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Sample records for duplex dna effect

  1. Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex.

    Science.gov (United States)

    Ueda, Yu-Mi; Zouzumi, Yu-Ki; Maruyama, Atsushi; Nakano, Shu-Ichi; Sugimoto, Naoki; Miyoshi, Daisuke

    2016-01-01

    We systematically investigated effects of molecular crowding with trimethylamine N -oxide (TMAO) as a zwitterionic and protective osmolyte and urea as a nonionic denaturing osmolyte on conformation and thermodynamics of the canonical DNA duplex and the non-canonical DNA G-quadruplex. It was found that TMAO and urea stabilized and destabilized, respectively, the G-quadruplex. On the other hand, these osmolytes generally destabilize the duplex; however, it was observed that osmolytes having the trimethylamine group stabilized the duplex at the lower concentrations because of a direct binding to a groove of the duplex. These results are useful not only to predict DNA structures and their thermodynamics under physiological environments in living cells, but also design of polymers and materials to regulate structure and stability of DNA sequences.

  2. Effect of Cavity Size of Mesoporous Silica on Short DNA Duplex Stability.

    Science.gov (United States)

    Masuda, Tsubasa; Shibuya, Yuuta; Arai, Shota; Kobayashi, Sayaka; Suzuki, Sotaro; Kijima, Jun; Itoh, Tetsuji; Sato, Yusuke; Nishizawa, Seiichi; Yamaguchi, Akira

    2018-05-15

    We studied the stabilities of short (4- and 3-bp) DNA duplexes within silica mesopores modified with a positively charged trimethyl aminopropyl (TMAP) monolayer (BJH pore diameter 1.6-7.4 nm). The DNA fragments with fluorescent dye were introduced into the pores, and their fluorescence resonance energy transfer (FRET) response was measured to estimate the structuring energies of the short DNA duplexes under cryogenic conditions (temperature 233-323 K). The results confirmed the enthalpic stability gain of the duplex within size-matched pores (1.6 and 2.3 nm). The hybridization equilibrium constants found for the size-matched pores were 2 orders of magnitude larger than those for large pores (≥3.5 nm), and this size-matching effect for the enhanced duplex stability was explained by a tight electrostatic interaction between the duplex and the surface TMAP groups. These results indicate the requirement of the precise regulation of mesopore size to ensure the stabilization of hydrogen-bonded supramolecular assemblies.

  3. DNA oligonucleotide duplexes containing intramolecular platinated cross-links: energetics, hydration, sequence, and ionic effects.

    Science.gov (United States)

    Kankia, Besik I; Soto, Ana Maria; Burns, Nicole; Shikiya, Ronald; Tung, Chang-Shung; Marky, Luis A

    2002-11-05

    The anticancer activity of cisplatin arises from its ability to bind covalently to DNA, forming primarily intrastrand cross-links to adjacent purine residues; the most common adducts involve d(GpG) (65%) and d(ApG) (25%) intrastrand cross-links. The incorporation of these platinum adducts in a B-DNA helix induces local distortions, causing bending and unwinding of the DNA. In this work, we used temperature-dependent UV spectroscopy to investigate the unfolding thermodynamics, and associated ionic effects, of two sets of DNA decamer duplexes containing either cis-[Pt(NH(3))(2)[d(GpG

  4. Effect of Radiofrequency Radiation on DNA Duplex Stability and Replication.

    Science.gov (United States)

    1983-08-01

    Ando, T. A nuclease specific for heat-denatured DNA isolated from a product of Aspergillus oryzae . Biochim Biophys Acta 114:158-168 (1966). Blakeley...metabolic acti- vation. Mutation Res 64:315-328 (1979). Vogt,. V.M. Purification and further properties of single-strand-specific nuclease from Aspergillus oryzae . Eur J Biochem 33:192-200 (1973). 42

  5. Effect of structure variation of the aptamer-DNA duplex probe on the performance of displacement-based electrochemical aptamer sensors.

    Science.gov (United States)

    Pang, Jie; Zhang, Ziping; Jin, Haizhu

    2016-03-15

    Electrochemical aptamer-based (E-AB) sensors employing electrode-immobilized, redox-tagged aptamer probes have emerged as a promising platform for the sensitive and quick detection of target analytes ranging from small molecules to proteins. Signal generation in this class of sensor is linked to change in electron transfer efficiency upon binding-induced change in flexibility/conformation of the aptamer probe. Because of this signaling mechanism, signal gains of these sensors can be improved by employing a displacement-based recognition system, which links target binding with a large-scale flexibility/conformation shift from the aptamer-DNA duplex to the single-stranded DNA or the native aptamer. Despite the relatively large number of displacement-based E-AB sensor samples, little attention has been paid to the structure variation of the aptamer-DNA duplex probe. Here we detail the effects of complementary length and position of the aptamer-DNA duplex probe on the performance of a model displacement-based E-AB sensor for ATP. We find that, greater background suppression and signal gain are observed with longer complementary length of the aptamer-DNA duplex probe. However, sensor equilibration time slows monotonically with increasing complementary length; and with too many target binding sites in aptamer sequence being occupied by the complementary DNA, the aptamer-target binding does not occur and no signal gain observed. We also demonstrate that signal gain of the displacement-based E-AB sensor is strongly dependent on the complementary position of the aptamer-DNA duplex probe, with complementary position located at the electrode-attached or redox-tagged end of the duplex probe, larger background suppression and signal increase than that of the middle position are observed. These results highlight the importance of rational structure design of the aptamer-DNA duplex probe and provide new insights into the optimization of displacement-based E-AB sensors. Copyright

  6. Capturing a DNA duplex under near-physiological conditions

    Science.gov (United States)

    Zhang, Huijuan; Xu, Wei; Liu, Xiaogang; Stellacci, Francesco; Thong, John T. L.

    2010-10-01

    We report in situ trapping of a thiolated DNA duplex with eight base pairs into a polymer-protected gold nanogap device under near-physiological conditions. The double-stranded DNA was captured by electrophoresis and covalently attached to the nanogap electrodes through sulfur-gold bonding interaction. The immobilization of the DNA duplex was confirmed by direct electrical measurements under near-physiological conditions. The conductance of the DNA duplex was estimated to be 0.09 μS. We also demonstrate the control of DNA dehybridization by heating the device to temperatures above the melting point of the DNA.

  7. Thermal stability of DNA quadruplex-duplex hybrids.

    Science.gov (United States)

    Lim, Kah Wai; Khong, Zi Jian; Phan, Anh Tuân

    2014-01-14

    DNA has the capacity to adopt several distinct structural forms, such as duplex and quadruplex helices, which have been implicated in cellular processes and shown to exhibit important functional properties. Quadruplex-duplex hybrids, generated from the juxtaposition of these two structural elements, could find applications in therapeutics and nanotechnology. Here we used NMR and CD spectroscopy to investigate the thermal stability of two classes of quadruplex-duplex hybrids comprising fundamentally distinct modes of duplex and quadruplex connectivity: Construct I involves the coaxial orientation of the duplex and quadruplex helices with continual base stacking across the two components; Construct II involves the orthogonal orientation of the duplex and quadruplex helices with no base stacking between the two components. We have found that for both constructs, the stability of the quadruplex generally increases with the length of the stem-loop incorporated, with respect to quadruplexes comprising nonstructured loops of the same length, which showed a continuous drop in stability with increasing loop length. The stability of these complexes, particularly Construct I, can be substantially influenced by the base-pair steps proximal to the quadruplex-duplex junction. Bulges at the junction are largely detrimental to the adoption of the desired G-quadruplex topology for Construct I but not for Construct II. These findings should facilitate future design and prediction of quadruplex-duplex hybrids.

  8. Quantification of Chemical and Mechanical Effects on the Formation of the G-Quadruplex and i-Motif in Duplex DNA.

    Science.gov (United States)

    Selvam, Sangeetha; Mandal, Shankar; Mao, Hanbin

    2017-09-05

    The formation of biologically significant tetraplex DNA species, such as G-quadruplexes and i-motifs, is affected by chemical (ions and pH) and mechanical [superhelicity (σ) and molecular crowding] factors. Because of the extremely challenging experimental conditions, the relative importance of these factors on tetraplex folding is unknown. In this work, we quantitatively evaluated the chemical and mechanical effects on the population dynamics of DNA tetraplexes in the insulin-linked polymorphic region using magneto-optical tweezers. By mechanically unfolding individual tetraplexes, we found that ions and pH have the largest effects on the formation of the G-quadruplex and i-motif, respectively. Interestingly, superhelicity has the second largest effect followed by molecular crowding conditions. While chemical effects are specific to tetraplex species, mechanical factors have generic influences. The predominant effect of chemical factors can be attributed to the fact that they directly change the stability of a specific tetraplex, whereas the mechanical factors, superhelicity in particular, reduce the stability of the competing species by changing the kinetics of the melting and annealing of the duplex DNA template in a nonspecific manner. The substantial dependence of tetraplexes on superhelicity provides strong support that DNA tetraplexes can serve as topological sensors to modulate fundamental cellular processes such as transcription.

  9. Micromechanics of base pair unzipping in the DNA duplex

    International Nuclear Information System (INIS)

    Volkov, Sergey N; Paramonova, Ekaterina V; Yakubovich, Alexander V; Solov’yov, Andrey V

    2012-01-01

    All-atom molecular dynamics (MD) simulations of DNA duplex unzipping in a water environment were performed. The investigated DNA double helix consists of a Drew-Dickerson dodecamer sequence and a hairpin (AAG) attached to the end of the double-helix chain. The considered system is used to examine the process of DNA strand separation under the action of an external force. This process occurs in vivo and now is being intensively investigated in experiments with single molecules. The DNA dodecamer duplex is consequently unzipped pair by pair by means of the steered MD. The unzipping trajectories turn out to be similar for the duplex parts with G⋅C content and rather distinct for the parts with A⋅T content. It is shown that during the unzipping each pair experiences two types of motion: relatively quick rotation together with all the duplex and slower motion in the frame of the unzipping fork. In the course of opening, the complementary pair passes through several distinct states: (i) the closed state in the double helix, (ii) the metastable preopened state in the unzipping fork and (iii) the unbound state. The performed simulations show that water molecules participate in the stabilization of the metastable states of the preopened base pairs in the DNA unzipping fork. (paper)

  10. Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: predictive thermodynamic model.

    Science.gov (United States)

    Moreira, Bernardo G; You, Yong; Owczarzy, Richard

    2015-03-01

    Cyanine dyes are important chemical modifications of oligonucleotides exhibiting intensive and stable fluorescence at visible light wavelengths. When Cy3 or Cy5 dye is attached to 5' end of a DNA duplex, the dye stacks on the terminal base pair and stabilizes the duplex. Using optical melting experiments, we have determined thermodynamic parameters that can predict the effects of the dyes on duplex stability quantitatively (ΔG°, Tm). Both Cy dyes enhance duplex formation by 1.2 kcal/mol on average, however, this Gibbs energy contribution is sequence-dependent. If the Cy5 is attached to a pyrimidine nucleotide of pyrimidine-purine base pair, the stabilization is larger compared to the attachment to a purine nucleotide. This is likely due to increased stacking interactions of the dye to the purine of the complementary strand. Dangling (unpaired) nucleotides at duplex terminus are also known to enhance duplex stability. Stabilization originated from the Cy dyes is significantly larger than the stabilization due to the presence of dangling nucleotides. If both the dangling base and Cy3 are present, their thermodynamic contributions are approximately additive. New thermodynamic parameters improve predictions of duplex folding, which will help design oligonucleotide sequences for biophysical, biological, engineering, and nanotechnology applications. Copyright © 2015. Published by Elsevier B.V.

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

    Science.gov (United States)

    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. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: complex theoretical and experimental studies.

    Science.gov (United States)

    Kratochvílová, Irena; Vala, Martin; Weiter, Martin; Špérová, Miroslava; Schneider, Bohdan; Páv, Ondřej; Šebera, Jakub; Rosenberg, Ivan; Sychrovský, Vladimír

    2013-01-01

    Oligonucleotides conduct electric charge via various mechanisms and their characterization and understanding is a very important and complicated task. In this work, experimental (temperature dependent steady state fluorescence spectroscopy, time-resolved fluorescence spectroscopy) and theoretical (Density Functional Theory) approaches were combined to study charge transfer processes in short DNA/DNA and RNA/DNA duplexes with virtually equivalent sequences. The experimental results were consistent with the theoretical model - the delocalized nature of HOMO orbitals and holes, base stacking, electronic coupling and conformational flexibility formed the conditions for more effective short distance charge transfer processes in RNA/DNA hybrids. RNA/DNA and DNA/DNA charge transfer properties were strongly connected with temperature affected structural changes of molecular systems - charge transfer could be used as a probe of even tiny changes of molecular structures and settings. © 2013. Published by Elsevier B.V. All rights reserved.

  13. Protein complexation with DNA phosphates as a cause for DNA duplex destabilization : a thermodynamic model

    NARCIS (Netherlands)

    Genderen, van M.H.P.; Buck, H.M.

    1989-01-01

    Complexation of positively charged sites in a protein with the negative DNA phosphate groups shields the phosphate charges. This diminishes interstrand electrostatic repulsions, which stabilizes the duplex. When phosphate shidlding is present in one DNA strand only, the conformation of this strand

  14. Duplex Alu Screening for Degraded DNA of Skeletal Human Remains

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    Fabian Haß

    2017-10-01

    Full Text Available The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs, have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. We developed duplex Alu screening PCRs with flanking primers for two Alu elements, each combined with a single internal Alu primer. By adding an internal primer, the approximately 400–500 bp presence signals of Alu elements can be detected within a range of less than 200 bp. Thus, our PCR approach is suited for highly fragmented ancient DNA samples, whereas NGS analyses frequently are unable to handle repetitive elements. With this analysis system, we examined remains of 12 individuals from the Lichtenstein cave with different degrees of DNA degradation. The duplex PCRs showed fully informative amplification results for all of the chosen Alu loci in eight of the 12 samples. Our analysis system showed that Alu presence/absence analysis is possible in samples with different degrees of DNA degradation and it reduces the amount of valuable skeletal material needed by a factor of four, as compared with a singleplex approach.

  15. Structure of DNA toroids and electrostatic attraction of DNA duplexes

    International Nuclear Information System (INIS)

    Cherstvy, A G

    2005-01-01

    DNA-DNA electrostatic attraction is considered as the driving force for the formation of DNA toroids in the presence of DNA condensing cations. This attraction comes from the DNA helical charge distribution and favours hexagonal toroidal cross-sections. The latter is in agreement with recent cryo-electron microscopy studies on DNA condensed with cobalt hexammine. We treat the DNA-DNA interactions within the modern theory of electrostatic interaction between helical macromolecules. The size and thickness of the toroids is calculated within a simple model; other models of stability of DNA toroids are discussed and compared

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

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    Anna Aviñó

    2016-02-01

    Full Text Available 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.

  17. A duplex DNA-gold nanoparticle probe composed as a colorimetric biosensor for sequence-specific DNA-binding proteins.

    Science.gov (United States)

    Ahn, Junho; Choi, Yeonweon; Lee, Ae-Ree; Lee, Joon-Hwa; Jung, Jong Hwa

    2016-03-21

    Using duplex DNA-AuNP aggregates, a sequence-specific DNA-binding protein, SQUAMOSA Promoter-binding-Like protein 12 (SPL-12), was directly determined by SPL-12-duplex DNA interaction-based colorimetric actions of DNA-Au assemblies. In order to prepare duplex DNA-Au aggregates, thiol-modified DNA 1 and DNA 2 were attached onto the surface of AuNPs, respectively, by the salt-aging method and then the DNA-attached AuNPs were mixed. Duplex-DNA-Au aggregates having the average size of 160 nm diameter and the maximum absorption at 529 nm were able to recognize SPL-12 and reached the equivalent state by the addition of ∼30 equivalents of SPL-12 accompanying a color change from red to blue with a red shift of the maximum absorption at 570 nm. As a result, the aggregation size grew to about 247 nm. Also, at higher temperatures of the mixture of duplex-DNA-Au aggregate solution and SPL-12, the equivalent state was reached rapidly. On the contrary, in the control experiment using Bovine Serum Albumin (BSA), no absorption band shift of duplex-DNA-Au aggregates was observed.

  18. Probing of miniPEGγ-PNA-DNA Hybrid Duplex Stability with AFM Force Spectroscopy.

    Science.gov (United States)

    Dutta, Samrat; Armitage, Bruce A; Lyubchenko, Yuri L

    2016-03-15

    Peptide nucleic acids (PNA) are synthetic polymers, the neutral peptide backbone of which provides elevated stability to PNA-PNA and PNA-DNA hybrid duplexes. It was demonstrated that incorporation of diethylene glycol (miniPEG) at the γ position of the peptide backbone increased the thermal stability of the hybrid duplexes (Sahu, B. et al. J. Org. Chem. 2011, 76, 5614-5627). Here, we applied atomic force microscopy (AFM) based single molecule force spectroscopy and dynamic force spectroscopy (DFS) to test the strength and stability of the hybrid 10 bp duplex. This hybrid duplex consisted of miniPEGγ-PNA and DNA of the same length (γ(MP)PNA-DNA), which we compared to a DNA duplex with a homologous sequence. AFM force spectroscopy data obtained at the same conditions showed that the γ(MP)PNA-DNA hybrid is more stable than the DNA counterpart, 65 ± 15 pN vs 47 ± 15 pN, respectively. The DFS measurements performed in a range of pulling speeds analyzed in the framework of the Bell-Evans approach yielded a dissociation constant, koff ≈ 0.030 ± 0.01 s⁻¹ for γ(MP)PNA-DNA hybrid duplex vs 0.375 ± 0.18 s⁻¹ for the DNA-DNA duplex suggesting that the hybrid duplex is much more stable. Correlating the high affinity of γ(MP)PNA-DNA to slow dissociation kinetics is consistent with prior bulk characterization by surface plasmon resonance. Given the growing interest in γ(MP)PNA as well as other synthetic DNA analogues, the use of single molecule experiments along with computational analysis of force spectroscopy data will provide direct characterization of various modifications as well as higher order structures such as triplexes and quadruplexes.

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

    Science.gov (United States)

    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.

  20. Nanopore Analysis of the 5-Guanidinohydantoin to Iminoallantoin Isomerization in Duplex DNA.

    Science.gov (United States)

    Zeng, Tao; Fleming, Aaron M; Ding, Yun; Ren, Hang; White, Henry S; Burrows, Cynthia J

    2018-04-06

    In DNA, guanine oxidation yields diastereomers of 5-guanidinohydantoin (Gh) as one of the major products. In nucleosides and single-stranded DNA, Gh is in a pH-dependent equilibrium with its constitutional isomer iminoallantoin (Ia). Herein, the isomerization reaction between Gh and Ia was monitored in duplex DNA using a protein nanopore by measuring the ionic current when duplex DNA interacts with the pore under an electrophoretic force. Monitoring current levels in this single-molecule method proved to be superior for analysis of population distributions in an equilibrating mixture of four isomers in duplex DNA as a function of pH. The results identified Gh as a major isomer observed when base paired with A, C, or G at pH 6.4-8.4, and Ia was a minor isomer of the reaction mixture that was only observed when the pH was >7.4 in the duplex DNA context. The present results suggest that Gh will be the dominant isomer in duplex DNA under physiological conditions regardless of the base-pairing partner in the duplex.

  1. Analysis of Structural Flexibility of Damaged DNA Using Thiol-Tethered Oligonucleotide Duplexes.

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    Masashi Fujita

    Full Text Available Bent structures are formed in DNA by the binding of small molecules or proteins. We developed a chemical method to detect bent DNA structures. Oligonucleotide duplexes in which two mercaptoalkyl groups were attached to the positions facing each other across the major groove were prepared. When the duplex contained the cisplatin adduct, which was proved to induce static helix bending, interstrand disulfide bond formation under an oxygen atmosphere was detected by HPLC analyses, but not in the non-adducted duplex, when the two thiol-tethered nucleosides were separated by six base pairs. When the insert was five and seven base pairs, the disulfide bond was formed and was not formed, respectively, regardless of the cisplatin adduct formation. The same reaction was observed in the duplexes containing an abasic site analog and the (6–4 photoproduct. Compared with the cisplatin case, the disulfide bond formation was slower in these duplexes, but the reaction rate was nearly independent of the linker length. These results indicate that dynamic structural changes of the abasic site- and (6–4 photoproduct-containing duplexes could be detected by our method. It is strongly suggested that the UV-damaged DNA-binding protein, which specifically binds these duplexes and functions at the first step of global-genome nucleotide excision repair, recognizes the easily bendable nature of damaged DNA.

  2. Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA.

    Science.gov (United States)

    Odell, M; Shuman, S

    1999-05-14

    The 298-amino acid ATP-dependent DNA ligase of Chlorella virus PBCV-1 is the smallest eukaryotic DNA ligase known. The enzyme has intrinsic specificity for binding to nicked duplex DNA. To delineate the ligase-DNA interface, we have footprinted the enzyme binding site on DNA and the DNA binding site on ligase. The size of the exonuclease III footprint of ligase bound a single nick in duplex DNA is 19-21 nucleotides. The footprint is asymmetric, extending 8-9 nucleotides on the 3'-OH side of the nick and 11-12 nucleotides on the 5'-phosphate side. The 5'-phosphate moiety is essential for the binding of Chlorella virus ligase to nicked DNA. Here we show that the 3'-OH moiety is not required for nick recognition. The Chlorella virus ligase binds to a nicked ligand containing 2',3'-dideoxy and 5'-phosphate termini, but cannot catalyze adenylation of the 5'-end. Hence, the 3'-OH is important for step 2 chemistry even though it is not itself chemically transformed during DNA-adenylate formation. A 2'-OH cannot substitute for the essential 3'-OH in adenylation at a nick or even in strand closure at a preadenylated nick. The protein side of the ligase-DNA interface was probed by limited proteolysis of ligase with trypsin and chymotrypsin in the presence and absence of nicked DNA. Protease accessible sites are clustered within a short segment from amino acids 210-225 located distal to conserved motif V. The ligase is protected from proteolysis by nicked DNA. Protease cleavage of the native enzyme prior to DNA addition results in loss of DNA binding. These results suggest a bipartite domain structure in which the interdomain segment either comprises part of the DNA binding site or undergoes a conformational change upon DNA binding. The domain structure of Chlorella virus ligase inferred from the solution experiments is consistent with the structure of T7 DNA ligase determined by x-ray crystallography.

  3. Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay

    Science.gov (United States)

    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. PMID:26544710

  4. Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay.

    Directory of Open Access Journals (Sweden)

    Yong Huang

    Full Text Available 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.

  5. Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay.

    Science.gov (United States)

    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.

  6. 6-Thioguanine alters the structure and stability of duplex DNA and inhibits quadruplex DNA formation.

    Science.gov (United States)

    Marathias, V M; Sawicki, M J; Bolton, P H

    1999-07-15

    The ability to chemically synthesize biomolecules has opened up the opportunity to observe changes in structure and activity that occur upon single atom substitution. In favorable cases this can provide information about the roles of individual atoms. The substitution of 6-thioguanine (6SG) for guanine is a potentially very useful single atom substitution as 6SG has optical, photocrosslinking, metal ion binding and other properties of potential utility. In addition, 6-mercaptopurine is a clinically important pro-drug that is activated by conversion into 6SG by cells. The results presented here indicate that the presence of 6SG blocks the formation of quadruplex DNA. The presence of 6SG alters the structure and lowers the thermal stability of duplex DNA, but duplex DNA can be formed in the presence of 6SG. These results indicate that some of the cytotoxic activity of 6SG may be due to disruption of the quadruplex structures formed by telomere and other DNAs. This additional mode of action is consistent with the delayed onset of cytotoxicity.

  7. NMR studies of abasic sites in DNA duplexes: Deoxyadenosine stacks into the helix opposite acyclic lesions

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Chang, Chienneng; Johnson, F.; Grollman, A.P.; Patel, D.J.

    1989-01-01

    Proton and phosphorus NMR studies are reported for two complementary nonanucleotide duplexes containing acyclic abasic sites. The first duplex, d(C-A-T-G-A-G-T-A-C)·d(G-T-A-C-P-C-A-T-G), contains an acyclic propanyl moiety, P, located opposite a deoxyadenosine at the center of the helix (designated AP P 9-mer duplex). The second duplex, d(C-A-T-G-A-G-T-A-C-)·d(G-T-A-C-E-C-A-T-G), contains a similarly located acyclic ethanyl moiety, E (designated AP E 9-mer duplex). The ethanyl moiety is one carbon shorter than the natural carbon-phosphodiester backbone of a single nucleotide unit of DNA. The majority of the exchangeable and nonexchangeable base and sugar protons in both the AP P 9-mer and AP E 9-mer duplexes, including those at the abasic site, have been assigned by recording and analyzing two-dimensional phase-sensitive NOESY data sets in H 2 O and D 2 O solution between -5 and 5 degree C. These spectroscopic observations establish that A5 inserts into the helix opposite the abasic site (P14 and El14) and stacks between the flanking G4·C15 and G6·C13 Watson-Crick base pairs in both the AP P 9-mer and AP E 9-mer duplexes. Proton NMR parameters for the Ap P 9-mer and AP E 9-mer duplexes are similar to those reported previously. These proton NMR experiments demonstrate that the structures at abasic sites are very similar whether the five-membered ring is open or closed or whether the phosphodiester backbone is shortened by one carbon atom. Phosphorus spectra of the AP P 9-mer and AP E 9-mer duplexes (5 degree C) indicate that the backbone conformation is similarly perturbed at three phosphodiester backbone torsion angles

  8. Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences

    Science.gov (United States)

    König, Sebastian L. B.; Huppert, Julian L.; Sigel, Roland K. O.; Evans, Amanda C.

    2013-01-01

    G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions. PMID:23771141

  9. Circularly polarized luminescence of helically assembled pyrene π-stacks on RNA and DNA duplexes.

    Science.gov (United States)

    Nakamura, Mitsunobu; Ota, Fuyuki; Takada, Tadao; Akagi, Kazuo; Yamana, Kazushige

    2018-05-01

    In this report, we describe the circularly polarized luminescence (CPL) of the RNA duplexes having one to four 2'-O-pyrene modified uridines (Upy) and the DNA duplexes having two, four, and six pyrene modified non-nucleosidic linkers (Py). Both the pyrene π-stack arrays formed on the RNA and DNA double helical structures exhibited pyrene excimer fluorescence. In the pyrene-modified RNA systems, the RNA duplex having four Upys gives CPL emission with g lum value of <0.01 at 480 nm. The structure of pyrene stacks on the RNA duplex may be rigidly regulated with increase in the Upy domains, which resulted in the CPL emission. In the DNA systems, the pyrene-modified duplexes containing two and four Pys exhibited CPL emission with g lum values of <0.001 at 505 nm. The pyrene π-stack arrays presented here show CPL emission. However, the g lum values are relatively small when compared with our previous system consisting of the pyrene-zipper arrays on RNA. © 2018 Wiley Periodicals, Inc.

  10. Exploring the Interactions of the Dietary Plant Flavonoids Fisetin and Naringenin with G-Quadruplex and Duplex DNA, Showing Contrasting Binding Behavior: Spectroscopic and Molecular Modeling Approaches.

    Science.gov (United States)

    Bhattacharjee, Snehasish; Chakraborty, Sandipan; Sengupta, Pradeep K; Bhowmik, Sudipta

    2016-09-01

    Guanine-rich sequences have the propensity to fold into a four-stranded DNA structure known as a G-quadruplex (G4). G4 forming sequences are abundant in the promoter region of several oncogenes and become a key target for anticancer drug binding. Here we have studied the interactions of two structurally similar dietary plant flavonoids fisetin and naringenin with G4 as well as double stranded (duplex) DNA by using different spectroscopic and modeling techniques. Our study demonstrates the differential binding ability of the two flavonoids with G4 and duplex DNA. Fisetin more strongly interacts with parallel G4 structure than duplex DNA, whereas naringenin shows stronger binding affinity to duplex rather than G4 DNA. Molecular docking results also corroborate our spectroscopic results, and it was found that both of the ligands are stacked externally in the G4 DNA structure. C-ring planarity of the flavonoid structure appears to be a crucial factor for preferential G4 DNA recognition of flavonoids. The goal of this study is to explore the critical effects of small differences in the structure of closely similar chemical classes of such small molecules (flavonoids) which lead to the contrasting binding properties with the two different forms of DNA. The resulting insights may be expected to facilitate the designing of the highly selective G4 DNA binders based on flavonoid scaffolds.

  11. Templated Chemistry for Sequence-Specific Fluorogenic Detection of Duplex DNA

    Science.gov (United States)

    Li, Hao; Franzini, Raphael M.; Bruner, Christopher; Kool, Eric T.

    2015-01-01

    We describe the development of templated fluorogenic chemistry for detection of specific sequences of duplex DNA in solution. In this approach, two modified homopyrimidine oligodeoxynucleotide probes are designed to bind by triple helix formation at adjacent positions on a specific purine-rich target sequence of duplex DNA. One fluorescein-labeled probe contains an α-azidoether linker to a fluorescence quencher; the second (trigger) probe carries a triarylphosphine, designed to reduce the azide and cleave the linker. The data showed that at pH 5.6 these probes yielded a strong fluorescence signal within minutes on addition to a complementary homopurine duplex DNA target. The signal increased by a factor of ca. 60, and was completely dependent on the presence of the target DNA. Replacement of cytosine in the probes with pseudoisocytosine allowed the templated chemistry to proceed readily at pH 7. Single nucleotide mismatches in the target oligonucleotide slowed the templated reaction considerably, demonstrating high sequence selectivity. The use of templated fluorogenic chemistry for detection of duplex DNAs has not been previously reported and may allow detection of double stranded DNA, at least for homopurine-homopyrimidine target sites, under native, non-disturbing conditions. PMID:20859985

  12. Sequence-specific protection of duplex DNA against restriction and methylation enzymes by pseudocomplementary PNAs

    DEFF Research Database (Denmark)

    Izvolsky, K I; Demidov, V V; Nielsen, P E

    2000-01-01

    I restriction endonuclease and dam methylase. The pcPNA-assisted protection against enzymatic methylation is more efficient when the PNA-binding site embodies the methylase-recognition site rather than overlaps it. We conclude that pcPNAs may provide the robust tools allowing to sequence-specifically manipulate...... DNA duplexes in a virtually sequence-unrestricted manner....

  13. G-quadruplexes Significantly Stimulate Pif1 Helicase-catalyzed Duplex DNA Unwinding*

    Science.gov (United States)

    Duan, Xiao-Lei; Liu, Na-Nv; Yang, Yan-Tao; Li, Hai-Hong; Li, Ming; Dou, Shuo-Xing; Xi, Xu-Guang

    2015-01-01

    The evolutionarily conserved G-quadruplexes (G4s) are faithfully inherited and serve a variety of cellular functions such as telomere maintenance, gene regulation, DNA replication initiation, and epigenetic regulation. Different from the Watson-Crick base-pairing found in duplex DNA, G4s are formed via Hoogsteen base pairing and are very stable and compact DNA structures. Failure of untangling them in the cell impedes DNA-based transactions and leads to genome instability. Cells have evolved highly specific helicases to resolve G4 structures. We used a recombinant nuclear form of Saccharomyces cerevisiae Pif1 to characterize Pif1-mediated DNA unwinding with a substrate mimicking an ongoing lagging strand synthesis stalled by G4s, which resembles a replication origin and a G4-structured flap in Okazaki fragment maturation. We find that the presence of G4 may greatly stimulate the Pif1 helicase to unwind duplex DNA. Further studies reveal that this stimulation results from G4-enhanced Pif1 dimerization, which is required for duplex DNA unwinding. This finding provides new insights into the properties and functions of G4s. We discuss the observed activation phenomenon in relation to the possible regulatory role of G4s in the rapid rescue of the stalled lagging strand synthesis by helping the replicator recognize and activate the replication origin as well as by quickly removing the G4-structured flap during Okazaki fragment maturation. PMID:25627683

  14. Electron transfer in DNA duplexes containing 2-methyl-1,4-naphthoquinone

    OpenAIRE

    Bergeron, François; Houde, Daniel; Hunting, Darel J.; Wagner, J. Richard

    2004-01-01

    2-Methyl-1,4-naphthoquinone (menadione, MQ) was linked to synthetic oligonucleotides and exposed to near-UV light to generate base radical cations in DNA. This model system of electron transfer induced alkali-labile breaks at GG doublets, similar to anthraquinone and metallointercalators systems. In sharp contrast to other systems, the photolysis of MQ–DNA duplexes gave interstrand cross-links and alkali-labile breaks at bases on the complementary strand opposite the MQ moiety. For sequences ...

  15. Mechanism of duplex DNA destabilization by RNA-guided Cas9 nuclease during target interrogation.

    Science.gov (United States)

    Mekler, Vladimir; Minakhin, Leonid; Severinov, Konstantin

    2017-05-23

    The prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 (Cas9) endonuclease cleaves double-stranded DNA sequences specified by guide RNA molecules and flanked by a protospacer adjacent motif (PAM) and is widely used for genome editing in various organisms. The RNA-programmed Cas9 locates the target site by scanning genomic DNA. We sought to elucidate the mechanism of initial DNA interrogation steps that precede the pairing of target DNA with guide RNA. Using fluorometric and biochemical assays, we studied Cas9/guide RNA complexes with model DNA substrates that mimicked early intermediates on the pathway to the final Cas9/guide RNA-DNA complex. The results show that Cas9/guide RNA binding to PAM favors separation of a few PAM-proximal protospacer base pairs allowing initial target interrogation by guide RNA. The duplex destabilization is mediated, in part, by Cas9/guide RNA affinity for unpaired segments of nontarget strand DNA close to PAM. Furthermore, our data indicate that the entry of double-stranded DNA beyond a short threshold distance from PAM into the Cas9/single-guide RNA (sgRNA) interior is hindered. We suggest that the interactions unfavorable for duplex DNA binding promote DNA bending in the PAM-proximal region during early steps of Cas9/guide RNA-DNA complex formation, thus additionally destabilizing the protospacer duplex. The mechanism that emerges from our analysis explains how the Cas9/sgRNA complex is able to locate the correct target sequence efficiently while interrogating numerous nontarget sequences associated with correct PAMs.

  16. Triple helical DNA in a duplex context and base pair opening

    Science.gov (United States)

    Esguerra, Mauricio; Nilsson, Lennart; Villa, Alessandra

    2014-01-01

    It is fundamental to explore in atomic detail the behavior of DNA triple helices as a means to understand the role they might play in vivo and to better engineer their use in genetic technologies, such as antigene therapy. To this aim we have performed atomistic simulations of a purine-rich antiparallel triple helix stretch of 10 base triplets flanked by canonical Watson–Crick double helices. At the same time we have explored the thermodynamic behavior of a flipping Watson–Crick base pair in the context of the triple and double helix. The third strand can be accommodated in a B-like duplex conformation. Upon binding, the double helix changes shape, and becomes more rigid. The triple-helical region increases its major groove width mainly by oversliding in the negative direction. The resulting conformations are somewhere between the A and B conformations with base pairs remaining almost perpendicular to the helical axis. The neighboring duplex regions maintain a B DNA conformation. Base pair opening in the duplex regions is more probable than in the triplex and binding of the Hoogsteen strand does not influence base pair breathing in the neighboring duplex region. PMID:25228466

  17. 5' modification of duplex DNA with a ruthenium electron donor-acceptor pair using solid-phase DNA synthesis

    Science.gov (United States)

    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.

  18. Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA.

    Science.gov (United States)

    Yang, Zhiyu; Price, Nathan E; Johnson, Kevin M; Wang, Yinsheng; Gates, Kent S

    2017-06-20

    Interstrand cross-links are exceptionally bioactive DNA lesions. Endogenous generation of interstrand cross-links in genomic DNA may contribute to aging, neurodegeneration, and cancer. Abasic (Ap) sites are common lesions in genomic DNA that readily undergo spontaneous and amine-catalyzed strand cleavage reactions that generate a 2,3-didehydro-2,3-dideoxyribose sugar remnant (3'ddR5p) at the 3'-terminus of the strand break. Interestingly, this strand scission process leaves an electrophilic α,β-unsaturated aldehyde residue embedded within the resulting nicked duplex. Here we present evidence that 3'ddR5p derivatives generated by spermine-catalyzed strand cleavage at Ap sites in duplex DNA can react with adenine residues on the opposing strand to generate a complex lesion consisting of an interstrand cross-link adjacent to a strand break. The cross-link blocks DNA replication by ϕ29 DNA polymerase, a highly processive polymerase enzyme that couples synthesis with strand displacement. This suggests that 3'ddR5p-derived cross-links have the potential to block critical cellular DNA transactions that require strand separation. LC-MS/MS methods developed herein provide powerful tools for studying the occurrence and properties of these cross-links in biochemical and biological systems. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA

    Science.gov (United States)

    Yang, Zhiyu; Price, Nathan E.; Johnson, Kevin M.

    2017-01-01

    Abstract Interstrand cross-links are exceptionally bioactive DNA lesions. Endogenous generation of interstrand cross-links in genomic DNA may contribute to aging, neurodegeneration, and cancer. Abasic (Ap) sites are common lesions in genomic DNA that readily undergo spontaneous and amine-catalyzed strand cleavage reactions that generate a 2,3-didehydro-2,3-dideoxyribose sugar remnant (3’ddR5p) at the 3’-terminus of the strand break. Interestingly, this strand scission process leaves an electrophilic α,β-unsaturated aldehyde residue embedded within the resulting nicked duplex. Here we present evidence that 3’ddR5p derivatives generated by spermine-catalyzed strand cleavage at Ap sites in duplex DNA can react with adenine residues on the opposing strand to generate a complex lesion consisting of an interstrand cross-link adjacent to a strand break. The cross-link blocks DNA replication by ϕ29 DNA polymerase, a highly processive polymerase enzyme that couples synthesis with strand displacement. This suggests that 3’ddR5p-derived cross-links have the potential to block critical cellular DNA transactions that require strand separation. LC-MS/MS methods developed herein provide powerful tools for studying the occurrence and properties of these cross-links in biochemical and biological systems. PMID:28531327

  20. Pulsed IR Heating Studies of Single-Molecule DNA Duplex Dissociation Kinetics and Thermodynamics

    Science.gov (United States)

    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) 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

  1. Correlation between the thermodynamic stability of DNA duplexes and the interaction and solvation energies of DNA building blocks

    Czech Academy of Sciences Publication Activity Database

    Řezáč, Jan; Hobza, Pavel

    2008-01-01

    Roč. 73, č. 2 (2008), s. 161-174 ISSN 0010-0765 R&D Projects: GA MŠk LC512; GA ČR GA203/05/0009; GA ČR(CZ) GD203/05/H001 Institutional research plan: CEZ:AV0Z40550506 Keywords : DNA duplex * interaction energy * stability Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.784, year: 2008

  2. Electrochemical single-molecule conductivity of duplex and quadruplex DNA

    DEFF Research Database (Denmark)

    Zhang, Ling; Zhang, Jingdong; Ulstrup, Jens

    2017-01-01

    Photoinduced and electrochemical charge transport in DNA (oligonucleotides, OGNs) and the notions “hopping”, superexchange, polaron, and vibrationally gated charge transport have been in focus over more than two decades. In recent years mapping of electrochemical charge transport of pure and redo...

  3. Long-Range Vibrational Dynamics Are Directed by Watson-Crick Base Pairing in Duplex DNA.

    Science.gov (United States)

    Hithell, Gordon; Shaw, Daniel J; Donaldson, Paul M; Greetham, Gregory M; Towrie, Michael; Burley, Glenn A; Parker, Anthony W; Hunt, Neil T

    2016-05-05

    Ultrafast two-dimensional infrared (2D-IR) spectroscopy of a 15-mer A-T DNA duplex in solution has revealed structure-dependent vibrational coupling and energy transfer processes linking bases with the sugar-phosphate backbone. Duplex melting induces significant changes in the positions of off-diagonal peaks linking carbonyl and ring-stretching vibrational modes of the adenine and thymine bases with vibrations of the phosphate group and phosphodiester linkage. These indicate that Watson-Crick hydrogen bonding and helix formation lead to a unique vibrational coupling arrangement of base vibrational modes with those of the phosphate unit. On the basis of observations from time-resolved 2D-IR data, we conclude that rapid energy transfer processes occur between base and backbone, mediated by additional modes located on the deoxyribose moiety within the same nucleotide. These relaxation dynamics are insensitive to duplex melting, showing that efficient intramolecular energy relaxation to the solvent via the phosphate groups is the key to excess energy dissipation in both single- and double-stranded DNA.

  4. G-quadruplex and G-rich sequence stimulate Pif1p-catalyzed downstream duplex DNA unwinding through reducing waiting time at ss/dsDNA junction

    Science.gov (United States)

    Zhang, Bo; Wu, Wen-Qiang; Liu, Na-Nv; Duan, Xiao-Lei; Li, Ming; Dou, Shuo-Xing; Hou, Xi-Miao; Xi, Xu-Guang

    2016-01-01

    Alternative DNA structures that deviate from B-form double-stranded DNA such as G-quadruplex (G4) DNA can be formed by G-rich sequences that are widely distributed throughout the human genome. We have previously shown that Pif1p not only unfolds G4, but also unwinds the downstream duplex DNA in a G4-stimulated manner. In the present study, we further characterized the G4-stimulated duplex DNA unwinding phenomenon by means of single-molecule fluorescence resonance energy transfer. It was found that Pif1p did not unwind the partial duplex DNA immediately after unfolding the upstream G4 structure, but rather, it would dwell at the ss/dsDNA junction with a ‘waiting time’. Further studies revealed that the waiting time was in fact related to a protein dimerization process that was sensitive to ssDNA sequence and would become rapid if the sequence is G-rich. Furthermore, we identified that the G-rich sequence, as the G4 structure, equally stimulates duplex DNA unwinding. The present work sheds new light on the molecular mechanism by which G4-unwinding helicase Pif1p resolves physiological G4/duplex DNA structures in cells. PMID:27471032

  5. Unstable Hoogsteen base pairs adjacent to echinomycin binding sites within a DNA duplex

    International Nuclear Information System (INIS)

    Gilbert, D.E.; van der Marel, G.A.; van Boom, J.H.; Feigon, J.

    1989-01-01

    The bisintercalation complex present between the DNA octamer [d(ACGTACGT)] 2 and the cyclic octadepsipeptide antibiotic echinomycin has been studied by one- and two-dimensional proton NMR, and the results obtained have been compared with the crystal structures of related DNA-echinomycin complexes. Two echinomycins are found to bind cooperatively to each DNA duplex at the CpG steps, with the two quinoxaline rings of each echinomycin bisintercalating between the C·G and A·T base pairs. At low temperatures, the A·T base pairs on either side of the intercalation site adopt the Hoogsteen conformation, as observed in the crystal structures. However, as the temperature is raised, the Hoogsteen base pairs in the interior of the duplex are destabilized and are observed to be exchanging between the Hoogsteen base pair and either an open or a Watson-Crick base-paired state. The terminal A·T base pairs, which are not as constrained by the helix as the internal base pairs, remain stably Hoogsteen base-paired up to at least 45 degree C. The implications of these results for the biological role of Hoogsteen base pairs in echinomycin-DNA complexes in vivo are discussed

  6. Combined Triplex/Duplex Invasion of Double-Stranded DNA by "Tail-Clamp" Peptide Nucleic Acid

    DEFF Research Database (Denmark)

    Bentin, Thomas; Larsen, H. J.; Nielsen, Peter E.

    2003-01-01

    as determined by T-m measurements. Binding to double-stranded (ds) DNA occurred by combined triplex and duplex invasion as analyzed by permanganate probing. Furthermore, C-50 measurements revealed that tail-clamp PNAs consistently bound the dsDNA target more efficiently, and kinetics experiments revealed...

  7. Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA

    Science.gov (United States)

    Mielke, Steven P.; Grønbech-Jensen, Niels; Krishnan, V. V.; Fink, William H.; Benham, Craig J.

    2005-09-01

    The topological state of DNA in vivo is dynamically regulated by a number of processes that involve interactions with bound proteins. In one such process, the tracking of RNA polymerase along the double helix during transcription, restriction of rotational motion of the polymerase and associated structures, generates waves of overtwist downstream and undertwist upstream from the site of transcription. The resulting superhelical stress is often sufficient to drive double-stranded DNA into a denatured state at locations such as promoters and origins of replication, where sequence-specific duplex opening is a prerequisite for biological function. In this way, transcription and other events that actively supercoil the DNA provide a mechanism for dynamically coupling genetic activity with regulatory and other cellular processes. Although computer modeling has provided insight into the equilibrium dynamics of DNA supercoiling, to date no model has appeared for simulating sequence-dependent DNA strand separation under the nonequilibrium conditions imposed by the dynamic introduction of torsional stress. Here, we introduce such a model and present results from an initial set of computer simulations in which the sequences of dynamically superhelical, 147 base pair DNA circles were systematically altered in order to probe the accuracy with which the model can predict location, extent, and time of stress-induced duplex denaturation. The results agree both with well-tested statistical mechanical calculations and with available experimental information. Additionally, we find that sites susceptible to denaturation show a propensity for localizing to supercoil apices, suggesting that base sequence determines locations of strand separation not only through the energetics of interstrand interactions, but also by influencing the geometry of supercoiling.

  8. The first example of a Hoogsteen base-paired DNA duplex in dynamic equilibrium with a Watson-Crick base-paired duplex--a structural (NMR), kinetic and thermodynamic study.

    Science.gov (United States)

    Isaksson, J; Zamaratski, E; Maltseva, T V; Agback, P; Kumar, A; Chattopadhyaya, J

    2001-06-01

    A single-point substitution of the O4' oxygen by a CH2 group at the sugar residue of A6 (i.e. 2'-deoxyaristeromycin moiety) in a self-complementary DNA duplex, 5'-d(C1G2C3G4A5A6T7T8C9G10C11G12)2(-3), has been shown to steer the fully Watson-Crick basepaired DNA duplex (1A), akin to the native counterpart, to a doubly A6:T7 Hoogsteen basepaired (1B) B-type DNA duplex, resulting in a dynamic equilibrium of (1A)(1B): Keq = k1/k(-1) = 0.56+/-0.08. The dynamic conversion of the fully Watson-Crick basepaired (1A) to the partly Hoogsteen basepaired (1B) structure is marginally kinetically and thermodynamically disfavoured [k1 (298K) = 3.9 0.8 sec(-1); deltaHdegrees++ = 164+/-14 kJ/mol; -TdeltaS degrees++ (298K) = -92 kJ/mol giving a deltaG degrees++ 298 of 72 kJ/mol. Ea (k1) = 167 14 kJ/mol] compared to the reverse conversion of the Hoogsteen (1B) to the Watson-Crick (1A) structure [k-1 (298K) = 7.0 0.6 sec-1, deltaH degrees++ = 153 13 kJ/mol; -TdeltaSdegrees++ (298K) = -82 kJ/mol giving a deltaGdegrees++(298) of 71 kJ/mol. Ea (k-1) = 155 13 kJ/mol]. Acomparison of deltaGdegrees++(298) of the forward (k1) and backward (k-1) conversions, (1A)(1B), shows that there is ca 1 kJ/mol preference for the Watson-Crick (1A) over the double Hoogsteen basepaired (1B) DNA duplex, thus giving an equilibrium ratio of almost 2:1 in favour of the fully Watson-Crick basepaired duplex. The chemical environments of the two interconverting DNA duplexes are very different as evident from their widely separated sets of chemical shifts connected by temperature-dependent exchange peaks in the NOESY and ROESY spectra. The fully Watson-Crick basepaired structure (1A) is based on a total of 127 intra, 97 inter and 17 cross-strand distance constraints per strand, whereas the double A6:T7 Hoogsteen basepaired (1B) structure is based on 114 intra, 92 inter and 15 cross-strand distance constraints, giving an average of 22 and 20 NOE distance constraints per residue and strand, respectively. In addition

  9. Sequence distribution of acetaldehyde-derived N2-ethyl-dG adducts along duplex DNA.

    Science.gov (United States)

    Matter, Brock; Guza, Rebecca; Zhao, Jianwei; Li, Zhong-ze; Jones, Roger; Tretyakova, Natalia

    2007-10-01

    Acetaldehyde (AA) is the major metabolite of ethanol and may be responsible for an increased gastrointestinal cancer risk associated with alcohol beverage consumption. Furthermore, AA is one of the most abundant carcinogens in tobacco smoke and induces tumors of the respiratory tract in laboratory animals. AA binding to DNA induces Schiff base adducts at the exocyclic amino group of dG, N2-ethylidene-dG, which are reversible on the nucleoside level but can be stabilized by reduction to N2-ethyl-dG. Mutagenesis studies in the HPRT reporter gene and in the p53 tumor suppressor gene have revealed the ability of AA to induce G-->A transitions and A-->T transversions, as well as frameshift and splice mutations. AA-induced point mutations are most prominent at 5'-AGG-3' trinucleotides, possibly a result of sequence specific adduct formation, mispairing, and/or repair. However, DNA sequence preferences for the formation of acetaldehyde adducts have not been previously examined. In the present work, we employed a stable isotope labeling-HPLC-ESI+-MS/MS approach developed in our laboratory to analyze the distribution of acetaldehyde-derived N2-ethyl-dG adducts along double-stranded oligodeoxynucleotides representing two prominent lung cancer mutational "hotspots" and their surrounding DNA sequences. 1,7,NH 2-(15)N-2-(13)C-dG was placed at defined positions within DNA duplexes derived from the K-ras protooncogene and the p53 tumor suppressor gene, followed by AA treatment and NaBH 3CN reduction to convert N2-ethylidene-dG to N2-ethyl-dG. Capillary HPLC-ESI+-MS/MS was used to quantify N2-ethyl-dG adducts originating from the isotopically labeled and unlabeled guanine nucleobases and to map adduct formation along DNA duplexes. We found that the formation of N2-ethyl-dG adducts was only weakly affected by the local sequence context and was slightly increased in the presence of 5-methylcytosine within CG dinucleotides. These results are in contrast with sequence

  10. Duplex Interrogation by a Direct DNA Repair Protein in Search of Base Damage

    Science.gov (United States)

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

    2012-01-01

    ALKBH2 is a direct DNA repair dioxygenase guarding mammalian genome against N1-methyladenine, N3-methylcytosine, and 1,N6-ethenoadenine damage. A prerequisite for repair is to identify these lesions in the genome. Here we present crystal structures of ALKBH2 bound to different duplex DNAs. Together with computational and biochemical analyses, our results suggest that DNA interrogation by ALKBH2 displays two novel features: i) ALKBH2 probes base-pair stability and detects base pairs with reduced stability; 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. PMID:22659876

  11. Structural studies of the 5'-phenazinium-tethered matched and G-A-mismatched DNA duplexes by NMR spectroscopy.

    Science.gov (United States)

    Maltseva, T; Sandström, A; Ivanova, I M; Sergeyev, D S; Zarytova, V F; Chattopadhyaya, J

    1993-05-01

    The mechanism through which modified oligo-DNA analogues act as antisense repressors at the transcriptional and translational level of gene expression is based on the information content in the nucleotide sequence which is determined by the specific base pairing. The efficiency of such action is largely determined by the stability of the duplex formed between the oligonucleotide reagent and the target sequence and also by the mismatched base pairing, such as G-A, that occurs during replication or recombination. We herein report that the phenazinium (Pzn)-tethered matched duplex p(d(TGTTTGGC)):(Pzn)-p(d(CCAAACA)) (III) (Tm = 50 degrees C) has a much larger stability than the parent matched duplex p(d(TGTTTGGC)):p(d(CCAAACA)) (I) (Tm = 30 degrees C). On the other hand, the Pzn-tethered G-A-mismatched duplex p(d(TGTTTGGC)):(Pzn)-p(d(ACAAACA)) (IV) (Tm = 34 degrees C) is only slightly more stable than its parent mismatched duplex p(d(TGTTTGGC)):p(d(ACAAACA)) (Tm = 25 degrees C). A detailed 500 MHz NMR study and constrained MD refinements of NMR-derived structures have been undertaken for the DNA duplexes (I), (II), (III) and (IV) in order to understand the structural basis of stabilization of Pzn-tethered matched DNA duplex (delta Tm = 20 degrees C) compared to mismatched duplex (delta Tm = 9 degrees C). Assignment of the 1H-NMR (500 MHz) spectra of the duplexes has been carried out by 2D NOESY, HOHAHA and DQF-COSY experiments. The torsion angles have been extracted from the J-coupling constants obtained by simulation of most of the DQF-COSY cross-peaks using program SMART. The solution structure of the duplexes were assessed by an iterative hybride relaxation matrix method (MORASS) combined with NOESY distances and torsion angles restrained molecular dynamics (MD) using program Amber 4.0. The standard Amber 4.0 force-field parameters were used for the oligonucleotide in conjunction with the new parameters for Pzn residue which was obtained by full geometry

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

    Science.gov (United States)

    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

  13. Crystal structure of metallo DNA duplex containing consecutive Watson-Crick-like T-Hg(II)-T base pairs.

    Science.gov (United States)

    Kondo, Jiro; Yamada, Tom; Hirose, Chika; Okamoto, Itaru; Tanaka, Yoshiyuki; Ono, Akira

    2014-02-24

    The metallo DNA duplex containing mercury-mediated T-T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II)-T base pairs. The Hg(II) ion occupies the center between two T residues. The N3-Hg(II) bond distance is 2.0 Å. The relatively short Hg(II)-Hg(II) distance (3.3 Å) observed in consecutive T-Hg(II)-T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B-form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of Hg(II). The structure of the metallo DNA duplex itself and the Hg(II)-induced structural switching from the nonhelical form to the B-form provide the basis for structure-based design of metal-conjugated nucleic acid nanomaterials. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Dual door entry to exciplex emission in a chimeric DNA duplex containing non-nucleoside-nucleoside pair.

    Science.gov (United States)

    Bag, Subhendu Sekhar; Talukdar, Sangita; Kundu, Rajen; Saito, Isao; Jana, Subhashis

    2014-01-25

    Dual door entry to exciplex formation was established in a chimeric DNA duplex wherein a fluorescent non-nucleosidic base surrogate () is paired against a fluorescent nucleosidic base surrogate (). Packing of the nucleobases via intercalative stacking interactions led to an exciplex emission either via FRET from the donor or direct excitation of the FRET acceptor .

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2015-03-19

    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.

  17. Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA

    NARCIS (Netherlands)

    Etson, Candice M.; Hamdan, Samir M.; Richardson, Charles C.; Oijen, Antoine M. van; Richardson, Charles C.

    2010-01-01

    The DNA polymerases involved in DNA replication achieve high processivity of nucleotide incorporation by forming a complex with processivity factors. A model system for replicative DNA polymerases, the bacteriophage T7 DNA polymerase (gp5), encoded by gene 5, forms a tight, 1:1 complex with

  18. EFFECT OF INTERMETALLIC PHASES ON CORROSION BEHAVIOR AND MECHANICAL PROPERTIES OF DUPLEX STAINLESS STEEL AND SUPER-DUPLEX STAINLESS STEEL

    Directory of Open Access Journals (Sweden)

    Prabhu Paulraj

    2015-08-01

    Full Text Available Duplex Stainless Steels (DSS and Super Duplex Stainless Steel (SDSS have excellent integration of mechanical and corrosion properties. However, the formation of intermetallic phases is a major problem in their usage. The mechanical and corrosion properties are deteriorated due to the presence of intermetallic phases. These phases are induced during welding, prolonged exposure to high temperatures, and improper heat treatments. The main emphasis of this review article is on intermetallic phases and their effects on corrosion and mechanical properties. First the effect of various alloying elements on DSS and SDSS has been discussed followed by formation of various intermetallic phases. The intermetallic phases affect impact toughness and corrosion resistance significantly. Their deleterious effect on weldments has also been reviewed.

  19. Simultaneous Binding of Hybrid Molecules Constructed with Dual DNA-Binding Components to a G-Quadruplex and Its Proximal Duplex.

    Science.gov (United States)

    Asamitsu, Sefan; Obata, Shunsuke; Phan, Anh Tuân; Hashiya, Kaori; Bando, Toshikazu; Sugiyama, Hiroshi

    2018-03-20

    A G-quadruplex (quadruplex) is a nucleic acid secondary structure adopted by guanine-rich sequences and is considered to be relevant to various pharmacological and biological contexts. Although a number of researchers have endeavored to discover and develop quadruplex-interactive molecules, poor ligand designability originating from topological similarity of the skeleton of diverse quadruplexes has remained a bottleneck for gaining specificity for individual quadruplexes. This work reports on hybrid molecules that were constructed with dual DNA-binding components, a cyclic imidazole/lysine polyamide (cIKP), and a hairpin pyrrole/imidazole polyamide (hPIP), with the aim toward specific quadruplex targeting by reading out the local duplex DNA sequence adjacent to designated quadruplexes in the genome. By means of circular dichroism (CD), fluorescence resonance energy transfer (FRET), surface plasmon resonance (SPR), and NMR techniques, we showed the dual and simultaneous recognition of the respective segment via hybrid molecules, and the synergistic and mutual effect of each binding component that was appropriately linked on higher binding affinity and modest sequence specificity. Monitoring quadruplex and duplex imino protons of the quadruplex/duplex motif titrated with hybrid molecules clearly revealed distinct features of the binding of hybrid molecules to the respective segments upon their simultaneous recognition. A series of the systematic and detailed binding assays described here showed that the concept of simultaneous recognition of quadruplex and its proximal duplex by hybrid molecules constructed with the dual DNA-binding components may provide a new strategy for ligand design, enabling targeting of a large variety of designated quadruplexes at specific genome locations. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Identification of pork contamination in meatball using genetic marker mitochondrial DNA cytochrome b gene by duplex-PCR

    Science.gov (United States)

    Novianty, E.; Kartikasari, L. R.; Lee, J. H.; Cahyadi, M.

    2017-04-01

    Meat based food products have a big opportunity to mix and adulterated with other meats. Muslim communities are prohibited to consume pork-containing product or other pig derivatives in food. Therefore, the high sensitivity, fast, cheap and accurate approach is needed to detect pig contamination in raw meat and meat-processed product such as meatball. The aim of this study was to identify pork contamination in meatball using genetic marker of mitochondrial DNA cytochrome b gene by duplex-PCR. Samples were prepared and designed by following the proportions 0, 1, 5, 10, 25% of pork in meatballs, respectively. The DNA genome was extracted from meatballs and polymerase chain reaction (PCR) was performed using species specific primer to isolate mt-DNA cytochrome b gene. The results showed that the DNA genome was successfully isolated from pork, beef, and contaminated meatballs. Furthermore, 2% agarose gels was able to visualize of duplex-PCR to identify pork contamination in meatballs up to very small proportion (1%). It can be concluded that duplex-PCR of mt-DNA cytochrome b gene was very sensitive to identify pork contamination in meatball with the presence of specific 398 bp DNA band.

  1. Toehold-Mediated Displacement of an Adenosine-Binding Aptamer from a DNA Duplex by its Ligand.

    Science.gov (United States)

    Monserud, Jon H; Macri, Katherine M; Schwartz, Daniel K

    2016-10-24

    DNA is increasingly used to engineer dynamic nanoscale circuits, structures, and motors, many of which rely on DNA strand-displacement reactions. The use of functional DNA sequences (e.g., aptamers, which bind to a wide range of ligands) in these reactions would potentially confer responsiveness on such devices, and integrate DNA computation with highly varied molecular stimuli. By using high-throughput single-molecule FRET methods, we compared the kinetics of a putative aptamer-ligand and aptamer-complement strand-displacement reaction. We found that the ligands actively disrupted the DNA duplex in the presence of a DNA toehold in a similar manner to complementary DNA, with kinetic details specific to the aptamer structure, thus suggesting that the DNA strand-displacement concept can be extended to functional DNA-ligand systems. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Widespread Transient Hoogsteen Base-Pairs in Canonical Duplex DNA with Variable Energetics

    Science.gov (United States)

    Alvey, Heidi S.; Gottardo, Federico L.; Nikolova, Evgenia N.; Al-Hashimi, Hashim M.

    2015-01-01

    Hoogsteen base-pairing involves a 180 degree rotation of the purine base relative to Watson-Crick base-pairing within DNA duplexes, creating alternative DNA conformations that can play roles in recognition, damage induction, and replication. Here, using Nuclear Magnetic Resonance R1ρ relaxation dispersion, we show that transient Hoogsteen base-pairs occur across more diverse sequence and positional contexts than previously anticipated. We observe sequence-specific variations in Hoogsteen base-pair energetic stabilities that are comparable to variations in Watson-Crick base-pair stability, with Hoogsteen base-pairs being more abundant for energetically less favorable Watson-Crick base-pairs. Our results suggest that the variations in Hoogsteen stabilities and rates of formation are dominated by variations in Watson-Crick base pair stability, suggesting a late transition state for the Watson-Crick to Hoogsteen conformational switch. The occurrence of sequence and position-dependent Hoogsteen base-pairs provide a new potential mechanism for achieving sequence-dependent DNA transactions. PMID:25185517

  3. NMR and molecular modeling evidence for a G·A mismatch base pair in a purine-rich DNA duplex

    International Nuclear Information System (INIS)

    Li, Ying; Wilson, W.D.; Zon, G.

    1991-01-01

    1 H NMR experiments indicate that the oligomer 5'-d(ATGAGCGAATA) forms an unusual 10-base-pair duplex with 4 G·A base pairs and a 3' unpaired adenosine. NMR results indicate that guanoxine imino protons of the F·A mismatches are not hydrogen bonded but are stacked in the helix. A G→ I substitution in either G·A base pair causes a dramatic decrtease in duplex stability and indicates that hydrogen bonding of the guanosine amino group is critical. Nuclear Overhauser effect spectroscopy (NOESY) and two-dimensional correlated spectroscopy (COSY) results indicate that the overall duplex conformation is in the B-family. Cross-strand NOEs in two-dimensional NOESY spectra between a mismatched AH2 and an AH1' of the other mismatched base pair and between a mismatched GH8 and GNH1 of the other mismatch establish a purine-purine stacking pattern, adenosine over adenosine and guanosine over guanosine, which strongly stabilizes the duplex. A computer graphics molecular model of the ususual duplex was constructed with G·A base pairs containing A-NH 2 to GN3 and G-NH 2 to AN7 hydrogen bonds and B-form base pairs on both sides of the G·A pairs [5'-d(ATGAGC)]. The energy-minimized duplex satisfies all experimental constraints from NOESY and COSY results. A hydrogen bond from G-NH 2 of the mismatch to a phosphate oxygen is predicted

  4. Structural features of an exocyclic adduct positioned opposite an abasic site in a DNA duplex

    International Nuclear Information System (INIS)

    Kouchakdjian, M.; Patel, D.J.; Eisenberg, M.; Johnson, F.; Grollman, A.P.

    1991-01-01

    Structural studies have been extended to dual lesions where an exocyclic adduct is positioned opposite an abasic site in the center of a DNA oligomer duplex. NMR and energy minimization studies were performed on the 1,N 2 -propanodeoxyguanosine exocyclic adduct (X) positioned opposite a tetrahydrofuran abasic site (F) with the dual lesions located in the center of the (C1-A2-T3-G4-X5-G6-T7-A8-C9)·(G10-T11-A12-C13-F14-C15-A16-T17-G18) X·F 9-mer duplex. Two-dimensional NMR experiments establish that the X·F 9-mer helix is right-handed with Watson-Crick A·T and G·C base pairing on either side of the lesion site. NOEs are detected from the methylene protons of the exocyclic ring of X5 to the imino protons of G4·C15 and G6·C13 which flank the lesion site, as well as to the H1' and H1 double-prime protons of the cross strand F14 tetrahydrofuran moiety. These NMR results establish that the exocyclic adduct X5 is positioned between flanking G4·C15 and G6·C13 base pairs and directed toward the abasic lesion F14 on the partner strand. These studies establish that the exocyclic ring of the 1,N 2 -propanodeoxyguanosine adduct fits into the cavity generated by the abasic site

  5. High-resolution NMR studies of chimeric DNA-RNA-DNA duplexes, heteronomous base pairing, and continuous base stacking at junctions

    International Nuclear Information System (INIS)

    Chou, Shanho; Flynn, P.; Wang, A.; Reid, B.

    1991-01-01

    Two symmetrical DNA-RNA-DNA duplex chimeras, d(CGCG)r(AAUU)d(CGCG) (designated rAAUU) and d(CGCG)r(UAUA)d(CGCG) (designated rUAUA), and a nonsymmetrical chimeric duplex, d(CGTT)r(AUAA)d(TGCG)/d(CGCA)r(UUAU)d(AACG) (designated rAUAA), as well as their pure DNA analogues, containing dU instead of T, have been synthesized by solid-phase phosphoramidite methods and studied by high-resolution NMR techniques. The 1D imino proton NOE spectra of these d-r-d chimeras indicate normal Watson-Crick hydrogen bonding and base stacking at the junction region. Preliminary qualitative NOESY, COSY, and chemical shift data suggest that the internal RNA segment contains C3'-endo (A-type) sugar conformations except for the first RNA residues (position 5 and 17) following the 3' end of the DNA block, which, unlike the other six ribonucleotides, exhibit detectable H1'-H2' J coupling. The nucleosides of the two flanking DNA segments appear to adopt a fairly normal C2'-endo B-DNA conformation except at the junction with the RNA blocks (residues 4 and 16), where the last DNA residue appears to adopt an intermediate sugar conformation. The data indicate that A-type and B-type conformations can coexist in a single short continuous nucleic acid duplex, but these results differ somewhat from previous theoretical model studies

  6. Electroporation and microinjection successfully deliver single-stranded and duplex DNA into live cells as detected by FRET measurements.

    Directory of Open Access Journals (Sweden)

    Rosemary A Bamford

    Full Text Available Förster resonance energy transfer (FRET technology relies on the close proximity of two compatible fluorophores for energy transfer. Tagged (Cy3 and Cy5 complementary DNA strands forming a stable duplex and a doubly-tagged single strand were shown to demonstrate FRET outside of a cellular environment. FRET was also observed after transfecting these DNA strands into fixed and live cells using methods such as microinjection and electroporation, but not when using lipid based transfection reagents, unless in the presence of the endosomal acidification inhibitor bafilomycin. Avoiding the endocytosis pathway is essential for efficient delivery of intact DNA probes into cells.

  7. DNA Duplex Length and Salt Concentration Dependence of Enthalpy−Entropy Compensation Parameters for DNA Melting

    KAUST Repository

    Starikov, E. B.; Nordén, Bengt

    2009-01-01

    of the DNA and their water-counterion surrounding. With this in mind, to reinterpret the most recent results of calorimetric experiments on DNA oligomers of such a kind, the recent enthalpy-entropy compensation theory has been used. It is demonstrated

  8. DNA Duplex Length and Salt Concentration Dependence of Enthalpy−Entropy Compensation Parameters for DNA Melting

    KAUST Repository

    Starikov, E. B.

    2009-08-20

    Systematical differential calorimetry experiments on DNA oligomers with different lengths and placed in water solutions with various added salt concentrations may, in principle, unravel important information about the structure and dynamics of the DNA and their water-counterion surrounding. With this in mind, to reinterpret the most recent results of calorimetric experiments on DNA oligomers of such a kind, the recent enthalpy-entropy compensation theory has been used. It is demonstrated that the application of the latter could enable direct estimation of thermodynamic parameters of the microphase transitions connected to the changes in DNA dynamical regimes versus the length of the biopolymers and the ionic strengths of their water solutions, and this calls for much more systematical experimental and theoretical studies in this field. © 2009 American Chemical Society.

