WorldWideScience

Sample records for surface bound dna

  1. NEXAFS characterization of DNA components and molecular-orientation of surface-bound DNA oligomers

    International Nuclear Information System (INIS)

    Samuel, Newton T.; Lee, C.-Y.; Gamble, Lara J.; Fischer, Daniel A.; Castner, David G.

    2006-01-01

    Single stranded DNA oligomers (ssDNA) immobilized onto solid surfaces forms the basis for several biotechnological applications such as DNA microarrays, affinity separations, and biosensors. Surface structure of Surface-bound oligomers is expected to significantly influence their biological activity and interactions with the environment. In this study near-edge X-ray absorption fine structure spectroscopy (NEXAFS) is used to characterize the components of DNA (nucleobases, nucleotides and nucleosides) and the orientation information of surface-bound ssDNA. The K-edges of carbon, nitrogen and oxygen have spectra with features that are characteristic of the different chemical species present in the nucleobases of DNA. The effect of addition of the DNA sugar and phosphate components on the NEXAFS K-edge spectra was also investigated. The polarization-dependent nitrogen K-edge NEXAFS data show significant changes for different orientations of surface bound ssDNA. These results establish NEXAFS as a powerful technique for chemical and structural characterization of surface-bound DNA oligomers

  2. The subglacial Lake Vostok (East Antarctica) surface snow is Earth-bound DNA (and dust)-free

    Science.gov (United States)

    Bulat, S.; Marie, D.; Bulat, E.; Alekhina, I.; Petit, J.-R.

    2012-09-01

    came up with only contaminant bacterial phylotypes (mostly of human source). The bioexposure trials showed that even in one day of open exposure the gDNA of rather complex microbial community composition was fatally damaged in terms of long-, mid-range and short-size amplicon generation in PCR. All this testify for very harsh conditions for life to survive the climate conditions of Central East Antarctica which could be considered as a presentday 'zone mortale' or 'polar desert' for known Earthbound microbial life forms. In addition this means that no life seeds are expected to reach subglacial lakes and water reservoirs and establish indigenous lake microbiota during their transit through the thick and aged Antarctic ice sheet upon its bottom melting. In general the subglacial Lake Vostok surface (ice sheet as well) environ represents the unique test area (sterile - in fact Earth-bound DNA-free and clean - in fact Earth-bound dust-free) for advancing extraterrestrial (ET) life detection technologies and searching for ET life indices in AMMs and IDPs.

  3. Hybridization thermodynamics of DNA bound to gold nanoparticles

    International Nuclear Information System (INIS)

    Lang, Brian

    2010-01-01

    Isothermal Titration Calorimetry (ITC) was used to study the thermodynamics of hybridization on DNA-functionalized colloidal gold nanoparticles. When compared to the thermodynamics of hybridization of DNA that is free in solution, the differences in the values of the Gibbs free energy of reaction, Δ r G o , the enthalpy, Δ r H o , and entropy, Δ r S o , were small. The change in Δ r G o between the free and bound states was always positive but with statistical significance outside the 95% confidence interval, implying the free DNA is slightly more stable than when in the bound state. Additionally, ITC was also able to reveal information about the binding stoichiometry of the hybridization reactions on the DNA-functionalized gold nanoparticles, and indicates that there is a significant fraction of the DNA on gold nanoparticle surface that is unavailable for DNA hybridization. Furthermore, the fraction of available DNA is dependent on the spacer group on the DNA that is used to span the gold surface from that to the probe DNA.

  4. Twisting, supercoiling and stretching in protein bound DNA

    Science.gov (United States)

    Lam, Pui-Man; Zhen, Yi

    2018-04-01

    We have calculated theoretical results for the torque and slope of the twisted DNA, with various proteins bound on it, using the Neukirch-Marko model, in the regime where plectonemes exist. We found that the torque in the protein bound DNA decreases compared to that in the bare DNA. This is caused by the decrease in the free energy g(f) , and hence the smaller persistence lengths, in the case of protein bound DNA. We hope our results will encourage experimental investigations of supercoiling in protein bound DNA, which can provide further tests of the Neukirch-Marko model.

  5. Generalized surface tension bounds in vacuum decay

    Science.gov (United States)

    Masoumi, Ali; Paban, Sonia; Weinberg, Erick J.

    2018-02-01

    Coleman and De Luccia (CDL) showed that gravitational effects can prevent the decay by bubble nucleation of a Minkowski or AdS false vacuum. In their thin-wall approximation this happens whenever the surface tension in the bubble wall exceeds an upper bound proportional to the difference of the square roots of the true and false vacuum energy densities. Recently it was shown that there is another type of thin-wall regime that differs from that of CDL in that the radius of curvature grows substantially as one moves through the wall. Not only does the CDL derivation of the bound fail in this case, but also its very formulation becomes ambiguous because the surface tension is not well defined. We propose a definition of the surface tension and show that it obeys a bound similar in form to that of the CDL case. We then show that both thin-wall bounds are special cases of a more general bound that is satisfied for all bounce solutions with Minkowski or AdS false vacua. We discuss the limit where the parameters of the theory attain critical values and the bound is saturated. The bounce solution then disappears and a static planar domain wall solution appears in its stead. The scalar field potential then is of the form expected in supergravity, but this is only guaranteed along the trajectory in field space traced out by the bounce.

  6. DNA ELECTROPHORESIS AT SURFACES

    Energy Technology Data Exchange (ETDEWEB)

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01

    During this year we performed two major projects: I. We developed a detailed theoretical model which complements our experiments on surface DNA electrophoresis. We found that it was possible to enhance the separation of DNA chains by imposing a chemical nanoscale pattern on the surface. This approach utilized the surface interaction effect of the DNA chains with the substrate and is a refinement to our previous method in which DNA chains were separated on homogeneous flat surfaces. By introducing the nano-patterns on the surface, the conformational changes of DNA chains of different lengths can be amplified, which results in the different friction strengths with the substrate surface. Our results also show that, when compared to the DNA electrophoresis performed on homogeneous flat surfaces, nanopatterned surfaces offer a larger window in choosing different surface interactions to achieve separation. II. In collaboration with a large international manufacturer of skin care products we also embarked on a project involving photo toxicity of titanium dioxide nanoparticles, which are a key ingredient in sunscreen and cosmetic lotions. The results clearly implicated the nanoparticles in catalyzing damage to chromosomal DNA. We then used this knowledge to develop a polymer/anti-oxidant coating which prevented the photocatalytic reaction on DNA while still retaining the UV absorptive properties of the nanoparticles. The standard gel electrophoresis was not sufficient in determining the extent of the DNA damage. The conclusions of this study were based predominantly on analysis obtained with the surface electrophoresis method.

  7. Surface-bound states in nanodiamonds

    Science.gov (United States)

    Han, Peng; Antonov, Denis; Wrachtrup, Jörg; Bester, Gabriel

    2017-05-01

    We show via ab initio calculations and an electrostatic model that the notoriously low, but positive, electron affinity of bulk diamond becomes negative for hydrogen passivated nanodiamonds and argue that this peculiar situation (type-II offset with a vacuum level at nearly midgap) and the three further conditions: (i) a surface dipole with positive charge on the outside layer, (ii) a spherical symmetry, and (iii) a dielectric mismatch at the surface, results in the emergence of a peculiar type of surface state localized just outside the nanodiamond. These states are referred to as "surface-bound states" and have consequently a strong environmental sensitivity. These type of states should exist in any nanostructure with negative electron affinity. We further quantify the band offsets of different type of nanostructures as well as the exciton binding energy and contrast the results with results for "conventional" silicon quantum dots.

