influence on tumor development in two mouse models of intestinal cancer, crosses between Mthfd1gt/+ and Apcmin/+ mice and azoxymethane (AOM)-induced colon cancer in Mthfd1gt/+ mice. Mthfd1 hemizygosity did not affect colon tumor incidence, number or load in Apcmin/+ mice. However, Mthfd1 deficiency increased tumor incidence 2.5-fold, tumor number 3.5-fold and tumor load 2-fold in AOM-treated mice. DNA uracil content in the colon was lower in Mthfd1gt/+ mice, indicating that thymidylate biosynthesis capacity does not play a significant role in AOM-induced colon tumorigenesis. Mthfd1 deficiency-modified cellular methylation potential, as indicated by the AdoMet: S-adenosylhomocysteine ratio and gene expression profiles, suggesting that changes in the transcriptome and/or decreased de novo purine biosynthesis and associated mutability cause cellular transformation in the AOM CRC model. This study emphasizes the impact and complexity of gene–nutrient interactions with respect to the relationships among folate metabolism and colon cancer initiation and progression. PMID:21156972

  3. Antisense oligonucleotide induction of progerin in human myogenic cells.

    PubMed

    Luo, Yue-Bei; Mitrpant, Chalermchai; Adams, Abbie M; Johnsen, Russell D; Fletcher, Sue; Mastaglia, Frank L; Wilton, Steve D

    2014-01-01

    We sought to use splice-switching antisense oligonucleotides to produce a model of accelerated ageing by enhancing expression of progerin, translated from a mis-spliced lamin A gene (LMNA) transcript in human myogenic cells. The progerin transcript (LMNA Δ150) lacks the last 150 bases of exon 11, and is translated into a truncated protein associated with the severe premature ageing disease, Hutchinson-Gilford progeria syndrome (HGPS). HGPS arises from de novo mutations that activate a cryptic splice site in exon 11 of LMNA and result in progerin accumulation in tissues of mesodermal origin. Progerin has also been proposed to play a role in the 'natural' ageing process in tissues. We sought to test this hypothesis by producing a model of accelerated muscle ageing in human myogenic cells. A panel of splice-switching antisense oligonucleotides were designed to anneal across exon 11 of the LMNA pre-mRNA, and these compounds were transfected into primary human myogenic cells. RT-PCR showed that the majority of oligonucleotides were able to modify LMNA transcript processing. Oligonucleotides that annealed within the 150 base region of exon 11 that is missing in the progerin transcript, as well as those that targeted the normal exon 11 donor site induced the LMNA Δ150 transcript, but most oligonucleotides also generated variable levels of LMNA transcript missing the entire exon 11. Upon evaluation of different oligomer chemistries, the morpholino phosphorodiamidate oligonucleotides were found to be more efficient than the equivalent sequences prepared as oligonucleotides with 2'-O-methyl modified bases on a phosphorothioate backbone. The morpholino oligonucleotides induced nuclear localised progerin, demonstrated by immunostaining, and morphological nuclear changes typical of HGPS cells. We show that it is possible to induce progerin expression in myogenic cells using splice-switching oligonucleotides to redirect splicing of LMNA. This may offer a model to investigate

  4. Bonding and reactivity of clean and chemically-modified semiconductor surfaces probed with STM

    SciTech Connect

    Hamers, R.J.

    1995-12-01

    Scanning tunneling microscopy has been used to directly study the interrelationships between chemical composition, chemical reactivity, electronic structure, and surface morphology at the atomic level on clean and chemically-modified semiconductor surfaces. Our work has focused recently on understanding the atomic-level interactions of dopants such as phosphorus and boron on the Si(001) surface, and the influence of these atoms on other chemical reactions such as the thermal decomposition of disilane to grow epitaxial silicon. Using STM to study how these atoms modify the surface in combination with tunneling spectroscopy to reveal the occupied and unoccupied molecular orbitals of these structures provides direct insight into the nature of chemical bonding on these surfaces. This talk will discuss the application of STM to understand chemical bonding at silicon surfaces.

  5. Highly Efficient Gene Suppression by Chemically Modified 27 Nucleotide Double-Stranded RNAs

    NASA Astrophysics Data System (ADS)

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

    2008-02-01

    RNA interference (RNAi) technology, described by Fire and Mello in 1998, is a powerful tool for the suppression of gene expression in mammalian cells. RNAi technology has several advantages over other chemical and genetic drugs. However, several problems in RNAi technology, such as cellular delivery, nuclease stability, and side effects, should be solved before applying it in the clinic. In this study, we focused on the development of novel chemically modified 27 nucleotide (nt) double-stranded RNAs (dsRNAs) with improved biological properties. Our chemically modified 27 nt dsRNAs exhibited an enhanced RNAi activity and a markedly increased stability in cell culture medium (containing 10% serum) in comparison with widely used 21 nt siRNAs and recently reported nonmodified 27 nt dsRNAs. The chemically modified 27 nt dsRNAs also exhibited a strong high long-term gene silencing effect after the 7 d treatment of viable cells. The chemically modified 27 nt dsRNAs in specific positions could be processed to 21 nt siRNAs by a recombinant Dicer enzyme. We suggested that the chemically modified 27 nt dsRNAs could be used for therapeutic applications (as genetic drugs) and bioanalyses.

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

    SciTech Connect

    Wang, J.

    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. siRNAmod: A database of experimentally validated chemically modified siRNAs.

    PubMed

    Dar, Showkat Ahmad; Thakur, Anamika; Qureshi, Abid; Kumar, Manoj

    2016-01-01

    Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod. PMID:26818131

  8. siRNAmod: A database of experimentally validated chemically modified siRNAs

    PubMed Central

    Dar, Showkat Ahmad; Thakur, Anamika; Qureshi, Abid; Kumar, Manoj

    2016-01-01

    Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod. PMID:26818131

  9. 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. PMID:23500788

  10. PET Imaging and biodistribution of chemically modified bacteriophage MS2.

    PubMed

    Farkas, Michelle E; Aanei, Ioana L; Behrens, Christopher R; Tong, Gary J; Murphy, Stephanie T; O'Neil, James P; Francis, Matthew B

    2013-01-01

    The fields of nanotechnology and medicine have merged in the development of new imaging and drug delivery agents based on nanoparticle platforms. As one example, a mutant of bacteriophage MS2 can be differentially modified on the exterior and interior surfaces for the concurrent display of targeting functionalities and payloads, respectively. In order to realize their potential for use in in vivo applications, the biodistribution and circulation properties of this class of agents must first be investigated. A means of modulating and potentially improving the characteristics of nanoparticle agents is the appendage of PEG chains. Both MS2 and MS2-PEG capsids possessing interior DOTA chelators were labeled with (64)Cu and injected intravenously into mice possessing tumor xenografts. Dynamic imaging of the agents was performed using PET-CT on a single animal per sample, and the biodistribution at the terminal time point (24 h) was assessed by gamma counting of the organs ex vivo for 3 animals per agent. Compared to other viral capsids of similar size, the MS2 agents showed longer circulation times. Both MS2 and MS2-PEG bacteriophage behaved similarly, although the latter agent showed significantly less uptake in the spleen. This effect may be attributed to the ability of the PEG chains to mask the capsid charge. Although the tumor uptake of the agents may result from the enhanced permeation and retention (EPR) effect, selective tumor imaging may be achieved in the future by using exterior targeting groups. PMID:23214968

  11. Gold Binding by Native and Chemically Modified Hops Biomasses

    DOE PAGESBeta

    López, M. Laura; Gardea-Torresdey, J. L.; Peralta-Videa, J. R.; de la Rosa, G.; Armendáriz, V.; Herrera, I.; Troiani, H.; Henning, J.

    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

  12. Theory of nanoscale friction on chemically modified graphene

    NASA Astrophysics Data System (ADS)

    Ko, Jae-Hyeon; Kim, Yong-Hyun

    2013-03-01

    Recently, it is known from FFM experiments that friction force on graphene is significantly increased by chemical modification such as hydrogenation, oxidization, and fluorination, whereas adhesion properties are altered marginally. A novel nanotribological theory on two-dimensional materials is proposed on the basis of experimental results and first-principles density-functional theory (DFT) calculations. The proposed theory indicates that the total lateral stiffness that is the proportional constant of friction force is mostly associated with the out-of-plane bending stiffness of two-dimensional materials. This contrasts to the case of three-dimensional materials, in which the shear strength of materials determines nanoscale friction. We will discuss details of DFT calculations and how to generalize the current theory to three dimensional materials.

  13. Equilibrium and thermodynamic studies of Cd (II) biosorption by chemically modified orange peel.

    PubMed

    Kumar, Arbind; Kumar, Vipin

    2016-03-01

    Agricultural wastes have great potential of removing heavy metal ions from aqueous solution. Removal of Cd (II) from aqueous solutions onto chemically modified orange peel was studied at different pH, contact time, initial metal concentrations, adsorbent doses and temperature. Batch experiments were carried out under optimized conditions to evaluate the adsorption capacity of orange peel chemically modified with NaOH. The results showed that maximum adsorption capacity of modified orange peel, approximately 97.0%, was observed 3 mg 1⁻¹ of initial Cd(II) concentration pH 6 for 4 g 1⁻¹ adsorbent dosage, 200 min contact time and 298 K temperature. Adsorption efficiency of modified orange peel decreased with increase in temperature indicated exothermic nature of adsorption. A negative value of ΔG⁰(-8.59 kJ mol⁻¹) confirmed the feasibility of adsorption process and spontaneous nature of adsorption. A negative value of ΔH⁰ (-28.08 kJ mol⁻¹) indicated exothermic nature while a negative ΔS⁰ (-66.86 J K⁻¹ mol⁻¹) value suggested decrease in degree of freedom of the adsorbed species. The results showed that biosorption process of Cd(II) ions by chemically modified orange peel is feasible, spontaneous and exothermic under studied conditions. Chemically by modified orange peel investigated in the present study showed good potential for the removal of cadmium from aqueous solutions. PMID:27097438

  14. 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.