  9. Hairpin and duplex formation in DNA fragments CCAATTTTGG, CCAATTTTTTGG, and CCATTTTTGG: a proton NMR study

    International Nuclear Information System (INIS)

    Pramanik, P.; Kanhouwa, N.; Kan, L.

    1988-01-01

    Three DNA fragments, CCAATTTTGG (1), CCAATTTTTTGG (2), AND CCATTTTTGG (3), were studied by proton NMR spectroscopy in aqueous solution. All these oligodeoxyribonucleotides contain common sequences at the 5' and 3' ends (5'-CCA and TGG-3'). 2 as well as 3 forms only hairpin structures with four unpaired thymidylyl units, four and three base pair stems, respectively, in neutral solution under low and high NaCl concentrations. At high salt concentration the oligomer 1 forms a duplex structure with -TT- internal loop. On the other hand, the same oligomer forms a stable hairpin structure at low salt and low strand concentrations at pH 7. The hairpin structure of 1 has a stem containing only three base pairs (CCA x TGG) and a loop containing four nucleotides (-ATTT-) that includes a dissociated A x T base pair. The two secondary structures of 1 coexist in an aqueous solution containing 0.1 M NaCl, at pH 7. The equilibrium shifts to the hairpin side when the temperature is raised. The stabilities and base-stacking modes of all three oligonucleotides in tow different structures are reported

  10. A ready-to-use duplex qPCR to detect Leishmania infantum DNA in naturally infected dogs.

    Science.gov (United States)

    Rampazzo, Rita de Cássia Pontello; Solcà, Manuela da Silva; Santos, Liliane Celestino Sales; Pereira, Lais de Novaes; Guedes, José Carlos Oliveira; Veras, Patrícia Sampaio Tavares; Fraga, Deborah Bittencourt Mothé; Krieger, Marco Aurélio; Costa, Alexandre Dias Tavares

    2017-11-15

    Canine visceral leishmaniasis (CVL) is a systemic disease caused by Leishmania infantum. A precise CVL diagnosis would allow for a faster and more specific treatment. Quantitative PCR (qPCR) is a sensitive and specific technique that can diagnose CVL and also monitor parasite load in the animal during the course of the infection or treatment. The aim of this study was to develop a ready-to-use (gelified and freezer-free) duplex qPCR for the identification of infected animals. We combined a new qPCR protocol that detects the canine 18S rRNA gene with an existing protocol for L. infantum kDNA detection, creating a duplex qPCR. This duplex method was then developed into a ready-to-use format. The performance of the duplex and singleplex reactions were compared in the traditional format (liquid and freezer-stored). Furthermore, the duplex qPCR performance was compared between the ready-to-use and traditional formats. The singleplex and new duplex qPCR exhibited the same detection limit in the traditional format (0.1 parasites/reaction). The ready-to-use format showed a detection limit of 1 parasite/reaction without affecting the reaction efficiency. The performance of the new qPCR protocol in the two formats was assessed using canine tissue samples from 82 dogs in an endemic CVL area that were previously characterized by standard serological and parasitological protocols. Splenic aspirates provided a higher rate of positivity (92.9%) followed by skin (50%) and blood (35.7%). The reported detection limits were observed for all tissues studied. Our results show that the amplification of L. infantum kDNA and canine DNA in a single tube, using either the traditional or ready-to-use format, exhibited the same diagnostic performance as amplification of the parasite kDNA alone. The detection of the host gene strengthens the qPCR results by confirming the presence and quality of DNA in the samples and the absence of polymerase inhibitors. The ready-to-use duplex qPCR format

  11. Assessing the effect of different operation techniques on postoperative duplex ultrasound quality after carotid endarterectomy.

    Science.gov (United States)

    Grambow, E; Heller, T; Wieneke, P; Weiß, C; Klar, E; Weinrich, M

    2018-01-01

    Duplex ultrasound is the first choice in diagnostics and surveillance of stenoses of the internal carotid arteries before and even after surgery. Therefore, the quality of duplex ultrasound is crucial to investigate these vascular pathologies. Aim of this study was the evaluation whether different surgical techniques affect the postoperative quality of duplex ultrasound. In a time period from January to May 2015 duplex ultrasound of the cervical vessels was performed in 75 patients after unilateral endarterectomy of the internal carotid artery at our department between 2006 and 2012. Thereby, the non-operated contralateral side served as a control. Study groups were defined by the surgical techniques of eversion- or thrombendarterectomy with patch plasty using different patch materials and/or a haemostatic sealant. Duplex ultrasound analysis included acoustic impedance, extinction of ultrasound, thickness of skin and individual anatomic aspects of the patients. Carotid endarterectomy itself reduced intravascular grey levels, skin thickness and increased extinction of duplex ultrasound when compared to the non-operated side of the neck. In contrast, neither the kind of chosen operative technique nor the use of different patch materials or the application of a haemostatic sealant showed an effect in this regards. Whereas carotid endarterectomy per se worsens the quality of postoperative duplex ultrasound, the different analysed surgical techniques as well as used patches and the application of a haemostatic sealant can be assumed to be equal regarding the quality of postoperative ultrasound.

  12. Binding modes and pathway of RHPS4 to human telomeric G-quadruplex and duplex DNA probed by all-atom molecular dynamics simulations with explicit solvent.

    Science.gov (United States)

    Mulholland, Kelly; Siddiquei, Farzana; Wu, Chun

    2017-07-19

    RHPS4, a potent binder to human telomeric DNA G-quadruplex, shows high efficacy in tumor cell growth inhibition. However, it's preferential binding to DNA G-quadruplex over DNA duplex (about 10 fold) remains to be improved toward its clinical application. A high resolution structure of the single-stranded telomeric DNA G-quadruplexes, or B-DNA duplex, in complex with RHPS4 is not available yet, and the binding nature of this ligand to these DNA forms remains to be elusive. In this study, we carried out 40 μs molecular dynamics binding simulations with a free ligand to decipher the binding pathway of RHPS4 to a DNA duplex and three G-quadruplex folders (parallel, antiparallel and hybrid) of the human telomeric DNA sequence. The most stable binding mode identified for the duplex, parallel, antiparallel and hybrid G-quadruplexes is an intercalation, bottom stacking, top intercalation and bottom intercalation mode, respectively. The intercalation mode with similar binding strength to both the duplex and the G-quadruplexes, explains the lack of binding selectivity of RHPS4 to the G-quadruplex form. Therefore, a ligand modification that destabilizes the duplex intercalation mode but stabilizes the G-quadruplex intercalation mode will improve the binding selectivity toward G-quadruplex. The intercalation mode of RHPS4 to both the duplex and the antiparallel and the hybrid G-quadruplex follows a base flipping-insertion mechanism rather than an open-insertion mechanism. The groove binding, the side binding and the intercalation with flipping out of base were observed to be intermediate states before the full intercalation state with paired bases.

  13. Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA

    Science.gov (United States)

    Yang, Changwon; Kim, Eunae; Pak, Youngshang

    2015-01-01

    Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. PMID:26250116

  14. Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNA.

    Science.gov (United States)

    Yang, Changwon; Kim, Eunae; Pak, Youngshang

    2015-09-18

    Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine-thymine (A-T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Duplex/quadruplex oligonucleotides: Role of the duplex domain in the stabilization of a new generation of highly effective anti-thrombin aptamers.

    Science.gov (United States)

    Russo Krauss, Irene; Napolitano, Valeria; Petraccone, Luigi; Troisi, Romualdo; Spiridonova, Vera; Mattia, Carlo Andrea; Sica, Filomena

    2018-02-01

    Recently, mixed duplex/quadruplex oligonucleotides have attracted great interest for use as biomedical aptamers. In the case of anti-thrombin aptamers, the addition of duplex-forming sequences to a G-quadruplex module identical or very similar to the best-known G-quadruplex of the Thrombin Binding Aptamer (HD1) results in new or improved biological properties, such as higher activity or different recognition properties with respect to HD1. Remarkably, this bimodular fold was hypothesized, based on its sequence, for the only anti-thrombin aptamer in advanced clinical trial, NU172. Whereas cation modulation of G-quadruplex conformation and stability is well characterized, only few data from similar analysis on duplex/quadruplex oligonucleotides exist. Here we have performed a characterization of structure and stability of four different duplex/quadruplex anti-thrombin aptamers, including NU172, in the presence of different cations and in physiological-mimicking conditions in comparison to HD1, by means of spectroscopic techniques (UV and circular dichroism) and differential scanning calorimetry. Our data show a strong reciprocal influence of each domain on the stability of the other and in particular suggest a stabilizing effect of the duplex region in the presence of solutions mimicking the physiological conditions, strengthening the idea that bimodular aptamers present better therapeutic potentialities than those containing a single G-quadruplex domain. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Site-Directed Spin-Labeling of Nucleic Acids by Click Chemistry. Detection of Abasic Sites in Duplex DNA by EPR Spectroscopy

    DEFF Research Database (Denmark)

    Sigurdsson, Snorri; Vogel, Stefan; Shelke, Sandip

    2010-01-01

    and the nitroxide spin label. The spin label was used to detect, for the first time, abasic sites in duplex DNA by X-band CW-EPR spectroscopy and give information about other structural deformations as well as local conformational changes in DNA. For example, reduced mobility of the spin label in a mismatched pair...... label out of the duplex and toward the solution. Thus, reposition of the spin label, when acting as a mercury(II)-controlled mechanical lever, can be readily detected by EPR spectroscopy. The ease of incorporation and properties of the new spin label make it attractive for EPR studies of nucleic acids...

  17. EFFECT OF INTERMETALLIC PHASES ON CORROSION BEHAVIOR AND MECHANICAL PROPERTIES OF DUPLEX STAINLESS STEEL AND SUPER-DUPLEX STAINLESS STEEL

    OpenAIRE

    Prabhu Paulraj; Rajnish Garg

    2015-01-01

    Duplex Stainless Steels (DSS) and Super Duplex Stainless Steel (SDSS) have excellent integration of mechanical and corrosion properties. However, the formation of intermetallic phases is a major problem in their usage. The mechanical and corrosion properties are deteriorated due to the presence of intermetallic phases. These phases are induced during welding, prolonged exposure to high temperatures, and improper heat treatments. The main emphasis of this review article is on intermetallic pha...

  18. Molecular Modeling of the Major DNA Adduct Formed from Food Mutagen Ochratoxin A in NarI Two-Base Deletion Duplexes: Impact of Sequence Context and Adduct Ionization on Conformational Preference and Mutagenicity.

    Science.gov (United States)

    Kathuria, Preetleen; Sharma, Purshotam; Manderville, Richard A; Wetmore, Stacey D

    2017-08-21

    Exposure to ochratoxin A (OTA), a possible human carcinogen, leads to many different DNA mutations. As a first step toward understanding the structural basis of OTA-induced mutagenicity, the present work uses a robust computational approach and a slipped mutagenic intermediate model previously studied for C 8 -dG aromatic amine adducts to analyze the conformational features of postreplication two-base deletion DNA duplexes containing OT-dG, the major OTA lesion at the C 8 position of guanine. Specifically, a total of 960 ns of molecular dynamics simulations (excluding trial simulations) were carried out on four OT-dG ionization states in three sequence contexts within oligomers containing the NarI recognition sequence, a known hotspot for deletion mutations induced by related adducts formed from known carcinogens. Our results indicate that the structural properties and relative stability of the competing "major groove" and "stacked" conformations of OTA adducted two-base deletion duplexes depend on both the OTA ionization state and the sequence context, mainly due to conformation-dependent deviations in discrete local (hydrogen-bonding and stacking) interactions at the lesion site, as well as DNA bending. When the structural characteristics of the OT-dG adducted two-base deletion duplexes are compared to those associated with previously studied C 8 -dG adducts, a greater understanding of the effects of the nucleobase-carcinogen linkage, and size of the carcinogenic moiety on the conformational preferences of damaged DNA is obtained. Most importantly, our work predicts key structural features for OT-dG-adducted deletion DNA duplexes, which in turn allow us to develop hypotheses regarding OT-dG replication outcomes. Thus, our computational results are valuable for the design and interpretation of future biochemical studies on the potentially carcinogenic OT-dG lesion.

  19. Effects of chitosan inhibitor on the electrochemical corrosion behavior of 2205 duplex stainless steel

    Science.gov (United States)

    Yang, Se-fei; Wen, Ying; Yi, Pan; Xiao, Kui; Dong, Chao-fang

    2017-11-01

    The effects of chitosan inhibitor on the corrosion behavior of 2205 duplex stainless steel were studied by electrochemical measurements, immersion tests, and stereology microscopy. The influences of immersion time, temperature, and chitosan concentration on the corrosion inhibition performance of chitosan were investigated. The optimum parameters of water-soluble chitosan on the corrosion inhibition performance of 2205 duplex stainless steel were also determined. The water-soluble chitosan showed excellent corrosion inhibition performance on the 2205 duplex stainless steel. Polarization curves demonstrated that chitosan acted as a mixed-type inhibitor. When the stainless steel specimen was immersed in the 0.2 g/L chitosan solution for 4 h, a dense and uniform adsorption film covered the sample surface and the inhibition efficiency (IE) reached its maximum value. Moreover, temperature was found to strongly influence the corrosion inhibition of chitosan; the inhibition efficiency gradually decreased with increasing temperature. The 2205 duplex stainless steel specimen immersed in 0.4 g/L water-soluble chitosan at 30°C displayed the best corrosion inhibition among the investigated specimens. Moreover, chitosan decreased the corrosion rate of the 2205 duplex stainless steel in an FeCl3 solution.

  20. Positive cooperativity of the specific binding between Hg2+ ion and T:T mismatched base pairs in duplex DNA

    International Nuclear Information System (INIS)

    Torigoe, Hidetaka; Miyakawa, Yukako; Ono, Akira; Kozasa, Tetsuo

    2012-01-01

    Highlights: ► Hg 2+ specifically bound with the T:T mismatched base pair at 1:1 molar ratio. ► The binding constant between Hg 2+ and the T:T mismatched base pair was 10 6 M −1 . ► The binding constant was larger than those for nonspecific metal–DNA interactions. ► The binding constant for the second Hg 2+ was larger than that for the first Hg 2+ . ► The positive cooperative binding was observed between Hg 2+ and multiple T:T. - Abstract: Metal-mediated base pairs by the interaction between metal ions and artificial bases in oligonucleotides have been developed for their potential applications in nanotechnology. We recently found that a natural T:T mismatched base pair bound with Hg 2+ ion to form a novel T–Hg–T base pair. Here, we examined the thermodynamic properties of the binding between Hg 2+ and each of the single and double T:T mismatched base pair duplex DNAs by isothermal titration calorimetry. Hg 2+ specifically bound with the T:T mismatched base pair at 1:1 molar ratio with 10 6 M −1 binding constant, which was significantly larger than those for nonspecific metal ion–DNA interactions. In the Hg 2+ –double T:T mismatched base pair interaction, the affinity for the second Hg 2+ binding was significantly larger than that for the first Hg 2+ binding. The positively cooperative binding may be favorable to align multiple Hg 2+ in duplex DNA for the application of the metal-mediated base pairs in nanotechnology.

  1. An unusual mode of DNA duplex association: Watson-Crick interaction of all-purine deoxyribonucleic acids.

    Science.gov (United States)

    Battersby, Thomas R; Albalos, Maria; Friesenhahn, Michel J

    2007-05-01

    Nucleic acid duplexes associating through purine-purine base pairing have been constructed and characterized in a remarkable demonstration of nucleic acids with mixed sequence and a natural backbone in an alternative duplex structure. The antiparallel deoxyribose all-purine duplexes associate specifically through Watson-Crick pairing, violating the nucleobase size-complementarity pairing convention found in Nature. Sequence-specific recognition displayed by these structures makes the duplexes suitable, in principle, for information storage and replication fundamental to molecular evolution in all living organisms. All-purine duplexes can be formed through association of purines found in natural ribonucleosides. Key to the formation of these duplexes is the N(3)-H tautomer of isoguanine, preferred in the duplex, but not in aqueous solution. The duplexes have relevance to evolution of the modern genetic code and can be used for molecular recognition of natural nucleic acids.

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

    Science.gov (United States)

    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.

  3. Pyrrolo-dC modified duplex DNA as a novel probe for the sensitive assay of base excision repair enzyme activity.

    Science.gov (United States)

    Lee, Chang Yeol; Park, Ki Soo; Park, Hyun Gyu

    2017-12-15

    We develop a novel approach to determine formamidopyrimidine DNA glycosylase (Fpg) activity by taking advantage of the unique fluorescence property of pyrrolo-dC (PdC) positioned opposite to 8-oxoguanine (8-oxoG) in duplex DNA. In its initial state, PdC in duplex DNA undergoes the efficient stacking and collisional quenching interactions, showing the low fluorescence signal. In contrast, the presence of Fpg, which specifically removes 8-oxoG and incises resulting apurinic (AP) site, transforms duplex DNA into single-stranded (ss) DNAs. As a result, the intrinsic fluorescence signal of PdC in ssDNA is recovered to exhibit the significantly enhanced fluorescence signal. Based on this Fpg-dependent fluorescence response of PdC, we could reliably determine Fpg activity down to 1.25U/ml with a linear response from 0 to 50U/ml. In addition, the diagnostic capability of this strategy was successfully demonstrated by reliably assaying Fpg activity in human blood serum, showing its great potential in the practical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional Structures

    Directory of Open Access Journals (Sweden)

    Yogini P. Bhavsar

    2011-01-01

    Full Text Available Topological variants of single-strand DNA (ssDNA structures, referred to as “functional DNA,” have been detected in regulatory regions of many genes and are thought to affect gene expression. Two fluorescent analogs of deoxycytidine, Pyrrolo-dC (PdC and 1,3-diaza-2-oxophenoxazine (tC∘, can be incorporated into DNA. Here, we describe spectroscopic studies of both analogs to determine fluorescent properties that report on structural transitions from double-strand DNA (dsDNA to ssDNA, a common pathway in the transition to functional DNA structures. We obtained fluorescence-detected circular dichroism (FDCD spectra, steady-state fluorescence spectra, and fluorescence lifetimes of the fluorophores in DNA. Our results show that PdC is advantageous in fluorescence lifetime studies because of a distinct ~2 ns change between paired and unpaired bases. However, tC∘ is a better probe for FDCD experiments that report on the helical structure of DNA surrounding the fluorophore. Both fluorophores provide complementary data to measure DNA structural transitions.

  5. Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA

    OpenAIRE

    Yang, Zhiyu; Price, Nathan E.; Johnson, Kevin M.; Wang, Yinsheng; Gates, Kent S.

    2017-01-01

    Abstract Interstrand cross-links are exceptionally bioactive DNA lesions. Endogenous generation of interstrand cross-links in genomic DNA may contribute to aging, neurodegeneration, and cancer. Abasic (Ap) sites are common lesions in genomic DNA that readily undergo spontaneous and amine-catalyzed strand cleavage reactions that generate a 2,3-didehydro-2,3-dideoxyribose sugar remnant (3?ddR5p) at the 3?-terminus of the strand break. Interestingly, this strand scission process leaves an electr...

  6. Capability of ds-DNA duplex structure in growing fluorescent silver nanoclusters

    International Nuclear Information System (INIS)

    Wu, Tao; Lin, Fan; Hu, Yuehua; Wang, Ying; Zhou, Xiaoshun; Shao, Yong

    2016-01-01

    Silver nanoclusters (AgNCs) have attracted wide interests in variant fields due to their easy synthesis and practical tunability in fluorescence properties. DNA has been generally used as the host to grow AgNCs due to the sequence-dependent fluorescence behavior. Actually, in such DNA, various ss-DNA segments that are structurally confined by the rigid ds-DNA counterparts have been used as the AgNCsГ—Ві growth sites. However, whether the ds-DNA structure plays somewhat role in AgNCsГ—Ві creation has not been well elucidated. Herein, we found that ds-DNA can also accommodate the growth of fluorescent AgNCs. The fluorescent AgNCs grown on ds-DNA should be separated each other and the G/C base pairs with right context sequences are the growth sites of fluorescent AgNCs. The intermediate A/T base pair among the continuous G/C ones seems to quench the growth of fluorescent AgNCs. For the repeat sequences, the fluorescence band position of AgNCs is not changed but the intensity is enhanced upon increasing the ds-DNA length, which is different from the results obtained with the previously reported ss-DNAs. AgNCs should be grown on the ds-DNA major groove, as convinced by the cytosine methylation experiment. Our work demonstrates that besides the ss-DNA role in defining AgNCs, one should also take into account the critical role of the ds-DNA segment in tuning the AgNCsГ—Ві fluorescence property.

  7. Recognition of base J in duplex DNA by J-binding protein

    NARCIS (Netherlands)

    Sabatini, Robert; Meeuwenoord, Nico; van Boom, Jacques H.; Borst, Piet

    2002-01-01

    beta-d-Glucosylhydroxymethyluracil, also called base J, is an unusual modified DNA base conserved among Kinetoplastida. Base J is found predominantly in repetitive DNA and correlates with epigenetic silencing of telomeric variant surface glycoprotein genes. We have previously found a J-binding

  8. Unfolding and Targeting Thermodynamics of a DNA Intramolecular Complex with Joined Triplex-Duplex Domains.

    Science.gov (United States)

    Johnson, Sarah E; Reiling-Steffensmeier, Calliste; Lee, Hui-Ting; Marky, Luis A

    2018-01-25

    Our laboratory is interested in developing methods that can be used for the control of gene expression. In this work, we are investigating the reaction of an intramolecular complex containing a triplex-duplex junction with partially complementary strands. We used a combination of isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC), and spectroscopy techniques to determine standard thermodynamic profiles for these targeting reactions. Specifically, we have designed single strands to target one loop (CTTTC) or two loops (CTTTC and GCAA) of this complex. Both reactions yielded exothermic enthalpies of -66.3 and -82.8 kcal/mol by ITC, in excellent agreement with the reaction enthalpies of -72.7 and -88.7 kcal/mol, respectively, obtained from DSC Hess cycles. The favorable heat contributions result from the formation of base-pair stacks involving mainly the unpaired bases of the loops. This shows that each complementary strand is able to invade and disrupt the secondary structure. The simultaneous targeting of two loops yielded a more favorable reaction free energy, by approximately -8 kcal/mol, which corresponds to the formation of roughly four base-pair stacks involving the unpaired bases of the 5'-GCAA loop. The main conclusion is that the targeting of loops with a large number of unpaired bases results in a more favorable reaction free energy.

  9. Structure of the DNA duplex d(ATTAAT2 with Hoogsteen hydrogen bonds.

    Directory of Open Access Journals (Sweden)

    Francisco J Acosta-Reyes

    Full Text Available The traditional Watson-Crick base pairs in DNA may occasionally adopt a Hoogsteen conformation, with a different organization of hydrogen bonds. Previous crystal structures have shown that the Hoogsteen conformation is favored in alternating AT sequences of DNA. Here we present new data for a different sequence, d(ATTAAT2, which is also found in the Hoogsteen conformation. Thus we demonstrate that other all-AT sequences of DNA with a different sequence may be found in the Hoogsteen conformation. We conclude that any all-AT sequence might acquire this conformation under appropriate conditions. We also compare the detailed features of DNA in either the Hoogsteen or Watson-Crick conformations.

  10. Effect of Temperature on the Intrinsic Flexibility of DNA and Its Interaction with Architectural Proteins

    NARCIS (Netherlands)

    Driessen, R.P.C.; Sitter, G.; Moolenaar, G.F.; Wuite, G.J.L.; Goosen, N.; Dame, R.T.

    2014-01-01

    The helical structure of double-stranded DNA is destabilized by increasing temperature. Above a critical temperature (the melting temperature), the two strands in duplex DNA become fully separated. Below this temperature, the structural effects are localized. Using tethered particle motion in a

  11. Conformation and dynamics of nucleotides in bulges and symmetric internal loops in duplex DNA studied by EPR and fluorescence spectroscopies

    International Nuclear Information System (INIS)

    Cekan, Pavol; Sigurdsson, Snorri Th.

    2012-01-01

    Highlights: ► Bulges and loops were studied by both EPR and fluorescence spectroscopies using the probe Ç/Ç f . ► One-base bulge was in a temperature-dependent equilibrium between looped-out and stacked states. ► Bases in two- and three-base bulges were stacked at all temperatures, resulting in DNA bending. ► Bases were stacked in symmetrical two- to five-base internal loops, according to EPR data. ► Unexpectedly high fluorescence for the smaller loops indicated local structural perturbations. -- Abstract: The dynamics and conformation of base bulges and internal loops in duplex DNA were studied using the bifunctional spectroscopic probe Ç, which becomes fluorescent (Ç f ) upon reduction of the nitroxide functional group, along with EPR and fluorescence spectroscopies. A one-base bulge was in a conformational equilibrium between looped-out and stacked states, the former favored at higher temperature and the latter at lower temperature. Stacking of bulge bases was favored in two- and three-base bulges, independent of temperature, resulting in DNA bending as evidenced by increased fluorescence of Ç f . EPR spectra of Ç-labeled three-, four- and five-base symmetrical interior DNA bulges at 20 °C showed low mobility, indicating that the spin-label was stacked within the loop. The spin-label mobility at 37 °C increased as the loops became larger. A considerable variation in fluorescence between different loops was observed, as well as a temperature-dependence within constructs. Fluorescence unexpectedly increased as the size of the loop decreased at 2 °C. Fluorescence of the smallest loops, where a single T·T mismatch was located between the stem region and the probe, was even larger than for the single strand, indicating a considerable local structural deformation of these loops from regular B-DNA. These results show the value of combining EPR and fluorescence spectroscopy to study non-helical regions of nucleic acids.

  12. Sequence-selective targeting of duplex DNA by peptide nucleic acids

    DEFF Research Database (Denmark)

    Nielsen, Peter E

    2010-01-01

    Sequence-selective gene targeting constitutes an attractive drug-discovery approach for genetic therapy, with the aim of reducing or enhancing the activity of specific genes at the transcriptional level, or as part of a methodology for targeted gene repair. The pseudopeptide DNA mimic peptide...

  13. 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

    Science.gov (United States)

    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

  14. Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.

    Science.gov (United States)

    Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K; Al-Hashimi, Hashim M

    2017-05-19

    In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02-0.4%) and short-lived (lifetimes ∼0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A

    Science.gov (United States)

    Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K.

    2017-01-01

    Abstract In the canonical DNA double helix, Watson–Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02–0.4%) and short-lived (lifetimes ∼0.2–2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. PMID:28369571

  16. Infrared Laser Heating Applied to Nanopore Sensing for DNA Duplex Analysis.

    Science.gov (United States)

    Angevine, Christopher E; Seashols-Williams, Sarah J; Reiner, Joseph E

    2016-03-01

    Temperature studies coupled with resistive-pulse nanopore sensing enable the quantification of a variety of important thermodynamic properties at the single-molecule limit. Previous demonstrations of nanopore sensing with temperature control have utilized bulk chamber heating methodologies. This approach makes it difficult to rapidly change temperatures and enable optical access for other analytical techniques (i.e., single-molecule fluorescence). To address these issues, researchers have explored laser-based methodologies through either direct infrared (IR) absorption or plasmonic assisted heating. In this paper, we demonstrate the use of IR-based direct absorption heating with the DNA sensing capabilities of a biological nanopore. The IR heating enables rapid changes of the temperature in and around an α-hemolysin pore, and we use this to explore melting properties for short (≤50 bp) double-stranded DNA homopolymers. We also demonstrate that the IR heating enables one to measure the percentage of different-sized DNA molecules in a binary mixture.

  17. Insights into the Structures of DNA Damaged by Hydroxyl Radical: Crystal Structures of DNA Duplexes Containing 5-Formyluracil

    Directory of Open Access Journals (Sweden)

    Masaru Tsunoda

    2010-01-01

    Full Text Available Hydroxyl radicals are potent mutagens that attack DNA to form various base and ribose derivatives. One of the major damaged thymine derivatives is 5-formyluracil (fU, which induces pyrimidine transition during replication. In order to establish the structural basis for such mutagenesis, the crystal structures of two kinds of DNA d(CGCGRATfUCGCG with R = A/G have been determined by X-ray crystallography. The fU residues form a Watson-Crick-type pair with A and two types of pairs (wobble and reversed wobble with G, the latter being a new type of base pair between ionized thymine base and guanine base. In silico structural modeling suggests that the DNA polymerase can accept the reversed wobble pair with G, as well as the Watson-Crick pair with A.

  18. Rolling replication of UV-irradiated duplex DNA in the phi X174 replicative-form----single-strand replication system in vitro

    International Nuclear Information System (INIS)

    Shavitt, O.; Livneh, Z.

    1989-01-01

    Cloning of the phi X174 viral origin of replication into phage M13mp8 produced an M13-phi X174 chimera, the DNA of which directed efficient replicative-form----single-strand rolling replication in vitro. This replication assay was performed with purified phi X174-encoded gene A protein, Escherichia coli rep helicase, single-stranded DNA-binding protein, and DNA polymerase III holoenzyme. The nicking of replicative-form I (RFI) DNA by gene A protein was essentially unaffected by the presence of UV lesions in the DNA. However, unwinding of UV-irradiated DNA by the rep helicase was inhibited twofold as compared with unwinding of the unirradiated substrate. UV irradiation of the substrate DNA caused a strong inhibition in its ability to direct DNA synthesis. However, even DNA preparations that contained as many as 10 photodimers per molecule still supported the synthesis of progeny full-length single-stranded DNA. The appearance of full-length radiolabeled products implied at least two full rounds of replication, since the first round released the unlabeled plus viral strand of the duplex DNA. Pretreatment of the UV-irradiated DNA substrate with purified pyrimidine dimer endonuclease from Micrococcus luteus, which converted photodimer-containing supercoiled RFI DNA into relaxed, nicked RFII DNA and thus prevented its replication, reduced DNA synthesis by 70%. Analysis of radiolabeled replication products by agarose gel electrophoresis followed by autoradiography revealed that this decrease was due to a reduction in the synthesis of progeny full-length single-stranded DNA. This implies that 70 to 80% of the full-length DNA products produced in this system were synthesized on molecules that carried photodimers

  19. Effect of laser shock processing on fatigue crack growth of duplex stainless steel

    International Nuclear Information System (INIS)

    Rubio-Gonzalez, C.; Felix-Martinez, C.; Gomez-Rosas, G.; Ocana, J.L.; Morales, M.; Porro, J.A.

    2011-01-01

    Research highlights: → LSP is an effective surface treatment to improve fatigue properties of duplex stainless steel. → Increasing pulse density, fatigue crack growth rate is reduced. → Microstructure is not affected by LSP. → Compressive residual stresses increases increasing pulse density. - Abstract: Duplex stainless steels have wide application in different fields like the ship, petrochemical and chemical industries that is due to their high strength and excellent toughness properties as well as their high corrosion resistance. In this work an investigation is performed to evaluate the effect of laser shock processing on some mechanical properties of 2205 duplex stainless steel. Laser shock processing (LSP) or laser shock peening is a new technique for strengthening metals. This process induces a compressive residual stress field which increases fatigue crack initiation life and reduces fatigue crack growth rate. A convergent lens is used to deliver 2.5 J, 8 ns laser pulses by a Q-switched Nd:YAG laser, operating at 10 Hz with infrared (1064 nm) radiation. The pulses are focused to a diameter of 1.5 mm. Effect of pulse density in the residual stress field is evaluated. Residual stress distribution as a function of depth is determined by the contour method. It is observed that the higher the pulse density the greater the compressive residual stress. Pulse densities of 900, 1600 and 2500 pul/cm 2 are used. Pre-cracked compact tension specimens were subjected to LSP process and then tested under cyclic loading with R = 0.1. Fatigue crack growth rate is determined and the effect of LSP process parameters is evaluated. In addition fracture toughness is determined in specimens with and without LSP treatment. It is observed that LSP reduces fatigue crack growth and increases fracture toughness if this steel.

  20. Effects of Ce, La and Ba addition on the electrochemical behavior of super duplex stainless steels

    International Nuclear Information System (INIS)

    Yoo, Yun-Ha; Choi, Yoon-Seok; Kim, Jung-Gu; Park, Yong-Soo

    2010-01-01

    The effects of rare earth metal (REM: Ce, La) and Ba addition on aqueous corrosion properties of super duplex stainless steels (SDSS) were investigated by electrochemical tests and surface analyses. The results of potentiodynamic test indicated that the passive range increased by the addition of Ce, La, and Ba, indicating increased relative resistance to localized corrosion. The EIS measurements showed that the Ce-La-Ba-bearing alloys exhibited higher R ct and R p values than the Ce-La-Ba-free alloy at the passive and breakdown states. Furthermore, the additions of REMs and Ba together promoted the formation of dense chromium-enriched passive film.

  1. Mg2+ Effect on Argonaute and RNA Duplex by Molecular Dynamics and Bioinformatics Implications

    Science.gov (United States)

    Nam, Seungyoon; Ryu, Hyojung; Son, Won-joon; Kim, Yon Hui; Kim, Kyung Tae; Balch, Curt; Nephew, Kenneth P.; Lee, Jinhyuk

    2014-01-01

    RNA interference (RNAi), mediated by small non-coding RNAs (e.g., miRNAs, siRNAs), influences diverse cellular functions. Highly complementary miRNA-target RNA (or siRNA-target RNA) duplexes are recognized by an Argonaute family protein (Ago2), and recent observations indicate that the concentration of Mg2+ ions influences miRNA targeting of specific mRNAs, thereby modulating miRNA-mRNA networks. In the present report, we studied the thermodynamic effects of differential [Mg2+] on slicing (RNA silencing cycle) through molecular dynamics simulation analysis, and its subsequent statistical analysis. Those analyses revealed different structural conformations of the RNA duplex in Ago2, depending on Mg2+ concentration. We also demonstrate that cation effects on Ago2 structural flexibility are critical to its catalytic/functional activity, with low [Mg2+] favoring greater Ago2 flexibility (e.g., greater entropy) and less miRNA/mRNA duplex stability, thus favoring slicing. The latter finding was supported by a negative correlation between expression of an Mg2+ influx channel, TRPM7, and one miRNA’s (miR-378) ability to downregulate its mRNA target, TMEM245. These results imply that thermodynamics could be applied to siRNA-based therapeutic strategies, using highly complementary binding targets, because Ago2 is also involved in RNAi slicing by exogenous siRNAs. However, the efficacy of a siRNA-based approach will differ, to some extent, based on the Mg2+ concentration even within the same disease type; therefore, different siRNA-based approaches might be considered for patient-to-patient needs. PMID:25330448

  2. Cost-effectiveness of identifying aortoiliac and femoropopliteal arterial disease with angiography or duplex scanning

    International Nuclear Information System (INIS)

    Coffi, S.B.; Ubbink, D.Th.; Dijkgraaf, M.G.W.; Reekers, J.A.; Legemate, D.A.

    2008-01-01

    Objectives: Cost-effectiveness analysis of three diagnostic imaging strategies for the assessment of aortoiliac and femoropopliteal arteries in patients with peripheral arterial occlusive disease. The strategies were: angiography as the reference strategy, duplex scanning (DS) plus supplementary angiography (S1) and DS plus confirmative angiography (S2). Design, materials and methods: A decision model was built with sensitivity and specificity data from literature, supplemented with prospective hospital cost data in Euro ( Euro ). The probability of correctly identifying the status of a lesion was taken as the primary outcome. We compared strategies by assessing the extra costs per additional correctly identified case. Results: Assuming no false positive or false negative results, angiography is the most effective strategy if the prevalence of significant obstructive lesions in the aortoiliac and femoropopliteal tract exceeds 70%, or if the sensitivity of duplex scanning is lower than 83%. In case of lower prevalence, strategy S1 becomes equally or even more effective than angiography. At a prevalence of 75%, performing angiography costs Euro 8443 per extra correctly identified case compared with strategy S1. Conclusions: In most situations angiography is more effective than diagnostic strategy S1. However, if society is unwilling to pay more than Euro 8443 for knowing a patient's disease status, diagnostic strategy S1 is a cost-effective alternative to angiography, especially at lower prevalence values

  3. Effects of fabrication conditions on mechanical properties and microstructure of duplex β″-Al2O3 solid electrolyte

    International Nuclear Information System (INIS)

    Canfield, Nathan L.; Kim, Jin Y.; Bonnett, Jeff F.; Pearson, R.L.; Sprenkle, Vincent L.; Jung, Keeyoung

    2015-01-01

    Highlights: • The concept of duplex BASEs is presented as a method to lower the ASR for NBBs. • Duplex BASEs consist of thin dense electrolyte and porous support. • Strength of converted BASEs shows a different trend from as-sintered samples. • Cell orientation gives significant impact on strength of duplex BASEs. - Abstract: Na-beta batteries are an attractive technology as a large-scale electrical energy storage for grid applications. However, additional improvements in performance and cost are needed for wide market penetration. To improve cell performance by minimizing polarizations, reduction of electrolyte thickness was attempted using a duplex structure consisting of a thin dense electrolyte layer and a porous support layer. In this paper, the effects of sintering conditions, dense electrolyte thickness, and cell orientation on the flexural strength of duplex BASEs fabricated using a vapor phase approach were investigated. It is shown that sintering at temperatures between 1500 and 1550 °C results in fine grained microstructures and the highest flexural strength after conversion. Increasing thickness of the dense electrolyte has a small impact on flexural strength, while the orientation of load such that the dense electrolyte is in tension instead of compression has major effects on strength for samples with a well-sintered dense electrolyte

  4. Accurate and rapid modeling of iron–bleomycin-induced DNA damage using tethered duplex oligonucleotides and electrospray ionization ion trap mass spectrometric analysis

    OpenAIRE

    Harsch, Andreas; Marzilli, Lisa A.; Bunt, Richard C.; Stubbe, Joanne; Vouros, Paul

    2000-01-01

    Bleomycin B2 (BLM) in the presence of iron [Fe(II)] and O2 catalyzes single-stranded (ss) and double-stranded (ds) cleavage of DNA. Electrospray ionization ion trap mass spectrometry was used to monitor these cleavage processes. Two duplex oligonucleotides containing an ethylene oxide tether between both strands were used in this investigation, allowing facile monitoring of all ss and ds cleavage events. A sequence for site-specific binding and cleavage by Fe–BLM was incorporated into each an...

  5. Effects of solution treatment on mechanical properties and corrosion resistance of 4A duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Panpan; Wang, Aiqin; Wang, Wenyan [Henan Univ. of Science and Technology, Luoyang (China). School of Material Science and Engineering; Xie, Jingpei [Henan Univ. of Science and Technology, Luoyang (China). Collaborative Innovation Center of Nonferrous Metals

    2018-02-15

    In this study, 4A duplex stainless steels were prepared via remelting in an intermediate frequency furnace and subsequently solution treated at different temperatures. The effects of solution treatment on the mechanical properties and corrosion resistance of 4A duplex stainless steel were investigated. Microstructures were characterized via optical microscopy and scanning electron microscopy. The mechanical properties were evaluated via hardness test, tensile test, and impact test experiments. The point corrosion resistance was studied via chemical immersion and potentiodynamic anodic polarization. The results showed that with increasing solution temperature in the range of 1223 - 1423 K, the tensile strength and hardness first decreased and then increased, and minimum values were obtained at 1323 K. The σ phase precipitated at the boundaries of the α/γ phases in samples solution treated at 1223 K, decreasing both impact energy and pitting potential of the experimental steels. When experimental steels were solution treated at 1373 K for 2 h, a suitable volume fraction of α/γ was uniformly distributed throughout the microstructure, and the steels exhibited optimal mechanical properties and pitting corrosion resistance.

  6. Effect of Plastic Deformation on the Corrosion Behavior of a Super-Duplex Stainless Steel

    Science.gov (United States)

    Renton, Neill C.; Elhoud, Abdu M.; Deans, William F.

    2011-04-01

    The role of plastic deformation on the corrosion behavior of a 25Cr-7Ni super-duplex stainless steel (SDSS) in a 3.5 wt.% sodium chloride solution at 90 °C was investigated. Different levels of plastic strain between 4 and 16% were applied to solution annealed tensile specimens and the effect on the pitting potential measured using potentiodynamic electrochemical techniques. A nonlinear relationship between the pitting potential and the plastic strain was recorded, with 8 and 16% causing a significant reduction in average E p, but 4 and 12% causing no significant change when compared with the solution-annealed specimens. The corrosion morphology revealed galvanic interaction between the anodic ferrite and the cathodic austenite causing preferential dissolution of the ferrite. Mixed potential theory and the changing surface areas of the two phases caused by the plastic deformation structures explain the reductions in pitting potential at certain critical plastic strain levels. End-users and manufacturers should evaluate the corrosion behavior of specific cold-worked duplex and SDSSs using their as-produced surface finishes assessing in-service corrosion performance.

  7. Excited-State Dynamics of a DNA Duplex in a Deep Eutectic Solvent Probed by Femtosecond Time-Resolved IR Spectroscopy.

    Science.gov (United States)

    de La Harpe, Kimberly; Kohl, Forrest R; Zhang, Yuyuan; Kohler, Bern

    2018-03-08

    To better understand how the solvent influences excited-state deactivation in DNA strands, femtosecond time-resolved IR (fs-TRIR) pump-probe measurements were performed on a d(AT) 9 ·d(AT) 9 duplex dissolved in a deep eutectic solvent (DES) made from choline chloride and ethylene glycol in a 1:2 mol ratio. This solvent, known as ethaline, is a member of a class of ionic liquids capable of solubilizing DNA with minimal disruption to its secondary structure. UV melting analysis reveals that the duplex studied here melts at 18 °C in ethaline compared to 50 °C in aqueous solution. Ethaline has an excellent transparency window that facilitates TRIR measurements in the double-bond stretching region. Transient spectra recorded in deuterated ethaline at room temperature indicate that photoinduced intrastrand charge transfer occurs from A to T, yielding the same exciplex state previously detected in aqueous solution. This state decays via charge recombination with a lifetime of 380 ± 10 ps compared to the 300 ± 10 ps lifetime measured earlier in D 2 O solution. The TRIR data strongly suggest that the long-lived exciplex forms exclusively in the solvated duplex, and not in the denatured single strands, which appear to have little, if any, base stacking. The longer lifetime of the exciplex state in the DES compared to aqueous solution is suggested to arise from reduced stabilization of the charge transfer state, resulting in slower charge recombination on account of Marcus inverted behavior.

  8. NMR studies of abasic sites in DNA duplexes: deoxyadenosine stacks into the helix opposite the cyclic analog of 2-deoxyribose

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Chang, C.N.; Grollman, A.P.; Patel, D.J.

    1988-01-01

    Proton and phosphorus NMR studies are reported for the complementary d(C-A-T-G-A-G-T-A-C) x d(G-T-A-C-F-C-A-T-G) nonanucleotide duplex (designated AP/sub F/ 9-mer duplex) which contains a stable abasic site analog, F, in the center of the helix. This oligodeoxynucleotide contains a modified tetrahydrofuran moiety, isosteric with 2-deoxyribofuranose, which serves as a structural analog of a natural apurinic/apyrimidinic site. Exchangeable and nonexchangeable base and sugar protons, including those located at the abasic site, have been assigned in the complementary AP/sub F/ 9-mer duplex by recording and analyzing two-dimensional phase-sensitive NOESY data sets in H 2 O and D 2 O solution at low temperature (0 0 C). These studies indicate that A5 inserts into the helix opposite the abasic site F14 and stacks with flanking G4 x C15 and G6 x C13 Watson-Crick base pairs. Base-sugar proton NOE connectivities were measured through G4-A5-G6 on the unmodified strand and between the base protons of C15 and the sugar protons of the 5'-flanking residue F14 on the modified strand. These studies establish that all glycosidic torsion angles are anti and that the helix is right-handed at and adjacent to the abasic site in the AP/sub F/ 9-mer duplex. Two of the 16 phosphodiester groups exhibit phosphorus resonances outside the normal spectral dispersion indicative of altered torsion angles at two of the phosphate groups in the backbone of the AP/sub F/ 9-mer duplex

  9. The Effect of Multiple Shot Peening on the Corrosion Behavior of Duplex Stainless Steel

    Science.gov (United States)

    Feng, Qiang; She, Jia; Wu, Xueyan; Wang, Chengxi; Jiang, Chuanhai

    2018-03-01

    Various types of shot peening treatments were applied to duplex stainless steel. The effects of shot peening intensity and working procedures on the microstructure were investigated. The domain size and microstrain evolution in the surface layer were characterized utilizing the Rietveld method. As the shot peening intensity increased, the surface roughness increased in the surface layer; however, it decreased after multiple (dual and triple) shot peening. The mole fraction of strain-induced martensite as a function of the intensity of shot peening was evaluated by XRD measurements. Both potentiodynamic polarization curves and salt spray tests of shot-peened samples in NaCl solution were investigated. The results indicate that traditional shot peening has negative effects on corrosion resistance with increasing shot peening intensity; however, the corrosion rate can be reduced by means of multiple shot peening.

  10. Effect of Continuous Cooling on Secondary Phase Precipitation in the Super Duplex Stainless Steel ZERON-100

    Science.gov (United States)

    Calliari, Irene; Bassani, Paola; Brunelli, Katya; Breda, Marco; Ramous, Emilio

    2013-12-01

    The precipitation of secondary phases in super duplex stainless steels (SDSS) is a subject of great relevance owing to their dangerous effects on both mechanical and corrosion-resistance properties. This paper examines the effect of continuous cooling after solution annealing treatment on secondary phase precipitation in the ZERON-100 SDSS. It considers the influence of cooling rate on volume fraction, morphology and chemical composition. It has been found that the formation of sigma and chi phases can be avoided only at cooling rates higher than 0.7 °C/s. In addition, at the lowest cooling rate the sigma phase amount approaches the equilibrium value, but the chi phase amount remains significantly low.

  11. Targeting human c-Myc promoter duplex DNA with actinomycin D by use of multi-way analysis of quantum-dot-mediated fluorescence resonance energy transfer

    DEFF Research Database (Denmark)

    Gholami, Somayeh; Kompany Zare, Mohsen

    2013-01-01

    Actinomycin D (Act D), an oncogenic c-Myc promoter binder, interferes with the action of RNA polymerase. There is great demand for high-throughput technology able to monitor the activity of DNA-binding drugs. To this end, binding of 7-aminoactinomycin D (7AAD) to the duplex c-Myc promoter...... pairs resulted in efficient energy transfer from drug to QD via fluorescence resonance energy transfer (FRET). Multi-way analysis of the three-way data array obtained from titration experiments was performed by use of restricted Tucker3 and hard trilinear decomposition (HTD). These techniques enable...... the important advantage over univariate classical methods of enabling us to investigate the source of variance in the fluorescence signal of the DNA-drug complex. It was established that hard trilinear decomposition analysis of FRET-measured data overcomes the problem of rank deficiency, enabling calculation...

  12. Development and Evaluation of a Duplex Real-Time PCR Assay With a Novel Internal Standard for Precise Quantification of Plasma DNA.

    Science.gov (United States)

    Chen, Dan; Pan, Shiyang; Xie, Erfu; Gao, Li; Xu, Huaguo; Xia, Wenying; Xu, Ting; Huang, Peijun

    2017-01-01

    Circulating levels of cell-free DNA increase in many pathologic conditions. However, notable discrepancies in the quantitative analysis of cell-free DNA from a large number of laboratories have become a considerable pitfall, hampering its clinical application. We designed a novel recombinant DNA fragment that could be applied as an internal standard in a newly developed and validated duplex real-time PCR assay for the quantitative analysis of total cell-free plasma DNA, which was tested in 5,442 healthy adults and 200 trauma patients. Compared with two traditional methods, this novel assay showed a lower detection limit of 0.1 ng/mL, lower intra- and inter-assay CVs, and higher accuracy in the recovery test. The median plasma DNA concentration of healthy males (20.3 ng/mL, n=3,092) was significantly higher than that of healthy females (16.1 ng/mL, n=2,350) (Mann-Whitney two-sample rank sum test, PDNA concentration were 0-45.8 ng/mL and 0-52.5 ng/mL for healthy females and males, respectively. The plasma DNA concentrations of the majority of trauma patients (96%) were higher than the upper normal cutoff values and were closely related to the corresponding injury severity scores (R²=0.916, PDNA, showing promising application in clinical diagnosis.

  13. The effect of S-substitution at the O6-guanine site on the structure and dynamics of a DNA oligomer containing a G:T mismatch.

    Directory of Open Access Journals (Sweden)

    Elaine Ann Moore

    Full Text Available The effect of S-substitution on the O6 guanine site of a 13-mer DNA duplex containing a G:T mismatch is studied using molecular dynamics. The structure, dynamic evolution and hydration of the S-substituted duplex are compared with those of a normal duplex, a duplex with S-substitution on guanine, but no mismatch and a duplex with just a G:T mismatch. The S-substituted mismatch leads to cell death rather than repair. One suggestion is that the G:T mismatch recognition protein recognises the S-substituted mismatch (GS:T as G:T. This leads to a cycle of futile repair ending in DNA breakage and cell death. We find that some structural features of the helix are similar for the duplex with the G:T mismatch and that with the S-substituted mismatch, but differ from the normal duplex, notably the helical twist. These differences arise from the change in the hydrogen-bonding pattern of the base pair. However a marked feature of the S-substituted G:T mismatch duplex is a very large opening. This showed considerable variability. It is suggested that this enlarged opening would lend support to an alternative model of cell death in which the mismatch protein attaches to thioguanine and activates downstream damage-response pathways. Attack on the sulphur by reactive oxygen species, also leading to cell death, would also be aided by the large, variable opening.

  14. Effect of preparative treatment on the corrosion resistance of duplex stainless steel

    International Nuclear Information System (INIS)

    Rieder, E.S.; Eagleton, T.S.; Farr, J.P.G.; Li, X.; Strangwood, M.; Ashworth, M.A.

    1999-01-01

    The effect of surface treatment on the characteristics of the passive film on a super duplex stainless steel is addressed. Auger Electron Spectroscopy (AES) has been used to provide in-depth chemical profile analyses of the passivation film. This study showed that the constitution of the film is largely dependent on the electrolytic conditions under which it is produced or to which it is submitted. The passive films formed by polarisation in an alkaline solution (boric-borate solution) consist of two regions, an inner region rich in chromium and an outer region rich in iron, whilst the films produced in acid solution only present the chromium - rich region. The film thickness is also greatly affected by the polarisation conditions. It can vary from ca. 8 monolayers to about 20 monolayers for cathodically and anodically polarised specimens respectively. The microstructure of weldmetal is also discussed. (author)

  15. Thermal treatments effect on the austenite-ferrite equilibrium in a duplex stainless steel weld beads

    International Nuclear Information System (INIS)

    Belkessa, Brahim; Badji, Riad; Bettahar, Kheireddine; Maza, Halim

    2006-01-01

    Heat treatments in the temperature range between 800 to 1200 C, with a keeping at high temperature of 60 min, followed by a water quenching at 20 C, have been carried out on austeno-ferritic stainless steel welds (of type SAF 2205-UNS S31803). The heat treatments carried out at temperatures below 1000 C have modified the structure of the duplex stainless steel 2205 in inducing the formation of precipitates, identified by X-ray diffraction as being the intermetallic compound σ and the chromium carbides M 23 C 6 . The treatments applied to temperatures superior to 1000 C shift the δ-γ equilibrium towards the δ phase. Indeed, the increase of the ferrite rate with the treatment temperature is approximately linear. The ferrite rates are higher in the heat-affected zone, which has been submitted to a ferritizing due to the welding thermal effects. (O.M.)

  16. Effect of Secondary Phase Precipitation on the Corrosion Behavior of Duplex Stainless Steels

    Directory of Open Access Journals (Sweden)

    Kai Wang Chan

    2014-07-01

    Full Text Available Duplex stainless steels (DSSs with austenitic and ferritic phases have been increasingly used for many industrial applications due to their good mechanical properties and corrosion resistance in acidic, caustic and marine environments. However, DSSs are susceptible to intergranular, pitting and stress corrosion in corrosive environments due to the formation of secondary phases. Such phases are induced in DSSs during the fabrication, improper heat treatment, welding process and prolonged exposure to high temperatures during their service lives. These include the precipitation of sigma and chi phases at 700–900 °C and spinodal decomposition of ferritic grains into Cr-rich and Cr-poor phases at 350–550 °C, respectively. This article gives the state-of the-art review on the microstructural evolution of secondary phase formation and their effects on the corrosion behavior of DSSs.

  17. Effects of heat input on pitting corrosion in super duplex stainless steel weld metals

    Science.gov (United States)

    Shin, Yong taek; Shin, Hak soo; Lee, Hae woo

    2012-12-01

    Due to the difference in reheating effects depending on the heat input of subsequent weld passes, the microstructure of the weld metal varies between acicular type austenite and a mixture of polygonal type and grain boundary mixed austenite. These microstructural changes may affect the corrosion properties of duplex stainless steel welds. This result indicates that the pitting resistance of the weld can be strongly influenced by the morphology of the secondary austenite phase. In particular, the ferrite phase adjacent to the acicular type austenite phase shows a lower Pitting Resistance Equivalent (PRE) value of 25.3, due to its lower chromium and molybdenum contents, whereas the secondary austenite phase maintains a higher PRE value of more than 38. Therefore, it can be inferred that the pitting corrosion is mainly due to the formation of ferrite phase with a much lower PRE value.

  18. Effect of Secondary Phase Precipitation on the Corrosion Behavior of Duplex Stainless Steels.

    Science.gov (United States)

    Chan, Kai Wang; Tjong, Sie Chin

    2014-07-22

    Duplex stainless steels (DSSs) with austenitic and ferritic phases have been increasingly used for many industrial applications due to their good mechanical properties and corrosion resistance in acidic, caustic and marine environments. However, DSSs are susceptible to intergranular, pitting and stress corrosion in corrosive environments due to the formation of secondary phases. Such phases are induced in DSSs during the fabrication, improper heat treatment, welding process and prolonged exposure to high temperatures during their service lives. These include the precipitation of sigma and chi phases at 700-900 °C and spinodal decomposition of ferritic grains into Cr-rich and Cr-poor phases at 350-550 °C, respectively. This article gives the state-of the-art review on the microstructural evolution of secondary phase formation and their effects on the corrosion behavior of DSSs.

  19. Effects of Solution Annealing Temperature on the Galvanic Corrosion Behavior of the Super Duplex Stainless Steels

    Science.gov (United States)

    Lee, Jun-Seob; Jeon, Soon-Hyeok; Park, Yong-Soo

    2013-02-01

    This study investigated the active dissolution of super duplex stainless steel (SDSS) at various solution annealing temperatures. The active dissolutions of the α-phase and γ-phase were compared, and the effects of the surface area ratio on the active dissolutions of both phases were investigated. There were two peaks in the active-passive transition region in the potentiodynamic test in the modified green-death solution. The two peaks changed as the solution annealing temperature was increased from 1050 to 1150 °C. The solution annealing temperature difference affected the critical anodic current densities. This provides useful information for determining the appropriate solution annealing temperature in the modified green-death solution for SDSS.

  20. Effects of REM and Ba Additions on the Characteristics of the Third Generation Duplex Stainless Steel

    International Nuclear Information System (INIS)

    Park, Yong Soo; Kim, Soon Tae

    2006-01-01

    The third generation super duplex stainless steel having excellent corrosion resistance, embrittlement resistance, castability, weldability and hot workability has been developed. REM and Ba added to the alloy, with larger atomic radius than those of Cr, Mo and W, seem to fill vacancies inside the matrix and around the grain boundaries, retarding formation of brittle σ and χ phases. In addition, fine oxides/ oxy-sulfides of REM and Ba (1∼3 μm in diameter) seem to enhance the retardation effects. The alloys have also shown higher strength and ductility resulting from phase and grain refinements caused by those oxides and oxy-sulfides. Accordingly it is judged that the core technology can provide the method for remarkably suppressing formation of intermetallic phases by adding new alloy elements, and improving a applied to sea water and flue gas desulfurization facility

  1. An exploration of sequence specific DNA-duplex/pyrene interactions for intercalated and surface-associated pyrene species. Final report, May 1, 1993--December 31, 1996

    Energy Technology Data Exchange (ETDEWEB)

    Netzel, T.L.

    1997-03-01

    The broad objective of this DOE sponsored work on photoinduced electron transfer (ET) within covalently modified DNA was to learn about the rates of Et among various DNA bases and commonly used organic electron donor (D) and acceptor (A) molecules. This hypothesis driven, multidisciplinary project combined skills in modified nucleic acid synthesis and in continuous and time-resolved optical spectroscopies. Covalently modified DNA chemistry as investigated in this program had two specific long term goals. The first was to use experimental and theoretical insights into the mechanisms of electron transfer (ET) reactions to design supramolecular assemblies of redox-active chromophores that function as efficient vectorial ET engines. The second was to construct oligonucleotide probes for real-time monitoring of intracellular processes involving DNA and RNA such as m-RNA expression and translocation. This research project laid the groundwork for studying ET reactions within DNA duplexes by examining the photophysics of uridine nucleosides which are covalently labeled at the 5-position with 1-pyrenyl chromophores.

  2. DNA secondary structure of the released strand stimulates WRN helicase action on forked duplexes without coordinate action of WRN exonuclease

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, Byungchan, E-mail: bbccahn@mail.ulsan.ac.kr [Department of Life Sciences, University of Ulsan, Ulsan (Korea, Republic of); Bohr, Vilhelm A. [Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, Baltimore, MD (United States)

    2011-08-12

    Highlights: {yields} In this study, we investigated the effect of a DNA secondary structure on the two WRN activities. {yields} We found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. {yields} These results imply that WRN helicase and exonuclease activities can act independently. -- Abstract: Werner syndrome (WS) is an autosomal recessive premature aging disorder characterized by aging-related phenotypes and genomic instability. WS is caused by mutations in a gene encoding a nuclear protein, Werner syndrome protein (WRN), a member of the RecQ helicase family, that interestingly possesses both helicase and exonuclease activities. Previous studies have shown that the two activities act in concert on a single substrate. We investigated the effect of a DNA secondary structure on the two WRN activities and found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. These results imply that WRN helicase and exonuclease activities can act independently, and we propose that the uncoordinated action may be relevant to the in vivo activity of WRN.

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

    Science.gov (United States)

    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.

  4. Accurate and rapid modeling of iron-bleomycin-induced DNA damage using tethered duplex oligonucleotides and electrospray ionization ion trap mass spectrometric analysis.

    Science.gov (United States)

    Harsch, A; Marzilli, L A; Bunt, R C; Stubbe, J; Vouros, P

    2000-05-01

    Bleomycin B(2)(BLM) in the presence of iron [Fe(II)] and O(2)catalyzes single-stranded (ss) and double-stranded (ds) cleavage of DNA. Electrospray ionization ion trap mass spectrometry was used to monitor these cleavage processes. Two duplex oligonucleotides containing an ethylene oxide tether between both strands were used in this investigation, allowing facile monitoring of all ss and ds cleavage events. A sequence for site-specific binding and cleavage by Fe-BLM was incorporated into each analyte. One of these core sequences, GTAC, is a known hot-spot for ds cleavage, while the other sequence, GGCC, is a hot-spot for ss cleavage. Incubation of each oligo-nucleotide under anaerobic conditions with Fe(II)-BLM allowed detection of the non-covalent ternary Fe-BLM/oligonucleotide complex in the gas phase. Cleavage studies were then performed utilizing O(2)-activated Fe(II)-BLM. No work-up or separation steps were required and direct MS and MS/MS analyses of the crude reaction mixtures confirmed sequence-specific Fe-BLM-induced cleavage. Comparison of the cleavage patterns for both oligonucleotides revealed sequence-dependent preferences for ss and ds cleavages in accordance with previously established gel electrophoresis analysis of hairpin oligonucleotides. This novel methodology allowed direct, rapid and accurate determination of cleavage profiles of model duplex oligonucleotides after exposure to activated Fe-BLM.

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

    Science.gov (United States)

    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. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Duplex Real-Time PCR Assay Distinguishes Aedes aegypti From Ae. albopictus (Diptera: Culicidae) Using DNA From Sonicated First-Instar Larvae.

    Science.gov (United States)

    Kothera, Linda; Byrd, Brian; Savage, Harry M

    2017-11-07

    Aedes aegypti (L.) and Ae. albopictus (Skuse) are important arbovirus vectors in the United States, and the recent emergence of Zika virus disease as a public health concern in the Americas has reinforced a need for tools to rapidly distinguish between these species in collections made by vector control agencies. We developed a duplex real-time PCR assay that detects both species and does not cross-amplify in any of the other seven Aedes species tested. The lower limit of detection for our assay is equivalent to ∼0.03 of a first-instar larva in a 60-µl sample (0.016 ng of DNA per real-time PCR reaction). The assay was sensitive and specific in mixtures of both species that reflected up to a 2,000-fold difference in DNA concentration. In addition, we developed a simple protocol to extract DNA from sonicated first-instar larvae, and used that DNA to test the assay. Because it uses real-time PCR, the assay saves time by not requiring a separate visualization step. This assay can reduce the time needed for vector control agencies to make species identifications, and thus inform decisions about surveillance and control. Published by Oxford University Press on behalf of Entomological Society of America 2017 This work is written by US Government employees and is in the public domain in the US.

  7. Single-Molecule Kinetics Reveal Cation-Promoted DNA Duplex Formation Through Ordering of Single-Stranded Helices

    Science.gov (United States)

    Dupuis, Nicholas F.; Holmstrom, Erik D.; Nesbitt, David J.

    2013-01-01

    In this work, the kinetics of short, fully complementary oligonucleotides are investigated at the single-molecule level. Constructs 6–9 bp in length exhibit single exponential kinetics over 2 orders of magnitude time for both forward (kon, association) and reverse (koff, dissociation) processes. Bimolecular rate constants for association are weakly sensitive to the number of basepairs in the duplex, with a 2.5-fold increase between 9 bp (k′on = 2.1(1) × 106 M−1 s−1) and 6 bp (k′on = 5.0(1) × 106 M−1 s−1) sequences. In sharp contrast, however, dissociation rate constants prove to be exponentially sensitive to sequence length, varying by nearly 600-fold over the same 9 bp (koff = 0.024 s−1) to 6 bp (koff = 14 s−1) range. The 8 bp sequence is explored in more detail, and the NaCl dependence of kon and koff is measured. Interestingly, konincreases by >40-fold (kon = 0.10(1) s−1 to 4.0(4) s−1 between [NaCl] = 25 mM and 1 M), whereas in contrast, koffdecreases by fourfold (0.72(3) s−1 to 0.17(7) s−1) over the same range of conditions. Thus, the equilibrium constant (Keq) increases by ≈160, largely due to changes in the association rate, kon. Finally, temperature-dependent measurements reveal that increased [NaCl] reduces the overall exothermicity (ΔΔH° > 0) of duplex formation, albeit by an amount smaller than the reduction in entropic penalty (−TΔΔS° duplex formation. PMID:23931323

  8. LNA effects on DNA binding and conformation

    DEFF Research Database (Denmark)

    Pabon-Martinez, Y Vladimir; Xu, You; Villa, Alessandra

    2017-01-01

    -substitution in the duplex pyrimidine strand alters the double helix structure, affecting x-displacement, slide and twist favoring triplex formation through enhanced TFO major groove accommodation. Collectively, these findings should facilitate the design of potent anti-gene ONs.......The anti-gene strategy is based on sequence-specific recognition of double-strand DNA by triplex forming (TFOs) or DNA strand invading oligonucleotides to modulate gene expression. To be efficient, the oligonucleotides (ONs) should target DNA selectively, with high affinity. Here we combined...... hybridization analysis and electrophoretic mobility shift assay with molecular dynamics (MD) simulations to better understand the underlying structural features of modified ONs in stabilizing duplex- and triplex structures. Particularly, we investigated the role played by the position and number of locked...

  9. Effect of point substitutions within the minimal DNA-binding domain of xeroderma pigmentosum group A protein on interaction with DNA intermediates of nucleotide excision repair.

    Science.gov (United States)

    Maltseva, E A; Krasikova, Y S; Naegeli, H; Lavrik, O I; Rechkunova, N I

    2014-06-01

    Xeroderma pigmentosum factor A (XPA) is one of the key proteins in the nucleotide excision repair (NER) process. The effects of point substitutions in the DNA-binding domain of XPA (positively charged lysine residues replaced by negatively charged glutamate residues: XPA K204E, K179E, K141E, and tandem mutant K141E/K179E) on the interaction of the protein with DNA structures modeling intermediates of the damage recognition and pre-incision stages in NER were analyzed. All these mutations decreased the affinity of the protein to DNA, the effect depending on the substitution and the DNA structure. The mutant as well as wild-type proteins bind with highest efficiency partly open damaged DNA duplex, and the affinity of the mutants to this DNA is reduced in the order: K204E > K179E > K141E = K141/179E. For all the mutants, decrease in DNA binding efficiency was more pronounced in the case of full duplex and single-stranded DNA than with bubble-DNA structure, the difference between protein affinities to different DNA structures increasing as DNA binding activity of the mutant decreased. No effect of the studied XPA mutations on the location of the protein on the partially open DNA duplex was observed using photoinduced crosslinking with 5-I-dUMP in different positions of the damaged DNA strand. These results combined with earlier published data suggest no direct correlation between DNA binding and activity in NER for these XPA mutants.

  10. Achieving single channel, full duplex wireless communication

    KAUST Repository

    Choi, Jung Il; Jain, Mayank; Srinivasan, Kannan; Levis, Phil; Katti, Sachin

    2010-01-01

    This paper discusses the design of a single channel full-duplex wireless transceiver. The design uses a combination of RF and baseband techniques to achieve full-duplexing with minimal effect on link reliability. Experiments on real nodes show the full-duplex prototype achieves median performance that is within 8% of an ideal full-duplexing system. This paper presents Antenna Cancellation, a novel technique for self-interference cancellation. In conjunction with existing RF interference cancellation and digital baseband interference cancellation, antenna cancellation achieves the amount of self-interference cancellation required for full-duplex operation. The paper also discusses potential MAC and network gains with full-duplexing. It suggests ways in which a full-duplex system can solve some important problems with existing wireless systems including hidden terminals, loss of throughput due to congestion, and large end-to-end delays. Copyright 2010 ACM.

  11. Effect of gold nanoparticle on stability of the DNA molecule: A study of molecular dynamics simulation.

    Science.gov (United States)

    Izanloo, Cobra

    2017-09-02

    An understanding of the mechanism of DNA interactions with gold nanoparticles is useful in today medicine applications. We have performed a molecular dynamics simulation on a B-DNA duplex (CCTCAGGCCTCC) in the vicinity of a gold nanoparticle with a truncated octahedron structure composed of 201 gold atoms (diameter ∼1.8 nm) to investigate gold nanoparticle (GNP) effects on the stability of DNA. During simulation, the nanoparticle is closed to DNA and phosphate groups direct the particles into the major grooves of the DNA molecule. Because of peeling and untwisting states that are occur at end of DNA, the nucleotide base lies flat on the surface of GNP. The configuration entropy is estimated using the covariance matrix of atom-positional fluctuations for different bases. The results show that when a gold nanoparticle has interaction with DNA, entropy increases. The results of conformational energy and the hydrogen bond numbers for DNA indicated that DNA becomes unstable in the vicinity of a gold nanoparticle. The radial distribution function was calculated for water hydrogen-phosphate oxygen pairs. Almost for all nucleotide, the presence of a nanoparticle around DNA caused water molecules to be released from the DNA duplex and cations were close to the DNA.