  8. The bounded complexity of DNA computing.

    Science.gov (United States)

    Garzon, M H; Jonoska, N; Karl, S A

    1999-10-01

    This paper proposes a new approach to analyzing DNA-based algorithms in molecular computation. Such protocols are characterized abstractly by: encoding, tube operations and extraction. Implementation of these approaches involves encoding in a multiset of molecules that are assembled in a tube having a number of physical attributes. The physico-chemical state of a tube can be changed by a prescribed number of elementary operations. Based on realistic definitions of these elementary operations, we define complexity of a DNA-based algorithm using the physico-chemical property of each operation. We show that new algorithms for Hamiltonian path are about twice as efficient as Adleman's original one and that a recent algorithm for Max-Clique provides a similar increase in efficiency. Consequences of this approach to tube complexity and DNA computing are discussed.

  9. UV-Visible Spectroscopy-Based Quantification of Unlabeled DNA Bound to Gold Nanoparticles.

    Science.gov (United States)

    Baldock, Brandi L; Hutchison, James E

    2016-12-20

    DNA-functionalized gold nanoparticles have been increasingly applied as sensitive and selective analytical probes and biosensors. The DNA ligands bound to a nanoparticle dictate its reactivity, making it essential to know the type and number of DNA strands bound to the nanoparticle surface. Existing methods used to determine the number of DNA strands per gold nanoparticle (AuNP) require that the sequences be fluorophore-labeled, which may affect the DNA surface coverage and reactivity of the nanoparticle and/or require specialized equipment and other fluorophore-containing reagents. We report a UV-visible-based method to conveniently and inexpensively determine the number of DNA strands attached to AuNPs of different core sizes. When this method is used in tandem with a fluorescence dye assay, it is possible to determine the ratio of two unlabeled sequences of different lengths bound to AuNPs. Two sizes of citrate-stabilized AuNPs (5 and 12 nm) were functionalized with mixtures of short (5 base) and long (32 base) disulfide-terminated DNA sequences, and the ratios of sequences bound to the AuNPs were determined using the new method. The long DNA sequence was present as a lower proportion of the ligand shell than in the ligand exchange mixture, suggesting it had a lower propensity to bind the AuNPs than the short DNA sequence. The ratio of DNA sequences bound to the AuNPs was not the same for the large and small AuNPs, which suggests that the radius of curvature had a significant influence on the assembly of DNA strands onto the AuNPs.

  10. Spatial imaging of proteins bound to nanochannel-linearized DNA

    Science.gov (United States)

    Wang, Yan Mei; Tegenfeldt, Jonas; Reisner, Walter; Austin, Robert; Cox, Ted

    2004-03-01

    One of the main questions in post genomic era is to understand how gene-regulating proteins control gene expression. We use single molecule techniques to image transcription factor fusion-proteins (LacI-GFP) bound to DNA by linearizing the DNA-protein construct molecule in quartz nanochannels. The nanochannels (down to 40nm wide) are fabricated using focused ion beam milling. These asymmetric (off center protein binding) DNA-protein molecules exhibit unusual behaviors upon entering nano-confinement - the longer tail always enters the channel first. Analysis considering free energy variation and charge distributions along the molecule will be presented. Polymer dynamics of DNA-protein complex and DNA in nanochannels will also be discussed.

  11. Computational structural analysis: multiple proteins bound to DNA.

    Directory of Open Access Journals (Sweden)

    Andrija Tomovic

    Full Text Available BACKGROUND: With increasing numbers of crystal structures of proteinratioDNA and proteinratioproteinratioDNA complexes publically available, it is now possible to extract sufficient structural, physical-chemical and thermodynamic parameters to make general observations and predictions about their interactions. In particular, the properties of macromolecular assemblies of multiple proteins bound to DNA have not previously been investigated in detail. METHODOLOGY/PRINCIPAL FINDINGS: We have performed computational structural analyses on macromolecular assemblies of multiple proteins bound to DNA using a variety of different computational tools: PISA; PROMOTIF; X3DNA; ReadOut; DDNA and DCOMPLEX. Additionally, we have developed and employed an algorithm for approximate collision detection and overlapping volume estimation of two macromolecules. An implementation of this algorithm is available at http://promoterplot.fmi.ch/Collision1/. The results obtained are compared with structural, physical-chemical and thermodynamic parameters from proteinratioprotein and single proteinratioDNA complexes. Many of interface properties of multiple proteinratioDNA complexes were found to be very similar to those observed in binary proteinratioDNA and proteinratioprotein complexes. However, the conformational change of the DNA upon protein binding is significantly higher when multiple proteins bind to it than is observed when single proteins bind. The water mediated contacts are less important (found in less quantity between the interfaces of components in ternary (proteinratioproteinratioDNA complexes than in those of binary complexes (proteinratioprotein and proteinratioDNA.The thermodynamic stability of ternary complexes is also higher than in the binary interactions. Greater specificity and affinity of multiple proteins binding to DNA in comparison with binary protein-DNA interactions were observed. However, protein-protein binding affinities are stronger in

  12. Random Coding Bounds for DNA Codes Based on Fibonacci Ensembles of DNA Sequences

    Science.gov (United States)

    2008-07-01

    Highway, Suite 1204, Arlington, VA 22202-4302, and to the Office of Management and Budget, Paperwork Reduction Project (0704-0188) Washington, DC...COVERED (From - To) 6 Jul 08 – 11 Jul 08 4. TITLE AND SUBTITLE RANDOM CODING BOUNDS FOR DNA CODES BASED ON FIBONACCI ENSEMBLES OF DNA SEQUENCES...sequences which are generalizations of the Fibonacci sequences. 15. SUBJECT TERMS DNA Codes, Fibonacci Ensembles, DNA Computing, Code Optimization 16

  13. Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States

    Energy Technology Data Exchange (ETDEWEB)

    Cotner-Gohara, Elizabeth; Kim, In-Kwon; Hammel, Michal; Tainer, John A.; Tomkinson, Alan E.; Ellenberger, Tom (Scripps); (Maryland-MED); (WU-MED); (LBNL)

    2010-09-13

    Human DNA ligase III has essential functions in nuclear and mitochondrial DNA replication and repair and contains a PARP-like zinc finger (ZnF) that increases the extent of DNA nick joining and intermolecular DNA ligation, yet the bases for ligase III specificity and structural variation among human ligases are not understood. Here combined crystal structure and small-angle X-ray scattering results reveal dynamic switching between two nick-binding components of ligase III: the ZnF-DNA binding domain (DBD) forms a crescent-shaped surface used for DNA end recognition which switches to a ring formed by the nucleotidyl transferase (NTase) and OB-fold (OBD) domains for catalysis. Structural and mutational analyses indicate that high flexibility and distinct DNA binding domain features in ligase III assist both nick sensing and the transition from nick sensing by the ZnF to nick joining by the catalytic core. The collective results support a 'jackknife model' in which the ZnF loads ligase III onto nicked DNA and conformational changes deliver DNA into the active site. This work has implications for the biological specificity of DNA ligases and functions of PARP-like zinc fingers.