  15. Chitosan and chemically modified chitosan beads for acid dyes sorption.

    PubMed

    Azlan, Kamari; Wan Saime, Wan Ngah; Lai Ken, Liew

    2009-01-01

    The capabilities of chitosan and chitosan-EGDE (ethylene glycol diglycidyl ether) beads for removing Acid Red 37 (AR 37) and Acid Blue 25 (AB 25) from aqueous solution were examined. Chitosan beads were cross-linked with EGDE to enhance its chemical resistance and mechanical strength. Experiments were performed as a function of pH, agitation period and concentration of AR 37 and AB 25. It was shown that the adsorption capacities of chitosan for both acid dyes were comparatively higher than those of chitosan-EGDE. This is mainly because cross-linking using EGDE reduces the major adsorption sites -NH3+ on chitosan. Langmuir isotherm model showed the best conformity compared to Freundlich and BET. The kinetic experimental data agreed very well to the pseudo second-order kinetic model. The desorption study revealed that after three cycles of adsorption and desorption by NaOH and HCl, both adsorbents retained their promising adsorption abilities. FT-IR analysis proved that the adsorption of acid dyes onto chitosan-based adsorbents was a physical adsorption. Results also showed that chitosan and chitosan-EGDE beads were favourable adsorbers and could be employed as low-cost alternatives for the removal of acid dyes in wastewater treatment. PMID:19634439

  16. miRNA-based therapies: Strategies and delivery platforms for oligonucleotide and non-oligonucleotide agents

    PubMed Central

    Baumann, V; Winkler, J

    2015-01-01

    The discovery of microRNAs as important regulatory agents for gene expression has expanded the therapeutic opportunities for oligonucleotides. In contrast to siRNA, miRNA-targeted therapy is able to influence not only a single gene, but entire cellular pathways or processes. It is possible to supplement down regulated or non-functional miRNAs by synthetic oligonucleotides, as well as alleviating effects caused by overexpression of malignant miRNAs through artificial antagonists, either oligonucleotides or small molecules. Chemical oligonucleotide modifications together with an efficient delivery system seem to be mandatory for successful therapeutic application. While miRNA-based therapy benefits from the decades of research spent on other therapeutic oligonucleotides, there are some specific challenges associated with miRNA therapy, mainly caused by the short target sequence. The current status and recent progress of miRNA-targeted therapeutics is described and future challenges and potential applications in treatment of cancer and viral infections are discussed. PMID:25495987

  17. 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.

  18. [Preparative isolation of tetra-, penta- and hexapurine oligonucleotides from partial hydrolysates of depyrimidinated herring sperm DNA].

    PubMed

    Schott, H; Schrade, H

    1984-02-01

    Herring sperm DNA is chemically degraded to a complex mixture of purine nucleotides. The oligonucleotides are separated from the partial hydrolysates by column chromatography. The resulting mixture of trimer to hexamer purine oligonucleotides is subsequently fractionated on QAE-Sephadex into different mixtures of sequence-isomeric purine oligonucleotides. In a final separation, which uses reversed-phase (Nucleosil C18) high-performance liquid chromatography, these mixtures are separated under isocratic conditions into 35 pure defined purine oligonucleotides with four to six monomer units, 14 defined mixtures of sequence-isomeric purine oligonucleotides and several unidentified products. Purity and sequence of the isolated oligonucleotides are determined by the "fingerprint" method. The results of the high-performance liquid chromatographic and the "fingerprint" methods of the isolated oligonucleotides are discussed. PMID:6707126

  19. 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

  20. 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. PMID:24603112

  1. 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.

  2. 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

  3. Stable dye-labelled oligonucleotide-nanoparticle conjugates for nucleic acid detection

    NASA Astrophysics Data System (ADS)

    Barrett, Lee; Dougan, Jennifer A.; Faulds, Karen; Graham, Duncan

    2011-08-01

    Metallic nanoparticles functionalized with oligonucleotides are used for a number of nucleic acid detection strategies. However, oligonucleotide-nanoparticle conjugates suffer from a lack of stability when exposed to certain conditions associated with DNA detection assays. In this study, we report the synthesis of thiol and thioctic acid-modified oligonucleotide gold nanoparticle (OGNs) conjugates functionalized with a dye label and varying spacer groups. The thioctic acid-modified conjugates exhibit increased stability when treated with dithiothreitol (DTT) compared to the more commonly used thiol modification. When the dye labelled oligonucleotide nanoparticle conjugates are exposed to the same conditions there is a pronounced increase in the stability for both thioctic acid and thiol modified sequences. These results open up the possibility of simply using a dye label to enhance the stability of oligonucleotide-nanoparticle conjugates in DNA detection assays where the enhanced stability of the conjugate system can be advantageous in more complex biological environments.

  4. CHARACTERIZATION OF CHEMICALLY MODIFIED HYPERTHERMOPHILIC ENZYMES FOR CHEMICAL SYNTHESES AND BIOREMEDIATION REACTIONS

    EPA Science Inventory

    Research developments in the area of biocatalysis in organic solvents are expected to greatly expand the role of bioprocessing in chemical synthesis, fuel processing, and bioremediation technologies. Many biological transformation reactions of interest to DOE site remediation inv...

  5. Optical characterization of pure and chemically modified chitosan bio-films

    NASA Astrophysics Data System (ADS)

    Nosal, William H.

    The purpose of this work was to apply spectroscopic ellipsometry (SE) to the study of monolayer thick chemically modified surfaces and then study the protein attachment or rejection of these films. Optical properties of spin-cast pure and chemically modified chitosan films have been determined in the infrared (IR), visible (vis), ultraviolet (UV), and vacuum ultraviolet (VUV) regions of the spectrum using spectroscopic ellipsometry (SE). Vis-SE data were used to monitor protein attachment or nonattachment to the surface of the chemically modified chitosan using real-time SE. Optical constants for the UV-Vis-near IR spectra from 130nm to 1700nm were determined on dried samples. Optical constants were modeled using Cauchy dispersion forms combined with Lorentzian oscillator models in the absorptive shorter wavelength regions. Infrared refraction index and extinction coefficients from 750cm -1 to 4000cm-1 were determined using ellipsometric data fits to dispersion models based on harmonic oscillators. This modeling determined that optical anisotropy was present and measurable over all wavelength regions of ellipsometric data. VUV adsorption was accounted for by including Gaussian and Tauc-Lorentz shaped oscillators in the optical model. IR-SE and VUV-SE data were used to confirm that chemical modifications to the surface occurred. IR spectra are well known for identifying resonant chemical bonds. However, VUV-SE simultaneously offers resonances for chemical identifications and high surface sensitivity due to shallow depth of optical penetration. To obtain additional information on the micro-scale and nano-scale surface structure, tapping mode AFM imaging was employed to determine morphology and roughness information of dry modified and pure spin-cast chitosan films.

  6. 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

  7. 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. PMID:27200340

  8. 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.

  9. Working with Oligonucleotide Arrays.

    PubMed

    Carvalho, Benilton S

    2016-01-01

    Preprocessing microarray data consists of a number of statistical procedures that convert the observed intensities into quantities that represent biological events of interest, like gene expression and allele-specific abundances. Here, we present a summary of the theory behind microarray data preprocessing for expression, whole transcriptome and SNP designs and focus on the computational protocol used to obtain processed data that will be used on downstream analyses. We describe the main features of the oligo Bioconductor package, an application designed to support oligonucleotide microarrays using the R statistical environment and the infrastructure provided by Bioconductor, allowing the researcher to handle probe-level data and interface with advanced statistical tools under a simplified framework. We demonstrate the use of the package by preprocessing data originated from three different designs. PMID:27008013

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

    SciTech Connect

    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.