  12. Effect of solution annealing temperature on precipitation in 2205 duplex stainless steel

    International Nuclear Information System (INIS)

    Kashiwar, A.; Vennela, N. Phani; Kamath, S.L.; Khatirkar, R.K.

    2012-01-01

    In the present study, effect of solution annealing temperature (1050 °C and 1100 °C) and isothermal ageing (700 °C: 15 min to 6 h) on the microstructural changes in 2205 duplex stainless steel has been investigated systematically. Scanning electron microscopy and X-ray diffraction were adopted to follow the microstructural evolution, while an energy dispersive spectrometer attached to scanning electron microscope was used to obtain localised chemical information of various phases. The ferritic matrix of the two phase 2205 duplex stainless steel (∼ 45% ferrite and ∼ 55% austenite) undergoes a series of metallurgical transformations during ageing—formation of secondary austenite (γ 2 ) and precipitation of Cr and Mo rich intermetallic (chi-χ and sigma-σ) phases. For solution annealing at 1050 °C, significant amount of carbides were observed in the ferrite grains after 1 h of ageing at 700 °C. χ Phase precipitated after the precipitation of carbides—preferentially at the ferrite–ferrite and also at the ferrite–austenite boundaries. σ Phase was not observed in significant quantity even after 6 h of ageing. The sequence of precipitation in samples solution annealed at 1050 °C was found to be carbides → χ → σ. On the contrary, for samples solution annealed at 1100 °C, the precipitation of χ phase was negligible. χ Phase precipitated before σ phase, preferentially along the ferrite–ferrite grain boundaries and was later consumed in the σ phase precipitation. The σ phase precipitated via the eutectoid transformation of ferrite to yield secondary austenite γ 2 and σ phase in the ferrite and along the ferrite–austenite grain boundaries. An increase in the volume fraction of γ 2 and σ phase with simultaneous decrease in the ferrite was evidenced with ageing. - Highlights: ► Effect of solution annealing temperature on microstructural evolution is studied. ► χ Phase precipitated preferentially in the samples solution annealed at

  13. Effect of solution annealing temperature on precipitation in 2205 duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Kashiwar, A., E-mail: akashiwar@gmail.com [Department of Metallurgical and Materials Engineering, Visvesvaraya National Institute of Technology (VNIT), South Ambazari Road, Nagpur-440010, Maharashtra (India); Vennela, N. Phani, E-mail: phanivennela@gmail.com [Department of Metallurgical and Materials Engineering, Visvesvaraya National Institute of Technology (VNIT), South Ambazari Road, Nagpur-440010, Maharashtra (India); Kamath, S.L., E-mail: kamath@iitb.ac.in [Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay (IITB), Powai, Mumbai-400076, Maharashtra (India); Khatirkar, R.K., E-mail: rajesh.khatirkar@gmail.com [Department of Metallurgical and Materials Engineering, Visvesvaraya National Institute of Technology (VNIT), South Ambazari Road, Nagpur-440010, Maharashtra (India)

    2012-12-15

    In the present study, effect of solution annealing temperature (1050 Degree-Sign C and 1100 Degree-Sign C) and isothermal ageing (700 Degree-Sign C: 15 min to 6 h) on the microstructural changes in 2205 duplex stainless steel has been investigated systematically. Scanning electron microscopy and X-ray diffraction were adopted to follow the microstructural evolution, while an energy dispersive spectrometer attached to scanning electron microscope was used to obtain localised chemical information of various phases. The ferritic matrix of the two phase 2205 duplex stainless steel ({approx} 45% ferrite and {approx} 55% austenite) undergoes a series of metallurgical transformations during ageing-formation of secondary austenite ({gamma}{sub 2}) and precipitation of Cr and Mo rich intermetallic (chi-{chi} and sigma-{sigma}) phases. For solution annealing at 1050 Degree-Sign C, significant amount of carbides were observed in the ferrite grains after 1 h of ageing at 700 Degree-Sign C. {chi} Phase precipitated after the precipitation of carbides-preferentially at the ferrite-ferrite and also at the ferrite-austenite boundaries. {sigma} Phase was not observed in significant quantity even after 6 h of ageing. The sequence of precipitation in samples solution annealed at 1050 Degree-Sign C was found to be carbides {yields} {chi} {yields} {sigma}. On the contrary, for samples solution annealed at 1100 Degree-Sign C, the precipitation of {chi} phase was negligible. {chi} Phase precipitated before {sigma} phase, preferentially along the ferrite-ferrite grain boundaries and was later consumed in the {sigma} phase precipitation. The {sigma} phase precipitated via the eutectoid transformation of ferrite to yield secondary austenite {gamma}{sub 2} and {sigma} phase in the ferrite and along the ferrite-austenite grain boundaries. An increase in the volume fraction of {gamma}{sub 2} and {sigma} phase with simultaneous decrease in the ferrite was evidenced with ageing. - Highlights

  14. Investigation of effects of boron additives and heat treatment on carbides and phase transition of highly alloyed duplex cast iron

    International Nuclear Information System (INIS)

    Tasgin, Yahya; Kaplan, Mehmet; Yaz, Mehmet

    2009-01-01

    The effect of boron additives and heat treatment on the microstructural morphology of the transition zone in a duplex cast iron, which has an outer shell of white cast iron (with a high Cr-content and containing boron additives) and an inner side composed of normal gray cast iron, has been investigated. For this purpose, two experimental materials possessing different compositions of white-gray duplex cast iron were produced. Subsequently, metallographic investigations were carried out to study the effect of heat treatment applied to the experimental materials by using the scanning electron microscopy technique, along with optical microscopy and energy dispersive X-ray spectroscopy. Moreover, the formation of various phases and carbide composites in the samples and their effects on the hardness were also investigated using X-ray diffraction techniques. The results of investigations, and hardness showed that addition of the elements Cr and B to high-alloyed white cast iron affected carbide formation significantly, while simultaneously hardening the microstructure, and consequently the carbide present in the transition area of white-gray cast iron was spread out and became thinner. However, B additives and heat treatment did not cause any damage to the transition region of high Cr-content duplex cast iron.

  15. The Effect of Surface Preparation on the Precipitation of Sigma During High Temperature Exposure of S32205 Duplex Stainless Steel

    Science.gov (United States)

    Jepson, Mark A. E.; Rowlett, Matthew; Higginson, Rebecca L.

    2017-03-01

    Although the formation of sigma phase in duplex stainless steels is reasonably well documented, the effect of surface finish on its formation rate in surface regions has not been previously noted. The growth of the sigma phase precipitated in the subsurface region (to a maximum depth of 120 μm) has been quantified after heat treatment of S32205 duplex stainless steel at 1073 K (800 °C) and 1173 K (900 °C) after preparation to two surface finishes. Here, results are presented that show that there is a change in the rate of sigma phase formation in the surface region of the material, with a coarser surface finish leading to a greater depth of precipitation at a given time and temperature of heat treatment. The growth rate and morphology of the precipitated sigma has been examined and explored in conjunction with thermodynamic equilibrium phase calculations.

  16. Effect of intermetallic precipitation on the properties of multi passed duplex stainless steel weldment

    Energy Technology Data Exchange (ETDEWEB)

    Bae, Seong Han [Technology research institute, Ulsan (Korea, Republic of); Lee, Hae Woo [Dong-A University, Busan (Korea, Republic of)

    2014-01-15

    This study investigated the effect of the aging time of weldment of 24Cr-3.5Mo duplex stainless steel on the microstructure and corrosion behavior. After performing FCAW, we carried out heat treatments at varying times at 850 ℃ and performed observation of microstructure, potentio dynamic test, SEM-EDS analysis, and X-ray diffraction analysis. As the aging time increased, the fraction of δ-ferrite decreased sharply, but the fraction of γ slightly increased. The σ phase was generated at a non-metallic inclusion along the grain boundaries of δ-ferrite and γ, while the χ phase was generated in the structure of δ-ferrite. As the intermetallic compounds increased, the critical pitting potential fell sharply, and PREN of the surrounding structure decreased by 5 due to precipitation of the σ phase in 3.5% NaCl at 60 ℃. Pitting occurred intensively under a multi-pass line which relatively had more intermetallic compounds, and the precipitation of the σ phase caused the formation of Cr carbide.

  17. Effect of intermetallic precipitation on the properties of multi passed duplex stainless steel weldment

    International Nuclear Information System (INIS)

    Bae, Seong Han; Lee, Hae Woo

    2014-01-01

    This study investigated the effect of the aging time of weldment of 24Cr-3.5Mo duplex stainless steel on the microstructure and corrosion behavior. After performing FCAW, we carried out heat treatments at varying times at 850 ℃ and performed observation of microstructure, potentio dynamic test, SEM-EDS analysis, and X-ray diffraction analysis. As the aging time increased, the fraction of δ-ferrite decreased sharply, but the fraction of γ slightly increased. The σ phase was generated at a non-metallic inclusion along the grain boundaries of δ-ferrite and γ, while the χ phase was generated in the structure of δ-ferrite. As the intermetallic compounds increased, the critical pitting potential fell sharply, and PREN of the surrounding structure decreased by 5 due to precipitation of the σ phase in 3.5% NaCl at 60 ℃. Pitting occurred intensively under a multi-pass line which relatively had more intermetallic compounds, and the precipitation of the σ phase caused the formation of Cr carbide.

  18. Effect of Aging Treatment on Impact Toughness and Corrosion Resistance of Super Duplex Stainless Steel

    Science.gov (United States)

    Kim, Jae-Hwan; Oh, Eun-Ji; Lee, Byung-Chan; Kang, Chang-Yong

    2016-01-01

    The effect of aging time on impact toughness and corrosion resistance of 25%Cr-7%Ni-2%Mo-4%W-0.2%N super duplex stainless steel from the viewpoint of intermetallic secondary phase variation was investigated with scanning electron microscopic observation with energy-dispersive x-ray spectroscopic analysis and transmission electron microscopy. The results clarified that R-phase is precipitated not only at the interface of ferrite and austenite but inside the ferrite at an initial stage of aging and then transformed into σ-phase from an aging time of 1 h, while the ferrite phase decomposed into γ2 and σ-phase with increase of aging time. This variation of the phases led to decrease of its impact toughness, and specifically, the R-phase was proved to be predominant in the degradation of the impact toughness at the initial stage of the aging. Additionally, these secondary phases led to deterioration of corrosion resistance because of Cr depletion.

  19. Alpha prime effect on mechanical properties and corrosion resistance of UR 52N+ duplex stainless steel

    International Nuclear Information System (INIS)

    Fontes, Talita Filier

    2009-01-01

    Alpha prime phase leads to decreased corrosion resistance and mechanical properties losses of duplex stainless steels. In this work mechanical and electrochemical tests were performed in duplex stainless steel UR 52N+ aged at 475 degree C for various periods in order to determine the sensibility of these tests to alpha prime presence. Hardness tests showed a gradual increase in its values; on the other hand, impact tests revealed that the material aged for 12h losses about 80% of energy absorption capacity of the solution annealed sample. Notwithstanding cyclic polarization tests showed that significant changes are only noted for aging times greater than 96h. (author)

  20. Effect of electromagnetic interaction during fusion welding of AISI 2205 duplex stainless steel on the corrosion resistance

    Energy Technology Data Exchange (ETDEWEB)

    García-Rentería, M.A., E-mail: marcogarciarenteria@uadec.edu.mx [Faculty of Metallurgy, Autonomous University of Coahuila, Carretera 57 Km. 5, CP 25720, Monclova, Coahuila (Mexico); López-Morelos, V.H., E-mail: vhlopez@umich.mx [Instituto de Investigación en Metalurgia y Materiales, Universidad Michoacana de San Nicolás de Hidalgo, A.P. 888, CP 58000, Morelia, Michoacán (Mexico); González-Sánchez, J., E-mail: jagonzal@uacam.mx [Centre for Corrosion Research, Autonomous University of Campeche, Av. Agustín Melgar s/n, Col. Buenavista, CP 24039, Campeche, Cam (Mexico); García-Hernández, R., E-mail: rgarcia@umich.mx [Instituto de Investigación en Metalurgia y Materiales, Universidad Michoacana de San Nicolás de Hidalgo, A.P. 888, CP 58000, Morelia, Michoacán (Mexico); Dzib-Pérez, L., E-mail: franciscocl7@yahoo.com.mx [Centre for Corrosion Research, Autonomous University of Campeche, Av. Agustín Melgar s/n, Col. Buenavista, CP 24039, Campeche, Cam (Mexico); Curiel-López, F.F., E-mail: franciscocl7@yahoo.com.mx [Faculty of Metallurgy, Autonomous University of Coahuila, Carretera 57 Km. 5, CP 25720, Monclova, Coahuila (Mexico)

    2017-02-28

    Highlights: • Application of EMILI during welding 2205 Duplex stainless steel hindered the coarsening of δ grains in HTHAZ and promoted regeneration of γ. • Welds made with simultaneous EMILI presented TPI values at the HTHAZ similar to those for BM. • Welds made under 3, 12 and 15 mT presented a mass loss by anodic polarisation similar to that observed for the as-received BM. • This behaviour is due to changes in the dynamics of microstructural evolution during welding with EMILI. - Abstract: The effect of electromagnetic interaction of low intensity (EMILI) applied during fusion welding of AISI 2205 duplex stainless steel on the resistance to localised corrosion in natural seawater was investigated. The heat affected zone (HAZ) of samples welded under EMILI showed a higher temperature for pitting initiation and lower dissolution under anodic polarisation in chloride containing solutions than samples welded without EMILI. The EMILI assisted welding process developed in the present work enhanced the resistance to localised corrosion due to a modification on the microstructural evolution in the HAZ and the fusion zone during the thermal cycle involved in fusion welding. The application of EMILI reduced the size of the HAZ, limited coarsening of the ferrite grains and promoted regeneration of austenite in this zone, inducing a homogeneous passive condition of the surface. EMILI can be applied during fusion welding of structural or functional components of diverse size manufactured with duplex stainless steel designed to withstand aggressive environments such as natural seawater or marine atmospheres.

  1. The effect of a simulation training package on skill acquisition for duplex arterial stenosis detection.

    Science.gov (United States)

    Jaffer, Usman; Normahani, Pasha; Singh, Prashant; Aslam, Mohammed; Standfield, Nigel J

    2015-01-01

    In vascular surgery, duplex ultrasonography is a valuable diagnostic tool in patients with peripheral vascular disease, and there is increasing demand for vascular surgeons to be able to perform duplex scanning. This study evaluates the role of a novel simulation training package on vascular ultrasound (US) skill acquisition. A total of 19 novices measured predefined stenosis in a simulated pulsatile vessel using both peak systolic velocity ratio (PSVR) and diameter reduction (DR) methods before and after a short period of training using a simulated training package. The training package consisted of a simulated pulsatile vessel phantom, a set of instructional videos, duplex ultrasound objective structured assessment of technical skills (DUOSATS) tool, and a portable US scanner. Quantitative metrics (procedure time, percentage error using PSVR and DR methods, DUOSAT scores, and global rating scores) before and after training were compared. Subjects spent a median time of 144 mins (IQR: 60-195) training using the simulation package. Subjects exhibited statistically significant improvements when comparing pretraining and posttraining DUOSAT scores (pretraining = 17 [16-19.3] vs posttraining = 30 [27.8-31.8]; p duplex images in a pulsatile simulated phantom following a short period of goal direct training using a simulation training package. A simulation training package may be a valuable tool for integration into a vascular training program. However, further work is needed to explore whether these newly attained skills are translated into clinical assessment. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

  2. Effect of welding processes on corrosion resistance of UNS S31803 duplex stainless steel

    International Nuclear Information System (INIS)

    Chiu, Liu Ho; Hsieh, Wen Chin

    2003-01-01

    An attractive combination of corrosion resistance and mechanical properties in the temperature range -50 to 250 .deg. C is offered by duplex stainless steel. However, undesirable secondary precipitation phase such as σ, γ 2 and Cr 2 N may taken place at the cooling stage from the welding processes. Therefore, this paper describes the influence of different welding procedures such as manual metal arc welding (MMA), tungsten inert gas welding (TIG) and vacuum brazing on corrosion resistance of the welded joint for UNS S31803 duplex stainless steel. Microstructure and chemical compositions of the welded joint were examined. The weight loss of specimens immersed in 6% FeCl 3 solution at 47.5 .deg. C for 24-hours was determined and used to evaluate the pitting resistance of duplex stainless steel and their welds. The region of heat-affected zone of specimen obtained by the MMA is much wider than that resulted from TIG, therefore, the weight loss of welds by MMA was larger than that of weld by TIG. The weight loss of brazed specimens cooled from slow cooling rate was larger than those of specimens cooled from high cooling rate, because the precipitation of σ phase. Beside that, the weight loss of brazed specimen is greater than those of the welded specimens. The galvanic corrosion was observed in brazed duplex stainless steel joints in the chloride solution

  3. Effects of Heat Input on Microstructure, Corrosion and Mechanical Characteristics of Welded Austenitic and Duplex Stainless Steels: A Review

    Directory of Open Access Journals (Sweden)

    Ghusoon Ridha Mohammed

    2017-01-01

    Full Text Available The effects of input heat of different welding processes on the microstructure, corrosion, and mechanical characteristics of welded duplex stainless steel (DSS are reviewed. Austenitic stainless steel (ASS is welded using low-heat inputs. However, owing to differences in the physical metallurgy between ASS and DSS, low-heat inputs should be avoided for DSS. This review highlights the differences in solidification mode and transformation characteristics between ASS and DSS with regard to the heat input in welding processes. Specifically, many studies about the effects of heat energy input in welding process on the pitting corrosion, intergranular stress, stresscorrosion cracking, and mechanical properties of weldments of DSS are reviewed.

  4. Effect of heat input on dissimilar welds of ultra high strength steel and duplex stainless steel: Microstructural and compositional analysis

    Energy Technology Data Exchange (ETDEWEB)

    Tasalloti, H., E-mail: hamed.tasalloti.kashani@student.lut.fi; Kah, P., E-mail: paul.kah@lut.fi; Martikainen, J., E-mail: jukka.martikainen@lut.fi

    2017-01-15

    The effect of heat input on the microstructure and compositional heterogeneity of welds of direct-quenched ultra high strength steel (Optim 960 QC) and duplex stainless steel (UNS S32205) was studied. The dissimilar welds were made using GMAW with a fully austenitic filler wire. In addition to grain coarsening in the heat affected zone (HAZ) of the ferritic side, it was found that an increase in heat input correlatively increased the proportional volume of bainitic to martensitic phases. Coarse ferritic grains were observed in the duplex HAZ. Higher heat input, however, had a beneficial effect on the nucleation of austenite in the HAZ. Heat input had a regulatory effect on grain growth within the austenitic weld and more favorable equiaxed austenite was obtained with higher heat input. On the ferritic side of the welds, macrosegregation in the form of a martensitic intermediate zone was observed for all the cooling rates studied. However, on the duplex side, macrosegregation in the fusion boundary was only noticed with higher cooling rates. Microstructural observations and compositional analysis suggest that higher heat input could be beneficial for the structural integrity of the weld despite higher heat input increasing the extent of adverse coarse grains in the HAZ, especially on the ferritic side. - Highlights: •The effect of heat input on dissimilar welds of UHSS and DSS was studied. •Transmutation of the microstructure was discussed in detail. •The influence of heat input on compositional heterogeneity of welds was described. •Higher heat input enhanced bainitic transformation on the ferritic side. •Macrosegregation was affected by the amount of heat input on the DSS side.

  5. Overall performance of the duplex Stirling refrigerator

    International Nuclear Information System (INIS)

    Erbay, L. Berrin; Ozturk, M. Mete; Doğan, Bahadır

    2017-01-01

    Highlights: • Overall performance coefficient of duplex Stirling refrigerator was investigated. • A definite region for the coefficient of performance of the refrigerator in duplex Stirling is identified. • A definite region for the thermal efficiency of the heat engine in duplex Stirling is identified. • Benchmark values and design bounds of the duplex Stirling refrigerator were obtained. - Abstract: The duplex Stirling refrigerator is an integrated refrigerator consists of Stirling cycle engine and Stirling cycle refrigerator used for cooling. The equality of the work generation of the heat engine to the work consumption of the refrigerator is the primary constraint of the duplex Stirling. The duplex Stirling refrigerator is investigated thermodynamically by considering the effects of constructional and operational parameters which are namely the temperature ratios for heat engine and refrigerator, and the compression ratios for both sides. The primary concern is given to the parametric effects on the overall coefficient of performance of the duplex Stirling refrigerator. The given diagrams provide a design bounds and benchmark results that allows seeing the big picture about the cooling load and heat input relation. Moreover they ease to determine the corresponding work rate to the target cooling load. As regard to the obtained results, a definite region for coefficient of performance of the refrigerator and a definite region for the thermal efficiency of the heat engine of the duplex Stirling are identified.

  6. Effect of Welding Process on Microstructure, Mechanical and Pitting Corrosion Behaviour of 2205 Duplex Stainless Steel Welds

    Science.gov (United States)

    Mohammed, Raffi; Madhusudhan Reddy, G.; Srinivasa Rao, K.

    2018-03-01

    An attempt has been made to weld 2205 Duplex stainless steel of 6mm thick plate using conventional gas tungsten arc welding (GTAW) and activated gas tungsten arc welding (A- GTAW) process using silica powder as activated flux. Present work is aimed at studying the effect of welding process on depth of penetration, width of weld zone of 2205 duplex stainless steel. It also aims to observe the microstructural changes and its effect on mechanical properties and pitting corrosion resistance of 2205 duplex stainless steel welds. Metallography is done to observe the microstructural changes of the welds using image analyzer attached to the optical microscopy. Hardness studies, tensile and ductility bend tests were evaluated for mechanical properties. Potentio-dynamic polarization studies were carried out using a basic GillAC electro-chemical system in 3.5% NaCl solution to observe the pitting corrosion behaviour. Results of the present investigation established that increased depth of penetration and reduction of weld width in a single pass by activated GTAW with the application of SiO2 flux was observed when compared with conventional GTAW process. It may be attributed to the arc constriction effect. Microstructure of the weld zones for both the welds is observed to be having combination of austenite and delta ferrite. Grain boundary austenite (GBA) with Widmanstatten-type austenite (WA) of plate-like feature was nucleated from the grain boundaries in the weld zone of A-GTAW process. Mechanical properties are relatively low in activated GTAW process and are attributed to changes in microstructural morphology of austenite. Improved pitting corrosion resistance was observed for the welds made with A-GTAW process.

  7. Effect of solution treatment on microstructure and properties of duplex stainless steel

    Science.gov (United States)

    Wang, X. Y.; Luo, J. M.; Huang, L. Q.; Wang, H. B.; Ma, C. W.

    2017-09-01

    The influence of solution treatment on microstructure and properties of 2205 duplex stainless steel (DSS) was studied. The microstructure, precipitates and corrosion resisting property were observed and analyzed by means of optical microscopy (OM), scanning electron microscopy (SEM) and electrochemical methods. The results showed that a large number of brittle σ-phase precipitates, which deteriorate the plasticity and corrosion resistance of the material, were easy to produce in the duplex stainless steel under the low temperature. The precipitation of σ-phase can be decreased and the plasticity and corrosion resistance can be improved by increasing solution temperature. In addition, the ferrite content increases with the increase of solution temperature, while less affected by cooling rate.

  8. 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.

    Science.gov (United States)

    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. Copyright © 2012 Elsevier

  9. Effects of rare earth metals addition on the resistance to pitting corrosion of super duplex stainless steel - Part 1

    International Nuclear Information System (INIS)

    Kim, Soon-Tae; Jeon, Soon-Hyeok; Lee, In-Sung; Park, Yong-Soo

    2010-01-01

    To elucidate the effects of rare earth metals addition on the resistance to pitting corrosion of super duplex stainless steel, a metallographic examination, potentiodynamic and potentiostatic polarization tests, a SEM-EDS and a SAM analysis of inclusion, austenite phase and ferrite phase were conducted. The addition of rare earth metals to the base alloy led to the formation of (Mn, Cr, Si, Al, Ce) oxides and (Mn, Cr, Si, Ce) oxides, which improved the resistance to pitting corrosion and caused a decrease in the preferential interface areas for the initiation of the pitting corrosion.

  10. The effect of fiber laser parameters on microhardness and microstructure of duplex stainless steel

    Directory of Open Access Journals (Sweden)

    Mohammed Ghusoon R.

    2017-01-01

    Full Text Available An investigation was implement to study the influence of laser power, and speed of the welding on hardness, microstructure, and penetration of laser welding bead on plate duplex stainless steel, which is not exhibited so far. A fiber laser was selected for welding duplex stainless steel sheet with 2 mm thickness. Then, optical microscope (OM was used in the morphologic observation of cross section, penetration depth, and bead width. Microhardness of the welded sheet was measured using Vickers hardness. Profiles of hardness and microstructure were utilized to discriminate welding line and to propose superior welding parameters. The experimental results displayed that, a good quality of duplex steel welds can be acquired when a suitable fiber laser welding parameters were selected. It was found that microhardness profiles showed a rise in the hardness of the weld and heat-affected zones as the solidification process proceeds rapidly. Additionally, the crystal solidification process induced by the fiber laser welding was schematically clarified and systematically exposed.

  11. Study of corrosive effect of oil in super duplex stainless steels; Estudo do efeito corrosivo do petroleo em acos super duplex

    Energy Technology Data Exchange (ETDEWEB)

    Gusmao, E.F.; Azambuja, V.M. [IFES, Coordenadoria de Metalurgia, Vitoria, ES (Brazil); Santos, D.S. [Universidade Federal do Rio de Janeiro (PEMM/COPPE/UFRJ), RJ (Brazil). Pos-Graduacao em Engenharia Metalurgica e de Materiais

    2010-07-01

    The super duplex stainless steel was exposed in an environment at 75 degree C with oil for days, weeks and month to observe the change in mass. The corrosion leads to loss of weight of material which could harm the economy of a company, as this will have to stop production to replace the corroded part. Hence the great importance of studies on ways to mitigate the corrosion. There was a chemical attack by the reagent Behara and testing to study the quality of the protective coating after the tests with oil by electrochemical impedance. (author)

  12. Development of bis-locked nucleic acid (bisLNA) oligonucleotides for efficient invasion of supercoiled duplex DNA

    DEFF Research Database (Denmark)

    Moreno, Pedro M D; Geny, Sylvain; Pabon, Y Vladimir

    2013-01-01

    In spite of the many developments in synthetic oligonucleotide (ON) chemistry and design, invasion into double-stranded DNA (DSI) under physiological salt and pH conditions remains a challenge. In this work, we provide a new ON tool based on locked nucleic acids (LNAs), designed for strand invasi...

  13. Development of dansyl-modified oligonucleotide probes responding to structural changes in a duplex.

    Science.gov (United States)

    Suzuki, Yoshio; Kowata, Keiko; Komatsu, Yasuo

    2013-11-15

    We have synthesized a nonnucleoside amidite block of dansyl fluorophore to prepare dansyl-modified oligonucleotides (ONTs). The fluorescence intensities of dansyl-ONT specifically increased by the presence of adjacent guanosine residues but, significantly reduced in a dansyl-flipping duplex. These changes were caused by solvatochromism effect due to the number of guanine which is hydrophobic functional group and the external environment of dansyl group. The fluorescence intensities could be plotted as a function of the ONTs concentrations and the increase in the fluorescence was observed to equimolar concentrations of target DNA. This duplex exhibited higher melting temperature relative to the corresponding duplexes containing other base pairs. Similar changes in fluorescence could be detected upon hybridization with complementary RNAs. Thus, the dansyl-modified ONTs provide sequence specific fluorescent probe of DNA and RNA. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. The Effects of Nitrogen Gas on Microstructural and Mechanical Properties of TIG Welded S32205 Duplex Stainless Steel

    Directory of Open Access Journals (Sweden)

    Aziz Barış Başyiğit

    2018-04-01

    Full Text Available Duplex stainless steels are gaining greater interest due to their increasing amounts of application fields. Accordingly, there is a need for awareness of problems associated with improper microstructural distributions such as δ-ferrite (delta-ferrite, austenite and other important intermetallic phases that may form in these steel weldments. Since δ-ferrite versus austenite ratio profoundly influences corrosion and mechanical properties, optimum δ-ferrite ratios must be kept approximately within 35–65 vol % and balance austenite to maintain satisfactory corrosion and mechanical properties on welding of these steels. Cooling rates of welds and alloying elements in base metal are the major factors that determine the final microstructure of these steels. In this work, 3 mm thickness of 2205 duplex stainless-steel plates were TIG (Tungsten Inert Gas welded with various amounts of nitrogen gas added to argon shielding gas. Specimens were joined within the same welding parameters and cooling conditions. As nitrogen is a potential austenite stabilizer and an interstitial solid solution hardener, the effects of nitrogen on mechanical properties such as hardness profiles, grain sizes and microstructural modifications are investigated thoroughly by changing the welding shielding gas compositions. Increasing the nitrogen content in argon shielding gas also increases the amount of austenitic phase while δ-ferrite ratios decreases. Nitrogen spherodized the grains of austenitic structure much more than observed in δ-ferrite. The strength values of specimens that welded with the addition of nitrogen gas into the argon shielding gas are increased more in both austenitic and delta-ferritic structure as compared to specimens that welded with plain argon shielding gas. The addition of 1 vol % of nitrogen gas into argon shielding gas provided the optimum phase balance of austenite and δ-ferrite in S32205 duplex stainless-steel TIG-welded specimens.

  15. Effects of fabrication conditions on mechanical properties and microstructure of duplex β″-Al{sub 2}O{sub 3} solid electrolyte

    Energy Technology Data Exchange (ETDEWEB)

    Canfield, Nathan L. [Energy Processes & Materials Division, Pacific Northwest National Laboratory, Richland, WA 99352 (United States); Kim, Jin Y., E-mail: Jin.Kim@pnnl.gov [Energy Processes & Materials Division, Pacific Northwest National Laboratory, Richland, WA 99352 (United States); Bonnett, Jeff F.; Pearson, R.L.; Sprenkle, Vincent L. [Energy Processes & Materials Division, Pacific Northwest National Laboratory, Richland, WA 99352 (United States); Jung, Keeyoung [Energy Storage Materials Research Center, Research Institute of Industrial Science and Technology (RIST), Pohang (Korea, Republic of)

    2015-07-15

    Highlights: • The concept of duplex BASEs is presented as a method to lower the ASR for NBBs. • Duplex BASEs consist of thin dense electrolyte and porous support. • Strength of converted BASEs shows a different trend from as-sintered samples. • Cell orientation gives significant impact on strength of duplex BASEs. - Abstract: Na-beta batteries are an attractive technology as a large-scale electrical energy storage for grid applications. However, additional improvements in performance and cost are needed for wide market penetration. To improve cell performance by minimizing polarizations, reduction of electrolyte thickness was attempted using a duplex structure consisting of a thin dense electrolyte layer and a porous support layer. In this paper, the effects of sintering conditions, dense electrolyte thickness, and cell orientation on the flexural strength of duplex BASEs fabricated using a vapor phase approach were investigated. It is shown that sintering at temperatures between 1500 and 1550 °C results in fine grained microstructures and the highest flexural strength after conversion. Increasing thickness of the dense electrolyte has a small impact on flexural strength, while the orientation of load such that the dense electrolyte is in tension instead of compression has major effects on strength for samples with a well-sintered dense electrolyte.

  16. Effect of Preaging Deformation on Aging Characteristics of 2507 Super Duplex Stainless Steel

    Science.gov (United States)

    Mishra, M. K.; Rao, A. G.; Sarkar, R.; Kashyap, B. P.; Prabhu, N.

    2016-02-01

    In the present study, precipitation of sigma (σ) phase was investigated over the temperature range of 700-850 °C in undeformed and deformed (60% cold rolling) samples of 2507 super duplex stainless steel. The fraction of sigma phase formed as a result of the transformation α → σ + γ2 increases with increasing time and temperature. The increase in sigma phase leads to increase in yield strength and decrease in ductility. Preaging deformation leads to accelerated precipitation of sigma phase. The activation energy for sigma phase precipitation in deformed sample is found to be lower than that in undeformed sample.

  17. Effect of Aging on Precipitation Behavior and Pitting Corrosion Resistance of SAF2906 Super Duplex Stainless Steel

    Science.gov (United States)

    Li, Jianchun; Li, Guoping; Liang, Wei; Han, Peide; Wang, Hongxia

    2017-09-01

    The effect of aging temperature and holding time on the precipitation of secondary phases and pitting corrosion resistance of SAF2906 super duplex stainless steel was examined. Chromium nitride and σ phase were observed to preferentially precipitate at the ferrite/austenite interface. An amount of nitrides was also observed within the ferrite grain. The precipitation of chromium nitride occurred before the σ phase. The increase in aging temperature and holding time did not affect the concentration of the nitrides but increased the area fraction of the σ phase at a faster rate. The Cr2N precipitation in SAF2906 is more evident than that of the other duplex stainless steels. The variation tendency of the precipitation concentrations is primarily consistent with the prediction results of Thermo-Calc software. The electrochemical results showed that Cr2N and σ phase significantly reduced the pitting potential. Scanning electron microscope observations revealed that pits appear mainly in regions adjacent to sigma phase and Cr2N.

  18. Effect of electromagnetic interaction during fusion welding of AISI 2205 duplex stainless steel on the corrosion resistance

    Science.gov (United States)

    García-Rentería, M. A.; López-Morelos, V. H.; González-Sánchez, J.; García-Hernández, R.; Dzib-Pérez, L.; Curiel-López, F. F.

    2017-02-01

    The effect of electromagnetic interaction of low intensity (EMILI) applied during fusion welding of AISI 2205 duplex stainless steel on the resistance to localised corrosion in natural seawater was investigated. The heat affected zone (HAZ) of samples welded under EMILI showed a higher temperature for pitting initiation and lower dissolution under anodic polarisation in chloride containing solutions than samples welded without EMILI. The EMILI assisted welding process developed in the present work enhanced the resistance to localised corrosion due to a modification on the microstructural evolution in the HAZ and the fusion zone during the thermal cycle involved in fusion welding. The application of EMILI reduced the size of the HAZ, limited coarsening of the ferrite grains and promoted regeneration of austenite in this zone, inducing a homogeneous passive condition of the surface. EMILI can be applied during fusion welding of structural or functional components of diverse size manufactured with duplex stainless steel designed to withstand aggressive environments such as natural seawater or marine atmospheres.

  19. Enantiospecific kinking of DNA by a partially intercalating metal complex

    KAUST Repository

    Reymer, Anna; Nordé n, Bengt

    2012-01-01

    Opposite enantiomers of [Ru(phenanthroline) 3] 2+ affect the persistence length of DNA differently, a long speculated effect of helix kinking. Our molecular dynamics simulations confirm a substantial change of duplex secondary structure produced

  20. Reversible Redox Activity by Ion-pH Dually Modulated Duplex Formation of i-Motif DNA with Complementary G-DNA

    Directory of Open Access Journals (Sweden)

    Soyoung Chang

    2018-04-01

    Full Text Available The unique biological features of supramolecular DNA have led to an increasing interest in biomedical applications such as biosensors. We have developed an i-motif and G-rich DNA conjugated single-walled carbon nanotube hybrid materials, which shows reversible conformational switching upon external stimuli such as pH (5 and 8 and presence of ions (Li+ and K+. We observed reversible electrochemical redox activity upon external stimuli in a quick and robust manner. Given the ease and the robustness of this method, we believe that pH- and ion-driven reversible DNA structure transformations will be utilized for future applications for developing novel biosensors.

  1. Effects of radiation on DNA

    International Nuclear Information System (INIS)

    Braddock, M.

    1985-07-01

    The hydroxyl radical (OH radical) is the most damaging radical produced by the effect of ionizing radiation in water. The rate of reaction of the OH radical with purified, native and isodisperse DNA has been determined as compared with calf thymus DNA. This has been achieved by direct observation of the rate of formation of the DNA-OH radical adduct, and by competition with SCN - . Results obtained from direct observation are consistent with calculations which have been performed using the encounter frequency model of Braams and Ebert. However, results obtained for OH radical with DNA derived from competition plots suggest a rate constant somewhat lower than that obtained from direct observation. The relative merits of both techniques are discussed. In order to study the effect of energy deposited directly in the DNA, dry films of purified plasmid DNA have been irradiated in a system where the indirect effects of radical interaction have been minimized. The present results indicate that with different molecular lengths of plasmid DNA, non-random breakage may occur, and that additional damage may be brought about at sites of previously existing damage. Differences in the sensitivity of plasmid DNA molecules of varying lengths to radiation induced double strand breaks have been demonstrated. (author)

  2. pH-Modulated Watson-Crick duplex-quadruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 base pairs upstream of the c-kit transcription initiation site.

    Science.gov (United States)

    Bucek, Pavel; Jaumot, Joaquim; Aviñó, Anna; Eritja, Ramon; Gargallo, Raimundo

    2009-11-23

    Guanine-rich regions of DNA are sequences capable of forming G-quadruplex structures. The formation of a G-quadruplex structure in a region 140 base pairs (bp) upstream of the c-kit transcription initiation site was recently proposed (Fernando et al., Biochemistry, 2006, 45, 7854). In the present study, the acid-base equilibria and the thermally induced unfolding of the structures formed by a guanine-rich region and by its complementary cytosine-rich strand in c-kit were studied by means of circular dichroism and molecular absorption spectroscopies. In addition, competition between the Watson-Crick duplex and the isolated structures was studied as a function of pH value and temperature. Multivariate data analysis methods based on both hard and soft modeling were used to allow accurate quantification of the various acid-base species present in the mixtures. Results showed that the G-quadruplex and i-motif coexist with the Watson-Crick duplex over the pH range from 3.0 to 6.5, approximately, under the experimental conditions tested in this study. At pH 7.0, the duplex is practically the only species present.

  3. Effect of residual stresses on individual phase mechanical properties of austeno-ferritic duplex stainless steel

    International Nuclear Information System (INIS)

    Dakhlaoui, R.; Baczmanski, A.; Braham, C.; Wronski, S.; Wierzbanowski, K.; Oliver, E.C.

    2006-01-01

    The mechanical properties of both phases in duplex stainless steel have been studied in situ using neutron diffraction during mechanical loading. Important differences in the evolution of lattice strains are observed between tests carried out in tension and compression. An elastoplastic self-consistent model is used to predict the evolution of internal stresses during loading and to identify critical resolved shear stresses and strain hardening parameters of the material. The differences between tensile and compressive behaviours of the phases are explained when the initial stresses are taken into account in model calculations. The yield stresses in each phase of the studied steel have been experimentally determined and successfully compared with the results of the elastoplastic self-consistent model

  4. Studies on the Parametric Effects of Plasma Arc Welding of 2205 Duplex Stainless Steel

    Science.gov (United States)

    Selva Bharathi, R.; Siva Shanmugam, N.; Murali Kannan, R.; Arungalai Vendan, S.

    2018-03-01

    This research study attempts to create an optimized parametric window by employing Taguchi algorithm for Plasma Arc Welding (PAW) of 2 mm thick 2205 duplex stainless steel. The parameters considered for experimentation and optimization are the welding current, welding speed and pilot arc length respectively. The experimentation involves the parameters variation and subsequently recording the depth of penetration and bead width. Welding current of 60-70 A, welding speed of 250-300 mm/min and pilot arc length of 1-2 mm are the range between which the parameters are varied. Design of experiments is used for the experimental trials. Back propagation neural network, Genetic algorithm and Taguchi techniques are used for predicting the bead width, depth of penetration and validated with experimentally achieved results which were in good agreement. Additionally, micro-structural characterizations are carried out to examine the weld quality. The extrapolation of these optimized parametric values yield enhanced weld strength with cost and time reduction.

  5. Effect of heat treatment on corrosion behavior of duplex stainless steel in orthodontic applications

    Science.gov (United States)

    Sabea Hammood, Ali; Faraj Noor, Ahmed; Talib Alkhafagy, Mohammed

    2017-12-01

    Heat treatment is necessary for duplex stainless steel (DSS) to remove or dissolve intermetallic phases, to remove segregation and to relieve any residual thermal stress in DSS, which may be formed during production processes. In the present study, the corrosion resistance of a DSS in artificial saliva was studied by potentiodynamic measurements. The microstructure was investigated by scanning electron microscopy (SEM),x-ray diffraction (XRD) and Vickers hardness (HV). The properties were tested in as-received and in thermally treated conditions (800-900 °C, 2-8 min). The research aims to evaluate the capability of DSS for orthodontic applications, in order to substitute the austenitic grades. The results indicate that the corrosion resistance is mainly affected by the ferrite/austenite ratio. The best result was obtained with a treatment at 900 °C for 2 min.

  6. Effect of friction stir welding speed on the microstructure and mechanical properties of a duplex stainless steel

    International Nuclear Information System (INIS)

    Saeid, T.; Abdollah-zadeh, A.; Assadi, H.; Malek Ghaini, F.

    2008-01-01

    The present study focuses on the effect of the welding speed on the microstructure and mechanical properties of the stir zone (SZ) in friction stir welding (FSW) of SAF 2205 duplex stainless steel. A single tool, made of a WC-base material, was used to weld 2 mm-thick plates at a constant rotational speed of 600 rpm. X-ray radiography revealed that sound welds were successfully obtained for the welding speeds in the range of 50-200 mm/min, whereas a groove-like defect was formed at the higher speed of 250 mm/min. Moreover, increasing the welding speed decreased the size of the α and γ grains in the SZ, and hence, improved the mean hardness value and the tensile strength of the SZ. These results are interpreted with respect to interplay between the welding speed and the peak temperature in FSW

  7. O6-ethylguanine carcinogenic lesions in DNA: An NMR study of O6etG·T pairing in dodecanucloetide duplexes

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Li, B.F.L.; Swann, P.F.; Patel, D.J.

    1989-01-01

    High-resolution two-dimensional NMR studies are reported on the self-complementary d-(C1-G2-C3-O 6 etG4-A5-G6-C7-T8-T9-G10-C11-G12) duplex (designated O 6 etG·T 12-mer) containing two symmetrically related O 6 etG·T lesion sites located four base pairs in from either end of the duplex. Parallel studies were undertaken on a related sequence containing O 6 meG·T lesion sites (designated O 6 meG·T 12-mer) in order to evaluate the influence of the size of the alkyl substituent on the structure of the duplex and were undertaken on a related sequence containing G·T mismatch sites (designated G·T 12-mer duplex), which served as the control duplex. The exchangeable and nonexchangeable proton and the phosphorus nuclei have been assigned from an analysis of two-dimensional nuclear Overhauser enhancement (NOE) and correlated spectra of the O 6 etG·T 12-mer, O 6 meG·T 12-mer, and G·T 12-mer duplexes in H 2 O and D 2 O solutions. The distance connectivities observed in the NOESY spectra of the O 6 alkG·T 12-mer duplexes establish that the helix is right-handed and all of the bases adopt an anti conformation of the glycosidic torsion angle including the O 6 alkG4 and T9 bases at the lesion site. These observations establish that the O 6 alkG4 and T9 residues are stacked into the duplex and that the O 6 CH 3 and O 6 CH 2 CH 3 groups of O 6 alkG4 adopt a syn orientation with respect to the N 1 of the alkylated guanine. Since the O 6 -alkyl group adopts a syn orientation, the separation between the O 6 of O 6 alkG4 and the O 4 of T9 in the major groove is increased, preventing the formation of a short hydrogen bond between the N 1 ring nitrogen of O 6 alkG4 and the imino proton of T9

  8. Mycobacterium smegmatis HelY Is an RNA-Activated ATPase/dATPase and 3'-to-5' Helicase That Unwinds 3'-Tailed RNA Duplexes and RNA:DNA Hybrids.

    Science.gov (United States)

    Uson, Maria Loressa; Ordonez, Heather; Shuman, Stewart

    2015-10-01

    Mycobacteria have a large and distinctive ensemble of DNA helicases that function in DNA replication, repair, and recombination. Little is known about the roster of RNA helicases in mycobacteria or their roles in RNA transactions. The 912-amino-acid Mycobacterium smegmatis HelY (MSMEG_3885) protein is a bacterial homolog of the Mtr4 and Ski2 helicases that regulate RNA 3' processing and turnover by the eukaryal exosome. Here we characterize HelY as an RNA-stimulated ATPase/dATPase and an ATP/dATP-dependent 3'-to-5' helicase. HelY requires a 3' single-strand RNA tail (a loading RNA strand) to displace the complementary strand of a tailed RNA:RNA or RNA:DNA duplex. The findings that HelY ATPase is unresponsive to a DNA polynucleotide cofactor and that HelY is unable to unwind a 3'-tailed duplex in which the loading strand is DNA distinguish HelY from other mycobacterial nucleoside triphosphatases/helicases characterized previously. The biochemical properties of HelY, which resemble those of Mtr4/Ski2, hint at a role for HelY in mycobacterial RNA catabolism. RNA helicases play crucial roles in transcription, RNA processing, and translation by virtue of their ability to alter RNA secondary structure or remodel RNA-protein interactions. In eukarya, the RNA helicases Mtr4 and Ski2 regulate RNA 3' resection by the exosome. Mycobacterium smegmatis HelY, a bacterial homolog of Mtr4/Ski2, is characterized here as a unidirectional helicase, powered by RNA-dependent ATP/dATP hydrolysis, that tracks 3' to 5' along a loading RNA strand to displace the complementary strand of a tailed RNA:RNA or RNA:DNA duplex. The biochemical properties of HelY suggest a role in bacterial RNA transactions. HelY homologs are present in pathogenic mycobacteria (e.g., M. tuberculosis and M. leprae) and are widely prevalent in Actinobacteria and Cyanobacteria but occur sporadically elsewhere in the bacterial domain. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  9. NMR studies of the exocyclic 1,N6-ethenodeoxyadenosine adduct (εdA) opposite thymidine in a DNA duplex. Nonplanar alignment of εdA(anti) and dT(anti) at the lesion site

    International Nuclear Information System (INIS)

    Kouchakdjian, M.; Patel, D.J.; Eisenberg, M.; Yarema, K.; Basu, A.; Essigmann, J.

    1991-01-01

    Two-dimensional proton NMR studies are reported on the complementary d(C-A-T-G-T-G-T-A-C)·d(G-T-A-C-εA-C-A-T-G) nonanucleotide duplex (designated εdA·dT 9-mer duplex) containing 1,N 6 -ethenodeoxyadenosine (εdA), a carcinogen-DNA adduct, positioned opposite thymidine in the center of the helix. The authors NMR studies have focused on the conformation of the εdA·dT 9-mer duplex at neutral pH with emphasis on defining the alignment at the dT5·εdA14 lesion site. The through-space NOE distance connectivities establish that both dT5 and εdA14 adopt anti glycosidic torsion angles, are directed into the interior of the helix, and stack with flanking Watson-Crick dG4·dC15 and dG6·dC13 pairs. Furthermore, the d(G4-T5-G6)·d(C13-εA14-C15) trinucleotide segment centered about the dT5·εdA14 lesion site adopts a right-handed helical conformation in solution. Energy minimization computations were undertaken starting from six different alignments of dT5(anti) and εdA14(anti) at the lesion site and were guided by distance constraints defined by lower and upper bounds estimated from NOESY data sets on the εdA·dT 9-mer duplex. The NMR data are consistent with a nonplanar alignment of εdA14(anti) and dT5(anti) with dT5 displaced toward the flanking dG4·dC15 base pair within the d(G4-T5-G6)·d(C13-εA14-C15) segment of the εdA·dT 9-mer duplex

  10. Effect of thermal treatments on the wear behaviour of duplex stainless steels

    International Nuclear Information System (INIS)

    Fargas, G; Mestra, A; Anglada, M; Mateo, A

    2009-01-01

    Duplex stainless steel (DSS) is a family of steels characterized by two-phase microstructure with similar percentages of ferrite (α) and austenite (γ).Their attractive combination of mechanical properties and corrosion resistance has increased its use in last decades in the marine and petrochemical industries. Nevertheless, an inappropriate heat treatment can induce the precipitation of secondary phases which affect directly their mechanical properties and corrosion resistance. There are few works dealing with the influence of heat treatments on wear behaviour of these steels in the literature. For instances, this paper aims to determine wear kinetic and sliding wear volume developed as a function of heat treatment conditions. Therefore, the samples were heat treated from 850 deg. C to 975 deg.C before sliding wear tests. These wear tests were carried out using ball on disk technique at constant sliding velocity and different sliding distances. Two methodologies were used to calculate the wear volume: weight loss and area measurement using a simplified contact model. Microstructural observations showed the presence of sigma phase for all studied conditions. The formation kinetics of this phase is faster at 875 deg. C and decrease at higher temperatures. Results related to wear showed that the hardness introduced due to the presence of sigma phase plays an important role on wear behaviour for this steel. It was observed also that wear rates decreased when increasing the percentage of sigma phase on the microstructure.

  11. SCC of 2304 Duplex Stainless Steel-Microstructure, Residual Stress and Surface Grinding Effects.

    Science.gov (United States)

    Zhou, Nian; Peng, Ru Lin; Schönning, Mikael; Pettersson, Rachel

    2017-02-23

    The influence of surface grinding and microstructure on chloride induced stress corrosion cracking (SCC) behavior of 2304 duplex stainless steel has been investigated. Grinding operations were performed both parallel and perpendicular to the rolling direction of the material. SCC tests were conducted in boiling magnesium chloride according to ASTM G36; specimens were exposed both without external loading and with varied levels of four-point bend loading. Residual stresses were measured on selected specimens before and after exposure using the X-ray diffraction technique. In addition, in-situ surface stress measurements subjected to four-point bend loading were performed to evaluate the deviation between the actual applied loading and the calculated values according to ASTM G39. Micro-cracks, initiated by grinding induced surface tensile residual stresses, were observed for all the ground specimens but not on the as-delivered surfaces. Loading transverse to the rolling direction of the material increased the susceptibility to chloride induced SCC. Grinding induced tensile residual stresses and micro-notches in the as-ground surface topography were also detrimental.

  12. SCC of 2304 Duplex Stainless Steel—Microstructure, Residual Stress and Surface Grinding Effects

    Directory of Open Access Journals (Sweden)

    Nian Zhou

    2017-02-01

    Full Text Available The influence of surface grinding and microstructure on chloride induced stress corrosion cracking (SCC behavior of 2304 duplex stainless steel has been investigated. Grinding operations were performed both parallel and perpendicular to the rolling direction of the material. SCC tests were conducted in boiling magnesium chloride according to ASTM G36; specimens were exposed both without external loading and with varied levels of four-point bend loading. Residual stresses were measured on selected specimens before and after exposure using the X-ray diffraction technique. In addition, in-situ surface stress measurements subjected to four-point bend loading were performed to evaluate the deviation between the actual applied loading and the calculated values according to ASTM G39. Micro-cracks, initiated by grinding induced surface tensile residual stresses, were observed for all the ground specimens but not on the as-delivered surfaces. Loading transverse to the rolling direction of the material increased the susceptibility to chloride induced SCC. Grinding induced tensile residual stresses and micro-notches in the as-ground surface topography were also detrimental.

  13. Effect of Mo contents on corrosion behaviors of welded duplex stainless steel

    Science.gov (United States)

    Bae, Seong Han; Lee, Hae Woo

    2013-05-01

    The corrosion behaviour and change of the phase fraction in welded 24Cr Duplex stainless steel was investigated for different chemical composition ranges of Mo contents. Filler metal was produced by fixing the contents of Cr, Ni, N, and Mn while adjusting the Mo content to 0.5, 1.4, 2.5, 3.5 wt%. The δ-ferrite fraction was observed to increase as the content of Mo increased. A polarisation test conducted in a salt solution, indicated the pitting corrosion potential increased continuously to 3.5 wt% Mo, while the corrosion potential changed most between 0.5 and 1.41 wt% Mo. The location of the pitting corrosion in 0.5 wt% Mo steel was randomly distributed, but it occurred selectively at the grain boundary between the γ- and δ-ferrite phases in 1.4, 2.5 and 3.5 wt% Mo steel. Energy dispersive X-ray spectroscopy mapping analysis showed that areas deficient in Cr, Mo, and Ni occurred around the grain boundary of the γ- and δ-ferrite phases. Non-metallic inclusions are thought to act as initiation points for the pitting corrosion that occurs in the salt solution initially as a result of the potential difference between the matrix structure and the incoherent inclusions.

  14. SCC of 2304 Duplex Stainless Steel—Microstructure, Residual Stress and Surface Grinding Effects

    Science.gov (United States)

    Zhou, Nian; Peng, Ru Lin; Schönning, Mikael; Pettersson, Rachel

    2017-01-01

    The influence of surface grinding and microstructure on chloride induced stress corrosion cracking (SCC) behavior of 2304 duplex stainless steel has been investigated. Grinding operations were performed both parallel and perpendicular to the rolling direction of the material. SCC tests were conducted in boiling magnesium chloride according to ASTM G36; specimens were exposed both without external loading and with varied levels of four-point bend loading. Residual stresses were measured on selected specimens before and after exposure using the X-ray diffraction technique. In addition, in-situ surface stress measurements subjected to four-point bend loading were performed to evaluate the deviation between the actual applied loading and the calculated values according to ASTM G39. Micro-cracks, initiated by grinding induced surface tensile residual stresses, were observed for all the ground specimens but not on the as-delivered surfaces. Loading transverse to the rolling direction of the material increased the susceptibility to chloride induced SCC. Grinding induced tensile residual stresses and micro-notches in the as-ground surface topography were also detrimental. PMID:28772582

  15. Dextranomer/hyaluronic acid endoscopic injection is effective in the treatment of intermediate and high grade vesicoureteral reflux in patients with complete duplex systems.

    Science.gov (United States)

    Hunziker, Manuela; Mohanan, Nochiparambil; Puri, Prem

    2013-05-01

    Endoscopic subureteral injection of dextranomer/hyaluronic acid has become an established alternative to long-term antibiotic prophylaxis or surgical treatment for vesicoureteral reflux. We evaluated the effectiveness of endoscopic injection of dextranomer/hyaluronic acid in intermediate and high grade vesicoureteral reflux in patients with complete duplex collecting systems. A total of 123 children underwent endoscopic correction of intermediate or high grade vesicoureteral reflux using injection of dextranomer/hyaluronic acid into complete duplex systems between 2001 and 2010. Vesicoureteral reflux was diagnosed by voiding cystourethrogram, and dimercapto-succinic acid scan was performed to evaluate the presence of renal scarring. Followup ultrasound and voiding cystourethrogram were performed 3 months after the outpatient procedure and renal ultrasound thereafter every 2 years. Mean followup was 6.7 years. Complete duplex systems were unilateral in 110 patients and bilateral in 13. Reflux severity in the 136 refluxing units was grade II in 1 (0.7%), III in 52 (38.2%), IV in 61 (44.9%) and V in 22 (16.2%). Dimercapto-succinic acid scan revealed renal functional abnormalities in 63 children (51.2%). Vesicoureteral reflux resolved after the first endoscopic injection of dextranomer/hyaluronic acid in 93 ureters (68.4%), after a second injection in 35 (25.7%) and after a third injection in 8 (5.9%). Febrile urinary tract infection developed in 5 patients (4.1%) during followup. No patient required ureteral reimplantation or experienced significant complications. Our results confirm the safety and efficacy of endoscopic injection of dextranomer/hyaluronic acid in eradicating intermediate and high grade vesicoureteral reflux in patients with complete duplex systems. We recommend this minimally invasive, 15-minute outpatient procedure as a viable option for treating intermediate and high grade vesicoureteral reflux in patients with complete duplex collecting systems

  16. Detecting deletions, insertions, and single nucleotide substitutions in cloned β-globin genes and new polymorphic nucleotide substitutions in β-globin genes in a Japanese population using ribonuclease cleavage at mismatches in RNA: DNA duplexes

    International Nuclear Information System (INIS)

    Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko.

    1990-08-01

    The applicability of ribonuclease (RNase) cleavage at mismatches in RNA:DNA duplexes (the RNase cleavage method) for determining nucleotide variant rates was examined in a Japanese population. DNA segments of various lengths obtained from four different regions of one normal and three thalassemic cloned human β-globin genes were inserted into transcription vectors. Sense and antisense RNA probes uniformly labeled with 32 P were prepared. When RNA probes of 771 nucleotides (nt) or less were hybridized with cloned DNAs and the resulting duplexes were treated with a mixture of RNases A and T1, the length of products agreed with theoretical values. Twelve possible mismatches were examined. Since both sense and antisense probes were used, uncleavable mismatches such as G:T and G:G which were made from one combination of RNA and DNA strands could be converted to the cleavable C:A and C:C mismatches, respectively, by using the opposite combination. Deletions and insertions of one (G), four(TTCT), five (ATTTT), and 10 (ATTTTATTTT) nt were easily detected. A polymorphic substitution of T to C at position 666 of the second intervening sequence (IVS2-666) of the β-globin gene was detected using genomic DNAs from cell lines established from the peripheral B lymphocytes of 59 unrelated Japanese from Hiroshima or those amplified by polymerase chain reaction (PCR). The frequency of the gene with C at the IVS2-666 (allele C) was 0.48 and that of the gene with T (allene T) was 0.52. Two new polymorphic substitutions of C to A and A to T were detected at nucleotide positions 1789 and 1945 from the capping site, respectively, using genomic DNAs amplified by PCR. We conclude that it would be feasible to use the RNase cleavage method combined with PCR for large-scale screening of variation in chromosomal DNA. (J.P.N.)

  17. Effects of benzo[a]pyrene-DNA adducts on a reconstituted replication system

    International Nuclear Information System (INIS)

    Brown, W.C.; Romano, L.J.

    1991-01-01

    The authors have used a partially reconstituted replication system consisting of T7 DNA polymerase and T7 gene 4 protein to examine the effect of benzo[a]pyrene (B[a]P) adducts on DNA synthesis and gene 4 protein activities. The gene 4 protein is required for T7 DNA replication because of its ability to act as both a primase and helicase. They show here that total synthesis decreases as the level of adducts per molecule of DNA increases, suggesting that the B[a]P adducts are blocking an aspect of the replication process. By challenging synthesis on oligonucleotide-primed B[a]P-modified DNA with unmodified DNA, they present evidence that the T7 DNA polymerase freely dissociates after encountering an adduct. Prior studies have shown that the gene 4 protein alone does not dissociate from the template during translocation upon encountering an adduct. However, when gene 4 protein primed DNA synthesis is challenged, they observe an increase in synthesis but to a lesser extent than observed on oligonucleotide-primed synthesis. Finally, they have examined DNA synthesis on duplex templates and show the B[a]P adducts inhibit synthesis by the T7 DNA polymerase and gene 4 protein to the same extent regardless of whether the adducts are positioned in the leading or lagging strand, while synthesis by the polymerase alone is inhibited only when the adducts are in the template strand

  18. Effect of Annealing Temperature on the Mechanical and Corrosion Behavior of a Newly Developed Novel Lean Duplex Stainless Steel.

    Science.gov (United States)

    Guo, Yanjun; Hu, Jincheng; Li, Jin; Jiang, Laizhu; Liu, Tianwei; Wu, Yanping

    2014-09-12

    The effect of annealing temperature (1000-1150 °C) on the microstructure evolution, mechanical properties, and pitting corrosion behavior of a newly developed novel lean duplex stainless steel with 20.53Cr-3.45Mn-2.08Ni-0.17N-0.31Mo was studied by means of optical metallographic microscopy (OMM), scanning electron microscopy (SEM), magnetic force microscopy (MFM), scanning Kelvin probe force microscopy (SKPFM), energy dispersive X-ray spectroscopy (EDS), uniaxial tensile tests (UTT), and potentiostatic critical pitting temperature (CPT). The results showed that tensile and yield strength, as well as the pitting corrosion resistance, could be degraded with annealing temperature increasing from 1000 up to 1150 °C. Meanwhile, the elongation at break reached the maximum of 52.7% after annealing at 1050 °C due to the effect of martensite transformation induced plasticity (TRIP). The localized pitting attack preferentially occurred at ferrite phase, indicating that the ferrite phase had inferior pitting corrosion resistance as compared to the austenite phase. With increasing annealing temperature, the pitting resistance equivalent number (PREN) of ferrite phase dropped, while that of the austenite phase rose. Additionally, it was found that ferrite possessed a lower Volta potential than austenite phase. Moreover, the Volta potential difference between ferrite and austenite increased with the annealing temperature, which was well consistent with the difference of PREN.

  19. Effects of nitrogen in shielding gas on microstructure evolution and localized corrosion behavior of duplex stainless steel welding joint

    Science.gov (United States)

    Zhang, Zhiqiang; Jing, Hongyang; Xu, Lianyong; Han, Yongdian; Zhao, Lei; Zhou, Chao

    2017-05-01

    The effects of nitrogen addition in shielding gas on microstructure evolution and localized corrosion behavior of duplex stainless steel (DSS) welds were studied. N2-supplemented shielding gas facilitated the primary austenite formation, suppressed the Cr2N precipitation in weld root, and increased the microhardnesses of weld metal. Furthermore, N2-supplemented shielding gas increased pitting resistance equivalent number (PREN) of austenite, but which decreased slightly PREN of ferrite. The modified double loop electrochemical potentiokinetic reactivation in 2 M H2SO4 + 1 M HCl was an effective method to study the localized corrosion of the different zones in the DSS welds. The adding 2% N2 to pure Ar shielding gas improved the localized corrosion resistance in the DSS welds, which was due to compensation for nitrogen loss and promoting nitrogen further solution in the austenite phases, suppression of the Cr2N precipitation in the weld root, and increase of primary austenite content with higher PREN than the ferrite and secondary austenite. Secondary austenite are prone to selective corrosion because of lower PREN compared with ferrite and primary austenite. Cr2N precipitation in the pure Ar shielding weld root and heat affected zone caused the pitting corrosion within the ferrite and the intergranular corrosion at the ferrite boundary. In addition, sigma and M23C6 precipitation resulted in the intergranular corrosion at the ferrite boundary.

  20. Effects of Tungsten on the Precipitation Kinetics of Secondary Phases and the Associated Susceptibility to Pitting Corrosion in Duplex Stainless Steels

    International Nuclear Information System (INIS)

    Park, Chan Jin; Kwon, Hyuk Sang

    2006-01-01

    Effects of tungsten (W) on the precipitation kinetics of secondary phases and the associated resistance to pitting corrosion of 25% Cr duplex stainless steels were investigated through microstructural and electrochemical noise analyses. With the partial substitution of W for Mo in duplex stainless steel, the potential and current noises of the alloy were significantly decreased in chloride solution due to retardation of the σ phase precipitation. The preferential precipitation of the χ phase in the W-containing alloy during the early period of aging contributed to retarding the precipitation of the σ phase by depleting W and Mo along grain boundaries. In addition, the retardation of the nucleation and growth of the σ phase in the W-containing alloy appears to be attributed to the inherently low diffusivity of W compared with that of Mo

  1. Effect of aging time on intergranular corrosion behavior of a newly developed LDX 2404 lean duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Hui [School of Materials Engineering, Shanghai University of Engineering Science, Shanghai 201620 (China); Zhang, Ziying, E-mail: zzying@sues.edu.cn [School of Materials Engineering, Shanghai University of Engineering Science, Shanghai 201620 (China); Zhang, Huizhen [School of Management, University of Shanghai for Science and Technology, Shanghai 200093 (China); Hu, Jun [School of Materials Engineering, Shanghai University of Engineering Science, Shanghai 201620 (China); Li, Jin [Department of Materials Science, Fudan University, Shanghai 200433 (China)

    2016-07-05

    The effect of aging at 700 °C for various times on the intergranular corrosion behavior of LDX 2404 duplex stainless steel is investigated by morphological observation and electrochemical detection. Scanning electronic microscopy and transmission electronic microscopy analysis reveal that Cr{sub 2}N, M{sub 23}C{sub 6} and the sigma and chi phases nucleate simultaneously at the initial stages of aging. The granular particles of sigma phase grow larger but fewer with the increase of aging time. The electrochemical detection results show that intergranular corrosion become more severe and the corrosion type evolves from intergranular corrosion into general corrosion as the holding time extends to 48 h. - Highlights: • The IGC behavior of aged LDX 2404 is investigated. • Cr{sub 2}N, M{sub 23}C{sub 6} and the σ and χ phases nucleate simultaneously at the initial stages of aging. • IGC resistance decreases with the increase of aging time. • The corrosion type evolves from IGC into general corrosion for longer aging times.

  2. Effect of Austenitic and Austeno-Ferritic Electrodes on 2205 Duplex and 316L Austenitic Stainless Steel Dissimilar Welds

    Science.gov (United States)

    Verma, Jagesvar; Taiwade, Ravindra V.

    2016-11-01

    This study addresses the effect of different types of austenitic and austeno-ferritic electrodes (E309L, E309LMo and E2209) on the relationship between weldability, microstructure, mechanical properties and corrosion resistance of shielded metal arc welded duplex/austenitic (2205/316L) stainless steel dissimilar joints using the combined techniques of optical, scanning electron microscope, energy-dispersive spectrometer and electrochemical. The results indicated that the change in electrode composition led to microstructural variations in the welds with the development of different complex phases such as vermicular ferrite, lathy ferrite, widmanstatten and intragranular austenite. Mechanical properties of welded joints were diverged based on compositions and solidification modes; it was observed that ferritic mode solidified weld dominated property wise. However, the pitting corrosion resistance of all welds showed different behavior in chloride solution; moreover, weld with E2209 was superior, whereas E309L exhibited lower resistance. Higher degree of sensitization was observed in E2209 weld, while lesser in E309L weld. Optimum ferrite content was achieved in all welds.

  3. The effect of sulphate-reducing bacteria biofilm on passivity and development of pitting on 2205 duplex stainless steel

    International Nuclear Information System (INIS)

    Dec, Weronika; Mosiałek, Michał; Socha, Robert P.; Jaworska-Kik, Marzena; Simka, Wojciech; Michalska, Joanna

    2016-01-01

    Results on biofilm formation and microbiologically influenced corrosion induced by pure D. desulfuricans strain on 2205 duplex stainless steel (DSS) are presented. Biofilm development stimulated by DSM642 standard strain was evaluated with reference to their metabolic activity and to the surface characterization including the structure and configuration of the biofilm. Electrochemical techniques (open circuit potential, electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization curves) and X-ray photoelectron spectroscopy (XPS) were carried out to determine the effect of bacteria on the passivity and corrosion resistance of 2205 DSS. The electrochemical results showed that the DSS corrosion resistance was affected in the presence of DSM642 biofilm. This statement was based on the significant decrease in the charge transfer resistance (R_1) obtained from EIS and the increase in the measured current densities obtained from potentiodynamic polarization curves. Although the breakdown potentials (E_b) were still high, SEM observations revealed micropits as well as signs of crevice attack on the steel surface. Significant sulphidation of the passive film affected the nature of cathodic behaviour of steel and helped to impede micropit growth. XPS analysis revealed the layered structure of the biofilm. Accumulation of sulphides and hydroxides was proved in the outermost layer, while the increasing contents of disulphides, organometallic and C−N bonds were detected along the biofilm thickness in the XPS analysis.

