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Sample records for dependent dna conductivity

  1. Electrical conduction through DNA molecule.

    PubMed

    Abdalla, S

    2011-09-01

    Several disorder parameters, inside the DNA molecule, lead to localization of charge carriers inside potential wells in the lowest unoccupied and highest occupied molecular orbits (LUMO and HOMO) which affects drastically the electrical conduction through the molecule, and demonstrates that the band carriers play an essential role in the conduction mechanism. So, a model is presented to shed light on the role of electrons of the LUMO in the electrical conduction through the DNA molecule. DC-, AC-conductivity and dielectric permittivity experimental data are well fitted with the presented model giving evidence that the free carriers in the LUMO and HOMO are responsible to make the DNA molecule conductor, insulator or semiconductor. The obtained results show that the localized charge carriers in the DNA molecule are characterized by four different types of relaxation phenomena which are thermally activated by corresponding four activation energies at 0.56 eV, 0.33 eV, 0.24 eV, and 0.05 eV respectively. Moreover, the calculations after the model, at room temperature, show that the time of the relaxation times of the current carriers are in the order of 5 × 10(-2)s, 1.74 × 10(-4)s, 5 × 10(-7)s, and 1.6 × 10(-10)s, respectively.

  2. Conductance of Dry DNA: Role of Environment

    NASA Technical Reports Server (NTRS)

    Anantram, M. P.; Adessi, Ch.; S. Walch

    2003-01-01

    This paper presents viewgraphs on the conductance of dry DNA and its effect on the surrounding environment. The topics include: 1) Approach; 2) Influence of Counter Ions; 3) Conductance Versus DNA Length; 4) Intrinsic Resonant Tunneling in Engineered DNA Sequence; and 5) Transmission Versus Energy.

  3. Gate-controlled conductance switching in DNA

    PubMed Central

    Xiang, Limin; Palma, Julio L.; Li, Yueqi; Mujica, Vladimiro; Ratner, Mark A.; Tao, Nongjian

    2017-01-01

    Extensive evidence has shown that long-range charge transport can occur along double helical DNA, but active control (switching) of single-DNA conductance with an external field has not yet been demonstrated. Here we demonstrate conductance switching in DNA by replacing a DNA base with a redox group. By applying an electrochemical (EC) gate voltage to the molecule, we switch the redox group between the oxidized and reduced states, leading to reversible switching of the DNA conductance between two discrete levels. We further show that monitoring the individual conductance switching allows the study of redox reaction kinetics and thermodynamics at single molecular level using DNA as a probe. Our theoretical calculations suggest that the switch is due to the change in the energy level alignment of the redox states relative to the Fermi level of the electrodes. PMID:28218275

  4. Gate-controlled conductance switching in DNA

    NASA Astrophysics Data System (ADS)

    Xiang, Limin; Palma, Julio L.; Li, Yueqi; Mujica, Vladimiro; Ratner, Mark A.; Tao, Nongjian

    2017-02-01

    Extensive evidence has shown that long-range charge transport can occur along double helical DNA, but active control (switching) of single-DNA conductance with an external field has not yet been demonstrated. Here we demonstrate conductance switching in DNA by replacing a DNA base with a redox group. By applying an electrochemical (EC) gate voltage to the molecule, we switch the redox group between the oxidized and reduced states, leading to reversible switching of the DNA conductance between two discrete levels. We further show that monitoring the individual conductance switching allows the study of redox reaction kinetics and thermodynamics at single molecular level using DNA as a probe. Our theoretical calculations suggest that the switch is due to the change in the energy level alignment of the redox states relative to the Fermi level of the electrodes.

  5. Environment and Structure Influence in DNA Conduction

    NASA Technical Reports Server (NTRS)

    Adessi, C.; Walch, S.; Anantram, M. P.; Biegel, Bryan (Technical Monitor)

    2002-01-01

    Results for transmission through the poly(G) DNA molecule are presented. We show that (i) periodically arranged sodium counter-ions in close proximity to dry DNA gives rise to a new conduction channel and aperiodicity in the counter-ion sequence can lead to a significant reduction in conduction, (ii) modification of the rise of B-DNA induces a change in the width of the transmission window, and (iii) specifically designed sequences are predicted to show intrinsic resonant tunneling behavior.

  6. Structure and Environment Influence in DNA Conduction

    NASA Technical Reports Server (NTRS)

    Adessi, C.; Walch, S.; Anantram, M. P.; Biegel, Bryan A. (Technical Monitor)

    2002-01-01

    Results for transmission through a poly(G) DNA molecule are presented. We show that a modification of the rise of a B-DNA form can induce a shift of the conduction channel toward the valence one. We clearly prove that deformation of the backbone of the molecule has a significant influence on hole transport. Finally, we observe that the presence of ionic species, such Na, near the molecule can create new conduction channels.

  7. Inhomogeneous DNA: Conducting exons and insulating introns

    NASA Astrophysics Data System (ADS)

    Krokhin, A. A.; Bagci, V. M. K.; Izrailev, F. M.; Usatenko, O. V.; Yampol'Skii, V. A.

    2009-08-01

    Parts of DNA sequences known as exons and introns play very different roles in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations among four basic nucleotides that form double-stranded DNA sequence, we calculate electron localization length for exon and intron regions. Analyzing different DNA molecules, we obtain that the exons have narrow bands of extended states, unlike the introns where all the states are well localized. The band of extended states is due to a specific form of the binary correlation function of the sequence of basic DNA nucleotides.

  8. Influence of Disorder on DNA Conductance

    NASA Technical Reports Server (NTRS)

    Adessi, Christophe; Anantram, M. P.; Biegel, Bryan A. (Technical Monitor)

    2003-01-01

    Disorder along a DNA strand due to non uniformity associated with the counter ion type and location, and in rise and twist are investigated using density functional theory. We then model the conductance through a poly(G) DNA strand by including the influence of disorder. We show that the conductance drops by a few orders of magnitude between typical lengths of 10 and 100 nm. Such a decrease occurs with on-site potential disorder that is larger than 100 meV.

  9. DNA sequencing using electrical conductance measurements of a DNA polymerase

    NASA Astrophysics Data System (ADS)

    Chen, Yu-Shiun; Lee, Chia-Hui; Hung, Meng-Yen; Pan, Hsu-An; Chiou, Jin-Chern; Huang, G. Steven

    2013-06-01

    The development of personalized medicine--in which medical treatment is customized to an individual on the basis of genetic information--requires techniques that can sequence DNA quickly and cheaply. Single-molecule sequencing technologies, such as nanopores, can potentially be used to sequence long strands of DNA without labels or amplification, but a viable technique has yet to be established. Here, we show that single DNA molecules can be sequenced by monitoring the electrical conductance of a phi29 DNA polymerase as it incorporates unlabelled nucleotides into a template strand of DNA. The conductance of the polymerase is measured by attaching it to a protein transistor that consists of an antibody molecule (immunoglobulin G) bound to two gold nanoparticles, which are in turn connected to source and drain electrodes. The electrical conductance of the DNA polymerase exhibits well-separated plateaux that are ~3 pA in height. Each plateau corresponds to an individual base and is formed at a rate of ~22 nucleotides per second. Additional spikes appear on top of the plateaux and can be used to discriminate between the four different nucleotides. We also show that the sequencing platform works with a variety of DNA polymerases and can sequence difficult templates such as homopolymers.

  10. Pressure dependence of electrical conductivity in forsterite

    NASA Astrophysics Data System (ADS)

    Yoshino, Takashi; Zhang, Baohua; Rhymer, Brandon; Zhao, Chengcheng; Fei, Hongzhan

    2017-01-01

    Electrical conductivity of dry forsterite has been measured in muli-anvil apparatus to investigate the pressure dependence of ionic conduction in forsterite. The starting materials for the conductivity experiments were a synthetic forsterite single crystal and a sintered forsterite aggregate synthesized from oxide mixture. Electrical conductivities were measured at 3.5, 6.7, 9.6, 12.1, and 14.9 GPa between 1300 and 2100 K. In the measured temperature range, the conductivity of single crystal forsterite decreases in the order of [001], [010], and [100]. In all cases, the conductivity decreases with increasing pressure and then becomes nearly constant for [100] and [001] and slightly increases above 7 GPa for [010] orientations and a polycrystalline forsterite sample. Pressure dependence of forsterite conductivity was considered as a change of the dominant conduction mechanism composed of migration of both magnesium and oxygen vacancies in forsterite. The activation energy (ΔE) and activation volume (ΔV) for ionic conduction due to migration of Mg vacancy were 1.8-2.7 eV and 5-19 cm3/mol, respectively, and for that due to O vacancy were 2.2-3.1 eV and -1.1 to 0.3 cm3/mol, respectively. The olivine conductivity model combined with small polaron conduction suggests that the most part of the upper mantle is controlled by ionic conduction rather than small polaron conduction. The previously observed negative pressure dependence of the conductivity of olivine with low iron content (Fo90) can be explained by ionic conduction due to migration of Mg vacancies, which has a large positive activation volume.

  11. Probing radiation damage by alternated current conductivity as a method to characterize electron hopping conduction in DNA molecules

    SciTech Connect

    Gomes, Paulo J.; Coelho, Margarida; Antonio Ribeiro, Paulo; Raposo, Maria; Dionisio, Madalena

    2012-09-17

    Analysis of AC electrical conductivity of deoxyribonucleic acid (DNA) thin films, irradiated with ultraviolet (UV) light, revealed that electrical conduction arises from DNA chain electron hopping between base-pairs and phosphate groups. The hopping distance calculated from correlated barrier hopping model equals the distance between DNA base-pairs, which is consistent with the loss of conductivity with irradiation time arising from a decrease in phosphates groups. In the high frequency regime, at a given frequency, real part of conductivity strongly depends on irradiation time particularly for low dose levels suggesting the use of DNA based films for UV radiation sensors.

  12. Conductance of DNA molecules: Effects of decoherence and bonding

    NASA Astrophysics Data System (ADS)

    Zilly, Matías; Ujsághy, Orsolya; Wolf, Dietrich E.

    2010-09-01

    The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently [M. Zilly, O. Ujsághy, and D. E. Wolf, Eur. Phys. J. B 68, 237 (2009)10.1140/epjb/e2009-00101-0] to experimental results. The DNA molecule itself is described by a tight-binding ladder model with parameters obtained from published ab initio calculations [K. Senthilkumar, F. C. Grozema, C. F. Guerra, F. M. Bickelhaupt, F. D. Lewis, Y. A. Berlin, M. A. Ratner, and L. D. A. Siebbeles, J. Am. Chem. Soc. 127, 14894 (2005)10.1021/ja054257e]. The good agreement with the experiments on sequence and length dependence gives a hint on the nature of conduction in DNA and at the same time provides a crucial test of the model.

  13. Temperature dependence of DNA translocations through solid-state nanopores.

    PubMed

    Verschueren, Daniel V; Jonsson, Magnus P; Dekker, Cees

    2015-06-12

    In order to gain a better physical understanding of DNA translocations through solid-state nanopores, we study the temperature dependence of λ-DNA translocations through 10 nm diameter silicon nitride nanopores, both experimentally and theoretically. The measured ionic conductance G, the DNA-induced ionic-conductance blockades [Formula: see text] and the event frequency Γ all increase with increasing temperature while the DNA translocation time τ decreases. G and [Formula: see text] are accurately described when bulk and surface conductances of the nanopore are considered and access resistance is incorporated appropriately. Viscous drag on the untranslocated part of the DNA coil is found to dominate the temperature dependence of the translocation times and the event rate is well described by a balance between diffusion and electrophoretic motion. The good fit between modeled and measured properties of DNA translocations through solid-state nanopores in this first comprehensive temperature study, suggest that our model captures the relevant physics of the process.

  14. Conformation-dependent DNA attraction

    NASA Astrophysics Data System (ADS)

    Li, Weifeng; Nordenskiöld, Lars; Zhou, Ruhong; Mu, Yuguang

    2014-05-01

    Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg2+ ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg2+ or Na+, benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg2+ bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription.Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by

  15. The contact area dependent interfacial thermal conductance

    SciTech Connect

    Liu, Chenhan; Wei, Zhiyong; Bi, Kedong; Yang, Juekuan; Chen, Yunfei; Wang, Jian

    2015-12-15

    The effects of the contact area on the interfacial thermal conductance σ are investigated using the atomic Green’s function method. Different from the prediction of the heat diffusion transport model, we obtain an interesting result that the interfacial thermal conductance per unit area Λ is positively dependent on the contact area as the area varies from a few atoms to several square nanometers. Through calculating the phonon transmission function, it is uncovered that the phonon transmission per unit area increases with the increased contact area. This is attributed to that each atom has more neighboring atoms in the counterpart of the interface with the increased contact area, which provides more channels for phonon transport.

  16. Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting

    PubMed Central

    Vlijm, Rifka; v.d. Torre, Jaco; Dekker, Cees

    2015-01-01

    The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, have determined that AT-rich sequences have a lower binding energy than GC-rich sequences. In cells, however, the double-stranded backbone of DNA is destabilized by negative supercoiling, and not by temperature. To investigate what the effect of GC content is on DNA melting induced by negative supercoiling, we studied DNA molecules with a GC content ranging from 38% to 77%, using single-molecule magnetic tweezer measurements in which the length of a single DNA molecule is measured as a function of applied stretching force and supercoiling density. At low force (<0.5pN), supercoiling results into twisting of the dsDNA backbone and loop formation (plectonemes), without inducing any DNA melting. This process was not influenced by the DNA sequence. When negative supercoiling is introduced at increasing force, local melting of DNA is introduced. We measured for the different DNA molecules a characteristic force Fchar, at which negative supercoiling induces local melting of the dsDNA. Surprisingly, GC-rich sequences melt at lower forces than AT-rich sequences: Fchar = 0.56pN for 77% GC but 0.73pN for 38% GC. An explanation for this counterintuitive effect is provided by the realization that supercoiling densities of a few percent only induce melting of a few percent of the base pairs. As a consequence, denaturation bubbles occur in local AT-rich regions and the sequence-dependent effect arises from an increased DNA bending/torsional energy associated with the plectonemes. This new insight indicates that an increased GC-content adjacent to AT-rich DNA regions will enhance local opening of the double-stranded DNA helix. PMID:26513573

  17. Large-Conductance Transmembrane Porin Made from DNA Origami

    PubMed Central

    2016-01-01

    DNA nanotechnology allows for the creation of three-dimensional structures at nanometer scale. Here, we use DNA to build the largest synthetic pore in a lipid membrane to date, approaching the dimensions of the nuclear pore complex and increasing the pore-area and the conductance 10-fold compared to previous man-made channels. In our design, 19 cholesterol tags anchor a megadalton funnel-shaped DNA origami porin in a lipid bilayer membrane. Confocal imaging and ionic current recordings reveal spontaneous insertion of the DNA porin into the lipid membrane, creating a transmembrane pore of tens of nanosiemens conductance. All-atom molecular dynamics simulations characterize the conductance mechanism at the atomic level and independently confirm the DNA porins’ large ionic conductance. PMID:27504755

  18. Large-Conductance Transmembrane Porin Made from DNA Origami.

    PubMed

    Göpfrich, Kerstin; Li, Chen-Yu; Ricci, Maria; Bhamidimarri, Satya Prathyusha; Yoo, Jejoong; Gyenes, Bertalan; Ohmann, Alexander; Winterhalter, Mathias; Aksimentiev, Aleksei; Keyser, Ulrich F

    2016-09-27

    DNA nanotechnology allows for the creation of three-dimensional structures at nanometer scale. Here, we use DNA to build the largest synthetic pore in a lipid membrane to date, approaching the dimensions of the nuclear pore complex and increasing the pore-area and the conductance 10-fold compared to previous man-made channels. In our design, 19 cholesterol tags anchor a megadalton funnel-shaped DNA origami porin in a lipid bilayer membrane. Confocal imaging and ionic current recordings reveal spontaneous insertion of the DNA porin into the lipid membrane, creating a transmembrane pore of tens of nanosiemens conductance. All-atom molecular dynamics simulations characterize the conductance mechanism at the atomic level and independently confirm the DNA porins' large ionic conductance.

  19. Theory of electron conductance across a DNA basepair

    NASA Astrophysics Data System (ADS)

    Lee, Myeong; Sankey, Otto

    2008-03-01

    In recent years, research on electron tunneling through DNA basepairs has become more important due to its potential application in DNA sequencing technology. The goal is to recognize and identify a specific DNA base by measuring the hydrogen bond mediated tunneling current across a DNA basepair junction. In this talk, we discuss the results of density functional theory on the intrinsic conduction through DNA basepairs (Watson-Crick basepairs, Wobble basepairs, etc), and in particular the role of the hydrogen bond on the tunneling current.

  20. Thickness dependent thermal conductivity of gallium nitride

    NASA Astrophysics Data System (ADS)

    Ziade, Elbara; Yang, Jia; Brummer, Gordie; Nothern, Denis; Moustakas, Theodore; Schmidt, Aaron J.

    2017-01-01

    As the size of gallium nitride (GaN) transistors is reduced in order to reach higher operating frequencies, heat dissipation becomes the critical bottleneck in device performance and longevity. Despite the importance of characterizing the physics governing the thermal transport in thin GaN films, the literature is far from conclusive. In this letter, we report measurements of thermal conductivity in a GaN film with thickness ranging from 15-1000 nm grown on 4H-SiC without a transition layer. Additionally, we measure the thermal conductivity in the GaN film when it is 1 μm-thick in the temperature range of 300 < T < 600 K and use a phonon transport model to explain the thermal conductivity in this film.

  1. Finite-element technique applied to heat conduction in solids with temperature dependent thermal conductivity

    NASA Technical Reports Server (NTRS)

    Aguirre-Ramirez, G.; Oden, J. T.

    1969-01-01

    Finite element method applied to heat conduction in solids with temperature dependent thermal conductivity, using nonlinear constitutive equation for heat ABCDEFGHIABCDEFGHIABCDEFGHIABCDEFGHIABCDEFGHIABCDEFGHIABCDEFGHIABCDEFGHIABCDEFGHIABCDEFGHIABCDEFGHIABCDEFGH

  2. Humidity dependence of charge transport through DNA revealed by silicon-based nanotweezers manipulation.

    PubMed

    Yamahata, Christophe; Collard, Dominique; Takekawa, Tetsuya; Kumemura, Momoko; Hashiguchi, Gen; Fujita, Hiroyuki

    2008-01-01

    The study of the electrical properties of DNA has aroused increasing interest since the last decade. So far, controversial arguments have been put forward to explain the electrical charge transport through DNA. Our experiments on DNA bundles manipulated with silicon-based actuated tweezers demonstrate undoubtedly that humidity is the main factor affecting the electrical conduction in DNA. We explain the quasi-Ohmic behavior of DNA and the exponential dependence of its conductivity with relative humidity from the adsorption of water on the DNA backbone. We propose a quantitative model that is consistent with previous studies on DNA and other materials, like porous silicon, subjected to different humidity conditions.

  3. Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field.

    PubMed

    Li, Chen-Yu; Hemmig, Elisa A; Kong, Jinglin; Yoo, Jejoong; Hernández-Ainsa, Silvia; Keyser, Ulrich F; Aksimentiev, Aleksei

    2015-02-24

    The DNA origami technique can enable functionalization of inorganic structures for single-molecule electric current recordings. Experiments have shown that several layers of DNA molecules, a DNA origami plate, placed on top of a solid-state nanopore is permeable to ions. Here, we report a comprehensive characterization of the ionic conductivity of DNA origami plates by means of all-atom molecular dynamics (MD) simulations and nanocapillary electric current recordings. Using the MD method, we characterize the ionic conductivity of several origami constructs, revealing the local distribution of ions, the distribution of the electrostatic potential and contribution of different molecular species to the current. The simulations determine the dependence of the ionic conductivity on the applied voltage, the number of DNA layers, the nucleotide content and the lattice type of the plates. We demonstrate that increasing the concentration of Mg(2+) ions makes the origami plates more compact, reducing their conductivity. The conductance of a DNA origami plate on top of a solid-state nanopore is determined by the two competing effects: bending of the DNA origami plate that reduces the current and separation of the DNA origami layers that increases the current. The latter is produced by the electro-osmotic flow and is reversible at the time scale of a hundred nanoseconds. The conductance of a DNA origami object is found to depend on its orientation, reaching maximum when the electric field aligns with the direction of the DNA helices. Our work demonstrates feasibility of programming the electrical properties of a self-assembled nanoscale object using DNA.

  4. Ionic Conductivity, Structural Deformation and Programmable Anisotropy of DNA Origami in Electric Field

    PubMed Central

    Li, Chen-Yu; Hemmig, Elisa A.; Kong, Jinglin; Yoo, Jejoong; Hernández-Ainsa, Silvia

    2015-01-01

    The DNA origami technique can enable functionalization of inorganic structures for single-molecule electric current recordings. Experiments have shown that several layers of DNA molecules—a DNA origami plate— placed on top of a solid-state nanopore is permeable to ions. Here, we report a comprehensive characterization of the ionic conductivity of DNA origami plates by means of all-atom molecular dynamics (MD) simulations and nanocapillary electric current recordings. Using the MD method, we characterize the ionic conductivity of several origami constructs, revealing the local distribution of ions, the distribution of the electrostatic potential and contribution of different molecular species to the current. The simulations determine the dependence of the ionic conductivity on the applied voltage, the number of DNA layers, the nucleotide content and the lattice type of the plates. We demonstrate that increasing the concentration of Mg2+ ions makes the origami plates more compact, reducing their conductivity. The conductance of a DNA origami plate on top of a solid-state nanopore is determined by the two competing effects: bending of the DNA origami plate that reduces the current and separation of the DNA origami layers that increases the current. The latter is produced by the electro-osmotic flow and is reversible at the time scale of a hundred nanoseconds. The conductance of a DNA origami object is found to depend on its orientation, reaching maximum when the electric field aligns with the direction of the DNA helices. Our work demonstrates feasibility of programming the electrical properties of a self-assembled nanoscale object using DNA. PMID:25623807

  5. Recombination-dependent concatemeric viral DNA replication.

    PubMed

    Lo Piano, Ambra; Martínez-Jiménez, María I; Zecchi, Lisa; Ayora, Silvia

    2011-09-01

    The initiation of viral double stranded (ds) DNA replication involves proteins that recruit and load the replisome at the replication origin (ori). Any block in replication fork progression or a programmed barrier may act as a factor for ori-independent remodelling and assembly of a new replisome at the stalled fork. Then replication initiation becomes dependent on recombination proteins, a process called recombination-dependent replication (RDR). RDR, which is recognized as being important for replication restart and stability in all living organisms, plays an essential role in the replication cycle of many dsDNA viruses. The SPP1 virus, which infects Bacillus subtilis cells, serves as a paradigm to understand the links between replication and recombination in circular dsDNA viruses. SPP1-encoded initiator and replisome assembly proteins control the onset of viral replication and direct the recruitment of host-encoded replisomal components at viral oriL. SPP1 uses replication fork reactivation to switch from ori-dependent θ-type (circle-to-circle) replication to σ-type RDR. Replication fork arrest leads to a double strand break that is processed by viral-encoded factors to generate a D-loop into which a new replisome is assembled, leading to σ-type viral replication. SPP1 RDR proteins are compared with similar proteins encoded by other viruses and their possible in vivo roles are discussed.

  6. Molecular conductance of double-stranded DNA evaluated by electrochemical capacitance spectroscopy

    NASA Astrophysics Data System (ADS)

    Ribeiro, W. C.; Gonçalves, L. M.; Liébana, S.; Pividori, M. I.; Bueno, P. R.

    2016-04-01

    Conductance was measured in two different double stranded DNA (both with 20 bases), the more conducting poly(dG)-poly(dC) (ds-DNAc) and the less conducting poly(dA)-poly(dT) (ds-DNAi), by means of Electrochemical Capacitance Spectroscopy (ECS). The use of the ECS approach, exemplified herein with DNA nanowires, is equally a suitable and time-dependent advantageous alternative for conductance measurement of molecular systems, additionally allowing better understanding of the alignment existing between molecular scale conductance and electron transfer rate.Conductance was measured in two different double stranded DNA (both with 20 bases), the more conducting poly(dG)-poly(dC) (ds-DNAc) and the less conducting poly(dA)-poly(dT) (ds-DNAi), by means of Electrochemical Capacitance Spectroscopy (ECS). The use of the ECS approach, exemplified herein with DNA nanowires, is equally a suitable and time-dependent advantageous alternative for conductance measurement of molecular systems, additionally allowing better understanding of the alignment existing between molecular scale conductance and electron transfer rate. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01076h

  7. Sequence-Dependent Persistence Lengths of DNA.

    PubMed

    Mitchell, Jonathan S; Glowacki, Jaroslaw; Grandchamp, Alexandre E; Manning, Robert S; Maddocks, John H

    2017-03-24

    A Monte Carlo code applied to the cgDNA coarse-grain rigid-base model of B-form double-stranded DNA is used to predict a sequence-averaged persistence length of lF = 53.5 nm in the sense of Flory, and of lp = 160 bp or 53.5 nm in the sense of apparent tangent-tangent correlation decay. These estimates are slightly higher than the consensus experimental values of 150 bp or 50 nm, but we believe the agreement to be good given that the cgDNA model is itself parametrized from molecular dynamics simulations of short fragments of length 10-20 bp, with no explicit fit to persistence length. Our Monte Carlo simulations further predict that there can be substantial dependence of persistence lengths on the specific sequence [Formula: see text] of a fragment. We propose, and confirm the numerical accuracy of, a simple factorization that separates the part of the apparent tangent-tangent correlation decay [Formula: see text] attributable to intrinsic shape, from a part [Formula: see text] attributable purely to stiffness, i.e., a sequence-dependent version of what has been called sequence-averaged dynamic persistence length l̅d (=58.8 nm within the cgDNA model). For ensembles of both random and λ-phage fragments, the apparent persistence length [Formula: see text] has a standard deviation of 4 nm over sequence, whereas our dynamic persistence length [Formula: see text] has a standard deviation of only 1 nm. However, there are notable dynamic persistence length outliers, including poly(A) (exceptionally straight and stiff), poly(TA) (tightly coiled and exceptionally soft), and phased A-tract sequence motifs (exceptionally bent and stiff). The results of our numerical simulations agree reasonably well with both molecular dynamics simulation and diverse experimental data including minicircle cyclization rates and stereo cryo-electron microscopy images.

  8. Sequence dependent hole evolution in DNA.

    PubMed

    Lakhno, V D

    2004-06-01

    The paper examines thedynamical behavior of a radical cation(G(+*)) generated in adouble stranded DNA for differentoligonucleotide sequences. The resonancehole tunneling through an oligonucleotidesequence is studied by the method ofnumerical integration of self-consistentquantum-mechanical equations. The holemotion is considered quantum mechanicallyand nucleotide base oscillations aretreated classically. The results obtaineddemonstrate a strong dependence of chargetransfer on the type of nucleotidesequence. The rates of the hole transferare calculated for different nucleotidesequences and compared with experimentaldata on the transfer from (G(+*))to a GGG unit.

  9. DNA strand breaks: the DNA template alterations that trigger p53-dependent DNA damage response pathways.

    PubMed Central

    Nelson, W G; Kastan, M B

    1994-01-01

    The tumor suppressor protein p53 serves as a critical regulator of a G1 cell cycle checkpoint and of apoptosis following exposure of cells to DNA-damaging agents. The mechanism by which DNA-damaging agents elevate p53 protein levels to trigger G1/S arrest or cell death remains to be elucidated. In fact, whether damage to the DNA template itself participates in transducing the signal leading to p53 induction has not yet been demonstrated. We exposed human cell lines containing wild-type p53 alleles to several different DNA-damaging agents and found that agents which rapidly induce DNA strand breaks, such as ionizing radiation, bleomycin, and DNA topoisomerase-targeted drugs, rapidly triggered p53 protein elevations. In addition, we determined that camptothecin-stimulated trapping of topoisomerase I-DNA complexes was not sufficient to elevate p53 protein levels; rather, replication-associated DNA strand breaks were required. Furthermore, treatment of cells with the antimetabolite N(phosphonoacetyl)-L-aspartate (PALA) did not cause rapid p53 protein increases but resulted in delayed increases in p53 protein levels temporally correlated with the appearance of DNA strand breaks. Finally, we concluded that DNA strand breaks were sufficient for initiating p53-dependent signal transduction after finding that introduction of nucleases into cells by electroporation stimulated rapid p53 protein elevations. While DNA strand breaks appeared to be capable of triggering p53 induction, DNA lesions other than strand breaks did not. Exposure of normal cells and excision repair-deficient xeroderma pigmentosum cells to low doses of UV light, under conditions in which thymine dimers appear but DNA replication-associated strand breaks were prevented, resulted in p53 induction attributable to DNA strand breaks associated with excision repair. Our data indicate that DNA strand breaks are sufficient and probably necessary for p53 induction in cells with wild-type p53 alleles exposed to DNA

  10. Electrically conductive gold- and copper-metallized DNA origami nanostructures.

    PubMed

    Geng, Yanli; Pearson, Anthony C; Gates, Elisabeth P; Uprety, Bibek; Davis, Robert C; Harb, John N; Woolley, Adam T

    2013-03-12

    This work demonstrates the use of a circuit-like DNA origami structure as a template to fabricate conductive gold and copper nanostructures on Si surfaces. We improved over previous results by using multiple Pd seeding steps to increase seed uniformity and density. Our process has also been characterized through atomic force microscopy, particle size distribution analysis, and scanning electron microscopy. We found that four successive Pd seeding steps yielded the best results for electroless metal plating on DNA origami. Electrical resistance measurements were done on both Au- and Cu-metallized nanostructures, with each showing ohmic behavior. Gold-plated DNA origami structures made under optimal conditions had an average resistivity of 7.0 × 10(-5) Ω·m, whereas copper-metallized structures had a resistivity as low as 3.6 × 10(-4) Ω·m. Importantly, this is the first demonstration of electrically conductive Cu nanostructures fabricated on either DNA or DNA origami templates. Although resistivities for both gold and copper samples were larger than those of the bulk metal, these metal nanostructures have the potential for use in electrically connecting small structures. In addition, these metallized objects might find use in surface-enhanced Raman scattering experiments.

  11. DNA-templated nanowires: morphology and electrical conductivity

    NASA Astrophysics Data System (ADS)

    Watson, Scott M. D.; Pike, Andrew R.; Pate, Jonathan; Houlton, Andrew; Horrocks, Benjamin R.

    2014-03-01

    DNA-templating has been used to create nanowires from metals, compound semiconductors and conductive polymers. The mechanism of growth involves nucleation at binding sites on the DNA followed by growth of spherical particles and then, under favourable conditions, a slow transformation to a smooth nanowire. The final transformation is favoured by restricting the amount of templated material per unit length of template and occurs most readily for materials of low surface tension. Electrical measurements on DNA-templated nanowires can be facilitated using three techniques: (i) standard current-voltage measurements with contact electrodes embedded in a dielectric so that there is a minimal step height at the dielectric/electrode boundary across which nanowires may be aligned by molecular combing, (ii) the use of a dried droplet technique and conductive AFM to determine contact resistance by moving the tip along the length of an individual nanowire and (iii) non-contact assessment of conductivity by scanned conductance microscopy on Si/SiO2 substrates.

  12. Frequency-dependent conductivity in bismuth-vanadate glassy semiconductors

    NASA Astrophysics Data System (ADS)

    Ghosh, Aswini

    1990-01-01

    The first measurements are reported for the frequency-dependent (ac) conductivity (real as well as imaginary parts) for various compositions of the bismuth-vanadate glassy semiconductors in the frequency range 102-105 Hz and in the temperature range 77-420 K. The behavior of the ac conductivity is broadly similar to what has been observed previously in many other types of amorphous semiconductors, namely, nearly linear frequency dependence and weak temperature dependence. The experimental results are analyzed with reference to various theoretical models based on quantum-mechanical tunneling and classical hopping over barriers. The analysis shows that the temperature dependence of the ac conductivity is consistent with the simple quantum-mechanical tunneling model at low temperatures; however, this model completely fails to predict the observed temperature dependence of the frequency exponent. The overlapping-large-polaron tunneling model can explain the temperature dependence of the frequency exponent at low temperatures. Fitting of this model to the low-temperature data yields a reasonable value of the wave-function decay constant. However, this model predicts the temperature dependence of the ac conductivity much higher than what actual data showed. The correlated barrier hopping model is consistent with the temperature dependence of both the ac conductivity and its frequency exponent. This model provides reasonable values of the maximum barrier heights but higher values of characteristic relaxation times.

  13. Electrochemical DNA Hybridization Sensors Based on Conducting Polymers

    PubMed Central

    Rahman, Md. Mahbubur; Li, Xiao-Bo; Lopa, Nasrin Siraj; Ahn, Sang Jung; Lee, Jae-Joon

    2015-01-01

    Conducting polymers (CPs) are a group of polymeric materials that have attracted considerable attention because of their unique electronic, chemical, and biochemical properties. This is reflected in their use in a wide range of potential applications, including light-emitting diodes, anti-static coating, electrochromic materials, solar cells, chemical sensors, biosensors, and drug-release systems. Electrochemical DNA sensors based on CPs can be used in numerous areas related to human health. This review summarizes the recent progress made in the development and use of CP-based electrochemical DNA hybridization sensors. We discuss the distinct properties of CPs with respect to their use in the immobilization of probe DNA on electrode surfaces, and we describe the immobilization techniques used for developing DNA hybridization sensors together with the various transduction methods employed. In the concluding part of this review, we present some of the challenges faced in the use of CP-based DNA hybridization sensors, as well as a future perspective. PMID:25664436

  14. Sequence and Structure Dependent DNA-DNA Interactions

    NASA Astrophysics Data System (ADS)

    Kopchick, Benjamin; Qiu, Xiangyun

    Molecular forces between dsDNA strands are largely dominated by electrostatics and have been extensively studied. Quantitative knowledge has been accumulated on how DNA-DNA interactions are modulated by varied biological constituents such as ions, cationic ligands, and proteins. Despite its central role in biology, the sequence of DNA has not received substantial attention and ``random'' DNA sequences are typically used in biophysical studies. However, ~50% of human genome is composed of non-random-sequence DNAs, particularly repetitive sequences. Furthermore, covalent modifications of DNA such as methylation play key roles in gene functions. Such DNAs with specific sequences or modifications often take on structures other than the canonical B-form. Here we present series of quantitative measurements of the DNA-DNA forces with the osmotic stress method on different DNA sequences, from short repeats to the most frequent sequences in genome, and to modifications such as bromination and methylation. We observe peculiar behaviors that appear to be strongly correlated with the incurred structural changes. We speculate the causalities in terms of the differences in hydration shell and DNA surface structures.

  15. Frequency dependence of ionic conductivity of electrolyte solutions

    NASA Astrophysics Data System (ADS)

    Chandra, Amalendu; Bagchi, Biman

    2000-01-01

    A theory for the frequency dependence of ionic conductivity of an electrolyte solution is presented. In this theory contributions to the conductivity from both the ion atmosphere relaxation and the electrophoretic effects are included in a self-consistent fashion. Mode coupling theory, combined with time-dependent density functional theory of ion atmosphere fluctuations, leads to expressions for these two contributions at finite frequencies. These expressions need to be solved self-consistently for the frequency dependence of the electrolyte friction and the ion conductivity at varying ion concentrations. In the limit of low concentration, the present theory reduces exactly to the well-known Debye-Falkenhagen (DF) expression of the frequency-dependent electrolyte friction when the non-Markovian effects in the ion atmosphere relaxation are ignored and in addition the ions are considered to be pointlike. The present theory also reproduces the expressions of the frequency-dependent conductivity derived by Chandra, Wei, and Patey when appropriate limiting situations are considered. We have carried out detailed numerical solutions of the self-consistent equations for concentrated solutions of a 1:1 electrolyte by using the expressions of pair correlation functions given by Attard. Numerical results reveal that the frequency dependence of the electrolyte friction at finite concentration can be quite different from that given by the DF expression. With the increase of ion concentration, the dispersion of the friction is found to occur at a higher frequency because of faster relaxation of the ion atmosphere. At low frequency, the real part of the conductivity shows a small increase with frequency which can be attributed to the well-known Debye-Falkenhagen effect. At high frequency, the conductivity decreases as expected. The extensions of the present theory to treat frequency-dependent diffusivities of charged colloid suspensions and conductivity of a dilute

  16. Using DNA looping to measure sequence dependent DNA elasticity

    NASA Astrophysics Data System (ADS)

    Kandinov, Alan; Raghunathan, Krishnan; Meiners, Jens-Christian

    2012-10-01

    We are using tethered particle motion (TPM) microscopy to observe protein-mediated DNA looping in the lactose repressor system in DNA constructs with varying AT / CG content. We use these data to determine the persistence length of the DNA as a function of its sequence content and compare the data to direct micromechanical measurements with constant-force axial optical tweezers. The data from the TPM experiments show a much smaller sequence effect on the persistence length than the optical tweezers experiments.

  17. Frequency-dependent effective hydraulic conductivity of strongly heterogeneous media.

    PubMed

    Caspari, E; Gurevich, B; Müller, T M

    2013-10-01

    The determination of the transport properties of heterogeneous porous rocks, such as an effective hydraulic conductivity, arises in a range of geoscience problems, from groundwater flow analysis to hydrocarbon reservoir modeling. In the presence of formation-scale heterogeneities, nonstationary flows, induced by pumping tests or propagating elastic waves, entail localized pressure diffusion processes with a characteristic frequency depending on the pressure diffusivity and size of the heterogeneity. Then, on a macroscale, a homogeneous equivalent medium exists, which has a frequency-dependent effective conductivity. The frequency dependence of the conductivity can be analyzed with Biot's equations of poroelasticity. In the quasistatic frequency regime of this framework, the slow compressional wave is a proxy for pressure diffusion processes. This slow compressional wave is associated with the out-of-phase motion of the fluid and solid phase, thereby creating a relative fluid-solid displacement vector field. Decoupling of the poroelasticity equations gives a diffusion equation for the fluid-solid displacement field valid in a poroelastic medium with spatial fluctuations in hydraulic conductivity. Then, an effective conductivity is found by a Green's function approach followed by a strong-contrast perturbation theory suggested earlier in the context of random dielectrics. This theory leads to closed-form expressions for the frequency-dependent effective conductivity as a function of the one- and two-point probability functions of the conductivity fluctuations. In one dimension, these expressions are consistent with exact solutions in both low- and high-frequency limits for arbitrary conductivity contrast. In 3D, the low-frequency limit depends on the details of the microstructure. However, the derived approximation for the effective conductivity is consistent with the Hashin-Shtrikman bounds.

  18. Magnetic and conductive magnetite nanowires by DNA-templating.

    PubMed

    Mohamed, Hasan Daw A; Watson, Scott M D; Horrocks, Benjamin R; Houlton, Andrew

    2012-09-28

    The synthesis of nanowires made of magnetite (Fe(3)O(4)) phase iron oxide was achieved using DNA as a template to direct formation of the metal oxide and confine its growth in two dimensions. This simple solution-based approach involves initial association of Fe(2+) and Fe(3+) to the DNA "template" molecules, and subsequent co-precipitation of the Fe(3)O(4) material, upon increasing the solution pH, to give the final metal oxide nanowires. Analysis of the DNA-templated material, using a combination of FTIR, XRD, XPS, and Raman spectroscopy, confirmed the iron oxide formed to be the Fe(3)O(4) crystal phase. Investigation of the structural character of the nanowires, carried out by AFM, revealed the metal oxide to form regular coatings of nanometre-scale thickness around the DNA templates. Statistical analysis showed the size distribution of the nanowires to follow a trimodal model, with the modal diameter values identified as 5-6 nm, 14-15 nm, and 23-24 nm. Additional scanning probe microscopy techniques (SCM, MFM) were also used to verify that the nanowire structures are electrically conducting and exhibit magnetic behaviour. Such properties, coupled with the small dimensions of these materials, make them potentially good candidates for application in a host of future nanoscale device technologies.

  19. DNA nanosensor surface grafting and salt dependence

    NASA Astrophysics Data System (ADS)

    Carvalho, B. G.; Fagundes, J.; Martin, A. A.; Raniero, L.; Favero, P. P.

    2013-02-01

    In this paper we investigated the Paracoccidoides brasiliensis fungus nanosensor by simulations of simple strand DNA grafting on gold nanoparticle. In order to improve the knowledge of nanoparticle environment, the addiction of salt solution was studied at the models proposed by us. Nanoparticle and DNA are represented by economic models validated by us in this paper. In addition, the DNA grafting and salt influences are evaluated by adsorption and bond energies calculations. This theoretical evaluation gives support to experimental diagnostics techniques of diseases.

  20. Temperature dependence of thermal conductivity of biological tissues.

    PubMed

    Bhattacharya, A; Mahajan, R L

    2003-08-01

    In this paper, we present our experimental results on the determination of the thermal conductivity of biological tissues using a transient technique based on the principles of the cylindrical hot-wire method. A novel, 1.45 mm diameter, 50 mm long hot-wire probe was deployed. Initial measurements were made on sponge, gelatin and Styrofoam insulation to test the accuracy of the probe. Subsequent experiments conducted on sheep collagen in the range of 25 degrees C < T < 55 degrees C showed the thermal conductivity to be a linear function of temperature. Further, these changes in the thermal conductivity were found to be reversible. However, when the tissue was heated beyond 55 degrees C, irreversible changes in thermal conductivity were observed. Similar experiments were also conducted for determining the thermal conductivity of cow liver. In this case, the irreversible effects were found to set in much later at around 90 degrees C. Below this temperature, in the range of 25 degrees C < T < 90 degrees C, the thermal conductivity, as for sheep collagen, varied linearly with temperature. In the second part of our study, in vivo measurements were taken on the different organs of a living pig. Comparison with reported values for dead tissues shows the thermal conductivities of living organs to be higher, indicating thereby the dominant role played by blood perfusion in enhancing the net heat transfer in living tissues. The degree of enhancement is different in different organs and shows a direct dependence on the blood flow rate.

  1. Sequence dependent proton conduction in self-assembled peptide nanostructures.

    PubMed

    Lerner Yardeni, Jenny; Amit, Moran; Ashkenasy, Gonen; Ashkenasy, Nurit

    2016-01-28

    The advancement of diverse electrochemistry technologies depends on the development of novel proton conducting polymers. Inspired by the efficacy of proton transport through proteins, we show in this work that self-assembling peptide nanostructures may be a promising alternative for such organic proton conducting materials. We demonstrate that aromatic amino acids, which participate in charge transport in nature, unprecedentedly promote proton conduction under both high and low relative humidity conditions for d,l α-cyclic peptide nanotubes. For dehydrated networks long-range order of the assemblies, induced by the aromatic side chains, is shown to be a dominating factor for promoting conductivity. However, for hydrated networks this order of effect is less significant and conductivity can be improved by the introduction of proton donating carboxylic acid peptide side chains in addition to the aromatic side chains despite the lower order of the assemblies. Based on these observations, a novel cyclic peptide that incorporates non-natural naphthyl side chains was designed. Self-assembled nanotubes of this peptide show greatly improved dehydrated conductivity, while maintaining high conductivity under hydrated conditions. We envision that the demonstrated modularity and versatility of these bio inspired nanostructures will make them extremely attractive building blocks for the fabrication of devices for energy conversion and storage applications, as well as other applications that involve proton transport, whether dry or wet conductivity is desired.

  2. Helix-Dependent Spin Filtering through the DNA Duplex.

    PubMed

    Zwang, Theodore J; Hürlimann, Sylvia; Hill, Michael G; Barton, Jacqueline K

    2016-12-07

    Recent work suggests that electrons can travel through DNA and other chiral molecules in a spin-selective manner, but little is known about the origin of this spin selectivity. Here we describe experiments on magnetized DNA-modified electrodes to explore spin-selective electron transport through hydrated duplex DNA. Our results show that the two spins migrate through duplex DNA with a different yield and that spin selectivity requires charge transport through the DNA duplex. Significantly, shifting the same duplex DNA between right-handed B- and left-handed Z-forms leads to a diode-like switch in spin selectivity; which spin moves more efficiently through the duplex depends upon the DNA helicity. With DNA, the supramolecular organization of chiral moieties, rather than the chirality of the individual monomers, determines the selectivity in spin, and thus a conformational change can switch the spin selectivity.

  3. Universal size-dependent conductance fluctuations in disordered organic semiconductors.

    PubMed

    Massé, A; Coehoorn, R; Bobbert, P A

    2014-09-12

    Numerically exact results of hopping charge transport in disordered organic semiconductors show for uncorrelated and dipole-correlated Gaussian energy disorder a universal, power-law, and non-power-law dependence, respectively, of the relative conductance fluctuations on the size of the considered region. Data collapse occurs upon scaling with a characteristic length having a power-law temperature dependence. Below this length, which can be as high as 100 nm for correlated disorder in a realistic case, fluctuations dominate and a continuum description of charge transport breaks down.

  4. DNA-DEPENDENT CONFORMATIONAL CHANGES IN THE KU HETERODIMER

    PubMed Central

    Lehman, Jason A.; Hoelz, Derek J.; Turchi, John J.

    2008-01-01

    Ionizing radiation induces DNA double-strand breaks which are repaired by the non-homologous end joining (NHEJ) pathway. NHEJ is initiated upon Ku binding to the DNA ends and facilitating an interaction with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This heterotrimeric DNA-PK complex is then active as a serine/threonine protein kinase. The molecular mechanisms involved in DNA-PK activation are unknown. Considering the crucial role of Ku in this process, we therefore determined the influence of DNA binding on the structure of the Ku heterodimer. Chemical modification with NHS-biotin and mass spectrometry was used to identify sites of modification. Biotinylation of free Ku revealed several reactive lysines on Ku70 and Ku80 which were reduced or eliminated upon DNA binding. Interestingly, in the predicted C-terminus SAP domain of Ku70, biotinylation patterns were observed which suggest a structural change in this region of the protein induced by DNA binding. Limited proteolytic digests of free and DNA-bound Ku revealed a series of unique peptides, again, indicative of a change in the accessibility of the Ku70 and Ku80 C-terminal domains. A 10 kDa peptide was also identified which was preferentially generated under non-DNA bound conditions and mapped to the Ku70 C-terminus. These results indicate a DNA-dependent movement or structural change in the C-terminal domains of Ku70 and Ku80 that may contribute to DNA-PKcs binding and activation. These results represent the first demonstration of DNA-induced changes in Ku structure and provide a framework for analysis of DNA-PKcs and the mechanism of DNA-PK activation. PMID:18355052

  5. Doping level dependent space charge limited conduction in polyaniline nanoparticles

    NASA Astrophysics Data System (ADS)

    Nath, Chandrani; Kumar, A.

    2012-11-01

    Spherical shaped polyaniline nanoparticles of average diameter ˜4 nm were doped with different concentration of hydrochloric acid. The x-ray diffraction studies reveal an increase in crystallinity with doping. Temperature dependent current-voltage measurements on the different nanoparticle samples indicate the prevalence of bulk-controlled space charge limited conduction (SCLC) mechanism in the high voltage (>1 V) region while the ohmic conduction dominates at the lower voltage (<1 V) region. With increasing doping the nature of SCLC changes from trap-free SCLC to Child-Langmuir type SCLC via exponential trap-limited SCLC. Moreover, the field and temperature dependence of mobility exhibits the universal Poole-Frenkel behavior. The energetic disorder parameter, spatial disorder parameter, inter-site distance, and localization length have been extracted employing the uncorrelated and the correlated Gaussian disorder model.

  6. Sequence dependent proton conduction in self-assembled peptide nanostructures

    NASA Astrophysics Data System (ADS)

    Lerner Yardeni, Jenny; Amit, Moran; Ashkenasy, Gonen; Ashkenasy, Nurit

    2016-01-01

    The advancement of diverse electrochemistry technologies depends on the development of novel proton conducting polymers. Inspired by the efficacy of proton transport through proteins, we show in this work that self-assembling peptide nanostructures may be a promising alternative for such organic proton conducting materials. We demonstrate that aromatic amino acids, which participate in charge transport in nature, unprecedentedly promote proton conduction under both high and low relative humidity conditions for d,l α-cyclic peptide nanotubes. For dehydrated networks long-range order of the assemblies, induced by the aromatic side chains, is shown to be a dominating factor for promoting conductivity. However, for hydrated networks this order of effect is less significant and conductivity can be improved by the introduction of proton donating carboxylic acid peptide side chains in addition to the aromatic side chains despite the lower order of the assemblies. Based on these observations, a novel cyclic peptide that incorporates non-natural naphthyl side chains was designed. Self-assembled nanotubes of this peptide show greatly improved dehydrated conductivity, while maintaining high conductivity under hydrated conditions. We envision that the demonstrated modularity and versatility of these bio inspired nanostructures will make them extremely attractive building blocks for the fabrication of devices for energy conversion and storage applications, as well as other applications that involve proton transport, whether dry or wet conductivity is desired.The advancement of diverse electrochemistry technologies depends on the development of novel proton conducting polymers. Inspired by the efficacy of proton transport through proteins, we show in this work that self-assembling peptide nanostructures may be a promising alternative for such organic proton conducting materials. We demonstrate that aromatic amino acids, which participate in charge transport in nature

  7. Diversification of DnaA dependency for DNA replication in cyanobacterial evolution.

    PubMed

    Ohbayashi, Ryudo; Watanabe, Satoru; Ehira, Shigeki; Kanesaki, Yu; Chibazakura, Taku; Yoshikawa, Hirofumi

    2016-05-01

    Regulating DNA replication is essential for all living cells. The DNA replication initiation factor DnaA is highly conserved in prokaryotes and is required for accurate initiation of chromosomal replication at oriC. DnaA-independent free-living bacteria have not been identified. The dnaA gene is absent in plastids and some symbiotic bacteria, although it is not known when or how DnaA-independent mechanisms were acquired. Here, we show that the degree of dependency of DNA replication on DnaA varies among cyanobacterial species. Deletion of the dnaA gene in Synechococcus elongatus PCC 7942 shifted DNA replication from oriC to a different site as a result of the integration of an episomal plasmid. Moreover, viability during the stationary phase was higher in dnaA disruptants than in wild-type cells. Deletion of dnaA did not affect DNA replication or cell growth in Synechocystis sp. PCC 6803 or Anabaena sp. PCC 7120, indicating that functional dependency on DnaA was already lost in some nonsymbiotic cyanobacterial lineages during diversification. Therefore, we proposed that cyanobacteria acquired DnaA-independent replication mechanisms before symbiosis and such an ancestral cyanobacterium was the sole primary endosymbiont to form a plastid precursor.

  8. Temperature dependence of DNA condensation at high ionic concentration

    NASA Astrophysics Data System (ADS)

    Mao, Wei; Gao, Qingqing; Liu, Yanhui; Fan, Yangtao; Hu, Lin; Xu, Houqiang

    2016-08-01

    A series of experiments pointed out that compact states of DNA condensed by multivalent cation prefer higher temperature. The condensed DNA takes elongated coil or compact globule states and the population of the compact globule states increases with an increase in temperature. At the same time, a recent experimental work carried out in buffer solution without multivalent cation points out that DNA persistence length strongly depends on the temperature. DNA persistence length is a key parameter for quantitative interpretation of the conformational properties of DNA and related to the bending rigidity of DNA. It is necessary to revolve the effects of temperature dependence of persistence length on DNA condensation, and a model including the temperature dependence of persistence length and strong correlation of multivalent cation on DNA is provided. The autocorrelation function of the tangent vectors is found as an effective way to detect the temperature dependence of toroid conformations. With an increase in temperature, the first periodic oscillation in the autocorrelation function shifts left and the number of segments containing the first periodic oscillation decreases gradually. According to the experiments mentioned above, the long-axis length is defined to estimate the temperature dependence of condensation process further. At the temperatures defined in experiments mentioned above, the relation between long-axis length and temperature matches the experimental results.

  9. Conformation dependent electronic transport in a DNA double-helix

    SciTech Connect

    Kundu, Sourav Karmakar, S. N.

    2015-10-15

    We present a tight-binding study of conformation dependent electronic transport properties of DNA double-helix including its helical symmetry. We have studied the changes in the localization properties of DNA as we alter the number of stacked bases within every pitch of the double-helix keeping fixed the total number of nitrogen bases within the DNA molecule. We take three DNA sequences, two of them are periodic and one is random and observe that in all the cases localization length increases as we increase the radius of DNA double-helix i.e., number of nucleobases within a pitch. We have also investigated the effect of backbone energetic on the I-V response of the system and found that in presence of helical symmetry, depending on the interplay of conformal variation and disorder, DNA can be found in either metallic, semiconducting and insulating phases, as observed experimentally.

  10. CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Characteristics of alternating current hopping conductivity in DNA sequences

    NASA Astrophysics Data System (ADS)

    Ma, Song-Shan; Xu, Hui; Wang, Huan-You; Guo, Rui

    2009-08-01

    This paper presents a model to describe alternating current (AC) conductivity of DNA sequences, in which DNA is considered as a one-dimensional (1D) disordered system, and electrons transport via hopping between localized states. It finds that AC conductivity in DNA sequences increases as the frequency of the external electric field rises, and it takes the form of øac(ω) ~ ω2 ln2(1/ω). Also AC conductivity of DNA sequences increases with the increase of temperature, this phenomenon presents characteristics of weak temperature-dependence. Meanwhile, the AC conductivity in an off-diagonally correlated case is much larger than that in the uncorrelated case of the Anderson limit in low temperatures, which indicates that the off-diagonal correlations in DNA sequences have a great effect on the AC conductivity, while at high temperature the off-diagonal correlations no longer play a vital role in electric transport. In addition, the proportion of nucleotide pairs p also plays an important role in AC electron transport of DNA sequences. For p < 0.5, the conductivity of DNA sequence decreases with the increase of p, while for p >= 0.5, the conductivity increases with the increase of p.

  11. Universality and the thermal dependence of the conductance of nanodevices

    NASA Astrophysics Data System (ADS)

    Oliveira, Luiz N.; Seridonio, Antonio C.; Yoshida, Makoto

    2008-03-01

    The conductance of a quantum wire side-coupled to a quantum dot will be discussed. In this device, plots of the conductance G vs. the gate voltage Vg applied to the dot display Fano antiresonances due to the interference between the current traversing the wire and the flux of electrons that hop to the dot to bypass the adjacent section of the wire; at fixed Vg's, the interference accounts for a variety of thermal dependences G(T). Analytical renormalization-group arguments will be presented that map G(T) to the universal curve g(T/TK) for the conductance of the spin-degenerate Anderson impurity Hamiltonian, with temperatures normalized by the Kondo temperature TK. This linear, universal mapping will be shown to (i) generate curves in excellent agreement with the measurements of Sato et al. [Phys. Rev. Lett. 95, 066801 (2005)] and justify those authors' phenomenological description of their data; (ii) fit novel numerical renormalization-group data for the conductance of the side-coupled device; and (iii) link G(T) to the conductance of the single-electron transistor.

  12. Sea salt dependent electrical conduction in polar ice

    SciTech Connect

    Moore, J.; Paren, J. ); Oerter, H. )

    1992-12-10

    A 45 m length of ice core from Dolleman Island, Antarctic Peninsula has been dielectrically analyzed at 5 cm resolution using the dielectric profiling (DEP) technique. The core has also been chemically analyzed for major ionic impurities. A statistical analysis of the measurements shows that the LF (low frequency) conductivity is determined both by neutral salt and acid concentrations. The statistical relationships have been compared with results from laboratory experiments on ice doped with HF (hydrogen fluoride). Salts (probably dispersed throughout the ice fabric) determine the dielectric conductivity. The salt conduction mechanism is probably due to Bjerrum L defects alone, created by the incorporation of chloride ions in the lattice. Samples of ice from beneath the Filchner-Ronne Ice Shelf were also measured and display a similar conduction mechanism below a solubility limit of about 400 [mu]M of chloride. The temperature dependence of the neutral salt, acid and pure ice contributions to the LF conductivity of natural ice between [approximately] 70[degrees]C and 0[degrees]C is discussed. These results allow a comprehensive comparison of dielectric and chemical data from natural ice.

  13. Electrical conductance of DNA molecules with varied density of itinerant pi electrons.

    PubMed

    Gao, Xu-Tuan; Fu, Xue; Mei, Liang-Mo; Xie, Shi-Jie

    2006-06-21

    The electrical transport of DNA is closely related to the density of itinerant pi electrons because of the strong electron-lattice interaction. The resistivities of two typical DNA molecules [poly(dG)-poly(dC) and lambda-DNA] with varied densities of itinerant pi electrons are calculated. It is found that the dependence of the resistivity on the density of itinerant pi electrons is symmetrical about the half-filling state of itinerant pi electrons in poly(dG)-poly(dC). At the half-filling state, the Peierls phase transition takes place and poly(dG)-poly(dC) has a large resistivity. When the density of itinerant pi electrons departs far from the half-filling state, the resistivity of poly(dG)-poly(dC) becomes small. For lambda-DNA, there is no Peierls phase transition due to the aperiodicity of its base pair arrangement. The resistivity of poly(dG)-poly(dC) decreases with increasing length of the molecular chain, but the resistivity of lambda-DNA increases with increasing length. The conducting mechanisms for poly(dG)-poly(dC) and a few lambda-DNA molecules with varied densities of itinerant pi electrons are analyzed.

  14. A context dependent role for DNA methylation in bivalves.

    PubMed

    Gavery, Mackenzie R; Roberts, Steven B

    2014-05-01

    The function of DNA methylation in species such as bivalves where the limited amount of DNA methylation is predominantly found in gene bodies remains unclear. An emerging possible explanation is that the role of gene body DNA methylation is dependent on gene function, a potential phenomenon that has arisen from selective pressure on lineage-specific life history traits. In genes contributing to phenotypes that benefit from increased plasticity, the absence of DNA methylation could contribute to stochastic transcriptional opportunities and increased transposable element activity. In genes where regulated control of activity is essential, DNA methylation may also play a role in targeted, predictable genome regulation. Here, we review the current knowledge concerning DNA methylation in bivalves and explore the putative role of DNA methylation in both an evolutionary and ecological context.

  15. Xenopus transcription factor IIIA-dependent DNA renaturation.

    PubMed

    Fiser-Littell, R M; Hanas, J S

    1988-11-15

    Kinetic and titration analyses are used to elucidate the mechanism by which Xenopus transcription factor IIIA (TFIIIA), a protein required for 5 S RNA synthesis by RNA polymerase III, promotes DNA renaturation. TFIIIA promotes 50% renaturation of complementary strands (303 bases) in 45 s. Analyses of the renaturation kinetics indicate the rate-limiting step in this TFIIIA-dependent reaction is first order. TFIIIA-dependent DNA renaturation is a stoichiometric rather than a catalytic process. The renaturation rates for specific and nonspecific DNA are very similar, indicating lack of sequence specificity in this TFIIIA-dependent process. In the nanomolar concentration range of protein and DNA, renaturation occurs at a ratio of about one TFIIIA molecule/single strand (303 bases). Elevated reaction temperatures strongly stimulate TFIIIA-dependent DNA renaturation; at 45 degrees C, renaturation of the 303-base pair fragment nears completion in about 5 s. The ability of TFIIIA to rapidly promote DNA renaturation is unique when compared with Escherichia coli recA protein, single-stranded DNA binding protein, or bacteriophage T4 gene 32 protein. This mechanism by which TFIIIA promotes DNA renaturation is compatible with features of 5 S RNA gene transcription.

  16. A time dependent anatomically detailed model of cardiac conduction

    NASA Technical Reports Server (NTRS)

    Saxberg, B. E.; Grumbach, M. P.; Cohen, R. J.

    1985-01-01

    In order to understand the determinants of transitions in cardiac electrical activity from normal patterns to dysrhythmias such as ventricular fibrillation, we are constructing an anatomically and physiologically detailed finite element simulation of myocardial electrical propagation. A healthy human heart embedded in paraffin was sectioned to provide a detailed anatomical substrate for model calculations. The simulation of propagation includes anisotropy in conduction velocity due to fiber orientation as well as gradients in conduction velocities, absolute and relative refractory periods, action potential duration and electrotonic influence of nearest neighbors. The model also includes changes in the behaviour of myocardial tissue as a function of the past local activity. With this model, we can examine the significance of fiber orientation and time dependence of local propagation parameters on dysrhythmogenesis.

  17. The calcium-dependent potassium conductance in rat sympathetic neurones.

    PubMed Central

    Belluzzi, O; Sacchi, O

    1990-01-01

    1. Adult and intact sympathetic neurones of isolated rat superior cervical ganglia were subjected to a two-electrode voltage-clamp analysis at 37 degrees C in order to investigate the Ca2(+)-dependent K+ conductance. 2. At each potential a Ca2(+)-dependent K+ current, IKCa, was determined as the difference between the current that could be attributed to the voltage-dependent K+ current, IKV, following Ca2+ channel blockade by Cd2+ and the total current generated. The final IKCa curves were obtained after correcting the experimental tracings for the underlying ICa current component. 3. IKCa became detectable during commands to -30 mV. About 3.6 x 10(5) Ca2+ ions are required to enter the cell before IKCa is initiated. The current was modelled on the basis of a 0.4-0.6 ms delay followed by an exponential activation of a fast component, IKCaf, simultaneously with a much slower exponential activation, IKCas. Experiments indicate a sigmoidal activation curve for the fast conductance, gKCf, with half-maximal activation at -13.0 mV and a slope factor of 4.7 mV (for 5 mM-Ca2+ in the bath). The associated time constant, tau kcf, ranged from 0.8 to 2.0 ms. The slow conductance exhibited a similar steady-state activation curve but an activation time constant in the 48-280 ms range. The maximum mean gKC was 0.32 microS per neurone for either the fast or slow component. 4. Excess K+ ions accumulate in the perineuronal space during K+ current flow giving rise to rapidly occurring, large K+ reversal potential (EK) modifications (up to -45 mV for the largest currents). The kinetics of K+ extracellular load can be described satisfactorily by a simple exponential function (tau = 0.9-2.8 ms). The characteristics of K+ wash-out appear similar to those of accumulation. 5. The immediate effect of such an extracellular K+ build-up is to make the apparent IKCa activation kinetics faster and to reduce (up to 50%) the true value of the K+ conductance. We simulated the predictions of a K

  18. Anti-DNA antibody mediated catalysis is isotype dependent.

    PubMed

    Xia, Yumin; Eryilmaz, Ertan; Zhang, Qiuting; Cowburn, David; Putterman, Chaim

    2016-01-01

    Anti-DNA antibodies are the serological hallmark of systemic lupus erythematosus, and participate in the pathogenesis of lupus nephritis by cross-reacting with multiple renal antigens. Previously, using a panel of murine anti-DNA IgGs that share identical variable regions but that differ in the constant regions, we demonstrated that the cross-reaction and renal pathogenicity of anti-DNA antibodies are isotype dependent. In this study, we investigated the catalytic potential of this anti-DNA antibody panel, and determined its isotype dependency. The three isotype switch variants (IgG1, IgG2a, IgG2b) and the parent IgG3 PL9-11 anti-DNA antibodies were compared in their catalysis of 500 base pair linear double stranded DNA and a 12-mer peptide (ALWPPNLHAWVP), by gel analysis, MALDI-TOF mass spectrometry, and nuclear magnetic resonance spectroscopy. The binding affinity of anti-DNA antibodies to double stranded DNA and peptide antigens were assessed by ELISA and surface plasmon resonance. We found that the PL9-11 antibody isotypes vary significantly in their potential to catalyze the cleavage of both linear and double stranded DNA and the proteolysis of peptides. The degree of the cleavage and proteolysis increases with the incubation temperature and time. While different PL9-11 isotypes have the same initial attack sites within the ALWPPNLHAWVP peptide, there was no correlation between binding affinity to the peptide and proteolysis rates. In conclusion, the catalytic properties of anti-DNA antibodies are isotype dependent. This finding provides further evidence that antibodies that share the same variable region, but which have different constant regions, are functionally distinct. The catalytic effects modulated by antibody constant regions need to be considered in the design of therapeutic antibodies (abzymes) and peptides designed to block pathogenic autoantibodies.

  19. Universal frequency-dependent conduction of electron glasses

    NASA Astrophysics Data System (ADS)

    Amir, Ariel

    2014-03-01

    Characterizing the frequency-dependent response of amorphous systems and glasses can provide important insights into their physics. Here, we study the response of an electronic glass, where Coulomb interactions are important and have previously been shown to significantly modify the conductance and lead to memory effects and aging. We propose a model which allows us to take the interactions into account in a self-consistent way, and explore the transport properties at all frequencies. Within the model, the response maps exactly to a (linear) network of resistors, self-capacitances and mutual capacitances. The response of this equivalent electric circuit is found numerically, and is shown to obey the universal scaling which is experimentally observed for a large class of amorphous solids.

  20. Empowering Malaysian dentists to tobacco dependence treatment conduct.

    PubMed

    Nordin, Amer Siddiq Amer; Kadir, Rahimah Abdul; Yahya, Nurul Asyikin; Zakaria, Hazli; Rashid, Rusdi Abdul; Habil, Mohamed Hussain

    2014-08-01

    As a signatory to the World Health Organisation 2003 Framework Convention on Tobacco Control, Malaysia has policies in place and funded 300 public Quit clinics. Unfortunately, government dentists are not included to run tobacco dependence treatment. A cross-sectional exploratory survey was carried out to seek Malaysian dentists' opinion on their knowledge, perception and willingness to conduct tobacco dependence treatment. Participation was voluntary from those who attended a specially designed one-day, four-module workshop on tobacco cessation intervention. Data were collected using the Audience-Response-System equipment which tracked immediate responses covering four domains namely: smoking as a public health problem, smoking as an addiction, the role of dentists in the programme and confidence in conducting smoking cessation in the clinic. Sample comprised more female dentists (73.5%), mean age 33.6 (SD 8.99) years and with more than 3 years working experience. Findings indicated that the majority agreed Malaysia has a rising problem in the prevalence of smoking (71.6%) and predicted that it will affect mostly the young (81.9%). Only half of the dentists surveyed (58.9%) routinely recorded their patients' smoking habits. The majority (71.6%) believed that dentists are effective in helping their patient to stop smoking and 76.3% agreed that dentists should discuss the smoking habit with their patients; however, 60% agreed that doing so is too time consuming. In addition, only 24.7% knew of more ways to treat a smoking habit. The majority felt comfortable giving advice to patients about changing their habits (76.5%) or discussing treatment options (60.5%): 75% would opt for a combined programme of counselling and use of medication if they have to do, 15% would choose to go on counselling only, while 8% did not want to treat. In conclusion, the findings suggest that dentists have a strong potential to contribute significantly to providing smoking cessation

  1. p53 inhibits DNA replication in vitro in a DNA-binding-dependent manner

    SciTech Connect

    Miller, S.D.; Farmer, G.; Prives, C.

    1995-12-01

    This report discusses new findings that the tumor supressor gene product p53 may play a role as a DNA-binding-dependent regulator of DNA replication. The results were obtained using polyomavirus in replication assays. Details regarding effects on cell growth arrest and transcriptional activation are discussed. 61 refs., 7 figs.

  2. Water percolation governs polymorphic transitions and conductivity of DNA.

    PubMed

    Brovchenko, Ivan; Krukau, Aliaksei; Oleinikova, Alla; Mazur, Alexey K

    2006-09-29

    We report on the first computer simulation studies of the percolation transition of water at the surface of the DNA double helix. With increased hydration, the ensemble of small clusters merges into a spanning water network via a quasi-two-dimensional percolation transition. This transition occurs strikingly close to the hydration level where the B form of DNA becomes stable in experiment. Formation of spanning water networks results in sigmoidlike acceleration of long-range ion transport in good agreement with experiment.

  3. DNA-protein recognition and sequence-dependent variations of DNA conformational properties

    NASA Astrophysics Data System (ADS)

    Vologodskii, Alexander

    2015-03-01

    Parameters of B-DNA, the major form of the double helix, depend on its sequence. This dependence can contribute to the recognition of specific DNA sequences by proteins. Here we try to analyze this contribution quantitatively. In the first approach to this goal we used experimental data on the sequence dependence of DNA bending rigidity and its helical repeat. The solution data on these parameters of B-DNA were derived from the experiments on cyclization of short DNA fragments with specially designed sequences. The data allowed calculating the sequence variations of DNA bending energy, as well as the variations of the energy of torsional deformation of the double helix associated with a protein binding. The results show that DNA conformational parameters can have very limited influence on the sequence specificity of protein binding. In the second approach we analyzed the experimental data on the binding affinity of the nucleosome core with DNA fragments of different sequences. The conclusions derived in these two approaches are in a good agreement with one another.

  4. Cation charge dependence of the forces driving DNA assembly.

    PubMed

    DeRouchey, Jason; Parsegian, V Adrian; Rau, Donald C

    2010-10-20

    Understanding the strength and specificity of interactions among biologically important macromolecules that control cellular functions requires quantitative knowledge of intermolecular forces. Controlled DNA condensation and assembly are particularly critical for biology, with separate repulsive and attractive intermolecular forces determining the extent of DNA compaction. How these forces depend on the charge of the condensing ion has not been determined, but such knowledge is fundamental for understanding the basis of DNA-DNA interactions. Here, we measure DNA force-distance curves for a homologous set of arginine peptides. All forces are well fit as the sum of two exponentials with 2.4- and 4.8-Å decay lengths. The shorter-decay-length force is always repulsive, with an amplitude that varies slightly with length or charge. The longer-decay-length force varies strongly with cation charge, changing from repulsion with Arg¹ to attraction with Arg². Force curves for a series of homologous polyamines and the heterogeneous protein protamine are quite similar, demonstrating the universality of these forces for DNA assembly. Repulsive amplitudes of the shorter-decay-length force are species-dependent but nearly independent of charge within each species. A striking observation was that the attractive force amplitudes for all samples collapse to a single curve, varying linearly with the inverse of the cation charge.

  5. Conductance hysteresis in the voltage-dependent anion channel.

    PubMed

    Rappaport, Shay M; Teijido, Oscar; Hoogerheide, David P; Rostovtseva, Tatiana K; Berezhkovskii, Alexander M; Bezrukov, Sergey M

    2015-09-01

    Hysteresis in the conductance of voltage-sensitive ion channels is observed when the transmembrane voltage is periodically varied with time. Although this phenomenon has been used in studies of gating of the voltage-dependent anion channel, VDAC, from the outer mitochondrial membrane for nearly four decades, full hysteresis curves have never been reported, because the focus was solely on the channel opening branches of the hysteresis loops. We studied the hysteretic response of a multichannel VDAC system to a triangular voltage ramp the frequency of which was varied over three orders of magnitude, from 0.5 mHz to 0.2 Hz. We found that in this wide frequency range the area encircled by the hysteresis curves changes by less than a factor of three, suggesting broad distribution of the characteristic times and strongly non-equilibrium behavior. At the same time, quasi-equilibrium two-state behavior is observed for hysteresis branches corresponding to VDAC opening. This enables calculation of the usual equilibrium gating parameters, gating charge and voltage of equipartitioning, which were found to be almost insensitive to the ramp frequency. To rationalize this peculiarity, we hypothesize that during voltage-induced closure and opening the system explores different regions of the complex free energy landscape, and, in the opening branch, follows quasi-equilibrium paths.

  6. Substrate dependent stability of conducting polymer coatings on medical electrodes.

    PubMed

    Green, Rylie A; Hassarati, Rachelle T; Bouchinet, Lucie; Lee, Chaekyung S; Cheong, Gin L M; Yu, Jin F; Dodds, Christopher W; Suaning, Gregg J; Poole-Warren, Laura A; Lovell, Nigel H

    2012-09-01

    Conducting polymer (CP) coatings on medical electrodes have the potential to provide superior performance when compared to conventional metallic electrodes, but their stability is strongly dependant on the substrate properties. The aim of this study was to examine the effect of laser roughening of underlying platinum (Pt) electrode surfaces on the mechanical, electrical and biological performance of CP coatings. In addition, the impact of dopant type on electrical performance and stability was assessed. The CP poly(ethylene dioxythiophene) (PEDOT) was coated on Pt microelectrode arrays, with three conventional dopant ions. The in vitro electrical characteristics were assessed by cyclic voltammetry and biphasic stimulation. Results showed that laser roughening of the underlying substrate did not affect the charge injection limit of the coated material, but significantly improved the passive stability and chronic stimulation lifetime without failure of the coating. Accelerated material ageing and long-term biphasic stimulus studies determined that some PEDOT variants experienced delamination within as little as 10 days when the underlying Pt was smooth, but laser roughening to produce a surface index of 2.5 improved stability, such that more than 1.3 billion stimulation cycles could be applied without evidence of failure. PEDOT doped with paratoluene sulfonate (PEDOT/pTS) was found to be the most stable CP on roughened Pt, and presented a surface topography which encouraged neural cell attachment.

  7. Aven-dependent activation of ATM following DNA damage

    PubMed Central

    Guo, Jessie Yanxiang; Yamada, Ayumi; Kajino, Taisuke; Wu, Judy Qiju; Tang, Wanli; Freel, Christopher D.; Feng, Junjie; Chau, B. Nelson; Wang, Michael Zhuo; Margolis, Seth; Yoo, Hae Yong; Wang, Xiao-Fan; Dunphy, William G.; Irusta, Pablo M.; Hardwick, J. Marie; Kornbluth, Sally

    2009-01-01

    Summary Background In response to DNA damage, cells either undergo cell cycle arrest or apoptosis, depending on the extent of damage and the cell’s capacity for DNA repair. Cell cycle arrest induced by double-stranded DNA breaks depends on activation of the ataxia-telangiectasia (ATM) protein kinase, which phosphorylates cell cycle effectors such as Chk2 and p53 to inhibit cell cycle progression. ATM is recruited to double stranded DNA breaks by a complex of sensor proteins including Mre11/Rad50/Nbs1, resulting in autophosphorylation, monomerization, and activation of ATM kinase. Results In characterizing Aven protein, a previously reported apoptotic inhibitor, we have found that Aven can function as an ATM activator to inhibit G2/M progression. Aven bound to ATM and Aven overexpression in cycling Xenopus egg extracts prevented mitotic entry and induced phosphorylation of ATM and its substrates. Immunodepletion of endogenous Aven allowed mitotic entry even in the presence of damaged DNA, and RNAi-mediated knock-down of Aven in human cells prevented autophosphorylation of ATM at an activating site (S1981) in response to DNA damage. Interestingly, Aven is also a substrate of the ATM kinase. Mutation of ATM-mediated phosphorylation sites on Aven reduced its ability to activate ATM, suggesting that Aven activation of ATM following DNA damage is enhanced by ATM-mediated Aven phosphorylation. Conclusions These results identify Aven as a new ATM activator and describe a positive feedback loop operating between Aven and ATM. In aggregate, these findings place Aven, a known apoptotic inhibitor, as a critical transducer of the DNA damage signal. PMID:18571408

  8. Effects of DNA nucleotide adsorption on the conductance of graphene nanoribbons from first principles

    NASA Astrophysics Data System (ADS)

    Lee, Eun-Cheol

    2012-04-01

    The effects of DNA nucleotide adsorption on the conductance of graphene nanoribbons are investigated through first-principles calculations. We find that, for the adsorption of a single nucleotide, the negatively charged phosphate produces conductance dips associated with quasibound states, reducing the hole conductance. The conductance of conduction electrons is also reduced by electron scattering at the Coulomb potential barriers produced by the phosphate, with no noticeable conductance dips near the Fermi level. Our results indicate that graphene nanoribbon is promising for the application to DNA sensor utilizing quantum carrier conductance.