  11. Catalytic conversion of biomass pyrolysis-derived compounds with chemical liquid deposition (CLD) modified ZSM-5.

    PubMed

    Zhang, Huiyan; Luo, Mengmeng; Xiao, Rui; Shao, Shanshan; Jin, Baosheng; Xiao, Guomin; Zhao, Ming; Liang, Junyu

    2014-03-01

    Chemical liquid deposition (CLD) with KH550, TEOS and methyl silicone oil as the modifiers was used to modify ZSM-5 and deposit its external acid sites. The characteristics of modified catalysts were tested by catalytic conversion of biomass pyrolysis-derived compounds. The effects of different modifying conditions (deposited amount, temperature, and time) on the product yields and selectivities were investigated. The results show KH550 modified ZSM-5 (deposited amount of 4%, temperature of 20°C and time of 6h) produced the maximum yields of aromatics (24.5%) and olefins (16.5%), which are much higher than that obtained with original ZSM-5 catalyst (18.8% aromatics and 9.8% olefins). The coke yield decreased from 44.1% with original ZSM-5 to 26.7% with KH550 modified ZSM-5. The selectivities of low-molecule-weight hydrocarbons (ethylene and benzene) decreased, while that of higher molecule-weight hydrocarbons (propylene, butylene, toluene, and naphthalene) increased comparing with original ZSM-5. PMID:24413482

  12. Towards electron transport measurements in chemically modified graphene: effect of a solvent

    NASA Astrophysics Data System (ADS)

    Jacobsen, Arnhild; Koehler, Fabian M.; Stark, Wendelin J.; Ensslin, Klaus

    2010-12-01

    The chemical functionalization of graphene modifies the local electron density of carbon atoms and hence electron transport. Measuring these changes allows for a closer understanding of the chemical interaction and the influence of functionalization on the graphene lattice. However, not only chemistry, in this case diazonium chemistry, has an effect on electron transport. The latter is also influenced by defects and dopants resulting from different processing steps. Here, we show that the solvents used in the chemical reaction process change the transport properties. In more detail, the investigated combination of isopropanol and heating treatment reduces the doping concentration and significantly increases the mobility of graphene. Furthermore, isopropanol treatment alone increases the concentration of dopants and introduces an asymmetry between electron and hole transport, which might be difficult to distinguish from the effect of functionalization. The results shown in this work demand a closer look at the influence of solvents used for chemical modification in order to understand their influence.

  13. In vivo natriuretic peptide reporter assay identifies chemical modifiers of hypertrophic cardiomyopathy signalling

    PubMed Central

    Becker, Jason R.; Robinson, Tamara Y.; Sachidanandan, Chetana; Kelly, Amy E.; Coy, Shannon; Peterson, Randall T.; MacRae, Calum A.

    2012-01-01

    Aims Despite increased understanding of the fundamental biology regulating cardiomyocyte hypertrophy and heart failure, it has been challenging to find novel chemical or genetic modifiers of these pathways. Traditional cell-based methods do not model the complexity of an intact cardiovascular system and mammalian models are not readily adaptable to chemical or genetic screens. Our objective was to create an in vivo model suitable for chemical and genetic screens for hypertrophy and heart failure modifiers Methods and results Using the developing zebrafish, we established that the cardiac natriuretic peptide genes (nppa and nppb), known markers of cardiomyocyte hypertrophy and heart failure, were induced in the embryonic heart by pathological cardiac stimuli. This pathological induction was distinct from the developmental regulation of these genes. We created a luciferase-based transgenic reporter line that accurately modelled the pathological induction patterns of the zebrafish nppb gene. Utilizing this reporter line, we were able to show remarkable conservation of pharmacological responses between the larval zebrafish heart and adult mammalian models. Conclusion By performing a focused screen of chemical agents, we were able to show a distinct response of a genetic model of hypertrophic cardiomyopathy to the histone deacetylase inhibitor, Trichostatin A, and the mitogen-activated protein kinase kinase 1/2 inhibitor, U0126. We believe this in vivo reporter line will offer a unique approach to the identification of novel chemical or genetic regulators of myocardial hypertrophy and heart failure. PMID:22198505

  14. 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.

  15. 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}.

  16. Annexin A2 facilitates endocytic trafficking of antisense oligonucleotides

    PubMed Central

    Wang, Shiyu; Sun, Hong; Tanowitz, Michael; Liang, Xue-hai; Crooke, Stanley T.

    2016-01-01

    Chemically modified antisense oligonucleotides (ASOs) designed to mediate site-specific cleavage of RNA by RNase H1 are used as research tools and as therapeutics. ASOs modified with phosphorothioate (PS) linkages enter cells via endocytotic pathways. The mechanisms by which PS-ASOs are released from membrane-enclosed endocytotic organelles to reach target RNAs remain largely unknown. We recently found that annexin A2 (ANXA2) co-localizes with PS-ASOs in late endosomes (LEs) and enhances ASO activity. Here, we show that co-localization of ANXA2 with PS-ASO is not dependent on their direct interactions or mediated by ANXA2 partner protein S100A10. Instead, ANXA2 accompanies the transport of PS-ASOs to LEs, as ANXA2/PS-ASO co-localization was observed inside LEs. Although ANXA2 appears not to affect levels of PS-ASO internalization, ANXA2 reduction caused significant accumulation of ASOs in early endosomes (EEs) and reduced localization in LEs and decreased PS-ASO activity. Importantly, the kinetics of PS-ASO activity upon free uptake show that target mRNA reduction occurs at least 4 hrs after PS-ASOs exit from EEs and is coincident with release from LEs. Taken together, our results indicate that ANXA2 facilitates PS-ASO trafficking from early to late endosomes where it may also contribute to PS-ASO release. PMID:27378781

  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. Gene-modified embryonic stem cell test to characterize chemical risks.

    PubMed

    Kitada, Kohei; Kizu, Akane; Teramura, Takeshi; Takehara, Toshiyuki; Hayashi, Masami; Tachibana, Daisuke; Wanibuchi, Hideki; Fukushima, Shoji; Koyama, Masayasu; Yoshida, Kayo; Morita, Takashi

    2015-11-01

    A high-throughput test of cell growth inhibition was performed using mouse embryonic stem (ES) cells to assess chemical toxicities. We herein demonstrated using a 96-well culture plate approach and the MTT assay that this method was suitable for prioritization of chemicals for their cytotoxic properties. In order to categorize chemicals, we used p53 gene-modified mouse ES cells as well as wild-type ES cells. The p53 gene is a well-known tumor suppressor and controls programmed cell death (apoptosis) and cellular senescence that is triggered by DNA-damaging agents such as alkylating agents and radiation. In the present study, p53-deficient ES cells were found to be more resistant to a tumor initiator, diethylnitrosamine (DEN), than wild-type ES cells, suggesting the inhibition of apoptosis or senescence by a dysfunction in p53. Chromosome aberrations were more frequently detected in p53-deficient ES cells than in wild-type cells, indicating genomic instability due to the deletion of p53. Other tumor initiators, methyl methanesulfonate (MMS) and N-methyl-N-nitrosourea (NMU), did not reveal apparent differences in cytotoxicity between wild-type and p53-deficient ES cells. Thus, ES test system using gene-modified ES cells may be used to categorize chemicals by detecting their characteristic effects on apoptosis, genotoxic potentials as well as general cytotoxicity. PMID:26206128

  19. Chemically modified biochar produced from conocarpus waste increases NO3 removal from aqueous solutions.

    PubMed

    Usman, Adel R A; Ahmad, Mahtab; El-Mahrouky, Mohamed; Al-Omran, Abdulrasoul; Ok, Yong Sik; Sallam, Abdelazeem Sh; El-Naggar, Ahmed H; Al-Wabel, Mohammad I

    2016-04-01

    Biochar has emerged as a universal sorbent for the removal of contaminants from water and soil. However, its efficiency is lower than that of commercially available sorbents. Engineering biochar by chemical modification may improve its sorption efficiency. In this study, conocarpus green waste was chemically modified with magnesium and iron oxides and then subjected to thermal pyrolysis to produce biochar. These chemically modified biochars were tested for NO3 removal efficiency from aqueous solutions in batch sorption isothermal and kinetic experiments. The results revealed that MgO-biochar outperformed other biochars with a maximum NO3 sorption capacity of 45.36 mmol kg(-1) predicted by the Langmuir sorption model. The kinetics data were well described by the Type 1 pseudo-second-order model, indicating chemisorption as the dominating mechanism of NO3 sorption onto biochars. Greater efficiency of MgO-biochar was related to its high specific surface area (391.8 m(2) g(-1)) and formation of strong ionic complexes with NO3. At an initial pH of 2, more than 89 % NO3 removal efficiency was observed for all of the biochars. We conclude that chemical modification can alter the surface chemistry of biochar, thereby leading to enhanced sorption capacity compared with simple biochar. PMID:26100325

  20. 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.