  4. Effects of the strain rate on the tensile properties of a TRIP-aided duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jeom Yong [Stainless Steel Product Group, Technical Research Laboratories, POSCO, Pohang 790-785 (Korea, Republic of); Lee, Jaeeun; Lee, Keunho; Koh, Ji-Yeon [Department of Materials Science and Engineering, RIAM, Seoul National University, Seoul 151–744 (Korea, Republic of); Cho, Jae-Hyung [Light Metal Division, Korea Institute of Materials Science, Changwon, Gyeongnam 642-831 (Korea, Republic of); Han, Heung Nam, E-mail: hnhan@snu.ac.kr [Department of Materials Science and Engineering, RIAM, Seoul National University, Seoul 151–744 (Korea, Republic of); Park, Kyung-Tae, E-mail: ktpark@hanbat.ac.kr [Department of Materials Science and Engineering, Hanbat National University, Daejeon 305-719 (Korea, Republic of)

    2016-06-01

    Factors influencing the strain-rate dependence of the tensile properties of TRIP-aided lean duplex stainless steel were investigated by employing several characterization techniques of EBSD, TEM, and nanoindentation. The steel exhibited excellent tensile strength over 800 MPa and elongation, which exceeded 70% at a strain rate of 10{sup −3} s{sup −1} due to strain-induced martensitic transformation (SIMT), but both values decreased considerably with an increase in the strain rate. The hardness and the maximum shear stress for dislocation nucleation of the austenite were found to be higher than those of the ferrite by sub-grain scale nanoindentation tests. As a result, strain partitioning to the ferrite rather than the austenite was more significant from an early stage of deformation, suppressing the SIMT in the austenite. An EBSD strain analysis on the intra- and inter-grain scale revealed that this strain partitioning became more pronounced as the strain rate increased. Adiabatic heating, which induces austenite stabilization, also became more significant as the strain rate increased. Therefore, the present results indicate that the diminishing TRIP effects at high strain rates can be attributed to preferential strain partitioning to the soft ferrite phase from an early stage of deformation, as well as adiabatic heating.

  5. Effects of Rare Earth Metal addition on the cavitation erosion-corrosion resistance of super duplex stainless steels

    Science.gov (United States)

    Shim, Sung-Ik; Park, Yong-Soo; Kim, Soon-Tae; Song, Chi-Bok

    2002-05-01

    Austenitic stainless steels such as AISI 316L have been used in equipment in which fluid flows at high speeds which can induce cavitation erosion on metallic surfaces due to the collapse of cavities, where the collapse is caused by the sudden change of local pressure within the liquid. Usually AISI 316L is susceptible to cavitation erosion. This research focuses on developing a better material to replace the AISI 316L used in equipment with high speed fluid flow, such as impellers. The effects of Rare Earth Metal (REM) additions on the cavitation erosion-corrosion resistance of duplex stainless steels were studied using metallographic examination, the potentiodynamic anodic polarization test, the tensile test, the X-ray diffraction test and the ultrasonic cavitation erosion test. The experimental alloys were found to have superior mechanical properties due to interstitial solid solution strengthening, by adding high nitrogen (0.4%), as well as by the refinement of phases and grains induced by fine REM oxides and oxy-sulfides. Corrosion resistance decreases in a gentle gradient as the REM content increases. However, REM containing alloys show superior corrosion resistance compared with that of other commercial alloys (SAF 2507, AISI 316L). Owing to their excellent mechanical properties and corrosion resistance, the alloys containing REM have high cavitation erosion-corrosion resistance.

  6. Effects of Rare Earth Metals addition and aging treatment on the corrosion resistance and mechanical properties of super duplex stainless steels

    Science.gov (United States)

    Park, Yong-Soo; Kim, Soon-Tae; Lee, In-Sung; Song, Chi-Bok

    2002-05-01

    Effects of rare earth metals addition and aging treatment on corrosion resistance and mechanical properties of super duplex stainless steels were investigated using optical/SEM/TEM metallographic examination, an X-ray diffraction test, a potentiodynamic anodic polarization test and a tensile test. The performance of the experimental alloy with 0.32% REM addition was compared with commercial super duplex stainless steel such as SAF 2507 when they were exposed to solution annealing heat treatment and aging treatment. The corrosion resistance in Cl- environments and mechanical properties of the experimental alloy were found superior to those of the commercial duplex stainless steel. The REM with larger atomic radii than those of Cr, Mo and W may fill vacancies inside the matrix and around the grain boundaries, retarding formation of harmful intermetallic σ and η phases. In addition, fine REM oxides/oxy-sulfides (1-3 μm) seemed to enhance the retardation effects. With REM additions, strength and ductility increased due to the phase and grain refinement caused by fine REM oxides and oxy-sulfides.

  7. A study on the effect of solution heat treatment on the corrosion resistance of super duplex stainless steels

    International Nuclear Information System (INIS)

    Park, Jee Yong; Park, Yong Soo; Kim, Soon Tae

    2001-01-01

    High temperature solution heat treatment(typically higher than 1100 .deg. C) is known generally to reduces the resistance to localized corrosion on super duplex stainless. This is attributed to the formation of zone depleted of alloying elements. In this study, the corrosion properties were investigated on super duplex stainless steels with various solution heat treatments. The corrosion resistance of these steels was evaluated in terms of critical pitting temperature and cyclic potentiodynamic polarization test. Chemical composition of the austenite and ferrite phases were analyzed by SEM-EDS. The following results were obtained. (1) By conducting furnace cooling, critical pitting temperature and repassivation potential increased. (2) By omitting furnace cooling, solution heat treatment produced Cr and Mo depleted zone in the phase boundary. (3) During furnace cooling, Cr and Mo rediffused through the phase boundary. This increased the corrosion resistance of super duplex stainless steels

  8. Structural Properties of G,T-Parallel Duplexes

    Directory of Open Access Journals (Sweden)

    Anna Aviñó

    2010-01-01

    Full Text Available The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.

  9. Effect of W substitution for Mo on stress corrosion cracking behavior of 25Cr-7Ni duplex stainless steel

    International Nuclear Information System (INIS)

    Ha, Tae Hong; Kim, Kyoo Young

    1998-01-01

    The effect of W substitution for Mo in duplex stainless steel (DSS) was investigated with respect to microstructure and stress corrosion cracking behavior. Homogenizing treatment was performed at 1100.deg.C for 10 minutes, while aging treatment was performed at 900.deg.C with different holding times. In homogenized condition, regardless of W substitution, all the specimens had the nearly equal volume-ratio of ferrite and austenite, and had no secondary phase precipitation. On aging, the W modification on suppression of secondary phase precipitation was very effective. Total amount of secondary phase precipitates was greatly reduced in the W-modified DSS in the early stage of the ageing treatment comparing to the commercial grade DSS without W modification. However, this effect was reduced rapidly as the aging time increased. Stress corrosion cracking(SCC) was examined in boil-ing 42% MgCl 2 solution by slow strain rate test(SSRT) and constant load test (CLT). Under the homogenized condition, the beneficial effect of W was clearly observed at the low applied stress levels where the electrochemical action plays a dominant role. In the commercial grade DSS without W modification, the crack propagated in a trans-phase mode,whereas in the W-modified DSS, the crack propagated in a mixed mode of trans-phase and inter-phase due to barrier effect of austenite phase against crack growth. Under the aged condition, the signification improvement in SCC resistance of the aged DSS specimens with W modification resulted from increase in toughness due to a relatively small amount of the brittle secondary phase precipitates. However, the cracks propagated in a trans-phase mode in the DSS specimens regardless of W modification

  10. Microstructural Characterization and the Effect of Phase Transformations on Toughness of the UNS S31803 Duplex Stainless Steel Aged Treated at 850 °C

    Directory of Open Access Journals (Sweden)

    Zucato Igor

    2002-01-01

    Full Text Available Duplex stainless steels, with ferritic-austenitic microstructure, have excellent mechanical properties and corrosion resistance. However, when duplex stainless steels are exposed to temperatures between 600 and 1000 °C, some phase transformations can occur such as chromium nitrides precipitation, chromium carbides precipitation and the sigma phase formation. The formation of such compounds leads to loss in both corrosion resistance and fracture toughness. The negative effects of the formation of chromium nitrides, carbides and the sigma phase are due to the chromium depletion in the matrix. The phase transformations cited above occur initially at ferritic-austenitic interfaces and at the grain boundaries. The aim of this work is to identify and characterize the phase transformations, which occur when aging heat treatments are carried out at temperatures at which the kinetics is the fastest for the reactions mentioned. At first, the samples were annealed at 1100 °C for 40 min. The aging heat treatments were then carried out at 850 °C for 6, 40 e 600 min. Microstructural characterization was done by using optical microscopy with different etchings, in order to identify each phase formed in the duplex stainless steel during aging heat treatments. The toughness was also evaluated by using Charpy impact test. Impact tests show that loss of toughness was related to phase transformations.

  11. Microstructural evolution during aging at 800 °C and its effect on the magnetic behavior of UNS S32304 lean duplex stainless steel

    International Nuclear Information System (INIS)

    Dille, J.; Areiza, M.C.L.; Tavares, S.S.M.; Pereira, G.R.; De Almeida, L.H.; Rebello, J.M.A.

    2017-01-01

    Duplex stainless steels are high strength and corrosion resistant alloys extensively used in chemical and petrochemical industries. However, exposition to temperatures in the range 300–1000 °C leads to precipitation of different phases having a detrimental effect on the mechanical properties and on the corrosion resistance of the alloy. In this work, the microstructural evolution during aging of a UNS S32304 lean duplex stainless steel was investigated by scanning electron microscopy, transmission electron microscopy and magnetic force microscopy. Formation of secondary austenite as well as Cr_2N and Cr_2_3C_6 precipitation and, consequently, a decrease of ferrite volume fraction were observed. EDX analysis indicated that secondary austenite is depleted in chromium which is detrimental to the corrosion resistance of the alloy. A variation of magnetic properties and Eddy current measurement parameters during aging was simultaneously detected and can be explained by the decrease of ferrite volume content. Therefore, Eddy current non-destructive testing can be successfully applied to detect the formation of deleterious phases during aging. - Highlights: • Aging of UNS S32304 lean duplex stainless steel at 800 °C is investigated. • STEM reveals formation of Cr-depleted secondary austenite and precipitation of Cr_2_3C_6 and Cr_2N. • Microstructural transformation occurs only during the first 30 min of aging. • Microstructural evolution during aging is correlated to magnetic properties evolution. • Eddy current testing permits to survey the formation of deleterious secondary austenite.

  12. A Location-Based Duplex Scheme for Cost Effective Rural Broadband Connectivity Using IEEE 802.22 Cognitive Radio Based Wireless Regional Area Networks

    Science.gov (United States)

    Kalidoss, R.; Bhagyaveni, M. A.; Vishvaksenan, K. S.

    2014-08-01

    The search for a method of utilizing the scarce spectrum in an efficient manner is an active area of research in both academic and industrial communities. IEEE 802.22 is a standard for wireless regional area network (WRAN) based on cognitive radio (CR) that operates over underutilized portions of TV bands (54-862 MHz). Time division duplex (TDD)-based WRAN cells have such advantages as dynamic traffic allocation, traffic asymmetry to users and ease of spectrum allocation. However, these cells suffer from severe cross time slot (CTS) interference when the frames of the cells are not synchronized with adjacent WRAN cells. In this paper, we evaluate the location-based duplex (LBD) scheme for eliminating the CTS interference. The proposed LBD system is much more flexible and efficient in providing asymmetric data service and eliminating CTS interference by exploiting the advantages of both TDD and frequency division duplex (FDD) schemes. We also compare the performance of LBD systems with virtual cell concepts. Furthermore, our simulation results reveal that LBD-based systems outperform the virtual cell approach in terms of the low signal-to-interference (SIR) ratio requirement by mitigating the effects of CTS.

  13. Thermodynamic and hydration effects for the incorporation of a cationic 3-aminopropyl chain into DNA

    Science.gov (United States)

    Soto, Ana Maria; Kankia, Besik I.; Dande, Prasad; Gold, Barry; Marky, Luis A.

    2002-01-01

    The introduction of cationic 5-(ω-aminoalkyl)-2′-deoxypyrimidines into duplex DNA has been shown to induce DNA bending. In order to understand the energetic and hydration contributions for the incorporation of a cationic side chain in DNA a combination of spectroscopy, calorimetry and density techniques were used. Specifically, the temperature unfolding and isothermal formation was studied for a pair of duplexes with sequence d(CGTAGUCG TGC)/d(GCACGACTACG), where U represents 2′-deoxyuridine (‘control’) or 5-(3-aminopropyl)-2′-deoxyuridine (‘modified’). Continuous variation experiments confirmed 1:1 stoichiometries for each duplex and the circular dichroism spectra show that both duplexes adopted the B conformation. UV and differential scanning calorimetry melting experiments reveal that each duplex unfolds in two-state transitions. In low salt buffer, the ‘modified’ duplex is more stable and unfolds with a lower endothermic heat and lower release of counterion and water. This electrostatic stabilization is entropy driven and disappears at higher salt concentrations. Complete thermodynamic profiles at 15°C show that the favorable formation of each duplex results from the compensation of a favorable exothermic heat with an unfavorable entropy contribution. However, the isothermal profiles yielded a differential enthalpy of 8.8 kcal/mol, which is 4.3 kcal/mol higher than the differential enthalpy observed in the unfolding profiles. This indicates that the presence of the aminopropyl chain induces an increase in base stacking interactions in the modified single strand and a decrease in base stacking interactions in the modified duplex. Furthermore, the formation of the ‘control’ duplex releases water while the ‘modified’ duplex takes up water. Relative to the control duplex, formation of the modified duplex at 15°C yielded a marginal differential ΔG° term, positive ΔΔHITC–Δ(TΔS) compensation, negative ΔΔV and a net release of

  14. Effect of local information within network layers on the evolution of cooperation in duplex public goods games

    International Nuclear Information System (INIS)

    Zhou, Yifeng; Zheng, Xiaoming; Wu, Weiwei

    2015-01-01

    Traditional works of public goods game (PGG) are often studied in simplex networks where agents play games through the same type of social interactions. In order to promote cooperation against the defection in PGGs in simplex network environment, many mechanisms have been proposed from different perspectives, such as the volunteering mechanisms, and the punishment and reward approaches. However, due to diverse types of interactions between agents in reality, the study of PGG should also consider the characteristic of multiplexity of networks. Hence, we firstly model the public goods game in the duplex network (for simplification of analysis, the duplex network is considered), in which agents have two types of social interactions, and thus the network is modeled as two network layers. This type of PGG is naturally named as duplex public goods game (D-PGG), in which agents can select one of the network layers to allocate their limited resources. Then for the new game environment (D-PGG), we propose a novel perspective to promote cooperation: degrading the information integrity, i.e., agents get information just from one network layer (local information) rather than from the whole duplex network (global information) in the evolution process. Finally, through theoretical analyses and simulations, we find that if agents imitate based on the local information of the payoff in the evolution, cooperation can be generally promoted; and the extent of promotion depends on both the network structure and the similarity of the network layers

  15. Enantiospecific kinking of DNA by a partially intercalating metal complex

    KAUST Repository

    Reymer, Anna

    2012-01-01

    Opposite enantiomers of [Ru(phenanthroline) 3] 2+ affect the persistence length of DNA differently, a long speculated effect of helix kinking. Our molecular dynamics simulations confirm a substantial change of duplex secondary structure produced by wedge-intercalation of one but not the other enantiomer. This effect is exploited by several classes of DNA operative proteins. © The Royal Society of Chemistry 2012.

  16. Development of duplex real-time PCR for the detection of WSSV and PstDV1 in cultivated shrimp.

    Science.gov (United States)

    Leal, Carlos A G; Carvalho, Alex F; Leite, Rômulo C; Figueiredo, Henrique C P

    2014-07-05

    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. 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. The standardized duplex qPCR was shown to be a robust, highly sensitive, and feasible diagnostic tool for the simultaneous detection of the

  17. Effect of ageing on phase evolution and mechanical properties of a high tungsten super-duplex stainless steel

    International Nuclear Information System (INIS)

    Akisanya, Alfred R.; Obi, Udoka; Renton, Neill C.

    2012-01-01

    Highlights: ► Secondary phases precipitate in a high tungsten SDSS aged between 700 and 900 °C. ► The volume fraction of the sigma phase increases as the holding time increases. ► The evolution of the sigma phase agrees with Johnson–Mehl–Avrami kinetic model. ► The secondary phases enhance the Young's modulus, hardness and strength. ► The ductility decreased significantly with increasing amount of sigma phase. - Abstract: The effect of ageing temperature and holding time on the precipitation of secondary phases and the mechanical properties of a 25Cr–6.7Ni–0.32N–3.0Mo–2.5W super duplex stainless steel is examined. The ageing temperature was varied from 600 to 900 °C and the holding time was varied from 1 to 240 min. Two types of Cr and Mo enriched intermetallic phases, sigma (σ) and chi (χ), were found to precipitate preferentially at the ferrite/austenite interface and within the ferrite grain. The precipitation of the χ-phase occurred preferentially before the σ-phase. The concentration of these secondary phases, which was quantified by a combination of microscopy and image analysis, increases with increasing ageing temperature and holding time, leading to significant reduction in the uniform strain and enhancement of the modulus, hardness and yield and tensile strengths. The measured concentration of the precipitated sigma phase is in agreement with the prediction by the Johnson–Mehl–Avrami kinetic model.

  18. Vesicoureteral Reflux and Duplex Systems

    OpenAIRE

    Thomas, John C.

    2008-01-01

    Vesicoureteral reflux (VUR) is the most common anomaly associated with duplex systems. In addition to an uncomplicated duplex system, reflux can also be secondary in the presence of an ectopic ureterocele with duplex systems. Controversy exists in regard to the initial and most definitive management of these anomalies when they coexist. This paper will highlight what is currently known about duplex systems and VUR, and will attempt to provide evidence supporting the various surgical approa...

  19. Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers.

    Science.gov (United States)

    Iadevaia, Giulia; Núñez-Villanueva, Diego; Stross, Alexander E; Hunter, Christopher A

    2018-06-06

    Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.

  20. Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.

    Science.gov (United States)

    Copp, William; Denisov, Alexey Y; Xie, Jingwei; Noronha, Anne M; Liczner, Christopher; Safaee, Nozhat; Wilds, Christopher J; Gehring, Kalle

    2017-09-29

    Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2'-deoxyribose, 2'-O-methyl-ribose, 2'-deoxy-2'-fluoro-ribose, arabinose and 2'-deoxy-2'-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2' modifications gave a variety of effects. Arabinose and 2'-deoxy-2'-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2'-O-methyl and 2'-deoxy-2'-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    Science.gov (United States)

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

    2016-01-01

    Abstract 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

  2. Increased Y-chromosome detection by SRY duplexing

    DEFF Research Database (Denmark)

    Hansen, Morten Høgh; Clausen, Frederik Banch; Dziegiel, Morten Hanefeld

    2012-01-01

    Determining fetal sex noninvasively is dependent of a robust assay. We designed a novel SRY assay and combined it with a SRY assay from literature forming a duplex assay with the same fluorescent dye to increase detection of Y-chromosome at low cell-free fetal DNA or chimeric DNA concentrations....

  3. Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins

    DEFF Research Database (Denmark)

    Kushon, S A; Jordan, J P; Seifert, J L

    2001-01-01

    The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using absorbance hypochromicity (ABS), circular dichroism (CD), and a colorimetric assay for PNA/DNA duplex detection. These results indicate that both stable PNA...... structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic...

  4. Effect of Multipass Friction Stir Processing on Mechanical and Corrosion Behavior of 2507 Super Duplex Stainless Steel

    Science.gov (United States)

    Mishra, M. K.; Gunasekaran, G.; Rao, A. G.; Kashyap, B. P.; Prabhu, N.

    2017-02-01

    The microstructure, mechanical properties, and corrosion behavior of 2507 super duplex stainless steel after multipass friction stir processing (FSP) were examined. A significant refinement in grain size of both ferrite and austenite was observed in stir zone resulting in improved yield and tensile strength. Electrochemical impedance spectroscopy and anodic polarization studies in 3.5 wt.% NaCl solution showed nobler corrosion characteristics with increasing number of FSP passes. This was evident from the decrease in corrosion current density, decrease in passive current density, and increase in polarization resistance. Also, the decrease in density of defects, based on Mott-Schottky analysis, further confirms the improvement in corrosion resistance of 2507 super duplex stainless steel after multipass FSP.

  5. Measuring secondary phases in duplex stainless steels

    Science.gov (United States)

    Calliari, I.; Brunelli, K.; Dabalà, M.; Ramous, E.

    2009-01-01

    The use of duplex stainless steels is limited by their susceptibility to the formation of dangerous intermetallic phases resulting in detrimental effects on impact toughness and corrosion resistance. This precipitation and the quantitative determinations of the phases have received considerable attention and different precipitation sequences (σ phase, χ phase, and carbides) have been suggested. This study investigates the phase transformation during continuous cooling and isothermal treatments in commercial duplex stainless steel grades and the effects on alloy properties, and compares the most common techniques of analysis.

  6. The Duplex Society.

    Science.gov (United States)

    Schorr, Alvin L.

    1984-01-01

    The duplex society, in which the poor live in close proximity to others but in a separate compartment, is already with us. Unless something deeply changes about family income, more than one-third of future generations will come to adulthood having spent a portion of their childhood in official poverty. (RM)

  7. Duplex tab exhaust nozzle

    Science.gov (United States)

    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.

  8. Considerations in Duplex Investment.

    Science.gov (United States)

    Wright, Arthur; Goen, Tom

    Problems of duplex investment are noted in the introduction to this booklet designed to provide a technique by which the investment decision can be approached, develop estimates of typical costs and returns under differing conditions, and encourage investors to analyze objectives and conditions before the decision to buy or build is made. A…

  9. Effect of seven Indian plant extracts on Fenton reaction-mediated damage to DNA constituents.

    Science.gov (United States)

    Kar, Indrani; Chattopadhyaya, Rajagopal

    2017-11-01

    The influences of substoichiometric amounts of seven plant extracts in the Fenton reaction-mediated damage to deoxynucleosides, deoxynucleoside monophosphates, deoxynucleoside triphosphates, and supercoiled plasmid DNA were studied to rationalize anticancer properties reported in some of these extracts. Extracts from Acacia catechu, Emblica officinalis, Spondias dulcis, Terminalia belerica, Terminalia chebula, as well as gallic acid, epicatechin, chebulagic acid and chebulinic acid enhance the extent of damage in Fenton reactions with all monomeric substrates but protect supercoiled plasmid DNA, compared to standard Fenton reactions. The damage to pyrimidine nucleosides/nucleotides is enhanced by these extracts and compounds to a greater extent than for purine ones in a concentration dependent manner. Dolichos biflorus and Hemidesmus indicus extracts generally do not show this enhancement for the monomeric substrates though they protect plasmid DNA. Compared to standard Fenton reactions for deoxynucleosides with ethanol, the presence of these five plant extracts render ethanol scavenging less effective as the radical is generated in the vicinity of the target. Since substoichiometric amounts of these extracts and the four compounds produce this effect, a catalytic mechanism involving the presence of a ternary complex of the nucleoside/nucleotide substrate, a plant compound and the hydroxyl radical is proposed. Such a mechanism cannot operate for plasmid DNA as the planar rings in the extract compounds cannot stack with the duplex DNA bases. These plant extracts, by enhancing Fenton reaction-mediated damage to deoxynucleoside triphosphates, slow down DNA replication in rapidly dividing cancer cells, thus contributing to their anticancer properties.

  10. O6-ethylguanine carcinogenic lesions in DNA: An NMR study of O6etG·C pairing in dodecanucleotide duplexes

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Li, B.F.L.; Swann, P.F.; Patel, D.J.

    1989-01-01

    The pairing of O 6 etG with C located four base pairs in from either end of the self-complementary d(C1-G2-C3-O 6 etG4-A5-G6-C7-T8-C9-G10-C11-G12) duplex (designated O 6 etG·C 12-mer) has been investigated from an analysis of proton and phosphorus two-dimensional NMR experiments. The structural consequences of increasing the alkyl group size were elucidated from a comparative study of the pairing of O 6 meG4 with C9 in a related sequence (designated O 6 meG·C 12-mer). The NMR parameters for both O 6 alkG-containing dodecanucleotides are also compared with those of the control sequence containing G4·C9 base pairs (designated G·C 12-mer). The NOE cross-peaks detected in the two-dimensional NOESY spectra of the O 6 alkG·C 12-mer duplexes in H 2 O solution establish that the O 6 etG4/O 6 meG4 and C9 bases at the lesion site stack into the helix between the flanking C3·G10 and A5·T8 Watson-Crick base pairs. The observed NOEs between the amino protons of C9 and the CH 3 protons of O 6 alkG4 establish a syn orientation of the O 6 -alkyl group with respect to the N 1 of alkylated guanine. A wobble alignment of the O 6 alkG4·C9 base pair stabilized by two hydrogen bonds, one between the amino group of C9 and N 1 of O 6 alkG and the other between the amino group of O 6 alkG and N 3 of C9, is tentatively proposed on the basis of the NOEs between the amino protons of C9 at the lesion site and the imino protons of flanking Watson-Crick base pairs

  11. Microstructural evolution during aging at 800 °C and its effect on the magnetic behavior of UNS S32304 lean duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Dille, J., E-mail: jdille@metalmat.ufrj.br [Metallurgical and Materials Engineering, COPPE - Federal University of Rio de Janeiro Cidade Universitária, Centro de Tecnologia, Bloco F, CEP 21941-914 Rio de Janeiro (Brazil); Areiza, M.C.L. [Laboratory of Nondestructive Testing, Corrosion and Welding, Department of Metallurgical and Materials Engineering, Federal University of Rio of Janeiro, CEP 21941-596 (Brazil); Tavares, S.S.M. [Universidade Federal Fluminense – Departamento de Engenharia Mecânica, Rua Passo da Pátria, 156, CEP 24210-240 Niterói (Brazil); Pereira, G.R.; De Almeida, L.H.; Rebello, J.M.A. [Metallurgical and Materials Engineering, COPPE - Federal University of Rio de Janeiro Cidade Universitária, Centro de Tecnologia, Bloco F, CEP 21941-914 Rio de Janeiro (Brazil)

    2017-03-15

    Duplex stainless steels are high strength and corrosion resistant alloys extensively used in chemical and petrochemical industries. However, exposition to temperatures in the range 300–1000 °C leads to precipitation of different phases having a detrimental effect on the mechanical properties and on the corrosion resistance of the alloy. In this work, the microstructural evolution during aging of a UNS S32304 lean duplex stainless steel was investigated by scanning electron microscopy, transmission electron microscopy and magnetic force microscopy. Formation of secondary austenite as well as Cr{sub 2}N and Cr{sub 23}C{sub 6} precipitation and, consequently, a decrease of ferrite volume fraction were observed. EDX analysis indicated that secondary austenite is depleted in chromium which is detrimental to the corrosion resistance of the alloy. A variation of magnetic properties and Eddy current measurement parameters during aging was simultaneously detected and can be explained by the decrease of ferrite volume content. Therefore, Eddy current non-destructive testing can be successfully applied to detect the formation of deleterious phases during aging. - Highlights: • Aging of UNS S32304 lean duplex stainless steel at 800 °C is investigated. • STEM reveals formation of Cr-depleted secondary austenite and precipitation of Cr{sub 23}C{sub 6} and Cr{sub 2}N. • Microstructural transformation occurs only during the first 30 min of aging. • Microstructural evolution during aging is correlated to magnetic properties evolution. • Eddy current testing permits to survey the formation of deleterious secondary austenite.

  12. Next-generation bis-locked nucleic acids with stacking linker and 2'-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes

    DEFF Research Database (Denmark)

    Geny, Sylvain; Moreno, Pedro M D; Krzywkowski, Tomasz

    2016-01-01

    Targeting and invading double-stranded DNA with synthetic oligonucleotides under physiological conditions remain a challenge. Bis-locked nucleic acids (bisLNAs) are clamp-forming oligonucleotides able to invade into supercoiled DNA via combined Hoogsteen and Watson-Crick binding. To improve the b...

  13. Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2-or 4-pyrenyl-functionalized O2 '-alkylated RNA monomers

    DEFF Research Database (Denmark)

    Karmakar, Saswata; Madsen, Andreas Stahl; Guenther, Dale C.

    2014-01-01

    '-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...

  14. Effects of radiation on DNA

    International Nuclear Information System (INIS)

    Medina, V.F.O.

    1978-01-01

    Irradiation has been shown to depress DNA (deoxyribonucleic acid) synthesis resulting in deficient DNA synthesis. In one experiment, Hela S 3 cells completed the next division after a dose of 500 rads to 200 kw X-rays. Another experiment showed that the amount of DNA synthesized was dependent on the stage in the generation cycle at which the cells are irradiated (Giffites and Tolmach, 1975). DNA synthesis was measured by radioactive thymidine incorporation. The smallest deficiency (20-35%) after a dose of 500 rad X-ray was observed in Hela S 3 cells irradiated in early G 1 or early G 2 , while the greatest deficiency (55-70*) after 500 rad X-ray was found in cells irradiated at mitosis or at the Gsub(1)/S transition. Using velocity sedimentation in alkaline gradients of the DNA from hamster, Elkind, et al 1972, studied repair processes as a function of X-ray dose. DNA containing material released by alkaline lysis was found initially contained in a complex-containing lipid, the sedimentation of which was anomalous relative to denatured RNA from unirradated cells. Doses of X-rays small enough to be in the range that permits high survival (100-800 rads) speed the resolution of single-stranded DNA from this DNA complex, giving rise to a species having a number average molecular weight of 2 x 10 8 daltons. Larger doses greater than 1000 to 2000 rads resulted in a degradation of these DNA strands. Incubation after irradiation resulted in the rapid repair of damage, although the rate of repair of damage to the complex resulted in a reassociation of lipid and DNA. This evidence supports the possibility that a large DNA-membrane structure is a principal target of radiation

  15. Effect of Dynamic Reheating Induced by Weaving on the Microstructure of GTAW Weld Metal of 25% Cr Super Duplex Stainless Steel Weld Metal

    Directory of Open Access Journals (Sweden)

    Hee-Joon Sung

    2017-11-01

    Full Text Available The importance of the additional growth and/or transformation of the austenite phase that occurs in weld metals of super duplex stainless steel upon reheating is known. However, the effects have not been fully investigated, especially with respect to reheating induced by weaving during single-pass welding. In this work, bead-on-pipe gas tungsten arc welding (GTAW was conducted on super duplex stainless steel to understand the effect of weaving on the microstructure of weld metal. Microstructural analysis, electron backscatter diffraction (EBSD, and focused ion beam transmission electron microscopy (FIB-TEM were carried out to investigate the relationship between weaving and microstructural change. The weaving of GTAW produced a dynamic reheated area just before the weld bead during welding. It was revealed that extensive reheated weld existed even after one welding pass, and that the content of the austenite phase in the reheated area was higher than that in the non-reheated area, indicating the existence of a large quantity of intragranular austenite phase. In addition, the Cr2N content in the reheated area was lower than that in the non-reheated area. This reduction of Cr2N was closely related to the reheating resulting from weaving. TEM analysis revealed that Cr2N in the non-reheated area was dispersed following heating and transformed to secondary austenite.

  16. Effects of sulfur addition on pitting corrosion and machinability behavior of super duplex stainless steel containing rare earth metals: Part 2

    International Nuclear Information System (INIS)

    Jeon, Soon-Hyeok; Kim, Soon-Tae; Lee, In-Sung; Park, Yong-Soo

    2010-01-01

    Research highlights: → The mechanisms on the effects of rare earth metals (REM) and sulfur (S) additions on the initiation and propagation of pitting corrosion and machinabillity of a super duplex stainless steel (SDSS) were elucidated → It was found that, in consideration of the ratio of lifetime (the resistance to pitting corrosion) to cost (machining and raw material), a costly austenitic stainless steel with high Ni , medium Mo and low N can be replaced by the high S and REM added SDSS with 7 wt.% Ni-4 wt% Mo-0.3 wt.% N → The resistance to pitting corrosion of the tested super duplex stainless steel was affected by the type of inclusions, the preferential interface areas between inclusions and the substrate, and the PREN difference between the γ-phase and the α-phase for the initiation and propagation of the pitting corrosion. - Abstract: To elucidate the effects of sulfur addition on pitting corrosion and machinability behavior of alloys containing rare earth metals, a potentiostatic polarization test, a critical pitting temperature test, a SEM-EDS analysis of inclusions, and a tool life test were conducted. As sulfur content increased, the resistance to pitting corrosion decreased due to the formation of numerous manganese sulfides deteriorating the corrosion resistance and an increase in the preferential interface areas for the initiation of the pitting corrosion. With an increase in sulfur content, the tool life increased due to the lubricating films of manganese sulfides adhering to tool surface.

  17. Effect of annealing treatment on microstructure evolution and the associated corrosion behavior of a super-duplex stainless steel

    International Nuclear Information System (INIS)

    Deng, B.; Jiang, Y.M.; Gao, J.; Li, J.

    2010-01-01

    The influence of annealing temperature on the pitting corrosion of a super-duplex stainless steel (SDSS) with mischmetal addition was investigated in chloride solution by critical pitting temperature (CPT) measurement. The corrosion behavior is strongly dependent on the microstructure, namely the presence of secondary phases, elemental partitioning behavior and volume fractions of ferrite and austenite. Based on CPT results and alloying rules, the optimal annealing temperature is determined as 1070 o C and a guideline for further development of improved SDSS is formulated.

  18. Effect of aging on impact properties of ASTM A890 Grade 1C super duplex stainless steel

    International Nuclear Information System (INIS)

    Martins, Marcelo; Forti, Leonardo Rodrigues Nogueira

    2008-01-01

    Super duplex stainless steels in the solution annealed condition are thermodynamically metastable systems which, when exposed to heat, present a strong tendency to 'seek' the most favorable thermodynamic condition. The main purpose of this study was to characterize the microstructure of a super duplex stainless steel in the as cast and solution annealed conditions, and to determine the influence of aging heat treatments on its impact strength, based on Charpy impact tests applied to V-notched test specimens. The sigma phase was found to begin precipitating at heat treatment temperatures above 760 deg. C and to dissolve completely only above 1040 deg. C, with the highest peak concentration of this phase appearing at close to 850 deg. C. Heat treatments conducted at temperatures of 580 deg. C to 740 deg. C led to a reduction of the energy absorbed in the Charpy impact test in response to the precipitation of a particulate phase with particle sizes ranging from 0.5 μm to 1.0 μm, with a chromium and iron-rich chemical composition

  19. LET-effects in DNA

    International Nuclear Information System (INIS)

    Kraft, G.; Taucher-Scholz, G.; Heilmann, J.

    1994-11-01

    In this contribution, an introductory view on the physical properties of ions is given and the cellular response to high LET radiation is summarized. Then the measurements of strand break induction of DNA in solution and in intracellular DNA are reported and compared to cell survival. The possibility of changes in the quality of the lesions is discussed and finally the present status of model calculations in comparison to the experiments is given. (orig./HSI)

  20. Detection and differentiation of wild-type and vaccine strains of canine distemper virus by a duplex reverse transcription polymerase chain reaction.

    Science.gov (United States)

    Dong, X Y; Li, W H; Zhu, J L; Liu, W J; Zhao, M Q; Luo, Y W; Chen, J D

    2015-01-01

    Canine distemper virus (CDV) is the cause of canine distemper (CD) which is a severe and highly contagious disease in dogs. In the present study, a duplex reverse transcription polymerase chain reaction (RT-PCR) method was developed for the detection and differentiation of wild-type and vaccine strains of CDV. Four primers were designed to detect and discriminate the two viruses by generating 638- and 781-bp cDNA products, respectively. Furthermore, the duplex RT-PCR method was used to detect 67 field samples suspected of CD from Guangdong province in China. Results showed that, 33 samples were to be wild-type-like. The duplex RT-PCR method exhibited high specificity and sensitivity which could be used to effectively detect and differentiate wild-type and vaccine CDV, indicating its use for clinical detection and epidemiological surveillance.

  1. C-5 Propynyl Modifications Enhance the Mechanical Stability of DNA.

    Science.gov (United States)

    Aschenbrenner, Daniela; Baumann, Fabian; Milles, Lukas F; Pippig, Diana A; Gaub, Hermann E

    2015-07-20

    Increased thermal or mechanical stability of DNA duplexes is desired for many applications in nanotechnology or -medicine where DNA is used as a programmable building block. Modifications of pyrimidine bases are known to enhance thermal stability and have the advantage of standard base-pairing and easy integration during chemical DNA synthesis. Through single-molecule force spectroscopy experiments with atomic force microscopy and the molecular force assay we investigated the effect of pyrimidines harboring C-5 propynyl modifications on the mechanical stability of double-stranded DNA. Utilizing these complementary techniques, we show that propynyl bases significantly increase the mechanical stability if the DNA is annealed at high temperature. In contrast, modified DNA complexes formed at room temperature and short incubation times display the same stability as non-modified DNA duplexes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Effect of weld metal chemistry and heat input on the structure and properties of duplex stainless steel welds

    Energy Technology Data Exchange (ETDEWEB)

    Muthupandi, V.; Bala Srinivasan, P.; Seshadri, S.K.; Sundaresan, S

    2003-10-15

    The excellent combination of strength and corrosion resistance in duplex stainless steels (DSS) is due to their strict composition control and microstructural balance. The ferrite-austenite ratio is often upset in DSS weld metals owing to the rapid cooling rates associated with welding. To achieve the desired ferrite-austenite balance and hence properties, either the weld metal composition and/or the heat input is controlled. In the current work, a low heat input process viz., EBW and another commonly employed process, gas tungsten-arc welding have been employed for welding of DSS with and without nickel enhancement. Results show that (i) chemical composition has got a greater influence on the ferrite-austenite ratio than the cooling rate, (ii) and even EBW which is considered an immature process in welding of DSS, can be employed provided means of filler addition could be devised.

  3. Effect of shot peening treatment in the behavior of residual stress in duplex stainless steel during medium cycle fatigue

    International Nuclear Information System (INIS)

    Pedrosa, Peter D.S.; Rebello, Joao Marcos A.; Fonseca, Maria P. Cindra

    2010-01-01

    The lifetime of duplex stainless steel parts experiencing cyclic fatigue is directly influenced by the residual stresses present in the ferrite and austenite phases. The motivation for this work was to analyze the behaviour of the residual stresses fields introduced by shot peening treatment in both phases, in the sample surface as in the subsurface layers, in low fatigue cycles, using the X-rays diffraction technique. The results shows that the compressive residual stresses introduced by the shot peening treatment in both phases improved fatigue life of the material. However, the cyclical loads produce partial or total relief in these residual stresses fields. It was verified that the shot peening process induced the formation of microcracks only in the ferrite phase. The largest variations in the total compressive residual stresses fields also occurred in this phase. The samples surfaces were analyzed by scanning electron microscopy. (author)

  4. Radiation effects on DNA methylation in mice

    International Nuclear Information System (INIS)

    Komura, J.; Kurishita, A.; Miyamura, Y.; Ono, T.; Tawa, R.; Sakurai, H.

    1992-01-01

    Effects of ionizing radiation on DNA methylation in liver, brain and spleen were examined by high performance liquid chromatography (HPLC). The total methylated cytosine level in the genome was reduced within 8 hours after 3.8 Gy of irradiation in liver of adult mice. But no appreciable effect was observed in brain and spleen. When mice were irradiated at newborn, liver DNA revealed no change in methylated cytosine level. Even though slight effects of radiation were detected in he methylation of the c-myc and c-fos genes, they were only temporary and no long-term effects were observed. These data suggest that the effect of radiation on DNA methylation in vivo is not prevailing a DNA damage, but rather influenced much through biological parameters. (author)

  5. Joint duplex mode selection, channel allocation, and power control for full-duplex cognitive femtocell networks

    Directory of Open Access Journals (Sweden)

    Mingjie Feng

    2015-02-01

    Full Text Available In this paper, we aim to maximize the sum rate of a full-duplex cognitive femtocell network (FDCFN as well as guaranteeing the quality of service (QoS of users in the form of a required signal to interference plus noise ratios (SINR. We first consider the case of a pair of channels, and develop optimum-achieving power control solutions. Then, for the case of multiple channels, we formulate joint duplex model selection, power control, and channel allocation as a mixed integer nonlinear problem (MINLP, and propose an iterative framework to solve it. The proposed iterative framework consists of a duplex mode selection scheme, a near-optimal distributed power control algorithm, and a greedy channel allocation algorithm. We prove the convergence of the proposed iterative framework as well as a lower bound for the greedy channel allocation algorithm. Numerical results show that the proposed schemes effectively improve the sum rate of FDCFNs.

  6. Effect O6-guanine alkylation on DNA flexibility studied by comparative molecular dynamics simulations.

    Science.gov (United States)

    Kara, Mahmut; Drsata, Tomas; Lankas, Filip; Zacharias, Martin

    2015-01-01

    Alkylation of guanine at the O6 atom is a highly mutagenic DNA lesion because it alters the coding specificity of the base causing G:C to A:T transversion mutations. Specific DNA repair enzymes, e.g. O(6)-alkylguanin-DNA-Transferases (AGT), recognize and repair such damage after looping out the damaged base to transfer it into the enzyme active site. The exact mechanism how the repair enzyme identifies a damaged site within a large surplus of undamaged DNA is not fully understood. The O(6)-alkylation of guanine may change the deformability of DNA which may facilitate the initial binding of a repair enzyme at the damaged site. In order to characterize the effect of O(6)-methyl-guanine (O(6)-MeG) containing base pairs on the DNA deformability extensive comparative molecular dynamics (MD) simulations on duplex DNA with central G:C, O(6)-MeG:C or O(6)-MeG:T base pairs were performed. The simulations indicate significant differences in the helical deformability due to the presence of O(6)-MeG compared to regular undamaged DNA. This includes enhanced base pair opening, shear and stagger motions and alterations in the backbone fine structure caused in part by transient rupture of the base pairing at the damaged site and transient insertion of water molecules. It is likely that the increased opening motions of O(6)-MeG:C or O(6)-MeG:T base pairs play a decisive role for the induced fit recognition or for the looping out of the damaged base by repair enzymes. © 2014 Wiley Periodicals, Inc.

  7. Effect of χ Phase Formation on the Mechanical Properties of 25Cr-7Ni-4Mo-0.2N Super Duplex Stainless Steel

    International Nuclear Information System (INIS)

    Kang, Chang Yong; Kim, Jae Hwan

    2011-01-01

    This study was carried out to investigate the precipitation behavior of χ phase and effect of χ-phase which precipitated at the initial stage of aging on mechanical properties of 25%Cr-7%Ni-4%Mo-0.2%N super duplex stainless steel. χ-phase was precipitated mainly at the interface of ferrite / austenite phases and inside of the ferrite phase at the initial stage of aging, and it was transformed into σ-phase with an increase of aging time. The ferrite phase was decomposed into new austenite(γ 2 )phase and σ-phase by aging treatment. The hardness and tensile strength of the initial stage of aging when χ-phase was precipitated did not changed considerably, while elongation rapidly decreased. Accordingly, it is considered that χ-phase didn't affect the hardness and strength significantly, but it affected the elongation.

  8. Effects of the Substitution of the Mo Element W of Super Duplex Stainless Steel Weld on the Secondary Phase Formation and Corrosion Resistance

    Energy Technology Data Exchange (ETDEWEB)

    Park, Hae-Ji; Lee, Hae-Woo [Dong-A University, Busan (Korea, Republic of)

    2014-03-15

    To investigate the effect of tungsten substitution of molybdenum on the formation of the second phase in Super Duplex Stainless Steel Weldments, welding wires with a composition of 3 wt% Mo, 2.2 wt% Mo-2.2 wt% W were designed for the flux cored arc welding process. As a result, the precipitation of the χ phase and σ phase increased in proportion to the decrease in the amount of δ ferrite content because the reaction, δ ferrite → σ + γ2, proceeded as the temperature rose. Under the same experimental conditions, the precipitation of the second phase, which degrades the properties of the material, was significantly reduced in the W substitution specimens compared to the Mo-only specimens. A polarization test conducted in a salt solution revealed that the pitting potential of the W substitution specimens was higher than that of the Mo-only specimens.

  9. [A Duplex PCR Method for Detection of Babesia caballi and Theileria equi].

    Science.gov (United States)

    Zhang, Yang; Zhang, Yu-ting; Wang, Zhen-bao; Bolati; Li, Hai; Bayinchahan

    2015-04-01

    To develop a duplex PCR assay for detection of Babesia caballi and Theileria equi. Two pairs of primers were designed according to the BC48 gene of B. caballi and 18 s rRNA gene of T. equi, and a duplex PCR assay was developed by the optimization of reaction conditions. The specificity, sensitivity and reliability of the method were tested. The horse blood samples of suspected cases were collected from Yili region, and detected by the duplex PCR, microspopy, conventional PCR, and fluorescence quantitative PCR, and the results were compared. Using the duplex PCR assay, the specific fragments of 155 bp and 280 bp were amplified from DNA samples of B. caballi and T. equi, respectively. No specific fragment was amplified from DNA samples of B. bigemina, Theilerdia annulata, Theilerdia sergenti, Toxoplasma gondii, Neospora caninum, and Trypanosoma evansi. The limit of detection was 4.85 x 10(5) copies/L for B. caballi DNA and 4.85 x 10(4) copies/µl for T. equi DNA, respectively. Among the 24 blood samples, 11 were found B. caballi-positive by the duplex PCR assay, and 18 were T. equi-positive. The coincidence rate of microscopy, conventional PCR, and fluorescence quantitative PCR with duplex PCR was 91.7% (22/24), 95.8% (23/24), and 95.8% (23/24), respectively. A duplex PCR assay for simultaneous detection of B. caballi and T. equi is established.

  10. LET-effects in DNA

    International Nuclear Information System (INIS)

    Kraft, G.; Taucher-Scholz, G.; Heilmann, J.

    1995-01-01

    The use of heavy particles in radiobiological experiments provides a fundamental tool to study the influence of different ionization densities and to prove the physical basis of models and theories. The knowledge of the interaction of high LET radiation (LET: linear energy transfer [keV/microm]) with biological matter is of great importance for the application of neutrons, protons and heavier ions in radiotherapy. It is also essential in radioprotection to estimate the risk in case of exposure to high LET radiation. In this contribution, an introductory view on the physical properties of ions is given and the cellular response to high LET radiation is summarized. Then the measurements of strand break induction of DNA in solution and in intracellular DNA are reported and compared to cell survival. The possibility of changes in the quality of the lesions is discussed and finally the present status of model calculations in comparison to the experiments is given

  11. Detection of chicken contamination in beef meatball using duplex-PCR Cyt b gene

    Science.gov (United States)

    Sari, E. P.; Kartikasari, L. R.; Cahyadi, M.

    2017-04-01

    Beef is one of expensive animal protein sources compared to other meats, on the other hand, chicken is cheap animal protein source. Mixing of chicken into beef meatball is possibly performed to decrease production cost. The aim of this study was to detect chicken contamination in beef meatball using Cytochrome b (Cyt b) gene by duplex-PCR. Sample was designed and prepared as follows, 100% of chicken meatball, 100% of beef meatball and serial level of chicken contaminations in beef meatball (1, 5, 10 and 25%, respectively). Isolation of DNA genome from meatball was according to the guideline of gSYNCTM DNA Extraction Kit for animal tissue. The PCR reaction was carried out using KAPA2G Fast Multiplex Mix. This study found that the DNA genome was succesfully extracted. Moreover, chicken contamination in beef meatball was indicated by the presence of 227 bp DNA band on 2% of agarose gels. Current study revealed that duplex-PCR using Cyt b gene as a genetic marker was able to detect chicken contamination in beef meatball until 1% of chicken meat in the sample. It can be effectively used to identify contamination and also authenticate species origin in animal products to protect consumer from undesirable contents in the food.

  12. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  13. Effect of Rolling and Subsequent Annealing on Microstructure, Microtexture, and Properties of an Experimental Duplex Stainless Steel

    Science.gov (United States)

    Mandal, Arka; Patra, Sudipta; Chakrabarti, Debalay; Singh, Shiv Brat

    2017-12-01

    A lean duplex stainless steel (LDSS) has been prepared with low-N content and processed by different thermo-mechanical schedules, similar to the industrial processing that comprised hot-rolling, cold-rolling, and annealing treatments. The microstructure developed in the present study on low-N LDSS has been compared to that of high-N LDSS as reported in the literature. As N is an austenite stabilizer, lower-N content reduced the stability of austenite and the austenite content in low-N LDSS with respect to the conventional LDSS. Due to low stability of austenite in low-N LDSS, cold rolling resulted in strain-induced martensitic transformation and the reversion of martensite to austenite during subsequent annealing contributed to significant grain refinement within the austenite regions. δ-ferrite grains in low-N LDSS, on the other hand, are refined by extended recovery mechanism. Initial solidification texture (mainly cube texture) within the δ-ferrite region finally converted into gamma-fiber texture after cold rolling and annealing. Although MS-brass component dominated the austenite texture in low-N LDSS after hot rolling and cold rolling, that even transformed into alpha-fiber texture after the final annealing. Due to the significant grain refinement and formation of beneficial texture within both austenite and ferrite, good combination of strength and ductility has been achieved in cold-rolled and annealed sample of low-N LDSS steel.

  14. Maximizing synchronizability of duplex networks

    Science.gov (United States)

    Wei, Xiang; Emenheiser, Jeffrey; Wu, Xiaoqun; Lu, Jun-an; D'Souza, Raissa M.

    2018-01-01

    We study the synchronizability of duplex networks formed by two randomly generated network layers with different patterns of interlayer node connections. According to the master stability function, we use the smallest nonzero eigenvalue and the eigenratio between the largest and the second smallest eigenvalues of supra-Laplacian matrices to characterize synchronizability on various duplexes. We find that the interlayer linking weight and linking fraction have a profound impact on synchronizability of duplex networks. The increasingly large inter-layer coupling weight is found to cause either decreasing or constant synchronizability for different classes of network dynamics. In addition, negative node degree correlation across interlayer links outperforms positive degree correlation when most interlayer links are present. The reverse is true when a few interlayer links are present. The numerical results and understanding based on these representative duplex networks are illustrative and instructive for building insights into maximizing synchronizability of more realistic multiplex networks.

  15. Effect of shot peening treatment in the behavior of residual stress in duplex stainless steel during medium cycle fatigue; Efeito do tratamento de shot peening no comportamento das tensoes residuais em aco inoxidavel duplex durante fadiga de medio ciclo

    Energy Technology Data Exchange (ETDEWEB)

    Pedrosa, Peter D.S.; Rebello, Joao Marcos A. [Coordenacao dos Programas de Pos-Graduacao de Engenharia (PEMM/COPPE/UFRJ), Rio de Janeiro, RJ (Brazil). Programa de Engenharia Metalurgica e de Materiais; Fonseca, Maria P. Cindra, E-mail: mcindra@vm.uff.b [Universidade Federal Fluminense (PGMEC/UFF), Niteroi, RJ (Brazil). Escola de Engenharia. Programa de Pos-Graduacao em Engenharia Mecanica

    2010-07-01

    The lifetime of duplex stainless steel parts experiencing cyclic fatigue is directly influenced by the residual stresses present in the ferrite and austenite phases. The motivation for this work was to analyze the behaviour of the residual stresses fields introduced by shot peening treatment in both phases, in the sample surface as in the subsurface layers, in low fatigue cycles, using the X-rays diffraction technique. The results shows that the compressive residual stresses introduced by the shot peening treatment in both phases improved fatigue life of the material. However, the cyclical loads produce partial or total relief in these residual stresses fields. It was verified that the shot peening process induced the formation of microcracks only in the ferrite phase. The largest variations in the total compressive residual stresses fields also occurred in this phase. The samples surfaces were analyzed by scanning electron microscopy. (author)

  16. The role of duplex stainless steels for downhole tubulars

    International Nuclear Information System (INIS)

    Francis, R.

    1993-01-01

    In sour conditions there is an increasing trend to turn to corrosion resistant alloys for downhole tubulars. The most commonly used CRA tubular is 13Cr, and there are thousands of feet in service. However, there are limits to the use of 13Cr, ie., the risk of sulphide stress corrosion cracking at high H 2 S levels, and the possibility of pitting or high corrosion rates in waters with high chloride contents. Where the service conditions are felt to be too severe for 13Cr alloys it has been traditional to switch to nickel base alloys such as alloys 825 and C-276 (UNS N08825 and N10276). The alloys are much more expensive than 13Cr, and in recent years the duplex stainless steels have been selected as alloys with superior corrosion and SSCC resistance compared with 13Cr, and having lower cost than nickel alloys. Originally the 22Cr duplex alloy (UNS 31803) was used, but more recently the 25Cr super duplex alloys (UNS S32760 and S32750) have become more available. The present paper reviews the data available for 13Cr and the limits of applicability. Data is also presented for laboratory tests for both the 22Cr and 25Cr super duplex alloys. There is extensive service experience with both 22Cr and 25Cr super duplex in the North Sea, covering both downhole tubulars, manifold and post wellhead equipment. Data is presented showing some of the sour condition being experienced in the North Sea by super duplex alloys. These results show that there is a substantial gap between the limits of use for 13Cr and the 25Cr super duplex stainless steel alloys. This means that in many sour environments super duplex stainless steel provides a cost effective alternative to nickel-base alloys

  17. Effect of Different Chromium Additions on the Microstructure and Mechanical Properties of Multipass Weld Joint of Duplex Stainless Steel

    Science.gov (United States)

    Kang, Dong Hoon; Lee, Hae Woo

    2012-12-01

    The correlation between the mechanical properties and ferrite volume fraction (approximately 40, 50, and 60 Ferrite Number [FN]) in duplex stainless steel weld metals were investigated by changing the Cr content in filler wires with a flux-cored arc-welding (FCAW) process. The interpass temperature was thoroughly maintained under a maximum of 423 K (150 °C), and the heat input was also sustained at a level under 15 KJ/cm in order to minimize defects. The microstructure examination demonstrated that the δ-ferrite volume fraction in the deposited metals increased as the Cr/Ni equivalent ratio increased, and consequently, chromium nitride (Cr2N) precipitation was prone to occur in the ferrite domains due to low solubility of nitrogen in this phase. Thus, more dislocations are pinned by the precipitates, thereby lowering the mobility of the dislocations. Not only can this lead to the strength improvement, but also it can accentuate embrittlement of the weld metal at subzero temperature. Additionally, the solid-solution strengthening by an increase of Cr and Mo content in austenite phase depending on the reduction of austenite proportion also made an impact on the increase of the tensile and yield strength. On the other hand, the impact test (at 293 K, 223 K, and 173 K [20 °C, -50 °C, and -100 °C]) showed that the specimen containing about 40 to 50 FN had the best result. The absorbed energy of about 40 to 50 J sufficiently satisfied the requirements for industrial applications at 223 K (-50 °C), while the ductile-to-brittle transition behavior exhibited in weldment containing 60 FN. As the test temperature decreased under 223 K (-50 °C), a narrow and deep dimple was transformed into a wide and shallow dimple, and a significant portion of the fracture surface was occupied by a flat cleavage facet with river patterns.

  18. A Dual-Specific Targeting Approach Based on the Simultaneous Recognition of Duplex and Quadruplex Motifs.

    Science.gov (United States)

    Nguyen, Thi Quynh Ngoc; Lim, Kah Wai; Phan, Anh Tuân

    2017-09-20

    Small-molecule ligands targeting nucleic acids have been explored as potential therapeutic agents. Duplex groove-binding ligands have been shown to recognize DNA in a sequence-specific manner. On the other hand, quadruplex-binding ligands exhibit high selectivity between quadruplex and duplex, but show limited discrimination between different quadruplex structures. Here we propose a dual-specific approach through the simultaneous application of duplex- and quadruplex-binders. We demonstrated that a quadruplex-specific ligand and a duplex-specific ligand can simultaneously interact at two separate binding sites of a quadruplex-duplex hybrid harbouring both quadruplex and duplex structural elements. Such a dual-specific targeting strategy would combine the sequence specificity of duplex-binders and the strong binding affinity of quadruplex-binders, potentially allowing the specific targeting of unique quadruplex structures. Future research can be directed towards the development of conjugated compounds targeting specific genomic quadruplex-duplex sites, for which the linker would be highly context-dependent in terms of length and flexibility, as well as the attachment points onto both ligands.

  19. Effect of a Dual Charge on the DNA-Conjugated Redox Probe on DNA Sensing by Short Hairpin Beacons Tethered to Gold Electrodes.

    Science.gov (United States)

    Kékedy-Nagy, László; Shipovskov, Stepan; Ferapontova, Elena E

    2016-08-16

    Charges of redox species can critically affect both the interfacial state of DNA and electrochemistry of DNA-conjugated redox labels and, as a result, the electroanalytical performance of those systems. Here, we show that the kinetics of electron transfer (ET) between the gold electrode and methylene blue (MB) label conjugated to a double-stranded (ds) DNA tethered to gold strongly depend on the charge of the MB molecule, and that affects the performance of genosensors exploiting MB-labeled hairpin DNA beacons. Positively charged MB binds to dsDNA via electrostatic and intercalative/groove binding, and this binding allows the DNA-mediated electrochemistry of MB intercalated into the duplex and, as a result, a complex mode of the electrochemical signal change upon hairpin hybridization to the target DNA, dominated by the "on-off" signal change mode at nanomolar levels of the analyzed DNA. When MB bears an additional carboxylic group, the negative charge provided by this group prevents intimate interactions between MB and DNA, and then the ET in duplexes is limited by the diffusion of the MB-conjugated dsDNA (the phenomenon first shown in Farjami , E. ; Clima , L. ; Gothelf , K. ; Ferapontova , E. E. Anal. Chem. 2011 , 83 , 1594 ) providing the robust "off-on" nanomolar DNA sensing. Those results can be extended to other intercalating redox probes and are of strategic importance for design and development of electrochemical hybridization sensors exploiting DNA nanoswitchable architectures.

  20. DNA Repair Mechanisms and the Bypass of DNA Damage in Saccharomyces cerevisiae

    Science.gov (United States)

    Boiteux, Serge; Jinks-Robertson, Sue

    2013-01-01

    DNA repair mechanisms are critical for maintaining the integrity of genomic DNA, and their loss is associated with cancer predisposition syndromes. Studies in Saccharomyces cerevisiae have played a central role in elucidating the highly conserved mechanisms that promote eukaryotic genome stability. This review will focus on repair mechanisms that involve excision of a single strand from duplex DNA with the intact, complementary strand serving as a template to fill the resulting gap. These mechanisms are of two general types: those that remove damage from DNA and those that repair errors made during DNA synthesis. The major DNA-damage repair pathways are base excision repair and nucleotide excision repair, which, in the most simple terms, are distinguished by the extent of single-strand DNA removed together with the lesion. Mistakes made by DNA polymerases are corrected by the mismatch repair pathway, which also corrects mismatches generated when single strands of non-identical duplexes are exchanged during homologous recombination. In addition to the true repair pathways, the postreplication repair pathway allows lesions or structural aberrations that block replicative DNA polymerases to be tolerated. There are two bypass mechanisms: an error-free mechanism that involves a switch to an undamaged template for synthesis past the lesion and an error-prone mechanism that utilizes specialized translesion synthesis DNA polymerases to directly synthesize DNA across the lesion. A high level of functional redundancy exists among the pathways that deal with lesions, which minimizes the detrimental effects of endogenous and exogenous DNA damage. PMID:23547164

  1. Atmospheric-Induced Stress Corrosion Cracking of Grade 2205 Duplex Stainless Steel—Effects of 475 °C Embrittlement and Process Orientation

    Directory of Open Access Journals (Sweden)

    Cem Örnek

    2016-07-01

    Full Text Available The effect of 475 °C embrittlement and microstructure process orientation on atmospheric-induced stress corrosion cracking (AISCC of grade 2205 duplex stainless steel has been investigated. AISCC tests were carried out under salt-laden, chloride-containing deposits, on U-bend samples manufactured in rolling (RD and transverse directions (TD. The occurrence of selective corrosion and stress corrosion cracking was observed, with samples in TD displaying higher propensity towards AISCC. Strains and tensile stresses were observed in both ferrite and austenite, with similar magnitudes in TD, whereas, larger strains and stresses in austenite in RD. The occurrence of 475 °C embrittlement was related to microstructural changes in the ferrite. Exposure to 475 °C heat treatment for 5 to 10 h resulted in better AISCC resistance, with spinodal decomposition believed to enhance the corrosion properties of the ferrite. The austenite was more susceptible to ageing treatments up to 50 h, with the ferrite becoming more susceptible with ageing in excess of 50 h. Increased susceptibility of the ferrite may be related to the formation of additional precipitates, such as R-phase. The implications of heat treatment at 475 °C and the effect of process orientation are discussed in light of microstructure development and propensity to AISCC.

  2. Effects of Energy Density and Shielding Medium on Performance of Laser Beam Welding (LBW) Joints on SAF2205 Duplex Stainless Steel

    Science.gov (United States)

    Zhang, W. W.; Cong, S.; Luo, S. B.; Fang, J. H.

    2018-05-01

    The corrosion resistance performance of SAF2205 duplex stainless steel depends on the amount of ferrite to austenite transformation, but the ferrite content after power beam welding is always excessively high. To obtain laser beam welding joints with better mechanical and corrosion resistance performance, the effects of the energy density and shielding medium on the austenite content, hardness distribution, and shear strength were investigated. The results showed that ferrite to austenite transformation was realized with increase in the energy density. When the energy density was increased from 120 J/mm to 200 J/mm, the austenite content of the welding joint changed from 2.6% to 38.5%. Addition of nitrogen gas to the shielding medium could promote formation of austenite. When the shielding medium contained 50% and 100% nitrogen gas, the austenite content of the welding joint was 42.7% and 47.2%, respectively. The hardness and shear strength were significantly improved by increase in the energy density. However, the shielding medium had less effect on the mechanical performance. Use of the optimal welding process parameters resulted in peak hardness of 375 HV and average shear strength of 670 MPa.

  3. Effect of the Addition of Nickel Powder and Post Weld Heat Treatment on the Metallurgical and Mechanical Properties of the Welded UNS S32304 Duplex Stainless Steel

    Directory of Open Access Journals (Sweden)

    Ali Tahaei

    Full Text Available Abstract In this research, the effect of the addition of nickel powder and the application of a post weld heat treatment (PWHT on the welding properties of the UNS S32304 lean duplex stainless steel were investigated in order to improve the microstructure and mechanical properties. Nickel powder was directly poured inside the joint gap and mixed with the filler metal during the Gas Tungsten Arc Welding (GTAW process; moreover, the solution heat treatment was performed at 1100 °C for 10 min. The joints were characterized by optical microscopy (OM and the evolution of the phase percentages in the different zones was studied by means of the image analysis technique. Tensile and hardness tests were carried out on the joints in order to evaluate the improvement of the mechanical properties. The results showed that both the addition of nickel powder during the welding process and the post weld heat treatment made it possible to improve the mechanical properties of the weld joints. PWHT had the best effect in restoring the equal percentage of ferrite and austenite compared to the addition of nickel powder.

  4. Clinical utility of carotid duplex ultrasound prior to cardiac surgery.

    Science.gov (United States)

    Lin, Judith C; Kabbani, Loay S; Peterson, Edward L; Masabni, Khalil; Morgan, Jeffrey A; Brooks, Sara; Wertella, Kathleen P; Paone, Gaetano

    2016-03-01

    Clinical utility and cost-effectiveness of carotid duplex examination prior to cardiac surgery have been questioned by the multidisciplinary committee creating the 2012 Appropriate Use Criteria for Peripheral Vascular Laboratory Testing. We report the clinical outcomes and postoperative neurologic symptoms in patients who underwent carotid duplex ultrasound prior to open heart surgery at a tertiary institution. Using the combined databases from our clinical vascular laboratory and the Society of Thoracic Surgery, a retrospective analysis of all patients who underwent carotid duplex ultrasound within 13 months prior to open heart surgery from March 2005 to March 2013 was performed. The outcomes between those who underwent carotid duplex scanning (group A) and those who did not (group B) were compared. Among 3233 patients in the cohort who underwent cardiac surgery, 515 (15.9%) patients underwent a carotid duplex ultrasound preoperatively, and 2718 patients did not (84.1%). Among the patients who underwent carotid screening vs no screening, there was no statistically significant difference in the risk factors of cerebrovascular disease (10.9% vs 12.7%; P = .26), prior stroke (8.2% vs 7.2%; P = .41), and prior transient ischemic attack (2.9% vs 3.3%; P = .24). For those undergoing isolated coronary artery bypass grafting (CABG), 306 (17.8%) of 1723 patients underwent preoperative carotid duplex ultrasound. Among patients who had carotid screening prior to CABG, the incidence of carotid disease was low: 249 (81.4%) had minimal or mild stenosis (duplex scanning and those who did not. Primary outcomes of patients who underwent open heart surgery also showed no difference in the perioperative mortality (5.1% vs 6.9%; P = .14) and stroke (2.6% vs 2.4%; P = .85) between patients undergoing preoperative duplex scanning and those who did not. Operative intervention of severe carotid stenosis prior to isolated CABG occurred in 2 of the 17 patients (11.8%) identified who

  5. Effect of Si and Mn additions on ferrite and austenite phase fractions in 25Cr-7Ni-1.5Mo-3W base super duplex stainless steels

    International Nuclear Information System (INIS)

    Jeong, S.W.; Lee, Z.-H.; Lee, H.M.

    2000-01-01

    The effect of heat treatment and Si and Mn additions on the ferrite and austenite phase fractions of the super duplex stainless steel (SDSS), Fe-25Cr-7Ni-1.5Mo-3W-Si-Mn-0.25N (numbers are all in wt.% unless specified otherwise), was investigated. The thermodynamic calculations of phase equilibria and phase fractions were performed using the Thermo-Calc program. Based on the calculated results, specific compositions of Si and Mn were selected and alloys with these compositions were analysed by Feritscope, X-ray diffractometry and scanning electron microscopy. The calculated phase fractions and experimentally analysed ones were compared and there was a good agreement between calculations and measurements. The optimum heat treatment condition for Fe-25Cr-7Ni-1.5Mo-3W-0.5Si-0.5Mn-0.25N is to hold at 1050 to 1100 C for 2 h in considering the ferrite to austenite ratio of 50:50 and to avoid second phase precipitation such as the σ phase. It was suggested that an excessive addition of more than 0.8Si and 1.0Mn may induce the σ phase precipitation. (orig.)

  6. Effect of electrolyte composition on the active-to-passive transition behavior of 2205 duplex stainless steel in H2SO4/HCl solutions

    International Nuclear Information System (INIS)

    Lo, I-H.; Fu Yan; Lin, C.-J.; Tsai, W.-T.