  9. Radiation Fluence dependent variation in Electrical conductivity of Cu nanowires

    SciTech Connect

    Gehlawat, Devender; Chauhan, R. P.; Sonkawade, R. G.

    2011-07-15

    Electrical conductivity of Cu nanowires varies with diameter of nanowires. However, keeping the diameter of nanowires constant, a variation in their electrical conductivity is observed after they irradiated with gamma rays and neutrons. On the basis of I-V characteristics drawn at room temperature, decrease in the conductivity of Cu nanowires is observed, as compared to that of pristine nanowires.

  10. Ku stimulation of DNA ligase IV-dependent ligation requires inward movement along the DNA molecule.

    PubMed

    Kysela, Boris; Doherty, Aidan J; Chovanec, Miroslav; Stiff, Thomas; Ameer-Beg, Simon M; Vojnovic, Borivoj; Girard, Pierre-Marie; Jeggo, Penny A

    2003-06-20

    The DNA ligase IV.XRCC4 complex (LX) functions in DNA non-homologous-end joining, the main pathway for double-strand break repair in mammalian cells. We show that, in contrast to ligation by T4 ligase, the efficiency of LX ligation of double-stranded (ds) ends is critically dependent upon the length of the DNA substrate. The effect is specific for ds ligation, and LX/DNA binding is not influenced by the substrate length. Ku stimulates LX ligation at concentrations resulting in 1-2 Ku molecules bound per substrate, whereas multiply Ku-bound DNA molecules inhibit ds ligation. The combined footprint of DNA with Ku and LX bound is the sum of each individual footprint suggesting that the two complexes are located in tandem at the DNA end. Inhibition of Ku translocation by the presence of cis-platinum adducts on the DNA substrate severely inhibits ligation by LX. Fluorescence resonance energy transfer analysis using fluorophore-labeled Ku and DNA molecules showed that, as expected, Ku makes close contact with the DNA end and that addition of LX can disrupt this close contact. Finally, we show that recruitment of LX by Ku is impaired in an adenylation-defective mutant providing further evidence that LX interacts directly with the DNA end, possibly via the 5'-phosphate as shown for prokaryotic ligases. Taken together, our results suggest that, when LX binds to a Ku-bound DNA molecule, it causes inward translocation of Ku and that freedom to move inward on the DNA is essential to Ku stimulation of LX activity.

  11. A DNA enzyme with Mg(2+)-Dependent RNA Phosphoesterase Activity

    NASA Technical Reports Server (NTRS)

    Breaker, Ronald R.; Joyce, Gerald F.

    1995-01-01

    Previously we demonstrated that DNA can act as an enzyme in the Pb(2+)-dependent cleavage of an RNA phosphoester. This is a facile reaction, with an uncatalyzed rate for a typical RNA phosphoester of approx. 10(exp -4)/ min in the presence of 1 mM Pb(OAc)2 at pH 7.0 and 23 C. The Mg(2+) - dependent reaction is more difficult, with an uncatalyzed rate of approx. 10(exp -7)/ min under comparable conditions. Mg(2+) - dependent cleavage has special relevance to biology because it is compatible with intracellular conditions. Using in vitro selection, we sought to develop a family of phosphoester-cleaving DNA enzymes that operate in the presence of various divalent metals, focusing particularly on the Mg(2+) - dependent reaction. Results: We generated a population of greater than 10(exp 13) DNAs containing 40 random nucleotides and carried out repeated rounds of selective amplification, enriching for molecules that cleave a target RNA phosphoester in the presence of 1 mM Mg(2+), Mn(2+), Zn(2+) or Pb(2+). Examination of individual clones from the Mg(2+) lineage after the sixth round revealed a catalytic motif comprised of a three-stem junction.This motif was partially randomized and subjected to seven additional rounds of selective amplification, yielding catalysts with a rate of 0.01/ min. The optimized DNA catalyst was divided into separate substrate and enzyme domains and shown to have a similar level of activity under multiple turnover conditions. Conclusions: We have generated a Mg(2+) - dependent DNA enzyme that cleaves a target RNA phosphoester with a catalytic rate approx. 10(exp 5) - fold greater than that of the uncatalyzed reaction. This activity is compatible with intracellular conditions, raising the possibility that DNA enzymes might be made to operate in vivo.

  12. The DnaE polymerase from Deinococcus radiodurans features RecA-dependent DNA polymerase activity

    PubMed Central

    Randi, Lorenzo; Perrone, Alessandro; Maturi, Mirko; Dal Piaz, Fabrizio; Camerani, Michela; Hochkoeppler, Alejandro

    2016-01-01

    We report in the present study on the catalytic properties of the Deinococcus radiodurans DNA polymerase III α subunit (αDr). The αDr enzyme was overexpressed in Escherichia coli, both in soluble form and as inclusion bodies. When purified from soluble protein extracts, αDr was found to be tightly associated with E. coli RNA polymerase, from which αDr could not be dissociated. On the contrary, when refolded from inclusion bodies, αDr was devoid of E. coli RNA polymerase and was purified to homogeneity. When assayed with different DNA substrates, αDr featured slower DNA extension rates when compared with the corresponding enzyme from E. coli (E. coli DNA Pol III, αEc), unless under high ionic strength conditions or in the presence of manganese. Further assays were performed using a ssDNA and a dsDNA, whose recombination yields a DNA substrate. Surprisingly, αDr was found to be incapable of recombination-dependent DNA polymerase activity, whereas αEc was competent in this action. However, in the presence of the RecA recombinase, αDr was able to efficiently extend the DNA substrate produced by recombination. Upon comparing the rates of RecA-dependent and RecA-independent DNA polymerase activities, we detected a significant activation of αDr by the recombinase. Conversely, the activity of αEc was found maximal under non-recombination conditions. Overall, our observations indicate a sharp contrast between the catalytic actions of αDr and αEc, with αDr more performing under recombination conditions, and αEc preferring DNA substrates whose extension does not require recombination events. PMID:27789781

  13. Effects of Ionic Dependence of DNA Persistence Length on the DNA Condensation at Room Temperature

    NASA Astrophysics Data System (ADS)

    Mao, Wei; Liu, Yan-Hui; Hu, Lin; Xu, Hou-Qiang

    2016-05-01

    DNA persistence length is a key parameter for quantitative interpretation of the conformational properties of DNA and related to the bending rigidity of DNA. A series of experiments pointed out that, in the DNA condensation process by multivalent cations, the condensed DNA takes elongated coil or compact globule states and the population of the compact globule states increases with an increase in ionic concentration. At the same time, single molecule experiments carried out in solution with multivalent cations (such as spermidine, spermine) indicated that DNA persistence length strongly depends on the ionic concentration. In order to revolve the effects of ionic concentration dependence of persistence length on DNA condensation, a model including the ionic concentration dependence of persistence length and strong correlation of multivalent cation on DNA is provided. The autocorrelation function of the tangent vectors is found as an effective way to detect the ionic concentration dependence of toroidal conformations. With an increase in ion concentration, the first periodic oscillation contained in the autocorrelation function shifts, the number of segment contained in the first periodic oscillation decreases gradually. According to the experiments, the average long-axis length is defined to estimate the ionic concentration dependence of condensation process further. The relation between long-axis length and ionic concentration matches the experimental results qualitatively. Supported by National Natural Science Foundation of China under Grant Nos. 11047022, 11204045, 11464004 and 31360215; The Research Foundation from Ministry of Education of China (212152), Guizhou Provincial Tracking Key Program of Social Development (SY20123089, SZ20113069); The General Financial Grant from the China Postdoctoral Science Foundation (2014M562341); The Research Foundation for Young University Teachers from Guizhou University (201311); The West Light Foundation (2015) and College

  14. Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity

    NASA Astrophysics Data System (ADS)

    Slone, Scott Michael; Li, Chen-Yu; Yoo, Jejoong; Aksimentiev, Aleksei

    2016-05-01

    The DNA bricks method exploits self-assembly of short DNA fragments to produce custom three-dimensional objects with subnanometer precision. In contrast to DNA origami, the DNA brick method permits a variety of different structures to be realized using the same library of DNA strands. As a consequence of their design, however, assembled DNA brick structures have fewer interhelical connections in comparison to equivalent DNA origami structures. Although the overall shape of the DNA brick objects has been characterized and found to conform to the features of the target designs, the microscopic properties of DNA brick objects remain yet to be determined. Here, we use the all-atom molecular dynamics method to directly compare the structure, mechanical properties and ionic conductivity of DNA brick and DNA origami structures different only by internal connectivity of their consistituent DNA strands. In comparison to equivalent DNA origami structures, the DNA brick structures are found to be less rigid and less dense and have a larger cross-section area normal to the DNA helix direction. At the microscopic level, the junction in the DNA brick structures are found to be right-handed, similar to the structure of individual Holliday junctions (HJ) in solution, which contrasts with the left-handed structure of HJ in DNA origami. Subject to external electric field, a DNA brick plate is more leaky to ions than an equivalent DNA origami plate because of its lower density and larger cross-section area. Overall, our results indicate that the structures produced by the DNA brick method are fairly similar in their overall appearance to those created by the DNA origami method but are more compliant when subject to external forces, which likely is a consequence of their single crossover design.

  15. DNA Template Dependent Accuracy Variation of Nucleotide Selection in Transcription

    PubMed Central

    Mellenius, Harriet; Ehrenberg, Måns

    2015-01-01

    It has been commonly assumed that the effect of erroneous transcription of DNA genes into messenger RNAs on peptide sequence errors are masked by much more frequent errors of mRNA translation to protein. We present a theoretical model of transcriptional accuracy. It uses experimentally estimated standard free energies of double-stranded DNA and RNA/DNA hybrids and predicts a DNA template dependent transcriptional accuracy variation spanning several orders of magnitude. The model also identifies high-error as well a high-accuracy transcription motifs. The source of the large accuracy span is the context dependent variation of the stacking free energy of pairs of correct and incorrect base pairs in the ever moving transcription bubble. Our model predictions have direct experimental support from recent single molecule based identifications of transcriptional errors in the C. elegans transcriptome. Our conclusions challenge the general view that amino acid substitution errors in proteins are mainly caused by translational errors. It suggests instead that transcriptional error hotspots are the dominating source of peptide sequence errors in some DNA template contexts, while mRNA translation is the major cause of protein errors in other contexts. PMID:25799551

  16. DNA template dependent accuracy variation of nucleotide selection in transcription.

    PubMed

    Mellenius, Harriet; Ehrenberg, Måns

    2015-01-01

    It has been commonly assumed that the effect of erroneous transcription of DNA genes into messenger RNAs on peptide sequence errors are masked by much more frequent errors of mRNA translation to protein. We present a theoretical model of transcriptional accuracy. It uses experimentally estimated standard free energies of double-stranded DNA and RNA/DNA hybrids and predicts a DNA template dependent transcriptional accuracy variation spanning several orders of magnitude. The model also identifies high-error as well a high-accuracy transcription motifs. The source of the large accuracy span is the context dependent variation of the stacking free energy of pairs of correct and incorrect base pairs in the ever moving transcription bubble. Our model predictions have direct experimental support from recent single molecule based identifications of transcriptional errors in the C. elegans transcriptome. Our conclusions challenge the general view that amino acid substitution errors in proteins are mainly caused by translational errors. It suggests instead that transcriptional error hotspots are the dominating source of peptide sequence errors in some DNA template contexts, while mRNA translation is the major cause of protein errors in other contexts.

  17. STING manifests self DNA-dependent inflammatory disease.

    PubMed

    Ahn, Jeonghyun; Gutman, Delia; Saijo, Shinobu; Barber, Glen N

    2012-11-20

    Inflammatory autoimmune diseases such as systemic lupus erythematosus (SLE) and polyarthritis are characterized by chronic cytokine overproduction, suggesting that the stimulation of host innate immune responses, speculatively by persistent infection or self nucleic acids, plays a role in the manifestation of these disorders. Mice lacking DNase II die during embryonic development through comparable inflammatory disease because phagocytosed DNA from apoptotic cells cannot be adequately digested and intracellular host DNA sensor pathways are engaged, resulting in the production of a variety of cytokines including type I IFN. The cellular sensor pathway(s) responsible for triggering DNA-mediated inflammation aggravated autoimmune disease remains to be determined. However, we report here that Stimulator of IFN Genes (STING) is responsible for inflammation-related embryonic death in DNase II defective mice initiated by self DNA. DNase II-dependent embryonic lethality was rescued by loss of STING function, and polyarthritis completely prevented because cytosolic DNA failed to robustly trigger cytokine production through STING-controlled signaling pathways. Our data provides significant molecular insight into the causes of DNA-mediated inflammatory disorders and affords a target that could plausibly be therapeutically controlled to help prevent such diseases.

  18. Thickness dependent ion conductivity of lithium borate network glasses

    NASA Astrophysics Data System (ADS)

    Berkemeier, F.; Shoar Abouzari, M.; Schmitz, G.

    2007-03-01

    Lithium borate network glasses are possible candidates for separator membranes in all-solid-state batteries. Thin films of a Li2O-borate glass were produced by argon beam sputtering and their specific ionic conductivities were measured by impedance spectroscopy. The conductivity of as-sputtered films is about two orders of magnitude higher compared to the conductivity of bulk glasses produced from the melt. Furthermore, thin films with a thickness of 7-125nm reveal a remarkable finite size effect after annealing: with decreasing thickness the specific dc conductivity increases about three orders of magnitude.

  19. Biomaterial-based Memory Device Development by Conducting Metallic DNA

    DTIC Science & Technology

    2013-05-28

    basis of the redshift of UV absorption spectra, we think that the incorporation of metal ions may result in a reduction of the original DNA band gap...memristor based on the changing of the boundary between the high-resistance and low-resistance layers of titanium dioxide TiO2 and TiO2 -x13. Their...electrode cell. These electrodes included a modified Au electrode (working electrode), a coiled platinum wire (counter electrode), and an Ag /AgCl

  20. The conductive properties of single DNA molecules studied by torsion tunneling atomic force microscopy.

    PubMed

    Wang, W; Niu, D X; Jiang, C R; Yang, X J

    2014-01-17

    The conductive properties of single natural λ-DNA molecules are studied by torsion tunneling atomic force microscopy (TR-TUNA). The currents both parallel to and perpendicular to the DNA chains are investigated, but only weak or even no current signals are detected by TR-TUNA. To improve the conductance of DNA molecules, silver and copper metallized DNAs are fabricated and their conductivities are checked by TR-TUNA. It is found that for both Cu- and Ag-DNAs, the conductivity perpendicular to the DNA chain is enhanced significantly as the metal clusters are attached to the DNA chains. But parallel to the chain the electrical transport is still weak, most probably due to the 'beads-on-a-string' constructions of metallized DNAs.

  1. The conductive properties of single DNA molecules studied by torsion tunneling atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Wang, W.; Niu, D. X.; Jiang, C. R.; Yang, X. J.

    2014-01-01

    The conductive properties of single natural λ-DNA molecules are studied by torsion tunneling atomic force microscopy (TR-TUNA). The currents both parallel to and perpendicular to the DNA chains are investigated, but only weak or even no current signals are detected by TR-TUNA. To improve the conductance of DNA molecules, silver and copper metallized DNAs are fabricated and their conductivities are checked by TR-TUNA. It is found that for both Cu- and Ag-DNAs, the conductivity perpendicular to the DNA chain is enhanced significantly as the metal clusters are attached to the DNA chains. But parallel to the chain the electrical transport is still weak, most probably due to the ‘beads-on-a-string’ constructions of metallized DNAs.

  2. Temperature-dependent electrical conductivity of soda-lime glass

    NASA Technical Reports Server (NTRS)

    Bunnell, L. Roy; Vertrees, T. H.

    1993-01-01

    The objective of this educational exercise was to demonstrate the difference between the electrical conductivity of metals and ceramics. A list of the equipment and supplies and the procedure for the experiment are presented.

  3. DnaK-Dependent Accelerated Evolutionary Rate in Prokaryotes

    PubMed Central

    Kadibalban, A. Samer; Bogumil, David; Landan, Giddy; Dagan, Tal

    2016-01-01

    Many proteins depend on an interaction with molecular chaperones in order to fold into a functional tertiary structure. Previous studies showed that protein interaction with the GroEL/GroES chaperonine and Hsp90 chaperone can buffer the impact of slightly deleterious mutations in the protein sequence. This capacity of GroEL/GroES to prevent protein misfolding has been shown to accelerate the evolution of its client proteins. Whether other bacterial chaperones have a similar effect on their client proteins is currently unknown. Here, we study the impact of DnaK (Hsp70) chaperone on the evolution of its client proteins. Evolutionary parameters were derived from comparison of the Escherichia coli proteome to 1,808,565 orthologous proteins in 1,149 proteobacterial genomes. Our analysis reveals a significant positive correlation between protein binding frequency with DnaK and evolutionary rate. Proteins with high binding affinity to DnaK evolve on average 4.3-fold faster than proteins in the lowest binding affinity class at the genus resolution. Differences in evolutionary rates of DnaK interactor classes are still significant after adjusting for possible effects caused by protein expression level. Furthermore, we observe an additive effect of DnaK and GroEL chaperones on the evolutionary rates of their common interactors. Finally, we found pronounced similarities in the physicochemical profiles that characterize proteins belonging to DnaK and GroEL interactomes. Our results thus implicate DnaK-mediated folding as a major component in shaping protein evolutionary dynamics in bacteria and supply further evidence for the long-term manifestation of chaperone-mediated folding on genome evolution. PMID:27189986

  4. pH-dependent specific binding and combing of DNA.

    PubMed Central

    Allemand, J F; Bensimon, D; Jullien, L; Bensimon, A; Croquette, V

    1997-01-01

    Recent developments in the rapid sequencing, mapping, and analysis of DNA rely on the specific binding of DNA to specially treated surfaces. We show here that specific binding of DNA via its unmodified extremities can be achieved on a great variety of surfaces by a judicious choice of the pH. On hydrophobic surfaces the best binding efficiency is reached at a pH of approximately 5.5. At that pH a approximately 40-kbp DNA is 10 times more likely to bind by an extremity than by a midsegment. A model is proposed to account for the differential adsorption of the molecule extremities and midsection as a function of pH. The pH-dependent specific binding can be used to align anchored DNA molecules by a receding meniscus, a process called molecular combing. The resulting properties of the combed molecules will be discussed. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 6 FIGURE 7 PMID:9336201

  5. Polarization and Angle Dependence of Fluorescence from Aligned DNA

    NASA Astrophysics Data System (ADS)

    Sridhar, Ashish; Bandler, Suri; Zhu, Ke; Gu, Yingzhan; Budassi, Julia; Sokolov, Jonathan

    2012-02-01

    DNA molecules can be deposited and aligned on various surfaces and imaged by confocal microscopy when labeled with fluorescent dyes. SyBr Gold dye, is known to possess a high angle and polarization dependence. We measured the emission intensity for various incident angles as a function of incident polarization angle. Samples were created by means of dipping PMMA-coated silicon wafers into dyed DNA solutions with DC electric field setup or drop evaporation. The blue laser as the imaging light source was mounted on an optical rail with a polarizer with rotatable half wave plate to change the incident polarization relative to the DNA molecular orientation. When applied to samples dyed using SyBr Gold, a clear change in the intensity of imaged DNA strands was observed though a range of input polarization angle. We have shown that it is possible to optimize the conditions in which aligned DNA is imaged using confocal microscopy by varying the polarization and angle of incidence of laser light on the sample. This study is supported by NSF-DMR-MRSEC program.

  6. Base-sequence-dependent sliding of proteins on DNA.

    PubMed

    Barbi, M; Place, C; Popkov, V; Salerno, M

    2004-10-01

    The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a noise-influenced sequence-dependent motion which deviate from the standard random walk usually assumed. The general validity and the implications of the results are discussed.

  7. Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays

    NASA Astrophysics Data System (ADS)

    Keller, Adrian; Rackwitz, Jenny; Cauët, Emilie; Liévin, Jacques; Körzdörfer, Thomas; Rotaru, Alexandru; Gothelf, Kurt V.; Besenbacher, Flemming; Bald, Ilko

    2014-12-01

    The electronic structure of DNA is determined by its nucleotide sequence, which is for instance exploited in molecular electronics. Here we demonstrate that also the DNA strand breakage induced by low-energy electrons (18 eV) depends on the nucleotide sequence. To determine the absolute cross sections for electron induced single strand breaks in specific 13 mer oligonucleotides we used atomic force microscopy analysis of DNA origami based DNA nanoarrays. We investigated the DNA sequences 5'-TT(XYX)3TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections between 2.66 . 10-14 cm2 and 7.06 . 10-14 cm2. The highest cross section was found for 5'-TT(ATA)3TT and 5'-TT(ABrUA)3TT, respectively. BrU is a radiosensitizer, which was discussed to be used in cancer radiation therapy. The replacement of T by BrU into the investigated DNA sequences leads to a slight increase of the absolute strand break cross sections resulting in sequence-dependent enhancement factors between 1.14 and 1.66. Nevertheless, the variation of strand break cross sections due to the specific nucleotide sequence is considerably higher. Thus, the present results suggest the development of targeted radiosensitizers for cancer radiation therapy.

  8. Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays

    PubMed Central

    Keller, Adrian; Rackwitz, Jenny; Cauët, Emilie; Liévin, Jacques; Körzdörfer, Thomas; Rotaru, Alexandru; Gothelf, Kurt V.; Besenbacher, Flemming; Bald, Ilko

    2014-01-01

    The electronic structure of DNA is determined by its nucleotide sequence, which is for instance exploited in molecular electronics. Here we demonstrate that also the DNA strand breakage induced by low-energy electrons (18 eV) depends on the nucleotide sequence. To determine the absolute cross sections for electron induced single strand breaks in specific 13 mer oligonucleotides we used atomic force microscopy analysis of DNA origami based DNA nanoarrays. We investigated the DNA sequences 5′-TT(XYX)3TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections between 2.66 · 10−14 cm2 and 7.06 · 10−14 cm2. The highest cross section was found for 5′-TT(ATA)3TT and 5′-TT(ABrUA)3TT, respectively. BrU is a radiosensitizer, which was discussed to be used in cancer radiation therapy. The replacement of T by BrU into the investigated DNA sequences leads to a slight increase of the absolute strand break cross sections resulting in sequence-dependent enhancement factors between 1.14 and 1.66. Nevertheless, the variation of strand break cross sections due to the specific nucleotide sequence is considerably higher. Thus, the present results suggest the development of targeted radiosensitizers for cancer radiation therapy. PMID:25487346

  9. Time resolved strain dependent morphological study of electrically conducting nanocomposites

    NASA Astrophysics Data System (ADS)

    Khan, Imran; Mitchell, Geoffrey; Mateus, Artur; Kamma-Lorger, Christina S.

    2015-10-01

    An efficient and reliable method is introduced to understand the network behaviour of nano-fillers in a polymeric matrix under uniaxial strain coupled with small angle x-ray scattering measurements. The nanoparticles (carbon nanotubes) are conductive and the particles form a percolating network that becomes apparent source of electrical conduction and consequently the samples behave as a bulk conductor. Polyurethane based nanocomposites containing 2% w/w multiwall carbon nanotubes are studied. The electrical conductivity of the nanocomposite was (3.28×10-5s/m).The sample was able to be extended to an extension ratio of 1.7 before fracture. A slight variation in the electrical conductivity is observed under uniaxial strain which we attribute to the disturbance of conductive pathways. Further, this work is coupled with in- situ time resolved small angle x-ray scattering measurements using a synchrotron beam line to enable its measurements to be made during the deformation cycle. We use a multiscale structure to model the small angle x-ray data. The results of the analysis are interpreted as the presence of aggregates which would also go some way towards understanding why there is no alignment of the carbon nanotubes.

  10. DNA-protected silver emitters: charge dependent switching of fluorescence.

    PubMed

    Berdakin, Matías; Taccone, Martin I; Pino, Gustavo A; Sánchez, Cristián G

    2017-02-22

    The relationship between the state of charge and spectroscopy of DNA-protected silver emitters is not yet well understood. This remains one of the major issues to unveil in order to fully disentangle the spectroscopic features of these novel systems. It is a well known fact that a fluorescence response arises upon chemical reduction of silver cations attached to DNA, leading to neutral (or partially oxidized) "bright" clusters. It is important to note that the absence of fluorescence in completely ionic complexes is universal in the sense that it does not depend on any experimental variable. This suggests that its origin may be founded on the nature of the interaction between DNA bases and silver cations. Nevertheless, to the best of our knowledge, no explanation exists for this charge dependent switching between dark completely ionic complexes and bright (neutral or partially oxidized) clusters. In this brief report we address this experimental fact on the basis of the electronic structure of the complex as a function of its charge and quantum dynamical simulations of the processes following photoexcitation. These data provide a dynamical picture of the correlation between charge and fluorescence.

  11. A sequence-dependent rigid-base model of DNA

    NASA Astrophysics Data System (ADS)

    Gonzalez, O.; Petkevičiutė, D.; Maddocks, J. H.

    2013-02-01

    A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all of its interactions. As a consequence, an arbitrary DNA oligomer has an intrinsic or pre-existing stress, with the level of this frustration dependent on the particular sequence of the oligomer. Attention is focussed on the particular model in the hierarchy that has nearest-neighbor interactions and dimer sequence dependence of the model parameters. For a Gaussian version of this model, a complete coarse-grain parameter set is estimated. The parameterized model allows, for an oligomer of arbitrary length and sequence, a simple and explicit construction of an approximation to the configuration-space equilibrium probability density function for the oligomer in solution. The training set leading to the coarse-grain parameter set is itself extracted from a recent and extensive database of a large number of independent, atomic-resolution molecular dynamics (MD) simulations of short DNA oligomers immersed in explicit solvent. The Kullback-Leibler divergence between probability density functions is used to make several quantitative assessments of our nearest-neighbor, dimer-dependent model, which is compared against others in the hierarchy to assess various assumptions pertaining both to the locality of the energetic couplings and to the level of sequence dependence of its parameters. It is also compared directly against all-atom MD simulation to assess its predictive capabilities. The results show that the nearest-neighbor, dimer-dependent model can successfully resolve sequence effects both within and between oligomers. For example, due to the presence of frustration, the model can

  12. Potential Dependence of the Conductivity of Highly Oxidized Polythiophenes, Polypyrroles, and Polyaniline: Finite Windows of High Conductivity

    DTIC Science & Technology

    1990-05-16

    protonation/deprotonation mechanism . Conductivity increases by at least 108 upon oxidizing polyani-ine from neutral to maximally conducting, and decreases...reversible, potential dependent changes in conductivity in liquid S02/electrolyte in the apparent absence of a protonation/deprotonation mechanism ...polyaniline is similar in 0.5 M H2SO4 ,1 liquid S02 /electrolyte, and poly(vinyl alchohol )/H 3PO4.nH20.8 However, the positive potential limit in aqueous

  13. DNA length and concentration dependencies of anisotropic phase transitions of DNA solutions.

    PubMed Central

    Merchant, K; Rill, R L

    1997-01-01

    Critical concentrations for the isotropic to cholesteric phase transitions of double-stranded DNA fragments in simple buffered saline (0.1 M NaCl) solutions were determined as a function of DNA contour length ranging from approximately 50 nm to 2700 nm, by solid-state 31P NMR spectroscopy and polarized light microscopy. As expected for semirigid chains, the critical concentrations decrease sharply with increasing DNA length near the persistence length in the range from 50 to 110 nm, and approach a plateau when the contour length exceeds 190 nm. The biphasic region is substantially wider than observed for xanthan, another semirigid polyelectrolyte approximately twice as stiff as DNA, primarily because of low critical concentrations for first appearance of the anisotropic phase, C(i)*, in DNA samples > or =110 nm (320 base pairs) long. The limiting C(i)* for DNA > or =490 nm long is exceptionally low (only 13 mg/ml) and is substantially lower than the C(i)* of approximately 40 mg/ml reported for the stiffer xanthan polyelectrolyte. The much higher values of the critical concentrations, C(a)*, for the disappearance of the isotropic DNA phase (> or =67 mg/ml) are modestly higher than those observed for xanthan and are predicted reasonably well by a theory that has been applied to other semirigid polymers, if a DNA persistence length in the consensus range of 50-100 nm is assumed. By contrast, the broad biphasic region and low C(i)* values of DNA fragments > or =190 nm long could only be reconciled with theory by assuming persistence lengths of 200-400 nm. The latter discrepancies are presumed to reflect some combination of deficiencies in current theory as applied to chiral, strong polyelectrolytes such as DNA, and sequence-dependent variations in DNA properties such as flexibility, curvature, or interaction potential. The propensity of DNA to spontaneously self-order at low concentrations well in the physiological range may have biological significance. PMID:9414227

  14. Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing

    PubMed Central

    Kording, Konrad; Schmidt, Daniel; Martin-Alarcon, Daniel; Tyo, Keith; Boyden, Edward S.; Church, George

    2012-01-01

    High-throughput recording of signals embedded within inaccessible micro-environments is a technological challenge. The ideal recording device would be a nanoscale machine capable of quantitatively transducing a wide range of variables into a molecular recording medium suitable for long-term storage and facile readout in the form of digital data. We have recently proposed such a device, in which cation concentrations modulate the misincorporation rate of a DNA polymerase (DNAP) on a known template, allowing DNA sequences to encode information about the local cation concentration. In this work we quantify the cation sensitivity of DNAP misincorporation rates, making possible the indirect readout of cation concentration by DNA sequencing. Using multiplexed deep sequencing, we quantify the misincorporation properties of two DNA polymerases – Dpo4 and Klenow exo− – obtaining the probability and base selectivity of misincorporation at all positions within the template. We find that Dpo4 acts as a DNA recording device for Mn2+ with a misincorporation rate gain of ∼2%/mM. This modulation of misincorporation rate is selective to the template base: the probability of misincorporation on template T by Dpo4 increases >50-fold over the range tested, while the other template bases are affected less strongly. Furthermore, cation concentrations act as scaling factors for misincorporation: on a given template base, Mn2+ and Mg2+ change the overall misincorporation rate but do not alter the relative frequencies of incoming misincorporated nucleotides. Characterization of the ion dependence of DNAP misincorporation serves as the first step towards repurposing it as a molecular recording device. PMID:22928047

  15. Cre-dependent DNA recombination activates a STING-dependent innate immune response

    PubMed Central

    Pépin, Geneviève; Ferrand, Jonathan; Höning, Klara; Jayasekara, W. Samantha N.; Cain, Jason E.; Behlke, Mark A.; Gough, Daniel J.; G. Williams, Bryan R.; Hornung, Veit; Gantier, Michael P.

    2016-01-01

    Gene-recombinase technologies, such as Cre/loxP-mediated DNA recombination, are important tools in the study of gene function, but have potential side effects due to damaging activity on DNA. Here we show that DNA recombination by Cre instigates a robust antiviral response in mammalian cells, independent of legitimate loxP recombination. This is due to the recruitment of the cytosolic DNA sensor STING, concurrent with Cre-dependent DNA damage and the accumulation of cytoplasmic DNA. Importantly, we establish a direct interplay between this antiviral response and cell–cell interactions, indicating that low cell densities in vitro could be useful to help mitigate these effects of Cre. Taking into account the wide range of interferon stimulated genes that may be induced by the STING pathway, these results have broad implications in fields such as immunology, cancer biology, metabolism and stem cell research. Further, this study sets a precedent in the field of gene-engineering, possibly applicable to other enzymatic-based genome editing technologies. PMID:27166376

  16. Spin-dependent conductance of small graphene flakes

    NASA Astrophysics Data System (ADS)

    Tugrul Senger, R.; Sahin, Hasan; Ciraci, Salim

    2010-03-01

    Using ab initio density-functional theory and quantum transport calculations based on nonequilibrium Green's function formalism we study structural, electronic, and transport properties of small graphene flakes. Rectangular and triangular graphene flakes are stable, having magnetically ordered edge states. We show that a spin-polarized current can be produced in pure, hydrogenated, rectangular graphene flakes by exploiting the spatially separated edge states of the flake using asymmetric, nonmagnetic contacts (1). Sharp discontinuities in the transmission spectra which arise from Fano resonances of localized states in the flake are also predicted. Functionalization of the graphene flake with magnetic adatoms such as vanadium also leads to spin-polarized currents even with symmetric contacts. Ground state of triangular flakes have non-zero magnetic moments and their conductance are spin polarized. (1) H. Sahin and R. T. Senger, Phys. Rev. B 78, 205423 (2008).

  17. Conductive magnetorheological elastomer: fatigue dependent impedance-mechanic coupling properties

    NASA Astrophysics Data System (ADS)

    Wang, Yu; Xuan, Shouhu; Ge, Lin; Wen, Qianqian; Gong, Xinglong

    2017-01-01

    This work investigated the relationship between the impedance properties and dynamic mechanical properties of magnetorheological elastomers (MREs) under fatigue loading. The storage modulus and the impedance properties of MREs were highly influenced by the pressure and magnetic field. Under the same experimental condition, the two characteristics exhibited similar fatigue dependent change trends. When pressure was smaller than 10 N, the capacitance of MRE could be divided into four sections with the increase of the cyclic numbers. The relative equivalent circuit model was established to fit the experimental results of the impedance spectra. Each parameter of circuit element reflected the change of fatigue loading, relative microstructure of MRE, MRE-electrode interface layer, respectively. Based on the above analysis, the real-time and nondestructive impedance method was demonstrated to be high potential on detecting the fatigue of the MRE device.

  18. High Electronic Conductance through Double-Helix DNA Molecules with Fullerene Anchoring Groups

    PubMed Central

    2017-01-01

    Determining the mechanism of charge transport through native DNA remains a challenge as different factors such as measuring conditions, molecule conformations, and choice of technique can significantly affect the final results. In this contribution, we have used a new approach to measure current flowing through isolated double-stranded DNA molecules, using fullerene groups to anchor the DNA to a gold substrate. Measurements were performed at room temperature in an inert environment using a conductive AFM technique. It is shown that the π-stacked B-DNA structure is conserved on depositing the DNA. As a result, currents in the nanoampere range were obtained for voltages ranging between ±1 V. These experimental results are supported by a theoretical model that suggests that a multistep hopping mechanism between delocalized domains is responsible for the long-range current flow through this specific type of DNA. PMID:28094940

  19. Proteasome inhibition enhances resistance to DNA damage via upregulation of Rpn4-dependent DNA repair genes.

    PubMed

    Karpov, Dmitry S; Spasskaya, Daria S; Tutyaeva, Vera V; Mironov, Alexander S; Karpov, Vadim L

    2013-09-17

    The 26S proteasome is an ATP-dependent multi-subunit protease complex and the major regulator of intracellular protein turnover and quality control. However, its role in the DNA damage response is controversial. We addressed this question in yeast by disrupting the transcriptional regulation of the PRE1 proteasomal gene. The mutant strain has decreased proteasome activity and is hyper-resistant to various DNA-damaging agents. We found that Rpn4-target genes MAG1, RAD23, and RAD52 are overexpressed in this strain due to Rpn4 stabilisation. These genes represent three different pathways of base excision, nucleotide excision and double strand break repair by homologous recombination (DSB-HR). Consistently, the proteasome mutant displays increased DSB-HR activity. Our data imply that the proteasome may have a negative role in DNA damage response.

  20. T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites

    PubMed Central

    Brunaud, Véronique; Balzergue, Sandrine; Dubreucq, Bertrand; Aubourg, Sébastien; Samson, Franck; Chauvin, Stéphanie; Bechtold, Nicole; Cruaud, Corinne; DeRose, Richard; Pelletier, Georges; Lepiniec, Loïc; Caboche, Michel; Lecharny, Alain

    2002-01-01

    A statistical analysis of 9000 flanking sequence tags characterizing transferred DNA (T-DNA) transformants in Arabidopsis sheds new light on T-DNA insertion by illegitimate recombination. T-DNA integration is favoured in plant DNA regions with an A-T-rich content. The formation of a short DNA duplex between the host DNA and the left end of the T-DNA sets the frame for the recombination. The sequence immediately downstream of the plant A-T-rich region is the master element for setting up the DNA duplex, and deletions into the left end of the integrated T-DNA depend on the location of a complementary sequence on the T-DNA. Recombination at the right end of the T-DNA with the host DNA involves another DNA duplex, 2–3 base pairs long, that preferentially includes a G close to the right end of the T-DNA. PMID:12446565

  1. Analysis of supercoiled DNA by agarose gel electrophoresis using low-conducting sodium threonine medium.

    PubMed

    Ishido, Tomomi; Ishikawa, Mitsuru; Hirano, Ken

    2010-05-01

    We describe a new low-ionic-strength sodium threonine (STh) medium with the advantage of avoiding relative DNA band migration changes following electrophoresis of supercoiled DNA in agarose gel when substituted for the standard conductive medium of TBE (Tris-boric acid-ethylenediaminetetraacetic acid [EDTA]) or TAE (Tris-acetic acid-EDTA) or the low-ionic-strength sodium boric acid medium. Low-ionic-strength STh medium provided better resolution, less heat generation, and prevention of relative migration order changes among linear, covalently closed circular-, and open circular-formed DNA in the range of 2-10 kilobase pairs in 1% agarose gel electrophoresis.

  2. A Device for Performing Lateral Conductance Measurements on Individual Double-Stranded DNA Molecules

    PubMed Central

    Menard, Laurent D.; Mair, Chad E.; Woodson, Michael E.; Alarie, Jean Pierre; Ramsey, J. Michael

    2012-01-01

    A nanofluidic device is described that is capable of electrically monitoring the driven translocation of DNA molecules through a nanochannel. This is achieved by intersecting a long transport channel with a shorter orthogonal nanochannel. The ionic conductance of this transverse nanochannel is monitored while DNA is electrokinetically driven through the transport channel. When DNA passes the intersection, the transverse conductance is altered, resulting in a transient current response. In 1 M KCl solutions, this was found to be a current enhancement of 5–25%, relative to the baseline transverse ionic current. Two different device geometries were investigated. In one device, the DNA was detected after it was fully inserted into and translocating through the transport nanochannel. In the other device, the DNA was detected while it was in the process of entering the nanochannel. It was found that these two conditions are characterized by different transport dynamics. Simultaneous optical and electrical monitoring of DNA translocation confirmed that the transient events originated from DNA transport through the nanochannel intersection. PMID:22950784

  3. Frequency-dependent conductivity contrast for tissue characterization using a dual-frequency range conductivity mapping magnetic resonance method.

    PubMed

    Kim, Dong-Hyun; Chauhan, Munish; Kim, Min-Oh; Jeong, Woo Chul; Kim, Hyung Joong; Sersa, Igor; Kwon, Oh In; Woo, Eung Je

    2015-02-01

    Electrical conductivities of biological tissues show frequency-dependent behaviors, and these values at different frequencies may provide clinically useful diagnostic information. MR-based tissue property mapping techniques such as magnetic resonance electrical impedance tomography (MREIT) and magnetic resonance electrical property tomography (MREPT) are widely used and provide unique conductivity contrast information over different frequency ranges. Recently, a new method for data acquisition and reconstruction for low- and high-frequency conductivity images from a single MR scan was proposed. In this study, we applied this simultaneous dual-frequency range conductivity mapping MR method to evaluate its utility in a designed phantom and two in vivo animal disease models. Magnetic flux density and B(1)(+) phase map for dual-frequency conductivity images were acquired using a modified spin-echo pulse sequence. Low-frequency conductivity was reconstructed from MREIT data by the projected current density method, while high-frequency conductivity was reconstructed from MREPT data by B(1)(+) mapping. Two different conductivity phantoms comprising varying ion concentrations separated by insulating films with or without holes were used to study the contrast mechanism of the frequency-dependent conductivities related to ion concentration and mobility. Canine brain abscess and ischemia were used as in vivo models to evaluate the capability of the proposed method to identify new electrical properties-based contrast at two different frequencies. The simultaneous dual-frequency range conductivity mapping MR method provides unique contrast information related to the concentration and mobility of ions inside tissues. This method has potential to monitor dynamic changes of the state of disease.

  4. Ancestry Dependent DNA Methylation and Influence of Maternal Nutrition

    PubMed Central

    Mozhui, Khyobeni; Smith, Alicia K.; Tylavsky, Frances A.

    2015-01-01

    There is extensive variation in DNA methylation between individuals and ethnic groups. These differences arise from a combination of genetic and non-genetic influences and potential modifiers include nutritional cues, early life experience, and social and physical environments. Here we compare genome-wide DNA methylation in neonatal cord blood from African American (AA; N = 112) and European American (EA; N = 91) participants of the CANDLE Study (Conditions Affecting Neurocognitive Development and Learning in Early Childhood). Our goal is to determine if there are replicable ancestry-specific methylation patterns that may implicate risk factors for diseases that have differential prevalence between populations. To identify the most robust ancestry-specific CpG sites, we replicate our results in lymphoblastoid cell lines from Yoruba African and CEPH European panels of HapMap. We also evaluate the influence of maternal nutrition—specifically, plasma levels of vitamin D and folate during pregnancy—on methylation in newborns. We define stable ancestry-dependent methylation of genes that include tumor suppressors and cell cycle regulators (e.g., APC, BRCA1, MCC). Overall, there is lower global methylation in African ancestral groups. Plasma levels of 25-hydroxy vitamin D are also considerably lower among AA mothers and about 60% of AA and 40% of EA mothers have concentrations below 20 ng/ml. Using a weighted correlation analysis, we define a network of CpG sites that is jointly modulated by ancestry and maternal vitamin D. Our results show that differences in DNA methylation patterns are remarkably stable and maternal micronutrients can exert an influence on the child epigenome. PMID:25742137

  5. Neutron energy-dependent initial DNA damage and chromosomal exchange.

    PubMed

    Tanaka, K; Gajendiran, N; Endo, S; Komatsu, K; Hoshi, M; Kamada, N

    1999-12-01

    This study was undertaken to investigate the biological effect of monoenergetic neutrons on human lymphocyte DNA and chromosomes. Monoenergetic neutrons of 2.3, 1.0, 0.79, 0.57, 0.37 and 0.186 MeV were generated, and 252Cf neutrons and 60Co gamma-rays were also used for comparison. Biological effect was evaluated two ways. The RBE values with the comet assay were estimated as 6.3 and 5.4 at 0.37 MeV and 0.57 MeV relative to that of 60Co gamma-rays, and chromosome aberration rates were also observed in these different levels of monoenergetic neutrons. The yield of chromosome aberrations per unit dose was high at lower neutron energies with a gradual decline with 0.186 MeV neutron energy. The RBE was increased to 10.7 at 0.57 MeV from 3.9 at 252Cf neutrons and reached 16.4 as the highest RBE at 0.37 MeV, but the value decreased to 11.2 at 0.186 MeV. The response patterns of initial DNA damage and chromosome exchange were quite similar to that of LET. These results show that the intensity of DNA damage and chromosomal exchange is LET dependent. RBE of low energy neutrons is higher than that of fission neutrons. Low energy neutrons containing Hiroshima atomic bomb radiation may have created a significantly higher incidence of biological effect in atomic bomb survivors.

  6. Nbs1-dependent binding of Mre11 to adenovirus E4 mutant viral DNA is important for inhibiting DNA replication

    SciTech Connect

    Mathew, Shomita S.; Bridge, Eileen

    2008-04-25

    Adenovirus (Ad) infections stimulate the activation of cellular DNA damage response and repair pathways. Ad early regulatory proteins prevent activation of DNA damage responses by targeting the MRN complex, composed of the Mre11, Rad50 and Nbs1 proteins, for relocalization and degradation. In the absence of these viral proteins, Mre11 colocalizes with viral DNA replication foci. Mre11 foci formation at DNA damage induced by ionizing radiation depends on the Nbs1 component of the MRN complex and is stabilized by the mediator of DNA damage checkpoint protein 1 (Mdc1). We find that Nbs1 is required for Mre11 localization at DNA replication foci in Ad E4 mutant infections. Mre11 is important for Mdc1 foci formation in infected cells, consistent with its role as a sensor of DNA damage. Chromatin immunoprecipitation assays indicate that both Mre11 and Mdc1 are physically bound to viral DNA, which could account for their localization in viral DNA containing foci. Efficient binding of Mre11 to E4 mutant DNA depends on the presence of Nbs1, and is correlated with a significant E4 mutant DNA replication defect. Our results are consistent with a model in which physical interaction of Mre11 with viral DNA is mediated by Nbs1, and interferes with viral DNA replication.

  7. Global strong solution to compressible Navier-Stokes equations with density dependent viscosity and temperature dependent heat conductivity

    NASA Astrophysics Data System (ADS)

    Duan, Ran; Guo, Ai; Zhu, Changjiang

    2017-04-01

    We obtain existence and uniqueness of global strong solution to one-dimensional compressible Navier-Stokes equations for ideal polytropic gas flow, with density dependent viscosity and temperature dependent heat conductivity under stress-free and thermally insulated boundary conditions. Here we assume viscosity coefficient μ (ρ) = 1 +ρα and heat conductivity coefficient κ (θ) =θβ for all α ∈ [ 0 , ∞) and β ∈ (0 , + ∞).

  8. Distance-Dependent Measurements of the Conductance of Porphyrin Nanorods Studied with Conductive Probe Atomic Force Microscopy.

    PubMed

    Zhai, Xianglin; Alexander, Denzel; Derosa, Pedro; Garno, Jayne C

    2017-02-07

    Protocols for nanopatterning porphyrins on Au(111) were developed based on immersion particle lithography. Porphyrins with and without a central metal ion, 5,10,15,20-tetraphenyl-21H,23H-porphyrin (TPP) and 5,10,15,20-tetraphenyl-21H,23H-porphyrin cobalt(II) (CoTPP), were selected for study, which spontaneously formed nanorod geometries depending on concentration parameters. The elongated shapes of the nanorods offers an opportunity for successive distance-dependent conductive probe atomic force microscopy (CP-AFM) measurements along the length of the nanorods. To prepare patterns of TPP and CoTPP nanorods, a mask of silica mesospheres was placed on gold substrates to generate nanoholes within an alkanethiol matrix film. The nanoholes prepared by particle lithography with an immersion step were backfilled with porphyrins by a second immersion step. By controlling the concentration and immersion interval, nanorods of porphyrins were generated with one end of the nanostructure attached to gold within a nanohole. The porphyrin nanorods exhibited slight differences in dimensions at the nanoscale to enable size-dependent measurements of conductive properties. The conductivity along the horizontal direction of the nanorods was evaluated with CP-AFM studies. Changes in conductivity were measured along the long axis of TPP and CoTPP nanorods. The TPP nanorods exhibited conductive profiles of an insulating material, and the CoTPP nanorods exhibited profiles of a semiconductor. The experiments demonstrate the applicability of particle lithography for preparing unique and functional surface platforms of porphyrins to measure distance-dependent conductive properties on gold.

  9. Temperature dependence of dc electrical conductivity of activated carbon-metal oxide nanocomposites. Some insight into conduction mechanisms

    NASA Astrophysics Data System (ADS)

    Barroso-Bogeat, Adrián; Alexandre-Franco, María; Fernández-González, Carmen; Sánchez-González, José; Gómez-Serrano, Vicente

    2015-12-01

    From a commercial activated carbon (AC) and six metal oxide (Al2O3, Fe2O3, SnO2, TiO2, WO3 and ZnO) precursors, two series of AC-metal oxide nanocomposites are prepared by wet impregnation, oven-drying at 120 °C, and subsequent heat treatment at 200 or 850 °C in inert atmosphere. The temperature-dependent dc electrical conductivity of AC and the as-prepared nanocomposites is measured from room temperature up to ca. 200 °C in air atmosphere by the four-probe method. The decrease in conductivity for the hybrid materials as compared to AC is the result of a complex interplay between several factors, including not only the intrinsic conductivity, crystallite size, content and chemical nature of the supported nanoparticles, which ultimately depend on the precursor and heat treatment temperature, but also the adsorption of oxygen and water from the surrounding atmosphere. The conductivity data are discussed in terms of a thermally activated process. In this regard, both AC and the prepared nanocomposites behave as semiconductors, and the temperature-dependent conductivity data have been interpreted on the basis of the classical model proposed by Mott and Davis. Because of its high content of heteroatoms, AC may be considered as a heavily doped semiconductor, so that conduction of thermally excited carriers via acceptor or donor levels is expected to be the dominant mechanism. The activation energies for the hybrid materials suggest that the supported metal oxide nanoparticles strongly modify the electronic band structure of AC by introducing new trap levels in different positions along its band gap. Furthermore, the thermally activated conduction process satisfies the Meyer-Neldel rule, which is likely connected with the shift of the Fermi level due to the introduction of the different metal oxide nanoparticles in the AC matrix.

  10. Charge conduction properties of a parallel-stranded DNA G-quadruplex: implications for chromosomal oxidative damage.

    PubMed

    Huang, Yu Chuan; Cheng, Alan K H; Yu, Hua-Zhong; Sen, Dipankar

    2009-07-28

    The charge-flow properties and concomitant guanine damage patterns of a number of intermolecular and wholly parallel-stranded DNA G-quadruplexes were investigated. The DNA constructs were structurally well-defined and consisted of the G-quadruplex sandwiched and stacked between two Watson-Crick base-paired duplexes. Such duplex-quadruplex-duplex constructs were designed to minimize torsional stress as well as steric crowding at the duplex-quadruplex junctions. When anthraquinone was used to induce charge flow within the constructs, it was found that the quadruplex served both as a sink and as a moderately good conductor of electron holes, relative to DNA duplexes. Most strikingly, the quadruplex suffered very little charge-flow generated oxidative damage relative to guanines in the duplex regions and, indeed, to guanines in antiparallel quadruplexes reported in prior studies. It is likely that these differences result from a combination of steric and electronic factors. A biological conclusion that may be drawn from these data is that if, as anticipated, G-quadruplex structures form in vivo at the telomeres and other loci in eukaryotic chromosomes, their ability to serve as protective sinks against chromosomal oxidative damage may depend on their specific character and topology. From a separate perspective, our results on the conduction properties of duplex-quadruplex-duplex DNA composites suggest the utility of G-quadruplexes as junction modules in the construction of DNA-based biosensors and nanocircuitry.

  11. Recognition tunneling measurement of the conductance of DNA bases embedded in self-assembled monolayers.

    PubMed

    Huang, Shuo; Chang, Shuai; He, Jin; Zhang, Peiming; Liang, Feng; Tuchband, Michael; Li, Shengqing; Lindsay, Stuart

    2010-12-09

    The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson Crick base pairs. When bases are embedded in a self-assembled alkane-thiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density-functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs.

  12. Simultaneous retrieval of temperature-dependent absorption coefficient and conductivity of participating media

    PubMed Central

    Ren, Yatao; Qi, Hong; Zhao, Fangzhou; Ruan, Liming; Tan, Heping

    2016-01-01

    A secondary optimization technique was proposed to estimate the temperature-dependent thermal conductivity and absorption coefficient. In the proposed method, the stochastic particle swarm optimization was applied to solve the inverse problem. The coupled radiation and conduction problem was solved in a 1D absorbing, emitting, but non-scattering slab exposed to a pulse laser. It is found that in the coupled radiation and conduction problem, the temperature response is highly sensitive to conductivity but slightly sensitive to the optical properties. On the contrary, the radiative intensity is highly sensitive to optical properties but slightly sensitive to thermal conductivity. Therefore, the optical and thermal signals should both be considered in the inverse problem to estimate the temperature-dependent properties of the transparent media. On this basis, the temperature-dependent thermal conductivity and absorption coefficient were both estimated accurately by measuring the time-dependent temperature, and radiative response at the boundary of the slab. PMID:26912418

  13. A robust assay to measure DNA topology-dependent protein binding affinity.

    PubMed

    Litwin, Tamara R; Solà, Maria; Holt, Ian J; Neuman, Keir C

    2015-04-20

    DNA structure and topology pervasively influence aspects of DNA metabolism including replication, transcription and segregation. However, the effects of DNA topology on DNA-protein interactions have not been systematically explored due to limitations of standard affinity assays. We developed a method to measure protein binding affinity dependence on the topology (topological linking number) of supercoiled DNA. A defined range of DNA topoisomers at equilibrium with a DNA binding protein is separated into free and protein-bound DNA populations using standard nitrocellulose filter binding techniques. Electrophoretic separation and quantification of bound and free topoisomers combined with a simple normalization procedure provide the relative affinity of the protein for the DNA as a function of linking number. Employing this assay we measured topology-dependent DNA binding of a helicase, a type IB topoisomerase, a type IIA topoisomerase, a non-specific mitochondrial DNA binding protein and a type II restriction endonuclease. Most of the proteins preferentially bind negatively supercoiled DNA but the details of the topology-dependent affinity differ among proteins in ways that expose differences in their interactions with DNA. The topology-dependent binding assay provides a robust and easily implemented method to probe topological influences on DNA-protein interactions for a wide range of DNA binding proteins.

  14. DNA base pair stacks with high electric conductance: a systematic structural search.

    PubMed

    Berlin, Yuri A; Voityuk, Alexander A; Ratner, Mark A

    2012-09-25

    We report a computational search for DNA π-stack structures exhibiting high electric conductance in the hopping regime, based on the INDO/S calculations of electronic coupling and the method of data analysis called k-means clustering. Using homogeneous poly(G)-poly(C) and poly(A)-poly(T) stacks as the simplest structural models, we identify the configurations of neighboring G:C and A:T pairs that allow strong electronic coupling and, therefore, molecular electric conductance much larger than the values reported for the corresponding reference systems in the literature. A computational approach for modeling the impact of thermal fluctuations on the averaged dimer structure was also proposed and applied to the [(G:C),(G:C)] and [(A:T),(A:T)] duplexes. The results of this work may provide guidance for the construction of DNA devices and DNA-based elements of nanoscale molecular circuits. Several factors that cause changes of step parameters favorable to the formation of the predicted stack conformation with high electric conductance of DNA molecules are also discussed; favorable geometries may enhance the conductivity by factors as large as 15.

  15. Study of the dependence the thermal conductivity of nanofluids on different parameters

    NASA Astrophysics Data System (ADS)

    Pryazhnikov, M. I.; Minakov, A. V.; Guzei, D. V.; Rudyak, V. Ya

    2016-10-01

    The paper presents the results of systematic measurements of the thermal conductivity coefficient of nanofluids at room temperature. It is shown that the thermal conductivity of all considered nanofluids depend on concentration, nanopartical size, as well as the base fluid properties. It was revealed that thermal conductivity coefficient of nanofluids increases with increasing concentration and size of nanoparticles.

  16. p53 inhibits DNA replication in vitro in a DNA-binding-dependent manner.

    PubMed Central

    Miller, S D; Farmer, G; Prives, C

    1995-01-01

    The p53 tumor suppressor gene product is a sequence-specific DNA-binding protein that is necessary for the G1 arrest of many cell types. Consistent with its role as a cell cycle checkpoint factor, p53 has been shown to be capable of both transcriptional activation and repression. Here we show a new potential role for p53 as a DNA-binding-dependent regulator of DNA replication. Constructs containing multiple copies of the ribosomal gene cluster (RGC) p53 binding site cloned on the late side of the polyomavirus origin were used in in vitro replication assays. In the presence of p53, the replication of these constructs was strongly inhibited, while the replication of constructs containing a mutant version of the RGC site was not affected by p53. Several tumor-derived mutant p53 proteins were unable to inhibit replication of the construct with wild-type RGC sites. Additionally, the transactivator GAL4-VP16 was unable to inhibit replication of a construct containing GAL4 binding sites adjacent to the polyomavirus origin. We also show that the inhibition by p53 can occur from sites cloned as far as 600 bp from the origin. Preincubation experiments suggest that p53 inhibits replication at a step mediated by ATP, possibly by inhibiting the binding of polyomavirus T antigen to the core origin. The presence of an endogenous p53 binding site in the polyomavirus origin suggests potential mechanisms for the observed inhibition. PMID:8524220

  17. The DNA-dependent protein kinase: A multifunctional protein kinase with roles in DNA double strand break repair and mitosis.

    PubMed

    Jette, Nicholas; Lees-Miller, Susan P

    2015-03-01

    The DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase composed of a large catalytic subunit (DNA-PKcs) and the Ku70/80 heterodimer. Over the past two decades, significant progress has been made in elucidating the role of DNA-PK in non-homologous end joining (NHEJ), the major pathway for repair of ionizing radiation-induced DNA double strand breaks in human cells and recently, additional roles for DNA-PK have been reported. In this review, we will describe the biochemistry, structure and function of DNA-PK, its roles in DNA double strand break repair and its newly described roles in mitosis and other cellular processes.

  18. Cell cycle regulation of DNA double-strand break end resection by Cdk1-dependent Dna2 phosphorylation.

    PubMed

    Chen, Xuefeng; Niu, Hengyao; Chung, Woo-Hyun; Zhu, Zhu; Papusha, Alma; Shim, Eun Yong; Lee, Sang Eun; Sung, Patrick; Ira, Grzegorz

    2011-08-14

    DNA recombination pathways are regulated by the cell cycle to coordinate with replication. Cyclin-dependent kinase (Cdk1) promotes efficient 5' strand resection at DNA double-strand breaks (DSBs), the initial step of homologous recombination and damage checkpoint activation. The Mre11-Rad50-Xrs2 complex with Sae2 initiates resection, whereas two nucleases, Exo1 and Dna2, and the DNA helicase-topoisomerase complex Sgs1-Top3-Rmi1 generate longer ssDNA at DSBs. Using Saccharomyces cerevisiae, we provide evidence for Cdk1-dependent phosphorylation of the resection nuclease Dna2 at Thr4, Ser17 and Ser237 that stimulates its recruitment to DSBs, resection and subsequent Mec1-dependent phosphorylation. Poorly recruited dna2T4A S17A S237A and dna2ΔN248 mutant proteins promote resection only in the presence of Exo1, suggesting cross-talk between Dna2- and Exo1-dependent resection pathways.

  19. On-chip DNA preconcentration in different media conductivities by electrodeless dielectrophoresis.

    PubMed

    Li, Shunbo; Ye, Ziran; Hui, Yu Sanna; Gao, Yibo; Jiang, Yusheng; Wen, Weijia

    2015-09-01

    Electrodeless dielectrophoresis is the best choice to achieve preconcentration of nanoparticles and biomolecules due to its simple, robust, and easy implementation. We designed a simple chip with microchannels and nano-slits in between and then studied the trapping of DNA in high conductive medium and low conductive medium, corresponding to positive and negative dielectrophoresis (DEP), respectively. It is very important to investigate the trapping in media with different conductivities since one always has to deal with the sample solutions with different conductivities. The trapping process was analyzed by the fluorescent intensity changes. The results showed that DNA could be trapped at the nano-slit in both high and low conductive media in a lower electric field strength (10 V/cm) compared to the existing methods. This is a significant improvement to suppress the Joule heating effect in DEP related experiments. Our work may give insight to researchers for DNA trapping by a simple and low cost device in the Lab-on-a-Chip system.

  20. pH- and voltage-dependent conductances in toad skin.

    PubMed

    Lacaz-Vieira, F

    1995-11-01

    The present study focuses on two closely related topics on ion conductance in toad skins: (i) the interaction of apical protons with the apical voltage-dependent Cl(-)-activated channels of the mitochondria-rich cells, and (ii) the description and characterization of a novel subject, a voltage-dependent H(+)-activated conductance. The Cl- conductance (GCl) is activated by tissue hyperpolarization (which leads to apical membrane depolarization) and the presence of Cl- ions in the apical solution. Increasing apical proton concentration (from pH 8 to pH 4) impairs the process of activation of the Cl- conductive pathway, slowing the kinetics of It activation and reducing the steady-stage values of Gt and It. This effect is markedly voltage-dependent since no effect is seen at Vt = -100 mv and is fully present at -50 mV. The voltage-dependence of the pH effect suggests that the critical protonation sites of the apical Cl- channels are not freely exposed to the apical solution but dwell within the membrane electric field. An also coherent interpretation is that titration of apical proton binding sites affects the gating of the voltage-dependent Cl- channels, shifting the conductance-vs.-voltage curve to more negative clamping potentials. Tissue conductance in the absence of apical Cl- ions can be importantly affected by the pH of the apical solution (pHa), the effect being markedly dependent on the clamping potential. Generally speaking, the effect of rising apical proton concentration can be conspicuous at negative clamping potentials, while at positive potentials changes in tissue conductance were never observed. For a clamping potential of -100 mV, a turning point somewhere between pHa = 4 and pHa = 3 was observed. Apical acidification to pH 4 has no effect upon tissue conductance while apical acidification to pH 3 leads to a marked, slow and reversible increase of tissue conductance. A striking similitude exists between the voltage-dependent Cl(-)-gated conductance

  1. Diameter Dependence of Lattice Thermal Conductivity of Single-Walled Carbon Nanotubes: Study from Ab Initio.

    PubMed

    Yue, Sheng-Ying; Ouyang, Tao; Hu, Ming

    2015-10-22

    The effects of temperature, tube length, defects, and surface functionalization on the thermal conductivity (κ) of single-walled carbon nanotubes (SWCNTs) were well documented in literature. However, diameter dependence of thermal conductivity of SWCNTs received less attentions. So far, diverse trends of the diameter dependence have been discussed by different methods and all the previous results were based on empirical interatomic potentials. In this paper, we emphasize to clarify accurate κ values of SWCNTs with different diameters and in-plane κ of graphene. All the studies were under the framework of anharmonic lattice dynamics and Boltzmann transport equation (BTE) based on first principle calculations. We try to infer the right trend of diameter dependent thermal conductivity of SWCNTs. We infer that graphene is the limitation as SWCNT with an infinite diameter. We analyzed the thermal conductivity contributions from each phonon mode in SWCNTs to explain the trend. Meanwhile, we also identify the extremely low thermal conductivity of ultra-thin SWCNTs.

  2. SIRT6 stabilizes DNA-dependent Protein Kinase at chromatin for DNA double-strand break repair

    PubMed Central

    McCord, Ronald A.; Michishita, Eriko; Hong, Tao; Berber, Elisabeth; Boxer, Lisa D.; Kusumoto, Rika; Guan, Shenheng; Shi, Xiaobing; Gozani, Or; Burlingame, Alma L.; Bohr, Vilhelm A.; Chua, Katrin F.

    2009-01-01

    The Sir2 chromatin regulatory factor links maintenance of genomic stability to life span extension in yeast. The mammalian Sir2 family member SIRT6 has been proposed to have analogous functions, because SIRT6-deficiency leads to shortened life span and an aging-like degenerative phenotype in mice, and SIRT6 knockout cells exhibit genomic instability and DNA damage hypersensitivity. However, the molecular mechanisms underlying these defects are not fully understood. Here, we show that SIRT6 forms a macromolecular complex with the DNA double-strand break (DSB) repair factor DNA-PK (DNA-dependent protein kinase) and promotes DNA DSB repair. In response to DSBs, SIRT6 associates dynamically with chromatin and is necessary for an acute decrease in global cellular acetylation levels on histone H3 Lysine 9. Moreover, SIRT6 is required for mobilization of the DNA-PK catalytic subunit (DNA-PKcs) to chromatin in response to DNA damage and stabilizes DNA-PKcs at chromatin adjacent to an induced site-specific DSB. Abrogation of these SIRT6 activities leads to impaired resolution of DSBs. Together, these findings elucidate a mechanism whereby regulation of dynamic interaction of a DNA repair factor with chromatin impacts on the efficiency of repair, and establish a link between chromatin regulation, DNA repair, and a mammalian Sir2 factor. PMID:20157594

  3. DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires

    PubMed Central

    Liu, Dage; Park, Sung Ha; Reif, John H.; LaBean, Thomas H.

    2004-01-01

    DNA-based nanotechnology is currently being developed as a general assembly method for nanopatterned materials that may find use in electronics, sensors, medicine, and many other fields. Here we present results on the construction and characterization of DNA nanotubes, a self-assembling superstructure composed of DNA tiles. Triple-crossover tiles modified with thiol-containing double-stranded DNA stems projected out of the tile plane were used as the basic building blocks. Triple-crossover nanotubes display a constant diameter of ≈25 nm and have been observed with lengths up to 20 μm. We present high-resolution images of the constructs, experimental evidence of their tube-like nature as well as data on metallization of the nanotubes to form nanowires, and electrical conductivity measurements through the nanowires. DNA nanotubes represent a potential breakthrough in the self-assembly of nanometer-scale circuits for electronics layout because they can be targeted to connect at specific locations on larger-scale structures and can subsequently be metallized to form nanometer-scale wires. The dimensions of these nanotubes are also perfectly suited for applications involving interconnection of molecular-scale devices with macroscale components fabricated by conventional photolithographic methods. PMID:14709674

  4. Modeling the electrical conduction in DNA nanowires: charge transfer and lattice fluctuation theories.

    PubMed

    Behnia, S; Fathizadeh, S

    2015-02-01

    An analytical approach is proposed for the investigation of the conductivity properties of DNA. The charge mobility of DNA is studied based on an extended Peyrard-Bishop-Holstein model when the charge carrier is also subjected to an external electrical field. We have obtained the values of some of the system parameters, such as the electron-lattice coupling constant, by using the mean Lyapunov exponent method. On the other hand, the electrical current operator is calculated directly from the lattice operators. Also, we have studied Landauer resistance behavior with respect to the external field, which could serve as the interface between chaos theory tools and electronic concepts. We have examined the effect of two types of electrical fields (dc and ac) and variation of the field frequency on the current flowing through DNA. A study of the current-voltage (I-V) characteristic diagram reveals regions with a (quasi-)Ohmic property and other regions with negative differential resistance (NDR). NDR is a phenomenon that has been observed experimentally in DNA at room temperature. We have tried to study the affected agents in charge transfer phenomena in DNA to better design nanostructures.

  5. Bias-dependent conductive characteristics of individual GeSi quantum dots studied by conductive atomic force microscopy.

    PubMed

    Wu, R; Zhang, S L; Lin, J H; Jiang, Z M; Yang, X J

    2011-03-04

    The bias-dependent electrical characteristics of individual self-assembled GeSi quantum dots (QDs) are investigated by conductive atomic force microscopy. The results reveal that the conductive characteristics of QDs are strongly influenced by the applied bias. At low (-0.5 to - 2.0 V) and high (-2.5 to - 4.0 V) biases, the current distributions of individual GeSi QDs exhibit ring-like and disc-like characteristics respectively. The current of the QD's central part increases more quickly than that of the other parts as the bias magnitude increases. Histograms of the magnitude of the current on a number of QDs exhibit the same single-peak feature at low biases, and double- or three-peak features at high biases, where additional peaks appear at large-current locations. On the other hand, histograms of the magnitude of the current on the wetting layers exhibit the same single-peak feature for all biases. This indicates the conductive mechanism is significantly different for QDs and wetting layers. While the small-current peak of QDs can be attributed to the Fowler-Nordheim tunneling model at low biases and the Schottky emission model at high biases respectively, the large-current peak(s) may be attributed to the discrete energy levels of QDs. The results suggest the conductive mechanisms of GeSi QDs can be regulated by the applied bias.

  6. Probing DNA by 2-OG-dependent dioxygenase

    PubMed Central

    Tsai, Chi-Lin; Tainer, John A.

    2014-01-01

    TET-mediated 5-methyl cytosine (5mC) oxidation acts in epigenetic regulation, stem cell development, and cancer. Hu et al. now determine the crystal structure of the TET2 catalytic domain bound to DNA, shedding light on 5mC-DNA substrate recognition and the catalytic mechanism of 5mC oxidation. PMID:24360270

  7. Structured DNA promotes phosphorylation of p53 by DNA-dependent protein kinase at serine 9 and threonine 18.

    PubMed

    Soubeyrand, Sébastien; Schild-Poulter, Caroline; Haché, Robert J G

    2004-09-01

    Phosphorylation at multiple sites within the N-terminus of p53 promotes its dissociation from hdm2/mdm2 and stimulates its transcriptional regulatory potential. The large phosphoinositide 3-kinase-like kinases ataxia telangiectasia mutated gene product and the ataxia telangectasia and RAD-3-related kinase promote phosphorylation of human p53 at Ser15 and Ser20, and are required for the activation of p53 following DNA damage. DNA-dependent protein kinase (DNA-PK) is another large phosphoinositide 3-kinase-like kinase with the potential to phosphorylate p53 at Ser15, and has been proposed to enhance phosphorylation of these sites in vivo. Moreover, recent studies support a role for DNA-PK in the regulation of p53-mediated apoptosis. We have shown previously that colocalization of p53 and DNA-PK to structured single-stranded DNA dramatically enhances the potential for p53 phosphorylation by DNA-PK. We report here the identification of p53 phosphorylation at two novel sites for DNA-PK, Thr18 and Ser9. Colocalization of p53 and DNA-PK on structured DNA was required for efficient phosphorylation of p53 at multiple sites, while specific recognition of Ser9 and Thr18 appeared to be dependent upon additional determinants of p53 beyond the N-terminal 65 amino acids. Our results suggest a role for DNA-PK in the modulation of p53 activity resultant from the convergence of p53 and DNA-PK on structured DNA.

  8. Doping, Ionic Conductivity and Photothermal Stability of Functionalized DNA for Solar Energy Conversion and Electrochromic Applications

    DTIC Science & Technology

    2011-06-01

    to 85 0C and the optical absorption spectra were monitored as function of time. Similar experiments were done using the UV light to degrade the...Rh590 – rhodamine 590 Rh610 – rhodamine 610 SHG – second harmonic generation THZ – Tetra Hertz UV – ultraviolet light VIS – visible light ...AFRL-AFOSR-UK-TR-2011-0025 DOPING , IONIC CONDUCTIVITY AND PHOTOTHERMAL STABILITY OF FUNCTIONALIZED DNA FOR SOLAR ENERGY CONVERSION

  9. Artemis phosphorylated by DNA-dependent protein kinase associates preferentially with discrete regions of chromatin.

    PubMed

    Soubeyrand, Sébastien; Pope, Louise; De Chasseval, Régina; Gosselin, Dominique; Dong, Fumin; de Villartay, Jean-Pierre; Haché, Robert J G

    2006-05-19

    Artemis is a nuclear phosphoprotein required for genomic integrity whose phosphorylation is increased subsequent to DNA damage. Artemis phosphorylation by the DNA-dependent protein kinase (DNA-PK) and the association of Artemis with DNA-PK catalytic subunit (DNA-PKcs) have been proposed to be crucial for the variable, diversity, joining (V(D)J) reaction, genomic stability and cell survival in response to double-stranded DNA breaks. The exact nature of the effectors of Artemis phosphorylation is presently being debated. Here, we have delimited the interface on Artemis required for its association with DNA-PKcs and present the characterization of six DNA-PK phosphorylation sites on Artemis whose phosphorylation shows dependence on its association with DNA-PKcs and is induced by double-stranded DNA damage. Surprisingly, DNA-PKcs Artemis association appeared to be dispensable in a V(D)J recombination assay with stably integrated DNA substrates. Phosphorylation at two of the sites on Artemis, S516 and S645, was verified in vivo using phosphospecific antibodies. Basal Artemis S516 and S645 phosphorylation in vivo showed a significant dependence on DNA-PKcs association. However, regardless of its association with DNA-PKcs, phosphorylation of Artemis at both S516 and S645 was stimulated in response to the double-stranded DNA-damaging agent bleomycin, albeit to a lesser extent. This suggests that additional factors contribute to promote DNA damage-induced Artemis phosphorylation. Intriguingly, pS516/pS645 Artemis was concentrated in chromatin-associated nuclear foci in naïve cells. These foci were maintained upon DNA damage but failed to overlap with the damage-induced gammaH2AX. These results provide the expectation of a specific role for DNA-PK-phosphorylated Artemis in both naïve and damaged cells.

  10. Frequency dependent optical conductivity of strained graphene at T=0 from an effective quantum field theory

    NASA Astrophysics Data System (ADS)

    Zhang, Shi-Jiang; Pan, Hui; Wang, Hai-Long

    2017-04-01

    An effective quantum field theory (EQFT) graphene sheet with arbitrary one dimensional strain field is derived from a microscopic effective low energy Hamiltonian. The geometric meaning of the strain-induced complex gauge field is clarified. The optical conductivity is also investigated, and a frequency dependent optical conductivity is obtained. The actual value of interband optical conductivity along the deformed direction is C0 + C1/ω2 in spite of the particular strain fields at T=0.

  11. Detecting ATM-Dependent Chromatin Modification in DNA Damage Response

    PubMed Central

    Udayakumar, Durga; Horikoshi, Nobuo; Mishra, Lope; Hunt, Clayton; Pandita, Tej K.

    2015-01-01

    Loss of function or mutation of the ataxia–telangiectasia mutated gene product (ATM) results in inherited genetic disorders characterized by neurodegeneration, immunodeficiency, and cancer. Ataxia-telangiectasia mutated (ATM) gene product belongs to the PI3K-like protein kinase (PIKKs) family and is functionally implicated in mitogenic signal transduction, chromosome condensation, meiotic recombination, cell-cycle control, and telomere maintenance. The ATM protein kinase is primarily activated in response to DNA double strand breaks (DSBs), the most deleterious form of DNA damage produced by ionizing radiation (IR) or radiomimetic drugs. It is detected at DNA damage sites, where ATM autophosphorylation causes dissociation of the inactive homodimeric form to the activated monomeric form. Interestingly, heat shock can activate ATM independent of the presence of DNA strand breaks. ATM is an integral part of the sensory machinery that detects DSBs during meiosis, mitosis, or DNA breaks mediated by free radicals. These DNA lesions can trigger higher order chromatin reorganization fuelled by posttranslational modifications of histones and histone binding proteins. Our group, and others, have shown that ATM activation is tightly regulated by chromatin modifications. This review summarizes the multiple approaches used to discern the role of ATM and other associated proteins in chromatin modification in response to DNA damage. PMID:25827888

  12. The dependence of the electronic conductivity of carbon molecular sieve electrodes on their charging states.

    PubMed

    Pollak, Elad; Genish, Isaschar; Salitra, Gregory; Soffer, Abraham; Klein, Lior; Aurbach, Doron

    2006-04-13

    The dependence of the electronic conductivity of activated carbon electrodes on their potential in electrolyte solutions was examined. Kapton polymer films underwent carbonization (1000 degrees C), followed by a mild oxidation process (CO(2) at 900 degrees C) for various periods of time, to obtain carbons of different pore structures. A specially designed cell was assembled in order to measure the conductivity of carbon electrodes at different potentials in solutions. When the carbon electrodes possessed molecular sieving properties, a remarkable dependence of their conductivity on their charging state was observed. Aqueous electrolyte solutions containing ions of different sizes were used in order to demonstrate this phenomenon. As the average pore size of the activated carbons was larger, their molecular sieving ability was lower, and the dependence of their conductivity on their charging state regained its classical form. This behavior is discussed herein.

  13. Enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface.

    PubMed

    Williamson, Adele; Rothweiler, Ulli; Leiros, Hanna Kirsti Schrøder

    2014-11-01

    DNA ligases are a structurally diverse class of enzymes which share a common catalytic core and seal breaks in the phosphodiester backbone of double-stranded DNA via an adenylated intermediate. Here, the structure and activity of a recombinantly produced ATP-dependent DNA ligase from the bacterium Psychromonas sp. strain SP041 is described. This minimal-type ligase, like its close homologues, is able to ligate singly nicked double-stranded DNA with high efficiency and to join cohesive-ended and blunt-ended substrates to a more limited extent. The 1.65 Å resolution crystal structure of the enzyme-adenylate complex reveals no unstructured loops or segments, and suggests that this enzyme binds the DNA without requiring full encirclement of the DNA duplex. This is in contrast to previously characterized minimal DNA ligases from viruses, which use flexible loop regions for DNA interaction. The Psychromonas sp. enzyme is the first structure available for the minimal type of bacterial DNA ligases and is the smallest DNA ligase to be crystallized to date.