  1. 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

    1998-05-01

    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. PMID:9600060

  2. Transfer of Chemically Modified Graphene with Retention of Functionality for Surface Engineering.

    PubMed

    Whitener, Keith E; Lee, Woo-Kyung; Bassim, Nabil D; Stroud, Rhonda M; Robinson, Jeremy T; Sheehan, Paul E

    2016-02-10

    Single-layer graphene chemically reduced by the Birch process delaminates from a Si/SiOx substrate when exposed to an ethanol/water mixture, enabling transfer of chemically functionalized graphene to arbitrary substrates such as metals, dielectrics, and polymers. Unlike in previous reports, the graphene retains hydrogen, methyl, and aryl functional groups during the transfer process. This enables one to functionalize the receiving substrate with the properties of the chemically modified graphene (CMG). For instance, magnetic force microscopy shows that the previously reported magnetic properties of partially hydrogenated graphene remain after transfer. We also transfer hydrogenated graphene from its copper growth substrate to a Si/SiOx wafer and thermally dehydrogenate it to demonstrate a polymer- and etchant-free graphene transfer for potential use in transmission electron microscopy. Finally, we show that the Birch reduction facilitates delamination of CMG by weakening van der Waals forces between graphene and its substrate. PMID:26784372

  3. Synthesis of chimeric oligonucleotides containing phosphodiester, phosphorothioate, and phosphoramidate linkages.

    PubMed

    Maier, M A; Guzaev, A P; Manoharan, M

    2000-06-29

    [reaction: see text] H-Phosphonate monomers of 2'-O-(2-methoxyethyl) ribonucleosides have been synthesized. Oxidation of oligonucleotide H-phosphonates has been optimized to allow the synthesis of oligonucleotides containing either 2'-deoxy or 2'-O-(2-methoxyethyl) ribonucleoside residues combined with three different phosphate modifications in the backbone, i.e., phosphodiester (PO), phosphorothioate (PS), and phosphoramidate (PN). Phosphodiester linkages were introduced by oxidation with a cocktail of 0.1 M Et(3)N in CCl(4)/Pyr/H(2)O (5:9:1) without affecting phosphorothioate or phosphoramidate linkages. For the synthesis of phosphoramidate-modified oligonucleotides, N(4)-acetyl deoxycytidine-3'-H-phosphonate monomers were used to avoid transamination during the oxidation step. PMID:10891166

  4. Chemically modified nucleic acid aptamers for in vitro selections: evolving evolution.

    PubMed

    Kusser, W

    2000-03-01

    Combinatorial library selections through the systematic evolution of ligands by exponential enrichment (SELEX) technique identify so-called nucleic acid aptamers that bind with high-affinity and specificity to a wide range of selected molecules. However, the modest chemical functionality of nucleic acids poses some limits on their versatility as binders and catalysts, and, furthermore, the sensitivity of pure RNA- and DNA-based aptamers to nucleases restricts their use as therapeutic and diagnostic agents. Here we review synthetic chemistries for modifying nucleotides that have been developed to enhance the affinity of aptamers for targets and to increase their stability in biological fluids. Implementation of in vitro selections with modified nucleotides promises to be an elegant technique for the creation of ligands with novel physical and chemical properties and is anticipated to have a significant impact on biotechnology, diagnostics and drug development. The current molecular designs and applications of modified nucleotides for in vitro selections are reviewed, along with a discussion of future developments expected to further the utility of this approach in both practical and theoretical terms. PMID:10943570

  5. 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

  6. Silencing of Inducible Immunoproteasome Subunit Expression by Chemically Modified siRNA and shRNA.

    PubMed

    Gvozdeva, Olga V; Prassolov, Vladimir S; Zenkova, Marina A; Vlassov, Valentin V; Chernolovskaya, Elena L

    2016-08-01

    Overexpression of inducible subunits of immunoproteasome is related to pathogenesis of some chronic diseases. Specific inhibition of the immunosubunits may be used for the treatment of these diseases and RNA interference is one of the potent methods used in this area. We designed 2'-O-methyl modified siRNAs with selectively protected nuclease-sensitive sites, which efficiently silence LMP2, LMP7, and MECL-1 genes expression. To provide stable long-lasting inhibition of target genes, short-hairpin RNAs (shRNA) expressed by lentiviral vectors were constructed. Our results demonstrated that chemically modified siRNAs inhibited the expression of target genes with similar efficiency or with efficiency exceeding that of corresponding shRNAs and provide silencing effect for 5 days. PMID:27351110

  7. 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.

  8. Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy.

    PubMed

    Manohar, Suresh; Mantz, Amber R; Bancroft, Kevin E; Hui, Chung-Yuen; Jagota, Anand; Vezenov, Dmitri V

    2008-12-01

    We measured the force required to peel single-stranded DNA molecules from single-crystal graphite using chemical force microscopy. Force traces during retraction of a tip chemically modified with oligonucleotides displayed characteristic plateaus with abrupt force jumps, which we interpreted as a steady state peeling process punctuated by complete detachment of one or more molecules. We were able to differentiate between bases in pyrimidine homopolymers; peeling forces were 85.3 - 4.7 pN for polythymine and 60.8 +/- 5.5 pN for polycytosine, substantially independent of salt concentration and the rate of detachment. We developed a model for peeling a freely jointed chain from the graphite surface and estimated the average binding energy per monomer to be 11.5 +/- 0.6 k(B)T and 8.3 +/- 0.7 k(B)T in the cases of thymine and cytosine nucleotides, respectively. The equilibrium free-energy profile simulated using molecular dynamics had a potential well of 18.9 k(B)T for thymidine, showing that nonelectrostatic interactions dominate the binding. The discrepancy between the experiment and theory indicates that not all bases are adsorbed on the surface or that there is a population of conformations in which they adsorb. Force spectroscopy using oligonucleotides covalently linked to AFM tips provides a flexible and unambiguous means to quantify the strength of interactions between DNA and a number of substrates, potentially including nanomaterials such as carbon nanotubes. PMID:19368004

  9. 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.

  10. An Efficient Protection-Free One-Pot Chemical Synthesis of Modified Nucleoside-5'-Triphosphates.

    PubMed

    Shanmugasundaram, Muthian; Senthilvelan, Annamalai; Xiao, Zejun; Kore, Anilkumar R

    2016-07-01

    A simple, reliable, and an efficient "one-pot, three step" chemical method for the synthesis of modified nucleoside triphosphates such as 5-methylcytidine-5'-triphosphate (5-MeCTP), pseudouridine-5'-triphosphate (pseudoUTP) and N(1)-methylpseudouridine-5'-triphosphate (N(1)-methylpseudoUTP) starting from the corresponding nucleoside is described. The overall reaction involves the monophosphorylation of nucleoside, followed by the reaction with pyrophosphate and subsequent hydrolysis of the cyclic intermediate to furnish the corresponding NTP in moderate yields with high purity (>99.5%). PMID:27159048

  11. 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.

  12. 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

  13. 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

  14. 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.

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

    PubMed

    Hendel, Ayal; Bak, Rasmus O; 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

    2015-09-01

    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

  16. Behaviour of chemical modifiers in the determination of arsenic by electrothermal atomic absorption spectrometry in petroleum products.

    PubMed

    Reboucas, Marcio V; Ferreira, Sergio L C; de Barros Neto, Benicio

    2005-07-15

    Most comparative studies on the efficiency of chemical modifiers have been conducted in aqueous media. In the present work, we proposed a detailed study of the use of different chemical modifiers for direct determination of arsenic in complex organic matrices by electrothermal atomic absorption spectrometry (ETAAS). Palladium, rhodium, tungsten, silver, lanthanum and a mixture of palladium and magnesium were tested. The figures of merit used for evaluation and comparison were acquired in the optimal conditions for each modifier, established by multivariate optimization of the main variables based on Doehlert designs. Singular features were observed for the chemical behaviour of some modifiers in organic matrices compared to aqueous media, such as the worse performance of Pd+Mg modifier and no notice of severe tube corrosion from La application. Lanthanum was chosen as the best chemical modifier for the present application, according to predefined criteria. Lanthanum showed the minimum limit of detection, characteristic concentration and blank signal among all tested species and no effect of the concomitants usually present in petrochemical feedstocks. Using a 200mgL(-1) lanthanum solution as a chemical modifier, the average relative standard deviations of 7 and 16% (at 3-15mugL(-1) level) and characteristic concentrations of 0.47 and 0.77mugL(-1) for naphtha and petroleum condensates, respectively, were observed. PMID:18970155

  17. 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

    2016-02-23

    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. PMID:26753184

  18. Physico-chemical properties of organically modified silicates' sol-gel layers for optical fibre sensors

    NASA Astrophysics Data System (ADS)

    Chodkowska, Eliza; Rayss, Jan

    2006-10-01

    The paper concerns the investigation of modified silica gel materials applied in optical fibre sensors. These materials are products of a sol-gel process in which three kinds of alkoxysilanes undergo hydrolysis and condensation and may play a role of the matrices containing transducer's molecules in the active layer of the sensor. In the experiment presented below three different compositions comprising tetraethoxysilane (TEOS), methyltriethoxysilane (MTES) and phenyltriethoxysilane (PhTES) were used. The alkoxysilanes underwent hydrolysis and condensation and the obtained gels were investigated in order to determine their texture, strucuture, composition and chemical properties as far as the dependence of those characteristics on the hydrolysis time and the molar ratio of the ingredients in the initial sols. The methods employed in the experiment were: Atomic Force Microscopy (AFM) which delivered vital information about the gels' textures, contact angles' and surface charge's measurements serving to estimate chemical properties of the gels' surfaces, Nuclear Magnetic Resonance (NMR) which helped to evaluate the hydrolysis' rate and porosimetric measurements enabling a determination of BET surface area and average diametres of the pores. The results may occur important for improving the construction of optical fibre sensors in which organically modified silicates (ORMOSILs)-TEOS layes are used.

