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Sample records for pairs duplex stability

  1. Molecular duplexes with encoded sequences and stabilities.

    PubMed

    Gong, Bing

    2012-12-18

    Through specific molecular shapes and repeating polymeric sequences, biomacromolecules encode information about both structure and function. Inspired by DNA molecules, we have conceived a strategy to encode linear molecular strands with sequences that specify intermolecular association, and we and our collaborators have supported this idea through our experimental work. This Account summarizes the design and development of a class of molecular duplexes with programmable hydrogen-bonding sequences and adjustable stabilities. The specific system involves oligoamide strands synthesized from readily available monomeric modules based on standard amide (peptide) chemistry. By covalently linking three types of basic building blocks in different orders, we create oligoamide strands with various arrangements of amide O and H atoms that provide arrays of hydrogen bonding sequences. Because one of the two edges of these molecules presents the sequences of hydrogen-bond donors and acceptors, these oligoamide strands associate via their hydrogen-bonding edges into double-stranded pairs or duplexes. Systematic studies have demonstrated the strict sequence specificity and tunable stability of this system. These structurally simple duplexes exhibit many features associated with DNA sequences such as programmable sequence specificity, shape and hydrogen-bonding complementarity, and cooperativity of multipoint interactions. Capable of specifying intermolecular associations, these duplexes have formed supramolecular structures such as β-sheets and non-covalent block copolymers and have templated chemical reactions. The incorporation of dynamic covalent interactions into these H-bonded duplexes has created association units that undergo sequence-specific association and covalent ligation in both nonpolar solvents and polar media including water. These new association units may facilitate the development of new dynamic covalent structures, and new properties are emerging from these

  2. Effect of 6-thioguanine on the stability of duplex DNA

    PubMed Central

    Bohon, Jen; de los Santos, Carlos R.

    2005-01-01

    The incorporation of 6-thioguanine (S6G) into DNA is a prerequisite for its cytotoxic action, but duplex structure is not significantly perturbed by the presence of the lesion [J. Bohon and C. R. de los Santos (2003) Nucleic Acids Res., 31, 1331–1338]. It is therefore possible that the mechanism of cytotoxicity relies on a loss of stability rather than a pathway involving direct structural recognition. The research described here focuses on the changes in thermodynamic properties of duplex DNA owing to the introduction of S6G as well as the kinetic properties of base pairs involving S6G. Replacement of a guanine in a G•C pair by S6G results in ∼1 kcal/mol less favorable Gibbs free energy of duplex formation at 37°C. S6G•T and G•T mismatch-containing duplexes have almost identical Gibbs free energy at 37°C, with values ∼3 kcal/mol less favorable than that of the control. Base pair stability is affected by S6G. The lifetime of the normal G•C base pair is ∼125 ms, whereas that of the G•T mismatch is below the detection limit. The lifetimes of S6G•C and S6G•T pairs are ∼7 and 2 ms, respectively, demonstrating that, although S6G significantly decreases the stability of the pairing with cytosine, it slightly increases that of a mismatch. PMID:15905476

  3. Nucleic acid duplexes incorporating a dissociable covalent base pair

    NASA Technical Reports Server (NTRS)

    Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    1999-01-01

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

  4. Nucleic acid duplexes incorporating a dissociable covalent base pair.

    PubMed

    Gao, K; Orgel, L E

    1999-12-21

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure. PMID:10611299

  5. Importance of minor groove functional groups for the stability of DNA duplexes.

    PubMed

    Sun, Zhenhua; Chen, Dongli; Lan, Tao; McLaughlin, Larry W

    2002-11-01

    Eight oligonucleotide duplexes have been prepared with four pairs of selected complementary pairs of native/analogue heterocyclic bases incorporated at a selected test site. The base pairs vary in the nature of their functionality in the minor groove. Each pair has a minor groove purine amino group present or absent, and correspondingly has a minor grove pyrimidine carbonyl present or absent. Loss of duplex stability is most notable when the minor groove pyrimidine carbonyl is absent although in other respects normal Watson-Crick hydrogen bonding is maintained in these sequences. These differences in stability are discussed in terms of possible variations in minor groove hydration.

  6. Base pairing and structural insights into the 5-formylcytosine in RNA duplex.

    PubMed

    Wang, Rui; Luo, Zhipu; He, Kaizhang; Delaney, Michael O; Chen, Doris; Sheng, Jia

    2016-06-01

    5-Formylcytidine (f(5)C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m(5)C) through 5-hydroxymethylcytidine (hm(5)C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f(5)C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5'-GUA(f(5)C)GUAC-3']2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f(5)C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex. PMID:27079978

  7. Base pairing and structural insights into the 5-formylcytosine in RNA duplex

    PubMed Central

    Wang, Rui; Luo, Zhipu; He, Kaizhang; Delaney, Michael O.; Chen, Doris; Sheng, Jia

    2016-01-01

    5-Formylcytidine (f5C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m5C) through 5-hydroxymethylcytidine (hm5C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f5C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5′-GUA(f5C)GUAC-3′]2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f5C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex. PMID:27079978

  8. 6-Pyrazolylpurine as an Artificial Nucleobase for Metal-Mediated Base Pairing in DNA Duplexes

    PubMed Central

    Léon, J. Christian; Sinha, Indranil; Müller, Jens

    2016-01-01

    The artificial nucleobase 6-pyrazol-1-yl-purine (6PP) has been investigated with respect to its usability in metal-mediated base pairing. As was shown by temperature-dependent UV spectroscopy, 6PP may form weakly stabilizing 6PP–Ag(I)–6PP homo base pairs. Interestingly, 6PP can be used to selectively recognize a complementary pyrimidine nucleobase. The addition of Ag(I) to a DNA duplex comprising a central 6PP:C mispair (C = cytosine) leads to a slight destabilization of the duplex. In contrast, a stabilizing 6PP–Ag(I)–T base pair is formed with a complementary thymine (T) residue. It is interesting to note that 6PP is capable of differentiating between the pyrimidine moieties despite the fact that it is not as sterically crowded as 6-(3,5-dimethylpyrazol-1-yl)purine, an artificial nucleobase that had previously been suggested for the recognition of nucleic acid sequences via the formation of a metal-mediated base pair. Hence, the additional methyl groups of 6-(3,5-dimethylpyrazol-1-yl)purine may not be required for the specific recognition of the complementary nucleobase. PMID:27089326

  9. Detection of base pair mismatches in duplex DNA and RNA oligonucleotides using electrospray mass spectrometry

    NASA Astrophysics Data System (ADS)

    Griffey, Richard H.; Greig, Michael J.

    1997-05-01

    The identify and location of base pair mismatches in non- covalent DNA:RNA duplexes are established using MS and MS-MS on a quadruple ion trap with electrospray ionization (ESI). MS-MS experiments on a 14mer duplex (D) with a single C:A base pair mismatch using lower activation energy results in selective cleavage of the mismatched A nucleobase, even in the presence of the wild-type duplex. The location of the mismatch base pair can be discerned via presence of the wild-type duplex. The location of the mismatch base pair can be discerned via selection of the (D-5H)5- ion and fragmentation of the backbone at that location in a n additional MS-MS experiment. Selective fragmentation is observed for C in a C-C mismatched base pair, which is very difficult to detect using chemical cleavage or E. coli mismatch binding protein. In an RNA:DNA duplex with a single base pair mismatch, the DNA base is removed without fragmentation of the RNA strand, greatly simplifying the interpretation of the resulting MS spectrum. A method is presented for detecting two DNA strands, for example a point mutation which generates an oncogenic phenotype, and the wild-type message. The results suggest that ESI-MS-MS may provide a rapid and selective method to identify and locate genetic mutations without the need for chemical degradation or protein binding followed by gel electrophoresis.

  10. 5' modification of duplex DNA with a ruthenium electron donor-acceptor pair using solid-phase DNA synthesis

    NASA Technical Reports Server (NTRS)

    Frank, Natia L.; Meade, Thomas J.

    2003-01-01

    Incorporation of metalated nucleosides into DNA through covalent modification is crucial to measurement of thermal electron-transfer rates and the dependence of these rates with structure, distance, and position. Here, we report the first synthesis of an electron donor-acceptor pair of 5' metallonucleosides and their subsequent incorporation into oligonucleotides using solid-phase DNA synthesis techniques. Large-scale syntheses of metal-containing oligonucleotides are achieved using 5' modified phosporamidites containing [Ru(acac)(2)(IMPy)](2+) (acac is acetylacetonato; IMPy is 2'-iminomethylpyridyl-2'-deoxyuridine) (3) and [Ru(bpy)(2)(IMPy)](2+) (bpy is 2,2'-bipyridine; IMPy is 2'-iminomethylpyridyl-2'-deoxyuridine) (4). Duplexes formed with the metal-containing oligonucleotides exhibit thermal stability comparable to the corresponding unmetalated duplexes (T(m) of modified duplex = 49 degrees C vs T(m) of unmodified duplex = 47 degrees C). Electrochemical (3, E(1/2) = -0.04 V vs NHE; 4, E(1/2) = 1.12 V vs NHE), absorption (3, lambda(max) = 568, 369 nm; 4, lambda(max) = 480 nm), and emission (4, lambda(max) = 720 nm, tau = 55 ns, Phi = 1.2 x 10(-)(4)) data for the ruthenium-modified nucleosides and oligonucleotides indicate that incorporation into an oligonucleotide does not perturb the electronic properties of the ruthenium complex or the DNA significantly. In addition, the absence of any change in the emission properties upon metalated duplex formation suggests that the [Ru(bpy)(2)(IMPy)](2+)[Ru(acac)(2)(IMPy)](2+) pair will provide a valuable probe for DNA-mediated electron-transfer studies.

  11. Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds

    PubMed Central

    Nakano, Shu-ichi; Kitagawa, Yuichi; Miyoshi, Daisuke; Sugimoto, Naoki

    2014-01-01

    Nucleic acids are useful for biomedical targeting and sensing applications in which the molecular environment is different from that of a dilute aqueous solution. In this study, the influence of various types of mixed solutions of water and water-soluble organic compounds on RNA was investigated by measuring the catalytic activity of the hammerhead ribozyme and the thermodynamic stability of an oligonucleotide duplex. The compounds with a net neutral charge, such as poly(ethylene glycol), small primary alcohols, amide compounds, and aprotic solvent molecules, added at high concentrations changed the ribozyme-catalyzed RNA cleavage rate, with the magnitude of the effect dependent on the NaCl concentration. These compounds also changed the thermodynamic stability of RNA base pairs of an oligonucleotide duplex and its dependence on the NaCl concentration. Specific interactions with RNA molecules and reduced water activity could account for the inhibiting effects on the ribozyme catalysis and destabilizing effects on the duplex stability. The salt concentration dependence data correlated with the dielectric constant, but not with water activity, viscosity, and the size of organic compounds. This observation suggests the significance of the dielectric constant effects on the RNA reactions under molecular crowding conditions created by organic compounds. PMID:25161873

  12. 2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes

    PubMed Central

    Sochacka, Elzbieta; Szczepanowski, Roman H.; Cypryk, Marek; Sobczak, Milena; Janicka, Magdalena; Kraszewska, Karina; Bartos, Paulina; Chwialkowska, Anna; Nawrot, Barbara

    2015-01-01

    2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon–anticodon interactions. The enhanced thermodynamic stability of S2U-containing RNA duplexes and the preferred S2U-A versus S2U-G base pairing are appreciated characteristics of S2U-modified molecular probes. Recently, we have demonstrated that 2-thiouridine (alone or within an RNA chain) is predominantly transformed under oxidative stress conditions to 4-pyrimidinone riboside (H2U) and not to uridine. Due to the important biological functions and various biotechnological applications for sulfur-containing nucleic acids, we compared the thermodynamic stabilities of duplexes containing desulfured products with those of 2-thiouracil-modified RNA and DNA duplexes. Differential scanning calorimetry experiments and theoretical calculations demonstrate that upon 2-thiouracil desulfuration to 4-pyrimidinone, the preferred base pairing of S2U with adenosine is lost, with preferred base pairing with guanosine observed instead. Therefore, biological processes and in vitro assays in which oxidative desulfuration of 2-thiouracil-containing components occurs may be altered. Moreover, we propose that the H2U-G base pair is a suitable model for investigation of the preferred recognition of 3′-G-ending versus A-ending codons by tRNA wobble nucleosides, which may adopt a 4-pyrimidinone-type structural motif. PMID:25690900

  13. Thermodynamic and structural properties of the specific binding between Ag⁺ ion and C:C mismatched base pair in duplex DNA to form C-Ag-C metal-mediated base pair.

    PubMed

    Torigoe, Hidetaka; Okamoto, Itaru; Dairaku, Takenori; Tanaka, Yoshiyuki; Ono, Akira; Kozasa, Tetsuo

    2012-11-01

    Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag(+) ion stabilized a C:C mismatched base pair duplex DNA. A C-Ag-C metal-mediated base pair was supposed to be formed by the binding between the Ag(+) ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C-Ag-C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag(+) ion. Isothermal titration calorimetry demonstrated that the Ag(+) ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 10(6) M(-1), which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag(+) ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag(+) ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C-Ag-C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C-Ag-C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences. PMID:22766014

  14. Thermodynamic and structural properties of the specific binding between Ag⁺ ion and C:C mismatched base pair in duplex DNA to form C-Ag-C metal-mediated base pair.

    PubMed

    Torigoe, Hidetaka; Okamoto, Itaru; Dairaku, Takenori; Tanaka, Yoshiyuki; Ono, Akira; Kozasa, Tetsuo

    2012-11-01

    Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag(+) ion stabilized a C:C mismatched base pair duplex DNA. A C-Ag-C metal-mediated base pair was supposed to be formed by the binding between the Ag(+) ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C-Ag-C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag(+) ion. Isothermal titration calorimetry demonstrated that the Ag(+) ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 10(6) M(-1), which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag(+) ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag(+) ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C-Ag-C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C-Ag-C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences.

  15. Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA.

    PubMed

    Nikolova, Evgenia N; Goh, Garrett B; Brooks, Charles L; Al-Hashimi, Hashim M

    2013-05-01

    G·C Hoogsteen base pairs can form transiently in duplex DNA and play important roles in DNA recognition, replication, and repair. G·C Hoogsteen base pairs are thought to be stabilized by protonation of cytosine N3, which affords a second key hydrogen bond, but experimental evidence for this is sparse because the proton cannot be directly visualized by X-ray crystallography and nuclear magnetic resonance spectroscopy. Here, we combine NMR and constant pH molecular dynamics simulations to directly investigate the pKa of cytosine N3 in a chemically trapped N1-methyl-G·C Hoogsteen base pair within duplex DNA. Analysis of NMR chemical shift perturbations and NOESY data as a function of pH revealed that cytosine deprotonation is coupled to a syn-to-anti transition in N1-methyl-G, which results in a distorted Watson-Crick geometry at pH >9. A four-state analysis of the pH titration profiles yields a lower bound pKa estimate of 7.2 ± 0.1 for the G·C Hoogsteen base pair, which is in good agreement with the pKa value (7.1 ± 0.1) calculated independently using constant pH MD simulations. Based on these results and pH-dependent NMR relaxation dispersion measurements, we estimate that under physiological pH (pH 7-8), G·C Hoogsteen base pairs in naked DNA have a population of 0.02-0.002%, as compared to 0.4% for A·T Hoogsteen base pairs, and likely exist primarily as protonated species.

  16. The thermodynamic stability of RNA duplexes and hairpins containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines.

    PubMed

    Kierzek, Elzbieta; Kierzek, Ryszard

    2003-08-01

    The N6-alkyladenosines and 2-methylthio-N6-alkyladenosines make up over half of the population of all naturally modified adenosines and they are present in the transfer ribonucleic acids (tRNA) at position 37. We measured effects of N6-alkyladenosines and 2-methylthio-N6-alkyladenosines on the thermodynamic stability of RNA duplexes containing a U-A(Mod) base pair at internal and terminal duplex positions, as well as containing modified adenosines as a 3'-terminal unpaired nucleotide. Beside naturally modified adenosines such as N6-isopentenyladenosine (i6A), N6-methyladenosine (m6A), 2-methylthio-N6-isopentenyladenosine (ms2i6A) and 2-methylthio-N6-methyladenosine (ms2m6A), we studied several artificial modifications to evaluate the steric and electronic effects of N6-alkyl substituents. Moreover, some N6-alkyladenosines and 2-methylthio-N6-alkyladenosines were placed in hairpins at positions corresponding to nucleotide 37 of the tRNA anticodon arm, and the thermodynamic stability of those hairpins was studied. The stability of the modified RNA hairpins was measured in standard melting buffer containing 1 M sodium chloride as well as in physiological buffer containing 10 mM magnesium chloride and 150 mM potassium chloride. The results obtained indicate that the nature of the adenosine modification and the position of U-A(Mod) base pairs within the duplex influence the thermodynamic stability of RNA duplexes. For most of the modification, the destabilization of duplexes was observed. Moreover, we found that the buffer composition and the structure of the modified adenosine very significantly affect the thermodynamic stability of RNA. PMID:12888507

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

    PubMed

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

    2016-01-01

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

  18. Silver-mediated base pairings: towards dynamic DNA nanostructures with enhanced chemical and thermal stability

    NASA Astrophysics Data System (ADS)

    Swasey, Steven M.; Gwinn, Elisabeth G.

    2016-04-01

    The thermal and chemical fragility of DNA nanomaterials assembled by Watson-Crick (WC) pairing constrain the settings in which these materials can be used and how they can be functionalized. Here we investigate use of the silver cation, Ag+, as an agent for more robust, metal-mediated self-assembly, focusing on the simplest duplex building blocks that would be required for more elaborate Ag+-DNA nanostructures. Our studies of Ag+-induced assembly of non-complementary DNA oligomers employ strands of 2-24 bases, with varied base compositions, and use electrospray ionization mass spectrometry to determine product compositions. High yields of duplex products containing narrowly distributed numbers of Ag+ can be achieved by optimizing solution conditions. These Ag+-mediated duplexes are stable to at least 60 mM Mg2+, higher than is necessary for WC nanotechnology schemes such as tile assemblies and DNA origami, indicating that sequential stages of Ag+-mediated and WC-mediated assembly may be feasible. Circular dichroism spectroscopy suggests simple helical structures for Ag+-mediated duplexes with lengths to at least 20 base pairs, and further indicates that the structure of cytosine-rich duplexes is preserved at high urea concentrations. We therefore propose an approach towards dynamic DNA nanomaterials with enhanced thermal and chemical stability through designs that combine sturdy silver-mediated ‘frames’ with WC paired ‘pictures’.

  19. Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes: A molecular dynamics simulation study.

    PubMed

    Suresh, Gorle; Priyakumar, U Deva

    2015-09-01

    Modified nucleic acids have found profound applications in nucleic acid based technologies such as antisense and antiviral therapies. Previous studies on chemically modified nucleic acids have suggested that modifications incorporated in furanose sugar especially at 2'-position attribute special properties to nucleic acids when compared to other modifications. 2'-O-methyl modification to deoxyribose sugars of DNA-RNA hybrids is one such modification that increases nucleic acid stability and has become an attractive class of compounds for potential antisense applications. It has been reported that modification of DNA strands with 2'-O-methyl group reverses the thermodynamic stability of DNA-RNA hybrid duplexes. Molecular dynamics simulations have been performed on two hybrid duplexes (DR and RD) which differ from each other and 2'-O-methyl modified counterparts to investigate the effect of 2'-O-methyl modification on their duplex stability. The results obtained suggest that the modification drives the conformations of both the hybrid duplexes towards A-RNA like conformation. The modified hybrid duplexes exhibit significantly contrasting dynamics and hydration patterns compared to respective parent duplexes. In line with the experimental results, the relative binding free energies suggest that the introduced modifications stabilize the less stable DR hybrid, but destabilize the more stable RD duplex. Binding free energy calculations suggest that the increased hydrophobicity is primarily responsible for the reversal of thermodynamic stability of hybrid duplexes. Free energy component analysis further provides insights into the stability of modified duplexes.

  20. Yeast Pif1 Helicase Exhibits a One-base-pair Stepping Mechanism for Unwinding Duplex DNA*

    PubMed Central

    Ramanagoudr-Bhojappa, Ramanagouda; Chib, Shubeena; Byrd, Alicia K.; Aarattuthodiyil, Suja; Pandey, Manjula; Patel, Smita S.; Raney, Kevin D.

    2013-01-01

    Kinetic analysis of the DNA unwinding and translocation activities of helicases is necessary for characterization of the biochemical mechanism(s) for this class of enzymes. Saccharomyces cerevisiae Pif1 helicase was characterized using presteady state kinetics to determine rates of DNA unwinding, displacement of streptavidin from biotinylated DNA, translocation on single-stranded DNA (ssDNA), and ATP hydrolysis activities. Unwinding of substrates containing varying duplex lengths was fit globally to a model for stepwise unwinding and resulted in an unwinding rate of ∼75 bp/s and a kinetic step size of 1 base pair. Pif1 is capable of displacing streptavidin from biotinylated oligonucleotides with a linear increase in the rates as the length of the oligonucleotides increased. The rate of translocation on ssDNA was determined by measuring dissociation from varying lengths of ssDNA and is essentially the same as the rate of unwinding of dsDNA, making Pif1 an active helicase. The ATPase activity of Pif1 on ssDNA was determined using fluorescently labeled phosphate-binding protein to measure the rate of phosphate release. The quantity of phosphate released corresponds to a chemical efficiency of 0.84 ATP/nucleotides translocated. Hence, when all of the kinetic data are considered, Pif1 appears to move along DNA in single nucleotide or base pair steps, powered by hydrolysis of 1 molecule of ATP. PMID:23596008

  1. Duplex stabilities of phosphorothioate, methylphosphonate, and RNA analogs of two DNA 14-mers.

    PubMed Central

    Kibler-Herzog, L; Zon, G; Uznanski, B; Whittier, G; Wilson, W D

    1991-01-01

    The duplex stabilities of various phosphorothioate, methylphosphonate, RNA and 2'-OCH3 RNA analogs of two self-complementary DNA 14-mers are compared. Phosphorothioate and/or methylphosphonate analogs of the two sequences d(TAATTAATTAATTA) [D1] and d(TAGCTAATTAGCTA) [D2] differ in the number, position, or chirality (at the 5' terminal linkage) of the modified phosphates. Phosphorothioate derivatives of D1 are found to be less destabilized when the linkage modified is between adenines rather than between thymines. Surprisingly, no base sequence effect on duplex stabilization is observed for any methylphosphonate derivatives of D1 or D2. Highly modified phosphorothioates or methylphosphonates are less stable than their partially modified counterparts which are less stable than the unmodified parent compounds. The 'normal' (2'-OH) RNA analog of duplex D1 is slightly destabilized, whereas the 2'-OCH3 RNA derivative is significantly stabilized relative to the unmodified DNA. For the D1 sequence, at approximately physiological salt concentration, the order of duplex stability is 2'-OCH3 RNA greater than unmodified DNA greater than 'normal' RNA greater than methylphosphonate DNA greater than phosphorothioate DNA. D2 and the various D2 methylphosphonate analogs investigated all formed hairpin conformations at low salt concentrations. PMID:1711677

  2. Effect of flanking bases on quadruplex stability and Watson-Crick duplex competition.

    PubMed

    Arora, Amit; Nair, Divya R; Maiti, Souvik

    2009-07-01

    Guanine-rich DNA sequences have the ability to fold into four-stranded structures called G-quadruplexes, and are considered as promising anticancer targets. Although the G-quadruplex structure is composed of quartets and interspersed loops, in the genome it is also flanked on each side by numerous bases. The effect of loop length and composition on quadruplex conformation and stability has been well investigated in the past, but the effect of flanking bases on quadruplex stability and Watson-Crick duplex competition has not been addressed. We have studied in detail the effect of flanking bases on quadruplex stability and on duplex formation by the G-quadruplex in the presence of complementary strands using the quadruplex-forming sequence located in the promoter region of the c-kit oncogene. The results obtained from CD, thermal difference spectrum and UV melting demonstrated the effect of flanking bases on quadruplex structure and stability. With the increase in flank length, the increase in the more favorable DeltaH(vH) is accompanied by a striking increase in the unfavorable DeltaS(vH), which resulted in a decrease in the overall DeltaG(vH) of quadruplex formation. Furthermore, CD, fluorescence and isothermal titration calorimetry studies demonstrated that the propensity to attain quadruplex structure decreases with increasing flank length.

  3. Process for stabilizing dimensions of duplex stainless steels for service at elevated temperatures

    DOEpatents

    Hull, Frederick C.; Tobin, John C.

    1981-01-01

    Duplex stainless steel materials containing austenite plus delta ferrite, are dimensionally stabilized by heating the material to a reaction temperature between about 1050.degree.-1450.degree. F. (566.degree.-788.degree. C.), holding it at this temperature during transformation of delta ferrite to austenite plus sigma phase, and subsequently heating to a reversion temperature between about 1625.degree.-1750.degree. F. (885.degree.-954.degree. C.), whereby the sigma phase transforms back to ferrite, but the austenite remains dispersed in the ferrite phase. Final controlled cooling permits transformation of ferrite to austenite plus sigma and, later, precipitation of carbides.

  4. MHF complex senses branched DNA via binding a pair of crossover DNA duplexes

    PubMed Central

    Zhao, Qi; Saro, Dorina; Sachpatzidis, Aristidis; Singh, Thiyam Ramsing; Schlingman, Daniel; Zheng, Xiao-Feng; Mack, Andrew; Tsai, Miaw-Sheue; Mochrie, Simon; Regan, Lynne; Meetei, Amom Ruhikanta; Sung, Patrick; Xiong, Yong

    2014-01-01

    The conserved MHF1-MHF2 (MHF) complex functions in the activation of the Fanconi anemia (FA) pathway of DNA damage response, in regulating homologous recombination, and in DNA replication fork maintenance. MHF facilitates the processing of multiple types of branched DNAs by the FA DNA translocase FANCM. Here we report the crystal structure of a human MHF-DNA complex that reveals the DNA binding mode of MHF. The structure suggests an MHF preference for branched DNA over double stranded DNA through engaging two duplex arms, which is supported by single molecule studies. Biochemical analyses verify that MHF preferentially engage DNA forks or various four-way junctions independent of the junction-site structure. Genetic experiments provide evidence that the observed DNA-binding interface of MHF is important for cellular resistance to DNA damage. These results provide insights into how the MHF complex recognizes branched DNA and stimulates FANCM activity at such a structure to promote genome maintenance. PMID:24390579

  5. Structure and stability of duplex DNA containing the 3-(deoxyguanosin-N2-yl)-2-acetylaminofluorene (dG(N2)-AAF) lesion: a bulky adduct that persists in cellular DNA.

    PubMed

    Zaliznyak, Tanya; Bonala, Radha; Johnson, Francis; de Los Santos, Carlos

    2006-06-01

    The carcinogenic environmental pollutant 2-nitrofluorene produces several DNA adducts including the minor 3-(deoxyguanosin-N(2)-yl)-2-acetylaminofluorene (dG(N(2))-AAF) lesion, which persists for long times in rat tissue DNA after discontinuation of carcinogen administration. Here, we present the solution structure of a dG(N(2))-AAF duplex as determined by NMR spectroscopy and restrained molecular dynamics. The data establish a regular right-handed conformation with Watson-Crick base pair alignments throughout the duplex. The AAF moiety resides in the minor grove of the helix with its long axis directed toward the 5'-end of the modified strand. Restrained molecular dynamics shows that the duplex structure adjusts to the AAF lesion, reducing its exposure to water molecules. Analysis of UV melting profiles shows that the presence of dG(N(2))-AAF increases the thermal and thermodynamic stability of duplex DNA, an effect that is driven by a favorable entropy. The structure and stability of the dG(N(2))-AAF duplex have important implications in understanding the recognition of bulky lesions by the DNA repair system. PMID:16780352

  6. The Contribution of the Activation Entropy to the Gas-Phase Stability of Modified Nucleic Acid Duplexes

    NASA Astrophysics Data System (ADS)

    Hari, Yvonne; Dugovič, Branislav; Istrate, Alena; Fignolé, Annabel; Leumann, Christian J.; Schürch, Stefan

    2016-07-01

    Tricyclo-DNA (tcDNA) is a sugar-modified analogue of DNA currently tested for the treatment of Duchenne muscular dystrophy in an antisense approach. Tandem mass spectrometry plays a key role in modern medical diagnostics and has become a widespread technique for the structure elucidation and quantification of antisense oligonucleotides. Herein, mechanistic aspects of the fragmentation of tcDNA are discussed, which lay the basis for reliable sequencing and quantification of the antisense oligonucleotide. Excellent selectivity of tcDNA for complementary RNA is demonstrated in direct competition experiments. Moreover, the kinetic stability and fragmentation pattern of matched and mismatched tcDNA heteroduplexes were investigated and compared with non-modified DNA and RNA duplexes. Although the separation of the constituting strands is the entropy-favored fragmentation pathway of all nucleic acid duplexes, it was found to be only a minor pathway of tcDNA duplexes. The modified hybrid duplexes preferentially undergo neutral base loss and backbone cleavage. This difference is due to the low activation entropy for the strand dissociation of modified duplexes that arises from the conformational constraint of the tc-sugar-moiety. The low activation entropy results in a relatively high free activation enthalpy for the dissociation comparable to the free activation enthalpy of the alternative reaction pathway, the release of a nucleobase. The gas-phase behavior of tcDNA duplexes illustrates the impact of the activation entropy on the fragmentation kinetics and suggests that tandem mass spectrometric experiments are not suited to determine the relative stability of different types of nucleic acid duplexes.

  7. Incorporation of 3-Aminobenzanthrone into 2′-Deoxyoligonucleotides and Its Impact on Duplex Stability

    PubMed Central

    Lukin, Mark; Zaliznyak, Tanya; Johnson, Francis; de los Santos, Carlos R.

    2011-01-01

    3-Nitrobenzanthrone (3NBA), an environmental pollutant and potent mutagen, causes DNA damage via the reaction of its metabolically activated form with the exocyclic amino groups of purines and the C-8 position of guanine. The present work describes a synthetic approach to the preparation of oligomeric 2′-deoxyribonucleotides containing a 2-(2′-deoxyguanosin-N2-yl)-3-aminobenzanthrone moiety, one of the major DNA adducts found in tissues of living organisms exposed to 3NBA. The NMR spectra indicate that the damaged oligodeoxyribonucleotide is capable of forming a regular double helical structure with the polyaromatic moiety assuming a single conformation at room temperature; the spectra suggest that the 3ABA moiety resides in the duplex minor groove pointing toward the 5′-end of the modified strand. Thermodynamic studies show that the dG(N2)-3ABA lesion has a stabilizing effect on the damaged duplex, a fact that correlates well with the long persistence of this damage in living organisms. PMID:22175001

  8. MD and NMR analyses of choline and TMA binding to duplex DNA: on the origins of aberrant sequence-dependent stability by alkyl cations in aqueous and water-free solvents.

    PubMed

    Portella, Guillem; Germann, Markus W; Hud, Nicholas V; Orozco, Modesto

    2014-02-26

    It has been known for decades that alkylammonium ions, such as tetramethyl ammonium (TMA), alter the usual correlation between DNA GC-content and duplex stability. In some cases it is even possible for an AT-rich duplex to be more stable than a GC-rich duplex of the same length. There has been much speculation regarding the origin of this aberration in sequence-dependent DNA duplex stability, but no clear resolution. Using a combination of molecular dynamics simulations and NMR spectroscopy we demonstrate that choline (2-hydroxy-N,N,N-trimethylethanaminium) and TMA are preferentially localized in the minor groove of DNA duplexes at A·T base pairs and these same ions show less pronounced localization in the major groove compared to what has been demonstrated for alkali and alkali earth metal ions. Furthermore, free energy calculations show that single-stranded GC-rich sequences exhibit more favorable solvation by choline than single-stranded AT-rich sequences. The sequence-specific nature of choline and TMA binding provides a rationale for the enhanced stability of AT-rich sequences when alkyl-ammonium ions are used as the counterions of DNA. Our combined theoretical and experimental study provides one of the most detailed pictures to date of cations localized along DNA in the solution state, and provides insights that go beyond understanding alkyl-ammonium ion binding to DNA. In particular, because choline and TMA bind to DNA in a manner that is found to be distinct from that previously reported for Na(+), K(+), Mg(2+), and Ca(2+), our results reveal the important but underappreciated role that most other cations play in sequence-specific duplex stability.

  9. Theoretical studies of d(A:T)-based parallel-stranded DNA duplexes.

    PubMed

    Cubero, E; Luque, F J; Orozco, M

    2001-12-01

    Poly d(A:T) parallel-stranded DNA duplexes based on the Hoogsteen and reverse Watson-Crick hydrogen bond pairing are studied by means of extensive molecular dynamics (MD) simulations and molecular mechanics coupled to Poisson-Boltzmann (MM-PB/SA) calculations. The structural, flexibility, and reactivity characteristics of Hoogsteen and reverse Watson-Crick parallel duplexes are described from the analysis of the trajectories. Theoretical calculations show that the two parallel duplexes are less stable than the antiparallel Watson-Crick duplex. The difference in stability between antiparallel and parallel duplexes increases steadily as the length of the duplex increases. The reverse Watson-Crick arrangement is slightly more stable than the Hoogsteen duplex, the difference being also increased linearly with the length of the duplex. A subtle balance of intramolecular and solvation terms is responsible for the preference of a given helical structure.

  10. Stability and size of particle pairs in complex plasmas

    SciTech Connect

    Nosenko, V.; Ivlev, A. V.; Kompaneets, R.; Morfill, G.

    2014-11-15

    Particle pairing in a complex plasma was experimentally studied with the emphasis on pair spatial extent and stability. Micron-size particles were suspended in the (pre)sheath area above the lower electrode in a capacitively coupled radio-frequency discharge in argon. They formed vertical pairs due to the ion wakes created by the flow of ions past particles. We discuss the confinement mechanism for the lower particle, resulting from a combination of the wake field and the field of non-uniform sheath. A model of particle pairs is proposed, which provides good description for the dependence of pair size and stability on experimental parameters.

  11. Evaluating the Effect of Ionic Strength on Duplex Stability for PNA Having Negatively or Positively Charged Side Chains

    PubMed Central

    De Costa, N. Tilani S.; Heemstra, Jennifer M.

    2013-01-01

    The enhanced thermodynamic stability of PNA:DNA and PNA:RNA duplexes compared with DNA:DNA and DNA:RNA duplexes has been attributed in part to the lack of electrostatic repulsion between the uncharged PNA backbone and negatively charged DNA or RNA backbone. However, there are no previously reported studies that systematically evaluate the effect of ionic strength on duplex stability for PNA having a charged backbone. Here we investigate the role of charge repulsion in PNA binding by synthesizing PNA strands having negatively or positively charged side chains, then measuring their duplex stability with DNA or RNA at varying salt concentrations. At low salt concentrations, positively charged PNA binds more strongly to DNA and RNA than does negatively charged PNA. However, at medium to high salt concentrations, this trend is reversed, and negatively charged PNA shows higher affinity for DNA and RNA than does positively charged PNA. These results show that charge screening by counterions in solution enables negatively charged side chains to be incorporated into the PNA backbone without reducing duplex stability with DNA and RNA. This research provides new insight into the role of electrostatics in PNA binding, and demonstrates that introduction of negatively charged side chains is not significantly detrimental to PNA binding affinity at physiological ionic strength. The ability to incorporate negative charge without sacrificing binding affinity is anticipated to enable the development of PNA therapeutics that take advantage of both the inherent benefits of PNA and the multitude of charge-based delivery technologies currently being developed for DNA and RNA. PMID:23484047

  12. Robust silver-mediated imidazolo-dC base pairs in metal DNA: dinuclear silver bridges with exceptional stability in double helices with parallel and antiparallel strand orientation.

    PubMed

    Jana, Sunit Kumar; Guo, Xiurong; Mei, Hui; Seela, Frank

    2015-12-18

    A new unprecedented metal-mediated base pair was designed that stabilizes reverse Watson-Crick DNA (parallel strand orientation, ps) as well as canonical Watson-Crick DNA (antiparallel strand orientation, aps). This base pair contains two imidazolo-dC units decorated with furan residues. Tm measurements and spectroscopic studies reveal that each silver-mediated furano-imidazolo-dC forms exceptionally stable duplexes with ps and aps chain orientation. This stability increase by a silver-mediated base pair is the highest reported so far for ps and aps DNA helices. PMID:26463426

  13. Chemical shifts assignments of the archaeal MC1 protein and a strongly bent 15 base pairs DNA duplex in complex.

    PubMed

    Loth, Karine; Landon, Céline; Paquet, Françoise

    2015-04-01

    MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55 in laboratory growth conditions and is structurally unrelated to other DNA-binding proteins. MC1 functions are to shape and to protect DNA against thermal denaturation by binding to it. Therefore, MC1 has a strong affinity for any double-stranded DNA. However, it recognizes and preferentially binds to bent DNA, such as four-way junctions and negatively supercoiled DNA minicircles. Combining NMR data, electron microscopy data, biochemistry, molecular modelisation and docking approaches, we proposed recently a new type of DNA/protein complex, in which the monomeric protein MC1 binds on the concave side of a strongly bent 15 base pairs DNA. We present here the NMR chemical shifts assignments of each partner in the complex, (1)H (15)N MC1 protein and (1)H (13)C (15)N bent duplex DNA, as first step towards the first experimental 3D structure of this new type of DNA/protein complex.

  14. Can copper(II) mediate Hoogsteen base-pairing in a left-handed DNA duplex? A pulse EPR study.

    PubMed

    Santangelo, Maria Grazia; Antoni, Philipp M; Spingler, Bernhard; Jeschke, Gunnar

    2010-02-22

    Pulse EPR spectroscopy is used to investigate possible structural features of the copper(II) ion coordinated to poly(dG-dC).poly(dG-dC) in a frozen aqueous solution, and the structural changes of the polynucleotide induced by the presence of the metal ion. Two different copper species were identified and their geometry explained by a molecular model. According to this model, one species is exclusively coordinated to a single guanine with the N7 nitrogen atom forming a coordinative bond with the copper. In the other species, a guanine and a cytosine form a ternary complex together with the copper ion. A copper crosslink between the N7 of guanine and N3 of cytosine is proposed as the most probable coordination site. Moreover, no evidence was found for an interaction of either copper species with a phosphate group or equatorial water molecules. In addition, circular dichroism (CD) spectroscopy showed that the DNA of the Cu(II)-poly(dG-dC).poly(dG-dC) adducts resembles the left-handed Z-form. These results suggest that metal-mediated Hoogsteen base pairing, as previously proposed for a right-handed DNA duplex, can also occur in a double-stranded left-handed DNA.

  15. Influence of local duplex stability and N6-methyladenine on uracil recognition by mismatch-specific uracil-DNA glycosylase (Mug).

    PubMed

    Valinluck, Victoria; Liu, Pingfang; Burdzy, Artur; Ryu, Junichi; Sowers, Lawrence C

    2002-12-01

    To maintain genomic integrity, DNA repair enzymes continually remove damaged bases and lesions resulting from endogenous and exogenous processes. These repair enzymes must distinguish damaged bases from normal bases to prevent the inadvertent removal of normal bases, which would promote genomic instability. The mechanisms by which this high level of specificity is accomplished are as yet unresolved. One member of the uracil-DNA glycosylase family of repair enzymes, Escherichia coli mismatch-specific uracil-DNA glycosylase (Mug), is reported to distinguish U:G mispairs from U:A base pairs based upon specific contacts with the mispaired guanine after flipping the target uracil out of the duplex. However, recent studies suggest other mechanisms for base selection, including local duplex stability. In this study, we used the modified base N6-methyladenine to probe the effect of local helix perturbation on Mug recognition of uracil. N6-Methyladenine is found in E. coli as part of both the mismatch repair and restriction-modification systems. In its cis isomer, N6-methyladenine destabilizes hydrogen bonding by interfering with pseudo-Watson-Crick base pairing. It is observed that the selection of uracil by Mug is sequence dependent and that uracil residues in sequences of reduced thermostability are preferentially removed. The replacement of adenine by N6-methyladenine increases the frequency of removal of the uracil residue paired opposite the modified adenine. These results are in accord with suggestions that local helix stability is an important determinant of base recognition by some DNA repair enzymes and provide a potential strategy for identifying the sequence location of modified bases in DNA. PMID:12482242

  16. The role of duplex stability for wavelength-shifting fluorescent DNA probes: energy transfer vs. exciton interactions in DNA "traffic lights".

    PubMed

    Barrois, Sebastian; Wörner, Samantha; Wagenknecht, Hans-Achim

    2014-08-01

    Exciton interactions between thiazole orange and thiazole red as nucleotide substitutes in DNA hairpins interfere with efficient energy transfer and fluorescence color change as readout. This interference can be tuned by two structural parameters that control the hairpin duplex stability.

  17. 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.

  18. Kinematic stability of roller pairs in free rolling contact

    NASA Technical Reports Server (NTRS)

    Savage, M.; Loewenthal, S. H.

    1976-01-01

    A set of generalized stability equations was developed for roller pairs in free rolling contact. A symmetric, dual contact model was used. Four possible external contact profiles that possess continuous contacting surfaces were studied. It was found that kinematic stability would be insured if the larger radius of transverse curvature, in absolute value, and the smaller rolling radius both exist on the roller that has the apex of its conical surface outboard of its main body. The stability criteria developed are considered to be useful for assessing axial restraint requirements for a variety of roller mechanisms and in the selection of roller contact geometry for traction drive devices.

  19. Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs

    SciTech Connect

    Patra, Amritraj; Harp, Joel; Pallan, Pradeep S.; Zhao, Linlin; Abramov, Mikhail; Herdewijn, Piet; Egli, Martin

    2012-12-28

    The thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli strain relies on the four building blocks 5-chloro-2'-deoxyuridine (ClU), A, C and G instead of the standard T, A, C, G alphabet [Marlière,P., Patrouix,J., Döring,V., Herdewijn,P., Tricot,S., Cruveiller,S., Bouzon,M. and Mutzel,R. (2011) Chemical evolution of a bacterium’s genome. Angew. Chem. Int. Ed., 50, 7109–7114]. The residual fraction of T in the DNA of adapted bacteria was <2% and the switch from T to ClU was accompanied by a massive number of mutations, including >1500 A to G or G to A transitions in a culture. The former is most likely due to wobble base pairing between ClU and G, which may be more common for ClU than T. To identify potential changes in the geometries of base pairs and duplexes as a result of replacement of T by ClU, we determined four crystal structures of a B-form DNA dodecamer duplex containing ClU:A or ClU:G base pairs. The structures reveal nearly identical geometries of these pairs compared with T:A or T:G, respectively, and no consequences for stability and cleavage by an endonuclease (EcoRI). The lack of significant changes in the geometry of ClU:A and ClU:G base pairs relative to the corresponding native pairs is consistent with the sustained unlimited self-reproduction of E. coli strains with virtually complete T→ClU genome substitution.

  20. Netropsin . dG-dG-dA-dA-dT-dT-dC-dC complex. Antibiotic binding at adenine . thymine base pairs in the minor groove of the self-complementary octanucleotide duplex.

    PubMed

    Patel, D J

    1979-09-01

    The structure of the netropsin . dG-dG-dA-dA-dT-dT-dC-dC complex (one antibiotic molecule/self-complementary octanucleodide duplex) and its dynamics as a function of temperature have been monitored by the nuclear magnetic resonances of the Watson-Crick protons, the nonexchangeable base and sugar protons and the backbone phosphates. The antibiotic forms a complex with the nucleic acid duplex at the dA . dT-containing tetranucleotide segment dA-dA-dT-dT, with slow migration amongst potential binding sites at low temperature. The downfield shifts in the exchangeable protons of netropsin on complex formation demonstrate the contributions of hydrogen-bonding interactions between the antibiotic and the nucleic acid to the stability of the complex. Complex formation results in changes in the glycosidic torsion angles of both thymidine residues and one deoxyadenosine residue as monitored by chemical shift changes in the thymine C-6 and adenine C-8 protons. The close proximity of the pyrrole rings of the antibiotic and the base-pair edges in the minor groove is manifested in the downfield shifts (0.3--0.5 ppm) of the pyrrole C-3 protons of netropsin and one adenine C-2 proton and one thymine N-3 base-pair proton on complex formation. The internucleotide phosphates of the octanucleotide undergo 31P chemical shift changes on addition of netropsin and these may reflect, in part, contributions from electrostatic interactions between the charged ends of the antibiotic and the backbone phosphates of the nucleic acid.

  1. Pairing geometry of the hydrophobic thymine analogue 2,4-difluorotoluene in duplex DNA as analyzed by X-ray crystallography.

    PubMed

    Pallan, Pradeep S; Egli, Martin

    2009-09-01

    Certain DNA polymerases (pols) were found to efficiently insert A opposite the hydrophobic T isostere 2,4-difluorotoluene (F) and vice versa, resulting in the widely held belief that some pols rely on shape rather than H-bonding for accurate replication. Using X-ray crystallography we have analyzed the geometry of F:A pairs in duplex DNA and observed a distance between fluorine and the exocyclic amino group of A that is consistent with a H-bond, thus challenging the assumption that the F analogue is unable to engage in H-bonding as well as the steric hypothesis of DNA replication. Therefore, shape and H-bonding are inherently related, and steric constraints at a pol active site, or conferred by stacking or the DNA backbone conformation, may enable H-bonding by F. PMID:19685868

  2. The Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography

    PubMed Central

    Pallan, Pradeep S.; Egli, Martin

    2009-01-01

    Certain DNA polymerases were found to efficiently insert A opposite the hydrophobic T isostere 2,4-difluorotoluene (F) and vice versa, resulting in the widely held belief that some pols rely on shape rather than H-bonding for accurate replication. Using X-ray crystallography we have analyzed the geometry of F:A pairs in duplex DNA and observed a distance between fluorine and the exocyclic amino group of A that is consistent with a H-bond, thus challenging the assumption that the F analog is unable to engage in H-bonding as well as the steric hypothesis of DNA replication. Therefore, shape and H-bonding are inherently related and steric constraints at a pol active site, or conferred by stacking or the DNA backbone conformation may enable H-bonding by F. PMID:19685868

  3. 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.

  4. 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

  5. Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability

    PubMed Central

    Knowles, D. B.; LaCroix, Andrew S.; Deines, Nickolas F.; Shkel, Irina; Record, M. Thomas

    2011-01-01

    Small solutes affect protein and nucleic acid processes because of favorable or unfavorable chemical interactions of the solute with the biopolymer surface exposed or buried in the process. Large solutes also exclude volume and affect processes where biopolymer molecularity and/or shape changes. Here, we develop an analysis to separate and interpret or predict excluded volume and chemical effects of a flexible coil polymer on a process. We report a study of the concentration-dependent effects of the full series from monomeric to polymeric PEG on intramolecular hairpin and intermolecular duplex formation by 12-nucleotide DNA strands. We find that chemical effects of PEG on these processes increase in proportion to the product of the amount of DNA surface exposed on melting and the amount of PEG surface that is accessible to this DNA, and these effects are completely described by two interaction terms that quantify the interactions between this DNA surface and PEG end and interior groups. We find that excluded volume effects, once separated from these chemical effects, are quantitatively described by the analytical theory of Hermans, which predicts the excluded volume between a flexible polymer and a rigid molecule. From this analysis, we show that at constant concentration of PEG monomer, increasing PEG size increases the excluded volume effect but decreases the chemical interaction effect, because in a large PEG coil a smaller fraction of the monomers are accessible to the DNA. Volume exclusion by PEG has a much larger effect on intermolecular duplex formation than on intramolecular hairpin formation. PMID:21742980

  6. Ligand-Induced Stabilization of a Duplex-like Architecture Is Crucial for the Switching Mechanism of the SAM-III Riboswitch.

    PubMed

    Suresh, Gorle; Srinivasan, Harini; Nanda, Shivani; Priyakumar, U Deva

    2016-06-21

    Riboswitches are structured RNA motifs that control gene expression by sensing the concentrations of specific metabolites and make up a promising new class of antibiotic targets. S-Adenosylmethionine (SAM)-III riboswitch, mainly found in lactic acid bacteria, is involved in regulating methionine and SAM biosynthetic pathways. SAM-III riboswitch regulates the gene expression by switching the translation process on and off with respect to the absence and presence of the SAM ligand, respectively. In this study, an attempt is made to understand the key conformational transitions involved in ligand binding using atomistic molecular dynamics (MD) simulations performed in an explicit solvent environment. G26 is found to recognize the SAM ligand by forming hydrogen bonds, whereas the absence of the ligand leads to opening of the binding pocket. Consistent with experimental results, the absence of the SAM ligand weakens the base pairing interactions between the nucleobases that are part of the Shine-Dalgarno (SD) and anti-Shine-Dalgarno (aSD) sequences, which in turn facilitates recognition of the SD sequence by ribosomes. Detailed analysis reveals that a duplex-like structure formed by nucleotides from different parts of the RNA and the adenine base of the ligand is crucial for the stability of the completely folded state in the presence of the ligand. Previous experimental studies have shown that the SAM-III riboswitch exists in equilibrium between the unfolded and partially folded states in the absence of the ligand, which completely folds upon binding of the ligand. Comparison of the results presented here to the available experimental data indicates the structures obtained using the MD simulations resemble the partially folded state. Thus, this study provides a detailed understanding of the fully and partially folded structures of the SAM-III riboswitch in the presence and absence of the ligand, respectively. This study hypothesizes a dual role for the SAM ligand

  7. Hybridization accompanying FRET event in labeled natural nucleoside-unnatural nucleoside containing chimeric DNA duplexes.

    PubMed

    Bag, Subhendu Sekhar; Das, Suman K; Pradhan, Manoj Kumar; Jana, Subhashis

    2016-09-01

    Förster resonance energy transfer (FRET) is a highly efficient strategy in illuminating the structures, structural changes and dynamics of DNA, proteins and other biomolecules and thus is being widely utilized in studying such phenomena, in designing molecular/biomolecular probes for monitoring the hybridization event of two single stranded DNA to form duplex, in gene detection and in many other sensory applications in chemistry, biology and material sciences. Moreover, FRET can give information about the positional status of chromophores within the associated biomolecules with much more accuracy than other methods can yield. Toward this end, we want to report here the ability of fluorescent unnatural nucleoside, triazolylphenanthrene ((TPhen)BDo) to show FRET interaction upon hybridization with fluorescently labeled natural nucleosides, (Per)U or (OxoPy)U or (Per)U, forming two stable chimeric DNA duplexes. The pairing selectivity and the thermal duplex stability of the chimeric duplexes are higher than any of the duplexes with natural nucleoside formed. The hybridization results in a Förster resonance energy transfer (FRET) from donor triazolylphenanthrene of (TPhen)BDo to acceptor oxopyrene of (OxoPy)U and/or to perylene chromophore of (Per)U, respectively, in two chimeric DNA duplexes. Therefore, we have established the FRET process in two chimeric DNA duplexes wherein a fluorescently labeled natural nucleoside ((OxoPy)U or (Per)U) paired against an unnatural nucleoside ((TPhen)BDo) without sacrificing the duplex stability and B-DNA conformation. The hybridization accompanying FRET event in these classes of interacting fluorophores is new. Moreover, there is no report of such designed system of chimeric DNA duplex. Our observed phenomenon and the design can potentially be exploited in designing more of such efficient FRET pairs for useful application in the detection and analysis of biomolecular interactions and in material science application. PMID:27498231

  8. Hybridization accompanying FRET event in labeled natural nucleoside-unnatural nucleoside containing chimeric DNA duplexes.

    PubMed

    Bag, Subhendu Sekhar; Das, Suman K; Pradhan, Manoj Kumar; Jana, Subhashis

    2016-09-01

    Förster resonance energy transfer (FRET) is a highly efficient strategy in illuminating the structures, structural changes and dynamics of DNA, proteins and other biomolecules and thus is being widely utilized in studying such phenomena, in designing molecular/biomolecular probes for monitoring the hybridization event of two single stranded DNA to form duplex, in gene detection and in many other sensory applications in chemistry, biology and material sciences. Moreover, FRET can give information about the positional status of chromophores within the associated biomolecules with much more accuracy than other methods can yield. Toward this end, we want to report here the ability of fluorescent unnatural nucleoside, triazolylphenanthrene ((TPhen)BDo) to show FRET interaction upon hybridization with fluorescently labeled natural nucleosides, (Per)U or (OxoPy)U or (Per)U, forming two stable chimeric DNA duplexes. The pairing selectivity and the thermal duplex stability of the chimeric duplexes are higher than any of the duplexes with natural nucleoside formed. The hybridization results in a Förster resonance energy transfer (FRET) from donor triazolylphenanthrene of (TPhen)BDo to acceptor oxopyrene of (OxoPy)U and/or to perylene chromophore of (Per)U, respectively, in two chimeric DNA duplexes. Therefore, we have established the FRET process in two chimeric DNA duplexes wherein a fluorescently labeled natural nucleoside ((OxoPy)U or (Per)U) paired against an unnatural nucleoside ((TPhen)BDo) without sacrificing the duplex stability and B-DNA conformation. The hybridization accompanying FRET event in these classes of interacting fluorophores is new. Moreover, there is no report of such designed system of chimeric DNA duplex. Our observed phenomenon and the design can potentially be exploited in designing more of such efficient FRET pairs for useful application in the detection and analysis of biomolecular interactions and in material science application.

  9. Increasing the Stability of DNA:RNA Duplexes by Introducing Stacking Phenyl-Substituted Pyrazole, Furan, and Triazole Moieties in the Major Groove.

    PubMed

    Hornum, Mick; Kumar, Pawan; Podsiadly, Patricia; Nielsen, Poul

    2015-10-01

    Consecutive incorporations of our previously published thymidine analogue, 5-(1-phenyl-1H-1,2,3-triazol-4-yl)-2'-deoxyuridine monomer W in oligonucleotides, has demonstrated significant duplex-stabilizing properties due to its efficient staking properties in the major groove of DNA:RNA duplexes. The corresponding 2'-deoxycytidine analogue is not as well-accommodated in duplexes, however, due to its clear preference for the ring-flipped coplanar conformation. In our present work, we have used ab initio calculations to design two new building blocks, 5-(5-phenylfuran-2-yl)-2'-deoxycytidine monomer Y and 5-(1-phenyl-1H-pyrazol-3-yl)-2'-deoxycytidine monomer Z, that emulate the conformation of W. These monomers were synthesized by Suzuki-Miyaura couplings, and the pyrazole moiety was obtained in a cycloaddition from N-phenylsydnone. We show that the novel analogues Y and Z engage in efficient stacking either with themselves or with W due to a better overlap of the aromatic moieties. Importantly, we demonstrate that this translates into very thermally stable DNA:RNA duplexes, thus making Y and especially Z good candidates for improving the binding affinities of oligonucleotide-based therapeutics. Since we now have both efficiently stacking T and C analogues in hand, any purine rich stretch can be effectively targeted using these simple analogues. Notably, we show that the introduction of the aromatic rings in the major groove does not significantly change the helical geometry. PMID:26334359

  10. Sequence specificity of mutagen-nucleic acid complexes in solution: Intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes

    PubMed Central

    Patel, Dinshaw J.; Canuel, Lita L.

    1977-01-01

    The complex formed between the mutagen proflavine and the dC-dC-dG-dG and dG-dG-dC-dC self-complementary tetranucleotide duplexes has been monitored by proton high resolution nuclear magnetic resonance spectroscopy in 0.1 M phosphate solution at high nucleotide/drug ratios. The large upfield shifts (0.5 to 0.85 ppm) observed at all the proflavine ring nonexchangeable protons on complex formation are consistent with intercalation of the mutagen between base pairs of the tetranucleotide duplex. We have proposed an approximate overlap geometry between the proflavine ring and nearest neighbor base pairs at the intercalation site from a comparison between experimental shifts and those calculated for various stacking orientations. We have compared the binding of actinomycin D, propidium diiodide, and proflavine to self-complementary tetranucleotide sequences dC-dC-dG-dG and dG-dG-dC-dC by UV absorbance changes in the drug bands between 400 and 500 nm. Actinomycin D exhibits a pronounced specificity for sequences with dG-dC sites (dG-dG-dC-dC), while propidium diiodide and proflavine exhibit a specificity for sequences with dC-dG sites (dC-dC-dG-dG). Actinomycin D binds more strongly than propidium diiodide and proflavine to dC-dG-dC-dG (contains dC-dG and dG-dC binding sites), indicative of the additional stabilization from hydrogen bonding and hydrophobic interactions between the pentapeptide lactone rings of actinomycin D and the base pair edges and sugar-phosphate backbone of the tetranucleotide duplex. PMID:268613

  11. Sequence specificity of mutagen-nucleic acid complexes in solution: intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes.

    PubMed

    Patel, D J; Canuel, L L

    1977-07-01

    The complex formed between the mutagen proflavine and the dC-dC-dG-dG and dG-dG-dC-dC self-complementary tetranucleotide duplexes has been monitored by proton high resolution nuclear magnetic resonance spectroscopy in 0.1 M phosphate solution at high nucleotide/drug ratios. The large upfield shifts (0.5 to 0.85 ppm) observed at all the proflavine ring nonexchangeable protons on complex formation are consistent with intercalation of the mutagen between base pairs of the tetranucleotide duplex. We have proposed an approximate overlap geometry between the proflavine ring and nearest neighbor base pairs at the intercalation site from a comparison between experimental shifts and those calculated for various stacking orientations. We have compared the binding of actinomycin D, propidium diiodide, and proflavine to self-complementary tetranucleotide sequences dC-dC-dG-dG and dG-dG-dC-dC by UV absorbance changes in the drug bands between 400 and 500 nm. Actinomycin D exhibits a pronounced specificity for sequences with dG-dC sites (dG-dG-dC-dC), while propidium diiodide and proflavine exhibit a specificity for sequences with dC-dG sites (dC-dC-dG-dG). Actinomycin D binds more strongly than propidium diiodide and proflavine to dC-dG-dC-dG (contains dC-dG and dG-dC binding sites), indicative of the additional stabilization from hydrogen bonding and hydrophobic interactions between the pentapeptide lactone rings of actinomycin D and the base pair edges and sugar-phosphate backbone of the tetranucleotide duplex.

  12. Silver Ions in Non-canonical DNA Base Pairs: Metal-Mediated Mismatch Stabilization of 2'-Deoxyadenosine and 7-Deazapurine Derivatives with 2'-Deoxycytidine and 2'-Deoxyguanosine.

    PubMed

    Yang, Haozhe; Seela, Frank

    2016-09-01

    Novel silver-mediated dA-dC, dA*-dC, and dA*-dG base pairs were formed in a natural DNA double helix environment (dA* denotes 7-deaza-dA, 7-deaza-7-iodo-dA, and 7-cyclopropyl-7-deaza-dA). 7-Deazapurine nucleosides enforce silver ion binding and direct metal-mediated base pair formation to their Watson-Crick face. New phosphoramidites were prepared from 7-deaza-dA, 7-deaza-7-iodo-dA, and 7-cyclopropyl-7-deaza-dA, which contain labile isobutyryl protecting groups. Solid-phase synthesis furnished oligonucleotides that contain mismatches in near central positions. Increased thermal stabilities (higher Tm values) were observed for oligonucleotide duplexes with non-canonical dA*-dC and dA-dC pairs in the presence of silver ions. The stability of the silver-mediated base pairs was pH dependent. Silver ion binding was not observed for the dA-dG mismatch but took place when mismatches were formed between 7-deazaadenine and guanine. The specific binding of silver ions was confirmed by stoichiometric UV titration experiments, which proved that one silver ion is captured by one mismatch. The stability increase of canonical DNA mismatches might have an impact on cellular DNA repair. PMID:27492501

  13. Pyrrolo-dC Metal-Mediated Base Pairs in the Reverse Watson-Crick Double Helix: Enhanced Stability of Parallel DNA and Impact of 6-Pyridinyl Residues on Fluorescence and Silver-Ion Binding.

    PubMed

    Yang, Haozhe; Mei, Hui; Seela, Frank

    2015-07-01

    Reverse Watson-Crick DNA with parallel-strand orientation (ps DNA) has been constructed. Pyrrolo-dC (PyrdC) nucleosides with phenyl and pyridinyl residues linked to the 6 position of the pyrrolo[2,3-d]pyrimidine base have been incorporated in 12- and 25-mer oligonucleotide duplexes and utilized as silver-ion binding sites. Thermal-stability studies on the parallel DNA strands demonstrated extremely strong silver-ion binding and strongly enhanced duplex stability. Stoichiometric UV and fluorescence titration experiments verified that a single (2py) PyrdC-(2py) PyrdC pair captures two silver ions in ps DNA. A structure for the PyrdC silver-ion base pair that aligns 7-deazapurine bases head-to-tail instead of head-to-head, as suggested for canonical DNA, is proposed. The silver DNA double helix represents the first example of a ps DNA structure built up of bidentate and tridentate reverse Watson-Crick base pairs stabilized by a dinuclear silver-mediated PyrdC pair.

  14. Pyrrolo-dC Metal-Mediated Base Pairs in the Reverse Watson-Crick Double Helix: Enhanced Stability of Parallel DNA and Impact of 6-Pyridinyl Residues on Fluorescence and Silver-Ion Binding.

    PubMed

    Yang, Haozhe; Mei, Hui; Seela, Frank

    2015-07-01

    Reverse Watson-Crick DNA with parallel-strand orientation (ps DNA) has been constructed. Pyrrolo-dC (PyrdC) nucleosides with phenyl and pyridinyl residues linked to the 6 position of the pyrrolo[2,3-d]pyrimidine base have been incorporated in 12- and 25-mer oligonucleotide duplexes and utilized as silver-ion binding sites. Thermal-stability studies on the parallel DNA strands demonstrated extremely strong silver-ion binding and strongly enhanced duplex stability. Stoichiometric UV and fluorescence titration experiments verified that a single (2py) PyrdC-(2py) PyrdC pair captures two silver ions in ps DNA. A structure for the PyrdC silver-ion base pair that aligns 7-deazapurine bases head-to-tail instead of head-to-head, as suggested for canonical DNA, is proposed. The silver DNA double helix represents the first example of a ps DNA structure built up of bidentate and tridentate reverse Watson-Crick base pairs stabilized by a dinuclear silver-mediated PyrdC pair. PMID:26096946

  15. Hydrophobic, Non-Hydrogen-Bonding Bases and Base Pairs in DNA

    PubMed Central

    Schweitzer, Barbara A.; Kool, Eric T.

    2009-01-01

    We report the properties of hydrophobic isosteres of pyrimidines and purines in synthetic DNA duplexes. Phenyl nucleosides 1 and 2 are nonpolar isosteres of the natural thymidine nucleoside, and indole nucleoside 3 is an analog of the complementary purine 2-aminodeoxyadenosine. The nucleosides were incorporated into synthetic oligodeoxynucleotides and were paired against each other and against the natural bases. Thermal denaturation experiments were used to measure the stabilities of the duplexes at neutral pH. It is found that the hydrophobic base analogs are nonselective in pairing with the four natural bases but selective for pairing with each other rather than with the natural bases. For example, compound 2 selectively pairs with itself rather than with A, T, G, or C; the magnitude of this selectivity is found to be 6.5–9.3 °C in Tm or 1.5–1.8 kcal/mol in free energy (25 °C). All possible hydrophobic pairing combinations of 1, 2, and 3 were examined. Results show that the pairing affinity depends on the nature of the pairs and on position in the duplex. The highest affinity pairs are found to be the 1–1 and 2–2 self-pairs and the 1–2 heteropair. The best stabilization occurs when the pairs are placed at the ends of duplexes rather than internally; the internal pairs may be destabilized by imperfect steric mimicry which leads to non-ideal duplex structure. In some cases the hydrophobic pairs are significantly stabilizing to the DNA duplex; for example, when situated at the end of a duplex, the 1–1 pair is more stabilizing than a T–A pair. When situated internally, the affinity of the 1–1 pair is the same as, or slightly better than, the analogous T–T mismatch pair, which is known to have two hydrogen bonds. The studies raise the possibility that hydrogen bonds may not always be required for the formation of stable duplex DNA-like structure. In addition, the results point out the importance of solvation and desolvation in natural base pairing

  16. Multi-quasiparticle isomers near stability and reduced pairing

    SciTech Connect

    Dracoulis, G.D.

    1996-12-31

    The proximity of high-{Omega} orbitals near both proton and neutron Fermi surfaces in nuclei near Z = 74 and N = 104 results in high-K states competing with collective rotation of low-seniority configurations to generate the yrast line. In favorable situations it is possible to observe both the intrinsic states and associated rotational bands. The band properties allow characterization of the configurations and evaluation of orbital and seniority-dependent effects, including pairing reduction and consequent loss of nuclear superfluidity.

  17. Sequence effects of aminofluorene-modified DNA duplexes: thermodynamic and circular dichroism properties

    PubMed Central

    Meneni, Srinivasa Rao; D'Mello, Rhijuta; Norigian, Gregory; Baker, Gregory; Gao, Lan; Chiarelli, M. Paul; Cho, Bongsup P.

    2006-01-01

    Circular dichroism (CD) and UV-melting experiments were conducted with 16 oligodeoxynucleotides modified by the carcinogen 2-aminofluorene, whose sequence around the lesion was varied systematically [d(CTTCTNG[AF]NCCTC), N = G, A, C, T], to gain insight into the factors that determine the equilibrium between base-displaced stacked (S) and external B-type (B) duplex conformers. Differing stabilities among the duplexes can be attributed to different populations of S and B conformers. The AF modification always resulted in sequence-dependent thermal (Tm) and thermodynamic (−ΔG°) destabilization. The population of B-type conformers derived from eight selected duplexes (i.e. -AG*N- and -CG*N-) was inversely proportional to the −ΔG° and Tm values, which highlights the importance of carcinogen/base stacking in duplex stabilization even in the face of disrupted Watson–Crick base pairing in S-conformation. CD studies showed that the extent of the adduct-induced negative ellipticities in the 290–350 nm range is correlated linearly with −ΔG° and Tm, but inversely with the population of B-type conformations. Taken together, these results revealed a unique interplay between the extent of carcinogenic interaction with neighboring base pairs and the thermodynamic properties of the AF-modified duplexes. The sequence-dependent S/B heterogeneities have important implications in understanding how arylamine–DNA adducts are recognized in nucleotide excision repair. PMID:16449208

  18. Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination.

    PubMed

    Takezawa, Yusuke; Nishiyama, Kotaro; Mashima, Tsukasa; Katahira, Masato; Shionoya, Mitsuhiko

    2015-10-12

    A novel bifacial ligand-bearing nucleobase, 5-hydroxyuracil (U(OH) ), which forms both a hydrogen-bonded base pair (U(OH) -A) and a metal-mediated base pair (U(OH) -M-U(OH) ) has been developed. The U(OH) -M-U(OH) base pairs were quantitatively formed in the presence of lanthanide ions such as Gd(III) when U(OH) -U(OH) pairs were consecutively incorporated into DNA duplexes. This result established metal-assisted duplex stabilization as well as DNA-templated assembly of lanthanide ions. Notably, a duplex possessing U(OH) -A base pairs was destabilized by addition of Gd(III) ions. This observation suggests that the hybridization behaviors of the U(OH) -containing DNA strands are altered by metal complexation. Thus, the U(OH) nucleobase with a bifacial base-pairing property holds great promise as a component for metal-responsive DNA materials.

  19. Structure and thermodynamic insights on acetylaminofluorene-modified deletion DNA duplexes as models for frameshift mutagenesis

    PubMed Central

    Sandineni, Anusha; Lin, Bin; MacKerell, Alexander D.; Cho, Bongsup P.

    2013-01-01

    2-Acetylaminofluorene (AAF) is a prototype arylamine carcinogen that forms C8-substituted dG-AAF and dG-AF as the major DNA lesions. The bulky N-acetylated dG-AAF lesion can induce various frameshift mutations depending on the base sequence around the lesion. We hypothesized that the thermodynamic stability of bulged-out slipped mutagenic intermediates (SMIs) is directly related to deletion mutations. The objective of the present study was to probe the structural/conformational basis of various dG-AAF–induced SMIs formed during a translesion synthesis. We performed spectroscopic, thermodynamic, and molecular dynamics studies of several AAF-modified 16-mer model DNA duplexes, including fully paired and −1, −2, and −3 deletion duplexes of the 5′-CTCTCGATG[FAAF]CCATCAC-3′ sequence and an additional −1 deletion duplex of the 5′-CTCTCGGCG[FAAF]CCATCAC-3′ NarI sequence. Modified deletion duplexes existed in a mixture of external B and stacked S conformers, with the population of the S conformer being ‘GC’ −1 (73%) > ‘AT’ −1 (72%) > full (60%) > −2 (55%) > −3 (37%). Thermodynamic stability was in the order of −1 deletion > −2 deletion > fully paired > −3 deletion duplexes. These results indicate that the stacked S-type conformer of SMIs are thermodynamically more stable than the conformationally flexible external B conformer. Results from the molecular dynamics simulations indicate perturbation of base stacking dominate the relative stability along with contributions from bending, duplex dynamics, solvation effects that are important in specific cases. Taken together, these results support a hypothesis that the conformational and thermodynamic stabilities of the SMIs are critical determinants for the induction of frameshift mutations. PMID:23688347

  20. Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

    PubMed Central

    Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

    2014-01-01

    The instability of Hoogsteen base pairs relative to Watson–Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson–Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson–Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo. PMID:24399194

  1. Structures and Energetics of Four Adjacent G·U Pairs That Stabilize an RNA Helix.

    PubMed

    Gu, Xiaobo; Mooers, Blaine H M; Thomas, Leonard M; Malone, Joshua; Harris, Steven; Schroeder, Susan J

    2015-10-22

    Consecutive G·U base pairs inside RNA helices can be destabilizing, while those at the ends of helices are thermodynamically stabilizing. To determine if this paradox could be explained by differences in base stacking, we determined the high-resolution (1.32 Å) crystal structure of (5'-GGUGGCUGUU-3')2 and studied three sequences with four consecutive terminal G·U pairs by NMR spectroscopy. In the crystal structure of (5'-GGUGGCUGUU-3')2, the helix is overwound but retains the overall features of A-form RNA. The penultimate base steps at each end of the helix have high base overlap and contribute to the unexpectedly favorable energetic contribution for the 5'-GU-3'/3'-UG-5' motif in this helix position. The balance of base stacking and helical twist contributes to the positional dependence of G·U pair stabilities. The energetic stabilities and similarity to A-form RNA helices suggest that consecutive G·U pairs would be recognized by RNA helix binding proteins, such as Dicer and Ago. Thus, these results will aid future searches for target sites of small RNAs in gene regulation. PMID:26425937

  2. PNA beacons for duplex DNA.

    PubMed

    Kuhn, H; Demidov, V V; Gildea, B D; Fiandaca, M J; Coull, J C; Frank-Kamenetskii, M D

    2001-08-01

    We report here on the hybridization of peptide nucleic acid (PNA)-based molecular beacons (MB) directly to duplex DNA sites locally exposed by PNA openers. Two stemless PNA beacons were tested, both featuring the same recognition sequence and fluorophore-quencher pair (Fluorescein and DABCYL, respectively) but differing in arrangement of these groups and net electrostatic charge. It was found that one PNA beacon rapidly hybridized, with the aid of openers, to its complementary target within duplex DNA at ambient conditions via formation of a PD-like loop. In contrast, the other PNA beacon bound more slowly to preopened duplex DNA target and only at elevated temperatures, although it readily hybridized to single-stranded (ss) DNA target. Besides a higher selectivity of hybridization provided by site-specific PNA openers, we expect this approach to be very useful in those MB applications when denaturation of the duplex DNA analytes is unfavorable or undesirable. Furthermore, we show that PNA beacons are advantageous over DNA beacons for analyzing unpurified/nondeproteinized DNA samples. This feature of PNA beacons and our innovative hybridization strategy may find applications in emerging fluorescent DNA diagnostics.

  3. Ion pair stabilization effects on a series of procaine structural analogs.

    PubMed

    Malvezzi, Alberto; do Amaral, Antonia T

    2010-12-23

    In this work, a series of 10 structural procaine analogs have been synthesized in order to investigate the structural features affecting the stability of ion pair formation and its influence on the lipophilicity of ionizable compounds. The structural variation within this series was focused on the terminal nitrogen substituents and on the intermediate chain linkage nature. The hydrophobic parameters logP(n) and logP(i) (partition coefficient of the neutral and ionic species, respectively), as well as the ionization constants pK(a) and pK(a)(oct), were obtained from logD-pH profiles measured at pH values ranging from 2 to 12. The difference between logP(i) and logP(n) values (i.e. difflogP) of each prepared compound was considered a measure of the stability of ion pair formation. In this set, the difflogP values varied nearly over one log unit, ranging from -2.40 to -3.37. It has been observed that the presence of hydrogen bonding groups (especially donor) and low steric hindrance around the terminal amine ionizable group increases the relative lipophilicity of the ionic species as compared to the corresponding neutral species. These results were interpreted as due to the increased stability of ion pairs of the compounds bearing these structural features.

  4. The Effect of Small Cosolutes that Mimic Molecular Crowding Conditions on the Stability of Triplexes Involving Duplex DNA

    PubMed Central

    Aviñó, Anna; Mazzini, Stefania; Gargallo, Raimundo; Eritja, Ramon

    2016-01-01

    Triplex stability is studied in crowding conditions using small cosolutes (ethanol, acetonitrile and dimethylsulfoxide) by ultraviolet (UV), circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopies. The results indicate that the triplex is formed preferentially when the triplex forming oligonucleotide (TFO) is RNA. In addition, DNA triplexes (D:D·D) are clearly less stable in cosolute solutions while the stability of the RNA triplexes (R:D·D) is only slightly decreased. The kinetic of triplex formation with RNA-TFO is slower than with DNA-TFO and the thermal stability of the triplex is increased with the salt concentration in EtOH-water solutions. Accordingly, RNA could be considered a potential molecule to form a stable triplex for regulatory purposes in molecular crowding conditions. PMID:26861295

  5. Conformational stability of fibrillar amyloid-beta oligomers via protofilament pair formation - a systematic computational study.