  14. BION web server: predicting non-specifically bound surface ions.

    Science.gov (United States)

    Petukh, Marharyta; Kimmet, Taylor; Alexov, Emil

    2013-03-15

    Ions are essential component of the cell and frequently are found bound to various macromolecules, in particular to proteins. A binding of an ion to a protein greatly affects protein's biophysical characteristics and needs to be taken into account in any modeling approach. However, ion's bounded positions cannot be easily revealed experimentally, especially if they are loosely bound to macromolecular surface. Here, we report a web server, the BION web server, which addresses the demand for tools of predicting surface bound ions, for which specific interactions are not crucial; thus, they are difficult to predict. The BION is easy to use web server that requires only coordinate file to be inputted, and the user is provided with various, but easy to navigate, options. The coordinate file with predicted bound ions is displayed on the output and is available for download.

  15. Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching Between Two DNA Bound States†

    OpenAIRE

    Cotner-Gohara, Elizabeth; Kim, In-Kwon; Hammel, Michal; Tainer, John A.; Tomkinson, Alan E.; Ellenberger, Tom

    2010-01-01

    Human DNA ligase III has essential functions in nuclear and mitochondrial DNA replication and repair and contains a PARP-like zinc finger (ZnF) that increases DNA nick-joining and intermolecular DNA ligation. Yet, the bases for ligase III specificity and structural variation among human ligases are not understood. Here combined crystal structure and small angle x-ray scattering results reveal dynamic switching between two nick-binding components of ligase III: the ZnF-DNA binding domain (DBD)...

  16. Regulating DNA Self-assembly by DNA-Surface Interactions.

    Science.gov (United States)

    Liu, Longfei; Li, Yulin; Wang, Yong; Zheng, Jianwei; Mao, Chengde

    2017-12-14

    DNA self-assembly provides a powerful approach for preparation of nanostructures. It is often studied in bulk solution and involves only DNA-DNA interactions. When confined to surfaces, DNA-surface interactions become an additional, important factor to DNA self-assembly. However, the way in which DNA-surface interactions influence DNA self-assembly is not well studied. In this study, we showed that weak DNA-DNA interactions could be stabilized by DNA-surface interactions to allow large DNA nanostructures to form. In addition, the assembly can be conducted isothermally at room temperature in as little as 5 seconds. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Subgap in the Surface Bound States Spectrum of Superfluid ^3 He-B with Rough Surface

    Science.gov (United States)

    Nagato, Y.; Higashitani, S.; Nagai, K.

    2017-12-01

    The subgap structure in the surface bound states spectrum of superfluid ^3 He-B with rough surface is discussed. The subgap is formed by the level repulsion between the surface bound state and the continuum states in the course of multiple scattering by the surface roughness. We show that the level repulsion is originated from the nature of the wave function of the surface bound state that is now recognized as Majorana fermion. We study the superfluid ^3 He-B with a rough surface and in a magnetic field perpendicular to the surface using the quasi-classical Green function together with a random S-matrix model. We calculate the self-consistent order parameters, the spin polarization density and the surface density of states. It is shown that the subgap is found also in a magnetic field perpendicular to the surface. The magnetic field dependence of the transverse acoustic impedance is also discussed.

  18. Surface plasmon oscillations in a semi-bounded semiconductor plasma

    Science.gov (United States)

    M, SHAHMANSOURI; A, P. MISRA

    2018-02-01

    We study the dispersion properties of surface plasmon (SP) oscillations in a semi-bounded semiconductor plasma with the effects of the Coulomb exchange (CE) force associated with the spin polarization of electrons and holes as well as the effects of the Fermi degenerate pressure and the quantum Bohm potential. Starting from a quantum hydrodynamic model coupled to the Poisson equation, we derive the general dispersion relation for surface plasma waves. Previous results in this context are recovered. The dispersion properties of the surface waves are analyzed in some particular cases of interest and the relative influence of the quantum forces on these waves are also studied for a nano-sized GaAs semiconductor plasma. It is found that the CE effects significantly modify the behaviors of the SP waves. The present results are applicable to understand the propagation characteristics of surface waves in solid density plasmas.

  19. Determining the limit of detection of surface bound antibody.

    Science.gov (United States)

    Madiona, Robert M T; Welch, Nicholas G; Scoble, Judith A; Muir, Benjamin W; Pigram, Paul J

    2017-08-11

    Determination of a limit of detection (LoD) for surface bound antibodies is crucial for the development and deployment of sensitive bioassays. The measurement of very low concentrations of surface bound antibodies is also important in the manufacturing of pharmaceutical products such as antibody-conjugated pharmaceuticals. Low concentrations are required to avoid an immune response from the target host. Enzyme-linked immunosorbent assay (ELISA), x-ray photoelectron spectroscopy (XPS), and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were used to determine the LoD for the surface bound antibody (antiepidermal growth factor receptor antibody) on silicon substrates. Antibody solution concentrations between 10 μg/ml and 1 ng/ml and a control (antibody-free buffer solution) were employed, and the detection performance of each technique was compared. For this system, the ELISA LoD was 100 ng/ml and the XPS LoD was 1 μg/ml, corresponding to an estimated surface concentration of 49  ± 7 ng/cm 2 using a 1 μg/ml solution. Due to the multivariate complexity of ToF-SIMS data, analysis was carried out using three different methods, peak ratio calculations, principal component analysis, and artificial neural network analysis. The use of multivariate analysis with this dataset offers an unbiased analytical approach based on the peaks selected from ToF-SIMS data. The results estimate a ToF-SIMS LoD between applied antibody concentrations of 10 and 100 ng/mL. For surface bound antibodies on a silicon substrate, the LoD is below an estimated surface concentration of 49 ng/cm 2 . The authors have determined the LoD for this system using ELISA, XPS, and ToF-SIMS with multivariate analyses, with ToF-SIMS offering an order of magnitude better detection over ELISA and 2 orders of magnitude better detection over XPS.

  20. Nanostructures and dynamics of macromolecules bound to attractive filler surfaces

    Science.gov (United States)

    Koga, Tad; Barkley, Deborah; Jiang, Naisheng; Endoh, Maya; Masui, Tomomi; Kishimoto, Hiroyuki; Nagao, Michihiro; Satija, Sushil; Taniguchi, Takashi

    We report in-situ nanostructures and dynamics of polybutadiene (PB) chains bound to carbon black (CB) fillers (the so-called ``bound polymer layer (BPL)'') in a good solvent. The BPL on the CB fillers were extracted by solvent leaching of a CB-filled PB compound and subsequently dispersed in deuterated toluene to label the BPL for small-angle neutron scattering and neutron spin echo techniques. Intriguingly, the results demonstrate that the BPL is composed of two regions regardless of molecular weights of PB: the inner unswollen region of ~ 0.5 nm thick and outer swollen region where the polymer chains display a parabolic profile with a diffuse tail. This two-layer formation on the filler surface is similar to that reported for polymer chains adsorbed on planar substrates from melts. In addition, the results show that the dynamics of the swollen bound chains can be explained by the so-called ``breathing mode'' and is generalized with the thickness of the swollen BPL. Furthermore, we will discuss how the breathing collective dynamics is affected by the presence of polymer chains in a matrix solution. We acknowledge the financial support from NSF Grant No. CMMI-1332499.