  19. Supported liquid membrane stability in chiral resolution by chemically and physically modified membranes.

    PubMed

    Molinari, R; Argurio, P

    2001-01-01

    In the present work some stability studies on Supported Liquid Membranes (SLMs) to be used for chiral separations were realized. In particular, primary aim was to determine how a modification of the support surface influences the SLM stability. First, the procedure for support modification was optimised, making a screening of various compounds (sulphuric acid, nitric acid, chromic acid, sodium dodecyl sulphate (SDS), glycerol, oleic alcohol, propylene glycol (PPG), bovine serum albumin (BSA)) and testing their performance by means of contact angle measurements. Next, a second screening was realized by permeation tests in a stirred cell. Finally, to compare the stability of modified with unmodified support in a process of interest for chemical and/or biochemical industries, some permeation tests for resolution of DNB-DL-Leucine were realized in a re-circulation system. Results showed a better surface hydrophilization of chemically modified support and better stability of the sulphonated support. However, in operating conditions a little high stability of the unmodified support was obtained. PMID:11381544

  20. 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

  1. 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

    2011-01-01

    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

  2. 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

  3. 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

    2015-01-01

    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

  4. Chemically and biologically synthesized CPP-modified gelonin for enhanced anti-tumor activity.

    PubMed

    Shin, Meong Cheol; Zhang, Jian; David, Allan E; Trommer, Wolfgang E; Kwon, Young Min; Min, Kyoung Ah; Kim, Jin H; Yang, Victor C

    2013-11-28

    The ineffectiveness of small molecule drugs against cancer has generated significant interest in more potent macromolecular agents. Gelonin, a plant-derived toxin that inhibits protein translation, has attracted much attention in this regard. Due to its inability to internalize into cells, however, gelonin exerts only limited tumoricidal effect. To overcome this cell membrane barrier, we modified gelonin, via both chemical conjugation and genetic recombination methods, with low molecular weight protamine (LMWP), a cell-penetrating peptide (CPP) which was shown to efficiently ferry various cargoes into cells. Results confirmed that gelonin-LMWP chemical conjugate (cG-L) and recombinant gelonin-LMWP chimera (rG-L) possessed N-glycosidase activity equivalent to that of unmodified recombinant gelonin (rGel); however, unlike rGel, both gelonin-LMWPs were able to internalize into cells. Cytotoxicity studies further demonstrated that cG-L and rG-L exhibited significantly improved tumoricidal effects, with IC50 values being 120-fold lower than that of rGel. Moreover, when tested against a CT26 s.c. xenograft tumor mouse model, significant inhibition of tumor growth was observed with rG-L doses as low as 2 μg/tumor, while no detectable therapeutic effects were seen with rGel at 10-fold higher doses. Overall, this study demonstrated the potential of utilizing CPP-modified gelonin as a highly potent anticancer drug to overcome limitations of current chemotherapeutic agents. PMID:23973813

  5. 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

  6. Kinetics of cadmium, chromium, and lead sorption onto chemically modified sugarcane bagasse and wheat straw.

    PubMed

    Mahmood-ul-Hassan, M; Suthar, V; Rafique, E; Ahmad, R; Yasin, M

    2015-07-01

    In this study, cadmium (Cd), chromium (Cr), and lead (Pb) adsorption potential of unmodified and modified sugarcane bagasse and ground wheat straw was explored from aqueous solution through batch equilibrium technique. Both the materials were chemically modified by treating with sodium hydroxide (NaOH) alone and in combination with nitric acid (HNO3) and sulfuric acid (H2SO4). Two kinetic models, pseudo-first order and pseudo-second order were used to follow the adsorption process and reaction fallowed the later model. The Pb removal by both the materials was highest and followed by Cr and Cd. The chemical treatment invariably increased the adsorption capacity and NaOH treatment proved more effective than others. Langmuir maximum sorption capacity (q m) of Pb was utmost (12.8-23.3 mg/g of sugarcane bagasse, 14.5-22.4 mg/g of wheat straw) and of Cd was least (1.5-2.2 mg/g of sugarcane bagasse, 2.5-3.8 mg/g of wheat straw). The q m was in the order of Pb > Cr > Cd for all the three adsorbents. Results demonstrate that agricultural waste materials used in this study could be used to remediate the heavy metal-polluted water. PMID:26116198

  7. 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…

  8. Dual-tracer method to estimate coral reef response to a plume of chemically modified seawater

    NASA Astrophysics Data System (ADS)

    Maclaren, J. K.; Caldeira, K.

    2013-12-01

    We present a new method, based on measurement of seawater samples, to estimate the response of a reef ecosystem to a plume of an additive (for example, a nutrient or other chemical). In the natural environment, where there may be natural variability in concentrations, it can be difficult to distinguish between changes in concentrations that would occur naturally and changes in concentrations that result from a chemical addition. Furthermore, in the unconfined natural environment, chemically modified water can mix with waters that have not been modified, making it difficult to distinguish between effects of dilution and effects of chemical fluxes or transformations. We present a dual-tracer method that extracts signals from observations that may be affected by both natural variability and dilution. In this dual-tracer method, a substance (in our example case, alkalinity) is added to the water in known proportion to a passive conservative tracer (in our example case, Rhodamine WT dye). The resulting plume of seawater is allowed to flow over the study site. Two transects are drawn across the plume at the front and back of the study site. If, in our example, alkalinity is plotted as a function of dye concentration for the front transect, the slope of the resulting mixing line is the ratio of alkalinity to dye in the added fluid. If a similar mixing line is measured and calculated for the back transect, the slope of this mixing line will indicate the amount of added alkalinity that remains in the water flowing out of the study site per unit of added dye. The ratio of the front and back slopes indicates the fraction of added alkalinity that was taken up by the reef. The method is demonstrated in an experiment performed on One Tree Reef (Queensland, Australia) aimed at showing that ocean acidification is already affecting coral reef growth. In an effort to chemically reverse some of the changes to seawater chemistry that have occurred over the past 200 years, we added

  9. 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.

  10. Optical second-harmonic spectroscopy of chemically-modified silicon and silicon-dioxide surfaces

    NASA Astrophysics Data System (ADS)

    Downer, M. C.; Jiang, Y. Y.; Lim, D.

    2002-03-01

    The optical second-harmonic generation (SHG) response of solid interfaces depends sensitively on chemical termination. We present a spectroscopic SHG study of chemically-modified Si and SiO2 surfaces that elucidates at the atomic level how adsorbates alter the electronic structure, and thereby the SHG response, of the surface. SHG spectra were measured on reconstructed Si(001) surfaces in UHV that were exposed to atomic H or to gas-phase precursors of Ge and B, and on the surfaces of 30 angstrom-thick silicon dioxide films on silicon substrates that were chemically functionalized to nucleate silicon nanocrystal formation. Microscopic models show that adsorbate-induced alterations of the surface SHG spectra are correlated with changes in near-surface charge polarization caused by surface dimer buckling, transfer of electrons to boron acceptors in second layer substitutional sites, or transfer of electrons from the silicon substrate, through the tunneling oxide, to the surface nanocrystals [1]. 1. M. C. Downer, B. S. Mendoza and V. I. Gavrilenko, Surf. Interface Anal. 31, 966 (2001).

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

    NASA Astrophysics Data System (ADS)

    Kalugin, Nikolai G.

    2014-03-01

    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.

  12. Allergenic components in modified and unmodified rosin. Chemical characterization and studies of allergenic activity.

    PubMed

    Gäfvert, E

    1994-01-01

    Gäfvert, E. 1994. Allergenic components in modified and unmodified rosin. Chemical characterization and studies of allergenic activity. Acta Dermato-Venereologica. Suppl. 184. 36pp. Uppsala. Unmodified rosin (colophony) is a well-known cause of contact allergy (delayed type hypersensitivity). Rosin is obtained from coniferous trees and consists mainly of diterpenoid resin acids. Most rosin used in technical products is chemically modified. In the common modification of rosin with maleic anhydride, the major product formed is maleopimaric acid (MPA). MPA was identified in experimental sensitization studies as a potent contact allergen. MPA is also formed when rosin is modified with fumaric acid at high temperature and with prolonged heating. The amounts of MPA in technical quality rosins modified with maleic anhydride or fumaric acid might be enough to sensitize individuals handling these rosins. The major product of the modification of rosin with fumaric acid, fumaropimaric acid (FPA), did not elicit any reactions in the animals tested. In another common rosin modification, glycerol esterification, the major product formed was identified as glyceryl triabietate (GTA). In an experimental sensitization study none of the animals reacted to GTA. However, a minor product formed, glyceryl 1-monoabietate (GMA) showed sensitizing capacity. The presence of new contact allergens due to the modification, together with remaining unmodified material, contributes to the risk of developing allergy from contact with these types of rosin. A new main contact allergen in unmodified rosin was identified; 13,14(beta)-epoxyabietic acid. The allergenicity of this epoxide was comparable to that of an earlier identified rosin allergen, 15-hydroperoxyabietic acid (15-HPA). The allergens were detected as their methyl esters. Experimental sensitization and cross-reactivity of oxidation products of resin acids were studied. A pattern of cross-reactivity was observed which indicates that the

  13. New oligonucleotide derivatives as unreactive substrate analogues and potential inhibitors of human apurinic/apyrimidinic endonuclease APE1.