    PubMed

    Kahler, Anna; Sticht, Heinrich; Horn, Anselm H C

    2013-01-01

    Amyloid-[Formula: see text] (A[Formula: see text]) oligomers play a crucial role in Alzheimer's disease due to their neurotoxic aggregation properties. Fibrillar A[Formula: see text] oligomerization can lead to protofilaments and protofilament pairs via oligomer elongation and oligomer association, respectively. Small fibrillar oligomers adopt the protofilament topology, whereas fibrils contain at least protofilament pairs. To date, the underlying growth mechanism from oligomers to the mature fibril still remains to be elucidated. Here, we performed all-atom molecular dynamics simulations in explicit solvent on single layer-like protofilaments and fibril-like protofilament pairs of different size ranging from the tetramer to the 48-mer. We found that the initial U-shaped topology per monomer is maintained over time in all oligomers. The observed deviations of protofilaments from the starting structure increase significantly with size due to the twisting of the in-register parallel [Formula: see text]-sheets. This twist causes long protofilaments to be unstable and leads to a breakage. Protofilament pairs, which are stabilized by a hydrophobic interface, exhibit more fibril-like properties such as the overall structure and the twist angle. Thus, they can act as stable conformational templates for further fibril growth. Key properties like the twist angle, shape complementarity, and energetics show a size-dependent behavior so that small oligomers favor the protofilament topology, whereas large oligomers favor the protofilament pair topology. The region for this conformational transition is at the size of approximately twelve A[Formula: see text] monomers. From that, we propose the following growth mechanism from A[Formula: see text] oligomers to fibrils: (1) elongation of short protofilaments; (2) breakage of large protofilaments; (3) formation of short protofilament pairs; and (4) elongation of protofilament pairs.

  6. Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy.

    PubMed

    Dairaku, Takenori; Furuita, Kyoko; Sato, Hajime; Šebera, Jakub; Nakashima, Katsuyuki; Kondo, Jiro; Yamanaka, Daichi; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Sychrovský, Vladimír; Kojima, Chojiro; Tanaka, Yoshiyuki

    2016-09-01

    The structure of an Ag(I) -mediated cytosine-cytosine base pair, C-Ag(I) -C, was determined with NMR spectroscopy in solution. The observation of 1-bond (15) N-(109) Ag J-coupling ((1) J((15) N,(109) Ag): 83 and 84 Hz) recorded within the C-Ag(I) -C base pair evidenced the N3-Ag(I) -N3 linkage in C-Ag(I) -C. The triplet resonances of the N4 atoms in C-Ag(I) -C demonstrated that each exocyclic N4 atom exists as an amino group (-NH2 ), and any isomerization and/or N4-Ag(I) bonding can be excluded. The 3D structure of Ag(I) -DNA complex determined with NOEs was classified as a B-form conformation with a notable propeller twist of C-Ag(I) -C (-18.3±3.0°). The (109) Ag NMR chemical shift of C-Ag(I) -C was recorded for cytidine/Ag(I) complex (δ((109) Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C-Ag(I) -C base pair. PMID:27505707

  7. Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy.

    PubMed

    Dairaku, Takenori; Furuita, Kyoko; Sato, Hajime; Šebera, Jakub; Nakashima, Katsuyuki; Kondo, Jiro; Yamanaka, Daichi; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Sychrovský, Vladimír; Kojima, Chojiro; Tanaka, Yoshiyuki

    2016-09-01

    The structure of an Ag(I) -mediated cytosine-cytosine base pair, C-Ag(I) -C, was determined with NMR spectroscopy in solution. The observation of 1-bond (15) N-(109) Ag J-coupling ((1) J((15) N,(109) Ag): 83 and 84 Hz) recorded within the C-Ag(I) -C base pair evidenced the N3-Ag(I) -N3 linkage in C-Ag(I) -C. The triplet resonances of the N4 atoms in C-Ag(I) -C demonstrated that each exocyclic N4 atom exists as an amino group (-NH2 ), and any isomerization and/or N4-Ag(I) bonding can be excluded. The 3D structure of Ag(I) -DNA complex determined with NOEs was classified as a B-form conformation with a notable propeller twist of C-Ag(I) -C (-18.3±3.0°). The (109) Ag NMR chemical shift of C-Ag(I) -C was recorded for cytidine/Ag(I) complex (δ((109) Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C-Ag(I) -C base pair.

  8. Effect of base-pair stability of nearest-neighbor nucleotides on the fidelity of deoxyribonucleic acid synthesis.

    PubMed

    Patten, J E; So, A G; Downey, K M

    1984-04-10

    The influence of the stability of base pairs formed by nearest-neighbor nucleotides on misincorporation frequency has been studied with the large fragment of DNA polymerase I, the alternating DNA copolymers, poly(dI-dC) and poly-(dG-dC), as template-primers, and dGTP, dITP, and dCTP as substrates. We have utilized the difference in thermodynamic stability between the doubly H-bonded I X C base pair and triply H-bonded G X C base pair to examine the effects of base-pair stability of both the "preceding" and the "following" nucleotides on the frequency of insertion of a mismatched nucleotide, as well as on its stable incorporation into polynucleotide. The present studies demonstrate that the stability of the base pairs formed by nearest-neighbor nucleotides affects the frequency of incorporation of noncomplementary nucleotides. Misincorporation frequency is increased when the nearest-neighbor nucleotides form more stable base pairs with the corresponding nucleotides in the template and is decreased when they form less stable base pairs. The stability of the base pair formed by a nucleotide either preceding (5' to) or following (3' to) a misincorporated nucleotide influences misincorporation frequency, but by different mechanisms. The stability of base pairs formed by preceding nucleotides affects the rate of insertion of mismatched nucleotide but does not protect the mismatched nucleotide from removal by the 3' to 5' exonuclease activity. In contrast, the stability of a base pair formed by a following nucleotide determines whether a misincorporated nucleotide is extended or excised by affecting the ability of the enzyme to edit errors of incorporation. PMID:6722115

  9. Effect of the stability of hydrogen-bonded ion pairs with organic amines on transdermal penetration of teriflunomide.

    PubMed

    Xi, Honglei; Cun, Dongmei; Wang, Zhongyan; Shang, Lei; Song, Wenting; Mu, Liwei; Fang, Liang

    2012-10-15

    The aim of this work was to investigate the effect of the stability of hydrogen-bonded ion pairs with organic amines on transdermal penetration of teriflunomide (TEF). Five organic amines, diethylamine (DEtA), triethylamine (TEtA), diethanolamine (DEA), triethanolamine (TEA), and N-(2'-hydroxyethanol)-piperdine (NP), were chosen to form ion pairs with TEF separately, and the passage of each TEF ion pair through the rabbit skin was evaluated in vitro. FTIR and (1)H NMR spectroscopy were performed to confirm the formation of ion pairs between TEF and organic amines in solution. The stability parameter of ion pairs in terms of ion-pair lifetimes (T(life)) was calculated from the NMR data. TEF could form ion pairs with these amines via hydrogen bond. The formation of ion pairs enhanced the percutaneous absorption of TEF except TEF-DEA. It was found that, for most studied organic amines, the longer the ion-pair lifetime, the higher the flux of skin permeation. The stability of TEF ion pairs was a pivotal factor influencing the skin permeation of TEF. PMID:22796174

  10. Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives.

    PubMed

    Cubero, Elena; Aviñó, Anna; de la Torre, Beatriz G; Frieden, Miriam; Eritja, Ramón; Luque, F Javier; González, Carlos; Orozco, Modesto

    2002-03-27

    The structure of parallel-stranded duplexes of DNA-containing a mixture of guanines (G) and adenines (A) is studied by means of molecular dynamics (MD) simulation, as well as NMR and circular dichroism (CD) spectroscopy. Results demonstrate that the structure is based on the Hoogsteen motif rather than on the reverse Watson-Crick one. Molecular dynamics coupled to thermodynamic integration (MD/TI) calculations and melting experiments allowed us to determine the effect of 8-amino derivatives of A and G and of 8-amino-2'-deoxyinosine on the stability of parallel-stranded duplexes. The large stabilization of the parallel-stranded helix upon 8-amino substitution agrees with a Hoogsteen pairing, confirming MD, NMR, and CD data, and suggests new methods to obtain DNA triplexes for antigene and antisense purposes.

  11. Water-like Anomalies and Phase Behavior of a Pair Potential that Stabilizes Diamond.

    PubMed

    Bertolazzo, Andressa A; Kumar, Abhinaw; Chakravarty, Charusita; Molinero, Valeria

    2016-03-01

    Water, silicon, silica, and other liquids that favor tetrahedral order display thermodynamic, dynamic, and structural anomalies in the pressure range in which they form tetrahedrally coordinated crystals. The tetrahedral order in these liquids is induced by anisotropic hydrogen bonding or covalent interactions, or, in ionic melts, by an appropriate size ratio of the ions. Simple isotropic two-length scale models have been extensively used to understand the origin of anomalies in complex liquids. However, single-component isotropic liquids characterized to date generally do not stabilize tetrahedral crystals, and in the few cases that they do, it was found that the liquids do not display anomalies in the region of the tetrahedral crystal. This poses the question of whether it is possible for isotropic pair potentials to display water-like phase behavior and anomalies. In this work, we use molecular dynamics simulations to investigate the phase behavior and the existence and loci of anomalies of a single-component purely repulsive isotropic pair potential that stabilizes diamond in the ground state over a wide range of pressures. We demonstrate that, akin to water, silica, and silicon, the isotropic potential of Marcotte, Stillinger, and Torquato (MST) presents structural, dynamic, and thermodynamic anomalies in the region of stability of the tetrahedral crystal. The regions of anomalies of MST are nested in the T-p plane following the same hierarchy as in silica: the region of diffusional anomalies encloses the region of structural anomalies, which in turn contains the region of thermodynamic anomalies. To our knowledge, MST is the first example of pair potential for which water-like anomalies are associated with the formation of tetrahedral order. PMID:26426477

  12. Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips.

    SciTech Connect

    Fotin, A. V.; Drobyshev, A. L.; Proudnikov, D. Y.; Perov, A. N.; Mirzabekov, A. D.; Center for Mechanistic Biology and Biotechnology; Engelhardt Inst. of Molecular Biology

    1998-03-15

    A microchip method has been developed for massive and parallel thermodynamic analyses of DNA duplexes. Fluorescently labeled oligonucleotides were hybridized with oligonucleotides immobilized in the 100 x 100 x 20 mum gel pads of the microchips. The equilibrium melting curves for all microchip duplexes were measured in real time in parallel for all microchip duplexes. Thermodynamic data for perfect and mismatched duplexes that were obtained using the microchip method directly correlated with data obtained in solution. Fluorescent labels or longer linkers between the gel and the oligonucleotides appeared to have no significant effect on duplex stability. Extending the immobilized oligonucleotides with a four-base mixture from the 3'-end or one or two universal bases (5-nitroindole) from the 3'- and/or 5'- end increased the stabilities of their duplexes. These extensions were applied to increase the stabilities of the duplexes formed with short oligonucleotides in microchips, to significantly lessen the differences in melting curves of the AT- and GC-rich duplexes, and to improve discrimination of perfect duplexes from those containing poorly recognized terminal mismatches. This study explored a way to increase the efficiency of sequencing by hybridization on oligonucleotide microchips.

  13. Fluctuations between stabilizing and destabilizing electrostatic contributions of ion pairs in conformers of the c-Myc-Max leucine zipper.

    PubMed

    Kumar, S; Nussinov, R

    2000-12-01

    In solution proteins often exhibit backbone and side-chain flexibility. Yet electrostatic interactions in proteins are sensitive to motions. Hence, here we study the contribution of ion pairs toward protein stability in a range of conformers which sample the conformational space in solution. Specifically, we focus on the electrostatic contributions of ion pairs to the stability of each of the conformers in the NMR ensemble of the c-Myc-Max leucine zipper and to their average energy minimized structure. We compute the electrostatic contributions of inter- and intra-helical ion pairs and of an ion pair network. We find that the electrostatic contributions vary considerably among the 40 NMR conformers. Each ion pair, and the network, fluctuates between being stabilizing and being destabilizing. This fluctation reflects the variability in the location of the ion pairing residues and in the geometric orientation of these residues, both with respect to each other and with respect to other charged groups in the rest of the protein. Ion pair interactions in the c-Myc-Max leucine zipper in solution depend on the protein conformer which is analyzed. Hence, the overall stabilizing (or destabilizing) contribution of an ion pair is conformer population-dependent. This study indicates that free energy calculations performed using the continuum electrostatics methodology are sensitive to protein conformational details.

  14. Mesophase stabilization in ionic liquid crystals through pairing equally shaped mesogenic cations and anions

    DOE PAGES

    Stappert, Kathrin; Lipinski, Gregor; Kopiec, Gabriel; Spielberg, Eike T.; Mudring, Anja -Verena

    2015-07-23

    The synthesis and properties of a set of novel ionic liquid crystals with congruently shaped cations and anions are reported to check whether pairing mesogenic cations with mesogenic anions leads to a stabilization of a liquid crystalline phase. To that avail 1-alkyl-3-methyl-triazolium cations with an alkyl chain length of 10, 12, and 14 carbon atoms have been combined with p-alkyloxy-benzenesulfonate anions with different alkyl chain lengths (n = 10, 12, and 14). The corresponding triazolium iodides have been synthesized as reference compounds where the cation and anion have strong size and shape mismatch. The mesomorphic behavior of all compounds ismore » studied by differential scanning calorimetry and polarizing optical microscopy. All compounds except 1-methyl-3-decyltriazolium iodide, which qualifies as an ionic liquid, are thermotropic ionic liquid crystals. All other compounds adopt smectic A phases. As a result, a comparison of the thermal phase behavior of the 1-methyl-3-decyltriazolium bromides to the corresponding p-alkoxy-benzensulfonates reveals that definitely the mesophase is stabilized by pairing the rod-shaped 1-alkyl-3-methyltriazolium cation with a rod-like anion of similar size.« less

  15. Mesophase stabilization in ionic liquid crystals through pairing equally shaped mesogenic cations and anions

    SciTech Connect

    Stappert, Kathrin; Lipinski, Gregor; Kopiec, Gabriel; Spielberg, Eike T.; Mudring, Anja -Verena

    2015-07-23

    The synthesis and properties of a set of novel ionic liquid crystals with congruently shaped cations and anions are reported to check whether pairing mesogenic cations with mesogenic anions leads to a stabilization of a liquid crystalline phase. To that avail 1-alkyl-3-methyl-triazolium cations with an alkyl chain length of 10, 12, and 14 carbon atoms have been combined with p-alkyloxy-benzenesulfonate anions with different alkyl chain lengths (n = 10, 12, and 14). The corresponding triazolium iodides have been synthesized as reference compounds where the cation and anion have strong size and shape mismatch. The mesomorphic behavior of all compounds is studied by differential scanning calorimetry and polarizing optical microscopy. All compounds except 1-methyl-3-decyltriazolium iodide, which qualifies as an ionic liquid, are thermotropic ionic liquid crystals. All other compounds adopt smectic A phases. As a result, a comparison of the thermal phase behavior of the 1-methyl-3-decyltriazolium bromides to the corresponding p-alkoxy-benzensulfonates reveals that definitely the mesophase is stabilized by pairing the rod-shaped 1-alkyl-3-methyltriazolium cation with a rod-like anion of similar size.

  16. Electrochemical properties of interstrand cross-linked DNA duplexes labeled with Nile blue.

    PubMed

    Mie, Yasuhiro; Kowata, Keiko; Kojima, Naoshi; Komatsu, Yasuo

    2012-12-11

    DNA molecules have attracted considerable attention as functional materials in various fields such as electrochemical sensors with redox-labeled DNA. However, the recently developed interstrand cross-link (ICL) technique for double-stranded DNA can adequately modify the electronic properties inside the duplex. Hence, the electrochemical investigation of ICL-DNA helps us to understand the electron transfer of redox-labeled DNA at an electrode surface, which would develop useful sensors. In this study, the first insight into this matter is presented. We prepared 17-mer DNA duplexes incorporating Nile blue (NB-DNA) at one end as a redox marker and a disulfide tether at the other end for immobilization onto an electrode. The duplexes were covalently cross-linked by bifunctional cross-linkers that utilize either a propyl or naphthalene residue to replace a base pair. Their electrochemical responses at the electrode surface were compared to evaluate the effect of the ICL on the electron-transfer reactions of the redox-labeled DNA duplexes. A direct transfer of electrons between NB and the electrode was observed for a standard DNA, as previously reported, whereas interstrand cross-linked DNA (CL-DNA) strands showed a decrease in the direct electron-transfer pathway. This is expected to result from constraining the elastic bending/flexibility of the duplex caused by the covalent cross-links. Interestingly, the CL-DNA incorporating naphthalene residues exhibited additional voltammetric peaks derived from DNA-mediated electron transfer (through base π stacking), which was not observed in the mismatched CL-DNA. The present results indicate that the ICL significantly affects electron transfer in the redox-labeled DNA at the electrode and can be an important determinant for electrochemical signaling in addition to its role in stabilizing the duplex structure. PMID:23153070

  17. Neomycin-neomycin dimer: an all-carbohydrate scaffold with high affinity for AT-rich DNA duplexes.

    PubMed

    Kumar, Sunil; Xue, Liang; Arya, Dev P

    2011-05-18

    A dimeric neomycin-neomycin conjugate 3 with a flexible linker, 2,2'-(ethylenedioxy)bis(ethylamine), has been synthesized and characterized. Dimer 3 can selectively bind to AT-rich DNA duplexes with high affinity. Biophysical studies have been performed between 3 and different nucleic acids with varying base composition and conformation by using ITC (isothermal calorimetry), CD (circular dichroism), FID (fluorescent intercalator displacement), and UV (ultraviolet) thermal denaturation experiments. A few conclusions can be drawn from this study: (1) FID assay with 3 and polynucleotides demonstrates the preference of 3 toward AT-rich sequences over GC-rich sequences. (2) FID assay and UV thermal denaturation experiments show that 3 has a higher affinity for the poly(dA)·poly(dT) DNA duplex than for the poly(dA)·2poly(dT) DNA triplex. Contrary to neomycin, 3 destabilizes poly(dA)·2poly(dT) triplex but stabilizes poly(dA)·poly(dT) duplex, suggesting the major groove as the binding site. (3) UV thermal denaturation studies and ITC experiments show that 3 stabilizes continuous AT-tract DNA better than DNA duplexes with alternating AT bases. (4) CD and FID titration studies show a DNA binding site size of 10-12 base pairs/drug, depending upon the structure/sequence of the duplex for AT-rich DNA duplexes. (5) FID and ITC titration between 3 and an intramolecular DNA duplex [d(5'-A(12)-x-T(12)-3'), x = hexaethylene glycol linker] results in a binding stoichiometry of 1:1 with a binding constant ∼10(8) M(-1) at 100 mM KCl. (6) FID assay using 3 and 512 hairpin DNA sequences that vary in their AT base content and placement also show a higher binding selectivity of 3 toward continuous AT-rich than toward DNA duplexes with alternate AT base pairs. (7) Salt-dependent studies indicate the formation of three ion pairs during binding of the DNA duplex d[5'-A(12)-x-T(12)-3'] and 3. (8) ITC-derived binding constants between 3 and DNA duplexes have the following order: AT

  18. Full-duplex optical communication system

    NASA Technical Reports Server (NTRS)

    Shay, Thomas M. (Inventor); Hazzard, David A. (Inventor); Horan, Stephen (Inventor); Payne, Jason A. (Inventor)

    2004-01-01

    A method of full-duplex electromagnetic communication wherein a pair of data modulation formats are selected for the forward and return data links respectively such that the forward data electro-magnetic beam serves as a carrier for the return data. A method of encoding optical information is used wherein right-hand and left-hand circular polarizations are assigned to optical information to represent binary states. An application for an earth to low earth orbit optical communications system is presented which implements the full-duplex communication and circular polarization keying modulation format.

  19. Wobble Pairs of the HDV Ribozyme Play Specific Roles in Stabilization of Active Site Dynamics

    PubMed Central

    Sripathi, Kamali N.; Banáš, Pavel; Reblova, Kamila; Šponer, Jiři; Otyepka, Michal

    2015-01-01

    The hepatitis delta virus (HDV) is the only known human pathogen whose genome contains a catalytic RNA motif (ribozyme). The overall architecture of the HDV ribozyme is that of a double-nested pseudoknot, with two GU pairs flanking the active site. Although extensive studies have shown that mutation of either wobble results in decreased catalytic activity, little work has focused on linking these mutations to specific structural effects on catalytic fitness. Here we use molecular dynamics simulations based on an activated structure to probe the active site dynamics as a result of wobble pair mutations. In both wild-type and mutant ribozymes, the in-line fitness of the active site (as a measure of catalytic proficiency) strongly depends on the presence of a C75(N3H3+)N1(O5′) hydrogen bond, which positions C75 as the general acid for the reaction. Our mutational analyses show that each GU wobble supports catalytically fit conformations in distinct ways; the reverse G25U20 wobble promotes high in-line fitness, high occupancy of the C75(N3H3+)G1(O5′) general-acid hydrogen bond and stabilization of the G1U37 wobble, while the G1U37 wobble acts more locally by stabilizing high in-line fitness and the C75(N3H3+)G1(O5′) hydrogen bond. We also find that stable type I A-minor and P1.1 hydrogen bonding above and below the active site, respectively, prevent local structural disorder from spreading and disrupting global conformation. Taken together, our results define specific, often redundant architectural roles for several structural motifs of the HDV ribozyme active site, expanding the known roles of these motifs within all HDV-like ribozymes and other structured RNAs. PMID:25631765

  20. Role of the Closing Base Pair for d(GCA) Hairpin Stability: Free Energy Analysis and Folding Simulations

    SciTech Connect

    Kannan, Srinivasaraghavan; Zacharias, Martin W.

    2011-06-30

    Hairpin loops belong to the most important structural motifs in folded nucleic acids. The d(GNA) sequence in DNA can form very stable trinucleotide hairpin loops depending, however, strongly on the closing base pair. Replica-exchange molecular dynamics (REMD) were employed to study hairpin folding of two DNA sequences, d(gcGCAgc) and d(cgGCAcg), with the same central loop motif but different closing base pairs starting from singlestranded structures. In both cases, conformations of the most populated conformational cluster at the lowest temperature showed close agreement with available experimental structures. For the loop sequence with the less stable G:C closing base pair, an alternative loop topology accumulated as second most populated conformational state indicating a possible loop structural heterogeneity. Comparative-free energy simulations on induced loop unfolding indicated higher stability of the loop with a C:G closing base pair by 3 kcal mol1 (compared to a G:C closing base pair) in very good agreement with experiment. The comparative energetic analysis of sampled unfolded, intermediate and folded conformational states identified electrostatic and packing interactions as the main contributions to the closing base pair dependence of the d(GCA) loop stability.

  1. Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues

    SciTech Connect

    Leszczynski, Jerzy; Sponer, Judit; Sponer, Jiri; Sumpter, Bobby G; Fuentes-Cabrera, Miguel A; Vazquez-Mayagoitia, Alvaro

    2010-01-01

    Recent experimental studies on the Watson Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH O hydrogen bonds separated by one NH N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the bases and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.

  2. The role of N7 protonation of guanine in determining the structure, stability and function of RNA base pairs.

    PubMed

    Halder, Antarip; Bhattacharya, Sohini; Datta, Ayan; Bhattacharyya, Dhananjay; Mitra, Abhijit

    2015-10-21

    The roles of protonated nucleobases in stabilizing different structural motifs and in facilitating catalytic functions of RNA are well known. Among different polar sites of all the nucleobases, N7 of guanine has the highest protonation propensity at physiological pH. However, unlike other easily protonable sites such as N1 and N3 of adenine or N3 of cytosine, N7 protonation of guanine does not lead to the stabilization of base pairs involving its protonated Hoogsteen edge. It also does not facilitate its participation in any acid-base catalysis process. To explore the possible roles of N7 protonated guanine, we have studied its base pairing potentials involving WatsonCrick and sugar edges, which undergo major charge redistribution upon N7 protonation. We have carried out quantum chemical geometry optimization at the M05-2X/6-311G+(2d,2p) level, followed by interaction energy calculation at the MP2/aug-cc-pVDZ level, along with the analysis of the context of occurrence for selected base pairs involving the sugar edge or the WatsonCrick edge of guanine within a non-redundant set of 167 RNA crystal structures. Our results suggest that, four base pairs - G:C W:W trans, G:rC W:S cis, G:G W:H cis and G:G S:H trans may involve N7 protonated guanine. These base pairs deviate significantly from their respective experimental geometries upon QM optimization, but they retain their experimental geometries if guanine N7 protonation is considered during optimization. Our study also reveals the role of guanine N7 protonation (i) in stabilizing important RNA structural motifs, (ii) in providing a framework for designing pH driven molecular motors and (iii) in providing an alternative strategy to mimic the effect of post-transcriptional changes. PMID:26382322

  3. The stability of calcium chloride ion pairs in aqueous solutions at temperatures between 100 and 360 degree C

    SciTech Connect

    Williams-Jones, A.E. ); Seward, T.M. )

    1989-02-01

    The speciation of calcium in chloride solutions has been investigated between 100 and 360{degree}C by measuring the solubility of AgCl in HCl-CaCl{sub 2} solutions in which chloride varies from 0.3 to 3.0 m and calcium is maintained constant at 0.1 m. Cumulative equilibrium formation constants of calcium chloride ion pairs were evaluated using a non-liner least squares procedure. Association constants of calcium chloride ion pairs from the data at 100{degree}C. However, at 150{degree}C the cumulative formation constants for CaCl{sup +} and CaCl{sup 0}{sub 2} are 0.85 and 1.73, respectively. The stability field for CaCl{sup +} decreases with increasing temperature, whereas that for CaCl{sup 0}{sub 2} increases sharply and at 360{degree}C K{sub 2} is 4.95 {center dot} 10{sup 4}. Higher order calcium chloride ion pairs either do not form or have stability fields too small to be detected by the methods used in this study. The neutral aqueous calcium chloride ion pair CaCl{sup 0}{sub 2} contributes significantly to calcium speciation in intermediate to high salinity hydrothermal solutions: at 250{degree}C, 50 mol percent of the calcium in a 1 m HCl solution occurs as CaCl{sup 0}{sub 2}. The effect of this ion pairing is to increase the pH stability limits and solubilities of calcium-bearing minerals in such solutions.

  4. Duplex tab exhaust nozzle

    NASA Technical Reports Server (NTRS)

    Gutmark, Ephraim Jeff (Inventor); Martens, Steven (nmn) (Inventor)

    2012-01-01

    An exhaust nozzle includes a conical duct terminating in an annular outlet. A row of vortex generating duplex tabs are mounted in the outlet. The tabs have compound radial and circumferential aft inclination inside the outlet for generating streamwise vortices for attenuating exhaust noise while reducing performance loss.

  5. Duplex interrogation by a direct DNA repair protein in search of base damage

    SciTech Connect

    Yi, Chengqi; Chen, Baoen; Qi, Bo; Zhang, Wen; Jia, Guifang; Zhang, Liang; Li, Charles J.; Dinner, Aaron R.; Yang, Cai-Guang; He, Chuan

    2012-08-31

    ALKBH2 is a direct DNA repair dioxygenase guarding the mammalian genome against N{sup 1}-methyladenine, N{sup 3}-methylcytosine and 1,N{sup 6}-ethenoadenine damage. A prerequisite for repair is to identify these lesions in the genome. Here we present crystal structures of human ALKBH2 bound to different duplex DNAs. Together with computational and biochemical analyses, our results suggest that DNA interrogation by ALKBH2 has two previously unknown features: (i) ALKBH2 probes base-pair stability and detects base pairs with reduced stability, and (ii) ALKBH2 does not have nor need a damage-checking site, which is critical for preventing spurious base cleavage for several glycosylases. The demethylation mechanism of ALKBH2 insures that only cognate lesions are oxidized and reversed to normal bases, and that a flipped, non-substrate base remains intact in the active site. Overall, the combination of duplex interrogation and oxidation chemistry allows ALKBH2 to detect and process diverse lesions efficiently and correctly.

  6. Non-nearest-neighbor dependence of stability for group III RNA single nucleotide bulge loops.

    PubMed

    Kent, Jessica L; McCann, Michael D; Phillips, Daniel; Panaro, Brandon L; Lim, Geoffrey F S; Serra, Martin J

    2014-06-01

    Thirty-five RNA duplexes containing single nucleotide bulge loops were optically melted and the thermodynamic parameters for each duplex determined. The bulge loops were of the group III variety, where the bulged nucleotide is either a AG/U or CU/G, leading to ambiguity to the exact position and identity of the bulge. All possible group III bulge loops with Watson-Crick nearest-neighbors were examined. The data were used to develop a model to predict the free energy of an RNA duplex containing a group III single nucleotide bulge loop. The destabilization of the duplex by the group III bulge could be modeled so that the bulge nucleotide leads to the formation of the Watson-Crick base pair rather than the wobble base pair. The destabilization of an RNA duplex caused by the insertion of a group III bulge is primarily dependent upon non-nearest-neighbor interactions and was shown to be dependent upon the stability of second least stable stem of the duplex. In-line structure probing of group III bulge loops embedded in a hairpin indicated that the bulged nucleotide is the one positioned further from the hairpin loop irrespective of whether the resulting stem formed a Watson-Crick or wobble base pair. Fourteen RNA hairpins containing group III bulge loops, either 3' or 5' of the hairpin loop, were optically melted and the thermodynamic parameters determined. The model developed to predict the influence of group III bulge loops on the stability of duplex formation was extended to predict the influence of bulge loops on hairpin stability.

  7. Computational comparison of oxidation stability: Solvent/salt monomers vs solvent-solvent/salt pairs

    NASA Astrophysics Data System (ADS)

    Kim, Dong Young; Park, Min Sik; Lim, Younhee; Kang, Yoon-Sok; Park, Jin-Hwan; Doo, Seok-Gwang

    2015-08-01

    A fundamental understanding of the anodic stabilities of electrolytes is important for the development of advanced high-voltage electrolytes. In this study, we calculated and systematically compared the oxidation stabilities of monomeric solvents and anions, and bimolecular solvent-solvent and anion-solvent systems that are considered to be high-voltage electrolyte components, using ab initio calculations. Oxidation stabilities of solvent or anion monomers without considering specific solvation molecules cannot represent experimental oxidation stabilities. The oxidation of electrolytes usually forms neutral or cationic radicals, which immediately undergo further reactions stabilizing the products. Oxidatively driven intermolecular reactions are the main reason for the lower oxidation stabilities of electrolytes compared with those of monomeric compounds. Electrolyte components such as tetramethylene sulfone (TMS), ethyl methyl sulfone (EMS), bis(oxalate)borate (BOB-), and bis(trifluoromethane)sulfonamide (TFSI-) that minimize such intermolecular chemical reactions on oxidation can maintain the oxidation stabilities of monomers. In predictions of the theoretical oxidation stabilities of electrolytes, simple comparisons of highest occupied molecular orbital energies can be misleading, even if microsolvation or bulk clusters are considered. Instead, bimolecular solvent complexes with a salt anion should be at least considered in oxidation calculations. This study provides important information on fundamental and applied aspects of the development of electrolytes.

  8. Finding the first cosmic explosions. IV. 90–140 $$\\;{{M}_{\\odot }}$$ pair-stability supernovae

    DOE PAGES

    Smidt, Joseph; Whalen, Daniel J.; Chatzopoulos, E.; Wiggins, Brandon; Chen, Ke-Jung; Kozyreva, Alexandra; Even, Wesley

    2015-05-19

    Population III stars that die as pair-instability supernovae are usually thought to fall in the mass range of 140 - 260 M⊙. However, several lines of work have now shown that rotation can build up the He cores needed to encounter the pair instability at stellar masses as low as 90 M⊙. Depending on the slope of the initial mass function of Population III stars, there could be 4 - 5 times as many stars from 90 - 140 M⊙ in the primordial universe than in the usually accepted range. We present numerical simulations of the pair-instability explosions of suchmore » stars performed with the MESA, FLASH and RAGE codes. We find that they will be visible to supernova factories such as Pan-STARRS and LSST in the optical out to z ~ 1-2 and JWST and the 30 m-class telescopes in the NIR out to z ~ 7-10. Such explosions will thus probe the stellar populations of the first galaxies and cosmic star formation rates in the era of cosmological reionization. These supernovae are also easily distinguished from more massive pair-instability explosions, underscoring the fact that there is far greater variety to the light curves of these events than previously understood.« less

  9. Finding the first cosmic explosions. IV. 90–140 $\\;{{M}_{\\odot }}$ pair-stability supernovae

    SciTech Connect

    Smidt, Joseph; Whalen, Daniel J.; Chatzopoulos, E.; Wiggins, Brandon; Chen, Ke-Jung; Kozyreva, Alexandra; Even, Wesley

    2015-05-19

    Population III stars that die as pair-instability supernovae are usually thought to fall in the mass range of 140 - 260 M. However, several lines of work have now shown that rotation can build up the He cores needed to encounter the pair instability at stellar masses as low as 90 M. Depending on the slope of the initial mass function of Population III stars, there could be 4 - 5 times as many stars from 90 - 140 M in the primordial universe than in the usually accepted range. We present numerical simulations of the pair-instability explosions of such stars performed with the MESA, FLASH and RAGE codes. We find that they will be visible to supernova factories such as Pan-STARRS and LSST in the optical out to z ~ 1-2 and JWST and the 30 m-class telescopes in the NIR out to z ~ 7-10. Such explosions will thus probe the stellar populations of the first galaxies and cosmic star formation rates in the era of cosmological reionization. These supernovae are also easily distinguished from more massive pair-instability explosions, underscoring the fact that there is far greater variety to the light curves of these events than previously understood.

  10. Thermal Stability Comparison of Nanocrystalline Fe-Based Binary Alloy Pairs

    NASA Astrophysics Data System (ADS)

    Clark, B. G.; Hattar, K.; Marshall, M. T.; Chookajorn, T.; Boyce, B. L.; Schuh, C. A.

    2016-06-01

    The widely recognized property improvements of nanocrystalline (NC) materials have generated significant interest; yet, they have been difficult to realize in engineering applications due to the propensity for grain growth in these interface-dominated systems. Although traditional pathways to thermal stabilization can slow the mobility of grain boundaries, recent theories suggest that solute segregation in NC alloys can reduce the grain boundary energy such that thermodynamic stabilization is achieved. Following the predictions of Murdoch et al., here we compare for the first time the thermal stability of a predicted NC stable alloy (Fe-10 at.% Mg) with a predicted non-NC stable alloy (Fe-10 at.% Cu) using the same processing and characterization methodologies. Results show improved thermal stability of the Fe-Mg alloy in comparison with the Fe-Cu, and thermally-evolved microstructures that are consistent with those predicted by Monte Carlo simulations.

  11. Thermal stability comparison of nanocrystalline Fe-based binary alloy pairs

    DOE PAGES

    Clark, Blythe G.; Hattar, Khalid Mikhiel; Marshall, Michael Thomas; Chookajorn, Tonghai; Boyce, Brad L.; Schuh, Christopher A.

    2016-02-01

    Here, the widely recognized property improvements of nanocrystalline (NC) materials have generated significant interest, yet have been difficult to realize in engineering applications due to the propensity for grain growth in these interface-dense systems. While traditional pathways to thermal stabilization can slow the mobility of grain boundaries, recent theories suggest that solute segregation in NC alloy can reduce the grain boundary energy such that thermodynamic stabilization is achieved. Following the predictions of Murdock et al., here we compare for the first time the thermal stability of a predicted NC stable alloy (Fe-10at.% Mg) with a predicted non-NC stable alloy (Fe-10at.%more » Cu) using the same processing and characterization methodologies. Results indicate improved thermal stability of the Fe-Mg alloy in comparison to the Fe-Cu, and observed microstructures are consistent with those predicted by Monte Carlo simulations.« less

  12. The Crystal Structure of Non-Modified and Bipyridine-Modified PNA Duplexes

    SciTech Connect

    Yeh, Joanne I.; Pohl, Ehmke; Truan, Daphne; He, Wei; Sheldrick, George M.; Du, Shoucheng; Achim, Catalina

    2011-09-28

    Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N-aminoethyl glycine backbone. The crystal structures of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATGCC)2, and the other containing the same nucleobase pairs and a central pair of bipyridine ligands, have been solved with a resolution of 1.22 and 1.10 {angstrom}, respectively. The non-modified PNA duplex adopts a P-type helical structure similar to that of previously characterized PNAs. The atomic-level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and the nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. Our results support the notion that whereas PNA typically adopts a P-type helical structure, its flexibility is relatively high. For example, the base-pair rise in the bipyridine-containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines bulge out of the duplex and are aligned parallel to the major groove of the PNA. In addition, two bipyridines from adjacent PNA duplexes form a p-stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl-modified DNA duplexes in solution, where the biphenyls are p stacked with adjacent nucleobase pairs and adopt an intrahelical geometry. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes.

  13. Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m5dCyd: Implications for the Stability of DNA i-Motif Conformations

    NASA Astrophysics Data System (ADS)

    Yang, Bo; Rodgers, M. T.

    2015-08-01

    Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m5dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m5dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m5dCyd)H+(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

  14. Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m(5)dCyd: Implications for the Stability of DNA i-Motif Conformations.

    PubMed

    Yang, Bo; Rodgers, M T

    2015-08-01

    Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m(5)dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m(5)dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m(5)dCyd)H(+)(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

  15. The roles of entropy and enthalpy in stabilizing ion-pairs at transition states in zeolite acid catalysis.

    PubMed

    Gounder, Rajamani; Iglesia, Enrique

    2012-02-21

    Acidic zeolites are indispensable catalysts in the petrochemical industry because they select reactants and their chemical pathways based on size and shape. Voids of molecular dimensions confine reactive intermediates and transition states that mediate chemical reactions, stabilizing them by van der Waals interactions. This behavior is reminiscent of the solvation effects prevalent within enzyme pockets and has analogous consequences for catalytic specificity. Voids provide the "right fit" for certain transition states, reflected in their lower free energies, thus extending the catalytic diversity of zeolites well beyond simple size discrimination. This catalytic diversity is even more remarkable because acid strength is essentially unaffected by confinement among known crystalline aluminosilicates. In this Account, we discuss factors that determine the "right fit" for a specific chemical reaction, exploring predictive criteria that extend the prevailing discourse based on size and shape. We link the structures of reactants, transition states, and confining voids to chemical reactivity and selectivity. Confinement mediates enthalpy-entropy compromises that determine the Gibbs free energies of transition states and relevant reactants; these activation free energies determine turnover rates via transition state theory. At low temperatures (400-500 K), dimethyl ether carbonylation occurs with high specificity within small eight-membered ring (8-MR) voids in FER and MOR zeolite structures, but at undetectable rates within larger voids (MFI, BEA, FAU, and SiO(2)-Al(2)O(3)). More effective van der Waals stabilization within 8-MR voids leads to lower ion-pair enthalpies but also lower entropies; taken together, carbonylation activation free energies are lower within 8-MR voids. The "right fit" is a "tight fit" at low temperatures, a consequence of how temperature appears in the defining equation for Gibbs free energy. In contrast, entropy effects dominate in high

  16. Theoretical study on the structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA.

    PubMed

    Fuentes-Cabrera, Miguel; Sumpter, Bobby G; Sponer, Judit E; Sponer, Jirí; Petit, Leon; Wells, Jack C

    2007-02-01

    M-DNA is a type of metalated DNA that forms at high pH and in the presence of Zn, Ni, and Co, with the metals placed in between each base pair, as in G-Zn-C. Experiments have found that M-DNA could be a promising candidate for a variety of nanotechnological applications, as it is speculated that the metal d-states enhance the conductivity, but controversy still clouds these findings. In this paper, we carry out a comprehensive ab initio study of eight G-Zn-C models in the gas phase to help discern the structure and electronic properties of Zn-DNA. Specifically, we study whether a model prefers to be planar and has electronic properties that correlate with Zn-DNA having a metallic-like conductivity. Out of all the studied models, there is only one which preserves its planarity upon full geometry optimization. Nevertheless, starting from this model, one can deduce a parallel Zn-DNA architecture only. This duplex would contain the imino proton, in contrast to what has been proposed experimentally. Among the nonplanar models, there is one that requires less than 8 kcal/mol to flatten (both in gas and solvent conditions), and we propose that it is a plausible model for building an antiparallel duplex. In this duplex, the imino proton would be replaced by Zn, in accordance with experimental models. Neither planar nor nonplanar models have electronic properties that correlate with Zn-DNA having a metallic-like conductivity due to Zn d-states. To understand whether density functional theory (DFT) can describe appropriately the electronic properties of M-DNAs, we have investigated the electronic properties of G-Co-C base pairs. We have found that when self-interaction corrections (SIC) are not included the HOMO state contains Co d-levels, whereas these levels are moved below the HOMO state when SIC are considered. This result indicates that caution should be exercised when studying the electronic properties of M-DNAs with functionals that do not account for strong

  17. Role of the heat capacity change in understanding and modeling melting thermodynamics of complementary duplexes containing standard and nucleobase-modified LNA.

    PubMed

    Hughesman, Curtis B; Turner, Robin F B; Haynes, Charles A

    2011-06-14

    Melting thermodynamic data obtained by differential scanning calorimetry (DSC) are reported for 43 duplexed oligonucleotides containing one or more locked nucleic acid (LNA) substitutions. The measured heat capacity change (ΔC(p)) for the helix-to-coil transition is used to compute the changes in enthalpy and entropy for melting of an LNA-bearing duplex at the T(m) of its corresponding isosequential unmodified DNA duplex to allow rigorous thermodynamic analysis of the stability enhancements provided by LNA substitutions. Contrary to previous studies, our analysis shows that the origin of the improved stability is almost exclusively a net reduction (ΔΔS° < 0) in the entropy gain accompanying the helix-to-coil transition, with the magnitude of the reduction dependent on the type of nucleobase and its base pairing properties. This knowledge and our average measured value for ΔC(p) of 42 ± 11 cal mol(-1) K(-1) bp(-1) are then used to derive a new model that accurately predicts melting thermodynamics and the increased melting temperature (ΔT(m)) of heteroduplexes formed between an unmodified DNA strand and a complementary strand containing any number and configuration of standard LNA nucleotides A, T, C, and G. This single-base thermodynamic (SBT) model requires only four entropy-related parameters in addition to ΔC(p). Finally, DSC data for 20 duplexes containing the nucleobase-modified LNAs 2-aminoadenine (D) and 2-thiothymine (H) are reported and used to determine SBT model parameters for D and H. The data and model suggest that along with the greater stability enhancement provided by D and H bases relative to their corresponding A and T analogues, the unique pseudocomplementary properties of D-H base pairs may make their use appealing for in vitro and in vivo applications.

  18. Stability of 100 homo and heterotypic coiled-coil a-a' pairs for ten amino acids (A, L, I, V, N, K, S, T, E, and R).

    PubMed

    Acharya, Asha; Rishi, Vikas; Vinson, Charles

    2006-09-26

    We present the thermal stability monitored by circular dichroism (CD) spectroscopy at 222 nm of 100 heterodimers that contain all possible coiled-coil a-a' pairs for 10 amino acids (I, V, L, N, A, K S, T, E, and R). This includes the stability of 36 heterodimers for 6 amino acids (I, V, L, N, A, and K) previously described and 64 new heterodimers including the 4 amino acids (S, T, E, and R). We have calculated a double mutant alanine thermodynamic cycle to determine a-a' pair coupling energies to evaluate which a-a' pairs encourage specific dimerization partners. The four new homotypic a-a' pairs (T-T, S-S, R-R, E-E) are repulsive relative to A-A and have destabilizing coupling energies. Among the 90 heterotypic a-a' pairs, the stabilizing coupling energies contain lysine or arginine paired with either an aliphatic or a polar amino acid. The range in coupling energies for each amino acid reveals its potential to regulate dimerization specificity. The a-a' pairs containing isoleucine and asparagine have the greatest range in coupling energies and thus contribute dramatically to dimerization specificity, which is to encourage homodimerization. In contrast, the a-a' pairs containing charged amino acids (K, R, and E) show the least range in coupling energies and promiscuously encourage heterodimerization.

  19. Unique Dynamic Properties of DNA Duplexes Containing Interstrand Crosslinks†

    PubMed Central

    Friedman, Joshua I.; Jiang, Yu Lin; Miller, Paul S.; Stivers, James T.

    2010-01-01

    Bifunctional DNA alkylating agents form a diverse assortment of covalent DNA interstrand crosslinked (ICL) structures that are potent cytotoxins. Since it is implausible that cells could possess distinct DNA repair systems for each individual ICL, it is believed that common structural and dynamic features of ICL damage are recognized, rather than specific structural characteristics of each cross-linking agent. Investigation of the structural and dynamic properties of ICLs that might be important for recognition has been complicated by heterogeneous incorporation of these lesions into DNA. To address this problem we have synthesized and characterized several homogenous ICL-DNAs containing site–specific staggered N4-cytosine-ethyl-N4-cytosine crosslinks. Staggered crosslinks were introduced in two ways: in a manner that preserves the overall structure of B-form duplex DNA, and in a manner that highly distorts the DNA structure, with the goal of understanding how structural and dynamic properties of diverse ICL duplexes might flag these sites for repair. Measurements of base pair opening dynamics in the B-form ICL duplex by 1H NMR linewidth or imino proton solvent exchange showed that the guanine base opposite to the crosslinked cytosine opened at least an order of magnitude more slowly than when in a control matched normal duplex. To a lesser degree, the B-form ICL also induced a decrease in base pair opening dynamics that extended from the site of the crosslink to adjacent base pairs. In contrast, the non-B-form ICL showed extensive conformational dynamics at the site of the cross link, which extended over the entire DNA sequence. Since DNA duplexes containing the B-form and non-B-form ICL crosslinks have both been shown to be incised when incubated in mammalian whole cell extracts, while a matched normal duplex is not, we conclude that intrinsic DNA dynamics is not a requirement for specific damage incision of these ICLs. Instead, we propose a general model where

  20. Physical stability of coconut oil lotions formulated using hydrophile-lipophile balance system of various emulsifier pairs.

    PubMed

    Boonme, Prapaporn; Maneenuan, Duangkhae; Channarong, Sunee

    2013-01-01

    The aim of this study was to prepare coconut oil lotions using a hydrophile-lipophile balance system to calculate the proportion of each nonionic surfactant used. The effects of emulsifier pairs in the formulations on physical properties (i.e., appearance, emulsion type, pH, flow type, viscosity) were investigated. The physical stability of the lotions was determined at ambient temperature (approximatley 30 degrees C) after the lotions were kept for 30 as well as 60 days and in accelerated conditions (6 freeze-thaw cycles). It was found that the formulations most tolerant to such harsh conditions were F1 and F2, o/w lotions containing 40% w/w coconut oil, 50% w/w water and 10% w/w of the mixed emulsifier of a low hydrophile-lipophile balance surfactant (sorbitan monostearate) and a high hydrophile-lipophile balance surfactant (either polyoxyethylene [20] sorbitan monooleate or polyethylene [20] sorbitan monolaurate).

  1. Single-pair fluorescence resonance energy transfer of nucleosomes in free diffusion: optimizing stability and resolution of subpopulations.

    PubMed

    Gansen, Alexander; Hauger, Florian; Tóth, Katalin; Langowski, Jörg

    2007-09-15

    We applied fluorescence detection methods on the single-molecule level to study structural variations and dynamic processes occurring within nucleosomes. Four fluorescent nucleosome constructs were made by attaching donor and acceptor fluorophores to different positions of two nucleosome positioning sequences and reconstituting nucleosomes by salt dialysis. The photochemical and biochemical stability of nucleosomes under single-molecule conditions was optimized by adding inert protein and free radical capturing additives, allowing us to define the best experimental conditions for single-molecule spectroscopy on highly diluted solutions of nucleosome complexes. We could demonstrate for the first time the resolution of conformational subpopulations of nucleosomes by single-pair fluorescence resonance energy transfer in a freely diffusing system and could show the effect of thermally induced nucleosome repositioning.

  2. Determination of sensor oversize for stereo-pair mismatch compensation and image stabilization

    NASA Astrophysics Data System (ADS)

    Kulkarni, Prajit

    2013-03-01

    Stereoscopic cameras consist of two camera modules that in theory are mounted parallel to each other at a fixed distance along a single plane. Practical tolerances in the manufacturing and assembly process can, however, cause mismatches in the relative orientation of the modules. One solution to this problem is to design sensors that image a larger field-of-view than is necessary to meet system specifications. This requires the computation of the sensor oversize needed to compensate for the various types of mismatch. This work presents a mathematical framework to determine these oversize values for mismatch along each of the six degrees of freedom. One module is considered as the reference and the extreme rays of the field-of-view of the second sensor are traced in order to derive equations for the required horizontal and vertical oversize. As a further application, by modeling user hand-shake as the displacement of the sensor from its intended position, these deterministic equations could be used to estimate the sensor oversize required to stabilize images that are captured using cell phones.

  3. The solution structure of double helical arabino nucleic acids (ANA and 2'F-ANA): effect of arabinoses in duplex-hairpin interconversion.

    PubMed

    Martín-Pintado, Nerea; Yahyaee-Anzahaee, Maryam; Campos-Olivas, Ramón; Noronha, Anne M; Wilds, Christopher J; Damha, Masad J; González, Carlos

    2012-10-01

    We report here the first structure of double helical arabino nucleic acid (ANA), the C2'-stereoisomer of RNA, and the 2'-fluoro-ANA analogue (2'F-ANA). A chimeric dodecamer based on the Dickerson sequence, containing a contiguous central segment of arabino nucleotides, flanked by two 2'-deoxy-2'F-ANA wings was studied. Our data show that this chimeric oligonucleotide can adopt two different structures of comparable thermal stabilities. One structure is a monomeric hairpin in which the stem is formed by base paired 2'F-ANA nucleotides and the loop by unpaired ANA nucleotides. The second structure is a bimolecular duplex, with all the nucleotides (2'F-ANA and ANA) forming Watson-Crick base pairs. The duplex structure is canonical B-form, with all arabinoses adopting a pure C2'-endo conformation. In the ANA:ANA segment, steric interactions involving the 2'-OH substituent provoke slight changes in the glycosidic angles and, therefore, in the ANA:ANA base pair geometry. These distortions are not present in the 2'F-ANA:2'F-ANA regions of the duplex, where the -OH substituent is replaced by a smaller fluorine atom. 2'F-ANA nucleotides adopt the C2'-endo sugar pucker and fit very well into the geometry of B-form duplex, allowing for favourable 2'F···H8 interactions. This interaction shares many features of pseudo-hydrogen bonds previously observed in 2'F-ANA:RNA hybrids and in single 2'F-ANA nucleotides.

  4. Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors.

    PubMed

    Mosayebi, Majid; Louis, Ard A; Doye, Jonathan P K; Ouldridge, Thomas E

    2015-12-22

    The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article, we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed force sensors and nanotechnological devices. We argue that rupture must be understood as an activated process, where the duplex state is metastable and the strands will separate in a finite time that depends on the duplex length and the force applied. Thus, the critical shearing force required to rupture a duplex depends strongly on the time scale of observation. We use simple models of DNA to show that this approach naturally captures the observed dependence of the force required to rupture a duplex within a given time on duplex length. In particular, this critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the long length limit. The prevailing approach, based on identifying when the presence of each additional base pair within the duplex is thermodynamically unfavorable rather than allowing for metastability, does not predict a time-scale-dependent critical force and does not naturally incorporate a critical force of zero for the shortest duplexes. We demonstrate that our findings have important consequences for the behavior of a new force-sensing nanodevice, which operates in a mixed mode that interpolates between shearing and unzipping. At a fixed time scale and duplex length, the critical force exhibits a sigmoidal dependence on the fraction of the duplex that is subject to shearing.

  5. Corrosion induced by cathodic hydrogen in 2205 duplex stainless steel

    NASA Astrophysics Data System (ADS)

    Michalska, J.

    2011-05-01

    In this work new results about the influence of cathodic hydrogen on passivity and corrosion resistance of 2205 duplex stainless steel are described. The results were discussed by taking into account hydrogen charged samples and without hydrogen. The corrosion resistance to pitting was qualified with the polarization curves. The conclusion is that, hydrogen deteriorated the passive film stability and corrosion resistance to pitting of 2205 duplex stainless steel. The presence of hydrogen in passive films increases corrosion current density and decreases the potential of the film breakdown. It was also found that degree of susceptibility to hydrogen action was dependent on the hydrogen charging conditions.

  6. Ion mobility spectrometry reveals duplex DNA dissociation intermediates.

    PubMed

    Burmistrova, Anastasia; Gabelica, Valérie; Duwez, Anne-Sophie; De Pauw, Edwin

    2013-11-01

    Electrospray ionization (ESI) soft desolvation is widely used to investigate fragile species such as nucleic acids. Tandem mass spectrometry (MS/MS) gives access to the gas phase energetics of the intermolecular interactions in the absence of solvent, by following the dissociation of mass-selected ions. Ion mobility mass spectrometry (IMS) provides indications on the tridimensional oligonucleotide structure by attributing a collision cross section (CCS) to the studied ion. Electrosprayed duplexes longer than eight bases pairs retain their helical structure in a solvent-free environment. However, the question of conformational changes under activation in MS/MS studies remains open. The objective of this study is to probe binding energetics and characterize the unfolding steps occurring prior to oligonucleotide duplex dissociation. Comparing the evolution of CCS with collision energy and breakdown curves, we characterize dissociation pathways involved in CID-activated DNA duplex separation into single strands, and we demonstrate here the existence of stable dissociation intermediates. At fixed duplex length, dissociation pathways were found to depend on the percentage of GC base pairs and on their position in the duplex. Our results show that pure GC sequences undergo a gradual compaction until reaching the dissociation intermediate: A-helix. Mixed AT-GC sequences were found to present at least two conformers: a classic B-helix and an extended structure where the GC tract is a B-helix and the AT tract(s) fray. The dissociation in single strands takes place from both conformers when the AT base pairs are enclosed between two GC tracts or only from the extended conformer when the AT tract is situated at the end(s) of the sequence.

  7. The hybridization-stabilization assay: a solution-based isothermal method for rapid screening and determination of sequence preference of ligands that bind to duplexed nucleic acids.

    PubMed

    Gonzalez, C; Moore, M; Ribeiro, S; Schmitz, U; Schroth, G P; Turin, L; Bruice, T W

    2001-08-15

    The gene-to-drug quest will be most directly served by the discovery and development of small molecules that bind to nucleic acids and modulate gene expression at the level of transcription and/or inhibit replication of infectious agents. Full realization of this potential will require implementation of a complete suite of modern drug discovery technologies. Towards this end, here we describe our initial results with a new assay for identification and characterization of novel nucleic acid binding ligands. It is based on the well recognized property of stabilization of hybridization of complementary oligonucleotides by groove and/or intercalation binding ligands. Unlike traditional thermal melt methodologies, this assay is isothermal and, unlike gel-based footprinting techniques, the assay also is performed in solution and detection can be by any number of highly sensitive, non-radioisotopic modalities, such as fluorescence resonance energy transfer, described herein. Thus, the assay is simple to perform, versatile in design and amenable to miniaturization and high throughput automation. Assay validation was performed using various permutations of direct and competitive binding formats and previously well studied ligands, including pyrrole polyamide and intercalator natural products, designed hairpin pyrrole-imidazole polyamides and furan-based non-polyamide dications. DNA specific ligands were identified and their DNA binding site size and sequence preference profiles were determined. A systematic approach to studying the relationship of binding sequence specificity with variation in ligand structure was demonstrated, and preferred binding sites in longer DNA sequences were found by pseudo-footprinting, with results that are in accord with established findings. This assay methodology should promote a more rapid discovery of novel nucleic acid ligands and potential drug candidates.

  8. Relative stability of guanosine-cytidine diribonucleotide cores: a 1H NMR assessment.

    PubMed

    Sinclair, A; Alkema, D; Bell, R A; Coddington, J M; Hughes, D W; Neilson, T; Romaniuk, P J

    1984-06-01

    Proton NMR was used to study the secondary structure and melting behavior of six self-complementary oligoribonucleotide tetramers, each containing two guanosine and two cytidine residues (GGCC, CCGG, GCCG, CGGC, GCGC, and CGCG). GGCC and CCGG formed perfect duplexes containing four G.C base pairs with Tms of 54 and 47.8 degrees C, respectively; GCCG and CGGC formed staggered duplexes with two G.C base pairs and four 3' double-dangling bases, with Tms of 35.5 and 29.2 degrees C, respectively; GCGC formed a perfect duplex with a Tm of 49.9 degrees C, while CGCG formed a staggered duplex with a Tm of 36.9 degrees C. From these results, an order of stability of the cores containing two G.C base pairs was proposed: GC:GC is more stable than GG:CC which is more stable than CG:CG. The RY model for secondary structure stability prediction was applied to the above tetramers with reasonable success. Suggestions for refinements are discussed.

  9. Determination of borate ion-pair stability constants by potentiometry and non-approximative linearization of titration data.

    PubMed

    Rogers, H R; van den Berg, C M

    1988-04-01

    Borate anions, B(OH)(-)(4), are known to associate with alkali and alkaline-earth metal cations in sea-water. The borate cation ion-pairs are of the general form MB(OH)((n-1)+)(4), where M(n+) is the cation. In this work, the cation borate stability constants (K*(MB)) have been evaluated for Na(+), Li(+), Mg(2+), Ca(2+) and Sr(2+) where K*(MB) = [MB(OH(4))((n-1)+)]/[M(n+)][B(OH)(-)(4)]. The K*(MB) values were obtained from values found for the stability constant of boric acid (K*(B)) in various electrolyte media at 25 degrees and an ionic strength of 0.7. Acid-base potentiometric titrations were performed in the electrolyte media with a standard Pt/H(2) electrode and a junctionless Ag/AgCl reference electrode to monitor the emf. A non-approximative equation was used to linearize the titration data. The values obtained were: K*(Lib) = 0.89 +/- 0.02, K*(NaB) = 0.44 +/- 0.01, K*(MgB) = 13.6 +/- 0.7, K*(CaB) = 11.4 +/- 0.15, K*(SrB) = 3.47 +/- 0.06. The values for K*(MB) correlate with the charge-density parameter z(2)/(r + 0.85), where r is the radius of the cation. The speciation of boron in sea-water was predicted from the K*(MB), data for the major cations present.

  10. The coupling between stability and ion pair formation in magnesium electrolytes from first-principles quantum mechanics and classical molecular dynamics.

    PubMed

    Rajput, Nav Nidhi; Qu, Xiaohui; Sa, Niya; Burrell, Anthony K; Persson, Kristin A

    2015-03-11

    In this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectric constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg(2+) → Mg(+)), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI(-) exhibits a significant bond weakening while paired with the transient, partially reduced Mg(+). In contrast, BH4(-) and BF4(-) are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.

  11. The coupling between stability and ion pair formation in magnesium electrolytes from first-principles quantum mechanics and classical molecular dynamics

    SciTech Connect

    Rajput, Nav Nidhi; Qu, Xiaohuui; Sa, Niya; Burrell, Anthony K.; Persson, Kristin A.

    2015-03-11

    In this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectric constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg2+ -> Mg+), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI exhibits a significant bond weakening while paired with the transient, partially reduced Mg+. In contrast, BH4 and BF4 are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.

  12. Dissecting the contributions of β-hairpin tyrosine pairs to the folding and stability of long-lived human γD-crystallins

    NASA Astrophysics Data System (ADS)

    Yang, Zaixing; Xia, Zhen; Huynh, Tien; King, Jonathan A.; Zhou, Ruhong

    2014-01-01

    Ultraviolet-radiation-induced damage to and aggregation of human lens crystallin proteins are thought to be a significant pathway to age-related cataract. The aromatic residues within the duplicated Greek key domains of γ- and β-crystallins are the main ultraviolet absorbers and are susceptible to direct and indirect ultraviolet damage. The previous site-directed mutagenesis studies have revealed a striking difference for two highly conserved homologous β-hairpin Tyr pairs, at the N-terminal domain (N-td) and C-terminal domain (C-td), respectively, in their contribution to the overall stability of HγD-Crys, but why they behave so differently still remains a mystery. In this paper, we systematically investigated the underlying molecular mechanism and detailed contributions of these two Tyr pairs with large scale molecular dynamics simulations. A series of different tyrosine-to-alanine pair(s) substitutions were performed in either the N-td, the C-td, or both. Our results suggest that the Y45A/Y50A pair substitution in the N-td mainly affects the stability of the N-td itself, while the Y133A/Y138A pair substitution in the C-td leads to a more cooperative unfolding of both N-td and C-td. The stability of motif 2 in the N-td is mainly determined by the interdomain interface, while motif 1 in the N-td or motifs 3 and 4 in the C-td are mainly stabilized by the intradomain hydrophobic core. The damage to any tyrosine pair(s) can directly introduce some apparent water leakage to the hydrophobic core at the interface, which in turn causes a serious loss in the stability of the N-td. However, for the C-td substitutions, it may further impair the stable ``sandwich-like'' Y133-R167-Y138 cluster (through cation-π interactions) in the wild-type, thus causing the loop regions near the residue A138 to undergo large fluctuations, which in turn results in the intrusion of water into the hydrophobic core of the C-td and induces the C-td to lose its stability. These findings help

  13. Stability of miRNA 5′terminal and seed regions is correlated with experimentally observed miRNA-mediated silencing efficacy

    PubMed Central

    Hibio, Naoki; Hino, Kimihiro; Shimizu, Eigo; Nagata, Yoshiro; Ui-Tei, Kumiko

    2012-01-01

    MicroRNAs (miRNAs) are key regulators of sequence-specific gene silencing. However, crucial factors that determine the efficacy of miRNA-mediated target gene silencing are poorly understood. Here we mathematized base-pairing stability and showed that miRNAs with an unstable 5′ terminal duplex and stable seed-target duplex exhibit strong silencing activity. The results are consistent with the previous findings that an RNA strand with unstable 5′ terminal in miRNA duplex easily loads onto the RNA-induced silencing complex (RISC), and miRNA recognizes target mRNAs with seed-complementary sequences to direct posttranscriptional repression. Our results suggested that both the unwinding and target recognition processes of miRNAs could be proficiently controlled by the thermodynamics of base-pairing in protein-free condition. Interestingly, such thermodynamic parameters might be evolutionarily well adapted to the body temperatures of various species. PMID:23251782

  14. A cationic dye triplet as a unique "glue" that can connect fully matched termini of DNA duplexes.

    PubMed

    Kashida, Hiromu; Hayashi, Takamitsu; Fujii, Taiga; Asanuma, Hiroyuki

    2011-02-25

    In this study, we propose that three consecutive cationic p-methylstilbazoles tethered on D-threoninols (Z residues) at 5' termini act as a unique "glue" connecting DNA duplexes by their interstrand cluster formation. Interstrand clustering of p-methylstilbazoles (ZZZ triplets) induces narrowing and hypsochromic shift of bands at 350 nm, which can be assigned to the absorption of p-methylstilbazole. However, single-stranded DNA conjugates involving a ZZZ triplet at the 5' terminus of 8-mer native nucleotides is found not to induce such large spectral changes, which implies that the intrinsic self-assembling property of ZZZ triplets is weak. Interestingly, when this conjugate is hybridized with a complementary 8-mer native oligonucleotide, a remarkable spectral change is observed, indicating the dimerization of a duplex through the interstrand clustering of ZZZ triplets. Dimerization of the duplex is also evidenced by cold-spray ionization mass spectrometry. This interstrand clustering is observed only when a ZZZ triplet is tethered to a 5' rather than 3' terminus. Furthermore, the stability of the interstrand cluster increases by increasing the number of nucleobases of the DNA portion, and when mismatched base pairs are incorporated or when a base next to the Z residue is deleted, the stability substantially drops. When we apply the ZZZ triplet to the formation of a nanowire using two complementary DNA conjugates, each of which has a ZZZ triplet at the 5' termini as overhang, we demonstrate the successful formation of a nanowire by native PAGE analysis. Since native sticky ends that have three nucleotides do not serve as "glue", ZZZ triplets with their unique glue-like properties are prime candidates for constructing DNA-based nanoarchitectures. PMID:21305625

  15. Water-evaporation reduction by duplex films: application to the human tear film.

    PubMed

    Cerretani, Colin F; Ho, Nghia H; Radke, C J

    2013-09-01

    Water-evaporation reduction by duplex-oil films is especially important to understand the physiology of the human tear film. Secreted lipids, called meibum, form a duplex film that coats the aqueous tear film and purportedly reduces tear evaporation. Lipid-layer deficiency is correlated with the occurrence of dry-eye disease; however, in-vitro experiments fail to show water-evaporation reduction by tear-lipid duplex films. We review the available literature on water-evaporation reduction by duplex-oil films and outline the theoretical underpinnings of spreading and evaporation kinetics that govern behavior of these systems. A dissolution-diffusion model unifies the data reported in the literature and identifies dewetting of duplex films into lenses as a key challenge to obtaining significant evaporation reduction. We develop an improved apparatus for measuring evaporation reduction by duplex-oil films including simultaneous assessment of film coverage, stability, and temperature, all under controlled external mass transfer. New data reported in this study fit into the larger body of work conducted on water-evaporation reduction by duplex-oil films. Duplex-oil films of oxidized mineral oil/mucin (MOx/BSM), human meibum (HM), and bovine meibum (BM) reduce water evaporation by a dissolution-diffusion mechanism, as confirmed by agreement between measurement and theory. The water permeability of oxidized-mineral-oil duplex films agrees with those reported in the literature, after correction for the presence of mucin. We find that duplex-oil films of bovine and human meibum at physiologic temperature reduce water evaporation only 6-8% for a 100-nm film thickness pertinent to the human tear film. Comparison to in-vivo human tear-evaporation measurements is inconclusive because evaporation from a clean-water surface is not measured and because the mass-transfer resistance is not characterized.

  16. ARGONAUTE PIWI domain and microRNA duplex structure regulate small RNA sorting in Arabidopsis

    PubMed Central

    Zhang, Xiaoming; Niu, DongDong; Carbonell, Alberto; Wang, Airong; Lee, Angel; Tun, Vinnary; Wang, Zonghua; Carrington, James C.; Chang, Chia-en A.; Jin, Hailing

    2014-01-01

    Small RNAs (sRNAs) are loaded into ARGONAUTE (AGO) proteins to induce gene silencing. In plants, the 5′-terminal nucleotide is important for sRNA sorting into different AGOs. Here, we show that miRNA duplex structure also contributes to miRNA sorting. Base-pairing at the 15th nucleotide of a miRNA duplex is important for miRNA sorting in both Arabidopsis AGO1 and AGO2. AGO2 favors miRNA duplexes with no middle mismatches, whereas AGO1 tolerates, or prefers, duplexes with central mismatches. AGO structure modeling and mutational analyses reveal that the QF-V motif within the conserved PIWI domain contributes to recognition of base-pairing at the 15th nucleotide of a duplex, while the DDDE catalytic core of AtAGO2 is important for recognition of the central nucleotides. Finally, we rescued the adaxialized phenotype of ago1-12, which is largely due to miR165 loss-of-function, by changing miR165 duplex structure which we predict redirects it to AGO2. PMID:25406978

  17. On the stability analysis of a pair of van der Pol oscillators with delayed self-connection, position and velocity couplings

    SciTech Connect

    Hu, Kun; Chung, Kwok-wai

    2013-11-15

    In this paper, we perform a stability analysis of a pair of van der Pol oscillators with delayed self-connection, position and velocity couplings. Bifurcation diagram of the damping, position and velocity coupling strengths is constructed, which gives insight into how stability boundary curves come into existence and how these curves evolve from small closed loops into open-ended curves. The van der Pol oscillator has been considered by many researchers as the nodes for various networks. It is inherently unstable at the zero equilibrium. Stability control of a network is always an important problem. Currently, the stabilization of the zero equilibrium of a pair of van der Pol oscillators can be achieved only for small damping strength by using delayed velocity coupling. An interesting question arises naturally: can the zero equilibrium be stabilized for an arbitrarily large value of the damping strength? We prove that it can be. In addition, a simple condition is given on how to choose the feedback parameters to achieve such goal. We further investigate how the in-phase mode or the out-of-phase mode of a periodic solution is related to the stability boundary curve that it emerges from a Hopf bifurcation. Analytical expression of a periodic solution is derived using an integration method. Some illustrative examples show that the theoretical prediction and numerical simulation are in good agreement.

  18. Novel reference gene, PKABA1, used in a duplex real-time polymerase chain reaction for detection and quantitation of wheat- and barley-derived DNA.

    PubMed

    Rønning, Sissel B; Berdal, Knut G; Andersen, Charlotte Bøydler; Holst-Jensen, Arne

    2006-02-01

    We report the development of a duplex real-time Polymerase Chain Reaction (PCR) for the simultaneous detection and quantification of wheat- and barley-derived DNA. We used a single primer pair to amplify the single-copy gene PKABA1 from wheat and barley, using minor-groove-binding probes to distinguish between the two cereals. The assay was fully specific, and different wheat and barley cultivars exhibited similar Ct values, indicating stability across cultivars with respect to allelic and copy number composition. The limits of detection were 5 and 10 PCR-forming units for wheat and barley, respectively, making the duplex assay as sensitive as other singleplex reference gene systems published. We were able to detect both wheat and barley simultaneously in real food samples, and the duplex assay is considered to be suitable as an endogenous reference gene system for the detection and quantification of wheat and barley in genetically modified organisms (GMO) and other food and feed analyses.

  19. Laser Safety Method For Duplex Open Loop Parallel Optical Link

    DOEpatents

    Baumgartner, Steven John; Hedin, Daniel Scott; Paschal, Matthew James

    2003-12-02

    A method and apparatus are provided to ensure that laser optical power does not exceed a "safe" level in an open loop parallel optical link in the event that a fiber optic ribbon cable is broken or otherwise severed. A duplex parallel optical link includes a transmitter and receiver pair and a fiber optic ribbon that includes a designated number of channels that cannot be split. The duplex transceiver includes a corresponding transmitter and receiver that are physically attached to each other and cannot be detached therefrom, so as to ensure safe, laser optical power in the event that the fiber optic ribbon cable is broken or severed. Safe optical power is ensured by redundant current and voltage safety checks.

  20. Thermodynamic Profiles and NMR Studies of Oligonucleotide Duplexes Containing Single Diastereomeric Spiroiminodihydantoin Lesions

    PubMed Central

    Khutsishvili, Irine; Zhang, Na; Marky, Luis A.; Crean, Conor; Patel, Dinshaw J.; Geacintov, Nicholas E.; Shafirovich, Vladimir

    2013-01-01

    The spiroiminodihydantoins (Sp) are highly mutagenic oxidation products of guanine and 8-oxo-7,8-dihydroguanine in DNA. The Sp lesions have been recently detected in the liver and colon of mice infected with H. hepaticus that induces inflammation and development of liver and colon cancers in murine model systems [Mangerich, A., et al. (2012) Proc. Natl. Acad. Sci. U.S.A. 109, E1820–E1829]. The impact of Sp lesions on the thermodynamic characteristics and the effects of the diastereomeric Sp-R and Sp-S lesions on the conformational features of double-stranded 11-mer oligonucleotide duplexes have been studied by a combination of microcalorimetric, analysis of DNA melting curves, and two-dimensional NMR methods. The non-planar, propeller-like shapes of the Sp residues strongly diminish the local base stacking interactions that destabilize the DNA duplexes characterized by unfavorable enthalpy contributions. Relative to an unmodified duplex, the thermally induced unfolding of the duplexes with centrally positioned Sp-R and Sp-S lesions into single strands is accompanied by a smaller release of cationic counterions (ΔnNa+ = 0.6 mol Na+ per mol duplex) and water molecules (Δnw = 17 mol H2O per mol duplex). The unfolding parameters are similar for the Sp-R and Sp-S lesions although their orientations in the duplexes are different. The structural disturbances radiate one base pair beyond the flanking C:G pair, although Watson-Crick hydrogen bonding is maintained at all flanking base pairs. The observed relatively strong destabilization of B-form DNA by the physically small Sp lesions are expected to have a significant impact on the processing of these lesions in biological environments. PMID:23360616

  1. Resonance energy transfer in DNA duplexes labeled with localized dyes.

    PubMed

    Cunningham, Paul D; Khachatrian, Ani; Buckhout-White, Susan; Deschamps, Jeffrey R; Goldman, Ellen R; Medintz, Igor L; Melinger, Joseph S

    2014-12-18

    The growing maturity of DNA-based architectures has raised considerable interest in applying them to create photoactive light harvesting and sensing devices. Toward optimizing efficiency in such structures, resonant energy transfer was systematically examined in a series of dye-labeled DNA duplexes where donor-acceptor separation was incrementally changed from 0 to 16 base pairs. Cyanine dyes were localized on the DNA using double phosphoramidite attachment chemistry. Steady state spectroscopy, single-pair fluorescence, time-resolved fluorescence, and ultrafast two-color pump-probe methods were utilized to examine the energy transfer processes. Energy transfer rates were found to be more sensitive to the distance between the Cy3 donor and Cy5 acceptor dye molecules than efficiency measurements. Picosecond energy transfer and near-unity efficiencies were observed for the closest separations. Comparison between our measurements and the predictions of Förster theory based on structural modeling of the dye-labeled DNA duplex suggest that the double phosphoramidite linkage leads to a distribution of intercalated and nonintercalated dye orientations. Deviations from the predictions of Förster theory point to a failure of the point dipole approximation for separations of less than 10 base pairs. Interactions between the dyes that alter their optical properties and violate the weak-coupling assumption of Förster theory were observed for separations of less than four base pairs, suggesting the removal of nucleobases causes DNA deformation and leads to enhanced dye-dye interaction. PMID:25397906

  2. Superstructure of linear duplex DNA.

    PubMed Central

    Vollenweider, H J; Koller, T; Parello, J; Sogo, J M

    1976-01-01

    The superstructure of a covalently closed circular DNA (of bacteriophage PM 2) was compared by electron microscopy with that of a linear duplex DNA (of bacteriophage T7) when ionic strength and benzyldimethylalkylammonium chloride concentration were varied. In parallel studies the sedimentation behavior of these DNAs was studied by analytical ultracentrifugation, but for technical reasons these had to be without benzyldimethylalkylammonium chloride. By combining the information from the two methods one has to conclude that with increasing ionic strength the linear duplex T7 DNA spontaneously forms a structure similar to that of the superhelical structure of closed circular PM 2 DNA. The superstructure is destroyed under premelting conditions and in the presence of an excess of ethidium bromide. Images PMID:1069302

  3. Optimized production of ultracold ground-state molecules: Stabilization employing potentials with ion-pair character and strong spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Tomza, Michał; Goerz, Michael H.; Musiał, Monika; Moszynski, Robert; Koch, Christiane P.

    2012-10-01

    We discuss the production of ultracold molecules in their electronic ground state by photoassociation employing electronically excited states with ion-pair character and strong spin-orbit interaction. A short photoassociation laser pulse drives a nonresonant three-photon transition for alkali-metal atoms colliding in their lowest triplet state. The excited-state wave packet is transferred to the ground electronic state by a second laser pulse, driving a resonant two-photon transition. After analyzing the transition matrix elements governing the stabilization step, we discuss the efficiency of population transfer using transform-limited and linearly chirped laser pulses. Finally, we employ optimal control theory to determine the most efficient stabilization pathways. We find that the stabilization efficiency can be increased by one and two orders of magnitude when using linearly chirped and optimally shaped laser pulses, respectively.