    2006-01-01

    Selective dissolution could occur in duplex stainless steels (DSSs) due to the difference in chemical composition between the two constituent phases. In this study, the effect of H 2 SO 4 /HCl composition on the selective dissolution behavior was investigated. The results indicated that there were two distinct peaks appeared in the active-to-passive transition region in the polarization curve. The peak appeared at a lower potential region was associated with the preferential dissolution of ferrite phase while that for austenite at a higher potential. In the concentration ranges of 0.25-2 M of H 2 SO 4 and 0.25-2 M of HCl, the magnitude of the peak anodic current density and the resolution between these two peaks greatly depended on the composition of H 2 SO 4 /HCl. However, the anodic peaks corresponding to the respective dissolutions of ferrite and austenite became less distinguishable when the concentrations of HCl exceeded 1.2 M. Image analysis using scanning electron microscopy (SEM) was performed to confirm the selective dissolution of each constituent phase after potentiostatic polarization at the respective anodic peak potential

  7. Welding of duplex and super-duplex stainless steels

    International Nuclear Information System (INIS)

    Van Nassau, L.; Meelker, H.; Hilkes, J.

    1994-01-01

    After a recall of the commercial designation of duplex or super-duplex steels (22-27% Cr, 4-8% Ni, 0.1-0.3% N with or without Mo (1.5-4%)) and of some metallurgical properties (phase diagrams, microstructure, ferrite determination, heat treatment and aging), welding technologies are synthetically presented (advantages-disadvantages of each process, metals filler, parameters of the welding processes, heat treatments after welding, cleaning, passivation, properties (mechanical, corrosion resistance) of the welded pieces). (A.B.). 28 refs. 5 figs., 15 tabs., 1 annexe

  8. Effects of irregular basement structure on the geometry and emplacement of frontal thrusts and duplexes in the Quebec Appalachians: Interpretations from well and seismic reflection data

    Science.gov (United States)

    Konstantinovskaya, E.; Malo, M.; Badina, F.

    2014-12-01

    Irregular basement geometry may affect thrust propagation in foreland fold-thrust belts creating a perturbation in structural continuity of hydrocarbon fields. Here we investigate how the irregular pattern of normal faults, along with the presence of uplifts and transverse faults in the Grenvillian basement has influenced the geometry and emplacement of frontal thrusts and duplexes in the parautochthonous domain of the southern Quebec Appalachians during the middle-late Ordovician Taconian orogeny. Integration of data from surface geology, wells, and 2D and 3D seismic reflection surveys into a regional-scale structural model is used to reconstruct the 3D geometry and emplacement history of one- and two-horse duplexes in the Joly-Saint-Flavien gas storage area. The normal hinterland to foreland sequence of thrusting in this area is complicated by the differential emplacement of tectonic slices along strike of the orogenic front, starting in the SW and developing subsequently to the NE within each structural level. The shortening related to duplex emplacement decreases laterally over the distance of 20 km from - 49% in the SW (Joly area) to - 31% in the NE (Saint-Flavien area). Duplex emplacement resulted from the differential forward propagation, deflexion and vertical-axis rotation of the roof thrust (Logan's Line), which, in turn, has been induced by the presence of frontal uplift and transverse faults in the basement. The structural-lithological analysis of tectonic slices and restoration of their initial location allows us to consider the lower slice of the Joly duplex as a structural trap comparable to the fractured reservoir in lower Ordovician dolomites of the Saint-Flavien duplex.

  9. Base pair mismatches and carcinogen-modified bases in DNA: an NMR study of G x T and G x O4meT pairing in dodecanucleotide duplexes

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Kouchakdjian, M.; Li, B.F.L.; Swann, P.F.; Patel, D.J.

    1988-01-01

    High-resolution two-dimensional NMR studies have been completed on the self-complementary d(C-G-C-G-A-G-C-T-T-G-C-G) duplex (designated G x T 12-mer) and the self-complementary d(C-G-C-G-A-G-C-T-O 4 meT-G-C-G) duplex (designated G x O 4 meT 12-mer) containing G x T and G x O 4 meT pairs at identical positions four base pairs in from either end of the duplex. The exchangeable and nonexchangeable proton resonances have been assigned from an analysis of two-dimensional nuclear Overhauser enhancement (NOESY) spectra for the G x T 12-mer and G x O 4 meT 12-mer duplexes in H 2 O and D 2 O solution. The guanosine and thymidine imino protons in the G x T mismatch resonate at 10.57 and 11.98 ppm, respectively, and exhibit a strong NOE between themselves and to imino protons of flanking base pairs in the G x T 12-mer duplex. The large upfield chemical shift of this proton relative to that of the imino proton resonance of G in the G x T mismatch or in G x C base pairs indicates that hydrogen bonding to O 4 meT is either very weak or absent. This guanosine imino proton has an NOE to the OCH 3 group of O 4 meT across the pair and NOEs to the imino protons of flanking base pairs. Taken together with data from the NMR of nonexchangeable protons, this shows that both G and O 4 meT have anti-glycosidic torsion angles and are stacked into the duplex. Comparison of the intensity of the NOEs between the guanosine imino proton and the OCH 3 of O 4 meT as well as other protons in its vicinity demonstrates that the OCH 3 group of O 4 meT adopts the syn orientation with respect to N3 of the methylated thymidine. The authors propose an alternate base pairing mode stabilized by one short hydrogen bond between the 2-amino group of guanosine and the 2-carbonyl group of O 4 met

  10. The effect of σ-phase precipitation at 800°C on the corrosion resistance in sea-water of a high alloyed duplex stainless steel

    NARCIS (Netherlands)

    Wilms, M.E.; Gadgil, V.J.; Krougman, J.M.; Ijsseling, F.P.

    1994-01-01

    Super-duplex stainless steels are recently developed high alloyed stainless steels that combine good mechanical properties with excellent corrosion resistance. Because of a high content of chromium and molybdenum, these alloys are susceptible to σ-phase precipitation during short exposure to

  11. Superimposed Code Theorectic Analysis of DNA Codes and DNA Computing

    Science.gov (United States)

    2010-03-01

    that the hybridization that occurs between a DNA strand and its Watson - Crick complement can be used to perform mathematical computation. This research...ssDNA single stranded DNA WC Watson – Crick A Adenine C Cytosine G Guanine T Thymine ... Watson - Crick (WC) duplex, e.g., TCGCA TCGCA . Note that non-WC duplexes can form and such a formation is called a cross-hybridization. Cross

  12. Determination of the major tautomeric form of the covalently modified adenine in the (+)-CC-1065-DNA adduct by 1H and 15N NMR studies

    International Nuclear Information System (INIS)

    Lin, Chin Hsiung; Hurley, L.H.

    1990-01-01

    (+)-CC-1065 is an extremely potent antitumor antibiotic produced by Streptomyces zelensis. The potent cytotoxic effects of the drug are thought to be due to the formation of a covalent adduct with DNA through N3 of adenine. Although the covalent linkage sites between (+)-CC-1065 and DNA have been determined, the tautomeric form of the covalently modified adenine in the (+)-CC-1065-DNA duplex adduct was not defined. The [6- 15 N]deoxyadenosine-labeled 12-mer duplex adduct was then studied by 1 H and 15 N NMR. One-dimensional NOE difference and two-dimensional NOESY 1 H NMR experiments on the nonisotopically labeled 12-mer duplex adduct demonstrate that the 6-amino protons of the covalently modified adenine exhibit two signals at 9.19 and 9.08 ppm. Proton NMR experiments on the [6- 15 N]deoxyadenosine-labeled 12-mer duplex adduct show that the two resonance signals for adenine H6 observed on the nonisotopically labeled duplex adduct were split into doublets by the 15 N nucleus with coupling constants of 91.3 Hz for non-hydrogen-bonded and 86.8 Hz for hydrogen-bonded amino protons. The authors conclude that the covalently modified adenine N6 of the (+)-CC-1065-12-mer duplex adduct is predominantly in the doubly protonated form, in which calculations predict that the C6-N6 bond is shortened and the positive charge is delocalized over the entire adenine molecule

  13. Induced effect of irradiated exogenous DNA on wheat

    International Nuclear Information System (INIS)

    Li Zhongjie; Sun Guangzu; Wang Guangjin

    1996-01-01

    Irradiated exogenous DNA introduced into wheat can give rise to break of DNA-chain and damage of part of alkali radicals. Introducing exogenous DNA irradiated by γ rays could increase Do fructification rate and decrease seed size and plumpness. These tendencies became obvious with dose increase. In comparison with control DNA, introducing DNA irradiated could raise evidently mutagenic effect of pollen tube pathway technique

  14. The value and economic analysis of routine postoperative carotid duplex ultrasound surveillance after carotid endarterectomy.

    Science.gov (United States)

    AbuRahma, Ali F; Srivastava, Mohit; AbuRahma, Zachary; Jackson, Will; Mousa, Albeir; Stone, Patrick A; Dean, L Scott; Green, Jason

    2015-08-01

    Several studies have reported on the role of postoperative duplex ultrasound surveillance after carotid endarterectomy (CEA) with varying results. Most of these studies had a small sample size or did not analyze cost-effectiveness. We analyzed 489 of 501 CEA patients with patch closure. All patients had immediate postoperative duplex ultrasound examination and were routinely followed up both clinically and with duplex ultrasound at regular intervals of 1 month, 6 months, 12 months, and every 12 months thereafter. A Kaplan-Meier analysis was used to estimate the rate of ≥50% and ≥80% post-CEA restenosis over time and the time frame of progression from normal to ≥50% or ≥80% restenosis. The cost of post-CEA duplex surveillance was also estimated. Overall, 489 patients with a mean age of 68.5 years were analyzed. Ten of these had residual postoperative ≥50% stenosis, and 37 did not undergo a second duplex ultrasound examination and therefore were not included in the final analysis. The mean follow-up was 20.4 months (range, 1-63 months), with a mean number of duplex ultrasound examinations of 3.6 (range, 1-7). Eleven of 397 patients (2.8%) with a normal finding on immediate postoperative duplex ultrasound vs 4 of 45 (8.9%) with mild stenosis on immediate postoperative duplex ultrasound progressed to ≥50% restenosis (P = .055). Overall, 15 patients (3.1%) had ≥50% restenosis, 9 with 50% to duplex ultrasound), which equals $1,408,320, to detect only four patients with ≥80% to 99% restenosis who may have been potential candidates for reintervention. This study shows that the value of routine postoperative duplex ultrasound surveillance after CEA with patch closure may be limited, particularly if the finding on immediate postoperative duplex ultrasound is normal or shows minimal disease. Copyright © 2015 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

  15. Detection of DNA damage based on metal-mediated molecular beacon and DNA strands displacement reaction

    Science.gov (United States)

    Xiong, Yanxiang; Wei, Min; Wei, Wei; Yin, Lihong; Pu, Yuepu; Liu, Songqin

    2014-01-01

    DNA hairpin structure probes are usually designed by forming intra-molecular duplex based on Watson-Crick hydrogen bonds. In this paper, a molecular beacon based on silver ions-mediated cytosine-Ag+-cytosine base pairs was used to detect DNA. The inherent characteristic of the metal ligation facilitated the design of functional probe and the adjustment of its binding strength compared to traditional DNA hairpin structure probes, which make it be used to detect DNA in a simple, rapid and easy way with the help of DNA strands displacement reaction. The method was sensitive and also possesses the good specificity to differentiate the single base mismatched DNA from the complementary DNA. It was also successfully applied to study the damage effect of classic genotoxicity chemicals such as styrene oxide and sodium arsenite on DNA, which was significant in food science, environmental science and pharmaceutical science.

  16. Effect of Dynamic Reheating Controlled by the Weaving Width on the Microstructure of GTA Bead-On-Pipe Weld Metal of 25% Cr Super Duplex Stainless Steel

    Directory of Open Access Journals (Sweden)

    Hee-Joon Sung

    2018-05-01

    Full Text Available Gas tungsten arc welding (GTAW with three different heat inputs controlled by the weaving width was performed to understand their effects on the microstructural changes during bead-on-pipe welding of super duplex stainless steel. The microstructure of the weld metals was categorized into three different types of zones: non-reheated, reheated type, and reheating-free zone. Even though single-pass welding with different weaving widths was employed, a reheated microstructure was detected, which has been previously observed with multiple pass welding. This phenomenon was called “dynamic reheating”, because it was produced by the weaving operation during welding regardless of the weaving width. The categorized area fraction varied with the weaving width change. Electron backscatter diffraction (EBSD results at the edge (the area near the fusion line of the low-heat-input condition indicated a higher austenite volume fraction and a lower Cr2N fraction than that of the medium heat input condition. Thus, it described an inverse relationship, because higher heat input provided a lower austenite fraction. In addition, it was observed clearly that the austenite fraction at the medium heat input condition was dramatically increased by reheating, while the Cr2N fraction was reduced. Regardless of the weaving width, reheating contributed to the increase of the austenite fraction, further reducing the Cr2N quantity. The edge areas in the map showed an inverse relationship in the reheated area fraction between low heat input and medium heat input. For this reason, the austenite fraction on the weld metal was determined not only by the heat input, but also by the amount of reheating.

  17. Effects of the Cooling Rate After Annealing Treatment on the Microstructure and the Mechanical Properties of Super-Duplex Stainless Steel

    International Nuclear Information System (INIS)

    Kwon, Gi-Hyoun; Park, Yong-Ho; Na, Young-Sang; Yoo, Wee-Do; Lee, Jong-Hoon

    2012-01-01

    The aim of this study was to analyze the effect of the cooling rate after heat treatment on the microstructure and mechanical properties of 2507 duplex stainless steels. Heat treatment was carried out at 1050°C for 1 hr, followed by controlled cooling. The cooling rates were 175.6 × 10 - 3°C/s, 47.8 × 10 - 3°C/s, 33.3 × 10 - 3°C/s, 16.7 × 10 - 3°C/s, 11.7 × 10 - 3°C/s, 5.8 × 10 - 3°C/s and 2.8 × 10 - 3°C/s, which resulted in variations of the microstructure, such as the fractional change of the ferrite phase and sigma phase formation. Fatigue, hardness, impact and tensile tests were performed on the specimens with different cooling rates. The precipitation of the σ phase caused a hardness increase and a sharp decrease of toughness and tensile elongation. The fatigue limit of the sample with a cooling rate of 5.8 × 10 - 3°C/s was 26 MPa higher than that of the sample with a cooling rate of 175.6 × 10 - 3°C/s. Our observations of the fracture surface confirmed that the higher fatigue resistance of the specimen with a cooling rate of 5.8 × 10 - 3°C/s was caused by the delay of the fatigue crack growth, in addition to higher yield strength.

  18. Effects of the Cooling Rate After Annealing Treatment on the Microstructure and the Mechanical Properties of Super-Duplex Stainless Steel

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Gi-Hyoun; Park, Yong-Ho [Pusan National University, Pusan (Korea, Republic of); Na, Young-Sang; Yoo, Wee-Do; Lee, Jong-Hoon [Korea Institute of Materials Science, Changwon (Korea, Republic of)

    2012-10-15

    The aim of this study was to analyze the effect of the cooling rate after heat treatment on the microstructure and mechanical properties of 2507 duplex stainless steels. Heat treatment was carried out at 1050°C for 1 hr, followed by controlled cooling. The cooling rates were 175.6 × 10{sup -}3°C/s, 47.8 × 10{sup -}3°C/s, 33.3 × 10{sup -}3°C/s, 16.7 × 10{sup -}3°C/s, 11.7 × 10{sup -}3°C/s, 5.8 × 10{sup -}3°C/s and 2.8 × 10{sup -}3°C/s, which resulted in variations of the microstructure, such as the fractional change of the ferrite phase and sigma phase formation. Fatigue, hardness, impact and tensile tests were performed on the specimens with different cooling rates. The precipitation of the σ phase caused a hardness increase and a sharp decrease of toughness and tensile elongation. The fatigue limit of the sample with a cooling rate of 5.8 × 10{sup -}3°C/s was 26 MPa higher than that of the sample with a cooling rate of 175.6 × 10{sup -}3°C/s. Our observations of the fracture surface confirmed that the higher fatigue resistance of the specimen with a cooling rate of 5.8 × 10{sup -}3°C/s was caused by the delay of the fatigue crack growth, in addition to higher yield strength.

  19. Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study

    Czech Academy of Sciences Publication Activity Database

    Krepl, Miroslav; Otyepka, M.; Banáš, Pavel; Šponer, Jiří

    2013-01-01

    Roč. 117, č. 6 (2013), s. 1872-1879 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GBP305/12/G034 Grant - others:GA ČR(CZ) GPPP301/11/P558; GA MŠk(CZ) ED1.1.00/02.0068 Program:ED Institutional research plan: CEZ:AV0Z50040702 Institutional support: RVO:68081707 Keywords : FREE-ENERGY CALCULATIONS * PARTICLE MESH EWALD * ACID BASE-PAIRS Subject RIV: BO - Biophysics Impact factor: 3.377, year: 2013

  20. Base Pair Opening in a Deoxynucleotide Duplex Containing a cis-syn Thymine Cyclobutane Dimer Lesion

    Science.gov (United States)

    Wenke, Belinda B.; Huiting, Leah N.; Frankel, Elisa B.; Lane, Benjamin F.; Núñez, Megan E.

    2014-01-01

    The cis-syn thymine cyclobutane dimer is a DNA photoproduct implicated in skin cancer. We compared the stability of individual base pairs in thymine dimer-containing duplexes to undamaged parent 10-mer duplexes. UV melting thermodynamic measurements, CD spectroscopy, and 2D NOESY NMR spectroscopy confirm that the thymine dimer lesion is locally and moderately destabilizing within an overall B-form duplex conformation. We measured the rates of exchange of individual imino protons by NMR using magnetization transfer from water and determined the equilibrium constant for the opening of each base pair Kop. In the normal duplex Kop decreases from the frayed ends of the duplex toward the center, such that the central TA pair is the most stable with a Kop of 8×10−7. In contrast, base pair opening at the 5’T of the thymine dimer is facile. The 5’T of the dimer has the largest equilibrium constant (Kop =3×10−4) in its duplex, considerably larger than even the frayed penultimate base pairs. Notably, base pairing by the 3’T of the dimer is much more stable than by the 5’T, indicating that the predominant opening mechanism for the thymine dimer lesion is not likely to be flipping out into solution as a single unit. The dimer asymmetrically affects the stability of the duplex in its vicinity, destabilizing base pairing on its 5’ side more than on the 3’ side. The striking differences in base pair opening between parent and dimer duplexes occur independently of the duplex-single strand melting transitions. PMID:24328089

  1. Normalized cDNA libraries

    Science.gov (United States)

    Soares, Marcelo B.; Efstratiadis, Argiris

    1997-01-01

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library.

  2. Proteins mediating DNA loops effectively block transcription.

    Science.gov (United States)

    Vörös, Zsuzsanna; Yan, Yan; Kovari, Daniel T; Finzi, Laura; Dunlap, David

    2017-07-01

    Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop-mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

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

    Science.gov (United States)

    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.

  4. Probabilistic Medium Access Control for Full-Duplex Networks with Half-Duplex Clients

    OpenAIRE

    Chen, Shih-Ying; Huang, Ting-Feng; Lin, Kate Ching-Ju; Hong, H. -W. Peter; Sabharwal, Ashutosh

    2016-01-01

    The feasibility of practical in-band full-duplex radios has recently been demonstrated experimentally. One way to leverage full-duplex in a network setting is to enable three-node full-duplex, where a full- duplex access point (AP) transmits data to one node yet simultaneously receives data from another node. Such three-node full-duplex communication however introduces inter-client interference, directly impacting the full-duplex gain. It hence may not always be beneficial to enable three-nod...

  5. Effect of Hecogenin on DNA instability

    Directory of Open Access Journals (Sweden)

    Marina Sampaio Cruz

    Full Text Available Hecogenin is a sapogenin found in Agave species in high quantities and is responsible for the many therapeutic effects of these medicinal plants. In addition, this compound is also widely used in the pharmaceutical industry as a precursor for the synthesis of steroidal hormones and anti-inflammatory drugs. Despite Hecogenin being widely used, little is known about its toxicological properties. Therefore, the present study aimed to investigate the cytotoxic, genotoxic and mutagenic effects of Hecogenin on HepG2 cells. Cytotoxicity was analyzed using the MTT test. Then, genotoxic and mutagenic potentials were assessed by comet assay and cytokinesis-block micronucleus assay, respectively. Cytotoxic effect was observed only when cells were exposed to concentrations of Hecogenin equal or higher than 100 μM. Although a lower concentration of Hecogenin caused DNA damage, a reduction on nuclear mutagenic markers in HepG2 cells was observed. The results indicated that Hecogenin treatment generated DNA damage, but in fact it would be repaired, avoiding dissemination of the damage throughout the cell division. Further studies need to be performed to confirm the observed protective effect of Hecogenin against genomic instability. Keywords: Hecogenin, CBMN, Genotoxicity, Comet assay

  6. Effects of charged particles on DNA

    International Nuclear Information System (INIS)

    Eguchi-Kasai, Kiyomi; Itsukaichi, Hiromi; Murakami, Masahiro

    1995-01-01

    It can be noted that it is not simple double strand breaks (dsb) but the non-reparable breaks that are associated with high biological effectiveness in the cell killing effect for high LET radiation. Here, we have examined the effectiveness of fast neutrons and low (initial energy = 12 MeV/u) or high (135 MeV/u) energy charged particles on cell death in 19 mammalian cell lines including radiosensitive mutants. Some of the radiosensitive lines were deficient in DNA dsb repair such as LX830, M10, V3, and L5178Y-S cells and showed lower values of relative biological effectiveness (RBE) for fast neutrons if compared with their parent cell lines. The other lines of human ataxia-telangiectasia fibroblasts, irs 1, irs 2, irs 3 and irs 1SF cells, which were also radiosensitive but known as proficient in dsb repair, showed moderate RBEs. Dsb repair deficient mutants showed low RBE values for heavy ions. These experimental findings suggest that the DNA repair system does not play a major role against the attack of high linear energy transfer (LET) radiations. Therefore, we hypothesize that a main cause of cell death induced by high LET radiations is due to non-reparable dsb, which are produced at a higher rate compared to low LET radiations. (author)

  7. Evaluation of Microstructure and Mechanical Properties in Dissimilar Austenitic/Super Duplex Stainless Steel Joint

    Science.gov (United States)

    Rahmani, Mehdi; Eghlimi, Abbas; Shamanian, Morteza

    2014-10-01

    To study the effect of chemical composition on microstructural features and mechanical properties of dissimilar joints between super duplex and austenitic stainless steels, welding was attempted by gas tungsten arc welding process with a super duplex (ER2594) and an austenitic (ER309LMo) stainless steel filler metal. While the austenitic weld metal had vermicular delta ferrite within austenitic matrix, super duplex stainless steel was mainly comprised of allotriomorphic grain boundary and Widmanstätten side plate austenite morphologies in the ferrite matrix. Also the heat-affected zone of austenitic base metal comprised of large austenite grains with little amounts of ferrite, whereas a coarse-grained ferritic region was observed in the heat-affected zone of super duplex base metal. Although both welded joints showed acceptable mechanical properties, the hardness and impact strength of the weld metal produced using super duplex filler metal were found to be better than that obtained by austenitic filler metal.

  8. Photochemistry of psoralen-DNA adducts, biological effects of psoralen-DNA adducts, applications of psoralen-DNA photochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Yun-bo

    1988-03-01

    This thesis consists of three main parts and totally eight chapters. In Part I, The author will present studies on the photochemistry of psoralen-DNA adducts, specifically, the wavelength dependencies for the photoreversals of thymidine-HMT (4'-hydroxymethyl-4, 5', 8-trimenthylpsoralen) monoadducts and diadduct and the same adducts incorporated in DNA helices and the wavelength dependecies for the photocrossslinking of thymidine-HMT monoadducts in double-stranded helices. In Part II, The author will report some biological effects of psoralen-DNA adducts, i.e., the effects on double-stranded DNA stability, DNA structure, and transcription by E. coli and T7 RNA polymerases. Finally, The author will focus on the applications of psoralen-DNA photochemistry to investigation of protein-DNA interaction during transcription, which includes the interaction of E. coli and T7 RNA polymerases with DNA in elongation complexes arrested at specific psoralen-DNA adduct sites as revealed by DNase I footprinting experiments. 123 refs., 52 figs., 12 tabs.

  9. Photochemistry of psoralen-DNA adducts, biological effects of psoralen-DNA adducts, applications of psoralen-DNA photochemistry

    International Nuclear Information System (INIS)

    Shi, Yun-bo.

    1988-03-01

    This thesis consists of three main parts and totally eight chapters. In Part I, The author will present studies on the photochemistry of psoralen-DNA adducts, specifically, the wavelength dependencies for the photoreversals of thymidine-HMT (4'-hydroxymethyl-4, 5', 8-trimenthylpsoralen) monoadducts and diadduct and the same adducts incorporated in DNA helices and the wavelength dependecies for the photocrossslinking of thymidine-HMT monoadducts in double-stranded helices. In Part II, The author will report some biological effects of psoralen-DNA adducts, i.e., the effects on double-stranded DNA stability, DNA structure, and transcription by E. coli and T7 RNA polymerases. Finally, The author will focus on the applications of psoralen-DNA photochemistry to investigation of protein-DNA interaction during transcription, which includes the interaction of E. coli and T7 RNA polymerases with DNA in elongation complexes arrested at specific psoralen-DNA adduct sites as revealed by DNase I footprinting experiments. 123 refs., 52 figs., 12 tabs

  10. Thermodynamics of sequence-specific binding of PNA to DNA

    DEFF Research Database (Denmark)

    Ratilainen, T; Holmén, A; Tuite, E

    2000-01-01

    For further characterization of the hybridization properties of peptide nucleic acids (PNAs), the thermodynamics of hybridization of mixed sequence PNA-DNA duplexes have been studied. We have characterized the binding of PNA to DNA in terms of binding affinity (perfectly matched duplexes) and seq......For further characterization of the hybridization properties of peptide nucleic acids (PNAs), the thermodynamics of hybridization of mixed sequence PNA-DNA duplexes have been studied. We have characterized the binding of PNA to DNA in terms of binding affinity (perfectly matched duplexes...

  11. Intersegmental interactions in supercoiled DNA: atomic force microscope study

    Energy Technology Data Exchange (ETDEWEB)

    Shlyakhtenko, Luda S.; Miloseska, Lela; Potaman, Vladimir N.; Sinden, Richard R.; Lyubchenko, Yuri L

    2003-10-15

    Intersegmental interactions in DNA facilitated by the neutralization of electrostatic repulsion was studied as a function of salt concentration and DNA supercoiling. DNA samples with defined superhelical densities were deposited onto aminopropyl mica at different ionic conditions and imaged in air after drying of the samples. Similar to hydrodynamic data, we did not observe a collapse of supercoiled DNA, as proposed earlier by cryo-EM studies. Instead, the formation of the contacts between DNA helices within supercoiled loops with no visible space between the duplexes was observed. The length of such close contacts increased upon increasing NaCl concentration. DNA supercoiling was a critical factor for the stabilization of intersegmental contacts. Implications of the observed effect for understanding DNA compaction in the cell and for regulation DNA transactions via interaction of distantly separated DNA regions are discussed.

  12. Dideoxynucleoside triphosphate-sensitive DNA polymerase from rice is involved in base excision repair and immunologically similar to mammalian DNA pol beta.

    Science.gov (United States)

    Sarkar, Sailendra Nath; Bakshi, Sankar; Mokkapati, Sanath K; Roy, Sujit; Sengupta, Dibyendu N

    2004-07-16

    A single polypeptide with ddNTP-sensitive DNA polymerase activity was purified to near homogeneity from the shoot tips of rice seedlings and analysis of the preparations by SDS-PAGE followed by silver staining showed a polypeptide of 67 kDa size. The DNA polymerase activity was found to be inhibitory by ddNTP in both in vitro DNA polymerase activity assay and activity gel analysis. Aphidicolin, an inhibitor of other types of DNA polymerases, had no effect on plant enzyme. The 67 kDa rice DNA polymerase was found to be recognized by the polyclonal antibody (purified IgG) made against rat DNA polymerase beta (pol beta) both in solution and also on Western blot. The recognition was found to be very specific as the activity of Klenow enzyme was unaffected by the antibody. The ability of rice nuclear extract to correct G:U mismatch of oligo-duplex was observed when oligo-duplex with 32P-labeled lower strand containing U (at 22nd position) was used as substrate. Differential appearance of bands at 21-mer, 22-mer, and 51-mer position in presence of dCTP was visible only with G:U mismatch oligo-duplex, but not with G:C oligo-duplex. While ddCTP or polyclonal antibody against rat-DNA pol beta inhibits base excision repair (BER), aphidicolin had no effect. These results for the first time clearly demonstrate the ability of rice nuclear extract to run BER and the involvement of ddNTP-sensitive pol beta type DNA polymerase. Immunological similarity of the ddNTP-sensitive DNA polymerase beta of rice and rat and its involvement in BER revealed the conservation of structure and function of ddNTP-sensitive DNA pol beta in plant and animal.

  13. Nucleic acid nanomaterials: Silver-wired DNA

    Science.gov (United States)

    Auffinger, Pascal; Ennifar, Eric

    2017-10-01

    DNA double helical structures are supramolecular assemblies that are typically held together by classical Watson-Crick pairing. Now, nucleotide chelation of silver ions supports an extended silver-DNA hybrid duplex featuring an uninterrupted silver array.

  14. Molecular mechanisms of DNA photodamage

    Energy Technology Data Exchange (ETDEWEB)

    Starrs, S.M

    2000-05-01

    Photodamage in DNA, caused by ultraviolet (UV) light, can occur by direct excitation of the nucleobases or indirectly via the action of photosensitisers. Such, DNA photodamage can be potentially mutagenic or lethal. Among the methods available for detecting UV-induced DNA damage, gel sequencing protocols, utilising synthetic oligodeoxyribonucleotides as targets for UV radiation, allow photolesions to be mapped at nucleotide resolution. This approach has been applied to investigate both DNA damage mechanisms. Following a general overview of DNA photoreactivity, and a description of the main experimental procedures, Chapter 3 identifies the origin of an anomalous mobility shift observed in purine chemical sequence ladders that can confuse the interpretation of DNA cleavage results; measures to abolish this shift are also described. Chapters 4 and 5 examine the alkali-labile DNA damage photosensitised by representative nonsteroidal antiinflammatory drugs (NSAIDs) and the fluoroquinolone antibiotics. Suprofen was the most photoactive NSAID studied, producing different patterns of guanine-specific damage in single-stranded and duplex DNA. Uniform modification of guanine bases, typifying attack by singlet oxygen, was observed in single-stranded oligodeoxyribonucleotides. In duplex molecules, modification was limited to the 5'-G of GG doublets, which is indicative of an electron transfer. The effect of quenchers and photoproduct analysis substantiated these findings. The quinolone, nalidixic acid, behaves similarly. The random base cleavage photosensitised by the fluoroquinolones, has been attributed to free radicals produced during their photodecomposition. Chapter 6 addresses the photoreactivity of purines within unusual DNA structures formed by the repeat sequences (GGA){sub n} and (GA){sub n}, and a minihairpin. There was no definitive evidence for enhanced purine reactivity caused by direct excitation. Finally, Chapter 7 investigates the mutagenic potential of a

  15. Molecular mechanisms of DNA photodamage

    International Nuclear Information System (INIS)

    Starrs, S.M.

    2000-05-01

    Photodamage in DNA, caused by ultraviolet (UV) light, can occur by direct excitation of the nucleobases or indirectly via the action of photosensitisers. Such, DNA photodamage can be potentially mutagenic or lethal. Among the methods available for detecting UV-induced DNA damage, gel sequencing protocols, utilising synthetic oligodeoxyribonucleotides as targets for UV radiation, allow photolesions to be mapped at nucleotide resolution. This approach has been applied to investigate both DNA damage mechanisms. Following a general overview of DNA photoreactivity, and a description of the main experimental procedures, Chapter 3 identifies the origin of an anomalous mobility shift observed in purine chemical sequence ladders that can confuse the interpretation of DNA cleavage results; measures to abolish this shift are also described. Chapters 4 and 5 examine the alkali-labile DNA damage photosensitised by representative nonsteroidal antiinflammatory drugs (NSAIDs) and the fluoroquinolone antibiotics. Suprofen was the most photoactive NSAID studied, producing different patterns of guanine-specific damage in single-stranded and duplex DNA. Uniform modification of guanine bases, typifying attack by singlet oxygen, was observed in single-stranded oligodeoxyribonucleotides. In duplex molecules, modification was limited to the 5'-G of GG doublets, which is indicative of an electron transfer. The effect of quenchers and photoproduct analysis substantiated these findings. The quinolone, nalidixic acid, behaves similarly. The random base cleavage photosensitised by the fluoroquinolones, has been attributed to free radicals produced during their photodecomposition. Chapter 6 addresses the photoreactivity of purines within unusual DNA structures formed by the repeat sequences (GGA) n and (GA) n , and a minihairpin. There was no definitive evidence for enhanced purine reactivity caused by direct excitation. Finally, Chapter 7 investigates the mutagenic potential of a dimeric

  16. Development of a panel of seven duplex real-time PCR assays for detecting 13 streptococcal superantigens.

    Science.gov (United States)

    Yang, Peng; Peng, Xiaomin; Cui, Shujuan; Shao, Junbin; Zhu, Xuping; Zhang, Daitao; Liang, Huijie; Wang, Quanyi

    2013-07-30

    Streptococcal superantigens (SAgs) are the major virulence factors of infection in humans for group A Streptococcus (GAS) bacteria. A panel consisting of seven duplex real-time PCR assays was developed to simultaneously detect 13 streptococcal SAgs and one internal control which may be important in the control of GAS-mediated diseases. Primer and probe sequences were selected based on the highly conserved region from an alignment of nucleotide sequences of the 13 streptococcal SAgs. The reaction conditions of the duplex real-time PCR were optimized and the specificity of the duplex assays was evaluated using SAg positive strains. The limit of detection of the duplex assays was determined by using 10-fold serial dilutions of the DNA of 13 streptococcal SAgs and compared to a conventional polymerase chain reaction (PCR) method for evaluating the duplex assays sensitivity. Using the duplex assays, we were able to differentiate between 13 SAgs from Streptococcus strains and other non-Streptococcus bacteria without cross-reaction. On the other hand, the limit of detection of the duplex assays was at least one or two log dilutions lower than that of the conventional PCR. The panel was highly specific (100%) and the limit of detection of these duplex groups was at least ten times lower than that obtained by using a conventional PCR method.

  17. Reducing duplex examinations in patients with iatrogenic pseudoaneurysms.

    Science.gov (United States)

    Stone, Patrick A; Aburahma, Ali F; Flaherty, Sarah K

    2006-06-01

    results in an estimated cost savings of $12,000, based on treating 15 small IPSAs per year. Ultrasound-guided thrombin injection is safe and effective for the treatment of nearly all iatrogenic pseudoaneurysms. We recommend primary treatment of small pseudoaneurysms by ultrasound-guided thrombin injection rather than observation with serial duplex scans. A point-of-care treatment algorithm can result in cost savings by reducing the number of necessary duplex examinations.

  18. ON SECURE FULL DUPLEX COMMUNICATION IN MOBILE AD HOC NETWORK

    OpenAIRE

    S. C. Dutta; Sudha Singh; D. K. Singh

    2013-01-01

    This paper is to establish Ad Hoc network in mobile phones and start fully secured full duplex communication in any situation. This type of communication will be cost effective and it will be fastest way of communication in case of any server failure or server error.

  19. An improved method for detecting genetic variation in DNA using denaturing gradient gel electrophoresis

    International Nuclear Information System (INIS)

    Takahashi, Norio; Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko.

    1990-05-01

    We have examined the feasibility of denaturing gradient gel electrophoresis (DGGE) of RNA:DNA duplexes to detect variations in genomic and cloned DNAs. The result has demonstrated that use of RNA:DNA duplexes makes DGGE much more practical for screening a large number of samples than use of DNA:DNA heteroduplexes, because preparation of RNA probes is easier than that of DNA probes. Three different 32 P-labeled RNA probes were produced. Genomic or cloned DNAs were digested with restriction enzymes and hybridized to labeled RNA probes, and resulting RNA:DNA duplexes were examined by DGGE. The presence of a mismatch(es) was detected as a difference in the mobility of bands on the gel. The experimental conditions were determined using DNA segments from cloned normal and three thalassemic human β-globin genes. The results from experiments on the cloned DNAs suggest that DGGE of RNA:DNA duplexes will detect nucleotide substitutions and deletions in DNA. In the course of these studies, a polymorphism due to a single-base substitution at position 666 of IVS2 (IVS2-666) of the human β-globin gene was directly identified using genomic DNA samples. A study of 59 unrelated Japanese from Hiroshima was undertaken in which the frequency of the allele with C at IVS2-666 was 0.48 and that of the allele with T was 0.52. This approach was found to be very effective for detecting heritable variation and should be a powerful tool for detecting fresh mutations in DNA, which occur outside the known restriction sites. (author)

  20. Effect of γ-irradiated DNA on the activity of DNA polymerase

    International Nuclear Information System (INIS)

    Leadon, S.A.; Ward, J.F.

    1981-01-01

    A cell-free assay was developed to measure the effect of γ-irradiated DNA template on the ability of DNA polymerase to copy unirradiated template. Doses as low as 1 krad were able to decrease (approx. 15%) the activity of both bacterial and mammalian DNA polymerases in the assay. The percentage of polymerase activity decreased as the dose received by the template increased. The reduction in DNA polymerase activity was shown to be due to an inhibition of the enzyme by the irradiated DNA. Irradiated poly(dA-dT) was more effective in reducing polymerase activity than calf thymus DNA. Thus the polymerase-inhibition site(s) appears to be associated with base damage, specifically adenine or thymine. Using a free-radical scavenger, OH radicals were found to be involved in producing the damage sites. The interaction between irradiated DNA and DNA polymerase was found to be specific for the enzyme and not for other proteins present in the assay. The inhibition of DNA polymerase occurred prior to or during the initiation of DNA synthesis rather than after initiation of synthesis, i.e., during elongation

  1. The Effect of Basepair Mismatch on DNA Strand Displacement

    OpenAIRE

    Broadwater, D.?W.?Bo; Kim, Harold?D.

    2016-01-01

    DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single base pair mismatch. The apparent displacement rate varied si...

  2. Effect of friction time on the microstructure and mechanic properties of friction welded AISI 1040/Duplex stainless steel

    Directory of Open Access Journals (Sweden)

    İhsan Kırık

    2000-06-01

    Full Text Available In this study, the effect on the characteristic microstructure and mechanic properties of friction time on the couple steels AISI 1040/AISI 2205 stainless steel joining with friction welding method was experimentally investigated. Friction welding experiment were carried out in privately prepared PLC controlled continuous friction welding machine by us. Joints were carried out under 1700 rpm rotation speed, with 30MPa process friction pressure, 60MPa forging pressure, 4 second forging pressure and under 3, 5, 7, 9 and 11 second friction time, respectively. After friction welding, the bonding interface microstructures of the specimens were examined by SEM microscopy and EDS analysis. After weld microhardness and tensile strength of specimens were carried out. The result of applied tests and observations pointed out that the properties of microstructure were changed with friction time increased. The excellent tensile strength of joint observed on 1700 rpm rotation speed and 3 second friction time sample.

  3. Effect of R-phase on impact toughness of 25Cr-7Ni-4Mo super duplex stainless steel

    Science.gov (United States)

    Hwang, T. H.; Kim, J. H.; Kim, K. H.; Moon, W. J.; Kang, C. Y.

    2014-01-01

    Effect of R-phase at an initial stage of aging on impact toughness was investigated in this study. Microstructure observation and energy dispersive x-ray analysis obviously clarified that the R-phase was mainly precipitated at interface of ferrite and austenite phases and inside of the ferrite phase at the initial stage of aging, and it was transformed into σ-phase with an increase of aging time. The ferrite phase was decomposed into new γ2-phase and σ-phase by aging treatment. These variations of phase during the aging affected the mechanical property. In other words, the impact toughness value rapidly decreased with an increase of the R-phase at the initial stage of aging while it sharply decreased and then slowly decreased with an increase of the σ-phase. This decrease of the toughness at the initial stage of aging was predominantly due to the precipitation of R-phase.

  4. Effect of Mn on σ Phase and Toughness of 22%Cr Duplex Stainless Steel by Aging Treatment at 700℃

    Directory of Open Access Journals (Sweden)

    BAI Yu-liang

    2017-05-01

    Full Text Available The effect of different Mn contents on the σ phase and toughness of 22%Cr (mass fraction, the same below low-nickel DSS by means of OM, XRD, SEM, TEM, precipitation kinetics and Charpy impact tests was studied. The results show that the morphology of precipitated phases changes from tiny granulated σ phase in δ/γ phase boundary to σ/γ2 eutectoid structure within δ phase with the addition of Mn from 4.3% to 9.7% and 76 hours aging. The increase of Mn content can decrease Avrami exponent n and increase reaction constant B, and the accelerating of σ-phase precipitation with higher Mn addition is due to the participation of Mn. Increasing Mn content can make initial time and ending time of σ-phase precipitation earlier and expand the interval between the initial time and ending time of σ-phase precipitation, that is, the more Mn addition, the earlier precipitation beginning time of σ-phase and the lower precipitation rate of it. The impact toughness is not sensitive to 1% transformation fraction of δ-ferrite, but it drops rapidly while the transformation fraction of δ-ferrite increases from 1% to 5%. More addition of Mn is good to impact toughness at the early stage of aging treatment, but the impact toughness decreases rapidly by accelerating the transformation fraction of δ-ferrite more than 1% earlier at the middle stage of aging time.

  5. The effects of low fugacity hydrogen in duplex- and beta-annealed Ti-6Al-4V alloy

    International Nuclear Information System (INIS)

    Tal-Gutelmacher, E.; Eliezer, D.; Eylon, D.

    2004-01-01

    Due to its excellent combination of a high strength/weight ratio and good corrosion behavior, Ti-6Al-4V alloys are ranked among the most important advanced materials for a variety of aerospace, chemical engineering, biomaterials, marine and commercial applications. However, in many of these technological applications, this alloy is exposed to environments which can act as sources of hydrogen, and severe problems may arise based on its susceptibility to hydrogen embrittlement. Even small hydrogen concentrations might lead to failure. Consequently, a comprehensive knowledge of hydrogen-trapping interactions is necessary to better understand the trapping mechanisms, the types of the trap sites, the trapped hydrogen content, in order to determine the safe service conditions of this alloy in the aerospace industry. The objective of this paper is to investigate the role of microstructure on hydrogen absorption/desorption behavior in Ti-6Al-4V alloy, with specific emphasis on the nature of the interaction between microstructural traps and hydrogen atoms. The effect of low fugacity hydrogen on the microstructure is studied using X-ray diffraction (XRD), and electron microscopy (SEM and TEM), while the absorption and desorption characteristics are determined by means of a hydrogen determinator and thermal desorption spectroscopy (TDS), respectively. The role of microstructure on hydrogen absorption and desorption behavior is discussed in detail

  6. Effect of DNA type on response of DNA biosensor for carcinogens

    Science.gov (United States)

    Sani, Nor Diyana bt. Md.; Heng, Lee Yook; Surif, Salmijah; Lazim, Azwani Mat

    2013-11-01

    Carcinogens are cancer causing chemicals that can bind to DNA and cause damage to the DNA. These chemicals are available everywhere including in water, air, soil and food. Therefore, a sensor that can detect the presence of these chemicals will be a very useful tool. Since carcinogens bind to DNA, DNA can be used as the biological element in a biosensor. This study has utilized different types of DNA in a biosensor for carcinogen detection. The DNAs include double stranded calf thymus DNA, single stranded calf thymus DNA and guanine rich single stranded DNA. The modified SPE was exposed to a carcinogen followed by interaction with methylene blue which acts as the electroactive indicator. The SPE was then analysed using differential pulse voltammetry (DPV). Optimization studies were conducted for MB concentration and accumulation time, DNA concentration, as well as effect of buffer concentration, buffer pH and ionic strength. The performance of the biosensor was tested on a group 1 carcinogen, formaldehyde. The results indicated that the usage of guanine rich single stranded DNA also gives higher response as carcinogens prefer to bind with guanine compared to other bases.

  7. The effect of chronic alcohol consumption on mitochondrial DNA mutagenesis in human blood

    Energy Technology Data Exchange (ETDEWEB)

    Wurmb-Schwark, N. von [Institute of Legal Medicine, Christian Albrecht University of Kiel, Arnold-Heller-Str. 12, 24105 Kiel (Germany)], E-mail: nvonwurmb@rechtsmedizin.uni-kiel.de; Ringleb, A.; Schwark, T. [Institute of Legal Medicine, Christian Albrecht University of Kiel, Arnold-Heller-Str. 12, 24105 Kiel (Germany); Broese, T.; Weirich, S.; Schlaefke, D. [Clinic of Psychiatry and Psychotherapy, University of Rostock, Gehlsheimer Str. 20, Rostock (Germany); Wegener, R. [Institute of Legal Medicine, St-Georg-Str. 108, University of Rostock, 18055 Rostock (Germany); Oehmichen, M. [Institute of Legal Medicine, Christian Albrecht University of Kiel, Arnold-Heller-Str. 12, 24105 Kiel (Germany)

    2008-01-01

    The 4977 bp deletion of mitochondrial DNA (mtDNA) is known to accumulate with increasing age in post mitotic tissues. Recently, studies came out detecting this specific alteration also in fast replicating cells, e.g. in blood or skin tissue, often in correlation to specific diseases or - specifically in skin - external stressors such as UV radiation. In this study, we investigated mitochondrial mutagenesis in 69 patients with a chronic alcoholic disease and 46 age matched controls with a moderate drinking behavior. Two different fragments, specific for total and for deleted mtDNA (dmtDNA) were amplified in a duplex-PCR. A subsequent fragment analysis was performed and for relative quantification, the quotient of the peak areas of amplification products specific for deleted and total mtDNA was determined. Additionally, a real time PCR was performed to quantify mtDNA copy number. The relative amount of 4977 bp deleted mtDNA in alcoholics was significantly increased compared to controls. On the other hand, no difference regarding the mtDNA/nuclear DNA ratio in both investigated groups was detected. Additionally, no age dependence could be found nor in alcoholics, neither in the control group. These findings indicate that mtDNA mutagenesis in blood can be influenced by stressors such as alcohol. Ethanol seems to be a significant factor to alter mitochondrial DNA in blood and might be an additional contributor for the cellular aging process.

  8. The effect of chronic alcohol consumption on mitochondrial DNA mutagenesis in human blood

    International Nuclear Information System (INIS)

    Wurmb-Schwark, N. von; Ringleb, A.; Schwark, T.; Broese, T.; Weirich, S.; Schlaefke, D.; Wegener, R.; Oehmichen, M.

    2008-01-01

    The 4977 bp deletion of mitochondrial DNA (mtDNA) is known to accumulate with increasing age in post mitotic tissues. Recently, studies came out detecting this specific alteration also in fast replicating cells, e.g. in blood or skin tissue, often in correlation to specific diseases or - specifically in skin - external stressors such as UV radiation. In this study, we investigated mitochondrial mutagenesis in 69 patients with a chronic alcoholic disease and 46 age matched controls with a moderate drinking behavior. Two different fragments, specific for total and for deleted mtDNA (dmtDNA) were amplified in a duplex-PCR. A subsequent fragment analysis was performed and for relative quantification, the quotient of the peak areas of amplification products specific for deleted and total mtDNA was determined. Additionally, a real time PCR was performed to quantify mtDNA copy number. The relative amount of 4977 bp deleted mtDNA in alcoholics was significantly increased compared to controls. On the other hand, no difference regarding the mtDNA/nuclear DNA ratio in both investigated groups was detected. Additionally, no age dependence could be found nor in alcoholics, neither in the control group. These findings indicate that mtDNA mutagenesis in blood can be influenced by stressors such as alcohol. Ethanol seems to be a significant factor to alter mitochondrial DNA in blood and might be an additional contributor for the cellular aging process

  9. DE-NE0000724 - Research Performance Final Report - Investigation of Thermal Aging Effects on the Evolution of Microstructure and Mechanical Properties of Cast Duplex Stainless Steels

    Energy Technology Data Exchange (ETDEWEB)

    Ankem, Sreeramamurthy [University of Maryland, College Park, MD (United States); Perea, Daniel E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kolli, R. Prakash [University of Maryland, College Park, MD (United States); Mburu, Sarah [University of Maryland, College Park, MD (United States); Schwarm, Samuel C. [University of Maryland, College Park, MD (United States)

    2017-12-11

    This report details the research activities carried out under DOE-NEUP award number DE-NE0000724 concerning the evolution of structural and mechanical properties during thermal aging of CF–3 and CF–8 cast duplex stainless steels (CDSS). The overall objective of this project was to use state-of-the-art characterization techniques to elucidate trends and phenomena in the mechanical and structural evolution of cast duplex stainless steels (CDSS) during thermal aging. These steels are commonly used as structural materials in commercial light water nuclear power plants, undergoing aging for decades in operation as cooling water pipes, pump casings, valve bodies, etc. During extended exposure to these conditions, CDSS are known to undergo a change in mechanical properties resulting in a loss of ductility, i.e. embrittlement. While it is generally accepted that structural changes within the ferrite phase, such as decomposition into iron (Fe)-rich and chromium (Cr)-rich domains, lead to the bulk embrittlement of the steels, many questions remain as to the mechanisms of embrittlement at multiple length scales. This work is intended to shed insight into the atomic level composition changes, associated kinetic mechanisms, and effects of changing phase structure on micro- and nano-scale deformation that lead to loss of impact toughness and tensile ductility in these steels. In general, this project provides a route to answer some of these major questions using techniques such as 3-dimensional (3-D) atom probe tomography (APT) and real-microstructure finite element method (FEM) modeling, which were not readily available when these steels were originally selected for service in light water reactors. Mechanical properties evaluated by Charpy V-notch impact testing (CVN), tensile testing, and microhardness and nanohardness measurements were obtained for each condition and compared with the initial baseline properties to view trends in deformation behavior during aging

  10. Effects of humic substances on fluorometric DNA quantification and DNA hybridization

    NARCIS (Netherlands)

    Bachoon, DS; Otero, E; Hodson, RE

    2001-01-01

    DNA extracts from sediment and water samples are often contaminated with coextracted humic-like impurities, Estuarine humic substances and vascular plant extract were used to evaluate the effect of the presence of such impurities on DNA hybridization and quantification. The presence of humic

  11. The effect of low radiation doses on DNA repair processes

    International Nuclear Information System (INIS)

    Tuschl, H.

    1978-08-01

    Error free DNA repair processes are an important preprequisite for the maintenance of genetic integrity of cells. They are of special importance for persons therapeutically or occupationally exposed to radiation. Therefore the effect of radiation therapy and elevated natural background radiation on unscheduled DNA synthesis was tested in peripheral lymphocytes of exposed persons. Both, autoradiographic studies of unscheduled DNA synthesis and measurement of 3 H-thymidine uptake into double stranded and single-strand containing DNA fractions revealed an increase of capacity for DNA repair. (author)

  12. Reaction of misonidazole with DNA radicals and its effect on the template activity of DNA

    International Nuclear Information System (INIS)

    Endoh, Daiji; Kuwabara, Mikinori; Sato, Fumiaki; Yoshii, Giichi.

    1985-01-01

    After calf thymus DNA was gamma-irradiated in the solid state in vacuo and subsequently dissolved in aqueous solution containing misonidazole (3 mM) under hypoxic condition, the frequency of single-strand breaks and alkali-labile sites in DNA and the amount of misonidazole bound to DNA were measured. The presence of misonidazole converted the precursor radicals, which otherwise results in single-strand breaks, to alkali-labile sites, and the amount of alkali-labile sites increased linearly with increasing radiation dose. The amount of misonidazole bound to DNA also increased linearly with increasing radiation dose. The biological meaning of the changes in the frequency of single-strand breaks and alkali-labile sites by the reaction of misonidazole with DNA radicals and of binding misonidazole with DNA was examined using a model system to measure the template activity of DNA for RNA synthesis in vitro. The conversion of DNA radicals to alkali-labile sites protected the radiation-induced decrease in the template activity of DNA, while the adduct formation of misonidazole had no effect on it. (author)

  13. Targeting G-quadruplex DNA Structures by EMICORON has a strong antitumor efficacy against advanced models of human colon cancer

    DEFF Research Database (Denmark)

    Porru, Manuela; Artuso, Simona; Salvati, Erica

    2015-01-01

    We previously identified EMICORON as a novel G-quadruplex (G4) ligand showing high selectivity for G4 structures over the duplex DNA, causing telomere damage and inhibition of cell proliferation in transformed and tumor cells. Here, we evaluated the antitumoral effect of EMICORON on advanced mode...

  14. Duplex gall bladder: bystander or culprit.

    Science.gov (United States)

    Kumar, Jogender; Yadav, Arushi

    2017-08-30

    Gall bladder (GB) duplication is a rare anatomical malformation, which can be detected by preoperative imaging study. We present a case of duplex gall bladder in a 14-year-old boy who presented with abdominal pain. On ultrasound, he had right nephrolithiasis and duplex gall bladder. Duplex gall bladder was confirmed on MR cholangiopancreatography. There was a dilemma for surgical management of duplex gall bladder; however, he became asymptomatic after conservative treatment. Prophylactic surgery is not recommended for asymptomatic incidentally detected duplex gall bladder. Radiologists and paediatric surgeons should be sensitised about the exact anatomy of this entity. © BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  15. Hot-Dip Aluminizing on AISI F55–UNS S32760 Super Duplex Stainless Steel Properties: Effect of Thermal Treatments

    Directory of Open Access Journals (Sweden)

    Andrea Francesco Ciuffini

    2017-11-01

    Full Text Available The behavior of super duplex stainless steels AISI F55-UNS S32760 in hot-dip aluminizing process has been studied, investigating the influence of cold working and of different initial microstructures obtained through a preliminary thermal treatment. The microstructural features examined are the secondary austenite precipitation, the static recovery of ferrite and the thermal dissolution of austenite within ferritic matrix. The hot-dip aluminizing temperature has been optimized through sessile drop tests. The treatment has been performed at 1100 °C for 300 s, 900 s and 2700 s. A strong chemical interaction occurs, generating intermetallic compounds at the interface. Molten aluminum interacts exclusively with the ferritic phase due to its much higher diffusivity in this phase coupled with its marked ferrite-stabilizer behavior. Thus, the influence of cold working is not remarkable, since the strains are mainly allocated by austenitic phase. The diffusivity of aluminum increases due to lattice defects thermally generated and, mainly, to influence given by grain boundaries, multiplied by secondary austenite precipitation, which act as short-circuit diffusion paths. Ni and Cr contents in the ferritic matrix have an influence but not highly relevant. Then, the best starting condition of the super duplex stainless steel substrates, to obtain a thick interfacial layer, are the thermal annealing at 1080 °C for 360 s/mm after a solution thermal treatment at 1300 °C for 60 s/mm.

  16. Effect of welding process on the microstructure and properties of dissimilar weld joints between low alloy steel and duplex stainless steel

    Science.gov (United States)

    Wang, Jing; Lu, Min-xu; Zhang, Lei; Chang, Wei; Xu, Li-ning; Hu, Li-hua

    2012-06-01

    To obtain high-quality dissimilar weld joints, the processes of metal inert gas (MIG) welding and tungsten inert gas (TIG) welding for duplex stainless steel (DSS) and low alloy steel were compared in this paper. The microstructure and corrosion morphology of dissimilar weld joints were observed by scanning electron microscopy (SEM); the chemical compositions in different zones were detected by energy-dispersive spectroscopy (EDS); the mechanical properties were measured by microhardness test, tensile test, and impact test; the corrosion behavior was evaluated by polarization curves. Obvious concentration gradients of Ni and Cr exist between the fusion boundary and the type II boundary, where the hardness is much higher. The impact toughness of weld metal by MIG welding is higher than that by TIG welding. The corrosion current density of TIG weld metal is higher than that of MIG weld metal in a 3.5wt% NaCl solution. Galvanic corrosion happens between low alloy steel and weld metal, revealing the weakness of low alloy steel in industrial service. The quality of joints produced by MIG welding is better than that by TIG welding in mechanical performance and corrosion resistance. MIG welding with the filler metal ER2009 is the suitable welding process for dissimilar metals jointing between UNS S31803 duplex stainless steel and low alloy steel in practical application.

  17. Contribution to the metallurgy of welding processes in stainless ferritic-austenitic (duplex) steels

    International Nuclear Information System (INIS)

    Perteneder, E.; Toesch, J.; Rabensteiner, G.

    1989-01-01

    Duplex steels have a ferritic austenitic structure. Therefore, to obtain a successful welding, special metallurgical regulations must be observed. The effect of energy per unit length and plate thickness onto the heat influence zone in case of manual arc welding is examined. Practice-oriented instructions for the welding technique to be applied are deduced from the results. Finally, the effect of the alloy composition onto the welding capacity of duplex steels is examined. (orig.) [de

  18. Two-dimensional 1H and 31P NMR spectra of a decamer oligodeoxyribonucleotide duplex and a quinoxaline ([MeCys3, MeCys7]TANDEM) drug duplex complex

    International Nuclear Information System (INIS)

    Powers, R.; Olsen, R.K.; Gorenstein, D.G.

    1989-01-01

    Assignment of the 1H and 31P NMR spectra of a decamer oligodeoxyribonucleotide duplex, d(CCCGATCGGG), and its quinoxaline ([MeCys3, MeCys7]TANDEM) drug duplex complex has been made by two-dimensional 1H-1H and heteronuclear 31P-1H correlated spectroscopy. The 31P chemical shifts of this 10 base pair oligonucleotide follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence, the more upfield the 31P resonance occurs. While the 31P chemical shifts show sequence-specific variations, they also do not generally follow the Calladine rules previously demonstrated. 31P NMR also provides a convenient monitor of the phosphate ester backbone conformational changes upon binding of the drug to the duplex. Although the quinoxaline drug, [MeCys3, MeCys7]TANDEM, is generally expected to bind to duplex DNA by bis-intercalation, only small 31P chemical shift changes are observed upon binding the drug to duplex d(CCCGATCGGG). Additionally, only small perturbations in the 1H NMR and UV spectra are observed upon binding the drug to the decamer, although association of the drug stabilizes the duplex form relative to the other states. These results are consistent with a non-intercalative mode of association of the drug. Modeling and molecular mechanics energy minimization demonstrate that a novel structure in which the two quinoxaline rings of the drug binds in the minor groove of the duplex is possible

  19. A duplex endpoint PCR assay for rapid detection and differentiation of Leptospira strains.

    Science.gov (United States)

    Benacer, Douadi; Zain, Siti Nursheena Mohd; Lewis, John W; Khalid, Mohd Khairul Nizam Mohd; Thong, Kwai Lin

    2017-01-01

    This study aimed to develop a duplex endpoint PCR assay for rapid detection and differentiation of Leptospira strains. Primers were designed to target the rrs (LG1/LG2) and ligB (LP1/LP2) genes to confirm the presence of the Leptospira genus and the pathogenic species, respectively. The assay showed 100% specificity against 17 Leptospira strains with a limit of detection of 23.1pg/µl of leptospiral DNA and sensitivity of 103 leptospires/ml in both spiked urine and water. Our duplex endpoint PCR assay is suitable for rapid early detection of Leptospira with high sensitivity and specificity.

  20. Specificity of binding to four-way junctions in DNA by bacteriophage T7 endonuclease I.

    OpenAIRE

    Parsons, C A; West, S C

    1990-01-01

    T7 endonuclease I binds specifically to four-way junctions in duplex DNA and promotes their resolution into linear duplexes. Under conditions in which the nuclease activity is blocked by the absence of divalent cations, the enzyme forms a distinct protein-DNA complex with the junction, as detected by gel retardation and filter binding assays. The formation of this complex is structure-specific and contrasts with the short-lived binding complexes formed on linear duplex DNA. The binding comple...

  1. Quantitative structure of a complex between a minor-groove-specific drug and a bent DNA decamer duplex: Use of 2D NMR data and NOESY constrained energy minimization

    International Nuclear Information System (INIS)

    Sarma, M.H.; Gupta, G.; Garcia, A.E.; Umemoto, K.; Sarma, R.H.

    1990-01-01

    Two-dimensional nuclear magnetic resonance (2D NMR) studies on d(GA4T4C)2 and d(GT4A4C)2 showed that A.T pairs are propeller twisted. As a result, A/T tracts form a straight rigid structural block with an array of bifurcated inter base pair H bonds in the major groove. It was demonstrated (previous paper) that replacement of methyl group by hydrogen (changing from T to U) in the major groove does not disrupt the array of bifurcated H bonds in the major groove. In this article, we summarize results of 2D NMR and molecular mechanic studies on the effect of a minor-groove-binding A.T-specific drug on the structure d(GA4T4C)2. A distamycin analogue (Dst2) was used for this study. It is shown that Dst2 binds to the minor groove of d(GA4T4C)2 mainly driven by van der Waals interaction between A.T pairs and the drug; as a consequence, an array of bifurcated H bonds can be formed in the minor groove between amide/amino protons of Dst2 and A.T pairs of DNA. NOESY data suggest that Dst2 predominantly binds at the central 5 A.T pairs. NOESY data also reveal that, upon drug binding, d(GA4T4C)2 does not undergo any significant change in conformation from the free state; i.e., propeller-twisted A.T pairs are still present in DNA and hence the array of bifurcated H bonds must be preserved in the major groove. NOESY data for the A5-T6 sequence also indicate that there is little change in junction stereochemistry upon drug binding

  2. Effect of uv irradiation on lambda DNA transcription

    Energy Technology Data Exchange (ETDEWEB)

    Ranade, S S [Cancer Research Inst., Bombay (India)

    1977-05-01

    The effect of uv irradiation of template DNA has been studied in vitro in the E.coli RNA polymerase system with native and uv treated lambda DNA. Lambda DNA was more susceptible to uv than was calf-thymus DNA, yet a residual activity was observed at a uv dose of 0.5 x 10/sup 4/ erg/mm/sup 2/. From the kinetic analysis of the reaction and the incorporation of lambda /sup 32/P-labelled nucleoside triphosphates, it seems reasonable to conclude that uv irradiation probably did not affect the DNA initiation sites, recognizable by RNA polymerase. The transcription products made with uv irradiated lambda DNA were asymmetrical, and hybridized to the right half (R) and the left half (L) of lambda DNA with the ratio of R/L=4/1, and they showed a lower hybridizability than the transcripts with native lambda DNA. The initiation sites recognizable by RNA polymerase seemed to be the same on both native and uv irradiated lambda DNA, though the transcription of uv treated lambda DNA appeared to terminate with rather short RNA chains.

  3. Prolonged CT urography in duplex kidney.

    Science.gov (United States)

    Gong, Honghan; Gao, Lei; Dai, Xi-Jian; Zhou, Fuqing; Zhang, Ning; Zeng, Xianjun; Jiang, Jian; He, Laichang

    2016-05-13

    Duplex kidney is a common anomaly that is frequently associated with multiple complications. Typical computed tomography urography (CTU) includes four phases (unenhanced, arterial, parenchymal and excretory) and has been suggested to considerably aid in the duplex kidney diagnosi. Unfortunately, regarding duplex kidney with prolonged dilatation, the affected parenchyma and tortuous ureters demonstrate a lack of or delayed excretory opacification. We used prolonged-delay CTU, which consists of another prolonged-delay phase (1- to 72-h delay; mean delay: 24 h) to opacify the duplicated ureters and affected parenchyma. Seventeen patients (9 males and 8 females; age range: 2.5-56 y; mean age: 40.4 y) with duplex kidney were included in this study. Unenhanced scans did not find typical characteristics of duplex kidney, except for irregular perirenal morphology. Duplex kidney could not be confirmed on typical four-phase CTU, whereas it could be easily diagnosed in axial and CT-3D reconstruction using prolonged CTU (prolonged-delay phase). Between January 2005 and October 2010, in this review board-approved study (with waived informed consent), 17 patients (9 males and 8 females; age range: 2.5 ~ 56 y; mean age: 40.4 y) with suspicious duplex kidney underwent prolonged CTU to opacify the duplicated ureters and confirm the diagnosis. Our results suggest the validity of prolonged CTU to aid in the evaluation of the function of the affected parenchyma and in the demonstration of urinary tract malformations.

  4. The effect of irradiation on the DNA of cauliflower

    International Nuclear Information System (INIS)

    Harmey, M.A.

    1991-01-01

    The cellular DNA is one of the components most affected by ionizing radiation. Lesions caused range from single and double stranded breaks to chemical modification of bases depending on the radiation dosage and the metabolic status of the tissue. In attempting to assess the DNA damage induced by irradiation of vegetables in a speedy and convenient manner, we examined the effect on the DNA by subjecting cauliflower to a dose of 1 kGy. If DNA is nicked by irradiation, the extent of the damage can be assessed by using DNA polymerase to repair the nicks. Comparisons were made between irradiated and non irradiated cauliflower and incorporation of 32 p deoxy GTP in the presence of the Klenow fragment of DNA polymerase measured

  5. Effect of thermal aging on the low cycle fatigue behavior of Z3CN20.09M cast duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Weifeng [School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 (China); Xue, Fei [Suzhou Nuclear Power Research Institute, Suzhou 215004 (China); Tian, Yang [School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 (China); Yu, Dunji, E-mail: djyu@tju.edu.cn [School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 (China); Yu, Weiwei [Suzhou Nuclear Power Research Institute, Suzhou 215004 (China); Chen, Xu [School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 (China)

    2015-10-14

    Nuclear grade Z3CN20.09M cast duplex stainless steel exhibits enhanced cyclic stress response and prolonged low cycle fatigue life at room temperature after thermal aging at 400 °C for up to 6000 h. The threshold strain amplitude for the onset of secondary hardening is shifted to a lower value after thermal aging. Microstructural observations reveal that fatigue cracks tend to initiate from phase boundaries in virgin specimens, but to initiate in the ferrite phase in aged ones. Denser fatigue striations are found on the fracture surface of fatigued specimen subjected to longer thermal aging duration. These observations are explained in the context of thermal aging induced embrittlement of the ferrite phase and deformation induced martensitic phase transformation in the austenite phase.

  6. The Effect of Constant and Pulsed Current Gas Tungsten Arc Welding on Joint Properties of 2205 Duplex Stainless Steel to 316L Austenitic Stainless Steel

    Science.gov (United States)

    Neissi, R.; Shamanian, M.; Hajihashemi, M.

    2016-05-01

    In this study, dissimilar 316L austenitic stainless steel/2205 duplex stainless steel (DSS) joints were fabricated by constant and pulsed current gas tungsten arc welding process using ER2209 DSS as a filler metal. Microstructures and joint properties were characterized using optical and electron scanning microscopy, tensile, Charpy V-notch impact and micro-hardness tests, and cyclic polarization measurements. Microstructural observations confirmed the presence of chromium nitride and delta ferrite in the heat-affected zone of DSS and 316L, respectively. In addition, there was some deviation in the austenite/ferrite ratio of the surface welding pass in comparison to the root welding pass. Besides having lower pitting potential, welded joints produced by constant current gas tungsten arc welding process, consisted of some brittle sigma phase precipitates, which resulted in some impact energy reduction. The tensile tests showed high tensile strength for the weld joints in which all the specimens were broken in 316L base metal.