  1. Error bounds for surface area estimators based on Crofton's formula

    DEFF Research Database (Denmark)

    Kiderlen, Markus; Meschenmoser, Daniel

    2009-01-01

    According to Crofton’s formula, the surface area S(A) of a sufficiently regular compact set A in R^d is proportional to the mean of all total projections pA (u) on a linear hyperplane with normal u, uniformly averaged over all unit vectors u. In applications, pA (u) is only measured in k directio...... in the sense that the relative error of the surface area estimator is very close to the minimal error....... and the mean is approximated by a finite weighted sum S(A) of the total projections in these directions. The choice of the weights depends on the selected quadrature rule. We define an associated zonotope Z (depending only on the projection directions and the quadrature rule), and show that the relative error...... S (A)/S (A) is bounded from below by the inradius of Z and from above by the circumradius of Z. Applying a strengthened isoperimetric inequality due to Bonnesen, we show that the rectangular quadrature rule does not give the best possible error bounds for d = 2. In addition, we derive asymptotic...

  2. Hybridization Efficiency of Molecular Beacons Bound to Gold Nanowires: Effect of Surface Coverage and Target Length

    Science.gov (United States)

    2010-01-01

    Surface-bound nucleic acid probes designed to adopt specific secondary structures are becoming increasingly important in a range of biosensing applications but remain less well characterized than traditional single-stranded probes, which are typically designed to avoid secondary structure. We report the hybridization efficiency for surface-immobilized hairpin DNA probes. Our probes are molecular beacons, carrying a 3′ dye moiety and a 5′ thiol for attachment to gold nanowires, which serve as both scaffolds for probe attachment and quenchers. Hybridization efficiency was dependent on probe surface coverage, reaching a maximum of ∼90% at intermediate coverages of (1−2) × 1012 probes/cm2 and dropping to ≤20% at higher or lower coverages. Fluorescence intensity did not track with the number of target molecules bound, and was highest for high probe coverage despite the lower bound targets per square centimeter. Backfilling with short thiolated oligoethylene glycol spacers increased hybridization efficiency at low hairpin probe coverages (∼(3−4) × 1011 probes/cm2), but not at higher probe coverages (1 × 1012/cm2). We also evaluated the effect of target length by adding up to 50 nonhybridizing nucleotides to the 3′ or 5′ end of the complementary target sequence. Additional nucleotides on the 3′ end of the complementary target sequence (i.e., the end near the nanowire surface) had a much greater impact on hybridization efficiency as compared to nucleotides added to the 5′ end. This work provides guidance in designing sensors in which surface-bound probes designed to adopt secondary structures are used to detect target sequences from solution. PMID:21038880

  3. Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site.

    Science.gov (United States)

    Li, Jun; Dantas Machado, Ana Carolina; Guo, Ming; Sagendorf, Jared M; Zhou, Zhan; Jiang, Longying; Chen, Xiaojuan; Wu, Daichao; Qu, Lingzhi; Chen, Zhuchu; Chen, Lin; Rohs, Remo; Chen, Yongheng

    2017-07-25

    FOXA2, a member of the forkhead family of transcription factors, plays essential roles in liver development and bile acid homeostasis. In this study, we report a 2.8 Å co-crystal structure of the FOXA2 DNA-binding domain (FOXA2-DBD) bound to a DNA duplex containing a forkhead consensus binding site (GTAAACA). The FOXA2-DBD adopts the canonical winged-helix fold, with helix H3 and wing 1 regions mainly mediating the DNA recognition. Although the wing 2 region was not defined in the structure, isothermal titration calorimetry assays suggested that this region was required for optimal DNA binding. Structure comparison with the FOXA3-DBD bound to DNA revealed more major groove contacts and fewer minor groove contacts in the FOXA2 structure than in the FOXA3 structure. Structure comparison with the FOXO1-DBD bound to DNA showed that different forkhead proteins could induce different DNA conformations upon binding to identical DNA sequences. Our findings provide the structural basis for FOXA2 protein binding to a consensus forkhead site and elucidate how members of the forkhead protein family bind different DNA sites.

  4. DNA unwinding assay using streptavidin-bound oligonucleotides

    Directory of Open Access Journals (Sweden)

    Kelman Zvi

    2006-11-01

    Full Text Available Abstract Background Helicases play essential roles in many cellular processes including replication, transcription and translation. Most helicases translocate along one strand of the duplex while displacing the complementary strand (of either DNA or RNA. Thus, helicases have directionality. They move along nucleic acids in either the 3'→ 5' or 5'→ 3' direction. The directionality of helicases with low activity or of those that cannot initiate duplex unwinding from a substrate that contains only one single-stranded overhang region is difficult to determine. Results An improved assay to determine helicase directionality was developed that uses a substrate containing biotinylated oligonucleotides. As a proof of concept, it was shown that the substrates substantially improve helicase activity and directionality determination for several DNA helicases in comparison to more traditional substrates. In addition, a universal substrate that can be used to determine the directionality of both 3'→ 5' and 5'→ 3' helicases was developed. Conclusion It is shown here that the use of a biotin-streptavidin complex as a helicase substrate improves helicase activity and the determination of helicase directionality. The method described is simpler that the currently available techniques.

  5. Sea level: measuring the bounding surfaces of the ocean.

    Science.gov (United States)

    Tamisiea, Mark E; Hughes, Chris W; Williams, Simon D P; Bingley, Richard M

    2014-09-28

    The practical need to understand sea level along the coasts, such as for safe navigation given the spatially variable tides, has resulted in tide gauge observations having the distinction of being some of the longest instrumental ocean records. Archives of these records, along with geological constraints, have allowed us to identify the century-scale rise in global sea level. Additional data sources, particularly satellite altimetry missions, have helped us to better identify the rates and causes of sea-level rise and the mechanisms leading to spatial variability in the observed rates. Analysis of all of the data reveals the need for long-term and stable observation systems to assess accurately the regional changes as well as to improve our ability to estimate future changes in sea level. While information from many scientific disciplines is needed to understand sea-level change, this review focuses on contributions from geodesy and the role of the ocean's bounding surfaces: the sea surface and the Earth's crust. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  6. Rigorous bounds on buoyancy flux in surface driven flows

    Science.gov (United States)

    Caulfield, C. P.

    2004-11-01

    Stably stratified shear flows, where both the velocity and density vary with height, are common in environmentally and geophysically relevant flows. An understanding of constraints on mixing processes is essential for an improved parameterization of geophysical turbulence, in particular for appropriate modelling of the budgets of heat, salinity and momentum in larger scale models. Flows that are principally driven by surface-localized stresses (e.g. caused by wind) are particularly prevalent in geophysical flows. In this talk, I will derive rigorous bounds on the long-time averaged buoyancy flux for a class of such flows, using the background method developed by Doering & Constantin. Interestingly, flows that maximize the buoyancy flux can be directly related to laminar flows with stronger forcing. This is qualitatively different from other stratified mixing problems, for example in stratified plane Couette flow. This result suggests that quasi-laminar mixing, which is typically much more efficient than strongly turbulent mixing, may be the dominant process by which irreversible changes in density occur within such surface driven flows.