  4. ESI-MS Investigation of an Equilibrium between a Bimolecular Quadruplex DNA and a Duplex DNA/RNA Hybrid

    NASA Astrophysics Data System (ADS)

    Birrento, Monica L.; Bryan, Tracy M.; Samosorn, Siritron; Beck, Jennifer L.

    2015-07-01

    Electrospray ionization mass spectrometry (ESI-MS) conditions were optimized for simultaneous observation of a bimolecular qDNA and a Watson-Crick base-paired duplex DNA/RNA hybrid. The DNA sequence used was telomeric DNA, and the RNA contained the template for telomerase-mediated telomeric DNA synthesis. Addition of RNA to the quadruplex DNA (qDNA) resulted in formation of the duplex DNA/RNA hybrid. Melting profiles obtained using circular dichroism spectroscopy confirmed that the DNA/RNA hybrid exhibited greater thermal stability than the bimolecular qDNA in solution. Binding of a 13-substituted berberine ( 1) derivative to the bimolecular qDNA stabilized its structure as evidenced by an increase in its stability in the mass spectrometer, and an increase in its circular dichroism (CD) melting temperature of 10°C. The DNA/RNA hybrid did not bind the ligand extensively and its thermal stability was unchanged in the presence of ( 1). The qDNA-ligand complex resisted unfolding in the presence of excess RNA, limiting the formation of the DNA/RNA hybrid. Previously, it has been proposed that DNA secondary structures, such as qDNA, may be involved in the telomerase mechanism. DNA/RNA hybrid structures occur at the active site of telomerase. The results presented in the current work show that if telomeric DNA was folded into a qDNA structure, it is possible for a DNA/RNA hybrid to form as is required during template alignment. The discrimination of ligand ( 1) for binding to the bimolecular qDNA over the DNA/RNA hybrid positions it as a useful compound for probing the role(s), if any, of antiparallel qDNA in the telomerase mechanism.

  5. The first crystal structures of RNA–PNA duplexes and a PNA-PNA duplex containing mismatches—toward anti-sense therapy against TREDs

    PubMed Central

    Kiliszek, Agnieszka; Banaszak, Katarzyna; Dauter, Zbigniew; Rypniewski, Wojciech

    2016-01-01

    PNA is a promising molecule for antisense therapy of trinucleotide repeat disorders. We present the first crystal structures of RNA–PNA duplexes. They contain CUG repeats, relevant to myotonic dystrophy type I, and CAG repeats associated with poly-glutamine diseases. We also report the first PNA–PNA duplex containing mismatches. A comparison of the PNA homoduplex and the PNA–RNA heteroduplexes reveals PNA's intrinsic structural properties, shedding light on its reported sequence selectivity or intolerance of mismatches when it interacts with nucleic acids. PNA has a much lower helical twist than RNA and the resulting duplex has an intermediate conformation. PNA retains its overall conformation while locally there is much disorder, especially peptide bond flipping. In addition to the Watson–Crick pairing, the structures contain interesting interactions between the RNA's phosphate groups and the Π electrons of the peptide bonds in PNA. PMID:26717983

  6. 60 Years of duplex stainless steel applications

    SciTech Connect

    Olsson, J.; Liljas, M.

    1994-12-31

    In this paper the history of wrought duplex stainless steel development and applications is described. Ferritic-austenitic stainless steels were introduced only a few decades after stainless steels were developed. The paper gives details from the first duplex stainless steels in the 1930`s to the super duplex stainless steel development during the 1980`s. During the years much effort has been devoted to production and welding metallurgy as well as corrosion research of the duplex stainless steels. Therefore, duplex stainless steels are to-day established in a wide product range. Numerous important applications are exemplified. In most cases the selection of a duplex steel has been a result of the combination high strength excellent corrosion resistance. In the pulp and paper industry the most interesting use is as vessel material in digesters. For chemical process industry, the duplex steels are currently used in heat exchangers. The largest application of duplex steels exists in the oil and gas/offshore industry. Hundreds of kms of pipelines are installed and are still being installed. An increased use of duplex steels is foreseen in areas where the strength is of prime importance.

  7. Covalent Bonding of Pyrrolobenzodiazepines (PBDs) to Terminal Guanine Residues within Duplex and Hairpin DNA Fragments

    PubMed Central

    Mantaj, Julia; Jackson, Paul J. M.; Karu, Kersti; Rahman, Khondaker M.; Thurston, David E.

    2016-01-01

    Pyrrolobenzodiazepines (PBDs) are covalent-binding DNA-interactive agents with growing importance as payloads in Antibody Drug Conjugates (ADCs). Until now, PBDs were thought to covalently bond to C2-NH2 groups of guanines in the DNA-minor groove across a three-base-pair recognition sequence. Using HPLC/MS methodology with designed hairpin and duplex oligonucleotides, we have now demonstrated that the PBD Dimer SJG-136 and the C8-conjugated PBD Monomer GWL-78 can covalently bond to a terminal guanine of DNA, with the PBD skeleton spanning only two base pairs. Control experiments with the non-C8-conjugated anthramycin along with molecular dynamics simulations suggest that the C8-substituent of a PBD Monomer, or one-half of a PBD Dimer, may provide stability for the adduct. This observation highlights the importance of PBD C8-substituents, and also suggests that PBDs may bind to terminal guanines within stretches of DNA in cells, thus representing a potentially novel mechanism of action at the end of DNA strand breaks. PMID:27055050

  8. Dynamics of spontaneous flipping of a mismatched base in DNA duplex

    PubMed Central

    Yin, Yandong; Yang, Lijiang; Zheng, Guanqun; Gu, Chan; Yi, Chengqi; He, Chuan; Gao, Yi Qin; Zhao, Xin Sheng

    2014-01-01

    DNA base flipping is a fundamental theme in DNA biophysics. The dynamics for a B-DNA base to spontaneously flip out of the double helix has significant implications in various DNA–protein interactions but are still poorly understood. The spontaneous base-flipping rate obtained previously via the imino proton exchange assay is most likely the rate of base wobbling instead of flipping. Using the diffusion-decelerated fluorescence correlation spectroscopy together with molecular dynamics simulations, we show that a base of a single mismatched base pair (T–G, T–T, or T–C) in a double-stranded DNA can spontaneously flip out of the DNA duplex. The extrahelical lifetimes are on the order of 10 ms, whereas the intrahelical lifetimes range from 0.3 to 20 s depending on the stability of the base pairs. These findings provide detailed understanding on the dynamics of DNA base flipping and lay down foundation to fully understand how exactly the repair proteins search and locate the target mismatched base among a vast excess of matched DNA bases. PMID:24843124

  9. Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine

    SciTech Connect

    Lee, S.; Bowman, B.R.; Ueno, Y.; Wang, S.; Verdine, G.L.

    2008-11-03

    The predominant product of aberrant DNA methylation is the genotoxic lesion N7-methyl-2{prime}-deoxyguanosine (m{sup 7}dG). M{sup 7}dG is recognized and excised by lesion-specific DNA glycosylases, namely AlkA in E. coli and Aag in humans. Structural studies of m{sup 7}dG recognition and catalysis by these enzymes have been hampered due to a lack of efficient means by which to incorporate the chemically labile m{sup 7}dG moiety site-specifically into DNA on a preparative scale. Here we report a solution to this problem. We stabilized the lesion toward acid-catalyzed and glycosylase-catalyzed depurination by 2{prime}-fluorination and toward base-catalyzed degradation using mild, nonaqueous conditions in the DNA deprotection reaction. Duplex DNA containing 2{prime}-fluoro-m{sup 7}dG (Fm{sup 7}dG) cocrystallized with AlkA as a host-guest complex in which the lesion-containing segment of DNA was nearly devoid of protein contacts, thus enabling the first direct visualization of the N7-methylguanine lesion nucleobase in DNA. The structure reveals that the base-pairing mode of Fm{sup 7}dG:C is nearly identical to that of G:C, and Fm{sup 7}dG does not induce any apparent structural disturbance of the duplex structure. These observations suggest that AlkA and Aag must perform a structurally invasive interrogation of DNA in order to detect the presence of intrahelical m{sup 7}dG lesions.

  10. Partial base flipping is sufficient for strand slippage near DNA duplex termini.

    PubMed

    Banavali, Nilesh K

    2013-06-01

    Strand slippage is a structural mechanism by which insertion-deletion (indel) mutations are introduced during replication by polymerases. Three-dimensional atomic-resolution structural pathways are still not known for the decades-old template slippage description. The dynamic nature of the process and the higher energy intermediates involved increase the difficulty of studying these processes experimentally. In the present study, restrained and unrestrained molecular dynamics simulations, carried out using multiple nucleic acid force fields, are used to demonstrate that partial base-flipping can be sufficient for strand slippage at DNA duplex termini. Such strand slippage can occur in either strand, i.e. near either the 3' or the 5' terminus of a DNA strand, which suggests that similar structural flipping mechanisms can cause both primer and template slippage. In the repetitive mutation hot-spot sequence studied, non-canonical base-pairing with exposed DNA groove atoms of a neighboring G:C base-pair stabilizes a partially flipped state of the cytosine. For its base-pair partner guanine, a similar partially flipped metastable intermediate was not detected, and the propensity for sustained slippage was also found to be lower. This illustrates that a relatively small metastable DNA structural distortion in polymerase active sites could allow single base insertion or deletion mutations to occur, and stringent DNA groove molecular recognition may be required to maintain intrinsic DNA polymerase fidelity. The implications of a close relationship between base-pair dissociation, base unstacking, and strand slippage are discussed in the context of sequence dependence of indel mutations. PMID:23692220

  11. Role of a Guanidinium Cation-Phosphodianion Pair in Stabilizing the Vinyl Carbanion Intermediate of Orotidine 5'-Phosphate Decarboxylase-Catalyzed Reactions.†

    PubMed Central

    Goryanova, Bogdana; Goldman, Lawrence M.; Amyes, Tina L.; Gerlt, John A; Richard, John P.

    2013-01-01

    The side chain cation of Arg235 provides a 5.6 and 2.6 kcal/mol stabilization of the transition states for orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae (OMPDC) catalyzed reactions of OMP and 5-fluoroorotidine 5'-monophosphate (FOMP), respectively, a 7.2 kcal/mol stabilization of the vinyl carbanion-like transition state for enzyme-catalyzed exchange of the C-6 proton of 5-fluorouridine 5'-monophosphate (FUMP), but no stabilization of the transition states for enzyme-catalyzed decarboxylation of truncated substrates 1-(β-d-erythrofuranosyl)orotic acid and 1-(β-d-erythrofuranosyl) 5-fluorouracil. These observations show that the transition state stabilization results from formation of a protein cation-phosphodianion pair, and that there is no detectable stabilization from an interaction between the side chain and the pyrimidine ring of substrate. The 5.6 kcal/mol side chain interaction with the transition state for the decarboxylation reaction is 50% of the total 11.2 kcal/mol transition state stabilization by interactions with the phosphodianion of OMP, while the 7.2 kcal/mol side-chain interaction with the transition state for the deuterium exchange reaction is a larger 78% of the total 9.2 kcal/mol transition state stabilization by interactions with the phosphodianion of FUMP. The effect of the R235A mutation on the enzyme-catalyzed deuterium exchange is expressed predominantly as a change in the turnover number kex while the effect on the enzyme-catalyzed decarboxylation of OMP is expressed predominantly as a change in the Michaelis constant Km. These results are rationalized by a mechanism in which the binding of OMP, compared with FUMP, provides a larger driving force for conversion of OMPDC from an inactive open conformation to a productive, active, closed conformation. PMID:24053466

  12. Phase Transformations in Cast Duplex Stainless Steels

    SciTech Connect

    Kim, Yoon-Jun

    2004-01-01

    Duplex stainless steels (DSS) constitute both ferrite and austenite as a matrix. Such a microstructure confers a high corrosion resistance with favorable mechanical properties. However, intermetallic phases such as σ and χ can also form during casting or high-temperature processing and can degrade the properties of the DSS. This research was initiated to develop time-temperature-transformation (TTT) and continuous-cooling-transformation (CCT) diagrams of two types of cast duplex stainless steels, CD3MN (Fe-22Cr-5Ni-Mo-N) and CD3MWCuN (Fe-25Cr-7Ni-Mo-W-Cu-N), in order to understand the time and temperature ranges for intermetallic phase formation. The alloys were heat treated isothermally or under controlled cooling conditions and then characterized using conventional metallographic methods that included tint etching, and also using electron microscopy (SEM, TEM) and wavelength dispersive spectroscopy (WDS). The kinetics of intermetallic-phase (σ + χ) formation were analyzed using the Johnson-Mehl-Avrami (MA) equation in the case of isothermal transformations and a modified form of this equation in the case of continuous cooling transformations. The rate of intermetallic-phase formation was found to be much faster in CD3MWCuN than CD3MN due mainly to differences in the major alloying contents such as Cr, Ni and Mo. To examine in more detail the effects of these elements of the phase stabilities; a series of eight steel castings was designed with the Cr, Ni and Mo contents systematically varied with respect to the nominal composition of CD3MN. The effects of varying the contents of alloying additions on the formation of intermetallic phases were also studied computationally using the commercial thermodynamic software package, Thermo-Calc. In general, σ was stabilized with increasing Cr addition and χ by increasing Mo addition. However, a delicate balance among Ni and other minor elements such as N and Si also exists. Phase equilibria in DSS can be affected by

  13. Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

    PubMed Central

    Hudson, Graham A.; Bloomingdale, Richard J.; Znosko, Brent M.

    2013-01-01

    Pseudouridine (Ψ) is the most common noncanonical nucleotide present in naturally occurring RNA and serves a variety of roles in the cell, typically appearing where structural stability is crucial to function. Ψ residues are isomerized from native uridine residues by a class of highly conserved enzymes known as pseudouridine synthases. In order to quantify the thermodynamic impact of pseudouridylation on U-A base pairs, 24 oligoribonucleotides, 16 internal and eight terminal Ψ-A oligoribonucleotides, were thermodynamically characterized via optical melting experiments. The thermodynamic parameters derived from two-state fits were used to generate linearly independent parameters for use in secondary structure prediction algorithms using the nearest-neighbor model. On average, internally pseudouridylated duplexes were 1.7 kcal/mol more stable than their U-A counterparts, and terminally pseudouridylated duplexes were 1.0 kcal/mol more stable than their U-A equivalents. Due to the fact that Ψ-A pairs maintain the same Watson-Crick hydrogen bonding capabilities as the parent U-A pair in A-form RNA, the difference in stability due to pseudouridylation was attributed to two possible sources: the novel hydrogen bonding capabilities of the newly relocated imino group as well as the novel stacking interactions afforded by the electronic configuration of the Ψ residue. The newly derived nearest-neighbor parameters for Ψ-A base pairs may be used in conjunction with other nearest-neighbor parameters for accurately predicting the most likely secondary structure of A-form RNA containing Ψ-A base pairs. PMID:24062573

  14. Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides.

    PubMed

    Hudson, Graham A; Bloomingdale, Richard J; Znosko, Brent M

    2013-11-01

    Pseudouridine (Ψ) is the most common noncanonical nucleotide present in naturally occurring RNA and serves a variety of roles in the cell, typically appearing where structural stability is crucial to function. Ψ residues are isomerized from native uridine residues by a class of highly conserved enzymes known as pseudouridine synthases. In order to quantify the thermodynamic impact of pseudouridylation on U-A base pairs, 24 oligoribonucleotides, 16 internal and eight terminal Ψ-A oligoribonucleotides, were thermodynamically characterized via optical melting experiments. The thermodynamic parameters derived from two-state fits were used to generate linearly independent parameters for use in secondary structure prediction algorithms using the nearest-neighbor model. On average, internally pseudouridylated duplexes were 1.7 kcal/mol more stable than their U-A counterparts, and terminally pseudouridylated duplexes were 1.0 kcal/mol more stable than their U-A equivalents. Due to the fact that Ψ-A pairs maintain the same Watson-Crick hydrogen bonding capabilities as the parent U-A pair in A-form RNA, the difference in stability due to pseudouridylation was attributed to two possible sources: the novel hydrogen bonding capabilities of the newly relocated imino group as well as the novel stacking interactions afforded by the electronic configuration of the Ψ residue. The newly derived nearest-neighbor parameters for Ψ-A base pairs may be used in conjunction with other nearest-neighbor parameters for accurately predicting the most likely secondary structure of A-form RNA containing Ψ-A base pairs.

  15. Triple helices formed at oligopyrimidine*oligopurine sequences with base pair inversions: effect of a triplex-specific ligand on stability and selectivity.

    PubMed Central

    Kukreti, S; Sun, J S; Loakes, D; Brown, D M; Nguyen, C H; Bisagni, E; Garestier, T; Helene, C

    1998-01-01

    Oligonucleotide-directed triple helix formation is mostly restricted to oligopyrimidine*oligopurine sequences of double helical DNA. An interruption of one or two pyrimidines in the oligopurine target strand leads to a strong triplex destabilisation. We have investigated the effect of nucleotide analogues introduced in the third strand at the site opposite the base pair inversion(s). We show that a 3-nitropyrrole derivative (M) discriminates G*C from C*G, A*T and T*A in the presence of a triplex-specific ligand (a benzo[e]pyridoindole derivative, BePI). N6-methoxy-2,6-diaminopurine (K) binds to an A*T base pair better than a T*A, G*C or C*G base pair. Some discrimination is still observed in the presence of BePI and triplex stability is markedly increased. These findings should help in designing BePI-oligonucleotide conjugates to extend the range of DNA sequences available for triplex formation. PMID:9547278

  16. Partition function and base pairing probabilities of RNA heterodimers

    PubMed Central

    Bernhart, Stephan H; Tafer, Hakim; Mückstein, Ulrike; Flamm, Christoph; Stadler, Peter F; Hofacker, Ivo L

    2006-01-01

    Background RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. Methods The standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs. Results We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures. Availability RNAcofold is distributed as part of the Vienna RNA Package, . Contact Stephan H. Bernhart – berni@tbi.univie.ac.at PMID:16722605

  17. Kinetic Monte Carlo Investigation of the Effects of Vacancy Pairing on Oxygen Diffusivity in Yttria-Stabilized Zirconia

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2011-01-01

    Yttria-stabilized zirconia s high oxygen diffusivity and corresponding high ionic conductivity, and its structural stability over a broad range of temperatures, have made the material of interest for use in a number of applications, for example, as solid electrolytes in fuel cells. At low concentrations, the stabilizing yttria also serves to increase the oxygen diffusivity through the presence of corresponding oxygen vacancies, needed to maintain charge neutrality. At higher yttria concentration, however, diffusivity is impeded by the larger number of relatively high energy migration barriers associated with yttrium cations. In addition, there is evidence that oxygen vacancies preferentially occupy nearest-neighbor sites around either dopant or Zr cations, further affecting vacancy diffusion. We present the results of ab initio calculations that indicate that it is energetically favorable for oxygen vacancies to occupy nearest-neighbor sites adjacent to Y ions, and that the presence of vacancies near either species of cation lowers the migration barriers. Kinetic Monte Carlo results from simulations incorporating this effect are presented and compared with results from simulations in which the effect is not present.

  18. Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex

    PubMed Central

    Mandal, Pradeep Kumar; Venkadesh, Sarkarai; Gautham, Namasivayam

    2012-01-01

    The crystal structure of the tetradecanucleotide sequence d(CCCCGGTACC­GGGG)2 has been determined at 2.5 Å resolution in the tetragonal space group P41. This sequence was designed with the expectation of a four-way junction. However, the sequence crystallized as an A-DNA duplex and represents more than one full turn of the A-helix. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex. The structural parameters of the A-type DNA duplex structure and the crystal-packing arrangement are described. One Mn2+ ion was identified with direct coordination to the N7 position of G13 and a water molecule at the major-groove side of the C2·G13 base pair. PMID:22505405

  19. Tandem 5'-GA:GA-3' mismatches account for the high stability of the fold-back structures formed by the centromeric Drosophila dodeca-satellite.

    PubMed

    Ortiz-Lombardía, M; Cortés, A; Huertas, D; Eritja, R; Azorín, F

    1998-04-10

    The centromeric dodeca-satellite of Drosophila forms unusual DNA structures in which its purine-rich strand (GTACGGGACCGA)n folds into very stable intramolecular hairpins. These intramolecular hairpins contain groups of tandem 5'-GA:GA-3' mismatches that, as judged by gel electrophoresis analysis and UV-melting studies, have a determinant contribution to their stability. Duplexes of the dodeca-satellite purine-rich strand, carrying tandem 5'-GA:GA-3' mismatches, are as stable as equivalent fully Watson-Crick duplexes containing tandem 5'-TA:TA-3' Watson-Crick pairs in place of the non-Watson-Crick G.A pairs. On the other hand, duplexes carrying any of the other three possible tandem combinations of purine.purine mismatches, including G.A pairs on the opposite orientation 5'-AG:AG-3', are very unstable. The high stability of the dodeca-satellite hairplus suggests that the tandem G.A pairs are on the sheared configuration although they are found within the less favourable 5'-G-(G-A)-C-3' sequence context. Other centromeres DNA sequences, including the AAGAG satellite of Drosophila and the mammalian CENP-B box sequence, have the potential of forming intramolecular hairpins stabilised by similar purine.purine interactions.

  20. A new general model for predicting melting thermodynamics of complementary and mismatched B-form duplexes containing locked nucleic acids: application to probe design for digital PCR detection of somatic mutations.

    PubMed

    Hughesman, Curtis; Fakhfakh, Kareem; Bidshahri, Roza; Lund, H Louise; Haynes, Charles

    2015-02-17

    Advances in real-time polymerase chain reaction (PCR), as well as the emergence of digital PCR (dPCR) and useful modified nucleotide chemistries, including locked nucleic acids (LNAs), have created the potential to improve and expand clinical applications of PCR through their ability to better quantify and differentiate amplification products, but fully realizing this potential will require robust methods for designing dual-labeled hydrolysis probes and predicting their hybridization thermodynamics as a function of their sequence, chemistry, and template complementarity. We present here a nearest-neighbor thermodynamic model that accurately predicts the melting thermodynamics of a short oligonucleotide duplexed either to its perfect complement or to a template containing mismatched base pairs. The model may be applied to pure-DNA duplexes or to duplexes for which one strand contains any number and pattern of LNA substitutions. Perturbations to duplex stability arising from mismatched DNA:DNA or LNA:DNA base pairs are treated at the Gibbs energy level to maintain statistical significance in the regressed model parameters. This approach, when combined with the model's accounting of the temperature dependencies of the melting enthalpy and entropy, permits accurate prediction of T(m) values for pure-DNA homoduplexes or LNA-substituted heteroduplexes containing one or two independent mismatched base pairs. Terms accounting for changes in solution conditions and terminal addition of fluorescent dyes and quenchers are then introduced so that the model may be used to accurately predict and thereby tailor the T(m) of a pure-DNA or LNA-substituted hydrolysis probe when duplexed either to its perfect-match template or to a template harboring a noncomplementary base. The model, which builds on classic nearest-neighbor thermodynamics, should therefore be of use to clinicians and biologists who require probes that distinguish and quantify two closely related alleles in either a

  1. Duplex Direct Data Distribution System

    NASA Technical Reports Server (NTRS)

    Greenfield, Israel (Technical Monitor)

    2001-01-01

    The NASA Glenn Research Center (GRC) is developing and demonstrating communications and network technologies that are helping to enable the near-Earth space Internet. GRC envisions several service categories. The first of these categories is direct data distribution or D3 (pronounced "D-cubed"). Commercially provided D3 will make it possible to download a data set from a spacecraft, like the International Space Station. as easily as one can extract a file from a remote server today, using a file transfer protocol. In a second category, NASA spacecraft will make use of commercial satellite communication (SATCOM) systems. Some of those services will come from purchasing time on unused transponders that cover landmasses. While it is likely there will be gaps in service coverage, Internet services should be available using these systems. This report addresses alternative methods of implementing a full duplex enhancement of the GRC developed experimental Ka-Band Direct Data Distribution (D3) space-to-ground communication link. The resulting duplex version is called the Duplex Direct Data Distribution (D4) system. The D4 system is intended to provide high-data-rate commercial direct or internet-based communications service between the NASA spacecraft in low earth orbit (LEO) and the respective principal investigators associated with these spacecraft. Candidate commercial services were assessed regarding their near-term potential to meet NASA requirements. Candidates included Ka-band and V-band geostationary orbit and non-geostationary orbit satellite relay services and direct downlink ("LEO teleport") services. End-to-end systems concepts were examined and characterized in terms of alternative link layer architectures. Alternatives included a Direct Link, a Relay Link, a Hybrid Link, and a Dual Mode Link. The direct link assessment examined sample ground terminal placements and antenna angle issues. The SATCOM-based alternatives examined existing or proposed commercial

  2. Structural, Dynamical and Electronic Transport Properties of Modified DNA Duplexes Containing Size-Expanded Nucleobases

    SciTech Connect

    Sumpter, Bobby G; Fuentes-Cabrera, Miguel A

    2011-01-01

    Among the distinct strategies proposed to expand the genetic alphabet, size-expanded nucleobases are promising for the development of modified DNA duplexes with improved biotechnological properties. In particular, duplexes built up by replacing canonical bases with the corresponding benzo-fused counterparts could be valuable as molecular nanowires. In this context, this study reports the results of classical molecular dynamics simulations carried out to examine the structural and dynamical features of size-expanded DNAs, including both hybrid duplexes containing mixed pairs of natural and benzo-fused bases (xDNA) and pure size-expanded (xxDNA) duplexes. Furthermore, the electronic structure of both natural and size-expanded duplexes is examined by means of density functional computations. The results confirm that the structural and flexibility properties of the canonical DNA are globally little affected by the presence of benzo-fused bases. The most relevant differences are found in the enhanced size of the grooves, and the reduction in the twist. However, the analysis also reveals subtle structural effects related to the nature and sequence of benzo-fused bases in the duplex. On the other hand, electronic structure calculations performed for xxDNAs confirm the reduction in the HOMO-LUMO gap predicted from the analysis of the natural bases and their size-expanded counterparts, which suggests that pure size-expanded DNAs can be good conductors. A more complex situation is found for xDNAs, where fluctuations in the electrostatic interaction between base pairs exerts a decisive influence on the modulation of the energy gap.

  3. Structural, Dynamical, and Electronic Transport Properties of Modified DNA Duplexes Containing Size-Expanded Nucleobases

    SciTech Connect

    Fuentes-Cabrera, Miguel A; Orozco, Modesto; Luque, Javier; Sumpter, Bobby G; Blas, Jose; Ordejon, Pablo J; Huertas, Oscar; Tabares, Carolina

    2011-01-01

    Among the distinct strategies proposed to expand the genetic alphabet, sizeexpanded nucleobases are promising for the development of modified DNA duplexes with improved biotechnological properties. In particular, duplexes built up by replacing canonical bases with the corresponding benzo-fused counterparts could be valuable as molecular nanowires. In this context, this study reports the results of classical molecular dynamics simulations carried out to examine the structural and dynamical features of size-expanded DNAs, including both hybrid duplexes containing mixed pairs of natural and benzo-fused bases (xDNA) and pure size-expanded (xxDNA) duplexes. Furthermore, the electronic structure of both natural and size-expanded duplexes is examined by means of density functional computations. The results confirm that the structural and flexibility properties of the canonical DNA are globally little affected by the presence of benzo-fused bases. Themost relevant differences are found in the enhanced size of the grooves, and the reduction in the twist. However, the analysis also reveals subtle structural effects related to the nature and sequence of benzo-fused bases in the duplex. On the other hand, electronic structure calculations performed for xxDNAs confirm the reduction in the HOMOLUMO gap predicted from the analysis of the natural bases and their size-expanded counterparts, which suggests that pure size-expanded DNAs can be good conductors. A more complex situation is found for xDNAs, where fluctuations in the electrostatic interaction between base pairs exerts a decisive influence on the modulation of the energy gap.

  4. Effect of thiazole orange doubly labeled thymidine on DNA duplex formation.

    PubMed

    Kimura, Yasumasa; Hanami, Takeshi; Tanaka, Yuki; de Hoon, Michiel J L; Soma, Takahiro; Harbers, Matthias; Lezhava, Alexander; Hayashizaki, Yoshihide; Usui, Kengo

    2012-08-01

    Nucleic acid oligonucleotides are widely used in hybridization experiments for specific detection of complementary nucleic acid sequences. For design and application of oligonucleotides, an understanding of their thermodynamic properties is essential. Recently, exciton-controlled hybridization-sensitive fluorescent oligonucleotides (ECHOs) were developed as uniquely labeled DNA oligomers containing commonly one thymidine having two covalently linked thiazole orange dye moieties. The fluorescent signal of an ECHO is strictly hybridization-controlled, where the dye moieties have to intercalate into double-stranded DNA for signal generation. Here we analyzed the hybridization thermodynamics of ECHO/DNA duplexes, and thermodynamic parameters were obtained from melting curves of 64 ECHO/DNA duplexes measured by ultraviolet absorbance and fluorescence. Both methods demonstrated a substantial increase in duplex stability (ΔΔG°(37) ~ -2.6 ± 0.7 kcal mol(-1)) compared to that of DNA/DNA duplexes of the same sequence. With the exception of T·G mismatches, this increased stability was mostly unaffected by other mismatches in the position opposite the labeled nucleotide. A nearest neighbor model was constructed for predicting thermodynamic parameters for duplex stability. Evaluation of the nearest neighbor parameters by cross validation tests showed higher predictive reliability for the fluorescence-based than the absorbance-based parameters. Using our experimental data, a tool for predicting the thermodynamics of formation of ECHO/DNA duplexes was developed that is freely available at http://genome.gsc.riken.jp/echo/thermodynamics/. It provides reliable thermodynamic data for using the unique features of ECHOs in fluorescence-based experiments.

  5. Cisplatin-induced duplex dissociation of complementary and destabilized short GG-containing duplex RNAs.

    PubMed

    Polonyi, Christopher; Alshiekh, Alak; Sarsam, Lamya A; Clausén, Maria; Elmroth, Sofi K C

    2014-08-21

    The ability of the anticancer active drug cisplatin to exert biological activity through interference with nucleic acid function is well documented. Since kinetics play a key role in determining product distributions in these systems, methods for accurate documentation of reactivity serve the purpose to identify preferential metal binding sites. In the present study, the aim has been to further explore a recently communicated approach (C. Polonyi and S. K. C. Elmroth, J. Chem. Soc., Dalton Trans., 2013, 42, 14959-14962) utilizing UV/vis spectroscopy and metal induced duplex RNA melting for monitoring of kinetics. More specifically, the sensitivity of the UV/vis-methodology has been evaluated by investigation of how overall length and changes of base-pairing in the close vicinity of a centrally located GG-site affect the rate of cisplatin binding, using the intracellularly active mono-aquated form of cisplatin (cis-Pt(NH3)2Cl(OH2)(+), ()) as the platination reagent. For this purpose, the reactivity of five different 13- to 17 base-pair duplex RNAs was monitored at 38 °C. A common trend of a ca. 10-fold reduction in reactivity was found to accompany an increase of bulk sodium concentration from CNa+ = 122 mM to 1.0 M. Typical half-lives are exemplified by the interaction of with the fully complementary 15-mer RNA-1 with t1/2 = ca. 0.5 and 4.8 hours, at CNa+ = 122 mM and 1.0 M respectively, and C = 45 μM. Lowering of melting temperature (Tm) was found to promote reactivity regardless of whether the change involved a decrease or increase of the RNA length. For example, at CNa+ = 1.0 M, truncation of the fully complementary and GG-containing 15-mer RNA-1 (Tm = 68.9 °C) to the 13-mer RNA-1-1-S (Tm = 63.9 °C) resulted in an increase of k2,app from ca. 0.9 M(-1) s(-1) to 2.0 M(-1) s(-1). Further, the 17-mer RNA-1-4 (Tm = 42.0 °C) with a central U4 bulge exhibited the highest reactivity of the sequences studied with k2,app = 4.0 M(-1) s(-1). The study shows that the

  6. The hydrogen-bonding structure in parallel-stranded duplex DNA is reverse Watson-Crick

    SciTech Connect

    Otto, C., Thomas, G.A.; Peticolas, W.L. ); Rippe, K.; Jovin, T.M. )

    1991-03-26

    Raman spectra of the parallel-stranded duplex formed from the deoxyoligonucleotides 5{prime}-d-((A){sub 10}TAATTTTAAATATTT)-3{prime} (D1) and 5{prime}-d((T){sub 10}ATTAAAATTTATAAA)-3{prime} (D2) in H{sub 2}O and D{sub 2}O have been acquired. The spectra of the parallel-stranded DNA are then compared to the spectra of the antiparallel double helix formed from the deoxyoligonucleotides D1 and 5{prime}-d(AAATATTTAAAATTA-(T){sub 10})-3{prime} (D3). The Raman spectra of the antiparallel-stranded (aps) duplex are reminiscent of the spectra of poly(d(A)){center dot}poly(d(T)) and a B-form structure similar to that adopted by the homopolymer duplex is assigned to the antiparallel double helix. The spectra of the parallel-stranded (ps) and antiparallel-stranded duplexes differ significantly due to changes in helical organization, i.e., base pairing, base stacking, and backbone conformation. Large changes observed in the carbonyl stretching region implicate the involvement of the C(2) carbonyl of thymine in base pairing. The interaction of adenine with the C(2) carbonyl of thymine is consistent with formation of reverse Watson-Crick base pairing in parallel-stranded DNA. Phosphate-furanose vibrations similar to those observed for B-form DNA of heterogeneous sequence and high A,T content are observed at 843 and 1,092 cm{sup {minus}1} in the spectra of the parallel-stranded duplex.

  7. Comparison of Proteins Involved in Pilus Synthesis and Mating Pair Stabilization from the Related Plasmids F and R100-1: Insights into the Mechanism of Conjugation

    PubMed Central

    Anthony, Karen G.; Klimke, William A.; Manchak, Jan; Frost, Laura S.

    1999-01-01

    F and R100-1 are closely related, derepressed, conjugative plasmids from the IncFI and IncFII incompatibility groups, respectively. Heteroduplex mapping and genetic analyses have revealed that the transfer regions are extremely similar between the two plasmids. Plasmid specificity can occur at the level of relaxosome formation, regulation, and surface exclusion between the two transfer systems. There are also differences in pilus serology, pilus-specific phage sensitivity, and requirements for OmpA and lipopolysaccharide components in the recipient cell. These phenotypic differences were exploited in this study to yield new information about the mechanism of pilus synthesis, mating pair stabilization, and surface and/or entry exclusion, which are collectively involved in mating pair formation (Mpf). The sequence of the remainder of the transfer region of R100-1 (trbA to traS) has been completed, and the complete sequence is compared to that of F. The differences between the two transfer regions include insertions and deletions, gene duplications, and mosaicism within genes, although the genes essential for Mpf are conserved in both plasmids. F+ cells carrying defined mutations in each of the Mpf genes were complemented with the homologous genes from R100-1. Our results indicate that the specificity in recipient cell recognition and entry exclusion are mediated by TraN and TraG, respectively, and not by the pilus. PMID:10464182

  8. Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.

    PubMed

    Kumar, S; Reed, M W; Gamper, H B; Gorn, V V; Lukhtanov, E A; Foti, M; West, J; Meyer, R B; Schweitzer, B I

    1998-02-01

    The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restrained molecular dynamics and relaxation matrix refinement, the solution structure of the CDPI3-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and that the CDPI3moiety was bound snugly in the minor groove, where it was stabilized by extensive van der Waal's interactions.

  9. Effect of loop length variation on quadruplex-Watson Crick duplex competition

    PubMed Central

    Kumar, Niti; Sahoo, Bankanidhi; Varun, K. A. S.; Maiti, Sudipta; Maiti, Souvik

    2008-01-01

    The effect of loop length on quadruplex stability has been studied when the G-rich strand is present along with its complementary C-rich strand, thereby resulting in competition between quadruplex and duplex structures. Using model sequences with loop lengths varying from T to T5, we carried out extensive FRET to discover the influence of loop length on the quadruplex-Watson Crick duplex competition. The binding data show an increase in the binding affinity of quadruplexes towards their complementary strands upon increasing the loop length. Our kinetic data reveal that unfolding of the quadruplex in presence of a complementary strand involves a contribution from a predominant slow and a small population of fast opening conformer. The contribution from the fast opening conformer increases upon increasing the loop length leading to faster duplex formation. FCS data show an increase in the interconversion between the quadruplex conformers in presence of the complementary strand, which shifts the equilibrium towards the fast opening conformer with an increase in loop length. The relative free-energy difference (ΔΔG°) between the duplex and quadruplex indicates that an increase in loop length favors duplex formation and out competes the quadruplex. PMID:18599514

  10. Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.

    PubMed

    Kumar, S; Reed, M W; Gamper, H B; Gorn, V V; Lukhtanov, E A; Foti, M; West, J; Meyer, R B; Schweitzer, B I

    1998-02-01

    The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restrained molecular dynamics and relaxation matrix refinement, the solution structure of the CDPI3-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and that the CDPI3moiety was bound snugly in the minor groove, where it was stabilized by extensive van der Waal's interactions. PMID:9443977

  11. Duplex sampling apparatus and method

    DOEpatents

    Brown, Paul E.; Lloyd, Robert

    1992-01-01

    An improved apparatus is provided for sampling a gaseous mixture and for measuring mixture components. The apparatus includes two sampling containers connected in series serving as a duplex sampling apparatus. The apparatus is adapted to independently determine the amounts of condensable and noncondensable gases in admixture from a single sample. More specifically, a first container includes a first port capable of selectively connecting to and disconnecting from a sample source and a second port capable of selectively connecting to and disconnecting from a second container. A second container also includes a first port capable of selectively connecting to and disconnecting from the second port of the first container and a second port capable of either selectively connecting to and disconnecting from a differential pressure source. By cooling a mixture sample in the first container, the condensable vapors form a liquid, leaving noncondensable gases either as free gases or dissolved in the liquid. The condensed liquid is heated to drive out dissolved noncondensable gases, and all the noncondensable gases are transferred to the second container. Then the first and second containers are separated from one another in order to separately determine the amount of noncondensable gases and the amount of condensable gases in the sample.

  12. Polymorphism of nucleic acid duplexes as revealed by X-ray diffraction analysis of oriented fibers

    SciTech Connect

    Arnott, S.

    1980-10-01

    Complementary base-paired polynucleotide duplexes are quite polymorphic. This is not surprising when one considers that the shape of their usual unit of structure, the nucleotide, has six endocyclic bonds and a fairly flexible furanose ring with which to contrive changes in shape. These different residue shapes confer very distinctive morphologies on the polymer helices which incorporate them. These differences are indicated by the axial translation (h) and rotation (t) per nucleotide residue in each helix.

  13. The cardiac muscle duplex as a method to study myocardial heterogeneity

    PubMed Central

    Solovyova, O.; Katsnelson, L.B.; Konovalov, P.V.; Kursanov, A.G.; Vikulova, N.A.; Kohl, P.; Markhasin, V.S.

    2014-01-01

    This paper reviews the development and application of paired muscle preparations, called duplex, for the investigation of mechanisms and consequences of intra-myocardial electro-mechanical heterogeneity. We illustrate the utility of the underlying combined experimental and computational approach for conceptual development and integration of basic science insight with clinically relevant settings, using previously published and new data. Directions for further study are identified. PMID:25106702

  14. Ion-pairing ability, chemical stability, and selectivity behavior of halogenated dodecacarborane cation exchangers in neutral carrier-based ion-selective electrodes.

    PubMed

    Peper, Shane; Qin, Yu; Almond, Philip; McKee, Michael; Telting-Diaz, Martin; Albrecht-Schmitt, Thomas; Bakker, Eric

    2003-05-01

    Recently, it has been discovered that carba-closo-dodecaborates can be used as cation exchangers in neutral carrier-based ion-selective chemical sensors. Because of their inherent chemical stability and versatile functionalization chemistries, they offer many advantages that may potentially be exploited for ion analyses that require nontraditional sample conditions, including strongly acidic media. In this work, trimethylammonium salts of undecachlorinated (UCC), undecabrominated (UBC), hexabrominated (HBC), and undecaiodinated (UIC) carborane anions were prepared and evaluated for their potential use in solvent polymeric membrane-based sensors. Computational methods including Natural population analysis and electrostatic mapping were used to predict the ion-exchanging ability of each lipophilic anion. In addition, the sandwich membrane technique was used to evaluate the ion-pairing ability of each carborane anion in situ (i.e., within bis(2-ethylhexyl) sebacate (DOS)- and 2-nitrophenyl octyl ether (o-NPOE)-plasticized ISE membranes). The results of the computational and potentiometric studies found that binding affinity of the anions followed the generalized trend HBC > UCC > UBC > UIC. PVC-DOS bulk optode thin films containing the chromoionophore ETH 5315 and a respective anion were used to determine the chemical stability/lipophilicity of the carboranes and tetrakis[3,5-bis(trifluoromethyl)phenyl] borate (TFPB) in acidic media (0.2 M HOAc) under flowing conditions. The studies found that in terms of stability/lipophilicity UIC > UBC > TFPB approximately UCC > HBC. Electrodes containing a Pb(2+)-selective ionophore, tert-butylcalix[4]arene-tetrakis(N,N-dimethylthioacetamide)(lead IV), were used to evaluate the functionality of each cation exchanger. An evaluation of response characteristics such as slope and selectivity found that UIC and UBC were quite comparable to the behavior of TFPB. Interestingly, both UIC and UBC showed a marked selectivity improvement

  15. The Contribution of DNA Single-Stranded Order to the Thermodynamics of Duplex Formation

    NASA Astrophysics Data System (ADS)

    Vesnaver, Gorazd; Breslauer, Kenneth J.

    1991-05-01

    We report a direct determination of the thermodynamic contribution that DNA single-stranded order makes to DNA duplex formation. By using differential scanning calorimetry (DSC) and temperature-dependent UV absorbance spectroscopy, we have characterized thermodynamically the thermally induced disruption of the 13-mer duplex [d(CGCATGAGTACGC)]\\cdot[d(GCGTACTCATGCG)] (henceforth called S_1\\cdotS_2) and its component single strands,[d(CGCATGAGTACGC)] (henceforth called S_1) and ]d(GCGTACTCATGCG)] (henceforth called S_2). These spectroscopic and calorimetric measurements yield the following thermodynamic profiles at 25^circC: Δ G^circ = 20.0 kcal/mol, Δ H^circ = 117.0 kcal/mol, and Δ S^circ = 325.4 cal\\cdotdegree-1\\cdotmol-1 for duplex melting of S_1\\cdotS_2; Δ G^circ = 0.45 kcal/mol, Δ H^circ = 29.1 kcal/mol, and Δ S^circ = 96.1 cal\\cdotdegree-1\\cdotmol-1 for single-strand melting of S_1; Δ G^circ = 1.44 kcal/mol, Δ H^circ = 27.2 kcal/mol, and Δ S^circ = 86.4 cal\\cdotdegree-1\\cdotmol-1 for single-strand melting of S_2 (1 cal = 4.184 J). These data reveal that the two single-stranded structures S_1 and S_2 are only marginally stable at 25^circC, despite exhibiting rather substantial transition enthalpies. This behavior results from enthalpy and entropy contributions of similar magnitudes that compensate each other, thereby giving rise to relatively small free energies of stabilization for the single strands at 25^circC. By contrast, the S_1\\cdotS_2 duplex state is very stable at 25^circC since the favorable transition entropy associated with duplex disruption (325.4 cal\\cdotdegree-1\\cdotmol-1) is more than compensated for by the extremely large duplex transition enthalpy (117.0 kcal/mol). We also measured directly an enthalpy change (Δ H^circ) of -56.4 kcal/mol for duplex formation at 25^circC using isothermal batch-mixing calorimetry. This duplex formation enthalpy of -56.4 kcal/mol at 25^circC is very different in magnitude from the duplex

  16. Defusing Complexity in Intermetallics: How Covalently Shared Electron Pairs Stabilize the FCC Variant Mo2Cu(x)Ga(6-x) (x ≈ 0.9).

    PubMed

    Kilduff, Brandon J; Yannello, Vincent J; Fredrickson, Daniel C

    2015-08-17

    Simple sphere packings of metallic atoms are generally assumed to exhibit highly delocalized bonding, often visualized in terms of a lattice of metal cations immersed in an electron gas. In this Article, we present a compound that demonstrates how covalently shared electron pairs can, in fact, play a key role in the stability of such structures: Mo2Cu(x)Ga(6-x) (x ≈ 0.9). Mo2Cu(x)Ga(6-x) adopts a variant of the common TiAl3 structure type, which itself is a binary coloring of the fcc lattice. Electronic structure calculations trace the formation of this compound to a magic electron count of 14 electrons/T atom (T = transition metal) for the TiAl3 type, for which the Fermi energy coincides with an electronic pseudogap. This count is one electron/T atom lower than the electron concentration for a hypothetical MoGa3 phase, making this structure less competitive relative to more complex alternatives. The favorable 14 electron count can be reached, however, through the partial substitution of Ga with Cu. Using DFT-calibrated Hückel calculations and the reversed approximation Molecular Orbital (raMO) method, we show that the favorability of the 14 electron count has a simple structural origin in terms of the 18 - n rule of T-E intermetallics (E = main group element): the T atoms of the TiAl3 type are arranged into square nets whose edges are bridged by E atoms. The presence of shared electron pairs along these T-T contacts allows for 18 electron configurations to be achieved on the T atoms despite possessing only 18 - 4 = 14 electrons/T atom. This bonding scheme provides a rationale for the observed stability range of TiAl3 type TE3 phases of ca. 13-14 electrons/T atom, and demonstrates how the concept of the covalent bond can extend even to the most metallic of structure types.

  17. FACILITY 810, REAR OF DUPLEX SHOWING COURTYARD BETWEEN WINGS, OBLIQUE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    FACILITY 810, REAR OF DUPLEX SHOWING COURTYARD BETWEEN WINGS, OBLIQUE VIEW FACING EAST. - Schofield Barracks Military Reservation, Duplex Housing Type with Corner Entries, Between Hamilton & Tidball Streets near Williston Avenue, Wahiawa, Honolulu County, HI

  18. Overstretching of a 30 bp DNA duplex studied with steered molecular dynamics simulation: Effects of structural defects on structure and force-extension relation

    NASA Astrophysics Data System (ADS)

    Li, H.; Gisler, T.

    2009-11-01

    Single-molecule experiments on polymeric DNA show that the molecule can be overstretched at nearly constant force by about 70% beyond its relaxed contour length. In this publication we use steered molecular dynamics (MD) simulation to study the effect of structural defects on force-extension curves and structures at high elongation in a 30 base pair duplex pulled by its torsionally unconstrained 5' -5' ends. The defect-free duplex shows a plateau in the force-extension curve at 120pN in which large segments with inclined and paired bases (“S-DNA”) near both ends of the duplex coexist with a central B-type segment separated from the former by small denaturation bubbles. In the presence of a base mismatch or a nick, force-extension curves are very similar to the ones of the defect-free duplex. For the duplex with a base mismatch, S-type segments with highly inclined base pairs are not observed; rather, the overstretched duplex consists of B-type segments separated by denaturation bubbles. The nicked duplex evolves, via a two-step transition, into a two-domain structure characterized by a large S-type segment coexisting with several short S-type segments which are separated by short denaturation bubbles. Our results suggest that in the presence of nicks the force-extension curve of highly elongated duplex DNA might reflect locally highly inhomogeneous stretching. Supplementary material in the form of a PDF file available from the Journal web page at 10.1140/epje/i2009-10524-5 and is accessible for authorised users.

  19. Extensional duplex in the Purcell Mountains of southeastern British Columbia

    SciTech Connect

    Root, K.G. )

    1990-05-01

    An extensional duplex consisting of fault-bounded blocks (horses) located between how-angle normal faults is exposed in Proterozoic strata in the Purcell Mountains of British Columbia, Canada. This is one of the first documented extensional duplexes, and it is geometrically and kinematically analogous to duplexes developed in contractional and strike-slip fault systems. The duplex formed within an extensional fault with a ramp and flat geometry when horses were sliced from the ramp and transported within the fault system.

  20. Introduction of a thermophile-sourced ion pair network in the fourth beta/alpha unit of a psychophile-derived triosephosphate isomerase from Methanococcoides burtonii significantly increases its kinetic thermal stability.

    PubMed

    Dhaunta, Neeraj; Arora, Kanika; Chandrayan, Sanjeev K; Guptasarma, Purnananda

    2013-06-01

    Hyperthermophile proteins commonly have higher numbers of surface ionic interactions than homologous proteins from other domains of life. PfuTIM, a triosephosphate isomerase (TIM) from the hyperthermophile archaeon, Pyrococcus furiosus, contains an intricate network of 4 ion pairs in its 4th beta/alpha unit, (β/α)4, whereas MbuTIM, a triosephosphate isomerase from a psychrophile archaeon, Methanococcoides burtonii, lacks this network. Notably, (β/α)4 is the first element of the structure formed during folding of certain TIM-type (beta/alpha)8 barrel proteins. Previously, we have shown that elimination of PfuTIM's ion pair network in PfuTIM significantly decreases its kinetic structural stability. Here, we describe the reciprocal experiment in which this ion pair network is introduced into MbuTIM, to produce MutMbuTIM. Recombinant MbuTIM displays multi-state unfolding with apparent Tm values of autonomous structural elements approaching, or above, 70°C, when a temperature scanning rate of 90°C/h is used. The protein displays significant intrinsic kinetic stability, i.e., there is a marked temperature scan rate-dependence of the Tm values associated with unfolding transitions. The Tm values drop by as much as ~10°C when the temperature scanning rate is lowered to 5°C/h. MutMbuTIM, incorporating PfuTIM's ion pair network, shows significantly higher apparent Tm values (raised by 4-6°C over those displayed by MbuTIM). MutMbuTIM also displays significantly higher kinetic thermal stability. Thus, it appears that the thermal stability of triosephosphate isomerase can be increased, or decreased, by either enhancing, or reducing, the strength of ion pair interactions stabilizing (β/α)4, presumably through reduced cooperativity (and increased autonomy) in unfolding transitions.

  1. Crystal structure of an RNA helix recognized by a zinc-finger protein: an 18-bp duplex at 1.6 A resolution.

    PubMed Central

    Lima, Susana; Hildenbrand, Jayne; Korostelev, Andrei; Hattman, Stanley; Li, Hong

    2002-01-01

    The crystal structure of the 19-mer RNA, 5'-GAAUGCCUGCGAGCAUCCC-3' has been determined from X-ray diffraction data to 1.6 A resolution by the multiwavelength anomalous diffraction method from crystals containing a brominated uridine. In the crystal, this RNA forms an 18-mer self-complementary double helix with the 19th nucleotide flipped out of the helix. This helix contains most of the target stem recognized by the bacteriophage Mu Com protein (control of mom), which activates translation of an unusual DNA modification enzyme, Mom. The 19-mer duplex, which contains one A.C mismatch and one A.C/G.U tandem wobble pair, was shown to bind to the Com protein by native gel electrophoresis shift assay. Comparison of the geometries and base stacking properties between Watson-Crick base pairs and the mismatches in the crystal structure suggest that both hydrogen bonding and base stacking are important for stabilizing these mismatched base pairs, and that the unusual geometry adopted by the A.C mismatch may reveal a unique structural motif required for the function of Com. PMID:12166647

  2. Ultra-short silicon MMI duplexer

    NASA Astrophysics Data System (ADS)

    Yi, Huaxiang; Huang, Yawen; Wang, Xingjun; Zhou, Zhiping

    2012-11-01

    The fiber-to-the-home (FTTH) systems are growing fast these days, where two different wavelengths are used for upstream and downstream traffic, typically 1310nm and 1490nm. The duplexers are the key elements to separate these wavelengths into different path in central offices (CO) and optical network unit (ONU) in passive optical network (PON). Multimode interference (MMI) has some benefits to be a duplexer including large fabrication tolerance, low-temperature dependence, and low-polarization dependence, but its size is too large to integrate in conventional case. Based on the silicon photonics platform, ultra-short silicon MMI duplexer was demonstrated to separate the 1310nm and 1490nm lights. By studying the theory of self-image phenomena in MMI, the first order images are adopted in order to keep the device short. A cascaded MMI structure was investigated to implement the wavelength splitting, where both the light of 1310nm and 1490nm was input from the same port, and the 1490nm light was coupling cross the first MMI and output at the cross-port in the device while the 1310nm light was coupling through the first and second MMI and output at the bar-port in the device. The experiment was carried on with the SOI wafer of 340nm top silicon. The cascaded MMI was investigated to fold the length of the duplexer as short as 117μm with the extinct ratio over 10dB.

  3. Microhydration of guanine...cytosine base pairs, a theoretical Study on the role of water in stability, structure and tautomeric equilibrium.

    PubMed

    Zelený, Tomás; Hobza, Pavel; Kabelác, Martin

    2009-05-14

    The potential energy surfaces of guanine...cytosine complexes and microhydrated guanine...cytosine (one and two water molecules) were investigated by the molecular dynamics/quenching method (MD/Q), using the empirical potential Parm94 force field, implemented in the Amber program package. The calculations were conducted for all the possible combinations of the four most stable tautomers of guanine and three of cytosine (covering the canonical forms in both cases). The obtained structures were sorted by their structural motifs into three main groups: planar hydrogen-bonded; stacked; and T-shaped structures. The most stable structures found at the empirical potential energy surfaces were fully reoptimised at the second-order Møller-Plesset perturbation theory as well as using the density functional method with an empirical dispersion term (DFT-D). A combination of the canonical form of guanine and cytosine and canonical cytosine with a guanine tautomer where the hydrogen is switched from position N9 to N7 are energetically preferred in microsolvated systems as well as those without the presence of a solvent. The rising number of water molecules leads to smaller differences between the stability of the various combinations of the tautomers of bases in the base pairs. For some of the tautomer combinations (mainly the enol-enol combination), two water molecules are sufficient for the preference of stacked structures over the H-bonded ones. The interaction energies and geometries obtained by the second-order Møller-Plesset perturbation theory method and the much less computationally demanding DFT-D method are comparable, except for stacked complexes, where the interaction energies are overestimated on average by 3 kcal mol(-1) at the MP2 level. PMID:19421545

  4. Effects of a Protecting Osmolyte on The Ion Atmosphere Surrounding DNA Duplexes

    PubMed Central

    Blose, Joshua M.; Pabit, Suzette A.; Meisburger, Steve P.; Li, Li; Jones, Christopher D.; Pollack, Lois

    2012-01-01

    Osmolytes are small, chemically diverse, organic solutes that function as an essential component of cellular stress response. Protecting osmolytes enhance protein stability via preferential exclusion, and non-protecting osmolytes, such as urea, destabilize protein structures. Although much is known about osmolyte effects on proteins, less is understood about osmolyte effects on nucleic acids and their counterion atmospheres. Non-protecting osmolytes destabilize nucleic acid structures, but effects of protecting osmolytes depend on numerous factors including the type of nucleic acid and the complexity of the functional fold. To begin quantifying protecting osmolyte effects on nucleic acid interactions we used small angle x-ray scattering (SAXS) techniques to monitor DNA duplexes in the presence of sucrose. This protecting osmolyte is a commonly used contrast matching agent in SAXS studies of protein-nucleic acid complexes, thus it is important to characterize interaction changes induced by sucrose. Measurements of interactions between duplexes showed no dependence on the presence of up to 30% sucrose except under high Mg2+ conditions where stacking interactions were disfavored. The number of excess ions associated with DNA duplexes, reported by anomalous small angle x-ray scattering (ASAXS) experiments, was sucrose independent. Although protecting osmolytes can destabilize secondary structures, our results suggest that ion atmospheres of individual duplexes remain unperturbed by sucrose. PMID:21882885

  5. Mechanistic studies of hairpin to duplex conversion for trinucleotide repeat sequences.

    PubMed

    Avila Figueroa, Amalia; Delaney, Sarah

    2010-05-01

    The expansion of a trinucleotide repeat sequence, such as CAG/CTG, has been pinpointed as the molecular basis for a number of neurodegenerative disorders. It has been proposed that as part of the expansion process, these repetitive sequences adopt non-B conformations such as hairpins. However, the prevalence of these hairpins and their contributions to the DNA expansion have not been well defined. In this work, we utilized a molecular beacon strategy to examine the stability of the (CAG)(10) hairpin and also its behavior in the presence of the complementary (CTG)(10) hairpin. We find that the two hairpins represent kinetically trapped species that can coexist but irreversibly convert to duplex upon thermal induction. Furthermore, as monitored by fluorescence and optical analysis, modifications to the base composition of either the loop or stem region have a profound effect on the ability of the trinucleotide repeat hairpins to convert to duplex. Additionally, the rate of duplex formation is also reduced with these loop and stem-modified hairpins. These results demonstrate that the trinucleotide repeat hairpins can convert to duplex via two independent mechanisms as follows: the loop-loop interactions found in kissing hairpins or the stem-stem interactions of a cruciform.

  6. Hydrogen effects in duplex stainless steel welded joints - electrochemical studies

    NASA Astrophysics Data System (ADS)

    Michalska, J.; Łabanowski, J.; Ćwiek, J.

    2012-05-01

    In this work results on the influence of hydrogen on passivity and corrosion resistance of 2205 duplex stainless steel (DSS) welded joints are described. The results were discussed by taking into account three different areas on the welded joint: weld metal (WM), heat-affected zone (HAZ) and parent metal. The corrosion resistance was qualified with the polarization curves registered in a synthetic sea water. The conclusion is that, hydrogen may seriously deteriorate the passive film stability and corrosion resistance to pitting of 2205 DSS welded joints. The presence of hydrogen in passive films increases corrosion current density and decreases the potential of the film breakdown. It was also found that degree of susceptibility to hydrogen degradation was dependent on the hydrogen charging conditions. WM region has been revealed as the most sensitive to hydrogen action.

  7. Water and ion binding around r(UpA)12 and d(TpA)12 oligomers--comparison with RNA and DNA (CpG)12 duplexes.

    PubMed

    Auffinger, P; Westhof, E

    2001-02-01

    The structural and dynamic properties of the water and ion first coordination shell of the r(A-U) and d(A-T) base-pairs embedded within the r(UpA)12 and d(TpA)12 duplexes are described on the basis of two 2.4 ns molecular dynamics simulations performed in a neutralizing aqueous environment with 0.25 M added KCl. The results are compared to previous molecular dynamics simulations of the r(CpG)12 and d(CpG)12 structures performed under similar conditions. It can be concluded that: (i) RNA helices are more rigid than DNA helices of identical sequence, as reflected by the fact that RNA duplexes keep their initial A-form shape while DNA duplexes adopt more sequence-specific shapes. (ii) Around these base-pairs, the water molecules occupy 21 to 22 well-defined hydration sites, some of which are partially occupied by potassium ions. (iii) These hydration sites are occupied by an average of 21.9, 21.0, 20.1, and 19.8 solvent molecules (water and ions) around the r(G=C), r(A-U), d(G=C), and d(A-T) pairs, respectively. (iv) From a dynamic point of view, the stability of the hydration shell is the strongest for the r(G=C) pairs and the weakest for the d(A-T) pairs. (v) For RNA, the observed long-lived hydration patterns are essentially non-sequence dependent and involve water bridges located in the deep groove and linking OR atoms of adjacent phosphate groups. Maximum lifetimes are close to 400 ps. (vi) In contrast, for DNA, long-lived hydration patterns are sequence dependent and located in the minor groove. For d(CpG)12, water bridges linking the (G)N3 and (C)O2 with the O4' atoms of adjacent nucleotides with 400 ps maximum lifetimes are characterized while no such bridges are observed for d(TpA)12. (vii) Potassium ions are observed to bind preferentially to deep/major groove atoms at RpY steps, essentially d(GpC), r(GpC), and r(ApU), by forming ion-bridges between electronegative atoms of adjacent base-pairs. On average, about half an ion is observed per base-pair

  8. Pick a Pair. Pancake Pairs

    ERIC Educational Resources Information Center

    Miller, Pat

    2005-01-01

    Cold February weather and pancakes are a traditional pairing. Pancake Day began as a way to eat up the foods that were abstained from in Lent--traditionally meat, fat, eggs and dairy products. The best-known pancake event is The Pancake Day Race in Buckinghamshire, England, which has been run since 1445. This column describes pairs of books that…

  9. Helix-coil transition of the self-complementary dG-dG-dA-dA-dT-dT-dC-dC duplex.

    PubMed

    Patel, D J; Canuel, L L

    1979-05-15

    The helix-coil transition of the octanucleotide self-complementary duplex dG-dG-dA-dA-dT-dT-dC-dC has been monitored at the Watson-Crick protons, the base and sugar nonexchangeable protons and the backbone phosphates by high-resolution nuclear magnetic resonance (NMR) spectroscopy. The melting transition of the octanucleotide monitored by ultraviolet absorbance spectroscopy is characterized by the thermodynamic parameters delta H degree = -216.7 kJ/mol and delta S degree (25 degrees C) = -0.632 KJ mol-1 K-1 in 0.1 M NaCl, 10 mM phosphate solution. Correlation of the transition midpoint values monitored by the ultraviolet absorbance studies at strand concentrations below 0.2 mM and by NMR studies at 5.3 mM suggest that both methods are monitoring the octanucleotide duplex-to-strand transition. The NMR spectra of the Watson-Crick ring NH protons of the octanucleotide duplex have been followed as a function of temperature. The resonance from the terminal dG.dC base pairs broadens out at room temperature while the resonances from the other base pairs broaden simultaneously with the onset of the melting transition. The nonexchangeable base and sugar H-1' protons are resolved in the duplex and strand states and shift as average peaks through the melting transition. The experimental shifts on duplex formation have been compared with calculated values based on ring-current and atomic diamagnetic anisotropy contributions for a B-DNA base-pair-overlap geometry in solution. Several nonexchangeable proton resonances broaden in the fast-exchange region during the duplex-to-strand transition and the excess widths yield a duplex dissociation rate constant for the octanucleotide of 1.9 x 10(3) s-1 at 32 degrees C (fraction of duplex = 0.86) in 0.1 M NaCl, 10 mM phosphate buffer. The 31P resonances of the seven internucleotide phosphates are distributed over 0.6 ppm in the duplex state, shift downfield during the duplex-to-strand transition and undergo additional downfield shifts

  10. Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

    NASA Technical Reports Server (NTRS)

    Egli, M.; Usman, N.; Rich, A.

    1993-01-01

    We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

  11. Thermodynamics of Oligonucleotide Duplex Melting

    NASA Astrophysics Data System (ADS)

    Schreiber-Gosche, Sherrie; Edwards, Robert A.

    2009-05-01

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

  12. Identification of a pKa-regulating motif stabilizing imidazole-modified double-stranded DNA

    PubMed Central

    Buyst, Dieter; Gheerardijn, Vicky; Fehér, Krisztina; Van Gasse, Bjorn; Van Den Begin, Jos; Martins, José C.; Madder, Annemieke

    2015-01-01

    The predictable 3D structure of double-stranded DNA renders it ideally suited as a template for the bottom-up design of functionalized nucleic acid-based active sites. We here explore the use of a 14mer DNA duplex as a scaffold for the precise and predictable positioning of catalytic functionalities. Given the ubiquitous participation of the histidine-based imidazole group in protein recognition and catalysis events, single histidine-like modified duplexes were investigated. Tethering histamine to the C5 of the thymine base via an amide bond, allows the flexible positioning of the imidazole function in the major groove. The mutual interactions between the imidazole and the duplex and its influence on the imidazolium pKaH are investigated by placing a single modified thymine at four different positions in the center of the 14mer double helix. Using NMR and unrestrained molecular dynamics, a structural motif involving the formation of a hydrogen bond between the imidazole and the Hoogsteen side of the guanine bases of two neighboring GC base pairs is established. The motif contributes to a stabilization against thermal melting of 6°C and is key in modulating the pKaH of the imidazolium group. The general features, prerequisites and generic character of the new pKaH-regulating motif are described. PMID:25520197

  13. Spectroscopic data for the G-quadruplex DNA to duplex DNA reaction

    PubMed Central

    Mendoza, Oscar; Elezgaray, Juan; Mergny, Jean-Louis

    2015-01-01

    This article describes additional data related to a research article entitled “Kinetics of Quadruplex to Duplex Conversion” (Mendoza et al. 2015 [1]). We followed the opening reaction of a series of intramolecular G-quadruplex structures by the addition of their corresponding complementary strand. Fluorolabeled complementary strands allowed to monitor the reaction in real-time. An adapted kinetic model was then applied in order to obtain the kinetic parameters of this reaction. We present a series of kinetic traces providing raw data of the G4 opening reaction and the fitting model applied in every case. In addition CD spectra and UV melting data is also provided to confirm the stability of all the DNA structures considered (G-quadruplex and duplex DNA). PMID:26693518

  14. A Density Functional Theory Examination of the Local Conformational Energetics of Normal and Epigenetically Modified Duplex DNA

    NASA Astrophysics Data System (ADS)

    Yusufaly, Tahir; Olson, Wilma

    2013-03-01

    We report density functional theory calculations of various local regions of duplex DNA, including hydrogen bonded base pairs, stacked nearest-neighbor bases, and sugar-phosphate backbones. Special attention is given to the methylation of 5-cytosine, an epigenetic modification believed to play a key role in eukaryotic gene regulation. Energetically stable molecular conformations are identified and their elastic properties analyzed. Our results are compared with previous ab initio studies and high-resolution crystalline structural data.

  15. Allele-Selective Inhibition of Huntingtin and Ataxin-3 Expression by RNA Duplexes Containing Unlocked Nucleic Acid (UNA) Substitutions

    PubMed Central

    Aiba, Yuichiro; Hu, Jiaxin; Liu, Jing; Xiang, Qin; Martinez, Carlos; Corey, David R.

    2014-01-01

    Unlocked nucleic acid (UNA) is an acyclic analog of RNA that can be introduced into RNA or DNA oligonucleotides. The increased flexibility conferred by the acyclic structure fundamentally affects the strength of base-pairing, createing opportunities for improved applications and new insights into molecular recognition. Here we test how UNA substitutions affect allele-selective inhibition of trinucleotide-repeat genes Huntingtin (HTT) and Ataxin-3 (ATX-3) expression. We find that the either the combination of mismatched bases and UNA substitutions or UNA substitutions alone can improve potency and selectivity. Inhibition is potent and selectivities of > 40-fold for inhibiting mutant versus wild-type expression can be achieved. Surprisingly, even though UNA preserves the potential for complete base-pairing, the introduction of UNA substitutions at central positions within fully complementary duplexes leads to >19-fold selectivity. Like mismatched bases, the introduction of central UNA bases disrupts the potential for cleavage of substrate by Argonaute 2 (AGO2) during gene silencing. UNA-substituted duplexes are as effective as other strategies for allele-selective silencing of trinucleotide repeat disease genes. Modulation of AGO2 activity by the introduction of UNA substitutions demonstrates that backbone flexibility is as important as base-pairing for catalysis of fully complementary duplex substrates. UNA can be used to tailor RNA silencing for optimal properties and allele-selective action. PMID:24266403

  16. Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2;#8242;-deoxyadenosine:dT Base Pairing in DNA

    SciTech Connect

    Kowal, Ewa A.; Ganguly, Manjori; Pallan, Pradeep S.; Marky, Luis A.; Gold, Barry; Egli, Martin; Stone, Michael P.

    2012-02-15

    As part of an ongoing effort to explore the effect of major groove electrostatics on the thermodynamic stability and structure of DNA, a 7-deaza-2'-deoxyadenosine:dT (7-deaza-dA:dT) base pair in the Dickerson-Drew dodecamer (DDD) was studied. The removal of the electronegative N7 atom on dA and the replacement with an electropositive C-H in the major groove was expected to have a significant effect on major groove electrostatics. The structure of the 7-deaza-dA:dT base pair was determined at 1.1 {angstrom} resolution in the presence of Mg{sup 2+}. The 7-deaza-dA, which is isosteric for dA, had minimal effect on the base pairing geometry and the conformation of the DDD in the crystalline state. There was no major groove cation association with the 7-deaza-dA heterocycle. In solution, circular dichroism showed a positive Cotton effect centered at 280 nm and a negative Cotton effect centered at 250 nm that were characteristic of a right-handed helix in the B-conformation. However, temperature-dependent NMR studies showed increased exchange between the thymine N3 imino proton of the 7-deaza-dA:dT base pair and water, suggesting reduced stacking interactions and an increased rate of base pair opening. This correlated with the observed thermodynamic destabilization of the 7-deaza-dA modified duplex relative to the DDD. A combination of UV melting and differential scanning calorimetry experiments were conducted to evaluate the relative contributions of enthalpy and entropy in the thermodynamic destabilization of the DDD. The most significant contribution arose from an unfavorable enthalpy term, which probably results from less favorable stacking interactions in the modified duplex, which was accompanied by a significant reduction in the release of water and cations from the 7-deaza-dA modified DNA.

  17. Influence of the incorporation of (S)-9-(3,4-dihydroxybutyl)adenine on the enzymatic stability and base-pairing properties of oligodeoxynucleotides.

    PubMed Central

    Augustyns, K; Van Aerschot, A; Van Schepdael, A; Urbanke, C; Herdewijn, P

    1991-01-01

    (S)-9-(3,4-dihydroxybutyl)adenine was used at several positions as nucleoside substitute in the synthesis of dimers and 13-mers. Therefore we used the phosporamidite and the H-phosphonate chemistry. The nuclease susceptibilities and the base-pairing properties of these oligomers have been evaluated. PMID:2041735

  18. Full Duplex, Spread Spectrum Radio System

    NASA Technical Reports Server (NTRS)

    Harvey, Bruce A.

    2000-01-01

    The goal of this project was to support the development of a full duplex, spread spectrum voice communications system. The assembly and testing of a prototype system consisting of a Harris PRISM spread spectrum radio, a TMS320C54x signal processing development board and a Zilog Z80180 microprocessor was underway at the start of this project. The efforts under this project were the development of multiple access schemes, analysis of full duplex voice feedback delays, and the development and analysis of forward error correction (FEC) algorithms. The multiple access analysis involved the selection between code division multiple access (CDMA), frequency division multiple access (FDMA) and time division multiple access (TDMA). Full duplex voice feedback analysis involved the analysis of packet size and delays associated with full loop voice feedback for confirmation of radio system performance. FEC analysis included studies of the performance under the expected burst error scenario with the relatively short packet lengths, and analysis of implementation in the TMS320C54x digital signal processor. When the capabilities and the limitations of the components used were considered, the multiple access scheme chosen was a combination TDMA/FDMA scheme that will provide up to eight users on each of three separate frequencies. Packets to and from each user will consist of 16 samples at a rate of 8,000 samples per second for a total of 2 ms of voice information. The resulting voice feedback delay will therefore be 4 - 6 ms. The most practical FEC algorithm for implementation was a convolutional code with a Viterbi decoder. Interleaving of the bits of each packet will be required to offset the effects of burst errors.

  19. Methods And Devices For Characterizing Duplex Nucleic Acid Molecules

    DOEpatents

    Akeson, Mark; Vercoutere, Wenonah; Haussler, David; Winters-Hilt, Stephen

    2005-08-30

    Methods and devices are provided for characterizing a duplex nucleic acid, e.g., a duplex DNA molecule. In the subject methods, a fluid conducting medium that includes a duplex nucleic acid molecule is contacted with a nanopore under the influence of an applied electric field and the resulting changes in current through the nanopore caused by the duplex nucleic acid molecule are monitored. The observed changes in current through the nanopore are then employed as a set of data values to characterize the duplex nucleic acid, where the set of data values may be employed in raw form or manipulated, e.g., into a current blockade profile. Also provided are nanopore devices for practicing the subject methods, where the subject nanopore devices are characterized by the presence of an algorithm which directs a processing means to employ monitored changes in current through a nanopore to characterize a duplex nucleic acid molecule responsible for the current changes. The subject methods and devices find use in a variety of applications, including, among other applications, the identification of an analyte duplex DNA molecule in a sample, the specific base sequence at a single nulceotide polymorphism (SNP), and the sequencing of duplex DNA molecules.

  20. 52. Photocopy of copy of original Officers' Duplex Quarters drawing ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    52. Photocopy of copy of original Officers' Duplex Quarters drawing by Copeland, 7 April 1932 (Original in possession of Veterans Administration, Wichita, Kansas, copy at Ablah Library, Wichita State University). Heating - Veterans Administration Center, Officers Duplex Quarters, 5302 East Kellogg (Legal Address); 5500 East Kellogg (Common Address), Wichita, Sedgwick County, KS

  1. 51. Photocopy of copy of original Officers' Duplex Quarters drawing ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    51. Photocopy of copy of original Officers' Duplex Quarters drawing by B.S. Elliott, 7 April 1932 (original in possession of Veterans Administration, Wichita, Kansas, copy at Ablah Library, Wichita State University). Plumbing - Veterans Administration Center, Officers Duplex Quarters, 5302 East Kellogg (Legal Address); 5500 East Kellogg (Common Address), Wichita, Sedgwick County, KS

  2. Scintigraphic features of duplex kidneys on DMSA renal cortical scans.

    PubMed

    Kwatra, Neha; Shalaby-Rana, Eglal; Majd, Massoud

    2013-09-01

    The spectrum of manifestations of duplex kidneys on (99m)Tc-dimercaptosuccinic acid (DMSA) renal cortical scans and correlating findings on other imaging modalities are presented. Relevant embryology of the duplex systems and technical aspects of DMSA scintigraphy are reviewed.