  14. Prooxidant action of chebulinic acid and tellimagrandin I: causing copper-dependent DNA strand breaks.

    PubMed

    Yi, Zong-Chun; Liu, Yan-Ze; Li, Hai-Xia; Wang, Zhao

    2009-04-01

    The prooxidant activity of two hydrolysable tannins, chebulinic acid and tellimagrandin I, on plasmid DNA and genomic DNA of cultured MRC-5 human embryo lung fibroblasts was assessed. The results revealed that both hydrolysable tannins in combination with Cu(II) induced DNA strand breaks in pBR322 plasmid DNA in a concentration-dependent manner. Chebulinic acid and tellimagrandin I also induced genomic DNA strand breaks of MRC-5 human embryo lung fibroblasts in the presence of Cu(II). After treatment with chebulinic acid or tellimagrandin I alone, the pBR322 plasmid DNA and genomic DNA in MRC-5 cells kept intact. In addition, addition of Cu(I) reagent bathocuproinedisulfonic acid or catalase markedly inhibited the copper-dependent DNA strand breaks by both tannins. However, three typical hydroxyl radical scavengers, DMSO, ethanol and mannitol, did not inhibit the DNA strand breaks. Both tannins were able to reduce Cu(II) to Cu(I). These results indicated that chebulinic acid and tellimagrandin I induced the copper-dependent strand breaks of pBR322 plasmid DNA and MRC-5 genomic DNA with prooxidant action, in which Cu(II)/Cu(I) redox cycle and H(2)O(2) were involved and hydroxyl radical formation is important in the hypothetical mechanism by which DNA strand breaks are formed.

  15. Atomistic Simulation of the Size and Orientation Dependences of Thermal Conductivity in GaN Nanowires

    SciTech Connect

    Wang, Zhiguo; Zu, Xiaotao; Gao, Fei; Weber, William J.; Crocombette, J.-P.

    2007-04-16

    The thermal conductivity of GaN nanowires has been determined computationally, by applying nonequilibrium atomistic simulation methods using the Stillinger-Weber [Phys. Rev. B 31, 5262 (1985)] potentials. The simulation results show that the thermal conductivity of the GaN nanowires is smaller than that of a bulk crystal and increases with increasing diameter. Surface scattering of phonons and the high surface to volume ratios of the nanowires are primarily responsible for the reduced thermal conductivity and its size dependence behavior. The thermal conductivity is also found to decrease with increasing temperature, which is due to phonon-phonon interactions at high temperatures. The thermal conductivity also exhibits a dependence on axial orientation of the nanowires.

  16. Orientation dependent thermal conductance in single-layer MoS2.

    PubMed

    Jiang, Jin-Wu; Zhuang, Xiaoying; Rabczuk, Timon

    2013-01-01

    We investigate the thermal conductivity in the armchair and zigzag MoS2 nanoribbons, by combining the non-equilibrium Green's function approach and the first-principles method. A strong orientation dependence is observed in the thermal conductivity. Particularly, the thermal conductivity for the armchair MoS2 nanoribbon is about 673.6 Wm(-1) K(-1) in the armchair nanoribbon, and 841.1 Wm(-1) K(-1) in the zigzag nanoribbon at room temperature. By calculating the Caroli transmission, we disclose the underlying mechanism for this strong orientation dependence to be the fewer phonon transport channels in the armchair MoS2 nanoribbon in the frequency range of [150, 200] cm(-1). Through the scaling of the phonon dispersion, we further illustrate that the thermal conductivity calculated for the MoS2 nanoribbon is esentially in consistent with the superior thermal conductivity found for graphene.

  17. Orientation Dependent Thermal Conductance in Single-Layer MoS2

    NASA Astrophysics Data System (ADS)

    Jiang, Jin-Wu; Zhuang, Xiaoying; Rabczuk, Timon

    2013-07-01

    We investigate the thermal conductivity in the armchair and zigzag MoS2 nanoribbons, by combining the non-equilibrium Green's function approach and the first-principles method. A strong orientation dependence is observed in the thermal conductivity. Particularly, the thermal conductivity for the armchair MoS2 nanoribbon is about 673.6 Wm-1 K-1 in the armchair nanoribbon, and 841.1 Wm-1 K-1 in the zigzag nanoribbon at room temperature. By calculating the Caroli transmission, we disclose the underlying mechanism for this strong orientation dependence to be the fewer phonon transport channels in the armchair MoS2 nanoribbon in the frequency range of [150, 200] cm-1. Through the scaling of the phonon dispersion, we further illustrate that the thermal conductivity calculated for the MoS2 nanoribbon is esentially in consistent with the superior thermal conductivity found for graphene.

  18. Evidence that recBC-dependent degradation of duplex DNA in Escherichia coli recD mutants involves DNA unwinding.

    PubMed Central

    Rinken, R; Thomas, B; Wackernagel, W

    1992-01-01

    Infection of Escherichia coli with phage T4 gene 2am was used to transport 3H-labeled linear duplex DNA into cells to follow its degradation in relation to the cellular genotype. In wild-type cells, 49% of the DNA was made acid soluble within 60 min; in recB or recC cells, only about 5% of the DNA was made acid soluble. Remarkably, in recD cells about 25% of the DNA was rendered acid soluble. The DNA degradation in recD cells depended on intact recB and recC genes. The degradation in recD cells was largely decreased by mutations in recJ (which eliminates the 5' single-strand-specific exonuclease coded by this gene) or xonA (which abolishes the 3' single-strand-specific exonuclease I). In a recD recJ xonA triple mutant, the degradation of linear duplex DNA was roughly at the level of a recB mutant. Results similar to those with the set of recD strains were also obtained with a recC++ mutant (in which the RecD protein is intact but does not function) and its recJ, xonA, and recJ xonA derivatives. The observations provide evidence for a recBC-dependent DNA-unwinding activity that renders unwound DNA susceptible to exonucleolytic degradation. It is proposed that the DNA-unwinding activity causes the efficient recombination, DNA repair, and SOS induction (after application of nalidixic acid) in recD mutants. The RecBC helicase indirectly detected here may have a central function in Chi-dependent recombination and in the recombinational repair of double-strand breaks by the RecBCD pathway. PMID:1322885

  19. Electronic density of states in sequence dependent DNA molecules

    NASA Astrophysics Data System (ADS)

    de Oliveira, B. P. W.; Albuquerque, E. L.; Vasconcelos, M. S.

    2006-09-01

    We report in this work a numerical study of the electronic density of states (DOS) in π-stacked arrays of DNA single-strand segments made up from the nucleotides guanine G, adenine A, cytosine C and thymine T, forming a Rudin-Shapiro (RS) as well as a Fibonacci (FB) polyGC quasiperiodic sequences. Both structures are constructed starting from a G nucleotide as seed and following their respective inflation rules. Our theoretical method uses Dyson's equation together with a transfer-matrix treatment, within an electronic tight-binding Hamiltonian model, suitable to describe the DNA segments modelled by the quasiperiodic chains. We compared the DOS spectra found for the quasiperiodic structure to those using a sequence of natural DNA, as part of the human chromosome Ch22, with a remarkable concordance, as far as the RS structure is concerned. The electronic spectrum shows several peaks, corresponding to localized states, as well as a striking self-similar aspect.

  20. Age dependency of base modification in rabbit liver DNA

    NASA Technical Reports Server (NTRS)

    Yamamoto, O.; Fuji, I.; Yoshida, T.; Cox, A. B.; Lett, J. T.

    1988-01-01

    Age-related modifications of DNA bases have been observed in the liver of the New Zealand white (NZW) rabbit (Oryctolagus cuniculus), a lagomorph with a median life span in captivity of 5-7 yr. The ages of the animals studied ranged from 6 wk to 9 yr. After the DNA had been extracted from the liver cell nuclei and hydrolyzed with acid, the bases were analyzed by column chromatography with Cellulofine gels (GC-15-m). Two peaks in the chromatogram, which eluted before the four DNA bases, contained modified bases. Those materials, which were obtained in relatively large amounts from old animals, were highly fluorescent, and were shown to be crosslinked base products by mass spectrometry. The yield of crosslinked products versus rabbit age (greater than 0.5 yr) can be fitted by an exponential function (correlation coefficient: 0.76 +/- 0.09).

  1. Hydrogen Peroxide-Dependent DNA Release and Transfer of Antibiotic Resistance Genes in Streptococcus gordonii ▿

    PubMed Central

    Itzek, Andreas; Zheng, Lanyan; Chen, Zhiyun; Merritt, Justin; Kreth, Jens

    2011-01-01

    Certain oral streptococci produce H2O2 under aerobic growth conditions to inhibit competing species like Streptococcus mutans. Additionally, H2O2 production causes the release of extracellular DNA (eDNA). eDNA can participate in several important functions: biofilm formation and cell-cell aggregation are supported by eDNA, while eDNA can serve as a nutrient and as an antimicrobial agent by chelating essential cations. eDNA contains DNA fragments of a size that has the potential to transfer genomic information. By using Streptococcus gordonii as a model organism for streptococcal H2O2 production, H2O2-dependent eDNA release was further investigated. Under defined growth conditions, the eDNA release process was shown to be entirely dependent on H2O2. Chromosomal DNA damage seems to be the intrinsic signal for the release, although only actively growing cells were proficient eDNA donors. Interestingly, the process of eDNA production was found to be coupled with the induction of the S. gordonii natural competence system. Consequently, the production of H2O2 triggered the transfer of antibiotic resistance genes. These results suggest that H2O2 is potentially much more than a simple toxic metabolic by-product; rather, its production could serve as an important environmental signal that facilitates species evolution by transfer of genetic information and an increase in the mutation rate. PMID:21984796

  2. Resistance of Adenoviral DNA Replication to Aphidicolin Is Dependent on the 72-Kilodalton DNA-Binding Protein

    PubMed Central

    Foster, David A.; Hantzopoulos, Petros; Zubay, Geoffrey

    1982-01-01

    Aphidicolin is a highly specific inhibitor of DNA polymerase α and has been most useful for assessing the role of this enzyme in various replication processes (J. A. Huberman, Cell 23:647-648, 1981). Both nuclear DNA replication and simian virus 40 DNA replication are highly sensitive to this drug (Krokan et al., Biochemistry 18:4431-4443, 1979), whereas mitochondrial DNA synthesis is completely insensitive (Zimmerman et al., J. Biol. Chem. 255:11847-11852, 1980). Adenovirus DNA replication is sensitive to aphidicolin, but only at much higher concentrations. These patterns of sensitivity are seen both in vivo and in vitro (Krokan et al., Biochemistry 18:4431-4443, 1979). A temperature-sensitive mutant of adenovirus type 5 known as H5ts125 is able to complete but not initiate new rounds of replication at nonpermissive temperatures (P. C. van der Vliet and J. S. Sussenbach, Virology 67:415-426, 1975). When cells infected with H5ts125 were shifted from permissive (33°C) to nonpermissive (41°C) conditions, the residual DNA synthesis (elongation) showed a striking increase in sensitivity to aphidicolin. The temperature-sensitive mutation of H5ts125 is in the gene for the 72-kilodalton single-stranded DNA-binding protein. This demonstrated that the increased resistance to aphidicolin shown by adenovirus DNA replication was dependent on that protein. It also supports an elongation role for both DNA polymerase α and the 72-kilodalton single-stranded DNA-binding protein in adenovirus DNA replication. Further support for an elongation role of DNA polymerase α came from experiments with permissive temperature conditions and inhibiting levels of aphidicolin in which it was shown that newly initiated strands failed to elongate to completion. Images PMID:6809958

  3. E2F-7 couples DNA damage-dependent transcription with the DNA repair process.

    PubMed

    Zalmas, Lykourgos-Panagiotis; Coutts, Amanda S; Helleday, Thomas; La Thangue, Nicholas B

    2013-09-15

    The cellular response to DNA damage, mediated by the DNA repair process, is essential in maintaining the integrity and stability of the genome. E2F-7 is an atypical member of the E2F family with a role in negatively regulating transcription and cell cycle progression under DNA damage. Surprisingly, we found that E2F-7 makes a transcription-independent contribution to the DNA repair process, which involves E2F-7 locating to and binding damaged DNA. Further, E2F-7 recruits CtBP and HDAC to the damaged DNA, altering the local chromatin environment of the DNA lesion. Importantly, the E2F-7 gene is a target for somatic mutation in human cancer and tumor-derived mutant alleles encode proteins with compromised transcription and DNA repair properties. Our results establish that E2F-7 participates in 2 closely linked processes, allowing it to directly couple the expression of genes involved in the DNA damage response with the DNA repair machinery, which has relevance in human malignancy.

  4. Theoretical and Experimental Analysis of Moisture-Dependent Thermal Conductivity of Lightweight Ceramic Bricks

    NASA Astrophysics Data System (ADS)

    Pavlík, Zbyšek; Fiala, Lukáš; Jerman, Miloš; Vejmelková, Eva; Pavlíková, Milena; Keppert, Martin; Černý, Robert

    2014-10-01

    The moisture-dependent thermal conductivity of two types of lightweight ceramic brick body is analyzed using both theoretical and experimental approaches. The basic physical properties are determined at first. Then, an impulse method is applied for the thermal-conductivity measurement. Initially, the material samples are dried, after that, they are exposed to liquid water for specific time intervals, and finally the moisture content is allowed to homogenize within the whole volume. The thermal-conductivity measurement is performed for different moisture contents achieved in this way. In the theoretical part, the homogenization principles are used for the calculation of the moisture-dependent thermal conductivity, utilizing the distribution functions based on the pore-size distribution measurement. Finally, a comparison of the measured and calculated data is done, and the validity of the applied effective media treatment is assessed.

  5. Reversibility, Dopant Desorption, and Tunneling in the Temperature-Dependent Conductivity of Type-Separated, Conductive Carbon Nanotube Networks

    SciTech Connect

    Barnes, T. M.; Blackburn, J. L.; van de Lagemaat, J.; Coutts, T. J.; Heben, M. J.

    2008-09-01

    We present a comprehensive study of the effects of doping and temperature on the conductivity of single-walled carbon nanotube (SWNT) networks. We investigated nearly type-pure networks as well as networks comprising precisely tuned mixtures of metallic and semiconducting tubes. Networks were studied in their as-produced state and after treatments with nitric acid, thionyl chloride, and hydrazine to explore the effects of both intentional and adventitious doping. For intentionally and adventitiously doped networks, the sheet resistance (R{sub s}) exhibits an irreversible increase with temperature above {approx}350 K. Dopant desorption is shown to be the main cause of this increase and the observed hysteresis in the temperature-dependent resistivity. Both thermal and chemical dedoping produced networks free of hysteresis. Temperature-programmed desorption data showed that dopants are most strongly bound to the metallic tubes and that networks consisting of metallic tubes exhibit the best thermal stability. At temperatures below the dopant desorption threshold, conductivity in the networks is primarily controlled by thermally assisted tunneling through barriers at the intertube or interbundle junctions.

  6. Spin-dependent electrical conduction in a pentacene Schottky diode explored by electrically detected magnetic resonance

    NASA Astrophysics Data System (ADS)

    Fukuda, Kunito; Asakawa, Naoki

    2017-02-01

    Reported is the observation of dark spin-dependent electrical conduction in a Schottky barrier diode with pentacene (PSBD) using electrically detected magnetic resonance at room temperature. It is suggested that spin-dependent conduction exists in pentacene thin films, which is explored by examining the anisotropic linewidth of the EDMR signal and current density-voltage (J-V) measurements. The EDMR spectrum can be decomposed to Gaussian and Lorentzian components. The dependency of the two signals on the applied voltage was consistent with the current density-voltage (J-V) of the PSBD rather than that of the electron-only device of Al/pentacene/Al, indicating that the spin-dependent conduction is due to bipolaron formation associated with hole polaronic hopping processes. The applied-voltage dependence of the ratio of intensity of the Gaussian line to the Lorentzian may infer that increasing current density should make conducting paths more dispersive, thereby resulting in an increased fraction of the Gaussian line due to the higher dispersive g-factor.

  7. Suppression of DNA-dependent protein kinase sensitize cells to radiation without affecting DSB repair.

    PubMed

    Gustafsson, Ann-Sofie; Abramenkovs, Andris; Stenerlöw, Bo

    2014-11-01

    Efficient and correct repair of DNA double-strand break (DSB) is critical for cell survival. Defects in the DNA repair may lead to cell death, genomic instability and development of cancer. The catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) is an essential component of the non-homologous end joining (NHEJ) which is the major DSB repair pathway in mammalian cells. In the present study, by using siRNA against DNA-PKcs in four human cell lines, we examined how low levels of DNA-PKcs affected cellular response to ionizing radiation. Decrease of DNA-PKcs levels by 80-95%, induced by siRNA treatment, lead to extreme radiosensitivity, similar to that seen in cells completely lacking DNA-PKcs and low levels of DNA-PKcs promoted cell accumulation in G2/M phase after irradiation and blocked progression of mitosis. Surprisingly, low levels of DNA-PKcs did not affect the repair capacity and the removal of 53BP1 or γ-H2AX foci and rejoining of DSB appeared normal. This was in strong contrast to cells completely lacking DNA-PKcs and cells treated with the DNA-PKcs inhibitor NU7441, in which DSB repair were severely compromised. This suggests that there are different mechanisms by which loss of DNA-PKcs functions can sensitize cells to ionizing radiation. Further, foci of phosphorylated DNA-PKcs (T2609 and S2056) co-localized with DSB and this was independent of the amount of DNA-PKcs but foci of DNA-PKcs was only seen in siRNA-treated cells. Our study emphasizes on the critical role of DNA-PKcs for maintaining survival after radiation exposure which is uncoupled from its essential function in DSB repair. This could have implications for the development of therapeutic strategies aiming to radiosensitize tumors by affecting the DNA-PKcs function.

  8. Lead-position dependent regular oscillations and random fluctuations of conductance in graphene quantum dots.

    PubMed

    Huang, Liang; Yang, Rui; Lai, Ying-Cheng; Ferry, David K

    2013-02-27

    Quantum interference causes a wavefunction to have sensitive spatial dependence, and this has a significant effect on quantum transport. For example, in a quantum-dot system, the conductance can depend on the lead positions. We investigate, for graphene quantum dots, the conductance variations with the lead positions. Since for graphene the types of boundaries, e.g., zigzag and armchair, can fundamentally affect the quantum transport characteristics, we focus on rectangular graphene quantum dots, for which the effects of boundaries can be systematically studied. For both zigzag and armchair horizontal boundaries, we find that changing the positions of the leads can induce significant conductance variations. Depending on the Fermi energy, the variations can be either regular oscillations or random conductance fluctuations. We develop a physical theory to elucidate the origin of the conductance oscillation/fluctuation patterns. In particular, quantum interference leads to standing-wave-like-patterns in the quantum dot which, in the absence of leads, are regulated by the energy-band structure of the corresponding vertical graphene ribbon. The observed 'coexistence' of regular oscillations and random fluctuations in the conductance can be exploited for the development of graphene-based nanodevices.

  9. Conditions for Using DNA Polymerase I as an RNA-Dependent DNA Polymerase

    PubMed Central

    Gulati, S. C.; Kacian, D. L.; Spiegelman, S.

    1974-01-01

    Conditions are described for using Escherichia coli DNA polymerase I for synthesizing complementary DNA copies of natural RNA molecules, which are suitable for use in hybridization experiments. The molar ratio of enzyme to template is critical; below a certain level, synthesis is not observed. Hybrids formed with the complementary DNA are of comparable specificity and stability to those formed with complementary DNAs synthesized by viral RNA-directed DNA polymerase. Synthesis of dA-dT polymers, a common occurrence with this enzyme, can be eliminated by including distamycin in the reaction mixture. PMID:4133845

  10. pH- and salt-dependent molecular combing of DNA: experiments and phenomenological model.

    PubMed

    Benke, Annegret; Mertig, Michael; Pompe, Wolfgang

    2011-01-21

    λ-DNA as well as plasmids can be successfully deposited by molecular combing on hydrophobic surfaces, for pH values ranging from 4 to 10. On polydimethylsiloxane (PDMS) substrates, the deposited DNA molecules are overstretched by about 60-100%. There is a significant influence of sodium ions (NaCl) on the surface density of the deposited DNA, with a maximum near to 100 mM NaCl for a DNA solution (28 ng µl(-1)) at pH 8. The combing process can be described by a micromechanical model including: (i) the adsorption of free moving coiled DNA at the substrate; (ii) the stretching of the coiled DNA by the preceding meniscus; (iii) the relaxation of the deposited DNA to the final length. The sticky ends of λ-DNA cause an adhesion force in the range of about 400 pN which allows a stable overstretching of the DNA by the preceding meniscus. The exposing of hidden hydrophobic bonds of the overstretched DNA leads to a stable deposition on the hydrophobic substrate. The pH-dependent density of deposited DNA as well as the observed influence of sodium ions can be explained by their screening of the negatively charged DNA backbone and sticky ends, respectively. The final DNA length can be derived from a balance of the stored elastic energy of the overstretched molecules and the energy of adhesion.

  11. Structure of the adenylation domain of NAD[superscript +]-dependent DNA ligase from Staphylococcus aureus

    SciTech Connect

    Han, Seungil; Chang, Jeanne S.; Griffor, Matt; Pfizer

    2010-09-17

    DNA ligase catalyzes phosphodiester-bond formation between immediately adjacent 5'-phosphate and 3''-hydroxyl groups in double-stranded DNA and plays a central role in many cellular and biochemical processes, including DNA replication, repair and recombination. Bacterial NAD{sup +}-dependent DNA ligases have been extensively characterized as potential antibacterial targets because of their essentiality and their structural distinction from human ATP-dependent DNA ligases. The high-resolution structure of the adenylation domain of Staphylococcus aureus NAD{sup +}-dependent DNA ligase establishes the conserved domain architecture with other bacterial adenylation domains. Two apo crystal structures revealed that the active site possesses the preformed NAD{sup +}-binding pocket and the 'C2 tunnel' lined with hydrophobic residues: Leu80, Phe224, Leu287, Phe295 and Trp302. The C2 tunnel is unique to bacterial DNA ligases and the Leu80 side chain at the mouth of the tunnel points inside the tunnel and forms a narrow funnel in the S. aureus DNA ligase structure. Taken together with other DNA ligase structures, the S. aureus DNA ligase structure provides a basis for a more integrated understanding of substrate recognition and catalysis and will be also be of help in the development of small-molecule inhibitors.

  12. Structure of the adenylation domain of NAD(+)-dependent DNA ligase from Staphylococcus aureus.

    PubMed

    Han, Seungil; Chang, Jeanne S; Griffor, Matt

    2009-11-01

    DNA ligase catalyzes phosphodiester-bond formation between immediately adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA and plays a central role in many cellular and biochemical processes, including DNA replication, repair and recombination. Bacterial NAD(+)-dependent DNA ligases have been extensively characterized as potential antibacterial targets because of their essentiality and their structural distinction from human ATP-dependent DNA ligases. The high-resolution structure of the adenylation domain of Staphylococcus aureus NAD(+)-dependent DNA ligase establishes the conserved domain architecture with other bacterial adenylation domains. Two apo crystal structures revealed that the active site possesses the preformed NAD(+)-binding pocket and the 'C2 tunnel' lined with hydrophobic residues: Leu80, Phe224, Leu287, Phe295 and Trp302. The C2 tunnel is unique to bacterial DNA ligases and the Leu80 side chain at the mouth of the tunnel points inside the tunnel and forms a narrow funnel in the S. aureus DNA ligase structure. Taken together with other DNA ligase structures, the S. aureus DNA ligase structure provides a basis for a more integrated understanding of substrate recognition and catalysis and will be also be of help in the development of small-molecule inhibitors.

  13. The E1 protein of bovine papilloma virus 1 is an ATP-dependent DNA helicase.

    PubMed Central

    Yang, L; Mohr, I; Fouts, E; Lim, D A; Nohaile, M; Botchan, M

    1993-01-01

    For efficient DNA replication of papillomaviruses, only two viral-encoded proteins, E1 and E2, are required. Other proteins and factors are provided by the host cell. E2 is an enhancer of both transcription and replication and is known to help E1 bind cooperatively to the origin of DNA replication. E1 is sufficient for replication in extracts prepared from permissive cells, but the activity is enhanced by E2. Here we show that purified E1 can act as an ATP-dependent DNA helicase. To measure this activity, we have used strand displacement, unwinding of topologically constrained DNA, denaturation of duplex fragments, and electron microscopy. The ability of E1 to unwind circular DNA is found to be independent of origin-specific viral DNA sequences under a variety of experimental conditions. In unfractionated cellular extracts, E1-dependent viral DNA replication is origin-dependent, but at elevated E1 concentrations, replication can occur on non-origin-containing DNA templates. This conversion from an origin-dependent replication system to a nonspecific initiator system is discussed in the context of the current understanding of the initiation of chromosomal DNA replication. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:8389467

  14. Temperature-dependent statistical behavior of single molecular conductance in aqueous solution.

    PubMed

    Cao, Hui; Jiang, Jun; Ma, Jing; Luo, Yi

    2008-05-28

    We have combined molecular dynamics simulations with first principles calculations to study electron transport in a single molecule of perylene tetracarboxylic diimide (PTCDI) sandwiched between two gold electrodes with an aqueous electrolyte. This combination has for the first time allowed one to reveal statistical behavior of molecular conductance in solution at different temperatures and to produce conductance histograms that can be directly compared with experiments. Our calculations show that experimentally observed temperature-dependent conductance can be attributed to the thermal effect on the hydrogen bonding network around the molecule and can be described by the radial distribution of water molecules surrounding the oxygen atom in the PTCDI molecule.

  15. Reduced temperature-dependent thermal conductivity of magnetite thin films by controlling film thickness

    NASA Astrophysics Data System (ADS)

    Park, No-Won; Lee, Won-Yong; Kim, Jin-A.; Song, Kyungjun; Lim, Hyuneui; Kim, Wan-Doo; Yoon, Soon-Gil; Lee, Sang-Kwon

    2014-02-01

    We report on the out-of-plane thermal conductivities of epitaxial Fe3O4 thin films with thicknesses of 100, 300, and 400 nm, prepared using pulsed laser deposition (PLD) on SiO2/Si substrates. The four-point probe three-omega (3- ω) method was used for thermal conductivity measurements of the Fe3O4 thin films in the temperature range of 20 to 300 K. By measuring the temperature-dependent thermal characteristics of the Fe3O4 thin films, we realized that their thermal conductivities significantly decreased with decreasing grain size and thickness of the films. The out-of-plane thermal conductivities of the Fe3O4 films were found to be in the range of 0.52 to 3.51 W/m · K at 300 K. For 100-nm film, we found that the thermal conductivity was as low as approximately 0.52 W/m · K, which was 1.7 to 11.5 order of magnitude lower than the thermal conductivity of bulk material at 300 K. Furthermore, we calculated the temperature dependence of the thermal conductivity of these Fe3O4 films using a simple theoretical Callaway model for comparison with the experimental data. We found that the Callaway model predictions agree reasonably with the experimental data. We then noticed that the thin film-based oxide materials could be efficient thermoelectric materials to achieve high performance in thermoelectric devices.

  16. Structural-dependent thermal conductivity of aluminium nitride produced by reactive direct current magnetron sputtering

    SciTech Connect

    Belkerk, B. E.; Soussou, A.; Carette, M.; Djouadi, M. A.; Scudeller, Y.

    2012-10-08

    This Letter reports the thermal conductivity of aluminium nitride (AlN) thin-films deposited by reactive DC magnetron sputtering on single-crystal silicon substrates (100) with varying plasma and magnetic conditions achieving different crystalline qualities. The thermal conductivity of the films was measured at room temperature with the transient hot-strip technique for film thicknesses ranging from 100 nm to 4000 nm. The thermal conductivity was found to increase with the thickness depending on the synthesis conditions and film microstructure. The conductivity in the bulk region of the films, so-called intrinsic conductivity, and the boundary resistance were in the range [120-210] W m{sup -1} K{sup -1} and [2-30 Multiplication-Sign 10{sup -9}] K m{sup 2} W{sup -1}, respectively, in good agreement with microstructures analysed by x-ray diffraction, high-resolution-scanning-electron-microscopy, and transmission-electron-microscopy.

  17. The basal proton conductance of mitochondria depends on adenine nucleotide translocase content

    PubMed Central

    2005-01-01

    The basal proton conductance of mitochondria causes mild uncoupling and may be an important contributor to metabolic rate. The molecular nature of the proton-conductance pathway is unknown. We show that the proton conductance of muscle mitochondria from mice in which isoform 1 of the adenine nucleotide translocase has been ablated is half that of wild-type controls. Overexpression of the adenine nucleotide translocase encoded by the stress-sensitive B gene in Drosophila mitochondria increases proton conductance, and underexpression decreases it, even when the carrier is fully inhibited using carboxyatractylate. We conclude that half to two-thirds of the basal proton conductance of mitochondria is catalysed by the adenine nucleotide carrier, independently of its ATP/ADP exchange or fatty-acid-dependent proton-leak functions. PMID:16076285

  18. Anisotropic Electroless Deposition on DNA Origami Templates To Form Small Diameter Conductive Nanowires.

    PubMed

    Uprety, Bibek; Westover, Tyler; Stoddard, Michael; Brinkerhoff, Kamron; Jensen, John; Davis, Robert C; Woolley, Adam T; Harb, John N

    2017-01-24

    An improved method for the metallization of DNA origami is examined in this work. DNA origami, a simple and robust method for creating a wide variety of nanostructured shapes and patterns, provides an enabling template for bottom-up fabrication of next-generation nanodevices. Selective metallization of these DNA templates is needed to make nanoelectronic devices. Here, we demonstrate a metallization process that uses gold nanorod seeds followed by anisotropic plating to provide improved morphology and greater control of the final metallized width of the structure. In our approach, gold nanorods are attached to an origami template to create a seed layer. Electroless gold deposition is then used to fill the gaps between seeds in order to create continuous, conductive nanowires. Importantly, growth during electroless deposition occurs preferentially in the length direction at a rate that is approximately 4 times the growth rate in the width direction, which enables fabrication of narrow, continuous wires. The electrical properties of 49 nanowires with widths ranging from 13 to 29 nm were characterized, and resistivity values as low as 8.9 × 10(-7) Ω·m were measured. The anisotropic metallization process presented here represents important progress toward the creation of nanoelectronic devices by molecularly directed placement of functional components onto self-assembled biological templates.

  19. GADD45α inhibition of DNMT1 dependent DNA methylation during homology directed DNA repair

    PubMed Central

    Lee, Bongyong; Morano, Annalisa; Porcellini, Antonio; Muller, Mark T.

    2012-01-01

    In this work, we examine regulation of DNA methyltransferase 1 (DNMT1) by the DNA damage inducible protein, GADD45α. We used a system to induce homologous recombination (HR) at a unique double-strand DNA break in a GFP reporter in mammalian cells. After HR, the repaired DNA is hypermethylated in recombinant clones showing low GFP expression (HR-L expressor class), while in high expressor recombinants (HR-H clones) previous methylation patterns are erased. GADD45α, which is transiently induced by double-strand breaks, binds to chromatin undergoing HR repair. Ectopic overexpression of GADD45α during repair increases the HR-H fraction of cells (hypomethylated repaired DNA), without altering the recombination frequency. Conversely, silencing of GADD45α increases methylation of the recombined segment and amplifies the HR-L expressor (hypermethylated) population. GADD45α specifically interacts with the catalytic site of DNMT1 and inhibits methylation activity in vitro. We propose that double-strand DNA damage and the resulting HR process involves precise, strand selected DNA methylation by DNMT1 that is regulated by GADD45α. Since GADD45α binds with high avidity to hemimethylated DNA intermediates, it may also provide a barrier to spreading of methylation during or after HR repair. PMID:22135303

  20. Diffusion of isolated DNA molecules: dependence on length and topology.

    PubMed

    Robertson, Rae M; Laib, Stephan; Smith, Douglas E

    2006-05-09

    The conformation and dynamics of circular polymers is a subject of considerable theoretical and experimental interest. DNA is an important example because it occurs naturally in different topological states, including linear, relaxed circular, and supercoiled circular forms. A fundamental question is how the diffusion coefficients of isolated polymers scale with molecular length and how they vary for different topologies. Here, diffusion coefficients D for relaxed circular, supercoiled, and linear DNA molecules of length L ranging from approximately 6 to 290 kbp were measured by tracking the Brownian motion of single molecules. A topology-independent scaling law D approximately L(-nu) was observed with nu(L) = 0.571 +/- 0.014, nu(C) = 0.589 +/- 0.018, and nu(S) = 0.571 +/- 0.057 for linear, relaxed circular, and supercoiled DNA, respectively, in good agreement with the scaling exponent of nu congruent with 0.588 predicted by renormalization group theory for polymers with significant excluded volume interactions. Our findings thus provide evidence in support of several theories that predict an effective diameter of DNA much greater than the Debye screening length. In addition, the measured ratio D(Circular)/D(Linear) = 1.32 +/- 0.014 was closer to the value of 1.45 predicted by using renormalization group theory than the value of 1.18 predicted by classical Kirkwood hydrodynamic theory and agreed well with a value of 1.31 predicted when incorporating a recently proposed expression for the radius of gyration of circular polymers into the Zimm model.

  1. Dendritic star polymers for efficient DNA binding and stimulus-dependent DNA release.

    PubMed

    Yin, Meizhen; Ding, Ke; Gropeanu, Radu A; Shen, Jie; Berger, Rüdiger; Weil, Tanja; Müllen, Klaus

    2008-11-01

    Water-soluble core-shell star polymers consisting of a dendritic polyphenylene core and an outer shell containing a defined number of amino groups have been synthesized via atom transfer radical polymerization (ATRP). All macromolecules efficiently interacted with a diverse set of DNA fragments, and stable complexes were formed and visualized by atomic force microscopy. The observed tight binding of DNA, which was found in the sub-nanomolar range, was mainly attributed to strong electrostatic interactions. Complex stoichiometries between the polyelectrolytes were controlled via the number of amino groups of the star polymers, and well-defined nanoscopic architectures were formed. DNA was released from the complexes after treatment with high concentrations of sodium chloride in aqueous solution. Such star polymers, which allow the binding and release of DNA, represent attractive candidates for the development of novel anion-exchange resins for DNA purification or as nonviral vector systems for gene delivery.

  2. Temperature and Thickness Dependences of the Anisotropic In-Plane Thermal Conductivity of Black Phosphorus.

    PubMed

    Smith, Brandon; Vermeersch, Bjorn; Carrete, Jesús; Ou, Eric; Kim, Jaehyun; Mingo, Natalio; Akinwande, Deji; Shi, Li

    2017-02-01

    The anisotropic basal-plane thermal conductivities of thin black phosphorus obtained from a new four-probe measurement exhibit much higher peak values at low temperatures than previous reports. First principles calculations reveal the important role of crystal defects and weak thickness dependence that is opposite to the case of graphene and graphite due to the absence of reflection symmetry in puckered phosphorene.

  3. Time dependent variation of human blood conductivity as a method for an estimation of RBC aggregation.

    PubMed

    Antonova, Nadia; Riha, Pavel; Ivanov, Ivan

    2008-01-01

    Time variation of whole human blood conductivity and shear stresses were investigated at rectangular and trapezium-shaped Couette viscometric flow under electric field of 2 kHz. The kinetics of conductivity signals were recorded both under transient flow and after the complete stoppage of shearing at shear rates from 0.94 to 94.5 s(-1) and temperatures T=25 degrees C and 37 degrees C. Contraves Low Shear 30 rotational viscometer as a base unit and a concurrent measuring system, including a device, developed by the conductometric method with a software for measurement of conductivity of biological fluids (data acquisition system), previously described (IFMBE Proceedings Series, Vol. 11, 2005, pp. 4247-4252; Clin. Hemorheol. Microcirc. 35(1/2) (2006), 19-29), were used for the experiments. The obtained experimental relationships show that the human blood conductivity is time, shear rate, hematocrit and temperature dependent under transient flow. It is also dependent on the regime of the applied shear rates. Non-linear curve approximation of the growth and relaxation curves is done. The results show that valuable information could be received about the kinetics of "rouleaux formation" and the time dependences of the blood conductivity follow the structural transformations of RBC aggregates during the aggregation-disaggregation processes. The results suggest that this technique may be used to clarify the mechanism of dynamics of RBC aggregates.

  4. ATM Dependent Silencing Links Nucleolar Chromatin Reorganization to DNA Damage Recognition.

    PubMed

    Harding, Shane M; Boiarsky, Jonathan A; Greenberg, Roger A

    2015-10-13

    Resolution of DNA double-strand breaks (DSBs) is essential for the suppression of genome instability. DSB repair in transcriptionally active genomic regions represents a unique challenge that is associated with ataxia telangiectasia mutated (ATM) kinase-mediated transcriptional silencing. Despite emerging insights into the underlying mechanisms, how DSB silencing connects to DNA repair remains undefined. We observe that silencing within the rDNA depends on persistent DSBs. Non-homologous end-joining was the predominant mode of DSB repair allowing transcription to resume. ATM-dependent rDNA silencing in the presence of persistent DSBs led to the large-scale reorganization of nucleolar architecture, with movement of damaged chromatin to nucleolar cap regions. These findings identify ATM-dependent temporal and spatial control of DNA repair and provide insights into how communication between DSB signaling and ongoing transcription promotes genome integrity.

  5. Conducting polymer based DNA biosensor for the detection of the Bacillus cereus group species

    NASA Astrophysics Data System (ADS)

    Velusamy, Vijayalakshmi; Arshak, Khalil; Korostynska, Olga; Oliwa, Kamila; Adley, Catherine

    2009-05-01

    Biosensor designs are emerging at a significant rate and play an increasingly important role in foodborne pathogen detection. Conducting polymers are excellent tools for the fabrication of biosensors and polypyrrole has been used in the detection of biomolecules due to its unique properties. The prime intention of this paper was to pioneer the design and fabrication of a single-strand (ss) DNA biosensor for the detection of the Bacillus cereus (B.cereus) group species. Growth of B. cereus, results in production of several highly active toxins. Therefore, consumption of food containing >106 bacteria/gm may results in emetic and diarrhoeal syndromes. The most common source of this bacterium is found in liquid food products, milk powder, mixed food products and is of particular concern in the baby formula industry. The electrochemical deposition technique, such as cyclic voltammetry, was used to develop and test a model DNA-based biosensor on a gold electrode electropolymerized with polypyrrole. The electrically conducting polymer, polypyrrole is used as a platform for immobilizing DNA (1μg) on the gold electrode surface, since it can be more easily deposited from neutral pH aqueous solutions of pyrrolemonomers. The average current peak during the electrodeposition event is 288μA. There is a clear change in the current after hybridization of the complementary oligonucleotide (6.35μA) and for the noncomplementary oligonucleotide (5.77μA). The drop in current after each event was clearly noticeable and it proved to be effective.

  6. RCC1-dependent activation of Ran accelerates cell cycle and DNA repair, inhibiting DNA damage–induced cell senescence

    PubMed Central

    Cekan, Pavol; Hasegawa, Keisuke; Pan, Yu; Tubman, Emily; Odde, David; Chen, Jin-Qiu; Herrmann, Michelle A.; Kumar, Sheetal; Kalab, Petr

    2016-01-01

    The coordination of cell cycle progression with the repair of DNA damage supports the genomic integrity of dividing cells. The function of many factors involved in DNA damage response (DDR) and the cell cycle depends on their Ran GTPase–regulated nuclear–cytoplasmic transport (NCT). The loading of Ran with GTP, which is mediated by RCC1, the guanine nucleotide exchange factor for Ran, is critical for NCT activity. However, the role of RCC1 or Ran⋅GTP in promoting cell proliferation or DDR is not clear. We show that RCC1 overexpression in normal cells increased cellular Ran⋅GTP levels and accelerated the cell cycle and DNA damage repair. As a result, normal cells overexpressing RCC1 evaded DNA damage–induced cell cycle arrest and senescence, mimicking colorectal carcinoma cells with high endogenous RCC1 levels. The RCC1-induced inhibition of senescence required Ran and exportin 1 and involved the activation of importin β–dependent nuclear import of 53BP1, a large NCT cargo. Our results indicate that changes in the activity of the Ran⋅GTP–regulated NCT modulate the rate of the cell cycle and the efficiency of DNA repair. Through the essential role of RCC1 in regulation of cellular Ran⋅GTP levels and NCT, RCC1 expression enables the proliferation of cells that sustain DNA damage. PMID:26864624

  7. Concentration-dependent thermophoretic accumulation for the detection of DNA using DNA-functionalized nanoparticles.

    PubMed

    Yu, Li-Hsien; Chen, Yih-Fan

    2015-03-03

    Thermophoresis is a phenomenon about the migration of particles along a temperature gradient and is sensitive to the properties of particles and the surrounding medium. While a few studies have investigated its mechanisms and effects on particle motion in recent years, the applications of thermophoresis in biosensing has not been well explored. In this study, we demonstrate a thermophoresis-based method for detecting DNA. We use DNA-functionalized gold nanoparticles and fluorescent DNA probes to capture target DNA in free solution, and we demonstrate that the hybridization between the specially designed capture probes and the target DNA significantly changes the thermophoretic properties of the fluorescent probes. As a result, the target DNA can be specifically detected in serum-containing buffers based on the spatial distribution of the fluorescent probes in a laser-induced temperature gradient. The optical setup consists of only a laser and an epifluorescence microscope, and the detection does not rely on any micro- or nanofabricated devices. In addition, because the detection is based on the thermophoretic motion of molecules in free solution, no capture probes need to be immobilized on a fixed surface before detection, and no channels or pumps are needed for washing away unbound molecules. The thermophoresis-based biosensing method is found to be simple and effective for detecting DNA.

  8. DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation

    NASA Astrophysics Data System (ADS)

    Boedicker, James Q.; Garcia, Hernan G.; Johnson, Stephanie; Phillips, Rob

    2013-12-01

    As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as through nucleosome positioning. Here we examine the sequence-dependent flexibility of DNA in bacterial transcription factor-mediated looping, a context for which the role of sequence remains poorly understood. Using a suite of synthetic constructs repressed by the Lac repressor and two well-known sequences that show large flexibility differences in vitro, we make precise statistical mechanical predictions as to how DNA sequence influences loop formation and test these predictions using in vivo transcription and in vitro single-molecule assays. Surprisingly, sequence-dependent flexibility does not affect in vivo gene regulation. By theoretically and experimentally quantifying the relative contributions of sequence and the DNA-bending protein HU to DNA mechanical properties, we reveal that bending by HU dominates DNA mechanics and masks intrinsic sequence-dependent flexibility. Such a quantitative understanding of how mechanical regulatory information is encoded in the genome will be a key step towards a predictive understanding of gene regulation at single-base pair resolution.

  9. Length Dependent Thermal Conductivity Measurements Yield Phonon Mean Free Path Spectra in Nanostructures

    PubMed Central

    Zhang, Hang; Hua, Chengyun; Ding, Ding; Minnich, Austin J.

    2015-01-01

    Thermal conductivity measurements over variable lengths on nanostructures such as nanowires provide important information about the mean free paths (MFPs) of the phonons responsible for heat conduction. However, nearly all of these measurements have been interpreted using an average MFP even though phonons in many crystals possess a broad MFP spectrum. Here, we present a reconstruction method to obtain MFP spectra of nanostructures from variable-length thermal conductivity measurements. Using this method, we investigate recently reported length-dependent thermal conductivity measurements on SiGe alloy nanowires and suspended graphene ribbons. We find that the recent measurements on graphene imply that 70% of the heat in graphene is carried by phonons with MFPs longer than 1 micron. PMID:25764977

  10. Magnetic field dependent electric conductivity of the magnetorheological fluids: the influence of oscillatory shear

    NASA Astrophysics Data System (ADS)

    Ruan, Xiaohui; Wang, Yu; Xuan, Shouhu; Gong, Xinglong

    2017-03-01

    In this work, the influence of oscillatory shear on the magnetic field dependent electric conductivity of the magnetorheological fluid (MRF) was reported. Upon applying a 0.96 T magnetic field, the electric conductivity could increase about 1500 times larger than the one without magnetic field. By increasing the volume fraction of carbonyl iron particles in the MRF from 5% to 30%, the electric conductivity increased about 565 times. Under applying an oscillatory shear, the resistance of the MRF decreased and it oscillated synchronously with the oscillatory shear. Interestingly, the larger shear strain led to larger oscillatory amplitude of the resistance. A particle–particle resistance model and a semi-empirical formula were proposed to investigate the influence of the oscillatory shear on the electric conductivity. The fitting results matched the experimental results very well. At last, a possible mechanism was proposed to explain the changes of resistance.

  11. Unique ligation properties of eukaryotic NAD+-dependent DNA ligase from Melanoplus sanguinipes entomopoxvirus.

    PubMed

    Lu, Jing; Tong, Jie; Feng, Hong; Huang, Jianmin; Afonso, Claudio L; Rock, Dan L; Barany, Francis; Cao, Weiguo

    2004-09-01

    The eukaryotic Melanoplus sanguinipes entomopoxvirus (MsEPV) genome reveals a homologous sequence to eubacterial nicotinamide adenine dinucleotide (NAD(+))-dependent DNA ligases [J. Virol. 73 (1999) 533]. This 522-amino acid open reading frame (ORF) contains all conserved nucleotidyl transferase motifs but lacks the zinc finger motif and BRCT domain found in conventional eubacterial NAD(+) ligases. Nevertheless, cloned MsEPV ligase seals DNA nicks in a NAD(+)-dependent fashion, while adenosine 5'-monophosphate (ATP) cannot serve as an adenylation cofactor. The ligation activity of MsEPV ligase requires Mg(2+) or Mn(2+). MsEPV ligase seals sticky ends efficiently, but has little activity on 1-nucleotide gap or blunt-ended DNA substrates even in the presence of polyethylene glycol. In comparison, bacterial NAD(+)-dependent ligases seal blunt-ended DNA substrates in the presence of polyethylene glycol. MsEPV DNA ligase readily joins DNA nicks with mismatches at either side of the nick junction, except for mismatches at the nick junction containing an A base in the template strand (A/A, G/A, and C/A). MsEPV NAD(+)-dependent DNA ligase can join DNA probes on RNA templates, a unique property that distinguishes this enzyme from other conventional bacterial NAD(+) DNA ligases. T4 ATP-dependent DNA ligase shows no detectable mismatch ligation at the 3' side of the nick but substantial 5' T/G mismatch ligation on an RNA template. In contrast, MsEPV ligase joins mismatches at the 3' side of the nick more frequently than at the 5' side of the nick on an RNA template. The complementary specificities of these two enzymes suggest alternative primer design for genomic profiling approaches that use allele-specific detection directly from RNA transcripts.

  12. Dependence on radiation quality of DNA fragmentation spectra

    NASA Astrophysics Data System (ADS)

    Campa, Alessandro; Ottolenghi, Andrea; Alloni, Daniele; Ballarini, Francesca; Belli, Mauro; Esposito, Giuseppe; Facoetti, Angelica; Friedland, Werner; Liotta, Marco; Paretzke, Herwig

    Energy deposition by radiation initially gives rise to cellular critical lesions such as DNA doublestrand breaks (DSB), that later lead to the formation of relevant biological endpoints. Studies on fragment size distributions induced by radiations of various qualities can be of great help in linking the characteristics of radiation to cellular endpoints, providing information for understanding the main mechanisms of cell damage. Here we are concerned with the damage induced by heavy charged particles; this issue is very important in the field of radioprotection of astronauts participating in long term space missions, besides being relevant also in other fields, like hadrontherapy. Galactic Cosmic Rays contain a large component of high-LET particles (HZE), e.g. helium and carbon ions, as well as highcharge particles such as iron ions. These particles are characterized by complex track structures with energy depositions not only along the path of the primary particle, but also at relatively large distance form the path, due to the presence of high energy secondary electrons. In this work we have simulated the irradiation of human fibroblasts with γ-rays, protons, helium, carbon and iron ions at a fixed dose with the biophysical Monte Carlo code PARTRAC,and calculated the induction of DSB. The PARTRAC code includes accurate representation of the chromatin geometry and of the physical and physico-chemical processes associated with the energy deposition by radiation. The results of a first validation of the code have been reported in A. Campa et al. (2005) and D. Alloni et al. (2007a, 2007b). DNA fragment spectra were calculated based on the DSB induction patterns and compared in particular for particles of the same specific energy and for particles of the same LET. Special emphasis has been directed to the calculation of very small fragments (< 1 kbp) that are not detectable by the most common experimental techniques and that can significantly influence the RBE

  13. Temperature and frequency dependent conductivity of lithium doped bismuth zinc vanadate semiconducting glassy system

    NASA Astrophysics Data System (ADS)

    Dahiya, S.; Punia, R.; Murugavel, S.; Maan, A. S.

    2014-11-01

    The ac conductivity of bismuth zinc vanadate glasses of compositions x Li2O (100 - x) (50V2O5·20 Bi2O3·30 ZnO); x = 0, 2, 4, 6, and 8 has been studied in the frequency range 10-1 Hzb-2 MHz and in temperature range 313-533 K. The temperature and frequency dependent conductivity is found to obey Almond-West universal power law for all the studied lithium doped bismuth zinc vanadate glassy systems. Various parameters such as dc conductivity ( σ dc ), crossover frequency ( ω H ) and frequency exponent ( s) have been estimated by fitting the experimental data of ac conductivity to Almond-West universal power law. It has been observed that the ac conductivity of bismuth zinc vanadate glass system decreases with the increase in Li2O content. The ac conductivity and its frequency exponent have been analyzed in the frame work of various theoretical models. The ac conduction seems to take place via tunneling of overlapping large polarons in all the compositions.

  14. Self-consistent modeling of terahertz waveguide and cavity with frequency-dependent conductivity

    NASA Astrophysics Data System (ADS)

    Huang, Y. J.; Chu, K. R.; Thumm, M.

    2015-01-01

    The surface resistance of metals, and hence the Ohmic dissipation per unit area, scales with the square root of the frequency of an incident electromagnetic wave. As is well recognized, this can lead to excessive wall losses at terahertz (THz) frequencies. On the other hand, high-frequency oscillatory motion of conduction electrons tends to mitigate the collisional damping. As a result, the classical theory predicts that metals behave more like a transparent medium at frequencies above the ultraviolet. Such a behavior difference is inherent in the AC conductivity, a frequency-dependent complex quantity commonly used to treat electromagnetics of metals at optical frequencies. The THz region falls in the gap between microwave and optical frequencies. However, metals are still commonly modeled by the DC conductivity in currently active vacuum electronics research aimed at the development of high-power THz sources (notably the gyrotron), although a small reduction of the DC conductivity due to surface roughness is sometimes included. In this study, we present a self-consistent modeling of the gyrotron interaction structures (a metallic waveguide or cavity) with the AC conductivity. The resulting waveguide attenuation constants and cavity quality factors are compared with those of the DC-conductivity model. The reduction in Ohmic losses under the AC-conductivity model is shown to be increasingly significant as the frequency reaches deeper into the THz region. Such effects are of considerable importance to THz gyrotrons for which the minimization of Ohmic losses constitutes a major design consideration.

  15. Recombinant expression and purification of an ATP-dependent DNA ligase from Aliivibrio salmonicida.

    PubMed

    Williamson, Adele; Pedersen, Hege

    2014-05-01

    The genome of the psychrophilic fish-pathogen Aliivibrio salmonicida encodes a putative ATP-dependent DNA ligase in addition to a housekeeping NAD-dependent enzyme. In order to study the structure and activity of the ATP dependent ligase in vitro we have undertaken its recombinant production and purification from an Escherichia coli based expression system. Expression and purification of this protein presented two significant challenges. First, the gene product was moderately toxic to E. coli cells, second it was necessary to remove the large amounts of E. coli DNA present in bacterial lysates without contamination of the protein preparation by nucleases which might interfere with future assaying. The toxicity problem was overcome by fusion of the putative ligase to large solubility tags such as maltose-binding protein (MBP) or Glutathione-S-transferase (GST), and DNA was removed by treatment with a nuclease which could be inhibited by reducing agents. As the A. salmonicida ATP-dependent DNA ligase gene encodes a predicted leader peptide, both the full-length and mature forms of the protein were produced. Both possessed ATP-dependent DNA ligase activity, but the truncated form was significantly more active. Here we detail the first reported production, purification and preliminary characterization of active A. salmonicida ATP-dependent DNA ligase.

  16. Orientation Dependent Thermal Conductance in Single-Layer MoS2

    PubMed Central

    Jiang, Jin-Wu; Zhuang, Xiaoying; Rabczuk, Timon

    2013-01-01

    We investigate the thermal conductivity in the armchair and zigzag MoS2 nanoribbons, by combining the non-equilibrium Green's function approach and the first-principles method. A strong orientation dependence is observed in the thermal conductivity. Particularly, the thermal conductivity for the armchair MoS2 nanoribbon is about 673.6 Wm−1 K−1 in the armchair nanoribbon, and 841.1 Wm−1 K−1 in the zigzag nanoribbon at room temperature. By calculating the Caroli transmission, we disclose the underlying mechanism for this strong orientation dependence to be the fewer phonon transport channels in the armchair MoS2 nanoribbon in the frequency range of [150, 200] cm−1. Through the scaling of the phonon dispersion, we further illustrate that the thermal conductivity calculated for the MoS2 nanoribbon is esentially in consistent with the superior thermal conductivity found for graphene. PMID:23860436

  17. DNA-PKcs-Dependent Modulation of Cellular Radiosensitivity by a Selective Cyclooxygenase-2 Inhibitor

    SciTech Connect

    Kodym, Elisabeth; Kodym, Reinhard; Chen, Benjamin P.; Chen, David J.; Morotomi-Yano, Keiko; Choy, Hak; Saha, Debabrata

    2007-09-01

    Purpose: Inhibition of cyclooxygenase-2 has been shown to increase radiosensitivity. Recently, the suppression of radiation-induced DNA-dependant protein kinase (DNA-PK) activity by the selective cyclooxygenase-2 inhibitor celecoxib was reported. Given the importance of DNA-PK for repair of radiation-induced DNA double-strand breaks by nonhomologous end-joining and the clinical use of the substance, we investigated the relevance of the DNA-PK catalytic subunit (DNA-PKcs) for the modulation of cellular radiosensitivity by celecoxib. Methods and Materials: We used a syngeneic model of Chinese hamster ovarian cell lines: AA8, possessing a wild-type DNK-PKcs; V3, lacking a functional DNA-PKcs; and V3/WT11, V3 stably transfected with the DNA-PKcs. The cells were treated with celecoxib (50 {mu}M) for 24 h before irradiation. The modulation of radiosensitivity was determined using the colony formation assay. Results: Treatment with celecoxib increased the cellular radiosensitivity in the DNA-PKcs-deficient cell line V3 with a dose-enhancement ratio of 1.3 for a surviving fraction of 0.5. In contrast, clonogenic survival was increased in DNA-PKcs wild-type-expressing AA8 cells and in V3 cells transfected with DNA-PKcs (V3/WT11). The decrease in radiosensitivity was comparable to the radiosensitization in V3 cells, with a dose-enhancement ratio of 0.76 (AA8) and 0.80 (V3/WT11) for a survival of 0.5. Conclusions: We have demonstrated a DNA-PKcs-dependent differential modulation of cellular radiosensitivity by celecoxib. These effects might be attributed to alterations in signaling cascades downstream of DNA-PK toward cell survival. These findings offer an explanation for the poor outcomes in some recently published clinical trials.

  18. Frequency-dependent stability of parallel-plate electrostatic actuators in conductive fluids

    NASA Astrophysics Data System (ADS)

    Sounart, T. L.; Panchawagh, H. V.; Mahajan, R. L.

    2010-05-01

    We present an electromechanical stability analysis of passivated parallel-plate electrostatic actuators in conductive dielectric media and show that the pull-in instability can be eliminated by tuning the applied frequency below a design-dependent stability limit. A partial instability region is also obtained, where the actuator jumps from the pull-in displacement to another stable position within the gap. The results predict that the stability limit is always greater than the critical actuation frequency, and therefore any device that is feasible to actuate in a conductive fluid can be operated with stability over the full range of motion.

  19. Bias-dependent amino-acid-induced conductance changes in short semi-metallic carbon nanotubes.

    PubMed

    Abadir, G B; Walus, K; Pulfrey, D L

    2010-01-08

    We study the interaction between short semi-metallic carbon nanotubes and different amino acids using molecular dynamics and ab initio (density functional theory/non-equilibrium Green's function) simulations. We identify two different mechanisms of nanotube conductance change upon adsorption of amino acids: one due to the change of the coordinates of the nanotube arising from van der Waals forces of interaction with the adsorbed amino acid; and one due to electrostatic interactions, which appear only in the case of charged amino acids. We also find that the transport mechanism and the changes in the conductance of the tube upon amino acid adsorption are bias dependent.

  20. Temperature Dependence of the Thermal Conductivity of Single Wall Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Osman, Mohamed A.; Srivastava, Deepak

    2000-01-01

    The thermal conductivity of several single wall carbon nanotubes (CNT) has been calculated over a temperature range of 100-500 K using molecular dynamics simulations with Tersoff-Brenner potential for C-C interactions. In all cases, starting from similar values at 100K, thermal conductivities show a peaking behavior before falling off at higher temperatures. The peak position shifts to higher temperatures for nanotubes of larger diameter, and no significant dependence on the tube chirality is observed. It is shown that this phenomenon is due to onset of Umklapp scattering, which shifts to higher temperatures for nanotubes of larger diameter.

  1. Human ClCa1 modulates anionic conduction of calcium-dependent chloride currents

    PubMed Central

    Hamann, Martine; Gibson, Adele; Davies, Noel; Jowett, Amanda; Walhin, Jean Philippe; Partington, Leanne; Affleck, Karen; Trezise, Derek; Main, Martin

    2009-01-01

    Proteins of the CLCA gene family including the human ClCa1 (hClCa1) have been suggested to constitute a new family of chloride channels mediating Ca2+-dependent Cl− currents. The present study examines the relationship between the hClCa1 protein and Ca2+-dependent Cl− currents using heterologous expression of hClCa1 in HEK293 and NCIH522 cell lines and whole cell recordings. By contrast to previous reports claiming the absence of Cl− currents in HEK293 cells, we find that HEK293 and NCIH522 cell lines express constitutive Ca2+-dependent Cl− currents and show that hClCa1 increases the amplitude of Ca2+-dependent Cl− currents in those cells. We further show that hClCa1 does not modify the permeability sequence but increases the Cl− conductance while decreasing the GSCN−/GCl− conductance ratio from ∼2–3 to ∼1. We use an Eyring rate theory (two barriers, one site channel) model and show that the effect of hClCa1 on the anionic channel can be simulated by its action on lowering the first and the second energy barriers. We conclude that hClCa1 does not form Ca2+-dependent Cl− channels per se or enhance the trafficking/insertion of constitutive channels in the HEK293 and NCIH522 expression systems. Rather, hClCa1 elevates the single channel conductance of endogenous Ca2+-dependent Cl− channels by lowering the energy barriers for ion translocation through the pore. PMID:19307298

  2. Efficiency of coaxial stacking depends on the DNA duplex structure.

    PubMed

    Pyshnyi, Dmitrii V; Goldberg, Eugenii L; Ivanova, Eugenia M

    2003-12-01

    Thermodynamic parameters of coaxial stacking at complementary helix-helix interfaces GX*pYG/CZVC (X,Y=A,C,T,G;*-nick) created by contiguous oligonucleotide hybridization were determined. The data obtained were compared to the thermodynamic parameters of coaxial stacking at the interfaces CX*pYC/GZVG. Multiple linear regression analysis has revealed that the free-energy increments of interaction for the contacts GX*pYG/CZVC and CX*pYC/GZVG can be described by a set of uniform Delta G degrees(X*pY/ZV) values. The difference in the observed free-energy of the coaxial stacking between the two sets is defined by the contribution from the factors reflecting structural differences between compared DNA duplexes.

  3. Situation-dependent repair of DNA damage in yeast

    SciTech Connect

    von Borstel, R.C.; Hastings, P.J.

    1985-01-01

    The concept of channelling of lesions in DNA into defined repair systems has been used to explain many aspects of induced and spontaneous mutation. The channelling hypothesis states that lesions excluded from one repair process will be taken up by another repair process. This is a simplification. The three known modes of repair of damage induced by radiation are not equivalent modes of repair; they are, instead, different solutions to the problem of replacement of damaged molecules with new molecules which have the same informational content as those that were damaged. The mode of repair that is used is the result of the response to the situation in which the damage takes place. Thus, when the most likely mode of repair does not take place, then the situation changes with respect to the repair of the lesion; the lesion may enter the replication fork and be reparable by another route.

  4. Time Dependent Universal Conductance Fluctuations In AuPd, Ag, And Au Wires

    NASA Astrophysics Data System (ADS)

    Trionfi, A.; Lee, S.; Natelson, D.

    2006-09-01

    Quantum transport phenomena allow experimental determinations of the phase coherence information in metals. We report quantitative comparisons of inferred coherence lengths from independent measurements of the weak localization magnetoresistance and time-dependent universal conductance fluctuations' magnetic field dependence. Strong agreement is observed in both quasi-2D and quasi-1D AuPd samples. However, quantitative agreement is not seen in quasi-1D Ag wires below 10 K and quasi-1D Au wires below 14 K. A possible explanation for this disagreement will be discussed. Attempts to produce changes in the coherence length in Au by annealing have also been made and results will be reported.

  5. Size-dependent conductivity dispersion of gold nanoparticle colloids in a microchip: contactless measurements

    NASA Astrophysics Data System (ADS)

    Khalafalla, M. A. H.; Mesli, A.; Widattallah, H. M.; Sellai, A.; Al-harthi, S.; Al-Lawati, Haider A. J.; Suliman, F. O.

    2014-08-01

    We performed admittance measurements to investigate the particle size dependence of the conductivity of gold nanoparticle (Diameters: 6-100 nm) colloids in electrophoresis microchip in the frequency range of 0.03-1.00 MHz. The admittance was measured with two electrodes capacitively coupled to the colloid contained in a microchip capillary channel. The imaginary and real components of the admittance showed low-frequency dispersion associated with the polarization of the nanoparticles induced by the AC electric field. This was evident from the linear dependence of the process relaxation time as a function of the square of the radius of the nanoparticle.

  6. Thermoelectric Property Dependence and Geometry Optimization of Peltier Current Leads Using Highly Electrically Conductive Thermoelectric Materials

    NASA Astrophysics Data System (ADS)

    Fujii, Tomohiro; Fukuda, Shinji; Emoto, Masahiko; Osada, Koudai; Kawahara, Toshio; Hamabe, Makoto; Watanabe, Hirofumi; Ivanov, Yury; Sun, Jian; Yamaguchi, Satarou

    2011-05-01

    Thermoelectric materials are promising candidates for use in energy-saving devices in many fields. They are also useful in superconducting applications such as those using Peltier current leads (PCLs) to reduce system heat loss. In the case of PCLs, consideration must be given to Joule heating. Furthermore, the performance of PCLs is intricately dependent on their thermoelectric properties. In addition to the figure of merit Z, consideration of the electrical conductivity is also important for the design of high-performance PCLs. In this paper, we discuss the resistivity dependence of the performance of PCLs using model parameters obtained from real devices.

  7. Reduced temperature-dependent thermal conductivity of magnetite thin films by controlling film thickness.

    PubMed

    Park, No-Won; Lee, Won-Yong; Kim, Jin-A; Song, Kyungjun; Lim, Hyuneui; Kim, Wan-Doo; Yoon, Soon-Gil; Lee, Sang-Kwon

    2014-02-26

    We report on the out-of-plane thermal conductivities of epitaxial Fe3O4 thin films with thicknesses of 100, 300, and 400 nm, prepared using pulsed laser deposition (PLD) on SiO2/Si substrates. The four-point probe three-omega (3-ω) method was used for thermal conductivity measurements of the Fe3O4 thin films in the temperature range of 20 to 300 K. By measuring the temperature-dependent thermal characteristics of the Fe3O4 thin films, we realized that their thermal conductivities significantly decreased with decreasing grain size and thickness of the films. The out-of-plane thermal conductivities of the Fe3O4 films were found to be in the range of 0.52 to 3.51 W/m · K at 300 K. For 100-nm film, we found that the thermal conductivity was as low as approximately 0.52 W/m · K, which was 1.7 to 11.5 order of magnitude lower than the thermal conductivity of bulk material at 300 K. Furthermore, we calculated the temperature dependence of the thermal conductivity of these Fe3O4 films using a simple theoretical Callaway model for comparison with the experimental data. We found that the Callaway model predictions agree reasonably with the experimental data. We then noticed that the thin film-based oxide materials could be efficient thermoelectric materials to achieve high performance in thermoelectric devices.

  8. A Review of the Role of the Sequence-Dependent Electrostatic Landscape in DNA Alkylation Patterns

    PubMed Central

    Gold, Barry; Marky, Luis M.; Stone, Michael P.; Williams, Loren D.

    2008-01-01

    Alkylating agents, including environmental and endogenous carcinogens, and DNA targeting antineoplastic agents, that adduct DNA via intermediates with significant cationic charge show a sequence selectively in their covalent bonding to nucleobases. The resulting patterns of alkylation eventually contribute to the agent-dependent distributions and types of mutations. The origin of the regioselective modification of DNA by electrophiles has been attributed to steric and/or electronic factors, but attempts to mechanistically model and predict alkylation patterns have had limited success. In this review, we present data consistent with the role of the intrinsic sequence-dependent electrostatic landscape (SDEL) in DNA that modulates the equilibrium binding of cations and the bonding of reactive charged alkylating agents to atoms that line the floor of the major groove of DNA. PMID:17112226

  9. Down-regulation of histone H2B by DNA-dependent protein kinase in response to DNA damage through modulation of octamer transcription factor 1.

    PubMed

    Schild-Poulter, Caroline; Shih, Amy; Yarymowich, Nicholas C; Haché, Robert J G

    2003-11-01

    Cells respond to double-stranded DNA breaks (DSBs) by pausing cell cycle progression to allow the repair machinery to restore genomic integrity. DNA-dependent protein kinase (DNA-PK), comprising a large catalytic subunit (DNA-PK(cs)) and the Ku antigen regulatory subunit (Ku70/Ku80), is activated in response to DSBs and is required for DNA repair through the nonhomologous end-joining pathway. Here we provide evidence that DNA-PK participates in altering specific gene expression in response to DNA damage by modulating the stability and transcriptional regulatory potential of the essential transcription factor octamer transcription factor 1 (Oct-1). Histone H2B and U2 RNA, whose expression are highly dependent on Oct-1, were strongly decreased in response to ionizing radiation in a DNA-PK-dependent manner, and Oct-1-dependent reporter gene transcription was repressed. Furthermore, Oct-1 phosphorylation in response to ionizing radiation increased in a DNA-PK-dependent manner. Paradoxically, down-regulation of transactivation correlated with the rapid DNA-PK-dependent stabilization of Oct-1. Stabilization of Oct-1 was dependent on the NH(2)-terminal region of Oct-1, which contains a transcriptional activation domain and which was phosphorylated by DNA-PK in vitro. These results suggest a mechanism for the regulation of Oct-1 in response to DNA damage through specific phosphorylation within the NH(2)-terminal transcriptional regulatory domain.

  10. Sequence-Dependent Fluorescence of Cy3- and Cy5-Labeled Double-Stranded DNA.

    PubMed

    Kretschy, Nicole; Sack, Matej; Somoza, Mark M

    2016-03-16

    The fluorescent intensity of Cy3 and Cy5 dyes is strongly dependent on the nucleobase sequence of the labeled oligonucleotides. Sequence-dependent fluorescence may significantly influence the data obtained from many common experimental methods based on fluorescence detection of nucleic acids, such as sequencing, PCR, FRET, and FISH. To quantify sequence dependent fluorescence, we have measured the fluorescence intensity of Cy3 and Cy5 bound to the 5' end of all 1024 possible double-stranded DNA 5mers. The fluorescence intensity was also determined for these dyes bound to the 5' end of fixed-sequence double-stranded DNA with a variable sequence 3' overhang adjacent to the dye. The labeled DNA oligonucleotides were made using light-directed, in situ microarray synthesis. The results indicate that the fluorescence intensity of both dyes is sensitive to all five bases or base pairs, that the sequence dependence is stronger for double- (vs single-) stranded DNA, and that the dyes are sensitive to both the adjacent dsDNA sequence and the 3'-ssDNA overhang. Purine-rich sequences result in higher fluorescence. The results can be used to estimate measurement error in experiments with fluorescent-labeled DNA, as well as to optimize the fluorescent signal by considering the nucleobase environment of the labeling cyanine dye.

  11. Temperature and frequency dependent conductivity of bismuth zinc vanadate semiconducting glassy system

    NASA Astrophysics Data System (ADS)

    Punia, R.; Kundu, R. S.; Dult, Meenakshi; Murugavel, S.; Kishore, N.

    2012-10-01

    The ac conductivity of bismuth zinc vanadate glasses with compositions 50V2O5. xBi2O3. (50-x) ZnO has been studied in the frequency range 10-1 Hz to 2 MHz and in temperature range 333.16 K to 533.16 K. The temperature and frequency dependent conductivity is found to obey Jonscher's universal power law for all the compositions of bismuth zinc vanadate glass system. The dc conductivity (σdc), crossover frequency (ωH), and frequency exponent (s) have been estimated from the fitting of experimental data of ac conductivity with Jonscher's universal power law. Enthalpy to dissociate the cation from its original site next to a charge compensating center (Hf) and enthalpy of migration (Hm) have also been estimated. It has been observed that mobility of charge carriers and ac conductivity in case of zinc vanadate glass system increases with increase in Bi2O3 content. In order to determine the conduction mechanism, the ac conductivity and its frequency exponent have been analyzed in the frame work of various theoretical models based on classical hopping over barriers and quantum mechanical tunneling. The ac conduction takes place via tunneling of overlapping large polarons in all the compositions of presently studied vanadate glasses. The fitting of experimental data of ac conductivity with overlapping large polarons tunneling model has also been done. The parameters; density of states at Fermi level (N(EF)), activation energy associated with charge transfer between the overlapping sites (WHO), inverse localization length (α) and polaron radius (rp) obtained from fitting of this model with experimental data are reasonable.

  12. Measurement of the position-dependent electrophoretic force on DNA in a glass nanocapillary.

    PubMed

    Bulushev, Roman D; Steinbock, Lorenz J; Khlybov, Sergey; Steinbock, Julian F; Keyser, Ulrich F; Radenovic, Aleksandra

    2014-11-12

    The electrophoretic force on a single DNA molecule inside a glass nanocapillary depends on the opening size and varies with the distance along the symmetrical axis of the nanocapillary. Using optical tweezers and DNA-coated beads, we measured the stalling forces and mapped the position-dependent force profiles acting on DNA inside nanocapillaries of different sizes. We showed that the stalling force is higher in nanocapillaries of smaller diameters. The position-dependent force profiles strongly depend on the size of the nanocapillary opening, and for openings smaller than 20 nm, the profiles resemble the behavior observed in solid-state nanopores. To characterize the position-dependent force profiles in nanocapillaries of different sizes, we used a model that combines information from both analytical approximations and numerical calculations.

  13. Preparation, characterization and scanned conductance microscopy studies of DNA-templated one-dimensional copper nanostructures.

    PubMed

    Watson, Scott M D; Wright, Nicholas G; Horrocks, Benjamin R; Houlton, Andrew

    2010-02-02

    The synthesis of one-dimensional metal nanostructures can be achieved through the use of DNA molecules as templates to control and direct metal deposition. Copper nanostructures have been fabricated using this strategy, through association of Cu(2+) ions to DNA templates and reduced with ascorbic acid. Due to the possibility that the reduction of the Cu(2+) can result in the preferential formation of Cu(2)O over metallic Cu(0), X-ray photoelectron spectroscopy and X-ray diffraction have been carried out to establish the chemical identity of the nanostructures. Conclusive evidence is found that reduction of the Cu(2+) ions does result in the formation of the desired metallic Cu(0) structures. The morphology of the nanostructured Cu(0) material has also been observed by atomic force microscopy, showing the structures to have a "beads-on-a-string" appearance and being 3.0-5.5 nm in height. The electrical properties of the structures have been investigated by scanned conductance microscopy, showing the Cu(0) structures exhibit much larger electrical resistance than expected for a metallic nanowire. This is thought to be a consequence of their "beads-on-a-string" morphology and small lateral dimensions (sub-10 nm); both these factors would be expected to increase the electron scattering rate, and, further, there are likely to be significant tunneling barriers at the Cu(0) particle-particle junctions.

  14. Alternating current electrokinetic separation and detection of DNA nanoparticles in high-conductance solutions.

    PubMed

    Krishnan, Rajaram; Sullivan, Benjamin D; Mifflin, Robert L; Esener, Sadik C; Heller, Michael J

    2008-05-01

    In biomedical research and diagnostics, it is a significant challenge to directly isolate and identify rare cells and potential biomarkers in blood, plasma and other clinical samples. Additionally, the advent of bionanotechnology is leading to numerous drug delivery approaches that involve encapsulation of drugs and imaging agents within nanoparticles, which now will also have to be identified and separated from blood and plasma. Alternating current (AC) electrokinetic techniques such as dielectrophoresis (DEP) offer a particularly attractive mechanism for the separation of cells and nanoparticles. Unfortunately, present DEP techniques require the dilution of blood/plasma, thus making the technology less suitable for clinical sample preparation. Using array devices with microelectrodes over-coated with porous hydrogel layers, AC electric field conditions have been found which allow the separation of DNA nanoparticles to be achieved under high-conductance (ionic strength) conditions. At AC frequencies in the 3000 Hz to 10,000 Hz range and 10 volts peak-to-peak, the separation of 10-microm polystyrene particles into low field regions, and 60-nm DNA-derivatized nanoparticles and 200-nm nanoparticles into high-field regions was carried out in 149 mM 1xPBS buffer (1.68 S/m). These results may allow AC electrokinetic systems to be developed that can be used with clinically relevant samples under physiological conditions.