  7. Sea level: measuring the bounding surfaces of the ocean

    Science.gov (United States)

    Tamisiea, Mark E.; Hughes, Chris W.; Williams, Simon D. P.; Bingley, Richard M.

    2014-01-01

    The practical need to understand sea level along the coasts, such as for safe navigation given the spatially variable tides, has resulted in tide gauge observations having the distinction of being some of the longest instrumental ocean records. Archives of these records, along with geological constraints, have allowed us to identify the century-scale rise in global sea level. Additional data sources, particularly satellite altimetry missions, have helped us to better identify the rates and causes of sea-level rise and the mechanisms leading to spatial variability in the observed rates. Analysis of all of the data reveals the need for long-term and stable observation systems to assess accurately the regional changes as well as to improve our ability to estimate future changes in sea level. While information from many scientific disciplines is needed to understand sea-level change, this review focuses on contributions from geodesy and the role of the ocean's bounding surfaces: the sea surface and the Earth's crust. PMID:25157196

  8. Structures of mithramycin analogues bound to DNA and implications for targeting transcription factor FLI1.

    Science.gov (United States)

    Hou, Caixia; Weidenbach, Stevi; Cano, Kristin E; Wang, Zhonghua; Mitra, Prithiba; Ivanov, Dmitri N; Rohr, Jürgen; Tsodikov, Oleg V

    2016-10-14

    Transcription factors have been considered undruggable, but this paradigm has been recently challenged. DNA binding natural product mithramycin (MTM) is a potent antagonist of oncogenic transcription factor EWS-FLI1. Structural details of MTM recognition of DNA, including the FLI1 binding sequence GGA(A/T), are needed to understand how MTM interferes with EWS-FLI1. We report a crystal structure of an MTM analogue MTM SA-Trp bound to a DNA oligomer containing a site GGCC, and two structures of a novel analogue MTM SA-Phe in complex with DNA. MTM SA-Phe is bound to sites AGGG and GGGT on one DNA, and to AGGG and GGGA(T) (a FLI1 binding site) on the other, revealing how MTM recognizes different DNA sequences. Unexpectedly, at sub-micromolar concentrations MTMs stabilize FLI1-DNA complex on GGAA repeats, which are critical for the oncogenic function of EWS-FLI1. We also directly demonstrate by nuclear magnetic resonance formation of a ternary FLI1-DNA-MTM complex on a single GGAA FLI1/MTM binding site. These biochemical and structural data and a new FLI1-DNA structure suggest that MTM binds the minor groove and perturbs FLI1 bound nearby in the major groove. This ternary complex model may lead to development of novel MTM analogues that selectively target EWS-FLI1 or other oncogenic transcription factors, as anti-cancer therapeutics. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers.

    Directory of Open Access Journals (Sweden)

    Marijn T J van Loenhout

    Full Text Available The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that acts as a scanning probe, is created by looping an optically trapped DNA tether around a DNA molecule that is held with magnetic tweezers. Upon scanning the loop along the λ-DNA molecule, EcoRI proteins were detected with ~17 nm spatial resolution. An offset of 33 ± 5 nm for the detected protein positions was found between back and forwards scans, corresponding to the size of the DNA loop and in agreement with theoretical estimates. At higher applied stretching forces, the scanning loop was able to remove bound proteins from the DNA, showing that the method is in principle also capable of measuring the binding strength of proteins to DNA with a force resolution of 0.1 pN/[Formula: see text]. The use of magnetic tweezers in this assay allows the facile preparation of many single-molecule tethers, which can be scanned one after the other, while it also allows for direct control of the supercoiling state of the DNA molecule, making it uniquely suitable to address the effects of torque on protein-DNA interactions.

  10. Strategies for optimizing DNA hybridization on surfaces.

    Science.gov (United States)

    Ravan, Hadi; Kashanian, Soheila; Sanadgol, Nima; Badoei-Dalfard, Arastoo; Karami, Zahra

    2014-01-01

    Specific and predictable hybridization of the polynucleotide sequences to their complementary counterparts plays a fundamental role in the rational design of new nucleic acid nanodevices. Generally, nucleic acid hybridization can be performed using two major strategies, namely hybridization of DNA or RNA targets to surface-tethered oligonucleotide probes (solid-phase hybridization) and hybridization of the target nucleic acids to randomly distributed probes in solution (solution-phase hybridization). Investigations into thermodynamic and kinetic parameters of these two strategies showed that hybridization on surfaces is less favorable than that of the same sequence in solution. Indeed, the efficiency of DNA hybridization on surfaces suffers from three constraints: (1) electrostatic repulsion between DNA strands on the surface, (2) steric hindrance between tethered DNA probes, and (3) nonspecific adsorption of the attached oligonucleotides to the solid surface. During recent years, several strategies have been developed to overcome the problems associated with DNA hybridization on surfaces. Optimizing the probe surface density, application of a linker between the solid surface and the DNA-recognizing sequence, optimizing the pH of DNA hybridization solutions, application of thiol reagents, and incorporation of a polyadenine block into the terminal end of the recognizing sequence are among the most important strategies for enhancing DNA hybridization on surfaces. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Peptides containing antigenic and cationic domains have enhanced, multivalent immunogenicity when bound to DNA vaccines.

    Science.gov (United States)

    Riedl, Petra; Reimann, Jörg; Schirmbeck, Reinhold

    2004-02-01

    We explored strategies to codeliver DNA- and peptide-based vaccines in a way that enhances the immunogenicity of both components of the combination vaccine for T cells. Specific CD8(+) T cell responses to an antigenic peptide are primed when the peptide is fused to a cationic peptide domain that is bound to plasmid DNA or oligonucleotides (ODN; with or without CpG motifs). Plasmid DNA mixed with antigenic/cationic peptides or histones forms large complexes with different biological properties depending on the molar ratios of peptide/protein and polynucleotide. Complexes containing high (but not low) molar ratios of cationic peptide to DNA facilitate transfection (DNA uptake and expression of the plasmid-encoded product) of cells. In contrast, complexes containing low (but not high) molar ratios of cationic peptide to DNA prime potent multispecific T cell responses after a single intramuscular injection of the complexes. The general validity of this observation was confirmed mixing different antigenic/cationic peptides with different DNA vaccines. In these vaccine formulations, multispecific CD8(+) T cell responses specific for epitopes of the peptide- as well as the DNA-based vaccine were efficiently coprimed, together with humoral antibody responses to conformational determinants of large viral antigens encoded by the DNA vaccine. The data indicate that mixtures of DNA vaccines with antigenic, cationic peptides are immunogenic vaccine formulations particularly suited for the induction of multispecific T cell responses.