  3. 48. Photocopy of copy of original Officers' Duplex Quarters drawing ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    48. Photocopy of copy of original Officers' Duplex Quarters drawing by Turner, 7 April 1932 (original in possession of Veterans Administration, Wichita, Kansas, copy at Ablah Library, Wichita State University). Attic and roof, basement, first floor, and second floor plans - Veterans Administration Center, Officers Duplex Quarters, 5302 East Kellogg (Legal Address); 5500 East Kellogg (Common Address), Wichita, Sedgwick County, KS

  4. 50. Photocopy of copy of original Officers' Duplex Quarters drawing ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    50. Photocopy of copy of original Officers' Duplex Quarters drawing by Turner, 7 April 1932 (original in possession of Veterans Administration, Wichita, Kansas, copy at Ablah Library, Wichita State University. Detail of front entrance and of gable dormer - Veterans Administration Center, Officers Duplex Quarters, 5302 East Kellogg (Legal Address); 5500 East Kellogg (Common Address), Wichita, Sedgwick County, KS

  5. 49. Photocopy of copy of original Officers' Duplex Quarters drawing ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    49. Photocopy of copy of original Officers' Duplex Quarters drawing by Turner, 7 April 1932 (original in possession of Veterans Administration, Wichita, Kansas, copy at Ablah Library, Wichita State University). Front, rear, and side elevations, and cross-section - Veterans Administration Center, Officers Duplex Quarters, 5302 East Kellogg (Legal Address); 5500 East Kellogg (Common Address), Wichita, Sedgwick County, KS

  6. Acoustical and perceptual influence of duplex stringing in grand pianos.

    PubMed

    Öberg, Fredrik; Askenfelt, Anders

    2012-01-01

    This study investigates the acoustical and perceptual influence of the string parts outside the speaking length in grand pianos (front and rear duplex strings). Acoustical measurements on a grand piano in concert condition were conducted, measuring the fundamental frequencies of all main and duplex strings in the four octaves D4-C8. Considerable deviations from the nominal harmonic relations between the rear duplex and main string frequencies, as described by the manufacturer in a patent, were observed. Generally the rear duplex strings were tuned higher than the nominal harmonic relations with average and median deviations approaching +50 cent. Single keys reached +190 and -100 cent. The spread in deviation from harmonic relations within trichords was also substantial with average and median values around 25 cent, occasionally reaching 60 cent. Contributions from both front and rear duplex strings were observed in the bridge motion and sound. The audibility of the duplex strings was studied in an ABX listening test. Complete dampening of the front duplex was clearly perceptible both for an experiment group consisting of musicians and a control group with naive subjects. The contribution from the rear duplex could also be perceived, but less pronounced. PMID:22280708

  7. Duplex structures connecting fault segments in Entrada Sandstone

    NASA Astrophysics Data System (ADS)

    Cruikshank, Kenneth M.; Zhao, Guozhu; Johnson, Arvid M.

    All stages in the development of a duplex structure—from isolated, stepped fault segments, to segments joined by a single ramp, to segments joined by tens of ramps—are preserved along strike-slip and normal faults in Entrada Sandstone in Arches National Park, Utah. Bedding is either absent or at a high angle to the duplex-like structures in Entrada Sandstone, thus it had no significant role in constraining their geometry. We can reproduce the essential features of a duplex structure along a normal fault with mechanical and kinematic models previously used to simulate duplex structures along thrust faults. However the models do not account for the amount of observed thickening at the step where the structure forms. This suggests that the geometry of duplex-like structures along these strike-slip faults may be a result of interaction between the fault segments.

  8. Carbonic acid ionization and the stability of sodium bicarbonate and carbonate ion pairs to 200 °C - A potentiometric and spectrophotometric study

    NASA Astrophysics Data System (ADS)

    Stefánsson, Andri; Bénézeth, Pascale; Schott, Jacques

    2013-11-01

    Carbonic acid ionization and sodium bicarbonate and carbonate ion pair formation constants have been experimentally determined in dilute hydrothermal solutions to 200 °C. Two experimental approaches were applied, potentiometric acid-base titrations at 10-60 °C and spectrophotometric pH measurements using the pH indicators, 2-napthol and 4-nitrophenol, at 25-200 °C. At a given temperature, the first and second ionization constants of carbonic acid (K1, K2) and the ion pair formation constants for NaHCO(aq)(K) and NaCO3-(aq)(K) were simultaneously fitted to the data. Results of this study compare well with previously determined values of K1 and K2. The NaHCO(aq) and NaCO3-(aq) ion pair formation constants vary between 25 and 200 °C having values of logK=-0.18 to 0.58 and logK=1.01 to 2.21, respectively. These ion pairs are weak at low-temperatures but become increasingly important with increasing temperature under neutral to alkaline conditions in moderately dilute to concentrated NaCl solutions, with NaCO3-(aq) predominating over CO32-(aq) in ⩾0.1 M NaCl solution at temperatures above 100 °C. The results demonstrate that NaCl cannot be considered as an inert (non-complexing) electrolyte in aqueous carbon dioxide containing solutions at elevated temperatures.

  9. Potentiometric and spectrophotometric study of the stability of magnesium carbonate and bicarbonate ion pairs to 150 °C and aqueous inorganic carbon speciation and magnesite solubility

    NASA Astrophysics Data System (ADS)

    Stefánsson, Andri; Bénézeth, Pascale; Schott, Jacques

    2014-08-01

    The formation constants of magnesium bicarbonate and carbonate ion pairs have been experimentally determined in dilute hydrothermal solutions to 150 °C. Two experimental approaches were applied, potentiometric acid-base titrations at 10-60 °C and spectrophotometric pH measurements using two pH indicators, 2-naphthol and 4-nitrophenol, at 25 and 80-150 °C. At a given temperature, the first and second ionization constants of carbonic acid (K1, K2) and the ion pair formation constants for MgHCO3+(aq) (KMgHCO3+) and MgCO3(aq) (KMgCO3) were simultaneously fitted to the data. Results of this study compare well with previously determined values of K1 and K2. The formation constants of MgHCO3+(aq) and MgCO3(aq) ion pairs increased significantly with increasing temperature, with values of logKMgHCO3+ = 1.14 and 1.75 and of logKMgCO3 = 2.86 and 3.48 at 10 °C and 100 °C, respectively. These ion pairs are important aqueous species under neutral to alkaline conditions in moderately dilute to concentrated Mg-containing solutions, with MgCO3(aq) predominating over CO32-(aq) in solutions at pH >8. The predominance of magnesium carbonate over carbonate is dependent on the concentration of dissolved magnesium and the ratio of magnesium over carbonate. With increasing temperature and at alkaline pH, brucite solubility further reduced the magnesium concentration to levels below 1 mmol kg-1, thus limiting availability of Mg2+(aq) for magnesite precipitation.

  10. Natural isoflavones regulate the quadruplex-duplex competition in human telomeric DNA.

    PubMed

    Zhang, Jin-li; Fu, Yan; Zheng, Lin; Li, Wei; Li, Hao; Sun, Qian; Xiao, Ying; Geng, Feng

    2009-05-01

    Effects of natural isoflavones on the structural competition of human telomeric G-quadruplex d[AG(3)(T(2)AG(3))(3)] and its related Watson-Crick duplex d[AG(3)(T(2)AG(3))(3)-(C(3)TA(2))(3)C(3)T] are investigated by using circular dichroism (CD), ESI-MS, fluorescence quenching measurement, CD stopped-flow kinetic experiment, UV spectroscopy and molecular modeling methods. It is intriguing to find out that isoflavones can stabilize the G-quadruplex structure but destabilize its corresponding Watson-Crick duplex and this discriminated interaction is intensified by molecular crowding environments. Kinetic experiments indicate that the dissociation rate of quadruplex (k(obs290 nm)) is decreased by 40.3% at the daidzin/DNA molar ratio of 1.0 in K(+), whereas in Na(+) the observed rate constant is reduced by about 12.0%. Furthermore, glycosidic daidzin significantly induces a structural transition of the polymorphic G-quadruplex into the antiparallel conformation in K(+). This is the first report on the recognition of isoflavones with conformational polymorphism of G-quadruplex, which suggests that natural isoflavone constituents potentially exhibit distinct regulation on the structural competition of quadruplex versus duplex in human telomeric DNA. PMID:19261597

  11. A nanoscale duplex precipitation approach for improving the properties of Fe-base alloys

    SciTech Connect

    Zhang, Zhongwu; Liu, C T; Wang, Xun-Li; Wen, Y. R.; Fujita, T.; Hirata, A.; Chen, M.W.; Miller, Michael K; Chen, Guang; Chin, Bryan

    2013-01-01

    The precipitate size and number density are important factors for tailoring the mechanical behaviors of nanoscale precipitate-hardened alloys. However during thermal aging, the precipitate size and number density change leading to either poor strength or high strength but significantly reduced ductility. Here we demonstrate, by producing nanoprecipitates with unusual duplex structures in a composition-optimized multicomponent precipitation-hardened alloy, a unique approach to improve the stability of the alloy against the effects of thermal aging and consequently change in the mechanical properties. Our study provides compelling experimental evidence that these nanoscale precipitates consist of a duplex structures with a Cu-enriched bcc core that is partially encased by a B2-ordered Ni(Mn,Al) phase. This duplex structure enables the precipitate size and number density to be independently optimized, provides a more complex obstacle for dislocation movement due to the ordering and an additional interphase interface, and yields a high yield strength alloy without sacrificing the ductility.

  12. High base pair opening rates in tracts of GC base pairs.

    PubMed

    Dornberger, U; Leijon, M; Fritzsche, H

    1999-03-12

    Sequence-dependent structural features of the DNA double helix have a strong influence on the base pair opening dynamics. Here we report a detailed study of the kinetics of base pair breathing in tracts of GC base pairs in DNA duplexes derived from 1H NMR measurements of the imino proton exchange rates upon titration with the exchange catalyst ammonia. In the limit of infinite exchange catalyst concentration, the exchange times of the guanine imino protons of the GC tracts extrapolate to much shorter base pair lifetimes than commonly observed for isolated GC base pairs. The base pair lifetimes in the GC tracts are below 5 ms for almost all of the base pairs. The unusually rapid base pair opening dynamics of GC tracts are in striking contrast to the behavior of AT tracts, where very long base pair lifetimes are observed. The implication of these findings for the structural principles governing spontaneous helix opening as well as the DNA-binding specificity of the cytosine-5-methyltransferases, where flipping of the cytosine base has been observed, are discussed.

  13. Sequence-dependent dynamics of duplex DNA: the applicability of a dinucleotide model.

    PubMed Central

    Okonogi, T M; Alley, S C; Reese, A W; Hopkins, P B; Robinson, B H

    2002-01-01

    The short-time (submicrosecond) bending dynamics of duplex DNA were measured to determine the effect of sequence on dynamics. All measurements were obtained from a single site on duplex DNA, using a single, site-specific modified base containing a rigidly tethered, electron paramagnetic resonance active spin probe. The observed dynamics are interpreted in terms of single-step sequence-dependent bending force constants, determined from the mean squared amplitude of bending relative to the end-to-end vector using the modified weakly bending rod model. The bending dynamics at a single site are a function of the sequence of the nucleotides constituting the duplex DNA. We developed and examined several dinucleotide-based models for flexibility. The models indicate that the dominant feature of the dynamics is best explained in terms of purine- and pyrimidine-type steps, although distinction is made among all 10 unique steps: It was found that purine-purine steps (which are the same as pyrimidine-pyrimidine steps) were near average in flexibility, but the pyrimidine-purine steps (5' to 3') were nearly twice as flexible, whereas purine-pyrimidine steps were more than half as flexible as average DNA. Therefore, the range of stepwise flexibility is approximately fourfold and is characterized by both the type of base pair step (pyrimidine/purine combination) and the identity of the bases within the pair (G, A, T, or C). All of the four models considered here underscore the complexity of the dependence of dynamics on DNA sequence with certain sequences not satisfactorily explainable in terms of any dinucleotide model. These findings provide a quantitative basis for interpreting the dynamics and kinetics of DNA-sequence-dependent biological processes, including protein recognition and chromatin packaging. PMID:12496111

  14. Hybrid recursive active filters for duplexing in RF transmitter front-ends

    NASA Astrophysics Data System (ADS)

    Gottardo, Giuseppe; Donati, Giovanni; Musolff, Christian; Fischer, Georg; Felgentreff, Tilman

    2016-08-01

    Duplex filters in modern base transceiver stations shape the channel in order to perform common frequency division duplex operations. Usually, they are designed as cavity filters, which are expensive and have large dimensions. Thanks to the emerging digital technology and fast digital converters, it is possible to transfer the efforts of designing analog duplex filters into digital numeric algorithms applied to feedback structures, operating on power. This solution provides the shaping of the signal spectrum directly at the output of the radio frequency (RF) power amplifiers (PAs) relaxing the transmitter design especially in the duplexer and in the antenna sections. The design of a digital baseband feedback applied to the analog power RF amplifiers (hybrid filter) is presented and verified by measurements. A model to describe the hybrid system is investigated, and the relation between phase and resonance peaks of the resulting periodic band-pass transfer function is described. The stability condition of the system is analyzed using Nyquist criterion. A solution involving a number of digital feedback and forward branches is investigated defining the parameters of the recursive structure. This solution allows the closed loop system to show a periodic band pass with up to 500 kHz bandwidth at the output of the RF amplifier. The band-pass magnitude reaches up to 17 dB selectivity. The rejection of the PA noise in the out-of-band frequencies is verified by measurements. The filter is tested with a modulated LTE (Long Term Evolution) signal showing an ACPR (Adjacent Channel Power Ratio) enhancement of 10 dB of the transmitted signal.

  15. Nitrogen containing shielding gases for GTAW duplex stainless steels

    SciTech Connect

    Creffield, G.K.; Cole, M.H.; Paciej, R.; Huang, W.; Urmston, S.

    1993-12-31

    The duplex stainless steel are alloys characterized as consisting of two phases; austenite and ferrite. As such, they combine the benefits of both phases i.e. good ductility and general corrosion resistance of austenite, but with improved stress corrosion cracking resistance and strength associate with ferrite. Carefully controlled manufacturing techniques are employed to produce this combination in roughly equal proportions to ensure optimum properties. The range of duplex alloys studied in this work covered both the standard grade (2205) and the latest generation of super duplex (2507) alloys; typical compositions are shown in Table 1. Although the standard duplex is the most commonly available and widely used, super duplexes, which are characterized by higher chromium, nickel, molybdenum and nitrogen contents, have even better corrosion properties and are finding increasing applications in the offshore industry. To benefit from the superior properties of duplex, it is vital that these alloys can be welded effectively and that the properties of the welded joint match those of the parent weld. The objective of the current investigation was to study the effect of nitrogen, in both the shielding and purge gas, on the weld metal nitrogen content, microstructure and corrosion resistance, with the eventual aim of recommending an effective shielding gas mixture for duplex stainless steels.

  16. Streamlined analysis of duplex sequencing data with Du Novo.

    PubMed

    Stoler, Nicholas; Arbeithuber, Barbara; Guiblet, Wilfried; Makova, Kateryna D; Nekrutenko, Anton

    2016-01-01

    Duplex sequencing was originally developed to detect rare nucleotide polymorphisms normally obscured by the noise of high-throughput sequencing. Here we describe a new, streamlined, reference-free approach for the analysis of duplex sequencing data. We show the approach performs well on simulated data and precisely reproduces previously published results and apply it to a newly produced dataset, enabling us to type low-frequency variants in human mitochondrial DNA. Finally, we provide all necessary tools as stand-alone components as well as integrate them into the Galaxy platform. All analyses performed in this manuscript can be repeated exactly as described at http://usegalaxy.org/duplex . PMID:27566673

  17. Streamlined analysis of duplex sequencing data with Du Novo.

    PubMed

    Stoler, Nicholas; Arbeithuber, Barbara; Guiblet, Wilfried; Makova, Kateryna D; Nekrutenko, Anton

    2016-08-26

    Duplex sequencing was originally developed to detect rare nucleotide polymorphisms normally obscured by the noise of high-throughput sequencing. Here we describe a new, streamlined, reference-free approach for the analysis of duplex sequencing data. We show the approach performs well on simulated data and precisely reproduces previously published results and apply it to a newly produced dataset, enabling us to type low-frequency variants in human mitochondrial DNA. Finally, we provide all necessary tools as stand-alone components as well as integrate them into the Galaxy platform. All analyses performed in this manuscript can be repeated exactly as described at http://usegalaxy.org/duplex .

  18. Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNA i-Motif

    NASA Astrophysics Data System (ADS)

    Yang, Bo; Wu, R. R.; Rodgers, M. T.

    2015-09-01

    (CCG)n•(CGG)n trinucleotide repeats have been found to be associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical proton-bound dimers of cytosine (C+•C). Halogenated cytosine residues are one form of DNA damage that may be important in altering the structure and stability of DNA or DNA-protein interactions and, hence, regulate gene expression. Previously, we investigated the effects of 5-halogenation and 1-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present study, we extend our work to include proton-bound homo- and heterodimers of cytosine, 1-methyl-5-fluorocytosine, and 1-methyl-5-bromocytosine. All modifications examined here are found to produce a decrease in the BPEs. However, the BPEs of all of the proton-bound dimers examined significantly exceed those of Watson-Crick G•C, neutral C•C base pairs, and various methylated variants such that DNA i-motif conformations should still be preserved in the presence of these modifications. The proton affinities (PAs) of the halogenated cytosines are also obtained from the experimental data by competitive analysis of the primary dissociation pathways that occur in parallel for the proton-bound heterodimers. 5-Halogenation leads to a decrease in the N3 PA of cytosine, whereas 1-methylation leads to an increase in the N3 PA. Thus, the 1-methyl-5-halocytosines exhibit PAs that are intermediate.

  19. Lubrication for high load duplex bearings

    SciTech Connect

    Steinhoff, R.G.

    1997-08-01

    Three ES and H-compatible lubricants (Environment, Safety and Health) for high load duplex bearing applications were evaluated and compared against trichlorotrifluoroethane (Freon) deposition of low molecular weight polytetrafluoroethylene (PTFE) bearing lubricant extracted from Vydax{trademark}. Vydax is a product manufactured by DuPont consisting of various molecular weights of PTFE suspended in trichlorotrifluoroethane (Freon) which is an ozone-depleting solvent. Bearings with Supercritical CO{sub 2} deposition of PTFE extracted from Vydax AR/IPA, bearings with titanium carbide coated balls, and bearings with diamond-like carbon races and retainers were evaluated. Bearings with Supercritical CO{sub 2} deposition of PTFE from Vydax AR/IPA performed as well as bearings with Freon deposition of PTFE from Freon-based Vydax.

  20. Force measurements reveal how small binders perturb the dissociation mechanisms of DNA duplex sequences

    NASA Astrophysics Data System (ADS)

    Burmistrova, Anastasia; Fresch, Barbara; Sluysmans, Damien; de Pauw, Edwin; Remacle, Françoise; Duwez, Anne-Sophie

    2016-06-01

    The force-driven separation of double-stranded DNA is crucial to the accomplishment of cellular processes like genome transactions. Ligands binding to short DNA sequences can have a local stabilizing or destabilizing effect and thus severely affect these processes. Although the design of ligands that bind to specific sequences is a field of intense research with promising biomedical applications, so far, their effect on the force-induced strand separation has remained elusive. Here, by means of AFM-based single molecule force spectroscopy, we show the co-existence of two different mechanisms for the separation of a short DNA duplex and demonstrate how they are perturbed by small binders. With the support of Molecular Dynamics simulations, we evidence that above a critical pulling rate one of the dissociation pathways becomes dominant, with a dramatic effect on the rupture forces. Around the critical threshold, we observe a drop of the most probable rupture forces for ligand-stabilized duplexes. Our results offer a deep understanding of how a stable DNA-ligand complex behaves under force-driven strand separation.The force-driven separation of double-stranded DNA is crucial to the accomplishment of cellular processes like genome transactions. Ligands binding to short DNA sequences can have a local stabilizing or destabilizing effect and thus severely affect these processes. Although the design of ligands that bind to specific sequences is a field of intense research with promising biomedical applications, so far, their effect on the force-induced strand separation has remained elusive. Here, by means of AFM-based single molecule force spectroscopy, we show the co-existence of two different mechanisms for the separation of a short DNA duplex and demonstrate how they are perturbed by small binders. With the support of Molecular Dynamics simulations, we evidence that above a critical pulling rate one of the dissociation pathways becomes dominant, with a dramatic effect

  1. [Analysis of Conformational Features of Watson-Crick Duplex Fragments by Molecular Mechanics and Quantum Mechanics Methods].

    PubMed

    Poltev, V I; Anisimov, V M; Sanchez, C; Deriabina, A; Gonzalez, E; Garcia, D; Rivas, F; Polteva, N A

    2016-01-01

    limits typical for the corresponding family. We observe that popular functionals in density functional theory calculations lead to the overestimated distances between base pairs, while MP2 computations and the newer complex functionals produce the structures that have too close atom-atom contacts. A detailed study of some complementary desoxydinucleoside monophosphate complexes with Na-ions highlights the existence of several energy minima corresponding to BI-conformations, in other words, the complexity of the relief pattern of the potential energy surface of complementary desoxydinucleoside monophosphate complexes. This accounts for variability of conformational parameters of duplex fragments with the same base sequence. Popular molecular mechanics force fields AMBER and CHARMM reproduce most of the conformational characteristics of desoxydinucleoside monophosphates and their complementary complexes with Na-ions but fail to reproduce some details of the dependence of the Watson-Crick duplex conformation on the nucleotide sequence.

  2. Formation and stability of a Janus-Wedge type of DNA triplex.

    PubMed

    Chen, Dongli; Meena, Meena; Sharma, Sunil K; McLaughlin, Larry W

    2004-01-14

    A new type of DNA targeting with the formation of a Janus-Wedge (J-W) triple helix is described. The "wedge" residue (W) attached to a PNA backbone is designed to insert itself into double-stranded DNA and base pair with both Watson-Crick faces. To study the stability of such an assembly, we have examined the formation of the J-W triplex with dC8 - T8 target sequence. The use of this target sequence permits the study of this new helix form without competing Watson-Crick interactions between the two target residues. Studies indicate that the W strand binds to both target strands, with defined polarity and a stability (-15.2 kcal/mol) that is roughly the sum of the two independent duplex interactions.

  3. NMR structural studies of the ionizing radiation adduct 7-hydro-8-oxodeoxyguanosine (8-oxo-7H-dG) opposite deoxyadenosine in a DNA duplex. 8-Oxo-7H-dG(syn).dA(anti) alignment at lesion site.

    PubMed

    Kouchakdjian, M; Bodepudi, V; Shibutani, S; Eisenberg, M; Johnson, F; Grollman, A P; Patel, D J

    1991-02-01

    Proton NMR studies are reported on the complementary d(C1-C2-A3-C4-T5-A6-oxo-G7-T8-C9-A10-C11-C12).d(G13-G14-T15- G16-A17-A18-T19- A20-G21-T22-G23-G24) dodecanucleotide duplex (designated 8-oxo-7H-dG.dA 12-mer), which contains a centrally located 7-hydro-8-oxodeoxyguanosine (8-oxo-7H-dG) residue, a group commonly found in DNA that has been exposed to ionizing radiation or oxidizing free radicals. From the NMR spectra it can be deduced that this moiety exists as two tautomers, or gives rise to two DNA conformations, that are in equilibrium and that exchange slowly. The present study focuses on the major component of the equilibrium that originates in the 6,8-dioxo tautomer of 8-oxo-7H-dG. We have assigned the exchangeable NH1, NH7, and NH2-2 base protons located on the Watson-Crick and Hoogsteen edges of 8-oxo-7H-dG7 in the 8-oxo-7H-dG.dA 12-mer duplex, using an analysis of one- and two-dimensional nuclear Overhauser enhancement (NOE) data in H2O solution. The observed NOEs derived from the NH7 proton of 8-oxo-7H-dG7 to the H2 and NH2-6 protons of dA18 establish an 8-oxo-7H-dG7(syn).dA 18(anti) alignment at the lesion site in the 8-oxo-7H-dG.dA 12-mer duplex in solution. This alignment, which places the 8-oxo group in the minor groove, was further characterized by an analysis of the NOESY spectrum of the 8-oxo-7H-dG.dA 12-mer duplex in D2O solution. We were able to detect a set of intra- and interstrand NOEs between protons (exchangeable and nonexchangeable) on adjacent residues in the d(A6-oxo-G7-T8).d(A17-A18-T19) trinucleotide segment centered about the lesion site that establishes stacking of the oxo-dG7(syn).dA(anti) pair between stable Watson-Crick dA6.dT19 and dT8.dA17 base pairs with minimal perturbation of the helix. Thus, both strands of the 8-oxo-7H-dG.dA 12-mer duplex adopt right-handed conformations at and adjacent to the lesion site, the unmodified bases adopt anti glycosidic torsion angles, and the bases are stacked into the helix. The energy

  4. Thermoacoustic Duplex Technology for Cooling and Powering a Venus Lander

    NASA Astrophysics Data System (ADS)

    Walker, A. R.; Haberbusch, M. S.; Sasson, J.

    2015-04-01

    A Thermoacoustic Stirling Heat Engine (TASHE) is directly coupled to a Pulse Tube Refrigerator (PTR) in a duplex configuration, providing simultaneous cooling and electrical power, thereby suiting the needs of a long-lived Venus lander.

  5. 43. View of station from southwest side with duplex keepers' ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    43. View of station from southwest side with duplex keepers' dwelling to the left. USLHB photo by Herbert Bamber, June 9, 1893. - Bodie Island Light Station, Off Highway 12, Nags Head, Dare County, NC

  6. Synthesis of oligodiaminomannoses and analysis of their RNA duplex binding properties and their potential application as siRNA-based drugs.

    PubMed

    Iwata, Rintaro; Doi, Akiko; Maeda, Yusuke; Wada, Takeshi

    2015-09-28

    The synthesis of artificial cationic oligodiaminosaccharides, α-(1 → 4)-linked-2,6-diamino-2,6-dideoxy-d-mannopyranose oligomers (ODAMans), and their interactions with RNA duplexes are described. The monomer through the pentamer, all of which bear unnatural 2,6-diaminomannose moieties, were successfully prepared. UV melting and fluorescence anisotropy analyses revealed that the ODAMans bound and thermodynamically stabilized both 12mer RNA duplexes and an siRNA. Furthermore, it was clearly shown that the siRNA acquired substantial RNase A resistance due to its binding to the ODAMan 4mer. PMID:26256756

  7. [Composites of peptide nucleic acids with titanium dioxide nanoparticles. III. Kinetics of PNA dissociation from nanocomposites containing DNA/PNA duplexes].

    PubMed

    Amirkhanov, R N; Zarytova, V F; Amirkhanov, N V

    2014-01-01

    When delivering peptide nucleic acids (PNA) to the cells in the nanocomposites TiO2 · PL · DNA/PNA, containing titanium dioxide nanoparticles coated with polylysine (PL) and immobilized DNA/PNA duplexes, it is important not only to transport them to the cell, but also ability to control the release rate of the PNA-drug from the carrier. PNA desorption from TiO2 · PL · DNA/PNA nanocomposite in time has been shown. Desorption is caused by dissociation of immobilized DNA/PNA duplex while the DNA remains on the carrier and PNA goes away in solution. It has been found that the half-retention times of PNA on TiO2 · PL · DNA/PNA nanocomposites containing DNA/PNA duplexes with overlapping complementary base pairs equal to 10, 12, 14, and 16 are 10, 14, 22 and 70 minutes, respectively. Thus, it has been shown that the release rate of the PNA-drug from nanocomposites can be adjusted by varying the overlap of complementary base pairs in the immobilized DNA/PNA duplex. This method of PNA immobilization may be used for designing of nanocomposites with optimum release time of the PNA-drugs. Created TiO2 · PL · DNA/PNA nanocomposites can be used to efficiently deliver therapeutically significant drug PNA and their selective effect on the pathogenic nucleic acid in the cell.

  8. Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability.

    PubMed

    Zrimec, Jan; Lapanje, Ales

    2015-01-01

    DNA melting bubbles are the basis of many DNA-protein interactions, such as those in regulatory DNA regions driving gene expression, DNA replication and bacterial horizontal gene transfer. Bubble formation is affected by DNA duplex stability and thermally induced duplex destabilization (TIDD). Although prediction of duplex stability with the nearest neighbor (NN) method is much faster than prediction of TIDD with the Peyrard-Bishop-Dauxois (PBD) model, PBD predicted TIDD defines regulatory DNA regions with higher accuracy and detail. Here, we considered that PBD predicted TIDD is inherently related to the intrinsic duplex stabilities of destabilization regions. We show by regression modeling that NN duplex stabilities can be used to predict TIDD almost as accurately as is predicted with PBD. Predicted TIDD is in fact ascribed to non-linear transformation of NN duplex stabilities in destabilization regions as well as effects of neighboring regions relative to destabilization size. Since the prediction time of our models is over six orders of magnitude shorter than that of PBD, the models present an accessible tool for researchers. TIDD can be predicted on our webserver at http://tidd.immt.eu.

  9. Perspective view of Building No. 61 from northwest. These duplex ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Perspective view of Building No. 61 from northwest. These duplex quarters were built during the 1920s on the south edge of the Northwestern Branch campus. This building is sited on a rise and shares paths and lawn with two similar structures - Buildings 56 and 79. Now located directly adjacent to the current hospital complex (background), all three duplexes are slated for demolition. - National Home for Disabled Volunteer Soldiers, Northwestern Branch, Quarters, 5000 West National Avenue, Milwaukee, Milwaukee County, WI

  10. Silver (I) as DNA glue: Ag+-mediated guanine pairing revealed by removing Watson-Crick constraints

    NASA Astrophysics Data System (ADS)

    Swasey, Steven M.; Leal, Leonardo Espinosa; Lopez-Acevedo, Olga; Pavlovich, James; Gwinn, Elisabeth G.

    2015-05-01

    Metal ion interactions with DNA have far-reaching implications in biochemistry and DNA nanotechnology. Ag+ is uniquely interesting because it binds exclusively to the bases rather than the backbone of DNA, without the toxicity of Hg2+. In contrast to prior studies of Ag+ incorporation into double-stranded DNA, we remove the constraints of Watson-Crick pairing by focusing on homo-base DNA oligomers of the canonical bases. High resolution electro-spray ionization mass spectrometry reveals an unanticipated Ag+-mediated pairing of guanine homo-base strands, with higher stability than canonical guanine-cytosine pairing. By exploring unrestricted binding geometries, quantum chemical calculations find that Ag+ bridges between non-canonical sites on guanine bases. Circular dichroism spectroscopy shows that the Ag+-mediated structuring of guanine homobase strands persists to at least 90 °C under conditions for which canonical guanine-cytosine duplexes melt below 20 °C. These findings are promising for DNA nanotechnology and metal-ion based biomedical science.

  11. Silver (I) as DNA glue: Ag+-mediated guanine pairing revealed by removing Watson-Crick constraints

    PubMed Central

    Swasey, Steven M.; Leal, Leonardo Espinosa; Lopez-Acevedo, Olga; Pavlovich, James; Gwinn, Elisabeth G.

    2015-01-01

    Metal ion interactions with DNA have far-reaching implications in biochemistry and DNA nanotechnology. Ag+ is uniquely interesting because it binds exclusively to the bases rather than the backbone of DNA, without the toxicity of Hg2+. In contrast to prior studies of Ag+ incorporation into double-stranded DNA, we remove the constraints of Watson-Crick pairing by focusing on homo-base DNA oligomers of the canonical bases. High resolution electro-spray ionization mass spectrometry reveals an unanticipated Ag+-mediated pairing of guanine homo-base strands, with higher stability than canonical guanine-cytosine pairing. By exploring unrestricted binding geometries, quantum chemical calculations find that Ag+ bridges between non-canonical sites on guanine bases. Circular dichroism spectroscopy shows that the Ag+-mediated structuring of guanine homobase strands persists to at least 90 °C under conditions for which canonical guanine-cytosine duplexes melt below 20 °C. These findings are promising for DNA nanotechnology and metal-ion based biomedical science. PMID:25973536

  12. Silver (I) as DNA glue: Ag(+)-mediated guanine pairing revealed by removing Watson-Crick constraints.

    PubMed

    Swasey, Steven M; Leal, Leonardo Espinosa; Lopez-Acevedo, Olga; Pavlovich, James; Gwinn, Elisabeth G

    2015-01-01

    Metal ion interactions with DNA have far-reaching implications in biochemistry and DNA nanotechnology. Ag(+) is uniquely interesting because it binds exclusively to the bases rather than the backbone of DNA, without the toxicity of Hg(2+). In contrast to prior studies of Ag(+) incorporation into double-stranded DNA, we remove the constraints of Watson-Crick pairing by focusing on homo-base DNA oligomers of the canonical bases. High resolution electro-spray ionization mass spectrometry reveals an unanticipated Ag(+)-mediated pairing of guanine homo-base strands, with higher stability than canonical guanine-cytosine pairing. By exploring unrestricted binding geometries, quantum chemical calculations find that Ag(+) bridges between non-canonical sites on guanine bases. Circular dichroism spectroscopy shows that the Ag(+)-mediated structuring of guanine homobase strands persists to at least 90 °C under conditions for which canonical guanine-cytosine duplexes melt below 20 °C. These findings are promising for DNA nanotechnology and metal-ion based biomedical science. PMID:25973536

  13. Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA.

    PubMed

    Zgarbová, Marie; Otyepka, Michal; Šponer, Jiří; Lankaš, Filip; Jurečka, Petr

    2014-08-12

    Terminal base pairs of DNA and RNA molecules in solution are known to undergo frequent transient opening events (fraying). Accurate modeling of this process is important because of its involvement in nucleic acid end recognition and enzymatic catalysis. In this article, we describe fraying in molecular dynamics simulations with the ff99bsc0, ff99bsc0χOL3, and ff99bsc0χOL4 force fields, both for DNA and RNA molecules. Comparison with the experiment showed that while some features of fraying are consistent with the available data, others indicate potential problems with the force field description. In particular, multiple noncanonical structures are formed at the ends of the DNA and RNA duplexes. Among them are tWC/sugar edge pair, C-H edge/Watson-Crick pair, and stacked geometries, in which the terminal bases are stacked above each other. These structures usually appear within the first tens to hundreds of nanoseconds and substantially limit the usefulness of the remaining part of the simulation due to geometry distortions that are transferred to several neighboring base pairs ("end effects"). We show that stability of the noncanonical structures in ff99bsc0 may be partly linked to inaccurate glycosidic (χ) torsion potentials that overstabilize the syn region and allow for rapid anti to syn transitions. The RNA refined glycosidic torsion potential χOL3 provides an improved description and substantially more stable MD simulations of RNA molecules. In the case of DNA, the χOL4 correction gives only partial improvement. None of the tested force fields provide a satisfactory description of the terminal regions, indicating that further improvement is needed to achieve realistic modeling of fraying in DNA and RNA molecules. PMID:26588288

  14. Topologically non-linked circular duplex DNA.

    PubMed

    Biegeleisen, Ken

    2002-05-01

    The discovery of circular DNA, over 30 years ago, introduced an element of uneasiness in what had been, up to that point, the almost picture-perfect story of the elucidation of the molecular biology of heredity. If DNA indeed has the Watson-Crick right-handed helical secondary structure, then in circular DNA, thousands, or perhaps even millions of twists must be removed in each generation, and re-wound in the next generation. Although enzyme systems adequate for this task have long since been found and characterized, there have nevertheless arisen a number of proposals for alternative DNA structures in which the strands are topologically non-linked, so that they might separate during replication without having to be unwound. These structures have generally been put forth as theory only, and have been largely unaccompanied by experimental evidence to support their applicability to native DNA from living systems. Recently, however, a report has emerged suggesting that it might be possible to separate, intact, the individual single-stranded circular half-chromosomes which constitute the double-stranded circular chromosomes of certain plasmids. This would not be possible unless the chromosomes had one of the alternative, topologically non-linked structures. It is widely believed that after a half-century of worldwide DNA research, any significant change to the Watson-Crick structure is unlikely to stand up to scrutiny. Nevertheless, the present author has found that in many instances in which the behavior of circular duplex DNA is considered to be explicable only in terms of the topologically linked helical model, it is also possible to explain that same behavior in terms of a topologically non-linked model. It is necessary, in these instances, to make certain logical assumptions which cannot be conclusively proven at the present time. The author herein offers an example of one such instance, namely an examination of the behavior of circular duplex DNA in an alkaline

  15. Pairing Learners in Pair Work Activity

    ERIC Educational Resources Information Center

    Storch, Neomy; Aldosari, Ali

    2013-01-01

    Although pair work is advocated by major theories of second language (L2) learning and research findings suggest that pair work facilitates L2 learning, what is unclear is how to best pair students in L2 classes of mixed L2 proficiency. This study investigated the nature of pair work in an English as a Foreign Language (EFL) class in a college in…

  16. Force measurements reveal how small binders perturb the dissociation mechanisms of DNA duplex sequences.

    PubMed

    Burmistrova, Anastasia; Fresch, Barbara; Sluysmans, Damien; De Pauw, Edwin; Remacle, Françoise; Duwez, Anne-Sophie

    2016-06-01

    The force-driven separation of double-stranded DNA is crucial to the accomplishment of cellular processes like genome transactions. Ligands binding to short DNA sequences can have a local stabilizing or destabilizing effect and thus severely affect these processes. Although the design of ligands that bind to specific sequences is a field of intense research with promising biomedical applications, so far, their effect on the force-induced strand separation has remained elusive. Here, by means of AFM-based single molecule force spectroscopy, we show the co-existence of two different mechanisms for the separation of a short DNA duplex and demonstrate how they are perturbed by small binders. With the support of Molecular Dynamics simulations, we evidence that above a critical pulling rate one of the dissociation pathways becomes dominant, with a dramatic effect on the rupture forces. Around the critical threshold, we observe a drop of the most probable rupture forces for ligand-stabilized duplexes. Our results offer a deep understanding of how a stable DNA-ligand complex behaves under force-driven strand separation. PMID:27221618

  17. Kinematic model for out-of-sequence thrusting: Motion of two ramp-flat faults and the production of upper plate duplex systems

    NASA Astrophysics Data System (ADS)

    Pavlis, Terry L.

    2013-06-01

    Kinematic models developed here suggest a bewildering array of structural styles can be generated during out-of-sequence thrusting. Many of these structures would be difficult to distinguish from a normally stacked thrust sequence and the process can produce younger-on-older faults that could easily be misinterpreted as normal faults. This paper considers a small subset of this problem within a large model space by considering structures that develop along a pair of ramp-flat faults that are moving simultaneously, or sequentially. Motion on the lower ramp warps the structurally higher fault due to fault-bend folding and when the fault ruptures through the warp it transfers a horse to the upper hanging wall. Continuity of the process generates what is referred to here as an "upper plate duplex" to distinguish the structure from a conventional duplex. Kinematic parameters are developed for two models within this general problem: 1) a system with a fixed ramp in the lower thrust, overridden by an upper thrust; and 2) a double-duplex system where a conventional duplex develops along the lower fault at the same time as an upper plate duplex is formed along the upper fault. The theory is tested with forward models using 2D Move software and these tests indicate different families of structural styles form in association with relative scaling of ramp systems, slip-ratio between faults, and aspect ratios of horse blocks formed in the upper-plate duplex. A first-order result of the analysis is that an upper plate duplex can be virtually indistinguishable from a conventional duplex unless the trailing branch lines of the horses are exposed or imaged; a condition seldom met in natural exposures. Restoration of an upper-plate duplex produces counterintuitive fault geometry in the restored state, and thus, restorations of upper plate duplexes that erroneously assume a conventional duplex model would produce restored states that are seriously in error. In addition, in most of

  18. ES and H-compatible lubrication for duplex bearings

    SciTech Connect

    Steinhoff, R.G.

    1997-10-01

    Two ES and H-compatible lubricants (environment, safety, and health) for duplex bearing applications and one hybrid material duplex bearing were evaluated and compared against duplex bearings with trichlorotrifluoroethane (Freon) deposition of low molecular weight polytetrafluoroethylene (PTFE) bearing lubricant extracted from Vydax{trademark}. Vydax is a product manufactured by DuPont consisting of various molecular weights of PTFE suspended in trichlorotrifluoroethane (Freon), which is an ozone-depleting solvent. Vydax has been used as a bearing lubricant in strong link mechanisms since 1974. Hybrid duplex bearings with silicon nitride balls and molded glass-nylon-Teflon retainers, duplex bearings lubricated with sputtered MoS{sub 2} on races and retainers, and duplex bearings lubricated with electrophoretic deposited MoS{sub 2} were evaluated. Bearings with electrophoretic deposited MoS{sub 2} performed as well as bearings with Freon deposition of PTFE from Freon-based Vydax. Hybrid bearings with silicon nitride balls performed worse than bearings lubricated with Vydax, but their performance would still be acceptable for most applications. Bearings lubricated with sputtered MoS{sub 2} on the races and retainers had varying amounts of film on the bearings. This affected the performance of the bearings. Bearings with a uniform coating performed to acceptable levels, but bearings with no visible MoS{sub 2} on the races and retainers did not perform as well as bearings with the other coatings. Unless process controls are incorporated in the sputtering process or the bearings are screened, they do not appear to be acceptable for duplex bearing applications.

  19. Hardware Impairments Aware Transceiver for Full-Duplex Massive MIMO Relaying

    NASA Astrophysics Data System (ADS)

    Xia, Xiaochen; Zhang, Dongmei; Xu, Kui; Ma, Wenfeng; Xu, Youyun

    2015-12-01

    This paper studies the massive MIMO full-duplex relaying (MM-FDR), where multiple source-destination pairs communicate simultaneously with the help of a common full-duplex relay equipped with very large antenna arrays. Different from the traditional MM-FDR protocol, a general model where sources/destinations are allowed to equip with multiple antennas is considered. In contrast to the conventional MIMO system, massive MIMO must be built with low-cost components which are prone to hardware impairments. In this paper, the effect of hardware impairments is taken into consideration, and is modeled using transmit/receive distortion noises. We propose a low complexity hardware impairments aware transceiver scheme (named as HIA scheme) to mitigate the distortion noises by exploiting the statistical knowledge of channels and antenna arrays at sources and destinations. A joint degree of freedom and power optimization algorithm is presented to further optimize the spectral efficiency of HIA based MM-FDR. The results show that the HIA scheme can mitigate the "ceiling effect" appears in traditional MM-FDR protocol, if the numbers of antennas at sources and destinations can scale with that at the relay.

  20. A single-tube duplex and multiplex PCR for simultaneous detection of four cassava mosaic begomovirus species in cassava plants.

    PubMed

    Aloyce, R C; Tairo, F; Sseruwagi, P; Rey, M E C; Ndunguru, J

    2013-04-01

    A single-tube duplex and multiplex PCR was developed for the simultaneous detection of African cassava mosaic virus (ACMV), East African cassava mosaic Cameroon virus (EACMCV), East African cassava mosaic Malawi virus (EACMMV) and East African cassava mosaic Zanzibar virus (EACMZV), four cassava mosaic begomoviruses (CMBs) affecting cassava in sub-Saharan Africa. Co-occurrence of the CMBs in cassava synergistically enhances disease symptoms and complicates their detection and diagnostics. Four primer pairs were designed to target DNA-A component sequences of cassava begomoviruses in a single tube PCR amplification using DNA extracted from dry-stored cassava leaves. Duplex and multiplex PCR enabled the simultaneous detection and differentiation of the four CMBs, namely ACMV (940bp), EACMCV (435bp), EACMMV (504bp) and EACMZV (260bp) in single and mixed infections, and sequencing results confirmed virus identities according to the respective published sequences of begomovirus species. In addition, we report here a modified Dellapotra et al. (1983) protocol, which was used to extract DNA from dry and fresh cassava leaves with comparable results. Using the duplex and multiplex techniques, time was saved and amount of reagents used were reduced, which translated into reduced cost of the diagnostics. This tool can be used by cassava breeders screening for disease resistance; scientists doing virus diagnostic studies; phytosanitary officers checking movement of diseased planting materials, and seed certification and multipliers for virus indexing.

  1. Regulated incorporation of two different metal ions into programmed sites in a duplex by DNA polymerase catalyzed primer extension.

    PubMed

    Funai, Tatsuya; Nakamura, Junko; Miyazaki, Yuki; Kiriu, Risa; Nakagawa, Osamu; Wada, Shun-ichi; Ono, Akira; Urata, Hidehito

    2014-06-23

    Metal-mediated base pairs formed by the coordination of metal ions to natural or artificial bases impart unique chemical and physical properties to nucleic acids and have attracted considerable interest in the field of nanodevices. Ag(I) ions were found to mediate DNA polymerase catalyzed primer extension through the formation of a C-Ag(I)-T base pair, as well as the previously reported C-Ag(I)-A base pair. The comparative susceptibility of dNTPs to Ag(I)-mediated enzymatic incorporation into the site opposite cytosine in the template was shown to be dATP>dTTP≫dCTP. Furthermore, two kinds of metal ions, Ag(I) and Hg(II), selectively mediate the incorporation of thymidine 5'-triphosphate into sites opposite cytosine and thymine in the template, respectively. In other words, the regulated incorporation of different metal ions into programmed sites in the duplex by DNA polymerase was successfully achieved.

  2. Regulated incorporation of two different metal ions into programmed sites in a duplex by DNA polymerase catalyzed primer extension.

    PubMed

    Funai, Tatsuya; Nakamura, Junko; Miyazaki, Yuki; Kiriu, Risa; Nakagawa, Osamu; Wada, Shun-ichi; Ono, Akira; Urata, Hidehito

    2014-06-23

    Metal-mediated base pairs formed by the coordination of metal ions to natural or artificial bases impart unique chemical and physical properties to nucleic acids and have attracted considerable interest in the field of nanodevices. Ag(I) ions were found to mediate DNA polymerase catalyzed primer extension through the formation of a C-Ag(I)-T base pair, as well as the previously reported C-Ag(I)-A base pair. The comparative susceptibility of dNTPs to Ag(I)-mediated enzymatic incorporation into the site opposite cytosine in the template was shown to be dATP>dTTP≫dCTP. Furthermore, two kinds of metal ions, Ag(I) and Hg(II), selectively mediate the incorporation of thymidine 5'-triphosphate into sites opposite cytosine and thymine in the template, respectively. In other words, the regulated incorporation of different metal ions into programmed sites in the duplex by DNA polymerase was successfully achieved. PMID:24719384

  3. Optimization of fluorescent 8-heteroaryl-guanine probes for monitoring protein-mediated duplex → G-quadruplex exchange.

    PubMed

    Fadock, Kaila L; Manderville, Richard A; Sharma, Purshotam; Wetmore, Stacey D

    2016-05-11

    In this study, we describe the thermal and optical properties of the thrombin binding aptamer (TBA) that has been modified at syn-G-tetrad positions with fluorescent 8-heteroaryl-2'-deoxyguanosine derivatives consisting of pyrrolyl ((Pyr)dG), furyl ((Fur)dG), thienyl ((Th)dG), benzofuryl ((Bfur)dG), indolyl ((Ind)dG) and benzothienyl ((Bth)dG). Insertion of the modified base into the syn-G5 position of TBA decreases duplex stability, but enhances stability of the antiparallel G-quadruplex (GQ) structure produced by TBA in the presence of K(+) ion and its molecular target, thrombin. The resulting modified TBA (mTBA) oligonucleotides have been employed in duplex → GQ exchange to monitor thrombin binding affinity and rates of GQ formation driven by thrombin binding. Our studies demonstrate that 8-heteroaryl-dG bases can be inserted into syn-G-tetrad positions of TBA without perturbing thrombin binding affinity and that the 8-thienyl-dG ((Th)dG) analog is particularly useful as an emissive probe for monitoring duplex → GQ exchange due to its heightened emissive sensitivity to change in DNA topology compared to the other 8-heteroaryl-dG analogs. The positional impact of a single (Th)dG probe versus multiple (Th)dG incorporation at syn-G sites of TBA highlight an advantage for di-substituted mTBA oligonucleotides for increased emission intensity and rates of duplex → GQ exchange that can be vital for diagnostics through aptamer detection strategies. PMID:27040462

  4. Duplex Ultrasonography in Assessing Restenosis of Renal Artery Stents

    SciTech Connect

    Bakker, Jeannette; Beutler, Jaap J.; Elgersma, Otto E.H.; Lange, Eduard E. de; Kort, Gerard A.P. de; Beek, Frederik J. A.

    1999-11-15

    Purpose: To determine the accuracy and optimal threshold values of duplex ultrasonography (US) in assessing restenosis of renal artery stents. Methods: Twenty-four consecutive patients with 33 renal arteries that had previously been treated with placement of a Palmaz stent underwent duplex US prior to intraarterial digital subtraction angiography (DSA), which was the reference standard. Diagnostic accuracy of in-stent peak systolic velocity (PSV) and reno-aortic ratio (RAR = PSV renal stent/PSV aorta) in detecting > 50% in-stent restenosis were evaluated by the receiver operating characteristic curve. Sensitivity and specificity were determined using the optimal threshold values, and using published threshold values: RAR > 3.5 and in-stent PSV > 180 cm/sec. Results: Six examinations were technically inadequate. Nine stents had residual or restenosis > 50% at DSA. The two duplex parameters were equally accurate since areas under the curves were similar (0.943). With optimal threshold values of 226 cm/sec for PSV and 2.7 for RAR, sensitivities and specificities were 100% and 90%, and 100% and 84%, respectively. Using the published duplex criteria resulted in sensitivities and specificities of 100% and 74% for PSV, and 50% and 89% for RAR. Conclusion: Duplex US is a sensitive modality for detecting in-stent restenosis if laboratory-specific threshold values are used.

  5. Calculation of nucleation free energy for duplex oligomers in the context of nearest neighbor models.

    PubMed

    Guerra, João Carlos de Oliveira

    2013-08-01

    Additive physical properties of DNA double strand polymers have been expanded in terms of 8 irreducible parameters. This provided consistency relations among the corresponding 10 duplex dimer contributions. To allow for oligomer analysis, end parameters were often added, and this would add extra degrees of freedom to the fore mentioned parameters. Statistical mechanics approaches were then connected to the nearest neighbor (NN) approach in the framework of the two-states model. Ad hoc end effects were thus (wrongly) correlated to nucleation phenomena and this lead to a critique for its role in NN modeling. With this motivation, a new NN model is proposed that accommodates the nucleation free energies. The model relates the nucleation free energy to the mean composition of the chain and permits to obtain a good estimate for the free energy associated only to the Watson-Crick base pairings.

  6. Alkyl phosphotriester modified oligodeoxyribonucleotides. VI. NMR and UV spectroscopic studies of ethyl phosphotriester (Et) modified Rp-Rp and Sp-Sp duplexes, (d[GGAA(Et)TTCC])2.

    PubMed Central

    Summers, M F; Powell, C; Egan, W; Byrd, R A; Wilson, W D; Zon, G

    1986-01-01

    1H NMR chemical shift assignments for the title compounds were made for all but a few H5' and H5" signals using two-dimensional nuclear Overhauser effect (2D-NOE) data, which was also used for the first time to assign absolute configuration at phosphorus. The chemical shifts were, in general, similar to those reported [Broido, M.S., et al. (1985) Eur. J. Biochem. 150, 117-128] for the B-like conformation of the unmodified, parent duplex, [d(GGAATTCC)]2. Differences in chemical shifts for corresponding protons were mostly localized to the AA(Et)TT region, and showed some stereochemical dependence. Unambiguous assignment of the phosphotriester 31P signals was achieved in a novel way using selective insensitive nucleus enhancement by polarization transfer (selective INEPT) NMR. The Rp-Rp duplex melted ca. 11 degrees C lower than either the Sp-Sp or parent duplexes, as evidenced by Tm and variable temperature 1H/31P NMR measurements. The 2D-NOE data for the Rp-Rp duplex suggested possible steric interactions between the ethyl group and the H3' of the flanking A residue. At low ionic strength, the Sp-Sp and parent duplexes had similar stability but at high ionic strength the Sp-Sp duplex was less stable. Images PMID:3763408

  7. Defined presentation of carbohydrates on a duplex DNA scaffold.

    PubMed

    Schlegel, Mark K; Hütter, Julia; Eriksson, Magdalena; Lepenies, Bernd; Seeberger, Peter H

    2011-12-16

    A new method for the spatially defined alignment of carbohydrates on a duplex DNA scaffold is presented. The use of an N-hydroxysuccinimide (NHS)-ester phosphoramidite along with carbohydrates containing an alkylamine linker allows for on-column labeling during solid-phase oligonucleotide synthesis. This modification method during solid-phase synthesis only requires the use of minimal amounts of complex carbohydrates. The covalently attached carbohydrates are presented in the major groove of the B-form duplex DNA as potential substrates for murine type II C-type lectin receptors mMGL1 and mMGL2. CD spectroscopy and thermal melting revealed only minimal disturbance of the overall helical structure. Surface plasmon resonance and cellular uptake studies with bone-marrow-derived dendritic cells were used to assess the capability of these carbohydrate-modified duplexes to bind to mMGL receptors.

  8. Cavitation Erosion of Sensitized UNS S31803 Duplex Stainless Steels

    NASA Astrophysics Data System (ADS)

    Mitelea, Ion; Micu, Lavinia Mădălina; Bordeaşu, Ilare; Crăciunescu, Corneliu Marius

    2016-05-01

    During processing or use, duplex steels can be subjected to heating at high temperatures that can affect their behavior. This work aims to correlate the influence of the sensitization treatment on the ultrasonic cavitation erosion behavior of a UNS S31803 (X2CrNiMoN22-5-3) duplex stainless steel. Duplex stainless steels, formed as a result of rapid cooling after solution annealing, are sensitized at temperatures of 475 and 850 °C, respectively, leading to hardening and embrittlement due to the spinodal decomposition of the ferrite and the precipitation of secondary phases. The ultrasonic cavitation erosion experiments showed that the sensitization at 850 °C reduced the mean depth of erosion by about 11% and the mean depth of erosion rate by 28%. By contrast, the sensitization at 475 °C deteriorates the cavitation erosion resistance, increasing the erosion parameters by up to 22%, compared to the solution annealed state.

  9. Chemical structure and properties of interstrand cross-links formed by reaction of guanine residues with abasic sites in duplex DNA.

    PubMed

    Catalano, Michael J; Liu, Shuo; Andersen, Nisana; Yang, Zhiyu; Johnson, Kevin M; Price, Nathan E; Wang, Yinsheng; Gates, Kent S

    2015-03-25

    A new type of interstrand cross-link resulting from the reaction of a DNA abasic site with a guanine residue on the opposing strand of the double helix was recently identified, but the chemical connectivity of the cross-link was not rigorously established. The work described here was designed to characterize the chemical structure and properties of dG-AP cross-links generated in duplex DNA. The approach involved characterization of the nucleoside cross-link "remnant" released by enzymatic digestion of DNA duplexes containing the dG-AP cross-link. We first carried out a chemical synthesis and complete spectroscopic structure determination of the putative cross-link remnant 9b composed of a 2-deoxyribose adduct attached to the exocyclic N(2)-amino group of dG. A reduced analogue of the cross-link remnant was also prepared (11b). Liquid chromatography-tandem mass spectrometric (LC-MS/MS) analysis revealed that the retention times and mass spectral properties of synthetic standards 9b and 11b matched those of the authentic cross-link remnants released by enzymatic digestion of duplexes containing the native and reduced dG-AP cross-link, respectively. These results establish the chemical connectivity of the dG-AP cross-link released from duplex DNA and provide a foundation for detection of this lesion in biological samples. The dG-AP cross-link in duplex DNA was remarkably stable, decomposing with a half-life of 22 days at pH 7 and 23 °C. The intrinsic chemical stability of the dG-AP cross-link suggests that this lesion in duplex DNA may have the power to block DNA-processing enzymes involved in transcription and replication.

  10. Renal cell carcinoma arising in ipsilateral duplex system.

    PubMed

    Mohan, Harsh; Kundu, Reetu; Dalal, Usha

    2014-09-01

    Congenital anomalies of the kidney and urinary tract are common and include a wide anatomic spectrum. Duplex systems are one of the more common renal anomalies, with the majority being asymptomatic. Little is known about the molecular pathogenesis of these anomalies; however, certain causative genes have been implicated. The finding of renal cell carcinoma arising in a kidney with the duplication of pelvicalyceal system and ureters, as in the present case, is uncommon. The association between a duplex system and renal cell carcinoma may be more than a coincidence, requiring a deeper insight and further elucidation. PMID:26328175

  11. Chirality- and sequence-selective successive self-sorting via specific homo- and complementary-duplex formations

    PubMed Central

    Makiguchi, Wataru; Tanabe, Junki; Yamada, Hidekazu; Iida, Hiroki; Taura, Daisuke; Ousaka, Naoki; Yashima, Eiji

    2015-01-01

    Self-recognition and self-discrimination within complex mixtures are of fundamental importance in biological systems, which entirely rely on the preprogrammed monomer sequences and homochirality of biological macromolecules. Here we report artificial chirality- and sequence-selective successive self-sorting of chiral dimeric strands bearing carboxylic acid or amidine groups joined by chiral amide linkers with different sequences through homo- and complementary-duplex formations. A mixture of carboxylic acid dimers linked by racemic-1,2-cyclohexane bis-amides with different amide sequences (NHCO or CONH) self-associate to form homoduplexes in a completely sequence-selective way, the structures of which are different from each other depending on the linker amide sequences. The further addition of an enantiopure amide-linked amidine dimer to a mixture of the racemic carboxylic acid dimers resulted in the formation of a single optically pure complementary duplex with a 100% diastereoselectivity and complete sequence specificity stabilized by the amidinium–carboxylate salt bridges, leading to the perfect chirality- and sequence-selective duplex formation. PMID:26051291

  12. A duplex recombinant viral nucleoprotein microbead immunoassay for simultaneous detection of seroresponses to human respiratory syncytial virus and metapneumovirus infections.

    PubMed

    Zhang, Yange; Brooks, W Abdullah; Goswami, Doli; Rahman, Mustafizur; Luby, Stephen P; Erdman, Dean D

    2014-09-01

    Serologic diagnosis of human respiratory syncytial virus (hRSV) and human metapneumovirus (hMPV) infections has been shown to complement virus detection methods in epidemiologic studies. Enzyme immunoassays (EIAs) using cultured virus lysate antigens are often used to diagnose infection by demonstration of a ≥4-fold rises in antibody titer between acute and convalescent serum pairs. In this study, hRSV and hMPV nucleocapsid (recN) proteins were expressed in a baculovirus system and their performance compared with virus culture lysate antigen in EIAs using paired serum specimens collected from symptomatic children. The recN proteins were also used to develop a duplex assay based on the Luminex microbead-based suspension array technology, where diagnostic rises in antibody levels could be determined simultaneously at a single serum dilution. Antibody levels measured by the recN and viral lysate EIAs correlated moderately (hRSV, r(2)=0.72; hMPV, r(2)=0.76); the recN EIAs identified correctly 35 of 37 (94.6%) and 48 of 50 (96%) serum pairs showing diagnostic antibody rises by viral lysate EIAs. Purified recN proteins were then coupled to microbeads and serum pairs were tested at a single dilution on a Luminex MAGPIX(®) analyzer. The duplex recN assay identified correctly 33 of 39 (85%) and 41 of 47 (86.7%) serum pairs showing diagnostic rises to hRSV and hMPV, respectively. The recN assay permits simultaneous testing for acute hRSV and hMPV infections and offers a platform for expanded multiplexing of other respiratory virus assays.

  13. [Interaction of Dystamycin Dimeric Analog with Poly(dA) x poly(dT), Poly[d(A-T)] x poly[d(A-T)] and Duplex O23 at Origin of Replication of the Herpes Simplex Virus].

    PubMed

    Surovaya, A N; Bazhulina, N P; Lepehina, S Yu; Andronova, V L; Galegov, G A; Moiseeva, E D; Grokhovsky, S L; Gursky, G V

    2016-01-01

    The binding of distamycin dimeric analog (Pt-bis-Dst) to poly[d(A-T)] x poly[d(A-T)1, poly(dA) x poly(dT) and duplex O23 with the sequence 5'-GCCAATATATATATATTATTAGG-3' which is present at the origin of replication of herpes simplex virus OriS is investigated with the use of UV and CD spectroscopy. The distinction of the synthetic polyamide from a natural antibiotic lies in the fact that in the synthetic polyamide there are two distamycin moieties bound via a glycine cis-diamino platinum group. It was shown that the binding of Pt-bis-Dst to poly[d(A-T)] x poly[d(A-T)] and poly(dA) x poly(dT) reaches saturation if one molecule of the ligand occurs at approximately every 8 bp. With further increase in the ratio of the added ligand to the base pairs in CD spectra of complexes with poly[d(A-T)] x poly[d(A-T)], we observed that the maximum wavelength band tend to be shifted towards longer wavelengths, while in the spectral region of 290-310 nm a "shoulder", that was absent in the spectra of the complexes obtained at low polymer coverages by the ligand, appeared. At high molar concentration ratios of ligand to oligonucleotide Pt-bis-Dst can bind to poly[d(A-T)] x poly[d(A-T)] in the form of hairpins or may form associates by the interaction between the distamycin moieties of neighboring molecules of Pt-bis-Dst. The structure of the complexes is stabilized by interactions between pirrolcarboxamide moieties of two molecules of Pt-bis-Dst adsorbed on adjacent overlapping binding sites. These interactions are probably also responsible for the concentration-dependent spectral changes observed during the formation of a complex between Pt-bis-Dst and poly[d(A-T)] x poly[d(A-T)]. Spectral changes are almost absent in binding of Pt-bis-Dst to poly(dA) x poly(dT). Binding of Pt-bis-Dst to duplex O23 reaches saturation if two ligand molecules occur in a duplex that contains a cluster of 18 AT pairs. With increasing the molar concentration ratio of the ligand to the duplex CD

  14. Stability of Electron Pairs--A Myth.

    ERIC Educational Resources Information Center

    Duke, B. J.

    1978-01-01

    This article discusses errors in the presentation of valence theory in undergraduate chemistry textbooks, and the resulting misunderstandings in the minds of many students. Particular emphasis is given to the explanation of the trend in ionization energies along the first row of the periodic table. (BB)

  15. A Standard Duplex Fiber Optic Receptacle/Connector: Requirements And Test Methods

    NASA Astrophysics Data System (ADS)

    Barrett, Mike; Khalil, Ragai

    1988-12-01

    The concept for using a duplex connector for the Fiber Distributed Data Interface (FDDI) was formalized in late 1983. The duplex requirements were driven by both the token ring topology and by the need to simplify connectivity between stations. Though most users speak in terms of a duplex connector or Medium Interface Connector (MIC), the FDDI Physical Medium Dependent (PMD) document only defines the physical parameters for a duplex receptacle. The receptacle is the boundary between the station and the cable plant of an FDDI network and hence the only location at which station conformance can be verified. The duplex connector or plug is therefore part of the FDDI cable plant.

  16. Computer Maintenance Operations Center (CMOC), showing duplexed cyber 170174 computers ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Computer Maintenance Operations Center (CMOC), showing duplexed cyber 170-174 computers - Beale Air Force Base, Perimeter Acquisition Vehicle Entry Phased-Array Warning System, Techinical Equipment Building, End of Spencer Paul Road, north of Warren Shingle Road (14th Street), Marysville, Yuba County, CA

  17. FRONT VIEW OF FACILITY 561, WHICH WAS ORIGINALLY A DUPLEX. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    FRONT VIEW OF FACILITY 561, WHICH WAS ORIGINALLY A DUPLEX. PHOTO SHOWS THE ONLY UNIT REMAINING, UNIT B (UNIT A WAS DEMOLISHED AFTER A FIRE). VIEW FACING NORTH - Camp H.M. Smith and Navy Public Works Center Manana Title VII (Capehart) Housing, Intersection of Acacia Road and Brich Circle, Pearl City, Honolulu County, HI

  18. Renal pelvis urothelial carcinoma of the upper moiety in complete right renal duplex: a case report

    PubMed Central

    Zhang, Yiran; Yu, Quanfeng; Zhang, Zhihong; Liu, Ranlu; Xu, Yong

    2015-01-01

    Urothelial carcinoma (UC) originated from renal pelvis is the common tumor of the urinary system, however, neoplasia of the renal pelvis in duplex kidneys is extremely rare, especially in the complete renal and ureteral duplex cases. We present the first case of renal pelvis UC of the upper moiety in a complete right renal duplex. This male patient has bilateral complete renal and ureteral duplex. To the best of our knowledge, this is the first reported case of renal pelvis UC in a complete renal duplex system. After this experience we feel that the diagnosis of renal pelvis UC in duplex kidneys is not so easy, and once the diagnosis is determined, the whole renal duplex units and bladder cuff or ectopic orifice should be excised radically. PMID:26823906

  19. Powered Tate Pairing Computation

    NASA Astrophysics Data System (ADS)

    Kang, Bo Gyeong; Park, Je Hong

    In this letter, we provide a simple proof of bilinearity for the eta pairing. Based on it, we show an efficient method to compute the powered Tate pairing as well. Although efficiency of our method is equivalent to that of the Tate pairing on the eta pairing approach, but ours is more general in principle.

  20. Development and evaluation of a single-step duplex PCR for simultaneous detection of Fasciola hepatica and Fasciola gigantica (family Fasciolidae, class Trematoda, phylum Platyhelminthes).

    PubMed

    Le, Thanh Hoa; Nguyen, Khue Thi; Nguyen, Nga Thi Bich; Doan, Huong Thi Thanh; Le, Xuyen Thi Kim; Hoang, Chau Thi Minh; De, Nguyen Van

    2012-08-01

    A single-step multiplex PCR (here referred to as a duplex PCR) has been developed for simultaneous detection and diagnosis of Fasciola hepatica and F. gigantica. These species overlap in distribution in many countries of North and East Africa and Central and Southeast Asia and are similar in egg morphology, making identification from fecal samples difficult. Based on a comparative alignment of mitochondrial DNA (mtDNA) spanning the region of cox1-trnT-rrnL, two species-specific forward primers were designed, FHF (for F. hepatica) and FGF (for F. gigantica), and a single reverse primer, FHGR (common for both species). Conventional PCR followed by sequencing was applied using species-specific primer pairs to verify the specificity of primers and the identity of Fasciola DNA templates. Duplex PCR (using three primers) was used for testing with the DNA extracted from adult worms, miracidia, and eggs, producing amplicons of 1,031 bp for F. hepatica and 615 bp for F. gigantica. The duplex PCR failed to amplify from DNA of other common liver and intestinal trematodes, including two opisthorchiids, three heterophyids, an echinostomid, another fasciolid, and a taeniid cestode. The sensitivity assay showed that the duplex PCR limit of detection for each Fasciola species was between 0.012 ng and 0.006 ng DNA. Evaluation using DNA templates from 32 Fasciola samples (28 adults and 4 eggs) and from 25 field-collected stools of ruminants and humans revealed specific bands of the correct size and the presence of Fasciola species. This novel mtDNA duplex PCR is a sensitive and fast tool for accurate identification of Fasciola species in areas of distributional and zonal overlap.

  1. Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes

    NASA Astrophysics Data System (ADS)

    Kimsey, Isaac J.; Petzold, Katja; Sathyamoorthy, Bharathwaj; Stein, Zachary W.; Al-Hashimi, Hashim M.

    2015-03-01

    Rare tautomeric and anionic nucleobases are believed to have fundamental biological roles, but their prevalence and functional importance has remained elusive because they exist transiently, in low abundance, and involve subtle movements of protons that are difficult to visualize. Using NMR relaxation dispersion, we show here that wobble dG•dT and rG•rU mispairs in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-populated Watson-Crick-like mispairs that are stabilized by rare enolic or anionic bases. These mispairs can evade Watson-Crick fidelity checkpoints and form with probabilities (10-3 to 10-5) that strongly imply a universal role in replication and translation errors. Our results indicate that rare tautomeric and anionic bases are widespread in nucleic acids, expanding their structural and functional complexity beyond that attainable with canonical bases.

  2. Visualizing Transient Watson-Crick Like Mispairs in DNA and RNA Duplexes

    PubMed Central

    Kimsey, Isaac J.; Petzold, Katja; Sathyamoorthy, Bharathwaj; Stein, Zachary W.; Al-Hashimi, Hashim M.

    2015-01-01

    Rare tautomeric and anionic nucleobases are believed to play fundamental biological roles but their prevalence and functional importance has remained elusive because they exist transiently, in low-abundance, and involve subtle movements of protons that are difficult to visualize. Using NMR relaxation dispersion, we show that wobble dG•dT and rG•rU mispairs in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-populated Watson-Crick like mispairs that are stabilized by rare enolic or anionic bases. These mispairs can evade Watson-Crick fidelity checkpoints and form with probabilities (10−3-10−5) that strongly imply a universal role in replication and translation errors. Our results indicate that rare tautomeric and anionic bases are widespread in nucleic acids, expanding their structural and functional complexity beyond that attainable with canonical bases. PMID:25762137

  3. Assessment of thermal embrittlement in duplex stainless steels 2003 and 2205 for nuclear power applications

    DOE PAGES

    Tucker, J. D.; Miller, M. K.; Young, G. A.

    2015-04-01

    Duplex stainless steels are desirable for use in power generation systems due to their attractive combination of strength, corrosion resistance, and cost. However, thermal embrittlement at intermediate homologous temperatures of ~887°F (475°C) and below, via spinodal decomposition, limits upper service temperatures for many applications. New lean grade duplex alloys have improved thermal stability over standard grades and potentially increase the upper service temperature or the lifetime at a given temperature for this class of material. The present work compares the thermal stability of lean grade, alloy 2003 to standard grade, alloy 2205, through a series of isothermal agings between 500°Fmore » (260°C) and 900°F (482°C) for times between 1 and 10,000 hours. Aged samples were characterized by changes in microhardness and impact toughness. Additionally, atom probe tomography was performed to illustrate the evolution of the α-α' phase separation in both alloys at select conditions. Atom probe tomography confirmed that phase separation occurs via spinodal decomposition for both alloys and identified the formation of Ni-Cu-Si-Mn-P clusters in alloy 2205 that may contribute to embrittlement of this alloy. The impact toughness model predictions for upper service temperature show that alloy 2003 can be considered for use in 550°F applications for 80 year service lifetimes based on a Charpy V-notch criteria of 35 ft-lbs at 70°F. Alloy 2205 should be limited to 500°F applications.« less

  4. Assessment of thermal embrittlement in duplex stainless steels 2003 and 2205 for nuclear power applications

    SciTech Connect

    Tucker, J. D.; Miller, M. K.; Young, G. A.

    2015-04-01

    Duplex stainless steels are desirable for use in power generation systems due to their attractive combination of strength, corrosion resistance, and cost. However, thermal embrittlement at intermediate homologous temperatures of ~887°F (475°C) and below, via spinodal decomposition, limits upper service temperatures for many applications. New lean grade duplex alloys have improved thermal stability over standard grades and potentially increase the upper service temperature or the lifetime at a given temperature for this class of material. The present work compares the thermal stability of lean grade, alloy 2003 to standard grade, alloy 2205, through a series of isothermal agings between 500°F (260°C) and 900°F (482°C) for times between 1 and 10,000 hours. Aged samples were characterized by changes in microhardness and impact toughness. Additionally, atom probe tomography was performed to illustrate the evolution of the α-α' phase separation in both alloys at select conditions. Atom probe tomography confirmed that phase separation occurs via spinodal decomposition for both alloys and identified the formation of Ni-Cu-Si-Mn-P clusters in alloy 2205 that may contribute to embrittlement of this alloy. The impact toughness model predictions for upper service temperature show that alloy 2003 can be considered for use in 550°F applications for 80 year service lifetimes based on a Charpy V-notch criteria of 35 ft-lbs at 70°F. Alloy 2205 should be limited to 500°F applications.

  5. Target-controlled formation of silver nanoclusters in abasic site-incorporated duplex DNA for label-free fluorescence detection of theophylline

    NASA Astrophysics Data System (ADS)

    Park, Ki Soo; Oh, Seung Soo; Soh, H. Tom; Park, Hyun Gyu

    2014-08-01

    A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to the cytosine nucleobase is prevented. Consequently, fluorescent silver nanoclusters are not formed causing a significant reduction of the fluorescence signal. By employing this new sensor, theophylline can be highly selectively detected at a concentration as low as 1.8 μM. Finally, the diagnostic capability and practical application of this sensor were demonstrated by its use in detecting theophylline in human blood serum.A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to

  6. Electron interaction with a DNA duplex: dCpdC:dGpdG.

    PubMed

    Gu, Jiande; Wang, Jing; Leszczynski, Jerzy

    2016-05-21

    Electron attachment to double-stranded cytosine-rich DNA, dCpdC:dGpdG, has been studied by density functional theory. This system represents a minimal descriptive unit of a cytosine-rich double-stranded DNA helix. A significant electron affinity for the formation of a cytosine-centered radical anion is revealed to be about 2.2 eV. The excess electron may reside on the nucleobase at the 5' position (dC˙(-)pdC:dGpdG) or at the 3' position (dCpdC˙(-):dGpdG). The inter-strand proton transfer between the radical anion centered cytosine (N3) and the paired guanine (HN1) results in the formation of radical anion center separated complexes dC1H˙pdC:dG2-H(-)pdG and dCpdC2H˙:dGpdG1-H(-). These distonic radical anions are found to be approximately 1 to 4 kcal mol(-1) more stable than the normal radical anions. Intra-strand cytosine π→π transition energies are below the electron detachment energy. Inter-strand π→π transitions of the excess electron from C to G are predicted to be less than 2.79 eV. Electron transfer might also be possible through the inter-strand base-jumping mode. An analysis of absorption visible spectra reveals the absorption bands ranging from 500 nm to 700 nm for the cytosine-rich radical anions of the DNA duplex. Electron attachment to cytidine oligomers might add color to the DNA duplex. PMID:27139598

  7. 31P NMR conformational studies of non-palindromic DNA duplexes related to HIV-1 enhancer

    NASA Astrophysics Data System (ADS)

    Tisne, C.; Simenel, C.; Hantz, E.; Delepierre, M.

    1998-02-01

    Assignment of all 31P resonances of 16 base-pair DNA duplexes, 5' d(CTGGGGACTTTCCAGG)3' 5' d(CCTGGAAAGTCCCCAG)3', related to the DNA kappaB site of the HIV-1 LTR together with a mutated sequence 5' d(CTGCTCACTTTCCAGG)3' 5' d(CCTGGAAAGTGAGCAG)3' was determined by 2D heteronuclear inverse NMR spectroscopy (HSQC-TOCSY and heteronuclear COSY). ^3JH{3'}-P coupling constants for most of the phosphates of the mutated oligomer were obtained using heteronuclear selective COSY. L'attribution des résonances 31P du fragment d'ADN de seize paires de base 5' d(CTGGGGACTTTCCAGG)3' 5' d(CCTGGAAAGTCCCCAG)3' (16N) correspondant au site kappaB du LTR du HIV-1 et de la séquence mutée 5' d(CTGCTCACTTTCCAGG)3' 5' d(CCTGGAAAGTGAGCAG)3' (16M) a été déterminée à l'aide de méthodes 2D hétéronucléaires à détection indirecte (HSQC-TOCSY et COSY hétéronucléaires). Les constantes de couplage ^3JH{3'}-P ont été mesurées pour la plupart des phosphates de 16 M à l'aide d'expérience COSY hétéronucléaires sélectives.

  8. Use of duplex polymerase chain reaction (duplex-PCR) technique to identify bovine and water buffalo milk used in making mozzarella cheese.