  15. In Situ Study of Strain-Dependent Ion Conductivity of Stretchable Polyethylene Oxide Electrolyte

    PubMed Central

    Kelly, Taylor; Ghadi, Bahar Moradi; Berg, Sean; Ardebili, Haleh

    2016-01-01

    There is a strong need in developing stretchable batteries that can accommodate stretchable or irregularly shaped applications including medical implants, wearable devices and stretchable electronics. Stretchable solid polymer electrolytes are ideal candidates for creating fully stretchable lithium ion batteries mainly due to their mechanical and electrochemical stability, thin-film manufacturability and enhanced safety. However, the characteristics of ion conductivity of polymer electrolytes during tensile deformation are not well understood. Here, we investigate the effects of tensile strain on the ion conductivity of thin-film polyethylene oxide (PEO) through an in situ study. The results of this investigation demonstrate that both in-plane and through-plane ion conductivities of PEO undergo steady and linear growths with respect to the tensile strain. The coefficients of strain-dependent ion conductivity enhancement (CSDICE) for in-plane and through-plane conduction were found to be 28.5 and 27.2, respectively. Tensile stress-strain curves and polarization light microscopy (PLM) of the polymer electrolyte film reveal critical insights on the microstructural transformation of stretched PEO and the potential consequences on ionic conductivity. PMID:26831948

  16. In Situ Study of Strain-Dependent Ion Conductivity of Stretchable Polyethylene Oxide Electrolyte

    NASA Astrophysics Data System (ADS)

    Kelly, Taylor; Ghadi, Bahar Moradi; Berg, Sean; Ardebili, Haleh

    2016-02-01

    There is a strong need in developing stretchable batteries that can accommodate stretchable or irregularly shaped applications including medical implants, wearable devices and stretchable electronics. Stretchable solid polymer electrolytes are ideal candidates for creating fully stretchable lithium ion batteries mainly due to their mechanical and electrochemical stability, thin-film manufacturability and enhanced safety. However, the characteristics of ion conductivity of polymer electrolytes during tensile deformation are not well understood. Here, we investigate the effects of tensile strain on the ion conductivity of thin-film polyethylene oxide (PEO) through an in situ study. The results of this investigation demonstrate that both in-plane and through-plane ion conductivities of PEO undergo steady and linear growths with respect to the tensile strain. The coefficients of strain-dependent ion conductivity enhancement (CSDICE) for in-plane and through-plane conduction were found to be 28.5 and 27.2, respectively. Tensile stress-strain curves and polarization light microscopy (PLM) of the polymer electrolyte film reveal critical insights on the microstructural transformation of stretched PEO and the potential consequences on ionic conductivity.

  17. Characterization and dynamic charge dependent modeling of conducting polymer trilayer bending

    NASA Astrophysics Data System (ADS)

    Farajollahi, Meisam; Sassani, Farrokh; Naserifar, Naser; Fannir, Adelyne; Plesse, Cédric; Nguyen, Giao T. M.; Vidal, Frédéric; Madden, John D. W.

    2016-11-01

    Trilayer bending actuators are charge driven devices that have the ability to function in air and provide large mechanical amplification. The electronic and mechanical properties of these actuators are known to be functions of their charge state making prediction of their responses more difficult when they operate over their full range of deformation. In this work, a combination of state space representation and a two-dimensional RC transmission line model are used to implement a nonlinear time variant model for conducting polymer-based trilayer actuators. Electrical conductivity and Young’s modulus of electromechanically active PEDOT conducting polymer containing films as a function of applied voltage were measured and incorporated into the model. A 16% drop in Young’s modulus and 24 times increase in conductivity are observed by oxidizing the PEDOT. A closed form formulation for radius of curvature of trilayer actuators considering asymmetric and location dependent Young’s modulus and conductivity in the conducting polymer layers is derived and implemented in the model. The nonlinear model shows the capability to predict the radius of curvature as a function of time and position with reasonable consistency (within 4%). The formulation is useful for general trilayer configurations to calculate the radius of curvature as a function of time. The proposed electrochemical modeling approach may also be useful for modeling energy storage devices.

  18. Modeling activity-dependent changes of axonal spike conduction in primary afferent C-nociceptors

    PubMed Central

    Tigerholm, Jenny; Petersson, Marcus E.; Obreja, Otilia; Lampert, Angelika; Carr, Richard; Schmelz, Martin

    2013-01-01

    Action potential initiation and conduction along peripheral axons is a dynamic process that displays pronounced activity dependence. In patients with neuropathic pain, differences in the modulation of axonal conduction velocity by activity suggest that this property may provide insight into some of the pathomechanisms. To date, direct recordings of axonal membrane potential have been hampered by the small diameter of the fibers. We have therefore adopted an alternative approach to examine the basis of activity-dependent changes in axonal conduction by constructing a comprehensive mathematical model of human cutaneous C-fibers. Our model reproduced axonal spike propagation at a velocity of 0.69 m/s commensurate with recordings from human C-nociceptors. Activity-dependent slowing (ADS) of axonal propagation velocity was adequately simulated by the model. Interestingly, the property most readily associated with ADS was an increase in the concentration of intra-axonal sodium. This affected the driving potential of sodium currents, thereby producing latency changes comparable to those observed for experimental ADS. The model also adequately reproduced post-action potential excitability changes (i.e., recovery cycles) observed in vivo. We performed a series of control experiments replicating blockade of particular ion channels as well as changing temperature and extracellular ion concentrations. In the absence of direct experimental approaches, the model allows specific hypotheses to be formulated regarding the mechanisms underlying activity-dependent changes in C-fiber conduction. Because ADS might functionally act as a negative feedback to limit trains of nociceptor activity, we envisage that identifying its mechanisms may also direct efforts aimed at alleviating neuronal hyperexcitability in pain patients. PMID:24371290

  19. Fluorescence quenching studies of potential-dependent DNA reorientation dynamics at glassy carbon electrode surfaces.

    PubMed

    Li, Qin; Cui, Chenchen; Higgins, Daniel A; Li, Jun

    2012-09-05

    The potential-dependent reorientation dynamics of double-stranded DNA (ds-DNA) attached to planar glassy carbon electrode (GCE) surfaces were investigated. The orientation state of surface-bound ds-DNA was followed by monitoring the fluorescence from a 6-carboxyfluorescein (FAM6) fluorophore covalently linked to the distal end of the DNA. Positive potentials (i.e., +0.2 V vs open circuit potential, OCP) caused the ds-DNA to align parallel to the electrode surface, resulting in strong dipole-electrode quenching of FAM6 fluorescence. Switching of the GCE potential to negative values (i.e., -0.2 V vs OCP) caused the ds-DNA to reorient perpendicular to the electrode surface, with a concomitant increase in FAM6 fluorescence. In addition to the very fast (submilliseconds) dynamics of the initial reorientation process, slow (0.1-0.9 s) relaxation of FAM6 fluorescence to intermediate levels was also observed after potential switching. These dynamics have not been previously described in the literature. They are too slow to be explained by double layer charging, and chronoamperometry data showed no evidence of such effects. Both the amplitude and rate of the dynamics were found to depend upon buffer concentration, and ds-DNA length, demonstrating a dependence on the double layer field. The dynamics are concluded to arise from previously undetected complexities in the mechanism of potential-dependent ds-DNA reorientation. The possible origins of these dynamics are discussed. A better understanding of these dynamics will lead to improved models for potential-dependent ds-DNA reorientation at electrode surfaces and will facilitate the development of advanced electrochemical devices for detection of target DNAs.

  20. Sieving DNA molecules by length dependence in artificial nano-channel matrices

    NASA Astrophysics Data System (ADS)

    Wang, Chung-Hsuan; Hua Ho, Chia; Chou, Y. C.

    2013-01-01

    Nano-channel matrices are designed and fabricated for sieving DNA molecules by length. The length dependence is found to change with the size of the channels. Three regimes can be distinguished: (a) for the matrices with the size of the channels comparable to the persistence length (lp) of DNA molecules (45 nm), the mobility of DNA is found to decrease with the length of the molecules, similar to that found for the gel electrophoresis; (b) as the size of the nano-channel increases, the successful attacking frequency increases for the long molecules. The length-dependence of the mobility reverses; and (c) the Ogston mechanism holds for even larger channels. The short DNA molecules drift faster for the channels with diameter larger than 10 lp. Such a variety of the length dependence is observed for the first time in the electrophoresis in the artificial structures.

  1. DNA electrophoresis in agarose gels: A new mobility vs. DNA length dependence

    NASA Astrophysics Data System (ADS)

    Beheshti, Afshin

    2002-04-01

    Separations were performed on double stranded DNA (dsDNA) using electrophoresis. Electrophoresis is the steady transport of particles under the influence of an external electric field. Double stranded DNA fragments ranging in length from 200 base pairs (bp) to 194,000 bp (0.34 nm = 1 bp) were electrophoresed at agarose gel concentrations T = 0.4%--1.5%. The electric field was varied from 0.62 V/cm to 6.21 V/cm. A wide range of electric fields and gel concentrations were used to study the usefulness of a new interpolation equation, 1mL =1mL-( 1mL-1 ms)e-L/g , where mL,ms , and g are independent free fitting parameters. The long length mobility limit is interpreted as mL , the short length mobility limit is ms , and g is the crossover between the long length limit and the short length limit. This exponential relation fit very well (chi2 ≥ 0.999) when there are two smooth transitions observed in the "reptation plots" (plotting 3mL/m∘ vs. L) (J. Rousseau, G. Drouin, and G. W. Slater, Phys Rev Lett. 1997, 79, 1945--1948). Fits deviate from the data when three different slopes were observed in the reptation plots. Reptation plots were used to determine a phase diagram for dsDNA migration regimes. The phase diagrams define different regions where mechanisms for molecular transport affect the migration of dsDNA in agarose gels during electrophoresis. The parameters from the equation have also been interpreted to provide a physical description of the structure of the agarose gel by calculating the pore sizes. The relations between the values for the pore sizes and the phase diagrams are interpreted to better understand the migration of the DNA through agarose gels.

  2. Defect association mediated ionic conductivity of rare earth doped nanoceria: Dependency on ionic radius

    NASA Astrophysics Data System (ADS)

    Anirban, Sk.; Sinha, A.; Bandyopadhyay, S.; Dutta, A.

    2016-05-01

    Rare earth doped nanoceria Ce0.9RE0.1O1.95 (RE = Pr, Nd, Eu and Gd) were prepared through citrate auto-ignition method. The single phase cubic fluorite structure with space group Fm3 ¯m of the compositions were confirmed from Rietveld analysis of XRD data. The particle size of the compositions were in the range 49.77 nm to 66.20 nm. An ionic radius dependent lattice parameter variation was found. The DC conductivity of each composition was evaluated using Random Barrier Model. The conductivity decreased and activation energy increased with increasing ionic radius from Gd to Pr doping due to the size mismatch with host ions and formation of stable defect associate. The formation of different defect associates and their correlation with ionic conductivity has been discussed.

  3. Methods to detect replication-dependent and replication-independent DNA structure-induced genetic instability

    PubMed Central

    Wang, Guliang; Gaddis, Sally; Vasquez, Karen M.

    2013-01-01

    DNA can adopt a variety of alternative secondary (i.e., non-B DNA) conformations that play important roles in cellular metabolism, including genetic instability, disease etiology, and evolution. While we still have much to learn, research in this field has expanded dramatically in the past decade. We have summarized in our previous Methods review (Wang et al., Methods, 2009) some commonly used techniques to determine non-B DNA structural conformations and non-B DNA-induced genetic instability in prokaryotes and eukaryotes. Since that time, we and others have further characterized mechanisms involved in DNA structure-induced mutagenesis and have proposed both replication-dependent and replication-independent models. Thus, in this review, we highlight some current methodologies to identify DNA replication-related and replication-independent mutations occurring at non-B DNA regions to allow for a better understanding of the mechanisms underlying DNA structure-induced genetic instability. We also describe a new web-based search engine to identify potential intramolecular triplex (H-DNA) and left-handed Z-DNA-forming motifs in entire genomes or at selected sequences of interest. PMID:23954565

  4. Large Conductance Switching in a Single-Molecule Device through Room Temperature Spin-Dependent Transport.

    PubMed

    Aragonès, Albert C; Aravena, Daniel; Cerdá, Jorge I; Acís-Castillo, Zulema; Li, Haipeng; Real, José Antonio; Sanz, Fausto; Hihath, Josh; Ruiz, Eliseo; Díez-Pérez, Ismael

    2016-01-13

    Controlling the spin of electrons in nanoscale electronic devices is one of the most promising topics aiming at developing devices with rapid and high density information storage capabilities. The interface magnetism or spinterface resulting from the interaction between a magnetic molecule and a metal surface, or vice versa, has become a key ingredient in creating nanoscale molecular devices with novel functionalities. Here, we present a single-molecule wire that displays large (>10000%) conductance switching by controlling the spin-dependent transport under ambient conditions (room temperature in a liquid cell). The molecular wire is built by trapping individual spin crossover Fe(II) complexes between one Au electrode and one ferromagnetic Ni electrode in an organic liquid medium. Large changes in the single-molecule conductance (>100-fold) are measured when the electrons flow from the Au electrode to either an α-up or a β-down spin-polarized Ni electrode. Our calculations show that the current flowing through such an interface appears to be strongly spin-polarized, thus resulting in the observed switching of the single-molecule wire conductance. The observation of such a high spin-dependent conductance switching in a single-molecule wire opens up a new door for the design and control of spin-polarized transport in nanoscale molecular devices at room temperature.

  5. RNA dependent DNA replication fidelity of HIV-1 reverse transcriptase: evidence of discrimination between DNA and RNA substrates.

    PubMed

    Kerr, S G; Anderson, K S

    1997-11-18

    The RNA dependent DNA replication fidelity of HIV-1 reverse transcriptase has been investigated using pre-steady-state kinetics under single turnover conditions. In contrast to previous estimates of low replication fidelity of HIV-1 reverse transcriptase, the present study finds the enzyme to be more highly discriminating when an RNA/DNA template-primer is employed as compared with the corresponding DNA/DNA template-primer. The basis of this selectivity is due to extremely slow polymerization kinetics for incorporation of an incorrect deoxynucleotide. The maximum rates for misincorporation (kpol) of dGTP, dCTP, and dTTP opposite a template uridine were 0.2, 0.03, and 0.003 s-1, respectively. The equilibrium dissociation constants (Kd) for the incorrect nucleotide opposite a template uridine were 1.0, 1.1, and 0.7 mM for dGTP, dCTP, and dTTP, respectively. These kinetic values provide fidelity estimates of 26 000 for discrimination against dGTP, 176 000 for dCTP, and 1 x 10(6) for dTTP misincorporation at this position. Similar observations were obtained when incorrect nucleotide misincorporation was examined opposite a template adenine. Thus in a direct comparison of RNA/DNA and DNA/DNA template-primer substrates, HIV-1 RT exhibits approximately a 10-60-fold increase in fidelity. This study augments our current understanding of the similarities and differences of catalytic activity of HIV-1 reverse transcriptase using RNA and DNA substrates. Moreover, these studies lend further support for a model for nucleotide incorporation by HIV-1 reverse transcriptase involving a two-step binding mechanism governed by a rate-limiting conformational change for correct incorporation.

  6. WEE1 inhibition in pancreatic cancer cells is dependent on DNA repair status in a context dependent manner

    PubMed Central

    Lal, Shruti; Zarei, Mahsa; Chand, Saswati N.; Dylgjeri, Emanuela; Mambelli-Lisboa, Nicole C.; Pishvaian, Michael J.; Yeo, Charles J.; Winter, Jordan M.; Brody, Jonathan R.

    2016-01-01

    Pancreatic ductal adenocarcinoma (PDA) is a lethal disease, in part, because of the lack of effective targeted therapeutic options. MK-1775 (also known as AZD1775), a mitotic inhibitor, has been demonstrated to enhance the anti-tumor effects of DNA damaging agents such as gemcitabine. We evaluated the efficacy of MK-1775 alone or in combination with DNA damaging agents (MMC or oxaliplatin) in PDA cell lines that are either DNA repair proficient (DDR-P) or deficient (DDR-D). PDA cell lines PL11, Hs 766T and Capan-1 harboring naturally selected mutations in DNA repair genes FANCC, FANCG and BRCA2 respectively, were less sensitive to MK-1775 as compared to two out of four representative DDR-P (MIA PaCa2 and PANC-1) cell lines. Accordingly, DDR-P cells exhibit reduced sensitivity to MK-1775 upon siRNA silencing of DNA repair genes, BRCA2 or FANCD2, compared to control cells. Only DDR-P cells showed increased apoptosis as a result of early mitotic entry and catastrophe compared to DDR-D cells. Taken together with other recently published reports, our results add another level of evidence that the efficacy of WEE1 inhibition is influenced by the DNA repair status of a cell and may also be dependent on the tumor type and model evaluated. PMID:27616351

  7. Temperature gating and competing temperature-dependent effects in DNA molecular wires

    NASA Astrophysics Data System (ADS)

    Wibowo, Denni; Narenji, Alaleh; Kassegne, Sam

    2017-02-01

    While recent research in electron-transport mechanism on a double strands DNA seems to converge into a consensus, experiments in direct electrical measurements on a long DNA molecules still lead to a conflicting result This study is the continuation of our previous research in electrical characterization of DNA molecular wires, where we furtherly investigate the effects of temperature on the electrical conductivity of DNA molecular wires by measuring its impedance response. We found that at higher temperatures, the expected increase in charge hopping mechanism may account for the decrease in impedance (and hence increase in conductivity) supporting the 'charge hopping mechanism' theory. UV light exposure, on the other hand, causes damage to GC base pairs reducing the path available for hopping mechanism and hence resulting in increased impedance - this again supporting the 'charge hopping mechanism' theory. We also report that λ-DNA molecular wires have differing impedance responses at two temperature regimes: impedance increases between 4 °C - 40 °C and then decreases between 40 °C - melting point (˜110 °C), after which λ-DNA denatures resulting in no current transduction. We submit that the low impedance of λ-DNA molecular wires observed at moderate to high frequencies may have significant implications to the field of DNA-based bionanoelectronics.

  8. Pilus-dependent, double-stranded DNA bacteriophage for Caulobacter.

    PubMed Central

    Scholl, D R; Jollick, J D

    1980-01-01

    Caulobacter phage phi 6, previously reported to adsorb specifically to bacterial flagella, was shown here to attach to pili more frequently than to flagella. Phage phi 6 was shown to contain double-stranded DNA by circular dichroism spectroscopy and thermal denaturation accompanied by a hyperchromic shift at 260 nm. Morphologically, phage phi 6 fits group B2 (H.-W. Ackermann, in A. I. Laskin and H. A. Lechevalier, ed., Handbook of Microbiology, vol. 1, p. 638-643, 1973) with a long, noncontractile tail and an elongate head. Pilus-less mutants of the host Caulobacter vibrioides CV6 are phage phi 6 resistant, whereas flagellum-less mutants, which produce pili, are phage susceptible. Treatments of susceptible cells which remove or immobilize pili and flagella, e.g., blending or cyanide, inhibited phage phi 6 infection. Our evidence suggests that phage of phi 6 initiates infection in a manner similar to the pilus-specific phages for Pseudomonas described previously (D. E. Bradley, Virology 51:489-492, 1973; D. E. Bradley and T. L. Pitt, J. Gen. Virol. 24:1-15, 1974). Images PMID:6106721

  9. Sequence dependence of isothermal DNA amplification via EXPAR

    PubMed Central

    Qian, Jifeng; Ferguson, Tanya M.; Shinde, Deepali N.; Ramírez-Borrero, Alissa J.; Hintze, Arend; Adami, Christoph; Niemz, Angelika

    2012-01-01

    Isothermal nucleic acid amplification is becoming increasingly important for molecular diagnostics. Therefore, new computational tools are needed to facilitate assay design. In the isothermal EXPonential Amplification Reaction (EXPAR), template sequences with similar thermodynamic characteristics perform very differently. To understand what causes this variability, we characterized the performance of 384 template sequences, and used this data to develop two computational methods to predict EXPAR template performance based on sequence: a position weight matrix approach with support vector machine classifier, and RELIEF attribute evaluation with Naïve Bayes classification. The methods identified well and poorly performing EXPAR templates with 67–70% sensitivity and 77–80% specificity. We combined these methods into a computational tool that can accelerate new assay design by ruling out likely poor performers. Furthermore, our data suggest that variability in template performance is linked to specific sequence motifs. Cytidine, a pyrimidine base, is over-represented in certain positions of well-performing templates. Guanosine and adenosine, both purine bases, are over-represented in similar regions of poorly performing templates, frequently as GA or AG dimers. Since polymerases have a higher affinity for purine oligonucleotides, polymerase binding to GA-rich regions of a single-stranded DNA template may promote non-specific amplification in EXPAR and other nucleic acid amplification reactions. PMID:22416064

  10. Response-coefficient method for heat-conduction transients with time-dependent inputs

    NASA Technical Reports Server (NTRS)

    Ceylan, Tamer

    1993-01-01

    A theoretical overview of the response coefficient method for heat conduction transients with time-dependent input forcing functions is presented with a number of illustrative applications. The method may be the most convenient and economical if the same problem is to be solved many times with different input-time histories or if the solution time is relatively long. The method is applicable to a wide variety of problems, including irregular geometries, position-dependent boundary conditions, position-dependent physical properties, and nonperiodic irregular input histories. Nonuniform internal energy generation rates within the structure can also be handled by the method. The area of interest is long-time solutions, in which initial condition is unimportant, and not the early transient period. The method can be applied to one dimensional problems in cartesian, cylindrical, and spherical coordinates as well as to two dimensional problems in cartesian and cylindrical coordinates.

  11. Burning off DNA methylation: new evidence for oxygen-dependent DNA demethylation.

    PubMed

    Jurkowski, Tomasz P; Jeltsch, Albert

    2011-11-25

    Where do you stop? Three recent publications have described how the oxidation of 5-methylcytosine by Tet dioxygenases does not stop at the 5-hydroxymethylcytosine (5hmC) state, rather further oxidation of 5hmC is involved in DNA demethylation. The nature of the enzymes involved in this process shed light on the dynamics of epigenetic signaling and its evolutionary origin.

  12. Force and twist dependence of RepC nicking activity on torsionally-constrained DNA molecules

    PubMed Central

    Pastrana, Cesar L.; Carrasco, Carolina; Akhtar, Parvez; Leuba, Sanford H.; Khan, Saleem A.; Moreno-Herrero, Fernando

    2016-01-01

    Many bacterial plasmids replicate by an asymmetric rolling-circle mechanism that requires sequence-specific recognition for initiation, nicking of one of the template DNA strands and unwinding of the duplex prior to subsequent leading strand DNA synthesis. Nicking is performed by a replication-initiation protein (Rep) that directly binds to the plasmid double-stranded origin and remains covalently bound to its substrate 5′-end via a phosphotyrosine linkage. It has been proposed that the inverted DNA sequences at the nick site form a cruciform structure that facilitates DNA cleavage. However, the role of Rep proteins in the formation of this cruciform and the implication for its nicking and religation functions is unclear. Here, we have used magnetic tweezers to directly measure the DNA nicking and religation activities of RepC, the replication initiator protein of plasmid pT181, in plasmid sized and torsionally-constrained linear DNA molecules. Nicking by RepC occurred only in negatively supercoiled DNA and was force- and twist-dependent. Comparison with a type IB topoisomerase in similar experiments highlighted a relatively inefficient religation activity of RepC. Based on the structural modeling of RepC and on our experimental evidence, we propose a model where RepC nicking activity is passive and dependent upon the supercoiling degree of the DNA substrate. PMID:27488190

  13. Layer thickness-dependent phonon properties and thermal conductivity of MoS2

    NASA Astrophysics Data System (ADS)

    Gu, Xiaokun; Li, Baowen; Yang, Ronggui

    2016-02-01

    For conventional materials, the thermal conductivity of thin films is usually suppressed when the thickness decreases due to phonon-boundary scattering. However, this is not necessarily true for the van der Waals solids if the thickness is reduced to only a few layers. In this letter, the layer thickness-dependent phonon properties and thermal conductivity in the few-layer MoS2 are studied using the first-principles-based Peierls-Boltzmann transport equation approach. The basal-plane thermal conductivity of 10-μm-long samples is found to monotonically reduce from 138 W/mK to 98 W/mK for naturally occurring MoS2, and from 155 W/mK to 115 W/mK for isotopically pure MoS2, when its thickness increases from one layer to three layers. The thermal conductivity of tri-layer MoS2 approaches to that of bulk MoS2. Both the change of phonon dispersion and the thickness-induced anharmonicity are important for explaining such a thermal conductivity reduction. The increased anharmonicity in bi-layer MoS2 results in stronger phonon scattering for ZAi modes, which is linked to the breakdown of the symmetry in single-layer MoS2.

  14. Spatial dependence of polycrystalline FTO’s conductance analyzed by conductive atomic force microscope (C-AFM)

    SciTech Connect

    Peixoto, Alexandre Pessoa; Costa, J. C. da

    2014-05-15

    Fluorine-doped Tin oxide (FTO) is a highly transparent, electrically conductive polycrystalline material frequently used as an electrode in organic solar cells and optical-electronic devices [1–2]. In this work a spatial analysis of the conductive behavior of FTO was carried out by Conductive-mode Atomic Force Microscopy (C-AFM). Rare highly oriented grains sample give us an opportunity to analyze the top portion of polycrystalline FTO and compare with the border one. It is shown that the current flow essentially takes place through the polycrystalline edge at grain boundaries.

  15. Examination of the causes of covariation between conduct disorder symptoms and vulnerability to drug dependence.

    PubMed

    Button, Tanya M M; Hewitt, John K; Rhee, Soo Hyun; Young, Susan E; Corley, Robin P; Stallings, Michael C

    2006-02-01

    Conduct disorder (CD) symptoms and substance dependence commonly co-occur. Both phenotypes are highly heritable and a common genetic influence on the covariation has been suggested. The aim of this study was to determine the extent to which genes and environment contribute to the covariance between CD and drug dependence using twins from the Colorado Longitudinal Twin Sample and the Colorado Twin Registry. A total of 880 twin pairs (237 monozygotic [MZ] female, 195 MZ male, 116 dizygotic [DZ] female, 118 DZ male and 214 DZ opposite-sex) aged 13 to 18 (mean = 15.65) were included in the analysis. CD was assessed by lifetime Diagnostic and Statistical Manual of Mental Disorders (4th ed.; DSM-IV; American Psychiatric Association, 1994) symptom count and a polysubstance dependence vulnerability index was developed from responses to the Composite International Diagnostic Interview--Substance Abuse Module. A bivariate Cholesky Decomposition model was used to partition the cause of variation and covariation of the two phenotypes. No sex-limitation was observed in our data, and male and female parameter estimates were constrained to be equal. Both CD symptoms and dependence vulnerability were significantly heritable, and genes, shared environment and nonshared environment all contributed to the covariation between them. Genes contributed 35% of the phenotypic covariance, shared environment contributed 46%, and nonshared environmental influences contributed the remaining 19% to the phenotypic covariance. Therefore, there appears to be pleiotropic genetic influence on CD symptoms and dependence vulnerability.

  16. Concentration-dependent organization of DNA by the dinoflagellate histone-like protein HCc3

    PubMed Central

    Chan, Yuk-Hang; Wong, Joseph T. Y.

    2007-01-01

    The liquid crystalline chromosomes of dinoflagellates are the alternative to the nucleosome-based organization of chromosomes in the eukaryotes. These nucleosome-less chromosomes have to devise novel ways to maintain active parts of the genome. The dinoflagellate histone-like protein HCc3 has significant sequence identity with the bacterial DNA-binding protein HU. HCc3 also has a secondary structure resembling HU in silico. We have examined HCc3 in its recombinant form. Experiments on DNA-cellulose revealed its DNA-binding activity is on the C-terminal domain. The N-terminal domain is responsible for intermolecular oligomerization as demonstrated by cross-linking studies. However, HCc3 could not complement Escherichia coli HU-deficient mutants, suggesting functional differences. In ligation assays, HCc3-induced DNA concatenation but not ring closure as the DNA-bending HU does. The basic HCc3 was an efficient DNA condensing agent, but it did not behave like an ordinary polycationic compound. HCc3 also induced specific structures with DNA in a concentration-dependent manner, as demonstrated by atomic force microscopy (AFM). At moderate concentration of HCc3, DNA bridging and bundling were observed; at high concentrations, the complexes were even more condensed. These results are consistent with a biophysical role for HCc3 in maintaining extended DNA loops at the periphery of liquid crystalline chromosomes. PMID:17412706

  17. Mutation dependance of the mitochondrial DNA copy number in the first stages of human embryogenesis.

    PubMed

    Monnot, Sophie; Samuels, David C; Hesters, Laetitia; Frydman, Nelly; Gigarel, Nadine; Burlet, Philippe; Kerbrat, Violaine; Lamazou, Frédéric; Frydman, René; Benachi, Alexandra; Feingold, Josué; Rotig, Agnes; Munnich, Arnold; Bonnefont, Jean-Paul; Steffann, Julie

    2013-05-01

    Mitochondrial DNA (mtDNA) content is thought to remain stable over the preimplantation period of human embryogenesis that is, therefore, suggested to be entirely dependent on ooplasm mtDNA capital. We have explored the impact of two disease-causing mutations [m.3243A>G myopathy, encephalopathy, lactic acidosis and stroke-like syndrome (MELAS) and m.8344A>G myoclonic epilepsy associated with ragged-red fibers (MERRF)] on mtDNA amounts in human oocytes and day 4-5 preimplantation embryos. The mtDNA amount was stable in MERRF and control materials, whereas gradually increasing from the germinal vesicle of oogenesis to the blastocyst stage of embryogenesis in MELAS cells, MELAS embryos carrying ∼3-fold higher mtDNA amount than control embryos (P = 0.0003). A correlation between mtDNA copy numbers and mutant loads was observed in MELAS embryos (R(2) = 0.42, P < 0.0013), suggestive of a compensation for the respiratory chain defect resulting from high mutation levels. These results suggest that mtDNA can replicate in early embryos and emphasize the need for sufficient amount of wild-type mtDNA to sustain embryonic development in humans.

  18. Mycobacterium tuberculosis NAD+-dependent DNA ligase is selectively inhibited by glycosylamines compared with human DNA ligase I

    PubMed Central

    Srivastava, Sandeep Kumar; Dube, Divya; Tewari, Neetu; Dwivedi, Namrata; Tripathi, Rama Pati; Ramachandran, Ravishankar

    2005-01-01

    DNA ligases are important enzymes which catalyze the joining of nicks between adjacent bases of double-stranded DNA. NAD+-dependent DNA ligases (LigA) are essential in bacteria and are absent in humans. They have therefore been identified as novel, validated and attractive drug targets. Using virtual screening against an in-house database of compounds and our recently determined crystal structure of the NAD+ binding domain of the Mycobacterium tuberculosis LigA, we have identified N1, Nn-bis-(5-deoxy-α-d-xylofuranosylated) diamines as a novel class of inhibitors for this enzyme. Assays involving M.tuberculosis LigA, T4 ligase and human DNA ligase I show that these compounds specifically inhibit LigA from M.tuberculosis. In vitro kinetic and inhibition assays demonstrate that the compounds compete with NAD+ for binding and inhibit enzyme activity with IC50 values in the µM range. Docking studies rationalize the observed specificities and show that among several glycofuranosylated diamines, bis xylofuranosylated diamines with aminoalkyl and 1, 3-phenylene carbamoyl spacers mimic the binding modes of NAD+ with the enzyme. Assays involving LigA-deficient bacterial strains show that in vivo inhibition of ligase by the compounds causes the observed antibacterial activities. They also demonstrate that the compounds exhibit in vivo specificity for LigA over ATP-dependent ligase. This class of inhibitors holds out the promise of rational development of new anti-tubercular agents. PMID:16361267

  19. Mycobacterium tuberculosis NAD+-dependent DNA ligase is selectively inhibited by glycosylamines compared with human DNA ligase I.

    PubMed

    Srivastava, Sandeep Kumar; Dube, Divya; Tewari, Neetu; Dwivedi, Namrata; Tripathi, Rama Pati; Ramachandran, Ravishankar

    2005-01-01

    DNA ligases are important enzymes which catalyze the joining of nicks between adjacent bases of double-stranded DNA. NAD+-dependent DNA ligases (LigA) are essential in bacteria and are absent in humans. They have therefore been identified as novel, validated and attractive drug targets. Using virtual screening against an in-house database of compounds and our recently determined crystal structure of the NAD+ binding domain of the Mycobacterium tuberculosis LigA, we have identified N1, N(n)-bis-(5-deoxy-alpha-D-xylofuranosylated) diamines as a novel class of inhibitors for this enzyme. Assays involving M.tuberculosis LigA, T4 ligase and human DNA ligase I show that these compounds specifically inhibit LigA from M.tuberculosis. In vitro kinetic and inhibition assays demonstrate that the compounds compete with NAD+ for binding and inhibit enzyme activity with IC50 values in the microM range. Docking studies rationalize the observed specificities and show that among several glycofuranosylated diamines, bis xylofuranosylated diamines with aminoalkyl and 1, 3-phenylene carbamoyl spacers mimic the binding modes of NAD+ with the enzyme. Assays involving LigA-deficient bacterial strains show that in vivo inhibition of ligase by the compounds causes the observed antibacterial activities. They also demonstrate that the compounds exhibit in vivo specificity for LigA over ATP-dependent ligase. This class of inhibitors holds out the promise of rational development of new anti-tubercular agents.

  20. Dependence of interface conductivity on relevant physical parameters in polarized Fermi mixtures

    NASA Astrophysics Data System (ADS)

    Ebrahimian, N.; Mehrafarin, M.; Afzali, R.

    2012-10-01

    We consider a mass-asymmetric polarized Fermi system in the presence of Hartree-Fock (HF) potentials. We concentrate on the BCS regime with various interaction strengths and numerically obtain the allowed values of the chemical and HF potentials, as well as the mass ratio. The functional dependence of the heat conductivity of the N-SF interface on relevant physical parameters, namely the temperature, the mass ratio, and the interaction strength, is obtained. In particular, we show that the interface conductivity starts to drop with decreasing temperature at the temperature, Tm, where the mean kinetic energy of the particles is just sufficient to overcome the SF gap. We obtain Tm as a function of the mass ratio and the interaction strength. The variation of the heat conductivity, at fixed temperature, with the HF potentials and the imbalance chemical potential is also obtained. Finally, because the range of relevant temperatures increases for larger values of the mass ratio, we consider the 6Li-40K mixture separately by taking the temperature dependence of the pair potential into account.

  1. Instabilities of thin layers of conducting fluids produced by time dependent magnetic fields

    NASA Astrophysics Data System (ADS)

    Burguete, Javier

    2011-11-01

    We present the recent results of an experiment where thin layers of conducting fluids are forced by time-dependent magnetic fields perpendicular to their surface. We use as conducting fluid an In-Ga-Sn alloy, immersed in a 5% hydrocloric acid solution to prevent oxidation. The conducting layers have a circular shape, and are placed inside a set-up that produces the vertical magnetic field. Due to MHD effects, the competition between the Lorentz force and gravity triggers an instability of the free surface. The shape of this surface can adopt many different configurations, with a very rich dynamics, presenting azimuthal wave numbers between 3 and 8 for the explored parameters. The magnetic field evolves harmonically with a frequency up to 10Hz, small enough to not to observe skin depth effects and with a magnitude up to 0.1 T. Different resonant regions have been observed, for narrow windows of the forcing frequency. We have analysed the existence of thresholds for these instabilities, depending on the wave number and experimental parameters. These results are compared with others present in the literature.

  2. Facet-dependent electrical conductivity properties of Cu2O crystals.

    PubMed

    Tan, Chih-Shan; Hsu, Shih-Chen; Ke, Wei-Hong; Chen, Lih-Juann; Huang, Michael H

    2015-03-11

    It is interesting to examine facet-dependent electrical properties of single Cu2O crystals, because such study greatly advances our understanding of various facet effects exhibited by semiconductors. We show a Cu2O octahedron is highly conductive, a cube is moderately conductive, and a rhombic dodecahedron is nonconductive. The conductivity differences are ascribed to the presence of a thin surface layer having different degrees of band bending. When electrical connection was made on two different facets of a rhombicuboctahedron, a diode-like response was obtained, demonstrating the potential of using single polyhedral nanocrystals as functional electronic components. Density of state (DOS) plots for three layers of Cu2O (111), (100), and (110) planes show respective metallic, semimetal, and semiconducting band structures. By examining DOS plots for varying number of planes, the surface layer thicknesses responsible for the facet-dependent electrical properties of Cu2O crystals have been determined to be below 1.5 nm for these facets.

  3. Growth factor-dependent initiation of DNA replication in nuclei isolated from an interleukin 3-dependent murine myeloid cell line.

    PubMed

    Munshi, N C; Gabig, T G

    1990-01-01

    To study the proliferative response of hematopoietic cells to growth factors at the molecular level, we developed a cell-free system for growth factor-dependent initiation of genomic DNA replication. Nuclei were isolated from the IL-3-dependent cell line NFS/N1-H7 after a 10-h period of IL-3 deprivation. Cytosolic and membrane-containing subcellular fractions were prepared from proliferating NFS/N1-H7 cells. Nuclei from the nonproliferating cells (+/- IL-3) showed essentially no incorporation of [3H]thymidine during a 16-h incubation with a mixture of unlabeled GTP, ATP, UTP, CTP, dGTP, dATP, dCTP, and [3H]dTTP. When the combination of IL-3, a cytosolic fraction, and a membrane-containing fraction from proliferating cells was added to nuclei from nonproliferating cells, a burst of [3H]thymidine incorporation into DNA began after a 12-h lag period, attained a maximal rate at 16 h, and reached a level of 860 pmol thymidine/10(6) nuclei at 24 h (corresponding to replication of approximately 56% total mouse genomic DNA). This DNA synthesis was inhibited approximately 90% by the specific DNA polymerase alpha inhibitor aphidicolin. Deletion of a single cellular component or IL-3 from the system resulted in a marked reduction of DNA replication (-membrane, 80 +/- 4%; -cytosol, 90% +/- 4%; -IL-3, 74 +/- 7% inhibition). This model requires a growth factor (IL-3), a sedimentable cell fraction containing its receptor and possibly additional membrane-associated components, and a cytosolic fraction. It appears to recapitulate the molecular events required for progression from early G1 to S phase of the cell cycle induced by IL-3 binding to its receptor.

  4. Growth factor-dependent initiation of DNA replication in nuclei isolated from an interleukin 3-dependent murine myeloid cell line.

    PubMed Central

    Munshi, N C; Gabig, T G

    1990-01-01

    To study the proliferative response of hematopoietic cells to growth factors at the molecular level, we developed a cell-free system for growth factor-dependent initiation of genomic DNA replication. Nuclei were isolated from the IL-3-dependent cell line NFS/N1-H7 after a 10-h period of IL-3 deprivation. Cytosolic and membrane-containing subcellular fractions were prepared from proliferating NFS/N1-H7 cells. Nuclei from the nonproliferating cells (+/- IL-3) showed essentially no incorporation of [3H]thymidine during a 16-h incubation with a mixture of unlabeled GTP, ATP, UTP, CTP, dGTP, dATP, dCTP, and [3H]dTTP. When the combination of IL-3, a cytosolic fraction, and a membrane-containing fraction from proliferating cells was added to nuclei from nonproliferating cells, a burst of [3H]thymidine incorporation into DNA began after a 12-h lag period, attained a maximal rate at 16 h, and reached a level of 860 pmol thymidine/10(6) nuclei at 24 h (corresponding to replication of approximately 56% total mouse genomic DNA). This DNA synthesis was inhibited approximately 90% by the specific DNA polymerase alpha inhibitor aphidicolin. Deletion of a single cellular component or IL-3 from the system resulted in a marked reduction of DNA replication (-membrane, 80 +/- 4%; -cytosol, 90% +/- 4%; -IL-3, 74 +/- 7% inhibition). This model requires a growth factor (IL-3), a sedimentable cell fraction containing its receptor and possibly additional membrane-associated components, and a cytosolic fraction. It appears to recapitulate the molecular events required for progression from early G1 to S phase of the cell cycle induced by IL-3 binding to its receptor. Images PMID:2104881

  5. ATP-dependent chromatin remodeling and DNA double-strand break repair.

    PubMed

    van Attikum, Haico; Gasser, Susan M

    2005-08-01

    The repair of DNA double-strand breaks (DSBs) is critical for the maintenance of genomic stability. Two pathways for the repair of DBSs, nonhomologous end-joining (NHEJ) and homologous recombination (HR), have evolved in eukaryotes. These pathways, like processes such as transcription and replication, act on DNA that is embedded in nucleosomes. Recent studies have shown that DNA repair, like transcription, is facilitated both by histone tail modification and by ATP-dependent chromatin remodeling. This review emphasizes recent reports that demonstrate a function for the ATP-dependent chromatin remodeling complexes INO80 and RSC in NHEJ and HR. We also discuss the possible role of SWR1- and TIP60-mediated nucleosomal histone exchange in DNA repair.

  6. A DNA break– and phosphorylation-dependent positive feedback loop promotes immunoglobulin class-switch recombination

    PubMed Central

    Vuong, Bao Q; Ucher, Anna J; Donghia, Nina M; Gu, Xiwen; Nicolas, Laura; Nowak, Urszula; Rahman, Numa; Strout, Matthew P; Mills, Kevin D; Stavnezer, Janet; Chaudhuri, Jayanta

    2014-01-01

    The ability of activation-induced cytidine deaminase (AID) to efficiently mediate class-switch recombination (CSR) is dependent on its phosphorylation at Ser38; however, the trigger that induces AID phosphorylation and the mechanism by which phosphorylated AID drives CSR have not been elucidated. Here we found that phosphorylation of AID at Ser38 was induced by DNA breaks. Conversely, in the absence of AID phosphorylation, DNA breaks were not efficiently generated at switch (S) regions in the immunoglobulin heavy-chain locus (Igh), consistent with a failure of AID to interact with the endonuclease APE1. Additionally, deficiency in the DNA-damage sensor ATM impaired the phosphorylation of AID at Ser38 and the interaction of AID with APE1. Our results identify a positive feedback loop for the amplification of DNA breaks at S regions through the phosphorylation- and ATM-dependent interaction of AID with APE1. PMID:24097111

  7. Viral DNA Replication-Dependent DNA Damage Response Activation during BK Polyomavirus Infection

    PubMed Central

    Verhalen, Brandy; Justice, Joshua L.; Imperiale, Michael J.

    2015-01-01

    ABSTRACT BK polyomavirus (BKPyV) reactivation is associated with severe human disease in kidney and bone marrow transplant patients. The interplay between viral and host factors that regulates the productive infection process remains poorly understood. We have previously reported that the cellular DNA damage response (DDR) is activated upon lytic BKPyV infection and that its activation is required for optimal viral replication in primary kidney epithelial cells. In this report, we set out to determine what viral components are responsible for activating the two major phosphatidylinositol 3-kinase-like kinases (PI3KKs) involved in the DDR: ataxia telangiectasia mutated (ATM) kinase and ATM and Rad3-related (ATR) kinase. Using a combination of UV treatment, lentivirus transduction, and mutant virus infection experiments, our results demonstrate that neither the input virus nor the expression of large T antigen (TAg) alone is sufficient to trigger the activation of ATM or ATR in our primary culture model. Instead, our data suggest that the activation of both the ATM- and ATR-mediated DDR pathways is linked to viral DNA replication. Intriguingly, a TAg mutant virus that is unable to activate the DDR causes substantial host DNA damage. Our study provides insight into how DDRs are activated by polyomaviruses in primary cells with intact cell cycle checkpoints and how the activation might be linked to the maintenance of host genome stability. IMPORTANCE Polyomaviruses are opportunistic pathogens that are associated with several human diseases under immunosuppressed conditions. BK polyomavirus (BKPyV) affects mostly kidney and bone marrow transplant patients. The detailed replication mechanism of these viruses remains to be determined. We have previously reported that BKPyV activates the host DNA damage response (DDR), a response normally used by the host cell to combat genotoxic stress, to aid its own replication. In this study, we identified that the trigger for DDR

  8. DNAPKcs-dependent arrest of RNA polymerase II transcription in the presence of DNA breaks.

    PubMed

    Pankotai, Tibor; Bonhomme, Céline; Chen, David; Soutoglou, Evi

    2012-02-12

    DNA double-strand break (DSB) repair interferes with ongoing cellular processes, including replication and transcription. Although the process of replication stalling upon collision of replication forks with damaged DNA has been extensively studied, the fate of elongating RNA polymerase II (RNAPII) that encounters a DSB is not well understood. We show that the occurrence of a single DSB at a human RNAPII-transcribed gene leads to inhibition of transcription elongation and reinitiation. Upon inhibition of DNA protein kinase (DNAPK), RNAPII bypasses the break and continues transcription elongation, suggesting that it is not the break per se that inhibits the processivity of RNAPII, but the activity of DNAPK. We also show that the mechanism of DNAPK-mediated transcription inhibition involves the proteasome-dependent pathway. The results point to the pivotal role of DNAPK activity in the eviction of RNAPII from DNA upon encountering a DNA lesion.

  9. Pressure dependence of ionic conductivity of hydrated and dehydrated zeolites A

    NASA Astrophysics Data System (ADS)

    Goryainov, S. V.; Secco, R. A.; Huang, Y.; Liu, H.

    2007-03-01

    Hydrated and dehydrated zeolites MA (where M=Li, Na and K) with LTA structure have been studied by impedance spectroscopy with scanning frequency from 1 Hz to 1 MHz at high pressure up to 4.5 GPa and high temperature up to 250 °C. Anomalous increase in electrical AC conductivity at about 1.5-2 GPa observed in hydrated zeolites is associated with changes in crystalline structure leading to the formation of high-diffusion state of cation and water stuffing of the channels. In dehydrated zeolites, electrical conductivity is controlled by diffusion of cations (Li +, Na + and K +), which is determined by cation sites and aluminosilicate ring windows. LiA and NaA zeolites show normal decrease of conductivity with pressure, whereas KA zeolite exhibits the anomalous dependence with considerable increase and then fast decrease of conductivity. The behaviour of KA zeolite is associated with nearly central location of cation site in 8-membered ring, different from that in LiA and NaA zeolites.

  10. [Sound reception of marine mammales depending on parameters and sound-conducting tracks].

    PubMed

    Babushina, E S

    2000-01-01

    Underwater audiograms of a northern fur seal, a Caspic seal and a dolphin aphalina were measured under conditions of full or partial (the head above the water) submergence of animals using the method of instrumental conditioned reflexes with food reinforcement. The possibility and peculiarities of sound conduction through the body of marine mammals were investigated by isolating the auricle from the medium of sound spreading (under conditions of partial submergence). By the same technique, the hearing thresholds of Caspic seal were measured in the presence of broad- and narrow-band noises with different central frequencies depending on the medium (underwater or in air) the signal and the noise masker were presented and on the sound-conducting ways (under conditions of full or partial submergence of animals). It was found that aerial and underwater sound-conducting canals of the Caspic seal were functionally connected with each other. The level of hearing masking in the Caspic seal is determined by the tracts of signal and noise conduction, by the differences in sensitivity to the signal and masker, and by their spectral structure. Apparently, the tissues of the seal body considerably change the amplitude-frequency characteristics of the sound.

  11. Transitional Metal/Chalcogen Dependant Interactions of Hairpin DNA with Transition Metal Dichalcogenides, MX2.

    PubMed

    Loo, Adeline Huiling; Bonanni, Alessandra; Sofer, Zdenek; Pumera, Martin

    2015-08-03

    Owing to the attractive properties that transition metal dichalcogenides (TMDs) display, they have found recent application in the fabrication of biosensing devices. These devices involve the immobilization of a recognition element such as DNA onto the surface of TMDs. Therefore, it is imperative to examine the interactions between TMDs and DNA. Herein, we explore the effect of different transition metals (Mo and W) and chalcogens (S and Se) on the interactions between hairpin DNA and TMDs of both bulk and t-BuLi exfoliated forms. We discovered that the interactions are strongly dependent on the metal/chalcogen composition in TMDs.

  12. Disparate Strain Dependent Thermal Conductivity of Two-dimensional Penta-Structures.

    PubMed

    Liu, Huake; Qin, Guangzhao; Lin, Yuan; Hu, Ming

    2016-06-08

    Two-dimensional (2D) carbon allotrope called penta-graphene was recently proposed from first-principles calculations and various similar penta-structures emerged. Despite significant effort having been dedicated to electronic structures and mechanical properties, little research has been focused on thermal transport in penta-structures. Motivated by this, we performed a comparative study of thermal transport properties of three representative pentagonal structures, namely penta-graphene, penta-SiC2, and penta-SiN2, by solving the phonon Boltzmann transport equation with interatomic force constants extracted from first-principles calculations. Unexpectedly, the thermal conductivity of the three penta-structures exhibits diverse strain dependence, despite their very similar geometry structures. While the thermal conductivity of penta-graphene exhibits standard monotonic reduction by stretching, penta-SiC2 possesses an unusual nonmonotonic up-and-down behavior. More interestingly, the thermal conductivity of penta-SiN2 has 1 order of magnitude enhancement due to the strain induced buckled to planar structure transition. The mechanism governing the diverse strain dependence is identified as the competition between the change of phonon group velocity and phonon lifetime of acoustic phonon modes with combined effect from the unique structure transition for penta-SiN2. The disparate thermal transport behavior is further correlated to the fundamentally different bonding nature in the atomic structures with solid evidence from the distribution of deformation charge density and more in-depth molecular orbital analysis. The reported giant and robust tunability of thermal conductivity may inspire intensive research on other derivatives of penta-structures as potential materials for emerging nanoelectronic devices. The fundamental physics understood from this study also solidifies the strategy to engineer thermal transport properties of broad 2D materials by simple mechanical

  13. Ionic conduction in non-uniform nanopores and DNA translocation: a Nernst-Planck-Jacobs one-dimensional description

    NASA Astrophysics Data System (ADS)

    Marini Bettolo Marconi, Umberto; Melchionna, Simone

    2013-12-01

    The conduction of an electrolyte solution in the presence of a DNA intruder in a synthetic charged pore is studied by theoretical means. The pore conductivity is controlled by two competing mechanisms: the steric effect of the DNA decreases the current and the extra-surface charges determine an increase in the number of charge carriers that increase the current. By using a Nernst-Planck description of the electrolyte and a one-dimensional advection-diffusion equation similar to the Jacobs-Zwanzig method, we obtain the characteristic curve within the local electroneutrality approximation. Such an information allows predicting the variation of the conductance caused by the DNA intruder and determining the current blockage/enhancement phase diagram.

  14. Dynamic DNA methylation in the brain: a new epigenetic mark for experience-dependent plasticity

    PubMed Central

    Tognini, Paola; Napoli, Debora; Pizzorusso, Tommaso

    2015-01-01

    Experience-dependent plasticity is the ability of brain circuits to undergo molecular, structural and functional changes as a function of neural activity. Neural activity continuously shapes our brain during all the stages of our life, from infancy through adulthood and beyond. Epigenetic modifications of histone proteins and DNA seem to be a leading molecular mechanism to modulate the transcriptional changes underlying the fine-tuning of synaptic connections and circuitry rewiring during activity-dependent plasticity. The recent discovery that cytosine methylation is an epigenetic mark particularly dynamic in brain cells has strongly increased the interest of neuroscientists in understanding the role of covalent modifications of DNA in activity-induced remodeling of neuronal circuits. Here, we provide an overview of the role of DNA methylation and hydroxylmethylation in brain plasticity both during adulthood, with emphasis on learning and memory related processes, and during postnatal development, focusing specifically on experience-dependent plasticity in the visual cortex. PMID:26379502

  15. The Borrelia burgdorferi telomere resolvase, ResT, possesses ATP-dependent DNA unwinding activity.

    PubMed

    Huang, Shu Hui; Cozart, McKayla R; Hart, Madison A; Kobryn, Kerri

    2016-12-09

    Spirochetes of the genus Borrelia possess unusual genomes harboring multiple linear and circular replicons. The linear replicons are terminated by covalently closed hairpin (hp) telomeres. Hairpin telomeres are formed from replicated intermediates by the telomere resolvase, ResT, in a phosphoryl transfer reaction with mechanistic similarities to those promoted by type 1B topoisomerases and tyrosine recombinases. There is growing evidence that ResT is multifunctional. Upon ResT depletion DNA replication unexpectedly ceases. Additionally, ResT possesses RecO-like biochemical activities being able to promote single-strand annealing on both free ssDNA and ssDNA complexed with cognate single-stranded DNA binding protein. We report here that ResT possesses DNA-dependent ATPase activity that promotes DNA unwinding with a 3'-5' polarity. ResT can unwind a variety of substrates including synthetic replication forks and D-loops. We demonstrate that ResT's twin activities of DNA unwinding and annealing can drive regression of a model replication fork. These properties are similar to those of the RecQ helicase of the RecF pathway involved in DNA gap repair. We propose that ResT's combination of activities implicates it in replication and recombination processes operating on the linear chromosome and plasmids of Borrelia burgdorferi.

  16. Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging

    PubMed Central

    Keller, Nicholas; Grimes, Shelley; Jardine, Paul J.; Smith, Douglas E.

    2016-01-01

    In many viruses molecular motors forcibly pack single DNA molecules to near-crystalline density into ~50–100 nm prohead shells1, 2. Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA-DNA interactions3. Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems4–8. Experiments in which conditions are changed during packaging to switch DNA-DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles5 we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles.9, 10 PMID:27540410

  17. Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging.

    PubMed

    Keller, Nicholas; Grimes, Shelley; Jardine, Paul J; Smith, Douglas E

    2016-08-01

    In many viruses molecular motors forcibly pack single DNA molecules to near-crystalline density into ~50-100 nm prohead shells(1, 2). Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA-DNA interactions(3). Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems(4-8). Experiments in which conditions are changed during packaging to switch DNA-DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles(5) we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles.(9, 10).

  18. Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging

    NASA Astrophysics Data System (ADS)

    Keller, Nicholas; Grimes, Shelley; Jardine, Paul J.; Smith, Douglas E.

    2016-08-01

    In many viruses, molecular motors forcibly pack single DNA molecules to near-crystalline density into ~50-100 nm prohead shells. Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA-DNA interactions. Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems. Experiments in which conditions are changed during packaging to switch DNA-DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles.

  19. Characterization of the DNA dependent activation of human ARTD2/PARP2

    PubMed Central

    Obaji, Ezeogo; Haikarainen, Teemu; Lehtiö, Lari

    2016-01-01

    Human ADP-ribosyltransferase 2 (ARTD2/PARP2) is an enzyme catalyzing a post-translational modification, ADP-ribosylation. It is one of the three DNA dependent ARTDs in the 17 member enzyme family. ADP-ribosylation catalyzed by ARTD2 is involved in the regulation of multiple cellular processes such as control of chromatin remodeling, transcription and DNA repair. Here we used a combination of biochemical and biophysical methods to elucidate the structure and function of ARTD2. The solution structures revealed the binding mode of the ARTD2 monomer and dimer to oligonucleotides that mimic damaged DNA. In the complex, DNA binds between the WGR domain and the catalytic fragment. The binding mode is supported by biophysical data that indicate all domains contribute to DNA binding. Also, our study showed that ARTD2 is preferentially activated by short 5′-phosphorylated DNA oligonucleotides. We demonstrate that the N-terminus functions as a high-affinity DNA-binding module, while the WGR domain contributes to DNA binding specificity and subsequent catalytic activation. Our data further suggest that ARTD2 would function in double strand break repair as a dimeric module, while in single strand break repair it would function as a monomer. PMID:27708353

  20. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    NASA Astrophysics Data System (ADS)

    Snodin, Benedict E. K.; Randisi, Ferdinando; Mosayebi, Majid; Šulc, Petr; Schreck, John S.; Romano, Flavio; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.; Doye, Jonathan P. K.

    2015-06-01

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na+] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  1. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    SciTech Connect

    Snodin, Benedict E. K. Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.; Randisi, Ferdinando; Šulc, Petr; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.

    2015-06-21

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  2. Proteasome-dependent degradation of replisome components regulates faithful DNA replication.

    PubMed

    Roseaulin, Laura C; Noguchi, Chiaki; Noguchi, Eishi

    2013-08-15

    The replication machinery, or the replisome, collides with a variety of obstacles during the normal process of DNA replication. In addition to damaged template DNA, numerous chromosome regions are considered to be difficult to replicate owing to the presence of DNA secondary structures and DNA-binding proteins. Under these conditions, the replication fork stalls, generating replication stress. Stalled forks are prone to collapse, posing serious threats to genomic integrity. It is generally thought that the replication checkpoint functions to stabilize the replisome and replication fork structure upon replication stress. This is important in order to allow DNA replication to resume once the problem is solved. However, our recent studies demonstrated that some replisome components undergo proteasome-dependent degradation during DNA replication in the fission yeast Schizosaccharomyces pombe. Our investigation has revealed the involvement of the SCF(Pof3) (Skp1-Cullin/Cdc53-F-box) ubiquitin ligase in replisome regulation. We also demonstrated that forced accumulation of the replisome components leads to abnormal DNA replication upon replication stress. Here we review these findings and present additional data indicating the importance of replisome degradation for DNA replication. Our studies suggest that cells activate an alternative pathway to degrade replisome components in order to preserve genomic integrity.

  3. Matching base-pair number dependence of the kinetics of DNA-DNA hybridization studied by surface plasmon fluorescence spectroscopy.

    PubMed

    Tawa, Keiko; Yao, Danfeng; Knoll, Wolfgang

    2005-08-15

    Two single-stranded DNA oligonucleotides consisting of complementary base-pairs can form double strands. This phenomenon is well studied in solutions, however, in order to clarify the physical mechanism of the hybridization occurring at a solid/solution interface, we studied the kinetics by surface plasmon fluorescence spectroscopy (SPFS): one single-stranded oligo-DNA (probe-DNA) was immobilized on the substrate, the other one (target-DNA) labelled with a fluorescent probe was added to the flow cell. After hybridization, the chromophores could be excited by the surface plasmon mode and their fluorescence detected with high sensitivity. The dependence of the k(on) and k(off) rate constants on the length of the hybridizing oligonucleotides was investigated by using a MM0 series (no mismatch) and the kinetics was found to be well described by a Langmuir adsorption model. From these measurements we found that also in the case of surface hybridization the affinity of the duplexes decreases as the number of matching base-pairs decreases from 15 to 10. In order to show that SPFS is the powerful technique with high sensitivity, the hybridization process for mixed target-oligos was measured by SPFS and analyzed by an expanded Langmuir model in which two components of target-oligo can bind to probe-DNA at the sensor surface competitively. Two sets of the k(on) and k(off) obtained from the experiment are successfully consistent with the k(on) and k(off) obtained from experiments for single (pure) target-DNA.

  4. Adenylation-Dependent Conformation and Unfolding Pathways of the NAD+-Dependent DNA Ligase from the Thermophile Thermus scotoductus

    PubMed Central

    Georlette, Daphné; Blaise, Vinciane; Bouillenne, Fabrice; Damien, Benjamin; Thorbjarnardóttir, Sigridur H.; Depiereux, Eric; Gerday, Charles; Uversky, Vladimir N.; Feller, Georges

    2004-01-01

    In the last few years, an increased attention has been focused on NAD+-dependent DNA ligases. This is mostly due to their potential use as antibiotic targets, because effective inhibition of these essential enzymes would result in the death of the bacterium. However, development of an efficient drug requires that the conformational modifications involved in the catalysis of NAD+-dependent DNA ligases are understood. From this perspective, we have investigated the conformational changes occurring in the thermophilic Thermus scotoductus NAD+-DNA ligase upon adenylation, as well as the effect of cofactor binding on protein resistance to thermal and chemical (guanidine hydrochloride) denaturation. Our results indicate that cofactor binding induces conformational rearrangement within the active site and promotes a compaction of the enzyme. These data support an induced “open-closure” process upon adenylation, leading to the formation of the catalytically active enzyme that is able to bind DNA. These conformational changes are likely to be associated with the protein function, preventing the formation of nonproductive complexes between deadenylated ligases and DNA. In addition, enzyme adenylation significantly increases resistance of the protein to thermal denaturation and GdmCl-induced unfolding, establishing a thermodynamic link between ligand binding and increased conformational stability. Finally, chemical unfolding of deadenylated and adenylated enzyme is accompanied by accumulation of at least two equilibrium intermediates, the molten globule and premolten globule states. Maximal populations of these intermediates are shifted toward higher GdmCl concentrations in the case of the adenylated ligase. These data provide further insights into the properties of partially folded intermediates. PMID:14747344

  5. Dependence of current switching dynamics on contact conductivity in semiconductor superlattices

    NASA Astrophysics Data System (ADS)

    Teitsworth, Stephen W.; Xu, Huidong

    2006-03-01

    Numerical simulation results are presented for a discrete drift-diffusion electronic transport model appropriate to weakly-coupled semiconductor superlattices [1]. Sequential resonant tunneling between adjacent quantum wells is the primary conduction mechanism for this model which also incorporates an effective contact conductivity σc. We study the dependence on σc of time-averaged current-voltage characteristics and transient current response to abrupt steps in applied voltage. For intermediate values of σc, three qualitatively distinct transient responses -- each associated with a different mechanism for the relocation of a static charge accumulation layer [1] - are observed for different values of voltage step Vstep; these involve, respectively, 1) the motion of a single charge accumulation layer, 2) the simultaneous motion of one depletion and two accumulation layers [2], and 3) the simultaneous motion of two accumulation layers. The range of Vstep values for each mechanism and the relocation times associated with each are studied as a function of σc; a critical value of σc is identified above which the second relocation mechanism is not observed for any value of Vstep. Relocation times are found to depend sensitively on specific values of σc and Vstep. [1] L. L. Bonilla and H. T. Grahn, Rep. Prog. Phys. 68, pp. 577-683 (2005), and refs. therein. [2] A. Amann, A. Wacker, L. L. Bonilla, and E. Schoell, Phys. Rev. E 63, 066207 (2001).

  6. Characterization of a voltage-dependent conductance in the basolateral membrane of leech skin epithelium.

    PubMed

    Schnizler, M; Clauss, W

    1998-05-01

    Voltage clamp studies were performed on the dorsal integument of Hirudo medicinalis. Under apical calcium-free conditions an inward-directed component of transepithelial current was activated by changes of transepithelial voltage. Depolarization caused up to 50% increase of the transepithelial sodium current. Hyperpolarization had no comparable effects. With calcium (1.8 mM) or amiloride (100 microM) in the apical solution and in sodium-free solutions the inward-directed current failed to increase after depolarization. Activation also occurred under chloride-free conditions. Permeabilization of the apical membrane by nystatin (5 microM) increased the current activation significantly. After nystatin, calcium as well as amiloride lost their inhibitory effects. This indicates a basolateral localization of the voltage-dependent conductance. Vesicle insertion or cytoskeletal structures are probably not involved in regulation, as seen by the lack of effects of brefeldin A and the cytochalasins B and D. However, serosal hyposmolar solutions (170 mosmol.1(-1)) caused a reinforced activation of the current. Our results indicate a voltage-dependent conductance in a tight sodium-absorbing epithelium.

  7. Carrier interactions and porosity initiated reversal of temperature dependence of thermal conduction in nanoscale tin films

    SciTech Connect

    Kaul, Pankaj B.; Prakash, Vikas

    2014-01-14

    Recently, tin has been identified as an attractive electrode material for energy storage/conversion technologies. Tin thin films have also been utilized as an important constituent of thermal interface materials in thermal management applications. In this regards, in the present paper, we investigate thermal conductivity of two nanoscale tin films, (i) with thickness 500 ± 50 nm and 0.45% porosity and (ii) with thickness 100 ± 20 nm and 12.21% porosity. Thermal transport in these films is characterized over the temperature range from 40 K–310 K, using a three-omega method for multilayer configurations. The experimental results are compared with analytical predictions obtained by considering both phonon and electron contributions to heat conduction as described by existing frequency-dependent phenomenological models and BvK dispersion for phonons. The thermal conductivity of the thicker tin film (500 nm) is measured to be 46.2 W/m-K at 300 K and is observed to increase with reduced temperatures; the mechanisms for thermal transport are understood to be governed by strong phonon-electron interactions in addition to the normal phonon-phonon interactions within the temperature range 160 K–300 K. In the case of the tin thin film with 100 nm thickness, porosity and electron-boundary scattering supersede carrier interactions, and a reversal in the thermal conductivity trend with reduced temperatures is observed; the thermal conductivity falls to 1.83 W/m-K at 40 K from its room temperature value of 36.1 W/m-K. In order to interpret the experimental results, we utilize the existing analytical models that account for contributions of electron-boundary scattering using the Mayadas-Shatzkes and Fuchs-Sondheimer models for the thin and thick films, respectively. Moreover, the effects of porosity on carrier transport are included using a previous treatment based on phonon radiative transport involving frequency-dependent mean free paths

  8. Role of acoustic phonons in frequency dependent electronic thermal conductivity of graphene

    NASA Astrophysics Data System (ADS)

    Bhalla, Pankaj

    2017-03-01

    We study the effect of the electron-phonon interaction on the finite frequency dependent electronic thermal conductivity of two dimensional graphene. We calculate it for various acoustic phonons present in graphene and characterized by different dispersion relations using the memory function approach. It is found that the electronic thermal conductivity κe (T) in the zero frequency limit follows different power law for the longitudinal/transverse and the flexural acoustic phonons. For the longitudinal/transverse phonons, κe (T) ∼T-1 at the low temperature and saturates at the high temperature. These signatures qualitatively agree with the results calculated by solving the Boltzmann equation analytically and numerically. Similarly, for the flexural phonons, we find that κe (T) shows T 1 / 2 law at the low temperature and then saturates at the high temperature. In the finite frequency regime, we observe that the real part of the electronic thermal conductivity, Re [κe (ω , T) ] follows ω-2 behavior at the low frequency and becomes frequency independent at the high frequency.

  9. Substrate-dependent thermal conductivity of aluminum nitride thin-films processed at low temperature

    SciTech Connect

    Belkerk, B. E.; Bensalem, S.; Soussou, A.; Carette, M.; Djouadi, M. A.; Scudeller, Y.; Al Brithen, H.

    2014-12-01

    In this paper, we report on investigation concerning the substrate-dependent thermal conductivity (k) of Aluminum Nitride (AlN) thin-films processed at low temperature by reactive magnetron sputtering. The thermal conductivity of AlN films grown at low temperature (<200 °C) on single-crystal silicon (Si) and amorphous silicon nitride (SiN) with thicknesses ranging from 100 nm to 4000 nm was measured with the transient hot-strip technique. The k values for AlN films on SiN were found significantly lower than those on Silicon consistently with their microstructures revealed by X-ray diffraction, high resolution scanning electron microscopy, and transmission electron microscopy. The change in k was due to the thermal boundary resistance found to be equal to 10 × 10{sup −9} Km{sup 2}W{sup −1} on SiN against 3.5 × 10{sup −9} Km{sup 2}W{sup −1} on Si. However, the intrinsic thermal conductivity was determined with a value as high as 200 Wm{sup −1}K{sup −1} whatever the substrate.

  10. Modeling the Time-dependent Changes in Electrical Conductivity of Basaltic Melts With Redox State

    NASA Astrophysics Data System (ADS)

    Pommier, A.; Gaillard, F.; Pichavant, M.

    2008-12-01

    The electrical conductivity σ is an efficient probe of mass transfer processes within silicate melts and magmas. Little attention has been given to the influence of redox state (fO2) on the melts conductivity. We present an experimental setup allowing electrical conductivity measurements for basaltic melts under variable fO2. We demonstrate a significant dependence of σ with fO2, allowing to characterize in situ the mechanisms and kinetics of redox changes in the melt. Experiments were conducted on basalts from Pu'u 'O'o, Hawaii, and Mt.Vesuvius, Italy. Measurements were performed cylindrical glass samples (OD: 6mm, ID: 1mm, L: 8mm) using an impedance spectrometer. Experiments were conducted in a 1atm vertical furnace, from 1200°C to 1400°C. Variable gas atmosphere (air, CO2 or CO-CO2 gas mixtures) were used, imposing ΔNNO from -1 to +7. Electrical conductivities were determined for the two melts at constant fO2, different T (constant fO2) and constant T, different fO2 (variable fO2) obtained by changing the gas composition. Isothermal reduction and oxidation cycles were performed. Glasses quenched from different T and fO2 conditions were analyzed by electron microprobe, the FeO concentration was determined by wet chemistry. In constant fO2 experiments, a small but detectable effect of fO2 on σ is evidenced. At 1300°C, the difference in the Kilauea sample conductivity between reduced (ΔNNO=-1) and oxidized (ΔNNO=+7) fO2 is <1(ohm.m)-1, the sample being more conductive when reduced. The temperature dependence of σ was fitted using Arrhenian equations, the activation energy Ea being 100kJ/mol. Sodium was identified as the main charge carrier in the melts. The fO2-effect on σ can thus be attributed to the influence of the Fe2+/Fe3+ ratio on sodium mobility. The fO2-dependence of σ was included in the model of Pommier et al.(2008), allowing the conductivity of natural melts to be calculated as a function of T, P, H2O, and fO2. Variable fO2 experiments

  11. Antecedents of opioid dependence and personality disorder: attention-deficit/hyperactivity disorder and conduct disorder.

    PubMed

    Modestin, J; Matutat, B; Würmle, O

    2001-01-01

    Both attention-deficit/hyperactivity disorder (ADHD) and conduct disorder (CD) were explored as possible antecedents of opioid dependence and personality disorder. One hundred adult opioid-dependent, treatment-seeking male inpatients were explored; an extended clinical semistructured interview to collect sociodemographic, drug use related, and clinical data and the Structured Clinical Interview for DSM-IV personality disorders SCID-II were carried out. Four groups of patients, namely ADHD alone (4 patients), ADHD + CD (7 patients), CD alone (47 patients) and no ADHD/no CD (42 patients) were identified and compared with each other. The results indicate that ADHD alone does not predispose to the development of opioid dependence in male inpatients. Childhood ADHD may nevertheless be found more frequently in male opioid addicts due to its comorbidity with CD, which was identified in more than half of our sample. Patients with ADHD history seemed to go through the drug abuse career earlier and to develop more frequently histrionic and obsessive-compulsive personality disorder. Over half of the CD patients developed borderline and/or antisocial personality disorder; both ADHD and CD predispose significantly to the PD development. Early substance use preventive measures are necessary in children and adolescents suffering from CD and from ADHD comorbid with CD.

  12. Time-Dependent Soil Hydraulic Conductivity in Salt-Affected Soils

    NASA Astrophysics Data System (ADS)

    Russo, D.

    2012-04-01

    Mixed salts such as sodium-calcium salts interact with the soil matrix. The physico chemical interactions between the soil solution and the soil matrix (SS-SM), particularly in the presence of smectite minerals (e.g., montmorillonite), may change the soil pore-size distribution; the latter could affect the soil hydraulic properties, i.e., the soil hydraulic conductivity and soil water retention. Since the magnitude of the SS-SM interactions depend on time-dependent flow-controlled attributes, i.e., soil solution concentration and composition and water content, the resultant hydraulic properties are also time-dependent. The present talk focuses on the effect of mixed-ion solutions on soil hydraulic properties relevant to water flow and solute transport. Experimental evidence on, and an approach for modeling of the effect of soil solution concentration and composition on the local- (Darcy) scale soil hydraulic properties are presented and discussed. Long-term effect of the soil solution concentration and composition on the soil hydraulic properties, and, concurrently, on water flow and solute transport are presented through simulations of field-scale flow and transport.

  13. Viral Single-Strand DNA Induces p53-Dependent Apoptosis in Human Embryonic Stem Cells

    PubMed Central

    Hirsch, Matthew L.; Fagan, B. Matthew; Dumitru, Raluca; Bower, Jacquelyn J.; Yadav, Swati; Porteus, Matthew H.; Pevny, Larysa H.; Samulski, R. Jude

    2011-01-01

    Human embryonic stem cells (hESCs) are primed for rapid apoptosis following mild forms of genotoxic stress. A natural form of such cellular stress occurs in response to recombinant adeno-associated virus (rAAV) single-strand DNA genomes, which exploit the host DNA damage response for replication and genome persistence. Herein, we discovered a unique DNA damage response induced by rAAV transduction specific to pluripotent hESCs. Within hours following rAAV transduction, host DNA damage signaling was elicited as measured by increased gamma-H2AX, ser15-p53 phosphorylation, and subsequent p53-dependent transcriptional activation. Nucleotide incorporation assays demonstrated that rAAV transduced cells accumulated in early S-phase followed by the induction of apoptosis. This lethal signaling sequalae required p53 in a manner independent of transcriptional induction of Puma, Bax and Bcl-2 and was not evident in cells differentiated towards a neural lineage. Consistent with a lethal DNA damage response induced upon rAAV transduction of hESCs, empty AAV protein capsids demonstrated no toxicity. In contrast, DNA microinjections demonstrated that the minimal AAV origin of replication and, in particular, a 40 nucleotide G-rich tetrad repeat sequence, was sufficient for hESC apoptosis. Our data support a model in which rAAV transduction of hESCs induces a p53-dependent lethal response that is elicited by a telomeric sequence within the AAV origin of replication. PMID:22114676

  14. DNA-Dependent Protein Kinase As Molecular Target for Radiosensitization of Neuroblastoma Cells.

    PubMed

    Dolman, M Emmy M; van der Ploeg, Ida; Koster, Jan; Bate-Eya, Laurel Tabe; Versteeg, Rogier; Caron, Huib N; Molenaar, Jan J

    2015-01-01

    Tumor cells might resist therapy with ionizing radiation (IR) by non-homologous end-joining (NHEJ) of IR-induced double-strand breaks. One of the key players in NHEJ is DNA-dependent protein kinase (DNA-PK). The catalytic subunit of DNA-PK, i.e. DNA-PKcs, can be inhibited with the small-molecule inhibitor NU7026. In the current study, the in vitro potential of NU7026 to radiosensitize neuroblastoma cells was investigated. DNA-PKcs is encoded by the PRKDC (protein kinase, DNA-activated, catalytic polypeptide) gene. We showed that PRKDC levels were enhanced in neuroblastoma patients and correlated with a more advanced tumor stage and poor prognosis, making DNA-PKcs an interesting target for radiosensitization of neuroblastoma tumors. Optimal dose finding for combination treatment with NU7026 and IR was performed using NGP cells. One hour pre-treatment with 10 μM NU7026 synergistically sensitized NGP cells to 0.63 Gy IR. Radiosensitizing effects of NU7026 increased in time, with maximum effects observed from 96 h after IR-exposure on. Combined treatment of NGP cells with 10 μM NU7026 and 0.63 Gy IR resulted in apoptosis, while no apoptotic response was observed for either of the therapies alone. Inhibition of IR-induced DNA-PK activation by NU7026 confirmed the capability of NGP cells to, at least partially, resist IR by NHEJ. NU7026 also synergistically radiosensitized other neuroblastoma cell lines, while no synergistic effect was observed for low DNA-PKcs-expressing non-cancerous fibroblasts. Results obtained for NU7026 were confirmed by PRKDC knockdown in NGP cells. Taken together, the current study shows that DNA-PKcs is a promising target for neuroblastoma radiosensitization.

  15. Revisiting the Valence and Conduction Band Size Dependence of PbS Quantum Dot Thin Films

    SciTech Connect

    Miller, Elisa M.; Kroupa, Daniel M.; Zhang, Jianbing; Schulz, Philip; Marshall, Ashley R.; Kahn, Antoine; Lany, Stephan; Luther, Joseph M.; Beard, Matthew C.; Perkins, Craig L.; van de Lagemaat, Jao

    2016-03-22

    We use a high signal-to-noise X-ray photoelectron spectrum of bulk PbS, GW calculations, and a model assuming parabolic bands to unravel the various X-ray and ultraviolet photoelectron spectral features of bulk PbS as well as determine how to best analyze the valence band region of PbS quantum dot (QD) films. X-ray and ultraviolet photoelectron spectroscopy (XPS and UPS) are commonly used to probe the difference between the Fermi level and valence band maximum (VBM) for crystalline and thin-film semiconductors. However, we find that when the standard XPS/UPS analysis is used for PbS, the results are often unrealistic due to the low density of states at the VBM. Instead, a parabolic band model is used to determine the VBM for the PbS QD films, which is based on the bulk PbS experimental spectrum and bulk GW calculations. Our analysis highlights the breakdown of the Brillioun zone representation of the band diagram for large band gap, highly quantum confined PbS QDs. We have also determined that in 1,2-ethanedithiol-treated PbS QD films the Fermi level position is dependent on the QD size; specifically, the smallest band gap QD films have the Fermi level near the conduction band minimum and the Fermi level moves away from the conduction band for larger band gap PbS QD films. This change in the Fermi level within the QD band gap could be due to changes in the Pb:S ratio. In addition, we use inverse photoelectron spectroscopy to measure the conduction band region, which has similar challenges in the analysis of PbS QD films due to a low density of states near the conduction band minimum.