  7. The effect of polyamines on the photochemical reactivity of DNA

    International Nuclear Information System (INIS)

    Ben-Hur, E.; Hebrew Univ., Jerusalem

    1975-01-01

    The effects of diaminopentane (cadaverine), diaminoethane and the polyamine, spermine, on the photoreactions of 4,5', 8-trimethylpsoralen with DNA were studied. Near ultraviolet (UV) light (360 nm) irradiation of psoralen with DNA results in the formation of psoralen monoadducts with pyrimidine bases and DNA interstrand crosslinks. The polyamines studied reduced the rate of both photoreactions to the same extent by a factor of 1.5-2.0. The magnitude of the effect increased with polyamine concentration. Effectiveness was in the order spermine > cadaverine > diaminoethane. This is also the same order for stabilization of the DNA double-helix. Under conditions of higher DNA stability (higher ionic strength), higher polyamine concentrations were required to obtain an effect which was smaller than at low ionic strength. It is concluded that the photoreactions of psoralen with pyrimidines in DNA require some distortion of the double-helix. This distortion is made more difficult in the presence of stabilizing agents like polyamines and therefore the rate of the reaction is reduced. If crosslinking of DNA by psoralen is a two-step reaction then it must be concluded that the second step does not require further distortion. Consistently with the above, polyamines also reduced the UV-induced dimerization of thymine in DNA, although to a lesser extent. (author)

  8. The effect of vinblastine on DNA metabolism in tumour cells

    International Nuclear Information System (INIS)

    Cabela, E.; Klein, W.

    1976-01-01

    Studies on the influence of Vinblastine on normal and tumor cells show that semiconservative DNA-synthesis correlates with the enzymatic activity of thymidinkinase. DNA-repair-investigations performed with Yoshida-Ascites cells indicate an inhibition effect on the ligase system after Vinblastine-treatment and gamma irradiation. (author)

  9. 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

    International Nuclear Information System (INIS)

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

    1991-01-01

    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. The authors have assigned the exchangeable NH1, NH7, and NH 2 -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 H 2 O solution. They 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·A17 base pairs with minimal perturbation of the helix. The structural studies demonstrate that 8-oxo-7H-dG(syn)·dA(anti) forms a stable pair in the interior of the helix, providing a basis for the observed incorporation of dA opposite 8-oxo-7H-dG when readthrough occurs past this oxidized nucleoside base

  10. Effects of tritium on DNA, 3

    International Nuclear Information System (INIS)

    Yamamoto, Osamu; Fuji, Izumi

    1984-01-01

    Lambda DNA solution was prepared at a concentration of 125μg/ml of 10mM Tris-HCl-5mM NaCl-1mM Na 2 EDTA (pH 7.4). Solutions were irradiated with 60 Co gamma-rays and 3 H beta-rays ( 3 HHO addition), respectively. After irradiation of DNA solutions, single-strand breaks and double-strand breaks were detected by a vertical gel electrophoretic system (BRL Model V16). In both strand breaks higher oxygen enhancement ratios were obtained with 60 Co erradiation. (J.P.N.)

  11. Screening of Modified RNA duplexes

    DEFF Research Database (Denmark)

    Schyth, Brian Dall; Bramsen, Jesper Bertram; Kjems, Jørgen

    protection against a fish pathogenic virus. This protection corresponded with an interferon response in the fish. Here we use this fish model to screen siRNAs containing various chemical modifications of the RNA backbone for their antiviral activity, the overall aim being identification of an siRNA form......Because of sequence specific gene targeting activity siRNAs are regarded as promising active compounds in gene medicine. But one serious problem with delivering siRNAs as treatment is the now well-established non-specific activities of some RNA duplexes. Cellular reactions towards double stranded...... RNAs include the 2´-5´ oligoadenylate synthetase system, the protein kinase R, RIG-I and Toll-like receptor activated pathways all resulting in antiviral defence mechanism. We have previously shown that antiviral innate immune reactions against double stranded RNAs could be detected in vivo as partial...

  12. Duplex Healing of Selectively Thiolated Guanosine Mismatches through a Cd2+ Chemical Stimulus.

    Science.gov (United States)

    Lunn, Samantha M L; Hribesh, Samira; Whitfield, Colette J; Hall, Michael J; Houlton, Andrew; Bronowska, Agnieszka K; Tuite, Eimer M; Pike, Andrew R

    2018-03-25

    The on-column selective conversion of guanosine to thioguanosine (tG) yields modified oligomers that exhibit destabilisation over the fully complementary duplex. Restoration to a stabilised duplex is induced through thio-directed Cd 2+ coordination; a route for healing DNA damage. Short oligomers are G-specifically thiolated through a modified on-column protocol without the need for costly thioguanosine phosphoramidites. Addition of Cd 2+ ions to a duplex containing a highly disrupted tG central mismatch sequence, 3'-A 6 tG 4 T 6 -5', suggests a (tG) 8 Cd 2 central coordination regime, resulting in increased base stacking and duplex stability. Equilibrium molecular dynamic calculations support the hypothesis of metal-induced healing of the thiolated duplex. The 2 nm displacement of the central tG mismatched region is dramatically reduced after the addition of a chemical stimuli, Cd 2+ ions, returning to a minimized fluctuational state comparable to the unmodified fully complementary oligomer. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Concurrent infections of pseudorabies virus and porcine bocavirus in China detected by duplex nanoPCR.

    Science.gov (United States)

    Luo, Yakun; Liang, Lin; Zhou, Ling; Zhao, Kai; Cui, Shangjin

    2015-07-01

    Nanoparticle-assisted polymerase chain reaction (nanoPCR) is a novel method for the simple, rapid, and specific amplification of DNA and has been used to detect viruses. A duplex nanoPCR molecular detection system was developed to detect pseudorabies virus (PRV) and porcine bocavirus (PBoV). Primers were selected to target conserved regions within the PRV gE gene and the PBoV NS1 gene. Under optimized nanoPCR reaction conditions, two specific fragments of 316 bp (PRV) and 996 bp (PBoV) were amplified by the duplex nanoPCR with a detection limit of 6 copies for PRV and 95 copies for PBoV; no fragments were amplified when other porcine viruses were used as template. When used to test 550 clinical samples, the duplex nanoPRC assay and a conventional duplex PCR assay provided very similar results (98.1% consistency); single PRV infections, single PBoV infections, and concurrent PRV and PBoV infections were detected in 37%, 15%, and 9% of the samples, respectively. The results indicate that the novel duplex nanoPCR assay is useful for the rapid detection of PRV and PBoV in pigs. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Interactions of tetracationic porphyrins with DNA and their effects on DNA cleavage

    Science.gov (United States)

    Lebedeva, Natalya Sh.; Yurina, Elena S.; Gubarev, Yury A.; Syrbu, Sergey A.

    2018-06-01

    The interaction of tetracationic porphyrins with DNA was studied using UV-Vis absorption, fluorescence spectroscopy and viscometry, and the particle sizes were determined. Аs cationic porphyrins, two isomer porphyrins, 3,3‧,3″,3‴-(5,10,15,20-Porphyrintetrayl)tetrakis(1-methylpyridinium) (TMPyP3) and 4,4‧,4″,4‴-(5,10,15,20-Porphyrintetrayl)tetrakis(1-methylpyridinium) (TMPyP4), were studied. They differ in the position of NCH3+ group in phenyl ring of the porphyrins and hence, in degree of freedom of rotation of the phenyl rings about the central macrocycle. It was found that intercalated complexes are formed at DNA/porphyrin molar ratios (R) of 2.2 and 3.9 for TMPyP3 и TMPyP4, respectively. Decreasing R up to 0.4 and 0.8 for TMPyP3 и TMPyP4, respectively, leads mainly to formation of outside complexes due to π-π stacking between the porphyrin chromophores interacting electrostatically with phosphate framework of DNA. Each type of the obtained complexes was characterized using Scatchard approach. It was ascertained that the affinity of TMPyP4 to DNA is stronger than TMPyP3, meanwhile the wedge effect of the latter is higher. The differences between the porphyrin isomers become more evident at irradiation of their complexes with DNA. It was established that irradiation of the intercalated complexes results in DNA fragmentation. In the case of TMPyP4, DNA fragments of different size are formed. The irradiation of the outside DNA/porphyrin complexes leads to cleavage of DNA (TMPyP3 and TMPyP4) and partial destruction of the complex due to photolysis of the porphyrin (TMPyP3).

  15. Identification of a premature termination of DNA polymerization in ...

    Indian Academy of Sciences (India)

    2013-04-25

    Apr 25, 2013 ... strands to the 5′ end of the template strands, forming double- stranded DNA with ... duplex stem is important for high processive polymerization. HIV-1 reverse ... KF has been used as a model to study DNA polymerase.

  16. Full Duplex Emulation via Spatial Separation of Half Duplex Nodes in a Planar Cellular Network

    DEFF Research Database (Denmark)

    Thomsen, Henning; Kim, Dong Min; Popovski, Petar

    2016-01-01

    A Full Duplex Base Station (FD-BS) can be used to serve simultaneously two Half-Duplex (HD) Mobile Stations (MSs), one working in the uplink and one in the downlink, respectively. The same functionality can be realized by having two interconnected and spatially separated Half Duplex Base Stations...... (HD-BSs), which is a scheme termed CoMPflex (CoMP for In-Band Wireless Full Duplex). A FD-BS can be seen as a special case of CoMPflex with separation distance zero. In this paper we study the performance of CoMPflex in a two-dimensional cellular scenario using stochastic geometry and compare...

  17. Dwell-Time Distribution, Long Pausing and Arrest of Single-Ribosome Translation through the mRNA Duplex.

    Science.gov (United States)

    Xie, Ping

    2015-10-09

    Proteins in the cell are synthesized by a ribosome translating the genetic information encoded on the single-stranded messenger RNA (mRNA). It has been shown that the ribosome can also translate through the duplex region of the mRNA by unwinding the duplex. Here, based on our proposed model of the ribosome translation through the mRNA duplex we study theoretically the distribution of dwell times of the ribosome translation through the mRNA duplex under the effect of a pulling force externally applied to the ends of the mRNA to unzip the duplex. We provide quantitative explanations of the available single molecule experimental data on the distribution of dwell times with both short and long durations, on rescuing of the long paused ribosomes by raising the pulling force to unzip the duplex, on translational arrests induced by the mRNA duplex and Shine-Dalgarno(SD)-like sequence in the mRNA. The functional consequences of the pauses or arrests caused by the mRNA duplex and the SD sequence are discussed and compared with those obtained from other types of pausing, such as those induced by "hungry" codons or interactions of specific sequences in the nascent chain with the ribosomal exit tunnel.

  18. Role of minor groove width and hydration pattern on amsacrine interaction with DNA.

    Directory of Open Access Journals (Sweden)

    Deepak K Jangir

    Full Text Available Amsacrine is an anilinoacridine derivative anticancer drug, used to treat a wide variety of malignancies. In cells, amsacrine poisons topoisomerase 2 by stabilizing DNA-drug-enzyme ternary complex. Presence of amsacrine increases the steady-state concentration of these ternary complexes which in turn hampers DNA replication and results in subsequent cell death. Due to reversible binding and rapid slip-out of amsacrine from DNA duplex, structural data is not available on amsacrine-DNA complexes. In the present work, we designed five oligonucleotide duplexes, differing in their minor groove widths and hydration pattern, and examined their binding with amsacrine using attenuated total reflection Fourier transform infrared (ATR-FTIR spectroscopy. Complexes of amsacrine with calf thymus DNA were also evaluated for a comparison. Our results demonstrate for the first time that amsacrine is not a simple intercalator; rather mixed type of DNA binding (intercalation and minor groove takes place between amsacrine and DNA. Further, this binding is highly sensitive towards the geometries and hydration patterns of different minor grooves present in the DNA. This study shows that ligand binding to DNA could be very sensitive to DNA base composition and DNA groove structures. Results demonstrated here could have implication for understanding cytotoxic mechanism of aminoacridine based anticancer drugs and provide directions to modify these drugs for better efficacy and few side-effects.

  19. Effects of polyamines on the DNA-reactive properties of dimeric mithramycin complexed with cobalt(II): implications for anticancer therapy.

    Science.gov (United States)

    Hou, Ming-Hon; Lu, Wen-Je; Huang, Chun-Yu; Fan, Ruey-Jane; Yuann, Jeu-Ming P

    2009-06-09

    Few studies have examined the effects of polyamines on the action of DNA-binding anticancer drugs. Here, a Co(II)-mediated dimeric mithramycin (Mith) complex, (Mith)(2)-Co(II), was shown to be resistant to polyamine competition toward the divalent metal ion when compared to the Fe(II)-mediated drug complexes. Surface plasmon resonance experiments demonstrated that polyamines interfered with the binding capacity and association rates of (Mith)(2)-Co(II) binding to DNA duplexes, while the dissociation rates were not affected. Although (Mith)(2)-Co(II) exhibited the highest oxidative activity under physiological conditions (pH 7.3 and 37 degrees C), polyamines (spermine in particular) inhibited the DNA cleavage activity of the (Mith)(2)-Co(II) in a concentration-dependent manner. Depletion of intracellular polyamines by methylglyoxal bis(guanylhydrazone) (MGBG) enhanced the sensitivity of A549 lung cancer cells to (Mith)(2)-Co(II), most likely due to the decreased intracellular effect of polyamines on the action of (Mith)(2)-Co(II). Our study suggests a novel method for enhancing the anticancer activity of DNA-binding metalloantibiotics through polyamine depletion.

  20. Three-dimensional solution structure of a DNA duplex containing the BclI restriction sequence: Two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the NOESY spectrum

    International Nuclear Information System (INIS)

    Banks, K.M.; Hare, D.R.; Reid, B.R.

    1989-01-01

    A three-dimensional solution structure for the self-complementary dodecanucleotide [(d-GCCTGATCAGGC)] 2 has been determined by distance geometry with further refinements being performed after back-calculation of the NOESY spectrum. This DNA dodecamer contains the hexamer [d(TGATCA)] 2 recognized and cut by the restriction endonuclease BclI, and its structure was determined in hopes of obtaining a better understanding of the sequence-specific interactions which occur between proteins and DNA. Preliminary examination of the structure indicates the structure is underwound with respect to idealized B-form DNA though some of the local structural parameters (glycosyl torsion angle and pseudorotation angle) suggest a B-family type of structure is present. This research demonstrates the requirements (resonance assignments, interproton distance measurements, distance geometry calculations, and NOESY spectra back-calculation) to generate experimentally self-consistent solution structures for short DNA sequences

  1. Full-Duplex Communications in Large-Scale Cellular Networks

    KAUST Repository

    AlAmmouri, Ahmad

    2016-04-01

    In-band full-duplex (FD) communications have been optimistically promoted to improve the spectrum utilization and efficiency. However, the penetration of FD communications to the cellular networks domain is challenging due to the imposed uplink/downlink interference. This thesis presents a tractable framework, based on stochastic geometry, to study FD communications in multi-tier cellular networks. Particularly, we assess the FD communications effect on the network performance and quantify the associated gains. The study proves the vulnerability of the uplink to the downlink interference and shows that the improved FD rate gains harvested in the downlink (up to 97%) comes at the expense of a significant degradation in the uplink rate (up to 94%). Therefore, we propose a novel fine-grained duplexing scheme, denoted as α-duplex scheme, which allows a partial overlap between the uplink and the downlink frequency bands. We derive the required conditions to harvest rate gains from the α-duplex scheme and show its superiority to both the FD and half-duplex (HD) schemes. In particular, we show that the α-duplex scheme provides a simultaneous improvement of 28% for the downlink rate and 56% for the uplink rate. We also show that the amount of the overlap can be optimized based on the network design objective. Moreover, backward compatibility is an essential ingredient for the success of new technologies. In the context of in-band FD communication, FD base stations (BSs) should support HD users\\' equipment (UEs) without sacrificing the foreseen FD gains. The results show that FD-UEs are not necessarily required to harvest rate gains from FD-BSs. In particular, the results show that adding FD-UEs to FD-BSs offers a maximum of 5% rate gain over FD-BSs and HD-UEs case, which is a marginal gain compared to the burden required to implement FD transceivers at the UEs\\' side. To this end, we shed light on practical scenarios where HD-UEs operation with FD-BSs outperforms the

  2. Self-DNA inhibitory effects: Underlying mechanisms and ecological implications.

    Science.gov (United States)

    Cartenì, Fabrizio; Bonanomi, Giuliano; Giannino, Francesco; Incerti, Guido; Vincenot, Christian Ernest; Chiusano, Maria Luisa; Mazzoleni, Stefano

    2016-01-01

    DNA is usually known as the molecule that carries the instructions necessary for cell functioning and genetic inheritance. A recent discovery reported a new functional role for extracellular DNA. After fragmentation, either by natural or artificial decomposition, small DNA molecules (between ∼50 and ∼2000 bp) exert a species specific inhibitory effect on individuals of the same species. Evidence shows that such effect occurs for a wide range of organisms, suggesting a general biological process. In this paper we explore the possible molecular mechanisms behind those findings and discuss the ecological implications, specifically those related to plant species coexistence.

  3. Sampling the potential energy surface of a DNA duplex damaged by a food carcinogen: Force field parameterization by ab initio quantum calculations and conformational searching using molecular mechanics computations

    Science.gov (United States)

    Wu, Xiangyang

    1999-07-01

    The heterocyclic amine 2-amino-3-methylimidazo (4, 5-f) quinoline (IQ) is one of a number of carcinogens found in barbecued meat and fish. It induces tumors in mammals and is probably involved in human carcinogenesis, because of great exposure to such food carcinogens. IQ is biochemically activated to a derivative which reacts with DNA to form a covalent adduct. This adduct may deform the DNA and consequently cause a mutation. which may initiate carcinogenesis. To understand this cancer initiating event, it is necessary to obtain atomic resolution structures of the damaged DNA. No such structures are available experimentally due to synthesis difficulties. Therefore, we employ extensive molecular mechanics and dynamics calculations for this purpose. The major IQ-DNA adduct in the specific DNA sequence d(5'G1G2C G3CCA3') - d(5'TGGCGCC3') with IQ modified at G3 is studied. The d(5'G1G2C G3CC3') sequence has recently been shown to be a hot-spot for mutations when IQ modification is at G3. Although this sequence is prone to -2 deletions via a ``slippage mechanism'' even when unmodified, a key question is why IQ increases the mutation frequency of the unmodified DNA by about 104 fold. Is there a structural feature imposed by IQ that is responsible? The molecular mechanics and dynamics program AMBER for nucleic acids with the latest force field was chosen for this work. This force field has been demonstrated to reproduce well the B-DNA structure. However, some parameters, the partial charges, bond lengths and angles, dihedral parameters of the modified residue, are not available in the AMBER database. We parameterized the force field using high level ab initio quantum calculations. We created 800 starting conformations which uniformly sampled in combination at 18° intervals three torsion angles that govern the IQ-DNA orientations, and energy minimized them. The most important structures are abnormal; the IQ damaged guanine is rotated out of its standard B-DNA

  4. Weld oxide formation on lean duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Westin, E.M. [Outokumpu Stainless, Avesta Research Centre, P.O. Box 74, SE-774 22 Avesta (Sweden)], E-mail: elin.westin@outokumpu.com; Olsson, C.-O.A. [Outokumpu Stainless, Avesta Research Centre, P.O. Box 74, SE-774 22 Avesta (Sweden); Hertzman, S. [Outokumpu Stainless Research Foundation, Brinellvaegen 23, SE-100 44 Stockholm (Sweden)

    2008-09-15

    Weld oxides have a strong influence on corrosion resistance, but have hitherto only been studied to a limited extent for duplex stainless steels. X-ray photoelectron spectroscopy (XPS) has here been used to study heat tint formed on gas tungsten arc (GTA) welds on the commercial duplex grades LDX 2101 (EN 1.4162/UNS S32101) and 2304 (EN 1.4362/UNS S32304) welded with and without nitrogen additions to the shielding gas. The process of heat tint formation is discussed in terms of transport phenomena to explain the effect of atmosphere, temperature and composition. The oxides formed were found to be enriched in manganese and corrosion testing shows that nitrogen has a strong influence on the weld oxide. A mechanism is proposed including evaporation from the weld pool and subsequent redeposition.

  5. Weld oxide formation on lean duplex stainless steel

    International Nuclear Information System (INIS)

    Westin, E.M.; Olsson, C.-O.A.; Hertzman, S.

    2008-01-01

    Weld oxides have a strong influence on corrosion resistance, but have hitherto only been studied to a limited extent for duplex stainless steels. X-ray photoelectron spectroscopy (XPS) has here been used to study heat tint formed on gas tungsten arc (GTA) welds on the commercial duplex grades LDX 2101 (EN 1.4162/UNS S32101) and 2304 (EN 1.4362/UNS S32304) welded with and without nitrogen additions to the shielding gas. The process of heat tint formation is discussed in terms of transport phenomena to explain the effect of atmosphere, temperature and composition. The oxides formed were found to be enriched in manganese and corrosion testing shows that nitrogen has a strong influence on the weld oxide. A mechanism is proposed including evaporation from the weld pool and subsequent redeposition

  6. Practical, real-time, full duplex wireless

    KAUST Repository

    Jain, Mayank; Choi, Jung Il; Kim, Taemin; Bharadia, Dinesh; Seth, Siddharth; Srinivasan, Kannan; Levis, Philip; Katti, Sachin; Sinha, Prasun

    2011-01-01

    This paper presents a full duplex radio design using signal inversion and adaptive cancellation. Signal inversion uses a simple design based on a balanced/unbalanced (Balun) transformer. This new design, unlike prior work, supports wideband and high power systems. In theory, this new design has no limitation on bandwidth or power. In practice, we find that the signal inversion technique alone can cancel at least 45dB across a 40MHz bandwidth. Further, combining signal inversion cancellation with cancellation in the digital domain can reduce self-interference by up to 73dB for a 10MHz OFDM signal. This paper also presents a full duplex medium access control (MAC) design and evaluates it using a testbed of 5 prototype full duplex nodes. Full duplex reduces packet losses due to hidden terminals by up to 88%. Full duplex also mitigates unfair channel allocation in AP-based networks, increasing fairness from 0.85 to 0.98 while improving downlink throughput by 110% and uplink throughput by 15%. These experimental results show that a re- design of the wireless network stack to exploit full duplex capability can result in significant improvements in network performance. © 2011 ACM.

  7. Energy balance and deformation mechanisms of duplexes

    Science.gov (United States)

    Mitra, Gautam; Boyer, Steven E.

    A duplex consists of a series of imbricate faults that are asymptotic to a roof thrust and a floor thrust. Depending on the final orientations of the imbricate faults and the final position of the branch lines, a duplex may be hinterland-dipping, foreland-dipping, or an antiformal stack. The exact geometry depends on various factors such as the initial dimensions of the individual slices (horses), their lithology, the amount of displacement (normalized to size of horse) on each fault, and the mechanics of movement along each fault. The energy required in duplex formation can be determined by calculating the total work involved in emplacing each horse: this is given by where W t=W p+W b+W g+W iWp is the work involved in initiating and propagating a fracture. Wb is the work involved in basal sliding, which may be frictional or some form of ductile flow, Wg is the work done against gravity during the emplacement of the horse, and Wi is the work involved in the internal deformation of the horse. By calculating and comparing these work terms it is possible to predict the conditions under which the different types of duplexes will form. Normally, the development of a hinterland-dipping duplex is most likely. However, if deformation conditions are favorable, displacements on individual imbricate faults may be very large compared to the size of the horses, leading to the formation of either antiformal stacks or foreland-dipping duplexes.

  8. Duplex recombinase polymerase amplification assays incorporating competitive internal controls for bacterial meningitis detection.

    Science.gov (United States)

    Higgins, Owen; Clancy, Eoin; Forrest, Matthew S; Piepenburg, Olaf; Cormican, Martin; Boo, Teck Wee; O'Sullivan, Nicola; McGuinness, Claire; Cafferty, Deirdre; Cunney, Robert; Smith, Terry J

    2018-04-01

    Recombinase polymerase amplification (RPA) is an isothermal nucleic acid amplification technology that provides rapid and robust infectious disease pathogen detection, ideal for point-of-care (POC) diagnostics in disease-prevalent low-resource countries. We have developed and evaluated three duplex RPA assays incorporating competitive internal controls for the detection of leading bacterial meningitis pathogens. Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae singleplex RPA assays were initially developed and evaluated, demonstrating 100% specificity with limits of detection of 4.1, 8.5 and 3.9 genome copies per reaction, respectively. Each assay was further developed into internally controlled duplex RPA assays via the incorporation of internal amplification control templates. Clinical performance of each internally controlled duplex RPA assay was evaluated by testing 64 archived PCR-positive clinical samples. Compared to real-time PCR, all duplex RPA assays demonstrated 100% diagnostic specificity, with diagnostic sensitivities of 100%, 86.3% and 100% for the S. pneumoniae, N. meningitidis and H. influenzae assays, respectively. This study details the first report of internally controlled duplex RPA assays for the detection of bacterial meningitis pathogens: S. pneumoniae, N. meningitidis and H. influenzae. We have successfully demonstrated the clinical diagnostic utility of each duplex RPA assay, introducing effective diagnostic technology for POC bacterial meningitis identification in disease-prevalent developing countries. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. In-Band α-Duplex Scheme for Cellular Networks: A Stochastic Geometry Approach

    KAUST Repository

    Alammouri, Ahmad

    2016-07-13

    In-band full-duplex (FD) communications have been optimistically promoted to improve the spectrum utilization and efficiency. However, the penetration of FD communications to the cellular networks domain is challenging due to the imposed uplink/downlink interference. This paper presents a tractable framework, based on stochastic geometry, to study FD communications in cellular networks. Particularly, we assess the FD communications effect on the network performance and quantify the associated gains. The study proves the vulnerability of the uplink to the downlink interference and shows that FD rate gains harvested in the downlink (up to 97%) come at the expense of a significant degradation in the uplink rate (up to 94%). Therefore, we propose a novel fine-grained duplexing scheme, denoted as -duplex scheme, which allows a partial overlap between the uplink and the downlink frequency bands. We derive the required conditions to harvest rate gains from the -duplex scheme and show its superiority to both the FD and half-duplex (HD) schemes. In particular, we show that the -duplex scheme provides a simultaneous improvement of 28% for the downlink rate and 56% for the uplink rate. Finally, we show that the amount of the overlap can be optimized based on the network design objective.

  10. The effect of volume exclusion on the formation of DNA minicircle networks: implications to kinetoplast DNA

    International Nuclear Information System (INIS)

    Diao, Y; Hinson, K; Sun, Y; Arsuaga, J

    2015-01-01

    Kinetoplast DNA (kDNA) is the mitochondrial of DNA of disease causing organisms such as Trypanosoma Brucei (T. Brucei) and Trypanosoma Cruzi (T. Cruzi). In most organisms, KDNA is made of thousands of small circular DNA molecules that are highly condensed and topologically linked forming a gigantic planar network. In our previous work we have developed mathematical and computational models to test the confinement hypothesis, that is that the formation of kDNA minicircle networks is a product of the high DNA condensation achieved in the mitochondrion of these organisms. In these studies we studied three parameters that characterize the growth of the network topology upon confinement: the critical percolation density, the mean saturation density and the mean valence (i.e. the number of mini circles topologically linked to any chosen minicircle). Experimental results on insect-infecting organisms showed that the mean valence is equal to three, forming a structure similar to those found in medieval chain-mails. These same studies hypothesized that this value of the mean valence was driven by the DNA excluded volume. Here we extend our previous work on kDNA by characterizing the effects of DNA excluded volume on the three descriptive parameters. Using computer simulations of polymer swelling we found that (1) in agreement with previous studies the linking probability of two minicircles does not decrease linearly with the distance between the two minicircles, (2) the mean valence grows linearly with the density of minicircles and decreases with the thickness of the excluded volume, (3) the critical percolation and mean saturation densities grow linearly with the thickness of the excluded volume. Our results therefore suggest that the swelling of the DNA molecule, due to electrostatic interactions, has relatively mild implications on the overall topology of the network. Our results also validate our topological descriptors since they appear to reflect the changes in the

  11. The effect of volume exclusion on the formation of DNA minicircle networks: implications to kinetoplast DNA

    Science.gov (United States)

    Diao, Y.; Hinson, K.; Sun, Y.; Arsuaga, J.

    2015-10-01

    Kinetoplast DNA (kDNA) is the mitochondrial of DNA of disease causing organisms such as Trypanosoma Brucei (T. Brucei) and Trypanosoma Cruzi (T. Cruzi). In most organisms, KDNA is made of thousands of small circular DNA molecules that are highly condensed and topologically linked forming a gigantic planar network. In our previous work we have developed mathematical and computational models to test the confinement hypothesis, that is that the formation of kDNA minicircle networks is a product of the high DNA condensation achieved in the mitochondrion of these organisms. In these studies we studied three parameters that characterize the growth of the network topology upon confinement: the critical percolation density, the mean saturation density and the mean valence (i.e. the number of mini circles topologically linked to any chosen minicircle). Experimental results on insect-infecting organisms showed that the mean valence is equal to three, forming a structure similar to those found in medieval chain-mails. These same studies hypothesized that this value of the mean valence was driven by the DNA excluded volume. Here we extend our previous work on kDNA by characterizing the effects of DNA excluded volume on the three descriptive parameters. Using computer simulations of polymer swelling we found that (1) in agreement with previous studies the linking probability of two minicircles does not decrease linearly with the distance between the two minicircles, (2) the mean valence grows linearly with the density of minicircles and decreases with the thickness of the excluded volume, (3) the critical percolation and mean saturation densities grow linearly with the thickness of the excluded volume. Our results therefore suggest that the swelling of the DNA molecule, due to electrostatic interactions, has relatively mild implications on the overall topology of the network. Our results also validate our topological descriptors since they appear to reflect the changes in the

  12. Structural Insights into the Quadruplex-Duplex 3' Interface Formed from a Telomeric Repeat: A Potential Molecular Target.

    Science.gov (United States)

    Russo Krauss, Irene; Ramaswamy, Sneha; Neidle, Stephen; Haider, Shozeb; Parkinson, Gary N

    2016-02-03

    We report here on an X-ray crystallographic and molecular modeling investigation into the complex 3' interface formed between putative parallel stranded G-quadruplexes and a duplex DNA sequence constructed from the human telomeric repeat sequence TTAGGG. Our crystallographic approach provides a detailed snapshot of a telomeric 3' quadruplex-duplex junction: a junction that appears to have the potential to form a unique molecular target for small molecule binding and interference with telomere-related functions. This unique target is particularly relevant as current high-affinity compounds that bind putative G-quadruplex forming sequences only rarely have a high degree of selectivity for a particular quadruplex. Here DNA junctions were assembled using different putative quadruplex-forming scaffolds linked at the 3' end to a telomeric duplex sequence and annealed to a complementary strand. We successfully generated a series of G-quadruplex-duplex containing crystals, both alone and in the presence of ligands. The structures demonstrate the formation of a parallel folded G-quadruplex and a B-form duplex DNA stacked coaxially. Most strikingly, structural data reveals the consistent formation of a TAT triad platform between the two motifs. This triad allows for a continuous stack of bases to link the quadruplex motif with the duplex region. For these crystal structures formed in the absence of ligands, the TAT triad interface occludes ligand binding at the 3' quadruplex-duplex interface, in agreement with in silico docking predictions. However, with the rearrangement of a single nucleotide, a stable pocket can be produced, thus providing an opportunity for the binding of selective molecules at the interface.

  13. Effects of sequence on DNA wrapping around histones

    Science.gov (United States)

    Ortiz, Vanessa

    2011-03-01

    A central question in biophysics is whether the sequence of a DNA strand affects its mechanical properties. In epigenetics, these are thought to influence nucleosome positioning and gene expression. Theoretical and experimental attempts to answer this question have been hindered by an inability to directly resolve DNA structure and dynamics at the base-pair level. In our previous studies we used a detailed model of DNA to measure the effects of sequence on the stability of naked DNA under bending. Sequence was shown to influence DNA's ability to form kinks, which arise when certain motifs slide past others to form non-native contacts. Here, we have now included histone-DNA interactions to see if the results obtained for naked DNA are transferable to the problem of nucleosome positioning. Different DNA sequences interacting with the histone protein complex are studied, and their equilibrium and mechanical properties are compared among themselves and with the naked case. NLM training grant to the Computation and Informatics in Biology and Medicine Training Program (NLM T15LM007359).

  14. Collaborating functions of BLM and DNA topoisomerase I in regulating human rDNA transcription

    International Nuclear Information System (INIS)

    Grierson, Patrick M.; Acharya, Samir; Groden, Joanna

    2013-01-01

    Bloom's syndrome (BS) is an inherited disorder caused by loss of function of the recQ-like BLM helicase. It is characterized clinically by severe growth retardation and cancer predisposition. BLM localizes to PML nuclear bodies and to the nucleolus; its deficiency results in increased intra- and inter-chromosomal recombination, including hyper-recombination of rDNA repeats. Our previous work has shown that BLM facilitates RNA polymerase I-mediated rRNA transcription in the nucleolus (Grierson et al., 2012 [18]). This study uses protein co-immunoprecipitation and in vitro transcription/translation (IVTT) to identify a direct interaction of DNA topoisomerase I with the C-terminus of BLM in the nucleolus. In vitro helicase assays demonstrate that DNA topoisomerase I stimulates BLM helicase activity on a nucleolar-relevant RNA:DNA hybrid, but has an insignificant effect on BLM helicase activity on a control DNA:DNA duplex substrate. Reciprocally, BLM enhances the DNA relaxation activity of DNA topoisomerase I on supercoiled DNA substrates. Our study suggests that BLM and DNA topoisomerase I function coordinately to modulate RNA:DNA hybrid formation as well as relaxation of DNA supercoils in the context of nucleolar transcription

  15. Collaborating functions of BLM and DNA topoisomerase I in regulating human rDNA transcription

    Energy Technology Data Exchange (ETDEWEB)

    Grierson, Patrick M. [Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210 (United States); Acharya, Samir, E-mail: samir.acharya@osumc.edu [Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210 (United States); Groden, Joanna [Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210 (United States)

    2013-03-15

    Bloom's syndrome (BS) is an inherited disorder caused by loss of function of the recQ-like BLM helicase. It is characterized clinically by severe growth retardation and cancer predisposition. BLM localizes to PML nuclear bodies and to the nucleolus; its deficiency results in increased intra- and inter-chromosomal recombination, including hyper-recombination of rDNA repeats. Our previous work has shown that BLM facilitates RNA polymerase I-mediated rRNA transcription in the nucleolus (Grierson et al., 2012 [18]). This study uses protein co-immunoprecipitation and in vitro transcription/translation (IVTT) to identify a direct interaction of DNA topoisomerase I with the C-terminus of BLM in the nucleolus. In vitro helicase assays demonstrate that DNA topoisomerase I stimulates BLM helicase activity on a nucleolar-relevant RNA:DNA hybrid, but has an insignificant effect on BLM helicase activity on a control DNA:DNA duplex substrate. Reciprocally, BLM enhances the DNA relaxation activity of DNA topoisomerase I on supercoiled DNA substrates. Our study suggests that BLM and DNA topoisomerase I function coordinately to modulate RNA:DNA hybrid formation as well as relaxation of DNA supercoils in the context of nucleolar transcription.

  16. Harvesting full-duplex rate gains in cellular networks with half-duplex user terminals

    KAUST Repository

    Alammouri, Ahmad; Elsawy, Hesham; Alouini, Mohamed-Slim

    2016-01-01

    Full-Duplex (FD) transceivers may be expensive in terms of complexity, power consumption, and price to be implemented in all user terminals. Therefore, techniques to exploit in-band full-duplex communication with FD base stations (BSs) and half

  17. One-electron oxidation of DNA: mechanism and consequences.

    Science.gov (United States)

    Schuster, Gary B

    2009-01-01

    All living organisms store the information necessary to maintain life in their DNA. Any process that damages DNA and causes loss or corruption of that information threatens the viability of the organism. One-electron oxidation is such a process. Loss of an electron from DNA generates a radical cation that is located primarily on its nucleobases. The radical cation migrates reversibly through duplex DNA by hopping until it is eventually trapped in an irreversible chemical reaction. The particular sequence of nucleobases in a DNA oligomer determines both the efficiency of hopping and the specific location and nature of the damaging chemical reaction. In its normal aqueous solutions, DNA is a polyanion because of the negative charge carried by its phosphate groups. Counter ions (typically Na(+)) to the phosphate groups play an important role in facilitating both the migration of the radical cation and in its eventual reaction with H(2)O. Irreversible reaction of a radical cation with H(2)O in duplex DNA occurs preferentially at the most reactive site. In normal DNA that is comprised of the four common DNA nucleobases, reaction occurs most commonly at a guanine and results in its conversion primarily to 8-oxo-7,8-dihydroguanine (8-OxoG). Both electronic and steric effects control the outcome of this process. If the DNA oligomer does not contain a suitable guanine, then reaction of the radical cation occurs at the thymine of a TT step primarily by a tandem process. The general outcomes revealed in the one-electron oxidation of DNA oligomers in solution appear to be generally valid also for more complex DNA structures and for the cellular DNA of living organisms.

  18. Development of a duplex droplet digital PCR assay for absolute quantitative detection of "Candidatus Liberibacter asiaticus".

    Science.gov (United States)

    Selvaraj, Vijayanandraj; Maheshwari, Yogita; Hajeri, Subhas; Chen, Jianchi; McCollum, Thomas Greg; Yokomi, Raymond

    2018-01-01

    Huanglongbing (HLB, citrus greening) is a devastating citrus disease affecting citrus production worldwide. It is associated with the bacterium "Candidatus Liberibacter asiaticus" (CLas) and is vectored by the Asian citrus psyllid (ACP). Currently, diagnosis of CLas in regulatory samples is based on real-time quantitative polymerase chain reaction (qPCR) using 16S rRNA gene specific primers/probe. The detection of CLas using qPCR is challenging due to low pathogen titer and uneven distribution in infected plants and exacerbated by sampling issues and presence of inhibitors. This study evaluated a duplex droplet digital polymerase chain reaction (ddPCR) using multi-copy gene targets, 16S and RNR, to simultaneously detect CLas DNA targets in the same sample for unambiguous detection of the HLB pathogen in DNA extracts from citrus leaves and ACP. Standard curve analyses on tenfold dilution series with plasmid, citrus leaf and ACP DNA showed that both ddPCR and qPCR exhibited good linearity and efficiency in the duplex assay. CLas-infected low titer samples were used to validate the duplex ddPCR and qPCR performance and demonstrated that detection rate is higher when both 16S and RNR primers were used in duplex assay. However, the receiver operating characteristic analysis indicated that area under the curve for RNR primer was significantly broader, compared to 16S primers for CLas detection at low target titer. The absolute quantification of CLas at variable titers was reproducible and repeatable for both primer sets and the ddPCR showed higher resilience to PCR inhibitors with citrus leaf and ACP extracts. Hence, the resultant duplex ddPCR assay resulted in a significantly improved detection platform for diagnosis of CLas in samples with low pathogen titer.

  19. Effect of Sintering Atmosphere and Solution Treatment on Density, Microstructure and Tensile Properties of Duplex Stainless Steels Developed from Pre-alloyed Powders

    Science.gov (United States)

    Murali, Arun Prasad; Mahendran, Sudhahar; Ramajayam, Mariappan; Ganesan, Dharmalingam; Chinnaraj, Raj Kumar

    2017-10-01

    In this research, Powder Metallurgy (P/M) of Duplex Stainless Steels (DSS) of different compositions were prepared through pre-alloyed powders and elemental powders with and without addition of copper. The powder mix was developed by pot mill for 12 h to obtain the homogeneous mixture of pre-alloyed powder with elemental compositions. Cylindrical green compacts with the dimensions of 30 mm diameter and 12 mm height were compacted through universal testing machine at a pressure level of 560 ± 10 MPa. These green compacts were sintered at 1350 °C for 2 h in hydrogen and argon atmospheres. Some of the sintered stainless steel preforms were solution treated at 1050 °C followed by water quenching. The sintered as well as solution treated samples were analysed by metallography examination, Scanning Electron Microscopy and evaluation of mechanical properties. Ferrite content of sintered and solution treated DSS were measured by Fischer Ferritoscope. It is inferred that the hydrogen sintered DSS depicted better density (94% theoretical density) and tensile strength (695 MPa) than the argon sintered steels. Similarly the microstructure of solution treated DSS revealed existence of more volume of ferrite grains than its sintered condition. Solution treated hydrogen sintered DSS A (50 wt% 316L + 50 wt% 430L) exhibited higher tensile strength of 716 MPa and elongation of 17%, which are 10-13% increment than the sintered stainless steels.

  20. Effect of heat input on microstructure and mechanical properties of dissimilar joints between super duplex stainless steel and high strength low alloy steel

    International Nuclear Information System (INIS)

    Sadeghian, M.; Shamanian, M.; Shafyei, A.

    2014-01-01

    Highlights: • The microstructure of weld metal consists of austenite and ferrite. • The HAZ of the API X-65 shows different transformation. • Impact strength of sample with low heat input was lower than base metals. • The heat input at 0.506 kJ/mm is not the suitable for dissimilar joining between UNS S32750/API X-65. - Abstract: In the present study, microstructure and mechanical properties of UNS S32750 super duplex stainless steel (SDSS)/API X-65 high strength low alloy steel (HSLA) dissimilar joint were investigated. For this purpose, gas tungsten arc welding (GTAW) was used in two different heat inputs: 0.506 and 0.86 kJ/mm. The microstructures investigation with optical microscope, scanning electron microscope and X-ray diffraction showed that an increase in heat input led to a decrease in ferrite percentage, and that detrimental phases were not present. It also indicated that in heat affected zone of HSLA base metal in low heat input, bainite and ferrite phases were created; but in high heat input, perlite and ferrite phases were created. The results of impact tests revealed that the specimen with low heat input exhibited brittle fracture and that with high heat input had a higher strength than the base metals

  1. On full duplex Gaussian relay channels with self-interference

    KAUST Repository

    Behboodi, Arash

    2016-08-15

    Self interference (SI) in full duplex (FD) systems is the interference caused by the transmission stream on the reception stream. Being one of the main restrictive factors for performance of practical full duplex systems, however, not too much is known about its effect on the fundamental limits of relaying systems. In this work, we consider the full duplex three-node relay channel with SI where SI is modeled as an additive Gaussian noise whose variance is dependent on instantaneous input power. The classical achievable rates and upper bounds for the single three-node relay channel no longer apply due to the structure of SI. Achievable rates for Decode-and-Forward (DF) and Compress-and-Forward (CF) and upper bounds on the capacity are derived assuming Gaussian inputs and SI. The deterministic model is also introduced and its capacity is characterized. The optimal joint source-relay distributions is discussed. Numerical results are provided comparing the achievable rates and upper bound. © 2016 IEEE.

  2. Assessment of okadaic acid effects on cytotoxicity, DNA damage and DNA repair in human cells.

    Science.gov (United States)

    Valdiglesias, Vanessa; Méndez, Josefina; Pásaro, Eduardo; Cemeli, Eduardo; Anderson, Diana; Laffon, Blanca

    2010-07-07

    Okadaic acid (OA) is a phycotoxin produced by several types of dinoflagellates causing diarrheic shellfish poisoning (DSP) in humans. Symptoms induced by DSP toxins are mainly gastrointestinal, but the intoxication does not appear to be fatal. Despite this, this toxin presents a potential threat to human health even at concentrations too low to induce acute toxicity, since previous animal studies have shown that OA has very potent tumour promoting activity. However, its concrete action mechanism has not been described yet and the results reported with regard to OA cytotoxicity and genotoxicity are often contradictory. In the present study, the genotoxic and cytotoxic effects of OA on three different types of human cells (peripheral blood leukocytes, HepG2 hepatoma cells, and SHSY5Y neuroblastoma cells) were evaluated. Cells were treated with a range of OA concentrations in the presence and absence of S9 fraction, and MTT test and Comet assay were performed in order to evaluate cytotoxicity and genotoxicity, respectively. The possible effects of OA on DNA repair were also studied by means of the DNA repair competence assay, using bleomycin as DNA damage inductor. Treatment with OA in absence of S9 fraction induced not statistically significant decrease in cell viability and significant increase in DNA damage in all cell types at the highest concentrations investigated. However, only SHSY5Y cells showed OA induced genotoxic and cytotoxic effects in presence of S9 fraction. Furthermore, we found that OA can induce modulations in DNA repair processes when exposure was performed prior to BLM treatment, in co-exposure, or during the subsequent DNA repair process. Copyright 2010 Elsevier B.V. All rights reserved.

  3. Phase Transformations in Cast Duplex Stainless Steels

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yoon-Jun [Iowa State Univ., Ames, IA (United States)

    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

  4. Duplex kidney: not just a drooping lily.

    Science.gov (United States)

    Doery, Ashlea J; Ang, Eileen; Ditchfield, Michael R

    2015-04-01

    Duplex kidneys are common, mostly asymptomatic and of no clinical significance. However, they can be associated with significant pathology, often with long-term morbidity. There is minimal literature on the review of the duplex kidney, its associated anomalies and complications. The purpose of this paper is to review our experience of imaging the spectrum of abnormalities associated with duplex kidneys in the paediatric population and correlate this with contemporary literature. A retrospective review of the radiology database in a tertiary paediatric centre was performed. A word search of the Radiology Information System for 'duplex' of patients under the age of 16 was undertaken and limited to studies performed between 2006 and 2013. Two hundred seventy-four patients were identified (age range 0-16, median 3 years, gender 59.9% female) who had 836 studies: ultrasound 598/836 (71.6%), nuclear medicine 180/836 (21.5%), micturating cystourethrogram 52/836 (6.2%), MRI 5/836 (duplex and no complication (151/274 = 55.1%), upper moiety obstruction, lower moiety reflux/scarring, multicystic dysplastic kidney, abnormal ureteric insertion and other pathology. Duplex kidneys are common and often not clinically significant. However, this study demonstrates almost 50% of paediatric patients investigated for duplex kidneys had complications requiring treatment. The most common complications were upper moiety obstruction associated with a ureterocele and lower moiety vesicoureteric reflux. Ultrasound was the most common modality for early detection of these complications. © 2015 The Royal Australian and New Zealand College of Radiologists.

  5. AUTENTIKASI DAGING AYAM SEGAR DARI KONTAMINASI DAGING BABI MENGGUNAKAN GEN CYT-B DENGAN ANALISIS DUPLEX- POLYMERASE CHAIN REACTION

    Directory of Open Access Journals (Sweden)

    Bayu Setya Hertanto

    2017-05-01

    Full Text Available Halal is one of important aspects in consumer protection. Meat and processed meat products are food that should be controlled strictly because those are prone to be adulterated by pork contamination. Therefore, it is necessary to provide detection technique which is accurate, fast and cheap. The objective of this research was to identify the presence of impurities of pork meat on raw chicken meat using gene Cyt-b with duplex-PCR analysis. This research used six samples of raw chicken meat and raw pork. Raw chicken meat was bought from supermarkets in the city of Surakarta and raw pork was obtained from pig slaughterhouse. The percentage of raw pork contamination on raw chicken meat was designed as much as 1, 5, 10, and 25%, respectively. The DNA genome was isolated according to DNA isolation protocol from Genomic DNA Mini Kit. In addition, duplex-PCR was performed based on protocol of KAPA2G Fast Multiplex PCR kit. The data was descriptively analyzed by directly looking the DNA bands on the gel documentation apparatus. The result showed that specific DNA bands for chicken and pig were completely appeared on 1.5% of agarose gels. Duplex-PCR detect contamination of pork on raw meat of chicken at all contamination levels. This research proved that the duplex-PCR detect the contamination of pork until the level of 1%.

  6. Improved quantification accuracy for duplex real-time PCR detection of genetically modified soybean and maize in heat processed foods

    Directory of Open Access Journals (Sweden)

    CHENG Fang

    2013-04-01

    Full Text Available Real-time PCR technique has been widely used in quantitative GMO detection in recent years.The accuracy of GMOs quantification based on the real-time PCR methods is still a difficult problem,especially for the quantification of high processed samples.To develop the suitable and accurate real-time PCR system for high processed GM samples,we made ameliorations to several real-time PCR parameters,including re-designed shorter target DNA fragment,similar lengths of amplified endogenous and exogenous gene targets,similar GC contents and melting temperatures of PCR primers and TaqMan probes.Also,one Heat-Treatment Processing Model (HTPM was established using soybean flour samples containing GM soybean GTS 40-3-2 to validate the effectiveness of the improved real-time PCR system.Tested results showed that the quantitative bias of GM content in heat processed samples were lowered using the new PCR system.The improved duplex real-time PCR was further validated using processed foods derived from GM soybean,and more accurate GM content values in these foods was also achieved.These results demonstrated that the improved duplex real-time PCR would be quite suitable in quantitative detection of high processed food products.

  7. Effect of sample storage time on detection of hybridization signals in Checkerboard DNA-DNA hybridization.

    Science.gov (United States)

    do Nascimento, Cássio; Muller, Katia; Sato, Sandra; Albuquerque Junior, Rubens Ferreira

    2012-04-01

    Long-term sample storage can affect the intensity of the hybridization signals provided by molecular diagnostic methods that use chemiluminescent detection. The aim of this study was to evaluate the effect of different storage times on the hybridization signals of 13 bacterial species detected by the Checkerboard DNA-DNA hybridization method using whole-genomic DNA probes. Ninety-six subgingival biofilm samples were collected from 36 healthy subjects, and the intensity of hybridization signals was evaluated at 4 different time periods: (1) immediately after collecting (n = 24) and (2) after storage at -20 °C for 6 months (n = 24), (3) for 12 months (n = 24), and (4) for 24 months (n = 24). The intensity of hybridization signals obtained from groups 1 and 2 were significantly higher than in the other groups (p  0.05). The Checkerboard DNA-DNA hybridization method was suitable to detect hybridization signals from all groups evaluated, and the intensity of signals decreased significantly after long periods of sample storage.

  8. Plastomes of the green algae Hydrodictyon reticulatum and Pediastrum duplex (Sphaeropleales, Chlorophyceae

    Directory of Open Access Journals (Sweden)

    Hilary A. McManus

    2017-05-01

    Full Text Available Background Comparative studies of chloroplast genomes (plastomes across the Chlorophyceae are revealing dynamic patterns of size variation, gene content, and genome rearrangements. Phylogenomic analyses are improving resolution of relationships, and uncovering novel lineages as new plastomes continue to be characterized. To gain further insight into the evolution of the chlorophyte plastome and increase the number of representative plastomes for the Sphaeropleales, this study presents two fully sequenced plastomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae, one from Hydrodictyon reticulatum and the other from Pediastrum duplex. Methods Genomic DNA from Hydrodictyon reticulatum and Pediastrum duplex was subjected to Illumina paired-end sequencing and the complete plastomes were assembled for each. Plastome size and gene content were characterized and compared with other plastomes from the Sphaeropleales. Homology searches using BLASTX were used to characterize introns and open reading frames (orfs ≥ 300 bp. A phylogenetic analysis of gene order across the Sphaeropleales was performed. Results The plastome of Hydrodictyon reticulatum is 225,641 bp and Pediastrum duplex is 232,554 bp. The plastome structure and gene order of H. reticulatum and P. duplex are more similar to each other than to other members of the Sphaeropleales. Numerous unique open reading frames are found in both plastomes and the plastome of P. duplex contains putative viral protein genes, not found in other Sphaeropleales plastomes. Gene order analyses support the monophyly of the Hydrodictyaceae and their sister relationship to the Neochloridaceae. Discussion The complete plastomes of Hydrodictyon reticulatum and Pediastrum duplex, representing the largest of the Sphaeropleales sequenced thus far, once again highlight the variability in size, architecture, gene order and content across the Chlorophyceae. Novel intron insertion sites and unique

  9. Synthesis and structural characterization of piperazino-modified DNA that favours hybridization towards DNA over RNA

    DEFF Research Database (Denmark)

    Skov, Joan; Bryld, Torsten; Lindegaard, Dorthe

    2011-01-01

    We report the synthesis of two C4'-modified DNA analogues and characterize their structural impact on dsDNA duplexes. The 4'-C-piperazinomethyl modification stabilizes dsDNA by up to 5°C per incorporation. Extension of the modification with a butanoyl-linked pyrene increases the dsDNA stabilizati...

  10. Duplex ultrasound surveillance after carotid artery endarterectomy.

    Science.gov (United States)

    Al Shakarchi, Julien; Lowry, Danielle; Nath, Jay; Khawaja, Aurangzaib Z; Inston, Nicholas; Tiwari, Alok

    2016-06-01

    After carotid endarterectomy (CEA), patients have been regularly followed up by duplex ultrasound imaging. However, the evidence for long-term follow-up is not clear, especially if the results from an early duplex scan are normal. This study assessed and systematically reviewed the evidence base for long-term surveillance after CEA and a normal early scan. Electronic databases were searched for studies assessing duplex surveillance after CEA in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The primary outcome for this study was the incidence of restenosis after a normal early scan. The secondary outcome was the number of reinterventions after a normal early scan. The review included seven studies that reported 2317 procedures. Of those patients with a normal early scan, 2.8% (95% confidence interval, 0.7%-6%) developed a restenosis, and 0.4% (95% confidence interval, 0%-0.9%) underwent a reintervention for their restenosis during the follow-up period. This review confirms that routine postoperative duplex ultrasound surveillance after CEA is not necessary if the early duplex scan is normal. Copyright © 2016 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

  11. Mycobacterium smegmatis RqlH defines a novel clade of bacterial RecQ-like DNA helicases with ATP-dependent 3'-5' translocase and duplex unwinding activities.

    Science.gov (United States)

    Ordonez, Heather; Unciuleac, Mihaela; Shuman, Stewart

    2012-05-01

    The Escherichia coli RecQ DNA helicase participates in a pathway of DNA repair that operates in parallel to the recombination pathway driven by the multisubunit helicase-nuclease machine RecBCD. The model mycobacterium Mycobacterium smegmatis executes homologous recombination in the absence of its helicase-nuclease machine AdnAB, though it lacks a homolog of E. coli RecQ. Here, we identify and characterize M. smegmatis RqlH, a RecQ-like helicase with a distinctive domain structure. The 691-amino acid RqlH polypeptide consists of a RecQ-like ATPase domain (amino acids 1-346) and tetracysteine zinc-binding domain (amino acids 435-499), separated by an RqlH-specific linker. RqlH lacks the C-terminal HRDC domain found in E. coli RecQ. Rather, the RqlH C-domain resembles bacterial ComF proteins and includes a phosphoribosyltransferase-like module. We show that RqlH is a DNA-dependent ATPase/dATPase that translocates 3'-5' on single-stranded DNA and has 3'-5' helicase activity. These functions inhere to RqlH-(1-505), a monomeric motor unit comprising the ATPase, linker and zinc-binding domains. RqlH homologs are distributed widely among bacterial taxa. The mycobacteria that encode RqlH lack a classical RecQ, though many other Actinobacteria have both RqlH and RecQ. Whereas E. coli K12 encodes RecQ but lacks a homolog of RqlH, other strains of E. coli have both RqlH and RecQ.

  12. Buffer management in wireless full-duplex systems

    KAUST Repository

    Bouacida, Nader; Showail, Ahmad; Shihada, Basem

    2015-01-01

    , we address the problem of buffer management in full-duplex networks by using Wireless Queue Management (WQM), which is an active queue management technique for wireless networks. Our solution is based on Relay Full-Duplex MAC (RFD

  13. On full duplex Gaussian relay channels with self-interference

    KAUST Repository

    Behboodi, Arash; Chaaban, Anas; Mathar, Rudolf; Alouini, Mohamed-Slim

    2016-01-01

    Self interference (SI) in full duplex (FD) systems is the interference caused by the transmission stream on the reception stream. Being one of the main restrictive factors for performance of practical full duplex systems, however, not too much

  14. Molecular mechanism of DNA replication-coupled inactivation of the initiator protein in Escherichia coli: interaction of DnaA with the sliding clamp-loaded DNA and the sliding clamp-Hda complex.

    Science.gov (United States)

    Su'etsugu, Masayuki; Takata, Makoto; Kubota, Toshio; Matsuda, Yusaku; Katayama, Tsutomu

    2004-06-01

    In Escherichia coli, the ATP-DnaA protein initiates chromosomal replication. After the DNA polymerase III holoenzyme is loaded on to DNA, DnaA-bound ATP is hydrolysed in a manner depending on Hda protein and the DNA-loaded form of the DNA polymerase III sliding clamp subunit, which yields ADP-DnaA, an inactivated form for initiation. This regulatory DnaA-inactivation represses extra initiation events. In this study, in vitro replication intermediates and structured DNA mimicking replicational intermediates were first used to identify structural prerequisites in the process of DnaA-ATP hydrolysis. Unlike duplex DNA loaded with sliding clamps, primer RNA-DNA heteroduplexes loaded with clamps were not associated with DnaA-ATP hydrolysis, and duplex DNA provided in trans did not rescue this defect. At least 40-bp duplex DNA is competent for the DnaA-ATP hydrolysis when a single clamp was loaded. The DnaA-ATP hydrolysis was inhibited when ATP-DnaA was tightly bound to a DnaA box-bearing oligonucleotide. These results imply that the DnaA-ATP hydrolysis involves the direct interaction of ATP-DnaA with duplex DNA flanking the sliding clamp. Furthermore, Hda protein formed a stable complex with the sliding clamp. Based on these, we suggest a mechanical basis in the DnaA-inactivation that ATP-DnaA interacts with the Hda-clamp complex with the aid of DNA binding. Copyright Blackwell Publishing Limited

  15. Molecular detection of infectious bronchitis and Newcastle disease viruses in broiler chickens with respiratory signs using Duplex RT-PCR.

    Science.gov (United States)

    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.

  16. Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base Pairing

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2014-08-01

    Full Text Available The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic stability of oligonucleotide duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I and 2'-deoxyribo-2,6-diaminopurine (D as non-canonical nucleotides. The stability of DNA duplexes was changed by substitution of a single base pair in the following order: G•C > D•T ≈ I•C > A•T > G•T > I•T. The apparent stabilization energy due to the presence of the 2-amino group of G and D varied depending on the salt concentration, and decreased in the water-ethanol mixed solvent. The effects of salt concentration on the thermodynamics of DNA duplexes were found to be partially sequence-dependent, and the 2-amino group of the purine bases might have an influence on the binding of ions to DNA through the formation of a stable base-paired structure. Our results also showed that physiological salt conditions were energetically favorable for complementary base recognition, and conversely, low salt concentration media and ethanol-containing solvents were effective for low stringency oligonucleotide hybridization, in the context of conditions employed in this study.

  17. Targeting DNA double strand break repair with hyperthermia and DNA-PKcs inhibition to enhance the effect of radiation treatment.

    Science.gov (United States)

    van Oorschot, Bregje; Granata, Giovanna; Di Franco, Simone; Ten Cate, Rosemarie; Rodermond, Hans M; Todaro, Matilde; Medema, Jan Paul; Franken, Nicolaas A P

    2016-10-04

    Radiotherapy is based on the induction of lethal DNA damage, primarily DNA double-strand breaks (DSB). Efficient DSB repair via Non-Homologous End Joining or Homologous Recombination can therefore undermine the efficacy of radiotherapy. By suppressing DNA-DSB repair with hyperthermia (HT) and DNA-PKcs inhibitor NU7441 (DNA-PKcsi), we aim to enhance the effect of radiation.The sensitizing effect of HT for 1 hour at 42°C and DNA-PKcsi [1 μM] to radiation treatment was investigated in cervical and breast cancer cells, primary breast cancer sphere cells (BCSCs) enriched for cancer stem cells, and in an in vivo human tumor model. A significant radio-enhancement effect was observed for all cell types when DNA-PKcsi and HT were applied separately, and when both were combined, HT and DNA-PKcsi enhanced radio-sensitivity to an even greater extent. Strikingly, combined treatment resulted in significantly lower survival rates, 2 to 2.5 fold increase in apoptosis, more residual DNA-DSB 6 h post treatment and a G2-phase arrest. In addition, tumor growth analysis in vivo showed significant reduction in tumor growth and elevated caspase-3 activity when radiation was combined with HT and DNA-PKcsi compared to radiation alone. Importantly, no toxic side effects of HT or DNA-PKcsi were found.In conclusion, inhibiting DNA-DSB repair using HT and DNA-PKcsi before radiotherapy leads to enhanced cytotoxicity in cancer cells. This effect was even noticed in the more radio-resistant BCSCs, which are clearly sensitized by combined treatment. Therefore, the addition of HT and DNA-PKcsi to conventional radiotherapy is promising and might contribute to more efficient tumor control and patient outcome.

  18. Full-Duplex Relay Selection in Cognitive Underlay Networks

    KAUST Repository

    Khafagy, Mohammad Galal; Alouini, Mohamed-Slim; Aissa, Sonia

    2017-01-01

    In this work, we analyze the performance of full-duplex relay selection (FDRS) in spectrum-sharing networks. Contrary to half-duplex relaying, full-duplex relaying (FDR) enables simultaneous listening/forwarding at the secondary relay(s), thereby

  19. The Effect of Basepair Mismatch on DNA Strand Displacement.

    Science.gov (United States)

    Broadwater, D W Bo; Kim, Harold D

    2016-04-12

    DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single basepair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term the concurrent displacement model, and used the first passage time approach to quantitatively explain the salient features of the observed relationship. We also introduce the concept of splitting probabilities to justify that the concurrent model can be simplified into a three-step sequential model in the presence of an invader mismatch. We expect our model to become a powerful tool to design DNA-based reaction schemes with broad functionality. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  20. Full-duplex optical communication system

    Science.gov (United States)

    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.

  1. Effects of ionising radiation on isolated and cellular DNA

    International Nuclear Information System (INIS)

    Cadet, J.; Artignan, X.; Berger, M.; Douki, T.; Gromova, M.; Polverelli, M.; Ravanat, J.L.

    1997-01-01

    In the present survey, emphasis has been placed on mechanistic aspects of the radiation-induced decomposition of the base moities of DNA and model compounds. An almost complete description of the radical reactions mediated by both OH radicals (indirect effects) and one-electron oxidation (direct effects) is now possible for guanine compounds in aerated aqueous solution. In addition, the results of a comparison of a targeted assay (high performance liquid chromatography-electrochemical method) and a non specific method ('comet assay') for monitoring radiation-induced DNA damage within human cells are reported. (authors)

  2. Trabectedin – the DNA minor groove binder

    Directory of Open Access Journals (Sweden)

    G. A. Belitsky

    2015-01-01

    Full Text Available Trabectedin (ET-743, Yondelis is an alkaloid that was originally isolated from the Caribbean Sea squirt, Ecteinascidia turbinata and is now produced synthetically. Its chemical structure consists in three fused tetrahydroisoquinoline rings. Two of them, A and B, binds covalently to guanine residues in the minor groove of the DNA double helix to bend the molecule toward the major groove and the third ring C protrudes from the DNA duplex, apparently allowing interactions with several nuclear proteins. Binding to the minor groove of DNA, trabectedin trigger a cascade of events that interfere with several transcription factors, DNA binding proteins, and DNA repair pathways in particular nucleotide excision repair. It acts both as a DNA-alkylating drug and topoisomerase poison. Trabectedin-DNA adduct traps the nucleotide excision repair proteins repairing the DNA damage in transcribing genes and induces DNA strand breaks. Cells deficient in homologous recombination pathway which repairs these double-strand breaks show increased sensitivity to trabectedin. The most sensitive of them were myxoid liposarcomas. Trabectedin is also effective in chemotherapy-experienced patients with advanced, recurrent liposarcoma or leiomyosarcoma as well as in women with ovarian cancer and breast cancer with BRCAness phenotype. Besides of tumor cells Trabectedin inhibits inflammatory cells by affecting directly monocytes and tumorassociated macrophages and indirectly by inhibiting production of inflammatory mediators, the cytokines and chemokines. It inhibits also the MDR-1 gene, which is responsible for the resistance of cancer cells to chemotherapeutic agents and strikes tumor angiogenesis.

  3. Interactions Between Fibroblast Cells and Laser Beam Welded AISI 2205 Duplex Stainless Steel

    Directory of Open Access Journals (Sweden)

    Ceyhun KÖSE

    2018-05-01

    Full Text Available Because of their high mechanical strength, excellent corrosion resistance and good weldability, duplex stainless steels are mostly used in industries such as oil, chemistry, petrochemistry, food and occasionally used in medical industry. These properties have enabled us to use duplex stainless steels in biomedical applications recently. Accordingly, duplex stainless steel material can be highly important to examine the toxic effect on the cells. In this study, the effect of the AISI 2205 duplex stainless steels which are joined by CO2 laser beam welding on viability of L929 fibroblast cells has been studied in vitro for the first time. For this aim, the cells were kept in DMEM/F-12 (Thermofisher Scientific 31331-028 medium for 7 days. The viability study was experimentally studied using the MTT (Thiazolyl Blue Tetrazolium Bromide method for 7 days. The cell viability of the laser beam welded sample has been detected to be higher than that of the base metal and the control based on 7th day data. According to the obtained results, it was revealed that laser beam welded and base metal AISI 2205 duplex stainless steel has been found suitable to study for biomedical applications. DOI: http://dx.doi.org/10.5755/j01.ms.24.2.18006

  4. Detection of DNA damage by using hairpin molecular beacon probes and graphene oxide.

    Science.gov (United States)

    Zhou, Jie; Lu, Qian; Tong, Ying; Wei, Wei; Liu, Songqin

    2012-09-15

    A hairpin molecular beacon tagged with carboxyfluorescein in combination with graphene oxide as a quencher reagent was used to detect the DNA damage by chemical reagents. The fluorescence of molecular beacon was quenched sharply by graphene oxide; while in the presence of its complementary DNA the quenching efficiency decreased because their hybridization prevented the strong adsorbability of molecular beacon on graphene oxide. If the complementary DNA was damaged by a chemical reagent and could not form intact duplex structure with molecular beacon, more molecular beacon would adsorb on graphene oxide increasing the quenching efficiency. Thus, damaged DNA could be detected based on different quenching efficiencies afforded by damaged and intact complementary DNA. The damage effects of chlorpyrifos-methyl and three metabolites of styrene such as mandelieaeids, phenylglyoxylieaeids and epoxystyrene on DNA were studied as models. The method for detection of DNA damage was reliable, rapid and simple compared to the biological methods. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Rapid assessment of the effect of ciprofloxacin on chromosomal DNA from Escherichia coli using an in situ DNA fragmentation assay

    Directory of Open Access Journals (Sweden)

    Gosalvez Jaime

    2009-04-01

    Full Text Available Abstract Background Fluoroquinolones are extensively used antibiotics that induce DNA double-strand breaks (DSBs by trapping DNA gyrase and topoisomerase IV on DNA. This effect is usually evaluated using biochemical or molecular procedures, but these are not effective at the single-cell level. We assessed ciprofloxacin (CIP-induced chromosomal DNA breakage in single-cell Escherichia coli by direct visualization of the DNA fragments that diffused from the nucleoid obtained after bacterial lysis in an agarose microgel on a slide. Results Exposing the E. coli strain TG1 to CIP starting at a minimum inhibitory concentration (MIC of 0.012 μg/ml and at increasing doses for 40 min increased the DNA fragmentation progressively. DNA damage started to be detectable at the MIC dose. At a dose of 1 μg/ml of CIP, DNA damage was visualized clearly immediately after processing, and the DNA fragmentation increased progressively with the antibiotic incubation time. The level of DNA damage was much higher when the bacteria were taken from liquid LB broth than from solid LB agar. CIP treatment produced a progressively slower rate of DNA damage in bacteria in the stationary phase than in the exponentially growing phase. Removing the antibiotic after the 40 min incubation resulted in progressive DSB repair activity with time. The magnitude of DNA repair was inversely related to CIP dose and was noticeable after incubation with CIP at 0.1 μg/ml but scarce after 10 μg/ml. The repair activity was not strictly related to viability. Four E. coli strains with identified mechanisms of reduced sensitivity to CIP were assessed using this procedure and produced DNA fragmentation levels that were inversely related to MIC dose, except those with very high MIC dose. Conclusion This procedure for determining DNA fragmentation is a simple and rapid test for studying and evaluating the effect of quinolones.