    PubMed

    Rea, S; Chikuni, K; Branciari, R; Sangamayya, R S; Ranucci, D; Avellini, P

    2001-11-01

    Molecular biology techniques have been used for species identification in food of animal origin in relatively recent years. A polymerase chain reaction (PCR) based method, the multiplex PCR, was recently applied to species identification in meat and meat products. It allows co-amplification of separate regions of a single gene or specific fragments, each typical of a different animal species in a single PCR reaction, using different pairs of primers in the same reaction mix. In the present paper, the duplex-PCR technique is proposed to identify bovine and water buffalo DNA in a single PCR assay in milk and mozzarella cheese (a typical Italian cheese, originally made from pure water buffalo milk). Because of its lower cost, undeclared bovine milk is added to water buffalo milk for making different kinds of mozzarella cheese. The results of this experiment indicate the applicability of this method, which showed an absolute specificity for the two species and a high sensitivity even down to low DNA concentrations (1 pg). In bovine and water buffalo mixtures of both milk and mozzarella cheese, the minimum concentration tested was 1% of bovine in water buffalo milk and water buffalo in bovine milk. The importance of the somatic cell content in raw milk is also discussed with special reference to the evaluation of mixtures (milk or cheese) of the two species.

  9. Role of helical constraints of the EBS1-IBS1 duplex of a group II intron on demarcation of the 5' splice site.

    PubMed

    Popovic, Milena; Greenbaum, Nancy L

    2014-01-01

    Recognition of the 5' splice site by group II introns involves pairing between an exon binding sequence (EBS) 1 within the ID3 stem-loop of domain 1 and a complementary sequence at the 3' end of exon 1 (IBS1). To identify the molecular basis for splice site definition of a group IIB ai5γ intron, we probed the solution structure of the ID3 stem-loop alone and upon binding of its IBS1 target by solution NMR. The ID3 stem was structured. The base of the ID3 loop was stacked but displayed a highly flexible EBS1 region. The flexibility of EBS1 appears to be a general feature of the ai5γ and the smaller Oceanobacillus iheyensis (O.i.) intron and may help in effective search of conformational space and prevent errors in splicing as a result of fortuitous base-pairing. Binding of IBS1 results in formation of a structured seven base pair duplex that terminates at the 5' splice site in spite of the potential for additional A-U and G•U pairs. Comparison of these data with conformational features of EBS1-IBS1 duplexes extracted from published structures suggests that termination of the duplex and definition of the splice site are governed by constraints of the helical geometry within the ID3 loop. This feature and flexibility of the uncomplexed ID3 loop appear to be common for both the ai5γ and O.i. introns and may help to fine-tune elements of recognition in group II introns. PMID:24243113

  10. Kinetics of DNA duplex formation: A-tracts versus AT-tracts.

    PubMed

    Wyer, Jean Ann; Kristensen, Mads Bejder; Jones, Nykola C; Hoffmann, Søren Vrønning; Nielsen, Steen Brøndsted

    2014-09-21

    The hybridisation and melting of DNA strands are critical steps in many biological processes, but still a deeper understanding of the kinetics is lacking. This is evident from the absence of a clear correlation between rate constants for duplex formation and the number of bases in the strand or the sequence. Here we have probed differences between formation times of A-tracts and AT-tracts by studying complementary model strands mainly comprised of adenine (A) and thymine (T) in stopped-flow (SF) experiments. These strands are relevant as DNA replication begins in regions with a large number of AT base pairs. Interpretation of our results is aided by secondary-structure modelling where both the fractions of the different types of structures and the number of paired bases in the lowest-energy ones are determined. The model is based on calculation of free energies using fixed values for enthalpies and entropies associated with base pairing and a stochastic sampling of the possible structures. We find that the strand length affects rates: the activation energy for the formation of short (16-base pairs) A-tracts is larger than that for longer ones (20-base pairs). Activation energies for the formation of AT-tracts are an order of magnitude larger, and larger for shorter strands than for long ones. These higher activation energies are in agreement with the fact that the fraction of unpaired bases in the constituent AT-tract strands is less than in those which comprise the A-tracts. That the pre-structures of the single strands significantly affect rates is also used to rationalise the results obtained for two pairs of complementary 12-mer strands that have the same bases but in a different sequence; we report here similar activation energies as reported earlier and that these are strongly sequence dependent. Finally, we demonstrate that SF can be coupled with the measurement of circular dichroism (CD) in the vacuum ultraviolet (VUV) region, taking advantage of a

  11. Hangingwall strain: A function of duplex shape and footwall topography

    NASA Astrophysics Data System (ADS)

    Butler, Robert W. H.

    1982-10-01

    The concept of piggy-back thrust tectonics implies that foreland is progressively accreted onto a developing thrust sheet during duplex formation. Lateral shape changes in duplexes in the hangingwall of a thrust and corrugations in the footwall will fold higher thrust sheets to give culminations and depressions. Balancing of parts of high level thrust sheets with lower sheets and foreland requires a sequence of extensional and compressional strains orientated normal to the thrust transport direction. Culmination walls will be sites of strike-parallel extension. Subsequent adjacent culminations will compress early culmination walls which will result in a sequence of irrotational strains. Examples of this geometry are given from the Moine Thrust zone of Northwest Scotland. The model allows a re-examination of strains and hangingwall evolution in some thrust sheets in the Helvetic and external zones of the Alps.

  12. Duplex stainless steels for the pulp and paper industry

    SciTech Connect

    Alfonsson, E.; Olsson, J.

    1999-07-01

    The metallurgy and corrosion resistance of duplex stainless steel, particularly with regards to applications in the pulp and paper industry, are described. Practical experiences from pressure vessel installations in cooking plants and bleach plants as well as from non-pressurized items in different parts along the fiber line, are given. The paper also reviews corrosion test results presented previously and compares these with recent test data and the practical experiences. Though most of the installations have been successful, some cases of corrosion attacks on duplex stainless steel have been reported, although these are very limited in number: one digester, one calorifier, two pulp storage towers, and two bleach plant filter washers, of a total of more than 700 identified installations.

  13. Investigation of plastic deformation heterogeneities in duplex steel by EBSD

    SciTech Connect

    Wronski, S.; Tarasiuk, J.; Bacroix, B.; Baczmanski, A.; Braham, C.

    2012-11-15

    An EBSD analysis of a duplex steel (austeno-ferritic) deformed in tension up to fracture is presented. The main purpose of the paper is to describe, qualitatively and quantitatively, the differences in the behavior of the two phases during plastic deformation. In order to do so, several topological maps are measured on the deformed state using the electron backscatter diffraction technique. Distributions of grain size, misorientation, image quality factor and texture are then analyzed in detail. - Highlights: Black-Right-Pointing-Pointer Heterogeneities in duplex steel is studied. Black-Right-Pointing-Pointer The behavior of the two phases during plastic deformation is studied. Black-Right-Pointing-Pointer IQ factor distribution and misorientation characteristics are examined using EBSD.

  14. Investigation of hot cracking resistance of 2205 duplex steel

    NASA Astrophysics Data System (ADS)

    Adamiec, J.; Ścibisz, B.

    2010-02-01

    Austenitic duplex steel of the brand 2205 according to Avesta Sheffield is used for welded constructions (pipelines, tanks) in the petrol industry, chemical industry and food industry. It is important to know the range of high-temperature brittleness in designing welding technology for constructions made of this steel type. There is no data in literature concerning this issue. High-temperature brittleness tests using the simulator of heat flow device Gleeble 3800 were performed. The tests results allowed the evaluation of the characteristic temperatures in the brittleness temperature range during the joining of duplex steels, specifically the nil-strength temperature (NST) and nil-ductility temperatures (NDT) during heating, the strength and ductility recovery temperatures (DRT) during cooling, the Rfparameter (Rf = (Tliquidus - NDT)/NDT) describing the duplex steel inclination for hot cracking, and the brittleness temperature range (BTR). It has been stated that, for the examined steel, this range is wide and amounts to ca. 90 °C. The joining of duplex steels with the help of welding techniques creates a significant risk of hot cracks. After analysis of the DTA curves a liquidus temperature of TL = 1465 °C and a solidus temperature of TS = 1454 °C were observed. For NST a mean value was assumed, in which the cracks appeared for six samples; the temperature was 1381 °C. As the value of the NDT temperature 1367 °C was applied while for DRT the assumed temperature was 1375 °C. The microstructure of the fractures was observed using a Hitachi S-3400N scanning electron microscope (SEM). The analyses of the chemical composition were performed using an energy-dispersive X-ray spectrometer (EDS), Noran System Six of Thermo Fisher Scientific. Essential differences of fracture morphology type over the brittle temperature range were observed and described.

  15. View from east to west of family housing unit (duplex; ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View from east to west of family housing unit (duplex; either #27 or #87, as only the 7 is visible). Unit #27 was three-bedroom and located on 9th Street south. Unit #87 was a two-bedroom located on 4th Street north. These housing units have been removed - Stanley R. Mickelsen Safeguard Complex, Family Housing Units, In area bounded by Tenth Street North, Avenue A, & Avenue J, Nekoma, Cavalier County, ND

  16. All-atom crystal simulations of DNA and RNA duplexes

    PubMed Central

    Liu, Chunmei; Janowski, Pawel A.; Case, David A.

    2014-01-01

    Background Molecular dynamics simulations can complement experimental measures of structure and dynamics of biomolecules. The quality of such simulations can be tested by comparisons to models refined against experimental crystallographic data. Methods We report simulations of a DNA and RNA duplex in their crystalline environment. The calculations mimic the conditions for PDB entries 1D23 [d(CGATCGATCG)2] and 1RNA [(UUAUAUAUAUAUAA)2], and contain 8 unit cells, each with 4 copies of the Watson-Crick duplex; this yields in aggregate 64 µs of duplex sampling for DNA and 16 µs for RNA. Results The duplex structures conform much more closely to the average structure seen in the crystal than do structures extracted from a solution simulation with the same force field. Sequence-dependent variations in helical parameters, and in groove widths, are largely maintained in the crystal structure, but are smoothed out in solution. However, the integrity of the crystal lattice is slowly degraded in both simulations, with the result that the interfaces between chains become heterogeneous. This problem is more severe for the DNA crystal, which has fewer inter-chain hydrogen bond contacts than does the RNA crystal. Conclusions Crystal simulations using current force fields reproduce many features of observed crystal structures, but suffer from a gradual degradation of the integrity of the crystal lattice. General significance The results offer insights into force-field simulations that tests their ability to preserve weak interactions between chains, which will be of importance also in non-crystalline applications that involve binding and recognition. PMID:25255706

  17. Rapid commutation duplexer with phase-related outputs

    NASA Astrophysics Data System (ADS)

    Roveda, R.; Cattarin, G.; Digregorio, C.; Parrucci, U.

    Design criteria and the realization of an X-band waveguide rapid commutation duplexer, in production, are presented. By means of a digital TTL command it is capable of operating in three different conditions: all the power is conveyed to a single output; the poweer is equally divided between two in-phase outputs; and it is equally divided between two counter-phase outputs. In a monopulse radar this permits the electronic scanning of the antenna beam.

  18. Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses

    NASA Technical Reports Server (NTRS)

    Urakawa, Hidetoshi; Noble, Peter A.; El Fantroussi, Said; Kelly, John J.; Stahl, David A.

    2002-01-01

    The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (T(d)) and signal intensity of short DNA duplexes were determined by using oligonucleotide microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-base-pair mismatch at positions 1 to 5 from the 5' terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the mismatch, type of mismatch, and formamide concentration significantly affected the T(d) and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the T(d) and signal intensity, and it decreased the variability of the signal. Although T(d)s of probe-target duplexes with mismatches in the first or second position were not significantly different from one another, duplexes with mismatches in the third to fifth positions had significantly lower T(d)s than those with mismatches in the first or second position. The trained NNs predicted the T(d) with high accuracies (R(2) = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R(2) = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in T(d)s, followed by position of the mismatch (19%) and type of mismatch (6%). The results suggest that position of the mismatch at or near the 5' terminus plays a greater role in determining the T(d) and signal intensity of duplexes than the type of mismatch.

  19. Duplex-Selective Ruthenium-based DNA Intercalators

    PubMed Central

    Shade, Chad M.; Kennedy, Robert D.; Rouge, Jessica L.; Rosen, Mari S.; Wang, Mary X.; Seo, Soyoung E.; Clingerman, Daniel J.

    2016-01-01

    We report the design and synthesis of small molecules that exhibit enhanced luminescence in the presence of duplex rather than single-stranded DNA. The local environment presented by a well-known [Ru(dipyrido[2,3-a:3',2'-c]phenazine)L2]2+-based DNA intercalator was modified by functionalizing the bipyridine ligands with esters and carboxylic acids. By systematically varying the number and charge of the pendant groups, it was determined that decreasing the electrostatic interaction between the intercalator and the anionic DNA backbone reduced single-strand interactions and translated to better duplex specificity. In studying this class of complexes, a single RuII complex emerged that selectively luminesces in the presence of duplex DNA with little to no background from interacting with single stranded DNA. This complex shows promise as a new dye capable of selectively staining double versus single-stranded DNA in gel electrophoresis, which cannot be done with conventional SYBR dyes. PMID:26119581

  20. Antisense properties of duplex- and triplex-forming PNAs.

    PubMed Central

    Knudsen, H; Nielsen, P E

    1996-01-01

    The potential of peptide nucleic acids (PNAs) as specific inhibitors of translation has been studied. PNAs with a mixed purine/pyrimidine sequence form duplexes, while homopyrimidine PNAs form (PNA)2/RNA triplexes with complementary sequences on RNA. We show here that neither of these PNA/RNA structures are substrates for RNase H. Translation experiments in cell-free extracts showed that a 15mer duplex-forming PNA blocked translation in a dose-dependent manner when the target was 5'-proximal to the AUG start codon on the RNA, whereas similar 10-, 15- or 20mer PNAs had no effect when targeted towards sequences in the coding region. Triplex-forming 10mer PNAs were efficient and specific antisense agents with a target overlapping the AUG start codon and caused arrest of ribosome elongation with a target positioned in the coding region of the mRNA. Furthermore, translation could be blocked with a 6mer bisPNA or with a clamp PNA, forming partly a triplex, partly a duplex, with its target sequence in the coding region of the mRNA. PMID:8602363

  1. Transpressive duplex and flower structure: Dent Fault System, NW England

    NASA Astrophysics Data System (ADS)

    Woodcock, Nigel H.; Rickards, Barrie

    2003-12-01

    Revised mapping along the Dent Fault (northwest England) has improved the resolution of folds and faults formed during Variscan (late Carboniferous) sinistral transpression. A NNE-trending east-down monocline, comprising the Fell End Syncline and Taythes Anticline, was forced in Carboniferous cover above a reactivated precursor to the Dent Fault within the Lower Palaeozoic basement. The Taythes Anticline is periclinal due to interference with earlier Acadian folds. The steep limb of the monocline was eventually cut by the west-dipping Dent Fault. The hangingwall of the Dent Fault was dissected by sub-vertical or east dipping faults, together forming a positive flower structure in cross-section and a contractional duplex in plan view. The footwall to the Dent Fault preserves evidence of mostly dip-slip displacements, whereas strike-slip was preferentially partitioned into the hangingwall faults. This pattern of displacement partitioning may be typical of transpressive structures in general. The faults of the Taythes duplex formed in a restraining overlap zone between the Dent Fault and the Rawthey Fault to the west. The orientations of the duplex faults were a response to kinematic boundary conditions rather than to the regional stress field directly. Kinematic constraints provided by the Dent and neighbouring Variscan faults yield a NNW-SSE regional shortening direction in this part of the Variscan foreland.

  2. Regulation of DNA Pairing in Homologous Recombination

    PubMed Central

    Daley, James M.; Gaines, William A.; Kwon, YoungHo; Sung, Patrick

    2014-01-01

    Homologous recombination (HR) is a major mechanism for eliminating DNA double-strand breaks from chromosomes. In this process, the break termini are resected nucleolytically to form 3′ ssDNA (single-strand DNA) overhangs. A recombinase (i.e., a protein that catalyzes homologous DNA pairing and strand exchange) assembles onto the ssDNA and promotes pairing with a homologous duplex. DNA synthesis then initiates from the 3′ end of the invading strand, and the extended DNA joint is resolved via one of several pathways to restore the integrity of the injured chromosome. It is crucial that HR be carefully orchestrated because spurious events can create cytotoxic intermediates or cause genomic rearrangements and loss of gene heterozygosity, which can lead to cell death or contribute to the development of cancer. In this review, we will discuss how DNA motor proteins regulate HR via a dynamic balance of the recombination-promoting and -attenuating activities that they possess. PMID:25190078

  3. Deformable nature of various damaged DNA duplexes estimated by an electrochemical analysis on electrodes.

    PubMed

    Chiba, J; Aoki, S; Yamamoto, J; Iwai, S; Inouye, M

    2014-10-01

    We report bending flexibility of damaged duplexes possessing an apurinic/apyrimidinic (AP) site analogue, a cyclobutane pyrimidine dimer (CPD), and a pyrimidine(6-4)pyrimidone photoproduct (6-4PP). Based on the electrochemical evaluation on electrodes, the duplex flexibilities of the lesions increased in the following order: CPD < AP < 6-4PP. We discussed the possibility that the emerging local flexibility might be a good sign for UV-damaged DNA-binding proteins on duplexes.

  4. Characterization of microstructure and texture across dissimilar super duplex/austenitic stainless steel weldment joint by super duplex filler metal

    SciTech Connect

    Eghlimi, Abbas; Shamanian, Morteza; Eskandarian, Masoomeh; Zabolian, Azam; Szpunar, Jerzy A.

    2015-08-15

    In the present paper, microstructural changes across an as-welded dissimilar austenitic/duplex stainless steel couple welded by a super duplex stainless steel filler metal using gas tungsten arc welding process is characterized with optical microscopy and electron back-scattered diffraction techniques. Accordingly, variations of microstructure, texture, and grain boundary character distribution of base metals, heat affected zones, and weld metal were investigated. The results showed that the weld metal, which was composed of Widmanstätten austenite side-plates and allotriomorphic grain boundary austenite morphologies, had the weakest texture and was dominated by low angle boundaries. The welding process increased the ferrite content but decreased the texture intensity at the heat affected zone of the super duplex stainless steel base metal. In addition, through partial ferritization, it changed the morphology of elongated grains of the rolled microstructure to twinned partially transformed austenite plateaus scattered between ferrite textured colonies. However, the texture of the austenitic stainless steel heat affected zone was strengthened via encouraging recrystallization and formation of annealing twins. At both interfaces, an increase in the special character coincident site lattice boundaries of the primary phase as well as a strong texture with <100> orientation, mainly of Goss component, was observed. - Graphical abstract: Display Omitted - Highlights: • Weld metal showed local orientation at microscale but random texture at macroscale. • Intensification of <100> orientated grains was observed adjacent to the fusion lines. • The austenite texture was weaker than that of the ferrite in all duplex regions. • Welding caused twinned partially transformed austenites to form at SDSS HAZ. • At both interfaces, the ratio of special CSL boundaries of the primary phase increased.

  5. Ratiometric pulsed alkylation/mass spectrometry of the cysteine pairs in individual zinc fingers of MRE-binding transcription factor-1 (MTF-1) as a probe of zinc chelate stability.

    PubMed

    Apuy, J L; Chen, X; Russell, D H; Baldwin, T O; Giedroc, D P

    2001-12-18

    Metal-response element (MRE)-binding transcription factor-1 (MTF-1) is a zinc-regulated transcriptional activator of metallothionein (MT) genes in mammalian cells. The MRE-binding domain of MTF-1 (MTF-zf) has six canonical Cys(2)-His(2) zinc finger domains that are distinguished on the basis of their apparent affinities for zinc and their specific roles in MRE-binding. In this paper, pulsed alkylation of the zinc-liganding cysteine thiolate pairs with the sulfhydryl-specific alkylating reagent d(5)-N-ethylmaleimide (d(5)-NEM) is used as a residue-specific probe of the relative stabilities of the individual zinc finger coordination complexes in Zn(6) MTF-zf. A chase with excess H(5)-N-ethylmaleimide (H(5)-NEM) to fully derivatize MTF-zf concomitant with complete proteolysis, followed by MALDI-TOF mass spectrometry allows quantitation of the mole fraction of d(5),d(5)-, d(5),H(5)-, and H(5),H(5)-NEM derivatized peptides corresponding to each individual zinc finger domain as a function of d(5)-NEM pulse time. This experiment establishes the hierarchy of cysteine thiolate reactivity in MTF-zf as F5 > F6 > F1 > F2 approximately F3 approximately F4. The apparent second-order rate of reaction of F1 thiolates is comparable to that determined for the DNA binding domain of Sp1, Zn(3) Sp1-zf, under identical solution conditions. The reactivities of all Cys residues in MTF-zf are significantly reduced when bound to an MREd-containing oligonucleotide. An identical experiment carried out with Zn(5) MTF-zf26, an MTF-zf domain lacking the N-terminal F1 zinc finger, reveals that MTF-zf26 binds to the MREd very weakly, and is characterized by strongly increased reactivity of nonadjacent F4 thiolates. These findings are discussed in the context of existing models for metalloregulation by MTF-1. PMID:11735399

  6. Effect of ultrafine grain on tensile behaviour and corrosion resistance of the duplex stainless steel.

    PubMed

    Jinlong, Lv; Tongxiang, Liang; Chen, Wang; Limin, Dong

    2016-05-01

    The ultrafine grained 2205 duplex stainless steel was obtained by cold rolling and annealing. The tensile properties were investigated at room temperature. Comparing with coarse grained stainless steel, ultrafine grained sample showed higher strength and plasticity. In addition, grain size changed deformation orientation. The strain induced α'-martensite was observed in coarse grained 2205 duplex stainless steel with large strain. However, the grain refinement inhibited the transformation of α'-martensite;nevertheless, more deformation twins improved the strength and plasticity of ultrafine grained 2205 duplex stainless steel. In addition, the grain refinement improved corrosion resistance of the 2205 duplex stainless steel in sodium chloride solution. PMID:26952459

  7. Effect of ultrafine grain on tensile behaviour and corrosion resistance of the duplex stainless steel.

    PubMed

    Jinlong, Lv; Tongxiang, Liang; Chen, Wang; Limin, Dong

    2016-05-01

    The ultrafine grained 2205 duplex stainless steel was obtained by cold rolling and annealing. The tensile properties were investigated at room temperature. Comparing with coarse grained stainless steel, ultrafine grained sample showed higher strength and plasticity. In addition, grain size changed deformation orientation. The strain induced α'-martensite was observed in coarse grained 2205 duplex stainless steel with large strain. However, the grain refinement inhibited the transformation of α'-martensite;nevertheless, more deformation twins improved the strength and plasticity of ultrafine grained 2205 duplex stainless steel. In addition, the grain refinement improved corrosion resistance of the 2205 duplex stainless steel in sodium chloride solution.

  8. Evaluation of the Gibbs Free Energy Changes and Melting Temperatures of DNA/DNA Duplexes Using Hybridization Enthalpy Calculated by Molecular Dynamics Simulation.

    PubMed

    Lomzov, Alexander A; Vorobjev, Yury N; Pyshnyi, Dmitrii V

    2015-12-10

    A molecular dynamics simulation approach was applied for the prediction of the thermal stability of oligonucleotide duplexes. It was shown that the enthalpy of the DNA/DNA complex formation could be calculated using this approach. We have studied the influence of various simulation parameters on the secondary structure and the hybridization enthalpy value of Dickerson-Drew dodecamer. The optimal simulation parameters for the most reliable prediction of the enthalpy values were determined. The thermodynamic parameters (enthalpy and entropy changes) of a duplex formation were obtained experimentally for 305 oligonucleotides of various lengths and GC-content. The resulting database was studied with molecular dynamics (MD) simulation using the optimized simulation parameters. Gibbs free energy changes and the melting temperatures were evaluated using the experimental correlation between enthalpy and entropy changes of the duplex formation and the enthalpy values calculated by the MD simulation. The average errors in the predictions of enthalpy, the Gibbs free energy change, and the melting temperature of oligonucleotide complexes were 11%, 10%, and 4.4 °C, respectively. We have shown that the molecular dynamics simulation gives a possibility to calculate the thermal stability of native DNA/DNA complexes a priori with an unexpectedly high accuracy.

  9. Ladderphanes: a new type of duplex polymers.

    PubMed

    Luh, Tien-Yau

    2013-02-19

    A polymeric ladderphane is a step-like structure comprising multiple layers of linkers covalently connected to two or more polymeric backbones. The linkers can be planar aromatic, macrocyclic metal complexes, or three-dimensional organic or organometallic moieties. Structurally, a DNA molecule is a special kind of ladderphane, where the cofacially aligned base-pair pendants are linked through hydrogen bonding. A greater understanding of this class of molecules could help researchers develop new synthetic molecules capable of a similar transfer of chemical information. In this Account, we summarize our studies of the strategy, design, synthesis, characterization, replications, chemical and photophysical properties, and assembly of a range of double-stranded ladderphanes with many fascinating structures. We employed two norbornene moieties fused with N-arylpyrrolidine to connect covalently with a range of relatively rigid linkers. Ring opening metathesis polymerizations (ROMP) of these bis-norbornenes using the first-generation Grubbs ruthenium-benzylidene catalyst produced the corresponding symmetrical double-stranded ladderphanes. The N-arylpyrrolidene moiety in the linker controls the isotactic selectivity and the trans configuration for all double bonds in both single- and double-stranded polynorbornenes. The π-π interactions between these aryl pendants may contribute to the high stereoselectivity in the ROMP of these substrates. We synthesized chiral helical ladderphanes by incorporating asymmetric center(s) in the linkers. Replication protocols and sequential polymerization of a monomer that includes two different polymerizable groups offer methods for producing unsymmetical ladderphanes. These routes furnish template synthesis of daughter polymers with well-controlled chain lengths and polydispersities. The linkers in these ladderphanes are well aligned in the center along the longitudinal axis of the polymer. Fluorescence quenching, excimer formation, or

  10. A novel electrochemical method to detect theophylline utilizing silver ions captured within abasic site-incorporated duplex DNA.

    PubMed

    Ahn, Jun Ki; Park, Ki Soo; Won, Byoung Yeon; Park, Hyun Gyu

    2015-05-15

    We herein describe a novel and label-free electrochemical system to detect theophylline. The system was constructed by immobilizing duplex DNA containing an abasic site opposite cytosine on the gold electrode surface. In the absence of theophylline in a sample, silver ions freely bind to the empty abasic site in the duplex DNA leading to the highly elevated electrochemical signal by the redox reaction of silver ions. On the other hand, when theophylline is present, it binds to the abasic site by pseudo base pairing with the opposite cytosine nucleobase, which consequently prevents silver ions from binding to the abasic site. As a result, redox reaction of silver ions would be greatly reduced resulting in the accordingly decreased electrochemical signal. By employing this electrochemical strategy, theophylline was reliably detected at a concentration as low as 3.2 μM with the high selectivity over structurally similar substances such as caffeine and theobromine. Finally, the diagnostic capability of this method was also successfully verified by reliably detecting theophylline present in a real human serum sample with an excellent recovery ratio within 100±6%.

  11. Structure of the E. coli DNA Glycosylase AlkA Bound to the Ends of Duplex DNA: A System for the Structure Determination of Lesion-Containing DNA

    SciTech Connect

    Bowman, B.R.; Lee, S.; Wang, S.; Verdine, G.L.

    2008-10-24

    The constant attack on DNA by endogenous and exogenous agents gives rise to nucleobase modifications that cause mutations, which can lead to cancer. Visualizing the effects of these lesions on the structure of duplex DNA is key to understanding their biologic consequences. The most definitive method of obtaining such structures, X-ray crystallography, is troublesome to employ owing to the difficulty of obtaining diffraction-quality crystals of DNA. Here, we present a crystallization system that uses a protein, the DNA glycosylase AlkA, as a scaffold to mediate the crystallization of lesion-containing duplex DNA. We demonstrate the use of this system to facilitate the rapid structure determination of DNA containing the lesion 8-oxoguanine in several different sequence contexts, and also deoxyinosine and 1,N{sup 6}-ethenoadenine, each stabilized as the corresponding 2{prime}-flouro analog. The structures of 8-oxoguanine provide a correct atomic-level view of this important endogenous lesion in DNA.

  12. Pairing forces in nuclei

    SciTech Connect

    Chasman, R.R.

    1996-12-31

    In this contribution, the author mentions some features of pairing forces that are unique to nuclei and cover some areas of major interest in nuclear structure research, that involve pairing. At the level of most nuclear structure studies, nuclei are treated as consisting of two kinds of fermions (protons and neutrons) in a valence space with rather few levels. These features give rise to unique aspects of pairing forces in nuclei: (1) n-p pairing in T = 0 as well as the usual T = 1 pairing that is characteristic of like fermions; (2) a need to correct pairing calculations for the (1/N) effects that can typically be neglected in superconducting solids. An issue of current concern is the nature of the pairing interaction: several recent studies suggest a need for a density dependent form of the pairing interaction. There is a good deal of feedback between the questions of accurate calculations of pairing interactions and the form and magnitude of the pairing interaction. Finally, the authors discuss some many-body wave functions that are a generalization of the BCS wave function form, and apply them to a calculation of energy level spacings in superdeformed rotational bands.

  13. DNA terminal base pairs have weaker hydrogen bonds especially for AT under low salt concentration

    NASA Astrophysics Data System (ADS)

    Ferreira, Izabela; Amarante, Tauanne D.; Weber, Gerald

    2015-11-01

    DNA base pairs are known to open more easily at the helix terminal, a process usually called end fraying, the details of which are still poorly understood. Here, we present a mesoscopic model calculation based on available experimental data where we consider separately the terminal base pairs of a DNA duplex. Our results show an important reduction of hydrogen bond strength for terminal cytosine-guanine (CG) base pairs which is uniform over the whole range of salt concentrations, while for AT base pairs, we obtain a nearly 1/3 reduction but only at low salt concentrations. At higher salt concentrations, terminal adenine-thymine (AT) pair has almost the same hydrogen bond strength than interior bases. The calculated terminal stacking interaction parameters display some peculiarly contrasting behavior. While there is mostly no perceptible difference to internal stacking, for some cases, we observe an unusually strong dependence with salt concentration which does not appear follow any pattern or trend.

  14. Target-controlled formation of silver nanoclusters in abasic site-incorporated duplex DNA for label-free fluorescence detection of theophylline.

    PubMed

    Park, Ki Soo; Oh, Seung Soo; Soh, H Tom; Park, Hyun Gyu

    2014-09-01

    A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to the cytosine nucleobase is prevented. Consequently, fluorescent silver nanoclusters are not formed causing a significant reduction of the fluorescence signal. By employing this new sensor, theophylline can be highly selectively detected at a concentration as low as 1.8 μM. Finally, the diagnostic capability and practical application of this sensor were demonstrated by its use in detecting theophylline in human blood serum.

  15. Influence of 5-N-carboxamide modifications on the thermodynamic stability of oligonucleotides.

    PubMed

    Wolk, Steven K; Shoemaker, Richard K; Mayfield, Wes S; Mestdagh, Andrew L; Janjic, Nebojsa

    2015-10-30

    We have recently shown that the incorporation of modified nucleotides such as 5-N-carboxamide-deoxyuridines into random nucleic acid libraries improves success rates in SELEX experiments and facilitates the identification of ligands with slow off-rates. Here we report the impact of these modifications on the thermodynamic stability of both duplexes and intramolecular 'single-stranded' structures. Within duplexes, large, hydrophobic naphthyl groups were destabilizing relative to the all natural DNA duplex, while the hydrophilic groups exhibited somewhat improved duplex stability. All of the significant changes in stability were driven by opposing contributions from the enthalpic and entropic terms. In contrast, both benzyl and naphthyl modifications stabilized intramolecular single-stranded structures relative to their natural DNA analogs, consistent with the notion that intramolecular folding allows formation of novel, stabilizing hydrophobic interactions. Imino proton NMR data provided evidence that elements of the folded structure form at temperatures well below the Tm, with a melting transition that is distinctly less cooperative when compared to duplex DNA. Although there are no data to suggest that the unmodified DNA sequences fold into structures similar to their modified analogs, this still represents clear evidence that these modifications impart thermodynamic stability to the folded structure not achievable with unmodified DNA.

  16. Matched-pair classification

    SciTech Connect

    Theiler, James P

    2009-01-01

    Following an analogous distinction in statistical hypothesis testing, we investigate variants of machine learning where the training set comes in matched pairs. We demonstrate that even conventional classifiers can exhibit improved performance when the input data has a matched-pair structure. Online algorithms, in particular, converge quicker when the data is presented in pairs. In some scenarios (such as the weak signal detection problem), matched pairs can be generated from independent samples, with the effect not only doubling the nominal size of the training set, but of providing the structure that leads to better learning. A family of 'dipole' algorithms is introduced that explicitly takes advantage of matched-pair structure in the input data and leads to further performance gains. Finally, we illustrate the application of matched-pair learning to chemical plume detection in hyperspectral imagery.

  17. Paired watershed study design

    SciTech Connect

    Clausen, J.C.; Spooner, J.

    1993-09-01

    The purpose of the fact sheet is to describe the paired watershed approach for conducting nonpoint source (NPS) water quality studies. The basic approach requires a minimum of two watersheds - control and treatment - and two periods of study - calibration and treatment. The basis of the paired watershed approach is that there is a quantifiable relationship between paired water quality data for the two watersheds, and that this relationship is valid until a major change is made in one of the watersheds.

  18. Crystal Structures of Non-Natural Nucleobase Pairs in A- and B-DNA†

    PubMed Central

    Georgiadis, Millie M.; Singh, Isha; Kellett, Whitney F.; Hoshika, Shuichi; Benner, Steven A.; Richards, Nigel G. J.

    2015-01-01

    The extent to which synthetic biology can be used to expand genetic information systems compatible with natural enzymes and cells will depend on the extent to which multiple and contiguous non-natural nucleobase pairs fit within the standard double helical conformations of DNA. Toward this goal, two non-standard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) were designed to form a Z:P pair with a standard “edge on” Watson-Crick geometry, but with rearranged hydrogen bond donor and acceptor groups. Here, we present the crystal structures of two self-complementary 16-mer oligonucleotides containing Z:P pairs. The first contained two consecutive Z:P nucleobase pairs and was found to crystallize within a host-guest complex in B-form. The second contained six consecutive Z:P pairs; it was found to crystallize as an A-form DNA duplex, although it can adopt B-form in solution as inferred from circular dichroism spectra. Although Z:P pairs have some structural properties that are similar to those of G:C pairs, unique features include stacking of the nitro group on Z with the adjacent heterocyclic nucleobase ring in A-DNA. In both B-and A-DNA, major groove widths associated with the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs potentially due to the presence of the nitro group in Z. Thus, our structural studies suggest that multiple and consecutive Z:P pairs are readily accommodated in DNA duplex structures recognized by natural polymerases, and therefore the GACTZP synthetic genetic system has the requisite properties to expand sequence space. PMID:25961938

  19. Purification and characterization of a DNA-pairing and strand transfer activity from mitotic Saccharomyces cerevisiae.

    PubMed

    Halbrook, J; McEntee, K

    1989-12-15

    An enzyme catalyzing homologous pairing of DNA chains has been extensively purified from mitotic yeast. The most highly purified fractions are enriched for a polypeptide with a molecular mass of approximately 120 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Protein-dependent pairing of single-stranded DNAs requires a divalent cation (Mg2+ or Ca2+) but proceeds rapidly in the absence of any nucleoside triphosphates. The kinetics of reassociation are extremely rapid, with more than 60% of the single-stranded DNA becoming resistant to S1 nuclease within 1 min at a ratio of 1 protein monomer/50 nucleotides. The results of enzyme titration and DNA challenge experiments suggest that this protein does not act catalytically during renaturation but is required stoichiometrically. The protein promotes formation of joint molecules between linear M13 replicative form DNA (form III) containing short single-stranded tails and homologous single-stranded M13 viral DNA. Removal of approximately 50 nucleotides from the ends of the linear duplex using either exonuclease III (5' ends) or T7 gene 6 exonuclease (3' ends) activates the duplex for extensive strand exchange. Electron microscopic analysis of product molecules suggests that the homologous circular DNA initially associates with the single-stranded tails of the duplexes, and the heteroduplex region is extended with displacement of the noncomplementary strand. The ability of this protein to pair and to promote strand transfer using either exonuclease III or T7 gene 6 exonuclease-treated duplex substrates suggests that this activity promotes heteroduplex extension in a nonpolar fashion. The biochemical properties of the transferase are consistent with a role for this protein in heteroduplex joint formation during mitotic recombination in Saccharomyces cerevisiae.

  20. Vortex pairs on surfaces

    SciTech Connect

    Koiller, Jair

    2009-05-06

    A pair of infinitesimally close opposite vortices moving on a curved surface moves along a geodesic, according to a conjecture by Kimura. We outline a proof. Numerical simulations are presented for a pair of opposite vortices at a close but nonzero distance on a surface of revolution, the catenoid. We conjecture that the vortex pair system on a triaxial ellipsoid is a KAM perturbation of Jacobi's geodesic problem. We outline some preliminary calculations required for this study. Finding the surfaces for which the vortex pair system is integrable is in order.

  1. Pairing Beyond BCS

    NASA Astrophysics Data System (ADS)

    Volya, Alexander; Zelevinsky, Vladimir

    2013-01-01

    We concentrate on the specifics of the nuclear pairing problem from the standpoint of the BCS approach. We consider the properties of nuclear pairing which usually are not discussed in standard texts: how good is the BCS theory in nuclear context compared to the exact large-scale diagonalization, whether it can be improved by the particle number conservation, how to mark the phase transition regions in a mesoscopic system like a nucleus, how may effective many-body forces influence the formation and structure of the pairing condensate, what effect the decay instability has on the paired nuclear structure, etc.

  2. Full duplex transmission operation of a 2.45-GHz asynchronous spread spectrum using a SAN convolver.

    PubMed

    Tsubouchi, K; Nakase, H; Namba, A; Masu, K

    1993-01-01

    An asynchronous spread spectrum (SS) modem in the 2.45-GHz band has been implemented using an efficient ZnO-SiO(2)-Si surface acoustic wave (SAW) convolver. The modem, which can operate under full duplex transmission is based on a direct-sequence/code-shift-keying (DS/CSK) method for the modulation. Pseudonoise (PN) codes are chosen from a preferred pair of m-sequences of period 127, and the code rate is 14 MHz. The demodulation is carried out asynchronously, utilizing the coherent correlation characteristics of the SAW convolver. The main interference caused by a transmitted signal in the modem itself is effectively reduced by an RF isolator and the SS process gain. Adequate self-jamming rejection capability has been confirmed; a bit error rate of 10(-6) is observed at -78.3 dB of a desired-to-undesired-signal ratio using an artificial transmission line. PMID:18263209

  3. Ultrasonic Attenuation Measurements in Thermally Degraded 2205 Duplex Stainless Steel

    NASA Astrophysics Data System (ADS)

    Ruiz, A.; Ortiz, N.; Carreón, H.; Sánchez, A.

    2009-03-01

    Ultrasonic attenuation plays an important role in materials characterization of metal components. This paper present data and discuss ultrasonic attenuation variations in a 2205 duplex stainless steel aged isothermally at 700° C and 900° C for different time intervals. Attenuation measurements as function of frequency where performed using pulse-echo immersion method and broad band planar transducers. Evidence is found of changes in the attenuation coefficient as aging time increases. The corresponding microstructure of aged specimens was observed and impact toughness was measured. Comparison is made with measurements of ferrite content for the two temperatures and different aging times.

  4. Use of duplex stainless steel castings in control valves

    SciTech Connect

    Gossett, J.L.

    1996-07-01

    Duplex stainless steels have enjoyed rapidly increasing popularity in recent years. For numerous reasons the availability of these alloys in the cast form has lagged behind the availability of the wrought form. Commercial demand for control valves in these alloys has driven development of needed information to move into production. A systematic approach was used to develop specifications, suppliers and weld procedures. Corrosion, stress corrosion cracking (SCC), sulfide stress cracking (SSC) and hardness results are also presented for several alloys including; CD3MN (UNS J92205), CD4MCu (UNS J93370) and CD7MCuN (cast UNS S32550).

  5. Local THz time domain spectroscopy of duplex DNA via fluorescence of an embedded probe.

    PubMed

    Dallmann, André; Pfaffe, Matthias; Mügge, Clemens; Mahrwald, Rainer; Kovalenko, Sergey A; Ernsting, Nikolaus P

    2009-11-26

    We demonstrate that THz vibrational activity of a biopolymer can be measured locally, on the effective length scale for polar solvation, with an embedded molecular probe. For this purpose, the polarity probe 2-hydroxy-7-nitrofluorene was linked into a 13mer DNA duplex opposite an abasic site. The NMR solution structure shows that the fluorene moiety occupies a well-defined position in place of a base pair but can flip around the long axis on a millisecond time scale. Femtosecond optical pump-probe experiments are used to measure the time-resolved Stokes shift of emission from the probe. The dynamic shifts for solution in H(2)O and D(2)O are quantified. Their difference is much larger than that expected for free water, implying that only bound water is observed. A weak 26 cm(-1) spectral oscillation of the emission band is observed, which is not present when the probe is free in solution and is therefore caused by the supramolecular structure (DNA and hydration water). PMID:19764701

  6. Pair contact process with diffusion of pairs

    NASA Astrophysics Data System (ADS)

    Santos, F. L.; Dickman, Ronald; Fulco, U. L.

    2011-03-01

    The pair contact process (PCP) is a nonequilibrium stochastic model which, like the basic contact process (CP), exhibits a phase transition to an absorbing state. The two models belong to the directed percolation (DP) universality class, despite the fact that the PCP possesses infinitely many absorbing configurations whereas the CP has but one. The critical behavior of the PCP with hopping by particles (PCPD) is as yet unclear. Here we study a version of the PCP in which nearest-neighbor particle pairs can hop but individual particles cannot. Using quasistationary simulations for three values of the diffusion probability (D = 0.1, 0.5 and 0.9), we find convincing evidence of DP-like critical behavior.

  7. Cooper Pairs in Insulators?!

    SciTech Connect

    James Valles

    2008-07-23

    Nearly 50 years elapsed between the discovery of superconductivity and the emergence of the microscopic theory describing this zero resistance state. The explanation required a novel phase of matter in which conduction electrons joined in weakly bound pairs and condensed with other pairs into a single quantum state. Surprisingly, this Cooper pair formation has also been invoked to account for recently uncovered high-resistance or insulating phases of matter. To address this possibility, we have used nanotechnology to create an insulating system that we can probe directly for Cooper pairs. I will present the evidence that Cooper pairs exist and dominate the electrical transport in these insulators and I will discuss how these findings provide new insight into superconductor to insulator quantum phase transitions. 

  8. Critical Schwinger Pair Production.

    PubMed

    Gies, Holger; Torgrimsson, Greger

    2016-03-01

    We investigate Schwinger pair production in spatially inhomogeneous electric backgrounds. A critical point for the onset of pair production can be approached by fields that marginally provide sufficient electrostatic energy for an off-shell long-range electron-positron fluctuation to become a real pair. Close to this critical point, we observe features of universality which are analogous to continuous phase transitions in critical phenomena with the pair-production rate serving as an order parameter: electric backgrounds can be subdivided into universality classes and the onset of pair production exhibits characteristic scaling laws. An appropriate design of the electric background field can interpolate between power-law scaling, essential Berezinskii-Kosterlitz-Thouless-type scaling, and a power-law scaling with log corrections. The corresponding critical exponents only depend on the large-scale features of the electric background, whereas the microscopic details of the background play the role of irrelevant perturbations not affecting criticality. PMID:26991162

  9. Cooper Pairs in Insulators?!

    ScienceCinema

    James Valles

    2016-07-12

    Nearly 50 years elapsed between the discovery of superconductivity and the emergence of the microscopic theory describing this zero resistance state. The explanation required a novel phase of matter in which conduction electrons joined in weakly bound pairs and condensed with other pairs into a single quantum state. Surprisingly, this Cooper pair formation has also been invoked to account for recently uncovered high-resistance or insulating phases of matter. To address this possibility, we have used nanotechnology to create an insulating system that we can probe directly for Cooper pairs. I will present the evidence that Cooper pairs exist and dominate the electrical transport in these insulators and I will discuss how these findings provide new insight into superconductor to insulator quantum phase transitions. 

  10. A Novel Pretreatment-Free Duplex Chamber Digital PCR Detection System for the Absolute Quantitation of GMO Samples.

    PubMed

    Zhu, Pengyu; Wang, Chenguang; Huang, Kunlun; Luo, Yunbo; Xu, Wentao

    2016-01-01

    Digital polymerase chain reaction (PCR) has developed rapidly since it was first reported in the 1990s. However, pretreatments are often required during preparation for digital PCR, which can increase operation error. The single-plex amplification of both the target and reference genes may cause uncertainties due to the different reaction volumes and the matrix effect. In the current study, a quantitative detection system based on the pretreatment-free duplex chamber digital PCR was developed. The dynamic range, limit of quantitation (LOQ), sensitivity and specificity were evaluated taking the GA21 event as the experimental object. Moreover, to determine the factors that may influence the stability of the duplex system, we evaluated whether the pretreatments, the primary and secondary structures of the probes and the SNP effect influence the detection. The results showed that the LOQ was 0.5% and the sensitivity was 0.1%. We also found that genome digestion and single nucleotide polymorphism (SNP) sites affect the detection results, whereas the unspecific hybridization within different probes had little side effect. This indicated that the detection system was suited for both chamber-based and droplet-based digital PCR. In conclusion, we have provided a simple and flexible way of achieving absolute quantitation for genetically modified organism (GMO) genome samples using commercial digital PCR detection systems. PMID:26999129

  11. A Novel Pretreatment-Free Duplex Chamber Digital PCR Detection System for the Absolute Quantitation of GMO Samples.

    PubMed

    Zhu, Pengyu; Wang, Chenguang; Huang, Kunlun; Luo, Yunbo; Xu, Wentao

    2016-03-18

    Digital polymerase chain reaction (PCR) has developed rapidly since it was first reported in the 1990s. However, pretreatments are often required during preparation for digital PCR, which can increase operation error. The single-plex amplification of both the target and reference genes may cause uncertainties due to the different reaction volumes and the matrix effect. In the current study, a quantitative detection system based on the pretreatment-free duplex chamber digital PCR was developed. The dynamic range, limit of quantitation (LOQ), sensitivity and specificity were evaluated taking the GA21 event as the experimental object. Moreover, to determine the factors that may influence the stability of the duplex system, we evaluated whether the pretreatments, the primary and secondary structures of the probes and the SNP effect influence the detection. The results showed that the LOQ was 0.5% and the sensitivity was 0.1%. We also found that genome digestion and single nucleotide polymorphism (SNP) sites affect the detection results, whereas the unspecific hybridization within different probes had little side effect. This indicated that the detection system was suited for both chamber-based and droplet-based digital PCR. In conclusion, we have provided a simple and flexible way of achieving absolute quantitation for genetically modified organism (GMO) genome samples using commercial digital PCR detection systems.

  12. A Novel Pretreatment-Free Duplex Chamber Digital PCR Detection System for the Absolute Quantitation of GMO Samples

    PubMed Central

    Zhu, Pengyu; Wang, Chenguang; Huang, Kunlun; Luo, Yunbo; Xu, Wentao

    2016-01-01

    Digital polymerase chain reaction (PCR) has developed rapidly since it was first reported in the 1990s. However, pretreatments are often required during preparation for digital PCR, which can increase operation error. The single-plex amplification of both the target and reference genes may cause uncertainties due to the different reaction volumes and the matrix effect. In the current study, a quantitative detection system based on the pretreatment-free duplex chamber digital PCR was developed. The dynamic range, limit of quantitation (LOQ), sensitivity and specificity were evaluated taking the GA21 event as the experimental object. Moreover, to determine the factors that may influence the stability of the duplex system, we evaluated whether the pretreatments, the primary and secondary structures of the probes and the SNP effect influence the detection. The results showed that the LOQ was 0.5% and the sensitivity was 0.1%. We also found that genome digestion and single nucleotide polymorphism (SNP) sites affect the detection results, whereas the unspecific hybridization within different probes had little side effect. This indicated that the detection system was suited for both chamber-based and droplet-based digital PCR. In conclusion, we have provided a simple and flexible way of achieving absolute quantitation for genetically modified organism (GMO) genome samples using commercial digital PCR detection systems. PMID:26999129

  13. Clean cast steel technology. Determination of transformation diagrams for duplex stainless steel

    SciTech Connect

    Chumbley, S. L.

    2005-09-01

    Duplex stainless steels (DSS) constitute both ferrite and austenite as a matrix. Such a microstructure confers a high corrosion resistance with favorable mechanical properties. However, intermetallic phases such as sigma ( can also form during casting or high-temperature processing and can degrade the properties of the DSS. This research was initiated to develop time-temperature-transformation (TTT) and continuous-cooling- transformation (CCT) diagrams of two types of cast duplex stainless steels, CD3MN (Fe 22Cr-5Ni-Mo-N) and CD3MWCuN (Fe-25Cr-7Ni-Mo-W-Cu-N), in order to understand the time and temperature ranges for intermetallic phase formation. The alloys were heat treated isothermally or under controlled cooling conditions and then characterized using conventional metallographic methods that included tint etching, and also using electron microscopy (SEM, TEM) and wavelength dispersive spectroscopy (WDS). The kinetics of intermetallic-phase ( formation were analyzed using the Johnson-Mehl-Avrami (JMA) equation in the case of isothermal transformations and a modified form of this equation in the case of continuous cooling transformations, The rate of intermetallic-phase formation was found to be much faster in CD3MWCuN than CD3MN due mainly to differences in the major alloying contents such as Cr, Ni and Mo. To examine in more detail the effects of these elements of the phase stabilities, a series of eight steel castings was designed with the Cr, Ni and Mo contents systematically varied with respect to the nominal composition of CD3MN. The effects of varying the contents of alloying additions on the formation of intermetallic phases were also studied computationally using the commercial thermodynamic software package, Thermo-Calc. In general, was stabilized with increasing Cr addition and by increasing Mo addition. However, a delicate balance among Ni and other minor elements such as N and Si also exists. Phase equilibria in DSS can be affected by local

  14. Duplex development and abandonment during evolution of the Lewis thrust system, southern Glacier National Park, Montana

    NASA Astrophysics Data System (ADS)

    Yin, An; Kelty, Thomas K.; Davis, Gregory A.

    1989-09-01

    Geologic mapping in southern Glacier National Park, Montana, reveals the presence of two duplexes sharing the same floor thrust fault, the Lewis thrust. The westernmost duplex (Brave Dog Mountain) includes the low-angle Brave Dog roof fault and Elk Mountain imbricate system, and the easternmost (Rising Wolf Mountain) duplex includes the low-angle Rockwell roof fault and Mt. Henry imbricate system. The geometry of these duplexes suggests that they differ from previously described geometric-kinematic models for duplex development. Their low-angle roof faults were preexisting structures that were locally utilized as roof faults during the formation of the imbricate systems. Crosscutting of the Brave Dog fault by the Mt. Henry imbricate system indicates that the two duplexes formed at different times. The younger Rockwell-Mt. Henry duplex developed 20 km east of the older Brave Dog-Elk Mountain duplex; the roof fault of the former is at a higher structural level. Field relations confirm that the low-angle Rockwell fault existed across the southern Glacier Park area prior to localized formation of the Mt. Henry imbricate thrusts beneath it. These thrusts kinematically link the Rockwell and Lewis faults and may be analogous to P shears that form between two synchronously active faults bounding a simple shear system. The abandonment of one duplex and its replacement by another with a new and higher roof fault may have been caused by (1) warping of the older and lower Brave Dog roof fault during the formation of the imbricate system (Elk Mountain) beneath it, (2) an upward shifting of the highest level of a simple shear system in the Lewis plate to a new decollement level in subhorizontal belt strata (= the Rockwell fault) that lay above inclined strata within the first duplex, and (3) a reinitiation of P-shear development (= Mt. Henry imbricate faults) between the Lewis thrust and the subparallel, synkinematic Rockwell fault.

  15. Duplex Identification of Staphylococcus aureus by Aptamer and Gold Nanoparticles.

    PubMed

    Chang, Tianjun; Wang, Libo; Zhao, Kexu; Ge, Yu; He, Meng; Li, Gang

    2016-06-01

    Staphylococcus aureus is the top common pathogen causing infections and food poisoning. Identification of S. aureus is crucial for the disease diagnosis and regulation of food hygiene. Herein, we report an aptamer-AuNPs based method for duplex identification of S. aureus. Using AuNPs as an indicator, SA23, an aptamer against S. aureus, can well identify its target from Escherichia coli, Listeria monocytogenes and Pseudomonas aeruginosa. Furthermore, we find citrate-coated AuNPs can strongly bind to S. aureus, but not bind to Salmonella enterica and Proteus mirabilis, which leads to different color changes in salt solution. This colorimetric response is capable of distinguishing S. aureus from S. enteritidis and P. mirabilis. Thus, using the aptasensor and AuNPs together, S. aureus can be accurately identified from the common pathogens. This duplex identification system is a promising platform for simple visual identification of S. aureus. Additionally, in the aptasensing process, bacteria are incubated with aptamers and then be removed before the aptamers adding to AuNPs, which may avoid the interactions between bacteria and AuNPs. This strategy can be potentially applied in principle to detect other cells by AuNPs-based aptasensors.

  16. Thermal Aging Phenomena in Cast Duplex Stainless Steels

    NASA Astrophysics Data System (ADS)

    Byun, T. S.; Yang, Y.; Overman, N. R.; Busby, J. T.

    2016-02-01

    Cast stainless steels (CASSs) have been extensively used for the large components of light water reactor (LWR) power plants such as primary coolant piping and pump casing. The thermal embrittlement of CASS components is one of the most serious concerns related to the extended-term operation of nuclear power plants. Many past researches have concluded that the formation of Cr-rich α'-phase by Spinodal decomposition of δ-ferrite phase is the primary mechanism for the thermal embrittlement. Cracking mechanism in the thermally-embrittled duplex stainless steels consists of the formation of cleavage at ferrite and its propagation via separation of ferrite-austenite interphase. This article intends to provide an introductory overview on the thermal aging phenomena in LWR-relevant conditions. Firstly, the thermal aging effect on toughness is discussed in terms of the cause of embrittlement and influential parameters. An approximate analysis of thermal reaction using Arrhenius equation was carried out to scope the aging temperatures for the accelerated aging experiments to simulate the 60 and 80 years of services. Further, an equilibrium precipitation calculation was performed for model CASS alloys using the CALPHAD program, and the results are used to describe the precipitation behaviors in duplex stainless steels. These results are also to be used to guide an on-going research aiming to provide knowledge-based conclusive prediction for the integrity of the CASS components of LWR power plants during the service life extended up to and beyond 60 years.

  17. Cosmetic leg veins: evaluation using duplex venous imaging.

    PubMed

    Thibault, P; Bray, A; Wlodarczyk, J; Lewis, W

    1990-07-01

    The records of 305 consecutive patients who had presented with cosmetic symptoms related to varicose and/or spider veins over a 12-month period were studied. Following clinical assessment, 250 (82%) patients were referred for duplex venous imaging. A total of 500 lower limbs were evaluated; 236 (47%) were documented to have incompetence in the superficial venous system (long or short saphenous veins). Only 6 (1%) limbs had deep venous incompetence and 45 (9%) limbs were found to have perforator incompetence. Short saphenous vein incompetence was found in 59 (12%) limbs. In the long saphenous vein there was a consistent pattern of an increasing incidence of incompetence from the saphenofemoral junction down to the below-knee segment. The duplex imaging findings were applied to determine the optimal treatment, ie, whether surgery, sclerotherapy, or a combination of both would provide the best short- and long-term results. The possible etiology and pathophysiology of spider and varicose veins are discussed in relation to these results.

  18. Thermal Aging Phenomena in Cast Duplex Stainless Steels

    SciTech Connect

    Byun, T. S.; Yang, Y.; Overman, N. R.; Busby, J. T.

    2015-11-12

    We used cast stainless steels (CASSs)for the large components of light water reactor (LWR) power plants such as primary coolant piping and pump casing. The thermal embrittlement of CASS components is one of the most serious concerns related to the extended-term operation of nuclear power plants. Many past researches have concluded that the formation of Cr-rich alpha-phase by Spinodal decomposition of delta-ferrite phase is the primary mechanism for the thermal embrittlement. Cracking mechanism in the thermally-embrittled duplex stainless steels consists of the formation of cleavage at ferrite and its propagation via separation of ferrite-austenite interphase. This article intends to provide an introductory overview on the thermal aging phenomena in LWR-relevant conditions. Firstly, the thermal aging effect on toughness is discussed in terms of the cause of embrittlement and influential parameters. Moreover, an approximate analysis of thermal reaction using Arrhenius equation was carried out to scope the aging temperatures for the accelerated aging experiments to simulate the 60 and 80 years of services. Further, an equilibrium precipitation calculation was performed for model CASS alloys using the CALPHAD program, and the results are used to describe the precipitation behaviors in duplex stainless steels. Our results are also to be used to guide an on-going research aiming to provide knowledge-based conclusive prediction for the integrity of the CASS components of LWR power plants during the service life extended up to and beyond 60 years.

  19. Duplex carburetor and intake system for internal combustion engines

    SciTech Connect

    Yokoyama, H.; Ishida, T.

    1984-06-05

    A duplex carburetor for an internal combustion engine has a primary barrel having a primary venturi for supplying an air-fuel mixture to an intake manifold under a full range of engine loads and a secondary barrel having a secondary venturi for supplying an air-fuel mixture to the manifold under higher engine loads. The primary venturi has a cross section which ranges from 20% to 30% of that of the secondary venturi. The secondary barrel has a flattened cross-sectional shape such as of a segment of a circle of an ellipse, and is located adjacent to the primary barrel. The intake manifold is of a duplex construction having primary and secondary common passages connected to the primary and secondary barrels, respectively, of the carburetor. The secondary passage of the manifold has a flattened cross-sectional shape such as of a segment of a circle or an ellipse, and is positioned adjacent to the primary passage. The primary passage extends through a region where the secondary passage is divided into a plurality of secondary branches, and is located immediately in front of the shortest one of the secondary branch. The primary passage is also branched into a plurality of primary branches, the shortest of which is displaced out of axial alignment with a central axis of the intake manifold.

  20. Duplex Identification of Staphylococcus aureus by Aptamer and Gold Nanoparticles.

    PubMed

    Chang, Tianjun; Wang, Libo; Zhao, Kexu; Ge, Yu; He, Meng; Li, Gang

    2016-06-01

    Staphylococcus aureus is the top common pathogen causing infections and food poisoning. Identification of S. aureus is crucial for the disease diagnosis and regulation of food hygiene. Herein, we report an aptamer-AuNPs based method for duplex identification of S. aureus. Using AuNPs as an indicator, SA23, an aptamer against S. aureus, can well identify its target from Escherichia coli, Listeria monocytogenes and Pseudomonas aeruginosa. Furthermore, we find citrate-coated AuNPs can strongly bind to S. aureus, but not bind to Salmonella enterica and Proteus mirabilis, which leads to different color changes in salt solution. This colorimetric response is capable of distinguishing S. aureus from S. enteritidis and P. mirabilis. Thus, using the aptasensor and AuNPs together, S. aureus can be accurately identified from the common pathogens. This duplex identification system is a promising platform for simple visual identification of S. aureus. Additionally, in the aptasensing process, bacteria are incubated with aptamers and then be removed before the aptamers adding to AuNPs, which may avoid the interactions between bacteria and AuNPs. This strategy can be potentially applied in principle to detect other cells by AuNPs-based aptasensors. PMID:27427591

  1. Thermal treatment effects on laser surface remelting duplex stainless steel

    NASA Astrophysics Data System (ADS)

    do Nascimento, Alex M.; Ierardi, Maria Clara F.; Aparecida Pinto, M.; Tavares, Sérgio S. M.

    2008-10-01

    In this paper the microstructural changes and effects on corrosion resistance of duplex stainless steels UNS S32304 and UNS S32205, commonly used by the petroleum industry, were studied, following the execution of laser surface remelting (LSM) and post-thermal treatments (TT). In this way, data was obtained, which could then be compared with the starting condition of the alloys. In order to analyze the corrosion behaviour of the alloys in the as-received conditions, treated with laser and after post-thermal treatments, cyclic polarization tests were carried out. A solution of 3.5% NaCl (artificial sea water) was used, as duplex stainless steels are regularly used by the petroleum industry in offshore locations. The results obtained showed that when laser surface treated, due to rapid resolidification, the alloys became almost ferritic, and since the level of nitrogen in the composition of both alloys is superior to their solubility limit in ferrite, a precipitation of Cr2N (chromium nitrides) occurred in the ferritic matrix, causing loss of corrosion resistance, thus resulting in an increase in surface hardness. However, after the post-thermal treatment the alloys corrosion resistance was restored to values close to those of the as-received condition.

  2. Electron pairing without superconductivity.

    PubMed

    Cheng, Guanglei; Tomczyk, Michelle; Lu, Shicheng; Veazey, Joshua P; Huang, Mengchen; Irvin, Patrick; Ryu, Sangwoo; Lee, Hyungwoo; Eom, Chang-Beom; Hellberg, C Stephen; Levy, Jeremy

    2015-05-14

    Strontium titanate (SrTiO3) is the first and best known superconducting semiconductor. It exhibits an extremely low carrier density threshold for superconductivity, and possesses a phase diagram similar to that of high-temperature superconductors--two factors that suggest an unconventional pairing mechanism. Despite sustained interest for 50 years, direct experimental insight into the nature of electron pairing in SrTiO3 has remained elusive. Here we perform transport experiments with nanowire-based single-electron transistors at the interface between SrTiO3 and a thin layer of lanthanum aluminate, LaAlO3. Electrostatic gating reveals a series of two-electron conductance resonances-paired electron states--that bifurcate above a critical pairing field Bp of about 1-4 tesla, an order of magnitude larger than the superconducting critical magnetic field. For magnetic fields below Bp, these resonances are insensitive to the applied magnetic field; for fields in excess of Bp, the resonances exhibit a linear Zeeman-like energy splitting. Electron pairing is stable at temperatures as high as 900 millikelvin, well above the superconducting transition temperature (about 300 millikelvin). These experiments demonstrate the existence of a robust electronic phase in which electrons pair without forming a superconducting state. Key experimental signatures are captured by a model involving an attractive Hubbard interaction that describes real-space electron pairing as a precursor to superconductivity. PMID:25971511

  3. Electron pairing without superconductivity

    NASA Astrophysics Data System (ADS)

    Levy, Jeremy

    Strontium titanate (SrTiO3) is the first and best known superconducting semiconductor. It exhibits an extremely low carrier density threshold for superconductivity, and possesses a phase diagram similar to that of high-temperature superconductors--two factors that suggest an unconventional pairing mechanism. Despite sustained interest for 50 years, direct experimental insight into the nature of electron pairing in SrTiO3 has remained elusive. Here we perform transport experiments with nanowire-based single-electron transistors at the interface between SrTiO3 and a thin layer of lanthanum aluminate, LaAlO3. Electrostatic gating reveals a series of two-electron conductance resonances--paired electron states--that bifurcate above a critical pairing field Bp of about 1-4 tesla, an order of magnitude larger than the superconducting critical magnetic field. For magnetic fields below Bp, these resonances are insensitive to the applied magnetic field; for fields in excess of Bp, the resonances exhibit a linear Zeeman-like energy splitting. Electron pairing is stable at temperatures as high as 900 millikelvin, well above the superconducting transition temperature (about 300 millikelvin). These experiments demonstrate the existence of a robust electronic phase in which electrons pair without forming a superconducting state. Key experimental signatures are captured by a model involving an attractive Hubbard interaction that describes real-space electron pairing as a precursor to superconductivity. Support from AFOSR, ONR, ARO, NSF, DOE and NSSEFF is gratefully acknowledged.

  4. Hyperconjugation with lone pair of morpholine nitrogen stabilizes transition state for phenyl hydroxylation in CYP3A4 metabolism of ( S)- N-[1-(3-morpholin-4-yl phenyl) ethyl]-3-phenylacrylamide

    NASA Astrophysics Data System (ADS)

    Shaikh, Abdul Rajjak; Broclawik, Ewa; Ismael, Mohamed; Tsuboi, Hideyuki; Koyama, Michihisa; Kubo, Momoji; Del Carpio, Carlos A.; Miyamoto, Akira

    2006-02-01

    Using quantum chemical modelling we describe a novel effect in the mechanism of CYP3A4 metabolism for the arene substrate with o-substituent yielding a lone pair donation to conjugate π system; this will compensate for the loss of aromaticity on formation of the tetrahedral complex and lower the rate-determining energy barrier.

  5. Stress corrosion cracking of duplex stainless steels in caustic solutions

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Ananya

    Duplex stainless steels (DSS) with roughly equal amount of austenite and ferrite phases are being used in industries such as petrochemical, nuclear, pulp and paper mills, de-salination plants, marine environments, and others. However, many DSS grades have been reported to undergo corrosion and stress corrosion cracking in some aggressive environments such as chlorides and sulfide-containing caustic solutions. Although stress corrosion cracking of duplex stainless steels in chloride solution has been investigated and well documented in the literature but the SCC mechanisms for DSS in caustic solutions were not known. Microstructural changes during fabrication processes affect the overall SCC susceptibility of these steels in caustic solutions. Other environmental factors, like pH of the solution, temperature, and resulting electrochemical potential also influence the SCC susceptibility of duplex stainless steels. In this study, the role of material and environmental parameters on corrosion and stress corrosion cracking of duplex stainless steels in caustic solutions were investigated. Changes in the DSS microstructure by different annealing and aging treatments were characterized in terms of changes in the ratio of austenite and ferrite phases, phase morphology and intermetallic precipitation using optical micrography, SEM, EDS, XRD, nano-indentation and microhardness methods. These samples were then tested for general and localized corrosion susceptibility and SCC to understand the underlying mechanisms of crack initiation and propagation in DSS in the above-mentioned environments. Results showed that the austenite phase in the DSS is more susceptible to crack initiation and propagation in caustic solutions, which is different from that in the low pH chloride environment where the ferrite phase is the more susceptible phase. This study also showed that microstructural changes in duplex stainless steels due to different heat treatments could affect their SCC

  6. Paired Straight Hearth Furnace

    SciTech Connect

    2009-04-01

    This factsheet describes a research project whose goals are to design, develop, and evaluate the scalability and commercial feasibility of the PSH Paired Straight Hearth Furnace alternative ironmaking process.

  7. Adaptive Pairing Reversible Watermarking.

    PubMed

    Dragoi, Ioan-Catalin; Coltuc, Dinu

    2016-05-01

    This letter revisits the pairwise reversible watermarking scheme of Ou et al., 2013. An adaptive pixel pairing that considers only pixels with similar prediction errors is introduced. This adaptive approach provides an increased number of pixel pairs where both pixels are embedded and decreases the number of shifted pixels. The adaptive pairwise reversible watermarking outperforms the state-of-the-art low embedding bit-rate schemes proposed so far.

  8. Resonantly paired fermionic superfluids

    NASA Astrophysics Data System (ADS)

    Gurarie, V.; Radzihovsky, L.

    2007-01-01

    We present a theory of a degenerate atomic Fermi gas, interacting through a narrow Feshbach resonance, whose position and therefore strength can be tuned experimentally, as demonstrated recently in ultracold trapped atomic gases. The distinguishing feature of the theory is that its accuracy is controlled by a dimensionless parameter proportional to the ratio of the width of the resonance to Fermi energy. The theory is therefore quantitatively accurate for a narrow Feshbach resonance. In the case of a narrow s-wave resonance, our analysis leads to a quantitative description of the crossover between a weakly paired BCS superconductor of overlapping Cooper pairs and a strongly paired molecular Bose-Einstein condensate of diatomic molecules. In the case of pairing via a p-wave resonance, that we show is always narrow for a sufficiently low density, we predict a detuning-temperature phase diagram, that in the course of a BCS-BEC crossover can exhibit a host of thermodynamically distinct phases separated by quantum and classical phase transitions. For an intermediate strength of the dipolar anisotropy, the system exhibits a px + i py paired superfluidity that undergoes a topological phase transition between a weakly coupled gapless ground state at large positive detuning and a strongly paired fully gapped molecular superfluid for a negative detuning. In two dimensions the former state is characterized by a Pfaffian ground state exhibiting topological order and non-Abelian vortex excitations familiar from fractional quantum Hall systems.

  9. Cooper Pair Insulators

    NASA Astrophysics Data System (ADS)

    Valles, James

    One of the recent advances in the field of the Superconductor to Insulator Transition (SIT) has been the discovery and characterization of the Cooper Pair Insulator phase. This bosonic insulator, which consists of localized Cooper pairs, exhibits activated transport and a giant magneto-resistance peak. These features differ markedly from the weakly localized transport that emerges as pairs break at a ``fermionic'' SIT. I will describe how our experiments on films nano-patterned with a nearly triangular array of holes have enabled us to 1) distinguish bosonic insulators from fermionic insulators, 2) show that Cooper pairs, rather than quasi-particles dominate the transport in the Cooper Pair insulator phase, 3) demonstrate that very weak, sub nano-meter thickness inhomogeneities control whether a bosonic or fermionic insulator forms at an SIT and 4) reveal that Cooper pairs disintegrate rather than becoming more tightly bound deep in the localized phase. We have also developed a method, using a magnetic field, to tune flux disorder reversibly in these films. I will present our latest results on the influence of magnetic flux disorder and random gauge fields on phenomena near bosonic SITs. This work was performed in collaboration with M. D. Stewart, Jr., Hung Q. Nguyen, Shawna M. Hollen, Jimmy Joy, Xue Zhang, Gustavo Fernandez, Jeffrey Shainline and Jimmy Xu. It was supported by NSF Grants DMR 1307290 and DMR-0907357.

  10. Preparation and property of duplex Ni-B-TiO2/Ni nano-composite coatings

    NASA Astrophysics Data System (ADS)

    Wang, Shu-Jen; Wang, Yuxin; Shu, Xin; Tay, Seeleng; Gao, Wei; Shakoor, R. A.; Kahraman, Ramazan

    2015-03-01

    The duplex Nickel-Boron-Titania/Nickel (Ni-B-TiO2/Ni) coatings were deposited on mild steel by using two baths with Ni as the inner layer. TiO2 nanoparticles were incorporated into the Ni-B coatings as the outer layer by using solid particle mixing method. The microstructure, morphology and corrosion resistance of the duplex Ni-B-TiO2/Ni nanocomposite coatings were systemically investigated. The results show that the duplex interface was uniform and the adhesion between two layers was very good. The microhardness of duplex Ni-B-TiO2/Ni coating was much higher than the Ni coating due to the outer layer of Ni-B-TiO2 coating. The corrosion resistance of the duplex Ni-B-TiO2/Ni coating was also significantly improved comparing with single Ni-B coating. The Ni-B-10 g/L TiO2/Ni coating was found to have the best corrosion resistance among these duplex coatings. This type of duplex Ni-B-TiO2/Ni coating, with high hardness and good corrosion resistance properties, should be able to find broad applications under adverse environmental conditions.

  11. Resistance to Nucleotide Excision Repair of Bulky Guanine Adducts Opposite Abasic Sites in DNA Duplexes and Relationships between Structure and Function

    PubMed Central

    Liu, Zhi; Ding, Shuang; Kropachev, Konstantin; Lei, Jia; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas E.

    2015-01-01

    The nucleotide excision repair of certain bulky DNA lesions is abrogated in some specific non-canonical DNA base sequence contexts, while the removal of the same lesions by the nucleotide excision repair mechanism is efficient in duplexes in which all base pairs are complementary. Here we show that the nucleotide excision repair activity in human cell extracts is moderate-to-high in the case of two stereoisomeric DNA lesions derived from the pro-carcinogen benzo[a]pyrene (cis- and trans-B[a]P-N2-dG adducts) in a normal DNA duplex. By contrast, the nucleotide excision repair activity is completely abrogated when the canonical cytosine base opposite the B[a]P-dG adducts is replaced by an abasic site in duplex DNA. However, base excision repair of the abasic site persists. In order to understand the structural origins of these striking phenomena, we used NMR and molecular spectroscopy techniques to evaluate the conformational features of 11mer DNA duplexes containing these B[a]P-dG lesions opposite abasic sites. Our results show that in these duplexes containing the clustered lesions, both B[a]P-dG adducts adopt base-displaced intercalated conformations, with the B[a]P aromatic rings intercalated into the DNA helix. To explain the persistence of base excision repair in the face of the opposed bulky B[a]P ring system, molecular modeling results suggest how the APE1 base excision repair endonuclease, that excises abasic lesions, can bind productively even with the trans-B[a]P-dG positioned opposite the abasic site. We hypothesize that the nucleotide excision repair resistance is fostered by local B[a]P residue—DNA base stacking interactions at the abasic sites, that are facilitated by the absence of the cytosine partner base in the complementary strand. More broadly, this study sets the stage for elucidating the interplay between base excision and nucleotide excision repair in processing different types of clustered DNA lesions that are substrates of nucleotide

  12. Low-temperature NMR studies on inosine wobble base pairs.

    PubMed

    Janke, Eline M Basílio; Riechert-Krause, Fanny; Weisz, Klaus

    2011-07-01

    Base pairs formed by the inosine nucleoside (I) play an important role in many physiological processes as well as in various DNA technologies. Relative stabilities and favored base pair geometries of free inosine wobble base pairs in aprotic solvents have been determined through (1)H NMR measurements at room temperature and at very low temperatures in a freonic solvent. As indicated by its significantly deshielded imino proton, the Watson-Crick-type I·C base pair forms a remarkably strong NHN hydrogen bond. For the thermodynamically less stable I·A wobble base pair, two configurations of similar population coexist at 133 K in the slow hydrogen bond exchange regime, namely a Watson-Crick(I)-Watson-Crick(A) geometry and a Watson-Crick(I)-Hoogsteen(A) geometry. I·U base pairs are stabilized by two rather weak hydrogen bonds and are significantly disfavored over inosine self-associates in a low-temperature Freon solution. PMID:21644523

  13. Duplex development and abandonment during evolution of the Lewis thrust system, southern Glacier National Park, Montana

    SciTech Connect

    Yin, An; Kelty, T.K.; Davis, G.A. )

    1989-09-01

    The westernmost duplex (Brave Dog Mountain) includes the low-angle Brave Dog roof fault and Elk Mountain imbricate system, and the easternmost (Rising Wolf Mountain) duplex includes the low-angle Rockwell roof fault and Mt. Henry imbricate system. The geometry of these duplexes suggests that they differ from previously described geometric-kinematic models for duplex development. Their low-angle roof faults were preexisting structures that were locally utilized as roof faults during the formation of the imbricate systems. Crosscutting of the Brave Dog fault by the Mt. Henry imbricate system indicates that the two duplexes formed at different times. The younger Rockwell-Mt. Henry duplex developed 20 km east of the older Brave Dog-Elk Mountain duplex; the roof fault of the former is at a higher structural level. Field relations confirm that the low-angle Rockwell fault existed across the southern Glacier Park area prior to localized formation of the Mt. Henry imbricate thrusts beneath it. These thrusts kinematically link the Rockwell and Lewis faults and may be analogous to P shears that form between two synchronously active faults bounding a simple shear system. The abandonment of one duplex and its replacement by another with a new and higher roof fault may have been caused by (1) warping of the older and lower Brave Dog roof fault during the formation of the imbricate system (Elk Mountain) beneath it, (2) an upward shifting of the highest level of a simple shear system in the Lewis plate to a new decollement level in subhorizontal belt strata (= the Rockwell fault) that lay above inclined strata within the first duplex, and (3) a reinitiation of P-shear development (= Mt. Henry imbricate faults) between the Lewis thrust and the subparallel, synkinematic Rockwell fault.