    PubMed

    Kuznetsov, Nikita A; Kupryushkin, Maxim S; Abramova, Tatyana V; Kuznetsova, Alexandra A; Miroshnikova, Anastasia D; Stetsenko, Dmitry A; Pyshnyi, Dmitrii V; Fedorova, Olga S

    2016-01-01

    Human apurinic/apyrimidinic endonuclease APE1 is one of the key enzymes of the base excision DNA repair system. The main biological function of APE1 is the hydrolysis of the phosphodiester bond on the 5'-side of an apurinic/apyrimidinic site (AP-site) to give the 5'-phosphate and 3'-hydroxyl group. It has long been known that AP-sites have mutagenic and cytotoxic effects and their accumulation in DNA is a potential hazard to the cell lifecycle. The structural and biochemical studies of APE1 are complicated by its high catalytic activity towards the AP-site and its cyclic or acyclic analogues. This work has focussed on the design, synthesis and analysis of oligonucleotide derivatives as potentially unreactive APE1 substrates. We have shown that the replacement of oxygen atoms in the phosphate group on the 5'-side from the AP-site analogue tetrahydrofuran (F) considerably decreases the rate of enzymatic hydrolysis of modified oligonucleotides. We have calculated that a N3'-P5' phosphoramidate linkage is hydrolysed about 30 times slower than the native phosphodiester bond while phosphorothioate or primary phosphoramidate linkages are cleaved more than three orders of magnitude slower. The value of IC50 of the oligonucleotide duplex containing a primary phosphoramidate linkage is 2.5 × 10(-7) M, which is in accordance with the APE1 association constant of DNA duplexes containing AP-sites. Thus, it is demonstrated that oligonucleotide duplexes with chemical modifications could be used as unreactive substrates and potential competitive inhibitors of APE1. PMID:26548492

  14. Chemically modified and nanostructured porous silicon as a drug delivery material and device

    NASA Astrophysics Data System (ADS)

    Anglin, Emily Jessica

    This thesis describes the fabrication, chemical modification, drug release, and toxicity studies of nanostructured porous silicon for the purposes of developing a smart drug delivery device. The first chapter is an introductory chapter, presenting the chemical and physical properties of porous silicon, the concepts and issues of current drug delivery devices and materials, and how porous silicon can address the issues regarding localized and controlled drug therapies. The second chapter discusses chemical modifications of nanostructured porous Si for stabilizing the material in biologically relevant media while providing an extended release of a therapeutic in vitro. This chapter also demonstrates the utility of the porous silicon optical signatures for effectively monitoring drug release from the system and its applications for development of a self-reporting drug delivery device. In chapter three, the concept of providing a triggered release of a therapeutic from porous silicon microparticles through initiation by an external stimulus is demonstrated. The microparticles are chemically modified, and the release is enhanced by a short application of ultrasound to the particulate system. The effect of ultrasound on the drug release and particle size is discussed. Chapter four presents a new method for sustaining the release of a monoclonal antibody from the porous matrix of porous SiO2. The therapeutic is incorporated into the films through electrostatic adsorption and a slow release is observed in vitro. A new method of quantifying the extent of drug loading is monitored with interferometry. The last chapter of the thesis provides a basic in vivo toxicity study of various porous Si microparticles for intraocular applications. Three types of porous Si particles are fabricated and studied in a rabbit eye model. The toxicity studies were conducted by collaborators at the Shiley Eye Center, La Jolla, CA. This work, demonstrates the feasibility of developing a self

  15. [Study toward practical use of oligonucleotide therapeutics].

    PubMed

    Inoue, Takao; Yoshida, Tokuyuki

    2014-01-01

    Over the past decade, oligonucleotide-based therapeutics such as antisense oligonucleotides and small interfering RNAs (siRNAs) have been developed extensively. For example, mipomersen (Kynamro; ISIS Pharmaceuticals), which is a second-generation antisense oligonucleotide administered by subcutaneous injection, has recently been approved by the FDA for the treatment of homozygous familial hypercholesterolemia. On the other hands, methods for the evaluation of quality, efficacy and safety of oligonucleotide therapeutics have not been fully discussed. Furthermore, the regulatory guidance specific for oligonucleotide therapeutics has not been established yet. Under these circumstances, we started to collaborate with Osaka University and PMDA to discuss regulatory science focused on oligonucleotide therapeutics. Through the collaboration, we would like to propose the possible design of quality evaluation and preclinical safety-evaluation of oligonucleotide therapeutics. PMID:25707197

  16. Extensive sugar modification improves triple helix forming oligonucleotide activity in vitro but reduces activity in vivo.

    PubMed

    Alam, Md Rowshon; Majumdar, Alokes; Thazhathveetil, Arun Kalliat; Liu, Su-Ting; Liu, Ji-Lan; Puri, Nitin; Cuenoud, Bernard; Sasaki, Shigeki; Miller, Paul S; Seidman, Michael M

    2007-09-01

    We are developing triple helix forming oligonucleotides (TFOs) for gene targeting. Previously, we synthesized bioactive TFOs containing 2'-O-methylribose (2'-OMe) and 2'-O-aminoethylribose (2'-AE) residues. Active TFOs contained four contiguous 2'-AE residues and formed triplexes with high thermal stability and rapid association kinetics. In an effort to further improve bioactivity, we synthesized three series of TFOs containing the 2'-AE patch and additional ribose modifications distributed throughout the remainder of the oligonucleotide. These were either additional 2'-AE residues, the conformationally locked BNA/LNA ribose with a 2'-O,4'-C-methylene bridge, or the 2'-O,4'-C-ethylene analogue (ENA). The additionally modified TFOs formed triplexes with greater thermal stability than the reference TFO, and some had improved association kinetics. However, the most active TFOs in the biochemical and biophysical assays were the least active in the bioassay. We measured the thermal stability of triplexes formed by the TFOs in each series on duplex targets containing a change in sequence at a single position. The Tm value of the variant sequence triplexes increased as the number of all additional modifications increased. A simple explanation for the failure of the improved TFOs in the bioassay was that the increased affinity for nonspecific targets lowered the effective nuclear concentration. Enhancement of TFO bioactivity will require chemical modifications that improve interaction with the specific targets while retaining selectivity against mismatched sequences. PMID:17691818

  17. Effect of three biological response modifiers on chemical carcinogenesis in mice.

    PubMed

    Bogdanović, Z; Culo, F; Marusić, M

    1993-01-01

    The modulation of chemical carcinogenesis by three biological response modifiers was assessed in a mouse model. CBA mice given 20-methylcholanthrene s.c. were treated with peptidoglycan monomer, azure B and indomethacin for one month, either from day 0 or 75 after methylcholanthrene injection to assess their effects on tumor incidence (on days 150 and 300), time of tumor appearance, time of death, and duration and dynamics of tumor growth. All three agents significantly influenced some of the parameters of tumor growth, except tumor incidence on day 300. Highly significant sex differences in tumor appearance and growth were observed. Tumors with late appearance grew faster in comparison to tumors with early appearance. The data presented indicate that the effectiveness of anti-cancer body defense mechanisms can be best defined by the time of tumor appearance. PMID:8272149

  18. 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.

  19. Nanometric dispersion of a Mg/Al layered double hydroxide into a chemically modified polycaprolactone.

    PubMed

    Mangiacapra, Pasqualina; Raimondo, Marialuigia; Tammaro, Loredana; Vittoria, Vittoria; Malinconico, Mario; Laurienzo, Paola

    2007-03-01

    Polycaprolactone (PCL) was chemically modified by grafting maleic anhydride on it, through a radical reaction induced by benzoyl peroxide as initiator. To improve the grafting degree, a second unsaturated comonomer such as glycidyl methacrylate (GMA) has been added, demonstrating a good reactivity in melt grafting without leading to long grafted chains. The quantitative determination of grafted maleic anhydride, performed by FTIR analysis, revealed a grafting weight percentage of 9.5 +/- 0.9, and the NMR characterization made it possible to propose a structure for the grafted polymer (PCLgMA). The modified polymer was analyzed by DSC and X-ray diffraction, showing a structural organization even better than that of the pristine polymer. An exchange reaction with a layered double hydroxide (LDH), hydrotalcite-like solid in the nitrate form, led to the disappearance of the crystalline basal peak of LDH in the X-ray diffractograms, suggesting a possible exfoliation of the inorganic sample. An oxidative etching on the composite surface followed by atomic force microscopy analysis made it possible to enlighten the lamellar structure in the pristine sample. In the composite sample, the well identifiable narrow fissures homogeneously distributed on the surface demonstrate that nanometer stacks of LDH sheets, embedded in a highly textured PCLgMA matrix, are present in the composite sample. The comparison of X-ray diffractograms and AFM analysis suggests either a partial exfoliation or an intercalation of the polymer in a lamellar texture with a basal spacing higher than 5 nm. In any case, the process of ionic exchange between nitrate LDH and PCLgMA led to the formation of nanocomposites, in which no large hydrotalcite aggregates are present. This is an interesting method to obtain a direct intercalation of the modified polymer into the inorganic solid with a simple ionic exchange reaction. PMID:17319719

  20. Chemical drug stability in lipids, modified lipids, and polyethylene oxide-containing formulations.

    PubMed

    Stella, Valentino J

    2013-12-01

    To critique the stability complications seen in formulating poorly water-soluble, problematic drugs in lipids, modified lipids, and polyethylene oxide solvents and surfactants in hard and soft gelatin capsules as well as some parenterals, a literature search was performed and personal experiences, and those of colleagues, collated. The literature is replete with examples of molecules undergoing rapid oxidative degradation in the presence of polyethylene oxide based solvents and surfactants as well as in the presence of unsaturated lipids. More recently appreciated is instability caused by the reaction of amine and amide drugs, with formaldehyde, formic acid found in many of these solvents as impurities and other degradation byproducts of the solvents themselves. One would expect acylation and transacylation reactions to be more common than reported but the literature has some good examples. An added complexity is occasionally seen with the use of hard and soft gelatin capsules with these solvents. The chemical stability of drugs in liquid and semi-solid formulations in the presence of lipids, modified lipids, and polyoxyethylene oxide-based solvents and surfactants can be complex, further exacerbated by the use of gelatin capsules, and can lead to a plethora of degradation pathways often not seen when the same drugs are formulated in solid dosage forms. PMID:23636838

  1. 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

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

    PubMed

    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

  3. 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.