  16. Composition, Temperature, and Pressure Dependence of the Phonon (Thermal) Conductivity of Silicate Geoliquids

    NASA Astrophysics Data System (ADS)

    Tikunoff, Dane Michael

    The study of geoliquids and their transport properties is a burgeoning field that sheds light on many critical geological problems. One such property, the thermal conductivity, measures the heat conduction capacity of a material and plays an important role in mantle and crust dynamics. Previous research has suggested that an increased insulation factor in rocks of the crust, regulated by relatively small values of the thermal conductivity, promotes anatexis and alleviates radiogenic heating requirements for the inducement of dehydration-triggered partial melting (Whittington et al., 2009). At greater depths, the proposed existence of melt patches along and immediately above the Core-Mantle Boundary (CMB) at ~2900 km depth could explain the discrete rather than graduated thermal gradient seen across the CMB (Murakami and Bass, 2011). This thesis describes the use of Molecular Dynamics (MD) simulations to compute thermal conductivity for three liquid silicates: CaMgSi2O6, NaAlSi3 O8 and MgSi2O4. The motivation for this study was to examine the temperature, pressure and compositional dependencies of thermal conductivity approximating conditions in the upper mantle (0-30 GPa, 2000-4500 K) for a few end member geosilicate liquids of natural importance. Results at low pressure and temperature show good agreement with recent laboratory measurements on CaMgSi2O6 and NaAlSi3O8 suggesting that MD simulation can provide realistic values at elevated pressure and temperature, conditions not readily accessible without great expense and time in the laboratory. For example, simulation results for molten diopside at 1763+/-13 K and 0.36+/-0.017 GPa provide a thermal conductivity value of k=1.186+/-0.019 W/m K while laser-flash data from Hofmeister et al. (2009) provides a value of k=1.178 +/-0.06 W/m K, agreement to within a percent. Further, a positive correlation between atomic structure and thermal conductivity is confirmed. At low pressure, the polymeric liquid NaAlSi3O8, in

  17. A DNA-dependent stress response involving DNA-PK occurs in hypoxic cells and contributes to cellular adaptation to hypoxia.

    PubMed

    Bouquet, Fanny; Ousset, Marielle; Biard, Denis; Fallone, Frédérique; Dauvillier, Stéphanie; Frit, Philippe; Salles, Bernard; Muller, Catherine

    2011-06-01

    DNA-dependent protein kinase (DNA-PK) is involved in DNA double-strand break (DSB) signalling and repair. We report that DNA-PK is activated by mild hypoxia conditions (0.1-1% O₂) as shown by (1) its autophosphorylation on Ser2056, and (2) its mobilisation from a soluble nucleoplasmic compartment to a less extractable nuclear fraction. The recruitment of DNA-PK was not followed by activation and recruitment of the XRCC4-DNA-ligase-IV complex, suggesting that DSBs are not responsible for activation of DNA-PK. To unravel the mechanism of DNA-PK activation, we show that exposure of cells to trichostatin A, a histone deacetylase inhibitor, leads to DNA-PK autophosphorylation and relocalisation to DNA. Histone acetylation (mainly H3K14) is increased in hypoxic cells and treatment with anacardic acid, an inhibitor of histone acetyl transferase, prevented both histone modifications and DNA-PK activation in hypoxic conditions. Importantly, in using either silenced DNA-PK cells or cells exposed to a specific DNA-PK inhibitor (NU7026), we demonstrated that hypoxic DNA-PK activation positively regulates the key transcription factor HIF-1 and one subsequent target gene, GLUT1. Our results show that hypoxia initiates chromatin modification and consequently DNA-PK activation, which positively regulate cellular oxygen-sensing and oxygen-signalling pathways.

  18. Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners

    PubMed Central

    Alves da Silva, Antônio Francisco; Machado, Filipe Brum; Pavarino, Érika Cristina; Biselli-Périco, Joice Matos; Zampieri, Bruna Lancia; da Silva Francisco Junior, Ronaldo; Mozer Rodrigues, Pedro Thyago; Terra Machado, Douglas; Santos-Rebouças, Cíntia Barros; Gomes Fernandes, Maria; Chuva de Sousa Lopes, Susana Marina; Lopes Rios, Álvaro Fabricio

    2016-01-01

    The supernumerary chromosome 21 in Down syndrome differentially affects the methylation statuses at CpG dinucleotide sites and creates genome-wide transcriptional dysregulation of parental alleles, ultimately causing diverse pathologies. At present, it is unknown whether those effects are dependent or independent of the parental origin of the nondisjoined chromosome 21. Linkage analysis is a standard method for the determination of the parental origin of this aneuploidy, although it is inadequate in cases with deficiency of samples from the progenitors. Here, we assessed the reliability of the epigenetic 5mCpG imprints resulting in the maternally (oocyte)-derived allele methylation at a differentially methylated region (DMR) of the candidate imprinted WRB gene for asserting the parental origin of chromosome 21. We developed a methylation-sensitive restriction enzyme-specific PCR assay, based on the WRB DMR, across single nucleotide polymorphisms (SNPs) to examine the methylation statuses in the parental alleles. In genomic DNA from blood cells of either disomic or trisomic subjects, the maternal alleles were consistently methylated, while the paternal alleles were unmethylated. However, the supernumerary chromosome 21 did alter the methylation patterns at the RUNX1 (chromosome 21) and TMEM131 (chromosome 2) CpG sites in a parent-of-origin-independent manner. To evaluate the 5mCpG imprints, we conducted a computational comparative epigenomic analysis of transcriptome RNA sequencing (RNA-Seq) and histone modification expression patterns. We found allele fractions consistent with the transcriptional biallelic expression of WRB and ten neighboring genes, despite the similarities in the confluence of both a 17-histone modification activation backbone module and a 5-histone modification repressive module between the WRB DMR and the DMRs of six imprinted genes. We concluded that the maternally inherited 5mCpG imprints at the WRB DMR are uncoupled from the parental allele

  19. DNA-dependent RNA polymerase detects hidden giant viruses in published databanks.

    PubMed

    Sharma, Vikas; Colson, Philippe; Giorgi, Roch; Pontarotti, Pierre; Raoult, Didier

    2014-06-13

    Environmental metagenomic studies show that there is a "dark matter," composed of sequences not linked to any known organism, as determined mainly using ribosomal DNA (rDNA) sequences, which therefore ignore giant viruses. DNA-dependent RNA polymerase (RNAP) genes are universal in microbes and conserved in giant viruses and may replace rDNA for identifying microbes. We found while reconstructing RNAP subunit 2 (RNAP2) phylogeny that a giant virus sequenced together with the genome of a large eukaryote, Hydra magnipapillata, has been overlooked. To explore the dark matter, we used viral RNAP2 and reconstructed putative ancestral RNAP2, which were significantly superior in detecting distant clades than current sequences, and we revealed two additional unknown mimiviruses, misclassified as an euryarchaeote and an oomycete plant pathogen, and detected unknown putative viral clades. We suggest using RNAP systematically to decipher the black matter and identify giant viruses.

  20. Inhibiting Mitochondrial DNA Ligase IIIα Activates Caspase 1-Dependent Apoptosis in Cancer Cells.

    PubMed

    Sallmyr, Annahita; Matsumoto, Yoshihiro; Roginskaya, Vera; Van Houten, Bennett; Tomkinson, Alan E

    2016-09-15

    Elevated levels of DNA ligase IIIα (LigIIIα) have been identified as a biomarker of an alteration in DNA repair in cancer cells that confers hypersensitivity to a LigIIIα inhibitor, L67, in combination with a poly (ADP-ribose) polymerase inhibitor. Because LigIIIα functions in the nucleus and mitochondria, we examined the effect of L67 on these organelles. Here, we show that, although the DNA ligase inhibitor selectively targets mitochondria, cancer and nonmalignant cells respond differently to disruption of mitochondrial DNA metabolism. Inhibition of mitochondrial LigIIIα in cancer cells resulted in abnormal mitochondrial morphology, reduced levels of mitochondrial DNA, and increased levels of mitochondrially generated reactive oxygen species that caused nuclear DNA damage. In contrast, these effects did not occur in nonmalignant cells. Furthermore, inhibition of mitochondrial LigIIIα activated a caspase 1-dependent apoptotic pathway, which is known to be part of inflammatory responses induced by pathogenic microorganisms in cancer, but not nonmalignant cells. These results demonstrate that the disruption of mitochondrial DNA metabolism elicits different responses in nonmalignant and cancer cells and suggests that the abnormal response in cancer cells may be exploited in the development of novel therapeutic strategies that selectively target cancer cells. Cancer Res; 76(18); 5431-41. ©2016 AACR.

  1. DNA-dependent protein kinase mediates V(D)J recombination via RAG2 phosphorylation.

    PubMed

    Hah, Young-Sool; Lee, Jung Hwa; Kim, Deok Ryong

    2007-05-31

    V(D)J recombination, a site-specific gene rearrangement process occurring during the lymphocyte development, begins with DNA double strand breaks by two recombination activating gene products (RAG1/2) and finishes with the repair process by several proteins including DNA-dependent protein kinase (DNA-PK). In this report, we found that RAG2 was specifically phosphorylated by DNA-PK at the 365(th) serine residue, and this phosphorylated RAG2 affected the V(D)J recombination activity in cells in the GFP expression-based assay. While the V(D)J recombination activity between wild-type RAG2 and mutant S365A RAG2 in the assay using a signal joint substrate was undistinguishable in DNA-PK deficient cells (M059J), the activity with wild-type RAG2 was largely increased in DNA-PK proficient cells (M059K) in comparison with mutant RAG2, suggesting that RAG2 phosphorylation by DNA-PK plays a crucial role in the signal joint formation during V(D)J recombination.

  2. Direction- and Salt-Dependent Ionic Current Signatures for DNA Sensing with Asymmetric Nanopores.

    PubMed

    Chen, Kaikai; Bell, Nicholas A W; Kong, Jinglin; Tian, Yu; Keyser, Ulrich F

    2017-02-28

    Solid-state nanopores are promising tools for single-molecule detection of both DNA and proteins. In this study, we investigated the patterns of ionic current blockades as DNA translocates into or out of the geometric confinement of conically shaped pores across a wide range of salt conditions. We studied how the geometry of a nanopore affects the detected ionic current signal of a translocating DNA molecule over a wide range of salt concentration. The blockade level in the ionic current depends on the translocation direction at a high salt concentration, and at lower salt concentrations we find a nonintuitive ionic current decrease and increase within each single event for the DNA translocations exiting from confinement. We use a recently developed method for synthesizing DNA molecules with multiple position markers, which provides further experimental characterization by matching the position of the DNA in the pore with the observed ionic current signal. Finally, we employ finite element calculations to explain the shapes of the signals observed at all salt concentrations and show that the unexpected current decrease and increase are due to the competing effects of ion concentration polarization and geometric exclusion of ions. Our analysis shows that over a wide range of geometries, voltages, and salt concentrations, we are able to understand the ionic current signals of DNA in asymmetric nanopores, enabling signal optimization in molecular sensing applications.

  3. Processing of meiotic DNA double strand breaks requires cyclin-dependent kinase and multiple nucleases.

    PubMed

    Manfrini, Nicola; Guerini, Ilaria; Citterio, Andrea; Lucchini, Giovanna; Longhese, Maria Pia

    2010-04-09

    Meiotic recombination requires the formation of programmed Spo11-dependent DNA double strand breaks (DSBs). In Saccharomyces cerevisiae, the Sae2 protein and the Mre11-Rad50-Xrs2 complex are necessary to remove the covalently attached Spo11 protein from the DNA ends, which are then resected by so far unknown nucleases. Here, we demonstrate that phosphorylation of Sae2 Ser-267 by cyclin-dependent kinase 1 (Cdk1) is required to initiate meiotic DSB resection by allowing Spo11 removal from DSB ends. This finding suggests that Cdk1 activity is required for the processing of Spo11-induced DSBs, thus providing a mechanism for coordinating DSB resection with progression through meiotic prophase. Furthermore, the helicase Sgs1 and the nucleases Exo1 and Dna2 participate in lengthening the 5'-3' resection tracts during meiosis by controlling a step subsequent to Spo11 removal.

  4. Discovery of bacterial NAD+-dependent DNA ligase inhibitors: optimization of antibacterial activity.

    PubMed

    Stokes, Suzanne S; Huynh, Hoan; Gowravaram, Madhusudhan; Albert, Robert; Cavero-Tomas, Marta; Chen, Brendan; Harang, Jenna; Loch, James T; Lu, Min; Mullen, George B; Zhao, Shannon; Liu, Ce-Feng; Mills, Scott D

    2011-08-01

    Optimization of adenosine analog inhibitors of bacterial NAD(+)-dependent DNA ligase is discussed. Antibacterial activity against Streptococcus pneumoniae and Staphylococcus aureus was improved by modification of the 2-position substituent on the adenine ring and 3'- and 5'-substituents on the ribose. Compounds with logD values 1.5-2.5 maximized potency and maintained drug-like physical properties.

  5. Genome-derived cytosolic DNA mediates type I interferon-dependent rejection of B cell lymphoma cells.

    PubMed

    Shen, Yu J; Le Bert, Nina; Chitre, Anuja A; Koo, Christine Xing'Er; Nga, Xing H; Ho, Samantha S W; Khatoo, Muznah; Tan, Nikki Y; Ishii, Ken J; Gasser, Stephan

    2015-04-21

    The DNA damage response (DDR) induces the expression of type I interferons (IFNs), but the underlying mechanisms are poorly understood. Here, we show the presence of cytosolic DNA in different mouse and human tumor cells. Treatment of cells with genotoxic agents increased the levels of cytosolic DNA in a DDR-dependent manner. Cloning of cytosolic DNA molecules from mouse lymphoma cells suggests that cytosolic DNA is derived from unique genomic loci and has the potential to form non-B DNA structures, including R-loops. Overexpression of Rnaseh1, which resolves R-loops, reduced the levels of cytosolic DNA, type I Ifn transcripts, and type I IFN-dependent rejection of lymphoma cells. Live-cell imaging showed a dynamic contact of cytosolic DNA with mitochondria, an important organelle for innate immune recognition of cytosolic nucleotides. In summary, we found that cytosolic DNA is present in many tumor cells and contributes to the immunogenicity of tumor cells.

  6. Anomalous temperature dependent magneto-conductance in organic light-emitting diodes with multiple emissive states

    SciTech Connect

    Zhao, Chen-xiao; Jia, Wei-yao; Huang, Ke-Xun; Zhang, Qiao-ming; Yang, Xiao-hui; Xiong, Zu-hong

    2015-07-13

    The temperature dependence of the magneto-conductance (MC) in organic electron donor-acceptor hybrid and layer heterojunction diodes was studied. The MC value increased with temperature in layer heterojunction and in 10 wt. % hybrid devices. An anomalous decrease of the MC with temperature was observed in 25 wt. %–50 wt. % hybrid devices. Further increasing donor concentration to 75 wt. %, the MC again increased with temperature. The endothermic exciplex-exciton energy transfer and the change in electroplex/exciton ratio caused by change in charge transport with temperature may account for these phenomena. Comparative studies of the temperature evolutions of the IV curves and the electroluminescence and photoluminescence spectra back our hypothesis.

  7. Estimation of temperature-dependent thermal conductivity of a packed bed of 13X molecular sieves

    SciTech Connect

    Vyas, R.K.; Kumar, S.

    1995-11-01

    Modeling and simulation of packed bed systems operating non-isothermally require sufficiently accurate knowledge of thermal transport properties.Effective thermal conductivity (k) of packed bed of molecular sieves is rarely reported. In this paper, dependence of k on temperature for a packed bed of 13X molecular sieves has been determined. An electrical heater embedded coaxially in the bed was used to heat it, and the radical temperature profiles thus obtained under transient conditions were utilized for estimation. The estimated relationship is k = 8.17635 {times} 10{sup {minus}5} + 10.915427 {times} 10{sup {minus}7}(T {minus} T{sub 0}). Statistical analysis of the estimated parameters has also been carried out. The deviations between experimental and predicted temperatures are less than 5%.

  8. Anomalous pressure dependence of thermal conductivities of large mass ratio compounds

    NASA Astrophysics Data System (ADS)

    Lindsay, L.; Broido, D. A.; Carrete, Jesús; Mingo, Natalio; Reinecke, T. L.

    2015-03-01

    The lattice thermal conductivities (κ) of binary compound materials are examined as a function of hydrostatic pressure P using a first-principles approach. Compounds with relatively small mass ratios, such as MgO, show an increase in κ with P , consistent with measurements. Conversely, compounds with large mass ratios that create significant frequency gaps between acoustic and optic phonons (e.g., BSb, BAs, BeTe, BeSe) exhibit decreasing κ with increasing P , a behavior that cannot be understood using simple theories of κ. This anomalous P dependence of κ arises from the fundamentally different nature of the intrinsic scattering processes for heat-carrying acoustic phonons in large mass ratio compounds compared to those with small mass ratios. This work demonstrates the power of first-principles methods for thermal properties and advances a broad paradigm for understanding thermal transport in nonmetals.

  9. Anomalous pressure dependence of thermal conductivities of large mass ratio compounds

    DOE PAGES

    Lindsay, Lucas R; Broido, David A.; Carrete, Jesus; ...

    2015-03-27

    The lattice thermal conductivities (k) of binary compound materials are examined as a function of hydrostatic pressure P using a first-principles approach. Compound materials with relatively small mass ratios, such as MgO, show an increase in k with P, consistent with measurements. Conversely, compounds with large mass ratios (e.g., BSb, BAs, BeTe, BeSe) exhibit decreasing with increasing P, a behavior that cannot be understood using simple theories of k. This anomalous P dependence of k arises from the fundamentally different nature of the intrinsic scattering processes for heat-carrying acoustic phonons in large mass ratio compounds compared to those with smallmore » mass ratios. We find this work demonstrates the power of first principles methods for thermal properties and advances the understanding of thermal transport in non-metals.« less

  10. Anomalous pressure dependence of thermal conductivities of large mass ratio compounds

    SciTech Connect

    Lindsay, Lucas R; Broido, David A.; Carrete, Jesus; Mingo, Natalio; Reinecke, Tom L.

    2015-03-27

    The lattice thermal conductivities (k) of binary compound materials are examined as a function of hydrostatic pressure P using a first-principles approach. Compound materials with relatively small mass ratios, such as MgO, show an increase in k with P, consistent with measurements. Conversely, compounds with large mass ratios (e.g., BSb, BAs, BeTe, BeSe) exhibit decreasing with increasing P, a behavior that cannot be understood using simple theories of k. This anomalous P dependence of k arises from the fundamentally different nature of the intrinsic scattering processes for heat-carrying acoustic phonons in large mass ratio compounds compared to those with small mass ratios. We find this work demonstrates the power of first principles methods for thermal properties and advances the understanding of thermal transport in non-metals.

  11. Use of Data Comm by Flight Crew to Conduct Interval Management Operations to Parallel Dependent Runways

    NASA Technical Reports Server (NTRS)

    Baxley, Brian T.; Hubbs, Clay; Shay, Rick; Karanian, James

    2011-01-01

    The Interval Management (IM) concept is being developed as a method to maintain or increase high traffic density airport arrival throughput while allowing aircraft to conduct near idle thrust descents. The Interval Management with Spacing to Parallel Dependent Runways (IMSPiDR1) experiment at NASA Langley Research Center used 24 commercial pilots to examine IM procedures to conduct parallel dependent runway arrival operations while maintaining safe but efficient intervals behind the preceding aircraft. The use of IM procedures during these operations requires a lengthy and complex clearance from Air Traffic Control (ATC) to the participating aircraft, thereby making the use of Controller Pilot Data Link Communications (CPDLC) highly desirable as the communication method. The use of CPDLC reduces the need for voice transmissions between controllers and flight crew, and enables automated transfer of IM clearance elements into flight management systems or other aircraft avionics. The result is reduced crew workload and an increase in the efficiency of crew procedures. This paper focuses on the subset of data collected related to the use of CPDLC for IM operations into a busy airport. Overall, the experiment and results were very successful, with the mean time under 43 seconds for the flight crew to load the clearance into the IM spacing tool, review the calculated speed, and respond to ATC. An overall mean rating of Moderately Agree was given when the crews were asked if the use of CPDLC was operationally acceptable as simulated in this experiment. Approximately half of the flight crew reported the use of CPDLC below 10,000 for IM operations was unacceptable, with 83% reporting below 5000 was unacceptable. Also described are proposed modifications to the IM operations that may reduce CPDLC Respond time to less than 30 seconds and should significantly reduce the complexity of crew procedures, as well as follow-on research issues for operational use of CPDLC during IM

  12. Polo-like kinase 1 (PLK1) and protein phosphatase 6 (PP6) regulate DNA-dependent protein kinase catalytic subunit (DNA-PKcs) phosphorylation in mitosis.

    PubMed

    Douglas, Pauline; Ye, Ruiqiong; Trinkle-Mulcahy, Laura; Neal, Jessica A; De Wever, Veerle; Morrice, Nick A; Meek, Katheryn; Lees-Miller, Susan P

    2014-06-25

    The protein kinase activity of the DNA-PKcs (DNA-dependent protein kinase catalytic subunit) and its autophosphorylation are critical for DBS (DNA double-strand break) repair via NHEJ (non-homologous end-joining). Recent studies have shown that depletion or inactivation of DNA-PKcs kinase activity also results in mitotic defects. DNA-PKcs is autophosphorylated on Ser2056, Thr2647 and Thr2609 in mitosis and phosphorylated DNA-PKcs localize to centrosomes, mitotic spindles and the midbody. DNA-PKcs also interacts with PP6 (protein phosphatase 6), and PP6 has been shown to dephosphorylate Aurora A kinase in mitosis. Here we report that DNA-PKcs is phosphorylated on Ser3205 and Thr3950 in mitosis. Phosphorylation of Thr3950 is DNA-PK-dependent, whereas phosphorylation of Ser3205 requires PLK1 (polo-like kinase 1). Moreover, PLK1 phosphorylates DNA-PKcs on Ser3205 in vitro and interacts with DNA-PKcs in mitosis. In addition, PP6 dephosphorylates DNA-PKcs at Ser3205 in mitosis and after IR (ionizing radiation). DNA-PKcs also phosphorylates Chk2 on Thr68 in mitosis and both phosphorylation of Chk2 and autophosphorylation of DNA-PKcs in mitosis occur in the apparent absence of Ku and DNA damage. Our findings provide mechanistic insight into the roles of DNA-PKcs and PP6 in mitosis and suggest that DNA-PKcs' role in mitosis may be mechanistically distinct from its well-established role in NHEJ.

  13. Lead titanate/cyclic carbonate dependence on ionic conductivity of ferro/acrylate blend polymer composites

    NASA Astrophysics Data System (ADS)

    Jayaraman, R.; Vickraman, P.; Subramanian, N. M. V.; Justin, A. Simon

    2016-05-01

    Impedance, XRD, DSC and FTIR studies had been carried out for PVdF-co-HFP/LIBETI based system for three plasticizer (EC/DMC) - filler (PbTiO3) weight ratios. The enhanced conductivity 4.18 × 10-5 Scm-1 was noted for 57.5 wt% -7.5 wt% plasticizer - filler. while blending PEMA to PVdF-co-HFP respectively 7.5: 22.5 wt % (3/7), 15 wt%: 15 wt % (5/5) and 22.5wt %: 7.5 wt % (7/3), the improved conductivity was noted for 3/7 ratio 1.22 × 10-5 S cm-1 and its temperature dependence abide Arrhenius behavior. The intensity of peaks in XRD diffractogram registered dominance of lead titanate, from 2θ = 10° to 80° and absence of VdF crystallites (α+β phase) was noted. In DSC studies, the presence of the exotherm events, filler effect was distinctively seen exhibiting recrystallization of VdF crystallites. In blending PEMA, however, no trace of exotherms was found suggestive of PEMA better inhibiting recrystallization. FTIR study confirmed molecular interactions of various constituents in the vibrational band 500 - 1000 cm-1 both in pristine PVdF-co-HFP and PEMA blended composites with reference to C-F stretching, C-H stretching and C=O carbonyl bands.

  14. Thickness, humidity, and polarization dependent ferroelectric switching and conductivity in Mg doped lithium niobate

    SciTech Connect

    Neumayer, Sabine M.; Rodriguez, Brian J.; Strelcov, Evgheni; Kravchenko, Ivan I.; Kalinin, Sergei V.; Manzo, Michele; Gallo, Katia; Kholkin, Andrei L.

    2015-12-28

    Mg doped lithium niobate (Mg:LN) exhibits several advantages over undoped LN such as resistance to photorefraction, lower coercive fields, and p-type conductivity that is particularly pronounced at domain walls and opens up a range of applications, e.g., in domain wall electronics. Engineering of precise domain patterns necessitates well founded knowledge of switching kinetics, which can differ significantly from that of undoped LN. In this work, the role of humidity and sample composition in polarization reversal has been investigated under application of the same voltage waveform. Control over domain sizes has been achieved by varying the sample thickness and initial polarization as well as atmospheric conditions. In addition, local introduction of proton exchanged phases allows for inhibition of domain nucleation or destabilization, which can be utilized to modify domain patterns. Polarization dependent current flow, attributed to charged domain walls and band bending, demonstrates the rectifying ability of Mg:LN in combination with suitable metal electrodes that allow for further tailoring of conductivity.

  15. Surface conductivity dependent dynamic behaviour of an ultrafine atmospheric pressure plasma jet for microscale surface processing

    NASA Astrophysics Data System (ADS)

    Abuzairi, Tomy; Okada, Mitsuru; Bhattacharjee, Sudeep; Nagatsu, Masaaki

    2016-12-01

    An experimental study on the dynamic behaviour of microcapillary atmospheric pressure plasma jets (APPJs) with 5 μm tip size for surfaces of different conductivity is reported. Electrical and spatio-temporal characteristics of the APPJs are monitored using high voltage probe, current monitor and high speed intensified charge couple device camera. From these experimental results, we presented a simple model to understand the electrical discharge characteristics of the capillary APPJs with double electrodes, and estimated the velocity of the ionization fronts in the jet and the electron density to be 3.5-4.2 km/s and 2-7 × 1017 m-3. By analyzing the dynamics of the microcapillary APPJs for different substrate materials, it was found that the surface irradiation area strongly depended on the substrate conductivity and permittivity, especially in the case of polymer-like substrate, surface irradiation area was significantly broadened probably due to the repelling behaviour of the plasma jets from the accumulated electrical charges on the polymer surface. The effect of applying a substrate bias in the range from -900 V to +900 V on the plasma irradiation onto the substrates was also investigated. From the knowledge of the present results, it is helpful for choosing the substrate materials for microscale surface modification.

  16. Observation of a magnetic field dependence of the lattice thermal conductivity

    NASA Astrophysics Data System (ADS)

    Jin, Hyungyu; Restrepo, Oscar; Antolin, Nikolas; Windl, Wolfgang; Barnes, Stewart; Heremans, Joseph

    2014-03-01

    Can phonons respond to magnetic fields? From the simple point of view of the classical lattice vibrations, there is no clue that phonons possess any magnetic characteristics. Here, we report for the first time that the lattice thermal conductivity can show a response to an external magnetic field in a non-magnetic semiconductor crystal. We observe a magnetic field dependence of the lattice thermal conductivity in a high quality 2x1015 Te doped single crystal of InSb. The electronic contribution is over 106 times smaller than the lattice. The effect is observed in the temperature regime where the Umklapp processes start appearing, and still mainly involve phonons with long mean free paths. A special thermal design is employed to obtain a high accuracy heat flux measurement. Detailed experimental procedures and results are presented along with a brief discussion about possible origins of the effect. HJ and JPH are supported by AFOSR MURI ``Cryogenic Peltier Cooling'' Contract #FA9550-10-1-0533; ODR and WW are supported by the Center for Emergent Materials, an NSF MRSEC at The Ohio State University (Grant DMR-0820414).

  17. Thickness, humidity, and polarization dependent ferroelectric switching and conductivity in Mg doped lithium niobate

    SciTech Connect

    Neumayer, Sabine M.; Strelcov, Evgheni; Manzo, Michele; Gallo, Katia; Kravchenko, Ivan I.; Kholkin, Andrei L.; Kalinin, Sergei V.; Rodriguez, Brian J.

    2015-12-28

    Mg doped lithium niobate (Mg:LN) exhibits several advantages over undoped LN such as resistance to photorefraction, lower coercive fields, and p-type conductivity that is particularly pronounced at domain walls and opens up a range of applications, e.g., in domain wall electronics. Engineering of precise domain patterns necessitates well founded knowledge of switching kinetics, which can differ significantly from that of undoped LN. In this work, the role of humidity and sample composition in polarization reversal has been investigated under application of the same voltage waveform. Control over domain sizes has been achieved by varying the sample thickness and initial polarization as well as atmospheric conditions. Additionally, local introduction of proton exchanged phases allows for inhibition of domain nucleation or destabilization, which can be utilized to modify domain patterns. In polarization dependent current flow, attributed to charged domain walls and band bending, it the rectifying ability of Mg: LN in combination with suitable metal electrodes that allow for further tailoring of conductivity is demonstrated.

  18. Temperature Dependent Thermal Conductivity and Thermal Interface Resistance of Pentacene Thin Films with Varying Morphology.

    PubMed

    Epstein, Jillian; Ong, Wee-Liat; Bettinger, Christopher J; Malen, Jonathan A

    2016-07-27

    Temperature dependent thermal conductivities and thermal interface resistances of pentacene (Pn) thin films deposited on silicon substrates and self-assembled monolayer-modified [octadecyltrichlorosilane (OTS) and (3-aminopropyl)triethoxysilane (APTES)] silicon substrates were measured using frequency domain thermoreflectance. Atomic force microscopy images were used to derive an effective film thickness for thermal transport that accounts for surface roughness. Data taken over a temperature range of 77-300 K for various morphologies and film thicknesses show that the thermal conductivity increases with increasing Pn grain size. The sum of the substrate-Pn and Pn-gold thermal interface resistances was isolated from the intrinsic thermal resistance of the Pn films and found to be independent of surface chemistry. Corresponding Kapitza lengths of approximately 150 nm are larger than the physical thicknesses of typical Pn thin films and indicate that the interfaces play a dominant role in the total thermal resistance. This study has implications for increasing the performance and effective thermal management of small molecule electronic and energy conversion devices.

  19. Thickness, humidity, and polarization dependent ferroelectric switching and conductivity in Mg doped lithium niobate

    DOE PAGES

    Neumayer, Sabine M.; Strelcov, Evgheni; Manzo, Michele; ...

    2015-12-28

    Mg doped lithium niobate (Mg:LN) exhibits several advantages over undoped LN such as resistance to photorefraction, lower coercive fields, and p-type conductivity that is particularly pronounced at domain walls and opens up a range of applications, e.g., in domain wall electronics. Engineering of precise domain patterns necessitates well founded knowledge of switching kinetics, which can differ significantly from that of undoped LN. In this work, the role of humidity and sample composition in polarization reversal has been investigated under application of the same voltage waveform. Control over domain sizes has been achieved by varying the sample thickness and initial polarizationmore » as well as atmospheric conditions. Additionally, local introduction of proton exchanged phases allows for inhibition of domain nucleation or destabilization, which can be utilized to modify domain patterns. In polarization dependent current flow, attributed to charged domain walls and band bending, it the rectifying ability of Mg: LN in combination with suitable metal electrodes that allow for further tailoring of conductivity is demonstrated.« less

  20. Ion concentration-dependence of rat cardiac unitary L-type calcium channel conductance.

    PubMed Central

    Guia, A; Stern, M D; Lakatta, E G; Josephson, I R

    2001-01-01

    Little is known about the native properties of unitary cardiac L-type calcium currents (i(Ca)) measured with physiological calcium (Ca) ion concentration, and their role in excitation-contraction (E-C) coupling. Our goal was to chart the concentration-dependence of unitary conductance (gamma) to physiological Ca concentration and compare it to barium ion (Ba) conductance in the absence of agonists. In isolated, K-depolarized rat myocytes, i(Ca) amplitudes were measured using cell-attached patches with 2 to 70 mM Ca or 2 to 105 mM Ba in the pipette. At 0 mV, 2 mM of Ca produced 0.12 pA, and 2 mM of Ba produced 0.19 pA unitary currents. Unitary conductance was described by a Langmuir isotherm relationship with a maximum gammaCa of 5.3 +/- 0.2 pS (n = 15), and gammaBa of 15 +/- 1 pS (n = 27). The concentration producing half-maximal gamma, Kd(gamma), was not different between Ca (1.7 +/- 0.3 mM) and Ba (1.9 +/- 0.4 mM). We found that quasi-physiological concentrations of Ca produced currents that were as easily resolvable as those obtained with the traditionally used higher concentrations. This study leads to future work on the molecular basis of E-C coupling with a physiological concentration of Ca ions permeating the Ca channel. PMID:11371449

  1. History dependence of human muscle-fiber conduction velocity during voluntary isometric contractions

    PubMed Central

    Lateva, Zoia C.

    2011-01-01

    The conduction velocity (CV) of a muscle fiber is affected by the fiber's discharge history going back ∼1 s. We investigated this dependence by measuring CV fluctuations during voluntary isometric contractions of the human brachioradialis muscle. We recorded electromyogram (EMG) signals simultaneously from multiple intramuscular electrodes, identified potentials belonging to the same motor unit using EMG decomposition, and estimated the CV of each discharge from the interpotential interval. In 12 of 14 subjects, CV increased by ∼10% during the first second after recruitment and then fluctuated by about ±2% in a way that mirrored the fluctuations in the instantaneous firing rate. The CV profile could be precisely described in terms of the discharge history by a simple mathematical model. In the other two subjects, and one subject retested after cooling the arm, the CV fluctuations were inversely correlated with instantaneous firing rate. In all subjects, CV was additionally affected by very short interdischarge intervals (<25 ms): it was increased in doublets at recruitment, but decreased in doublets during continuous firing and after short interdischarge intervals in doubly innervated fibers. CV also exhibited a slow trend of about −0.05%/s that did not depend on the immediate discharge history. We suggest that measurements of CV fluctuations during voluntary contractions, or during stimulation protocols that involve longer and more complex stimulation patterns than are currently being used, may provide a sensitive approach for estimating the dynamic characteristics of ion channels in the human muscle-fiber membrane. PMID:21565985

  2. Inactivation of a high conductance calcium dependent potassium current in rat hippocampal neurons.

    PubMed

    McLarnon, J G

    1995-06-23

    Inactivating, high conductance BK-type currents have been recorded from inside-out patches (internal and external K+ of 140 mM and 5 mM, respectively), obtained from cultured rat hippocampal neurons. The presence of prominent inactivation, not normally associated with BK channel activity, was dependent on two factors: a depolarizing step to 0 mV from a holding level of -80 mV and internal calcium at a concentration of 0.7 microM. Without the prior conditioning step to a negative potential, unitary currents were not evident at 0 mV; in addition, such currents were not elicited with the stimulus protocol if the internal Ca2+ was reduced to a level of 0.3 microM. Concomitant with current inactivation was the finding of a delayed activation of BK currents following the depolarizing step. Higher internal calcium, at 100 microM, led to persistent and sustained channel activity at 0 mV which was not dependent on a prior step to -80 mV. These results may be relevant to the complex nature of the repolarizing neuronal current Ic which is the macroscopic analogue of the unitary BK current.

  3. Calcium activates the light-dependent conductance in melanopsin-expressing photoreceptors of amphioxus.

    PubMed

    Peinado, Gabriel; Osorno, Tomás; Gomez, María del Pilar; Nasi, Enrico

    2015-06-23

    Melanopsin, the photopigment of the "circadian" receptors that regulate the biological clock and the pupillary reflex in mammals, is homologous to invertebrate rhodopsins. Evidence supporting the involvement of phosphoinositides in light-signaling has been garnered, but the downstream effectors that control the light-dependent conductance remain unknown. Microvillar photoreceptors of the primitive chordate amphioxus also express melanopsin and transduce light via phospholipase-C, apparently not acting through diacylglycerol. We therefore examined the role of calcium in activating the photoconductance, using simultaneous, high time-resolution measurements of membrane current and Ca(2+) fluorescence. The light-induced calcium rise precedes the onset of the photocurrent, making it a candidate in the activation chain. Moreover, photolysis of caged Ca elicits an inward current of similar size, time course and pharmacology as the physiological photoresponse, but with a much shorter latency. Internally released calcium thus emerges as a key messenger to trigger the opening of light-dependent channels in melanopsin-expressing microvillar photoreceptors of early chordates.

  4. The calcium-dependent protein kinase CPK7 acts on root hydraulic conductivity.

    PubMed

    Li, Guowei; Boudsocq, Marie; Hem, Sonia; Vialaret, Jérôme; Rossignol, Michel; Maurel, Christophe; Santoni, Véronique

    2015-07-01

    The hydraulic conductivity of plant roots (Lp(r)) is determined in large part by the activity of aquaporins. Mechanisms occurring at the post-translational level, in particular phosphorylation of aquaporins of the plasma membrane intrinsic protein 2 (PIP2) subfamily, are thought to be of critical importance for regulating root water transport. However, knowledge of protein kinases and phosphatases acting on aquaporin function is still scarce. In the present work, we investigated the Lp(r) of knockout Arabidopsis plants for four Ca(2+)-dependent protein kinases. cpk7 plants showed a 30% increase in Lp(r) because of a higher aquaporin activity. A quantitative proteomic analysis of wild-type and cpk7 plants revealed that PIP gene expression and PIP protein quantity were not correlated and that CPK7 has no effect on PIP2 phosphorylation. In contrast, CPK7 exerts a negative control on the cellular abundance of PIP1s, which likely accounts for the higher Lp(r) of cpk7. In addition, this study revealed that the cellular amount of a few additional proteins including membrane transporters is controlled by CPK7. The overall work provides evidence for CPK7-dependent stability of specific membrane proteins.

  5. Calcium activates the light-dependent conductance in melanopsin-expressing photoreceptors of amphioxus

    PubMed Central

    Peinado, Gabriel; Osorno, Tomás; Gomez, María del Pilar; Nasi, Enrico

    2015-01-01

    Melanopsin, the photopigment of the “circadian” receptors that regulate the biological clock and the pupillary reflex in mammals, is homologous to invertebrate rhodopsins. Evidence supporting the involvement of phosphoinositides in light-signaling has been garnered, but the downstream effectors that control the light-dependent conductance remain unknown. Microvillar photoreceptors of the primitive chordate amphioxus also express melanopsin and transduce light via phospholipase-C, apparently not acting through diacylglycerol. We therefore examined the role of calcium in activating the photoconductance, using simultaneous, high time-resolution measurements of membrane current and Ca2+ fluorescence. The light-induced calcium rise precedes the onset of the photocurrent, making it a candidate in the activation chain. Moreover, photolysis of caged Ca elicits an inward current of similar size, time course and pharmacology as the physiological photoresponse, but with a much shorter latency. Internally released calcium thus emerges as a key messenger to trigger the opening of light-dependent channels in melanopsin-expressing microvillar photoreceptors of early chordates. PMID:26056310

  6. Zwitterionic peptide anchored to conducting polymer PEDOT for the development of antifouling and ultrasensitive electrochemical DNA sensor.

    PubMed

    Wang, Guixiang; Han, Rui; Su, Xiaoli; Li, Yinan; Xu, Guiyun; Luo, Xiliang

    2017-06-15

    Zwitterionic peptides were anchored to a conducting polymer of citrate doped poly(3,4-ethylenedioxythiophene) (PEDOT) via the nickel cation coordination, and the obtained peptide modified PEDOT, with excellent antifouling ability and good conductivity, was further used for the immobilization of a DNA probe to construct an electrochemical biosensor for the breast cancer marker BRCA1. The DNA biosensor was highly sensitive (with detection limit of 0.03fM) and selective, and it was able to detect BRCA1 in 5% (v/v) human plasma with satisfying accuracy and low fouling. The marriage of antifouling and biocompatible peptides with conducting polymers opened a new avenue to construct electrochemical biosensors capable of assaying targets in complex biological media with high sensitivity and without biofouling.

  7. Highly thymine-dependent formation of fluorescent copper nanoparticles templated by ss-DNA

    NASA Astrophysics Data System (ADS)

    Liu, Guiying; Shao, Yong; Peng, Jian; Dai, Wei; Liu, Lingling; Xu, Shujuan; Wu, Fei; Wu, Xiaohua

    2013-08-01

    Double-stranded DNAs (ds-DNAs) have been identified as efficient templates favoring the formation of fluorescent copper nanoparticles (Cu NPs). Herein, we have tried to synthesize fluorescent Cu NPs using single-stranded DNAs (ss-DNAs) as templates and to identify the critical DNA sequences. By comparing the results using homopolymer DNAs, hairpin DNAs, and pristine ss-DNAs as templates, we found that DNA thymine base plays a dominant role in producing red-emissive fluorescent Cu NPs on ss-DNA templates. The thymine-dependent growth of the fluorescent Cu NPs is confirmed by Hg2+ mediated T-T base pair in comparison with the other non-specific metal ions, which could be developed into a practical sensor for turn-on fluorescence detection of Hg2+ with a high selectivity. The mechanism is briefly discussed according the DNA sequence-dependent formation of fluorescent Cu NPs. This work demonstrates the sequence role in producing fluorescent Cu NPs that could serve as promising fluorescent nanoprobes in biosensing and DNA-hosted Cu nanomaterials.

  8. Involvement of a Rac1-Dependent Macropinocytosis Pathway in Plasmid DNA Delivery by Electrotransfection.

    PubMed

    Mao, Mao; Wang, Liangli; Chang, Chun-Chi; Rothenberg, Katheryn E; Huang, Jianyong; Wang, Yingxiao; Hoffman, Brenton D; Liton, Paloma B; Yuan, Fan

    2017-03-01

    Electrotransfection is a widely used method for delivering genes into cells with electric pulses. Although different hypotheses have been proposed, the mechanism of electrotransfection remains controversial. Previous studies have indicated that uptake and intracellular trafficking of plasmid DNA (pDNA) are mediated by endocytic pathways, but it is still unclear which pathways are directly involved in the delivery. To this end, the present study investigated the dependence of electrotransfection on macropinocytosis. Data from the study demonstrated that electric pulses induced cell membrane ruffling and actin cytoskeleton remodeling. Using fluorescently labeled pDNA and a macropinocytosis marker (i.e., dextran), the study showed that electrotransfected pDNA co-localized with dextran in intracellular vesicles. Furthermore, electrotransfection efficiency could be decreased significantly by reducing temperature or treatment of cells with a pharmacological inhibitor of Rac1 and could be altered by changing Rac1 activity. Taken together, the findings suggested that electrotransfection of pDNA involved Rac1-dependent macropinocytosis.

  9. DNA polymerase β-dependent cell survival independent of XRCC1 expression

    PubMed Central

    Horton, Julie K.; Gassman, Natalie R.; Dunigan, Brittany B.; Stefanick, Donna F.; Wilson, Samuel H.

    2014-01-01

    Base excision repair (BER) is a primary mechanism for repair of base lesions in DNA such as those formed by exposure to the DNA methylating agent methyl methanesulfonate (MMS). Both DNA polymerase β (pol β)- and XRCC1-deficient mouse fibroblasts are hypersensitive to MMS. This is linked to a repair deficiency as measured by accumulation of strand breaks and poly(ADP-ribose) (PAR). The interaction between pol β and XRCC1 is important for recruitment of pol β to sites of DNA damage. Endogenous DNA damage can substitute for MMS-induced damage such that BER deficiency as a result of either pol β- or XRCC1-deletion is associated with sensitivity to PARP inhibitors. Pol β shRNA was used to knock down pol β in Xrcc1+/+ and Xrcc1−/− mouse fibroblasts. We determined whether pol β-mediated cellular resistance to MMS and PARP inhibitors resulted entirely from coordination with XRCC1 within the same BER sub-pathway. We find evidence for pol β- dependent cell survival independent of XRCC1 expression for both types of agents. The results suggest a role for pol β-dependent, XRCC1-independent repair. PAR immunofluorescence data are consistent with the hypothesis of a decrease in repair in both pol β knock down cell variants. PMID:25541391

  10. Erythroblast transformation by FLI-1 depends upon its specific DNA binding and transcriptional activation properties.

    PubMed

    Ano, Sabine; Pereira, Rui; Pironin, Martine; Lesault, Isabelle; Milley, Caroline; Lebigot, Ingrid; Quang, Christine Tran; Ghysdael, Jacques

    2004-01-23

    FLI-1 is a transcriptional regulator of the ETS family of proteins. Insertional activation at the FLI-1 locus is an early event in F-murine leukemia virus-induced erythroleukemia. Consistent with its essential role in erythroid transformation, enforced expression of FLI-1 in primary erythroblasts strongly impairs the response of these cells to erythropoietin (Epo), a cytokine essential to erythropoiesis. We show here that point mutations in the ETS domain that abolished FLI-1 binding to specific DNA elements (ETS-binding sites) suppressed the ability of FLI-1 to transform erythroblasts. The exchange of the entire ETS domain (DNA binding domain) of FLI-1 for that of PU.1 changed the DNA binding specificity of FLI-1 for that of PU.1 and impaired FLI-1 transforming properties. In contrast, ETS domain swapping mutants that maintained the DNA binding specificity of FLI-1 did not affect the ability of FLI-1 to transform erythroblasts. Deletion and swapping mutants that failed to inhibit the DNA binding activity of FLI-1 but impaired its transcriptional activation properties were also transformation-defective. Taken together, these results show that both the ability of FLI-1 to inhibit Epo-induced differentiation of erythroblasts and to confer enhanced cell survival in the absence of Epo critically depend upon FLI-1 ETS-binding site-dependent transcriptional activation properties.

  11. Pulse Shape and Timing Dependence on the Spike-Timing Dependent Plasticity Response of Ion-Conducting Memristors as Synapses

    PubMed Central

    Campbell, Kristy A.; Drake, Kolton T.; Barney Smith, Elisa H.

    2016-01-01

    Ion-conducting memristors comprised of the layered materials Ge2Se3/SnSe/Ag are promising candidates for neuromorphic computing applications. Here, the spike-timing dependent plasticity (STDP) application is demonstrated for the first time with a single memristor type operating as a synapse over a timescale of 10 orders of magnitude, from nanoseconds through seconds. This large dynamic range allows the memristors to be useful in applications that require slow biological times, as well as fast times such as needed in neuromorphic computing, thus allowing multiple functions in one design for one memristor type—a “one size fits all” approach. This work also investigated the effects of varying the spike pulse shapes on the STDP response of the memristors. These results showed that small changes in the pre- and postsynaptic pulse shape can have a significant impact on the STDP. These results may provide circuit designers with insights into how pulse shape affects the actual memristor STDP response and aid them in the design of neuromorphic circuits and systems that can take advantage of certain features in the memristor STDP response that are programmable via the pre- and postsynaptic pulse shapes. In addition, the energy requirement per memristor is approximated based on the pulse shape and timing responses. The energy requirement estimated per memristor operating on slower biological timescales (milliseconds to seconds) is larger (nanojoules range), as expected, than the faster (nanoseconds) operating times (~0.1 pJ in some cases). Lastly, the memristors responded in a similar manner under normal STDP conditions (pre- and post-spikes applied to opposite memristor terminals) as they did to the case where a waveform corresponding to the difference between pre- and post-spikes was applied to only one electrode, with the other electrode held at ground potential. By applying the difference signal to only one terminal, testing of the memristor in various

  12. Delineating Species with DNA Barcodes: A Case of Taxon Dependent Method Performance in Moths

    PubMed Central

    Kekkonen, Mari; Mutanen, Marko; Kaila, Lauri; Nieminen, Marko; Hebert, Paul D. N.

    2015-01-01

    The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work. PMID:25849083

  13. Strain dependent UV degradation of Escherichia coli DNA monitored by Fourier transform infrared spectroscopy.

    PubMed

    Muntean, Cristina M; Lapusan, Alexandra; Mihaiu, Liora; Stefan, Razvan

    2014-01-05

    In this work we present a method for detection of DNA isolated from nonpathogenic Escherichia coli strains, respectively. Untreated and UV irradiated bacterial DNAs were analyzed by FT-IR spectroscopy, to investigate their screening characteristic features and their structural radiotolerance at 253.7nm. FT-IR spectra, providing a high molecular structural information, have been analyzed in the wavenumber range 800-1800cm(-1). FT-IR signatures, spectroscopic band assignments and structural interpretations of these DNAs are reported. Also, UV damage at the DNA molecular level is of interest. Strain dependent UV degradation of DNA from E. coli has been observed. Particularly, alterations in nucleic acid bases, base pairing and base stacking have been found. Also changes in the DNA conformation and deoxyribose were detected. Based on this work, specific E. coli DNA-ligand interactions, drug development and vaccine design for a better understanding of the infection mechanism caused by an interference between pathogenic and nonpathogenic bacteria and for a better control of disease, respectively, might be further investigated using Fourier transform infrared spectroscopy. Besides, understanding the pathways for UV damaged DNA response, like nucleic acids repair mechanisms is appreciated.

  14. Electrochemical DNA biosensor based on the proximity-dependent surface hybridization assay.

    PubMed

    Zhang, Yanli; Wang, Ying; Wang, Haibo; Jiang, Jian-Hui; Shen, Guo-Li; Yu, Ru-Qin; Li, Jinghong

    2009-03-01

    This paper describes a novel electrochemical DNA (E-DNA) biosensor for simple, rapid, and specific detection of nucleic acids based on the proximity-dependent surface hybridization assay. This E-DNA biosensor was constructed by self-assembly of a 3' short thiolated capture probe on the gold electrode. DNA detection was realized by outputting a remarkable redox current of the 5' ferrocene (Fc) tail labeled probe. When the target DNA was introduced into the system, it was complementary to the 5' Fc labeled probe at the one-half-segment and complementary to the 3' short thiolated capture probe at the other half-segment, resulting in forming a stable duplex complex. As a result, the Fc probe was proximate to the electrode surface, and the Faradaic current was observed. This E-DNA biosensor was proved to have a low detection limit (1 fM) and a wide dynamic range (from 1 fM to 1 nM) due to the stable hybridization mode. In addition, the sensing system could discriminate the complementary sequence from mismatch sequences, with high sensitivity, stability, and reusability.

  15. Sodium selenide toxicity is mediated by O2-dependent DNA breaks.

    PubMed

    Peyroche, Gérald; Saveanu, Cosmin; Dauplais, Marc; Lazard, Myriam; Beuneu, François; Decourty, Laurence; Malabat, Christophe; Jacquier, Alain; Blanquet, Sylvain; Plateau, Pierre

    2012-01-01

    Hydrogen selenide is a recurrent metabolite of selenium compounds. However, few experiments studied the direct link between this toxic agent and cell death. To address this question, we first screened a systematic collection of Saccharomyces cerevisiae haploid knockout strains for sensitivity to sodium selenide, a donor for hydrogen selenide (H(2)Se/HSe(-/)Se(2-)). Among the genes whose deletion caused hypersensitivity, homologous recombination and DNA damage checkpoint genes were over-represented, suggesting that DNA double-strand breaks are a dominant cause of hydrogen selenide toxicity. Consistent with this hypothesis, treatment of S. cerevisiae cells with sodium selenide triggered G2/M checkpoint activation and induced in vivo chromosome fragmentation. In vitro, sodium selenide directly induced DNA phosphodiester-bond breaks via an O(2)-dependent reaction. The reaction was inhibited by mannitol, a hydroxyl radical quencher, but not by superoxide dismutase or catalase, strongly suggesting the involvement of hydroxyl radicals and ruling out participations of superoxide anions or hydrogen peroxide. The (•)OH signature could indeed be detected by electron spin resonance upon exposure of a solution of sodium selenide to O(2). Finally we showed that, in vivo, toxicity strictly depended on the presence of O(2). Therefore, by combining genome-wide and biochemical approaches, we demonstrated that, in yeast cells, hydrogen selenide induces toxic DNA breaks through an O(2)-dependent radical-based mechanism.

  16. Inhibition of RNA-dependent DNA polymerase of Rous sarcoma virus by thiosemicarbazones and several cations.

    PubMed

    Levinson, W; Faras, A; Woodson, B; Jackson, J; Bishop, J M

    1973-01-01

    The RNA-dependent DNA polymerase of Rous sarcoma virus is inhibited by N-methyl isatin beta-thiosemicarbazone and by thiosemicarbazide, but not by semicarbazide. These inhibitors also inactivate, upon contact with the virion, the transforming ability of Rous sarcoma virus. Sulfhydryl donors, such as 2-mercapto-ethanol, can prevent these effects. The RNA-directed activity of the purified polymerase is inhibited to a greater degree than is the DNA-directed activity. Two cations, Cu(++) and Hg(++), can inhibit RNA-dependent DNA polymerase and inactivate the transforming ability of the virus. Synergism between N-methyl isatin beta-thiosemicarbazone and Cu(++) occurs, since treatment of the virus with a low dose of either N-methyl isatin beta-thiosemicarbazone or Cu(++) has little effect; however, when the two compounds are mixed together, significant inactivation occurs. This observation supports the hypothesis that the antiviral action of thiosemicarbazones is a function of their ability to act as a ligand for metallic ions. Several cations (Ag(+), Co(++), Zn(++), Cd(++), and Ni(++)) significantly inactivate the RNA-dependent DNA polymerase, but have little effect on the transforming ability. In view of this result, the conclusion that the enzyme activity is required for transformation remains open to question.

  17. Dimorphic DNA methylation during temperature-dependent sex determination in the sea turtle Lepidochelys olivacea.

    PubMed

    Venegas, Daniela; Marmolejo-Valencia, Alejandro; Valdes-Quezada, Christian; Govenzensky, Tzipe; Recillas-Targa, Félix; Merchant-Larios, Horacio

    2016-09-15

    Sex determination in vertebrates depends on the expression of a conserved network of genes. Sea turtles such as Lepidochelys olivacea have temperature-dependent sex determination. The present work analyses some of the epigenetic processes involved in this. We describe sexual dimorphism in global DNA methylation patterns between ovaries and testes of L. olivacea and show that the differences may arise from a combination of DNA methylation and demethylation events that occur during sex determination. Irrespective of incubation temperature, 5-hydroxymethylcytosine was abundant in the bipotential gonad; however, following sex determination, this modification was no longer found in pre-Sertoli cells in the testes. These changes correlate with the establishment of the sexually dimorphic DNA methylation patterns, down regulation of Sox9 gene expression in ovaries and irreversible gonadal commitment towards a male or female differentiation pathway. Thus, DNA methylation changes may be necessary for the stabilization of the gene expression networks that drive the differentiation of the bipotential gonad to form either an ovary or a testis in L. olivacea and probably among other species that manifest temperature-dependent sex determination.

  18. Requirement of Rad5 for DNA Polymerase ζ-Dependent Translesion Synthesis in Saccharomyces cerevisiae

    PubMed Central

    Pagès, Vincent; Bresson, Anne; Acharya, Narottam; Prakash, Satya; Fuchs, Robert P.; Prakash, Louise

    2008-01-01

    In yeast, Rad6–Rad18-dependent lesion bypass involves translesion synthesis (TLS) by DNA polymerases η or ζ or Rad5-dependent postreplication repair (PRR) in which error-free replication through the DNA lesion occurs by template switching. Rad5 functions in PRR via its two distinct activities—a ubiquitin ligase that promotes Mms2–Ubc13-mediated K63-linked polyubiquitination of PCNA at its lysine 164 residue and a DNA helicase that is specialized for replication fork regression. Both these activities are important for Rad5's ability to function in PRR. Here we provide evidence for the requirement of Rad5 in TLS mediated by Polζ. Using duplex plasmids carrying different site-specific DNA lesions—an abasic site, a cis–syn TT dimer, a (6-4) TT photoproduct, or a G-AAF adduct—we show that Rad5 is needed for Polζ-dependent TLS. Rad5 action in this role is likely to be structural, since neither the inactivation of its ubiquitin ligase activity nor the inactivation of its helicase activity impairs its role in TLS. PMID:18757916

  19. Single-Molecule Studies of the Temperature Dependence of Viral DNA Packaging Motors

    NASA Astrophysics Data System (ADS)

    White, Michael; Raymer, Dorian; Rickgauer, Peter; Fuller, Derek; Grimes, Shelley; Jardine, Paul; Anderson, Dwight; Smith, Doug

    2007-03-01

    A key step in the assembly of many viruses is the packaging of dsDNA into a preformed capsid by the action of a portal molecular motor complex. We have developed methods for directly measuring viral DNA translocation at the single molecule level using optical tweezers and applied these methods to study bacteriophages φ29, lambda, and T4. Our previous measurements with φ29 were performed at room temperature. Here we report that the rate of DNA translocation is strongly temperature dependent. Preliminary measurements indicate that the motor velocity increases ˜2-fold, to ˜250-300 bp/s when the temperature is increased from ˜20 to 30 degrees C. As the viral packaging motors are enzymes that catalyze ATP hydrolysis, such a trend with increasing temperature is to be expected, at least up to the point where the motor complex is thermally dissociated or denatured. However, the detailed form of the temperature dependence is difficult to quantify using standard bulk assay methods. We have installed a heating/cooling system in our optical tweezers instrument that allows us to precisely control the temperature in our sample chamber. This system allows us to systematically study the temperature dependence of the DNA translocation rate.

  20. Early days of DNA repair: discovery of nucleotide excision repair and homology-dependent recombinational repair.

    PubMed

    Rupp, W Dean

    2013-12-13

    The discovery of nucleotide excision repair in 1964 showed that DNA could be repaired by a mechanism that removed the damaged section of a strand and replaced it accurately by using the remaining intact strand as the template. This result showed that DNA could be actively metabolized in a process that had no precedent. In 1968, experiments describing postreplication repair, a process dependent on homologous recombination, were reported. The authors of these papers were either at Yale University or had prior Yale connections. Here we recount some of the events leading to these discoveries and consider the impact on further research at Yale and elsewhere.

  1. Computational Study of the Force Dependence of Phosphoryl Transfer during DNA Synthesis by a High Fidelity Polymerase

    NASA Astrophysics Data System (ADS)

    Venkatramani, Ravindra; Radhakrishnan, Ravi

    2008-02-01

    High fidelity polymerases are efficient catalysts of phosphodiester bond formation during DNA replication or repair. We interpret molecular dynamics simulations of a polymerase bound to its substrate DNA and incoming nucleotide using a quasiharmonic model to study the effect of external forces applied to the bound DNA on the kinetics of phosphoryl transfer. The origin of the force dependence is shown to be an intriguing coupling between slow, delocalized polymerase-DNA modes and fast catalytic site motions. Using noncognate DNA substrates we show that the force dependence is context specific.

  2. Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors

    PubMed Central

    Liu, Jiajian; Stormo, Gary D.

    2008-01-01

    Motivation: Modeling and identifying the DNA-protein recognition code is one of the most challenging problems in computational biology. Several quantitative methods have been developed to model DNA-protein interactions with specific focus on the C2H2 zinc-finger proteins, the largest transcription factor family in eukaryotic genomes. In many cases, they performed well. But the overall the predictive accuracy of these methods is still limited. One of the major reasons is all these methods used weight matrix models to represent DNA-protein interactions, assuming all base-amino acid contacts contribute independently to the total free energy of binding. Results: We present a context-dependent model for DNA–zinc-finger protein interactions that allows us to identify inter-positional dependencies in the DNA recognition code for C2H2 zinc-finger proteins. The degree of non-independence was detected by comparing the linear perceptron model with the non-linear neural net (NN) model for their predictions of DNA–zinc-finger protein interactions. This dependency is supported by the complex base-amino acid contacts observed in DNA–zinc-finger interactions from structural analyses. Using extensive published qualitative and quantitative experimental data, we demonstrated that the context-dependent model developed in this study can significantly improves predictions of DNA binding profiles and free energies of binding for both individual zinc fingers and proteins with multiple zinc fingers when comparing to previous positional-independent models. This approach can be extended to other protein families with complex base-amino acid residue interactions that would help to further understand the transcriptional regulation in eukaryotic genomes. Availability:The software implemented as c programs and are available by request. http://ural.wustl.edu/softwares.html Contact: stormo@ural.wustl.edu PMID:18586699

  3. Hydroxyl-radical-dependent DNA damage by ambient particulate matter from contrasting sampling locations

    SciTech Connect

    Shi Tingming; Duffin, Rodger; Borm, Paul J.A.; Li Hui; Weishaupt, Christel; Schins, Roel P.F. . E-mail: roel.schins@uni-duesseldorf.de

    2006-05-15

    Exposure to ambient particulate matter (PM) has been reported to be associated with increased respiratory, cardiovascular, and malignant lung disease. Previously we have shown that PM can induce oxidative DNA damage in A549 human lung epithelial cells. The aims of the present study were to investigate the variability of the DNA-damaging properties of PM sampled at different locations and times and to relate the observed effects to the hydroxyl-radical ({center_dot}OH)-generating activities of these samples. Weekly samples of coarse (10-2.5 {mu}m) and fine (<2.5 {mu}m) PM from four sites (Nordrheim Westfalen, Germany) were analyzed for hydrogen-peroxide-dependent {center_dot}OH formation using electron paramagnetic resonance and formation of 8-hydroxydeoxyguanosine (8-OHdG) in calf thymus DNA using an immuno-dot-blot assay. DNA strand breakage by fine PM in A549 human lung epithelial cells was quantified using the alkaline comet assay. Both PM size distribution fractions elicited {center_dot}OH generation and 8-OHdG formations in calf thymus DNA. Significantly higher {center_dot}OH generation was observed for PM sampled at urban/industrial locations and for coarse PM. Samples of fine PM also caused DNA strand breakage in A549 cells and this damage could be prevented using the hydroxyl-radical scavengers 5,5-dimethyl-1-pyrroline-N-oxide and dimethyl sulfoxide. The observed DNA strand breakage appeared to correlate with the hydroxyl-radical-generating capacities of the PM samples but with different profiles for rural versus urban/industrial samples. In conclusion, when considered at equal mass, {center_dot}OH formation of PM shows considerable variability with regard to the sampling location and time and is correlated with its ability to cause DNA damage.

  4. Unusual sequence length-dependent gold nanoparticles aggregation of the ssDNA sticky end and its application for enzyme-free and signal amplified colorimetric DNA detection

    NASA Astrophysics Data System (ADS)

    He, Hongfei; Dai, Jianyuan; Duan, Zhijuan; Zheng, Baozhan; Meng, Yan; Guo, Yong; Dan Xiao, A1"/>

    2016-08-01

    It is known that the adsorption of short single-stranded DNA (ssDNA) on unmodified gold nanoparticles (AuNPs) is much faster than that for long ssDNA, and thus leads to length-dependent AuNPs aggregation after addition of salt, the color of the solutions sequentially changed from red to blue in accordance with the increase of ssDNA length. However, we found herein that the ssDNA sticky end of hairpin DNA exhibited a completely different adsorption behavior compared to ssDNA, an inverse blue-to-red color variation was observed in the colloid solution with the increase of sticky end length when the length is within a certain range. This unusual sequence length-dependent AuNPs aggregation might be ascribed to the effect of the stem of hairpin DNA. On the basis of this unique phenomenon and catalytic hairpin assembly (CHA) based signal amplification, a novel AuNPs-based colorimetric DNA assay with picomolar sensitivity and specificity was developed. This unusual sequence length-dependent AuNPs aggregation of the ssDNA sticky end introduces a new direction for the AuNPs-based colorimetric assays.

  5. STING-Dependent Cytosolic DNA Sensing Promotes Radiation-Induced Type I Interferon-Dependent Antitumor Immunity in Immunogenic Tumors.

    PubMed

    Deng, Liufu; Liang, Hua; Xu, Meng; Yang, Xuanming; Burnette, Byron; Arina, Ainhoa; Li, Xiao-Dong; Mauceri, Helena; Beckett, Michael; Darga, Thomas; Huang, Xiaona; Gajewski, Thomas F; Chen, Zhijian J; Fu, Yang-Xin; Weichselbaum, Ralph R

    2014-11-20

    Ionizing radiation-mediated tumor regression depends on type I interferon (IFN) and the adaptive immune response, but several pathways control I IFN induction. Here, we demonstrate that adaptor protein STING, but not MyD88, is required for type I IFN-dependent antitumor effects of radiation. In dendritic cells (DCs), STING was required for IFN-? induction in response to irradiated-tumor cells. The cytosolic DNA sensor cyclic GMP-AMP (cGAMP) synthase (cGAS) mediated sensing of irradiated-tumor cells in DCs. Moreover, STING was essential for radiation-induced adaptive immune responses, which relied on type I IFN signaling on DCs. Exogenous IFN-? treatment rescued the cross-priming by cGAS or STING-deficient DCs. Accordingly, activation of STING by a second messenger cGAMP administration enhanced antitumor immunity induced by radiation. Thus radiation-mediated antitumor immunity in immunogenic tumors requires a functional cytosolic DNA-sensing pathway and suggests that cGAMP treatment might provide a new strategy to improve radiotherapy.

  6. Electrical conductivity and magnetic field dependent current-voltage characteristics of nanocrystalline nickel ferrite

    NASA Astrophysics Data System (ADS)

    Ghosh, P.; Bhowmik, R. N.; Das, M. R.; Mitra, P.

    2017-04-01

    We have studied the grain size dependent electrical conductivity, dielectric relaxation and magnetic field dependent current voltage (I - V) characteristics of nickel ferrite (NiFe2O4) . The material has been synthesized by sol-gel self-combustion technique, followed by ball milling at room temperature in air environment to control the grain size. The material has been characterized using X-ray diffraction (refined with MAUD software analysis) and Transmission electron microscopy. Impedance spectroscopy and I - V characteristics in the presence of variable magnetic fields have confirmed the increase of resistivity for the fine powdered samples (grain size 5.17±0.6 nm), resulted from ball milling of the chemical routed sample. Activation energy of the material for electrical charge hopping process has increased with the decrease of grain size by mechanical milling of chemical routed sample. The I - V curves showed many highly non-linear and irreversible electrical features, e.g., I - V loop and bi-stable electronic states (low resistance state-LRS and high resistance state-HRS) on cycling the electrical bias voltage direction during I-V curve measurement. The electrical dc resistance for the chemically routed (without milled) sample in HRS (∼3.4876×104 Ω) at 20 V in presence of magnetic field 10 kOe has enhanced to ∼3.4152×105 Ω for the 10 h milled sample. The samples exhibited an unusual negative differential resistance (NDR) effect that gradually decreased on decreasing the grain size of the material. The magneto-resistance of the samples at room temperature has been found substantially large (∼25-65%). The control of electrical charge transport properties under magnetic field, as observed in the present ferrimagnetic material, indicate the magneto-electric coupling in the materials and the results could be useful in spintronics applications.

  7. Simultaneous detection of DNA from 10 food allergens by ligation-dependent probe amplification.

    PubMed

    Ehlert, Alexandra; Demmel, Anja; Hupfer, Christine; Busch, Ulrich; Engel, Karl-Heinz

    2009-04-01

    The simultaneous detection of DNA from different allergenic food ingredients by a ligation-dependent probe amplification (LPA) system is described. The approach allows detection of several targets in a one-tube assay. Synthetic oligonucleotides were designed to detect DNA from peanuts, cashews, pecans, pistachios, hazelnuts, sesame seeds, macadamia nuts, almonds, walnuts and brazil nuts. The specificity of the system was tested with DNA from more than 50 plant and animal species. The sensitivity of the method was suitable to detect allergenic ingredients in the low mg kg(-1) range. The limit of detection (LOD) for single allergens in different food matrices was 5 mg kg(-1). The novel analytical strategy represents a useful tool for the surveillance of established legislation on food allergens within the European Union.

  8. Mechanism of RAD51-dependent DNA interstrand cross-link repair.

    PubMed

    Long, David T; Räschle, Markus; Joukov, Vladimir; Walter, Johannes C

    2011-07-01

    DNA interstrand cross-links (ICLs) are toxic DNA lesions whose repair in S phase of eukaryotic cells is incompletely understood. In Xenopus egg extracts, ICL repair is initiated when two replication forks converge on the lesion. Dual incisions then create a DNA double-strand break (DSB) in one sister chromatid, whereas lesion bypass restores the other sister. We report that the broken sister chromatid is repaired via RAD51-dependent strand invasion into the regenerated sister. Recombination acts downstream of FANCI-FANCD2, yet RAD51 binds ICL-stalled replication forks independently of FANCI-FANCD2 and before DSB formation. Our results elucidate the functional link between the Fanconi anemia pathway and the recombination machinery during ICL repair. In addition, they demonstrate the complete repair of a DSB via homologous recombination in vitro.

  9. Electronic promotion effect of double proton transfer on conduction of DNA through improvement of transverse electronic communication of base pairs

    NASA Astrophysics Data System (ADS)

    Liu, Haiying; Li, Genqin; Zhang, Laibin; Li, Jilai; Wang, Meishan; Bu, Yuxiang

    2011-10-01

    The effect of double proton transfer (DPT) on charge migration of DNA was investigated by the nonequilibrium Green's function method combined with density functional theory. The results revealed that DPT not only lowers ionization potentials, but also improves the delocalization of the localized π-orbitals at each base moiety through adjusting energy levels and spatial distributions of their molecular orbitals. Furthermore, DPT leads to both the strengthening of the second-order interactions of the Watson-Crick H-bond zones, and the promotion of the charge transfer transitions between two pairing bases in the UV absorption spectra. Electronic transport calculations indicated that DPT can improve the charge migration along the DNA duplex for specific sequences through enhancing transverse base-to-base electronic communication. This work will provide a new insight into the understanding of DNA charge conduction which can be electronically promoted or regulated by DPT.

  10. Opposing roles of RNF8/RNF168 and deubiquitinating enzymes in ubiquitination-dependent DNA double-strand break response signaling and DNA-repair pathway choice

    PubMed Central

    Nakada, Shinichiro

    2016-01-01

    The E3 ubiquitin ligases ring finger protein (RNF) 8 and RNF168 transduce the DNA double-strand break (DSB) response (DDR) signal by ubiquitinating DSB sites. The depletion of RNF8 or RNF168 suppresses the accumulation of DNA-repair regulating factors such as 53BP1 and RAP80 at DSB sites, suggesting roles for RNF8- and RNF168-mediated ubiquitination in DSB repair. This mini-review provides a brief overview of the RNF8- and RNF168-dependent DDR-signaling and DNA-repair pathways. The choice of DNA-repair pathway when RNF8- and RNF168-mediated ubiquitination-dependent DDR signaling is negatively regulated by deubiquitinating enzymes (DUBs) is reviewed to clarify how the opposing roles of RNF8/RNF168 and DUBs regulate ubiquitination-dependent DDR signaling and the choice of DNA-repair pathway. PMID:26983989

  11. Temperature-Dependent Charge Transport through Individually Contacted DNA Origami-Based Au Nanowires.

    PubMed

    Teschome, Bezu; Facsko, Stefan; Schönherr, Tommy; Kerbusch, Jochen; Keller, Adrian; Erbe, Artur

    2016-10-11

    DNA origami nanostructures have been used extensively as scaffolds for numerous applications such as for organizing both organic and inorganic nanomaterials, studying single molecule reactions, and fabricating photonic devices. Yet, little has been done toward the integration of DNA origami nanostructures into nanoelectronic devices. Among other challenges, the technical difficulties in producing well-defined electrical contacts between macroscopic electrodes and individual DNA origami-based nanodevices represent a serious bottleneck that hinders the thorough characterization of such devices. Therefore, in this work, we have developed a method to electrically contact individual DNA origami-based metallic nanowires using electron beam lithography. We then characterize the charge transport of such nanowires in the temperature range from room temperature down to 4.2 K. The room temperature charge transport measurements exhibit ohmic behavior, whereas at lower temperatures, multiple charge transport mechanisms such as tunneling and thermally assisted transport start to dominate. Our results confirm that charge transport along metallized DNA origami nanostructures may deviate from pure metallic behavior due to several factors including partial metallization, seed inhomogeneities, impurities, and weak electronic coupling among AuNPs. Besides, this study further elucidates the importance of variable temperature measurements for determining the dominant charge transport mechanisms for conductive nanostructures made by self-assembly approaches.

  12. Time-dependent conductive heat transfer in rarefied polyatomic gases confined between parallel plates

    NASA Astrophysics Data System (ADS)

    Tsimpoukis, A.; Tantos, C.; Valougeorgis, D.

    2017-01-01

    The transient conductive heat transfer through a rarefied gas confined between two infinite parallel plates due to a sudden jump in the temperature of one of the plates is investigated in the whole range of the Knudsen number via kinetic theory. More specifically, the time-dependent heat transfer flow is modelled by the Holway kinetic model subject to diffuse boundary conditions. The governing integro-differential equation is numerically solved using the discrete velocity method in the molecular velocity space and typical finite control volume schemes in time and physical spaces. The time evolution of the density and temperature distributions as well as of the translational and rotational heat fluxes in terms of the two parameters characterizing the heat flow, namely the Knudsen number and the imposed temperature ratio between the plates is provided. The investigation is focused on the effect of the rotational degrees of freedom and a comparison between monatomic and polyatomic gases is performed. It is found that the time needed to reach the steady-state conditions varies between monatomic and polyatomic gases. In all cases the total time to recover the stationary solution in terms of the rarefaction parameter exhibits a minimum close to the well-known Knudsen minimum.

  13. State-dependent access of anions to the cystic fibrosis transmembrane conductance regulator chloride channel pore.

    PubMed

    Fatehi, Mohammad; Linsdell, Paul

    2008-03-07

    The cystic fibrosis transmembrane conductance regulator (CFTR) Cl(-) channel is gated by intracellular factors; however, conformational changes in the channel pore associated with channel activation have not been identified. We have used patch clamp recording to investigate the state-dependent accessibility of substituted cysteine residues in the CFTR channel pore to a range of cysteine-reactive reagents applied to the extracellular side of the membrane. Using functional modification of the channel current-voltage relationship as a marker of modification, we find that several positively charged reagents are able to penetrate deeply into the pore from the outside irrespective of whether or not the channels have been activated. In contrast, access of three anionic cysteine-reactive reagents, the methanesulfonate sodium (2-sulfonatoethyl)methanesulfonate, the organic mercurial p-chloromercuriphenylsulfonic acid, and the permeant anion Au(CN)(2)(-), to several different sites in the pore is strictly limited prior to channel activation. This suggests that in nonactivated channels some ion selectivity mechanism exists to exclude anions yet permit cations into the channel pore from the extracellular solution. We suggest that activation of CFTR channels involves a conformational change in the pore that removes a strong selectivity against anion entry from the extracellular solution. We propose further that this conformational change occurs in advance of channel opening, suggesting that multiple distinct closed pore conformations exist.

  14. Activation of cGAS-dependent antiviral responses by DNA intercalating agents

    PubMed Central

    Pépin, Geneviève; Nejad, Charlotte; Thomas, Belinda J.; Ferrand, Jonathan; McArthur, Kate; Bardin, Philip G.; Williams, Bryan R.G.; Gantier, Michael P.