  14. Solution structure of a DNA double helix with consecutive metal-mediated base pairs.

    PubMed

    Johannsen, Silke; Megger, Nicole; Böhme, Dominik; Sigel, Roland K O; Müller, Jens

    2010-03-01

    Metal-mediated base pairs represent a powerful tool for the site-specific functionalization of nucleic acids with metal ions. The development of applications of the metal-modified nucleic acids will depend on the availability of structural information on these double helices. We present here the NMR solution structure of a self-complementary DNA oligonucleotide with three consecutive imidazole nucleotides in its centre. In the absence of transition-metal ions, a hairpin structure is adopted with the artificial nucleotides forming the loop. In the presence of Ag(i) ions, a duplex comprising three imidazole-Ag(+)-imidazole base pairs is formed. Direct proof for the formation of metal-mediated base pairs was obtained from ¹J(¹⁵N,¹⁰⁷/¹⁰⁹Ag) couplings upon incorporation of ¹⁵N-labelled imidazole. The duplex adopts a B-type conformation with only minor deviations in the region of the artificial bases. This work represents the first structural characterization of a metal-modified nucleic acid with a continuous stretch of metal-mediated base pairs. PMID:21124482

  15. SnO2:F Coated Duplex Stainless Steel for PEM Fuel Cell Bipolar Plates

    SciTech Connect

    Wang, H.; Turner, J. A.

    2008-01-01

    Duplex 2205 stainless steel was deposited with 0.6 {micro}m thick SnO2:F coating; coated steel was characterized for PEMFC bipolar plate application. Compared with bare alloy, interfacial contact resistance (ICR) values of the coated 2205 steel are higher. SnO2:F coating adds its own resistance to the air-formed film on the steel. In a PEMFC anode environment, a current peak of ca. 25 {micro}A/cm2 registered at ca. 30 min for coated 2205 steel. It stabilized at ca. 2.0 {approx} -1.0 {micro}A/cm2. This peak is related to the complicated process of coating dissolution and oxide-layer formation. Anodic-cathodic current transfer occurred at ca. 200 min polarization. In a PEMFC cathode environment, current was stable immediately after polarization. The stable current was ca. 0.5 {approx} 2.0 {micro}A/cm2 during the entire polarization period. AES depth profiles with tested samples and ICP analysis with the tested solutions confirmed the excellent corrosion resistance of the SnO2:F coated 2205 alloy in simulated PEMFC environments.

  16. The effects of laser welding parameters on the microstructure of ferritic and duplex stainless steels welds

    NASA Astrophysics Data System (ADS)

    Pekkarinen, J.; Kujanpää, V.

    This study is focused to determine empirically, which microstructural changes occur in ferritic and duplex stainless steels when heat input is controlled by welding parameters. Test welds were done autogenously bead-on-plate without shielding gas using 5 kW fiber laser. For comparison, some gas tungsten arc welds were made. Used test material were 1.4016 (AISI 430) and 1.4003 (low-carbon ferritic) type steels in ferritic steels group and 1.4162 (low-alloyed duplex, LDX2101) and 1.4462 (AISI 2205) type steels in duplex steels group. Microstructural changes in welds were identified and examined using optical metallographic methods.

  17. Geometry of an outcrop-scale duplex in Devonian flysch, Maine

    USGS Publications Warehouse

    Bradley, D.C.; Bradley, L.M.

    1994-01-01

    We describe an outcrop-scale duplex consisting of 211 exposed repetitions of a single bed. The duplex marks an early Acadian (Middle Devonian) oblique thrust zone in the Lower Devonian flysch of northern Maine. Detailed mapping at a scale of 1:8 has enabled us to measure accurately parameters such as horse length and thickness, ramp angles and displacements; we compare these and derivative values with those of published descriptions of duplexes, and with theoretical models. Shortening estimates based on line balancing are consistently smaller than two methods of area balancing, suggesting that layer-parallel shortening preceded thrusting. ?? 1994.

  18. Researches upon cavitation erosion behavior of some duplex steels

    NASA Astrophysics Data System (ADS)

    Bordeasu, I.; Popoviciu, M. O.; Mitelea, I.; Micu, L. M.; Bordeasu, C.; Ghera, C.; Iosif, A.

    2016-02-01

    This paper presents the cavitation erosion behavior of two stainless steels having a duplex structure formed by austenite and ferrite. The conclusions were obtained by using both the cavitation erosion characteristic curves and the pictures of the eroded surfaces obtained with performing optic microscopes. The researches were focused upon the optimal correlation between the cavitation erosion resistance and the rate of the two structural constituents. The tests were done with T2 facility, with ceramic crystals, which integrally respects the ASTM G32-2010 Standard. The obtained results present the cumulative effect upon cavitation erosion of the chemical composition, mechanical properties and the structural constituents. The results of the researches are of importance for the specialists which establishes the composition of the stainless steels used for manufacturing hydraulic machineries or other devices subjected to cavitation erosion.

  19. The sequence dependence of circular dichroism spectra of DNA duplexes.

    PubMed

    Arnott, S; Arnott, S

    1975-09-01

    The three satellite DNAs of Drosophila virilis, that approximate to poly d(CAAACTA)-poly d(TAGTTTG), poly d(TAAACTA)-poly d(TAGTTTA), poly d(CAAATTA)-poly d(TAATTTG), the satellite DNA of Drosophila melanogaster that approximates to poly d(AATAT)-poly d(ATATT), the synthetic DNA duplexes, poly dG-poly dC, poly d(AT)-poly d(AT), poly d(AAT)-poly d(ATT), poly d(AAC)-poly d(GTT), poly d(TAC)-poly d(GTA) and the block copolymer d(C15A15)-d(T15G15) all have circular dichroism spectra consistent with the propositions that they have the same molecular geometry in solution and that it is the kind and frequency of nucleotide triplet sequences that determines their spectral characteristics. Poly dA-poly dT is apparently an exception.

  20. Pyrazinetetracarboxamide: A Duplex Ligand for Palladium(II).

    PubMed

    Lohrman, Jessica; Telikepalli, Hanumaiah; Johnson, Thomas S; Jackson, Timothy A; Day, Victor W; Bowman-James, Kristin

    2016-06-01

    Tetraethylpyrazine-2,3,5,6-tetracarboxamide forms a dipalladium(II) complex with acetates occupying the fourth coordination sites of the two bound metal ions. Crystallographic results indicate that the "duplex" dipincer has captured two protons that serve as the counterions. The protons lie between adjacent amide carbonyl groups with very short O···O distances of 2.435(5) Å. In the free base, the adjacent carbonyl groups are farther apart, averaging 3.196(3) Å. While the dipalladium(II) complexes stack in an ordered stepwise fashion along the a axis, the free base molecules stack on top of each other, with each pincer rotated by about 60° from the one below. PMID:27187158

  1. Electromagnetic non-destructive technique for duplex stainless steel characterization

    NASA Astrophysics Data System (ADS)

    Rocha, João Vicente; Camerini, Cesar; Pereira, Gabriela

    2016-02-01

    Duplex stainless steel (DSS) is a two-phase (ferrite and austenite) material, which exhibits an attractive combination of mechanical properties and high corrosion resistance, being commonly employed for equipment of petrochemical plants, refining units and oil & gas platforms. The best properties of DSS are achieved when the phases are in equal proportions. However, exposition to high temperatures (e.g. welding process) may entail undesired consequences, such as deleterious phases precipitation (e.g. sigma, chi) and different proportion of the original phases, impairing dramatically the mechanical and corrosion properties of the material. A detailed study of the magnetic behavior of DSS microstructure with different ferrite austenite ratios and deleterious phases content was accomplished. The non destructive method evaluates the electromagnetic properties changes in the material and is capable to identify the presence of deleterious phases into DSS microstructure.

  2. Isothermal DNA amplification strategies for duplex microorganism detection.

    PubMed

    Santiago-Felipe, Sara; Tortajada-Genaro, Luis Antonio; Morais, Sergi; Puchades, Rosa; Maquieira, Ángel

    2015-05-01

    A valid solution for micro-analytical systems is the selection of a compatible amplification reaction with a simple, highly-integrated efficient design that allows the detection of multiple genomic targets. Two approaches under isothermal conditions are presented: recombinase polymerase amplification (RPA) and multiple displacement amplification (MDA). Both methods were applied to a duplex assay specific for Salmonella spp. and Cronobacter spp., with excellent amplification yields (0.2-8.6 · 10(8) fold). The proposed approaches were successfully compared to conventional PCR and tested for the milk sample analysis as a microarray format on a compact disc (support and driver). Satisfactory results were obtained in terms of resistance to inhibition, selectivity, sensitivity (10(1)-10(2)CFU/mL) and reproducibility (below 12.5%). The methods studied are efficient and cost-effective, with a high potential to automate microorganisms detection by integrated analytical systems working at a constant low temperature.

  3. Duplex Doppler ultrasound study of the temporomandibular joint.

    PubMed

    Stagnitti, A; Marini, A; Impara, L; Drudi, F M; Lo Mele, L; Lillo Odoardi, G

    2012-06-01

    Sommario INTRODUZIONE: La fisiologia articolare dell’articolazione temporo-mandibolare (ATM) può essere esaminata sia dal punto di vista clinico che strumentale. La diagnostica per immagini ha da tempo contribuito con la risonanza magnetica (RM) e anche con la radiografia (Rx) e la tomografia computerizzata (TC) all’analisi della morfologia dei capi articolari e della cinetica condilare. L’esame duplex-ecodoppler è una metodica di largo impiego nello studio delle strutture in movimento in particolar modo a livello delle strutture del sistema vascolare. MATERIALI E METODI: È stata utilizzata un’apparecchiatura Toshiba APLIO SSA-770A, con l’uso di tecnica duplex-ecodoppler multi display, che consente la visualizzazione contemporanea dell’immagine ecografica e dei segnali Doppler utilizzando una sonda lineare del tipo phased array con cristalli trasduttori funzionanti ad una frequenza fondamentale di 6 MHz per gli spettri Doppler pulsati e 7.5 MHz per l’imaging ecografico. Sono stati esaminati nel Dipartimento di Scienze Radiologiche, Oncologiche e Anatomo-patologiche dell’Università “Sapienza” di Roma, 30 pazienti del reparto di Ortognatodonzia dell’Istituto di Odontoiatria della stessa Università. RISULTATI: Nei pazienti normali si è ottenuta un’alternanza regolare degli spettri Doppler, mentre nei soggetti con disfunzioni del complesso condilo-meniscale, si è persa la regolarità della sommatoria degli spettri di Fourier, con altezze incostanti in relazione a spostamenti irregolari del complesso condilo-meniscale. CONCLUSIONI: L’esame ecodoppler si è dimostrato, in tutti i pazienti, capace di discriminare quelli normali dai patologici e tra questi ultimi ha permesso di identificare gli aspetti più significativi delle patologie disfunzionali.

  4. Thermal Aging Phenomena in Cast Duplex Stainless Steels

    DOE PAGES

    Byun, T. S.; Yang, Y.; Overman, N. R.; Busby, J. T.

    2015-11-12

    We used cast stainless steels (CASSs)for the large components of light water reactor (LWR) power plants such as primary coolant piping and pump casing. The thermal embrittlement of CASS components is one of the most serious concerns related to the extended-term operation of nuclear power plants. Many past researches have concluded that the formation of Cr-rich alpha-phase by Spinodal decomposition of delta-ferrite phase is the primary mechanism for the thermal embrittlement. Cracking mechanism in the thermally-embrittled duplex stainless steels consists of the formation of cleavage at ferrite and its propagation via separation of ferrite-austenite interphase. This article intends to providemore » an introductory overview on the thermal aging phenomena in LWR-relevant conditions. Firstly, the thermal aging effect on toughness is discussed in terms of the cause of embrittlement and influential parameters. Moreover, an approximate analysis of thermal reaction using Arrhenius equation was carried out to scope the aging temperatures for the accelerated aging experiments to simulate the 60 and 80 years of services. Further, an equilibrium precipitation calculation was performed for model CASS alloys using the CALPHAD program, and the results are used to describe the precipitation behaviors in duplex stainless steels. Our results are also to be used to guide an on-going research aiming to provide knowledge-based conclusive prediction for the integrity of the CASS components of LWR power plants during the service life extended up to and beyond 60 years.« less

  5. Simultaneous detection of West Nile and Japanese encephalitis virus RNA by duplex TaqMan RT-PCR.

    PubMed

    Barros, Silvia C; Ramos, Fernanda; Zé-Zé, Líbia; Alves, Maria J; Fagulha, Teresa; Duarte, Margarida; Henriques, Margarida; Luís, Tiago; Fevereiro, Miguel

    2013-11-01

    West Nile virus (WNV) and Japanese encephalitis virus (JEV) are important mosquito-borne viruses of the Flaviviridae family, associated with encephalitis, mainly in humans and horses. WNV is also pathogen for many bird species. The incidence of human and animal WNV infections in Europe has risen, mostly in recent years, and JEV was detected in 2011 in mosquitoes collected in Italy and may emerge in Europe in the same way as other flaviviruses had emerged recently (USUTU and Bagaza virus) and should be regarded as a potential threat to public health. Prompt identification and discrimination between WNV and JEV provides critical epidemiological data for prevalence studies and public and animal health management policies. Here we describe a quantitative one-step duplex TaqMan RT-PCR, targeting non-structural protein 2A gene (NS2A-qRT-PCR), based on only one primer pair and two probes for differential diagnosis of WNV and JEV. Also this assay enables the detection of both WNV lineages (WNV-1 and WNV-2). To access the specificity of NS2A-qRT-PCR a panel of different arboviruses were used. The assay was shown to be specific for both WNV lineages (WNV-1 and WNV-2), WNV related Kunjin virus and JEV, since no cross-reactions were observed with other tested arboviruses. Sensitivity of the assay was determined using serial dilutions of in vitro-transcribed RNA from WNV and JEV. The duplex NS2A-qRT-PCR assay was shown to be very sensitive, being able to detect 10 copies of WNV and JEV RNA. This assay is a suitable tool for the diagnosis of WNV and JEV, and provides a valuable addition to the methods currently available for routine diagnosis of these zoonoses and for surveillance studies.

  6. Rapid method to detect duplex formation in sequencing by hybridization methods

    DOEpatents

    Mirzabekov, A.D.; Timofeev, E.N.; Florentiev, V.L.; Kirillov, E.V.

    1999-01-19

    A method for determining the existence of duplexes of oligonucleotide complementary molecules is provided. A plurality of immobilized oligonucleotide molecules, each of a specific length and each having a specific base sequence, is contacted with complementary, single stranded oligonucleotide molecules to form a duplex. Each duplex facilitates intercalation of a fluorescent dye between the base planes of the duplex. The invention also provides for a method for constructing oligonucleotide matrices comprising confining light sensitive fluid to a surface and exposing the light-sensitive fluid to a light pattern. This causes the fluid exposed to the light to coalesce into discrete units and adhere to the surface. This places each of the units in contact with a set of different oligonucleotide molecules so as to allow the molecules to disperse into the units. 13 figs.

  7. Applications and experiences with super duplex stainless steel in wet FGD scrubber systems

    SciTech Connect

    Francis, R.; Byrne, G.; Warburton, G.; Hebdon, S.

    1998-12-31

    The paper presents the properties of the author`s company`s proprietary super duplex stainless steel. Work is presented showing the development of a more realistic laboratory solution representing typical limestone slurries found in real flue gas desulfurization (FGD) systems. The importance of additions of metal ions such as Fe{sup 3+} and Mn{sup 2+} as well as partially oxidized sulfur species is demonstrated. Results are presented comparing the crevice corrosion resistance of super duplex stainless steel in these slurries with other commonly used wrought and cast stainless steels, for both simulated anthracite and lignite type slurries. Data from loop tests on the erosion resistance of a range of alloys in simulated FGD slurries is presented. The results clearly show the superior resistance of super duplex stainless steel to both crevice corrosion and erosion in FGD slurries. Finally the experiences in UK FGD systems with both cast and wrought super duplex stainless steel are presented.

  8. Electrochemical Investigation of Interaction between a Bifunctional Probe and GG Mismatch Duplex.

    PubMed

    Li, Jiao; He, Hanping; Peng, Xiaoqian; Huang, Min; Zhang, Xiuhua; Wang, Shengfu

    2015-01-01

    A bifunctional probe (FecNC), containing a recognition part and an electrochemical active center, was applied to electrochemical detection of GG mismatch duplexes. The preparation of gold electrodes modified by mismatch and complementatry duplexes was characterized by electrochemical impedance spectroscopy (EIS) and optimized for better detection in terms of self-assembly time, hybridization time, and incubation time. The interaction between FecNC and DNA duplexes modified on the surface of a gold electrode was explored by square wave voltammetry (SWV) and EIS. The results showed that the DNA duplexes with GG mismatch on the surface of a gold electrode was easily detected by the largest electrochemical signal of the bifunctional probe because of its selective binding to GG mismatches. The bifunctional probe could offer a simple, effective electrochemical detection of GG mismatches, and theoretical bases for development of electrochemical biosensors. Further, the method would be favorable for diagnosis of genetic diseases. PMID:26165289

  9. Electrochemical Investigation of Interaction between a Bifunctional Probe and GG Mismatch Duplex.

    PubMed

    Li, Jiao; He, Hanping; Peng, Xiaoqian; Huang, Min; Zhang, Xiuhua; Wang, Shengfu

    2015-01-01

    A bifunctional probe (FecNC), containing a recognition part and an electrochemical active center, was applied to electrochemical detection of GG mismatch duplexes. The preparation of gold electrodes modified by mismatch and complementatry duplexes was characterized by electrochemical impedance spectroscopy (EIS) and optimized for better detection in terms of self-assembly time, hybridization time, and incubation time. The interaction between FecNC and DNA duplexes modified on the surface of a gold electrode was explored by square wave voltammetry (SWV) and EIS. The results showed that the DNA duplexes with GG mismatch on the surface of a gold electrode was easily detected by the largest electrochemical signal of the bifunctional probe because of its selective binding to GG mismatches. The bifunctional probe could offer a simple, effective electrochemical detection of GG mismatches, and theoretical bases for development of electrochemical biosensors. Further, the method would be favorable for diagnosis of genetic diseases.

  10. Replication of linear duplex DNA in vitro with bacteriophage T5 DNA polymerase

    SciTech Connect

    Fujimura, R. K.; Das, S. K.; Allison, D. P.; Roop, B. C.

    1980-01-01

    Two sets of experiments are presented that attempt to contribute to understanding the mechanisms of DNA replication. The specific areas discussed are fidelity of DNA replication and initiation of replication of duplex DNA. (ACR)

  11. Two-flux transfer matrix model for predicting the reflectance and transmittance of duplex halftone prints.

    PubMed

    Mazauric, Serge; Hébert, Mathieu; Simonot, Lionel; Fournel, Thierry

    2014-12-01

    We introduce a model allowing convenient calculation of the spectral reflectance and transmittance of duplex prints. It is based on flux transfer matrices and enables retrieving classical Kubelka-Munk formulas, as well as extended formulas for nonsymmetric layers. By making different assumptions on the flux transfers, we obtain two predictive models for the duplex halftone prints: the "duplex Clapper-Yule model," which is an extension of the classical Clapper-Yule model, and the "duplex primary reflectance-transmittance model." The two models can be calibrated from either reflectance or transmittance measurements; only the second model can be calibrated from both measurements, thus giving optimal accuracy for both reflectance and transmittance predictions. The conceptual differences between the two models are deeply analyzed, as well as their advantages and drawbacks in terms of calibration. According to the test carried out in this study with paper printed in inkjet, their predictive performances are good provided appropriate calibration options are selected.

  12. Comparison of intraoperative completion flowmeter versus duplex ultrasonography and contrast arteriography for carotid endarterectomy.

    PubMed

    Winkler, Gabor A; Calligaro, Keith D; Kolakowski, Steven; Doerr, Kevin J; McAffee-Bennett, Sandy; Muller, Kathy; Dougherty, Matthew J

    Intraoperative completion studies of the internal carotid artery following carotid endarterectomy are recommended to ensure technical perfection of the repair. Transit time ultrasound flowmeter does not require trained technicians, requires less time than other completion studies such as duplex ultrasonography and contrast arteriography, and is noninvasive. Flowmetry was compared with duplex ultrasonography and contrast arteriography to determine if the relatively simpler flowmetry could replace these two more widely accepted completion studies in the intraoperative assessment of carotid endarterectomy. Comparative intraoperative assessment was performed in 116 carotid endarterectomies using all three techniques between December 1, 2000 and November 30, 2003. Eversion endarterectomy was performed in 51 cases and standard endarterectomy with prosthetic patching in 65 cases. Patients underwent completion flowmetry, duplex ultrasonography, and contrast arteriography studies of the exposed arteries, which were performed by vascular fellows or senior surgical residents under direct supervision of board-certified vascular surgeons. Duplex ultrasonography surveillance was performed 1 and 6 months postoperatively and annually thereafter. Mean follow-up was 18 months (range, 6-42 months). The combined ipsilateral stroke and death rate was 0%. The mean internal carotid artery flow using flowmetry was 249 mL/min (range, 60-750 mL/min). Five (4.3%) patients had flow < 100 mL/min as measured with flowmetry, but completion contrast arteriography and duplex ultrasonography were normal and none of the arteries were re-explored. One carotid endarterectomy was re-explored based on completion duplex ultrasonography that showed markedly elevated internal carotid artery peak systolic velocity (> 500 cm/sec); however, exploration was normal and completion flowmetry and contrast arteriography were normal. Duplex ultrasonography studies revealed internal carotid artery peak systolic

  13. Multi-pair states in electron-positron pair creation

    NASA Astrophysics Data System (ADS)

    Wöllert, Anton; Bauke, Heiko; Keitel, Christoph H.

    2016-09-01

    Ultra strong electromagnetic fields can lead to spontaneous creation of single or multiple electron-positron pairs. A quantum field theoretical treatment of the pair creation process combined with numerical methods provides a description of the fermionic quantum field state, from which all observables of the multiple electron-positron pairs can be inferred. This allows to study the complex multi-particle dynamics of electron-positron pair creation in-depth, including multi-pair statistics as well as momentum distributions and spin. To illustrate the potential benefit of this approach, it is applied to the intermediate regime of pair creation between nonperturbative Schwinger pair creation and perturbative multiphoton pair creation where the creation of multi-pair states becomes nonnegligible but cascades do not yet set in. Furthermore, it is demonstrated how spin and helicity of the created electrons and positrons are affected by the polarization of the counterpropagating laser fields, which induce the creation of electron-positron pairs.

  14. Metal-Mediated Assembly of 1,N(6)-Ethenoadenine: From Surfaces to DNA Duplexes.

    PubMed

    Mandal, Soham; Wang, Can; Prajapati, Rajneesh K; Kösters, Jutta; Verma, Sandeep; Chi, Lifeng; Müller, Jens

    2016-07-18

    The design of multinuclear metal complexes requires a match of the ligand-to-metal vectors and the preferred coordination geometries of the metal ions. Only a few ligands are known with a parallel orientation of N→M vectors that brings the metal ions into close proximity. We establish here the adenine derivative 1,N(6)-ethenoadenine (εA) as an ideal bis(monodentate) ligand. Scanning tunneling microscope images of alkylated εA on graphite surface clearly indicate that these ligands bind to Ag(I) ions. The molecular structures of [Ag2(1)2](ClO4)2 and [Ag2(2)2](ClO4)2 (1, 9-ethyl-1,N(6)-ethenoadenine; 2, 9-propyl-1,N(6)-propylenoadenine) confirm that dinuclear complexes with short Ag···Ag distances are formed (3.0256(3) and 2.984(1) Å, respectively). The structural motif can be extended to divalent metal ions, as was shown by determining the molecular structure of [Cu2(1)2(CHO2)2(OH2)2](NO3)2·2H2O with a Cu···Cu distance of 3.162(2) Å. Moreover, when introducing the 1,N(6)-ethenoadenine deoxyribonucleoside into parallel-stranded DNA duplexes, even dinuclear Ag(I)-mediated base pairs are formed, featuring the same transoid orientation of the glycosidic bonds as the model complexes. Hence, 1,N(6)-ethenoadenine and its derivatives are ideally suited as bis(monodentate) ligands with a parallel alignment of the N→M vectors for the construction of supramolecular metal complexes that require two metal ions at close distance. PMID:27347746

  15. Heat Capacity Changes Associated with DNA Duplex Formation: Salt- and Sequence-Dependent Effects†

    PubMed Central

    Mikulecky, Peter J.; Feig, Andrew L.

    2008-01-01

    Duplexes are the most fundamental elements of nucleic acid folding. Although it has become increasingly clear that duplex formation can be associated with a significant change in heat capacity (ΔCp), this parameter is typically overlooked in thermodynamic studies of nucleic acid folding. Analogy to protein folding suggests that base stacking events coupled to duplex formation should give rise to a ΔCp due to the release of waters solvating aromatic surfaces of nucleotide bases. In previous work, we showed that the ΔCp observed by isothermal titration calorimetry (ITC) for RNA duplex formation depended on salt and sequence. In the present work, we apply calorimetric and spectroscopic techniques to a series of designed DNA duplexes to demonstrate that both the salt dependence and sequence dependence of ΔCps observed by ITC reflect perturbations to the same fundamental phenomenon: stacking in the single-stranded state. By measuring the thermodynamics of single strand melting, one can accurately predict the ΔCps observed for duplex formation by ITC at high and low ionic strength. We discuss our results in light of the larger issue of contributions to ΔCp from coupled equilibria and conclude that observed ΔCps can be useful indicators of intermediate states in nucleic acid folding phenomena. PMID:16401089

  16. X-mas trees: A new application for duplex stainless steels

    SciTech Connect

    Hochoertler, G.; Zeiler, G.; Haberfellner, K.

    1995-12-31

    The development of fields in severe areas (subsea installations, deserts) necessitates the use of materials which can operate maintenance free in these conditions. Depending on production route and aggressivity of relevant media, the materials used until now, such as AISI 4130, are being superseded by higher alloyed materials such as F6NM, Duplex and Super Duplex Steels. Extensive investigation of metallurgical, mechanical, technological and stress aspects as well as research into the influence of melting, forging and heat treatment processes on high alloyed materials enables ``High Tech`` forgings to be manufactured. Based on investigations and experience gained by previously produced forgings (WYE-piece, Gate Valve components, Swivel forgings, line pipes made of Super Duplex Stainless Steels and Duplex Stainless Steels), the first X-mas trees made of solid Duplex Stainless Steel has been produced. Due to the excellent mechanical and corrosion properties of Duplex Stainless Steel, the expensive and time consuming cladding can be eliminated for most environments, which results in good economy and significantly reduced production time. To obtain information about the quality of such a large forging, samples were taken from one of these X-mas trees and the mechanical and corrosion properties were investigated.

  17. Recognition of triplex forming oligodeoxynucleotides incorporating abasic sites by 5-arylcytosine residues in duplex DNAs.

    PubMed

    Mizuta, Masahiro; Banba, Jun-Ichi; Kanamori, Takashi; Ohkubo, Akihiro; Sekine, Mitsuo; Seio, Kohji

    2007-01-01

    In this paper, we reported our attempt to use a 5arylcytosine (dC(ar)) and the abasic site () as an artificial base pair for DNA triplex. The idea was confirmed by the molecular modeling studied in which the aromatic group of (ph) which protrudes in the major groove was buried into the cleft formed by the residue in the TFO. We synthesized three kinds of dC(ar) and the oligonucleotides incorporating them. Our UV-melting experiments revealed that the DNA triplex containing the dC(ph).phi was more stable than that containing dC.phi pair. Moreover, the dC.phi pair was more stable than any other dC.Y pairs such as dC(ph).G, dC(ph).C, dC(ph).T and dC(ph).A. These results indicated the possibility that the appropriate pair of dC(Ar) and could be the new sequence code of DNA triplex. We also carried out the Tm analyses of other TFOs incorporating dC(Ar) and , and clarified the stability of these triplexes. PMID:18029568

  18. 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

  19. Discrimination of Single Base Pair Differences Among Individual DNA Molecules Using a Nanopore

    NASA Technical Reports Server (NTRS)

    Vercoutere, Wenonah; DeGuzman, Veronica

    2003-01-01

    The protein toxin alpha-hemolysin form nanometer scale channels across lipid membranes. Our lab uses a single channel in an artificial lipid bilayer in a patch clamp device to capture and examine individual DNA molecules. This nanopore detector used with a support vector machine (SVM) can analyze DNA hairpin molecules on the millisecond time scale. We distinguish duplex stem length, base pair mismatches, loop length, and single base pair differences. The residual current fluxes also reveal structural molecular dynamics elements. DNA end-fraying (terminal base pair dissociation) can be observed as near full blockades, or spikes, in current. This technique can be used to investigate other biological processes dependent on DNA end-fraying, such as the processing of HIV DNA by HIV integrase.

  20. Binding of T and T analogs to CG base pairs in antiparallel triplexes.

    PubMed

    Durland, R H; Rao, T S; Revankar, G R; Tinsley, J H; Myrick, M A; Seth, D M; Rayford, J; Singh, P; Jayaraman, K

    1994-08-11

    The goal of this study was to address antiparallel triplex formation at duplex targets that do not conform to a strict oligopurine.oligopyrimidine motif. We focused on the ability of natural bases and base analogs incorporated into oligonucleotide third strands to bind to so-called CG inversions. These are sites where a cytosine base is present in an otherwise purine-rich strand of a duplex target. Using a 26-base-triplet test system, we found that of the standard bases, only thymine (T) shows substantial binding to CG inversions. This is quantitatively similar to the report of Beal and Dervan [Science (1991), 251, 1360-1363]. Binding to CG inversions was only slightly weaker than binding to AT base pairs. Binding of T to CG inversions was also evaluated in two other sequences, with qualitatively similar results. Six different analogs of thymine were also tested for binding to CG inversions and AT base pairs. Significant changes in affinity were observed. In particular, 5-fluoro-2'-deoxyuridine was found to increase affinity for CG inversions as well as for AT base pairs. Studies with oligonucleotides containing pyridin-2-one or pyridin-4-one suggest that thymine O4 plays a critical role in the T.CG interaction. Possible models to account for these observations are discussed. PMID:8065940

  1. Low-Power Optical Feeder for VDSL Over Twisted Pair for Last Mile Access Networks

    NASA Astrophysics Data System (ADS)

    Dudley, Sandra E. M.; Quinlan, Terence J.; Henning, Ian D.; Walker, Stuart D.; Davey, Russell P.; Wallace, Andrew D.; Boyd, Ivan; Payne, Dave B.

    2006-01-01

    In this paper, we describe an ultra-low-power optoelectronic very-high-data-rate digital subscriber line (VDSL) system, enabling broadband access to the home over 10 km of optical fiber and 1 km of twisted pair. The cabinet/distribution point interface has a footprint of just 3 × 3 × 1 cm, and consumes only 165 mW. A quadrature-amplitude-modulation (QAM) scheme was used for system tests with 10 Mb/s full duplex achieved, and up to 40-dB up/downstream channel isolation is obtained using hybrid transformers.

  2. Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay.

    PubMed

    Huang, Yong; Xing, Na; Wang, Zengguo; Zhang, Xiujuan; Zhao, Xiaomin; Du, Qian; Chang, Lingling; Tong, Dewen

    2015-01-01

    Mixed infection of multiple viruses is common in modern intensive pig rearing. However, there are no methods available to detect DNA and RNA viruses in the same reaction system in preclinical level. In this study, we aimed to develop a duplex ultrasensitive nanoparticle DNA probe-based PCR assay (duplex UNDP-PCR) that was able to simultaneously detect DNA and RNA viruses in the same reaction system. PCV2 and TGEV are selected as representatives of the two different types of viruses. PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. After magnetic separation, DNA barcodes specific for PCV2 and TGEV were eluted using DTT and characterized by specific PCR assay for specific DNA barcodes subsequently. The duplex UNDP-PCR showed similar sensitivity as that of single UNDP-PCR and was able to detect 20 copies each of PCV2 and TGEV in the serum, showing approximately 250-fold more sensitivity than conventional duplex PCR/RT-PCR assays. No cross-reaction was observed with other viruses. The positive detection rate of single MMPs- and duplex MMPs-based duplex UNDP-PCR was identical, with 29.6% for PCV2, 9.3% for TGEV and 3.7% for PCV2 and TGEV mixed infection. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. Therefore, the established duplex UNDP-PCR is a rapid and economical detection method, exhibiting high sensitivity, specificity and reproducibility.

  3. Sole and stable RNA duplexes of G-rich sequences located in the 5'-untranslated region of protooncogenes.

    PubMed

    Saxena, Sarika; Miyoshi, Daisuke; Sugimoto, Naoki

    2010-08-24

    Guanine- (G-) rich nucleic acid sequences can form four-stranded structures called G-quadruplexes. It is widely held that the formation of a G-quadruplex in RNA is more feasible than in DNA because of the lack of a complementary strand in mRNA. Here, we analyzed sequences of 5'-untranslated regions of protooncogenes and surprisingly found that these regions showed an enrichment of not only guanine (G) but also cytosine (C) nucleotides. Since neighboring cytosine- (C-) rich regions can affect the formation and stability of a G-quadruplex structure, we further investigated the properties of DNA and RNA structures of G-rich and GC-rich regions. We selected typical GC-rich RNA sequences from protooncogenes and corresponding DNA sequences and investigated their structures. It was found that the GC-rich RNA sequences formed stable A-form duplexes as their major structure independent of the surrounding conditions, including the presence of different cations (Na(+), K(+), or Li(+)) or molecular crowding with 40 wt % poly(ethylene glycol) with an average molecular mass of 200 Da although there are a few exceptions in which only a combination of K(+) and molecular crowding induced a G-quadruplex structure of an extremely G-rich RNA sequence. In contrast, structural polymorphisms involving duplexes, G-quadruplexes, and i-motifs were observed for GC-rich DNA sequences depending on the surrounding factors. These results demonstrate the considerable structural and functional differences in GC-rich sequences of the genome (DNA) and transcriptosome (mRNA) with respect to the nucleic acid backbone. Moreover, it was suggested that structural study for a G-rich RNA sequence should be carried out under cell-mimicking condition where K(+) and crowding cosolutes exist.

  4. Beamforming Based Full-Duplex for Millimeter-Wave Communication.

    PubMed

    Liu, Xiao; Xiao, Zhenyu; Bai, Lin; Choi, Jinho; Xia, Pengfei; Xia, Xiang-Gen

    2016-01-01

    In this paper, we study beamforming based full-duplex (FD) systems in millimeter-wave (mmWave) communications. A joint transmission and reception (Tx/Rx) beamforming problem is formulated to maximize the achievable rate by mitigating self-interference (SI). Since the optimal solution is difficult to find due to the non-convexity of the objective function, suboptimal schemes are proposed in this paper. A low-complexity algorithm, which iteratively maximizes signal power while suppressing SI, is proposed and its convergence is proven. Moreover, two closed-form solutions, which do not require iterations, are also derived under minimum-mean-square-error (MMSE), zero-forcing (ZF), and maximum-ratio transmission (MRT) criteria. Performance evaluations show that the proposed iterative scheme converges fast (within only two iterations on average) and approaches an upper-bound performance, while the two closed-form solutions also achieve appealing performances, although there are noticeable differences from the upper bound depending on channel conditions. Interestingly, these three schemes show different robustness against the geometry of Tx/Rx antenna arrays and channel estimation errors. PMID:27455256

  5. Beamforming Based Full-Duplex for Millimeter-Wave Communication.

    PubMed

    Liu, Xiao; Xiao, Zhenyu; Bai, Lin; Choi, Jinho; Xia, Pengfei; Xia, Xiang-Gen

    2016-01-01

    In this paper, we study beamforming based full-duplex (FD) systems in millimeter-wave (mmWave) communications. A joint transmission and reception (Tx/Rx) beamforming problem is formulated to maximize the achievable rate by mitigating self-interference (SI). Since the optimal solution is difficult to find due to the non-convexity of the objective function, suboptimal schemes are proposed in this paper. A low-complexity algorithm, which iteratively maximizes signal power while suppressing SI, is proposed and its convergence is proven. Moreover, two closed-form solutions, which do not require iterations, are also derived under minimum-mean-square-error (MMSE), zero-forcing (ZF), and maximum-ratio transmission (MRT) criteria. Performance evaluations show that the proposed iterative scheme converges fast (within only two iterations on average) and approaches an upper-bound performance, while the two closed-form solutions also achieve appealing performances, although there are noticeable differences from the upper bound depending on channel conditions. Interestingly, these three schemes show different robustness against the geometry of Tx/Rx antenna arrays and channel estimation errors.

  6. Superplastic Forming of Duplex Stainless Steel for Aerospace Part

    SciTech Connect

    Lee, Ho-Sung; Yoon, Jong-Hoon; Yoo, Joon-Tae; Yi, Young-Moo

    2011-08-22

    In this study, the high temperature forming behavior of duplex stainless steel has been characterized and the outer shell of a combustion chamber was fabricated with pressure difference of hot gas. It consists of two parts which are the outer skin made of stainless steel to sustain the internal pressure and the inner shell made of copper alloy for regenerative cooling channels. Two outer skins partitioned to half with respect to the symmetric axis was prepared by hot gas forming process with a maximum pressure of 7 MPa following to FEM analysis. For inner layer, copper alloy was machined for cooling channels and then placed in the gas pressure welding fixture. It is shown that the optimum condition of gas pressure welding is 7 MPa at 890 deg. C, for one hour. EDX analysis and scanning electron microscope micrograph confirm the atomic diffusion process is observed at the interface and copper atoms diffuse into steel, while iron and chrome atoms diffuse into copper. The result shows that the manufacturing method with superplastic forming and gas pressure welding of steel and copper alloy has been successful for near net shape manufacturing of scaled combustion chamber of launch vehicle.

  7. Superplastic Forming of Duplex Stainless Steel for Aerospace Part

    NASA Astrophysics Data System (ADS)

    Lee, Ho-Sung; Yoon, Jong-Hoon; Yoo, Joon-Tae; Yi, Young-Moo

    2011-08-01

    In this study, the high temperature forming behavior of duplex stainless steel has been characterized and the outer shell of a combustion chamber was fabricated with pressure difference of hot gas. It consists of two parts which are the outer skin made of stainless steel to sustain the internal pressure and the inner shell made of copper alloy for regenerative cooling channels. Two outer skins partitioned to half with respect to the symmetric axis was prepared by hot gas forming process with a maximum pressure of 7 MPa following to FEM analysis. For inner layer, copper alloy was machined for cooling channels and then placed in the gas pressure welding fixture. It is shown that the optimum condition of gas pressure welding is 7 MPa at 890 °C, for one hour. EDX analysis and scanning electron microscope micrograph confirm the atomic diffusion process is observed at the interface and copper atoms diffuse into steel, while iron and chrome atoms diffuse into copper. The result shows that the manufacturing method with superplastic forming and gas pressure welding of steel and copper alloy has been successful for near net shape manufacturing of scaled combustion chamber of launch vehicle.

  8. Phase Separation in Lean Grade Duplex Stainless Steel 2101

    SciTech Connect

    Garfinkel, D.; Poplawsky, Jonathan D.; Guo, Wei; Young, Jr., George A.; Tucker, Julie

    2015-08-19

    The use of duplex stainless steels (DSS) in nuclear power generation systems is limited by thermal instability that leads to embrittlement in the temperature range of 204°C - 538°C. New lean grade alloys, such as 2101, offer the potential to mitigate these effects. Thermal embrittlement was quantified through impact toughness and hardness testing on samples of alloy 2101 after aging at 427°C for various durations (1-10,000 hours). Additionally, atom probe tomography (APT) was utilized in order to observe the kinetics of α-α’ separation and G-phase formation. Mechanical testing and APT data for two other DSS alloys, 2003 and 2205 were used as a reference to 2101. The results show that alloy 2101 exhibits superior performance compared to the standard grade DSS alloy, 2205, but inferior to the lean grade alloy, 2003, in mechanical testing. APT data demonstrates that the degree of α-α’ separation found in alloy 2101 closely resembles that of 2205, and greatly exceeds 2003. Additionally, contrary to what was observed in 2003, 2101 demonstrated G-phase like precipitates after long aging times, though precipitates were not as abundant as was observed in 2205.

  9. Electron beam welding produces improved duplex crack arrest specimens

    SciTech Connect

    King, J.F.; Hudson, J.D.

    1988-01-01

    The crack arrest toughness, K/sub Ia/, is generally determined using a monolithic compact type specimen which contains a brittle weld bead to act as a crack initiation site. To test at higher temperatures and toughnesses, electron beam (EB) welded duplex specimens were fabricated. These specimens required the joining of hardened 4340 steel, which acts as the crack initiator, to A533 grade B class 1 steel base material and submerged arc welds in this base metal. The successful fabrication of these specimens required the development of an EB welding procedure with a very narrow heat-affected zone (HAZ). A technique was also developed to eliminate the porosity which was always present in the EB welds through the submerged arc weld deposit region of the joint. The technique involved remelting the joint surface of the A533 steel containing the submerged arc weld to a controlled depth using an oscillated electron beam. This remelt in vacuum reduced the gaseous constituents to low levels and prevented porosity from forming in the deep penetration EB welds between this surface and the 4340 steel.

  10. JAEA Fatigue Analysis of EBR-II Duplex Tubing

    SciTech Connect

    J. H. Jackson; D. L. Porter; W. R. Lloyd

    2009-07-01

    This work addresses questions brought up concerning the mechanisms associated with fatigue crack growth retardation and/or arrest within the nickel bond layer in duplex 2¼ Cr-1Mo steel superheater tubes. Previous work performed at the Idaho National Laboratory (INL) indicated that the nickel bond layer did not function as a crack arrestor during fatigue crack propagation with the exception of one, isolated case involving an exceptionally low fatigue load and a high temperature (400 0C) environment. Since it is atypical for a fatigue crack to propagate from a relatively soft material (the nickel bond layer) to a harder material (the 2¼ Cr-1Mo steel) there has been speculation that the nickel bond layer was hardened in service. Additionally, there are questions surrounding the nature of the fatigue crack propagation within the nickel bond layer; specifically with regard to the presence of voids seen on micrographs of the bond layer and oxidation within the steel along the edge of the nickel bond layer. There is uncertainty as to the effect of these voids and/or oxide barriers with respect to potential fatigue crack arrest.

  11. JAEA Fatigue Analysis of EBR-II Duplex Tubing

    SciTech Connect

    J. H. Jackson; D. L. Porter; W. R. Lloyd; N. Kisohara

    2011-03-01

    Small, notched three-point bend specimens machined from duplex tubes, which were extracted from an EBR-II superheater, were fatigued through the nickel interlayer to determine propensity for crack arrest within this interlayer. Several of these specimens were fatigued in the near threshold, and steady state regimes of Paris Law behavior. Additionally, two specimens were fatigued to the edge of the nickel interlayer and then monotonically loaded. Micro-hardness profiles of the nickel interlayer were also measured. Fatigue behavior was found to be similar to previous studies in that arrest was only noted in the near threshold Paris regime (attributed to the presence of voids) and in the steady state regime exhibited an acceleration of crack growth rate through the nickel interlayer followed by a slight retardation. Monotonic loading resulted in crack branching or delamination along the interlayer. Although archival material was not available for this study, the hardness of the nickel interlayer was determined to have been lowered slightly during service by comparison to the expected hardness of a similar nickel braze prepared as specified for fabrication of these tubes.

  12. Reaction-diffusion processes and metapopulation models on duplex networks

    NASA Astrophysics Data System (ADS)

    Xuan, Qi; Du, Fang; Yu, Li; Chen, Guanrong

    2013-03-01

    Reaction-diffusion processes, used to model various spatially distributed dynamics such as epidemics, have been studied mostly on regular lattices or complex networks with simplex links that are identical and invariant in transferring different kinds of particles. However, in many self-organized systems, different particles may have their own private channels to keep their purities. Such division of links often significantly influences the underlying reaction-diffusion dynamics and thus needs to be carefully investigated. This article studies a special reaction-diffusion process, named susceptible-infected-susceptible (SIS) dynamics, given by the reaction steps β→α and α+β→2β, on duplex networks where links are classified into two groups: α and β links used to transfer α and β particles, which, along with the corresponding nodes, consist of an α subnetwork and a β subnetwork, respectively. It is found that the critical point of particle density to sustain reaction activity is independent of the network topology if there is no correlation between the degree sequences of the two subnetworks, and this critical value is suppressed or extended if the two degree sequences are positively or negatively correlated, respectively. Based on the obtained results, it is predicted that epidemic spreading may be promoted on positive correlated traffic networks but may be suppressed on networks with modules composed of different types of diffusion links.

  13. Eddy current techniques for super duplex stainless steel characterization

    NASA Astrophysics Data System (ADS)

    Camerini, C.; Sacramento, R.; Areiza, M. C.; Rocha, A.; Santos, R.; Rebello, J. M.; Pereira, G.

    2015-08-01

    Super duplex stainless steel (SDSS) is a two-phase material where the microstructure consists of grains of ferrite (δ) and austenite (γ). SDSS exhibit an attractive combination of properties, such as: strength, toughness and stress corrosion cracking resistance. Nevertheless, SDSS attain these properties after a controlled solution heat treatment, leading to a similar volumetric fraction of δ and γ. Any further heat treatment, welding operation for example, can change the balance of the original phases, or may also lead to precipitation of a deleterious phase, such as sigma (σ). For these situations, the material corrosion resistance is severely impaired. In the present study, several SDSS samples with low σ phase content and non-balanced microstructure were intentionally obtained by thermally treating SDSS specimens. Electromagnetic techniques, conventional Eddy Current Testing (ECT) and Saturated Low Frequency Eddy Current (SLOFEC), were employed to characterize the SDSS samples. The results showed that ECT and SLOFEC are reliable techniques to evaluate σ phase presence in SDSS and can provide an estimation of the δ content.

  14. Phase Separation in Lean-Grade Duplex Stainless Steel 2101

    NASA Astrophysics Data System (ADS)

    Garfinkel, David A.; Poplawsky, Jonathan D.; Guo, Wei; Young, George A.; Tucker, Julie D.

    2015-08-01

    The use of duplex stainless steels (DSS) in nuclear power generation systems is limited by thermal instability that leads to embrittlement in the temperature range of 204°C to 538°C. New lean-grade alloys, such as 2101, offer the potential to mitigate these effects. Thermal embrittlement was quantified through impact toughness and hardness testing on samples of alloy 2101 after aging at 427°C for various durations (1-10,000 h). Additionally, atom probe tomography (APT) was utilized in order to observe the kinetics of α-α' separation and G-phase formation. Mechanical testing and APT data for two other DSS alloys, 2003 and 2205, were used as a reference to 2101. The results show that alloy 2101 exhibits superior performance compared to the standard-grade DSS alloy 2205 but inferior to the lean-grade alloy 2003 in mechanical testing. APT data demonstrate that the degree of α-α' separation found in alloy 2101 closely resembles that of 2205 and greatly exceeds 2003. Additionally, contrary to what was observed in 2003, 2101 demonstrated G-phase like precipitates after long aging times, although precipitates were not as abundant as was observed in 2205.

  15. Phase Separation in Lean Grade Duplex Stainless Steel 2101

    DOE PAGES

    Garfinkel, D.; Poplawsky, Jonathan D.; Guo, Wei; Young, Jr., George A.; Tucker, Julie

    2015-08-19

    The use of duplex stainless steels (DSS) in nuclear power generation systems is limited by thermal instability that leads to embrittlement in the temperature range of 204°C - 538°C. New lean grade alloys, such as 2101, offer the potential to mitigate these effects. Thermal embrittlement was quantified through impact toughness and hardness testing on samples of alloy 2101 after aging at 427°C for various durations (1-10,000 hours). Additionally, atom probe tomography (APT) was utilized in order to observe the kinetics of α-α’ separation and G-phase formation. Mechanical testing and APT data for two other DSS alloys, 2003 and 2205 weremore » used as a reference to 2101. The results show that alloy 2101 exhibits superior performance compared to the standard grade DSS alloy, 2205, but inferior to the lean grade alloy, 2003, in mechanical testing. APT data demonstrates that the degree of α-α’ separation found in alloy 2101 closely resembles that of 2205, and greatly exceeds 2003. Additionally, contrary to what was observed in 2003, 2101 demonstrated G-phase like precipitates after long aging times, though precipitates were not as abundant as was observed in 2205.« less

  16. Detecting ultralow-frequency mutations by Duplex Sequencing

    PubMed Central

    Kennedy, Scott R; Schmitt, Michael W; Fox, Edward J; Kohrn, Brendan F; Salk, Jesse J; Ahn, Eun Hyun; Prindle, Marc J; Kuong, Kawai J; Shen, Jiang-Cheng; Risques, Rosa-Ana; Loeb, Lawrence A

    2014-01-01

    Duplex Sequencing (DS) is a next-generation sequencing methodology capable of detecting a single mutation among >1 × 107 wild-type nucleotides, thereby enabling the study of heterogeneous populations and very-low-frequency genetic alterations. DS can be applied to any double-stranded DNA sample, but it is ideal for small genomic regions of <1 Mb in size. The method relies on the ligation of sequencing adapters harboring random yet complementary double-stranded nucleotide sequences to the sample DNA of interest. Individually labeled strands are then PCR-amplified, creating sequence ‘families’ that share a common tag sequence derived from the two original complementary strands. Mutations are scored only if the variant is present in the PCR families arising from both of the two DNA strands. Here we provide a detailed protocol for efficient DS adapter synthesis, library preparation and target enrichment, as well as an overview of the data analysis workflow. The protocol typically takes 1–3 d. PMID:25299156

  17. Beamforming Based Full-Duplex for Millimeter-Wave Communication

    PubMed Central

    Liu, Xiao; Xiao, Zhenyu; Bai, Lin; Choi, Jinho; Xia, Pengfei; Xia, Xiang-Gen

    2016-01-01

    In this paper, we study beamforming based full-duplex (FD) systems in millimeter-wave (mmWave) communications. A joint transmission and reception (Tx/Rx) beamforming problem is formulated to maximize the achievable rate by mitigating self-interference (SI). Since the optimal solution is difficult to find due to the non-convexity of the objective function, suboptimal schemes are proposed in this paper. A low-complexity algorithm, which iteratively maximizes signal power while suppressing SI, is proposed and its convergence is proven. Moreover, two closed-form solutions, which do not require iterations, are also derived under minimum-mean-square-error (MMSE), zero-forcing (ZF), and maximum-ratio transmission (MRT) criteria. Performance evaluations show that the proposed iterative scheme converges fast (within only two iterations on average) and approaches an upper-bound performance, while the two closed-form solutions also achieve appealing performances, although there are noticeable differences from the upper bound depending on channel conditions. Interestingly, these three schemes show different robustness against the geometry of Tx/Rx antenna arrays and channel estimation errors. PMID:27455256

  18. Stabilization of the tertiary structure of yeast phenylalanine tRNA by [Co(NH3)6]3+. X-ray evidence for hydrogen bonding to pairs of guanine bases in the major groove.

    PubMed

    Hingerty, B E; Brown, R S; Klug, A

    1982-04-26

    The sites of three [Co(NH3)6]3+ ions bound to the phenylalanine tRNA of yeast have been determined by X-ray diffraction analysis. [Co(NH3)6]3+ binds to purine-purine sequences in yeast tRNA Phe. It is different from the binding fo Co2+, which binds to the base and phosphate of residue G15. There are no direct metal-nucleotide bonds, although hydrogen bonding of the coordinated ammines to double-helical guanylguanosine sequences in the major groove and to phosphate oxygen in neighboring polynucleotide strands increases the stability of the structure. Hydrogen-bonding appears to be via cis ammine ligands to N(7) and O(6) positions of adjacent purine bases.

  19. EHD3 Protein Is Required for Tubular Recycling Endosome Stabilization, and an Asparagine-Glutamic Acid Residue Pair within Its Eps15 Homology (EH) Domain Dictates Its Selective Binding to NPF Peptides.

    PubMed

    Bahl, Kriti; Xie, Shuwei; Spagnol, Gaelle; Sorgen, Paul; Naslavsky, Naava; Caplan, Steve

    2016-06-24

    An elaborate network of dynamic lipid membranes, termed tubular recycling endosomes (TRE), coordinates the process of endocytic recycling in mammalian cells. The C-terminal Eps15 homology domain (EHD)-containing proteins have been implicated in the bending and fission of TRE, thus regulating endocytic recycling. EHD proteins have an EH domain that interacts with proteins containing an NPF motif. We found that NPF-containing EHD1 interaction partners such as molecules interacting with CasL-like1 (MICAL-L1) and Syndapin2 are essential for TRE biogenesis. Also crucial for TRE biogenesis is the generation of phosphatidic acid, an essential lipid component of TRE that serves as a docking point for MICAL-L1 and Syndapin2. EHD1 and EHD3 have 86% amino acid identity; they homo- and heterodimerize and partially co-localize to TRE. Despite their remarkable identity, they have distinct mechanistic functions. EHD1 induces membrane vesiculation, whereas EHD3 supports TRE biogenesis and/or stabilization by an unknown mechanism. While using phospholipase D inhibitors (which block the conversion of glycerophospholipids to phosphatidic acid) to deplete cellular TRE, we observed that, upon inhibitor washout, there was a rapid and dramatic regeneration of MICAL-L1-marked TRE. Using this "synchronized" TRE biogenesis system, we determined that EHD3 is involved in the stabilization of TRE rather than in their biogenesis. Moreover, we identify the residues Ala-519/Asp-520 of EHD1 and Asn-519/Glu-520 of EHD3 as defining the selectivity of these two paralogs for NPF-containing binding partners, and we present a model to explain the atomic mechanism and provide new insight for their differential roles in vesiculation and tubulation, respectively. PMID:27189942

  20. Existence of best proximity pairs and equilibrium pairs

    NASA Astrophysics Data System (ADS)

    Kim, Won Kyu; Lee, Kyoung Hee

    2006-04-01

    In this paper, using the fixed point theorem for Kakutani factorizable multifunctions, we shall prove new existence theorems of best proximity pairs and equilibrium pairs for free abstract economies, which include the previous fixed point theorems and equilibrium existence theorems.

  1. Solution confirmation of the (-)-trans-anti-5-Methylchrysene-dG adduct oppposite dC in a DNA duplex: DNA bending associated with wedging of the Methyl group of 5-Methylchrysene to the 3{prime}-side of the modification site

    SciTech Connect

    Cosman, M.; Patel, D.J.

    1995-05-09

    This paper reports on NMR-molecular mechanics structural studies of the (-)-trans-anti-[MC]dG adduct positioned opposite dC in the sequence context of the d(Cl-C2-A3-T4-C5-[MC]G6-C7-T8-A9-C10-C11){sm_bullet}d(G12-G13-T14-A15-G16-C17-G 18-A19-T20-G21-G22) duplex [designated (-)-trans-anti-[MC]dG{sm_bullet}dC 11-mer duplex]. This adduct is derived from the trans addition at C{sup 4} of (-)-anti-1(S),2(R)-dihydroxy-3(R),4(S)-epoxy-1,2,3,4-tetrahydro-5-methylchrysene [(-)-anti-5-MeCDE] to the N{sup 2} position of dG6 in this duplex sequence. The 5-methyl group is located adjacent to the MC(C{sup 4}) binding site, with these groups juxtaposed in a sterically crowded bay region in the adduct duplex. The 5-methylchrysenyl and the nucleic acid exchangeable and nonexchangeable protons were assigned following analysis of two-dimensional NMR data sets in H{sub 2}O and D{sub 2}O buffer solution. The solution structure of the trans-anti-[MC]dG{sm_bullet}dC 11-mer duplex has been determined by incorporating DNA-DNA and carcinogen-DNA proton-proton distances defined by lower and upper bounds deduced from NOESY data sets as restraints in molecular mechanics computations in torsion angle space. The results establish that the [MC]dG6{sm_bullet}dC17 base pair and flanking dC5{sm_bullet}dG18 and dC7{sm_bullet}dG16 base pairs retain Watson-Crick alignments upon adduct formation. 61 refs., 9 figs., 2 tabs.

  2. Heat treatment temperature influence on ASTM A890 GR 6A super duplex stainless steel microstructure

    SciTech Connect

    Martins, Marcelo; E-mail: marcelo.martins@sulzer.com; Casteletti, Luiz Carlos

    2005-09-15

    Duplex and super duplex stainless steels are ferrous alloys with up to 26% chromium, 8% nickel, 5% molybdenum and 0.3% nitrogen, which are largely used in applications in media containing ions from the halogen family, mainly the chloride ion (Cl{sup -}). The emergence of this material aimed at substituting Copper-Nickel alloys (Cupro-Nickel) that despite presenting good corrosion resistance, has mechanical properties quite inferior to steel properties. The metallurgy of duplex and super duplex stainless steel is complex due to high sensitiveness to sigma phase precipitation that becomes apparent, due to the temperatures they are exposed on cooling from solidification as well as from heat treatment processes. The objective of this study was to verify the influence of heat treating temperatures on the microstructure and hardness of ASTM A890/A890M Gr 6A super duplex stainless steel type. Microstructure control is of extreme importance for castings, as the chemical composition and cooling during solidification inevitably provide conditions for precipitation of sigma phase. Higher hardness in these materials is directly associated to high sigma phase concentration in the microstructure, precipitated in the ferrite/austenite interface. While heat treatment temperature during solution treatment increases, the sigma phase content in the microstructure decreases and consequently, the material hardness diminishes. When the sigma phase was completely dissolved by the heat treatment, the material hardness was influenced only due to ferrite and austenite contents in the microstructure.

  3. Localization of duplex thrust-ramps by buckling: analog and numerical modelling

    NASA Astrophysics Data System (ADS)

    Liu, Shumin; Dixon, John M.

    1995-06-01

    Duplex structures in natural fold-thrust belts occur over a wide range of geometric scales. Duplex thrust ramps exhibit a regular spacing linearly related to the thickness of strata involved in the duplex. We suggest that buckling instability in layered systems can produce local stress concentrations which localize thrust ramps with regular spacing. This mechanism is demonstrated through analog (centrifuge) and numerical (finite element) modelling. Centrifuge models containing finely-laminated multilayers composed of plasticine and silicone putty (simulating rocks such as limestone and shale) are compressed from one edge; folds propagate from hinterland to foreland. As shortening continues, the lowest competent unit is thrust into a blind duplex structure by breakthrusting. The duplex develops by serial nucleation of faults from hinterland to foreland; the ramp locations are inherited from the initial buckling instability. Finite-element models based on the analog models and their natural prototypes demonstrate that stress concentrations develop in fore-limbs of anticlines within competent stratigraphie units. Models containing thrust discontinuities (at sites of calculated stress concentration) display additional stress concentrations in the forelimbs of unfaulted folds closer to the foreland. The locus of stress concentration thus propagates towards the foreland, consistent with foreland thrust propagation in nature. The location and regular spacing of ramps are inherited from early (possibly even incipient) buckle folds.

  4. Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2′-alkylated RNA monomers†

    PubMed Central

    Karmakar, Saswata; Madsen, Andreas S.; Guenther, Dale C.; Gibbons, Bradley C.; Hrdlicka, Patrick J.

    2014-01-01

    Despite advances with triplex-forming oligonucleotides, peptide nucleic acids, polyamides and - more recently - engineered proteins, there remains an urgent need for synthetic ligands that enable specific recognition of double-stranded (ds) DNA to accelerate studies aiming at detecting, regulating and modifying genes. Invaders, i.e., energetically activated DNA duplexes with interstrand zipper arrangements of intercalator-functionalized nucleotides, are emerging as an attractive approach toward this goal. Here, we characterize and compare Invaders based on 1-, 2- and 4-pyrenyl-functionalized O2′-alkylated uridine monomers X–Z by means of thermal denaturation experiments, optical spectroscopy, force-field simulations and recognition experiments using DNA hairpins as model targets. We demonstrate that Invaders with +1 interstrand zippers of X or Y monomers efficiently recognize mixed-sequence DNA hairpins with single nucleotide fidelity. Intercalator-mediated unwinding and activation of the double-stranded probe, coupled with extraordinary stabilization of probe-target duplexes (ΔTm/modification up to +14.0 °C), provides the driving force for dsDNA recognition. In contrast, Z-modified Invaders show much lower dsDNA recognition efficiency. Thus, even very conservative changes in the chemical makeup of the intercalator-functionalized nucleotides used to activate Invader duplexes, affects dsDNA-recognition efficiency of the probes, which highlights the importance of systematic structure-property studies. The insight from this study will guide future design of Invaders for applications in molecular biology and nucleic acid diagnostics. PMID:25144705

  5. STABILIZED OSCILLATOR

    DOEpatents

    Jessen, P.L.; Price, H.J.

    1958-03-18

    This patent relates to sine-wave generators and in particular describes a generator with a novel feedback circuit resulting in improved frequency stability. The generator comprises two triodes having a common cathode circuit connected to oscillate at a frequency and amplitude at which the loop galn of the circutt ls unity, and another pair of triodes having a common cathode circuit arranged as a conventional amplifier. A signal is conducted from the osciliator through a frequency selective network to the amplifier and fed back to the osciliator. The unique feature of the feedback circuit is the amplifier operates in the nonlinear portion of its tube characteristics thereby providing a relatively constant feedback voltage to the oscillator irrespective of the amplitude of its input signal.

  6. Full-Duplex Digital Communication on a Single Laser Beam

    NASA Technical Reports Server (NTRS)

    Hazzard, D. A.; MacCannell, J. A.; Lee, G.; Selves, E. R.; Moore, D.; Payne, J. A.; Garrett, C. D.; Dahlstrom, N.; Shay, T. M.

    2006-01-01

    A proposed free-space optical communication system would operate in a full-duplex mode, using a single constant-power laser beam for transmission and reception of binary signals at both ends of the free-space optical path. The system was conceived for two-way data communication between a ground station and a spacecraft in a low orbit around the Earth. It has been estimated that in this application, a data rate of 10 kb/s could be achieved at a ground-station-to-spacecraft distance of 320 km, using a laser power of only 100 mW. The basic system concept is also applicable to terrestrial free-space optical communications. The system (see figure) would include a diode laser at one end of the link (originally, the ground station) and a liquid-crystal- based retroreflecting modulator at the other end of the link (originally, the spacecraft). At the laser end, the beam to be transmitted would be made to pass through a quarter-wave plate, which would convert its linear polarization to right circular polarization. For transmission of data from the laser end to the retroreflector end, the laser beam would be modulated with subcarrier phase-shift keying (SC-PSK). The transmitted beam would then pass through an aperture- sharing element (ASE) - basically, a mirror with a hole in it, used to separate the paths of the transmitted and received light beams. The transmitted beam would continue outward through a telescope (which, in the original application, would be equipped with a spacecraft-tracking system) that would launch the transmitted beam along the free-space optical path to the retroreflector end.

  7. Use of Symmetry in Calibration of Looped Duplex DTS Measurements

    NASA Astrophysics Data System (ADS)

    Van De Giesen, N.; van der Spek, A.

    2014-12-01

    A looped duplex Distributed Temperature Sensing (DTS) deployment uses a bifilar arrangement of two optical fibres in the same cable or conduit. On one end of the cable the ends of the fibres are spliced together. The other ends are connected to a (double ended) DTS system or one end is connected to a (single ended) DTS system. A light pulse shot from one end will eventually emerge from the other end and vice versa. Back scattered Raman-shifted photons will thus be detected twice for each posistion along the cable or conduit but delayed in time by twice the distance from the symmetry point (turn around sub) divided by the speed of light in the fibre.Calibration of a DTS system requires, first and foremost that differential loss; i.e. the difference in optical attenuation between Stokes and anti-Stokes backscattered signals, is compensated for. It will be shown that residual errors due to uncompensated differential loss can only be due to the uneven part of the (non-uniform) differential loss distribution. A bifilar deployment is therefore highly insensitive to uncompensated differential loss because ageing, chemical or mechanical damage to the cable as well as thermal or mechanical strain may vary over the length of the cable but remain symmetrical and therefore even with respect to the turn around sub.By writing the (non-)uniform differential loss as the sum of an even and an uneven part it is possible to derive an equation for the residual error of a DTS temperature measurement expressed as an integral over the uneven part of the differential loss distribution only. Thus it is possible to estimate any residual temperature error under field conditions. Such a capability is especially useful where no access to one end of the cable is possible, such as is the case in borehole applications.

  8. Preoperative duplex ultrasound parameters predicting male fertility after successful varicocelectomy

    PubMed Central

    Alshehri, Fahad M.; Akbar, Mahboob H.; Altwairgi, Adel K.; AlThaqufi, Omar J.

    2015-01-01

    Objectives: To assess duplex ultrasound (DUS) parameters, and predicti the outcome of varicocele ligation in male infertility. Methods: This retrospective and follow up study was conducted at Dr. Sulaiman Al Habib Hospital, AlQassim, Saudi Arabia between January 2011 and December 2012. Eighty-two patients were selected, who presented with clinical/subclinical varicocele and male infertility. All these patients had DUS of the scrotum and underwent for low ligation varicocelectomy. These patients were followed for a period of 12-24 months after surgery for the occurrence of paternity. We reviewed pre-operative scrotal DUS of these 82 patients for the testicular size and volume, pampiniform veins caliber and duration of reflux in the dilated veins at rest, and after valsalva maneuver. These DUS parameters were correlated with the postoperative paternity rate. Results: Postoperative paternity was achieved in 18 patients (31.6%) with normal-sized testes, and in 3 patients (12%) with small size testes. The positive paternity rate was higher (38.5%) in patients with clinically detected varicocele, compared with only 16.7% of patients with subclinical varicocele (detected by ultrasound only). In addition, postoperative paternity was significantly higher in patients with bilateral varicocele (70.6%), with shunt-type varicocele (71.4%), and patients with a permanent grade of venous reflux (62.5%). Conclusion: Selection of patients for the successful paternity after varicocele repair depends mainly on DUS parameters, which includes normal size testicles with shunt type of bilateral varicocele and continuous reflux. PMID:26620986

  9. Direct versus limited-step reconstitution reveals key features of an RNA hairpin-stabilized paused transcription complex.

    PubMed

    Kyzer, Scotty; Ha, Kook Sun; Landick, Robert; Palangat, Murali

    2007-06-29

    We have identified minimal nucleic acid scaffolds capable of reconstituting hairpin-stabilized paused transcription complexes when incubated with RNAP either directly or in a limited step reconstitution assay. Direct reconstitution was achieved using a 29-nucleotide (nt) RNA whose 3'-proximal 9-10 nt pair to template DNA within an 11-nt noncomplementary bubble of a 39-bp duplex DNA; the 5'-proximal 18 nt of RNA forms the his pause RNA hairpin. Limited-step reconstitution was achieved on the same DNAs using a 27-nt RNA that can be 3'-labeled during reconstitution and then extended 2 nt past the pause site to assay transcriptional pausing. Paused complexes formed by either method recapitulated key features of a promoter-initiated, hairpin-stabilized paused complex, including a slow rate of pause escape, resistance to transcript cleavage and pyrophosphorolysis, and enhancement of pausing by the elongation factor NusA. These findings establish that RNA upstream from the pause hairpin and pyrophosphate are not essential for pausing and for NusA action. Reconstitution of the his paused transcription complex provides a valuable tool for future studies of protein-nucleic interactions involved in transcriptional pausing. PMID:17502377

  10. The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation

    PubMed Central

    Yamaguchi, Hiroshi; Šebera, Jakub; Kondo, Jiro; Oda, Shuji; Komuro, Tomoyuki; Kawamura, Takuya; Dairaku, Takenori; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Burda, Jaroslav V.; Kojima, Chojiro; Sychrovský, Vladimír; Tanaka, Yoshiyuki

    2014-01-01

    We have determined the three-dimensional (3D) structure of DNA duplex that includes tandem HgII-mediated T–T base pairs (thymine–HgII–thymine, T–HgII–T) with NMR spectroscopy in solution. This is the first 3D structure of metallo-DNA (covalently metallated DNA) composed exclusively of ‘NATURAL’ bases. The T–HgII–T base pairs whose chemical structure was determined with the 15N NMR spectroscopy were well accommodated in a B-form double helix, mimicking normal Watson–Crick base pairs. The Hg atoms aligned along DNA helical axis were shielded from the bulk water. The complete dehydration of Hg atoms inside DNA explained the positive reaction entropy (ΔS) for the T–HgII–T base pair formation. The positive ΔS value arises owing to the HgII dehydration, which was approved with the 3D structure. The 3D structure explained extraordinary affinity of thymine towards HgII and revealed arrangement of T–HgII–T base pairs in metallo-DNA. PMID:24371287

  11. Development and validation of fast duplex real-time PCR assays based on SYBER Green florescence for detection of bovine and poultry origins in feedstuffs.

    PubMed

    Safdar, Muhammad; Junejo, Yasmeen

    2015-04-15

    SYBR duplex real-time polymerase chain reaction (SDRT-PCR) with melting curve analysis was developed that can unite the reward of multiplex PCR with real-time PCR to recognize animal genes rapidly in feedstuffs. The method merges the use of bovine (Bos taurus) and poultry (Gallus gallus) specific primers that amplify small fragments (amplicons <200 base pairs) of the mitochondrial gene. Appropriate mixtures of bovine and poultry heat treated meat DNAs were used to develop the assay. Gene products of bovine and poultry were produced two distinct melting peaks simultaneously at 79.5 °C and 87.5 °C, respectively. Multiplex analysis of the reference feed samples showed that the detection limit of the assay was 0.001% for bovine and poultry species. Based upon the assay results it has been concluded that SDRT-PCR assay might be an efficient tool for the verification of species origin in feedstuffs. PMID:25466073

  12. Rapid method to detect duplex formation in sequencing by hybridization methods

    DOEpatents

    Mirzabekov, Andrei Darievich; Timofeev, Edward Nikolaevich; Florentiev, Vladimer Leonidovich; Kirillov, Eugene Vladislavovich

    1999-01-01

    A method for determining the existence of duplexes of oligonucleotide complementary molecules is provided whereby a plurality of immobilized oligonucleotide molecules, each of a specific length and each having a specific base sequence, is contacted with complementary, single stranded oligonucleotide molecules to form a duplex so as to facilitate intercalation of a fluorescent dye between the base planes of the duplex. The invention also provides for a method for constructing oligonucleotide matrices comprising confining light sensitive fluid to a surface, exposing said light-sensitive fluid to a light pattern so as to cause the fluid exposed to the light to coalesce into discrete units and adhere to the surface; and contacting each of the units with a set of different oligonucleotide molecules so as to allow the molecules to disperse into the units.

  13. Duplex in the assessment of the free radial forearm flaps: Is it time to change practice?

    PubMed

    Ganesan, K; Stead, L; Smith, A B; Ong, T K; Mitchell, D A; Kanatas, A N

    2010-09-01

    Radial forearm free flaps (RFFFs) are safe, but critical ischaemia of the hand has been described and is catastrophic. Every effort should therefore be made to improve the safety margin even further. Colour flow duplex ultrasound (US) is a simple, non-invasive and effective assessment tool. We compared it with Allen's test to identify serious vascular anomalies. We studied 121 patients who were listed to have a RFFF harvested, all of whom had both duplex US assessment and Allen's testing of the selected arm. The significance of differences in proportions was assessed using McNemar's test. Five of the 121 patients had an alternative flap selected as a consequence of the duplex assessment. A single flap failed. There were no ischaemic vascular complications that affected the hand.

  14. Experimental Analysis and Modelling of Fe-Mn-Al-C Duplex Steel Mechanical Behaviour

    SciTech Connect

    Shiekhelsouk, M. N.; Favier, V.; Cherkaoui, M.; Inal, K.; Bouaziz, O.

    2007-04-07

    A new variety of duplex steels with high content of manganese and aluminum has been elaborated in Arcelor Research. These steels contain two phases: austenite and ferrite combining the best features of austenitic and ferritic steels. In this work, four duplex steels with different chemical composition and phase volume fraction are studied. The evolution of internal stresses for the two phases has been determined by X-ray diffraction during an in situ tensile test. These measurements results were used to determine the mechanical behaviour of the duplex steel using a micromechanical approach by scale transition for tensile tests. Though a good agreement between experiments and simulations is found at the macroscopic level, the calculated internal stresses of the austenitic phase do not match experimental results. These discrepancies are attributed to (i) a bad estimation of the austenite yield stress or (ii) the presence of kinematic hardening in the austenitic phase. A new step is then proposed to test these two hypotheses.

  15. Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes.

    PubMed

    Iwasaki, Shintaro; Kobayashi, Maki; Yoda, Mayuko; Sakaguchi, Yuriko; Katsuma, Susumu; Suzuki, Tsutomu; Tomari, Yukihide

    2010-07-30

    Small silencing RNAs--small interfering RNAs (siRNAs) or microRNAs (miRNAs)--direct posttranscriptional gene silencing of their mRNA targets as guides for the RNA-induced silencing complex (RISC). Both siRNAs and miRNAs are born double stranded. Surprisingly, loading these small RNA duplexes into Argonaute proteins, the core components of RISC, requires ATP, whereas separating the two small RNA strands within Argonaute does not. Here we show that the Hsc70/Hsp90 chaperone machinery is required to load small RNA duplexes into Argonaute proteins, but not for subsequent strand separation or target cleavage. We envision that the chaperone machinery uses ATP and mediates a conformational opening of Ago proteins so that they can receive bulky small RNA duplexes. Our data suggest that the chaperone machinery may serve as the driving force for the RISC assembly pathway.

  16. Sequential and spatial organization of metal complexes inside a peptide duplex.

    PubMed

    Yamada, Yasuyuki; Kubota, Takayuki; Nishio, Motoki; Tanaka, Kentaro

    2014-04-30

    To generate integrated organized molecular properties, multiple molecular components are required to be assembled into the molecular system with sequential and spatial accuracy in accordance with the design of the molecular assembly. Herein, we present a novel programmable synthesis of a cofacially stacked porphyrin array via repetitive construction of a peptide duplex. We designed and synthesized a novel porphyrin having two artificial amino acid moieties at the trans meso-positions. The amino acid moieties can be connected with another porphyrin unit by repetitive doubly coupling reactions to afford the peptide duplex bridged by the porphyrins. In the duplex, the porphyrin units are stacked cofacially, and the efficient electronic communication among the arrayed porphyrin units was characterized by split redox waves in the cyclic voltammograms. We also demonstrated the three different square-planar metal ions, namely Cu(2+), Ni(2+), and Pd(2+), were arranged inside the ladder-type porphyrin array in a programmable fashion. PMID:24735178

  17. Final Report, Volume 3, Guidance Document for the Evaluation of Cast Super Duplex Stainless Steel

    SciTech Connect

    Hariharan, Vasudevan; Lundin, Carl, D.