  6. Effective DNA Inhibitors of Cathepsin G by In Vitro Selection

    Science.gov (United States)

    Gatto, Barbara; Vianini, Elena; Lucatello, Lorena; Sissi, Claudia; Moltrasio, Danilo; Pescador, Rodolfo; Porta, Roberto; Palumbo, Manlio

    2008-01-01

    Cathepsin G (CatG) is a chymotrypsin-like protease released upon degranulation of neutrophils. In several inflammatory and ischaemic diseases the impaired balance between CatG and its physiological inhibitors leads to tissue destruction and platelet aggregation. Inhibitors of CatG are suitable for the treatment of inflammatory diseases and procoagulant conditions. DNA released upon the death of neutrophils at injury sites binds CatG. Moreover, short DNA fragments are more inhibitory than genomic DNA. Defibrotide, a single stranded polydeoxyribonucleotide with antithrombotic effect is also a potent CatG inhibitor. Given the above experimental evidences we employed a selection protocol to assess whether DNA inhibition of CatG may be ascribed to specific sequences present in defibrotide DNA. A Selex protocol was applied to identify the single-stranded DNA sequences exhibiting the highest affinity for CatG, the diversity of a combinatorial pool of oligodeoxyribonucleotides being a good representation of the complexity found in defibrotide. Biophysical and biochemical studies confirmed that the selected sequences bind tightly to the target enzyme and also efficiently inhibit its catalytic activity. Sequence analysis carried out to unveil a motif responsible for CatG recognition showed a recurrence of alternating TG repeats in the selected CatG binders, adopting an extended conformation that grants maximal interaction with the highly charged protein surface. This unprecedented finding is validated by our results showing high affinity and inhibition of CatG by specific DNA sequences of variable length designed to maximally reduce pairing/folding interactions. PMID:19325843

  7. Effective DNA Inhibitors of Cathepsin G by In Vitro Selection

    Directory of Open Access Journals (Sweden)

    Manlio Palumbo

    2008-06-01

    Full Text Available Cathepsin G (CatG is a chymotrypsin-like protease released upon degranulation of neutrophils. In several inflammatory and ischaemic diseases the impaired balance between CatG and its physiological inhibitors leads to tissue destruction and platelet aggregation. Inhibitors of CatG are suitable for the treatment of inflammatory diseases and procoagulant conditions. DNA released upon the death of neutrophils at injury sites binds CatG. Moreover, short DNA fragments are more inhibitory than genomic DNA. Defibrotide, a single stranded polydeoxyribonucleotide with antithrombotic effect is also a potent CatG inhibitor. Given the above experimental evidences we employed a selection protocol to assess whether DNA inhibition of CatG may be ascribed to specific sequences present in defibrotide DNA. A Selex protocol was applied to identify the single-stranded DNA sequences exhibiting the highest affinity for CatG, the diversity of a combinatorial pool of oligodeoxyribonucleotides being a good representation of the complexity found in defibrotide. Biophysical and biochemical studies confirmed that the selected sequences bind tightly to the target enzyme and also efficiently inhibit its catalytic activity. Sequence analysis carried out to unveil a motif responsible for CatG recognition showed a recurrence of alternating TG repeats in the selected CatG binders, adopting an extended conformation that grants maximal interaction with the highly charged protein surface. This unprecedented finding is validated by our results showing high affinity and inhibition of CatG by specific DNA sequences of variable length designed to maximally reduce pairing/folding interactions.

  8. Ionization versus indirect effects of ionizing radiation on cellular DNA

    International Nuclear Information System (INIS)

    Cadet, Jean; Ravanat, Jean-Luc; Douki, Thierry

    2012-01-01

    Emphasis has been placed in the last decade on the elucidation of the main degradation pathways of isolated DNA mediated by hydroxyl radical (OH) and one-electron oxidation reactions as the result of indirect and direct effects of ionizing radiation respectively. This has led to the isolation and characterization of about 100 oxidized purine and pyrimidine nucleosides if hydroperoxide precursors and diastereomers are included. However, far less information is available on the mechanisms of radiation-induced degradation of bases in cellular DNA mostly due partly to analytical difficulties. It may be reminded that the measurement of oxidized nucleosides and bases in nuclear DNA is still a challenging issue which until recently has been hampered by the use of inappropriate methods such as the GC-MS that have led to overestimated values of the lesions by factors varying between two and three orders of magnitude. At the present, using the accurate and sensitive HPLC/MS/MS assay, 11 single modified nucleosides and bases were found to be generated in cellular DNA upon exposure to gamma rays and heavy ions. This validates several of the OH-mediated oxidation pathways of thymine, guanine and adenine that were previously inferred from model studies. The concomitant decrease in the yields of oxidized bases with the increase in the LET of heavy ions is accounted for by the preponderance of indirect effects in the damaging action of ionizing radiation on DNA. Further evidence for the major role played by .OH was provided by the results of exposure of cells to high intensity 266 nm laser pulses. Under these conditions 8-oxo-7,8-dihydroguanine is mostly produced by biphotonic ionization of DNA nucleobases and subsequent hole migration to guanine bases. It is likely that some of the oxidized bases that have been isolated as single lesions are in fact involved in clustered damage. Interestingly it was recently shown that a single oxidation hit is capable of generating complex

  9. Effect of Surfactants on Plasmid DNA Stability and Release from ...

    African Journals Online (AJOL)

    Purpose: To evaluate the effect of surfactants on plasmid DNA during preparation and release from polylactic glycolide (PLGA) microspheres. Methods: Various surfactants, both ionic and non-ionic (Span, Tween, Triton X100, cetyltrimethylammonium bromide and sodium dodecyl sulphate), were added during the ...

  10. Ultra-short silicon MMI duplexer

    Science.gov (United States)

    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.

  11. Duplex Design Project: Science Pilot Test.

    Science.gov (United States)

    Center for Research on Evaluation, Standards, and Student Testing, Los Angeles, CA.

    Work is reported towards the completion of a prototype duplex-design assessment instrument for grade-12 science. The student course-background questionnaire and the pretest section of the two-stage instrument that was developed were administered to all 134 12th-grade students at St. Clairsville High School (Ohio). Based on the information obtained…

  12. Duplex ultrasound for identifying renal artery stenosis

    DEFF Research Database (Denmark)

    Zachrisson, Karin; Herlitz, Hans; Lönn, Lars

    2017-01-01

    Background Renal artery duplex ultrasound (RADUS) is an established method for diagnosis of renal artery stenosis (RAS), but there is no consensus regarding optimal RADUS criteria. Purpose To define optimal cutoff values for RADUS parameters when screening for RAS using intra-arterial trans...

  13. Investigation of the effect of radiation of DNA methylation patterns

    International Nuclear Information System (INIS)

    Kalinich, J.F.

    1986-01-01

    Four lines of cultured mammalian cells were used in this project: V79A03, a Chinese hamster lung fibroblast; HeLa S-3, an epithelial cell line from a human cervix carcinoma; CHO K-1, an epithelial cell line from a Chinese hamster ovary; and C-1300 N1E-115, a mouse neuroblastoma line. The 5-methylcytosine levels in DNA following exposure to cobalt-60 gamma radiation were measured. Induction of metallothionein in V79A03 cells and acetylcholinesterase in C-1300 N1E-115 cells after irradiation was determined and the effect of radiation on cytoplasmic and nuclear levels of DNA methyltransferase was studied and nuclear demethylase activity assayed. This study showed gamma radiation resulted in a decrease of 5-methylcytosine levels in the DNA of cultured mammalian cells. This radiation-induced hypomethylation resulted in the induction of acetylcholinesterase in mouse neuroblastoma cells and metallothionein in Chinese hamster lung fibroblasts and was caused by a decrease in DNA methyltransferase activity in the nucleus after irradiation and not by the presence of DNA demethylase

  14. Conformational Effects of UV Light on DNA Origami.

    Science.gov (United States)

    Chen, Haorong; Li, Ruixin; Li, Shiming; Andréasson, Joakim; Choi, Jong Hyun

    2017-02-01

    The responses of DNA origami conformation to UV radiation of different wavelengths and doses are investigated. Short- and medium-wavelength UV light can cause photo-lesions in DNA origami. At moderate doses, the lesions do not cause any visible defects in the origami, nor do they significantly affect the hybridization capability. Instead, they help relieve the internal stress in the origami structure and restore it to the designed conformation. At high doses, staple dissociation increases which causes structural disintegration. Long-wavelength UV does not show any effect on origami conformation by itself. We show that this UV range can be used in conjunction with photoactive molecules for photo-reconfiguration, while avoiding any damage to the DNA structures.

  15. Protective effect of a polyvalent influenza DNA vaccine in pigs

    DEFF Research Database (Denmark)

    Karlsson, Ingrid; Borggren, Marie; Rosenstierne, Maiken Worsøe

    2018-01-01

    Background Influenza A virus in swine herds represents a major problem for the swine industry and poses a constant threat for the emergence of novel pandemic viruses and the development of more effective influenza vaccines for pigs is desired. By optimizing the vector backbone and using a needle...... needle-free delivery to the skin, we immunized pigs with two different doses (500 μg and 800 μg) of an influenza DNA vaccine based on six genes of pandemic origin, including internally expressed matrix and nucleoprotein and externally expressed hemagglutinin and neuraminidase as previously demonstrated....... Two weeks following immunization, the pigs were challenged with the 2009 pandemic H1N1 virus. Results When challenged with 2009 pandemic H1N1, 0/5 vaccinated pigs (800 μg DNA) became infected whereas 5/5 unvaccinated control pigs were infected. The pigs vaccinated with the low dose (500 μg DNA) were...

  16. Efeito da energia de soldagem sobre a microestrutura e propriedades mecânicas da zona afetada pelo calor de juntas de aço inoxidável duplex Effect of the welding heat input on the microstructure and mechanical properties of the heat affected zone of multipass welded joints of duplex stainless steel

    Directory of Open Access Journals (Sweden)

    Everton Barbosa Nunes

    2011-09-01

    Full Text Available O objetivo deste trabalho é analisar a influência da energia de soldagem na zona afetada pelo calor (ZAC, de juntas soldadas do aço inoxidável duplex UNS S31803. Foram realizadas soldagens com eletrodo revestido AWS E2209-17 em junta tipo V de Aço Inoxidável Duplex UNS S31803, com dois níveis de energia (15 e 20 kJ/cm. A condição soldada com energia mais elevada apresentou uma ZAC mais extensa e microestrutura mais grosseira nos passes de acabamento. No entanto, nos passes de enchimento e de raiz, as ZAC's destas regiões foram mais refinadas e menos extensa. Em relação à microdureza, a condição soldada com energia de 15 kJ/cm apresentou níveis menores. Em relação à tenacidade, não foi verificada diferença significativa nos resultados.The aim this work is to evaluate the influence of multipass welding heat input on the microstructure and mechanical properties of the heat affected zone (HAZ of UNS S31803 duplex stainless steel multipass welded joints. The shielded metal arc welding process using as filler metal the AWS E2209-17 covered electrode were employed had been carried through V joint groove UNS S31803 DSS, so that two levels of energy (15 and 20 kJ/cm had been used in this experiment. The condition welded with higher energy higher a HAZ extensive and coarser microstructure in the finishing passes. On the other hand, in the wadding passes and root pass, the HAZ this region was more refined and less extensive. In respect of microhardness, the condition welded with energy of 15 kJ/cm got lower levels. In relation to toughness, it was not observed significant differences.

  17. Comparison of duplex PCR and phenotypic analysis in differentiating Candida dubliniensis from Candida albicans from oral samples.

    Science.gov (United States)

    Sampath, Asanga; Weerasekera, Manjula; Dilhari, Ayomi; Gunasekara, Chinthika; Bulugahapitiya, Uditha; Fernando, Neluka; Samaranayake, Lakshman

    2017-12-01

    Candida dubliniensis shares a wide range of phenotypic characteristics with Candida albicans including a common trait called germ tube positivity. Hence, laboratory differentiation of these two species is cumbersome. Duplex PCR analyses for C. albicans and C. dubliniensis was performed directly on DNA extracted from a total of 122 germ tube positive isolates derived from 100 concentrated oral rinse samples from a random cohort of diabetics attending a clinic in Sri Lanka. These results were confirmed by DNA sequencing of internal transcribed spacer (ITS) region of rDNA of the yeasts. Performance efficacy of duplex PCR was then compared with phenotypic identification using a standard battery of phenotypic tests. Of the 122 germ tube positive isolates three were identified by duplex PCR as C. dubliniensis and the remainder as C. albicans. On the contrary, when the standard phenotypic tests, sugar assimilation and chlamydospore formation, were used to differentiate the two species 13 germ tube positive isolates were erroneously identified as C. dubliniensis. Duplex PCR was found to be rapid, sensitive and more specific than phenotypic identification methods in discriminating C. dubliniensis from C. albicans. This is also the first report on the oral carriage of C. dubliniensis in a Sri Lankan population.

  18. Numerical modeling and optimization of machining duplex stainless steels

    Directory of Open Access Journals (Sweden)

    Rastee D. Koyee

    2015-01-01

    Full Text Available The shortcomings of the machining analytical and empirical models in combination with the industry demands have to be fulfilled. A three-dimensional finite element modeling (FEM introduces an attractive alternative to bridge the gap between pure empirical and fundamental scientific quantities, and fulfill the industry needs. However, the challenging aspects which hinder the successful adoption of FEM in the machining sector of manufacturing industry have to be solved first. One of the greatest challenges is the identification of the correct set of machining simulation input parameters. This study presents a new methodology to inversely calculate the input parameters when simulating the machining of standard duplex EN 1.4462 and super duplex EN 1.4410 stainless steels. JMatPro software is first used to model elastic–viscoplastic and physical work material behavior. In order to effectively obtain an optimum set of inversely identified friction coefficients, thermal contact conductance, Cockcroft–Latham critical damage value, percentage reduction in flow stress, and Taylor–Quinney coefficient, Taguchi-VIKOR coupled with Firefly Algorithm Neural Network System is applied. The optimization procedure effectively minimizes the overall differences between the experimentally measured performances such as cutting forces, tool nose temperature and chip thickness, and the numerically obtained ones at any specified cutting condition. The optimum set of input parameter is verified and used for the next step of 3D-FEM application. In the next stage of the study, design of experiments, numerical simulations, and fuzzy rule modeling approaches are employed to optimize types of chip breaker, insert shapes, process conditions, cutting parameters, and tool orientation angles based on many important performances. Through this study, not only a new methodology in defining the optimal set of controllable parameters for turning simulations is introduced, but also

  19. Space Radiation Effects on Human Cells: Modeling DNA Breakage, DNA Damage Foci Distribution, Chromosomal Aberrations and Tissue Effects

    Science.gov (United States)

    Ponomarev, A. L.; Huff, J. L.; Cucinotta, F. A.

    2011-01-01

    Future long-tem space travel will face challenges from radiation concerns as the space environment poses health risk to humans in space from radiations with high biological efficiency and adverse post-flight long-term effects. Solar particles events may dramatically affect the crew performance, while Galactic Cosmic Rays will induce a chronic exposure to high-linear-energy-transfer (LET) particles. These types of radiation, not present on the ground level, can increase the probability of a fatal cancer later in astronaut life. No feasible shielding is possible from radiation in space, especially for the heavy ion component, as suggested solutions will require a dramatic increase in the mass of the mission. Our research group focuses on fundamental research and strategic analysis leading to better shielding design and to better understanding of the biological mechanisms of radiation damage. We present our recent effort to model DNA damage and tissue damage using computational models based on the physics of heavy ion radiation, DNA structure and DNA damage and repair in human cells. Our particular area of expertise include the clustered DNA damage from high-LET radiation, the visualization of DSBs (DNA double strand breaks) via DNA damage foci, image analysis and the statistics of the foci for different experimental situations, chromosomal aberration formation through DSB misrepair, the kinetics of DSB repair leading to a model-derived spectrum of chromosomal aberrations, and, finally, the simulation of human tissue and the pattern of apoptotic cell damage. This compendium of theoretical and experimental data sheds light on the complex nature of radiation interacting with human DNA, cells and tissues, which can lead to mutagenesis and carcinogenesis later in human life after the space mission.

  20. In-Band Full-Duplex Communications for Cellular Networks with Partial Uplink/Downlink Overlap

    KAUST Repository

    AlAmmouri, Ahmad

    2015-12-06

    In-band full-duplex (FD) communications have been optimistically promoted to improve the spectrum utilization in cellular networks. However, the explicit impact of spatial interference, imposed by FD communications, on uplink and downlink transmissions has been overlooked in the literature. This paper presents an extensive study of the explicit effect of FD communications on the uplink and downlink performances. For the sake of rigorous analysis, we develop a tractable framework based on stochastic geometry toolset. The developed model accounts for uplink truncated channel inversion power control in FD cellular networks. The study shows that FD communications improve the downlink throughput at the expense of significant degradation in the uplink throughput. Therefore, we propose a novel fine-grained duplexing scheme, denoted as α-duplex scheme, which allows a partial overlap between uplink and downlink frequency bands. To this end, we show that the amount of the overlap can be optimized via adjusting α to achieve a certain design objective.

  1. In-Band Full-Duplex Communications for Cellular Networks with Partial Uplink/Downlink Overlap

    KAUST Repository

    Alammouri, Ahmad; Elsawy, Hesham; Amin, Osama; Alouini, Mohamed-Slim

    2015-01-01

    In-band full-duplex (FD) communications have been optimistically promoted to improve the spectrum utilization in cellular networks. However, the explicit impact of spatial interference, imposed by FD communications, on uplink and downlink transmissions has been overlooked in the literature. This paper presents an extensive study of the explicit effect of FD communications on the uplink and downlink performances. For the sake of rigorous analysis, we develop a tractable framework based on stochastic geometry toolset. The developed model accounts for uplink truncated channel inversion power control in FD cellular networks. The study shows that FD communications improve the downlink throughput at the expense of significant degradation in the uplink throughput. Therefore, we propose a novel fine-grained duplexing scheme, denoted as α-duplex scheme, which allows a partial overlap between uplink and downlink frequency bands. To this end, we show that the amount of the overlap can be optimized via adjusting α to achieve a certain design objective.

  2. Approximation methods for the stability analysis of complete synchronization on duplex networks

    Science.gov (United States)

    Han, Wenchen; Yang, Junzhong

    2018-01-01

    Recently, the synchronization on multi-layer networks has drawn a lot of attention. In this work, we study the stability of the complete synchronization on duplex networks. We investigate effects of coupling function on the complete synchronization on duplex networks. We propose two approximation methods to deal with the stability of the complete synchronization on duplex networks. In the first method, we introduce a modified master stability function and, in the second method, we only take into consideration the contributions of a few most unstable transverse modes to the stability of the complete synchronization. We find that both methods work well for predicting the stability of the complete synchronization for small networks. For large networks, the second method still works pretty well.

  3. Noncovalent DNA Binding Drives DNA Alkylation by Leinamycin. Evidence That the Z,E-5-(Thiazol-4-yl)-penta-2,4-dienone Moiety of the Natural Product Serves As An Atypical DNA Intercalator

    Science.gov (United States)

    Fekry, Mostafa I.; Szekely, Jozsef; Dutta, Sanjay; Breydo, Leonid; Zang, Hong; Gates, Kent S.

    2012-01-01

    Molecular recognition and chemical modification of DNA are important in medicinal chemistry, toxicology, and biotechnology. Historically, natural products have revealed many interesting and unexpected mechanisms for noncovalent DNA binding and covalent DNA modification. The studies reported here characterize the molecular mechanisms underlying the efficient alkylation of duplex DNA by the Streptomyces-derived natural product leinamycin. Previous studies suggested that alkylation of duplex DNA by activated leinamycin (2) is driven by noncovalent association of the natural product with the double helix. This is striking because leinamycin does not contain a classical noncovalent DNA-binding motif such as an intercalating unit, a groove binder, or a polycation. The experiments described here provide evidence that leinamycin is an atypical DNA-intercalating agent. A competition binding assay involving daunomycin-mediated inhibition of DNA alkylation by leinamycin provided evidence that activated leinamycin binds to duplex DNA with an apparent binding constant of approximately 4.3 ± 0.4 × 103 M−1. Activated leinamycin caused duplex unwinding and hydrodynamic changes in DNA-containing solutions that are indicative of DNA intercalation. Characterization of the reaction of activated leinamycin with palindromic duplexes containing 5'-CG and 5'-GC target sites, bulge-containing duplexes, and 5-methylcytosine-containing duplexes provided evidence regarding the orientation of leinamycin with respect to target guanine residues. The data allows construction of a model for the leinamycin-DNA complex suggesting how a modest DNA-binding constant combines with proper positioning of the natural product to drive efficient alkylation of guanine residues in the major groove of duplex DNA. PMID:21954957

  4. Recovery Based Nanowire Field-Effect Transistor Detection of Pathogenic Avian Influenza DNA

    Science.gov (United States)

    Lin, Chih-Heng; Chu, Chia-Jung; Teng, Kang-Ning; Su, Yi-Jr; Chen, Chii-Dong; Tsai, Li-Chu; Yang, Yuh-Shyong

    2012-02-01

    Fast and accurate diagnosis is critical in infectious disease surveillance and management. We proposed a DNA recovery system that can easily be adapted to DNA chip or DNA biosensor for fast identification and confirmation of target DNA. This method was based on the re-hybridization of DNA target with a recovery DNA to free the DNA probe. Functionalized silicon nanowire field-effect transistor (SiNW FET) was demonstrated to monitor such specific DNA-DNA interaction using high pathogenic strain virus hemagglutinin 1 (H1) DNA of avian influenza (AI) as target. Specific electric changes were observed in real-time for AI virus DNA sensing and device recovery when nanowire surface of SiNW FET was modified with complementary captured DNA probe. The recovery based SiNW FET biosensor can be further developed for fast identification and further confirmation of a variety of influenza virus strains and other infectious diseases.

  5. Problems in repair-welding of duplex-treated tool steels

    Directory of Open Access Journals (Sweden)

    T. Muhič

    2009-01-01

    Full Text Available The present paper addresses problems in laser welding of die-cast tools used for aluminum pressure die-castings and plastic moulds. To extend life cycle of tools various surface improvements are used. These surface improvements significantly reduce weldability of the material. This paper presents development of defects in repair welding of duplex-treated tool steel. The procedure is aimed at reduction of defects by the newly developed repair laser welding techniques. Effects of different repair welding process parameters and techniques are considered. A microstructural analysis is conducted to detect defect formation and reveal the best laser welding method for duplex-treated tools.

  6. Determination of the chromium concentration of phase decomposition products in an aged duplex stainless steel

    International Nuclear Information System (INIS)

    Kuwano, Hisashi; Imamasu, Hisanao

    2006-01-01

    A commercial duplex stainless steel has been aged at 673 K for up to 55,000 h. The aging results in the phase decomposition of the ferrite in duplex stainless steel. The end products of the phase decomposition are a Fe-rich and a Cr-rich phase. The chromium concentration of these phases is determined by measuring the hyperfine magnetic field and the isomer shift using Moessbauer effect. The experimental results are compared with a phase diagram calculated for Fe-Cr-Ni ternary system at 673 K.

  7. Doppler color flow mapping of peripheral vessels: Comparison of angiodynography with conventional duplex US

    International Nuclear Information System (INIS)

    Merritt, C.R.B.; Bluth, E.I.; Sullivan, M.A.

    1986-01-01

    A new Doppler color flow imager was compared to duplex US in the evaluation of carotid and peripheral vessels in 50 patients. A 7.5-MHz transducer permitted simultaneous high-resolution real-time imaging of Doppler flow and tissue. The system was found to have excellent image quality and Doppler sensitivity. Flow characteristics and velocity measurements obtained with this system correlated well with those obtained using the duplex scanner and were obtained more quickly than with the conventional system, allowing more complete assessment of flow characteristics. Color Doppler flow imaging appears to be an extremely promising method for the rapid and effective evaluation of peripheral vascular flow

  8. Development of duplex PCR for simultaneous detection of Theileria spp. and Anaplasma spp. in sheep and goats.

    Science.gov (United States)

    Cui, Yanyan; Zhang, Yan; Jian, Fuchun; Zhang, Longxian; Wang, Rongjun; Cao, Shuxuan; Wang, Xiaoxing; Yan, Yaqun; Ning, Changshen

    2017-05-01

    Theileria spp. and Anaplasma spp., which are important tick-borne pathogens (TBPs), impact the health of humans and animals in tropical and subtropical areas. Theileria and Anaplasma co-infections are common in sheep and goats. Following alignment of the relevant DNA sequences, two primer sets were designed to specifically target the Theileria spp. 18S rRNA and Anaplasma spp. 16S rRNA gene sequences. Genomic DNA from the two genera was serially diluted tenfold for testing the sensitivities of detection of the primer sets. The specificities of the primer sets were confirmed when DNA from Anaplasma and Theileria (positive controls), other related hematoparasites (negative controls) and ddH 2 O were used as templates. Fifty field samples were also used to evaluate the utility of single PCR and duplex PCR assays, and the detection results were compared with those of the PCR methods previously published. An optimized duplex PCR assay was established from the two primer sets based on the relevant genes from the two TBPs, and this assay generated products of 298-bp (Theileria spp.) and 139-bp (Anaplasma spp.). The detection limit of the assay was 29.4 × 10 -3  ng per μl, and there was no cross-reaction with the DNA from other hematoparasites. The results showed that the newly developed duplex PCR assay had an efficiency of detection (P > 0.05) similar to other published PCR methods. In this study, a duplex PCR assay was developed that can simultaneously identify Theileria spp. and Anaplasma spp. in sheep and goats. This duplex PCR is a potentially valuable assay for epidemiological studies of TBPs in that it can detect cases of mixed infections of the pathogens. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Effects of coordination of diammineplatinum(II) with DNA on the activities of Escherichia coli DNA polymerase I

    International Nuclear Information System (INIS)

    Bernges, F.; Holler, E.

    1988-01-01

    The effects of the reaction of cis- and trans-diamminedichloroplatinum(II) with DNA have been measured with regard to DNA synthesis, 3'-5' exonuclease (proofreading), and 5'-3' exonuclease (repair) activities of Escherichia coli DNA polymerase I. Both isomers inhibit DNA synthetic activity of the polymerase through an increase in K/sub m/ values and a decrease in V/sub max/ values for platinated DNA but not for the nucleoside 5'-triphosphates as the varied substrates. The inhibition is a consequence of lowered binding affinity between platinated DNA and DNA polymerase, and of a platination-induced separation of template and primer strands. Strand separation enhances initial rates of 3'-5' excision of [ 3 H]dCMP from platinated DNA (proofreading), while total excision levels of nucleotides are decreased. In contrast to proofreading activity, the 5'-3' exonuclease activity (repair) discriminates between DNA which had reacted with cis- and with trans-diamminedichloroplatinum(II). While both initial rates and total excision are inhibited for the cis isomer, they are almost not affected for the trans isomer. This differential effect could explain why bacterial growth inhibition requires much higher concentrations of trans- than cis-diamminedichloroplatinum(II)

  10. Strip biosensor for amplified detection of nerve growth factor-beta based on a molecular translator and catalytic DNA circuit.

    Science.gov (United States)

    Liu, Jun; Lai, Ting; Mu, Kejie; Zhou, Zheng

    2014-10-07

    We have demonstrated a new visual detection approach based on a molecular translator and a catalytic DNA circuit for the detection of nerve growth factor-beta (NGF-β). In this assay, a molecular translator based on the binding-induced DNA strand-displacement reaction was employed to convert the input protein to an output DNA signal. The molecular translator is composed of a target recognition element and a signal output element. Target recognition is achieved by the binding of the anti-NGF-β antibody to the target protein. Polyclonal anti-NGF-β antibody is conjugated to DNA1 and DNA2. The antibody conjugated DNA1 is initially hybridized to DNA3 to form a stable DNA1/DNA3 duplex. In the presence of NGF-β, the binding of the same target protein brings DNA1 and DNA2 into close proximity, resulting in an increase in their local effective concentration. This process triggers the strand-displacement reaction between DNA2 and DNA3 and releases the output DNA3. The released DNA3 is further amplified by a catalytic DNA circuit. The product of the catalytic DNA circuit is detected by a strip biosensor. This proposed assay has high sensitivity and selectivity with a dynamic response ranging from 10 fM to 10 pM, and its detection limit is 10 fM of NGF-β. This work provides a sensitive, enzyme-free, and universal strategy for the detection of other proteins.

  11. Effect of DNA polymerase inhibitors on DNA repair in intact and permeable human fibroblasts: Evidence that DNA polymerases δ and β are involved in DNA repair synthesis induced by N-methyl-N'-nitro-N-nitrosoguanidine

    International Nuclear Information System (INIS)

    Hammond, R.A.; Miller, M.R.; McClung, J.K.

    1990-01-01

    The involvement of DNA polymerases α, β, and δ in DNA repair synthesis induced by N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) was investigated in human fibroblasts (HF). The effects of anti-(DNA polymerase α) monoclonal antibody, (p-n-butylphenyl)deoxyguanosine triphosphate (BuPdGTP), dideoxythymidine triphosphate (ddTTP), and aphidicolin on MNNG-induced DNA repair synthesis were investigated to dissect the roles of the different DNA polymerases. A subcellular system (permeable cells), in which DNA repair synthesis and DNA replication were differentiated by CsCl gradient centrifugation of BrdUMP density-labeled DNA, was used to examine the effects of the polymerase inhibitors. Another approach investigated the effects of several of these inhibitors of MNNG-induced DNA repair synthesis in intact cells by measuring the amount of [ 3 H]thymidine incorporated into repair DNA as determined by autoradiography and quantitation with an automated video image analysis system. In permeable cells, MNNG-induced DNA repair synthesis was inhibited 56% by 50 μg of aphidicolin/mL, 6% by 10 μM BuPdGTP, 13% by anti-(DNA polymerse α) monoclonal antibodies, and 29% by ddTTP. In intact cells, MNNG-induced DNA repair synthesis was inhibited 57% by 50 μg of aphidicolin/mL and was not significantly inhibited by microinjecting anti-(DNA polymerase α) antibodies into HF nuclei. These results indicate that both DNA polymerase δ and β are involved in repairing DNA damage caused by MNNG

  12. Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance

    Directory of Open Access Journals (Sweden)

    Haque Kashif A

    2005-09-01

    Full Text Available Abstract Background Whole genome amplification (WGA promises to eliminate practical molecular genetic analysis limitations associated with genomic DNA (gDNA quantity. We evaluated the performance of multiple displacement amplification (MDA WGA using gDNA extracted from lymphoblastoid cell lines (N = 27 with a range of starting gDNA input of 1–200 ng into the WGA reaction. Yield and composition analysis of whole genome amplified DNA (wgaDNA was performed using three DNA quantification methods (OD, PicoGreen® and RT-PCR. Two panels of N = 15 STR (using the AmpFlSTR® Identifiler® panel and N = 49 SNP (TaqMan® genotyping assays were performed on each gDNA and wgaDNA sample in duplicate. gDNA and wgaDNA masses of 1, 4 and 20 ng were used in the SNP assays to evaluate the effects of DNA mass on SNP genotyping assay performance. A total of N = 6,880 STR and N = 56,448 SNP genotype attempts provided adequate power to detect differences in STR and SNP genotyping performance between gDNA and wgaDNA, and among wgaDNA produced from a range of gDNA templates inputs. Results The proportion of double-stranded wgaDNA and human-specific PCR amplifiable wgaDNA increased with increased gDNA input into the WGA reaction. Increased amounts of gDNA input into the WGA reaction improved wgaDNA genotyping performance. Genotype completion or genotype concordance rates of wgaDNA produced from all gDNA input levels were observed to be reduced compared to gDNA, although the reduction was not always statistically significant. Reduced wgaDNA genotyping performance was primarily due to the increased variance of allelic amplification, resulting in loss of heterozygosity or increased undetermined genotypes. MDA WGA produces wgaDNA from no template control samples; such samples exhibited substantial false-positive genotyping rates. Conclusion The amount of gDNA input into the MDA WGA reaction is a critical determinant of genotyping performance of wgaDNA. At least 10 ng of

  13. Formamidopyrimidines in DNA: mechanisms of formation, repair, and biological effects.

    Science.gov (United States)

    Dizdaroglu, Miral; Kirkali, Güldal; Jaruga, Pawel

    2008-12-15

    Oxidatively induced damage to DNA results in a plethora of lesions comprising modified bases and sugars, DNA-protein cross-links, tandem lesions, strand breaks, and clustered lesions. Formamidopyrimidines, 4,6-diamino-5-formamidopyrimidine (FapyAde) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyGua), are among the major lesions generated in DNA by hydroxyl radical attack, UV radiation, or photosensitization under numerous in vitro and in vivo conditions. They are formed by one-electron reduction of C8-OH-adduct radicals of purines and thus have a common precursor with 8-hydroxypurines generated upon one-electron oxidation. Methodologies using mass spectrometry exist to accurately measure FapyAde and FapyGua in vitro and in vivo. Formamidopyrimidines are repaired by base excision repair. Numerous prokaryotic and eukaryotic DNA glycosylases are highly specific for removal of these lesions from DNA in the first step of this repair pathway, indicating their biological importance. FapyAde and FapyGua are bypassed by DNA polymerases with the insertion of the wrong intact base opposite them, leading to mutagenesis. In mammalian cells, the mutagenicity of FapyGua exceeds that of 8-hydroxyguanine, which is thought to be the most mutagenic of the oxidatively induced lesions in DNA. The background and formation levels of the former in vitro and in vivo equal or exceed those of the latter under various conditions. FapyAde and FapyGua exist in living cells at significant background levels and are abundantly generated upon exposure to oxidative stress. Mice lacking the genes that encode specific DNA glycosylases accumulate these lesions in different organs and, in some cases, exhibit a series of pathological conditions including metabolic syndrome and cancer. Animals exposed to environmental toxins accumulate formamidopyrimidines in their organs. Here, we extensively review the mechanisms of formation, measurement, repair, and biological effects of formamidopyrimidines

  14. Law of mixture used to model the flow behavior of a duplex stainless steel at high temperatures

    International Nuclear Information System (INIS)

    Momeni, A.; Dehghani, K.; Poletti, M.C.

    2013-01-01

    In this investigation the flow curves of a duplex stainless steel were drawn by performing hot compression tests over a wide temperature range of 950–1200 °C and strain rates of 0.001–100 s −1 . The flow curves of ferrite and austenite phases in the duplex structure were depicted by conducting similar hot compression tests on two steels that were cast and prepared with the same chemical compositions. The flow curves of the austenitic steel were found typical of dynamic recrystallization. They were successfully modeled by using the experimental exponential equation proposed by Cingara and McQueen. The flow curves of the ferritic steel were typical of dynamic recovery. They were modeled by the dislocation density evolution function proposed by Estrin and Meckning. Comparing the flow curves of three studied steels, it was found that the flow curves of the duplex steel were very similar and close to those of the ferrite steel. It was understood that in a duplex structure of ferrite and austenite the flow behavior is mostly controlled by the softer phase, i.e. ferrite. The law of mixture was modified to consider the strain partitioning between ferrite and austenite. The distribution coefficients of ferrite and austenite were described and determined at different deformation conditions. The results of modeling satisfactorily predicted the experimental curves. It was shown that the influence of austenite on the flow behavior of the duplex structure is almost low. However, it increases as strain rate or temperature rises. - Highlights: ► Flow curves of austenite and ferrite in the duplex steel were modeled separately. ► The flow behavior of the duplex steel is mostly controlled by ferrite. ► The effect of austenite on flow curve increases with temperature and strain rate. ► The flow curve of the duplex steel is modeled by the modified law of mixture

  15. A study of DNA protective effect of orange juice supplementation.

    Science.gov (United States)

    Szeto, Yim Tong; To, Tai Lun; Pak, Sok Cheon; Kalle, Wouter

    2013-05-01

    The potential acute genoprotective effect of orange juice supplementation was investigated. Six healthy subjects (aged 33 to 60 years; 3 women and 3 men) were asked to drink 400 mL of commercial orange juice, which contained 100 mg vitamin C and 40.8 g sugar. Venous blood (2 mL) was taken before and 2 h after ingestion (test trial). A week later, the subjects were asked to repeat the trial by drinking 400 mL water with 100 mg vitamin C and 40.8 g glucose (control trial). Lymphocytes isolated from blood samples underwent comet assay on the day of collection. Pre- and postingestion DNA damage scores were measured in both the test and control trials. Results showed that there was a significant decrease in DNA damage induced by hydrogen peroxide after 2 h of supplementation with orange juice, and no change in baseline DNA damage. There was no significant decrease in the DNA damage in lymphocytes in the control trial.

  16. RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes.

    Science.gov (United States)

    NandyMazumdar, Monali; Nedialkov, Yuri; Svetlov, Dmitri; Sevostyanova, Anastasia; Belogurov, Georgiy A; Artsimovitch, Irina

    2016-12-27

    Upon RNA polymerase (RNAP) binding to a promoter, the σ factor initiates DNA strand separation and captures the melted nontemplate DNA, whereas the core enzyme establishes interactions with the duplex DNA in front of the active site that stabilize initiation complexes and persist throughout elongation. Among many core RNAP elements that participate in these interactions, the β' clamp domain plays the most prominent role. In this work, we investigate the role of the β gate loop, a conserved and essential structural element that lies across the DNA channel from the clamp, in transcription regulation. The gate loop was proposed to control DNA loading during initiation and to interact with NusG-like proteins to lock RNAP in a closed, processive state during elongation. We show that the removal of the gate loop has large effects on promoter complexes, trapping an unstable intermediate in which the RNAP contacts with the nontemplate strand discriminator region and the downstream duplex DNA are not yet fully established. We find that although RNAP lacking the gate loop displays moderate defects in pausing, transcript cleavage, and termination, it is fully responsive to the transcription elongation factor NusG. Together with the structural data, our results support a model in which the gate loop, acting in concert with initiation or elongation factors, guides the nontemplate DNA in transcription complexes, thereby modulating their regulatory properties.

  17. Sequence specificity of alkali-labile DNA damage photosensitized by suprofen.

    Science.gov (United States)

    Starrs, S M; Davies, R J

    2000-09-01

    On irradiation at UVB wavelengths, in aerated neutral aqueous solution, the anti-inflammatory drug suprofen (SP) photosensitizes the production of alkali-labile cleavage sites in DNA much more efficiently than direct strand breaks. It is active at submillimolar concentrations despite having no significant binding affinity for DNA. Gel sequencing studies utilizing 32P-end-labeled oligonucleotides have revealed that piperidine-sensitive lesions are formed predominantly at the positions of guanine (G) bases, with the extent of modification being UV dose- and SP concentration-dependent. Quite distinct patterns of G-specific damage are observed in single-stranded and duplex DNA molecules. The uniform attack at all G residues in single-stranded DNA, which is enhanced in D2O, is compatible with a Type-II mechanism. SP is a known generator of singlet oxygen whose participation in the reaction is supported by the effects of quenchers and scavengers. In duplex DNA, piperidine-induced cleavage occurs with high selectivity at the 5'-G of GG and (less prominently) GA doublets. This behavior is characteristic of a Type-I process involving electron transfer from DNA to photoexcited SP molecules. The ability of SP to sensitize the formation of Type-I and Type-II photo-oxidation products from 2'-deoxyguanosine attests to the feasibility of competing mechanisms in DNA.

  18. Study of Sigma Phase in Duplex SAF 2507

    Science.gov (United States)

    Fellicia, D. M.; Sutarsis; Kurniawan, B. A.; Wulanari, D.; Purniawan, A.; Wibisono, A. T.

    2017-05-01

    Super duplex stainless steel is one of the stainless steel which has a combination between high strength properties and excellent corrosion resistance. However, the resistance can decrease by precipitation of sigma phase which is formed at high temperature, for example after welding processes. A series of experiments has been performed to study the effect of solution annealing to existence of sigma phase on super duplex SAF 2507. Variations of solution-annealing temperatures were 1000 °C, 1065 °C and 1125 °C with holding time of 15 and 30 minutes for each temperature. Effect of solution annealing process was characterized by using XRD, SEM, and Optical Microscopy. The result showed precipitation of sigma phase completely dissolved at 1065 °C and 1125 °C because it reformed to austenite. After it was heated at 1065 °C, chromium carbide appeared in ferrite site and grain boundary. The amount of chromium carbide increased with the increasing of solution annealing temperature.

  19. Detection of Toxoplasma gondii and Epstein-Barr virus in HIV patients with clinical symptoms of suspected central nervous system infection using duplex real-time polymerase chain reaction

    Science.gov (United States)

    Rahmawati, E.; Ibrahim, F.; Imran, D.; Sudarmono, P.

    2017-08-01

    Focal brain lesion is a neurological complication in HIV, which is marked as a space occupying lesion (SOL) and needs rapid and effective treatment. This lesion is mainly caused by encephalitis toxoplasma and primary central nervous system lymphoma related to the Epstein-Barr virus (EBV) infection, which is difficult to distinguish using CT scan or magnetic resonance imaging (MRI). The gold standard of diagnosing focal brain lesion has been brain biopsy, but this examination is an invasive procedure that causes complications. The objective of this study is to obtain the rapid laboratory diagnosis of Toxoplasma gondii (T. gondii) and EBV infection. In this experimental study, blood and cerebrospinal fluid were obtained from HIV patients who were admitted to the Neurology Department of Cipto Mangunkusumo Hospital. The samples were examined using duplex real-time polymerase chain reaction (PCR) to detect T. gondii and EBV. The first step was the optimization of duplex real-time PCR, including the annealing temperature, primer and probe concentration, elution volume, and template volume. Minimal DNA detection was used to measure minimal T. gondii and EBV. Cross reactions were determined for technical specificity using the bacteria and viruses Staphylococcus aureus, Klebsiella pneumonia, Pseudomonas aeruginosa, Mycobacterium tuberculosis H37Rv, Candida spp, cytomegalovirus, herpes zoster virus, and varicella zoster virus. Duplex real-time PCR was applied optimally to patients. In the optimization of duplex real-time PCR, the annealing temperature of T. gondii and EBV were 58 °C, the concentration of primer forward and reverse for T. gondii and EBV were 0.2 μM, the concentration of probe for T. gondii and EBV were 0.4μM and 0.2 μM, respectively. Minimal DNA detection of T. gondii and EBV were 5.68 copy/ml and 1.31 copy/ml, respectively. There was no cross reaction between another bacteria and virus that were used as the primer and probe for T. gondii and EBV. The

  20. Renal duplex Doppler ultrasound findings in diabetics

    International Nuclear Information System (INIS)

    Shim, Hyang Yee; Kim, Young Geun; Kook, Cheol Keu; Yoon, Chong Hyun; Lee, Shin Hyung; Lee, Chang Joon

    1993-01-01

    The correlation between clinical-laboratory findings and renal duplex Doppler ultrasound findings was studied in 45 patients with diabetes mellitus to see the role of duplex Doppler ultrasound in the detection of diabetic nephropathy. The resistive indices in patients with elevated serum creatinine, BUN, proteinuria, and systolic blood pressure levels were statistically significantly higher than those in patients with normal levels (p<0.05). Also resistive indics in patients with retinopathy were higher than that in patients without retinopathy (p<0.05). But the ultrasound morphologic changes of kidney such as renal length, cortical eye-catching, and corticomedullarycontrast were not well correlated with clinical-laboratory data and resistive index. The resistive index of the kidney in conjunction with clinical-laboratory data in diabetics may be helpful in the evaluation of diabetic nephropathy

  1. Renal duplex Doppler ultrasound findings in diabetics

    Energy Technology Data Exchange (ETDEWEB)

    Shim, Hyang Yee; Kim, Young Geun; Kook, Cheol Keu; Yoon, Chong Hyun; Lee, Shin Hyung; Lee, Chang Joon [National Medical Center, Seoul (Korea, Republic of)

    1993-12-15

    The correlation between clinical-laboratory findings and renal duplex Doppler ultrasound findings was studied in 45 patients with diabetes mellitus to see the role of duplex Doppler ultrasound in the detection of diabetic nephropathy. The resistive indices in patients with elevated serum creatinine, BUN, proteinuria, and systolic blood pressure levels were statistically significantly higher than those in patients with normal levels (p<0.05). Also resistive indics in patients with retinopathy were higher than that in patients without retinopathy (p<0.05). But the ultrasound morphologic changes of kidney such as renal length, cortical eye-catching, and corticomedullarycontrast were not well correlated with clinical-laboratory data and resistive index. The resistive index of the kidney in conjunction with clinical-laboratory data in diabetics may be helpful in the evaluation of diabetic nephropathy

  2. Characterization of selection effects on broiler lines using DNA fingerprinting

    Directory of Open Access Journals (Sweden)

    GS Schmidt

    2003-05-01

    Full Text Available The objective of this study was to evaluate the effect of selection for body weight on the genetic variability and diversity in broiler lines. Two paternal broiler lines (LL and LLc were used. LL line was selected for 12 generations for growth and carcass and reproduction characteristics. The LLc line was established from LL line in 1985 and mated at random. Blood samples from six chickens per line were collected and used for molecular analysis. Also, a DNA pool was made for each line to compare effects between lines. Data were analyzed considering the collected information on the presence or absence of DNA bands. Band sharing scores were calculated using the DICE coefficient. The pattern of the 21 most representative bands was used. DNA fingerprinting (DFP showed 90.48 % of polymorphism bands for both lines. Difference between lines was not due to the presence or absence of bands, but to the frequency of such bands in each genotype. Considering that both lines had the same genetic background, changes on band frequency were probably due to selection. Selection for body weight had an effect on the band frequency as evaluated by DFP, and for this reason this technique could be used as a tool in the selection process. Results also suggest that bands 4, 5 and 19 were linked to body weight traits, and bands 9, 10, 12, 13 and 21 were linked to reproductive traits such as egg production.

  3. Thermal ageing of duplex stainless steels

    International Nuclear Information System (INIS)

    Massoud, J.P.; Van Duysen, J.C.; Zacharie, G.; Auger, P.; Danoix, F.

    1992-03-01

    The evolution of the mechanical properties of Mobearing anf Mo-free cast duplex stainless steels, induced by long term ageing in the range 300-400 deg C, has been studied in relation with the evolution of their microstructure. The unmixing of the ferritic Fe-Cr-Ni, solid solution by three-dimensional (sponge-like) spinodal decomposition and the precipitation of intermetallic G-phase particles are the main characteristics of this microstructural evolution

  4. Effects of DNA polymerase inhibitors on replicative and repair DNA synthesis in ultraviolet-irradiated HeLa cells

    International Nuclear Information System (INIS)

    Morita, T.; Nakamura, H.; Tsutsui, Y.; Nishiyama, Y.; Yoshida, S.

    1982-01-01

    Aphidicolin specifically inhibits eukaryotic DNA polymerase α, while 2',3'-dideoxythymidine 5'-triphosphate (d 2 TTP) inhibits DNA polymerase ν and ν but not α. 1-ν-D-Arabinofuranosylcytosine 5'-triphosphate (araCTP) inhibits both DNA polymerase α and ν although to a different extent. Here we measured the effects of these inhibitors on repair DNA synthesis of U.V.-irradiated HeLa cells by two different methods. Firstly, aphidicolin, 1-ν-D-arabinofuranosylcytosine (araC, a precursor of araCTP) and 2',3'-dideoxythimidine (d 2 Thd, a precursor of d 2 TTP) were added directly to the culture medium. In this case, aphidicolin and araC strongly inhibited replicative DNA synthesis of HeLa cells, and they also inhibited repair synthesis after U.V.-irradiation but to a much lesser extent. In contrast, high concentrations of d 2 Thd inhibited repair DNA synthesis to a higher extent than replicative DNA synthesis. Secondly, the active form of inhibitor, d 2 TTP, was microinjected directly into cytoplasm or nuclei or U.V.-irradiated HeLa cells. Microinjection of d 2 TTP effectively inhibited repair synthesis. The microinjection of d 2 TTP, into either cytoplasm or nucleus, strongly inhibited replicative synthesis. These results might indicate that multiple DNA polymerases are involved in repair synthesis as well as in replicative synthesis

  5. Development and Evaluation of a Single-Step Duplex PCR for Simultaneous Detection of Fasciola hepatica and Fasciola gigantica (Family Fasciolidae, Class Trematoda, Phylum Platyhelminthes)

    Science.gov (United States)

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

    2012-01-01

    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. PMID:22692744

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

    Science.gov (United States)

    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.

  7. Development of a lean duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Liljas, M.; Johansson, P.; Liu Hui-Ping; Olsson, C.O.A. [Avesta Research Centre, Avesta (Sweden). Outokumpu Stainless

    2008-06-15

    The classic series of duplex stainless steels shows very high corrosion resistance and can be used for very demanding applications. A new lean duplex steel, LDX 2101 {sup registered} (EN 1.4162, UNS S32101), has been developed with corrosion resistance on a par with standard austenitic grades. Application areas include: structural components, chemical industry, tanks and containers. The steel was designed to have equal amounts of ferrite and austenite in annealed condition and with an austenite that is stable against strain-induced martensite. Thanks to its high nitrogen content, the steel has a fast austenite reformation when subjected to thermal cycling, e.g. welding. Unlike conventional duplex grades, the formation of intermetallic phase is very sluggish, although precipitation of nitrides and carbides has a certain impact on material properties after exposure in the temperature range 600 to 800 C. The precipitation behaviour after different isothermal treatments is described and its influence on different product properties is shown. A good agreement was found between impact toughness and corrosion resistance for a wide range of thermal treatments. (orig.)

  8. Characterization of thermal aging of duplex stainless steel by SQUID

    International Nuclear Information System (INIS)

    Isobe, Y.; Kamimura, A.; Aoki, K.; Nakayasu, F.

    1995-01-01

    Thermal aging is a growing concern for long-term-aged duplex stainless steel piping in nuclear power plants. Superconducting QUantum Interference Device (SQUID) was used for the detection of thermal aging of SUS329 rolled duplex stainless steel and SCS16 cast duplex stainless steel. It was found that the SQUID output signal pattern in the presence of AC magnetic field applied to the specimen was sensitive to the changes in electromagnetic properties due to thermal aging

  9. Full-Duplex MIMO Small-Cell Networks: Performance Analysis

    OpenAIRE

    Atzeni, Italo; Kountouris, Marios

    2015-01-01

    Full-duplex small-cell relays with multiple antennas constitute a core element of the envisioned 5G network architecture. In this paper, we use stochastic geometry to analyze the performance of wireless networks with full-duplex multiple-antenna small cells, with particular emphasis on the probability of successful transmission. To achieve this goal, we additionally characterize the distribution of the self-interference power of the full-duplex nodes. The proposed framework reveals useful ins...

  10. Electron Beam Welding of Duplex Steels with using Heat Treatment

    Science.gov (United States)

    Schwarz, Ladislav; Vrtochová, Tatiana; Ulrich, Koloman

    2010-01-01

    This contribution presents characteristics, metallurgy and weldability of duplex steels with using concentrated energy source. The first part of the article describes metallurgy of duplex steels and the influence of nitrogen on their solidification. The second part focuses on weldability of duplex steels with using electron beam aimed on acceptable structure and corrosion resistance performed by multiple runs of defocused beam over the penetration weld.

  11. Quantitative analysis of TALE-DNA interactions suggests polarity effects.

    Science.gov (United States)

    Meckler, Joshua F; Bhakta, Mital S; Kim, Moon-Soo; Ovadia, Robert; Habrian, Chris H; Zykovich, Artem; Yu, Abigail; Lockwood, Sarah H; Morbitzer, Robert; Elsäesser, Janett; Lahaye, Thomas; Segal, David J; Baldwin, Enoch P

    2013-04-01

    Transcription activator-like effectors (TALEs) have revolutionized the field of genome engineering. We present here a systematic assessment of TALE DNA recognition, using quantitative electrophoretic mobility shift assays and reporter gene activation assays. Within TALE proteins, tandem 34-amino acid repeats recognize one base pair each and direct sequence-specific DNA binding through repeat variable di-residues (RVDs). We found that RVD choice can affect affinity by four orders of magnitude, with the relative RVD contribution in the order NG > HD ≈ NN > NI > NK. The NN repeat preferred the base G over A, whereas the NK repeat bound G with 10(3)-fold lower affinity. We compared AvrBs3, a naturally occurring TALE that recognizes its target using some atypical RVD-base combinations, with a designed TALE that precisely matches 'standard' RVDs with the target bases. This comparison revealed unexpected differences in sensitivity to substitutions of the invariant 5'-T. Another surprising observation was that base mismatches at the 5' end of the target site had more disruptive effects on affinity than those at the 3' end, particularly in designed TALEs. These results provide evidence that TALE-DNA recognition exhibits a hitherto un-described polarity effect, in which the N-terminal repeats contribute more to affinity than C-terminal ones.

  12. On the Performance of In-Band Full-Duplex Cooperative Communications

    KAUST Repository

    Khafagy, Mohammad Galal

    2016-01-01

    -duplex potentials. Full-duplex relaying (FDR), where intermediate nodes may now support source-destination communication via simultaneous listening/forwarding, represents one of two full-duplex settings currently recommended for deployment in future fifth

  13. Repair of Clustered Damage and DNA Polymerase Iota.

    Science.gov (United States)

    Belousova, E A; Lavrik, O I

    2015-08-01

    Multiple DNA lesions occurring within one or two turns of the DNA helix known as clustered damage are a source of double-stranded DNA breaks, which represent a serious threat to the cells. Repair of clustered lesions is accomplished in several steps. If a clustered lesion contains oxidized bases, an individual DNA lesion is repaired by the base excision repair (BER) mechanism involving a specialized DNA polymerase after excising DNA damage. Here, we investigated DNA synthesis catalyzed by DNA polymerase iota using damaged DNA templates. Two types of DNA substrates were used as model DNAs: partial DNA duplexes containing breaks of different length, and DNA duplexes containing 5-formyluracil (5-foU) and uracil as a precursor of apurinic/apyrimidinic sites (AP) in opposite DNA strands. For the first time, we showed that DNA polymerase iota is able to catalyze DNA synthesis using partial DNA duplexes having breaks of different length as substrates. In addition, we found that DNA polymerase iota could catalyze DNA synthesis during repair of clustered damage via the BER system by using both undamaged and 5-foU-containing templates. We found that hPCNA (human proliferating cell nuclear antigen) increased efficacy of DNA synthesis catalyzed by DNA polymerase iota.

  14. The Role of Repulsion in Colloidal Crystal Engineering with DNA

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Soyoung E. [Department; Li, Tao [X-ray; Senesi, Andrew J. [X-ray; Mirkin, Chad A. [Department; Lee, Byeongdu [X-ray

    2017-11-07

    Hybridization interactions between DNA-functionalized nanoparticles (DNA-NPs) can be used to program the crystallization behavior of superlattices, yielding access to complex three-dimensional structures with more than 30 different lattice symmetries. The first superlattice structures using DNA-NPs as building blocks were identified almost two decades ago, yet the role of repulsive interactions in guiding structure formation is still largely unexplored. Here, a com-prehensive approach is taken to study the role of repulsion in the assembly behavior of DNA-NPs, enabling the calculation of interparticle interaction potentials based on experimental results. In this work, we used two different means to assemble DNA-NPs—Watson-Crick base pairing interactions and depletion interactions—and systematically varied the salt concen-tration to study the effective interactions in DNA-NP superlattices. A comparison between the two systems allows us to decouple the repulsive forces from the attractive hybridization interactions that are sensitive to the ionic environment. We find that the gap distance between adjacent DNA-NPs follows a simple power law dependence on solution ionic strength regardless of the type of attractive forces present. This result suggests that the observed trend is driven by repulsive inter-actions. To better understand such behavior, we propose a mean-field model that provides a mathematical description for the observed trend. This model shows that the trend is due to the variation in the effective cross-sectional diameter of DNA duplex and the thickness of DNA shell.

  15. Twist–radial normal mode analysis in double-stranded DNA chains

    International Nuclear Information System (INIS)

    Torrellas, Germán; Maciá, Enrique

    2012-01-01

    We study the normal modes of a duplex DNA chain at low temperatures. We consider the coupling between the hydrogen-bond radial oscillations and the twisting motion of each base pair within the Peyrard–Bishop–Dauxois model. The coupling is mediated by the stacking interaction between adjacent base pairs along the helix. We explicitly consider different mass values for different nucleotides, extending previous works. We disclose several resonance conditions of interest, determined by the fine-tuning of certain model parameters. The role of these dynamical effects on the DNA chain charge transport properties is discussed.

  16. On the Performance of In-Band Full-Duplex Cooperative Communications

    KAUST Repository

    Khafagy, Mohammad Galal

    2016-06-01

    In-band full-duplex, by which radios may simultaneously transmit and receive over the same channel, has been always considered practically-unfeasible due to the prohibitively strong self-interference. Indeed, a freshly-generated transmit signal power is typically ten orders of magnitude higher than that of a naturally-attenuated received signal. While unable to manage such an overwhelming interference, wireless communications resorted to half-duplex operation, transmitting and receiving over orthogonal channel resources. Recent research has demonstrated the practical feasibility of full-duplexing via successive sophisticated stages of signal suppression/cancellation, bringing this long-held assumption down and reviving the promising full-duplex potentials. Full-duplex relaying (FDR), where intermediate nodes may now support source-destination communication via simultaneous listening/forwarding, represents one of two full-duplex settings currently recommended for deployment in future fifth-generation (5G) systems. Theoretically, it has been widely accepted that FDR potentially doubles the channel capacity when compared to its half-duplex counterpart. Although FDR doubles the multiplexing gain, the effective signal-to-noise ratio (SNR) can be significantly degraded due to the residual self-interference (RSI) if not properly handled. In this work, efficient protocols are devised for different FDR settings. Selective cooperation is proposed for the canonical three-terminal FDR channel with RSI, which exploits the cooperative diversity offered by the independently fading source/relay message replicas arriving at the destination. Closed-form expressions are derived for the end-to-end SNR cumulative distribution function (CDF) under Rayleigh and Nakagami-m fading. Further, the offered diversity gain is presented as a function of the RSI scaling trend with the relay power. We show that the existing diversity problem in simple FDR protocols can be considerably fixed via

  17. Comparative analysis of the end-joining activity of several DNA ligases.

    Directory of Open Access Journals (Sweden)

    Robert J Bauer

    Full Text Available DNA ligases catalyze the repair of phosphate backbone breaks in DNA, acting with highest activity on breaks in one strand of duplex DNA. Some DNA ligases have also been observed to ligate two DNA fragments with short complementary overhangs or blunt-ended termini. In this study, several wild-type DNA ligases (phage T3, T4, and T7 DNA ligases, Paramecium bursaria chlorella virus 1 (PBCV1 DNA ligase, human DNA ligase 3, and Escherichia coli DNA ligase were tested for their ability to ligate DNA fragments with several difficult to ligate end structures (blunt-ended termini, 3'- and 5'- single base overhangs, and 5'-two base overhangs. This analysis revealed that T4 DNA ligase, the most common enzyme utilized for in vitro ligation, had its greatest activity on blunt- and 2-base overhangs, and poorest on 5'-single base overhangs. Other ligases had different substrate specificity: T3 DNA ligase ligated only blunt ends well; PBCV1 DNA ligase joined 3'-single base overhangs and 2-base overhangs effectively with little blunt or 5'- single base overhang activity; and human ligase 3 had highest activity on blunt ends and 5'-single base overhangs. There is no correlation of activity among ligases on blunt DNA ends with their activity on single base overhangs. In addition, DNA binding domains (Sso7d, hLig3 zinc finger, and T4 DNA ligase N-terminal domain were fused to PBCV1 DNA ligase to explore whether modified binding to DNA would lead to greater activity on these difficult to ligate substrates. These engineered ligases showed both an increased binding affinity for DNA and increased activity, but did not alter the relative substrate preferences of PBCV1 DNA ligase, indicating active site structure plays a role in determining substrate preference.

  18. Cytogenetic effects of tritium incorporated into DNA of human lymphocytes

    Energy Technology Data Exchange (ETDEWEB)

    Beno, M [Inst. of Preventive and Clinical Medicine, 83301 Bratislava (Slovakia)

    1996-12-31

    In the reported in vitro experiments the numbers of chromosomal aberrations (CA) in correlation to the physical dose as assessed by determining the specific radioactivity of DNA have been followed in vitro human lymphocytes from adult donors. Lymphocytes from healthy adult donors of age from 20 to 59 of both sexes (24 males and 20 females) were isolated from blood by centrifugation. After washing the cells were irradiated from tritium incorporated during in vitro incubation in phytohemagglutinin containing medium with tritium labelled thymidine. Slides for standard CA counting have been done from every sample 48 hours after the begin cultivation. The CA were counted in at least 200 metaphases on each slide. Parallel samples of lymphocytes served for preparation smears for autoradiography to determine the labeling index. Other parallel samples were used for the determination of tritium concentration in DNA by the diphenylamine method, as well as determination of the specific radioactivity in lymphocyte DNA by scintillation counting. The dose absorbed in DNA was estimated using the conversion factor implicating that 37 kBq of tritium uniformly distributed per gram of tissue of unit density delivers a dose rate of 121.4 {sup m}i{sup G}y/hour. The contamination of cells by precursors of nucleic acids - like tritiated thymidine - causes an uneven distribution of doses in the cell population. A proportion of the population of cells remains unlabelled. The dose-response curve is flat showing signs of loss of heavily damaged cells and signs of repair of damage. Both these signs are based on the nature of biological processes which lead to internal contamination of cells and to expression of effects in terms of numbers of CA. (J.K.) 5 figs., 4 refs.

  19. The effect of ancient DNA damage on inferences of demographic histories

    DEFF Research Database (Denmark)

    Axelsson, Erik; Willerslev, Eske; Gilbert, Marcus Thomas Pius

    2008-01-01

    The field of ancient DNA (aDNA) is casting new light on many evolutionary questions. However, problems associated with the postmortem instability of DNA may complicate the interpretation of aDNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates o...... for a change in effective population size in this data set vanishes once the effects of putative damage are removed. Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution....

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

    Science.gov (United States)

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

    2016-01-01

    It is generally accepted that the important characteristic features of the Watson-Crick duplex originate from the molecular structure of its subunits. However, it still remains to elucidate what properties of each subunit are responsible for the significant characteristic features of the DNA structure. The computations of desoxydinucleoside monophosphates complexes with Na-ions using density functional theory revealed a pivotal role of DNA conformational properties of single-chain minimal fragments in the development of unique features of the Watson-Crick duplex. We found that directionality of the sugar-phosphate backbone and the preferable ranges of its torsion angles, combined with the difference between purines and pyrimidines. in ring bases, define the dependence of three-dimensional structure of the Watson-Crick duplex on nucleotide base sequence. In this work, we extended these density functional theory computations to the minimal' fragments of DNA duplex, complementary desoxydinucleoside monophosphates complexes with Na-ions. Using several computational methods and various functionals, we performed a search for energy minima of BI-conformation for complementary desoxydinucleoside monophosphates complexes with different nucleoside sequences. Two sequences are optimized using ab initio method at the MP2/6-31++G** level of theory. The analysis of torsion angles, sugar ring puckering and mutual base positions of optimized structures demonstrates that the conformational characteristic features of complementary desoxydinucleoside monophosphates complexes with Na-ions remain within BI ranges and become closer to the corresponding characteristic features of the Watson-Crick duplex crystals. Qualitatively, the main characteristic features of each studied complementary desoxydinucleoside monophosphates complex remain invariant when different computational methods are used, although the quantitative values of some conformational parameters could vary lying within the

  1. Effect of UV-irradiation on DNA-membrane complex of Bacillus subtilis

    International Nuclear Information System (INIS)

    Chefranova, O.A.; Gaziev, A.I.

    1979-01-01

    The UV radiation effect on DNA membrane complex of Bacillus subtilis has been studied. Increase of DNA content in the DNA membrane complex in two strains of 168 and recA - and its decrease in the polA - strain are shown. The above effect in the first two stamms is suppressed with caffeine and correlates with the change in protein content in the DNA membrane complex, determined by a radioactive label, but not lipids in other words, fixation of DNA and membrane goes through proteins. Capability of DNA content increase in the DNA membrane complex after UV irradiation and subsequent bacteria incubation in a total medium correlates with the relative sensitivity of stamm UV sensitivity. It is suggested, that the reparation synthesis goes in cells on the membrane and that binding of DNA and the membrane is necessary for the normal DNA reparation process

  2. Effect of turmeric and curcumin on BP-DNA adducts.

    Science.gov (United States)

    Mukundan, M A; Chacko, M C; Annapurna, V V; Krishnaswamy, K

    1993-03-01

    Many human cancers that are widely prevalent today can be prevented through modifications in life-styles, of which diet appears to be an important agent. Several dietary constituents modulate the process of carcinogenesis and prevent genotoxicity. Many plant constituents including turmeric appear to be potent antimutagens and antioxidants. Therefore the modulatory effects of turmeric and curcumin on the levels of benzo[a]pyrene induced DNA adducts in the livers of rats were studied by the newly developed 32P-postlabelling assay method. Turmeric when fed at 0.1, 0.5 and 3% and the active principle of turmeric (curcumin) when fed at a level of 0.03% in the diet for 4 weeks significantly reduced the level of BP-DNA adducts including the major adduct dG-N2-BP, formed within 24 h in response to a single i.p. injection of benzo[a]pyrene. The significance of these effects in terms of the potential anticarcinogenic effects of turmeric is discussed. Further, these results strengthen the various other biological effects of turmeric which have direct relevance to anticarcinogenesis and chemoprevention.

  3. Spermine attenuates the action of the DNA intercalator, actinomycin D, on DNA binding and the inhibition of transcription and DNA replication.