    2017-01-01

    Acridine dyes, including proflavine and acriflavine, were commonly used as antiseptics before the advent of penicillins in the mid-1940s. While their mode of action on pathogens was originally attributed to their DNA intercalating activity, work in the early 1970s suggested involvement of the host immune responses, characterized by induction of interferon (IFN)-like activities through an unknown mechanism. We demonstrate here that sub-toxic concentrations of a mixture of acriflavine and proflavine instigate a cyclic-GMP-AMP (cGAMP) synthase (cGAS)-dependent type-I IFN antiviral response. This pertains to the capacity of these compounds to induce low level DNA damage and cytoplasmic DNA leakage, resulting in cGAS-dependent cGAMP-like activity. Critically, acriflavine:proflavine pre-treatment of human primary bronchial epithelial cells significantly reduced rhinovirus infection. Collectively, our findings constitute the first evidence that non-toxic DNA binding agents have the capacity to act as indirect agonists of cGAS, to exert potent antiviral effects in mammalian cells. PMID:27694309

  15. M. tuberculosis Sliding β-Clamp Does Not Interact Directly with the NAD+ -Dependent DNA Ligase

    PubMed Central

    Kukshal, Vandna; Khanam, Taran; Chopra, Deepti; Singh, Nidhi; Sanyal, Sabyasachi; Ramachandran, Ravishankar

    2012-01-01

    The sliding β-clamp, an important component of the DNA replication and repair machinery, is drawing increasing attention as a therapeutic target. We report the crystal structure of the M. tuberculosis β-clamp (Mtbβ-clamp) to 3.0 Å resolution. The protein crystallized in the space group C2221 with cell-dimensions a = 72.7, b = 234.9 & c = 125.1 Å respectively. Mtbβ-clamp is a dimer, and exhibits head-to-tail association similar to other bacterial clamps. Each monomer folds into three domains with similar structures respectively and associates with its dimeric partner through 6 salt-bridges and about 21 polar interactions. Affinity experiments involving a blunt DNA duplex, primed-DNA and nicked DNA respectively show that Mtbβ-clamp binds specifically to primed DNA about 1.8 times stronger compared to the other two substrates and with an apparent Kd of 300 nM. In bacteria like E. coli, the β-clamp is known to interact with subunits of the clamp loader, NAD+ -dependent DNA ligase (LigA) and other partners. We tested the interactions of the Mtbβ-clamp with MtbLigA and the γ-clamp loader subunit through radioactive gel shift assays, size exclusion chromatography, yeast-two hybrid experiments and also functionally. Intriguingly while Mtbβ-clamp interacts in vitro with the γ-clamp loader, it does not interact with MtbLigA unlike in bacteria like E. coli where it does. Modeling studies involving earlier peptide complexes reveal that the peptide-binding site is largely conserved despite lower sequence identity between bacterial clamps. Overall the results suggest that other as-yet-unidentified factors may mediate interactions between the clamp, LigA and DNA in mycobacteria. PMID:22545130

  16. CK2 phosphorylation-dependent interaction between aprataxin and MDC1 in the DNA damage response

    PubMed Central

    Becherel, Olivier J.; Jakob, Burkhard; Cherry, Amy L.; Gueven, Nuri; Fusser, Markus; Kijas, Amanda W.; Peng, Cheng; Katyal, Sachin; McKinnon, Peter J.; Chen, Junjie; Epe, Bernd; Smerdon, Stephen J.; Taucher-Scholz, Gisela; Lavin, Martin F.

    2010-01-01

    Aprataxin, defective in the neurodegenerative disorder ataxia oculomotor apraxia type 1, resolves abortive DNA ligation intermediates during DNA repair. Here, we demonstrate that aprataxin localizes at sites of DNA damage induced by high LET radiation and binds to mediator of DNA-damage checkpoint protein 1 (MDC1/NFBD1) through a phosphorylation-dependent interaction. This interaction is mediated via the aprataxin FHA domain and multiple casein kinase 2 di-phosphorylated S-D-T-D motifs in MDC1. X-ray structural and mutagenic analysis of aprataxin FHA domain, combined with modelling of the pSDpTD peptide interaction suggest an unusual FHA binding mechanism mediated by a cluster of basic residues at and around the canonical pT-docking site. Mutation of aprataxin FHA Arg29 prevented its interaction with MDC1 and recruitment to sites of DNA damage. These results indicate that aprataxin is involved not only in single strand break repair but also in the processing of a subset of double strand breaks presumably through its interaction with MDC1. PMID:20008512

  17. The temperature dependence of the electrical conductivity in Cu2O thin films grown by magnetron sputtering

    NASA Astrophysics Data System (ADS)

    Kudryashov, D.; Gudovskikh, A.; Zelentsov, K.; Mozharov, A.; Babichev, A.; Filimonov, A.

    2016-08-01

    The temperature dependence of the electrical conductivity in Cu2O thin films grown by magnetron sputtering at room temperature under different rf-power was investigated. Calculated activation energy of the conductivity for copper oxide (I) films linearly increases with increase in sputtering power reflecting an increasing in concentration of gap states.

  18. cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA.

    PubMed

    Petkevičiūtė, D; Pasi, M; Gonzalez, O; Maddocks, J H

    2014-11-10

    cgDNA is a package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any given length and sequence, cgDNA calculates the configuration of the associated free energy minimizer, i.e. the relative positions and orientations of each base, along with a stiffness matrix, which together govern differences in free energies. The model predicts non-local (i.e. beyond base-pair step) sequence dependence of the free energy minimizer. Configurations can be input or output in either the Curves+ definition of the usual helical DNA structural variables, or as a PDB file of coordinates of base atoms. We illustrate the cgDNA package by comparing predictions of free energy minimizers from (a) the cgDNA model, (b) time-averaged atomistic molecular dynamics (or MD) simulations, and (c) NMR or X-ray experimental observation, for (i) the Dickerson-Drew dodecamer and (ii) three oligomers containing A-tracts. The cgDNA predictions are rather close to those of the MD simulations, but many orders of magnitude faster to compute. Both the cgDNA and MD predictions are in reasonable agreement with the available experimental data. Our conclusion is that cgDNA can serve as a highly efficient tool for studying structural variations in B-form DNA over a wide range of sequences.

  19. Discovery of bacterial NAD⁺-dependent DNA ligase inhibitors: improvements in clearance of adenosine series.

    PubMed

    Stokes, Suzanne S; Gowravaram, Madhusudhan; Huynh, Hoan; Lu, Min; Mullen, George B; Chen, Brendan; Albert, Robert; O'Shea, Thomas J; Rooney, Michael T; Hu, Haiqing; Newman, Joseph V; Mills, Scott D

    2012-01-01

    Optimization of clearance of adenosine inhibitors of bacterial NAD(+)-dependent DNA ligase is discussed. To reduce Cytochrome P-450-mediated metabolic clearance, many strategies were explored; however, most modifications resulted in compounds with reduced antibacterial activity and/or unchanged total clearance. The alkyl side chains of the 2-cycloalkoxyadenosines were fluorinated, and compounds with moderate antibacterial activity and favorable pharmacokinetic properties in rat and dog were identified.

  20. Correlating Humidity-Dependent Ionically Conductive Surface Area with Transport Phenomena in Proton-Exchange Membranes

    SciTech Connect

    He, Qinggang; Kusoglu, Ahmet; Lucas, Ivan T.; Clark, Kyle; Weber, Adam Z.; Kostecki, Robert

    2011-08-01

    The objective of this effort was to correlate the local surface ionic conductance of a Nafion? 212 proton-exchange membrane with its bulk and interfacial transport properties as a function of water content. Both macroscopic and microscopic proton conductivities were investigated at different relative humidity levels, using electrochemical impedance spectroscopy and current-sensing atomic force microscopy (CSAFM). We were able to identify small ion-conducting domains that grew with humidity at the surface of the membrane. Numerical analysis of the surface ionic conductance images recorded at various relative humidity levels helped determine the fractional area of ion-conducting active sites. A simple square-root relationship between the fractional conducting area and observed interfacial mass-transport resistance was established. Furthermore, the relationship between the bulk ionic conductivity and surface ionic conductance pattern of the Nafion? membrane was examined.

  1. Sequence-dependent DNA curvature and flexibility from scanning force microscopy images.

    PubMed Central

    Scipioni, Anita; Anselmi, Claudio; Zuccheri, Giampaolo; Samori, Bruno; De Santis, Pasquale

    2002-01-01

    This paper reports a study of the sequence-dependent DNA curvature and flexibility based on scanning force microscopy (SFM) images. We used a palindromic dimer of a 1878-bp pBR322 fragment and collected a large pool of SFM images. The curvature of each imaged chain was measured in modulus and direction. It was found that the ensemble curvature modulus does not allow the separation of static and dynamic contributions to the curvature, whereas the curvature, when its direction in the two dimensions is taken into account, permits the direct separation of the intrinsic curvature contributions static and dynamic contributions. The palindromic symmetry also acted as an internal gauge of the validity of the SFM images statistical analysis. DNA static curvature resulted in good agreement with the predicted sequence-dependent intrinsic curvature. Furthermore, DNA sequence-dependent flexibility was found to correlate with the occurrence of A.T-rich dinucleotide steps along the chain and, in general, with the normalized basepair stacking energy distribution. PMID:12414677

  2. DNA unwinding by ASCC3 helicase is coupled to ALKBH3-dependent DNA alkylation repair and cancer cell proliferation.

    PubMed

    Dango, Sebastian; Mosammaparast, Nima; Sowa, Mathew E; Xiong, Li-Jun; Wu, Feizhen; Park, Keyjung; Rubin, Mark; Gygi, Steve; Harper, J Wade; Shi, Yang

    2011-11-04

    Demethylation by the AlkB dioxygenases represents an important mechanism for repair of N-alkylated nucleotides. However, little is known about their functions in mammalian cells. We report the purification of the ALKBH3 complex and demonstrate its association with the activating signal cointegrator complex (ASCC). ALKBH3 is overexpressed in various cancers, and both ALKBH3 and ASCC are important for alkylation damage resistance in these tumor cell lines. ASCC3, the largest subunit of ASCC, encodes a 3'-5' DNA helicase, whose activity is crucial for the generation of single-stranded DNA upon which ALKBH3 preferentially functions for dealkylation. In cell lines that are dependent on ALKBH3 and ASCC3 for alkylation damage resistance, loss of ALKBH3 or ASCC3 leads to increased 3-methylcytosine and reduced cell proliferation, which correlates with pH2A.X and 53BP1 foci formation. Our data provide a molecular mechanism by which ALKBH3 collaborates with ASCC to maintain genomic integrity in a cell-type specific manner.

  3. Rad18-dependent SUMOylation of human specialized DNA polymerase eta is required to prevent under-replicated DNA

    PubMed Central

    Despras, Emmanuelle; Sittewelle, Méghane; Pouvelle, Caroline; Delrieu, Noémie; Cordonnier, Agnès M; Kannouche, Patricia L

    2016-01-01

    Translesion polymerase eta (polη) was characterized for its ability to replicate ultraviolet-induced DNA lesions that stall replicative polymerases, a process promoted by Rad18-dependent PCNA mono-ubiquitination. Recent findings have shown that polη also acts at intrinsically difficult to replicate sequences. However, the molecular mechanisms that regulate its access to these loci remain elusive. Here, we uncover that polη travels with replication forks during unchallenged S phase and this requires its SUMOylation on K163. Abrogation of polη SUMOylation results in replication defects in response to mild replication stress, leading to chromosome fragments in mitosis and damage transmission to daughter cells. Rad18 plays a pivotal role, independently of its ubiquitin ligase activity, acting as a molecular bridge between polη and the PIAS1 SUMO ligase to promote polη SUMOylation. Our results provide the first evidence that SUMOylation represents a new way to target polη to replication forks, independent of the Rad18-mediated PCNA ubiquitination, thereby preventing under-replicated DNA. PMID:27811911

  4. Hippocampal adult neurogenesis is maintained by Neil3-dependent repair of oxidative DNA lesions in neural progenitor cells.

    PubMed

    Regnell, Christine Elisabeth; Hildrestrand, Gunn Annette; Sejersted, Yngve; Medin, Tirill; Moldestad, Olve; Rolseth, Veslemøy; Krokeide, Silje Zandstra; Suganthan, Rajikala; Luna, Luisa; Bjørås, Magnar; Bergersen, Linda H

    2012-09-27

    Accumulation of oxidative DNA damage has been proposed as a potential cause of age-related cognitive decline. The major pathway for removal of oxidative DNA base lesions is base excision repair, which is initiated by DNA glycosylases. In mice, Neil3 is the main DNA glycosylase for repair of hydantoin lesions in single-stranded DNA of neural stem/progenitor cells, promoting neurogenesis. Adult neurogenesis is crucial for maintenance of hippocampus-dependent functions involved in behavior. Herein, behavioral studies reveal learning and memory deficits and reduced anxiety-like behavior in Neil3(-/-) mice. Neural stem/progenitor cells from aged Neil3(-/-) mice show impaired proliferative capacity and reduced DNA repair activity. Furthermore, hippocampal neurons in Neil3(-/-) mice display synaptic irregularities. It appears that Neil3-dependent repair of oxidative DNA damage in neural stem/progenitor cells is required for maintenance of adult neurogenesis to counteract the age-associated deterioration of cognitive performance.

  5. Single molecule identification of homology-dependent interactions between long ssRNA and dsDNA

    PubMed Central

    Liu, Chenli; Danilowicz, Claudia; Kleckner, Nancy; Prentiss, Mara

    2017-01-01

    Long non-coding RNAs (lncRNAs) are prominently associated with chromosomes in an ever-increasing diversity of roles. To provide further insight into the potential nature of these associations, we have explored, for the first time, the interaction of long single-stranded (ss) RNAs with cognate homologous double-stranded (ds) DNA in vitro. Using magnetic tweezers, we measured the effects of ssRNA on force extension curves for dsDNA. We observe that the presence of ssRNA impedes the extension of dsDNA, specifically at low forces, dependent on homology between the RNA and DNA species, and dependent on ssRNA lengths (≥1 kb). The observed effect also depends on the concentration of ssRNA and is abolished by overstretching of the dsDNA. These findings show that significant homologous contacts can occur between long ssRNA and dsDNA in the absence of protein and that these contacts alter the mechanical properties of the dsDNA. We propose that long ssRNA interacts paranemically with long dsDNA via periodic short homologous interactions, e.g. mediated by RNA/DNA triplex-formation, and that dsDNA extension is impeded by formation of RNA secondary structure in the intervening unbound regions. Analogous interactions in vivo would permit lncRNAs to mediate the juxtaposition of two or more DNA regions on the same or different chromosomes. PMID:27580717

  6. DNA sequence-dependent ionic currents in ultra-small solid-state nanopores

    NASA Astrophysics Data System (ADS)

    Comer, Jeffrey; Aksimentiev, Aleksei

    2016-05-01

    Measurements of ionic currents through nanopores partially blocked by DNA have emerged as a powerful method for characterization of the DNA nucleotide sequence. Although the effect of the nucleotide sequence on the nanopore blockade current has been experimentally demonstrated, prediction and interpretation of such measurements remain a formidable challenge. Using atomic resolution computational approaches, here we show how the sequence, molecular conformation, and pore geometry affect the blockade ionic current in model solid-state nanopores. We demonstrate that the blockade current from a DNA molecule is determined by the chemical identities and conformations of at least three consecutive nucleotides. We find the blockade currents produced by the nucleotide triplets to vary considerably with their nucleotide sequences despite having nearly identical molecular conformations. Encouragingly, we find blockade current differences as large as 25% for single-base substitutions in ultra small (1.6 nm × 1.1 nm cross section; 2 nm length) solid-state nanopores. Despite the complex dependence of the blockade current on the sequence and conformation of the DNA triplets, we find that, under many conditions, the number of thymine bases is positively correlated with the current, whereas the number of purine bases and the presence of both purines and pyrimidines in the triplet are negatively correlated with the current. Based on these observations, we construct a simple theoretical model that relates the ion current to the base content of a solid-state nanopore. Furthermore, we show that compact conformations of DNA in narrow pores provide the greatest signal-to-noise ratio for single base detection, whereas reduction of the nanopore length increases the ionic current noise. Thus, the sequence dependence of the nanopore blockade current can be theoretically rationalized, although the predictions will likely need to be customized for each nanopore type.Measurements of ionic

  7. Extracellular sodium dependence of the conduction velocity-calcium relationship: evidence of ephaptic self-attenuation.

    PubMed

    George, Sharon A; Bonakdar, Mohammad; Zeitz, Michael; Davalos, Rafael V; Smyth, James W; Poelzing, Steven

    2016-05-01

    Our laboratory previously demonstrated that perfusate sodium and potassium concentrations can modulate cardiac conduction velocity (CV) consistent with theoretical predictions of ephaptic coupling (EpC). EpC depends on the ionic currents and intercellular separation in sodium channel rich intercalated disk microdomains like the perinexus. We suggested that perinexal width (WP) correlates with changes in extracellular calcium ([Ca(2+)]o). Here, we test the hypothesis that increasing [Ca(2+)]o reduces WP and increases CV. Mathematical models of EpC also predict that reducing WP can reduce sodium driving force and CV by self-attenuation. Therefore, we further hypothesized that reducing WP and extracellular sodium ([Na(+)]o) will reduce CV consistent with ephaptic self-attenuation. Transmission electron microscopy revealed that increasing [Ca(2+)]o (1 to 3.4 mM) significantly decreased WP Optically mapping wild-type (WT) (100% Cx43) mouse hearts demonstrated that increasing [Ca(2+)]o increases transverse CV during normonatremia (147.3 mM), but slows transverse CV during hyponatremia (120 mM). Additionally, CV in heterozygous (∼50% Cx43) hearts was more sensitive to changes in [Ca(2+)]o relative to WT during normonatremia. During hyponatremia, CV slowed in both WT and heterozygous hearts to the same extent. Importantly, neither [Ca(2+)]o nor [Na(+)]o altered Cx43 expression or phosphorylation determined by Western blotting, or gap junctional resistance determined by electrical impedance spectroscopy. Narrowing WP, by increasing [Ca(2+)]o, increases CV consistent with enhanced EpC between myocytes. Interestingly, during hyponatremia, reducing WP slowed CV, consistent with theoretical predictions of ephaptic self-attenuation. This study suggests that serum ion concentrations may be an important determinant of cardiac disease expression.

  8. A nucleotide-dependent and HRDC domain-dependent structural transition in DNA-bound RecQ helicase.

    PubMed

    Kocsis, Zsuzsa S; Sarlós, Kata; Harami, Gábor M; Martina, Máté; Kovács, Mihály

    2014-02-28

    The allosteric communication between the ATP- and DNA-binding sites of RecQ helicases enables efficient coupling of ATP hydrolysis to translocation along single-stranded DNA (ssDNA) and, in turn, the restructuring of multistranded DNA substrates during genome maintenance processes. In this study, we used the tryptophan fluorescence signal of Escherichia coli RecQ helicase to decipher the kinetic mechanism of the interaction of the enzyme with ssDNA. Rapid kinetic experiments revealed that ssDNA binding occurs in a two-step mechanism in which the initial binding step is followed by a structural transition of the DNA-bound helicase. We found that the nucleotide state of RecQ greatly influences the kinetics of the detected structural transition, which leads to a high affinity DNA-clamped state in the presence of the nucleotide analog ADP-AlF4. The DNA binding mechanism is largely independent of ssDNA length, indicating the independent binding of RecQ molecules to ssDNA and the lack of significant DNA end effects. The structural transition of DNA-bound RecQ was not detected when the ssDNA binding capability of the helicase-RNase D C-terminal domain was abolished or the domain was deleted. The results shed light on the nature of conformational changes leading to processive ssDNA translocation and multistranded DNA processing by RecQ helicases.

  9. Temperature and frequency dependence of AC conductivity of new quaternary Se-Te-Bi-Pb chalcogenide glasses

    NASA Astrophysics Data System (ADS)

    Yadav, Preeti; Sharma, Ambika

    2016-05-01

    The aim of the present work is to study the temperature and frequency dependence of ac conductivity of new quaternary Se84-xTe15Bi1.0Pbx chalcogenide glasses. The Se84-xTe15Bi1.0Pbx (x = 2, 6) glassy alloys are prepared by using melt quenching technique. The temperature and frequency dependent behavior of ac conductivity σac(ω) has been carried out in the frequency range 42 Hz to 5 MHz and in the temperature range of 298-323 K below glass transition temperature. The behavior of ac conductivity is described in terms of the power law ωs. The obtained temperature dependence behavior of ac conductivity and frequency component (s) are explained by means of correlated barrier hopping model recommended by Elliot.

  10. Effects of temperature dependence of electrical and thermal conductivities on the Joule heating of a one dimensional conductor

    NASA Astrophysics Data System (ADS)

    Antoulinakis, F.; Chernin, D.; Zhang, Peng; Lau, Y. Y.

    2016-10-01

    We examine the effects of temperature dependence of the electrical and thermal conductivities on Joule heating of a one-dimensional conductor by solving the coupled non-linear steady state electrical and thermal conduction equations. The spatial temperature distribution and the maximum temperature and its location within the conductor are evaluated for four cases: (i) constant electrical conductivity and linear temperature dependence of thermal conductivity, (ii) linear temperature dependence of both electrical and thermal conductivities, (iii) the Wiedemann-Franz relation for metals, and (iv) polynomial fits to measured data for carbon nanotube fibers and for copper. For (i) and (ii), it is found that there are conditions under which no steady state solution exists, which may indicate the possibility of thermal runaway. For (i), analytical solutions are constructed, from which explicit expressions for the parameter bounds for the existence of steady state solutions are obtained. The shifting of these bounds due to the introduction of linear temperature dependence of electrical conductivity (case (ii)) is studied numerically. These results may provide guidance in the design of circuits and devices in which the effects of coupled thermal and electrical conduction are important.

  11. ATM mediates repression of DNA end-degradation in an ATP-dependent manner.

    PubMed

    Rahal, Elias A; Henricksen, Leigh A; Li, Yuling; Turchi, John J; Pawelczak, Katherine S; Dixon, Kathleen

    2008-03-01

    Ataxia telangiectasia mutated (ATM) is a PI3-kinase-like kinase (PIKK) associated with DNA double-strand break (DSB) repair and cell cycle control. We have previously reported comparable efficiencies of DSB repair in nuclear extracts from both ATM deficient (A-T) and control (ATM+) cells; however, the repair products from the A-T nuclear extracts contained deletions encompassing longer stretches of DNA compared to controls. These deletions appeared to result from end-joining at sites of microhomology. These data suggest that ATM hinders error-prone repair pathways that depend on degradation of DNA ends at a break. Such degradation may account for the longer deletions we formerly observed in A-T cell extracts. To address this possibility we assessed the degradation of DNA duplex substrates in A-T and control nuclear extracts under DSB repair conditions. We observed a marked shift in signal intensity from full-length products to shorter products in A-T nuclear extracts, and addition of purified ATM to A-T nuclear extracts restored full-length product detection. This repression of degradation by ATM was both ATP-dependent and inhibited by the PIKK inhibitors wortmannin and caffeine. Addition of pre-phosphorylated ATM to an A-T nuclear extract in the presence of PIKK inhibitors was insufficient in repressing degradation, indicating that kinase activities are required. These results demonstrate a role for ATM in preventing the degradation of DNA ends possibly through repressing nucleases implicated in microhomology-mediated end-joining.

  12. DNA sequence-dependent ionic currents in ultra-small solid-state nanopores.

    PubMed

    Comer, Jeffrey; Aksimentiev, Aleksei

    2016-05-05

    Measurements of ionic currents through nanopores partially blocked by DNA have emerged as a powerful method for characterization of the DNA nucleotide sequence. Although the effect of the nucleotide sequence on the nanopore blockade current has been experimentally demonstrated, prediction and interpretation of such measurements remain a formidable challenge. Using atomic resolution computational approaches, here we show how the sequence, molecular conformation, and pore geometry affect the blockade ionic current in model solid-state nanopores. We demonstrate that the blockade current from a DNA molecule is determined by the chemical identities and conformations of at least three consecutive nucleotides. We find the blockade currents produced by the nucleotide triplets to vary considerably with their nucleotide sequences despite having nearly identical molecular conformations. Encouragingly, we find blockade current differences as large as 25% for single-base substitutions in ultra small (1.6 nm × 1.1 nm cross section; 2 nm length) solid-state nanopores. Despite the complex dependence of the blockade current on the sequence and conformation of the DNA triplets, we find that, under many conditions, the number of thymine bases is positively correlated with the current, whereas the number of purine bases and the presence of both purines and pyrimidines in the triplet are negatively correlated with the current. Based on these observations, we construct a simple theoretical model that relates the ion current to the base content of a solid-state nanopore. Furthermore, we show that compact conformations of DNA in narrow pores provide the greatest signal-to-noise ratio for single base detection, whereas reduction of the nanopore length increases the ionic current noise. Thus, the sequence dependence of the nanopore blockade current can be theoretically rationalized, although the predictions will likely need to be customized for each nanopore type.

  13. Long dwell-time passage of DNA through nanometer-scale pores: kinetics and sequence dependence of motion.

    PubMed

    Jetha, Nahid N; Feehan, Christopher; Wiggin, Matthew; Tabard-Cossa, Vincent; Marziali, Andre

    2011-06-22

    A detailed understanding of the kinetics of DNA motion though nanometer-scale pores is important for the successful development of many of the proposed next-generation rapid DNA sequencing and analysis methods. Many of these approaches require DNA motion through nanopores to be slowed by several orders of magnitude from its native translocation velocity so that the translocation times for individual nucleotides fall within practical timescales for detection. With the increased dwell time of DNA in the pore, DNA-pore interactions begin to play an increasingly important role in translocation kinetics. In previous work, we and others observed that when the DNA dwell time in the pore is substantial (>1 ms), DNA motion in α-hemolysin (α-HL) pores leads to nonexponential kinetics in the escape of DNA out of the pore. Here we show that a three-state model for DNA escape, involving stochastic binding interactions of DNA with the pore, accurately reproduces the experimental data. In addition, we investigate the sequence dependence of the DNA escape process and show that the interaction strength of adenine with α-HL is substantially lower relative to cytosine. Our results indicate a difference in the process by which DNA moves through an α-HL nanopore when the motion is fast (microsecond timescale) as compared with when it is slow (millisecond timescale) and strongly influenced by DNA-pore interactions of the kind reported here. We also show the ability of wild-type α-HL to detect and distinguish between 5-methylcytosine and cytosine based on differences in the absolute ionic current through the pore in the presence of these two nucleotides. The results we present here regarding sequence-dependent (and dwell-time-dependent) DNA-pore interaction kinetics will have important implications for the design of methods for DNA analysis through reduced-velocity motion in nanopores.

  14. Sequence-dependent structural changes in a self-assembling DNA oligonucleotide.

    PubMed

    Saoji, Maithili; Paukstelis, Paul J

    2015-12-01

    DNA has proved to be a remarkable molecule for the construction of sophisticated two-dimensional and three-dimensional architectures because of its programmability and structural predictability provided by complementary Watson-Crick base pairing. DNA oligonucleotides can, however, exhibit a great deal of local structural diversity. DNA conformation is strongly linked to both environmental conditions and the nucleobase identities inherent in the oligonucleotide sequence, but the exact relationship between sequence and local structure is not completely understood. This study examines how a single-nucleotide addition to a class of self-assembling DNA 13-mers leads to a significantly different overall structure under identical crystallization conditions. The DNA 13-mers self-assemble in the presence of Mg(2+) through a combination of Watson-Crick and noncanonical base-pairing interactions. The crystal structures described here show that all of the predicted Watson-Crick base pairs are present, with the major difference being a significant rearrangement of noncanonical base pairs. This includes the formation of a sheared A-G base pair, a junction of strands formed from base-triple interactions, and tertiary interactions that generate structural features similar to tandem sheared G-A base pairs. The adoption of this alternate noncanonical structure is dependent in part on the sequence in the Watson-Crick duplex region. These results provide important new insights into the sequence-structure relationship of short DNA oligonucleotides and demonstrate a unique interplay between Watson-Crick and noncanonical base pairs that is responsible for crystallization fate.

  15. DNA Based Micelles: Synthesis, Micellar Properties and Size-dependent Cell Permeability

    PubMed Central

    Liu, Haipeng; Zhu, Zhi; Kang, Huaizhi; Wu, Yanrong; Sefan, Kwame

    2012-01-01

    Functional nanomaterials based on molecular self-assembly hold great promise for applications in biomedicine and biotechnology. However, their efficacy could be a problem and can be improved by precisely controlling the size, structure and functions. This would require a molecular engineering design capable of producing monodispersed functional materials characterized by beneficial changes in size, shape and chemical structure. To address this challenge, we have designed and constructed a series of amphiphilic oligonucleotide molecules. In aqueous solutions, the amphiphilic oligonucleotide molecules, consisting of a hydrophilic oligonucleotide covalently linked to hydrophobic diacyllipid tails, spontaneously self-assemble into monodispersed, three dimensional micellar nanostructures with a lipid core and a DNA corona. These hierarchical architectures are results of intermolecular hydrophobic interactions. Experimental testing further showed that these types of micelles have excellent thermal stability and their size can be fine tuned by changing the length of the DNA sequence. Moreover, in the micelle system, the molecular recognition properties of DNA are intact, thus, our DNA micelles can hybridize with complimentary sequences while remain their structural integrity. Importantly, when interacting with cell membranes, the highly charged DNA micelles are able to disintegrate themselves and insert into cell membrane, completing the process of internalization by endocytosis. Interestingly, the fluorescence was found accumulated in confined regions of cytosole. Finally, we show that the kinetics of this internalization process is size-dependent. Therefore, cell permeability, combined with small sizes and natural nontoxicity, are all excellent features that make our DNA-micelles highly suitable for a variety of applications in nanobiotechnology, cell biology, and drug delivery systems. PMID:20162643

  16. Quantitative analysis of the ion-dependent folding stability of DNA triplexes

    NASA Astrophysics Data System (ADS)

    Chen, Gengsheng; Chen, Shi-Jie

    2011-12-01

    A DNA triplex is formed through binding of a third strand to the major groove of a duplex. Due to the high charge density of a DNA triplex, metal ions are critical for its stability. We recently developed the tightly bound ion (TBI) model for ion-nucleic acids interactions. The model accounts for the potential correlation and fluctuations of the ion distribution. We now apply the TBI model to analyze the ion dependence of the thermodynamic stability for DNA triplexes. We focus on two experimentally studied systems: a 24-base DNA triplex and a pair of interacting 14-base triplexes. Our theoretical calculations for the number of bound ions indicate that the TBI model provides improved predictions for the number of bound ions than the classical Poisson-Boltzmann (PB) equation. The improvement is more significant for a triplex, which has a higher charge density than a duplex. This is possibly due to the higher ion concentration around the triplex and hence a stronger ion correlation effect for a triplex. In addition, our analysis for the free energy landscape for a pair of 14-mer triplexes immersed in an ionic solution shows that divalent ions could induce an attractive force between the triplexes. Furthermore, we investigate how the protonated cytosines in the triplexes affect the stability of the triplex helices.

  17. Cell cycle-dependent resolution of DNA double-strand breaks

    PubMed Central

    Ambrosio, Susanna; Di Palo, Giacomo; Napolitano, Giuliana; Amente, Stefano; Dellino, Gaetano Ivan; Faretta, Mario; Pelicci, Pier Giuseppe; Lania, Luigi; Majello, Barbara

    2016-01-01

    DNA double strand breaks (DSBs) elicit prompt activation of DNA damage response (DDR), which arrests cell-cycle either in G1/S or G2/M in order to avoid entering S and M phase with damaged DNAs. Since mammalian tissues contain both proliferating and quiescent cells, there might be fundamental difference in DDR between proliferating and quiescent cells (or G0-arrested). To investigate these differences, we studied recruitment of DSB repair factors and resolution of DNA lesions induced at site-specific DSBs in asynchronously proliferating, G0-, or G1-arrested cells. Strikingly, DSBs occurring in G0 quiescent cells are not repaired and maintain a sustained activation of the p53-pathway. Conversely, re-entry into cell cycle of damaged G0-arrested cells, occurs with a delayed clearance of DNA repair factors initially recruited to DSBs, indicating an inefficient repair when compared to DSBs induced in asynchronously proliferating or G1-synchronized cells. Moreover, we found that initial recognition of DSBs and assembly of DSB factors is largely similar in asynchronously proliferating, G0-, or G1-synchronized cells. Our study thereby demonstrates that repair and resolution of DSBs is strongly dependent on the cell-cycle state. PMID:26700820

  18. Distance dependence of single-fluorophore quenching by gold nanoparticles studied on DNA origami.

    PubMed

    Acuna, Guillermo P; Bucher, Martina; Stein, Ingo H; Steinhauer, Christian; Kuzyk, Anton; Holzmeister, Phil; Schreiber, Robert; Moroz, Alexander; Stefani, Fernando D; Liedl, Tim; Simmel, Friedrich C; Tinnefeld, Philip

    2012-04-24

    We study the distance-dependent quenching of fluorescence due to a metallic nanoparticle in proximity of a fluorophore. In our single-molecule measurements, we achieve excellent control over structure and stoichiometry by using self-assembled DNA structures (DNA origami) as a breadboard where both the fluorophore and the 10 nm metallic nanoparticle are positioned with nanometer precision. The single-molecule spectroscopy method employed here reports on the co-localization of particle and dye, while fluorescence lifetime imaging is used to directly obtain the correlation of intensity and fluorescence lifetime for varying particle to dye distances. Our data can be well explained by exact calculations that include dipole-dipole orientation and distances. Fitting with a more practical model for nanosurface energy transfer yields 10.4 nm as the characteristic distance of 50% energy transfer. The use of DNA nanotechnology together with minimal sample usage by attaching the particles to the DNA origami directly on the microscope coverslip paves the way for more complex experiments exploiting dye-nanoparticle interactions.

  19. Quantitative analysis of the ion-dependent folding stability of DNA triplexes.

    PubMed

    Chen, Gengsheng; Chen, Shi-Jie

    2011-12-01

    A DNA triplex is formed through binding of a third strand to the major groove of a duplex. Due to the high charge density of a DNA triplex, metal ions are critical for its stability. We recently developed the tightly bound ion (TBI) model for ion-nucleic acids interactions. The model accounts for the potential correlation and fluctuations of the ion distribution. We now apply the TBI model to analyze the ion dependence of the thermodynamic stability for DNA triplexes. We focus on two experimentally studied systems: a 24-base DNA triplex and a pair of interacting 14-base triplexes. Our theoretical calculations for the number of bound ions indicate that the TBI model provides improved predictions for the number of bound ions than the classical Poisson-Boltzmann (PB) equation. The improvement is more significant for a triplex, which has a higher charge density than a duplex. This is possibly due to the higher ion concentration around the triplex and hence a stronger ion correlation effect for a triplex. In addition, our analysis for the free energy landscape for a pair of 14-mer triplexes immersed in an ionic solution shows that divalent ions could induce an attractive force between the triplexes. Furthermore, we investigate how the protonated cytosines in the triplexes affect the stability of the triplex helices.

  20. Time-dependent behavior of magnetic fields confined by conducting walls

    SciTech Connect

    Kidder, R.E.; Cecil, A.B.

    1983-03-09

    An equation is derived which describes the total current flowing in a moving conducting surface surrounding a magnetic field, where diffusion of the field into the conductor is taken into account. Analytic and numerical solutions of the current equation are obtained for the cases of exponential and linear compression of the magnetic field with time, respectively. It is assumed that the electrical conductivity is constant, that the conducting surfaces are axially symmetric, and that the thickness and radius of curvature of the conducting walls is large compared with the effective depth of penetration of the field.

  1. Template Supercoiling during ATP-Dependent DNA Helix Tracking: Studies with Simian Virus 40 Large Tumor Antigen

    NASA Astrophysics Data System (ADS)

    Yang, Liu; Jessee, C. Bret; Lau, Kawai; Zhang, Hui; Liu, Leroy F.

    1989-08-01

    Incubation of topologically relaxed plasmid DNA with simian virus 40 (SV40) large tumor antigen (T antigen), ATP, and eubacterial DNA topoisomerase I resulted in the formation of highly positively supercoiled DNA. Eukaryotic DNA topoisomerase I could not substitute for eubacterial DNA topoisomerase I in this reaction. Furthermore, the addition of eukaryotic topoisomerase I to a preincubated reaction mixture containing both T antigen and eubacterial topoisomerase I caused rapid relaxation of the positively supercoiled DNA. These results suggest that SV40 T antigen can introduce topoisomerase-relaxable supercoils into DNA in a reaction coupled to ATP hydrolysis. We interpret the observed T antigen supercoiling reaction in terms of a recently proposed twin-supercoiled-domain model that describes the mechanics of DNA helix-tracking processes. According to this model, positive and negative supercoils are generated ahead of and behind the moving SV40 T antigen, respectively. The preferential relaxation of negative supercoils by eubacterial DNA topoisomerase I explains the accumulation of positive supercoils in the DNA template. The supercoiling assay using DNA conformation-specific eubacterial DNA topoisomerase I may be of general use for the detection of ATP-dependent DNA helix-tracking proteins.

  2. Use-dependent effects of lidocaine on conduction in canine myocardium: application of the modulated receptor hypothesis in vivo.

    PubMed

    Davis, J; Matsubara, T; Scheinman, M M; Katzung, B; Hondeghem, L H

    1986-07-01

    Lidocaine is a commonly used antiarrhythmic drug that causes use-dependent blockade of sodium channels in vitro and reduces conduction velocity in vitro and in vivo. According to the modulated receptor hypothesis of antiarrhythmic drug action, lidocaine has a low affinity for rested sodium channels but a high affinity for open and inactivated channels. In the present experiments, we characterized use-dependent conduction slowing and recovery from slowing by lidocaine in anesthetized dogs. The His-to-ventricular conduction interval was used as the indicator of conduction velocity. We found that prolongation of conduction time was greater as the stimulation frequency was increased. Moreover, on abruptly changing the stimulation frequency, a new steady-state conduction time was approached in two to three depolarizations. On discontinuation of stimulation, the conduction time of progressively less premature extrastimuli shortened exponentially with a terminal phase time constant of 152 +/- 115 msec. These effects by lidocaine were enhanced during acidosis and enhancement was reversed by correction of the acidosis. It is concluded that the effects in vivo of lidocaine on conduction under several conditions of rate, rhythm, and pH are similar to its effects on the maximum upstroke velocity of the action potential in vitro. Although these experiments were not designed to validate the modulated receptor hypothesis, it appears that the modulated receptor hypothesis can predict the effects of lidocaine on conduction in vivo.

  3. Gli1/DNA interaction is a druggable target for Hedgehog-dependent tumors

    PubMed Central

    Infante, Paola; Mori, Mattia; Alfonsi, Romina; Ghirga, Francesca; Aiello, Federica; Toscano, Sara; Ingallina, Cinzia; Siler, Mariangela; Cucchi, Danilo; Po, Agnese; Miele, Evelina; D'Amico, Davide; Canettieri, Gianluca; De Smaele, Enrico; Ferretti, Elisabetta; Screpanti, Isabella; Uccello Barretta, Gloria; Botta, Maurizio; Botta, Bruno; Gulino, Alberto; Di Marcotullio, Lucia

    2015-01-01

    Hedgehog signaling is essential for tissue development and stemness, and its deregulation has been observed in many tumors. Aberrant activation of Hedgehog signaling is the result of genetic mutations of pathway components or other Smo-dependent or independent mechanisms, all triggering the downstream effector Gli1. For this reason, understanding the poorly elucidated mechanism of Gli1-mediated transcription allows to identify novel molecules blocking the pathway at a downstream level, representing a critical goal in tumor biology. Here, we clarify the structural requirements of the pathway effector Gli1 for binding to DNA and identify Glabrescione B as the first small molecule binding to Gli1 zinc finger and impairing Gli1 activity by interfering with its interaction with DNA. Remarkably, as a consequence of its robust inhibitory effect on Gli1 activity, Glabrescione B inhibited the growth of Hedgehog-dependent tumor cells in vitro and in vivo as well as the self-renewal ability and clonogenicity of tumor-derived stem cells. The identification of the structural requirements of Gli1/DNA interaction highlights their relevance for pharmacologic interference of Gli signaling. PMID:25476449

  4. Gel mobilities of linking-number topoisomers and their dependence on DNA helical repeat and elasticity

    PubMed Central

    Vetcher, Alexandre A.; McEwen, Abbye E.; Abujarour, Ramzey; Hanke, Andreas; Levene, Stephen D.

    2010-01-01

    Agarose-gel electrophoresis has been used for more than thirty years to characterize the linking-number (Lk) distribution of closed-circular DNA molecules. Although the physical basis of this technique remains poorly understood, the gel-electrophoretic behavior of covalently closed DNAs has been used to determine the local unwinding of DNA by proteins and small-molecule ligands, characterize supercoiling-dependent conformational transitions in duplex DNA, and to measure helical-repeat changes due to shifts in temperature and ionic strength. Those results have been analyzed by assuming that the absolute mobility of a particular topoisomer is mainly a function of the integral number of superhelical turns, and thus a slowly varying function of plasmid molecular weight. In examining the mobilities of Lk topoisomers for a series of plasmids that differ incrementally in size over more than one helical turn, we found that the size-dependent agarose-gel mobility of individual topoisomers with identical values of Lk (but different values of the excess linking number, ΔLk) vary dramatically over a duplex turn. Our results suggest that a simple semi-empirical relationship holds between the electrophoretic mobility of linking-number topoisomers and their average writhe in solution. PMID:20346570

  5. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites.

    PubMed

    Ma, Yufeng; Chiu, Pui Lam; Serrano, Arnaldo; Ali, Shah R; Chen, Alex M; He, Huixin

    2008-06-25

    We have found that the polymerization process was 4,500 times faster when a self-doped polyaniline nanocomposite was fabricated using in situ polymerization in the presence of single-stranded DNA-dispersed and -functionalized single-walled carbon nanotubes (ssDNA-SWNTs). More importantly, the quality of the composite was significantly improved: fewer short oligomers were produced, and the self-doped polyaniline backbone had a longer conjugation length and existed in the more stable and conductive emeraldine state. The functionality of the boronic acid group in the composite and the highly improved electronic performance may lead to broad applications of the composite in flexible electronic devices. Blending of preformed polymer with carbon nanotubes is straightforward and widely used to fabricate nanocomposites. We demonstrate that this simple mixing approach might not fully and synergistically combine the merits of each individual component. Surprisingly, these advantages also cannot be obtained using in situ polymerization with preoxidized ssDNA-SWNTs, which is renowned as the "seed" method for production of conducting-polymer nanowires. The electronic structures of the carbon nanotubes and the monomer-nanotube interaction during polymerization greatly impact the kinetics of nanocomposite fabrication and the electronic performance of the resulting composites.

  6. Coordinateendonucleolytic 5' and 3' trimming of terminally blocked blunt DNA double-strand break ends by Artemis nuclease and DNA-dependent protein kinase

    SciTech Connect

    Povirk, Lawrence; Yannone, Steven M.; Khan, Imran S.; Zhou, Rui-Zhe; Zhou, Tong; Valerie, Kristoffer; F., Lawrence

    2008-02-18

    Previous work showed that, in the presence of DNA-PK, Artemis slowly trims 3'-phosphoglycolate-terminated blunt ends. To examine the trimming reaction in more detail, long internally labeled DNA substrates were treated with Artemis. In the absence of DNA-PK, Artemis catalyzed extensive 5' {yields} 3' exonucleolytic resection of double-stranded DNA. This resection required a 5'-phosphate but did not require ATP, and was accompanied by endonucleolytic cleavage of the resulting 3' overhang. In the presence of DNA-PK, Artemis-mediated trimming was more limited, was ATP-dependent, and did not require a 5'-phosphate. For a blunt end with either a 3'-phosphoglycolate or 3'-hydroxyl terminus, endonucleolytic trimming of 2-4 nucleotides from the 3'-terminal strand was accompanied by trimming of 6 nucleotides from the 5'-terminal strand. The results suggest that autophosphorylated DNA-PK suppresses the exonuclease activity of Artemis toward blunt-ended DNA, and promotes slow and limited endonucleolytic trimming of the 5'-terminal strand, resulting in short 3' overhangs that are trimmed endonucleolytically. Thus, Artemis and DNA-PK can convert terminally blocked DNA ends of diverse geometry and chemical structure to a form suitable for polymerase mediated patching and ligation, with minimal loss of terminal sequence. Such processing could account for the very small deletions often found at DNA double-strand break repair sites.

  7. Lyn tyrosine kinase promotes silencing of ATM-dependent checkpoint signaling during recovery from DNA double-strand breaks

    SciTech Connect

    Fukumoto, Yasunori Kuki, Kazumasa; Morii, Mariko; Miura, Takahito; Honda, Takuya; Ishibashi, Kenichi; Hasegawa, Hitomi; Kubota, Sho; Ide, Yudai; Yamaguchi, Noritaka; Nakayama, Yuji; Yamaguchi, Naoto

    2014-09-26

    Highlights: • Inhibition of Src family kinases decreased γ-H2AX signal. • Inhibition of Src family increased ATM-dependent phosphorylation of Chk2 and Kap1. • shRNA-mediated knockdown of Lyn increased phosphorylation of Kap1 by ATM. • Ectopic expression of Src family kinase suppressed ATM-mediated Kap1 phosphorylation. • Src is involved in upstream signaling for inactivation of ATM signaling. - Abstract: DNA damage activates the DNA damage checkpoint and the DNA repair machinery. After initial activation of DNA damage responses, cells recover to their original states through completion of DNA repair and termination of checkpoint signaling. Currently, little is known about the process by which cells recover from the DNA damage checkpoint, a process called checkpoint recovery. Here, we show that Src family kinases promote inactivation of ataxia telangiectasia mutated (ATM)-dependent checkpoint signaling during recovery from DNA double-strand breaks. Inhibition of Src activity increased ATM-dependent phosphorylation of Chk2 and Kap1. Src inhibition increased ATM signaling both in G2 phase and during asynchronous growth. shRNA knockdown of Lyn increased ATM signaling. Src-dependent nuclear tyrosine phosphorylation suppressed ATM-mediated Kap1 phosphorylation. These results suggest that Src family kinases are involved in upstream signaling that leads to inactivation of the ATM-dependent DNA damage checkpoint.

  8. Sensing the water content of honey from temperature-dependent electrical conductivity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In order to predict water content in honey, electrical conductivity was measured on blossom honey types of milk-vetch, jujube and yellow-locust with water content of 18%-37% between 5-40ºC. Regression models of electrical conductivity were developed as functions of water content and temperature. The...

  9. Coarse-grained model of conformation-dependent electrophoretic mobility and its influence on DNA dynamics

    NASA Astrophysics Data System (ADS)

    Pandey, Harsh; Underhill, Patrick T.

    2015-11-01

    The electrophoretic mobility of molecules such as λ -DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model. Brownian dynamics simulations have been performed using this model. The model reproduces the cross-stream migration that occurs in capillary electrophoresis when pressure-driven flow is applied parallel or antiparallel to the electric field. The model also reproduces the change of mobility when the molecule is stretched significantly in an extensional field. We find that the conformation-dependent mobility can lead to a new type of unraveling of the molecule in strong fields. This occurs when different parts of the molecule have different mobilities and the electric field is large.

  10. Signalling of DNA damage and cytokines across cell barriers exposed to nanoparticles depends on barrier thickness

    NASA Astrophysics Data System (ADS)

    Sood, A.; Salih, S.; Roh, D.; Lacharme-Lora, L.; Parry, M.; Hardiman, B.; Keehan, R.; Grummer, R.; Winterhager, E.; Gokhale, P. J.; Andrews, P. W.; Abbott, C.; Forbes, K.; Westwood, M.; Aplin, J. D.; Ingham, E.; Papageorgiou, I.; Berry, M.; Liu, J.; Dick, A. D.; Garland, R. J.; Williams, N.; Singh, R.; Simon, A. K.; Lewis, M.; Ham, J.; Roger, L.; Baird, D. M.; Crompton, L. A.; Caldwell, M. A.; Swalwell, H.; Birch-Machin, M.; Lopez-Castejon, G.; Randall, A.; Lin, H.; Suleiman, M.-S.; Evans, W. H.; Newson, R.; Case, C. P.

    2011-12-01

    The use of nanoparticles in medicine is ever increasing, and it is important to understand their targeted and non-targeted effects. We have previously shown that nanoparticles can cause DNA damage to cells cultured below a cellular barrier without crossing this barrier. Here, we show that this indirect DNA damage depends on the thickness of the cellular barrier, and it is mediated by signalling through gap junction proteins following the generation of mitochondrial free radicals. Indirect damage was seen across both trophoblast and corneal barriers. Signalling, including cytokine release, occurred only across bilayer and multilayer barriers, but not across monolayer barriers. Indirect toxicity was also observed in mice and using ex vivo explants of the human placenta. If the importance of barrier thickness in signalling is a general feature for all types of barriers, our results may offer a principle with which to limit the adverse effects of nanoparticle exposure and offer new therapeutic approaches.

  11. The poly(ADP-ribose)-dependent chromatin remodeler Alc1 induces local chromatin relaxation upon DNA damage

    PubMed Central

    Sellou, Hafida; Lebeaupin, Théo; Chapuis, Catherine; Smith, Rebecca; Hegele, Anna; Singh, Hari R.; Kozlowski, Marek; Bultmann, Sebastian; Ladurner, Andreas G.; Timinszky, Gyula; Huet, Sébastien

    2016-01-01

    Chromatin relaxation is one of the earliest cellular responses to DNA damage. However, what determines these structural changes, including their ATP requirement, is not well understood. Using live-cell imaging and laser microirradiation to induce DNA lesions, we show that the local chromatin relaxation at DNA damage sites is regulated by PARP1 enzymatic activity. We also report that H1 is mobilized at DNA damage sites, but, since this mobilization is largely independent of poly(ADP-ribosyl)ation, it cannot solely explain the chromatin relaxation. Finally, we demonstrate the involvement of Alc1, a poly(ADP-ribose)- and ATP-dependent remodeler, in the chromatin-relaxation process. Deletion of Alc1 impairs chromatin relaxation after DNA damage, while its overexpression strongly enhances relaxation. Altogether our results identify Alc1 as an important player in the fast kinetics of the NAD+- and ATP-dependent chromatin relaxation upon DNA damage in vivo. PMID:27733626

  12. Oxygen partial pressure dependence of electrical conductivity in {gamma}'-Bi{sub 2}MoO{sub 6}

    SciTech Connect

    Vera, C.M.C. Aragon, R.

    2008-05-15

    The electrical conductivity of {gamma}'-Bi{sub 2}MoO{sub 6} was surveyed between 450 and 750 deg. C as a function of oxygen partial pressure, in the range 0.01-1 atm. A -1/6 power law dependence, consistent with a Frenkel defect model of doubly ionized oxygen vacancies and interstitials, is evidence for an n-type semiconductive component, with an optical band gap of 2.9 eV. The absence of this dependence is used to map the onset of dominant ionic conduction. - Graphical abstract: Temporal dependence of electrical conductivity at 500 deg. C for {gamma}'-Bi{sub 2}MoO{sub 6} at controlled partial pressures of oxygen.

  13. Activity-dependent depression of monosynaptic fast IPSCs in hippocampus: contributions from reductions in chloride driving force and conductance.

    PubMed

    Ling, D S; Benardo, L S

    1995-01-23

    Whole-cell recordings techniques were used to record pharmacologically isolated fast inhibitory postsynaptic currents (IPSCs) in CA1 pyramidal neurons from rat hippocampal slices. Repetitive extracellular stimulation up to 10 Hz progressively reduced steady-state fast IPSC amplitude. At low stimulation frequencies (up to 1 Hz), this attenuation was characterized by a positive shift of IPSC reversal potential with no change in IPSC conductance. Above 1 Hz stimulation, fast IPSC depression was associated with changes in both reversal potential and IPSC conductance. Use-dependent depression at low frequencies was prevented when cells were chloride-loaded using cesium chloride based intracellular solutions. These findings suggest that activity-dependent depression of fast IPSCs at low stimulus frequencies results entirely from a reduction in chloride driving force, stemming from intracellular chloride accumulation. Activity-dependent changes in fast IPSC conductance occur only at stimulation rates above 1 Hz.

  14. Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction.

    PubMed

    Kasahara, Kota; Shirota, Matsuyuki; Kinoshita, Kengo

    2016-01-01

    The mechanism of ion conduction by potassium channels is one of the central issues in physiology. In particular, it is still unclear how the ion concentration and the membrane voltage drive ion conduction. We have investigated the dynamics of the ion conduction processes in the Kv1.2 pore domain, by molecular dynamics (MD) simulations with several different voltages and ion concentrations. By focusing on the detailed ion movements through the pore including selectivity filter (SF) and cavity, we found two major conduction mechanisms, called the III-IV-III and III-II-III mechanisms, and the balance between the ion concentration and the voltage determines the mechanism preference. In the III-IV-III mechanism, the outermost ion in the pore is pushed out by a new ion coming from the intracellular fluid, and four-ion states were transiently observed. In the III-II-III mechanism, the outermost ion is pulled out first, without pushing by incoming ions. Increases in the ion concentration and voltage accelerated ion conductions, but their mechanisms were different. The increase in the ion concentrations facilitated the III-IV-III conductions, while the higher voltages increased the III-II-III conductions, indicating that the pore domain of potassium channels permeates ions by using two different driving forces: a push by intracellular ions and a pull by voltage.

  15. High-Capacity Conductive Nanocellulose Paper Sheets for Electrochemically Controlled Extraction of DNA Oligomers

    PubMed Central

    Razaq, Aamir; Nyström, Gustav; Strømme, Maria; Mihranyan, Albert; Nyholm, Leif

    2011-01-01

    Highly porous polypyrrole (PPy)-nanocellulose paper sheets have been evaluated as inexpensive and disposable electrochemically controlled three-dimensional solid phase extraction materials. The composites, which had a total anion exchange capacity of about 1.1 mol kg−1, were used for extraction and subsequent release of negatively charged fluorophore tagged DNA oligomers via galvanostatic oxidation and reduction of a 30–50 nm conformal PPy layer on the cellulose substrate. The ion exchange capacity, which was, at least, two orders of magnitude higher than those previously reached in electrochemically controlled extraction, originated from the high surface area (i.e. 80 m2 g−1) of the porous composites and the thin PPy layer which ensured excellent access to the ion exchange material. This enabled the extractions to be carried out faster and with better control of the PPy charge than with previously employed approaches. Experiments in equimolar mixtures of (dT)6, (dT)20, and (dT)40 DNA oligomers showed that all oligomers could be extracted, and that the smallest oligomer was preferentially released with an efficiency of up to 40% during the reduction of the PPy layer. These results indicate that the present material is very promising for the development of inexpensive and efficient electrochemically controlled ion-exchange membranes for batch-wise extraction of biomolecules. PMID:22195031

  16. Biochemical and genetic defects in the DNA-dependent protein kinase in murine scid lymphocytes.

    PubMed Central

    Danska, J S; Holland, D P; Mariathasan, S; Williams, K M; Guidos, C J

    1996-01-01

    The scid gene product has been identified as the 460-kDa catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs p460), a member of the phosphatidylinositol 3-kinase family. DNA-PK activity is undetectable in scid cells, but the molecular basis for this defect has not been identified. Here we report that expression of p460 in scid lymphocyte precursors is detectable but is reduced at least 10-fold relative to that in wild-type lymphocytes. In addition, we show that the scid mutation disturbs p460 nuclear association, presumably affecting its role in DNA repair pathways. To examine the molecular basis for our observations, we used a degenerate PCR strategy to clone the C-terminal p460 kinase domain from wild-type and scid thymocytes. Northern (RNA) analysis with these probes revealed normal steady-state p460 mRNA levels in scid cells, suggesting that the reduced abundance of p460 protein is due to a posttranscriptional defect. Sequence comparisons identified a single-base-pair alteration in the scid C-terminal p460 kinase domain, resulting in a premature stop codon. This mutation is predicted to truncate p460 by approximately 8 kDa, but it preserves the conserved motifs required for kinase activity in members of the phosphoinositidyl 3-kinase family. Despite a computed molecular weight alteration of less than 2%, we were able to visualize this difference by Western blot (immunoblot) analysis of wild-type and scid p460. These data demonstrate that the scid DNA-PKes mutation is not a null allele and suggest a molecular rationale for the well-described leakiness of the scid phenotype. PMID:8816463

  17. Targeting GLI by GANT61 involves mechanisms dependent on inhibition of both transcription and DNA licensing

    PubMed Central

    Zhang, Ruowen; Wu, Jiahui; Ferrandon, Sylvain; Glowacki, Katie J.; Houghton, Janet A.

    2016-01-01

    The GLI genes are transcription factors and in cancers are oncogenes, aberrantly and constitutively activated. GANT61, a specific GLI inhibitor, has induced extensive cytotoxicity in human models of colon cancer. The FOXM1 promoter was determined to be a transcriptional target of GLI1. In HT29 cells, inhibition of GLI1 binding at the GLI consensus sequence by GANT61 led to inhibited binding of Pol II, the pause-release factors DSIF, NELF and p-TEFb. The formation of R-loops (RNA:DNA hybrids, ssDNA), were reduced by GANT61 at the FOXM1 promoter. Pretreatment of HT29 cells with α-amanitin reduced GANT61-induced γH2AX foci. Co-localization of GLI1 and BrdU foci, inhibited by GANT61, indicated GLI1 and DNA replication to be linked. By co-immunoprecipitation and confocal microscopy, GLI1 co-localized with the DNA licensing factors ORC4, CDT1, and MCM2. Significant co-localization of GLI1 and ORC4 was inhibited by GANT61, and enrichment of ORC4 occurred at the GLI binding site in the FOXM1 promoter. CDT1 was found to be a transcription target of GLI1. Overexpression of CDT1 in HT29 and SW480 cells reduced GANT61-induced cell death, gH2AX foci, and cleavage of caspase-3. Data demonstrate involvement of transcription and of DNA replication licensing factors by non-transcriptional and transcriptional mechanisms in the GLI-dependent mechanism of action of GANT61. PMID:27863397

  18. The catalytic subunit of DNA-dependent protein kinase is required for cellular resistance to oxidative stress independent of DNA double-strand break repair.

    PubMed

    Li, Mengxia; Lin, Yu-Fen; Palchik, Guillermo A; Matsunaga, Shinji; Wang, Dong; Chen, Benjamin P C

    2014-11-01

    DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and ataxia telangiectasia mutated (ATM) are the two major kinases involved in DNA double-strand break (DSB) repair, and are required for cellular resistance to ionizing radiation. Whereas ATM is the key upstream kinase for DSB signaling, DNA-PKcs is primarily involved in DSB repair through the nonhomologous end-joining (NHEJ) mechanism. In addition to DSB repair, ATM has been shown to be involved in the oxidative stress response and could be activated directly in vitro on hydrogen peroxide (H2O2) treatment. However, the role of DNA-PKcs in cellular response to oxidative stress is not clear. We hypothesize that DNA-PKcs may participate in the regulation of ATM activation in response to oxidative stress, and that this regulatory role is independent of its role in DNA double-strand break repair. Our findings reveal that H2O2 induces hyperactivation of ATM signaling in DNA-PKcs-deficient, but not Ligase 4-deficient cells, suggesting an NHEJ-independent role for DNA-PKcs. Furthermore, DNA-PKcs deficiency leads to the elevation of reactive oxygen species (ROS) production, and to a decrease in cellular survival against H2O2. For the first time, our results reveal that DNA-PKcs plays a noncanonical role in the cellular response to oxidative stress, which is independent from its role in NHEJ. In addition, DNA-PKcs is a critical regulator of the oxidative stress response and contributes to the maintenance of redox homeostasis. Our findings reveal that DNA-PKcs is required for cellular resistance to oxidative stress and suppression of ROS buildup independently of its function in DSB repair.

  19. Temperature dependence of electronic heat capacity in Holstein model of DNA

    NASA Astrophysics Data System (ADS)

    Fialko, N.; Sobolev, E.; Lakhno, V.

    2016-04-01

    The dynamics of charge migration was modeled to calculate temperature dependencies of its thermodynamic equilibrium values such as energy and electronic heat capacity in homogeneous adenine fragments. The energy varies from nearly polaron one at T ∼ 0 to midpoint of the conductivity band at high temperatures. The peak on the graph of electronic heat capacity is observed at the polaron decay temperature.

  20. Length dependence of carbon nanotube thermal conductivity and the "problem of long waves"

    NASA Technical Reports Server (NTRS)

    Mingo, N.; Broido, D. A.

    2005-01-01

    We present the first calculations of finite length carbon nanotube thermal conductivity that extend from the ballistic to the diffusive regime, throughout a very wide range of lengths and temperatures. The long standing problem of vanishing scattering of the "long wavelength phonf dramatically here, making the thermal conductivity diverge as the nanotube length increases. We show that the divergence disappears if 3-phonon scattering processes are considered to second or higher order. Nevertheless, for defect free nanotubes, the thermal conductivity keeps increasing up to very large lengths (10 gm at 300 K). Defects in the nanotube are also able to remove the long wavelength divergence.

  1. Self similarity and sample length dependence of conductance in quasiperiodic lateral magnetic superlattices

    NASA Astrophysics Data System (ADS)

    Zeng, Z. Y.; Claro, F.

    2002-02-01

    We study the transport of electrons in a Fibonacci magnetic superlattice produced on a two-dimensional electron gas modulated by parallel magnetic-field stripes arranged in a Fibonacci sequence. Both the transmission coefficient and conductance exhibit self similarity and the six-circle property. The presence of extended states yields a finite conductivity at infinite length, that may be detected as an abrupt change in the conductance as the Fermi energy is varied, much as a metal-insulator transition. This is a unique feature of transport in this kind of structure, arising from its inherent two-dimensional nature.

  2. Regulation of ATM-Dependent DNA Damage Responses in Breast Cancer by the RhoGEF Net1

    DTIC Science & Technology

    2015-05-01

    Award Number: W81XWH-12-1-0014 TITLE: Regulation of ATM-Dependent DNA Damage Responses in Breast Cancer by the RhoGEF Net1 PRINCIPAL INVESTIGATOR... DNA breaks that are lethal to a cell if not repaired. In response to IR exposure a signal transduction cascade is initiated that activates cell...cycle checkpoints to cause cell cycle arrest, thereby allowing cells time to repair their damaged DNA (3). The ability of a cell to efficiently respond

  3. Polarization-Dependent Optical Response in Anisotropic Nanoparticle-DNA Superlattices.

    PubMed

    Sun, Lin; Lin, Haixin; Park, Daniel J; Bourgeois, Marc R; Ross, Michael B; Ku, Jessie C; Schatz, George C; Mirkin, Chad A

    2017-03-30

    DNA-programmable assembly has been used to prepare superlattices composed of octahedral and spherical nanoparticles, respectively. These superlattices have the same body-centered cubic lattice symmetry and macroscopic rhombic dodecahedron crystal habit but tunable lattice parameters by virtue of the DNA length, allowing one to study and determine the effect of nanoscale structure and lattice parameter on the light-matter interactions in the superlattices. Backscattering measurements and finite-difference time-domain simulations have been used to characterize these two classes of superlattices. Superlattices composed of octahedral nanoparticles exhibit polarization-dependent backscattering but via a trend that is opposite to that observed in the polarization dependence for analogous superlattices composed of spherical nanoparticles. Electrodynamics simulations show that this polarization dependence is mainly due to the anisotropy of the nanoparticles and is observed only if the octahedral nanoparticles are well-aligned within the superlattices. Both plasmonic and photonic modes are identified in such structures, both of which can be tuned by controlling the size and shape of the nanoparticle building blocks, the lattice parameters, and the overall size of the three-dimensional superlattices (without changing habit).

  4. Benchmark study of the length dependent thermal conductivity of individual suspended, pristine SWCNTs.

    PubMed

    Liu, Jinhui; Li, Tianyi; Hu, Yudong; Zhang, Xing

    2017-01-26

    The thermal conductivity of individual suspended single-walled carbon nanotubes (SWCNTs) has been theoretically predicated to increase with length but this has never been verified experimentally. This then leads to the question of whether the thermal conductivity saturates to a finite constant value in ultra-long SWCNTs. This paper reports on experimental measurements of the thermal conductivity of individual suspended SWCNTs as a function of the characteristic thermal transport length using the same individual suspended SWCNT sample. Interestingly, at around 360 K, the thermal conductivity first increases with increasing characteristic length and then saturates to a finite constant value at a characteristic length of ∼10 μm. These experimental results provide a fundamental understanding of the phonon transport characteristics in suspended, pristine SWCNTs.

  5. Effects of temperature dependence of electrical and thermal conductivities on the heating of a one dimensional conductor

    NASA Astrophysics Data System (ADS)

    Antoulinakis, Foivos; Zhang, Peng; Lau, Y. Y.; Chernin, David

    2016-10-01

    Dependence of electrical conductivity on temperature gives rise to electrotheramal instability, an important instability for Z-pinches. In other areas, ohmic heating limits the operation of nanoscale circuits such as graphene electronics, carbon nanofiber based field emitters, and nanolasers. For many applications, it is important to consider the temperature dependence of the thermal and electrical conductivities when calculating the effects of ohmic heating. We examine the effects of linear temperature dependence of the electrical and thermal conductivities on the heating of a one-dimensional conductor by solving the coupled non-linear steady state electrical and thermal conduction equations. We find that there are conditions under which no steady state solution exists. In the special case in which the temperature dependence of the electrical conductivity may be neglected, we have obtained explicit expressions for these conditions. The maximum temperature and its location within the conductor are examined for various boundary conditions. We note that the absence of a steady state solution may indicate the possibility of thermal runaway. Work supported by AFOSR No. FA9550-14-1-0309, and by L-3 Communications.

  6. Effects of Electron-phonon scattering on Conductance of Carbon nanotubes using Time-dependent wave-packet approach

    NASA Astrophysics Data System (ADS)

    Ishii, Hiroyuki; Kobayashi, Nobuhiko; Hirose, Kenji

    2007-03-01

    The application of single-walled carbon nanotubes as the ideal ballistic conductors is expected. However, the electronic current saturates at the high-bias regime due to electron-phonon scattering. In order to improve the conductivity, understanding of the scattering mechanism is highly required. We investigated the electron-phonon coupling effect on the conductance in single-walled carbon nanotubes using the time-dependent wave-packet approach under a tight-binding approximation [1]. The vibrational atomic displacements in real space are introduced through the time-dependent change of the transfer energies. We solve the time-dependent Schr"odinger equation and obtain the time-dependent diffusion coefficients of the electronic wave packets. From these data, we can extract the coherence length and then the conductance. We found that the optical phonon decreases the conductance of metallic carbon nanotubes, because the propagating speed of electron is reduced by the electron-phonon scattering. Furthermore, we clarify the difference of the scattering effects on the conductivity of the metallic nanotube and the semiconducting one. [1] S. Roche et al., PRL 95 (2005) 076803

  7. Saturation dependence of the quadrature conductivity of oil-bearing sands

    NASA Astrophysics Data System (ADS)

    Schmutz, M.; Blondel, A.; Revil, A.

    2012-02-01

    We have investigated the complex conductivity of oil-bearing sands with six distinct oil types including sunflower oil, silicone oil, gum rosin, paraffin, engine oil, and an industrial oil of complex composition. In all these experiments, the oil was the non-wetting phase. The in-phase (real) conductivity follows a power law relationship with the saturation (also known as the second Archie's law) but with a saturation exponent n raging from 1.1 to 3.1. In most experiments, the quadrature conductivity follows also a power law relationship with the water saturation but with a power law exponent p can be either positive or negative. For some samples, the quadrature conductivity first increases with saturation and then decreases indicating that two processes compete in controlling the quadrature conductivity. One is related to the insulating nature of the oil phase and a second could be associated with the surface area of the oil / water interface. The quadrature conductivity seems to be influenced not only by the value of the saturation exponent n (according to the Vinegar and Waxman model, p = n - 1), but also by the surface area between the oil phase and the water phase especially for very water-repellent oil having a fractal oil-water interface.

  8. Sensing the water content of honey from temperature-dependent electrical conductivity

    NASA Astrophysics Data System (ADS)

    Guo, Wenchuan; Liu, Yi; Zhu, Xinhua; Zhuang, Hong

    2011-08-01

    In order to predict the water content in honey, electrical conductivity was measured on blossom honey types milk-vetch, jujube and yellow-locust with the water content of 18-37% between 5 and 40 °C. The regression models of electrical conductivity were developed as functions of water content and temperature. The results showed that increases in either water content or temperature resulted in an increase in the electrical conductivity of honey with greater changes at higher water content and/or higher temperature. The linear terms of water content and temperature, a quadratic term of water content, and the interaction effect of water content and temperature had significant influence on the electrical conductivity of honey (p < 0.0001). Regardless of blossom honey type, the linear coefficient of the determination of measured and calculated electrical conductivities was 0.998 and the range error ratio was larger than 100. These results suggest that the electrical conductivity of honey might be used to develop a detector for rapidly predicting the water content in blossom honey.

  9. Universal scaling of crowding-induced DNA mobility is coupled with topology-dependent molecular compaction and elongation.

    PubMed

    Gorczyca, Stephanie M; Chapman, Cole D; Robertson-Anderson, Rae M

    2015-10-21

    Using single-molecule fluorescence microscopy and particle-tracking techniques, we elucidate the role DNA topology plays in the diffusion and conformational dynamics of crowded DNA molecules. We focus on large (115 kbp), double-stranded ring and linear DNA crowded by varying concentrations (0-40%) of dextran (10, 500 kDa) that mimic cellular conditions. By tracking the center-of-mass and measuring the lengths of the major and minor axes of single DNA molecules, we characterize both DNA mobility reduction as well as crowding-induced conformational changes (from random spherical coils). We reveal novel topology-dependent conformations, with single ring molecules undergoing compaction to ordered spherical configurations ∼20% smaller than dilute random coils, while linear DNA elongates by ∼2-fold. Surprisingly, these highly different conformations result in nearly identical exponential mobility reduction dependent solely on crowder volume fraction Φ, revealing a universal critical crowding concentration of Φc≅ 2.3. Beyond Φc DNA exhibits topology-independent conformational relaxation dynamics despite highly distinct topology-driven conformations. Our collective results reveal that topology-dependent conformational changes, unique to crowded environments, enable DNA to overcome the classically expected mobility reduction that high-viscosity crowded environments impose. Such coupled universal dynamics suggest a mechanism for DNA to maintain sufficient mobility required for wide-ranging biological processes despite severe cellular crowding.

  10. The unexpected non-monotonic inter-layer bonding dependence of the thermal conductivity of bilayered boron nitride.

    PubMed

    Gao, Yufei; Zhang, Xiaoliang; Jing, Yuhang; Hu, Ming

    2015-04-28

    Hexagonal boron nitride (BN) and its bilayer form are very fascinating two-dimensional materials that have attracted tremendous interest recently. Their realistic applications in emerging nanoelectronics usually quest for manipulating the thermal transport properties in a precise manner. Using nonequilibrium molecular dynamics simulations, we herein studied the effect of inter-layer covalent bonding on the thermal conductivity of bilayered BN. We found that the in-plane thermal conductivity of bilayered BN, which can be largely tuned by introducing covalent bonding between the two BN layers, depends not only on the inter-layer bonding density, but also on the detailed topological configuration of the inter-layer bonds. For randomly distributed inter-layer bonding the thermal conductivity of bilayered BN decreases monotonically with inter-layer bonding density, the same behavior already found for bilayered graphene. However, for regularly arranged inter-layer bonding the thermal conductivity of bilayered BN surprisingly possesses a non-monotonic dependence on the inter-layer bonding density. This non-intuitive non-monotonic dependence is further explained by performing spectral energy density analysis, where the peak and valley values of the thermal conductivity are governed by different mechanisms. These results suggest the application of inter-layer covalent bonding in designing nanoscale devices with precisely tunable thermal conductivities.

  11. Increased oxidative stress in AOA3 cells disturbs ATM-dependent DNA damage responses.

    PubMed

    Kobayashi, Junya; Saito, Yuichiro; Okui, Michiyo; Miwa, Noriko; Komatsu, Kenshi

    2015-04-01

    Ataxia telangiectasia (AT) is caused by a mutation in the ataxia-telangiectasia-mutated (ATM) gene; the condition is associated with hyper-radiosensitivity, abnormal cell-cycle checkpoints, and genomic instability. AT patients also show cerebellar ataxia, possibly due to reactive oxygen species (ROS) sensitivity in neural cells. The ATM protein is a key regulator of the DNA damage response. Recently, several AT-like disorders have been reported. The genes responsible for them are predicted to encode proteins that interact with ATM in the DNA-damage response. Ataxia with oculomotor apraxia types 1-3 (AOA1, 2, and 3) result in a neurodegenerative and cellular phenotype similar to AT; however, the basis of this phenotypic similarity is unclear. Here, we show that the cells of AOA3 patients display aberrant ATM-dependent phosphorylation and apoptosis following γ-irradiation. The ATM-dependent response to H2O2 treatment was abrogated in AOA3 cells. Furthermore, AOA3 cells had reduced ATM activity. Our results suggest that the attenuated ATM-related response is caused by an increase in endogenous ROS in AOA3 cells. Pretreatment of cells with pyocyanin, which induces endogenous ROS production, abolished the ATM-dependent response. Moreover, AOA3 cells had decreased homologous recombination (HR) activity, and pyocyanin pretreatment reduced HR activity in HeLa cells. These results indicate that excess endogenous ROS represses the ATM-dependent cellular response and HR repair in AOA3 cells. Since the ATM-dependent cell-cycle checkpoint is an important block to carcinogenesis, such inactivation of ATM may lead to tumorigenesis as well as neurodegeneration.

  12. On the dependence of the thermal conductivity of width-modulated nanowires on the number of modulations

    NASA Astrophysics Data System (ADS)

    Zianni, Xanthippi; Termentzidis, Konstantinos; Lacroix, David

    2017-01-01

    Our previous Monte Carlo simulations on the thermal conductivity of width-modulated nanowires indicated two distinct dependences of the decrease of the thermal conductivity κ relative to that of the non-modulated nanowire: (i) in the case of multiple constrictions κ scales with the nanowire transmissivity, (ii) in the case of a single constriction κ is determined by the ballistic constriction resistance. Here, we report on the transition between the two regimes. We discuss the thermal conductivity of width modulated nanowires as a function of the number of modulations. Phenomenology has been derived to interpret the MC simulations.