  12. Probing the run-on oligomer of activated SgrAI bound to DNA.

    Science.gov (United States)

    Shah, Santosh; Sanchez, Jonathan; Stewart, Andrew; Piperakis, Michael M; Cosstick, Richard; Nichols, Claire; Park, Chad K; Ma, Xin; Wysocki, Vicki; Bitinaite, Jurate; Horton, Nancy C

    2015-01-01

    SgrAI is a type II restriction endonuclease with an unusual mechanism of activation involving run-on oligomerization. The run-on oligomer is formed from complexes of SgrAI bound to DNA containing its 8 bp primary recognition sequence (uncleaved or cleaved), and also binds (and thereby activates for DNA cleavage) complexes of SgrAI bound to secondary site DNA sequences which contain a single base substitution in either the 1st/8th or the 2nd/7th position of the primary recognition sequence. This modulation of enzyme activity via run-on oligomerization is a newly appreciated phenomenon that has been shown for a small but increasing number of enzymes. One outstanding question regarding the mechanistic model for SgrAI is whether or not the activating primary site DNA must be cleaved by SgrAI prior to inducing activation. Herein we show that an uncleavable primary site DNA containing a 3'-S-phosphorothiolate is in fact able to induce activation. In addition, we now show that cleavage of secondary site DNA can be activated to nearly the same degree as primary, provided a sufficient number of flanking base pairs are present. We also show differences in activation and cleavage of the two types of secondary site, and that effects of selected single site substitutions in SgrAI, as well as measured collisional cross-sections from previous work, are consistent with the cryo-electron microscopy model for the run-on activated oligomer of SgrAI bound to DNA.

  13. Probing the run-on oligomer of activated SgrAI bound to DNA.

    Directory of Open Access Journals (Sweden)

    Santosh Shah

    Full Text Available SgrAI is a type II restriction endonuclease with an unusual mechanism of activation involving run-on oligomerization. The run-on oligomer is formed from complexes of SgrAI bound to DNA containing its 8 bp primary recognition sequence (uncleaved or cleaved, and also binds (and thereby activates for DNA cleavage complexes of SgrAI bound to secondary site DNA sequences which contain a single base substitution in either the 1st/8th or the 2nd/7th position of the primary recognition sequence. This modulation of enzyme activity via run-on oligomerization is a newly appreciated phenomenon that has been shown for a small but increasing number of enzymes. One outstanding question regarding the mechanistic model for SgrAI is whether or not the activating primary site DNA must be cleaved by SgrAI prior to inducing activation. Herein we show that an uncleavable primary site DNA containing a 3'-S-phosphorothiolate is in fact able to induce activation. In addition, we now show that cleavage of secondary site DNA can be activated to nearly the same degree as primary, provided a sufficient number of flanking base pairs are present. We also show differences in activation and cleavage of the two types of secondary site, and that effects of selected single site substitutions in SgrAI, as well as measured collisional cross-sections from previous work, are consistent with the cryo-electron microscopy model for the run-on activated oligomer of SgrAI bound to DNA.

  14. Internal charge transfer based ratiometric interaction of anionic surfactant with calf thymus DNA bound cationic surfactant: Study I

    Science.gov (United States)

    Mukherjee, Abhijit; Chaudhuri, Tandrima; Moulik, Satya Priya; Banerjee, Manas

    2016-01-01

    Cetyl trimethyl ammonium bromide (CTAB) binds calf thymus (ct-) DNA like anionic biopolymers electrostatically and established equilibrium both in the ground as well as in excited state in aqueous medium at pH 7. Anionic sodium dodecyl sulfate (SDS) does not show even hydrophobic interaction with ct-DNA at low concentration. On contrary, SDS can establish well defined equilibrium with DNA bound CTAB in ground state where the same CTAB-DNA isosbestic point reappears. First report of internal charge transfer (ICT) based binding of CTAB with ct-DNA as well as ICT based interaction of anionic SDS with DNA bound CTAB that shows dynamic quenching contribution also. The reappearance of anodic peak and slight increase in cathodic peak current with increasing concentration (at lower range) of anionic SDS, possibly reflect the release of CTAB from DNA bound CTAB by SDS.

  15. Protein sequences bound to mineral surfaces persist into deep time

    DEFF Research Database (Denmark)

    Demarchi, Beatrice; Hall, Shaun; Roncal-Herrero, Teresa

    2016-01-01

    Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites...

  16. Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA

    Directory of Open Access Journals (Sweden)

    Yijin Liu

    2015-12-01

    Full Text Available We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction.

  17. Covalently bound DNA on naked iron oxide nanoparticles: Intelligent colloidal nano-vector for cell transfection.

    Science.gov (United States)

    Magro, Massimiliano; Martinello, Tiziana; Bonaiuto, Emanuela; Gomiero, Chiara; Baratella, Davide; Zoppellaro, Giorgio; Cozza, Giorgio; Patruno, Marco; Zboril, Radek; Vianello, Fabio

    2017-11-01

    Conversely to common coated iron oxide nanoparticles, novel naked surface active maghemite nanoparticles (SAMNs) can covalently bind DNA. Plasmid (pDNA) harboring the coding gene for GFP was directly chemisorbed onto SAMNs, leading to a novel DNA nanovector (SAMN@pDNA). The spontaneous internalization of SAMN@pDNA into cells was compared with an extensively studied fluorescent SAMN derivative (SAMN@RITC). Moreover, the transfection efficiency of SAMN@pDNA was evaluated and explained by computational model. SAMN@pDNA was prepared and characterized by spectroscopic and computational methods, and molecular dynamic simulation. The size and hydrodynamic properties of SAMN@pDNA and SAMN@RITC were studied by electron transmission microscopy, light scattering and zeta-potential. The two nanomaterials were tested by confocal scanning microscopy on equine peripheral blood-derived mesenchymal stem cells (ePB-MSCs) and GFP expression by SAMN@pDNA was determined. Nanomaterials characterized by similar hydrodynamic properties were successfully internalized and stored into mesenchymal stem cells. Transfection by SAMN@pDNA occurred and GFP expression was higher than lipofectamine procedure, even in the absence of an external magnetic field. A computational model clarified that transfection efficiency can be ascribed to DNA availability inside cells. Direct covalent binding of DNA on naked magnetic nanoparticles led to an extremely robust gene delivery tool. Hydrodynamic and chemical-physical properties of SAMN@pDNA were responsible of the successful uptake by cells and of the efficiency of GFP gene transfection. SAMNs are characterized by colloidal stability, excellent cell uptake, persistence in the host cells, low toxicity and are proposed as novel intelligent DNA nanovectors for efficient cell transfection. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. DNA Adsorption to and Elution from Silica Surfaces: Influence of Amino Acid Buffers

    Science.gov (United States)

    Vandeventer, Peter E.; Mejia, Jorge; Nadim, Ali; Johal, Malkiat S.; Niemz, Angelika