  4. 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

  5. Biodistribution profiling of the chemical modified hyaluronic acid derivatives used for oral delivery system.

    PubMed

    Hsieh, Chien-Ming; Huang, Yu-Wen; Sheu, Ming-Thau; Ho, Hsiu-O

    2014-03-01

    A series of adipic acid dihydrazide (ADH)-modified hyaluronic acid (HA-ADH) compounds were synthesized and conjugated with QDots (QDots-HA conjugates) to assess the effects of the molecular weight (MW) and extent of chemical modification of HA on its biodistribution. Their physicochemical structures were confirmed by complementary application of GPC, (1)H NMR, FTIR, and UV-vis spectroscopic methods. In vivo imaging of QDots-HA conjugates after oral administration was analyzed to investigate their biodistribution in nude mice. Simultaneously, real-time bioimaging was confirmed by an anatomical analysis to investigate the organ-specific accumulation of conjugates. QDot-HA conjugates with a higher MW of HA or high modification presented relatively slow clearance leading to an extension of the retention time for up to 10 days, whereas those with lower MWs of HA or a low modification extent exhibited quick absorption and elimination after oral administration. Taken together, HA derivatives with suitable MWs and chemical modification extents can be used to design new, more-sophisticated, and intelligent HA-based vehicles for oral delivery with diverse characteristics. PMID:24315950

  6. 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.

  7. Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures.

    PubMed

    Kalinowski, Matthäus; Haug, Rüdiger; Said, Hassan; Piasecka, Sylwia; Kramer, Markus; Richert, Clemens

    2016-06-16

    The folding of long DNA strands into designed nanostructures has evolved into an art. Being based on linear chains only, the resulting nanostructures cannot readily be transformed into covalently linked frameworks. Covalently linking strands in the context of folded DNA structures requires a robust method that avoids sterically demanding reagents or enzymes. Here we report chemical ligation of the 3'-amino termini of oligonucleotides and 5'-phosphorylated partner strands in templated reactions that produce phosphoramidate linkages. These reactions produce inter-nucleotide linkages that are isoelectronic and largely isosteric to phosphodiesters. Ligations were performed at three levels of complexity, including the extension of branched DNA hybrids and the ligation of six scaffold strands in a small origami. PMID:27225865

  8. 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

  9. Characterization of chemically modified enzymes for bioremediation-reactions. 1997 annual progress report

    SciTech Connect

    Kaufman, E.N.; Adams, M.W.W.

    1997-09-01

    'Many, if not most, biological transformation reactions of interest to US Department of Energy (DOE) site remediation involve substrates that are only sparingly soluble in aqueous environments. Hence, destruction of these recalcitrant and toxic materials would benefit tremendously if their degradation could be performed in nonaqueous environments. Organic biocatalysis may be motivated by the nature of the substrate itself, augmented mass transport, ease of product recovery, or novel reaction pathways afforded by the organic solvent. For instance, polychlorinated biphenyls (PCBs) are sparingly soluble in water, but may be more effectively processed when solubilized by organic liquids. However, naturally-occurring enzymes are not soluble in organic solvents. Indeed, most spontaneously denature and, depending on the solvent used, typically form inactive and insoluble precipitates. The objective of the current work is to gain a fundamental understanding of the molecular and catalytic properties of enzymes that have been chemically-modified so that they are catalytically-active and chemically-thermally-stable in organic solvents. The premise for this study is that highly stable enzymes which are catalytically active in both water and in a range of organic solvents are optimally suited for bioremediation where substrates of interest are more soluble and may be processed with greater specificity in nonaqueous solvents. The proposed research program will enable the development of nonaqueous bioremediation technologies for the treatment of DOE sites contaminated with aqueous-insoluble organic compounds. Such compounds may include dense nonaqueous phase liquids, trichloroethylene (TCE), trichloroacetic acid, trans-dichloroethylene, diesel fuel, and PCBs. These compounds have been identified as targets for technology development in the ``EM Technology Needs Database,'''' and are contaminants at the following DOE sites: K-25 Site plumes; ORNL WAGS 1, 4, and 5; Paducah plumes

  10. Modified chemical synthesis of porous α-Sm{sub 2}S{sub 3} thin films

    SciTech Connect

    Kumbhar, V.S.; Jagadale, A.D.; Gaikwad, N.S.; Lokhande, C.D.

    2014-08-15

    Highlights: • A novel chemical route to prepare α-Sm{sub 2}S{sub 3} thin films. • A porous honeycomb like morphology of the α-Sm{sub 2}S{sub 3} thin film. • An application of α-Sm{sub 2}S{sub 3} thin film toward its supercapacitive behaviour. - Abstract: The paper reports synthesis of porous α-Sm{sub 2}S{sub 3} thin films using modified chemical synthesis, also known as successive ionic layer adsorption and reaction (SILAR) method. The X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), atomic force microscopy (AFM), wettability and ultraviolet–visible spectroscopy (UV–vis) techniques are used for the study of structural, elemental, morphological and optical properties of α-Sm{sub 2}S{sub 3} films. An orthorhombic crystal structure of α-Sm{sub 2}S{sub 3} is resulted from XRD study. The SEM and AFM observations showed highly porous α-Sm{sub 2}S{sub 3} film surface. An optical band gap of 2.50 eV is estimated from optical absorption spectrum. The porous α-Sm{sub 2}S{sub 3} thin film tuned for supercapacitive behaviour using cyclic voltammetry and galvanostatic charge discharge showed a specific capacitance and energy density of 294 Fg{sup –1} and 48.9 kW kg{sup –1}, respectively in 1 M LiClO{sub 4}–propylene carbonate electrolyte.

  11. Oligonucleotide-directed site-specific mutagenesis in Drosophila melanogaster.

    PubMed Central

    Banga, S S; Boyd, J B

    1992-01-01

    An efficient technique has been developed for performing in vivo site-directed mutagenesis in Drosophila melanogaster. This procedure involves directed repair of P-element-induced DNA lesions after injection of a modified DNA sequence into early embryos. An oligonucleotide of 50 base pairs, whose sequence spans the P-element insertion site, mediates base replacement in the endogenous gene. Restriction mapping, DNA sequencing, and polymerase chain reaction analysis demonstrate that base substitutions present in an injected oligonucleotide are incorporated into genomic sequences flanking a P insertion site in the white gene. This analysis suggests that progeny bearing directed mutations are recovered with a frequency of about 0.5 x 10(-3). Because Drosophila remains a premier organism for the analysis of eukaryotic gene regulation, this system should find strong application in that analysis as well as in the analysis of DNA recombination, conversion, repair, and mutagenesis. Images PMID:1311850

  12. A novel chemically modified curcumin reduces severity of experimental periodontal disease in rats: initial observations.

    PubMed

    Elburki, Muna S; Rossa, Carlos; Guimaraes, Morgana R; Goodenough, Mark; Lee, Hsi-Ming; Curylofo, Fabiana A; Zhang, Yu; Johnson, Francis; Golub, Lorne M

    2014-01-01

    Tetracycline-based matrix metalloproteinase- (MMP-) inhibitors are currently approved for two inflammatory diseases, periodontitis and rosacea. The current study addresses the therapeutic potential of a novel pleiotropic MMP-inhibitor not based on an antibiotic. To induce experimental periodontitis, endotoxin (LPS) was repeatedly injected into the gingiva of rats on one side of the maxilla; the contralateral (control) side received saline injections. Two groups of rats were treated by daily oral intubation with a chemically modified curcumin, CMC 2.24, for two weeks; the control groups received vehicle alone. After sacrifice, gingiva, blood, and maxilla were collected, the jaws were defleshed, and periodontal (alveolar) bone loss was quantified morphometrically and by μ-CT scan. The gingivae were pooled per experimental group, extracted, and analyzed for MMPs (gelatin zymography; western blot) and for cytokines (e.g., IL-1β; ELISA); serum and plasma samples were analyzed for cytokines and MMP-8. The LPS-induced pathologically excessive bone loss was reduced to normal levels based on either morphometric (P = 0.003) or μ-CT (P = 0.008) analysis. A similar response was seen for MMPs and cytokines in the gingiva and blood. This initial study, on a novel triketonic zinc-binding CMC, indicates potential efficacy on inflammatory mediators and alveolar bone loss in experimental periodontitis and warrants future therapeutic and pharmacokinetic investigations. PMID:25104884

  13. Structural and dynamics analysis of matrix metalloproteinases MMP-2 complexed with chemically modified tetracyclines (CMTs).