    2005-09-30

    Volume 3 comprises of the Development of Qualification Standards for Cast Super Duplex Stainless Steel (A890-5A) which is equivalent to wrought 2507. The objective of this work was to determine the suitability of ASTM A923 Standard Test methods for Detecting Detrimental Intermetallic Phase in Duplex Austenitic-Ferritic Stainless Steels for 25 Cr Cast Super Duplex Stainless Steels (ASTM A890-5A). The various tests which were carried out were ASTM A923 Test Method A, B and C (Sodium Hydroxide Etch Test, Charpy Impact Test and Ferric Chloride Corrosion Test), ferrite measurement using Feritscope{reg_sign}, ASTM E562 Manual Point Count Method and X-Ray Diffraction, hardness measurement using Rockwell B and C and microstructural analysis using SEM and EDS.

  18. Final Report, Volume 3, Guidance Document for the Evaluation of Cast Super Duplex Stainless Steel

    SciTech Connect

    Hariharan, Vasudevan; Lundin, Carl, W.

    2005-09-30

    Volume 3 is comprised of the Development of Qualification Standards for Cast Super Duplex Stainless Steel (A890-5A) which is equivalent to wrought 2507. The objective of this work was to determine the suitability of ASTM A923 Standard Test methods for Detecting Detrimental Intermetallic Phase in Duplex Austenitic-Ferritic Stainless Steels for 25 Cr Cast Super Duplex Stainless Steels (ASTM A890-5A). The various tests which were carried out were ASTM A923 Test Method A, B and C (Sodium Hydroxide Etch Test, Charpy Impact Test and Ferric Chloride Corrosion Test), ferrite measurement using Feritscope®, ASTM E562 Manual Point Count Method and X-Ray Diffraction, hardness measurement using Rockwell B and C and microstructural analysis using SEM and EDS.

  19. Primordial nuggets survival and QCD pairing

    NASA Astrophysics Data System (ADS)

    Lugones, G.; Horvath, J. E.

    2004-03-01

    We reexamine the problem of boiling and surface evaporation of quark nuggets in the cosmological quark-hadron transition with the explicit consideration of pairing between quarks in a color-flavor locked state. Assuming that primordial quark nuggets are actually formed, we analyze the consequences of pairing on the rates of boiling and surface evaporation in order to determine whether they could have survived with substantial mass. We find a substantial quenching of the evaporation+boiling processes, which suggests the survival of primordial nuggets for the currently considered range of the pairing gap Δ. Boiling is shown to depend on the competition of an increased stability window and the suppression of the rate, and is not likely to dominate the destruction of the nuggets. If surface evaporation dominates, the fate of the nuggets depends on the features of the initial mass spectrum of the nuggets, their evaporation rate, and the value of the pairing gap, as shown and discussed in the text.

  20. Multiprocessor switch with selective pairing

    DOEpatents

    Gara, Alan; Gschwind, Michael K; Salapura, Valentina

    2014-03-11

    System, method and computer program product for a multiprocessing system to offer selective pairing of processor cores for increased processing reliability. A selective pairing facility is provided that selectively connects, i.e., pairs, multiple microprocessor or processor cores to provide one highly reliable thread (or thread group). Each paired microprocessor or processor cores that provide one highly reliable thread for high-reliability connect with a system components such as a memory "nest" (or memory hierarchy), an optional system controller, and optional interrupt controller, optional I/O or peripheral devices, etc. The memory nest is attached to a selective pairing facility via a switch or a bus

  1. Prospective very young asteroid pairs

    NASA Astrophysics Data System (ADS)

    Galád, A.; Vokrouhlický, D.; Zizka, J.

    2014-07-01

    Several tens of asteroid pairs can be discerned from the background main-belt asteroids. The majority of them are thought to have formed within only the last few 10^6 yr. The youngest recognized pairs have formed more than ≈ 10 kyr ago. As some details of pair formation are still not understood well, the study of young pairs is of great importance. It is mainly because the conditions at the time of the pair formation could be deduced much more reliably for young pairs. For example, space weathering on the surfaces of the components, or changes in their rotational properties (in spin rates, tumbling, coordinates of rotational pole) could be negligible since the formation of young pairs. Also, possible strong perturbations by main-belt bodies on pair formation can be reliably studied only for extremely young pairs. Some pairs can quickly blend in with the background asteroids, so even the frequency of asteroid pair formation could be determined more reliably based on young pairs (though only after a statistically significant sample is at disposal). In our regular search for young pairs in the growing asteroid database, only multiopposition asteroids with very similar orbital and proper elements are investigated. Every pair component is represented by a number of clones within orbital uncertainties and drifting in semimajor axis due to the Yarkovsky effect. We found that, if the previously unrecognized pairs (87887) 2000 SS_{286} - 2002 AT_{49} and (355258) 2007 LY_{4} - 2013AF_{40} formed at the recent very close approach of their components, they could become the youngest known pairs. In both cases, the relative encounter velocities of the components were only ˜ 0.1 m s^{-1}. However, the minimum distances between some clones are too large and a few clones of the latter pair did not encounter recently (within ≈ 10 kyr). The age of some prospective young pairs cannot be determined reliably without improved orbital properties (e.g., the second component of a pair

  2. A Commentary on "Updating the Duplex Design for Test-Based Accountability in the Twenty-First Century"

    ERIC Educational Resources Information Center

    Brandt, Steffen

    2010-01-01

    This article presents the author's commentary on "Updating the Duplex Design for Test-Based Accountability in the Twenty-First Century," in which Isaac I. Bejar and E. Aurora Graf propose the application of a test design--the duplex design (which was proposed in 1988 by Bock and Mislevy) for application in current accountability assessments.…

  3. A one-step duplex rRT-PCR assay for the simultaneous detection of duck hepatitis A virus genotypes 1 and 3.

    PubMed

    Hu, Qin; Zhu, Dekang; Ma, Guangpeng; Cheng, Anchun; Wang, Mingshu; Chen, Shun; Jia, Renyong; Liu, Mafeng; Sun, Kunfeng; Yang, Qiao; Wu, Ying; Chen, Xiaoyue

    2016-10-01

    Duck hepatitis A virus (DHAV) is a highly infectious pathogen that causes significant bleeding lesions in the viscera of ducklings less than 3 weeks old. There are three serotypes of DHAV: serotype 1 (DHAV-1), serotype 2 (DHAV-2) and serotype 3 (DHAV-3). These serotypes have no cross-antigenicity with each other. To establish an rRT-PCR assay for the rapid detection of a mixed infection of DHAV-1 and DHAV-3, two pairs of primers and a pair of matching TaqMan probes were designed based on conserved regions of DHAV-1 VP0 and DHAV-3 VP3. Finally, we established a one-step duplex rRT-PCR assay with high specificity and sensitivity for the simultaneous detection of DHAV-1 and DHAV-3. This method showed no cross-antigenicity with the other pathogens tested, including duck plague virus, Muscovy duck parvovirus, Riemerella anatipestifer, and pathogenic E. coli from ducks. Sensitivity tests identified the minimum detection limits of this method as 98 (DHAV-1) and 10 (DHAV-3) copies/reaction. To validate the method, thirty-eight clinical samples and thirty artificially infected samples collected from dead duck embryos were studied. Thirty-seven samples were positive for DHAV-1, seventeen samples were positive for DHAV-3, and fourteen samples were positive for a mixed infection using the duplex rRT-PCR method. The method established in this study is specific, sensitive, convenient and timesaving and is a powerful tool for detecting DHAV-1, DHAV-3, and their mixed infection and for conducting surveys of pandemic virus strains. PMID:27435338

  4. A one-step duplex rRT-PCR assay for the simultaneous detection of duck hepatitis A virus genotypes 1 and 3.

    PubMed

    Hu, Qin; Zhu, Dekang; Ma, Guangpeng; Cheng, Anchun; Wang, Mingshu; Chen, Shun; Jia, Renyong; Liu, Mafeng; Sun, Kunfeng; Yang, Qiao; Wu, Ying; Chen, Xiaoyue

    2016-10-01

    Duck hepatitis A virus (DHAV) is a highly infectious pathogen that causes significant bleeding lesions in the viscera of ducklings less than 3 weeks old. There are three serotypes of DHAV: serotype 1 (DHAV-1), serotype 2 (DHAV-2) and serotype 3 (DHAV-3). These serotypes have no cross-antigenicity with each other. To establish an rRT-PCR assay for the rapid detection of a mixed infection of DHAV-1 and DHAV-3, two pairs of primers and a pair of matching TaqMan probes were designed based on conserved regions of DHAV-1 VP0 and DHAV-3 VP3. Finally, we established a one-step duplex rRT-PCR assay with high specificity and sensitivity for the simultaneous detection of DHAV-1 and DHAV-3. This method showed no cross-antigenicity with the other pathogens tested, including duck plague virus, Muscovy duck parvovirus, Riemerella anatipestifer, and pathogenic E. coli from ducks. Sensitivity tests identified the minimum detection limits of this method as 98 (DHAV-1) and 10 (DHAV-3) copies/reaction. To validate the method, thirty-eight clinical samples and thirty artificially infected samples collected from dead duck embryos were studied. Thirty-seven samples were positive for DHAV-1, seventeen samples were positive for DHAV-3, and fourteen samples were positive for a mixed infection using the duplex rRT-PCR method. The method established in this study is specific, sensitive, convenient and timesaving and is a powerful tool for detecting DHAV-1, DHAV-3, and their mixed infection and for conducting surveys of pandemic virus strains.

  5. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays

    NASA Technical Reports Server (NTRS)

    Urakawa, Hidetoshi; El Fantroussi, Said; Smidt, Hauke; Smoot, James C.; Tribou, Erik H.; Kelly, John J.; Noble, Peter A.; Stahl, David A.

    2003-01-01

    The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.

  6. Conformational Variants of Duplex DNA Correlated with Cytosine-rich Chromosomal Fragile Sites*S⃞

    PubMed Central

    Tsai, Albert G.; Engelhart, Aaron E.; Hatmal, Ma'mon M.; Houston, Sabrina I.; Hud, Nicholas V.; Haworth, Ian S.; Lieber, Michael R.

    2009-01-01

    We found that several major chromosomal fragile sites in human lymphomas, including the bcl-2 major breakpoint region, bcl-1 major translocation cluster, and c-Myc exon 1-intron 1 boundary, contain distinctive sequences of consecutive cytosines exhibiting a high degree of reactivity with the structure-specific chemical probe bisulfite. To assess the inherent structural variability of duplex DNA in these regions and to determine the range of structures reactive to bisulfite, we have performed bisulfite probing on genomic DNA in vitro and in situ; on duplex DNA in supercoiled and linearized plasmids; and on oligonucleotide DNA/DNA and DNA/2′-O-methyl RNA duplexes. Bisulfite is significantly more reactive at the frayed ends of DNA duplexes, which is expected given that bisulfite is an established probe of single-stranded DNA. We observed that bisulfite also distinguishes between more subtle sequence/structural differences in duplex DNA. Supercoiled plasmids are more reactive than linear DNA; and sequences containing consecutive cytosines, namely GGGCCC, are more reactive than those with alternating guanine and cytosine, namely GCGCGC. Circular dichroism and x-ray crystallography show that the GGGCCC sequence forms an intermediate B/A structure. Molecular dynamics simulations also predict an intermediate B/A structure for this sequence, and probe calculations suggest greater bisulfite accessibility of cytosine bases in the intermediate B/A structure over canonical B- or A-form DNA. Electrostatic calculations reveal that consecutive cytosine bases create electropositive patches in the major groove, predicting enhanced localization of the bisulfite anion at homo-C tracts over alternating G/C sequences. These characteristics of homo-C tracts in duplex DNA may be associated with DNA-protein interactions in vivo that predispose certain genomic regions to chromosomal fragility. PMID:19106104

  7. Characterizing the bending and flexibility induced by bulges in DNA duplexes

    NASA Astrophysics Data System (ADS)

    Schreck, John S.; Ouldridge, Thomas E.; Romano, Flavio; Louis, Ard A.; Doye, Jonathan P. K.

    2015-04-01

    Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages, two-dimensional arrays, and ribbons, is a bulged duplex, that is, two helical segments that connect at a bulge loop. We use a coarse-grained model of DNA to characterize such bulged duplexes. We find that this motif can adopt structures belonging to two main classes: one where the stacking of the helices at the center of the system is preserved, the geometry is roughly straight, and the bulge is on one side of the duplex and the other where the stacking at the center is broken, thus allowing this junction to act as a hinge and increasing flexibility. Small loops favor states where stacking at the center of the duplex is preserved, with loop bases either flipped out or incorporated into the duplex. Duplexes with longer loops show more of a tendency to unstack at the bulge and adopt an open structure. The unstacking probability, however, is highest for loops of intermediate lengths, when the rigidity of single-stranded DNA is significant and the loop resists compression. The properties of this basic structural motif clearly correlate with the structural behavior of certain nano-scale objects, where the enhanced flexibility associated with larger bulges has been used to tune the self-assembly product as well as the detailed geometry of the resulting nanostructures. We further demonstrate the role of bulges in determining the structure of a "Z-tile," a basic building block for nanostructures.

  8. Multiple origins of asteroid pairs

    NASA Astrophysics Data System (ADS)

    Jacobson, Seth A.

    2016-01-01

    Rotationally fissioned asteroids produce unbound asteroid pairs that have very similar heliocentric orbits. Backward integration of their current heliocentric orbits provides an age of closest proximity that can be used to date the rotational fission event. Most asteroid pairs follow a predicted theoretical relationship between the primary spin period and the mass ratio of the two pair members that is a direct consequence of the YORP-induced rotational fission hypothesis. If the progenitor asteroid has strength, asteroid pairs may have higher mass ratios or faster rotating primaries. However, the process of secondary fission leaves the originally predicted trend unaltered. We also describe the characteristics of pair members produced by four alternative routes from a rotational fission event to an asteroid pair. Unlike direct formation from the event itself, the age of closest proximity of these pairs cannot generally be used to date the rotational fission event since considerable time may have passed.

  9. Effect of sulphur crosslinking on the stability and transition of triple helical DNA.

    PubMed

    Srivastava, S; Gupta, V D; Singh, S

    1999-06-01

    In continuation to our work on order-order and order-disorder transition in triple stranded DNA when it is bounded to netropsin, we report in this communication the stabilizing/destabilizing effect of disulphide linkage on the phase dynamics of the triplex using the amended Zimm-Bragg theory. It is observed that in contrast to the sequential triplex-->duplex -->single strand melting of the uncrosslinked triplex, crosslinking causes the triplex state to melt directly to the single stranded state, with no apparent intermediary of a duplex state. Since there is no overall difference in the enthalpy of crosslinked and uncrosslinked triplexes, the transition is entropy driven.

  10. 'Passive-roof' duplex geometry in the frontal structures of the Kirthar and Sulaiman mountain belts, Pakistan

    NASA Astrophysics Data System (ADS)

    Banks, C. J.; Warburton, J.

    Exploration for hydrocarbons over the past few years has greatly improved our understanding of the geometry of frontal mountain belt structures. In this study we introduce and discuss the concept of the 'Passive-roof duplex', using as the main example the Kirthar and Sulaiman Ranges in the Baluchistan Province of Pakistan. Structures similar to those described here have been recognized previously in other mountain belts, and they appear to exist as a common feature in many more frontal regions of mountain belts. Our example of a Passive-roof duplex which we describe from Pakistan is compared briefly with similar structures reported by others. The Passive-roof duplex is here defined as a duplex whose roof thrust has backthrust sense ( Passive-roof thrust) and whose roof sequence (those rocks lying above the roof thrust) remains relatively 'stationary' during foreland directed piggy-back style propagation of horses within the duplex.

  11. A case report of laparoscopic ipsilateral ureteroureterostomy in children with renal duplex

    PubMed Central

    Wong, Yuen Shan; Tam, Yuk Him; Pang, Kristine Kit Yi

    2016-01-01

    We report on two children aged 2 and 6 years, who underwent laparoscopic ipsilateral ureteroureterostomy for their renal duplex anomalies. Both patients had complete duplex and were investigated by ultrasound, micturating cystourethrogram, magnetic resonance urography, and radioisotope scan. One patient had high-grade vesicoureteral reflux to lower moiety complicated with recurrent urinary tract infections, while the other had obstruction to upper moiety due to ectopic ureter. The pathological moieties of both patients were functional. Both patients underwent laparoscopic ipsilateral ureteroureterostomy uneventfully without any intraoperative complications. Postoperative imagings confirmed successful outcomes after surgery. PMID:27014651

  12. Stabilization of i-motif structures by 2'-β-fluorination of DNA.

    PubMed

    Assi, Hala Abou; Harkness, Robert W; Martin-Pintado, Nerea; Wilds, Christopher J; Campos-Olivas, Ramón; Mittermaier, Anthony K; González, Carlos; Damha, Masad J

    2016-06-20

    i-Motifs are four-stranded DNA structures consisting of two parallel DNA duplexes held together by hemi-protonated and intercalated cytosine base pairs (C:CH(+)). They have attracted considerable research interest for their potential role in gene regulation and their use as pH responsive switches and building blocks in macromolecular assemblies. At neutral and basic pH values, the cytosine bases deprotonate and the structure unfolds into single strands. To avoid this limitation and expand the range of environmental conditions supporting i-motif folding, we replaced the sugar in DNA by 2-deoxy-2-fluoroarabinose. We demonstrate that such a modification significantly stabilizes i-motif formation over a wide pH range, including pH 7. Nuclear magnetic resonance experiments reveal that 2-deoxy-2-fluoroarabinose adopts a C2'-endo conformation, instead of the C3'-endo conformation usually found in unmodified i-motifs. Nevertheless, this substitution does not alter the overall i-motif structure. This conformational change, together with the changes in charge distribution in the sugar caused by the electronegative fluorine atoms, leads to a number of favorable sequential and inter-strand electrostatic interactions. The availability of folded i-motifs at neutral pH will aid investigations into the biological function of i-motifs in vitro, and will expand i-motif applications in nanotechnology. PMID:27166371

  13. Stabilization of i-motif structures by 2′-β-fluorination of DNA

    PubMed Central

    Assi, Hala Abou; Harkness, Robert W.; Martin-Pintado, Nerea; Wilds, Christopher J.; Campos-Olivas, Ramón; Mittermaier, Anthony K.; González, Carlos; Damha, Masad J.

    2016-01-01

    i-Motifs are four-stranded DNA structures consisting of two parallel DNA duplexes held together by hemi-protonated and intercalated cytosine base pairs (C:CH+). They have attracted considerable research interest for their potential role in gene regulation and their use as pH responsive switches and building blocks in macromolecular assemblies. At neutral and basic pH values, the cytosine bases deprotonate and the structure unfolds into single strands. To avoid this limitation and expand the range of environmental conditions supporting i-motif folding, we replaced the sugar in DNA by 2-deoxy-2-fluoroarabinose. We demonstrate that such a modification significantly stabilizes i-motif formation over a wide pH range, including pH 7. Nuclear magnetic resonance experiments reveal that 2-deoxy-2-fluoroarabinose adopts a C2′-endo conformation, instead of the C3′-endo conformation usually found in unmodified i-motifs. Nevertheless, this substitution does not alter the overall i-motif structure. This conformational change, together with the changes in charge distribution in the sugar caused by the electronegative fluorine atoms, leads to a number of favorable sequential and inter-strand electrostatic interactions. The availability of folded i-motifs at neutral pH will aid investigations into the biological function of i-motifs in vitro, and will expand i-motif applications in nanotechnology. PMID:27166371

  14. Stereo Pair, Honolulu, Oahu

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Honolulu, on the island of Oahu, is a large and growing urban area. This stereoscopic image pair, combining a Landsat image with topography measured by the Shuttle Radar Topography Mission (SRTM), shows how topography controls the urban pattern. This color image can be viewed in 3-D by viewing the left image with the right eye and the right image with the left eye (cross-eyed viewing), or by downloading and printing the image pair, and viewing them with a stereoscope.

    Features of interest in this scene include Diamond Head (an extinct volcano near the bottom of the image), Waikiki Beach (just above Diamond Head), the Punchbowl National Cemetary (another extinct volcano, near the image center), downtown Honolulu and Honolulu harbor (image left-center), and offshore reef patterns. The slopes of the Koolau mountain range are seen in the right half of the image. Clouds commonly hang above ridges and peaks of the Hawaiian Islands, but in this synthesized stereo rendition appear draped directly on the mountains. The clouds are actually about 1000 meters (3300 feet) above sea level.

    This stereoscopic image pair was generated using topographic data from the Shuttle Radar Topography Mission, combined with a Landsat 7 Thematic Mapper image collected at the same time as the SRTM flight. The topography data were used to create two differing perspectives, one for each eye. When stereoscopically merged, the result is a vertically exaggerated view of the Earth's surface in its full three dimensions. The United States Geological Survey's Earth Resources Observations Systems (EROS) Data Center, Sioux Falls, South Dakota, provided the Landsat data.

    The Shuttle Radar Topography Mission (SRTM), launched on February 11, 2000, used the same radar instrument that comprised the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR-C/X-SAR) that flew twice on the Space Shuttle Endeavour in 1994. The mission was designed to collect three-dimensional measurements of the

  15. Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.

    SciTech Connect

    Robinson, H.; Gao, Y.-G.; Sanishvili, R.; Joachimiak, A.; Wang, A. H.-J.; Univ. of Illinois; Northwestern Univ.

    2000-01-01

    Magnesium ions play important roles in the structure and function of nucleic acids. Whereas the tertiary folding of RNA often requires magnesium ions binding to tight places where phosphates are clustered, the molecular basis of the interactions of magnesium ions with RNA helical regions is less well understood. We have refined the crystal structures of four decamer oligonucleotides, d(ACCGGCCGGT), r(GCG)d(TATACGC), r(GC)d(GTATACGC) and r(G)d(GCGTATACGC) with bound hexahydrated magnesium ions at high resolution. The structures reveal that A-form nucleic acid has characteristic [Mg(H2O)6]2+ binding modes. One mode has the ion binding in the deep major groove of a GpN step at the O6/N7 sites of guanine bases via hydrogen bonds. Our crystallographic observations are consistent with the recent NMR observations that in solution [Co(NH3)6]3+, a model ion of [Mg(H2O)6]2+, binds in an identical manner. The other mode involves the binding of the ion to phosphates, bridging across the outer mouth of the narrow major groove. These [Mg(H2O)6]2+ ions are found at the most negative electrostatic potential regions of A-form duplexes. We propose that these two binding modes are important in the global charge neutralization, and therefore stability, of A-form duplexes.

  16. Stereo Pair, Pasadena, California

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This stereoscopic image pair is a perspective view that shows the western part of the city of Pasadena, California, looking north toward the San Gabriel Mountains. Portions of the cities of Altadena and La Canada Flintridge are also shown. The cluster of large buildings left of center, at the base of the mountains, is the Jet Propulsion Laboratory. This image shows the power of combining data from different sources to create planning tools to study problems that affect large urban areas. In addition to the well-known earthquake hazards, Southern California is affected by a natural cycle of fire and mudflows. Data shown in this image can be used to predict both how wildfires spread over the terrain and how mudflows are channeled down the canyons.

    The image was created from three datasets: the Shuttle Radar Topography Mission (SRTM) supplied the elevation, U. S. Geological Survey digital aerial photography provided the image detail, and the Landsat Thematic Mapper provided the color. The United States Geological Survey's Earth Resources Observations Systems (EROS) Data Center, Sioux Falls, South Dakota, provided the Landsat data and the aerial photography. The image can be viewed in 3-D by viewing the left image with the right eye and the right image with the left eye (cross-eyed viewing), or by downloading and printing the image pair, and viewing them with a stereoscope.

    The Shuttle Radar Topography Mission (SRTM), launched on February 11, 2000, used the same radar instrument that comprised the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR-C/X-SAR) that flew twice on the Space Shuttle Endeavour in 1994. The mission was designed to collect three-dimensional measurements of the Earth's surface. To collect the 3-D data, engineers added a 60-meter-long (200-foot) mast, an additional C-band imaging antenna and improved tracking and navigation devices. The mission is a cooperative project between the National Aeronautics and Space Administration

  17. Numerically optimal Runge-Kutta pairs with interpolants

    NASA Astrophysics Data System (ADS)

    Verner, J.

    2010-03-01

    Explicit Runge-Kutta pairs are known to provide efficient solutions to initial value differential equations with inexpensive derivative evaluations. Two criteria for selection are proposed with a view to deriving pairs of all orders 6(5) to 9(8) which minimize computation while achieving a user-specified accuracy. Coefficients of improved pairs, their stability regions and coefficients of appended optimal interpolatory Runge-Kutta formulas are provided on the author's website (www.math.sfu.ca/~jverner). This note reports results of tests on these pairs to illustrate their effectiveness in solving nonstiff initial value problems. These pairs and interpolants may be used for implementation, or else to provide comparison targets for other new types of methods such as explicit general linear methods.

  18. Frustrated Lewis pairs: metal-free hydrogen activation and more.

    PubMed

    Stephan, Douglas W; Erker, Gerhard

    2010-01-01

    Sterically encumbered Lewis acid and Lewis base combinations do not undergo the ubiquitous neutralization reaction to form "classical" Lewis acid/Lewis base adducts. Rather, both the unquenched Lewis acidity and basicity of such sterically "frustrated Lewis pairs (FLPs)" is available to carry out unusual reactions. Typical examples of frustrated Lewis pairs are inter- or intramolecular combinations of bulky phosphines or amines with strongly electrophilic RB(C(6)F(5))(2) components. Many examples of such frustrated Lewis pairs are able to cleave dihydrogen heterolytically. The resulting H(+)/H(-) pairs (stabilized for example, in the form of the respective phosphonium cation/hydridoborate anion salts) serve as active metal-free catalysts for the hydrogenation of, for example, bulky imines, enamines, or enol ethers. Frustrated Lewis pairs also react with alkenes, aldehydes, and a variety of other small molecules, including carbon dioxide, in cooperative three-component reactions, offering new strategies for synthetic chemistry. PMID:20025001

  19. Pygmy stars: first pair.

    PubMed

    Zwicky, F

    1966-07-01

    The binary LP 101-15/16 having the proper motion of 1.62 seconds of arc per year has been studied with the prime-focus spectrograph of the 200-inch (508 cm) telescope. Indications are that LP 101-15/16 is the first pair of pygmy stars ever discovered. One of its components, LP 101-16, is probably a blue pygmy star which is at least four magnitudes fainter than the ordinary white dwarfs. Also, two of the Balmer lines in absorption appear to be displaced toward the red by amounts which indicate the existence of an Einstein gravitational red shift corresponding to about 1000 km sec-1. On the other hand LP 101-15 is red and shows an entirely new type of spectrum, which suggests that it may be a first representative of a type of red pygmy star which is 2.5 magnitudes fainter than the M-type dwarf stars of the main sequence. PMID:17730606

  20. Pygmy stars: first pair.

    PubMed

    Zwicky, F

    1966-07-01

    The binary LP 101-15/16 having the proper motion of 1.62 seconds of arc per year has been studied with the prime-focus spectrograph of the 200-inch (508 cm) telescope. Indications are that LP 101-15/16 is the first pair of pygmy stars ever discovered. One of its components, LP 101-16, is probably a blue pygmy star which is at least four magnitudes fainter than the ordinary white dwarfs. Also, two of the Balmer lines in absorption appear to be displaced toward the red by amounts which indicate the existence of an Einstein gravitational red shift corresponding to about 1000 km sec-1. On the other hand LP 101-15 is red and shows an entirely new type of spectrum, which suggests that it may be a first representative of a type of red pygmy star which is 2.5 magnitudes fainter than the M-type dwarf stars of the main sequence.

  1. DNA adduct-induced stabilization of slipped frameshift intermediates within repetitive sequences: implications for mutagenesis.

    PubMed Central

    Garcia, A; Lambert, I B; Fuchs, R P

    1993-01-01

    Chemical carcinogens such as the aromatic amide 2-acetylaminofluorene (AAF) are known to induce -1 frameshift mutation hotspots at repetitive sequences. This mutagenesis pathway was suggested to involve slipped intermediates formed during replication. To investigate the stability and structure of such intermediates we have constructed DNA duplexes containing single AAF adducts within a run of three guanine residues. The strand complementary to that bearing the AAF adducts contained either the wild-type sequence (homoduplexes) or lacked one cytosine directly opposite the run of guanines containing the AAF adduct and thus modeled the putative slipped mutagenic intermediates (SMIs). The melting temperature of AAF-modified homoduplexes or the unmodified SMI was reduced by approximately 10 degrees C relative to the unmodified homoduplex. Surprisingly, AAF adducts stabilized the SMIs as evidenced by an increase in melting temperature to a level approaching that of the unmodified homoduplex. The chemical probes hydroxylamine and bromoacetaldehyde were strongly reactive toward cytosine residues opposite the adduct in AAF-modified homoduplexes, indicating adduct-induced denaturation. In contrast, no cytosine reactivities were observed in the AAF-modified SMIs, suggesting that the two cytosines were paired with unmodified guanines. Use of diethyl pyrocarbonate to probe the guanine residues showed that all three guanines in the unmodified SMI adopted a transient single-stranded state which was delocalized along the repetitive sequence. However, when an AAF adduct was present, reduced diethyl pyrocarbonate reactivity at guanines adjacent to the adduct in AAF-modified SMIs reflected localization of the bulge to the adducted base. Our results suggest that AAF exerts a local denaturing and destabilizing effect within the homoduplex which is alleviated by the formation of a bulge. The stabilization by the AAF adduct of the SMIs may contribute to the dramatic increase in -1

  2. Dynamical evolution of comet pairs

    NASA Astrophysics Data System (ADS)

    Sosa, Andrea; Fernández, Julio A.

    2016-10-01

    Some Jupiter family comets in near-Earth orbits (thereafter NEJFCs) show a remarkable similarity in their present orbits, like for instance 169P/NEAT and P/2003 T12 (SOHO), or 252P/LINEAR and P/2016 BA14 (PANSTARRS). By means of numerical integrations we studied the dynamical evolution of these objects. In particular, for each pair of presumably related objects, we are interested in assessing the stability of the orbital parameters for several thousand years, and to find a minimum of their relative spatial distance, coincident with a low value of their relative velocity. For those cases for which we find a well defined minimum of their relative orbital separation, we are trying to reproduce the actual orbit of the hypothetical fragment by modeling a fragmentation of the parent body. Some model parameters are the relative ejection velocity (a few m/s), the orbital point at which the fragmentation could have happened (e.g. perihelion), and the elapsed time since fragmentation. In addition, some possible fragmentation mechanisms, like thermal stress, rotational instability, or collisions, could be explored. According to Fernández J.A and Sosa A. 2015 (Planetary and Space Science 118,pp.14-24), some NEJFCs might come from the outer asteroid belt, and then they would have a more consolidated structure and a higher mineral content than that of comets coming from the trans-Neptunian belt or the Oort cloud. Therefore, such objects would have a much longer physical lifetime in the near-Earth region, and could become potential candidates to produce visible meteor showers (as for example 169P/NEAT which has been identified as the parent body of the alpha-Capricornid meteoroid stream, according to Jenniskens, P., Vaubaillon, J., 2010 (Astron. J. 139), and Kasuga, T., Balam, D.D., Wiegert, P.A., 2010 (Astron. J. 139).

  3. Pairs of promoter pairs in a web of transcription.

    PubMed

    Kaplan, Craig D

    2016-08-30

    A new analysis has characterized a fundamental building block of complex transcribed loci. Constellations of core promoters can generally be reduced to pairs of divergent transcription units, where the distance between the pairs of transcription units correlates with constraints on genomic context, which in turn contribute to transcript fate. PMID:27573684

  4. Pairs of promoter pairs in a web of transcription.

    PubMed

    Kaplan, Craig D

    2016-08-30

    A new analysis has characterized a fundamental building block of complex transcribed loci. Constellations of core promoters can generally be reduced to pairs of divergent transcription units, where the distance between the pairs of transcription units correlates with constraints on genomic context, which in turn contribute to transcript fate.

  5. The {sigma} phase formation in annealed UNS S31803 duplex stainless steel: Texture aspects

    SciTech Connect

    Souza, C.M. Abreu, H.F.G.; Tavares, S.S.M.; Rebello, J.M.A.

    2008-09-15

    The influence of sigma phase precipitation on the texture of austenite in a duplex stainless steel UNS S31803 was investigated. Sigma phase quantification was precisely performed by electron backscattered scanning diffraction (EBSD) for some conditions. It was found that the increase of the sigma phase precipitation enhances the amount of Brass texture in the austenite phase.

  6. Real-Time Duplex Applications of Loop-Mediated AMPlification (LAMP) by Assimilating Probes

    PubMed Central

    Kubota, Ryo; Jenkins, Daniel M.

    2015-01-01

    Isothermal nucleic-acid amplification methods such as Loop-Mediated isothermal AMPlification (LAMP) are increasingly appealing alternatives to PCR for use in portable diagnostic system due to the low cost, weight, and power requirements of the instrumentation. As such, interest in developing new probes and other functionality based on the LAMP reaction has been intense. Here, we report on the development of duplexed LAMP assays for pathogen detection using spectrally unique Assimilating Probes. As proof of principle, we used a reaction for Salmonella enterica as a model coupled with a reaction for λ-phage DNA as an internal control, as well as a duplexed assay to sub-type specific quarantine strains of the bacterial wilt pathogen Ralstonia solanacearum. Detection limits for bacterial DNA analyzed in individual reactions was less than 100 genomic equivalents in all cases, and increased by one to two orders of magnitude when reactions were coupled in duplexed formats. Even so, due to the more robust activity of newly available strand-displacing polymerases, the duplexed assays reported here were more powerful than analogous individual reactions reported only a few years ago, and represent a significant advance for incorporation of internal controls to validate assay results in the field. PMID:25741765

  7. Duplex PCR for detection of Salmonella and Shigella spp in cockle samples.

    PubMed

    Senachai, Pachara; Chomvarin, Chariya; Wongboot, Warawan; Boonyanugomol, Wongwarut; Tangkanakul, Waraluk

    2013-09-01

    Salmonella and Shigella spp are important causative agents of foodborne diseases. A sensitive, specific and rapid method is essential for detection of these pathogens. In this study, a duplex PCR method was developed for simultaneous detection of Salmonella and Shigella spp in cockle samples and compared with the traditional culture method. Enrichment broths for Salmonella spp recovery were also compared. Sensitivity of the duplex PCR for simultaneous detection of Salmonella and Shigella spp from pure culture was 10(3) CFU/ml (40 CFU/PCR reaction), and that of sterile cockle samples spiked with these two pathogens was 1 CFU/10 g of cockle tissue after 9 hours enrichment [3 hours in buffered peptone water (BPW), followed by 6 hours in Rappaport Vasiliadis (RV) broth or tetrathionate (TT) broth for Salmonella spp and 6 hours enrichment in Shigella broth (SB) for Shigella spp]. There was no significant difference in detection sensitivity between enrichment in RV and TT broths. Salmonella spp detected in cockles in Khon Kaen, Thailand by duplex PCR and culture method was 17% and 13%, respectively but Shigella spp was not detected. The duplex PCR technique developed for simultaneous detection of Salmonella and Shigella spp in cockle samples was highly sensitive, specific and rapid and could serve as a suitable method for food safety assessment.

  8. Sigma phase morphologies in cast and aged super duplex stainless steel

    SciTech Connect

    Martins, Marcelo; Casteletti, Luiz Carlos

    2009-08-15

    Solution annealed and water quenched duplex and super duplex stainless steels are thermodynamically metastable systems at room temperature. These systems do not migrate spontaneously to a thermodynamically stable condition because an energy barrier separates the metastable and stable states. However, any heat input they receive, for example through isothermal treatment or through prolonged exposure to a voltaic arc in the welding process, cause them to reach a condition of stable equilibrium which, for super duplex stainless steels, means precipitation of intermetallic and carbide phases. These phases include the sigma phase, which is easily identified from its morphology, and its influence on the material's impact strength. The purpose of this work was to ascertain how 2-hour isothermal heat treatments at 920 deg. C and 980 deg. C affect the microstructure of ASTM A890/A890M GR 6A super duplex stainless steel. The sigma phase morphologies were found to be influenced by these two aging temperatures, with the material showing a predominantly lacy microstructure when heat treated at 920 deg. C and block-shaped when heat treated at 980 deg. C.

  9. On the stress corrosion cracking of lean duplex steel in chloride environment

    NASA Astrophysics Data System (ADS)

    Tayyaba, Qanita; Farooq, Hina; Shahid, Muhammad; Jadoon, Ammer Khan; Shahzad, M.; Qureshi, A. H.

    2014-06-01

    Duplex stainless steel having attractive combination of austenitic and ferritic properties is being used in industry such as petrochemical, pulp and paper mills. In this study, the corrosion and stress corrosion behavior of duplex stainless steel in 3.5% sodium chloride environment was investigated by weight loss measurements, electrochemical DC testing and slow strain rate test (SSRT). Weight loss data showed no significant corrosion after 1700 hours. Electrochemical polarization test in 3.5% NaCl solution exhibited a uniform corrosion rate of 0.008 mpy (calculated using Tafel analysis) showing passivity in the range of 735-950 mV. A comparison of the slow strain rate test in 3.5% NaCl solution with air shows almost a similar stress strain curve for duplex stainless steel. In comparison, the stress strain curves for 0.15% carbon steel show a loss of about 25% tensile elongation for the same comparison. The excellent corrosion and especially resistance to localized corrosion (pitting) is responsible for no loss of ductility in duplex stainless steel.

  10. Duplex PCR for detection of Salmonella and Shigella spp in cockle samples.

    PubMed

    Senachai, Pachara; Chomvarin, Chariya; Wongboot, Warawan; Boonyanugomol, Wongwarut; Tangkanakul, Waraluk

    2013-09-01

    Salmonella and Shigella spp are important causative agents of foodborne diseases. A sensitive, specific and rapid method is essential for detection of these pathogens. In this study, a duplex PCR method was developed for simultaneous detection of Salmonella and Shigella spp in cockle samples and compared with the traditional culture method. Enrichment broths for Salmonella spp recovery were also compared. Sensitivity of the duplex PCR for simultaneous detection of Salmonella and Shigella spp from pure culture was 10(3) CFU/ml (40 CFU/PCR reaction), and that of sterile cockle samples spiked with these two pathogens was 1 CFU/10 g of cockle tissue after 9 hours enrichment [3 hours in buffered peptone water (BPW), followed by 6 hours in Rappaport Vasiliadis (RV) broth or tetrathionate (TT) broth for Salmonella spp and 6 hours enrichment in Shigella broth (SB) for Shigella spp]. There was no significant difference in detection sensitivity between enrichment in RV and TT broths. Salmonella spp detected in cockles in Khon Kaen, Thailand by duplex PCR and culture method was 17% and 13%, respectively but Shigella spp was not detected. The duplex PCR technique developed for simultaneous detection of Salmonella and Shigella spp in cockle samples was highly sensitive, specific and rapid and could serve as a suitable method for food safety assessment. PMID:24437322

  11. DNA CTG triplet repeats involved in dynamic mutations of neurologically related gene sequences form stable duplexes

    NASA Technical Reports Server (NTRS)

    Smith, G. K.; Jie, J.; Fox, G. E.; Gao, X.

    1995-01-01

    DNA triplet repeats, 5'-d(CTG)n and 5'-d(CAG)n, are present in genes which have been implicated in several neurodegenerative disorders. To investigate possible stable structures formed by these repeating sequences, we have examined d(CTG)n, d(CAG)n and d(CTG).d(CAG)n (n = 2 and 3) using NMR and UV optical spectroscopy. These studies reveal that single stranded (CTG)n (n > 2) forms stable, antiparallel helical duplexes, while the single stranded (CAG)n requires at least three repeating units to form a duplex. NMR and UV melting experiments show that the Tm increases in the order of [(CAG)3]2 < [(CTG)3]2 << (CAG)3.(CTG)3. The (CTG)3 duplex is stable and exhibits similar NMR spectra in solutions containing 0.1-4 M NaCl and at a pH range from 4.6 to 8.8. The (CTG)3 duplex, which contains multiple-T.T mismatches, displays many NMR spectral characteristics similar to those of B-form DNA. However, unique NOE and 1H-31P coupling patterns associated with the repetitive T.T mismatches in the CTG repeats are discerned. These results, in conjunction with recent in vitro studies suggest that longer CTG repeats may form hairpin structures, which can potentially cause interruption in replication, leading to dynamic expansion or deletion of triplet repeats.

  12. Chemical Shift Assignments of Mouse HOXD13 DNA Binding Domain Bound to Duplex DNA

    PubMed Central

    Turner, Matthew; Zhang, Yonghong; Carlson, Hanqian L.; Stadler, H. Scott; Ames, James B.

    2014-01-01

    The homeobox gene (Hoxd13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of proteins that control embryonic morphogenesis. We report NMR chemical shift assignments of mouse Hoxd13 DNA binding domain bound to an 11-residue DNA duplex (BMRB no. 25133). PMID:25491407

  13. Final Report, Volume 1, Metallurgical Evaluation of Cast Duplex Stainless Steels and their Weldments

    SciTech Connect

    Wen, Songqing; Lundin, Carl, W.; Batten, Greg, W.

    2005-09-30

    Duplex stainless steels (DSS) are being specified for chloride containing environments due to their enhanced pitting and stress corrosion cracking resistance. They exhibit improved corrosion performance over the austenitic stainless steels. Duplex stainless steels also offer improved strength properties and are available in various wrought and cast forms. Selected grades of duplex stainless steel castings and their welds, in comparison with their wrought counterparts, were evaluated, regarding corrosion performance and mechanical properties and weldability. Multiple heats of cast duplex stainless steel were evaluated in the as-cast, solution annealed (SA) static cast and SA centrifugal cast conditions, while their wrought counterparts were characterized in the SA condition and in the form of as-rolled plate. Welding, including extensive assessment of autogenous welds and a preliminary study of composite welds (shielded metal arc weld (SMAW)), was performed. The evaluations included critical pitting temperature (CPT) testing, intergranular corrosion (IGC) testing, ASTM A923 (Methods A, B and C), Charpy impact testing, weldability testing (ASTM A494), ferrite measurement and microstructural evaluations. In the study, the corrosion performances of DSS castings were characterized and assessed, including the wrought counterparts for comparison. The evaluation filled the pore of lack of data for cast duplex stainless steels compared to wrought materials. A database of the pitting corrosion and IGC behavior of cast and wrought materials was generated for a greater depth of understanding for the behavior of cast duplex stainless steel. In addition, improved evaluation methods for DSS castings were developed according to ASTM A923, A262, G48 and A494. The study revealed that when properly heat treated according to the specification, (1) DSS castings have equal or better pitting and intergranular corrosion resistance than their wrought counterparts; (2) Welding reduces the

  14. Final Report, Volume 1, Metallurgical Evaluation of Cast Duplex Stainless Steels and their Weldments

    SciTech Connect

    Wen, Songqing; Lundin, Carl, W.; Batten, Greg, W.

    2005-09-30

    Duplex stainless steels (DSS) are being specified for chloride containing environments due to their enhanced pitting and stress corrosion cracking resistance. They exhibit improved corrosion performance over the austenitic stainless steels. Duplex stainless steels also offer improved strength properties and are available in various wrought and cast forms. Selected grades of duplex stainless steel castings and their welds, in comparison with their wrought counterparts, were evaluated, regarding corrosion performance and mechanical properties and weldability. Multiple heats of cast duplex stainless steel were evaluated in the as-cast, solution annealed (SA) static cast and SA centrifugal cast conditions, while their wrought counterparts were characterized in the SA condition and in the form of as-rolled plate. Welding, including extensive assessment of autogenous welds and a preliminary study of composite welds (shielded metal arc weld (SMAW)), was performed. The evaluations included critical pitting temperature (CPT) testing, intergranular corrosion (IGC) testing, ASTM A923 (Methods A, B and C), Charpy impact testing, weldability testing (ASTM A494), ferrite measurement and microstructural evaluations. In the study, the corrosion performances of DSS castings were characterized and assessed, including the wrought counterparts for comparison. The evaluation filled the pore of lack of data for cast duplex stainless steels compared to wrought materials. A database of the pitting corrosion and IGC behavior of cast and wrought materials was generated for a greater depth of understanding for the behavior of cast duplex stainless steel. In addition, improved evaluation methods for DSS castings were developed according to ASTM A923, A262, G48 and A494. The study revealed that when properly heat treated according to the specification, (1) DSS castings have equal or better pitting and intergranular corrosion resistance than their wrought counterparts; (2) Welding reduces the

  15. Development of nano-structured duplex and ferritic stainless steels by pulverisette planetary milling followed by pressureless sintering

    SciTech Connect

    R, Shashanka Chaira, D.

    2015-01-15

    Nano-structured duplex and ferritic stainless steel powders are prepared by planetary milling of elemental Fe, Cr and Ni powder for 40 h and then consolidated by conventional pressureless sintering. The progress of milling and the continuous refinement of stainless steel powders have been confirmed by means of X-ray diffraction and scanning electron microscopy. Activation energy for the formation of duplex and ferritic stainless steels is calculated by Kissinger method using differential scanning calorimetry and is found to be 159.24 and 90.17 KJ/mol respectively. Both duplex and ferritic stainless steel powders are consolidated at 1000, 1200 and 1400 °C in argon atmosphere to study microstructure, density and hardness. Maximum sintered density of 90% and Vickers microhardness of 550 HV are achieved for duplex stainless steel sintered at 1400 °C for 1 h. Similarly, 92% sintered density and 263 HV microhardness are achieved for ferritic stainless steel sintered at 1400 °C. - Highlights: • Synthesized duplex and ferritic stainless steels by pulverisette planetary milling • Calculated activation energy for the formation of duplex and ferritic stainless steels • Studied the effect of sintering temperature on density, hardness and microstructure • Duplex stainless steel exhibits 90% sintered density and microhardness of 550 HV. • Ferritic stainless steel shows 92% sintered density and 263 HV microhardness.

  16. Ab initio Study of the Structural, Tautomeric, Pairing and Electronic Properties of Seleno-Derivatives of Thymine

    SciTech Connect

    Vazquez-Mayagoitia, Alvaro; Fuentes-Cabrera, Miguel A; Sumpter, Bobby G; Luque, Javier; Huertas, Oscar; Orozco, Modesto; Felice, Rosa; Brancolini, Giorgia; Migliore, Agostino

    2009-01-01

    The structural, tautomeric, hydrogen-bonding, stacking and electronic properties of a seleno-derivative of thymine (T), denoted here as 4SeT and created by replacing O4 in T with Se, are investigated by means of ab initio computational techniques. The structural properties of T and 4SeT are very similar and the geometrical differences are mainly limited to the adjacent environment of the C-Se bond. The canonical keto form is the most stable tautomer, in gas phase and in aqueous solution, for both T and 4SeT. It is argued that the competition between two opposite trends, i.e. a decrease in the base-pairing ability and an increase of the stacking interaction upon incorporation of 4SeT into a duplex, likely explains the similar experimental melting points of a seleno-derivative duplex (Se-DNA) and its native counterpart. Interestingly, the underlying electronic structure shows that replacement of O4 with Se promotes a reduction in the HOMO-LUMO gap and an increase in inter-plane coupling, which suggests that Se-DNA could be potentially useful for nanodevice applications. This finding is further supported by the fact that transfer integrals between 4SeT---A stacked base pairs are larger than those determined for similarly stacked natural T---A pairs.

  17. On the Formation and Properties of Interstrand DNA-DNA Cross-links Forged by Reaction of an Abasic Site With the Opposing Guanine Residue of 5′-CAp Sequences in Duplex DNA

    PubMed Central

    Johnson, Kevin M.; Price, Nathan E.; Wang, Jin; Fekry, Mostafa I.; Dutta, Sanjay; Seiner, Derrick R.; Wang, Yinsheng; Gates, Kent S.

    2014-01-01

    We recently reported that the aldehyde residue of an abasic (Ap) site in duplex DNA can generate an interstrand cross-link via reaction with a guanine residue on the opposing strand. This finding is intriguing because the highly deleterious nature of interstrand cross-links suggests that even small amounts of Ap-derived cross-links could make a significant contribution to the biological consequences stemming from the generation of Ap sites in cellular DNA. Incubation of 21-bp duplexes containing a central 5′-CAp sequence under conditions of reductive amination (NaCNBH3, pH 5.2) generated much higher yields of cross-linked DNA than reported previously. At pH 7, in the absence of reducing agents, these Ap-containing duplexes also produced cross-linked duplexes that were readily detected on denaturing polyacrylamide gels. Cross-link formation was not highly sensitive to reaction conditions and, once formed, the cross-link was stable to a variety of work-up conditions. Results of multiple experiments including MALDI-TOF mass spectrometry, gel mobility, methoxyamine capping of the Ap aldehyde, inosine-for-guanine replacement, hydroxyl radical footprinting, and LCMS/MS were consistent with a cross-linking mechanism involving reversible reaction of the Ap aldehyde residue with the N2-amino group of the opposing guanine residue in 5′-CAp sequences to generate hemiaminal, imine, or cyclic hemiaminal cross-links (7-10) that were irreversibly converted under conditions of reductive amination (NaCNBH3/pH 5.2) to a stable amine linkage. Further support for the importance of the exocyclic N2-amino group in this reaction was provided by an experiment showing that installation of a 2-aminopurine-thymine base pair at the cross-linking site produced high yields (15-30%) of a cross-linked duplex at neutral pH, in the absence of NaCNBH3. PMID:23215239

  18. Bilayer Protograph Codes for Half-Duplex Relay Channels

    NASA Technical Reports Server (NTRS)

    Divsalar, Dariush; VanNguyen, Thuy; Nosratinia, Aria

    2013-01-01

    re-optimization. The main problem of half-duplex relay coding can be reduced to the simultaneous design of two codes at two rates and two SNRs (signal-to-noise ratios), such that one is a subset of the other. This problem can be addressed by forceful optimization, but a clever method of addressing this problem is via the bilayer lengthened (BL) LDPC structure. This method uses a bilayer Tanner graph to make the two codes while using a concept of "parity forwarding" with subsequent successive decoding that removes the need to directly address the issue of uneven SNRs among the symbols of a given codeword. This method is attractive in that it addresses some of the main issues in the design of relay codes, but it does not by itself give rise to highly structured codes with simple encoding, nor does it give rate-compatible codes. The main contribution of this work is to construct a class of codes that simultaneously possess a bilayer parity- forwarding mechanism, while also benefiting from the properties of protograph codes having an easy encoding, a modular design, and being a rate-compatible code.

  19. Multistory duplexes with forward dipping roofs, north central Brooks Range, Alaska

    USGS Publications Warehouse

    Wallace, W.K.; Moore, T.E.; Plafker, G.

    1997-01-01

    The Endicott Mountains allochthon has been thrust far northward over the North Slope parautochthon in the northern Brooks Range. Progressively younger units are exposed northward within the allochthon. To the south, the incompetent Hunt Fork Shale has thickened internally by asymmetric folds and thrust faults. Northward, the competent Kanayut Conglomerate forms a duplex between a floor thrust in Hunt Fork and a roof thrust in the Kayak Shale. To the north, the competent Lisburne Group forms a duplex between a floor thrust in Kayak and a roof thrust in the Siksikpuk Formation. Both duplexes formed from north vergent detachment folds whose steep limbs were later truncated by south dipping thrust faults that only locally breach immediately overlying roof thrusts. Within the parautochthon, the Kayak, Lisburne, and Siksikpuk-equivalent Echooka Formation form a duplex identical to that in the allochthon. This duplex is succeeded abruptly northward by detachment folds in Lisburne. These folds are parasitic to an anticlinorium interpreted to reflect a fault-bend folded horse in North Slope "basement," with a roof thrust in Kayak and a floor thrust at depth. These structures constitute two northward tapered, internally deformed wedges that are juxtaposed at the base of the allochthon. Within each wedge, competent units have been shortened independently between detachments, located mainly in incompetent units. The basal detachment of each wedge cuts upsection forward (northward) to define a wedge geometry within which units dip regionally forward. These dips reflect forward decrease in internal structural thickening by forward vergent folds and hindward dipping thrust faults. Copyright 1997 by the American Geophysical Union.

  20. Architecture Studies Done for High-Rate Duplex Direct Data Distribution (D4) Services

    NASA Technical Reports Server (NTRS)

    2002-01-01

    A study was sponsored to investigate a set of end-to-end system concepts for implementing a high-rate duplex direct data distribution (D4) space-to-ground communications link. The NASA Glenn Research Center is investigating these systems (both commercial and Government) as a possible method of providing a D4 communications service between NASA spacecraft in low Earth orbit and the respective principal investigators using or monitoring instruments aboard these spacecraft. Candidate commercial services were assessed regarding their near-term potential to provide a D4 type of service. The candidates included K-band and V-band geostationary orbit and nongeostationary orbit satellite relay services and direct downlink (D3) services. Internet protocol (IP) networking technologies were evaluated to enable the user-directed distribution and delivery of science data. Four realistic, near-future concepts were analyzed: 1) A duplex direct link (uplink plus downlink communication paths) between a low-Earth-orbit spacecraft and a principal-investigator-based autonomous Earth station; 2) A space-based relay using a future K-band nongeosynchronous-orbit system to handle both the uplink and downlink communication paths; 3) A hybrid link using both direct and relay services to achieve full duplex capability; 4) A dual-mode concept consisting of both a duplex direct link and a space relay duplex link operating independently. The concepts were analyzed in terms of contact time between the NASA spacecraft and the communications service and the achievable data throughput. Throughput estimates for the D4 systems were based on the infusion of advanced communications technology products (single and multibeam K-band phased-arrays and digital modems) being developed by Glenn. Cost estimates were also performed using extrapolated information from both terrestrial and current satellite communications providers. The throughput and cost estimates were used to compare the concepts.

  1. Adsorption on ordered and disordered duplex layers of porous anodic alumina.

    PubMed

    Bruschi, Lorenzo; Mistura, Giampaolo; Phadungbut, Poomiwat; Do, D D; Nicholson, D; Mayamei, Yashar; Lee, Woo

    2015-05-01

    We have carried out systematic experiments and numerical simulations of the adsorption on porous anodic aluminum oxide (AAO) duplex layers presenting either an ordered or a disordered interconnecting interface between the large (cavity) and small (constriction) sections of the structured pores. Selective blocking of the pore openings resulted in three different pore topologies: open structured pores, funnel pores, and ink-bottle pores. In the case of the structured pores having an ordered interface, the adsorption isotherms present a rich phenomenology characterized by the presence of two steps in the condensation branch and the opening of one (two) hysteresis loops during evaporation for the ink-bottle (open and funnel) pores. The isotherms can be obtained by summing the isotherms measured on uniform pores having the dimensions of the constrictions or of the cavities. The numerical analysis of the three different pore topologies indicates that the shape of the junction between the two pore sections is only important for the adsorption branch. In particular, a conic junction which resembles that of the AAO pores represents the experimental isotherms for the open and funnel pores better, but the shape of the junction in the ink bottle pores does not matter. The isotherms for the duplex layers with a disordered interface display the same general features found for the ordered duplex layers. In both cases, the adsorption branches coincide and have two steps which are shifted to lower relative pressures compared to those for the ordered duplex. Furthermore, the desorption branches comprise hysteresis loops much wider than those of the ordered duplex layers. Overall, this study highlights the important role played by morphologies where there are interconnections between large and small pores.

  2. Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair.

    PubMed Central

    Beuning, Penny J; Nagan, Maria C; Cramer, Christopher J; Musier-Forsyth, Karin; Gelpí, Josep-Lluis; Bashford, Donald

    2002-01-01

    Specific aminoacylation by aminoacyl-tRNA synthetases requires accurate recognition of cognate tRNA substrates. In the case of alanyl-tRNA synthetase (AlaRS), RNA duplexes that mimic the acceptor stem of the tRNA are efficient substrates for aminoacylation in vitro. It was previously shown that recognition by AlaRS is severely affected by a simple base pair transversion of the G2:C71 pair at the second position in the RNA helix. In this study, we determined the aminoacylation efficiencies of 50 variants of the tRNA(Ala) acceptor stem containing substitutions at the 2:71 position. We find that there is not a single functional group of the wild-type G2:C71 base pair that is critical for positive recognition. Rather, we observed that base-pair orientation plays an important role in recognition. In particular, pyrimidine2:purine71 combinations generally resulted in decreased aminoacylation efficiency compared to the corresponding purine:pyrimidine pair. Moreover, the activity of a pyrimidine:purine variant could be partially restored by the presence of a major groove amino group at position 71. In an attempt to understand this result further, dielectric continuum electrostatic calculations were carried out, in some cases with additional inclusion of van der Waals interaction energies, to determine interaction potentials of the wild-type duplexAla and seven 2:71 variants. This analysis revealed a positive correlation between major groove negative electrostatic potential in the vicinity of the 3:70 base pair and measured aminoacylation efficiency. PMID:12022232

  3. On the cryogenic magnetic transition and martensitic transformation of the austenite phase of 7MoPLUS duplex stainless steel

    NASA Astrophysics Data System (ADS)

    Lo, K. H.; Lai, J. K. L.

    2010-08-01

    The magnetic behaviour and martensitic transformation at cryogenic temperatures (down to 4 K) of the austenite phase of the duplex stainless steel (DSS), 7MoPLUS, were studied. As regards the prediction of Neel temperature, the empirical expressions for austenitic stainless steels are not applicable to the austenite phase of 7MoPLUS, although the composition of the austenite phase falls within the composition ranges within which the expressions were developed. Regarding the prediction of martensitic point Ms, the applicability of 'old' and recently developed expressions has been examined. The recently developed expressions, which take into account more alloying elements and their interactions, are not suitable for the austenite phase of 7MoPLUS. But for the 'old', simpler expressions, they seem to be valid in the sense that they all predict high stability of the austenite phase. Results obtained from 7MoPLUS were qualitatively the same as those obtained from another DSS, designated as 2205. Reasons for the applicability and inapplicability of these empirical expressions are suggested.

  4. Assessment Strategies for Pair Programming

    ERIC Educational Resources Information Center

    Hahn, Jan Hendrik; Mentz, Elsa; Meyer, Lukas

    2009-01-01

    Although pair programming has proved its usefulness in teaching and learning programming skills, it is difficult to assess the individual roles and abilities of students whilst programming in pairs. (Note that within this manuscript, the term assessment refers to evaluating individual student performance.) Assessing only the outcomes of a pair…

  5. Guanidinium Pairing Facilitates Membrane Translocation.

    PubMed

    Allolio, Christoph; Baxova, Katarina; Vazdar, Mario; Jungwirth, Pavel

    2016-01-14

    Ab initio free energy calculations of guanidinium pairing in aqueous solution confirm the counterintuitive conjecture that the like-charge ion pair is thermodynamically stable. Transferring the guanidinium pair to the inside of a POPC lipid bilayer, like-charge ion pairing is found to occur also inside the membrane defect. It is found to contribute to the nonadditivity of ion transfer, thereby facilitating the presence of ions inside the bilayer. The effect is quantified by free energy decomposition and comparison with ammonium ions, which do not form a stable pair. The presence of two charges inside the center of the bilayer leads to the formation of a pore. Potential consequences for cell penetrating peptides and ion conduction are drawn.

  6. Development of a self-similar strike-slip duplex system in the Atacama Fault system, Chile

    NASA Astrophysics Data System (ADS)

    Jensen, E.; Cembrano, J.; Faulkner, D.; Veloso, E.; Arancibia, G.

    2011-11-01

    Fault development models are crucial to predict geometry and distribution of fractures at all scales. We present here structures related to the development of the Bolfín Fault in the Atacama Fault System (AFS), covering a range of scales of 7 orders of magnitude. The AFS is a 1000 km-long trench-parallel fault system located in the Andean Forearc. The Bolfín Fault is a first-order fault of the Caleta Coloso Duplex, has a trend ∼170° and length >45 km. It cuts mainly meta-diorites and exhibits a 100-200 m thick core of subvertical bands of altered fractured host rock and of foliated cataclasites. This foliation is made up of several trend-parallel cm-thick shear bands, composed of plagioclase fragments (>0.1 mm) surrounded by epidote. In the compressive quadrant around the tip point of Bolfín Fault, the lower strain faults exhibit an unusual internal structure consisting of fractures arranged in a multi-duplex pattern. This pattern can be observed from meters to millimeters scale. The fractures in the strike-slip duplex pattern can be separated into two types. Main Faults: trend-parallel, longer and with larger offsets; and Secondary Fractures: sigmoid-shape fractures distributed in the regions between Main Faults, all oriented between 15° and 75° with respect to the Main Faults, measured counterclockwise (i.e. in P-diedra). On the basis of the distribution of the two types of recognized fractures, the relative sequence of propagation can be inferred. Main Faults, the more widely distributed, propagated earlier. The Secondary Fractures, in turn, distributed in thinner areas between the larger Main Faults, were propagated later as linking fractures. The duplex pattern is self-similar: Multiple-Core Faults with internal structure of multiple-duplex are itself in turn secondary faults within a larger km-scale duplex (Caleta Coloso Duplex). The duplex width (W) and the length (L) of the Main Faults forming the duplex show an almost linear relationship, for

  7. Base pairing and base mis-pairing in nucleic acids

    NASA Technical Reports Server (NTRS)

    Wang, A. H. J.; Rich, A.

    1986-01-01

    In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

  8. Stereo Pair: Patagonia, Argentina

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This view of northern Patagonia, near El Cain, Argentina shows complexly eroded volcanic terrain, with basalt mesas, sinkholes, landslide debris, playas, and relatively few integrated drainage channels. Surrounding this site (but also extending far to the east) is a broad plateau capped by basalt, the Meseta de Somuncura. Here, near the western edge of the plateau, erosion has broken through the basalt cap in a variety of ways. On the mesas, water-filled sinkholes (lower left) are most likely the result of the collapse of old lava tubes. Along the edges of the mesas (several locations) the basalt seems to be sliding away from the plateau in a series of slices. Water erosion by overland flow is also evident, particularly in canyons where vegetation blankets the drainage channels (green patterns, bottom of image). However, overland water flow does not extend very far at any location. This entire site drains to local playas, some of which are seen here (blue). While the water can reach the playas and then evaporate, what becomes of the eroded rock debris? Wind might excavate some of the finer eroded debris, but the fate of much of the missing bedrock remains mysterious.

    This cross-eyed stereoscopic image pair was generated using topographic data from the Shuttle Radar Topography Mission, combined with an enhanced Landsat 7 satellite color image. The topography data are used to create two differing perspectives of a single image, one perspective for each eye. In doing so, each point in the image is shifted slightly, depending on its elevation. When stereoscopically merged, the result is a vertically exaggerated view of the Earth's surface in its full three dimensions.

    Landsat satellites have provided visible light and infrared images of the Earth continuously since 1972. SRTM topographic data match the 30-meter (99-foot) spatial resolution of most Landsat images and provide a valuable complement for studying the historic and growing Landsat data archive. The

  9. Stereo Pair, Patagonia, Argentina

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This view of northern Patagonia, at Los Menucos, Argentina shows remnants of relatively young volcanoes built upon an eroded plain of much older and contorted volcanic, granitic, and sedimentary rocks. The large purple, brown, and green 'butterfly' pattern is a single volcano that has been deeply eroded. Large holes on the volcano's flanks indicate that they may have collapsed soon after eruption, as fluid molten rock drained out from under its cooled and solidified outer shell. At the upper left, a more recent eruption occurred and produced a small volcanic cone and a long stream of lava, which flowed down a gully. At the top of the image, volcanic intrusions permeated the older rocks resulting in a chain of small dark volcanic peaks. At the top center of the image, two halves of a tan ellipse pattern are offset from each other. This feature is an old igneous intrusion that has been split by a right-lateral fault. The apparent offset is about 6.6 kilometers (4 miles). Color, tonal, and topographic discontinuities reveal the fault trace as it extends across the image to the lower left. However, young unbroken basalt flows show that the fault has not been active recently.

    This cross-eyed stereoscopic image pair was generated using topographic data from the Shuttle Radar Topography Mission, combined with an enhanced Landsat 7satellite color image. The topography data are used to create two differing perspectives of a single image, one perspective for each eye. In doing so, each point in the image is shifted slightly, depending on its elevation. When stereoscopically merged, the result is a vertically exaggerated view of the Earth's surface in its full three dimensions.

    Landsat satellites have provided visible light and infrared images of the Earth continuously since 1972. SRTM topographic data match the 30-meter (99-foot) spatial resolution of most Landsat images and provide a valuable complement for studying the historic and growing Landsat data archive

  10. Electron backscatter diffraction study of deformation and recrystallization textures of individual phases in a cross-rolled duplex steel

    SciTech Connect

    Zaid, Md; Bhattacharjee, P.P.

    2014-10-15

    The evolution of microstructure and texture during cross-rolling and annealing was investigated by electron backscatter diffraction in a ferritic–austenitic duplex stainless steel. For this purpose an alloy with nearly equal volume fraction of the two phases was deformed by multi-pass cross-rolling process up to 90% reduction in thickness. The rolling and transverse directions were mutually interchanged in each pass by rotating the sample by 90° around the normal direction. In order to avoid deformation induced phase transformation and dynamic strain aging, the rolling was carried out at an optimized temperature of 898 K (625 °C) at the warm-deformation range. The microstructure after cross warm-rolling revealed a lamellar structure with alternate arrangement of the bands of two phases. Strong brass and rotated brass components were observed in austenite in the steel after processing by cross warm-rolling. The ferrite in the cross warm-rolling processed steel showed remarkably strong RD-fiber (RD//< 011 >) component (001)< 011 >. The development of texture in the two phases after processing by cross warm-rolling could be explained by the stability of the texture components. During isothermal annealing of the 90% cross warm-rolling processed material the lamellar morphology was retained before collapse of the lamellar structure to the mutual interpenetration of the phase bands. Ferrite showed recovery resulting in annealing texture similar to the deformation texture. In contrast, the austenite showed primary recrystallization without preferential orientation selection leading to the retention of deformation texture. The evolution of deformation and annealing texture in the two phases of the steel was independent of one another. - Highlights: • Effect of cross warm-rolling on texture formation is studied in duplex steel. • Brass texture in austenite and (001)<110 > in ferrite are developed. • Ferrite shows recovery during annealing retaining the (001

  11. Finite Wave Vector Pairing in Doped Two-leg Ladders

    SciTech Connect

    Robinson N. J.; Tsvelik A.; Essler, F.H.L.; Jeckelmann, E.

    2012-05-02

    We consider the effects of umklapp processes in doped two-leg fermionic ladders. These may emerge either at special band fillings or as a result of the presence of external periodic potentials. We show that such umklapp processes can lead to profound changes of physical properties and in particular stabilize pair-density wave phases.

  12. Pairing Correlations at High Spins

    NASA Astrophysics Data System (ADS)

    Ma, Hai-Liang; Dong, Bao-Guo; Zhang, Yan; Fan, Ping; Yuan, Da-Qing; Zhu, Shen-Yun; Zhang, Huan-Qiao; Petrache, C. M.; Ragnarsson, I.; Carlsson, B. G.

    The pairing correcting energies at high spins in 161Lu and 138Nd are studied by comparing the results of the cranked-Nilsson-Strutinsky (CNS) and cranked-Nilsson-Strutinsky-Bogoliubov (CNSB) models. It is concluded that the Coriolis effect rather than the rotational alignment effect plays a major role in the reduction of the pairing correlations in the high spin region. Then we proposed an average pairing correction method which not only better reproduces the experimental data comparing with the CNS model but also enables a clean-cut tracing of the configurations thus the full-spin-range discussion on the various rotating bands.

  13. Pairing Properties of Superheavy Nuclei

    SciTech Connect

    Staszczak, A.; Dobaczewski, J.; Nazarewicz, Witold

    2007-01-01

    Pairing properties of even-even superheavy N=184 isotones are studied within the Skyrme-Hartree-Fock+BCS approach. In the particle-hole channel we take the Skyrme energy density functional SLy4, while in the particle-particle channel we employ the seniority pairing force and zero-range delta-interactions with different forms of density dependence. We conclude that the calculated static fission trajectories weakly depend on the specific form of the delta-pairing interaction. We also investigate the impact of triaxiality on the inner fission barrier and find a rather strong Z dependence of the effect.

  14. Identification of homologous pairing and strand-exchange activity from a human tumor cell line based on Z-DNA affinity chromatography

    SciTech Connect

    Fishel, R.A.; Detmer, K.; Rich, A.

    1988-01-01

    An enzymatic activity that catalyzes ATP-dependent homologous pairing and strand exchange of duplex linear DNA and single-stranded circular DNA has been purified several thousand-fold from a human leukemic T-lymphoblast cell line. The activity was identified after chromatography of nuclear proteins on a Z-DNA column matrix. The reaction was shown to transfer the complementary single strand from a donor duplex linear substrate to a viral circular single-stranded acceptor beginning at the 5' end and proceeding in the 3' direction. Products of the strand-transfer reaction were characterized by electron microscopy. A 74-kDa protein was identified as the major ATP-binding peptide in active strand transferase fractions. The protein preparation described in this report binds more strongly to Z-DNA than to B-DNA.

  15. Detection of 12 respiratory viruses by duplex real time PCR assays in respiratory samples.

    PubMed

    Arvia, Rosaria; Corcioli, Fabiana; Ciccone, Nunziata; Della Malva, Nunzia; Azzi, Alberta

    2015-12-01

    Different viruses can be responsible for similar clinical manifestations of respiratory infections. Thus, the etiological diagnosis of respiratory viral diseases requires the detection of a large number of viruses. In this study, 6 duplex real-time PCR assays, using EvaGreen intercalating dye, were developed to detect 12 major viruses responsible for respiratory diseases: influenza A and B viruses, enteroviruses (including enterovirus spp, and rhinovirus spp), respiratory syncytial virus, human metapneumovirus, coronaviruses group I (of which CoV 229E and CoV NL63 are part) and II (including CoV OC43 and CoV HKU1), parainfluenza viruses type 1, 2, 3 and 4, human adenoviruses and human bocaviruses. The 2 target viruses of each duplex reaction were distinguishable by the melting temperatures of their amplicons. The 6 duplex real time PCR assays were applied for diagnostic purpose on 202 respiratory samples from 157 patients. One hundred fifty-seven samples were throat swabs and 45 were bronchoalveolar lavages. The results of the duplex PCR assays were confirmed by comparison with a commercial, validated, assay; in addition, the positive results were confirmed by sequencing. The analytical sensitivity of the duplex PCR assays varied from 10(3) copies/ml to 10(4) copies/ml. For parainfluenza virus 2 only it was 10(5) copies/ml. Seventy clinical samples (35%) from 55 patients (30 children and 25 adults) were positive for 1 or more viruses. In adult patients, influenza A virus was the most frequently detected respiratory virus followed by rhinoviruses. In contrast, respiratory syncytial virus was the most common virus in children, followed by enteroviruses, influenza A virus and coronavirus NL63. The small number of samples/patients does not allow us to draw any epidemiological conclusion. Altogether, the results of this study indicate that the 6 duplex PCR assays described in this study are sensitive, specific and cost-effective. Thus, this assay could be

  16. Development of self-similar duplex systems. Atacama Fault System, Chile

    NASA Astrophysics Data System (ADS)

    Jensen, E.; Cembrano, J. M.; Veloso, E. E.

    2009-12-01

    Fault development models are very important to predict geometry and distribution of fractures at all scales. However, models based on structures from microns to km are relatively scarce due to the lack of well-exposed structures. We present structures related to the development of the Bolfín fault in the Atacama Fault System (AFS), covering a scale range of 9 orders of magnitude. The AFS is a 1000 km-long trench-parallel fault system located in the Andean Forearc. The Bolfín fault is a first-order fault of the Caleta Coloso Duplex; it has a trend ~170° and a length >45 km (Fig 1A). It cuts meta-diorites and exhibits a 100-200m wide core of subvertical bands of altered fractured host rock and of foliated cataclasites. Foliation is made of trend-parallel cm-wide shear bands composed of plagioclase fragments (>0,1mm) surrounded by epidote. Around the bands there are many micro fractures oriented within the P-diedra. In the compressive quadrant around a tip point of Bolfín fault, the lower strain faults exhibit an unusual internal structure consisting of fractures arranged in a multi-duplex pattern. This pattern can be seen from metric- (Parulo fault, fig 1C) to mm-scale (Palmera fault fig 1B). Fractures in the pattern can be separated in 2 types: Main Faults: Trend-parallel, longer and with larger offsets. Secondary Fractures: sigmoid-shape fractures distributed in the regions between main faults, all oriented between 15° and 75° with respect to the main faults, meassured in the shear-sense (i.e. in P-diedra). On the basis of the distribution of the 2 types of fractures, the generation sequence can be inferred. The main faults are more widely distributed, and were propagated earlier. The secondary fractures are distributed in smaller areas between larger displacement main faults, and propagated later as linking fractures. The duplex pattern is thus self-similar: faults with multiple-duplex internal structure (Parulo and Palmera fault)are in turn secondary faults

  17. The coevolution of long-term pair bonds and cooperation.

    PubMed

    Song, Z; Feldman, M W

    2013-05-01

    The evolution of social traits may not only depend on but also change the social structure of the population. In particular, the evolution of pairwise cooperation, such as biparental care, depends on the pair-matching distribution of the population, and the latter often emerges as a collective outcome of individual pair-bonding traits, which are also under selection. Here, we develop an analytical model and individual-based simulations to study the coevolution of long-term pair bonds and cooperation in parental care, where partners play a Snowdrift game in each breeding season. We illustrate that long-term pair bonds may coevolve with cooperation when bonding cost is below a threshold. As long-term pair bonds lead to assortative interactions through pair-matching dynamics, they may promote the prevalence of cooperation. In addition to the pay-off matrix of a single game, the evolutionarily stable equilibrium also depends on bonding cost and accidental divorce rate, and it is determined by a form of balancing selection because the benefit from pair-bond maintenance diminishes as the frequency of cooperators increases. Our findings highlight the importance of ecological factors affecting social bonding cost and stability in understanding the coevolution of social behaviour and social structures, which may lead to the diversity of biological social systems. PMID:23496797

  18. Dynamical interactions of galaxy pairs

    NASA Technical Reports Server (NTRS)

    Athanassoula, E.

    1990-01-01

    Here the author briefly reviews the dynamics of sinking satellites and the effect of companions on elliptical galaxies. The author then discusses recent work on interacting disk systems, and finally focuses on a favorite interacting pair, NGC 5194/5195.