  13. Microbial diversity in fecal samples depends on DNA extraction method: easyMag DNA extraction compared to QIAamp DNA stool mini kit extraction

    PubMed Central

    2014-01-01

    Background There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE). Findings In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I’Etoile, France) and a manual one (QIAamp DNA Stool Mini Kit, Qiagen, Hilden, Germany) were tested on stool samples collected from 3 patients with Inflammatory Bowel disease (IBD) and 5 healthy individuals. DNA extracts obtained by the QIAamp DNA Stool Mini Kit yield a higher amount of DNA compared to DNA extracts obtained by easyMag® from the same fecal samples. Furthermore, DNA extracts obtained using easyMag® seemed to contain inhibitory compounds, since in order to perform a successful PCR-analysis, the sample should be diluted at least 10 times. DGGE performed on PCR from DNA extracted by QIAamp DNA Stool Mini Kit DNA was very successful. Conclusion QIAamp DNA Stool Mini Kit DNA extracts are optimal for DGGE runs and this extraction method yields a higher amount of DNA compared to easyMag®. PMID:24447346

  14. System to measure accurate temperature dependence of electric conductivity down to 20 K in ultrahigh vacuum.

    PubMed

    Sakai, C; Takeda, S N; Daimon, H

    2013-07-01

    We have developed the new in situ electrical-conductivity measurement system which can be operated in ultrahigh vacuum (UHV) with accurate temperature measurement down to 20 K. This system is mainly composed of a new sample-holder fixing mechanism, a new movable conductivity-measurement mechanism, a cryostat, and two receptors for sample- and four-probe holders. Sample-holder is pushed strongly against the receptor, which is connected to a cryostat, by using this new sample-holder fixing mechanism to obtain high thermal conductivity. Test pieces on the sample-holders have been cooled down to about 20 K using this fixing mechanism, although they were cooled down to only about 60 K without this mechanism. Four probes are able to be touched to a sample surface using this new movable conductivity-measurement mechanism for measuring electrical conductivity after making film on substrates or obtaining clean surfaces by cleavage, flashing, and so on. Accurate temperature measurement is possible since the sample can be transferred with a thermocouple and∕or diode being attached directly to the sample. A single crystal of Bi-based copper oxide high-Tc superconductor (HTSC) was cleaved in UHV to obtain clean surface, and its superconducting critical temperature has been successfully measured in situ. The importance of in situ measurement of resistance in UHV was demonstrated for this HTSC before and after cesium (Cs) adsorption on its surface. The Tc onset increase and the Tc offset decrease by Cs adsorption were observed.

  15. Spike Phase Locking in CA1 Pyramidal Neurons depends on Background Conductance and Firing Rate

    PubMed Central

    Broiche, Tilman; Malerba, Paola; Dorval, Alan D.; Borisyuk, Alla; Fernandez, Fernando R.; White, John A.

    2012-01-01

    Oscillatory activity in neuronal networks correlates with different behavioral states throughout the nervous system, and the frequency-response characteristics of individual neurons are believed to be critical for network oscillations. Recent in vivo studies suggest that neurons experience periods of high membrane conductance, and that action potentials are often driven by membrane-potential fluctuations in the living animal. To investigate the frequency-response characteristics of CA1 pyramidal neurons in the presence of high conductance and voltage fluctuations, we performed dynamic-clamp experiments in rat hippocampal brain slices. We drove neurons with noisy stimuli that included a sinusoidal component ranging, in different trials, from 0.1 to 500 Hz. In subsequent data analysis, we determined action potential phase-locking profiles with respect to background conductance, average firing rate, and frequency of the sinusoidal component. We found that background conductance and firing rate qualitatively change the phase-locking profiles of CA1 pyramidal neurons vs. frequency. In particular, higher average spiking rates promoted band-pass profiles, and the high-conductance state promoted phase-locking at frequencies well above what would be predicted from changes in the membrane time constant. Mechanistically, spike-rate adaptation and frequency resonance in the spike-generating mechanism are implicated in shaping the different phase-locking profiles. Our results demonstrate that CA1 pyramidal cells can actively change their synchronization properties in response to global changes in activity associated with different behavioral states. PMID:23055508

  16. Microstructure Dependence of Oxygen-Ion Conductivity of Samarium-Doped Ceria Ceramics

    NASA Astrophysics Data System (ADS)

    Huang, Duan-Ping; Xu, Qing; Liu, Han-Xing; Chen, Wen; Zhao, Kai; Kim, Bok-Hee

    2013-07-01

    Superfine and uniform Ce0.8Sm0.2O1.9 powder was derived from a urea-combustion process with a U/Mn+ ratio of 2.0. The microstructure and oxygen-ion conductivity of the ceramics sintered at 1050-1400 °C were investigated. The relative densities of the ceramics increased with sintering temperature through a maximum at 1200 °C and then slightly declined. The relatively densities of the specimens attained 95.8-98.0% at the sintering temperatures of 1100-1200 °C. The average grain size of the ceramics gradually enhanced from ˜110 to ˜500 nm with the elevation of sintering temperature from 1050 to 1350 °C. The specimens sintered at 1100-1200 °C achieved high oxygen-ion conductivities and low activation energies for the conduction. The results indicate an evident effect of the microstructure on the oxygen-ion conductivity. The superior oxygenion conducting properties of the specimens sintered at 1100-1200 °C are attributed to their low sintering temperatures, high densification levels and fine-grained microstructures.

  17. Scale-dependent hydraulic conductivity of mountain glacial sediments and implications for shallow groundwater recharge and stream baseflow

    NASA Astrophysics Data System (ADS)

    Houghton, T. B.; Ronayne, M. J.; Stednick, J. D.; Musselman, R. C.

    2011-12-01

    The hydraulic conductivity of shallow geologic material is a key control on water and nutrient cycling in mountain watersheds. Many high-elevation watersheds have a veneer of unconsolidated to semi-consolidated glacial sediments, which can serve as an important hydrologic pathway and water storage reservoir. This study utilized three different measurement techniques to characterize the saturated hydraulic conductivity of glacial till sediment across an alpine field site in the Snowy Range Mountains of southern Wyoming, USA. The measurements indicate that the conductivity ranges from approximately 0.05 to 5 m/d and is both spatially variable and scale dependent. The highest estimated conductivities were obtained with a double-ring infiltrometer that is strongly influenced by the coarse-grained fraction of the till. The lowest estimated conductivities were obtained with a mini-disk infiltrometer. The importance of accurately measuring hydraulic conductivity is demonstrated by considering water table fluctuations during snowmelt. A model that is parameterized with the lower, small-scale hydraulic conductivity will overestimate the potential for saturation-excess overland flow (rejected recharge) during peak snowmelt. Using a representative larger-scale hydraulic conductivity, model calculations indicate that the shallow subsurface has the capacity to accommodate all snowmelt. These results show that representative hydraulic conductivities measured at the appropriate scale are critical when quantifying groundwater recharge from snowmelt. This will support efforts to understand groundwater-surface water interaction and late season stream baseflow in mountain watersheds.

  18. RNF4 regulates DNA double-strand break repair in a cell cycle-dependent manner.

    PubMed

    Kuo, Ching-Ying; Li, Xu; Stark, Jeremy M; Shih, Hsiu-Ming; Ann, David K

    2016-01-01

    Both RNF4 and KAP1 play critical roles in the response to DNA double-strand breaks (DSBs), but the functional interplay of RNF4 and KAP1 in regulating DNA damage response remains unclear. We have previously demonstrated the recruitment and degradation of KAP1 by RNF4 require the phosphorylation of Ser824 (pS824) and SUMOylation of KAP1. In this report, we show the retention of DSB-induced pS824-KAP1 foci and RNF4 abundance are inversely correlated as cell cycle progresses. Following irradiation, pS824-KAP1 foci predominantly appear in the cyclin A (-) cells, whereas RNF4 level is suppressed in the G0-/G1-phases and then accumulates during S-/G2-phases. Notably, 53BP1 foci, but not BRCA1 foci, co-exist with pS824-KAP1 foci. Depletion of KAP1 yields opposite effect on the dynamics of 53BP1 and BRCA1 loading, favoring homologous recombination repair. In addition, we identify p97 is present in the RNF4-KAP1 interacting complex and the inhibition of p97 renders MCF7 breast cancer cells relatively more sensitive to DNA damage. Collectively, these findings suggest that combined effect of dynamic recruitment of RNF4 to KAP1 regulates the relative occupancy of 53BP1 and BRCA1 at DSB sites to direct DSB repair in a cell cycle-dependent manner.

  19. RNF4 regulates DNA double-strand break repair in a cell cycle-dependent manner

    PubMed Central

    Kuo, Ching-Ying; Li, Xu; Stark, Jeremy M.; Shih, Hsiu-Ming; Ann, David K.

    2016-01-01

    Abstract Both RNF4 and KAP1 play critical roles in the response to DNA double-strand breaks (DSBs), but the functional interplay of RNF4 and KAP1 in regulating DNA damage response remains unclear. We have previously demonstrated the recruitment and degradation of KAP1 by RNF4 require the phosphorylation of Ser824 (pS824) and SUMOylation of KAP1. In this report, we show the retention of DSB-induced pS824-KAP1 foci and RNF4 abundance are inversely correlated as cell cycle progresses. Following irradiation, pS824-KAP1 foci predominantly appear in the cyclin A (-) cells, whereas RNF4 level is suppressed in the G0-/G1-phases and then accumulates during S-/G2-phases. Notably, 53BP1 foci, but not BRCA1 foci, co-exist with pS824-KAP1 foci. Depletion of KAP1 yields opposite effect on the dynamics of 53BP1 and BRCA1 loading, favoring homologous recombination repair. In addition, we identify p97 is present in the RNF4-KAP1 interacting complex and the inhibition of p97 renders MCF7 breast cancer cells relatively more sensitive to DNA damage. Collectively, these findings suggest that combined effect of dynamic recruitment of RNF4 to KAP1 regulates the relative occupancy of 53BP1 and BRCA1 at DSB sites to direct DSB repair in a cell cycle-dependent manner. PMID:26766492

  20. DNA-dependent RNA polymerase subunits encoded within the vaccinia virus genome.

    PubMed Central

    Jones, E V; Puckett, C; Moss, B

    1987-01-01

    Antiserum to a multisubunit DNA-dependent RNA polymerase from vaccinia virions was prepared to carry out genetic studies. This antiserum selectively inhibited the activity of the viral polymerase but had no effect on calf thymus RNA polymerase II. The specificity of the antiserum was further demonstrated by immunoprecipitation of RNA polymerase subunits from dissociated virus particles. The presence in vaccinia virus-infected cells of mRNA that encodes the polymerase subunits was determined by in vitro translation. Immunoprecipitable polypeptides with Mrs of about 135,000, 128,000, 36,000, 34,000, 31,000, 23,000, 21,000, 20,000, and 17,000 were made when early mRNA was added to reticulocyte extracts. The subunits were encoded within the vaccinia virus genome, as demonstrated by translation of early mRNA that hybridized to vaccinia virus DNA. The locations of the subunit genes were determined initially by hybridization of RNA to a series of overlapping 40-kilobase-pair DNA fragments that were cloned in a cosmid vector. Further mapping was achieved with cloned HindIII restriction fragments. Results of these studies indicated that RNA polymerase subunit genes are transcribed early in infection and are distributed within the highly conserved central portion of the poxvirus genome in HindIII fragments E, J, H, D, and A. Images PMID:3033308

  1. Repressor activity of the RpoS/σS-dependent RNA polymerase requires DNA binding

    PubMed Central

    Lévi-Meyrueis, Corinne; Monteil, Véronique; Sismeiro, Odile; Dillies, Marie-Agnès; Kolb, Annie; Monot, Marc; Dupuy, Bruno; Duarte, Sara Serradas; Jagla, Bernd; Coppée, Jean-Yves; Beraud, Mélanie; Norel, Françoise

    2015-01-01

    The RpoS/σS sigma subunit of RNA polymerase (RNAP) activates transcription of stationary phase genes in many Gram-negative bacteria and controls adaptive functions, including stress resistance, biofilm formation and virulence. In this study, we address an important but poorly understood aspect of σS-dependent control, that of a repressor. Negative regulation by σS has been proposed to result largely from competition between σS and other σ factors for binding to a limited amount of core RNAP (E). To assess whether σS binding to E alone results in significant downregulation of gene expression by other σ factors, we characterized an rpoS mutant of Salmonella enterica serovar Typhimurium producing a σS protein proficient for EσS complex formation but deficient in promoter DNA binding. Genome expression profiling and physiological assays revealed that this mutant was defective for negative regulation, indicating that gene repression by σS requires its binding to DNA. Although the mechanisms of repression by σS are likely specific to individual genes and environmental conditions, the study of transcription downregulation of the succinate dehydrogenase operon suggests that σ competition at the promoter DNA level plays an important role in gene repression by EσS. PMID:25578965

  2. Determination of temperature-dependent heat conductivity and thermal diffusivity of waste glass melter feed

    SciTech Connect

    Pokorny, Richard; Rice, Jarrett A.; Schweiger, Michael J.; Hrma, Pavel R.

    2013-06-01

    The cold cap is a layer of reacting glass batch floating on the surface of melt in an all-electric continuous glass melter. The heat needed for the conversion of the melter feed to molten glass must be transferred to and through the cold cap. Since the heat flux into the cold cap determines the rate of melting, the heat conductivity is a key property of the reacting feed. We designed an experimental setup consisting of a large cylindrical crucible with an assembly of thermocouples that monitors the evolution of the temperature field while the crucible is heated at a constant rate. Then we used two methods to calculate the heat conductivity and thermal diffusivity of the reacting feed: the approximation of the temperature field by polynomial functions and the finite-volume method coupled with least-squares analysis. Up to 680°C, the heat conductivity of the reacting melter feed was represented by a linear function of temperature.

  3. Protein kinase A dependent membrane protein phosphorylation and chloride conductance in endosomal vesicles from kidney cortex

    SciTech Connect

    Reenstra, W.W.; Bae, H.R.; Verkman, A.S. Univ. of California, San Francisco ); Sabolic, I. Harvard Medical School, Charlestown, MA )

    1992-01-14

    Regulation of Cl conductance by protein kinase A action, cell-free measurements of Cl transport and membrane protein phosphorylation were carried out in apical endocytic vesicles from rabbit kidney proximal tubule. Cl transport was measured by a stopped-flow quenching assay in endosomes labeled in vivo with the fluorescent Cl indicator 6-methoxy-N-(3-sulfopropyl)quinolinium. Phosphorylation was studied in a purified endosomal preparation by SDS-PAGE and autoradiography of membrane proteins labeled by ({gamma}-{sup 32}P)ATP. These results suggest that, in a cell-free system, protein kinase A increases Cl conductance in endosomes from kidney proximal tubule by a phosphorylation mechanism. The labeled protein has a size similar to that of the 64-kDa putative kidney Cl channel reported by Landry et al. but is much smaller than the {approximately}170-kDa cystic fibrosis transmembrane conductance regulatory protein.

  4. Temperature dependent conduction and UV induced metal-to-insulator transition in ZnO nanowires

    SciTech Connect

    Chang, P.-C.; Lu, Jia Grace

    2008-05-26

    Thin ZnO nanowires with diameters of less than 50 nm are configured as field effect transistors and studied for their transport mechanisms at different temperatures under UV illumination and gate modulation. The conductivity exhibits two regimes: at T>50 K, thermally activated transport dominates with activation energy around 30-60 meV attributed to the shallow donor states and at T<50 K, three dimensional variable range hopping reveals in the conduction. In addition, UV irradiation leads to a metal-to-insulator transition at {approx}210 K. Furthermore, electrostatic gating results in a band bending giving rise to a change in the activation energy.

  5. Giant humidity dependence of conductivity in a single exfoliated titania nanosheet

    SciTech Connect

    Tanaka, Ayaka; Hatakeyama, Kazuto; Oku, Azusa; Matsuzaki, Koji; Saitou, Natsumi; Yokoi, Hiroyuki; Taniguchi, Takaaki; Matsumoto, Yasumichi; Hara, Masahiro

    2014-04-21

    We have investigated an in-plane electrical transport in an individual titania nanosheet, which forms a lepidocrocite structure with a few atomic layer thickness. The conductivity in the titania nanosheet varied five orders for the change of the relative humidity from 45% to 95%. The drastic change in the conductivity is due to a sensitive response with respect to water molecules adsorbed on the surface of the two-dimensional nanosheet. The results may open an avenue for nanodevices built from various oxide nanosheets.

  6. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs

    PubMed Central

    2016-01-01

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

  7. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs.

    PubMed

    Fang, Wei; Chen, Ji; Rossi, Mariana; Feng, Yexin; Li, Xin-Zheng; Michaelides, Angelos

    2016-06-02

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general.

  8. Tissue distribution of a plasmid DNA encoding Hsp65 gene is dependent on the dose administered through intramuscular delivery

    PubMed Central

    Coelho-Castelo, AAM; Trombone, AP; Rosada, RS; Santos, RR; Bonato, VLD; Sartori, A; Silva, CL

    2006-01-01

    In order to assess a new strategy of DNA vaccine for a more complete understanding of its action in immune response, it is important to determine the in vivo biodistribution fate and antigen expression. In previous studies, our group focused on the prophylactic and therapeutic use of a plasmid DNA encoding the Mycobacterium leprae 65-kDa heat shock protein (Hsp65) and achieved an efficient immune response induction as well as protection against virulent M. tuberculosis challenge. In the present study, we examined in vivo tissue distribution of naked DNA-Hsp65 vaccine, the Hsp65 message, genome integration and methylation status of plasmid DNA. The DNA-Hsp65 was detectable in several tissue types, indicating that DNA-Hsp65 disseminates widely throughout the body. The biodistribution was dose-dependent. In contrast, RT-PCR detected the Hsp65 message for at least 15 days in muscle or liver tissue from immunized mice. We also analyzed the methylation status and integration of the injected plasmid DNA into the host cellular genome. The bacterial methylation pattern persisted for at least 6 months, indicating that the plasmid DNA-Hsp65 does not replicate in mammalian tissue, and Southern blot analysis showed that plasmid DNA was not integrated. These results have important implications for the use of DNA-Hsp65 vaccine in a clinical setting and open new perspectives for DNA vaccines and new considerations about the inoculation site and delivery system. PMID:16445866

  9. Estimation of DNA sequence context-dependent mutation rates using primate genomic sequences.

    PubMed

    Zhang, Wei; Bouffard, Gerard G; Wallace, Susan S; Bond, Jeffrey P

    2007-09-01

    It is understood that DNA and amino acid substitution rates are highly sequence context-dependent, e.g., C --> T substitutions in vertebrates may occur much more frequently at CpG sites and that cysteine substitution rates may depend on support of the context for participation in a disulfide bond. Furthermore, many applications rely on quantitative models of nucleotide or amino acid substitution, including phylogenetic inference and identification of amino acid sequence positions involved in functional specificity. We describe quantification of the context dependence of nucleotide substitution rates using baboon, chimpanzee, and human genomic sequence data generated by the NISC Comparative Sequencing Program. Relative mutation rates are reported for the 96 classes of mutations of the form 5' alphabetagamma 3' --> 5' alphadeltagamma 3', where alpha, beta, gamma, and delta are nucleotides and beta not equal delta, based on maximum likelihood calculations. Our results confirm that C --> T substitutions are enhanced at CpG sites compared with other transitions, relatively independent of the identity of the preceding nucleotide. While, as expected, transitions generally occur more frequently than transversions, we find that the most frequent transversions involve the C at CpG sites (CpG transversions) and that their rate is comparable to the rate of transitions at non-CpG sites. A four-class model of the rates of context-dependent evolution of primate DNA sequences, CpG transitions > non-CpG transitions approximately CpG transversions > non-CpG transversions, captures qualitative features of the mutation spectrum. We find that despite qualitative similarity of mutation rates among different genomic regions, there are statistically significant differences.

  10. Current-dependent growth of silicon nitride lines using a conducting tip AFM

    NASA Astrophysics Data System (ADS)

    Workman, R. K.; Peterson, C. A.; Sarid, D.

    1999-03-01

    The measurement of a picoamp current accompanying silicon nitride line growth in an ammonia atmosphere, using a conducting tip atomic force microscope, is reported for the first time. The observed total charge per nanolithographed volume is found to be consistent with a process where the reduction of H + ions belonging to the ammonia gives rise to the nitridation of the silicon substrate.

  11. The Dependence of Peat Soil Hydraulic Conductivity on Dominant Vegetation Type in Mountain Fens

    NASA Astrophysics Data System (ADS)

    Crockett, A. C.; Ronayne, M. J.; Cooper, D. J.

    2014-12-01

    The peat soil within fen wetlands provides water storage that can substantially influence the hydrology of mountain watersheds. In this study, we investigated the relationship between hydraulic conductivity and vegetation type for fens occurring in Rocky Mountain National Park (RMNP), Colorado, USA. Vegetation in RMNP fens can be dominated by woody plants and shrubs, such as willows; by mosses; or by herbaceous plants such as sedges. Fens dominated by each vegetation type were selected for study. Six fens were investigated, all of which are in the Colorado River watershed on the west side of RMNP. For each site, soil hydraulic conductivity was measured at multiple locations using a single-ring infiltrometer. As a result of the shallow water table in these fens (the water table was always within 10 cm of the surface), horizontal hydraulic gradients were produced during the field tests. The measured infiltration rates were analyzed using the numerical model HYDRUS. In order to determine the hydraulic conductivity, a parameter estimation problem was solved using HYDRUS as the forward simulator. Horizontal flow was explicitly accounted for in the model. This approach produced more accurate estimates of hydraulic conductivity than would be obtained using an analytical solution that assumes strictly vertical flow. Significant differences in hydraulic properties between fens appear to result at least in part from the effects of different dominant vegetation types on peat soil formation.

  12. Ligation reaction specificities of an NAD(+)-dependent DNA ligase from the hyperthermophile Aquifex aeolicus.

    PubMed

    Tong, J; Barany, F; Cao, W

    2000-03-15

    An NAD(+)-dependent DNA ligase from the hyperthermophilic bacterium Aquifex aeolicus was cloned, expressed in Escherichia coli and purified to homogeneity. The enzyme is most active in slightly alkaline pH conditions with either Mg(2+)or Mn(2+)as the metal cofactor. Ca(2+)and Ni(2+)mainly support formation of DNA-adenylate intermediates. The catalytic cycle is characterized by a low k (cat)value of 2 min(-1)with concomitant accumulation of the DNA - adenylate intermediate when Mg(2+)is used as the metal cofactor. The ligation rates of matched substrates vary by up to 4-fold, but exhibit a general trend of T/A < or = G/C < C/G < A/T on both the 3'- and 5'-side of the nick. Consistent with previous studies on Thermus ligases, this Aquifex ligase exhibits greater discrimination against a mismatched base pair on the 3'-side of the nick junction. The requirement of 3' complementarity for a ligation reaction is reaffirmed by results from 1 nt insertions on either the 3'- or 5'-side of the nick. Furthermore, most of the unligatable 3' mismatched base pairs prohibit formation of the DNA-adenylate intermediate, indicating that the substrate adenylation step is also a control point for ligation fidelity. Unlike previously studied ATP ligases, gapped substrates cannot be ligated and intermediate accumulation is minimal, suggesting that complete elimination of base pair complementarity on one side of the nick affects substrate adenylation on the 5'-side of the nick junction. Relationships among metal cofactors, ligation products and intermediate, and ligation fidelity are discussed.

  13. Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding

    PubMed Central

    van Steensel, Bas; Delrow, Jeffrey; Bussemaker, Harmen J.

    2003-01-01

    The association of sequence-specific DNA-binding factors with their cognate target sequences in vivo depends on the local molecular context, yet this context is poorly understood. To address this issue, we have performed genomewide mapping of in vivo target genes of Drosophila GAGA factor (GAF). The resulting list of ≈250 target genes indicates that GAF regulates many cellular pathways. We applied unbiased motif-based regression analysis to identify the sequence context that determines GAF binding. Our results confirm that GAF selectively associates with (GA)n repeat elements in vivo. GAF binding occurs in upstream regulatory regions, but less in downstream regions. Surprisingly, GAF binds abundantly to introns but is virtually absent from exons, even though the density of (GA)n is roughly the same. Intron binding occurs equally frequently in last introns compared with first introns, suggesting that GAF may not only regulate transcription initiation, but possibly also elongation. We provide evidence for cooperative binding of GAF to closely spaced (GA)n elements and explain the lack of GAF binding to exons by the absence of such closely spaced GA repeats. Our approach for revealing determinants of context-dependent DNA binding will be applicable to many other transcription factors. PMID:12601174

  14. Drosophila factor 2, an RNA polymerase II transcript release factor, has DNA-dependent ATPase activity.

    PubMed

    Xie, Z; Price, D

    1997-12-12

    Drosophila factor 2 has been identified as a component of negative transcription elongation factor (N-TEF) that causes the release of RNA polymerase II transcripts in an ATP-dependent manner (Xie, Z. and Price D. H. (1996) J. Biol. Chem. 271, 11043-11046). We show here that the transcript release activity of factor 2 requires ATP or dATP and that adenosine 5'-O-(thiotriphosphate) (ATPgammaS), adenosine 5'-(beta,gamma-imino)triphosphate (AMP-PNP), or other NTPs do not support the activity. Factor 2 demonstrated a strong DNA-dependent ATPase activity that correlated with its transcript release activity. At 20 microg/ml DNA, the ATPase activity of factor 2 had an apparent Km(ATP) of 28 microM and an estimated Kcat of 140 min-1. Factor 2 caused the release of nascent transcripts associated with elongation complexes generated by RNA polymerase II on a dC-tailed template. Therefore, no other protein cofactors are required for the transcript release activity of factor 2. Using the dC-tailed template assay, it was found that renaturation of the template was required for factor 2 function.

  15. Replication-Dependent Unhooking of DNA Interstrand Cross-Links by the NEIL3 Glycosylase.

    PubMed

    Semlow, Daniel R; Zhang, Jieqiong; Budzowska, Magda; Drohat, Alexander C; Walter, Johannes C

    2016-10-06

    During eukaryotic DNA interstrand cross-link (ICL) repair, cross-links are resolved ("unhooked") by nucleolytic incisions surrounding the lesion. In vertebrates, ICL repair is triggered when replication forks collide with the lesion, leading to FANCI-FANCD2-dependent unhooking and formation of a double-strand break (DSB) intermediate. Using Xenopus egg extracts, we describe here a replication-coupled ICL repair pathway that does not require incisions or FANCI-FANCD2. Instead, the ICL is unhooked when one of the two N-glycosyl bonds forming the cross-link is cleaved by the DNA glycosylase NEIL3. Cleavage by NEIL3 is the primary unhooking mechanism for psoralen and abasic site ICLs. When N-glycosyl bond cleavage is prevented, unhooking occurs via FANCI-FANCD2-dependent incisions. In summary, we identify an incision-independent unhooking mechanism that avoids DSB formation and represents the preferred pathway of ICL repair in a vertebrate cell-free system.

  16. Quantitative site-specific ADP-ribosylation profiling of DNA-dependent PARPs.

    PubMed

    Gagné, Jean-Philippe; Ethier, Chantal; Defoy, Daniel; Bourassa, Sylvie; Langelier, Marie-France; Riccio, Amanda A; Pascal, John M; Moon, Kyung-Mee; Foster, Leonard J; Ning, Zhibin; Figeys, Daniel; Droit, Arnaud; Poirier, Guy G

    2015-06-01

    An important feature of poly(ADP-ribose) polymerases (PARPs) is their ability to readily undergo automodification upon activation. Although a growing number of substrates were found to be poly(ADP-ribosyl)ated, including histones and several DNA damage response factors, PARPs themselves are still considered as the main acceptors of poly(ADP-ribose). By monitoring spectral counts of specific hydroxamic acid signatures generated after the conversion of the ADP-ribose modification onto peptides by hydroxylamine hydrolysis, we undertook a thorough mass spectrometry mapping of the glutamate and aspartate ADP-ribosylation sites onto automodified PARP-1, PARP-2 and PARP-3. Thousands of hydroxamic acid-conjugated peptides were identified with high confidence and ranked based on their spectral count. This semi-quantitative approach allowed us to locate the preferentially targeted residues in DNA-dependent PARPs. In contrast to what has been reported in the literature, automodification of PARP-1 is not predominantly targeted towards its BRCT domain. Our results show that interdomain linker regions that connect the BRCT to the WGR module and the WGR to the PRD domain undergo prominent ADP-ribosylation during PARP-1 automodification. We also found that PARP-1 efficiently automodifies the D-loop structure within its own catalytic fold. Interestingly, additional major ADP-ribosylation sites were identified in functional domains of PARP-1, including all three zinc fingers. Similar to PARP-1, specific residues located within the catalytic sites of PARP-2 and PARP-3 are major targets of automodification following their DNA-dependent activation. Together our results suggest that poly(ADP-ribosyl)ation hot spots make a dominant contribution to the overall automodification process.

  17. DNA sequence-dependent variation in nucleosome structure, stability, and dynamics detected by a FRET-based analysis.

    PubMed

    Kelbauskas, L; Woodbury, N; Lohr, D

    2009-02-01

    Förster resonance energy transfer (FRET) techniques provide powerful and sensitive methods for the study of conformational features in biomolecules. Here, we review FRET-based studies of nucleosomes, focusing particularly on our work comparing the widely used nucleosome standard, 5S rDNA, and 2 promoter-derived regulatory element-containing nucleosomes, mouse mammary tumor virus (MMTV)-B and GAL10. Using several FRET approaches, we detected significant DNA sequence-dependent structure, stability, and dynamics differences among the three. In particular, 5S nucleosomes and 5S H2A/H2B-depleted nucleosomal particles have enhanced stability and diminished DNA dynamics, compared with MMTV-B and GAL10 nucleosomes and particles. H2A/H2B-depleted nucleosomes are of interest because they are produced by the activities of many transcription-associated complexes. Significant location-dependent (intranucleosomal) stability and dynamics variations were also observed. These also vary among nucleosome types. Nucleosomes restrict regulatory factor access to DNA, thereby impeding genetic processes. Eukaryotic cells possess mechanisms to alter nucleosome structure, to generate DNA access, but alterations often must be targeted to specific nucleosomes on critical regulatory DNA elements. By endowing specific nucleosomes with intrinsically higher DNA accessibility and (or) enhanced facility for conformational transitions, DNA sequence-dependent nucleosome dynamics and stability variations have the potential to facilitate nucleosome recognition and, thus, aid in the crucial targeting process. This and other nucleosome structure and function conclusions from FRET analyses are discussed.

  18. RSC facilitates Rad59-dependent homologous recombination between sister chromatids by promoting cohesin loading at DNA double-strand breaks.

    PubMed

    Oum, Ji-Hyun; Seong, Changhyun; Kwon, Youngho; Ji, Jae-Hoon; Sid, Amy; Ramakrishnan, Sreejith; Ira, Grzegorz; Malkova, Anna; Sung, Patrick; Lee, Sang Eun; Shim, Eun Yong

    2011-10-01

    Homologous recombination repairs DNA double-strand breaks by searching for, invading, and copying information from a homologous template, typically the homologous chromosome or sister chromatid. Tight wrapping of DNA around histone octamers, however, impedes access of repair proteins to DNA damage. To facilitate DNA repair, modifications of histones and energy-dependent remodeling of chromatin are required, but the precise mechanisms by which chromatin modification and remodeling enzymes contribute to homologous DNA repair are unknown. Here we have systematically assessed the role of budding yeast RSC (remodel structure of chromatin), an abundant, ATP-dependent chromatin-remodeling complex, in the cellular response to spontaneous and induced DNA damage. RSC physically interacts with the recombination protein Rad59 and functions in homologous recombination. Multiple recombination assays revealed that RSC is uniquely required for recombination between sister chromatids by virtue of its ability to recruit cohesin at DNA breaks and thereby promoting sister chromatid cohesion. This study provides molecular insights into how chromatin remodeling contributes to DNA repair and maintenance of chromatin fidelity in the face of DNA damage.

  19. Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer

    PubMed Central

    Mosig, Gisela; Gewin, John; Luder, Andreas; Colowick, Nancy; Vo, Daniel

    2001-01-01

    Two major pathways of recombination-dependent DNA replication, “join-copy” and “join-cut-copy,” can be distinguished in phage T4: join-copy requires only early and middle genes, but two late proteins, endonuclease VII and terminase, are uniquely important in the join-cut-copy pathway. In wild-type T4, timing of these pathways is integrated with the developmental program and related to transcription and packaging of DNA. In primase mutants, which are defective in origin-dependent lagging-strand DNA synthesis, the late pathway can bypass the lack of primers for lagging-strand DNA synthesis. The exquisitely regulated synthesis of endo VII, and of two proteins from its gene, explains the delay of recombination-dependent DNA replication in primase (as well as topoisomerase) mutants, and the temperature-dependence of the delay. Other proteins (e.g., the single-stranded DNA binding protein and the products of genes 46 and 47) are important in all recombination pathways, but they interact differently with other proteins in different pathways. These homologous recombination pathways contribute to evolution because they facilitate acquisition of any foreign DNA with limited sequence homology during horizontal gene transfer, without requiring transposition or site-specific recombination functions. Partial heteroduplex repair can generate what appears to be multiple mutations from a single recombinational intermediate. The resulting sequence divergence generates barriers to formation of viable recombinants. The multiple sequence changes can also lead to erroneous estimates in phylogenetic analyses. PMID:11459968

  20. Development of Single-Molecule DNA Sequencing Platform Based on Single-Molecule Electrical Conductance

    DTIC Science & Technology

    2015-05-25

    indicate that they are nearly harmless to cultured cells (17-20). The bio-distribution of injected GNPs has shown a size-dependent accumulation in liver ...Animals” of National Chiao Tung University. Four-week-old male BALB/C mice were housed at 22±2 C with a 12-h light/dark cycle and fed standard...Conference, Protein Folding Dynamics, 5-10 Jan, 2014, Hotel Galvez in Galveston TX, United States Guewha Steven Huang , Single-Molecule Kinetics of

  1. Efficient Capture and Isolation of Tumor-Related Circulating Cell-Free DNA from Cancer Patients Using Electroactive Conducting Polymer Nanowire Platforms

    PubMed Central

    Jeon, SeungHyun; Lee, HyungJae; Bae, Kieun; Yoon, Kyong-Ah; Lee, Eun Sook; Cho, Youngnam

    2016-01-01

    Circulating cell-free DNA (cfDNA) is currently recognized as a key non-invasive biomarker for cancer diagnosis and progression and therapeutic efficacy monitoring. Because cfDNA has been detected in patients with diverse types of cancers, the use of efficient strategies to isolate cfDNA not only provides valuable insights into tumour biology, but also offers the potential for developing new cancer-specific targets. However, the challenges associated with conventional cfDNA extraction methods prevent their further clinical applications. Here, we developed a nanostructured conductive polymer platform for the efficient capture and release of circulating cfDNA and demonstrated its potential clinical utility using unprocessed plasma samples from patients with breast and lung cancers. Our results confirmed that the platform's enhanced efficiency allows tumor-specific circulating cfDNA to be recovered at high yield and purity. PMID:27162553

  2. Shear Strength of Conductive Adhesive Joints on Rigid and Flexible Substrates Depending on Adhesive Quantity

    NASA Astrophysics Data System (ADS)

    Hirman, Martin; Steiner, Frantisek

    2016-05-01

    This article deals with the impact of electrically conductive adhesive quantity on the shear strength of joints glued by adhesives "EPO-TEKⓇ H20S" and "MG8331S" on three types of substrates (FR-4, MELINEXⓇST504, DuPont™ PyraluxⓇAC). These joints were made by gluing chip resistors 1206, 0805 and 0603, with two curing profiles for each adhesive. Different thicknesses of stencil and reductions in the size of the hole in stencils were used for this experiment. These differences have an effect on the quantity of conductive adhesives which must be used on the samples. Samples were measured after the curing process by using a shear strength test applied by the device LabTest 3.030. This article presents the effects of different curing profiles, various types of substrates, and different quantities of adhesives on the mechanical strength of the joint.

  3. Current-dependent anisotropic conductivity of locally assembled silver nanoparticles in hybrid polymer films.

    PubMed

    Goel, Pooja; Vinokur, Rostislav; Weichold, Oliver

    2010-12-15

    The electrical behaviour of hybrid poly(ethylene terephthalate) films containing localised, percolating networks of silver nanoparticles separated by pure polymer is studied. The films resemble an array of parallel wires in the submicron range and, thus, exhibit anisotropic conductivity. In the high-conductivity direction at low amplitudes, the films show Ohmic behaviour, while at moderate voltage, non-linearity and a decreasing resistance is observed. The samples were found to heat up during the measurements and the deviation from Ohm's law coincides with the Tg of the polymer. Microstructural analysis of the samples revealed an irreversible agglomeration of the particles at moderate voltages leading to the formation of filaments with higher metallic character than the random particle network.

  4. Frequency-dependent magneto-optical conductivity in the generalized α -T3 model

    NASA Astrophysics Data System (ADS)

    Kovács, Áron Dániel; Dávid, Gyula; Dóra, Balázs; Cserti, József

    2017-01-01

    We have studied a generalized three-band crossing model in 2D, the generalized α -T3 lattice, ranging from the pseudospin-1 Dirac equation through a quadratic+flat band touching to the pseudospin-1/2 Dirac equation. A general method is presented to determine the operator form of the Green's function, being gauge and representation independent. This yields the Landau level structure in a quantizing magnetic field and the longitudinal and transversal magneto-optical conductivities of the underlying system. Although the magneto-optical selection rules allow for many transitions between Landau levels, the dominant one stems from exciting a particle from/to the flat band to/from a propagating band. The Hall conductivity from each valley is rational (not quantized at all), in agreement with Berry phase considerations, though their sum is always integer quantized.

  5. Measurement of temperature-dependent viscosity and thermal conductivity of alumina and titania thermal oil nanofluids

    NASA Astrophysics Data System (ADS)

    Cieśliński, Janusz T.; Ronewicz, Katarzyna; Smoleń, Sławomir

    2015-12-01

    In this study the results of simultaneous measurements of dynamic viscosity, thermal conductivity, electrical conductivity and pH of two nanofluids, i.e., thermal oil/Al2O3 and thermal oil/TiO2 are presented. Thermal oil is selected as a base liquid because of possible application in ORC systems as an intermediate heating agent. Nanoparticles were tested at the concentration of 0.1%, 1%, and 5% by weight within temperature range from 20 °C to 60 °C. Measurement devices were carefully calibrated by comparison obtained results for pure base liquid (thermal oil) with manufacturer's data. The results obtained for tested nanofluids were compared with predictions made by use of existing models for liquid/solid particles mixtures.

  6. Temperature dependence of spin-dependent tunneling conductance of magnetic tunnel junctions with half-metallic C o2MnSi electrodes

    NASA Astrophysics Data System (ADS)

    Hu, Bing; Moges, Kidist; Honda, Yusuke; Liu, Hong-xi; Uemura, Tetsuya; Yamamoto, Masafumi; Inoue, Jun-ichiro; Shirai, Masafumi

    2016-09-01

    In order to elucidate the origin of the temperature (T ) dependence of spin-dependent tunneling conductance (G ) of magnetic tunnel junctions (MTJs), we experimentally investigated the T dependence of G for the parallel and antiparallel magnetization alignments, GP and GAP, of high-quality C o2MnSi (CMS)/MgO/CMS MTJs having systematically varied spin polarizations (P ) at 4.2 K by varying the Mn composition α in C o2M nαSi electrodes that exhibited giant tunneling magnetoresistance ratios. Results showed that GP normalized by its value at 4.2 K exhibited a notable, nonmonotonic T dependence although its variation with T was significantly smaller than that of GAP normalized by its value at 4.2 K, indicating that an analysis of the experimental GP(T ) is critical to revealing the origin of the T dependence of G . By analyzing the experimental GP(T ) , we clarified that both spin-flip inelastic tunneling via a thermally excited magnon and spin-conserving elastic tunneling in which P decays with increasing T play key roles. The experimental GAP(T ) , including its stronger T dependence for higher P at 4.2 K, was also consistently explained with this model. Our findings provide a unified picture for understanding the origin of the T dependence of G of MTJs with a wide range of P , including MTJs with high P close to a half-metallic value.

  7. Homology-dependent repair is involved in 45S rDNA loss in plant CAF-1 mutants.

    PubMed

    Muchová, Veronika; Amiard, Simon; Mozgová, Iva; Dvořáčková, Martina; Gallego, Maria E; White, Charles; Fajkus, Jiří

    2015-01-01

    Arabidopsis thaliana mutants in FAS1 and FAS2 subunits of chromatin assembly factor 1 (CAF1) show progressive loss of 45S rDNA copies and telomeres. We hypothesized that homology-dependent DNA damage repair (HDR) may contribute to the loss of these repeats in fas mutants. To test this, we generated double mutants by crossing fas mutants with knock-out mutants in RAD51B, one of the Rad51 paralogs of A. thaliana. Our results show that the absence of RAD51B decreases the rate of rDNA loss, confirming the implication of RAD51B-dependent recombination in rDNA loss in the CAF1 mutants. Interestingly, this effect is not observed for telomeric repeat loss, which thus differs from that acting in rDNA loss. Involvement of DNA damage repair in rDNA dynamics in fas mutants is further supported by accumulation of double-stranded breaks (measured as γ-H2AX foci) in 45S rDNA. Occurrence of the foci is not specific for S-phase, and is ATM-independent. While the foci in fas mutants occur both in the transcribed (intranucleolar) and non-transcribed (nucleoplasmic) fraction of rDNA, double fas rad51b mutants show a specific increase in the number of the intranucleolar foci. These results suggest that the repair of double-stranded breaks present in the transcribed rDNA region is RAD51B dependent and that this contributes to rDNA repeat loss in fas mutants, presumably via the single-stranded annealing recombination pathway. Our results also highlight the importance of proper chromatin assembly in the maintenance of genome stability.

  8. Fluence dependent electrical conductivity in aluminium thin films grown by infrared pulsed laser deposition

    NASA Astrophysics Data System (ADS)

    Rebollar, Esther; Martínez-Tong, Daniel E.; Sanz, Mikel; Oujja, Mohamed; Marco, José F.; Ezquerra, Tiberio A.; Castillejo, Marta

    2016-11-01

    We studied the effect of laser fluence on the morphology, composition, structure and electric conductivity of deposits generated by pulsed laser ablation of a metallic aluminium target in vacuum using a Q-switched Nd:YAG laser (1064 nm, 15 ns). Upon irradiation for one hour at a repetition rate of 10 Hz, a smooth layer of several tens of nanometres, as revealed by atomic force microscopy (AFM) was deposited on glass. Surface chemical composition was determined by X-ray photoelectron spectroscopy, and to study the conductivity of deposits both I-V curves and conductive-AFM measurements were performed. Irradiation at fluences around 2.7 J/cm2 resulted in deposition of amorphous aluminium oxide films. Differently, at higher fluences above 7 J/cm2, the films are constituted by metallic aluminium. Optical emission spectroscopy revealed that highly ionized species are more abundant in the ablation plumes generated at higher fluences. The results demonstrate the possibility to control by PLD the metal or dielectric character of the films.

  9. Shape Dependent Thermal Conductivity of TiO2-Deionized Water and Ethylene Glycol Dispersion.

    PubMed

    Pal, Bhupender; Mallick, Soumya Suddha; Pal, Bonamali

    2015-05-01

    This paper presents the importance of different shapes and crystal phases of TiO2 nanostructures such as TiO2 P-25 (70:30 anatase and rutile), as-prepared nanorods (pure anatase) and sodium titanate nanotubes (orthorhombic Na2Ti2O5 x H2O crystal) on the thermal conductivity of de-ionized water and ethylene glycol. It revealed that TiO2 nanorods (L x W = 81-134 nm x 8-13 nm and surface area = 79 m2 g(-1)) showed always higher thermal conductivity than porous nanotubes (L x W = 85-115 nm x 9-12 nm and surface area = 176 m2 g(-1)) and commercial TiO2 P-25 (30-55 nm surface area = 56 m2 g(-1)), which was explained by their differences in crystallinity, crystal phases, compactness, surface exposed atoms, surface area and much greater mean free path of longitudinal phonon vibrations along its lateral dimensions. The subsequent effect of sonication time from 5-10 h results into the breakdown of TiO2 nanorods cluster (42 to 28 nm) with the instantaneous increase in negative zeta potential values from -31 to -45 mV, respectively, seems to be an additional cause for enhancement in its thermal conductivity.

  10. Replication-Dependent and Transcription-Dependent Mechanisms of DNA Double-Strand Break Induction by the Topoisomerase 2-Targeting Drug Etoposide

    PubMed Central

    Tammaro, Margaret; Barr, Peri; Ricci, Brett; Yan, Hong

    2013-01-01

    Etoposide is a DNA topoisomerase 2-targeting drug widely used for the treatment of cancer. The cytoxicity of etoposide correlates with the generation of DNA double-strand breaks (DSBs), but the mechanism of how it induces DSBs in cells is still poorly understood. Catalytically, etoposide inhibits the re-ligation reaction of Top2 after it nicks the two strands of DNA, trapping it in a cleavable complex consisting of two Top2 subunits covalently linked to the 5’ ends of DNA (Top2cc). Top2cc is not directly recognized as a true DSB by cells because the two subunits interact strongly with each other to hold the two ends of DNA together. In this study we have investigated the cellular mechanisms that convert Top2ccs into true DSBs. Our data suggest that there are two mechanisms, one dependent on active replication and the other dependent on proteolysis and transcription. The relative contribution of each mechanism is affected by the concentration of etoposide. We also find that Top2α is the major isoform mediating the replication-dependent mechanism and both Top2α and Top2 mediate the transcription-dependent mechanism. These findings are potentially of great significance to the improvement of etoposide’s efficacy in cancer therapy. PMID:24244448

  11. Replication-dependent and transcription-dependent mechanisms of DNA double-strand break induction by the topoisomerase 2-targeting drug etoposide.

    PubMed

    Tammaro, Margaret; Barr, Peri; Ricci, Brett; Yan, Hong

    2013-01-01

    Etoposide is a DNA topoisomerase 2-targeting drug widely used for the treatment of cancer. The cytoxicity of etoposide correlates with the generation of DNA double-strand breaks (DSBs), but the mechanism of how it induces DSBs in cells is still poorly understood. Catalytically, etoposide inhibits the re-ligation reaction of Top2 after it nicks the two strands of DNA, trapping it in a cleavable complex consisting of two Top2 subunits covalently linked to the 5' ends of DNA (Top2cc). Top2cc is not directly recognized as a true DSB by cells because the two subunits interact strongly with each other to hold the two ends of DNA together. In this study we have investigated the cellular mechanisms that convert Top2ccs into true DSBs. Our data suggest that there are two mechanisms, one dependent on active replication and the other dependent on proteolysis and transcription. The relative contribution of each mechanism is affected by the concentration of etoposide. We also find that Top2α is the major isoform mediating the replication-dependent mechanism and both Top2α and Top2 mediate the transcription-dependent mechanism. These findings are potentially of great significance to the improvement of etoposide's efficacy in cancer therapy.

  12. The Arabidopsis HOMOLOGY-DEPENDENT GENE SILENCING1 Gene Codes for an S-Adenosyl-l-Homocysteine Hydrolase Required for DNA Methylation-Dependent Gene Silencing

    PubMed Central

    Rocha, Pedro S.C.F.; Sheikh, Mazhar; Melchiorre, Rosalba; Fagard, Mathilde; Boutet, Stéphanie; Loach, Rebecca; Moffatt, Barbara; Wagner, Conrad; Vaucheret, Hervé; Furner, Ian

    2005-01-01

    Genes introduced into higher plant genomes can become silent (gene silencing) and/or cause silencing of homologous genes at unlinked sites (homology-dependent gene silencing or HDG silencing). Mutations of the HOMOLOGY-DEPENDENT GENE SILENCING1 (HOG1) locus relieve transcriptional gene silencing and methylation-dependent HDG silencing and result in genome-wide demethylation. The hog1 mutant plants also grow slowly and have low fertility and reduced seed germination. Three independent mutants of HOG1 were each found to have point mutations at the 3′ end of a gene coding for S-adenosyl-l-homocysteine (SAH) hydrolase, and hog1-1 plants show reduced SAH hydrolase activity. A transposon (hog1-4) and a T-DNA tag (hog1-5) in the HOG1 gene each behaved as zygotic embryo lethal mutants and could not be made homozygous. The results suggest that the homozygous hog1 point mutants are leaky and result in genome demethylation and poor growth and that homozygous insertion mutations result in zygotic lethality. Complementation of the hog1-1 point mutation with a T-DNA containing the gene coding for SAH hydrolase restored gene silencing, HDG silencing, DNA methylation, fast growth, and normal seed viability. The same T-DNA also complemented the zygotic embryo lethal phenotype of the hog1-4 tagged mutant. A model relating the HOG1 gene, DNA methylation, and methylation-dependent HDG silencing is presented. PMID:15659630

  13. RNA-dependent DNA polymerase of an endogenous type C virus of mice: purification and partial characterization.

    PubMed Central

    Hizi, A; Yaniv, A

    1980-01-01

    An RNA-dependent DNA polymerase was isolated from purified virions of endogenous oncornaviruses released by the MOPC-315 murine myeloma cell line. Upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the purified enzyme was found to consist of two major polypeptides with molecular weights of about 28,000 and 26,500. The active enzyme had a molecular weight of approximately 56,000, as calculated from its sedimentation on glycerol density gradients, indicating that it is probably a dimer of the two subunit polypeptides. The isolated MOPC-315 virus polymerase exhibited all three activities known to be found in the DNA polymerase from oncornaviruses, namely, an RNA-dependent DNA polymerase, a DNA-dependent DNA polymerase, and an RNase H. The RNA-dependent polymerase activity showed a prounced preference for Mn2+ over Mg2+, whereas the DNA-dependent and RNase H reactions were catalyzed by these two cations to an almost equal extent. The purified polymerase was found to be immunologically related to the polymerase of Rauscher murine leukemia virus. Images PMID:6155478

  14. Realizing field-dependent conduction in ZnO nanowires without annealing.

    PubMed

    Burke-Govey, C P; Castanet, U; Warring, H; Nau, A; Ruck, B J; Majimel, J; Plank, N O V

    2017-03-24

    We report on the low-temperature fabrication of field-effect transistors by bridging pre-patterned electrodes using ZnO nanowires grown in situ, which operate without requiring post-growth processing or annealing. The devices show good performance using as-grown nanowires, with on-off ratios of 10(5) and threshold voltages of 2 V. Electron microscopy shows the field-dependent nanowires hierarchically nucleate from larger ZnO nanorods, and both are oriented along a common c-axis. A high nanowire surface-to-volume ratio allows depleting electron traps on the nanowire surface to compensate intrinsic electron donors present throughout the nanowire bulk. This eliminates the need to reduce the electron concentration through high-temperature annealing, making the nanowires naturally field-dependent in their as-grown state.

  15. Realizing field-dependent conduction in ZnO nanowires without annealing

    NASA Astrophysics Data System (ADS)

    Burke-Govey, C. P.; Castanet, U.; Warring, H.; Nau, A.; Ruck, B. J.; Majimel, J.; Plank, N. O. V.

    2017-03-01

    We report on the low-temperature fabrication of field-effect transistors by bridging pre-patterned electrodes using ZnO nanowires grown in situ, which operate without requiring post-growth processing or annealing. The devices show good performance using as-grown nanowires, with on–off ratios of 105 and threshold voltages of 2 V. Electron microscopy shows the field-dependent nanowires hierarchically nucleate from larger ZnO nanorods, and both are oriented along a common c-axis. A high nanowire surface-to-volume ratio allows depleting electron traps on the nanowire surface to compensate intrinsic electron donors present throughout the nanowire bulk. This eliminates the need to reduce the electron concentration through high-temperature annealing, making the nanowires naturally field-dependent in their as-grown state.

  16. A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases.

    PubMed

    Iyer, Lakshminarayan M; Abhiman, Saraswathi; Aravind, L

    2008-10-04

    Using sequence profile methods and structural comparisons we characterize a previously unknown family of nucleic acid polymerases in a group of mobile elements from genomes of diverse bacteria, an algal plastid and certain DNA viruses, including the recently reported Sputnik virus. Using contextual information from domain architectures and gene-neighborhoods we present evidence that they are likely to possess both primase and DNA polymerase activity, comparable to the previously reported prim-pol proteins. These newly identified polymerases help in defining the minimal functional core of superfamily A DNA polymerases and related RNA polymerases. Thus, they provide a framework to understand the emergence of both DNA and RNA polymerization activity in this class of enzymes. They also provide evidence that enigmatic DNA viruses, such as Sputnik, might have emerged from mobile elements coding these polymerases.

  17. Hypotonicity activates a voltage-dependent membrane conductance in N2a neuroblastoma cells.

    PubMed

    Taruno, Akiyuki; Marunaka, Yoshinori

    2017-03-04

    To maintain cellular and bodily homeostasis, cells respond to extracellular stimuli including osmotic stress by activating various ion channels, which have been implicated in many physiological and pathophysiological conditions. However, cellular osmosensory mechanisms remain elusive. Here, we report a novel voltage-dependent current in N2a cells activated by exposure to hypotonic stress. After a hypotonic challenge, N2a cells sequentially develop two distinct currents. The volume-regulated anion channel (VRAC) current emerges first and, after a delay, activation of a previously uncharacterized strongly outwardly rectifying current follows. The latter, delayed current (Id) is insensitive to NPPB, a nonspecific blocker of Cl(-) channels, and intracellular Mg(2+), which inhibits VRAC and swelling-activated TRPM3 and TRPM7 channels. Replacement of extracellular Na(+) with NMDG(+) reduces inward tail currents, suggesting that Id is mediated by cations. Finally, Id shows voltage-dependent activation with slow activation kinetics and half-maximal activation at +76 mV. These pharmacological and biophysical characteristics of Id are distinct from those of known osmotic cell swelling-activated ion channels. In conclusion, our data identify and characterize a novel osmotically-activated, voltage-dependent ion channel in N2a cells.

  18. Electrical conduction of ion tracks in tetrahedral amorphous carbon: temperature, field and doping dependence and comparison with matrix data

    NASA Astrophysics Data System (ADS)

    Krauser, J.; Gehrke, H.-G.; Hofsäss, H.; Amani, J.; Trautmann, C.; Weidinger, A.

    2015-12-01

    This paper gives an extended overview of the electrical properties of ion tracks in hydrogen-free tetrahedral amorphous carbon (ta-C) with a sp3 bond fraction of about 80%. The films were grown by mass selected ion beam deposition of 100 eV 12C+ ions. The ion tracks are generated by irradiation of ta-C films with uranium ions of 1 GeV kinetic energy. Along the ion path a conversion from diamond-like (sp3) carbon to graphite-like (sp2) carbon takes place. Topography and current measurements of individual ion tracks were performed by atomic force microscopy at ambient temperature. The temperature dependence of the electric conductivity was studied between 15 and 390 K by means of 0.28 mm2 large contact pads averaging over about 107 tracks. For each sample and at each temperature the conductivity as a function of the applied electrical field (non-ohmic behaviour) was measured separately and the data were extrapolated to field zero. In this way, the zero-field conductivity was determined independent from the field dependence. In spite of large differences in the absolute values, the temperature dependence of the zero-field conductivities is found to be very similar in shape for all samples. The conductivities follow a {T}-{1/4} law up to temperatures slightly below room temperature. At higher temperatures a transport mechanism based on over-barrier hopping dominates with an activation energy of about 220 meV for tracks and 260 meV for the ta-C matrix. The field dependence measurements show that the deviation of the I-V characteristics from ohmic behaviour decreases with increasing zero-field conductivity. We also tested Cu-doped ta-C samples and found that they conduct significantly better than pure ta-C. However, the doping also increases the zero-field conductivity resulting in a weaker contrast between the track and matrix. The data are interpreted within the so-called ‘barrier model’ where the electrons are assumed to move fairly freely in well-conducting sp2

  19. Salt-Dependent DNA-DNA Spacings in Intact Bacteriophage lambda Reflect Relative Importance of DNA Self-Repulsion and Bending Energies

    SciTech Connect

    X Qiu; D Rau; V Parsegian; L Fang; C Knobler; W Gelbart

    2011-12-31

    Using solution synchrotron x-ray scattering, we measure the variation of DNA-DNA d spacings in bacteriophage {lambda} with mono-, di-, and polyvalent salt concentrations, for wild-type [48.5 x 10{sup 3} base pairs (bp)] and short-genome-mutant (37.8 kbp) strains. From the decrease in d spacings with increasing salt, we deduce the relative contributions of DNA self-repulsion and bending to the energetics of packaged phage genomes. We quantify the DNA-DNA interaction energies within the intact phage by combining the measured d spacings in the capsid with measurements of osmotic pressure in DNA assemblies under the same salt conditions in bulk solution. In the commonly used Tris-Mg buffer, the DNA-DNA interaction energies inside the phage capsids are shown to be about 1 kT/bp, an order of magnitude larger than the bending energies.

  20. Stereochemistry-Dependent Proton Conduction in Proton Exchange Membrane Fuel Cells.

    PubMed

    Thimmappa, Ravikumar; Devendrachari, Mruthyunjayachari Chattanahalli; Kottaichamy, Alagar Raja; Tiwari, Omshanker; Gaikwad, Pramod; Paswan, Bhuneshwar; Thotiyl, Musthafa Ottakam

    2016-01-12

    Graphene oxide (GO) is impermeable to H2 and O2 fuels while permitting H(+) shuttling, making it a potential candidate for proton exchange membrane fuel cells (PEMFC), albeit with a large anisotropy in their proton transport having a dominant in plane (σIP) contribution over the through plane (σTP). If GO-based membranes are ever to succeed in PEMFC, it inevitably should have a dominant through-plane proton shuttling capability (σTP), as it is the direction in which proton gets transported in a real fuel-cell configuration. Here we show that anisotropy in proton conduction in GO-based fuel cell membranes can be brought down by selectively tuning the geometric arrangement of functional groups around the dopant molecules. The results show that cis isomer causes a selective amplification of through-plane proton transport, σTP, pointing to a very strong geometry angle in ionic conduction. Intercalation of cis isomer causes significant expansion of GO (001) planes involved in σTP transport due to their mutual H-bonding interaction and efficient bridging of individual GO planes, bringing down the activation energy required for σTP, suggesting the dominance of a Grotthuss-type mechanism. This isomer-governed amplification of through-plane proton shuttling resulted in the overall boosting of fuel-cell performance, and it underlines that geometrical factors should be given prime consideration while selecting dopant molecules for bringing down the anisotropy in proton conduction and enhancing the fuel-cell performance in GO-based PEMFC.

  1. Temperature dependence electrical conduction of solution-processed CZTS films in dark and under light

    NASA Astrophysics Data System (ADS)

    Ghediya, Prashant R.; Chaudhuri, Tapas K.; Patel, K. C.

    2016-09-01

    Electrical conduction of solution-processed Cu2ZnSnS4 (CZTS) films has been reported in dark and under light in the temperature range of 85 to 300 K. The films show nearest neighbor hopping mode of transport at below 200 K, while above 200 K the films were dominated by thermionic emission over grain boundary barriers, following, Seto's model for polycrystalline films. The hopping energy and grain boundary barrier height of CZTS films are found be decreases under illumination due to the photoconductivity. The films were pure kesterite CZTS as revealed from X-Ray diffraction and Raman spectroscopy.

  2. DNA Ligase I is an In Vivo Substrate of DNA-Dependent Protein Kinase and is Activated by Phosphorylation in Response to DNA Double-Strand Breaks

    DTIC Science & Technology

    2006-01-01

    anlysis. to the procedure described by Malanga and Althaus (8). Gel Electrophoresis and A utoradiography. Immunopre- DNA Ligase and Protein Assays. DNA...by casein kinase 11, EMBO J. 11, 2925-2933. In conclusion, we have demonstrated that DNA ligase I 8. Malanga , M., and Althaus, F. R. (1994) Poly (ADP

  3. Temperature dependence of electrical and thermal conduction in single silver nanowire.

    PubMed

    Cheng, Zhe; Liu, Longju; Xu, Shen; Lu, Meng; Wang, Xinwei

    2015-06-02

    In this work, the thermal and electrical transport in an individual silver nanowire is characterized down to 35 K for in-depth understanding of the strong structural defect induced electron scattering. The results indicate that, at room temperature, the electrical resistivity increases by around 4 folds from that of bulk silver. The Debye temperature (151 K) of the silver nanowire is found 36% lower than that (235 K) of bulk silver, confirming strong phonon softening. At room temperature, the thermal conductivity is reduced by 55% from that of bulk silver. This reduction becomes larger as the temperature goes down. To explain the opposite trends of thermal conductivity (κ) ~ temperature (T) of silver nanowire and bulk silver, a unified thermal resistivity (Θ ~ T/k ) is used to elucidate the electron scattering mechanism. A large residual Θ is observed for silver nanowire while that of the bulk silver is almost zero. The same Θ ~ T trend proposes that the silver nanowire and bulk silver share the similar phonon-electron scattering mechanism for thermal transport. Due to phonon-assisted electron energy transfer across grain boundaries, the Lorenz number of the silver nanowire is found much larger than that of bulk silver and decreases with decreasing temperature.

  4. DNA-Dependent Protein Kinase Phosphorylation of IκBα and IκBβ Regulates NF-κB DNA Binding Properties

    PubMed Central

    Liu, Li; Kwak, Youn-Tae; Bex, Françoise; García-Martínez, León F.; Li, Xiao-Hua; Meek, Katheryn; Lane, William S.; Gaynor, Richard B.

    1998-01-01

    Regulation of the IκBα and IκBβ proteins is critical for modulating NF-κB-directed gene expression. Both IκBα and IκBβ are substrates for cellular kinases that phosphorylate the amino and carboxy termini of these proteins and regulate their function. In this study, we utilized a biochemical fractionation scheme to purify a kinase activity which phosphorylates residues in the amino and carboxy termini of both IκBα and IκBβ. Peptide microsequence analysis by capillary high-performance liquid chromatography ion trap mass spectroscopy revealed that this kinase was the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). DNA-PK phosphorylates serine residue 36 but not serine residue 32 in the amino terminus of IκBα and also phosphorylates threonine residue 273 in the carboxy terminus of this protein. To determine the biological relevance of DNA-PK phosphorylation of IκBα, murine severe combined immunodeficiency (SCID) cell lines which lack the DNA-PKcs gene were analyzed. Gel retardation analysis using extract prepared from these cells demonstrated constitutive nuclear NF-κB DNA binding activity, which was not detected in extracts prepared from SCID cells complemented with the human DNA-PKcs gene. Furthermore, IκBα that was phosphorylated by DNA-PK was a more potent inhibitor of NF-κB binding than nonphosphorylated IκBα. These results suggest that DNA-PK phosphorylation of IκBα increases its interaction with NF-κB to reduce NF-κB DNA binding properties. PMID:9632806

  5. The dependence of radiofrequency induced pacemaker lead tip heating on the electrical conductivity of the medium at the lead tip.

    PubMed

    Langman, Deborah A; Goldberg, Ira B; Judy, Jack; Paul Finn, J; Ennis, Daniel B

    2012-08-01

    Radiofrequency induced pacemaker lead tip heating is one of the main reasons magnetic resonance imaging (MRI) is contraindicated for patients with pacemakers. The objective of this work was to evaluate the dependence of pacemaker lead tip heating during MRI scanning on the electrical conductivity of the medium surrounding the pacemaker lead tip. The effect of conductivity was measured using hydroxyethyl cellulose, polyacrylic acid, and saline with conductivities ranging from 0 to 3 S/m which spans the range of human tissue conductivity. The maximum lead tip heating observed in polyacrylic acid was 50.4 °C at 0.28 S/m, in hydroxyethyl cellulose the maximum was 36.8 °C at 0.52 S/m, and in saline the maximum was 12.5 °C at 0.51 S/m. The maximum power transfer theorem was used to calculate the relative power deposited in the solution based on the characteristic impedance of the pacemaker lead and test solution impedance. The results demonstrate a strong correlation between the relative power deposited and pacemaker lead tip heating for hydroxyethyl cellulose and saline solutions. Maximum power deposition occurred when the impedance of the solution matched the pacemaker lead impedance. Pacemaker lead tip heating is dependent upon the electrical conductivity of the solution at the lead tip and should be considered when planning in vitro gel or saline experiments.

  6. Superresolution imaging reveals activity-dependent plasticity of axon morphology linked to changes in action potential conduction velocity.

    PubMed

    Chéreau, Ronan; Saraceno, G Ezequiel; Angibaud, Julie; Cattaert, Daniel; Nägerl, U Valentin

    2017-02-07

    Axons convey information to nearby and distant cells, and the time it takes for action potentials (APs) to reach their targets governs the timing of information transfer in neural circuits. In the unmyelinated axons of hippocampus, the conduction speed of APs depends crucially on axon diameters, which vary widely. However, it is not known whether axon diameters are dynamic and regulated by activity-dependent mechanisms. Using time-lapse superresolution microscopy in brain slices, we report that axons grow wider after high-frequency AP firing: synaptic boutons undergo a rapid enlargement, which is mostly transient, whereas axon shafts show a more delayed and progressive increase in diameter. Simulations of AP propagation incorporating these morphological dynamics predicted bidirectional effects on AP conduction speed. The predictions were confirmed by electrophysiological experiments, revealing a phase of slowed down AP conduction, which is linked to the transient enlargement of the synaptic boutons, followed by a sustained increase in conduction speed that accompanies the axon shaft widening induced by high-frequency AP firing. Taken together, our study outlines a morphological plasticity mechanism for dynamically fine-tuning AP conduction velocity, which potentially has wide implications for the temporal transfer of information in the brain.

  7. Statistical inferences for data from studies conducted with an aggregated multivariate outcome-dependent sample design.

    PubMed

    Lu, Tsui-Shan; Longnecker, Matthew P; Zhou, Haibo

    2017-03-15

    Outcome-dependent sampling (ODS) scheme is a cost-effective sampling scheme where one observes the exposure with a probability that depends on the outcome. The well-known such design is the case-control design for binary response, the case-cohort design for the failure time data, and the general ODS design for a continuous response. While substantial work has been carried out for the univariate response case, statistical inference and design for the ODS with multivariate cases remain under-developed. Motivated by the need in biological studies for taking the advantage of the available responses for subjects in a cluster, we propose a multivariate outcome-dependent sampling (multivariate-ODS) design that is based on a general selection of the continuous responses within a cluster. The proposed inference procedure for the multivariate-ODS design is semiparametric where all the underlying distributions of covariates are modeled nonparametrically using the empirical likelihood methods. We show that the proposed estimator is consistent and developed the asymptotically normality properties. Simulation studies show that the proposed estimator is more efficient than the estimator obtained using only the simple-random-sample portion of the multivariate-ODS or the estimator from a simple random sample with the same sample size. The multivariate-ODS design together with the proposed estimator provides an approach to further improve study efficiency for a given fixed study budget. We illustrate the proposed design and estimator with an analysis of association of polychlorinated biphenyl exposure to hearing loss in children born to the Collaborative Perinatal Study. Copyright © 2016 John Wiley & Sons, Ltd.

  8. Temperature dependence of spin lifetime of conduction electrons in bulk germanium

    NASA Astrophysics Data System (ADS)

    Guite, Chinkhanlun; Venkataraman, V.

    2012-12-01

    Optically generated spin polarized electrons in bulk n-type Ge samples have been detected by using a radio-frequency modulation technique. Using the Hanle effect in an external magnetic field, the spin lifetime was measured as a function of temperature in the range 90 K to 180 K. The lifetime decreases with increasing temperature from ˜5 ns at 100 K to ˜2 ns at 180 K. We show that the temperature dependence is consistent with the Elliott-Yafet spin relaxation mechanism [R. J. Elliot, Phys. Rev. 96, 266 (1954)].

  9. PARP-2 domain requirements for DNA damage-dependent activation and localization to sites of DNA damage.

    PubMed

    Riccio, Amanda A; Cingolani, Gino; Pascal, John M

    2016-02-29

    Poly(ADP-ribose) polymerase-2 (PARP-2) is one of three human PARP enzymes that are potently activated during the cellular DNA damage response (DDR). DDR-PARPs detect DNA strand breaks, leading to a dramatic increase in their catalytic production of the posttranslational modification poly(ADP-ribose) (PAR) to facilitate repair. There are limited biochemical and structural insights into the functional domains of PARP-2, which has restricted our understanding of how PARP-2 is specialized toward specific repair pathways. PARP-2 has a modular architecture composed of a C-terminal catalytic domain (CAT), a central Trp-Gly-Arg (WGR) domain and an N-terminal region (NTR). Although the NTR is generally considered the key DNA-binding domain of PARP-2, we report here that all three domains of PARP-2 collectively contribute to interaction with DNA damage. Biophysical, structural and biochemical analyses indicate that the NTR is natively disordered, and is only required for activation on specific types of DNA damage. Interestingly, the NTR is not essential for PARP-2 localization to sites of DNA damage. Rather, the WGR and CAT domains function together to recruit PARP-2 to sites of DNA breaks. Our study differentiates the functions of PARP-2 domains from those of PARP-1, the other major DDR-PARP, and highlights the specialization of the multi-domain architectures of DDR-PARPs.

  10. PARP-2 domain requirements for DNA damage-dependent activation and localization to sites of DNA damage

    PubMed Central

    Riccio, Amanda A.; Cingolani, Gino; Pascal, John M.

    2016-01-01

    Poly(ADP-ribose) polymerase-2 (PARP-2) is one of three human PARP enzymes that are potently activated during the cellular DNA damage response (DDR). DDR-PARPs detect DNA strand breaks, leading to a dramatic increase in their catalytic production of the posttranslational modification poly(ADP-ribose) (PAR) to facilitate repair. There are limited biochemical and structural insights into the functional domains of PARP-2, which has restricted our understanding of how PARP-2 is specialized toward specific repair pathways. PARP-2 has a modular architecture composed of a C-terminal catalytic domain (CAT), a central Trp-Gly-Arg (WGR) domain and an N-terminal region (NTR). Although the NTR is generally considered the key DNA-binding domain of PARP-2, we report here that all three domains of PARP-2 collectively contribute to interaction with DNA damage. Biophysical, structural and biochemical analyses indicate that the NTR is natively disordered, and is only required for activation on specific types of DNA damage. Interestingly, the NTR is not essential for PARP-2 localization to sites of DNA damage. Rather, the WGR and CAT domains function together to recruit PARP-2 to sites of DNA breaks. Our study differentiates the functions of PARP-2 domains from those of PARP-1, the other major DDR-PARP, and highlights the specialization of the multi-domain architectures of DDR-PARPs. PMID:26704974

  11. CONDENSED MATTER: ELECTRONIC STRUCTURE, ELECTRICAL, MAGNETIC, AND OPTICAL PROPERTIES: Dependence of Conductance of Corrugated Graphene Quantum Dot on Geometrical Features

    NASA Astrophysics Data System (ADS)

    Li, Gui-Qin; Deng, Jing-Kang; Cai, Jun

    2009-11-01

    Dependence of conductance of corrugated graphene quantum dot (CGQD) on geometrical features including length, width, connection and edge is investigated by the first principles calculations. The results demonstrate that the conductance of CGQD with different geometrical features is different from each other. The positions and amplitudes of discrete levels in densities of states and transmission coefficients are sensitive to geometrical features. The I-V characteristics of graphene are modified by size and edge, it is surprise the current does not change monotonously but oscillatory with length. And they are slight change for different connections.

  12. The immunogenicity of viral haemorragic septicaemia rhabdovirus (VHSV) DNA vaccines can depend on plasmid regulatory sequences.

    PubMed

    Chico, V; Ortega-Villaizan, M; Falco, A; Tafalla, C; Perez, L; Coll, J M; Estepa, A

    2009-03-18

    A plasmid DNA encoding the viral hemorrhagic septicaemia virus (VHSV)-G glycoprotein under the control of 5' sequences (enhancer/promoter sequence plus both non-coding 1st exon and 1st intron sequences) from carp beta-actin gene (pAE6-G(VHSV)) was compared to the vaccine plasmid usually described the gene expression is regulated by the human cytomegalovirus (CMV) immediate-early promoter (pMCV1.4-G(VHSV)). We observed that these two plasmids produced a markedly different profile in the level and time of expression of the encoded-antigen, and this may have a direct effect upon the intensity and suitability of the in vivo immune response. Thus, fish genetic immunisation assays were carried out to study the immune response of both plasmids. A significantly enhanced specific-antibody response against the viral glycoprotein was found in the fish immunised with pAE6-G(VHSV). However, the protective efficacy against VHSV challenge conferred by both plasmids was similar. Later analysis of the transcription profile of a set of representative immune-related genes in the DNA immunized fish suggested that depending on the plasmid-related regulatory sequences controlling its expression, the plasmid might activate distinct patterns of the immune system. All together, the results from this study mainly point out that the selection of a determinate encoded-antigen/vector combination for genetic immunisation is of extraordinary importance in designing optimised DNA vaccines that, when required for inducing protective immune response, could elicit responses biased to antigen-specific antibodies or cytotoxic T cells generation.

  13. Chiral Differentiation of DNA Adducts Formed by Enantiomeric Analogues of Antitumor Cisplatin Is Sequence-Dependent

    PubMed Central

    Delalande, Olivier; Malina, Jaroslav; Brabec, Viktor; Kozelka, Jiří

    2005-01-01

    1,2-GG intrastrand cross-links formed in DNA by the enantiomeric complexes [PtCl2(R,R-2,3-diaminobutane (DAB))] and [PtCl2(S,S-DAB)] were studied by biophysical methods. Molecular modeling revealed that structure of the cross-links formed at the TGGT sequence was affected by repulsion between the 5′-directed methyl group of the DAB ligand and the methyl group of the 5′-thymine of the TGGT fragment. Molecular dynamics simulations of the solvated platinated duplexes and our recent structural data indicated that the adduct of [PtCl2(R,R-DAB)] alleviated this repulsion by unwinding the TpG step, whereas the adduct of [PtCl2(S,S-DAB)] avoided the unfavorable methyl-methyl interaction by decreasing the kink angle. Electrophoretic retardation measurements on DNA duplexes containing 1,2-GG intrastrand cross-links of Pt(R,R-DAB)2+ or Pt(S,S-DAB)2+ at a CGGA site showed that in this sequence both enantiomers distorted the double helix to the identical extent similar to that found previously for the same sequence containing the cross-links of the parent antitumor \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}cis-{\\mathrm{Pt}}({\\mathrm{NH}}_{3})_{2}^{2+}\\end{equation*}\\end{document} (cisplatin). In addition, the adducts showed similar affinities toward the high-mobility-group box 1 proteins. Hence, whereas the structural perturbation induced in DNA by 1,2-GG intrastrand cross-links of cisplatin does not depend largely on the bases flanking the cross-links, the perturbation related to GG cross-linking by bulkier platinum diamine derivatives does. PMID:15805172

  14. Length dependence of conductance and thermopower of hybrid alkyl-thiophene single molecule junctions

    NASA Astrophysics Data System (ADS)

    Kotiuga, Michele; Chang, William B.; Mai, Cheng-Kang; Pauly, Fabian; Bazan, Guillermo C.; Segalman, Rachel A.; Neaton, Jeffrey B.

    2014-03-01

    Single-molecule junctions are novel, controllable testbeds for understanding mixed electronic and thermal transport at interfaces. Here, we study a set of newly-synthesized molecules containing alkyl and thiophene units of increasing length in order to control junction level alignment and electronic coupling with a combination of theory and experiment. Using a first-principles scattering-state approach, based on self-energy corrected density functional theory, we calculate the conductance and thermopower of thiol-terminated alkyl-thiophene-Au junctions, elucidating the relationship between length and thermopower. We compare our work to statistical measurements with a scanning tunneling microscope-based break junction technique, and discuss the impact of junction geometry on our results. Work supported by ONR/AFOSR BAA 10-026 and computational resources provided by NERSC.

  15. [Sound reception in marine mammals depending on sound parameters and conduction pathways].

    PubMed

    Babushina, E S

    1999-01-01

    The interaction of complex sounds with the body tissues of Black Sea dolphin (Tursiops truncatus) was studied by the method of instrumental conditioned reflexes with food reinforcement. The thresholds of detecting underwater acoustic signals of different frequencies for dolphin and northern fur seal (Callorhinus ursinus) were measured as a function of pulse duration under conditions of full and partial (head above water) submergence of animals into water. It was found that sound conduction through dolphin tissues was more effective than that in a northern fur seal in a wide frequency range. Presumably, the process of sound propagation in dolphin is accompanied by changes in the amplitude-frequency structure of broad-band sounds. The temporal summation in dolphin hearing was observed at all frequencies under conditions of full and partial submergence, whereas in northern fur seal it was nearly absent at a frequency of 5 kHz under the conditions of head lifting above water.