    Science.gov (United States)

    Wang, Sheng-Yu; Lee, Alan Yueh-Luen; Lee, Yueh-Luen; Lai, Yi-Hua; Chen, Jeremy J W; Wu, Wen-Lin; Yuann, Jeu-Ming P; Su, Wang-Lin; Chuang, Show-Mei; Hou, Ming-Hon

    2012-01-01

    The anticancer activity of DNA intercalators is related to their ability to intercalate into the DNA duplex with high affinity, thereby interfering with DNA replication and transcription. Polyamines (spermine in particular) are almost exclusively bound to nucleic acids and are involved in many cellular processes that require nucleic acids. Until now, the effects of polyamines on DNA intercalator activities have remained unclear because intercalation is the most important mechanism employed by DNA-binding drugs. Herein, using actinomycin D (ACTD) as a model, we have attempted to elucidate the effects of spermine on the action of ACTD, including its DNA-binding ability, RNA and DNA polymerase interference, and its role in the transcription and replication inhibition of ACTD within cells. We found that spermine interfered with the binding and stabilization of ACTD to DNA. The presence of increasing concentrations of spermine enhanced the transcriptional and replication activities of RNA and DNA polymerases, respectively, in vitro treated with ActD. Moreover, a decrease in intracellular polyamine concentrations stimulated by methylglyoxal-bis(guanylhydrazone) (MGBG) enhanced the ACTD-induced inhibition of c-myc transcription and DNA replication in several cancer cell lines. The results indicated that spermine attenuates ACTD binding to DNA and its inhibition of transcription and DNA replication both in vitro and within cells. Finally, a synergistic antiproliferative effect of MGBG and ACTD was observed in a cell viability assay. Our findings will be of significant relevance to future developments in combination with cancer therapy by enhancing the anticancer activity of DNA interactors through polyamine depletion.

  4. Spermine attenuates the action of the DNA intercalator, actinomycin D, on DNA binding and the inhibition of transcription and DNA replication.

    Directory of Open Access Journals (Sweden)

    Sheng-Yu Wang

    Full Text Available The anticancer activity of DNA intercalators is related to their ability to intercalate into the DNA duplex with high affinity, thereby interfering with DNA replication and transcription. Polyamines (spermine in particular are almost exclusively bound to nucleic acids and are involved in many cellular processes that require nucleic acids. Until now, the effects of polyamines on DNA intercalator activities have remained unclear because intercalation is the most important mechanism employed by DNA-binding drugs. Herein, using actinomycin D (ACTD as a model, we have attempted to elucidate the effects of spermine on the action of ACTD, including its DNA-binding ability, RNA and DNA polymerase interference, and its role in the transcription and replication inhibition of ACTD within cells. We found that spermine interfered with the binding and stabilization of ACTD to DNA. The presence of increasing concentrations of spermine enhanced the transcriptional and replication activities of RNA and DNA polymerases, respectively, in vitro treated with ActD. Moreover, a decrease in intracellular polyamine concentrations stimulated by methylglyoxal-bis(guanylhydrazone (MGBG enhanced the ACTD-induced inhibition of c-myc transcription and DNA replication in several cancer cell lines. The results indicated that spermine attenuates ACTD binding to DNA and its inhibition of transcription and DNA replication both in vitro and within cells. Finally, a synergistic antiproliferative effect of MGBG and ACTD was observed in a cell viability assay. Our findings will be of significant relevance to future developments in combination with cancer therapy by enhancing the anticancer activity of DNA interactors through polyamine depletion.

  5. Radiation damage to DNA: the effect of LET

    Energy Technology Data Exchange (ETDEWEB)

    Ward, J F; Milligan, J R [California Univ., San Diego, La Jolla, CA (United States). School of Medicine

    1997-03-01

    Mechanisms whereby ionizing radiation induced damage are introduced into cellular DNA are discussed. The types of lesions induced are summarized and the rationale is presented which supports the statement that radiation induced singly damaged sites are biologically unimportant. The conclusion that multiply damaged sites are critical is discussed and the mechanisms whereby such lesions are formed are presented. Structures of multiply damaged sites are summarized and problems which they present to cellular repair systems are discussed. Lastly the effects of linear energy transfer on the complexity of multiply damaged sites are surveyed and the consequences of this increased complexity are considered in terms of cell survival and mutation. (author)

  6. Harvesting full-duplex rate gains in cellular networks with half-duplex user terminals

    KAUST Repository

    AlAmmouri, Ahmad

    2016-07-26

    Full-Duplex (FD) transceivers may be expensive in terms of complexity, power consumption, and price to be implemented in all user terminals. Therefore, techniques to exploit in-band full-duplex communication with FD base stations (BSs) and half-duplex (HD) users\\' equipment (UEs) are required. In this context, 3-node topology (3NT) has been recently proposed for FD BSs to reuse the uplink (UL) and downlink (DL) channels with HD terminals within the same cell. In this paper, we present a tractable mathematical framework, based on stochastic geometry, for 3NT in cellular networks. To this end, we propose a design paradigm via pulse-shaping and partial overlap between UL and DL channels to maximize the harvested rate gains in 3NT. The results show that 3NT achieves a close performance to networks with FD BSs and FD UEs, denoted by 2-node topology (2NT) networks. A maximum of 5% rate loss is reported when 3NT is compared to 2NT with efficient self-interference cancellation (SIC). If the SIC in 2NT is not efficient, 3NT highly outperforms 2NT. Consequently, we conclude that, irrespective to the UE duplexing scheme, it is sufficient to have FD BSs to harvest FD rate gains.

  7. Adenine radicals generated in alternating AT duplexes by direct absorption of low-energy UV radiation.

    Science.gov (United States)

    Banyasz, Akos; Ketola, Tiia; Martínez-Fernández, Lara; Improta, Roberto; Markovitsi, Dimitra

    2018-04-17

    There is increasing evidence that the direct absorption of photons with energies that are lower than the ionization potential of nucleobases may result in oxidative damage to DNA. The present work, which combines nanosecond transient absorption spectroscopy and quantum mechanical calculations, studies this process in alternating adenine-thymine duplexes (AT)n. We show that the one-photon ionization quantum yield of (AT)10 at 266 nm (4.66 eV) is (1.5 ± 0.3) × 10-3. According to our PCM/TD-DFT calculations carried out on model duplexes composed of two base pairs, (AT)1 and (TA)1, simultaneous base pairing and stacking does not induce important changes in the absorption spectra of the adenine radical cation and deprotonated radical. The adenine radicals, thus identified in the time-resolved spectra, disappear with a lifetime of 2.5 ms, giving rise to a reaction product that absorbs at 350 nm. In parallel, the fingerprint of reaction intermediates other than radicals, formed directly from singlet excited states and assigned to AT/TA dimers, is detected at shorter wavelengths. PCM/TD-DFT calculations are carried out to map the pathways leading to such species and to characterize their absorption spectra; we find that, in addition to the path leading to the well-known TA* photoproduct, an AT photo-dimerization path may be operative in duplexes.

  8. Estudo dos efeitos da restrição na microestrutura, microdureza e tenacidade em juntas soldadas em aço inoxidável duplex Study of restriction effects on mMicrostructure, microhardness and toughness in welded joints of duplex stainless steel

    Directory of Open Access Journals (Sweden)

    Everton Barbosa Nunes

    2011-06-01

    Full Text Available Os aços inoxidáveis duplex (AID apresentam em sua microestrutura ferrita e austenita, de modo a aliar boas propriedades mecânicas e resistência à corrosão. Estes materiais possuem grande aplicação na indústria petroquímica, sendo o UNS S31803 um dos mais conhecidos. Existem poucos trabalhos referentes ao estudo da influência da restrição na soldagem da junta na formação de Widmanstätten. Logo, este trabalho tem como objetivo analisar a influência da restrição no balanceamento de fases, na morfologia da austenita, na microdureza e na tenacidade da Zona Afetada pelo Calor (ZAC e da Zona Fundida (ZF. Foram realizadas soldagens em juntas tipo V utilizando eletrodo revestido AWS E2209-17com dois níveis de energia: 15 kJ/cm e 20 kJ/cm, com e sem restrição. De maneira geral, houve maior quantidade de ferrita nos passes de acabamento em relação aos passes de enchimento e de raiz. Foram observadas maiores quantidades de Widmanstätten nas condições soldadas com restrição. A ZAC apresentou uma microestrutura mais grosseira nos passes de acabamento. No entanto, não foram observadas diferenças significativas nas microestruturas quando comparadas as condições com e sem restrição. As condições que apresentaram maior quantidade de Widmanstätten obtiveram menores níveis de microdureza. Não foram observadas diferenças na energia absorvida na ZAC e ZF.Duplex stainless steels present ferrite and austenite in their microstructure in order to join good mechanical properties and corrosion resistance. These materials are very used in petrochemical industry, being the DSS UNS S31803 one of the most commercially known. There were not much published literature to study the influence of the precipitation of Widmanstätten austenite in joins with some restriction. This work has as objective to analyze the influence of the restriction in the phase balance of austenite and ferrite, in the morphology of the austenite, in the

  9. Effect of nickel chloride on Arabidopsis genomic DNA and methylation of 18S rDNA

    Directory of Open Access Journals (Sweden)

    Zhongai Li

    2015-01-01

    Conclusions: NiCl2 application caused variation of DNA methylation of the Arabidopsis genomic and offspring's. NiCl2 also resulted in nucleolar injury and deformity of root tip cells. The methylation rate of 18S rDNA also changed by adding NiCl2.

  10. Effects of temperature and relative humidity on DNA methylation.

    Science.gov (United States)

    Bind, Marie-Abele; Zanobetti, Antonella; Gasparrini, Antonio; Peters, Annette; Coull, Brent; Baccarelli, Andrea; Tarantini, Letizia; Koutrakis, Petros; Vokonas, Pantel; Schwartz, Joel

    2014-07-01

    Previous studies have found relationships between DNA methylation and various environmental contaminant exposures. Associations with weather have not been examined. Because temperature and humidity are related to mortality even on non-extreme days, we hypothesized that temperature and relative humidity may affect methylation. We repeatedly measured methylation on long interspersed nuclear elements (LINE-1), Alu, and 9 candidate genes in blood samples from 777 elderly men participating in the Normative Aging Study (1999-2009). We assessed whether ambient temperature and relative humidity are related to methylation on LINE-1 and Alu, as well as on genes controlling coagulation, inflammation, cortisol, DNA repair, and metabolic pathway. We examined intermediate-term associations of temperature, relative humidity, and their interaction with methylation, using distributed lag models. Temperature or relative humidity levels were associated with methylation on tissue factor (F3), intercellular adhesion molecule 1 (ICAM-1), toll-like receptor 2 (TRL-2), carnitine O-acetyltransferase (CRAT), interferon gamma (IFN-γ), inducible nitric oxide synthase (iNOS), and glucocorticoid receptor, LINE-1, and Alu. For instance, a 5°C increase in 3-week average temperature in ICAM-1 methylation was associated with a 9% increase (95% confidence interval: 3% to 15%), whereas a 10% increase in 3-week average relative humidity was associated with a 5% decrease (-8% to -1%). The relative humidity association with ICAM-1 methylation was stronger on hot days than mild days. DNA methylation in blood cells may reflect biological effects of temperature and relative humidity. Temperature and relative humidity may also interact to produce stronger effects.

  11. Effect of superoxide dismutase supplementation on sperm DNA fragmentation

    Directory of Open Access Journals (Sweden)

    Luciano Negri

    2017-10-01

    Full Text Available Background: antioxidants supplementation improves sperm quality, but few trials have analyzed the effects on sperm DNA fragmentation (SDF. This study compares the effectiveness of SOD-based antioxidant supplementation plus hydroxytyrosol and carnosol in reducing SDF with other antioxidants without SOD, hydroxytyrosol, and carnosol. Materials and methods: men with high SDF at baseline were selected in our clinical database. The patients taken into account had a 2-month control. SDF was measured by Sperm Chromatin Dispersion test (SCD. Untreated men were used as a control group. The remaining subjects received some oral antioxidant supplements (12 different combinations of both hydrophilic and lipophilic antioxidants, with some of them receiving nutritional support with a SOD-based antioxidant supplementation plus hydroxytyrosol and carnosol. Results: 118 men were selected for a retrospective study. Mean age 39.3 ± 5.4 years. Fifteen had no treatment, 55 were treated with a SOD-based antioxidant supplementation plus hydroxytyrosol and carnosol, and 48 took some antioxidant supplements for 2 months. Clinically, variations of at least 10% in baseline values of classic semen parameters and sperm DNA fragmentation were taken into consideration. Classic seminal parameters did not vary significantly in the three groups, with the exception of viability (p = 0.001. We assessed which of the active substances (no. 19 in different formulations were associated with variations in SDF. In the multivariable analysis of the 7 active substances that passed the univariable analysis, only the SOD molecule appeared to be linked to an improvement in SDF (< 0.0001. In detail, only one patient in the control group showed a spontaneous improvement in SDF (6%, compared to 16/48 (33% of those taking various oral antioxidant supplements, and 31/55 (56% of those taking a SOD-based antioxidant supplementation plus hydroxytyrosol and carnosol. Conclusions: SOD

  12. Duplex ultrasound: Indications and findings in a newly created ...

    African Journals Online (AJOL)

    Duplex ultrasound: Indications and findings in a newly created facility at the University of Calabar Teaching Hospital, Calabar. ... It is recommended that timely referrals be made, and mobile Doppler units be acquired to save more lives and limbs in the developing world. Keywords: Calabar, deep venous thrombosis, duplex ...

  13. Criteria for the Segmentation of Vowels on Duplex Oscillograms.

    Science.gov (United States)

    Naeser, Margaret A.

    This paper develops criteria for the segmentation of vowels on duplex oscillograms. Previous vowel duration studies have primarily used sound spectrograms. The use of duplex oscillograms, rather than sound spectrograms, permits faster production (real time) at less expense (adding machine paper may be used). The speech signal can be more spread…

  14. Zoster duplex: a clinical report and etiologic analysis.

    Science.gov (United States)

    Zhang, Feng; Zhou, Jin

    2015-01-01

    Herpes zoster (HZ) duplex is a rare disease presentation. The mechanisms of varicella zoster virus (VZV) reactivation in multiple dermal regions are unknown. To present a HZ duplex case occurring in an immunocompetent woman and to analyze the possible underlying causes of HZ duplex. We present a HZ duplex case in an immunocompetent woman and analyzed the possible contributing factors in 36 HZ duplex cases. Continuously distributed variables were categorized by numbers and percentages. In our study, 24 cases (66.7%) were from Asia, 16 cases (44.4%) were in individuals ≥ 50 years of age, and 17 cases (47.2%) occurred in immunocompromised patients. Of the 36 cases, 23 involved women (63.9%) and 13 involved men. Eighteen patients suffering from HZ duplex, 13 of which were women (72.2%), did not suffer from any chronic systemic disease or have a long history of taking drugs. HZ duplex is a rare event that can occur in both immunocompetent and immunosuppressed individuals. HZ duplex might be associated with the Asia region, advanced age, immunosuppression, and being female.

  15. Molecular architecture: construction of self-assembled organophosphonate duplexes and their electrochemical characterization.

    Science.gov (United States)

    Cattani-Scholz, Anna; Liao, Kung-Ching; Bora, Achyut; Pathak, Anshuma; Hundschell, Christian; Nickel, Bert; Schwartz, Jeffrey; Abstreiter, Gerhard; Tornow, Marc

    2012-05-22

    Self-assembled monolayers of phosphonates (SAMPs) of 11-hydroxyundecylphosphonic acid, 2,6-diphosphonoanthracene, 9,10-diphenyl-2,6-diphosphonoanthracene, and 10,10'-diphosphono-9,9'-bianthracene and a novel self-assembled organophosphonate duplex ensemble were synthesized on nanometer-thick SiO(2)-coated, highly doped silicon electrodes. The duplex ensemble was synthesized by first treating the SAMP prepared from an aromatic diphosphonic acid to form a titanium complex-terminated one; this was followed by addition of a second equivalent of the aromatic diphosphonic acid. SAMP homogeneity, roughness, and thickness were evaluated by AFM; SAMP film thickness and the structural contributions of each unit in the duplex were measured by X-ray reflection (XRR). The duplex was compared with the aliphatic and aromatic monolayer SAMPs to determine the effect of stacking on electrochemical properties; these were measured by impedance spectroscopy using aqueous electrolytes in the frequency range 20 Hz to 100 kHz, and data were analyzed using resistance-capacitance network based equivalent circuits. For the 11-hydroxyundecylphosphonate SAMP, C(SAMP) = 2.6 ± 0.2 μF/cm(2), consistent with its measured layer thickness (ca. 1.1 nm). For the anthracene-based SAMPs, C(SAMP) = 6-10 μF/cm(2), which is attributed primarily to a higher effective dielectric constant for the aromatic moieties (ε = 5-10) compared to the aliphatic one; impedance spectroscopy measured the additional capacitance of the second aromatic monolayer in the duplex (2ndSAMP) to be C(Ti/2ndSAMP) = 6.8 ± 0.7 μF/cm(2), in series with the first.

  16. Duplex tube steam reformer development program

    International Nuclear Information System (INIS)

    Lewe, C.K.; Nieto, J.M.; Papadopoulos, A.

    1978-09-01

    Work done in partial fulfillment of Task 7 of the Duplex Steam Reformer Development Program is described. The DSR concept acts as a double barrier between a process heat high temperature reactor plant (PNP) and a closed loop chemical heat pipe (CHP) for the long distance transport of chemical energy to a remote industrial user. The current state of the DSR design is described as well as related systems and equipment. The PNP concept presented is based upon work currently underway in the Federal Republic of Germany

  17. Duplex ultrasound evidence of fat embolism syndrome

    Directory of Open Access Journals (Sweden)

    Abdallah Naddaf, MD

    2016-12-01

    Full Text Available Fat embolism syndrome is a potentially fatal disease process most commonly associated with long-bone and pelvic fractures. Reports describing ultrasound evidence of fat emboli are restricted to echocardiography. We propose a new objective finding on venous duplex ultrasound imaging of the lower extremities as a useful diagnostic criterion by presenting the case reports of two patients with acute long-bone fractures, possibly leading to earlier orthopedic fixation and allocation of resources to those patients at higher risk of fat embolism syndrome.

  18. Timing, Coordination, and Rhythm : Acrobatics at the DNA Replication Fork

    NARCIS (Netherlands)

    Hamdan, Samir M.; Oijen, Antoine M. van

    2010-01-01

    In DNA replication, the antiparallel nature of the parental duplex imposes certain constraints on the activity of the DNA polymerases that synthesize new DNA. The leading-strand polymerase advances in a continuous fashion, but the lagging-strand polymerase is forced to restart at short intervals. In

  19. Full Duplex Communications in 5G Small Cells

    DEFF Research Database (Denmark)

    Mahmood, Nurul Huda; Gatnau, Marta; Berardinelli, Gilberto

    2017-01-01

    Full duplex communication promises system performance improvement over conventional half duplex communication by allowing simultaneous transmission and reception. However, such concurrent communication results in strong self interference and an increase in the overall network interference, and can...... only be exploited when traffic is available in both directions. The potential throughput gains of full duplex communication over conventional half duplex transmission in a small cell network with asymmetric traffic conditions is investigated in this contribution. The throughput performance gains...... are analysed using tools from stochastic geometry, and further confirmed through extensive system level simulations. Our findings explicitly quantify how the gains from full duplex communication depend on the traffic profile and the inter-cell interference coupling. The demonstrated throughput gains and delay...

  20. Effect of proton transfer on the electronic coupling in DNA

    International Nuclear Information System (INIS)

    Rak, Janusz; Makowska, Joanna; Voityuk, Alexander A.

    2006-01-01

    The effects of single and double proton transfer within Watson-Crick base pairs on donor-acceptor electronic couplings, V da , in DNA are studied on the bases of quantum chemical calculations. Four dimers [AT,AT], [GC,GC], [GC,AT] and [GC,TA)] are considered. Three techniques - the generalized Mulliken-Hush scheme, the fragment charge method and the diabatic states method - are employed to estimate V da for hole transfer between base pairs. We show that both single- and double proton transfer (PT) reactions may substantially affect the electronic coupling in DNA. The electronic coupling in [AT,AT] is predicted to be most sensitive to PT. Single PT within the first base pair in the dimer leads to increase in the hole transfer efficiency by a factor of 4, while proton transfer within the second pair should substantially, by 2.7 times, decrease the rate of charge transfer. Thus, directional asymmetry of the PT effects on the electronic coupling is predicted. The changes in the V da matrix elements correlate with the topological properties of orbitals of donor and acceptor and can be qualitatively rationalized in terms of resonance structures of donor and acceptor. Atomic pair contributions to the V da matrix elements are also analyzed

  1. Effect of temperature on DNA double helix: An insight from ...

    Indian Academy of Sciences (India)

    2012-06-25

    Jun 25, 2012 ... We have carried out detailed MD simulations of DNA double ..... Wireframe representation of B-DNA crystal structures with PDB identifier (a) 1EHV, ..... nucleic acid structures, PhD thesis, University of Calcutta, Kolkata.

  2. Raman study of magnesium induced conversion of polyU·polyA duplexes to polyU·polyA·polyU triplexes

    OpenAIRE

    Herrera, S. J. Espinoza; Štepánek, J.

    2010-01-01

    Raman titration experiment with magnesium salt added gradually to aqueous solution of duplexes formed by RNA homopolynucleotides polyU and polyA was performed to reveal its effect on homopolynucleotide complexes. Statistical analysis of obtained spectral set has confirmed the effect already found by less structurally sensitive methods [Nucleic Acids Res. 31(17) (2003), 5101–5107] that at sufficiently high concentrations magnesium causes transformation of polyU·polyA duplexes to polyU·polyA·po...

  3. Characterization of antibodies to dihydrothymine, a radiolysis product of DNA

    International Nuclear Information System (INIS)

    Hubbard, K.; Ide, H.; Erlanger, B.F.; Wallace, S.S.

    1989-01-01

    Antibodies to dihydrothymine were elicited by immunizing rabbits with dihydrothymidine monophosphate conjugated by carbodiimide to BSA. By use of an ELISA assay, the antibodies produced were found to be specific for dihydrothymine. Hapten inhibition studies showed that dihydrothymidine monophosphate was 3 orders of magnitude more effective as an inhibitor than thymidine monophosphate and 4 orders of magnitude more effective than thymidine glycol monophosphate. With DNA containing dihydrothymine, antibody reactivity was observed at 20 fmol of dihydrothymine, which is approximately 0.1 dihydrothymine per 10,000 bases. Thus, the assay is very sensitive. The antibody reacted with denatured DNA containing dihydrothymine but not with native DNA containing this lesion. The antibody was used for measurement of in vivo incorporation of dihydrothymidine in wild-type Escherichia coli or mutants defective in their ability to remove dihydrothymine from DNA or in the de novo synthesis of thymidylate. Lastly, antibodies to dihydrothymine were use to quantitate the formation of dihydrothymine in DNA X-irradiated under N2. Production of dihydrothymine in irradiated DNA correlated with the level of reducing species produced by X-rays, and dihydrothymine was produced preferentially in irradiated single-stranded or denatured DNA as compared to irradiated duplex DNA

  4. Measuring DNA hybridization using fluorescent DNA-stabilized silver clusters to investigate mismatch effects on therapeutic oligonucleotides.

    Science.gov (United States)

    de Bruin, Donny; Bossert, Nelli; Aartsma-Rus, Annemieke; Bouwmeester, Dirk

    2018-04-06

    Short nucleic acid oligomers have found a wide range of applications in experimental physics, biology and medicine, and show potential for the treatment of acquired and genetic diseases. These applications rely heavily on the predictability of hybridization through Watson-Crick base pairing to allow positioning on a nanometer scale, as well as binding to the target transcripts, but also off-target binding to transcripts with partial homology. These effects are of particular importance in the development of therapeutic oligonucleotides, where off-target effects caused by the binding of mismatched sequences need to be avoided. We employ a novel method of probing DNA hybridization using optically active DNA-stabilized silver clusters (Ag-DNA) to measure binding efficiencies through a change in fluorescence intensity. In this way we can determine their location-specific sensitivity to individual mismatches in the sequence. The results reveal a strong dependence of the hybridization on the location of the mismatch, whereby mismatches close to the edges and center show a relatively minor impact. In parallel, we propose a simple model for calculating the annealing ratios of mismatched DNA sequences, which supports our experimental results. The primary result shown in this work is a demonstration of a novel technique to measure DNA hybridization using fluorescent Ag-DNA. With this technique, we investigated the effect of mismatches on the hybridization efficiency, and found a significant dependence on the location of individual mismatches. These effects are strongly influenced by the length of the used oligonucleotides. The novel probe method based on fluorescent Ag-DNA functions as a reliable tool in measuring this behavior. As a secondary result, we formulated a simple model that is consistent with the experimental data.

  5. Effect of temperature on DNA double helix: An insight from ...

    Indian Academy of Sciences (India)

    The three-dimensional structure of DNA contains various sequence-dependent structural information, which control many cellular processes in life, such as replication, transcription, DNA repair, etc. For the above functions, DNA double helices need to unwind or melt locally, which is different from terminal melting, as often ...

  6. Duplex Tear Film Evaporation Analysis.

    Science.gov (United States)

    Stapf, M R; Braun, R J; King-Smith, P E

    2017-12-01

    Tear film thinning, hyperosmolarity, and breakup can cause irritation and damage to the human eye, and these form an area of active investigation for dry eye syndrome research. Recent research demonstrates that deficiencies in the lipid layer may cause locally increased evaporation, inducing conditions for breakup. In this paper, we explore the conditions for tear film breakup by considering a model for tear film dynamics with two mobile fluid layers, the aqueous and lipid layers. In addition, we include the effects of osmosis, evaporation as modified by the lipid, and the polar portion of the lipid layer. We solve the system numerically for reasonable parameter values and initial conditions and analyze how shifts in these cause changes to the system's dynamics.

  7. An effective and low-cost method for DNA extraction from herbal ...

    African Journals Online (AJOL)

    Rhubarb is an important traditional Chinese herbal drug with high secondary metabolites that interfere with DNA extraction procedures and downstream applications, such as DNA restriction and amplification. An effective and low-cost protocol for isolating genomic DNA from root of Rheum tanguticum is described in this ...

  8. Corrosion behavior of 2205 duplex stainless steel.

    Science.gov (United States)

    Platt, J A; Guzman, A; Zuccari, A; Thornburg, D W; Rhodes, B F; Oshida, Y; Moore, B K

    1997-07-01

    The corrosion of 2205 duplex stainless steel was compared with that of AISI type 316L stainless steel. The 2205 stainless steel is a potential orthodontic bracket material with low nickel content (4 to 6 wt%), whereas the 316L stainless steel (nickel content: 10 to 14 wt%) is a currently used bracket material. Both stainless steels were subjected to electrochemical and immersion (crevice) corrosion tests in 37 degrees C, 0.9 wt% sodium chloride solution. Electrochemical testing indicates that 2205 has a longer passivation range than 316L. The corrosion rate of 2205 was 0.416 MPY (milli-inch per year), whereas 316L exhibited 0.647 MPY. When 2205 was coupled to 316L with equal surface area ratio, the corrosion rate of 2205 reduced to 0.260 MPY, indicating that 316L stainless steel behaved like a sacrificial anode. When 316L is coupled with NiTi, TMA, or stainless steel arch wire and was subjected to the immersion corrosion test, it was found that 316L suffered from crevice corrosion. On the other hand, 2205 stainless steel did not show any localized crevice corrosion, although the surface of 2205 was covered with corrosion products, formed when coupled to NiTi and stainless steel wires. This study indicates that considering corrosion resistance, 2205 duplex stainless steel is an improved alternative to 316L for orthodontic bracket fabrication when used in conjunction with titanium, its alloys, or stainless steel arch wires.

  9. Electrolytic pickling of duplex stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Ipek, N.; Holm, B.; Pettersson, R. [Swedish Institute for Metals Research, Drottning Kristinas vaeg 48, 11428 Stockholm (Sweden); Runnsjoe, G.; Karlsson, M. [Outokumpu Stainless AB, 77422 Avesta (Sweden)

    2005-08-01

    Pickling of duplex stainless steels has proved to be much more difficult than that of standard austenitic grades. Electrolytic pre-pickling is shown to be a key process towards facilitating the pickling process for material annealed both in the production-line and in laboratory experiments. The mechanism for the neutral electrolytic process on duplex 2205 and austenitic 316 steels has been examined and the oxide scale found to become thinner as a function of electrolytic pickling time. Spallation or peeling of the oxide induced by gas evolution did not play a decisive role. A maximum of about 20% of the current supplied to the oxidised steel surface goes to dissolution reactions whereas about 80% of the current was consumed in oxygen gas production. This makes the current utilisation very poor, particularly against the background of reports that in indirect electrolytic pickling only about 30% of the total current, supplied to the process, actually goes into the strip. A parametric study was therefore carried out to determine whether adjustment of process variables could improve the current utilisation. (Abstract Copyright [2005], Wiley Periodicals, Inc.)

  10. On phase equilibria in duplex stainless steels

    Energy Technology Data Exchange (ETDEWEB)

    Wessman, S. [Swerea KIMAB AB, Stockholm (Sweden); Pettersson, R. [Outokumpu Stainless AB, Avesta Research Centre, Avesta (Sweden); Hertzman, S. [Outokumpu Stainless Research Foundation, Stockholm (Sweden)

    2010-05-15

    The equilibrium conditions of four duplex stainless steels; Fe-23Cr-4.5Ni-0.1N, Fe-22Cr-5.5Ni-3Mo-0.17N, Fe-25Cr-7Ni-4Mo-0.27N and Fe-25Cr-7Ni-4Mo-1W-1.5Cu-0.27N were studied in the temperature region from 700 to 1000 C. Phase compositions were determined with SEM EDS and the phase fractions using image analysis on backscattered SEM images. The results showed that below 1000 C the steels develop an inverse duplex structure with austenite and sigma phase, of which the former is the matrix phase. With decreasing temperature, the microstructure will be more and more complex and finely dispersed. The ferrite is, for the higher alloyed steels, only stable above 1000 C and at lower temperatures disappears in favour of intermetallic phases. The major intermetallic phase is sigma phase with small amounts of chi phase, the latter primarily in high Mo and W grades. Nitrides, not a focus in this investigation, were present as rounded particles and acicular precipitates at lower temperatures. The results were compared to theoretical predictions using the TCFE5 and TCFE6 databases. (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  11. Metallurgical Changes During Welding of Duplex Stainless Steel

    International Nuclear Information System (INIS)

    SLLam, Y.A.A.

    2004-01-01

    The aim of this study is to investigate the influence of the cooling rates on the transformation behavior of a duplex stainless steel deposited weld metal, subjected to isothermal heat treatments in the temperature range between 400 C to 700 C, for different aging times. cooling rates (air cooling, furnace cooling, and water quenching) followed all heat treatments. the effect of aging time on the ferrite content, and hardness value of the weld metal samples, for these cooling rates, and aging temperatures were evaluated. the ferrite content decreased and hardness value increased by increasing aging time. the microstructure of the weld metal in both as welded and isothermally heat-treated conditions has been investigated using optical microscopy, and X-ray diffraction techniques

  12. Charge transport through DNA/DNA duplexes and DNA/RNA hybrids: complex mechanism study

    Czech Academy of Sciences Publication Activity Database

    Kratochvílová, Irena; Vala, M.; Weiter, M.; Špérová, M.; Schneider, Bohdan; Páv, Ondřej; Šebera, Jakub; Rosenberg, Ivan; Sychrovský, Vladimír

    2013-01-01

    Roč. 20, č. 1 (2013), s. 9-9 ISSN 1211-5894. [Discussions in Structural Molecular Biology. Annual Meeting of the Czech Society for Structural Biology /11./. 14.03.2013-16.03.2013, Nové Hrady] Institutional support: RVO:61388963 ; RVO:68378271 ; RVO:86652036 Keywords : charge transport * fluorescence spectroscopy * DFT Subject RIV: CF - Physical ; Theoretical Chemistry

  13. Effects of microbial DNA on human DNA profiles generated using the PowerPlex® 16 HS system.

    Science.gov (United States)

    Dembinski, Gina M; Picard, Christine J

    2017-11-01

    Most crime scenes are not sterile and therefore may be contaminated with environmental DNA, especially if a decomposing body is found. Collecting biological evidence from this individual will yield DNA samples mixed with microbial DNA. This also becomes important if postmortem swabs are collected from sexually assaulted victims. Although genotyping kits undergo validation tests, including bacterial screens, they do not account for the diverse microbial load during decomposition. We investigated the effect of spiking human DNA samples with known concentrations of DNA from 17 microbe species associated with decomposition on DNA profiles produced using the Promega PowerPlex ® HS system. Two species, Bacillus subtilis and Mycobacterium smegmatis, produced an extraneous allele at the TPOX locus. When repeated with the PowerPlex ® Fusion kit, the extra allele no longer amplified with these two species. This experiment demonstrates that caution should be exhibited if microbial load is high and the PowerPlex ® 16HS system is used. Copyright © 2017 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  14. Effect of Cisplatin on the Flexibility of Linear DNA

    International Nuclear Information System (INIS)

    Ji Chao; Zhang Ling-Yun; Hou Xi-Miao; Dou Shuo-Xing; Wang Peng-Ye

    2011-01-01

    With the aid of an atomic force microscope (AFM), we study the interaction between linear DNA fragment and cisplatin. For different cisplatin concentrations, the AFM used to observe the conformation of DNA has a gradual change. The contour length, the end-to-end distance and the local bend angles of the linear DNA fragment can be accurately measured. The persistence length of DNA interacting with cisplatin is decreased with the increasing cisplatin concentration. Furthermore, it is demonstrated that the local bend angles of DNA chains are increased by the binding interaction of cisplatin. (cross-disciplinary physics and related areas of science and technology)

  15. DNA hybridization kinetics: zippering, internal displacement and sequence dependence.

    Science.gov (United States)

    Ouldridge, Thomas E; Sulc, Petr; Romano, Flavio; Doye, Jonathan P K; Louis, Ard A

    2013-10-01

    Although the thermodynamics of DNA hybridization is generally well established, the kinetics of this classic transition is less well understood. Providing such understanding has new urgency because DNA nanotechnology often depends critically on binding rates. Here, we explore DNA oligomer hybridization kinetics using a coarse-grained model. Strand association proceeds through a complex set of intermediate states, with successful binding events initiated by a few metastable base-pairing interactions, followed by zippering of the remaining bonds. But despite reasonably strong interstrand interactions, initial contacts frequently dissociate because typical configurations in which they form differ from typical states of similar enthalpy in the double-stranded equilibrium ensemble. Initial contacts must be stabilized by two or three base pairs before full zippering is likely, resulting in negative effective activation enthalpies. Non-Arrhenius behavior arises because the number of base pairs required for nucleation increases with temperature. In addition, we observe two alternative pathways-pseudoknot and inchworm internal displacement-through which misaligned duplexes can rearrange to form duplexes. These pathways accelerate hybridization. Our results explain why experimentally observed association rates of GC-rich oligomers are higher than rates of AT- rich equivalents, and more generally demonstrate how association rates can be modulated by sequence choice.

  16. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S K

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  17. Duplex ultrasound and computed tomography angiography in the follow-up of endovascular abdominal aortic aneurysm repair: a comparative study

    International Nuclear Information System (INIS)

    Cantador, Alex Aparecido; Siqueira, Daniel Emilio Dalledone; Jacobsen, Octavio Barcellos; Baracat, Jamal; Pereira, Ines Minniti Rodrigues; Menezes, Fabio 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. (author)

  18. Duplex ultrasound and computed tomography angiography in the follow-up of endovascular abdominal aortic aneurysm repair: a comparative study

    Energy Technology Data Exchange (ETDEWEB)

    Cantador, Alex Aparecido; Siqueira, Daniel Emilio Dalledone; Jacobsen, Octavio Barcellos; Baracat, Jamal; Pereira, Ines Minniti Rodrigues; Menezes, Fabio Hüsemann; Guillaumon, Ana Terezinha, E-mail: alex_cantador@yahoo.com.br [Universidade Estadual de Campinas (FCM/UNICAMP), Campinas, SP (Brazil). Faculdade de Ciencias Medicas

    2016-07-15

    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. (author)

  19. Dilution and Ferrite Number Prediction in Pulsed Current Cladding of Super-Duplex Stainless Steel Using RSM

    Science.gov (United States)

    Eghlimi, Abbas; Shamanian, Morteza; Raeissi, Keyvan

    2013-12-01

    Super-duplex stainless steels have an excellent combination of mechanical properties and corrosion resistance at relatively low temperatures and can be used as a coating to improve the corrosion and wear resistance of low carbon and low alloy steels. Such coatings can be produced using weld cladding. In this study, pulsed current gas tungsten arc cladding process was utilized to deposit super-duplex stainless steel on high strength low alloy steel substrates. In such claddings, it is essential to understand how the dilution affects the composition and ferrite number of super-duplex stainless steel layer in order to be able to estimate its corrosion resistance and mechanical properties. In the current study, the effect of pulsed current gas tungsten arc cladding process parameters on the dilution and ferrite number of super-duplex stainless steel clad layer was investigated by applying response surface methodology. The validity of the proposed models was investigated by using quadratic regression models and analysis of variance. The results showed an inverse relationship between dilution and ferrite number. They also showed that increasing the heat input decreases the ferrite number. The proposed mathematical models are useful for predicting and controlling the ferrite number within an acceptable range for super-duplex stainless steel cladding.

  20. Rietveld and impedance analysis of cold and hot rolled duplex and lean duplex steels for application in paper and pulp industry

    Energy Technology Data Exchange (ETDEWEB)

    Esteves, Luiza; Lins, Vanessa de Freitas Cunha, E-mail: luizaeq@yahoo.com.br [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Departamento de Engenharia Quimica; Paiva, Paulo Renato Perdigao [Centro Federal de Educacao Tecnologica de Minas Gerais (CEFET), Belo Horizonte, MG (Brazil); Viana, Adolfo Kalergis do Nascimento [APERAM South America, Timoteo, MG (Brazil)

    2017-01-15

    In this study, X-Ray Diffraction (XRD) and Rietveld Refinement were performed to identify and quantify the ferrite and austenite phase of cold and hot rolled duplex stainless steels (UNS S31803) and lean duplex stainless steels (UNS S32304). Electrochemical impedance spectroscopy (EIS) was applied to evaluate the chemical behavior of duplex and lean duplex stainless steels in white, green, and black liquors of paper and pulp industry. Rietveld analysis results showed a higher austenite content than the standard limit for duplex steels in the hot rolled condition. The hot rolling condition plays a major role in improving corrosion resistance in white liquor mainly for the lean duplex steel. (author)

  1. Rietveld and impedance analysis of cold and hot rolled duplex and lean duplex steels for application in paper and pulp industry

    International Nuclear Information System (INIS)

    Esteves, Luiza; Lins, Vanessa de Freitas Cunha; Viana, Adolfo Kalergis do Nascimento

    2017-01-01

    In this study, X-Ray Diffraction (XRD) and Rietveld Refinement were performed to identify and quantify the ferrite and austenite phase of cold and hot rolled duplex stainless steels (UNS S31803) and lean duplex stainless steels (UNS S32304). Electrochemical impedance spectroscopy (EIS) was applied to evaluate the chemical behavior of duplex and lean duplex stainless steels in white, green, and black liquors of paper and pulp industry. Rietveld analysis results showed a higher austenite content than the standard limit for duplex steels in the hot rolled condition. The hot rolling condition plays a major role in improving corrosion resistance in white liquor mainly for the lean duplex steel. (author)

  2. Effect of food processing on plant DNA degradation and PCR-based GMO analysis: a review.

    Science.gov (United States)

    Gryson, Nicolas

    2010-03-01

    The applicability of a DNA-based method for GMO detection and quantification depends on the quality and quantity of the DNA. Important food-processing conditions, for example temperature and pH, may lead to degradation of the DNA, rendering PCR analysis impossible or GMO quantification unreliable. This review discusses the effect of several food processes on DNA degradation and subsequent GMO detection and quantification. The data show that, although many of these processes do indeed lead to the fragmentation of DNA, amplification of the DNA may still be possible. Length and composition of the amplicon may, however, affect the result, as also may the method of extraction used. Also, many techniques are used to describe the behaviour of DNA in food processing, which occasionally makes it difficult to compare research results. Further research should be aimed at defining ingredients in terms of their DNA quality and PCR amplification ability, and elaboration of matrix-specific certified reference materials.

  3. Detection of influenza A virus using carbon nanotubes field effect transistor based DNA sensor

    Science.gov (United States)

    Tran, Thi Luyen; Nguyen, Thi Thuy; Huyen Tran, Thi Thu; Chu, Van Tuan; Thinh Tran, Quang; Tuan Mai, Anh

    2017-09-01

    The carbon nanotubes field effect transistor (CNTFET) based DNA sensor was developed, in this paper, for detection of influenza A virus DNA. Number of factors that influence the output signal and analytical results were investigated. The initial probe DNA, decides the available DNA strands on CNTs, was 10 μM. The hybridization time for defined single helix was 120 min. The hybridization temperature was set at 30 °C to get a net change in drain current of the DNA sensor without altering properties of any biological compounds. The response time of the DNA sensor was less than one minute with a high reproducibility. In addition, the DNA sensor has a wide linear detection range from 1 pM to 10 nM, and a very low detection limit of 1 pM. Finally, after 7-month storage in 7.4 pH buffer, the output signal of DNA sensor recovered 97%.

  4. Effect of neonatal undernutrition on various forms of DNA-dependent DNA polymerases in cerebellum and liver of rat

    International Nuclear Information System (INIS)

    Baksi, K.; Kumar, A.

    1978-01-01

    Effect of neonatal undernutrition on the two forms of DNA polymerases obtained by DEAF-cellulose column chromatography of the solubilized nuclei and the high speed supernatant fractions of cerebellum and liver of rats has been studied. The form of DNA polymerase eluting with 0.1 M potassium phosphate buffer (pH 7.5) was significantly reduced, whereas that eluting with 0.3 M buffer (pH 7.5) was devoid of neonatal undernutrition effect. The properties of the separated DNA polymerases, both from cerebellum and liver, of control and undernourished groups were also studied. [Me- 3 H]thymidine-5--'triphosphate has been used in the study. (author)

  5. Buffer management in wireless full-duplex systems

    KAUST Repository

    Bouacida, Nader

    2015-10-19

    Wireless full-duplex radios can simultaneously transmit and receive using the same frequency. In theory, this can double the throughput. In fact, there is only little work addressing aspects other than throughput gains in full-duplex systems. Over-buffering in today\\'s networks or the so-called “bufferbloat” phenomenon creates excessive end-to-end delays resulting in network performance degradation. Our analysis shows that full-duplex systems may suffer from high latency caused by bloated buffers. In this paper, we address the problem of buffer management in full-duplex networks by using Wireless Queue Management (WQM), which is an active queue management technique for wireless networks. Our solution is based on Relay Full-Duplex MAC (RFD-MAC), an asynchronous media access control protocol designed for relay full-duplexing. We compare the performance of WQM in full-duplex environment to Drop Tail mechanism over various scenarios. Our solution reduces the end-to-end delay by two orders of magnitude while achieving similar throughput in most of the cases.

  6. Ultra-low-energy (<10 eV/u) ion beam bombardment effect on naked DNA

    Energy Technology Data Exchange (ETDEWEB)

    Thopan, P. [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Thongkumkoon, P. [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Prakrajang, K. [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Faculty of Science, Maejo University, Chiang Mai 50290 (Thailand); Suwannakachorn, D. [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Yu, L.D., E-mail: yuld@thep-center.org [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok 10400 (Thailand)

    2014-05-01

    Highlights: • Decelerated ultra-low energy ion beam bombarded naked DNA. • DNA form change induced by ion bombardment was investigated. • N-ion bombardment at 32 eV induced DNA single and double strand breaks. • Ar-ion bombardment at a-few-hundreds eV induced DNA single strand break. - Abstract: Since ion energy deposition in the ion-bombarded materials dominantly occurs in the low-energy range, it is very interesting to know effects from ultra-low-energy ion interaction with DNA for understanding ion-beam-induced genetic mutation. Tens-keV Ar- and N-ion beams were decelerated to ultra-low energy ranging from 20 to 100 eV, or only a few to 10 eV/u, to bombard naked plasmid DNA. The bombarded DNA was analyzed using gel electrophoresis for DNA form changes. The original DNA supercoiled form was found to change to relaxed and linear forms, indicating single or double strand breaks after bombarded by tens-eV ion beam. N-ion beam was found more effective in inducing DNA change and mutation than Ar-ion beam. The study demonstrated that the ion bombardment with energy as low as several-tens eV was able to break DNA strands and thus potentially to cause genetic modification of biological cells. The experimental results were discussed in terms of direct atomic collision between the ions and DNA atoms.

  7. Ultra-low-energy (<10 eV/u) ion beam bombardment effect on naked DNA

    International Nuclear Information System (INIS)

    Thopan, P.; Thongkumkoon, P.; Prakrajang, K.; Suwannakachorn, D.; Yu, L.D.

    2014-01-01

    Highlights: • Decelerated ultra-low energy ion beam bombarded naked DNA. • DNA form change induced by ion bombardment was investigated. • N-ion bombardment at 32 eV induced DNA single and double strand breaks. • Ar-ion bombardment at a-few-hundreds eV induced DNA single strand break. - Abstract: Since ion energy deposition in the ion-bombarded materials dominantly occurs in the low-energy range, it is very interesting to know effects from ultra-low-energy ion interaction with DNA for understanding ion-beam-induced genetic mutation. Tens-keV Ar- and N-ion beams were decelerated to ultra-low energy ranging from 20 to 100 eV, or only a few to 10 eV/u, to bombard naked plasmid DNA. The bombarded DNA was analyzed using gel electrophoresis for DNA form changes. The original DNA supercoiled form was found to change to relaxed and linear forms, indicating single or double strand breaks after bombarded by tens-eV ion beam. N-ion beam was found more effective in inducing DNA change and mutation than Ar-ion beam. The study demonstrated that the ion bombardment with energy as low as several-tens eV was able to break DNA strands and thus potentially to cause genetic modification of biological cells. The experimental results were discussed in terms of direct atomic collision between the ions and DNA atoms

  8. Multicenter assessment of venous reflux by duplex ultrasound.

    Science.gov (United States)

    Lurie, Fedor; Comerota, Anthony; Eklof, Bo; Kistner, Robert L; Labropoulos, Nicos; Lohr, Joann; Marston, William; Meissner, Mark; Moneta, Gregory; Neglén, Peter; Neuhardt, Diana; Padberg, Frank; Welsh, Harold J

    2012-02-01

    This prospective multicenter investigation was conducted to define the repeatability of duplex-based identification of venous reflux and the relative effect of key parameters on the reproducibility of the test. Repeatability was studied by having the same technologist perform duplicate tests, at the same time of the day, using the same reflux-provoking maneuver and with the patient in the same position. Reproducibility was examined by having two different technologists perform the test at the same time of the day, using the same reflux-provoking maneuver and with the patient in the same position. Facilitated reproducibility was studied by having two different technologists examine the same patients immediately after an educational intervention. Limits of agreement between two duplex scans were studied by changing three elements of the test: time of the day (morning vs afternoon), patient's position (standing vs supine), and reflux initiation (manual vs automatic compression-decompression). The study enrolled 17 healthy volunteers and 57 patients with primary chronic venous disease. Repeatability of reflux time measurements in deep veins did not significantly differ with the time of day, the patient's position, or the reflux-provoking maneuver. Reflux measurements in the superficial veins were more repeatable (P ultrasound detection of venous reflux. Reports should include information on the time of the test, the patient's position, and the provoking maneuver used. Adopting a uniform cut point of 0.5 second for pathologic reflux can significantly improve the reliability of reflux detection. Implementation of a standard protocol should elevate the minimal standard for agreement between repeated tests from the current 70% to at least 80% and with more rigid standardization, to 90%. Copyright © 2012 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.

  9. Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

    Directory of Open Access Journals (Sweden)

    Yuji Miyahara

    2013-02-01

    Full Text Available Peptide nucleic acid (PNA has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry.

  10. Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

    Science.gov (United States)

    Goda, Tatsuro; Singi, Ankit Balram; Maeda, Yasuhiro; Matsumoto, Akira; Torimura, Masaki; Aoki, Hiroshi; Miyahara, Yuji

    2013-01-01

    Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry. PMID:23435052

  11. Molecular dynamics analysis of stabilities of the telomeric Watson-Crick duplex and the associated i-motif as a function of pH and temperature.

    Science.gov (United States)

    Panczyk, Tomasz; Wolski, Pawel

    2018-06-01

    This work deals with a molecular dynamics analysis of the protonated and deprotonated states of the natural sequence d[(CCCTAA) 3 CCCT] of the telomeric DNA forming the intercalated i-motif or paired with the sequence d[(CCCTAA) 3 CCCT] and forming the Watson-Crick (WC) duplex. By utilizing the amber force field for nucleic acids we built the i-motif and the WC duplex either with native cytosines or using their protonated forms. We studied, by applying molecular dynamics simulations, the role of hydrogen bonds between cytosines or in cytosine-guanine pairs in the stabilization of both structures in the physiological fluid. We found that hydrogen bonds exist in the case of protonated i-motif and in the standard form of the WC duplex. They, however, vanish in the case of the deprotonated i-motif and protonated form of the WC duplex. By determining potentials of mean force in the enforced unwrapping of these structures we found that the protonated i-motif is thermodynamically the most stable. Its deprotonation leads to spontaneous and observed directly in the unbiased calculations unfolding of the i-motif to the hairpin structure at normal temperature. The WC duplex is stable in its standard form and its slight destabilization is observed at the acidic pH. However, the protonated WC duplex unwraps very slowly at 310 K and its decomposition was not observed in the unbiased calculations. At higher temperatures (ca. 400 K or more) the WC duplex unwraps spontaneously. Copyright © 2018. Published by Elsevier B.V.

  12. Iodination as a probe for small regions of disrupted secondary structure in double-stranded DNA

    DEFF Research Database (Denmark)

    Jensen, Kaj Frank; Nes, Ingolf F.; Wells, Robert D.

    1976-01-01

    Conditions were established where the thallium-catalyzed iodination of random coil DNA proceeded 100–200 times faster than for native DNA. This reaction was explored as a probe for localized regions of disrupted base pairs in duplex DNA. A heteroduplex was constructed between DNA fragments produced...

  13. A Molecular Dynamics-Quantum Mechanics Theoretical Study of DNA-Mediated Charge Transport in Hydrated Ionic Liquids.

    Science.gov (United States)

    Meng, Zhenyu; Kubar, Tomas; Mu, Yuguang; Shao, Fangwei

    2018-05-08

    Charge transport (CT) through biomolecules is of high significance in the research fields of biology, nanotechnology, and molecular devices. Inspired by our previous work that showed the binding of ionic liquid (IL) facilitated charge transport in duplex DNA, in silico simulation is a useful means to understand the microscopic mechanism of the facilitation phenomenon. Here molecular dynamics simulations (MD) of duplex DNA in water and hydrated ionic liquids were employed to explore the helical parameters. Principal component analysis was further applied to capture the subtle conformational changes of helical DNA upon different environmental impacts. Sequentially, CT rates were calculated by a QM/MM simulation of the flickering resonance model based upon MD trajectories. Herein, MD simulation illustrated that the binding of ionic liquids can restrain dynamic conformation and lower the on-site energy of the DNA base. Confined movement among the adjacent base pairs was highly related to the increase of electronic coupling among base pairs, which may lead DNA to a CT facilitated state. Sequentially combining MD and QM/MM analysis, the rational correlations among the binding modes, the conformational changes, and CT rates illustrated the facilitation effects from hydrated IL on DNA CT and supported a conformational-gating mechanism.

  14. Label-free detection of DNA hybridization using carbon nanotube network field-effect transistors

    Science.gov (United States)

    Star, Alexander; Tu, Eugene; Niemann, Joseph; Gabriel, Jean-Christophe P.; Joiner, C. Steve; Valcke, Christian

    2006-01-01

    We report carbon nanotube network field-effect transistors (NTNFETs) that function as selective detectors of DNA immobilization and hybridization. NTNFETs with immobilized synthetic oligonucleotides have been shown to specifically recognize target DNA sequences, including H63D single-nucleotide polymorphism (SNP) discrimination in the HFE gene, responsible for hereditary hemochromatosis. The electronic responses of NTNFETs upon single-stranded DNA immobilization and subsequent DNA hybridization events were confirmed by using fluorescence-labeled oligonucleotides and then were further explored for label-free DNA detection at picomolar to micromolar concentrations. We have also observed a strong effect of DNA counterions on the electronic response, thus suggesting a charge-based mechanism of DNA detection using NTNFET devices. Implementation of label-free electronic detection assays using NTNFETs constitutes an important step toward low-cost, low-complexity, highly sensitive and accurate molecular diagnostics. hemochromatosis | SNP | biosensor

  15. Racemic DNA crystallography.

    Science.gov (United States)

    Mandal, Pradeep K; Collie, Gavin W; Kauffmann, Brice; Huc, Ivan

    2014-12-22

    Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. The current status of studies on mitochondrial DNA with tumor, radiation biological effects and aging

    International Nuclear Information System (INIS)

    Liu Qingjie; Sang Lu

    2004-01-01

    The mitochondrial plays a very important role in sustaining the normal physiological function, because it is the center of energy making and mitochondrial DNA (mtDNA) is the only genetic material outside the nuclear. The result of studies showed that many diseases have a close relationship with mtDNA mutation and deletion. This article reviewed the current status of research on mtDNA with tumor, radiation biological effects and aging, in order to initiate the application study of mtDNA in the circle of radiation medicine

  17. Corrosion behavior of sensitized duplex stainless steel.

    Science.gov (United States)

    Torres, F J; Panyayong, W; Rogers, W; Velasquez-Plata, D; Oshida, Y; Moore, B K

    1998-01-01

    The present work investigates the corrosion behavior of 2205 duplex stainless steel in 0.9% NaCl solution after various heat-treatments, and compares it to that of 316L austenitic stainless steel. Both stainless steels were heat-treated at 500, 650, and 800 degrees C in air for 1 h, followed by furnace cooling. Each heat-treated sample was examined for their microstructures and Vickers micro-hardness, and subjected to the X-ray diffraction for the phase identification. Using potentiostatic polarization method, each heat-treated sample was corrosion-tested in 37 degrees C 0.9% NaCl solution to estimate its corrosion rate. It was found that simulated sensitization showed an adverse influence on both steels, indicating that corrosion rates increased by increasing the sensitization temperatures.

  18. Duplex stainless steel surface bay laser cladding

    International Nuclear Information System (INIS)

    Amigo, V.; Pineda, Y.; Segovia, F.; Vicente, A.

    2004-01-01

    Laser cladding is one of the most promising techniques to restore damaged surfaces and achieve properties similar to those of the base metal. In this work, duplex stainless steels have been cladded by a nickel alloy under different processing conditions. The influence of the beam speed and defocusing variables ha been evaluated in the microstructure both of the cladding and heat affected zone, HAZ. These results have been correlated to mechanical properties by means of microhardness measurements from cladding area to base metal through the interface. This technique has shown to be very appropriate to obtain controlled mechanical properties as they are determined by the solidification microstructure, originated by the transfer of mass and heat in the system. (Author) 21 refs

  19. Duplex quantum communication through a spin chain

    Science.gov (United States)

    Wang, Zhao-Ming; Bishop, C. Allen; Gu, Yong-Jian; Shao, Bin

    2011-08-01

    Data multiplexing within a quantum computer can allow for the simultaneous transfer of multiple streams of information over a shared medium thereby minimizing the number of channels needed for requisite data transmission. Here, we investigate a two-way quantum communication protocol using a spin chain placed in an external magnetic field. In our scheme, Alice and Bob each play the role of a sender and a receiver as two states, cos((θ1)/(2))0+sin((θ1)/(2))eiφ11 and cos((θ2)/(2))0+sin((θ2)/(2))eiφ21, are transferred through one channel simultaneously. We find that the transmission fidelity at each end of a spin chain can usually be enhanced by the presence of a second party. This is an important result for establishing the viability of duplex quantum communication through spin chain networks.

  20. Numerical Simulation of Duplex Steel Multipass Welding

    Directory of Open Access Journals (Sweden)

    Giętka T.

    2016-12-01

    Full Text Available Analyses based on FEM calculations have significantly changed the possibilities of determining welding strains and stresses at early stages of product design and welding technology development. Such an approach to design enables obtaining significant savings in production preparation and post-weld deformation corrections and is also important for utility properties of welded joints obtained. As a result, it is possible to make changes to a simulated process before introducing them into real production as well as to test various variants of a given solution. Numerical simulations require the combination of problems of thermal, mechanical and metallurgical analysis. The study presented involved the SYSWELD software-based analysis of GMA welded multipass butt joints made of duplex steel sheets. The analysis of the distribution of stresses and displacements were carried out for typical welding procedure as during real welding tests.

  1. Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining

    Science.gov (United States)

    Kukshal, Vandna; Kim, In-Kwon; Hura, Gregory L.; Tomkinson, Alan E.; Tainer, John A.; Ellenberger, Tom

    2015-01-01

    Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation. PMID:26130724

  2. Novel DNA lesions generated by the interaction between therapeutic thiopurines and UVA light.

    Science.gov (United States)

    Zhang, Xiaohong; Jeffs, Graham; Ren, Xiaolin; O'Donovan, Peter; Montaner, Beatriz; Perrett, Conal M; Karran, Peter; Xu, Yao-Zhong

    2007-03-01

    The therapeutic effect of the thiopurines, 6-thioguanine (6-TG), 6-mercaptopurine, and its prodrug azathioprine, depends on the incorporation of 6-TG into cellular DNA. Unlike normal DNA bases, 6-TG absorbs UVA radiation, and UVA-mediated photochemical damage of DNA 6-TG has potentially harmful side effects. When free 6-TG is UVA irradiated in solution in the presence of molecular oxygen, reactive oxygen species are generated and 6-TG is oxidized to guanine-6-sulfonate (G(SO3)) and guanine-6-thioguanine in reactions involving singlet oxygen. This conversion is prevented by antioxidants, including the dietary vitamin ascorbate. DNA G(SO3) is also the major photoproduct of 6-TG in DNA and it can be selectively introduced into DNA or oligonucleotides in vitro by mild chemical oxidation. Thermal stability measurements indicate that G(SO3) does not form stable base pairs with any of the normal DNA bases in duplex oligonucleotides and is a powerful block for elongation by Klenow DNA polymerase in primer extension experiments. In cultured human cells, DNA damage produced by 6-TG and UVA treatment is associated with replication inhibition and provokes a p53-dependent DNA damage response.

  3. The Mechanical Behavior of a 25Cr Super Duplex Stainless Steel at Elevated Temperature

    Science.gov (United States)

    Lasebikan, B. A.; Akisanya, A. R.; Deans, W. F.

    2013-02-01

    Super duplex stainless steel (SDSS) is a candidate material for production tubing in oil and gas wells and subsea pipelines used to transport corrosive hydrocarbon fluids. The suitability of this material for high temperature applications is examined in this article. The uniaxial tensile properties are determined for a 25Cr SDSS over a range of temperature relevant to high pressure-high temperature oil and gas wells. It is shown that there is a significant effect of temperature on the uniaxial tensile properties. Elevated temperature was shown to reduce the Young's modulus and increase the strain hardening index; temperature effects on these two parameters are usually neglected in the design of subsea pipelines and oil well tubulars, and this could lead to wrong predictions of the collapse pressure. The manufacturing process of the super duplex tubular did not lead to significant anisotropy in the hardness and the ultimate tensile and uniaxial yield strengths.

  4. Four highly pseudosymmetric and/or twinned structures of d(CGCGCG) 2 extend the repertoire of crystal structures of Z-DNA

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Zhipu; Dauter, Zbigniew; Gilski, Miroslaw

    2017-10-30

    DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG)2duplexes are described here. They are characterized by a high degree of pseudosymmetry and/or twinning, with three or four independent duplexes differently oriented in a monoclinicP21lattice of hexagonal metric. The various twinning criteria give somewhat conflicting indications in these complicated cases of crystal pathology. The details of molecular packing in these crystal structures are compared with other known crystal forms of Z-DNA.

  5. Investigation of the charge effect on the electrochemical transduction in a quinone-based DNA sensor

    DEFF Research Database (Denmark)

    Reisberg, S.; Piro, B.; Noel, V.

    2008-01-01

    To elucidate the mechanism involved in the electrochemical transduction process of a conducting polymer-based DNA sensor, peptide nucleic acids (PNA) were used. PNA are DNA analogues having similar hybridization properties but are neutral. This allows to discriminate the electrostatic effect of D...... strands from the steric hindrance generated on the bioelectrode upon hybridization. It can be concluded that DNA conformational changes are determinant in the transduction process and that the electrostatic effect is negligible....

  6. Investigating the DNA-binding ability of GATA-1-N-terminal zinc finger

    International Nuclear Information System (INIS)

    Wong, R.; Newton, A.; Crossley, M.; Mackay, J.

    2001-01-01

    Erythroid transcription factor GATA-1 interacts with both DNA and other proteins through its zinc finger domains (ZnFs). While it has been known for me time that the C-terminal ZnF binds DNA at GATA sites, only recently has it been observed that the N-terminal finger (NF) is capable of interacting with GATC sites. Further, a number of naturally occurring mutations in NF (V205M, G208S, R216Q, D218G) that lead to anaemia and thrombocytopenia have been identified. We are interested in characterising the NF-DNA interaction and determining the effects of mutation upon this interaction. Using nuclear magnetic resonance (NMR) spectroscopy, we have observed an interaction between recombinant NF and a 16-mer DNA duplex containing a core GATC sequence. This result forms the basis from which residues in NF involved in DNA binding can be identified, and work is being carried out to improve the quality of the NMR data with the aim of determining the solution structure of the NF-DNA complex. The DNA-binding affinity of both wild-type and mutant NFs mentioned above is also being investigated using isothermal titration calorimetry. These data suggest that the strength of the interaction between NF and the 16-mer DNA duplex is in the sub-micromolar range, and comparisons between the DNA-binding affinities of the NF mutants are being made. Together, these studies will help us to understand how GATA-1 acts as a transcriptional regulator and how mutations in NF domain of GATA-1 may lead to blood disorders

  7. Targeting Ongoing DNA Damage in Multiple Myeloma: Effects of DNA Damage Response Inhibitors on Plasma Cell Survival

    Directory of Open Access Journals (Sweden)

    Ana Belén Herrero

    2017-05-01

    Full Text Available Human myeloma cell lines (HMCLs and a subset of myeloma patients with poor prognosis exhibit high levels of replication stress (RS, leading to DNA damage. In this study, we confirmed the presence of DNA double-strand breaks (DSBs in several HMCLs by measuring γH2AX and RAD51 foci and analyzed the effect of various inhibitors of the DNA damage response on MM cell survival. Inhibition of ataxia telangiectasia and Rad3-related protein (ATR, the main kinase mediating the response to RS, using the specific inhibitor VE-821 induced more cell death in HMCLs than in control lymphoblastoid cells and U266, an HMCL with a low level of DNA damage. The absence of ATR was partially compensated by ataxia telangiectasia-mutated protein (ATM, since chemical inhibition of both kinases using VE-821 and KU-55933 significantly increased the death of MM cells with DNA damage. We found that ATM and ATR are involved in DSB repair by homologous recombination (HR in MM. Inhibition of both kinases resulted in a stronger inhibition that may underlie cell death induction, since abolition of HR using two different inhibitors severely reduced survival of HMCLs that exhibit DNA damage. On the other hand, inhibition of the other route involved in DSB repair, non-homologous end joining (NHEJ, using the DNA-PK inhibitor NU7441, did not affect MM cell viability. Interestingly, we found that NHEJ inhibition did not increase cell death when HR was simultaneously inhibited with the RAD51 inhibitor B02, but it clearly increased the level of cell death when HR was inhibited with the MRE11 inhibitor mirin, which interferes with recombination before DNA resection takes place. Taken together, our results demonstrate for the first time that MM cells with ongoing DNA damage rely on an intact HR pathway, which thereby suggests therapeutic opportunities. We also show that inhibition of HR after the initial step of end resection might be more appropriate for inducing MM cell death, since it

  8. Initiation of the microgene polymerization reaction with non-repetitive homo-duplexes

    International Nuclear Information System (INIS)

    Itsko, Mark; Zaritsky, Arieh; Rabinovitch, Avinoam; Ben-Dov, Eitan

    2008-01-01

    Microgene Polymerization Reaction (MPR) is used as an experimental system to artificially simulate evolution of short, non-repetitive homo-duplex DNA into multiply-repetitive products that can code for functional proteins. Blunt-end ligation by DNA polymerase is crucial in expansion of homo-duplexes (HDs) into head-to-tail multiple repeats in MPR. The propagation mechanism is known, but formation of the initial doublet (ID) by juxtaposing two HDs and polymerization through the gap has been ambiguous. Initiation events with pairs of HDs using Real-Time PCR were more frequent at higher HD concentrations and slightly below the melting temperature. A process molecularity of about 3.1, calculated from the amplification efficiency and the difference in PCR cycles at which propagation was detected at varying HD concentrations, led to a simple mechanism for ID formation: the gap between two HDs is bridged by a third. Considering thermodynamic aspects of the presumed intermediate 'nucleation complex' can predict relative propensity for the process with other HDs

  9. Inhibitory effect of benzene metabolites on nuclear DNA synthesis in bone marrow cells

    International Nuclear Information System (INIS)

    Lee, E.W.; Johnson, J.T.; Garner, C.D.

    1989-01-01

    Effects of endogenously produced and exogenously added benzene metabolites on the nuclear DNA synthetic activity were investigated using a culture system of mouse bone marrow cells. Effects of the metabolites were evaluated by a 30-min incorporation of [ 3 H]thymidine into DNA following a 30-min interaction with the cells in McCoy's 5a medium with 10% fetal calf serum. Phenol and muconic acid did not inhibit nuclear DNA synthesis. However, catechol, 1,2,4-benzenetriol, hydroquinone, and p-benzoquinone were able to inhibit 52, 64, 79, and 98% of the nuclear DNA synthetic activity, respectively, at 24 μM. In a cell-free DNA synthetic system, catechol and hydroquinone did not inhibit the incorporation of [ 3 H]thymidine triphosphate into DNA up to 24 μM but 1,2,4-benzenetriol and p-benzoquinone did. The effect of the latter two benzene metabolites was completely blocked in the presence of 1,4-dithiothreitol (1 mM) in the cell-free assay system. Furthermore, when DNA polymerase α, which requires a sulfhydryl (SH) group as an active site, was replaced by DNA polymerase 1, which does not require an SH group for its catalytic activity, p-benzoquinone and 1,2,4-benzenetriol were unable to inhibit DNA synthesis. Thus, the data imply the p-benzoquinone and 1,2,4-benzenetriol inhibited DNA polymerase α, consequently resulting in inhibition of DNA synthesis in both cellular and cell-free DNA synthetic systems. The present study identifies catechol, hydroquinone, p-benzoquinone, and 1,2,4-benzenetriol as toxic benzene metabolites in bone marrow cells and also suggests that their inhibitory action on DNA synthesis is mediated by mechanism(s) other than that involving DNA damage as a primary cause

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

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2014-01-01

    Full Text Available 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.

  11. Detection and quantification of beef and pork materials in meat products by duplex droplet digital PCR

    OpenAIRE

    Cai, Yicun; He, Yuping; Lv, Rong; Chen, Hongchao; Wang, Qiang; Pan, Liangwen

    2017-01-01

    Meat products often consist of meat from multiple animal species, and inaccurate food product adulteration and mislabeling can negatively affect consumers. Therefore, a cost-effective and reliable method for identification and quantification of animal species in meat products is required. In this study, we developed a duplex droplet digital PCR (dddPCR) detection and quantification system to simultaneously identify and quantify the source of meat in samples containing a mixture of beef (Bos t...