  19. Pair Excitations in Fermi Fluids

    NASA Astrophysics Data System (ADS)

    Böhm, Helga M.; Krotscheck, Eckhard; Schörkhuber, Karl; Springer, Josef

    2006-09-01

    We present a theory of multi-pair excitations in strongly interacting Fermi systems. Based on an equations-of-motion approach for time-dependent pair correlations it leads to a qualitatively new structure of the density-density response function. Our theory reduces to both, i) the "correlated" random-phase approximation (RPA) for fermions if the two-pair excitations are ignored, and ii) the correlated Brillouin-Wigner perturbation theory for bosons in the appropriate limit. The theory preserves the two first energy-weighted sum rules. A familiar problem of the standard RPA is that its zero-sound mode is energetically much higher than found in experiments. The popular cure of introducing an average effective mass in the Lindhard function violates sum rules and describes the physics incorrectly. We demonstrate that the inclusion of correlated pair excitations gives the correct dispersion. As in 4He, a modification of the effective mass is unnecessary also in 3He.

  20. Assembly of pyrene-modified DNA/RNA duplexes incorporating a G-rich single strand region.

    PubMed

    Seio, Kohji; Tokugawa, Munefumi; Tsunoda, Hirosuke; Ohkubo, Akihiro; Arisaka, Fumio; Sekine, Mitsuo

    2013-12-15

    The structural properties of a DNA/RNA duplex having a pyrene residue at the 5' end of DNA and a G-rich single strand region at the 3' end of RNA were studied in detail. Fluorescence and ultracentrifugation analyses indicated the formation of a complex containing four DNA/RNA duplexes, which required a pyrene residue, G-rich sequence, RNA-type backbone, and high salt concentration. PMID:24183539

  1. Breathing fluctuations in position-specific DNA base pairs are involved in regulating helicase movement into the replication fork.

    PubMed

    Jose, Davis; Weitzel, Steven E; von Hippel, Peter H

    2012-09-01

    We previously used changes in the near-UV circular dichroism and fluorescence spectra of DNA base analogue probes placed site specifically to show that the first three base pairs at the fork junction in model replication fork constructs are significantly opened by "breathing" fluctuations under physiological conditions. Here, we use these probes to provide mechanistic snapshots of the initial interactions of the DNA fork with a tight-binding replication helicase in solution. The primosome helicase of bacteriophage T4 was assembled from six (gp41) helicase subunits, one (gp61) primase subunit, and nonhydrolyzable GTPγS. When bound to a DNA replication fork construct this complex advances one base pair into the duplex portion of the fork and forms a stably bound helicase "initiation complex." Replacement of GTPγS with GTP permits the completion of the helicase-driven unwinding process. Our spectroscopic probes show that the primosome in this stable helicase initiation complex binds the DNA of the fork primarily via backbone contacts and holds the first complementary base pair of the fork in an open conformation, whereas the second, third, and fourth base pairs of the duplex show essentially the breathing behavior that previously characterized the first three base pairs of the free fork. These spectral changes, together with dynamic fluorescence quenching results, are consistent with a primosome-binding model in which the lagging DNA strand passes through the central hole of the hexagonal helicase, the leading strand binds to the "outside" surfaces of subunits of the helicase hexamer, and the single primase subunit interacts with both strands.

  2. Stabilized floating platforms

    DOEpatents

    Thomas, David G.

    1976-01-01

    The subject invention is directed to a floating platform for supporting nuclear reactors and the like at selected offshore sites. The platform is provided with a stabilizer mechanism which significantly reduces the effects of wave action upon the platform and which comprises a pair of relatively small floats attached by rigid booms to the platform at locations spaced therefrom for reducing wave pitch, acceleration, and the resonance period of the wave.

  3. Activation Energies for Dissociation of Double Strand Oligonucleotide Anions: Evidence for Watson–Crick Base Pairing in Vacuo

    PubMed Central

    Schnier, Paul D.; Klassen, John S.; Strittmatter, Eric F.; Williams*, Evan R.

    2005-01-01

    The dissociation kinetics of a series of complementary and noncomplementary DNA duplexes, (TGCA)23−, (CCGG)23−, (AATTAAT)23−, (CCGGCCG)23−, A7·T73−, A7·A73−, T7·T73−, and A7·C73− were investigated using blackbody infrared radiative dissociation in a Fourier transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Activation energies range from 1.2 to 1.7 eV, and preexponential factors range from 1013 to 1019 s−1. Dissociation of the duplexes results in cleavage of the noncovalent bonds and/or cleavage of covalent bonds leading to loss of a neutral nucleobase followed by backbone cleavage producing sequence-specific (a – base) and w ions. Four pieces of evidence are presented which indicate that Watson–Crick (WC) base pairing is preserved in complementary DNA duplexes in the gas phase: i. the activation energy for dissociation of the complementary dimer, A7·T73−, to the single strands is significantly higher than that for the related noncomplementary A7·A73− and T7·T73− dimers, indicating a stronger interaction between strands with a specific base sequence, ii. extensive loss of neutral adenine occurs for A7·A73− and A7·C73− but not for A7·T73− consistent with this process being shut down by WC hydrogen bonding, iii. a correlation is observed between the measured activation energy for dissociation to single strands and the dimerization enthalpy (−ΔHd) in solution, and iv. molecular dynamics carried out at 300 and 400 K indicate that WC base pairing is preserved for A7·T73− duplex, although the helical structure is essentially lost. In combination, these results provide strong evidence that WC base pairing can exist in the complete absence of solvent. PMID:16498487

  4. Characterization of passive film on 2205 duplex stainless steel in sodium thiosulphate solution

    NASA Astrophysics Data System (ADS)

    Luo, H.; Dong, C. F.; Xiao, K.; Li, X. G.

    2011-10-01

    The electrochemical behaviour of passive film formed on 2205 duplex stainless steel in 0.1 M Na 2S 2O 3 solutions was investigated using potentiodynamic polarization, EIS, Mott-Schottky analysis and the compositions of oxide film in different passive regions were carried out by XPS. The results indicated that the impedance is dependent on the applied potential indicating the occurrence of a charge transfer reaction in a porous film. The doping densities evaluated from Mott-Schottky plots demonstrated that there existence of two donor levels in the space charge layer of the passive films. The donor density ( ND1 and ND2 ) values are in the range of 10 20-10 21 cm 3, and decreases exponentially with increasing film formation potential, which is in good agreement with the theoretical consequences of the PDM. The polarization curve and XPS results shows that in the passive regions the 2205 duplex stainless steel exhibits different electrochemical and semiconductor properties.

  5. Vacuum-ultraviolet circular dichroism reveals DNA duplex formation between short strands of adenine and thymine.

    PubMed

    Nielsen, Lisbeth Munksgaard; Hoffmann, Søren Vrønning; Brøndsted Nielsen, Steen

    2012-11-21

    Absorbance spectroscopy is used extensively to tell when two DNA single strands come together and form a double strand. Here we show that circular dichroism in the vacuum ultraviolet region provides an even stronger indication for duplex formation in the case of short strands of adenine and thymine (4 to 16 bases in each strand). Indeed, our results show that a strong positive CD band appears at 179 nm when double strands are formed. Melting experiments were done in aqueous solution with and without added Na(+) counter ions. With additional salt present a huge increase in the 179 nm CD band was observed when lowering the temperature. A 179 nm CD marker band for duplex formation can be used to measure the kinetics for the association of two single strands. Such experiments rely on large changes at one particular wavelength since it is too time-consuming to record a full-wavelength spectrum.

  6. Progress Towards the Development of a Long-Lived Venus Lander Duplex System

    NASA Technical Reports Server (NTRS)

    Dyson, Rodger, W.; Bruder, Geoffrey A.

    2011-01-01

    NASA has begun the development of a combined Stirling cycle power and cooling system (duplex) to enable the long-lived surface exploration of Venus and other harsh environments in the solar system. The duplex system will operate from the heat provided by decaying radioisotope plutonium-238 or its substitute. Since the surface of Venus has a thick, hot, and corrosive atmosphere, it is a challenging proposition to maintain sensitive lander electronics under survivable conditions. This development effort requires the integration of: a radioisotope or fission heat source; heat pipes; high-temperature, corrosion-resistant material; multistage cooling; a novel free-displacer Stirling convertor for the lander; and a minimal vibration thermoacoustic Stirling convertor for the seismometer. The first year effort includes conceptual system design and control studies, materials development, and prototype hardware testing. A summary of these findings and test results is presented in this report.

  7. Internal friction study of decomposition kinetics of SAF 2507 type duplex stainless steel

    SciTech Connect

    Smuk, O.; Smuk, S.; Hanninen, H.; Jagodzinski, Yu.; Tarasenko, O.

    1999-01-08

    During the last decade, super duplex stainless steels (DSSs) with increased nitrogen content have been an object of intensive studies. Present work is devoted to the study of the peculiarities of {delta}-ferrite decomposition in SAF 2507 type duplex steel, and redistribution of nitrogen between ferrite and austenite phases in a wide temperature range by means of internal fraction (IF). Unlike local methods of electron microscopy or engineering methods of hardness or impact toughness testing, which give basically information on the formation of brittle intermetallic phases, the internal friction technique allows to study the state of solid solution and kinetics of changes in the relative amounts of ferrite and austenite phases during thermal treatment.

  8. Distinguishing between chi and sigma phases in duplex stainless steels using potentiostatic etching

    SciTech Connect

    Jackson, E.M.L.E.M.; Visser, P.E. de . Physical Metallurgy Div.); Cornish, L.A. )

    1993-12-01

    A color interference film etching technique based on the principle of potentiostatic etching has been developed to distinguish, by optical metallography, between Cr-rich sigma and Mo-rich chi phases as well as with simultaneous identification of the ferrite and austenite phases in duplex stainless steels. The optical metallography results are confirmed by semiquantitative energy dispersive spectrometry analysis and back-scattered electron imaging. The technique is relatively simple and rapid, and makes use of low voltages and a hot etchant. Results have shown distinctively the sigma, chi, ferrite, and austenite phases, and enable observation of the microstructural development, morphology, and kinetics of formation of the phases in duplex alloys. The method, by giving excellent color contrast between sigma and chi, also facilitates quantitative image analysis of the sigma and chi volume fractions.

  9. Sites of Predicted Stress-Induced DNA Duplex Destabilization Occur Preferentially at Regulatory Loci

    NASA Astrophysics Data System (ADS)

    Benham, Craig J.

    1993-04-01

    This paper describes a computational method to predict the sites on a DNA molecule where imposed superhelical stresses destabilize the duplex. Several DNA sequences are analyzed in this way, including the pBR322 and ColE1 plasmids, bacteriophage f1, and the polyoma and bovine papilloma virus genomes. Superhelical destabilization in these molecules is predicted to occur at small numbers of discrete sites, most of which are within regulatory regions. The most destabilized sites include the terminator and promoter regions of specific plasmid operons, the LexA binding sites of genes under SOS control, the intergenic control region of bacteriophage f1, and the polyadenylylation sites in eukaryotic viruses. These results demonstrate the existence of close correspondences between sites of predicted superhelical duplex destabilization and specific types of regulatory regions. The use of these correspondences to supplement string-matching techniques in the search for regulatory loci is discussed.

  10. Progress Towards the Development of a Long-Lived Venus Lander Duplex System

    NASA Technical Reports Server (NTRS)

    Dyson, Roger W.; Bruder, Geoffrey A.

    2010-01-01

    NASA has begun the development of a combined Stirling cycle power and cooling system (duplex) to enable the long-lived surface exploration of Venus and other harsh environments in the solar system. The duplex system will operate from the heat provided by decaying radioisotope plutonium-238 or its substitute. Since the surface of Venus has a thick, hot, and corrosive atmosphere, it is a challenging proposition to maintain sensitive lander electronics under survivable conditions. This development effort requires the integration of: a radioisotope or fission heat source; heat pipes; high-temperature, corrosion-resistant material; multistage cooling; a novel free-displacer Stirling convertor for the lander; and a minimal vibration thermoacoustic Stirling convertor for the seismometer. The first year effort includes conceptual system design and control studies, materials development, and prototype hardware testing. A summary of these findings and test results is presented in this report.

  11. Corrosion failure of duplex stainless steel equipment in a PVC plant

    SciTech Connect

    Davies, M.; Potgieter, G.

    2000-05-01

    After <9 months of operation in a polyvinyl chloride (PVC) manufacturing plant, alloy 2205 duplex stainless steel (UNS 31803) columns and spiral heat exchangers (HXs) were corroding and cracking. The columns were repaired and remained in service but the HXs needed to be replaced. Candidate materials for the HXs were assessed, and it was found that the super-austenitic alloys containing 6% molybdenum would be more appropriate for this application.

  12. Is Duplex-Ultrasound a useful tool in defining rejection episodes in composite tissue allograft transplants?

    PubMed

    Loizides, Alexander; Kronberger, Irmgard-Elisabeth; Plaikner, Michaela; Gruber, Hannes

    2015-12-01

    Immunologic reactions in transplanted organs are in more or less all allograft patients detectable: clear parameters exist as e.g. in renal transplants where the clearance power reduces by rejection. On the contrary, in composite tissue allografts clear and objective indicators stating a rejection episode lack. We present the case of a hand-transplanted subject with signs of acute transplant rejection diagnosed by means of Duplex Ultrasound and confirmed by biopsy.

  13. Diagnosis of gastric cryptosporidiosis in birds using a duplex real-time PCR assay.

    PubMed

    Nakamura, Alex A; Homem, Camila G; da Silva, Adriana M J; Meireles, Marcelo V

    2014-09-15

    Three species and several genotypes of Cryptosporidium can infect the epithelial surface of the bursa of Fabricius, the respiratory tract, the proventriculus, the intestine, and the urinary tract in birds. There is reason to believe that gastric cryptosporidiosis in birds is caused by Cryptosporidium galli and Cryptosporidium avian genotype III, resulting in a chronic illness of the proventriculus that can lead to a debilitating and fatal clinical condition in birds of the orders Passeriformes and Psittaciformes. The objectives of the present study were to develop a duplex real-time polymerase chain reaction (PCR) that targets the 18S rRNA gene to simultaneously detect C. galli and Cryptosporidium avian genotype III DNA and to compare the duplex real-time PCR results to those of nested PCR targeting a partial fragment of the 18S rRNA gene, followed by sequencing of the amplified products (nPCR/S). A total of 1027 fecal samples were collected from birds of the orders Psittaciformes and Passeriformes originating either from captivity or the wild. Duplex real-time PCR results were positive in 580 (56.47%) and 21 (2.04%) samples, respectively, for C. galli and Cryptosporidium avian genotype III, whereas nPCR/S was positive in 28 (2.73%) and three (0.29%) samples, respectively, for C. galli and Cryptosporidium avian genotype III. Novel host birds were identified for both of the above gastric species, and it was also possible to identify Cryptosporidium baileyi and, for the first time in Brazil, Cryptosporidium avian genotype V. The duplex real-time PCR assay developed in the present study represents a sensitive and specific method for the detection of C. galli and Cryptosporidium avian genotype III in bird fecal samples. Moreover, this method may serve as an alternative to nPCR/S as a gold standard for the diagnosis of gastric cryptosporidiosis in birds.

  14. Detection of Pathogenic Yersinia enterocolitica by a Rapid and Sensitive Duplex PCR Assay

    PubMed Central

    Wannet, Wim J. B.; Reessink, Michiel; Brunings, Henk A.; Maas, Henny M. E.

    2001-01-01

    A duplex PCR assay targeting the ail and 16S rRNA genes of Yersinia enterocolitica was developed to specifically identify pathogenic Y. enterocolitica from pure culture. Validation of the assay was performed with 215 clinical Yersinia strains and 40 strains of other bacterial species. Within an assay time of 4 h, this assay offers a very specific, reliable, and inexpensive alternative to the conventional phenotypic assays used in clinical laboratories to identify pathogenic Y. enterocolitica. PMID:11724866

  15. Finite Element Stress Model of a Strike-Slip Duplex: A Case Study from Southern Chile

    NASA Astrophysics Data System (ADS)

    Iturrieta, P. C.; Hurtado, D.; Cembrano, J. M.; Valderrama, C.; Stanton-Yonge, A.

    2015-12-01

    The Liquiñe-Ofqui Fault System (LOFS) is spatially and genetically related to seismic activity, volcanic hazard and hydrothermal resources in southern Chile. The LOFS is a regional-scale shear zone, which accommodates part of the oblique component of the convergence vector. In the LOFS southern end, an extensional strike-slip duplex arises from the connection between two NNE-striking master faults, where two damaging earthquakes (6.1-6.2 Mw) occurred in 2007. In order to understand the nature and origin of the stress field within the duplex area, we calculate the ellipticity of the stress tensor field by means of a 3D finite element model. The model represents the brittle-plastic transition in the mid crust, within which the fault zone is mechanically distinguished from the host rock in a continuum fashion. The fault zone is modeled by using an elastic-plastic constitutive relation, which is built on the basis of a range of width and orientation of mylonitic bands, representing the fault zone as seen in the field. Boundary conditions reproduce the convergence velocity between Nazca and South-America plates. Results are broadly consistent with structural data and seismicity recorded in the region. Extensional-to-transtensional stress regimes match spatially with a seismic swarm recorded in the region in 2007, and with the spatial distribution of quaternary volcanic centers. The model also shows a transpressive state of stress in the western branch of the LOFS, whereas in the eastern branch, pure strike-slip is obtained. We propose that the current duplex kinematics can be explained by convergence obliquity, duplex geometry and the occurrence of plastic deformation, which are sufficient enough to deliver the current stress configuration. Sources of discrepancy between structural data and model results might be explained by other factors not considered by the model, such as the timing of deformation or the current activity of blind faults.

  16. Solution conformation of the (-)-trans-anti-5-methylchrysene-dG adduct opposite dC in a DNA duplex: DNA bending associated with wedging of the methyl group of 5-methylchrysene to the 3'-side of the modification site.

    PubMed

    Cosman, M; Xu, R; Hingerty, B E; Amin, S; Harvey, R G; Geacintov, N E; Broyde, S; Patel, D J

    1995-05-01

    This paper reports on NMR-molecular mechanics structural studies of the (-)-trans-anti-[MC]dG adduct positioned opposite dC in the sequence context of the d(C1-C2-A3-T4-C5-[MC]G6-C7-T8-A9-C10-C11).d(G12-G13-T14++ +-A15-G16-C17-G18- A19-T20-G21-G22) duplex [designated (-)-trans-anti-[MC]dG.dC 11-mer duplex]. This adduct is derived from the trans addition at C4 of (-)-anti-1(S),2(R)-dihydroxy-3(R),4(S)-epoxy-1,2,3,4-tetrahydro-5-met hylchrysen e [(-)-anti-5-MeCDE] to the N2 position of dG6 in this duplex sequence. The 5-methyl group is located adjacent to the MC(C4) binding site, with these groups juxtaposed in a sterically crowded bay region in the adduct duplex. The 5-methylchrysenyl and the nucleic acid exchangeable and nonexchangeable protons were assigned following analysis of two-dimensional NMR data sets in H2O and D2O buffer solution. The solution structure of the (-)-trans-anti-[MC]dG.dC 11-mer duplex has been determined by incorporating DNA-DNA and carcinogen-DNA proton-proton distances defined by lower and upper bounds deduced from NOESY data sets as restraints in molecular mechanics computations in torsion angle space. The results establish that the [MC]dG6.dC17 base pair and flanking dC5.dG18 and dC7.dG16 base pairs retain Watson-Crick alignments upon adduct formation. The aromatic chrysenyl ring is positioned in the minor groove of a right-handed B-DNA helix and stacks predominantly over the sugar of the dC17 residue across from it on the unmodified complementary strand. The chrysenyl ring points toward the 3'-end of the modified strand with its 5-methyl group inserting between the modified [MC]dG6.dC17 and dC7.dG16 base pairs. The adduct duplex bends by approximately 47 degrees as a result of the wedged insertion of the 5-methyl group from the minor groove face of the duplex. The solution structure of the (-)-trans-anti-[MC] dG.dC 11-mer duplex is compared with that of the corresponding (-)-trans-anti-[BP]dG.dC 11-mer [De los Santos et al. (1992

  17. Superconductivity: The persistence of pairs

    SciTech Connect

    Edelman, Alex; Littlewood, Peter

    2015-05-20

    Superconductivity stems from a weak attraction between electrons that causes them to form bound pairs and behave much like bosons. These so-called Cooper pairs are phase coherent, which leads to the astonishing properties of zero electrical resistance and magnetic flux expulsion typical of superconducting materials. This coherent state may be qualitatively understood within the Bose–Einstein condensate (BEC) model, which predicts that a gas of interacting bosons will become unstable below a critical temperature and condense into a phase of matter with a macroscopic, coherent population in the lowest energy state, as happens in 4He or cold atomic gases. The successful theory proposed by Bardeen, Cooper and Schrieffer (BCS) predicts that at the superconducting transition temperature Tc, electrons simultaneously form pairs and condense, with no sign of pairing above Tc. Theorists have long surmised that the BCS and BEC models are opposite limits of a single theory and that strong interactions or low density can, in principle, drive the system to a paired state at a temperature Tpair higher than Tc, making the transition to the superconducting state BEC-like (Fig. 1). Yet most superconductors to date are reasonably well described by BCS theory or its extensions, and there has been scant evidence in electronic materials for the existence of pairing independent of the full superconducting state (though an active debate rages over the cuprate superconductors). Writing in Nature, Jeremy Levy and colleagues have now used ingenious nanostructured devices to provide evidence for electron pairing1. Perhaps surprisingly, the material they have studied is a venerable, yet enigmatic, low-temperature superconductor, SrTiO3.

  18. Study of Aging Effects in 2205 Duplex Stainless Steel Using Thermoelectric Power Measurement

    NASA Astrophysics Data System (ADS)

    Lara, N.; Ruiz, A.; Carreón, H.; Medina, A.; Sánchez, A.

    2010-02-01

    Thermoelectric power (TEP) measurements have been used as an effective method for evaluating the metallurgical state of various alloys. In the steel industry, some fabrication processes promote phase transformation and second phase precipitations which affect the material properties. Assessment of mechanical properties is critical in order to ensure quality of components. This work was conducted in order to evaluate the influence of the aging state of 2205 duplex stainless steel on TEP values. Commercial 2205 duplex steel was isothermally aged at 650 °C 700 °C and 900 °C at different aging times. TEP measurement technique was applied as a non destructive assessment technique to characterize the aging kinetics of the aged 2205 duplex stainless steel, hardness Rockwell (RC) and Charpy impact test were preformed to observe the effect of aging time on the specimens. Metallographic analysis was used to monitor phase transformation and sigma phase precipitation caused by the spinodal decomposition process of ferrite into secondary austenite and sigma phase. Results indicate that that the TEP is sensitive to gradual microstructural changes produced by the aging treatments.

  19. A general strategy to inhibiting viral -1 frameshifting based on upstream attenuation duplex formation.

    PubMed

    Hu, Hao-Teng; Cho, Che-Pei; Lin, Ya-Hui; Chang, Kung-Yao

    2016-01-01

    Viral -1 programmed ribosomal frameshifting (PRF) as a potential antiviral target has attracted interest because many human viral pathogens, including human immunodeficiency virus (HIV) and coronaviruses, rely on -1 PRF for optimal propagation. Efficient eukaryotic -1 PRF requires an optimally placed stimulator structure downstream of the frameshifting site and different strategies targeting viral -1 PRF stimulators have been developed. However, accessing particular -1 PRF stimulator information represents a bottle-neck in combating the emerging epidemic viral pathogens such as Middle East respiratory syndrome coronavirus (MERS-CoV). Recently, an RNA hairpin upstream of frameshifting site was shown to act as a cis-element to attenuate -1 PRF with mechanism unknown. Here, we show that an upstream duplex formed in-trans, by annealing an antisense to its complementary mRNA sequence upstream of frameshifting site, can replace an upstream hairpin to attenuate -1 PRF efficiently. This finding indicates that the formation of a proximal upstream duplex is the main determining factor responsible for -1 PRF attenuation and provides mechanistic insight. Additionally, the antisense-mediated upstream duplex approach downregulates -1 PRF stimulated by distinct -1 PRF stimulators, including those of MERS-CoV, suggesting its general application potential as a robust means to evaluating viral -1 PRF inhibition as soon as the sequence information of an emerging human coronavirus is available. PMID:26612863

  20. A full-duplex CATV/wireless-over-fiber lightwave transmission system.

    PubMed

    Li, Chung-Yi; Lu, Hai-Han; Ying, Cheng-Ling; Cheng, Chun-Jen; Lin, Che-Yu; Wan, Zhi-Wei; Chen, Jian-Hua

    2015-04-01

    A full-duplex CATV/wireless-over-fiber lightwave transmission system consisting of one broadband light source (BLS), two optical interleavers (ILs), one intensity modulator, and one phase modulator is proposed and experimentally demonstrated. The downstream light is optically promoted from 10Gbps/25GHz microwave (MW) data signal to 10Gbps/100GHz and 10Gbps/50GHz millimeter-wave (MMW) data signals in fiber-wireless convergence, and intensity-modulated with 50-550 MHz CATV signal. For up-link transmission, the downstream light is phase-remodulated with 10Gbps/25GHz MW data signal in fiber-wireless convergence. Over a 40-km single-mode fiber (SMF) and a 10-m radio frequency (RF) wireless transport, bit error rate (BER), carrier-to-noise ratio (CNR), composite second-order (CSO), and composite triple-beat (CTB) are observed to perform well in such full-duplex CATV/wireless-over-fiber lightwave transmission systems. This full-duplex 100-GHz/50-GHz/25-GHz/550-MHz lightwave transmission system is an attractive alternative. This transmission system not only presents its advancement in the integration of fiber backbone and CATV/wireless feeder networks, but also it provides the advantages of a communication channel for higher data rates and bandwidth.

  1. Phase Transformations During the Low-Temperature Nitriding of AISI 2205 Duplex Stainless Steel

    NASA Astrophysics Data System (ADS)

    Yan, Jing; Gu, Tan; Qiu, Shaoyu; Wang, Jun; Xiong, Ji; Fan, Hongyuan

    2015-02-01

    Liquid nitriding of type AISI 2205 duplex stainless steel was conducted at 723 K (450 °C), using one type of novel low-temperature liquid chemical thermo-treatment. The transformation of the nitrided surface microstructure was systematically studied. Experimental results revealed that a nitrided layer formed on the sample surface with the thickness ranging from 3 to 28 μm, depending on nitriding time. After the 2205 duplex stainless steel was subjected to liquid nitriding 723 K (450 °C) for less than 8 hours, the pre-existing ferrite region on the surface transformed into the expanded austenite (S phase) by the infusion of nitrogen atoms, most of which stay in the interstitial sites. Generally, the dominant phase of the nitrided layer was the expanded austenite. When the nitriding time prolonged up to 16 hours, some pre-existing ferrite in expanded austenite was decomposed and ɛ-nitride precipitated subsequently. When the treatment time went up to 40 hours, large amount of ɛ-nitride and CrN precipitates were observed in the pre-existing ferritic region in the expanded austenite. Furthermore, many nitrides precipitated from the pre-austenite region. Acicular nitride was identified by transmission electron microscopy. The thickness of the nitrided layer increased with increasing nitriding time. The growth of the nitrided layer is mainly due to nitrogen diffusion in accordance with the expected parabolic rate law. Liquid nitriding effectively increased the surface hardness of 2205 duplex stainless steel by a factor of 3.

  2. STUDY OF AGING EFFECTS IN 2205 DUPLEX STAINLESS STEEL USING THERMOELECTRIC POWER MEASUREMENT

    SciTech Connect

    Lara, N.; Ruiz, A.; Carreon, H.; Medina, A.; Sanchez, A.

    2010-02-22

    Thermoelectric power (TEP) measurements have been used as an effective method for evaluating the metallurgical state of various alloys. In the steel industry, some fabrication processes promote phase transformation and second phase precipitations which affect the material properties. Assessment of mechanical properties is critical in order to ensure quality of components. This work was conducted in order to evaluate the influence of the aging state of 2205 duplex stainless steel on TEP values. Commercial 2205 duplex steel was isothermally aged at 650 deg. C 700 deg. C and 900 deg. C at different aging times. TEP measurement technique was applied as a non destructive assessment technique to characterize the aging kinetics of the aged 2205 duplex stainless steel, hardness Rockwell (RC) and Charpy impact test were preformed to observe the effect of aging time on the specimens. Metallographic analysis was used to monitor phase transformation and sigma phase precipitation caused by the spinodal decomposition process of ferrite into secondary austenite and sigma phase. Results indicate that that the TEP is sensitive to gradual microstructural changes produced by the aging treatments.

  3. Microstructure/property relationships in dissimilar welds between duplex stainless steels and carbon steels

    SciTech Connect

    Barnhouse, E.J.; Lippold, J.C.

    1998-12-01

    The metallurgical characteristics, toughness and corrosion resistance of dissimilar welds between duplex stainless steel Alloy 2205 and carbon steel A36 have been evaluated. Both duplex stainless steel ER2209 and Ni-based Alloy 625 filler metals were used to join this combination using a multipass, gas tungsten arc welding (GTAW) process. Defect-free welds were made with each filler metal. The toughness of both the 625 and 2209 deposits were acceptable, regardless of heat input. A narrow martensitic region with high hardness was observed along the A36/2209 fusion boundary. A similar region was not observed in welds made with the 625 filler metal. The corrosion resistance of the welds made with 2209 filler metal improved with increasing heat input, probably due to higher levels of austenite and reduced chromium nitride precipitation. Welds made with 625 exhibited severe attack in the root pass, while the bulk of the weld was resistant. This investigation has shown that both filler metals can be used to joint carbon steel to duplex stainless steels, but that special precautions may be necessary in corrosive environments.

  4. Development of quantitative duplex real-time PCR method for screening analysis of genetically modified maize.

    PubMed

    Oguchi, Taichi; Onishi, Mari; Minegishi, Yasutaka; Kurosawa, Yasunori; Kasahara, Masaki; Akiyama, Hiroshi; Teshima, Reiko; Futo, Satoshi; Furui, Satoshi; Hino, Akihiro; Kitta, Kazumi

    2009-06-01

    A duplex real-time PCR method was developed for quantitative screening analysis of GM maize. The duplex real-time PCR simultaneously detected two GM-specific segments, namely the cauliflower mosaic virus (CaMV) 35S promoter (P35S) segment and an event-specific segment for GA21 maize which does not contain P35S. Calibration was performed with a plasmid calibrant specially designed for the duplex PCR. The result of an in-house evaluation suggested that the analytical precision of the developed method was almost equivalent to those of simplex real-time PCR methods, which have been adopted as ISO standard methods for the analysis of GMOs in foodstuffs and have also been employed for the analysis of GMOs in Japan. In addition, this method will reduce both the cost and time requirement of routine GMO analysis by half. The high analytical performance demonstrated in the current study would be useful for the quantitative screening analysis of GM maize. We believe the developed method will be useful for practical screening analysis of GM maize, although interlaboratory collaborative studies should be conducted to confirm this. PMID:19602858

  5. Pulsed IR heating studies of single-molecule DNA duplex dissociation kinetics and thermodynamics.

    PubMed

    Holmstrom, Erik D; Dupuis, Nicholas F; Nesbitt, David J

    2014-01-01

    Single-molecule fluorescence spectroscopy is a powerful technique that makes it possible to observe the conformational dynamics associated with biomolecular processes. The addition of precise temperature control to these experiments can yield valuable thermodynamic information about equilibrium and kinetic rate constants. To accomplish this, we have developed a microscopy technique based on infrared laser overtone/combination band absorption to heat small (≈10(-11) liter) volumes of water. Detailed experimental characterization of this technique reveals three major advantages over conventional stage heating methods: 1), a larger range of steady-state temperatures (20-100°C); 2), substantially superior spatial (≤20 μm) control; and 3), substantially superior temporal (≈1 ms) control. The flexibility and breadth of this spatial and temporally resolved laser-heating approach is demonstrated in single-molecule fluorescence assays designed to probe the dissociation of a 21 bp DNA duplex. These studies are used to support a kinetic model based on nucleic acid end fraying that describes dissociation for both short (<10 bp) and long (>10 bp) DNA duplexes. These measurements have been extended to explore temperature-dependent kinetics for the 21 bp construct, which permit determination of single-molecule activation enthalpies and entropies for DNA duplex dissociation.

  6. Multivalent IDP assemblies: Unique properties of LC8-associated, IDP duplex scaffolds.

    PubMed

    Clark, Sarah A; Jespersen, Nathan; Woodward, Clare; Barbar, Elisar

    2015-09-14

    A wide variety of subcellular complexes are composed of one or more intrinsically disordered proteins (IDPs) that are multivalent, flexible, and characterized by dynamic binding of diverse partner proteins. These multivalent IDP assemblies, of broad functional diversity, are classified here into five categories distinguished by the number of IDP chains and the arrangement of partner proteins in the functional complex. Examples of each category are summarized in the context of the exceptional molecular and biological properties of IDPs. One type - IDP duplex scaffolds - is considered in detail. Its unique features include parallel alignment of two IDP chains, formation of new self-associated domains, enhanced affinity for additional bivalent ligands, and ubiquitous binding of the hub protein LC8. For two IDP duplex scaffolds, dynein intermediate chain IC and nucleoporin Nup159, these duplex features, together with the inherent flexibility of IDPs, are central to their assembly and function. A new type of IDP-LC8 interaction, distributed binding of LC8 among multiple IDP recognition sites, is described for Nup159 assembly. PMID:26226419

  7. Magnesium effect on premelting transitions in nucleic acids: DNA duplex and RNA hairpin models

    NASA Astrophysics Data System (ADS)

    Ottová, Pavla; Espinoza-Herrera, Shirly Josefina; Štěpánek, Josef

    2011-05-01

    The effect of magnesium ions on the conformational changes in the temperature region below the melting transition (premelting transitions) of a DNA duplex and an RNA hairpin was studied by difference Raman spectroscopy. The chosen model systems were the polynucleotide poly(dA)-poly(dT) duplex and the apical hairpin of the trans-activation response (TAR) element of HIV-1. Magnesium effect was displayed by differences of Raman spectra measured at various temperatures with and without magnesium ions. Our results have revealed that magnesium ions influence measurably the premelting transitions in both cases; the extent of the effect and its character is though quite different. In the case of the B' → B premelting transition of the polynucleotide poly(dA)-poly(dT) duplex, magnesium binds to the minor groove of the B but not of the B' form and acts again the rearrangement in the vicinity of the thymidine keto-groups. On the other hand, the magnesium effect on the TAR hairpin premelting consists in a weak support of the premelting structural change via more effective electrostatic shielding.

  8. Laser Shock Processing with Different Conditions of Treatment on Duplex Stainless Steel

    NASA Astrophysics Data System (ADS)

    Castañeda, E.; Rubio-Gonzalez, C.; Chavez-Chavez, A.; Gomez-Rosas, G.

    2015-06-01

    The laser shock processing (LSP) has been developed as an effective alternative to traditional methods for improvement of metallic materials properties and as surface treatment to metals. Duplex stainless steel is a material that has a microstructure formed by two phases, with approximately equal amounts of each one. This stainless steel has wide applications in different fields like shipping, petrochemical, and chemical industries. We present results of the LSP performance using two pulse density configurations of 2500 and 5000 pulses/cm2, both of them at laser irradiation of 532 and 1064 nm (keeping approximately constant power density), in order to treat in under water-jet the surface of 2205 duplex stainless steel samples without coating. A flat mirror and a converging lens is used to deliver 400 mJ/pulse, (5 ns FWHM, 1.1 mm spot diameter with 532 nm wavelength) and 850 mJ/pulse, (6 ns FWHM, 1.5 mm spot diameter with 1064 nm wavelength) laser pulse produced by 10 Hz Q-switched Nd:YAG laser. A motor-controlled x-y precision stage is used, for sweep the treated zone on sample. The use of two wavelengths with approximately the same power density is an effective way for obtaining high compressive residual stresses (~90% of the yield stress). An improvement of hardness (12-25%) at the surface of 2205 duplex stainless steel due to LSP is presented.

  9. Application of martensitic, modified martensitic and duplex stainless steel bar stock for completion equipment

    SciTech Connect

    Bhavsar, R.B.; Montani, R.

    1998-12-31

    Martensitic and duplex stainless steel tubing are commonly used for oil and gas applications containing CO{sub 2}. Completion equipment manufacturing requires use of solid round bar or heavy wall hollows. Material properties for this stock are not identical in all cases. Material properties as well as corrosion characteristics are discussed for 13Cr, 13Cr-5Ni-2Mo and 25Cr alloys. Corrosion testing of modified or Enhanced 13Cr solid bar stock, UNS S41425 and other compositions in H{sub 2}S-Cl{sup {minus}} and pH is reported in coupled and uncoupled condition. Corrosion testing of various super duplex bar stock at various H{sub 2}S-chlorides and temperature in CO{sub 2} environment is reported. Impact value requirements, welding issues and special consideration required for these alloys for completion equipment is discussed. Modified 13Cr and Super Duplex Oil Country Tubular Goods (OCTG) are readily available, however, availability of completion equipment raw material compatible with these OCTG is limited.

  10. Human CST has independent functions during telomere duplex replication and C-strand fill-in

    PubMed Central

    Wang, Feng; Stewart, Jason A.; Kasbek, Christopher; Zhao, Yong; Wright, Woodring E.; Price, Carolyn M.

    2012-01-01

    Summary Human CST (CTC1-STN1-TEN1) is an RPA-like complex that is needed for efficient replication through the telomere duplex and genome-wide replication restart after fork stalling. Here we show that STN1/CST has a second function in telomere replication during G-overhang maturation. Analysis of overhang structure after STN1 depletion revealed normal kinetics for telomerase-mediated extension in S-phase but a delay in subsequent overhang shortening. This delay resulted from a defect in C-strand fill-in. Short telomeres exhibited the fill-in defect but normal telomere duplex replication, indicating that STN1/CST functions independently in these processes. Our work also indicates that the requirement for STN1/CST in telomere duplex replication correlates with increasing telomere length and replication stress. Our results provide the first direct evidence that STN1/CST participates in C-strand fill-in. They also demonstrate that STN1/CST participates in two mechanistically separate steps during telomere replication and identify CST as a novel replication factor that solves diverse replication-associated problems. PMID:23142664

  11. Pulsed IR Heating Studies of Single-Molecule DNA Duplex Dissociation Kinetics and Thermodynamics

    PubMed Central

    Holmstrom, Erik D.; Dupuis, Nicholas F.; Nesbitt, David J.

    2014-01-01

    Single-molecule fluorescence spectroscopy is a powerful technique that makes it possible to observe the conformational dynamics associated with biomolecular processes. The addition of precise temperature control to these experiments can yield valuable thermodynamic information about equilibrium and kinetic rate constants. To accomplish this, we have developed a microscopy technique based on infrared laser overtone/combination band absorption to heat small (≈10−11 liter) volumes of water. Detailed experimental characterization of this technique reveals three major advantages over conventional stage heating methods: 1), a larger range of steady-state temperatures (20–100°C); 2), substantially superior spatial (≤20 μm) control; and 3), substantially superior temporal (≈1 ms) control. The flexibility and breadth of this spatial and temporally resolved laser-heating approach is demonstrated in single-molecule fluorescence assays designed to probe the dissociation of a 21 bp DNA duplex. These studies are used to support a kinetic model based on nucleic acid end fraying that describes dissociation for both short (<10 bp) and long (>10 bp) DNA duplexes. These measurements have been extended to explore temperature-dependent kinetics for the 21 bp construct, which permit determination of single-molecule activation enthalpies and entropies for DNA duplex dissociation. PMID:24411254

  12. Development of quantitative duplex real-time PCR method for screening analysis of genetically modified maize.

    PubMed

    Oguchi, Taichi; Onishi, Mari; Minegishi, Yasutaka; Kurosawa, Yasunori; Kasahara, Masaki; Akiyama, Hiroshi; Teshima, Reiko; Futo, Satoshi; Furui, Satoshi; Hino, Akihiro; Kitta, Kazumi

    2009-06-01

    A duplex real-time PCR method was developed for quantitative screening analysis of GM maize. The duplex real-time PCR simultaneously detected two GM-specific segments, namely the cauliflower mosaic virus (CaMV) 35S promoter (P35S) segment and an event-specific segment for GA21 maize which does not contain P35S. Calibration was performed with a plasmid calibrant specially designed for the duplex PCR. The result of an in-house evaluation suggested that the analytical precision of the developed method was almost equivalent to those of simplex real-time PCR methods, which have been adopted as ISO standard methods for the analysis of GMOs in foodstuffs and have also been employed for the analysis of GMOs in Japan. In addition, this method will reduce both the cost and time requirement of routine GMO analysis by half. The high analytical performance demonstrated in the current study would be useful for the quantitative screening analysis of GM maize. We believe the developed method will be useful for practical screening analysis of GM maize, although interlaboratory collaborative studies should be conducted to confirm this.

  13. Common carotid artery duplex for the bubble test to detect right-to-left shunt.

    PubMed

    Censori, Bruno; Partziguian, Tania; Poloni, Marco

    2010-04-01

    We prospectively compared the bubble test with agitated saline for right-to-left shunt using transcranial Doppler (TCD) of the right middle cerebral artery and second harmonic imaging duplex of the right common carotid artery (CCA) in 100 consecutive patients. Microembolic signals (MES) were counted offline. MES were classified into 6 classes: absent (class 0), 1-10 MES (class 1), 11-20 MES (class 2), 21-30 MES (class 3), 31-50 MES (class 4) and >50 MES or "curtain effect" (class 5). For TCD, classes 2-5 combined (i.e., "large" shunts), the sensitivity of duplex with the Valsalva maneuver was 95.3%, the specificity was 100%, the positive predictive 100%, the negative predictive value 96.6% and accuracy 98.0%. Second harmonic imaging duplex of the CCA may substitute TCD for the bubble test when an adequate cranial bone window is not available. This technique may also greatly increase the number of facilities where the bubble test can be carried out. However, tests with few or no MES need to be confirmed by TCD or transesophageal echocardiography.

  14. End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes.

    PubMed

    Smolina, Irina V; Demidov, Vadim V; Soldatenkov, Viatcheslav A; Chasovskikh, Sergey G; Frank-Kamenetskii, Maxim D

    2005-01-01

    Peptide nucleic acid (PNA) is a synthetic DNA mimic with valuable properties and a rapidly growing scope of applications. With the exception of recently introduced pseudocomplementary PNAs, binding of common PNA oligomers to target sites located inside linear double-stranded DNAs (dsDNAs) is essentially restricted to homopurine-homopyrimidine sequence motifs, which significantly hampers some of the PNA applications. Here, we suggest an approach to bypass this limitation of common PNAs. We demonstrate that PNA with mixed composition of ordinary nucleobases is capable of sequence-specific targeting of complementary dsDNA sites if they are located at the very termini of DNA duplex. We then show that such targeting makes it possible to perform capturing of designated dsDNA fragments via the DNA-bound biotinylated PNA as well as to signal the presence of a specific dsDNA sequence, in the case a PNA beacon is employed. We also examine the PNA-DNA conjugate and prove that it can initiate the primer-extension reaction starting from the duplex DNA termini when a DNA polymerase with the strand-displacement ability is used. We thus conclude that recognition of duplex DNA by mixed-base PNAs via the end invasion has a promising potential for site-specific and sequence-unrestricted DNA manipulation and detection.

  15. Phase transitions in the q -voter model with noise on a duplex clique

    NASA Astrophysics Data System (ADS)

    Chmiel, Anna; Sznajd-Weron, Katarzyna

    2015-11-01

    We study a nonlinear q -voter model with stochastic noise, interpreted in the social context as independence, on a duplex network. To study the role of the multilevelness in this model we propose three methods of transferring the model from a mono- to a multiplex network. They take into account two criteria: one related to the status of independence (LOCAL vs GLOBAL) and one related to peer pressure (AND vs OR). In order to examine the influence of the presence of more than one level in the social network, we perform simulations on a particularly simple multiplex: a duplex clique, which consists of two fully overlapped complete graphs (cliques). Solving numerically the rate equation and simultaneously conducting Monte Carlo simulations, we provide evidence that even a simple rearrangement into a duplex topology may lead to significant changes in the observed behavior. However, qualitative changes in the phase transitions can be observed for only one of the considered rules: LOCAL&AND. For this rule the phase transition becomes discontinuous for q =5 , whereas for a monoplex such behavior is observed for q =6 . Interestingly, only this rule admits construction of realistic variants of the model, in line with recent social experiments.

  16. The structure and duplex context of DNA interstrand crosslinks affects the activity of DNA polymerase η

    PubMed Central

    Roy, Upasana; Mukherjee, Shivam; Sharma, Anjali; Frank, Ekaterina G.; Schärer, Orlando D.

    2016-01-01

    Several important anti-tumor agents form DNA interstrand crosslinks (ICLs), but their clinical efficiency is counteracted by multiple complex DNA repair pathways. All of these pathways require unhooking of the ICL from one strand of a DNA duplex by nucleases, followed by bypass of the unhooked ICL by translesion synthesis (TLS) polymerases. The structures of the unhooked ICLs remain unknown, yet the position of incisions and processing of the unhooked ICLs significantly influence the efficiency and fidelity of bypass by TLS polymerases. We have synthesized a panel of model unhooked nitrogen mustard ICLs to systematically investigate how the state of an unhooked ICL affects pol η activity. We find that duplex distortion induced by a crosslink plays a crucial role in translesion synthesis, and length of the duplex surrounding an unhooked ICL critically affects polymerase efficiency. We report the synthesis of a putative ICL repair intermediate that mimics the complete processing of an unhooked ICL to a single crosslinked nucleotide, and find that it provides only a minimal obstacle for DNA polymerases. Our results raise the possibility that, depending on the structure and extent of processing of an ICL, its bypass may not absolutely require TLS polymerases. PMID:27257072

  17. Compact design of high-temperature superconducting duplexer and triplexer for satellite communications

    NASA Astrophysics Data System (ADS)

    Zhang, Xu; He, Ming; Ji, Lu; Zhao, Xinjie; Fang, Lan; Yan, Shaolin

    2012-10-01

    This paper presents a compact C-band high-temperature superconducting (HTS) input module duplexer, which can be scaled to a triplexer. The duplexer includes a common node as the input port, which is an extensible and effective structure for integrating a HTS multiplexer on a single superconducting film. The input node is realized by an open-loop microstrip line, which resonates at the frequency in the guard band between the two channels. In addition two four-pole bandpass filters consisting of rectangular spiral line resonators are used as output channels of the device. The duplexer is designed at 3995 MHz with a bandwidth of 226 MHz. The frequency ranges of the two channels are 3882-3942 MHz and 4048-4108 MHz, respectively. It is fabricated using double-sided Y Ba2Cu3O7 (YBCO) thin films on a piece of 30× 10 mm 2 MgO substrate. The experimental results show that the insertion loss is less than 0.1 dB for both channel filters and the isolation between the two channels is higher than 40 dB. Good agreement has been achieved between simulations and measurements to illustrate the effectiveness of the proposed approach. Moreover, the triplexer is also designed and measured and the scalability is verified by simulation and experiments.

  18. Microstructure and mechanical properties of duplex stainless steel subjected to hydrostatic extrusion

    SciTech Connect

    Maj, P.; Adamczyk-Cieślak, B.; Mizera, J.; Pachla, W.; Kurzydłowski, K.J.

    2014-07-01

    The nanostructure and mechanical properties of ferritic-austenitic duplex stainless steel subjected to hydrostatic extrusion were examined. The refinement of the structure in the initial state and in the two deformation states (ε = 1.4 and ε = 3.8) was observed in an optical microscope (OM) and a transmission electron microscope (TEM). The results indicate that the structure evolved from microcrystalline with a grain size of about 4 μm to nanocrystalline with a grain size of about 150 nm in ferrite and 70 nm in austenite. The material was characterized mechanically by tensile tests performed in the two deformation states. The ultimate strength appeared to increase significantly compared to that in the initial deformation stages, which can be attributed to the grain refinement and plastic deformation. The heterogeneity observed in microregions results from the dual-phase structure of the steel. The results indicate that hydrostatic extrusion is a highly potential technology suitable for improving the properties of duplex steels. - Highlights: • Duplex stainless steel was hydro extruded to a total strain of 3.8 • After the last stage of deformation heterogeneous structure was obtained in the material • As a result of stresses non-diffusive transformation γ→α’ occurred in the material • Nanometric (sub)grains were obtained in the austenite regions.

  19. Ion Channels Made from a Single Membrane-Spanning DNA Duplex

    PubMed Central

    2016-01-01

    Because of their hollow interior, transmembrane channels are capable of opening up pathways for ions across lipid membranes of living cells. Here, we demonstrate ion conduction induced by a single DNA duplex that lacks a hollow central channel. Decorated with six porpyrin-tags, our duplex is designed to span lipid membranes. Combining electrophysiology measurements with all-atom molecular dynamics simulations, we elucidate the microscopic conductance pathway. Ions flow at the DNA–lipid interface as the lipid head groups tilt toward the amphiphilic duplex forming a toroidal pore filled with water and ions. Ionic current traces produced by the DNA-lipid channel show well-defined insertion steps, closures, and gating similar to those observed for traditional protein channels or synthetic pores. Ionic conductances obtained through simulations and experiments are in excellent quantitative agreement. The conductance mechanism realized here with the smallest possible DNA-based ion channel offers a route to design a new class of synthetic ion channels with maximum simplicity. PMID:27324157

  20. Passive-roof duplexes under the Rocky Mountain foreland basin, Alberta

    SciTech Connect

    Skuce, A.G. ); Goody, N.P. ); Maloney, J. )

    1992-01-01

    Seismic reflection data in the Central Alberta Foothills near Edson reveal the presence of small passive-roof duplexes in Upper Cretaceous rocks within the otherwise undeformed foreland basin, as much as 40 km northeast of the mountain front monocline. The tops and bottoms of the duplexes are defined by backthrusts and sole thrusts, which follow bedding planes within Upper Cretaceous strata. Overlying the structures is an essentially uncontracted 1.8-km-thick section of Upper Cretaceous and Tertiary rocks, which is passively uplifted over the thickened duplexes. The underlying autochthonous sequence of Mesozoic and Paleozoic rocks exhibits some minor folding but is also uncontracted. The authors' interpretation extends both the upper and lower detachments of the widely accepted triangle-zone model more than 30 km farther under the foreland basin than has previously been supposed. The seismic data illustrate relatively clearly the form of the leading edge of the last phase of Rocky Mountain thrusting. The authors expect that similar features will be observed elsewhere in the Rocky Mountain foothills and, probably, at other mountain fronts worldwide.

  1. Development of duplex real-time PCR for the detection of WSSV and PstDV1 in cultivated shrimp

    PubMed Central

    2014-01-01

    Background The White spot syndrome virus (WSSV) and Penaeus stylirostris penstyldensovirus 1 (previously named Infectious hypodermal and hematopoietic necrosis virus-IHHNV) are two of the most important viral pathogens of penaeid shrimp. Different methods have been applied for diagnosis of these viruses, including Real-time PCR (qPCR) assays. A duplex qPCR method allows the simultaneous detection of two viruses in the same sample, which is more cost-effective than assaying for each virus separately. Currently, an assay for the simultaneous detection of the WSSV and the PstDV1 in shrimp is unavailable. The aim of this study was to develop and standardize a duplex qPCR assay for the simultaneous detection of the WSSV and the PstDV1 in clinical samples of diseased L. vannamei. In addition, to evaluate the performance of two qPCR master mixes with regard to the clinical sensitivity of the qPCR assay, as well as, different methods for qPCR results evaluation. Results The duplex qPCR assay for detecting WSSV and PstDV1 in clinical samples was successfully standardized. No difference in the amplification of the standard curves was observed between the duplex and singleplex assays. Specificities and sensitivities similar to those of the singleplex assays were obtained using the optimized duplex qPCR. The analytical sensitivities of duplex qPCR were two copies of WSSV control plasmid and 20 copies of PstDV1 control plasmid. The standardized duplex qPCR confirmed the presence of viral DNA in 28 from 43 samples tested. There was no difference for WSSV detection using the two kits and the distinct methods for qPCR results evaluation. High clinical sensitivity for PstDV1 was obtained with TaqMan Universal Master Mix associated with relative threshold evaluation. Three cases of simultaneous infection by the WSSV and the PstDV1 were identified with duplex qPCR. Conclusion The standardized duplex qPCR was shown to be a robust, highly sensitive, and feasible diagnostic tool for the

  2. Pair extended coupled cluster doubles

    SciTech Connect

    Henderson, Thomas M.; Scuseria, Gustavo E.; Bulik, Ireneusz W.

    2015-06-07

    The accurate and efficient description of strongly correlated systems remains an important challenge for computational methods. Doubly occupied configuration interaction (DOCI), in which all electrons are paired and no correlations which break these pairs are permitted, can in many cases provide an accurate account of strong correlations, albeit at combinatorial computational cost. Recently, there has been significant interest in a method we refer to as pair coupled cluster doubles (pCCD), a variant of coupled cluster doubles in which the electrons are paired. This is simply because pCCD provides energies nearly identical to those of DOCI, but at mean-field computational cost (disregarding the cost of the two-electron integral transformation). Here, we introduce the more complete pair extended coupled cluster doubles (pECCD) approach which, like pCCD, has mean-field cost and reproduces DOCI energetically. We show that unlike pCCD, pECCD also reproduces the DOCI wave function with high accuracy. Moreover, pECCD yields sensible albeit inexact results even for attractive interactions where pCCD breaks down.

  3. Solution structure of a five-adenine bulge loop within a DNA duplex.

    PubMed

    Dornberger, U; Hillisch, A; Gollmick, F A; Fritzsche, H; Diekmann, S

    1999-09-28

    The three-dimensional solution structure of a DNA molecule of the sequence 5'-d(GCATCGAAAAAGCTACG)-3' paired with 5'-d(CGTAGCCGATGC)-3' containing a five-adenine bulge loop (dA(5)-bulge) between two double helical stems was determined by 2D (1)H and (31)P NMR, infrared, and Raman spectroscopy. The DNA in both stems adopt a classical B-form double helical structure with Watson-Crick base pairing and C2'-endo sugar conformation. In addition, the two dG/dC base pairs framing the dA(5)-bulge loop are formed and are stable at least up to 30 degrees C. The five adenine bases of the bulge loop are localized at intrahelical positions within the double helical stems. Stacking on the double helical stem is continued for the first four 5'-adenines in the bulge loop. The total rise (the height) of these four stacked adenines roughly equals the diameter of the double helical stem. The stacking interactions are broken between the last of these four 5'-adenines and the fifth loop adenine at the 3'-end. This 3'-adenine partially stacks on the other stem. The angle between the base planes of the two nonstacking adenines (A10 and A11) in the bulge loop reflects the kinking angle of the global DNA structure. The neighboring cytosines opposite the dA(5)-bulge (being parts of the bulge flanking base pairs) do not stack on one another. This disruption of stacking is characterized by a partial shearing of these bases, such that certain sequential NOEs for this base step are preserved. In the base step opposite the loop, an extraordinary hydrogen bond is observed between the phosphate backbone of the 5'-dC and the amino proton of the 3'-dC in about two-thirds of the conformers. This hydrogen bond probably contributes to stabilizing the global DNA structure. The dA(5)-bulge induces a local kink into the DNA molecule of about 73 degrees (+/-11 degrees ). This kinking angle and the mutual orientation of the two double helical stems agree well with results from fluorescence resonance energy

  4. Odd frequency pairing of interacting Majorana fermions

    NASA Astrophysics Data System (ADS)

    Huang, Zhoushen; Woelfle, Peter; Balatsky, Alexandar

    Majorana fermions are rising as a promising key component in quantum computation. While the prevalent approach is to use a quadratic (i.e. non-interacting) Majorana Hamiltonian, when expressed in terms of Dirac fermions, generically the Hamiltonian involves interaction terms. Here we focus on the possible pair correlations in a simple model system. We study a model of Majorana fermions coupled to a boson mode and show that the anomalous correlator between different Majorana fermions, located at opposite ends of a topological wire, exhibits odd frequency behavior. It is stabilized when the coupling strength g is above a critical value gc. We use both, conventional diagrammatic theory and a functional integral approach, to derive the gap equation, the critical temperature, the gap function, the critical coupling, and a Ginzburg-Landau theory allowing to discuss a possible subleading admixture of even-frequency pairing. Work supported by USDOE DE-AC52-06NA25396 E304, Knut and Alice Wallenberg Foundation, and ERC DM-321031.

  5. Pair-Starved Pulsar Magnetospheres

    NASA Technical Reports Server (NTRS)

    Muslimov, Alex G.; Harding, Alice K.

    2009-01-01

    We propose a simple analytic model for the innermost (within the light cylinder of canonical radius, approx. c/Omega) structure of open-magnetic-field lines of a rotating neutron star (NS) with relativistic outflow of charged particles (electrons/positrons) and arbitrary angle between the NS spin and magnetic axes. We present the self-consistent solution of Maxwell's equations for the magnetic field and electric current in the pair-starved regime where the density of electron-positron plasma generated above the pulsar polar cap is not sufficient to completely screen the accelerating electric field and thus establish thee E . B = 0 condition above the pair-formation front up to the very high altitudes within the light cylinder. The proposed mode1 may provide a theoretical framework for developing the refined model of the global pair-starved pulsar magnetosphere.

  6. X-ray Crystal Structure of a Locked Nucleic Acid (LNA) Duplex Composed of a Palindromic 10-mer DNA Strand Containing One LNA Thymine Monomer

    SciTech Connect

    Egli, M.; Minasov, G.; Teplova, M.; Kumar, R.; Wengel, J.

    2010-03-05

    Locked nucleic acid (LNA), a recently introduced nucleic acid analogue with a bicyclic 2'-O,4'-C-methylene linked furanose sugar, exhibits enhanced affinities for DNA and RNA relative to the corresponding oligodeoxyribonucleotides and oligoribonucleotides; we report the first crystal structure of an LNA unit incorporated in an oligonucleotide duplex. The structure at 1.4 {angstrom} resolution of the DNA-LNA decamer duplex with one LNA thymine monomer per strand provides a detailed view of the conformation and hydration of locked nucleic acid residues in a duplex A-form. Our study provides a first look at the conformational properties of LNA in a crystal structure at relatively high resolution. The main characteristics of the structure are the standard A-type conformation induced by LNA residues and the capacity of the 2'-oxygen that is part of the bicyclic sugar framework to engage in a least two hydrogen bonds to water molecules. Circular dichroism spectra (CD) of LNA-LNA duplexes in solution indicated that such duplexes appear to adopt a conformation that closely resembles the A-form geometry of RNA-RNA duplexes. However, these spectra also manifested subtle differences between the two species (data not shown). The present analysis of a duplex with only a single LNA residue per strand does not provide any insight into potential conformational differences between LNA and RNA duplexes. Attempts to determine a crystal structure of a completely modified LNA-LNA duplex are underway.

  7. Development of one novel multiple-target plasmid for duplex quantitative PCR analysis of roundup ready soybean.

    PubMed

    Zhang, Haibo; Yang, Litao; Guo, Jinchao; Li, Xiang; Jiang, Lingxi; Zhang, Dabing

    2008-07-23

    To enforce the labeling regulations of genetically modified organisms (GMOs), the application of reference molecules as calibrators is becoming essential for practical quantification of GMOs. However, the reported reference molecules with tandem marker multiple targets have been proved not suitable for duplex PCR analysis. In this study, we developed one unique plasmid molecule based on one pMD-18T vector with three exogenous target DNA fragments of Roundup Ready soybean GTS 40-3-2 (RRS), that is, CaMV35S, NOS, and RRS event fragments, plus one fragment of soybean endogenous Lectin gene. This Lectin gene fragment was separated from the three exogenous target DNA fragments of RRS by inserting one 2.6 kb DNA fragment with no relatedness to RRS detection targets in this resultant plasmid. Then, we proved that this design allows the quantification of RRS using the three duplex real-time PCR assays targeting CaMV35S, NOS, and RRS events employing this reference molecule as the calibrator. In these duplex PCR assays, the limits of detection (LOD) and quantification (LOQ) were 10 and 50 copies, respectively. For the quantitative analysis of practical RRS samples, the results of accuracy and precision were similar to those of simplex PCR assays, for instance, the quantitative results were at the 1% level, the mean bias of the simplex and duplex PCR were 4.0% and 4.6%, respectively, and the statistic analysis ( t-test) showed that the quantitative data from duplex and simplex PCR had no significant discrepancy for each soybean sample. Obviously, duplex PCR analysis has the advantages of saving the costs of PCR reaction and reducing the experimental errors in simplex PCR testing. The strategy reported in the present study will be helpful for the development of new reference molecules suitable for duplex PCR quantitative assays of GMOs.

  8. Like-charge guanidinium pairing from molecular dynamics and ab initio calculations.

    PubMed

    Vazdar, Mario; Vymětal, Jiři; Heyda, Jan; Vondrášek, Jiři; Jungwirth, Pavel

    2011-10-20

    Pairing of guanidinium moieties in water is explored by molecular dynamics simulations of short arginine-rich peptides and ab initio calculations of a pair of guanidinium ions in water clusters of increasing size. Molecular dynamics simulations show that, in an aqueous environment, the diarginine guanidinium like-charged ion pairing is sterically hindered, whereas in the Arg-Ala-Arg tripeptide, this pairing is significant. This result is supported by the survey of protein structure databases, where it is found that stacked arginine pairs in dipeptide fragments exist solely as being imposed by the protein structure. In contrast, when two arginines are separated by a single amino acid, their guanidinium groups can freely approach each other and they frequently form stacked pairs. Molecular dynamics simulations results are also supported by ab initio calculations, which show stabilization of stacked guanidinium pairs in sufficiently large water clusters.

  9. Scaffolding along nucleic acid duplexes using 2'-amino-locked nucleic acids.

    PubMed

    Astakhova, I Kira; Wengel, Jesper

    2014-06-17

    CONSPECTUS: Incorporation of chemically modified nucleotide scaffolds into nucleic acids to form assemblies rich in function is an innovative area with great promise for nanotechnology and biomedical and material science applications. The intrinsic biorecognition potential of nucleic acids combined with advanced properties of the locked nucleic acids (LNAs) provide opportunities to develop new nanomaterials and devices like sensors, aptamers, and machines. In this Account, we describe recent research on preparation and investigation of the properties of LNA/DNA hybrids containing functionalized 2'-amino-LNA nucleotides. By application of different chemical reactions, modification of 2'-amino-LNA scaffolds can be efficiently performed in high yields and with various tags, postsynthetically or during the automated oligonucleotide synthesis. The choice of a synthetic method for scaffolding along 2'-amino-LNA mainly depends on the chemical nature of the modification, its price, its availability, and applications of the product. One of the most useful applications of the product LNA/DNA scaffolds containing 2'-amino-LNA is to detect complementary DNA and RNA targets. Examples of these applications include sensing of clinically important single-nucleotide polymorphisms (SNPs) and imaging of nucleic acids in vitro, in cell culture, and in vivo. According to our studies, 2'-amino-LNA scaffolds are efficient within diagnostic probes for DNA and RNA targets and as therapeutics, whereas both 2'-amino- and isomeric 2'-α-l-amino-LNA scaffolds have promising properties for stabilization and detection of DNA nanostructures. Attachment of fluorescent groups to the 2'-amino group results in very high fluorescent quantum yields of the duplexes and remarkable sensitivity of the fluorescence signal to target binding. Notably, fluorescent LNA/DNA probes bind nucleic acid targets with advantages of high affinity and specificity. Thus, molecular motion of nanodevices and programmable

  10. Scaffolding along nucleic acid duplexes using 2'-amino-locked nucleic acids.

    PubMed

    Astakhova, I Kira; Wengel, Jesper

    2014-06-17

    CONSPECTUS: Incorporation of chemically modified nucleotide scaffolds into nucleic acids to form assemblies rich in function is an innovative area with great promise for nanotechnology and biomedical and material science applications. The intrinsic biorecognition potential of nucleic acids combined with advanced properties of the locked nucleic acids (LNAs) provide opportunities to develop new nanomaterials and devices like sensors, aptamers, and machines. In this Account, we describe recent research on preparation and investigation of the properties of LNA/DNA hybrids containing functionalized 2'-amino-LNA nucleotides. By application of different chemical reactions, modification of 2'-amino-LNA scaffolds can be efficiently performed in high yields and with various tags, postsynthetically or during the automated oligonucleotide synthesis. The choice of a synthetic method for scaffolding along 2'-amino-LNA mainly depends on the chemical nature of the modification, its price, its availability, and applications of the product. One of the most useful applications of the product LNA/DNA scaffolds containing 2'-amino-LNA is to detect complementary DNA and RNA targets. Examples of these applications include sensing of clinically important single-nucleotide polymorphisms (SNPs) and imaging of nucleic acids in vitro, in cell culture, and in vivo. According to our studies, 2'-amino-LNA scaffolds are efficient within diagnostic probes for DNA and RNA targets and as therapeutics, whereas both 2'-amino- and isomeric 2'-α-l-amino-LNA scaffolds have promising properties for stabilization and detection of DNA nanostructures. Attachment of fluorescent groups to the 2'-amino group results in very high fluorescent quantum yields of the duplexes and remarkable sensitivity of the fluorescence signal to target binding. Notably, fluorescent LNA/DNA probes bind nucleic acid targets with advantages of high affinity and specificity. Thus, molecular motion of nanodevices and programmable

  11. Missing energies at pair creation

    NASA Technical Reports Server (NTRS)

    El-Ela, A. A.; Hassan, S.; Bagge, E. R.

    1985-01-01

    Wilson cloud chamber measurements of the separated spectra of positrons and electrons produced by gamma quanta of 6.14 MeV differ considerably from the theoretically predicted spectra by BETHE and HEITLER, but are in good agreement with those of a modified theory of pair creation.

  12. Cooper pair transfer in nuclei

    NASA Astrophysics Data System (ADS)

    Potel, G.; Idini, A.; Barranco, F.; Vigezzi, E.; Broglia, R. A.

    2013-10-01

    The second-order distorted wave Born approximation implementation of two-particle transfer direct reactions which includes simultaneous and successive transfer, properly corrected by non-orthogonality effects, is tested with the help of controlled nuclear structure and reaction inputs against data spanning the whole mass table, and showed to constitute a quantitative probe of nuclear pairing correlations.

  13. Pick a Pair. Being Bony

    ERIC Educational Resources Information Center

    Miller, Pat

    2004-01-01

    This column suggests pairings of fiction and nonfiction books to meet curricular needs and help students to compare/contrast the texts as they may be asked on state tests. The author of this paper focuses on activities surrounding Halloween. Since many schools are discouraged from teaching about Halloween, this can be a great time to investigate…

  14. Pairing Linguistic and Music Intelligences

    ERIC Educational Resources Information Center

    DiEdwardo, MaryAnn Pasda

    2005-01-01

    This article describes how music in the language classroom setting can be a catalyst for developing reading, writing, and understanding skills. Studies suggest that pairing music and linguistic intelligences in the college classroom improves students' grades and abilities to compose theses statements for research papers in courses that emphasize…

  15. Molecular dynamics simulation of DNA base-pair opening by sharp bending

    NASA Astrophysics Data System (ADS)

    Cong, Peiwen; Dai, Liang; van der Maarel, Johan R. C.; Yan, Jie

    2013-03-01

    Many biological processes require sharp bending of DNA. According to worm-like chain model, the bending energy dominates the free energy cost of those processes containing DNA loops shorter than 40 nm, such as DNA wrapping around histones, Lac repressor looping and virus DNA packaging. However, several recent experimental observations suggest that the WLC model s not applicable under tight bending conditions. In full atom molecular dynamics simulations, a double stranded, 20 base-pairs DNA fragment is forced to bend by an external spring. It is found that one or two AT-rich regions are disrupted for sufficiently small end-to-end distance. The disrupted DNA base-pairs separate and usually stack with the neighbouring base-pairs to form a defect. It is shown that these defects are more bendable than the bending rigidity of the duplex in the regular B-form. The simulation suggests a curvature dependent, non-harmonic bending elasticity of the DNA backbone is necessary to describe the DNA conformation under tight bending conditions.

  16. Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe

    PubMed Central

    Ding, Yuan; Zhang, Xiaojun; Tham, Kenneth W.; Qin, Peter Z.

    2014-01-01

    Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as ‘DNA shape’, critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA duplexes that contain response elements of the p53 tumor suppressor. An R5a nitroxide spin label, which was covalently attached at a specific phosphate group, was scanned consecutively through the DNA duplex. X-band continuous-wave electron paramagnetic resonance spectroscopy was used to monitor rotational motions of R5a, which report on DNA structure and dynamics at the labeling site. An approach based on Pearson's coefficient analysis was developed to collectively examine the degree of similarity among the ensemble of R5a spectra. The resulting Pearson's coefficients were used to generate maps representing variation of R5a mobility along the DNA duplex. The R5a mobility maps were found to correlate with maps of certain DNA helical parameters, and were capable of revealing similarity and deviation in the shape of the two closely related DNA duplexes. Collectively, the R5a probe and the Pearson's coefficient-based lineshape analysis scheme yielded a generalizable method for examining sequence-dependent DNA shapes. PMID:25092920

  17. Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe.

    PubMed

    Ding, Yuan; Zhang, Xiaojun; Tham, Kenneth W; Qin, Peter Z

    2014-10-01

    Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as 'DNA shape', critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA duplexes that contain response elements of the p53 tumor suppressor. An R5a nitroxide spin label, which was covalently attached at a specific phosphate group, was scanned consecutively through the DNA duplex. X-band continuous-wave electron paramagnetic resonance spectroscopy was used to monitor rotational motions of R5a, which report on DNA structure and dynamics at the labeling site. An approach based on Pearson's coefficient analysis was developed to collectively examine the degree of similarity among the ensemble of R5a spectra. The resulting Pearson's coefficients were used to generate maps representing variation of R5a mobility along the DNA duplex. The R5a mobility maps were found to correlate with maps of certain DNA helical parameters, and were capable of revealing similarity and deviation in the shape of the two closely related DNA duplexes. Collectively, the R5a probe and the Pearson's coefficient-based lineshape analysis scheme yielded a generalizable method for examining sequence-dependent DNA shapes.

  18. Molecular detection of infectious bronchitis and Newcastle disease viruses in broiler chickens with respiratory signs using Duplex RT-PCR

    PubMed Central

    Saba Shirvan, Aylar; Mardani, Karim

    2014-01-01

    Infectious bronchitis (IB) and Newcastle disease (ND) are highly contagious and the most economically important diseases of the poultry affecting respiratory tract and causing economic losses in poultry industry throughout the world. In the present study, the simultaneous detection and differentiation of causative agents of these diseases were investigated using duplex-RT-PCR. RNA was extracted from vaccinal and reference strains of infectious bronchitis virus (IBV) and Newcastle disease virus (NDV) and then cDNA was synthesized. Using two universal primer sets for detection of IBV and NDV, the duplex-RT-PCR was developed. In order to assess the efficiency of the developed duplex RT-PCR, a number of 12 broiler farms with the symptoms of respiratory tract infection was sampled (trachea, lung and kidney were sampled from affected birds suspicious for IBV and NDV infections). After RNA extraction from tissues and cDNA synthesis, the presence of IBV and NDV genome were investigated using duplex-PCR. The results showed that three of twelve examined broiler farms were positive for IBV and two farms were positive for NDV and IBV. The results revealed that the duplex-RT-PCR is a quick and sensitive procedure for simultaneously detecting IBV and NDV in birds with respiratory infections. PMID:25610585

  19. Duplex ultrasound and computed tomography angiography in the follow-up of endovascular abdominal aortic aneurysm repair: a comparative study*

    PubMed Central

    Cantador, Alex Aparecido; Siqueira, Daniel Emílio Dalledone; Jacobsen, Octavio Barcellos; Baracat, Jamal; Pereira, Ines Minniti Rodrigues; Menezes, Fábio Hüsemann; Guillaumon, Ana Terezinha

    2016-01-01

    Objective To compare duplex ultrasound and computed tomography (CT) angiography in terms of their performance in detecting endoleaks, as well as in determining the diameter of the aneurysm sac, in the postoperative follow-up of endovascular abdominal aortic aneurysm repair. Materials and Methods This was a prospective study involving 30 patients who had undergone endovascular repair of infrarenal aortoiliac aneurysms. Duplex ultrasound and CT angiography were performed simultaneously by independent radiologists. Measurements of the aneurysm sac diameter were assessed, and the presence or absence of endoleaks was determined. Results The average diameter of the aneurysm sac, as determined by duplex ultrasound and CT angiography was 6.09 ± 1.95 and 6.27 ± 2.16 cm, respectively. Pearson's correlation coefficient showing a statistically significant correlation (R = 0.88; p < 0.01). Comparing the duplex ultrasound and CT angiography results regarding the detection of endoleaks, we found that the former had a negative predictive value of 92.59% and a specificity of 96.15%. Conclusion Our results show that there is little variation between the two methods evaluated, and that the choice between the two would have no significant effect on clinical management. Duplex ultrasound could replace CT angiography in the postoperative follow-up of endovascular aneurysm repair of the infrarenal aorta, because it is a low-cost procedure without the potential clinical complications related to the use of iodinated contrast and exposure to radiation. PMID:27777476

  20. Study of E. coli Hfq’s RNA annealing acceleration and duplex destabilization activities using substrates with different GC-contents

    PubMed Central

    Doetsch, Martina; Stampfl, Sabine; Fürtig, Boris; Beich-Frandsen, Mads; Saxena, Krishna; Lybecker, Meghan; Schroeder, Renée

    2013-01-01

    Folding of RNA molecules into their functional three-dimensional structures is often supported by RNA chaperones, some of which can catalyse the two elementary reactions helix disruption and helix formation. Hfq is one such RNA chaperone, but its strand displacement activity is controversial. Whereas some groups found Hfq to destabilize secondary structures, others did not observe such an activity with their RNA substrates. We studied Hfq’s activities using a set of short RNAs of different thermodynamic stabilities (GC-contents from 4.8% to 61.9%), but constant length. We show that Hfq’s strand displacement as well as its annealing activity are strongly dependent on the substrate’s GC-content. However, this is due to Hfq’s preferred binding of AU-rich sequences and not to the substrate’s thermodynamic stability. Importantly, Hfq catalyses both annealing and strand displacement with comparable rates for different substrates, hinting at RNA strand diffusion and annealing nucleation being rate-limiting for both reactions. Hfq’s strand displacement activity is a result of the thermodynamic destabilization of the RNA through preferred single-strand binding whereas annealing acceleration is independent from Hfq’s thermodynamic influence. Therefore, the two apparently disparate activities annealing acceleration and duplex destabilization are not in energetic conflict with each other. PMID:23104381