    2014-01-01

    Solid phase extraction and purification of DNA from complex samples typically requires chaotropic salts that can inhibit downstream polymerase amplification if carried into the elution buffer. Amino acid buffers may serve as a more compatible alternative for modulating the interaction between DNA and silica surfaces. We characterized DNA binding to silica surfaces, facilitated by representative amino acid buffers, and the subsequent elution of DNA from the silica surfaces. Through bulk depletion experiments, we found that more DNA adsorbs to silica particles out of positively compared to negatively charged amino acid buffers. Additionally, the type of the silica surface greatly influences the amount of DNA adsorbed, and the final elution yield. Quartz crystal microbalance experiments with dissipation monitoring (QCM-D) revealed multiphasic DNA adsorption out of stronger adsorbing conditions such as arginine, glycine, and glutamine, with DNA more rigidly bound during the early stages of the adsorption process. The DNA film adsorbed out of glutamate was more flexible and uniform throughout the adsorption process. QCM-D characterization of DNA elution from the silica surface indicates an uptake in water mass during the initial stage of DNA elution for the stronger adsorbing conditions, which suggests that for these conditions the DNA film is partly dehydrated during the prior adsorption process. Overall, several positively charged and polar neutral amino acid buffers show promise as an alternative to methods based on chaotropic salts for solid phase DNA extraction. PMID:23931415

  19. Inhibition of surface bound carbonate stabilization of tetragonal zirconia

    DEFF Research Database (Denmark)

    Nielsen, Mette Skovgaard; Almdal, Kristoffer; Lelieveld, A. van

    2011-01-01

    Water is known to initiate a tetragonal to monoclinic phase transformation in zirconia particles. Carbonates on the zirconia surface react with water molecules and hence reduce the transformation rate. This study investigates the possibility of inhibition of the reaction between surface carbonates...... and water in order to increase the transformation rate in the zirconia crystals. It was found possible to limit the reaction by reacting the surface carbonates with alcohols, a thiol and a primary amide prior to reaction with water. It was also concluded that di- and trialcohols are able to stabilize...

  20. Mechanisms of Surface-Mediated DNA Hybridization

    Science.gov (United States)

    2015-01-01

    Single-molecule total internal reflection fluorescence microscopy was employed in conjunction with resonance energy transfer (RET) to observe the dynamic behavior of donor-labeled ssDNA at the interface between aqueous solution and a solid surface decorated with complementary acceptor-labeled ssDNA. At least 100 000 molecular trajectories were determined for both complementary strands and negative control ssDNA. RET was used to identify trajectory segments corresponding to the hybridized state. The vast majority of molecules from solution adsorbed nonspecifically to the surface, where a brief two-dimensional search was performed with a 7% chance of hybridization. Successful hybridization events occurred with a characteristic search time of ∼0.1 s, and unsuccessful searches resulted in desorption from the surface, ultimately repeating the adsorption and search process. Hybridization was reversible, and two distinct modes of melting (i.e., dehybridization) were observed, corresponding to long-lived (∼15 s) and short-lived (∼1.4 s) hybridized time intervals. A strand that melted back onto the surface could rehybridize after a brief search or desorb from the interface. These mechanistic observations provide guidance for technologies that involve DNA interactions in the near-surface region, suggesting a need to design surfaces that both enhance the complex multidimensional search process and stabilize the hybridized state. PMID:24708278

  1. Surface-bound microgels - From physicochemical properties to biomedical applications

    DEFF Research Database (Denmark)

    Nyström, Lina; Malmsten, Martin

    2016-01-01

    Microgels offer robust and facile approaches for surface modification, as well as opportunities to introduce biological functionality by loading such structures with bioactive agents, e.g., in the context of drug delivery, functional biomaterials, and biosensors. As such, they provide a versatile...

  2. A change in the composition of supramolecular DNA-bound phospholipids in thymus and liver of gamma-irradiated rats

    International Nuclear Information System (INIS)

    Krasichkova, Z.I.; Strazhevskaya, N.B.

    1984-01-01

    The composition of supramolecular DNA (SM DNA)-bound phospholipids (PL) of thymus and liver of intact rats and those 2 min, 2, 6 and 24 h after γ-irradiation (9.7 Gy) was studied. In norm, supramolecular DNA of the thymus was shown to contain 6.7 μg PL/mg DNA, and that of the liver, 6.1 μg PL/mg DNA, the main components of PL being cardiolipin (CL) and phosphatidylethanolamine (PEA). Substantial changes were detected in the PL composition of SM DNA of γ,irradiated rat organs. During the postirradiation period the concentration of PEA and CL in thymus SM DNA changed symbatically and irreversibly decAeased to traces; whereas in SM DNA of the liver, their concentrations changed antibatically and decreased only to a definite level thus maintaining the necessary ''lipid volume''. It was shown that PL were not restored in SM DNA of the radiopesistant liver

  3. Implementation of Bounding Surface Model into ABAQUS and Its Application to Wellbore Stability Analysis

    Science.gov (United States)

    Chen, S.; Al-Muntasheri, G.; Abousleiman, Y. N.

    2014-12-01

    The critical state concept based bounding surface model is one of the most widely used elastoplastic constitutive models for geomaterials, attributed mainly to its essential feature of allowing plastic deformation to occur for stress points within the bounding surface and thus the capability to represent the realistic non-recoverable behaviour of soils and rocks observed under the cyclic loading. This paper develops an implicit integration algorithm for the bounding surface model, using the standard return mapping approach (elastic predictor-plastic corrector), to obtain the updated stresses for the given strain increments. The formulation of the constitutive integration requires the derivation of a supplementary differential equation to describe the evolution of a key variable, i.e., the ratio between the image stress and the current stress quantities. It is essentially an extension of the integration scheme presented in an earlier work used for the simple bounding surface version of modified Cam Clay associated with a substantially simplified hardening rule. The integration algorithm for the bounding surface model is implemented into the finite element analysis commercial program, ABAQUS, through the material interface of UMAT (user defined material subroutine), and then used for the analysis of wellbore stability problem. The predictions from the ABAQUS simulations are generally in excellent agreement with the available analytical solutions, thus demonstrating the accuracy and robustness of the proposed integration scheme.

  4. Oxidation of DNA, proteins and lipids by DOPA, protein-bound DOPA, and related catechol(amine)s

    DEFF Research Database (Denmark)

    Pattison, David I; Dean, Roger T; Davies, Michael Jonathan

    2002-01-01

    Incubation of free 3,4-dihydroxyphenylalanine (DOPA), protein-bound DOPA (PB-DOPA) and related catechols with DNA, proteins and lipids has been shown to result in oxidative damage to the target molecule. This article reviews these reactions with particular emphasis on those that occur in the pres......Incubation of free 3,4-dihydroxyphenylalanine (DOPA), protein-bound DOPA (PB-DOPA) and related catechols with DNA, proteins and lipids has been shown to result in oxidative damage to the target molecule. This article reviews these reactions with particular emphasis on those that occur...

  5. Bound and resonant surface states at the (110) surfaces of AlSb, AlAs, and AlP

    International Nuclear Information System (INIS)

    Beres, R.P.; Allen, R.E.; Buisson, J.P.; Bowen, M.A.; Blackwell, G.F.; Hjalmarson, H.P.; Dow, J.D.

    1982-01-01

    The dispersion curves E(k-bar) have been calculated for bound and resonant (110) surface states of AlSb, AlAs, and AlP. AlSb is predicted to have no surface states within the bulk fundamental band gap, but AlAs and AlP are predicted to have surface state band minima which are very near the conduction band edge, and could lie either within the gap or immediately above the edge

  6. Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development.