  16. Scale-dependency of effective hydraulic conductivity on fire-affected hillslopes

    NASA Astrophysics Data System (ADS)

    Langhans, Christoph; Lane, Patrick N. J.; Nyman, Petter; Noske, Philip J.; Cawson, Jane G.; Oono, Akiko; Sheridan, Gary J.

    2016-07-01

    Effective hydraulic conductivity (Ke) for Hortonian overland flow modeling has been defined as a function of rainfall intensity and runon infiltration assuming a distribution of saturated hydraulic conductivities (Ks). But surface boundary condition during infiltration and its interactions with the distribution of Ks are not well represented in models. As a result, the mean value of the Ks distribution (KS¯), which is the central parameter for Ke, varies between scales. Here we quantify this discrepancy with a large infiltration data set comprising four different methods and scales from fire-affected hillslopes in SE Australia using a relatively simple yet widely used conceptual model of Ke. Ponded disk (0.002 m2) and ring infiltrometers (0.07 m2) were used at the small scales and rainfall simulations (3 m2) and small catchments (ca 3000 m2) at the larger scales. We compared KS¯ between methods measured at the same time and place. Disk and ring infiltrometer measurements had on average 4.8 times higher values of KS¯ than rainfall simulations and catchment-scale estimates. Furthermore, the distribution of Ks was not clearly log-normal and scale-independent, as supposed in the conceptual model. In our interpretation, water repellency and preferential flow paths increase the variance of the measured distribution of Ks and bias ponding toward areas of very low Ks during rainfall simulations and small catchment runoff events while areas with high preferential flow capacity remain water supply-limited more than the conceptual model of Ke predicts. The study highlights problems in the current theory of scaling runoff generation.

  17. Heat Capacity Changes Associated with DNA Duplex Formation: Salt- and Sequence-Dependent Effects†

    PubMed Central

    Mikulecky, Peter J.; Feig, Andrew L.

    2008-01-01

    Duplexes are the most fundamental elements of nucleic acid folding. Although it has become increasingly clear that duplex formation can be associated with a significant change in heat capacity (ΔCp), this parameter is typically overlooked in thermodynamic studies of nucleic acid folding. Analogy to protein folding suggests that base stacking events coupled to duplex formation should give rise to a ΔCp due to the release of waters solvating aromatic surfaces of nucleotide bases. In previous work, we showed that the ΔCp observed by isothermal titration calorimetry (ITC) for RNA duplex formation depended on salt and sequence. In the present work, we apply calorimetric and spectroscopic techniques to a series of designed DNA duplexes to demonstrate that both the salt dependence and sequence dependence of ΔCps observed by ITC reflect perturbations to the same fundamental phenomenon: stacking in the single-stranded state. By measuring the thermodynamics of single strand melting, one can accurately predict the ΔCps observed for duplex formation by ITC at high and low ionic strength. We discuss our results in light of the larger issue of contributions to ΔCp from coupled equilibria and conclude that observed ΔCps can be useful indicators of intermediate states in nucleic acid folding phenomena. PMID:16401089

  18. Chromosome Synapsis Alleviates Mek1-Dependent Suppression of Meiotic DNA Repair

    PubMed Central

    Subramanian, Vijayalakshmi V.; MacQueen, Amy J.; Vader, Gerben; Shinohara, Miki; Sanchez, Aurore; Borde, Valérie; Shinohara, Akira; Hochwagen, Andreas

    2016-01-01

    Faithful meiotic chromosome segregation and fertility require meiotic recombination between homologous chromosomes rather than the equally available sister chromatid, a bias that in Saccharomyces cerevisiae depends on the meiotic kinase, Mek1. Mek1 is thought to mediate repair template bias by specifically suppressing sister-directed repair. Instead, we found that when Mek1 persists on closely paired (synapsed) homologues, DNA repair is severely delayed, suggesting that Mek1 suppresses any proximal repair template. Accordingly, Mek1 is excluded from synapsed homologues in wild-type cells. Exclusion requires the AAA+-ATPase Pch2 and is directly coupled to synaptonemal complex assembly. Stage-specific depletion experiments further demonstrate that DNA repair in the context of synapsed homologues requires Rad54, a repair factor inhibited by Mek1. These data indicate that the sister template is distinguished from the homologue primarily by its closer proximity to inhibitory Mek1 activity. We propose that once pairing or synapsis juxtaposes homologues, exclusion of Mek1 is necessary to avoid suppression of all templates and accelerate repair progression. PMID:26870961

  19. 53BP1 and the LINC Complex Promote Microtubule-Dependent DSB Mobility and DNA Repair.

    PubMed

    Lottersberger, Francisca; Karssemeijer, Roos Anna; Dimitrova, Nadya; de Lange, Titia

    2015-11-05

    Increased mobility of chromatin surrounding double-strand breaks (DSBs) has been noted in yeast and mammalian cells but the underlying mechanism and its contribution to DSB repair remain unclear. Here, we use a telomere-based system to track DNA damage foci with high resolution in living cells. We find that the greater mobility of damaged chromatin requires 53BP1, SUN1/2 in the linker of the nucleoskeleton, and cytoskeleton (LINC) complex and dynamic microtubules. The data further demonstrate that the excursions promote non-homologous end joining of dysfunctional telomeres and implicated Nesprin-4 and kinesins in telomere fusion. 53BP1/LINC/microtubule-dependent mobility is also evident at irradiation-induced DSBs and contributes to the mis-rejoining of drug-induced DSBs in BRCA1-deficient cells showing that DSB mobility can be detrimental in cells with numerous DSBs. In contrast, under physiological conditions where cells have only one or a few lesions, DSB mobility is proposed to prevent errors in DNA repair.

  20. Topoisomerase II Inhibitors Induce DNA Damage-Dependent Interferon Responses Circumventing Ebola Virus Immune Evasion

    PubMed Central

    Luthra, Priya; Aguirre, Sebastian; Yen, Benjamin C.; Pietzsch, Colette A.; Sanchez-Aparicio, Maria T.; Tigabu, Bersabeh; Morlock, Lorraine K.; García-Sastre, Adolfo; Leung, Daisy W.; Williams, Noelle S.; Fernandez-Sesma, Ana; Bukreyev, Alexander

    2017-01-01

    ABSTRACT Ebola virus (EBOV) protein VP35 inhibits production of interferon alpha/beta (IFN) by blocking RIG-I-like receptor signaling pathways, thereby promoting virus replication and pathogenesis. A high-throughput screening assay, developed to identify compounds that either inhibit or bypass VP35 IFN-antagonist function, identified five DNA intercalators as reproducible hits from a library of bioactive compounds. Four, including doxorubicin and daunorubicin, are anthracycline antibiotics that inhibit topoisomerase II and are used clinically as chemotherapeutic drugs. These compounds were demonstrated to induce IFN responses in an ATM kinase-dependent manner and to also trigger the DNA-sensing cGAS-STING pathway of IFN induction. These compounds also suppress EBOV replication in vitro and induce IFN in the presence of IFN-antagonist proteins from multiple negative-sense RNA viruses. These findings provide new insights into signaling pathways activated by important chemotherapy drugs and identify a novel therapeutic approach for IFN induction that may be exploited to inhibit RNA virus replication. PMID:28377530

  1. DNA-binding dependent and independent functions of WT1 protein during human hematopoiesis

    SciTech Connect

    Svensson, Emelie; Eriksson, Helena; Gekas, Christos; Olofsson, Tor; Richter, Johan; Gullberg, Urban . E-mail: urban.gullberg@hematologi.lu.se

    2005-08-01

    The Wilms tumor gene 1 (WT1) encodes a zinc-finger-containing transcription factor highly expressed in immature hematopoietic progenitor cells. Overexpression and presence of somatic mutations in acute leukemia indicate a role for WT1 in the pathogenesis of leukemia. CD34{sup +} progenitor cells were transduced with one splice variant of human WT1 without the KTS insert in the zinc-finger domain, WT1(+/-), and with a deleted mutant of WT1 lacking the entire zinc-finger region, WT1(delZ), thus incapable of binding DNA. We show that inhibition of erythroid colony formation and differentiation is absolutely dependent on the DNA-binding zinc-finger domain of WT1. Unexpectedly, however, WT1(delZ) was equally effective as wild type protein in the reduction of myeloid clonogenic growth as well as in stimulation of myeloid differentiation, as judged by the expression of cell surface CD11b. Expression of neither WT1(+/-) nor WT1(delZ) upregulated mRNA for the cdk inhibitor p21{sup Waf1/Cip1} or p27{sup Kip1}. Our results demonstrate that WT1 affects proliferation and differentiation in erythroid and myeloid cells by different molecular mechanisms, and suggest that mutations affecting the zinc-finger domain of WT1 could interfere with normal differentiation in the pathogenesis of leukemia.

  2. Histamine potentiates neuronal excitation by blocking a calcium-dependent potassium conductance.

    PubMed

    Haas, H L

    1984-04-01

    Histaminergic neurones send their axons to the whole forebrain. The diffuse projection is consistent with a modulatory role of these pathways. In hippocampal slices from rats a mechanism for this modulation is described, on pyramidal neurones of the CA 1 area: Strong excitations induced by intracellular current injection, ionophoretic administration of glutamate or synaptic stimulation normally restrict themselves by the activation of the calcium-dependent potassium current (gK(Ca) ). This current causes a long lasting afterhyperpolarization and an accommodation of firing. Their block by histamine and impromidine (reversed by metiamide and cimetidine) leads to a profound potentiation of excitatory signals. It is suggested that HA, through H2 receptors, accelerates the removal of intracellular free Ca++ ions.

  3. Length dependence of the thermal conductance of alkane-based single-molecule junctions: An ab initio study

    NASA Astrophysics Data System (ADS)

    Klöckner, J. C.; Bürkle, M.; Cuevas, J. C.; Pauly, F.

    2016-11-01

    Motivated by recent experiments, we present here a systematic ab initio study of the length dependence of the thermal conductance of single-molecule junctions. We make use of a combination of density functional theory with nonequilibrium Green's function techniques to investigate the length dependence of the phonon transport in single-alkane chains, contacted with gold electrodes via both thiol and amine anchoring groups. Additionally, we study the effect of the substitution of the hydrogen atoms in the alkane chains by heavier fluorine atoms to form polytetrafluoroethylenes. Our results demonstrate that (i) the room-temperature thermal conductance is fairly length independent for chains with more than 5 methylene units and (ii) the efficiency of the thermal transport is strongly influenced by the strength of the phononic metal-molecule coupling. Our study sheds light on the phonon transport in molecular junctions, and it provides clear guidelines for the design of molecular junctions for thermal management.

  4. Temperature Dependence of Density, Viscosity and Electrical Conductivity for Hg-Based II-VI Semiconductor Melts

    NASA Technical Reports Server (NTRS)

    Li, C.; Ban, H.; Lin, B.; Scripa, R. N.; Su, C.-H.; Lehoczky, S. L.

    2004-01-01

    The relaxation phenomenon of semiconductor melts, or the change of melt structure with time, impacts the crystal growth process and the eventual quality of the crystal. The thermophysical properties of the melt are good indicators of such changes in melt structure. Also, thermophysical properties are essential to the accurate predication of the crystal growth process by computational modeling. Currently, the temperature dependent thermophysical property data for the Hg-based II-VI semiconductor melts are scarce. This paper reports the results on the temperature dependence of melt density, viscosity and electrical conductivity of Hg-based II-VI compounds. The melt density was measured using a pycnometric method, and the viscosity and electrical conductivity were measured by a transient torque method. Results were compared with available published data and showed good agreement. The implication of the structural changes at different temperature ranges was also studied and discussed.

  5. Concentration- and chromosome-organization-dependent regulator unbinding from DNA for transcription regulation in living cells

    PubMed Central

    Chen, Tai-Yen; Santiago, Ace George; Jung, Won; Krzemiński, Łukasz; Yang, Feng; Martell, Danya J.; Helmann, John D.; Chen, Peng

    2015-01-01

    Binding and unbinding of transcription regulators at operator sites constitute a primary mechanism for gene regulation. While many cellular factors are known to regulate their binding, little is known on how cells can modulate their unbinding for regulation. Using nanometer-precision single-molecule tracking, we study the unbinding kinetics from DNA of two metal-sensing transcription regulators in living Escherichia coli cells. We find that they show unusual concentration-dependent unbinding kinetics from chromosomal recognition sites in both their apo and holo forms. Unexpectedly, their unbinding kinetics further varies with the extent of chromosome condensation, and more surprisingly, varies in opposite ways for their apo-repressor versus holo-activator forms. These findings suggest likely broadly relevant mechanisms for facile switching between transcription activation and deactivation in vivo and in coordinating transcription regulation of resistance genes with the cell cycle. PMID:26145755

  6. Topoisomerase IIalpha-dependent induction of a persistent DNA damage response in response to transient etoposide exposure.

    PubMed

    Soubeyrand, Sébastien; Pope, Louise; Haché, Robert J G

    2010-02-01

    Cytotoxicity of the topoisomerase II (topoII) poison etoposide has been ascribed to the persistent covalent trapping of topoII in DNA cleavage complexes that become lethal as cells replicate their DNA. However, short term etoposide treatment also leads to subsequent cell death, suggesting that the lesions that lead to cytotoxicity arise rapidly and prior to the onset DNA replication. In the present study 1h treatment with 25muM etoposide was highly toxic and initiated a double-stranded DNA damage response as reflected by the recruitment of ATM, MDC1 and DNA-PKcs to gammaH2AX foci. While most DNA breaks were rapidly repaired upon withdrawal of the etoposide treatment, the repair machinery remained engaged in foci for at least 24h following withdrawal. TopoII siRNA ablation showed the etoposide toxicity and gammaH2AX response to correlate with the inability of the cell to correct topoIIalpha-initiated DNA damage. gammaH2AX induction was resistant to the inhibition of DNA replication and transcription, but was increased by pre-treatment with the histone deacetylase inhibitor trichostatin A. These results link the lethality of etoposide to the generation of persistent topoIIalpha-dependent DNA defects within topologically open chromatin domains.

  7. trans Autophosphorylation at DNA-Dependent Protein Kinase's Two Major Autophosphorylation Site Clusters Facilitates End Processing but Not End Joining▿

    PubMed Central

    Meek, Katheryn; Douglas, Pauline; Cui, Xiaoping; Ding, Qi; Lees-Miller, Susan P.

    2007-01-01

    Recent studies have established that DNA-dependent protein kinase (DNA-PK) undergoes a series of autophosphorylation events that facilitate successful completion of nonhomologous DNA end joining. Autophosphorylation at sites in two distinct clusters regulates DNA end access to DNA end-processing factors and to other DNA repair pathways. Autophosphorylation within the kinase's activation loop regulates kinase activity. Additional autophosphorylation events (as yet undefined) occur that mediate kinase dissociation. Here we provide the first evidence that autophosphorylation within the two major clusters (regulating end access) occurs in trans. Further, both UV-induced and double-strand break (DSB)-induced phosphorylation in the two major clusters is predominately autophosphorylation. Finally, we show that while autophosphorylation in trans on one of two synapsed DNA-PK complexes facilitates appropriate end processing, this is not sufficient to promote efficient end joining. This suggests that end joining in living cells requires additional phosphorylation events that either occur in cis or that occur on both sides of the DNA-PK synapse. These data support an emerging consensus that, via a series of autophosphorylation events, DNA-PK undergoes a sequence of conformational changes that promote efficient and appropriate repair of DSBs. PMID:17353268

  8. Wavelength dependence for the photoreactions of DNA-Psoralen monoadducts. 1. Photoreversal of monoadducts

    SciTech Connect

    Shi, Y.; Hearst, J.E.

    1987-06-30

    The authors have studied the wavelength dependence for the photoreversal of a monoadducted psoralen derivative, HMT (4'(hydroxymethyl)-4,5',8-trimethylpsoralen), in a single-stranded deoxyoligonucleotide (5'-GAAGCTACGAGC-3'). The psoralen was covalently attached to the thymidine residue in the oligonucleotide as either a furan-side monoadduct, which is formed through the cycloaddition between the 4',5' double bond of the psoralen and the 5,6 double bond of the thymidine, or a pyrone-side monoadduct, which is formed through the cycloaddition between the 3,4 double bond of the psoralen and the 5,6 double bond of the thymidine. As a comparison, they have also investigated the wavelength-dependent photoreversal of the isolated thymidine-HMT monoadducts. All photoreversal action spectra correlate with the extinction spectra of the isolate monoadducts. In the case of the pyrone-side monoadduct, two absorption bands contribute to the photoreversal with a quantum yield of 2 x 10/sup -2/ at wavelengths below 250 nm and 7 x 10/sup -3/ at wavelengths from 287 to 314 nm. The incorporation of the monoadduct into the DNA oligomer had little effect upon the photoreversal rate. For the furan-side monoadduct at least three absorption bands contribute to the photoreversal. The quantum yield varied from 5 x 10/sup -2/ at wavelengths below 250 nm to 7 x 10/sup -4/ at wavelengths between 295 and 365 nm. In contrast to the case of the pyrone-side monoadduct, the incorporation of the furan-side monoadduct into the DNA oligomer reduced the photoreversal rate constant at wavelengths above 285 nm.

  9. Single voltage-dependent chloride-selective channels of large conductance in cultured rat muscle.

    PubMed Central

    Blatz, A L; Magleby, K L

    1983-01-01

    Single-channel currents of an anion-selective channel in the plasma membrane of cultured rat muscle cells (myotubes) were recorded with the patch-clamp technique (Hamill, O.P., A. Marty, E. Neher, B. Sakmann, and F.J. Sigworth, 1981. Pfluegers Arch. Eur. J. Physiol., 391:85-100). The channel is selective for Cl- over cations, and has an unusually large single-channel conductance of approximately 430 pS in symmetrical 143 mM KCl. The channel is often active at 0 mV, opening and closing spontaneously. When active, steps from 0 mV to either negative or positive membrane potentials close the channel to an apparent inactivated state. The mean effective time that a channel is open before it inactivates is approximately 1.19 s for steps to -30 mV and 0.48 s for steps to +30 mV. Returning the membrane potential to 0 mV results in recovery from inactivation. Calcium ions are not required for channel activity. PMID:6311302

  10. Roughness-dependent dynamics of a point charge near a conducting plane

    SciTech Connect

    Gintautas, Vadas; Hubler, Alfred

    2008-01-01

    Nearly any surface in the real world is rough at some scale. Fmthermore, in most experiments there is some limit at which a surface is too rough to approximate by a smooth one. In this work the dynamics of a point charge near a rough surface are studied as the roughness of the surface is allowed to vary. The equation of motion of a charged pendulum near a rough, grounded, conducting plane is derived analytically and then analyzed both analytically and numerically . As the roughness is varied, a phase transition is observed in the fixed points of the pendulum. The consequences of a roughness phase transition on waveguide and electromagnetic scattering applications are considered. Also, the grounded plane may be considered to be a rough mirror and the point charge to be interacting with its image in this mirror. The quality of the image degrades with increasing roughness; the implications of this to interactions between systems in the real world and synthetic models are explored.

  11. Motor Nerve Conduction Velocity Depends on Stimuli Frequency in the Rat

    NASA Astrophysics Data System (ADS)

    Méndez, Ma C.; Cruz, Elizabeth; Caudillo, Cipriana; Sosa, Modesto; Gamiño, Sergio M.

    2003-09-01

    This study was performed to evaluate the effect of frequency and duration of stimuli on motor nerve conduction velocity (MNCV) in the rat. MNCV was evaluated in two separate series of records. In the first the frequency of stimuli was varied between 1.0 and 10.0 Hz, by 1 Hz steps, keeping the duration of the pulses constant at 0.1 ms. In a second experimental trial, the frequency of the stimuli was kept at 10.0 Hz, while duration increased from 0.05 to 1.00 ms, at customized steps. Supramaximal stimulation pulses were always used. Measures were performed in the right pelvic limb of 12 anesthetized rats. The active needle electrode was inserted in the second interosseus space of the paw, while a subcutaneous reference electrode was inserted in the third toe. The ground electrode was placed on dorsal surface of the limb. The proximal stimuli site was identified at the sciatic notch and the distal one at the ankle. Surface stimulation was used. Latency, duration, area under the curve and amplitude of the muscular action potential were also measured. MNCV was estimated by dividing distal to proximal latency difference by the distance between stimuli sites. MNCV exhibited an increase to a plateu with stimulus frequency growth. Duration also showed the same behavior.

  12. Investigation on Temperature-Dependent Electrical Conductivity of Carbon Nanotube/Epoxy Composites for Sustainable Energy Applications.

    PubMed

    Njuguna, Michael K; Galpaya, Dilini; Yan, Cheng; Colwell, John M; Will, Geoffrey; Hu, Ning; Yarlagadda, Prasad; Bell, John M

    2015-09-01

    Composites with carbon nanotubes are becoming increasingly used in energy storage and electronic devices, due to incorporated excellent properties from carbon nanotubes and polymers. Although their properties make them more attractive than conventional smart materials, their electrical properties have been found to be temperature-dependent which is important to consider for the design of devices. To study the effects of temperature in electrically conductive multi-wall carbon nanotube/epoxy composites, thin films were prepared and the effect of temperature on the resistivity, thermal properties and Raman spectral characteristics of the composite films was evaluated. Resistivity-temperature profiles showed three distinct regions in as-cured samples and only two regions in samples whose thermal histories had been erased. In the vicinity of the glass transition temperature, the as-cured composites exhibited pronounced resistivity and enthalpic relaxation peaks, which both disappeared after erasing the composites' thermal histories by temperature cycling. Combined DSC, Raman spectroscopy, and resistivity-temperature analyses indicated that this phenomenon can be attributed to the physical aging of the epoxy matrix and that, in the region of the observed thermal history-dependent resistivity peaks, structural rearrangement of the conductive carbon nanotube network occurs through a volume expansion/relaxation process. These results have led to an overall greater understanding of the temperature-dependent behaviour of conductive carbon nanotube/epoxy composites, including the positive temperature coefficient effect.

  13. Global analysis of ion dependence unveils hidden steps in DNA binding and bending by integration host factor

    NASA Astrophysics Data System (ADS)

    Vivas, Paula; Velmurugu, Yogambigai; Kuznetsov, Serguei V.; Rice, Phoebe A.; Ansari, Anjum

    2013-09-01

    Proteins that recognize and bind to specific sites on DNA often distort the DNA at these sites. The rates at which these DNA distortions occur are considered to be important in the ability of these proteins to discriminate between specific and nonspecific sites. These rates have proven difficult to measure for most protein-DNA complexes in part because of the difficulty in separating the kinetics of unimolecular conformational rearrangements (DNA bending and kinking) from the kinetics of bimolecular complex association and dissociation. A notable exception is the Integration Host Factor (IHF), a eubacterial architectural protein involved in chromosomal compaction and DNA recombination, which binds with subnanomolar affinity to specific DNA sites and bends them into sharp U-turns. The unimolecular DNA bending kinetics has been resolved using both stopped-flow and laser temperature-jump perturbation. Here we expand our investigation by presenting a global analysis of the ionic strength dependence of specific binding affinity and relaxation kinetics of an IHF-DNA complex. This analysis enables us to obtain each of the underlying elementary rates (DNA bending/unbending and protein-DNA association/dissociation), and their ionic strength dependence, even under conditions where the two processes are coupled. Our analysis indicates interesting differences in the ionic strength dependence of the bi- versus unimolecular steps. At moderate [KCl] (100-500 mM), nearly all the ionic strength dependence to the overall equilibrium binding affinity appears in the bimolecular association/dissociation of an initial, presumably weakly bent, encounter complex, with a slope SKbi ≈ 8 describing the loglog-dependence of the equilibrium constant to form this complex on [KCl]. In contrast, the unimolecular equilibrium constant to form the fully wrapped specific complex from the initial complex is nearly independent of [KCl], with SKuni < 0.5. This result is counterintuitive because there

  14. Temperature and frequency dependent dielectric properties of electrically conducting oxidatively synthesized polyazomethines and their structural, optical, and thermal characterizations

    NASA Astrophysics Data System (ADS)

    Dineshkumar, Sengottuvelu; Muthusamy, Athianna; Chandrasekaran, J.

    2017-01-01

    Three azomethine diol monomers were synthesized by condensing with methanolic solution of aromatic aldehydes with ethylenediamine. These monomers were oxidatively polymerized using NaOCl as an oxidant. The structures of the monomers and polymers were confirmed by various spectroscopic techniques. Spectral results showed that the repeating units are linked by Csbnd C and Csbnd Osbnd C couplings. The polyazomethines have fluorescent property with high stokes shift. Solid state electrical conductivity of polymers both in I2 doped and undoped states, temperature and frequency dependent dielectric measurements were made by two probe method. The electrical conductivities of polyazomethines were compared based on the charge densities on imine nitrogens obtained from Huckel calculation. The conductivity of polymers increases with increase in iodine vapour contact time. Among the synthesized polymers PHNAE has shown high dielectric constant at low applied frequency of 50 Hz at 393 K due the presence of bulky naphthalene unit in polymer chain.

  15. Direction dependent thermal conductivity of monolayer phosphorene: Parameterization of Stillinger-Weber potential and molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Xu, Wen; Zhu, Liyan; Cai, Yongqing; Zhang, Gang; Li, Baowen

    2015-06-01

    A Stillinger-Weber interatomic potential is parameterized for phosphorene. It well reproduces the crystal structure, cohesive energy, and phonon dispersion predicted by first-principles calculations. The thermal conductivity of phosphorene is explored by equilibrium molecular dynamics simulations adopting the optimal set of potential parameters. At room temperature, the intrinsic thermal conductivities along zigzag and armchair directions are about 152.7 and 33.0 W/mK, respectively, with a large anisotropy ratio of five. The remarkably directional dependence of thermal conductivity in phosphorene, consistent with previous reports, is mainly due to the strong anisotropy of phonon group velocities, and weak anisotropy of phonon lifetimes as revealed by lattice dynamics calculations. Moreover, the effective phonon mean free paths at zigzag and armchair directions are about 141.4 and 43.4 nm, respectively.

  16. Ataxia telangiectasia-mutated protein and DNA-dependent protein kinase have complementary V(D)J recombination functions.

    PubMed

    Zha, Shan; Jiang, Wenxia; Fujiwara, Yuko; Patel, Harin; Goff, Peter H; Brush, James W; Dubois, Richard L; Alt, Frederick W

    2011-02-01

    Antigen receptor variable region exons are assembled during lymphocyte development from variable (V), diversity (D), and joining (J) gene segments. Each germ-line gene segment is flanked by recombination signal sequences (RSs). Recombination-activating gene endonuclease initiates V(D)J recombination by cleaving a pair of gene segments at their junction with flanking RSs to generate covalently sealed (hairpinned) coding ends (CEs) and blunt 5'-phosphorylated RS ends (SEs). Subsequently, nonhomologous end joining (NHEJ) opens, processes, and fuses CEs to form coding joins (CJs) and precisely joins SEs to form signal joins (SJs). DNA-dependent protein kinase catalytic subunit (DNA-PKcs) activates Artemis endonuclease to open and process hairpinned CEs before their fusion into CJs by other NHEJ factors. Although DNA-PKcs is absolutely required for CJs, SJs are formed to variable degrees and with variable fidelity in different DNA-PKcs-deficient cell types. Thus, other factors may compensate for DNA-PKcs function in SJ formation. DNA-PKcs and the ataxia telangiectasia-mutated (ATM) kinase are members of the same family, and they share common substrates in the DNA damage response. Although ATM deficiency compromises chromosomal V(D)J CJ formation, it has no reported role in SJ formation in normal cells. Here, we report that DNA-PKcs and ATM have redundant functions in SJ formation. Thus, combined DNA-PKcs and ATM deficiency during V(D)J recombination leads to accumulation of unjoined SEs and lack of SJ fidelity. Moreover, treatment of DNA-PKcs- or ATM-deficient cells, respectively, with specific kinase inhibitors for ATM or DNA-PKcs recapitulates SJ defects, indicating that the overlapping V(D)J recombination functions of ATM and DNA-PKcs are mediated through their kinase activities.

  17. Protein–DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors

    PubMed Central

    Etheve, Loïc; Martin, Juliette; Lavery, Richard

    2016-01-01

    We have studied the dynamics of three transcription factor–DNA complexes using all-atom, microsecond-scale MD simulations. In each case, the salt bridges and hydrogen bond interactions formed at the protein–DNA interface are found to be dynamic, with lifetimes typically in the range of tens to hundreds of picoseconds, although some interactions, notably those involving specific binding to DNA bases, can be a hundred times longer lived. Depending on the complex studied, this dynamics may or may not lead to the existence of distinct conformational substates. Using a sequence threading technique, it has been possible to determine whether DNA sequence recognition is sensitive or not to such conformational changes, and, in one case, to show that recognition appears to be locally dependent on protein-mediated cation distributions. PMID:27658967

  18. FORTRAN 77 programs for conductive cooling of dikes with temperature-dependent thermal properties and heat of crystallization

    USGS Publications Warehouse

    Delaney, P.T.

    1988-01-01

    Temperature histories obtained from transient heat-conduction theory are applicable to most dikes despite potential complicating effects related to magma flow during emplacement, groundwater circulation, and metamorphic reaction during cooling. Here. machine-independent FORTRAN 77 programs are presented to calculate temperatures in and around dikes as they cool conductively. Analytical solutions can treat thermal-property contrasts between the dike and host rocks, but cannot address the release of magmatic heat of crystallization after the early stages of cooling or the appreciable temperature dependence of thermal conductivity and diffusivity displayed by most rock types. Numerical solutions can incorporate these additional factors. The heat of crystallization can raise the initial temperature at the dike contact, ??c1, about 100??C above that which would be estimated if it were neglected, and can decrease the rate at which the front of solidified magma moves to the dike center by a factor of as much as three. Thermal conductivity and diffusivity of rocks increase with decreasing temperature and, at low temperatures, these properties increase more if the rocks are saturated with water. Models that treat these temperature dependencies yield estimates of ??c1 that are as much as 75??C beneath those which would be predicted if they were neglected. ?? 1988.

  19. Temperature dependent dielectric and conductivity studies of polyvinyl alcohol-ZnO nanocomposite films by impedance spectroscopy

    NASA Astrophysics Data System (ADS)

    Hemalatha, K. S.; Sriprakash, G.; Ambika Prasad, M. V. N.; Damle, R.; Rukmani, K.

    2015-10-01

    Dielectric and conductivity behaviors of nano ZnO doped polyvinyl alcohol (PVA) composites for various concentrations of dopant were investigated using impedance spectroscopy for a wide range of temperatures (303 K-423 K) and frequencies (5 Hz-30 MHZ). The dielectric properties of host polymer matrix have been improved by the addition of nano ZnO and are found to be highly temperature dependent. Anomalous dielectric behavior was observed in the frequency range of 2.5 MHz-5 MHz. Increase in dielectric permittivity and dielectric loss was observed with respect to temperature. The Cole-Cole plot could be modeled by low resistance regions in a high resistance matrix and the lowest resistance was observed for the 10 mol. % films. The imaginary part of the electric modulus showed asymmetric peaks with the relaxation following Debye nature below and non-Debye nature above the peaks. The ac conductivity is found to obey Jonscher's power law, whereas the variation of dc conductivity with temperature was found to follow Arrhenius behavior. Two different activation energy values were obtained from Arrhenius plot indicating that two conduction mechanisms are involved in the composite films. Fitting the ac conductivity data to Jonscher's law indicates that large polaron assisted tunneling is the most likely conduction mechanism in the composites. Maximum conductivity is observed at 423 K for all the samples and it is optimum for 10 mol. % ZnO doped PVA composite film. Significant increase in dc and ac conductivities in these composite films makes them a potential candidate for application in electronic devices.

  20. Temperature dependent dielectric and conductivity studies of polyvinyl alcohol-ZnO nanocomposite films by impedance spectroscopy

    SciTech Connect

    Hemalatha, K. S.; Damle, R.; Rukmani, K.; Sriprakash, G.; Ambika Prasad, M. V. N.

    2015-10-21

    Dielectric and conductivity behaviors of nano ZnO doped polyvinyl alcohol (PVA) composites for various concentrations of dopant were investigated using impedance spectroscopy for a wide range of temperatures (303 K–423 K) and frequencies (5 Hz–30 MHZ). The dielectric properties of host polymer matrix have been improved by the addition of nano ZnO and are found to be highly temperature dependent. Anomalous dielectric behavior was observed in the frequency range of 2.5 MHz–5 MHz. Increase in dielectric permittivity and dielectric loss was observed with respect to temperature. The Cole-Cole plot could be modeled by low resistance regions in a high resistance matrix and the lowest resistance was observed for the 10 mol. % films. The imaginary part of the electric modulus showed asymmetric peaks with the relaxation following Debye nature below and non-Debye nature above the peaks. The ac conductivity is found to obey Jonscher's power law, whereas the variation of dc conductivity with temperature was found to follow Arrhenius behavior. Two different activation energy values were obtained from Arrhenius plot indicating that two conduction mechanisms are involved in the composite films. Fitting the ac conductivity data to Jonscher's law indicates that large polaron assisted tunneling is the most likely conduction mechanism in the composites. Maximum conductivity is observed at 423 K for all the samples and it is optimum for 10 mol. % ZnO doped PVA composite film. Significant increase in dc and ac conductivities in these composite films makes them a potential candidate for application in electronic devices.

  1. Temperature Field of Turbulent Flow in a Well with Account for the Dependence of Thermal Conductivity Coefficient on Temperature

    NASA Astrophysics Data System (ADS)

    Filippov, A. I.; Shabarov, A. B.; Akhmetova, O. V.

    2017-01-01

    A method of solving the problem on nonstationary heat transfer of turbulent flow with variable coefficients and nonlinearity caused by the dependence of the thermal conductivity of oil on temperature is considered. The method consists of the joint application of the asymptotic methods of small and formal parameters. Based on the analysis of experimental data on the dependence of the thermal conductivity coefficient on temperature, it is shown that this dependence can be presented by a linear function in the form of the Taylor series containing the small parameter. The expansion of the problem in the small parameter leads to a linear problem in zero approximation that can be solved by using the asymptotic method of formal parameter. To determine the first coefficient of the expansion in the small parameter, a unique procedure of uncoupling has been developed. Analytical dependences of temperature in a well and in the surrounding rocks on time and spatial coordinates have been found that account for the orthotropy of the thermophysical properties of the media.

  2. DNA Damage Response Checkpoint Activation Drives KP1019 Dependent Pre-Anaphase Cell Cycle Delay in S. cerevisiae

    PubMed Central

    Bierle, Lindsey A.; Reich, Kira L.; Taylor, Braden E.; Blatt, Eliot B.; Middleton, Sydney M.; Burke, Shawnecca D.; Stultz, Laura K.; Hanson, Pamela K.; Partridge, Janet F.; Miller, Mary E.

    2015-01-01

    Careful regulation of the cell cycle is required for proper replication, cell division, and DNA repair. DNA damage–including that induced by many anticancer drugs–results in cell cycle delay or arrest, which can allow time for repair of DNA lesions. Although its molecular mechanism of action remains a matter of debate, the anticancer ruthenium complex KP1019 has been shown to bind DNA in biophysical assays and to damage DNA of colorectal and ovarian cancer cells in vitro. KP1019 has also been shown to induce mutations and induce cell cycle arrest in Saccharomyces cerevisiae, suggesting that budding yeast can serve as an appropriate model for characterizing the cellular response to the drug. Here we use a transcriptomic approach to verify that KP1019 induces the DNA damage response (DDR) and find that KP1019 dependent expression of HUG1 requires the Dun1 checkpoint; both consistent with KP1019 DDR in budding yeast. We observe a robust KP1019 dependent delay in cell cycle progression as measured by increase in large budded cells, 2C DNA content, and accumulation of Pds1 which functions to inhibit anaphase. Importantly, we also find that deletion of RAD9, a gene required for the DDR, blocks drug-dependent changes in cell cycle progression, thereby establishing a causal link between the DDR and phenotypes induced by KP1019. Interestingly, yeast treated with KP1019 not only delay in G2/M, but also exhibit abnormal nuclear position, wherein the nucleus spans the bud neck. This morphology correlates with short, misaligned spindles and is dependent on the dynein heavy chain gene DYN1. We find that KP1019 creates an environment where cells respond to DNA damage through nuclear (transcriptional changes) and cytoplasmic (motor protein activity) events. PMID:26375390

  3. DNA Damage Response Checkpoint Activation Drives KP1019 Dependent Pre-Anaphase Cell Cycle Delay in S. cerevisiae.

    PubMed

    Bierle, Lindsey A; Reich, Kira L; Taylor, Braden E; Blatt, Eliot B; Middleton, Sydney M; Burke, Shawnecca D; Stultz, Laura K; Hanson, Pamela K; Partridge, Janet F; Miller, Mary E

    2015-01-01

    Careful regulation of the cell cycle is required for proper replication, cell division, and DNA repair. DNA damage--including that induced by many anticancer drugs--results in cell cycle delay or arrest, which can allow time for repair of DNA lesions. Although its molecular mechanism of action remains a matter of debate, the anticancer ruthenium complex KP1019 has been shown to bind DNA in biophysical assays and to damage DNA of colorectal and ovarian cancer cells in vitro. KP1019 has also been shown to induce mutations and induce cell cycle arrest in Saccharomyces cerevisiae, suggesting that budding yeast can serve as an appropriate model for characterizing the cellular response to the drug. Here we use a transcriptomic approach to verify that KP1019 induces the DNA damage response (DDR) and find that KP1019 dependent expression of HUG1 requires the Dun1 checkpoint; both consistent with KP1019 DDR in budding yeast. We observe a robust KP1019 dependent delay in cell cycle progression as measured by increase in large budded cells, 2C DNA content, and accumulation of Pds1 which functions to inhibit anaphase. Importantly, we also find that deletion of RAD9, a gene required for the DDR, blocks drug-dependent changes in cell cycle progression, thereby establishing a causal link between the DDR and phenotypes induced by KP1019. Interestingly, yeast treated with KP1019 not only delay in G2/M, but also exhibit abnormal nuclear position, wherein the nucleus spans the bud neck. This morphology correlates with short, misaligned spindles and is dependent on the dynein heavy chain gene DYN1. We find that KP1019 creates an environment where cells respond to DNA damage through nuclear (transcriptional changes) and cytoplasmic (motor protein activity) events.

  4. ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain.

    PubMed

    Petrova, T; Bezsudnova, E Y; Boyko, K M; Mardanov, A V; Polyakov, K M; Volkov, V V; Kozin, M; Ravin, N V; Shabalin, I G; Skryabin, K G; Stekhanova, T N; Kovalchuk, M V; Popov, V O

    2012-12-01

    DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5'-phosphate and 3'-hydroxyl termini. Their function is essential for maintaining genome integrity in the replication, recombination and repair of DNA. High flexibility is important for the function of DNA ligase molecules. Two types of overall conformations of archaeal DNA ligase that depend on the relative position of the OB-fold domain have previously been revealed: closed and open extended conformations. The structure of ATP-dependent DNA ligase from Thermococcus sp. 1519 (LigTh1519) in the crystalline state determined at a resolution of 3.02 Å shows a new relative arrangement of the OB-fold domain which is intermediate between the positions of this domain in the closed and the open extended conformations of previously determined archaeal DNA ligases. However, small-angle X-ray scattering (SAXS) measurements indicate that in solution the LigTh1519 molecule adopts either an open extended conformation or both an intermediate and an open extended conformation with the open extended conformation being dominant.

  5. Nucleotide excision repair-dependent DNA double-strand break formation and ATM signaling activation in mammalian quiescent cells.

    PubMed

    Wakasugi, Mitsuo; Sasaki, Takuma; Matsumoto, Megumi; Nagaoka, Miyuki; Inoue, Keiko; Inobe, Manabu; Horibata, Katsuyoshi; Tanaka, Kiyoji; Matsunaga, Tsukasa

    2014-10-10

    Histone H2A variant H2AX is phosphorylated at Ser(139) in response to DNA double-strand break (DSB) and single-stranded DNA (ssDNA) formation. UV light dominantly induces pyrimidine photodimers, which are removed from the mammalian genome by nucleotide excision repair (NER). We previously reported that in quiescent G0 phase cells, UV induces ATR-mediated H2AX phosphorylation plausibly caused by persistent ssDNA gap intermediates during NER. In this study, we have found that DSB is also generated following UV irradiation in an NER-dependent manner and contributes to an earlier fraction of UV-induced H2AX phosphorylation. The NER-dependent DSB formation activates ATM kinase and triggers the accumulation of its downstream factors, MRE11, NBS1, and MDC1, at UV-damaged sites. Importantly, ATM-deficient cells exhibited enhanced UV sensitivity under quiescent conditions compared with asynchronously growing conditions. Finally, we show that the NER-dependent H2AX phosphorylation is also observed in murine peripheral T lymphocytes, typical nonproliferating quiescent cells in vivo. These results suggest that in vivo quiescent cells may suffer from NER-mediated secondary DNA damage including ssDNA and DSB.

  6. Mutation of a Conserved Active Site Residue Converts Tyrosyl-DNA Phosphodiesterase l Into a DNA Topoisomerase l-Dependent Poison

    SciTech Connect

    He,X.; van Waardenburg, R.; Babaoglu, K.; Price, A.; Nitiss, K.; Nitiss, J.; Bjornsti, M.; White, S.

    2007-01-01

    Tyrosyl-DNA phosphodiesterase 1 (Tdp1) catalyzes the resolution of 3' and 5' phospho-DNA adducts. A defective mutant, associated with the recessive neurodegenerative disease SCAN1, accumulates Tdp1-DNA complexes in vitro. To assess the conservation of enzyme architecture, a 2.0 {angstrom} crystal structure of yeast Tdp1 was determined that is very similar to human Tdp1. Poorly conserved regions of primary structure are peripheral to an essentially identical catalytic core. Enzyme mechanism was also conserved, because the yeast SCAN1 mutant (H{sub 432}R) enhanced cell sensitivity to the DNA topoisomerase I (Top1) poison camptothecin. A more severe Top1-dependent lethality of Tdp1H{sub 432}N was drug-independent, coinciding with increased covalent Top1-DNA and Tdp1-DNA complex formation in vivo. However, both H432 mutants were recessive to wild-type Tdp1. Thus, yeast H{sub 432} acts in the general acid/base catalytic mechanism of Tdp1 to resolve 3' phosphotyrosyl and 3' phosphoamide linkages. However, the distinct pattern of mutant Tdp1 activity evident in yeast cells, suggests a more severe defect in Tdp1H{sub 432}N-catalyzed resolution of 3' phospho-adducts.

  7. Yields of clustered DNA damage induced by charged-particle radiations of similar kinetic energy per nucleon: LET dependence in different DNA microenvironments

    SciTech Connect

    Keszenman, D.J.; Sutherland, B. M.

    2010-08-01

    To determine the linear energy transfer (LET) dependence of the biological effects of densely ionizing radiation in relation to changes in the ionization density along the track, we measured the yields and spectrum of clustered DNA damages induced by charged particles of different atomic number but similar kinetic energy per nucleon in different DNA microenvironments. Yeast DNA embedded in agarose in solutions of different free radical scavenging capacity was irradiated with 1 GeV protons, 1 GeV/nucleon oxygen ions, 980 MeV/nucleon titanium ions or 968 MeV/nucleon iron ions. The frequencies of double-strand breaks (DSBs), abasic sites and oxypurine clusters were quantified. The total DNA damage yields per absorbed dose induced in non-radioquenching solution decreased with LET, with minor variations in radioquenching conditions being detected. However, the total damage yields per particle fluence increased with LET in both conditions, indicating a higher efficiency per particle to induce clustered DNA damages. The yields of DSBs and non-DSB clusters as well as the damage spectra varied with LET and DNA milieu, suggesting the involvement of more than one mechanism in the formation of the different types of clustered damages.

  8. Ionic strength-dependent persistence lengths of single-stranded RNA and DNA.

    PubMed

    Chen, Huimin; Meisburger, Steve P; Pabit, Suzette A; Sutton, Julie L; Webb, Watt W; Pollack, Lois

    2012-01-17

    Dynamic RNA molecules carry out essential processes in the cell including translation and splicing. Base-pair interactions stabilize RNA into relatively rigid structures, while flexible non-base-paired regions allow RNA to undergo conformational changes required for function. To advance our understanding of RNA folding and dynamics it is critical to know the flexibility of these un-base-paired regions and how it depends on counterions. Yet, information about nucleic acid polymer properties is mainly derived from studies of ssDNA. Here we measure the persistence lengths (l(p)) of ssRNA. We observe valence and ionic strength-dependent differences in l(p) in a direct comparison between 40-mers of deoxythymidylate (dT(40)) and uridylate (rU(40)) measured using the powerful combination of SAXS and smFRET. We also show that nucleic acid flexibility is influenced by local environment (an adjoining double helix). Our results illustrate the complex interplay between conformation and ion environment that modulates nucleic acid function in vivo.

  9. Shape-dependent bactericidal activity of copper oxide nanoparticle mediated by DNA and membrane damage

    SciTech Connect

    Laha, Dipranjan; Pramanik, Arindam; Laskar, Aparna; Jana, Madhurya; Pramanik, Panchanan; Karmakar, Parimal

    2014-11-15

    Highlights: • Spherical and sheet shaped copper oxide nanoparticles were synthesized. • Physical characterizations of these nanoparticles were done by TEM, DLS, XRD, FTIR. • They showed shape dependent antibacterial activity on different bacterial strain. • They induced both membrane damage and ROS mediated DNA damage in bacteria. - Abstract: In this work, we synthesized spherical and sheet shaped copper oxide nanoparticles and their physical characterizations were done by the X-ray diffraction, fourier transform infrared spectroscopy, transmission electron microscopy and dynamic light scattering. The antibacterial activity of these nanoparticles was determined on both gram positive and gram negative bacterial. Spherical shaped copper oxide nanoparticles showed more antibacterial property on gram positive bacteria where as sheet shaped copper oxide nanoparticles are more active on gram negative bacteria. We also demonstrated that copper oxide nanoparticles produced reactive oxygen species in both gram negative and gram positive bacteria. Furthermore, they induced membrane damage as determined by atomic force microscopy and scanning electron microscopy. Thus production of and membrane damage are major mechanisms of the bactericidal activity of these copper oxide nanoparticles. Finally it was concluded that antibacterial activity of nanoparticles depend on physicochemical properties of copper oxide nanoparticles and bacterial strain.

  10. Ionic strength-dependent persistence lengths of single-stranded RNA and DNA

    PubMed Central

    Chen, Huimin; Meisburger, Steve P.; Pabit, Suzette A.; Sutton, Julie L.; Webb, Watt W.; Pollack, Lois

    2012-01-01

    Dynamic RNA molecules carry out essential processes in the cell including translation and splicing. Base-pair interactions stabilize RNA into relatively rigid structures, while flexible non-base-paired regions allow RNA to undergo conformational changes required for function. To advance our understanding of RNA folding and dynamics it is critical to know the flexibility of these un-base-paired regions and how it depends on counterions. Yet, information about nucleic acid polymer properties is mainly derived from studies of ssDNA. Here we measure the persistence lengths (lp) of ssRNA. We observe valence and ionic strength-dependent differences in lp in a direct comparison between 40-mers of deoxythymidylate (dT40) and uridylate (rU40) measured using the powerful combination of SAXS and smFRET. We also show that nucleic acid flexibility is influenced by local environment (an adjoining double helix). Our results illustrate the complex interplay between conformation and ion environment that modulates nucleic acid function in vivo. PMID:22203973

  11. Self-catalytic growth of unmodified gold nanoparticles as conductive bridges mediated gap-electrical signal transduction for DNA hybridization detection.

    PubMed

    Zhang, Jing; Nie, Huagui; Wu, Zhan; Yang, Zhi; Zhang, Lijie; Xu, Xiangju; Huang, Shaoming

    2014-01-21

    A simple and sensitive gap-electrical biosensor based on self-catalytic growth of unmodified gold nanoparticles (AuNPs) as conductive bridges has been developed for amplifying DNA hybridization events. In this strategy, the signal amplification degree of such conductive bridges is closely related to the variation of the glucose oxidase (GOx)-like catalytic activity of AuNPs upon interaction with single- and double-stranded DNA (ssDNA and dsDNA), respectively. In the presence of target DNA, the obtained dsDNA product cannot adsorb onto the surface of AuNPs due to electrostatic interaction, which makes the unmodified AuNPs exhibit excellent GOx-like catalytic activity. Such catalytic activity can enlarge the diameters of AuNPs in the glucose and HAuCl4 solution and result in a connection between most of the AuNPs and a conductive gold film formation with a dramatically increased conductance. For the control sample, the catalytic activity sites of AuNPs are fully blocked by ssDNA due to the noncovalent interaction between nucleotide bases and AuNPs. Thus, the growth of the assembled AuNPs will not happen and the conductance between microelectrodes will be not changed. Under the optimal experimental conditions, the developed strategy exhibited a sensitive response to target DNA with a high signal-to-noise ratio. Moreover, this strategy was also demonstrated to provide excellent differentiation ability for single-nucleotide polymorphism. Such performances indicated the great potential of this label-free electrical strategy for clinical diagnostics and genetic analysis under real biological sample separation.

  12. Sequence-dependent Structural Variation in DNA Undergoing Intrahelical Inspection by the DNA glycosylase MutM

    SciTech Connect

    Sung, Rou-Jia; Zhang, Michael; Qi, Yan; Verdine, Gregory L.

    2012-08-31

    MutM, a bacterial DNA-glycosylase, plays a critical role in maintaining genome integrity by catalyzing glycosidic bond cleavage of 8-oxoguanine (oxoG) lesions to initiate base excision DNA repair. The task faced by MutM of locating rare oxoG residues embedded in an overwhelming excess of undamaged bases is especially challenging given the close structural similarity between oxoG and its normal progenitor, guanine (G). MutM actively interrogates the DNA to detect the presence of an intrahelical, fully base-paired oxoG, whereupon the enzyme promotes extrusion of the target nucleobase from the DNA duplex and insertion into the extrahelical active site. Recent structural studies have begun to provide the first glimpse into the protein-DNA interactions that enable MutM to distinguish an intrahelical oxoG from G; however, these initial studies left open the important question of how MutM can recognize oxoG residues embedded in 16 different neighboring sequence contexts (considering only the 5'- and 3'-neighboring base pairs). In this study we set out to understand the manner and extent to which intrahelical lesion recognition varies as a function of the 5'-neighbor. Here we report a comprehensive, systematic structural analysis of the effect of the 5'-neighboring base pair on recognition of an intrahelical oxoG lesion. These structures reveal that MutM imposes the same extrusion-prone ('extrudogenic') backbone conformation on the oxoG lesion irrespective of its 5'-neighbor while leaving the rest of the DNA relatively free to adjust to the particular demands of individual sequences.

  13. Efficient, Mg(2+)-dependent photochemical DNA cleavage by the antitumor quinobenzoxazine (S)-A-62176.

    PubMed

    Yu, H; Kwok, Y; Hurley, L H; Kerwin, S M

    2000-08-22

    The quinobenzoxazines, a group of structural analogues of the antibacterial fluoroquinolones, are topoisomerase II inhibitors that have demonstrated promising anticancer activity in mice. It has been proposed that the quinobenzoxazines form a 2:2 drug-Mg(2+) self-assembly complex on DNA. The quinobenzoxazine (S)-A-62176 is photochemically unstable and undergoes a DNA-accelerated photochemical reaction to afford a highly fluorescent photoproduct. Here we report that the irradiation of both supercoiled DNA and DNA oligonucleotides in the presence of (S)-A-62176 results in photochemical cleavage of the DNA. The (S)-A-62176-mediated DNA photocleavage reaction requires Mg(2+). Photochemical cleavage of supercoiled DNA by (S)-A-62176 is much more efficient that the DNA photocleavage reactions of the fluoroquinolones norfloxacin, ciprofloxacin, and enoxacin. The photocleavage of supercoiled DNA by (S)-A-62176 is unaffected by the presence of SOD, catalase, or other reactive oxygen scavengers, but is inhibited by deoxygenation. The photochemical cleavage of supercoiled DNA is also inhibited by 1 mM KI. Photochemical cleavage of DNA oligonucleotides by (S)-A-62176 occurs most extensively at DNA sites bound by drug, as determined by DNase I footprinting, and especially at certain G and T residues. The nature of the DNA photoproducts, and inhibition studies, indicate that the photocleavage reaction occurs by a free radical mechanism initiated by abstraction of the 4'- and 1'-hydrogens from the DNA minor groove. These results lend further support for the proposed DNA binding model for the quinobenzoxazine 2:2 drug-Mg(2+) complex and serve to define the position of this complex on the minor groove of DNA.

  14. Reconstitution of recombinant human replication factor C (RFC) and identification of an RFC subcomplex possessing DNA-dependent ATPase activity.

    PubMed

    Ellison, V; Stillman, B

    1998-03-06

    Replication factor C (RFC) is a five-subunit protein complex required for coordinate leading and lagging strand DNA synthesis during S phase and DNA repair in eukaryotic cells. It functions to load the proliferating cell nuclear antigen (PCNA), a processivity factor for polymerases delta and epsilon, onto primed DNA templates. This process, which is ATP-dependent, is carried out by 1) recognition of the primer terminus by RFC () binding to and disruption of the PCNA trimer, and then 3) topologically linking the PCNA to the DNA. In this report, we describe the purification and properties of recombinant human RFC expressed in Sf9 cells from baculovirus expression vectors. Like native RFC derived from 293 cells, recombinant RFC was found to support SV40 DNA synthesis and polymerase delta DNA synthesis in vitro and to possess an ATPase activity that was highly stimulated by DNA and further augmented by PCNA. Assembly of RFC was observed to involve distinct subunit interactions in which both the 36- and 38-kDa subunits interacted with the 37-kDa subunit, and the 40-kDa subunit interacted with the 36-kDa subunit-37-kDa subunit subcomplex. The 140-kDa subunit was found to require interactions primarily with the 38- and 40-kDa subunits for incorporation into the complex. In addition, a stable subcomplex lacking the 140-kDa subunit, although defective for DNA replication, was found to possess DNA-dependent ATPase activity that was not responsive to the addition of PCNA.

  15. DNA DSB induced by iron ions in human fibroblasts: LET dependence and shielding efficiency

    NASA Astrophysics Data System (ADS)

    Antonelli, F.; Belli, M.; Campa, A.; Dini, V.; Esposito, G.; Furusawa, Y.; Rydberg, B.; Simone, G.; Sorrentino, E.; Tabocchini, M. A.

    Galactic Cosmic Rays represent one of the main sources of charged particle radiation outside the magnetic field of the Earth, containing particles of all charges, in a wide energy range. As HZE particles interact with a shield, they fragment and deposit energy at rates depending on the nature and energy of the incident particles, and on the nature and thickness of the shield. We have studied the DNA DSB induction in human fibroblasts by iron ions of different energies (5 GeV/u, 1 GeV/u, 500 MeV/u and 200 MeV) in the absence or presence of different shields (PMMA, Al and Pb). Measure of DNA DSB was performed by gel electrophoresis and .fragmentation analysis. The RBE for unshielded and shielded beams has been plotted as a function of the dose average LET, and the relationship shows a maximum of 1.7 at about 140 keV/μ m (5 GeV/u iron ions). The dose average LET seems to adequately describe the effectiveness of degraded beams since their RBEs fall roughly on the same relationship of the unshielded beams. The cross section for unshielded beams increases with LET. The shielding efficiency has been evaluated by the ratio between the cross sections for unshielded and shielded beams (SPF, shielding protection factor). When this ratio is plotted as a function of the shield thickness (g/cm2), different relationships were found for beams with different energy. For 500 MeV/u iron ions, the presence of the shields gives SPF lower than unity, independently of thickness and material. For 1 GeV/u iron beams, SPF values are always higher than unity. Moreover, PMMA shield gives a higher SPF than Al or Pb shields having the same residual range but different thickness. The higher SPF of PMMA has been confirmed in experiments performed with 5 GeV/u iron beams and different shields having the same thickness. The SPF found for 1 and 5 GeV/u iron ions remain constant also when the fragmentation analysis used for evaluating DNA DSB is extended to fragments of smaller size. The fragment

  16. Generalized Procedure for Improved Accuracy of Thermal Contact Resistance Measurements for Materials With Arbitrary Temperature-Dependent Thermal Conductivity

    SciTech Connect

    Sayer, Robert A.

    2014-06-26

    Thermal contact resistance (TCR) is most commonly measured using one-dimensional steady-state calorimetric techniques. In the experimental methods we utilized, a temperature gradient is applied across two contacting beams and the temperature drop at the interface is inferred from the temperature profiles of the rods that are measured at discrete points. During data analysis, thermal conductivity of the beams is typically taken to be an average value over the temperature range imposed during the experiment. Our generalized theory is presented and accounts for temperature-dependent changes in thermal conductivity. The procedure presented enables accurate measurement of TCR for contacting materials whose thermal conductivity is any arbitrary function of temperature. For example, it is shown that the standard technique yields TCR values that are about 15% below the actual value for two specific examples of copper and silicon contacts. Conversely, the generalized technique predicts TCR values that are within 1% of the actual value. The method is exact when thermal conductivity is known exactly and no other errors are introduced to the system.

  17. Generalized Procedure for Improved Accuracy of Thermal Contact Resistance Measurements for Materials With Arbitrary Temperature-Dependent Thermal Conductivity

    DOE PAGES

    Sayer, Robert A.

    2014-06-26

    Thermal contact resistance (TCR) is most commonly measured using one-dimensional steady-state calorimetric techniques. In the experimental methods we utilized, a temperature gradient is applied across two contacting beams and the temperature drop at the interface is inferred from the temperature profiles of the rods that are measured at discrete points. During data analysis, thermal conductivity of the beams is typically taken to be an average value over the temperature range imposed during the experiment. Our generalized theory is presented and accounts for temperature-dependent changes in thermal conductivity. The procedure presented enables accurate measurement of TCR for contacting materials whose thermalmore » conductivity is any arbitrary function of temperature. For example, it is shown that the standard technique yields TCR values that are about 15% below the actual value for two specific examples of copper and silicon contacts. Conversely, the generalized technique predicts TCR values that are within 1% of the actual value. The method is exact when thermal conductivity is known exactly and no other errors are introduced to the system.« less

  18. Thermal resistance optimization of GaN/substrate stacks considering thermal boundary resistance and temperature-dependent thermal conductivity

    NASA Astrophysics Data System (ADS)

    Park, K.; Bayram, C.

    2016-10-01

    Here, we investigate the effects of thermal boundary resistance (TBR) and temperature-dependent thermal conductivity on the thermal resistance of GaN/substrate stacks. A combination of parameters such as substrates {diamond, silicon carbide, silicon, and sapphire}, thermal boundary resistance {10-60 m2K/GW}, heat source lengths {10 nm-20 μm}, and power dissipation levels {1-8 W} are studied by using technology computer-aided design (TCAD) software Synopsys. Among diamond, silicon carbide, silicon, and sapphire substrates, the diamond provides the lowest thermal resistance due to its superior thermal conductivity. We report that due to non-zero thermal boundary resistance and localized heating in GaN-based high electron mobility transistors, an optimum separation between the heat source and substrate exists. For high power (i.e., 8 W) heat dissipation on high thermal conductive substrates (i.e., diamond), the optimum separation between the heat source and substrate becomes submicron thick (i.e., 500 nm), which reduces the hotspot temperature as much as 50 °C compared to conventional multi-micron thick case (i.e., 4 μm). This is attributed to the thermal conductivity drop in GaN near the heat source. Improving the TBR between GaN and diamond increases temperature reduction by our further approach. Overall, we provide thermal management design guidelines for GaN-based devices.

  19. Aspartic Acid Residue D3 Critically Determines Cx50 Gap Junction Channel Transjunctional Voltage-Dependent Gating and Unitary Conductance

    PubMed Central

    Xin, Li; Nakagawa, So; Tsukihara, Tomitake; Bai, Donglin

    2012-01-01

    Previous studies have suggested that the aspartic acid residue (D) at the third position is critical in determining the voltage polarity of fast Vj-gating of Cx50 channels. To test whether another negatively charged residue (a glutamic acid residue, E) could fulfill the role of the D3 residue, we generated the mutant Cx50D3E. Vj-dependent gating properties of this mutant channel were characterized by double-patch-clamp recordings in N2A cells. Macroscopically, the D3E substitution reduced the residual conductance (Gmin) to near zero and outwardly shifted the half-inactivation voltage (V0), which is a result of both a reduced aggregate gating charge (z) and a reduced free-energy difference between the open and closed states. Single Cx50D3E gap junction channels showed reduced unitary conductance (γj) of the main open state, reduced open dwell time at ±40 mV, and absence of a long-lived substate. In contrast, a G8E substitution tested to compare the effects of the E residue at the third and eighth positions did not modify the Vj-dependent gating profile or γj. In summary, this study is the first that we know of to suggest that the D3 residue plays an essential role, in addition to serving as a negative-charge provider, as a critical determinant of the Vj-dependent gating sensitivity, open-closed stability, and unitary conductance of Cx50 gap junction channels. PMID:22404924

  20. Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule encoding a putative DNA-dependent DNA polymerase.

    PubMed

    Shao, Zhiyong; Graf, Shannon; Chaga, Oleg Y; Lavrov, Dennis V

    2006-10-15

    The 16,937-nuceotide sequence of the linear mitochondrial DNA (mt-DNA) molecule of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa) - the first mtDNA sequence from the class Scypozoa and the first sequence of a linear mtDNA from Metazoa - has been determined. This sequence contains genes for 13 energy pathway proteins, small and large subunit rRNAs, and methionine and tryptophan tRNAs. In addition, two open reading frames of 324 and 969 base pairs in length have been found. The deduced amino-acid sequence of one of them, ORF969, displays extensive sequence similarity with the polymerase [but not the exonuclease] domain of family B DNA polymerases, and this ORF has been tentatively identified as dnab. This is the first report of dnab in animal mtDNA. The genes in A. aurita mtDNA are arranged in two clusters with opposite transcriptional polarities; transcription proceeding toward the ends of the molecule. The determined sequences at the ends of the molecule are nearly identical but inverted and lack any obvious potential secondary structures or telomere-like repeat elements. The acquisition of mitochondrial genomic data for the second class of Cnidaria allows us to reconstruct characteristic features of mitochondrial evolution in this animal phylum.

  1. Interleukin-1 beta-converting enzyme-like protease cleaves DNA- dependent protein kinase in cytotoxic T cell killing

    PubMed Central

    1996-01-01

    Cytotoxic T cells (CTL) represent the major defense mechanism against the spread of virus infection. It is believed that the pore-forming protein, perforin, facilitates the entry of a series of serine proteases (particularly granzyme B) into the target cell which ultimately leads to DNA fragmentation and apoptosis. We demonstrate here that during CTL-mediated cytolysis the catalytic subunit of DNA- dependent protein kinase (DNA-PKcs), an enzyme implicated in the repair of double strand breaks in DNA, is specifically cleaved by an interleukin (IL)-1 beta-converting enzyme (ICE)-like protease. A serine protease inhibitor, 3,4-dichloroisocoumarin (DCl), which is known to block granzyme B activity, inhibited CTL-induced apoptosis and prevented the degradation of DNA-PKcs in cells but failed to prevent the degradation of purified DNA-PKcs by CTL extracts. However, Tyr-Val- Ala-Asp-CH2Cl (YVAD-CMK) and other cysteine protease inhibitors prevented the degradation of purified DNA-PKcs by CTL extracts. Furthermore, incubation of DNA-PKcs with granzyme B did not produce the same cleavage pattern observed in cells undergoing apoptosis and when this substrate was incubated with either CTL extracts or the ICE-like protease, CPP32. Sequence analysis revealed that the cleavage site in DNA-PKcs during CTL killing was the same as that when this substrate was exposed to CPP32. This study demonstrates for the first time that the cleavage of DNA-PKcs in this intact cell system is exclusively due to an ICE-like protease. PMID:8760815

  2. Fingerprints of a size-dependent crossover in the dimensionality of electronic conduction in Au-seeded Ge nanowires

    PubMed Central

    Koleśnik-Gray, Maria; Collins, Gillian; Holmes, Justin D

    2016-01-01

    We studied the electrical transport properties of Au-seeded germanium nanowires with radii ranging from 11 to 80 nm at ambient conditions. We found a non-trivial dependence of the electrical conductivity, mobility and carrier density on the radius size. In particular, two regimes were identified for large (lightly doped) and small (stronger doped) nanowires in which the charge-carrier drift is dominated by electron-phonon and ionized-impurity scattering, respectively. This goes in hand with the finding that the electrostatic properties for radii below ca. 37 nm have quasi one-dimensional character as reflected by the extracted screening lengths. PMID:28144508

  3. Temperature and voltage dependent current-voltage behavior of single-walled carbon nanotube transparent conducting films

    NASA Astrophysics Data System (ADS)

    Zhang, Ze-Chen; Geng, Hong-Zhang; Wang, Yan; Yang, Hai-Jie; Da, Shi-Xun; Ding, Er-Xiong; Liu, Juncheng; Yu, Ping; Fu, Yun-Qiao; Li, Xu; Pan, Hui

    2015-11-01

    High purified single-walled carbon nanotubes (SWCNTs) were dispersed in water and transparent conducting films (TCFs) were fabricated by a spray coating. The produced uniform SWCNT-TCFs treated by nitric acid have a relatively low sheet resistance and high transmittance. The current-voltage (I-V) behaviors of the TCFs were measured at room to higher temperature during the heating or cooling process. It was found that the I-V behavior of TCFs strongly dependent on the temperature and applied voltage. The sheet resistance showed semiconductor behavior at low temperature and low voltage, while it showed metallic behavior at high temperature and high voltage.

  4. Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation.

    PubMed

    Yoo, Jejoong; Kim, Hajin; Aksimentiev, Aleksei; Ha, Taekjip

    2016-03-22

    Although proteins mediate highly ordered DNA organization in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA-DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA-DNA interactions that we report here may play a role in the chromosome organization and gene regulation.

  5. Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

    NASA Astrophysics Data System (ADS)

    Yoo, Jejoong; Kim, Hajin; Aksimentiev, Aleksei; Ha, Taekjip

    2016-03-01

    Although proteins mediate highly ordered DNA organization in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA-DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA-DNA interactions that we report here may play a role in the chromosome organization and gene regulation.

  6. Small Conductance Ca2+-Activated K+ Channel Knock-Out Mice Reveal the Identity of Calcium-Dependent Afterhyperpolarization Currents

    PubMed Central

    Bond, Chris T.; Herson, Paco S.; Strassmaier, Timothy; Hammond, Rebecca; Stackman, Robert; Maylie, James; Adelman, John P.

    2010-01-01

    Action potentials in many central neurons are followed by a prolonged afterhyperpolarization (AHP) that influences firing frequency and affects neuronal integration. In hippocampal CA1 pyramidal neurons, the current ascribed to the AHP (IAHP) has three kinetic components. The IfastAHP is predominantly attributable to voltage-dependent K+ channels, whereas Ca2+-dependent and voltage-independent K+ channels contribute to the ImediumAHP (ImAHP) and IslowAHP (IsAHP). Apamin, which selectively suppresses a component of the mAHP, increases neuronal excitability and facilitates the induction of synaptic plasticity at Schaffer collateral synapses and hippocampal-dependent learning. The Ca2+-dependent components of the AHP have been attributed to the activity of small conductance Ca2+-activated K+(SK) channels. Examination of transgenic mice, each lacking one of the three SK channel genes expressed in the CNS, reveals that mice without the SK2 subunit completely lack the apamin-sensitive component of the ImAHP in CA1 neurons, whereas the IsAHP is not different in any of the SK transgenic mice. In each of the transgenic lines, the expression levels of the remaining SK genes are not changed. The results demonstrate that only SK2 channels are necessary for the ImAHP, and none of the SK channels underlie the IsAHP. PMID:15190101

  7. DNA Mutagenic Activity and Capacity for HIV-1 Restriction of the Cytidine Deaminase APOBEC3G Depends on Whether DNA or RNA Binds to Tyrosine 315.

    PubMed

    Polevoda, Bogdan; Joseph, Rebecca; Friedman, Alan E; Bennett, Ryan P; Greiner, Rebecca; De Zoysa, Thareendra; Stewart, Ryan A; Smith, Harold C

    2017-04-05

    APOBEC3G (A3G) belongs to the AID/APOBEC protein family of cytidine deaminases (CDA) that bind to nucleic acids. A3G mutates the HIV genome by deamination of dC to dU, leading to accumulation of virus-inactivating mutations. Binding to cellular RNAs inhibits A3G binding to substrate single-stranded (ss) DNA and CDA activity. RNA and ssDNA bind to the same three A3G tryptic peptides (amino acids 181-194, 314-320, and 345-374) that form parts of a continuously exposed protein surface extending from the catalytic domain in the C-terminus of A3G to its N-terminus. We show here that the A3G tyrosines 181 and 315 directly cross-link ssDNA. Binding experiments showed that a Y315A mutation alone significantly reduced A3G binding to both ssDNA and RNA, whereas Y181A and Y182A mutations only moderately affected A3G nucleic acid binding. Consistent with these findings, the Y315A mutant exhibited little to no deaminase activity in an E. coli DNA mutator reporter, while Y181A and Y182A mutants retained ~50% of wild-type A3G activity. The Y315A mutant also showed a markedly reduced ability to assemble into viral particles and had reduced antiviral activity. In uninfected cells, the impaired RNA-binding capacity of Y315A was evident by a shift of A3G from high-molecular-mass ribonucleoprotein complexes to low-molecular-mass complexes. We conclude that Y315 is essential for coordinating ssDNA interaction with or entry to the deaminase domain and hypothesize that RNA bound to Y315 may be sufficient to competitively inhibit ssDNA deaminase-dependent antiviral activity.

  8. DNA double helix unwinding triggers transcription block-dependent apoptosis: a semiquantitative probe of the response of ATM, RNAPII, and p53 to two DNA intercalators.

    PubMed

    Zhang, Zhichao; Wang, Yuanyuan; Song, Ting; Gao, Jin; Wu, Guiye; Zhang, Jing; Qian, Xuhong

    2009-03-16

    We have previously shown the binding modes of two DNA interacting analogues (1)a {3-(4-methyl-piperazin)-8-oxo-8H-acenaphtho[1,2-b]pyrrole-9-carbonitrile} and (3)a {3-(3-dimethylamino-propylamino)-8-oxo-8H-acenaphtho[1,2-b]pyrrole-9-carbonitrile} with the DNA double helix. In this study, we have determined the notably different DNA damage signal pathway elicited by (1)a and (3)a due to the different extents to which they unwind the DNA double helix. First, we have identified that ataxia-telangiectasia-mutated (ATM) protein kinase can respond to DNA double helix unwinding caused by both (1)a and (3)a. In addition, the amount of ATM activation is consistent with the degree to which the DNA double helix was unwound. Consequently, we used (1)a and (3)a to semiquantitatively probe the response of RNA polymerase II (RNAPII) and p53 toward DNA double helix unwinding in vivo. By means of flow cytometry, immunocytochemistry, ChIP, quantitative real-time polymerase chain reaction, and Western blot analyses, we measured the level of p53 and RNAPII phosphorylation, in addition to the dynamics of the RNAPII distribution along the c-Myc gene. These results provided novel evidence for the impact of subtle DNA structural changes on the activity of RNAPII and p53. Moreover, DNA double helix conformational damage-dependent apoptosis was studied for the first time. These results indicated that (1)a can induce transcriptional blockage following a shift of the unphosphorylated IIa form of RNAPII to the phosphorylated IIo form, while (3)a is unable to induce the same effect. Subsequently, p53 accumulation and phosphorylation events occur that lead to apoptosis in the case of (1)a exposure. This suggests that the transcriptional blockage is also correlated to the degree of double helix unwinding. Furthermore, we found that the degree of DNA conformational damage determines whether or not apoptosis occurs through transcriptional blockage. Under our experimental conditions, ATM does not

  9. Molecular Characterization of NAD+-Dependent DNA Ligase from Wolbachia Endosymbiont of Lymphatic Filarial Parasite Brugia malayi

    PubMed Central

    Shrivastava, Nidhi; Nag, Jeetendra Kumar; Misra-Bhattacharya, Shailja

    2012-01-01

    The lymphatic filarial parasite, Brugia malayi contains Wolbachia endobacteria that are essential for development, viability and fertility of the parasite. Therefore, wolbachial proteins have been currently seen as the potential antifilarial drug targets. NAD+-dependent DNA ligase is characterized as a promising drug target in several organisms due to its crucial, indispensable role in DNA replication, recombination and DNA repair. We report here the cloning, expression and purification of NAD+-dependent DNA ligase of Wolbachia endosymbiont of B. malayi (wBm-LigA) for its molecular characterization. wBm-LigA has all the domains that are present in nearly all the eubacterial NAD+-dependent DNA ligases such as N-terminal adenylation domain, OB fold, helix-hairpin-helix (HhH) and BRCT domain except zinc-binding tetracysteine domain. The purified recombinant protein (683-amino acid) was found to be biochemically active and was present in its native form as revealed by the circular dichroism and fluorescence spectra. The purified recombinant enzyme was able to catalyze intramolecular strand joining on a nicked DNA as well as intermolecular joining of the cohesive ends of BstEII restricted lamda DNA in an in vitro assay. The enzyme was localized in the various life-stages of B. malayi parasites by immunoblotting and high enzyme expression was observed in Wolbachia within B. malayi microfilariae and female adult parasites along the hypodermal chords and in the gravid portion as evident by the confocal microscopy. Ours is the first report on this enzyme of Wolbachia and these findings would assist in validating the antifilarial drug target potential of wBm-LigA in future studies. PMID:22815933

  10. Oversized AAV transductifon is mediated via a DNA-PKcs-independent, Rad51C-dependent repair pathway.

    PubMed

    Hirsch, Matthew L; Li, Chengwen; Bellon, Isabella; Yin, Chaoying; Chavala, Sai; Pryadkina, Marina; Richard, Isabelle; Samulski, Richard Jude

    2013-12-01

    A drawback of gene therapy using adeno-associated virus (AAV) is the DNA packaging restriction of the viral capsid (<4.7 kb). Recent observations demonstrate oversized AAV genome transduction through an unknown mechanism. Herein, AAV production using an oversized reporter (6.2 kb) resulted in chloroform and DNase-resistant particles harboring distinct "fragment" AAV (fAAV) genomes (5.0, 2.4, and 1.6 kb). Fractionation experiments determined that only the larger "fragments" mediated transduction in vitro, and relatively efficient transduction was also demonstrated in the muscle, the eye, and the liver. In contrast with concatemerization-dependent large-gene delivery by split AAV, fAAV transduction is independent of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) in vitro and in vivo while disproportionately reliant on the DNA strand-annealing protein Rad51C. Importantly, fAAV's unique dependence on DNA repair proteins, compared with intact AAV, strongly suggests that the majority of oversized AAV transduction is mediated by fragmented genomes. Although fAAV transduction is less efficient than intact AAV, it is enhanced fourfold in muscle and sevenfold in the retina compared with split AAV transduction. Furthermore, fAAV carrying codon-optimized therapeutic dysferlin cDNA in a 7.5 kb expression cassette restored dysferlin levels in a dystrophic model. Collectively, oversized AAV genome