    PubMed

    Marcial, B L; Sousa, S F; Santos, H F Dos; Ramos, M J

    2014-12-01

    Matrix metalloproteinases (MMPs) play a critical role in physiological processes and pathological conditions such tumor invasion and metastasis. In recent years, a number of MMP inhibitors have been proposed, including the chemically modified tetracyclines (CMTs), which have been evaluated in preclinical cancer models showing promising results. This work provides insights into the structure and dynamics of the MMP-2 catalytic domain complexed with seven CMT (CMT-n), based on the analysis of molecular dynamics trajectories in solution. The comparative analysis of various relevant molecular aspects of the different complexes of MMP-2 and CMT-n derivatives was performed aiming to elucidate the effect of ligands on the enzyme structure. These include the radial distribution function of the water molecules around the catalytic zinc, the solvent accessible surface area for the inhibitors and the root-mean-square fluctuation for all amino acid residues. The results help to understand the differences in the binding modes of related compounds and, therefore, add to further design of novel tetracycline-based inhibitors for MMP enzymes. PMID:24125013

  14. The effects of chemically modifying serum apolipoproteins on their ability to activate lipoprotein lipase.

    PubMed Central

    Dodds, P F; Lopez-Johnston, A; Welch, V A; Gurr, M I

    1987-01-01

    Lipoprotein lipase activity was measured in an acetone-dried-powder preparation from rat epididymal adipose tissue using pig serum or pig serum lipoprotein, which had been chemically modified, as activator. Modification of acidic amino acids of lipoproteins with NN-dimethyl-1,3-diamine resulted in a complete loss of ability to activate lipoprotein lipase. Modification of 34% of lipoprotein arginine groups with cyclohexanedione resulted in the loss of 75% of the activation of lipoprotein lipase; approx. 42% of the original activity was recovered after reversal of the modification. This effect was dependent on the cyclohexanedione concentration. Modification of 48% of lipoprotein lysine groups with malonaldehyde decreased the maximum activation by 20%, but three times as much lipoprotein was required to achieve this. Non-enzymic glycosylation of lipoprotein with glucose, under a variety of conditions resulting in up to 28 nmol of glucose/mg of protein, had no effect upon the ability to activate lipoprotein lipase. In contrast non-enzymic sialylation resulted in a time-dependent loss of up to 60% of ability to activate lipoprotein lipase. Reductive methylation and acetoacetylation of serum did not affect the ability to activate lipoprotein lipase. The results are compared to the effects of similar modifications to low density lipoproteins on receptor-mediated endocytosis. PMID:3593262

  15. 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. PMID:26986200

  16. 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

  17. A Novel Chemically Modified Curcumin Reduces Severity of Experimental Periodontal Disease in Rats: Initial Observations

    PubMed Central

    Elburki, Muna S.; Rossa, Carlos; Guimaraes, Morgana R.; Goodenough, Mark; Lee, Hsi-Ming; Curylofo, Fabiana A.; Zhang, Yu; Johnson, Francis; Golub, Lorne M.

    2014-01-01

    Tetracycline-based matrix metalloproteinase- (MMP-) inhibitors are currently approved for two inflammatory diseases, periodontitis and rosacea. The current study addresses the therapeutic potential of a novel pleiotropic MMP-inhibitor not based on an antibiotic. To induce experimental periodontitis, endotoxin (LPS) was repeatedly injected into the gingiva of rats on one side of the maxilla; the contralateral (control) side received saline injections. Two groups of rats were treated by daily oral intubation with a chemically modified curcumin, CMC 2.24, for two weeks; the control groups received vehicle alone. After sacrifice, gingiva, blood, and maxilla were collected, the jaws were defleshed, and periodontal (alveolar) bone loss was quantified morphometrically and by μ-CT scan. The gingivae were pooled per experimental group, extracted, and analyzed for MMPs (gelatin zymography; western blot) and for cytokines (e.g., IL-1β; ELISA); serum and plasma samples were analyzed for cytokines and MMP-8. The LPS-induced pathologically excessive bone loss was reduced to normal levels based on either morphometric (P = 0.003) or μ-CT (P = 0.008) analysis. A similar response was seen for MMPs and cytokines in the gingiva and blood. This initial study, on a novel triketonic zinc-binding CMC, indicates potential efficacy on inflammatory mediators and alveolar bone loss in experimental periodontitis and warrants future therapeutic and pharmacokinetic investigations. PMID:25104884

  18. Structural and dynamical properties of water on chemically modified surfaces: The role of the instantaneous surface

    NASA Astrophysics Data System (ADS)

    Bekele, Selemon; Tsige, Mesfin

    Surfaces of polymers such as atactic polystyrene (aPS) represent very good model systems for amorphous material surfaces. Such polymer surfaces are usually modified either chemically or physically for a wide range of applications that include friction, lubrication and adhesion. It is thus quite important to understand the structural and dynamical properties of liquids that come in contact with them to achieve the desired functional properties. Using molecular dynamics (MD) simulations, we investigate the structural and dynamical properties of water molecules in a slab of water in contact with atactic polystyrene surfaces of varying polarity. We find that the density of water molecules and the number distribution of hydrogen bonds as a function of distance relative to an instantaneous surface exhibit a structure indicative of a layering of water molecules near the water/PS interface. For the dynamics, we use time correlation functions of hydrogen bonds and the incoherent structure function for the water molecules. Our results indicate that the polarity of the surface dramatically affects the dynamics of the interfacial water molecules with the dynamics slowing down with increasing polarity. This work was supported by NSF Grant DMR1410290.

  19. 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.

  20. 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.

  1. 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. PMID:23064494

  2. 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

    2016-08-01

    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. PMID:27265308

  3. 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.

  4. 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.

  5. 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

  6. Surfactants as bubble surface modifiers in the flotation of algae: dissolved air flotation that utilizes a chemically modified bubble surface.

    PubMed

    Henderson, Rita K; Parsons, Simon A; Jefferson, Bruce

    2008-07-01

    In this paper we present an investigation into the use of bubbles modified with surfactants in dissolved air flotation (DAF). Bubble modification was investigated by dosing surfactants of varying character into the saturator of a DAF unit in turn. The cell removal efficiency only improved when using a cationic surfactant where optimum removal of Microcystis aeruginosa cells was obtained when using 0.0022-0.004 mequiv L(-1) surfactant. However, the magnitude of the removal differed according to the hydrophobicity of the surfactant. Typically, the more efficiently the surfactant adsorbed at the bubble interface, the better the removal efficiency. When the dose to saturator ratio was kept constant and the recycle ratio varied, the removal efficiency improved with increasing recycle ratio, reaching a maximum removal efficiency of 87% for M. aeruginosa. This value was comparable with that predicted by a theoretical model. The bubble collection efficiency of a maximum of two cells per bubble was constant irrespective of the influent cell number or recycle ratio. Treatment of additional species in this way revealed a relationship between increasing size and both increasing removal efficiency and decreasing surfactant dose, which is supported by theoretical relationships. PMID:18678021

  7. 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.

  8. 40 CFR 372.20 - Process for modifying covered chemicals and facilities.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... facilities that release the toxic chemical or to population centers, the history of releases of such chemical... (CONTINUED) SUPERFUND, EMERGENCY PLANNING, AND COMMUNITY RIGHT-TO-KNOW PROGRAMS TOXIC CHEMICAL RELEASE... toxic chemical listed under subsection (c) of section 313 of Title III if the Administrator...

  9. 40 CFR 372.20 - Process for modifying covered chemicals and facilities.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... facilities that release the toxic chemical or to population centers, the history of releases of such chemical... (CONTINUED) SUPERFUND, EMERGENCY PLANNING, AND COMMUNITY RIGHT-TO-KNOW PROGRAMS TOXIC CHEMICAL RELEASE... toxic chemical listed under subsection (c) of section 313 of Title III if the Administrator...

  10. Rational design of antisense oligonucleotides targeting single nucleotide polymorphisms for potent and allele selective suppression of mutant Huntingtin in the CNS

    PubMed Central

    Østergaard, Michael E.; Southwell, Amber L.; Kordasiewicz, Holly; Watt, Andrew T.; Skotte, Niels H.; Doty, Crystal N.; Vaid, Kuljeet; Villanueva, Erika B.; Swayze, Eric E.; Frank Bennett, C.; Hayden, Michael R.; Seth, Punit P.

    2013-01-01

    Autosomal dominant diseases such as Huntington’s disease (HD) are caused by a gain of function mutant protein and/or RNA. An ideal treatment for these diseases is to selectively suppress expression of the mutant allele while preserving expression of the wild-type variant. RNase H active antisense oligonucleotides (ASOs) or small interfering RNAs can achieve allele selective suppression of gene expression by targeting single nucleotide polymorphisms (SNPs) associated with the repeat expansion. ASOs have been previously shown to discriminate single nucleotide changes in targeted RNAs with ∼5-fold selectivity. Based on RNase H enzymology, we enhanced single nucleotide discrimination by positional incorporation of chemical modifications within the oligonucleotide to limit RNase H cleavage of the non-targeted transcript. The resulting oligonucleotides demonstrate >100-fold discrimination for a single nucleotide change at an SNP site in the disease causing huntingtin mRNA, in patient cells and in a completely humanized mouse model of HD. The modified ASOs were also well tolerated after injection into the central nervous system of wild-type animals, suggesting that their tolerability profile is suitable for advancement as potential allele-selective HD therapeutics. Our findings lay the foundation for efficient allele-selective downregulation of gene expression using ASOs—an outcome with broad application to HD and other dominant genetic disorders. PMID:23963702