    Science.gov (United States)

    Phanstiel, Douglas H; Van Bortle, Kevin; Spacek, Damek; Hess, Gaelen T; Shamim, Muhammad Saad; Machol, Ido; Love, Michael I; Aiden, Erez Lieberman; Bassik, Michael C; Snyder, Michael P

    2017-09-21

    The three-dimensional arrangement of the human genome comprises a complex network of structural and regulatory chromatin loops important for coordinating changes in transcription during human development. To better understand the mechanisms underlying context-specific 3D chromatin structure and transcription during cellular differentiation, we generated comprehensive in situ Hi-C maps of DNA loops in human monocytes and differentiated macrophages. We demonstrate that dynamic looping events are regulatory rather than structural in nature and uncover widespread coordination of dynamic enhancer activity at preformed and acquired DNA loops. Enhancer-bound loop formation and enhancer activation of preformed loops together form multi-loop activation hubs at key macrophage genes. Activation hubs connect 3.4 enhancers per promoter and exhibit a strong enrichment for activator protein 1 (AP-1)-binding events, suggesting that multi-loop activation hubs involving cell-type-specific transcription factors represent an important class of regulatory chromatin structures for the spatiotemporal control of transcription. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. On the bound states of Schrodinger operators with -interactions on conical surfaces

    Czech Academy of Sciences Publication Activity Database

    Lotoreichik, Vladimir; Ourmieres-Bonafos, T.

    2016-01-01

    Roč. 41, č. 6 (2016), s. 999-1028 ISSN 0360-5302 Institutional support: RVO:61389005 Keywords : conical and hyperconical surfaces * delta-interaction * existence of bound states * Schrodinger operator * spectral asymptotics Subject RIV: BE - Theoretical Physics Impact factor: 1.608, year: 2016

  8. In-situ observations of catalyst dynamics during surface-bound carbon nanotube nucleation

    DEFF Research Database (Denmark)

    Hofmann, S; Sharma, R; Du, G

    2007-01-01

    We present atomic-scale, video-rate environmental transmission electron microscopy and in situ time-resolved X-ray photoelectron spectroscopy of surface-bound catalytic chemical vapor deposition of single-walled carbon nanotubes and nanofibers. We observe that transition metal catalyst...

  9. Trade-off bounds for the Pareto surface approximation in multi-criteria IMRT planning.

    Science.gov (United States)

    Serna, J I; Monz, M; Küfer, K H; Thieke, C

    2009-10-21

    One approach to multi-criteria IMRT planning is to automatically calculate a data set of Pareto-optimal plans for a given planning problem in a first phase, and then interactively explore the solution space and decide on the clinically best treatment plan in a second phase. The challenge of computing the plan data set is to ensure that all clinically meaningful plans are covered and that as many clinically irrelevant plans as possible are excluded to keep computation times within reasonable limits. In this work, we focus on the approximation of the clinically relevant part of the Pareto surface, the process that constitutes the first phase. It is possible that two plans on the Pareto surface have a small, clinically insignificant difference in one criterion and a significant difference in another criterion. For such cases, only the plan that is clinically clearly superior should be included into the data set. To achieve this during the Pareto surface approximation, we propose to introduce bounds that restrict the relative quality between plans, the so-called trade-off bounds. We show how to integrate these trade-off bounds into the approximation scheme and study their effects. The proposed scheme is applied to two artificial cases and one clinical case of a paraspinal tumor. For all cases, the quality of the Pareto surface approximation is measured with respect to the number of computed plans, and the range of values occurring in the approximation for different criteria is compared. Through enforcing trade-off bounds, the scheme disregards clinically irrelevant plans during the approximation. Thereby, the number of plans necessary to achieve a good approximation quality can be significantly reduced. Thus, trade-off bounds are an effective tool to focus the planning and to reduce computation time.

  10. Trade-off bounds for the Pareto surface approximation in multi-criteria IMRT planning

    International Nuclear Information System (INIS)

    Serna, J I; Monz, M; Kuefer, K H; Thieke, C

    2009-01-01

    One approach to multi-criteria IMRT planning is to automatically calculate a data set of Pareto-optimal plans for a given planning problem in a first phase, and then interactively explore the solution space and decide on the clinically best treatment plan in a second phase. The challenge of computing the plan data set is to ensure that all clinically meaningful plans are covered and that as many clinically irrelevant plans as possible are excluded to keep computation times within reasonable limits. In this work, we focus on the approximation of the clinically relevant part of the Pareto surface, the process that constitutes the first phase. It is possible that two plans on the Pareto surface have a small, clinically insignificant difference in one criterion and a significant difference in another criterion. For such cases, only the plan that is clinically clearly superior should be included into the data set. To achieve this during the Pareto surface approximation, we propose to introduce bounds that restrict the relative quality between plans, the so-called trade-off bounds. We show how to integrate these trade-off bounds into the approximation scheme and study their effects. The proposed scheme is applied to two artificial cases and one clinical case of a paraspinal tumor. For all cases, the quality of the Pareto surface approximation is measured with respect to the number of computed plans, and the range of values occurring in the approximation for different criteria is compared. Through enforcing trade-off bounds, the scheme disregards clinically irrelevant plans during the approximation. Thereby, the number of plans necessary to achieve a good approximation quality can be significantly reduced. Thus, trade-off bounds are an effective tool to focus the planning and to reduce computation time.

  11. Tracking a Common Surface-Bound Intermediate during CO2-to-Fuels Catalysis

    Science.gov (United States)

    2016-01-01

    Rational design of selective CO2-to-fuels electrocatalysts requires direct knowledge of the electrode surface structure during turnover. Metallic Cu is the most versatile CO2-to-fuels catalyst, capable of generating a wide array of value-added products, including methane, ethylene, and ethanol. All of these products are postulated to form via a common surface-bound CO intermediate. Therefore, the kinetics and thermodynamics of CO adsorption to Cu play a central role in determining fuel-formation selectivity and efficiency, highlighting the need for direct observation of CO surface binding equilibria under catalytic conditions. Here, we synthesize nanostructured Cu films adhered to IR-transparent Si prisms, and we find that these Cu surfaces enhance IR absorption of bound molecules. Using these films as electrodes, we examine Cu-catalyzed CO2 reduction in situ via IR spectroelectrochemistry. We observe that Cu surfaces bind electrogenerated CO, derived from CO2, beginning at −0.60 V vs RHE with increasing surface population at more negative potentials. Adsorbed CO is in dynamic equilibrium with dissolved 13CO and exchanges rapidly under catalytic conditions. The CO adsorption profiles are pH independent, but adsorbed CO species undergo a reversible transformation on the surface in modestly alkaline electrolytes. These studies establish the potential, concentration, and pH dependencies of the CO surface population on Cu, which serve to maintain a pool of this vital intermediate primed for further reduction to higher order fuel products. PMID:27610413

  12. Detection of human papillomavirus (HPV) L1 gene DNA possibly bound to particulate aluminum adjuvant in the HPV vaccine Gardasil.

    Science.gov (United States)

    Lee, Sin Hang

    2012-12-01

    Medical practitioners in nine countries submitted samples of Gardasil (Merck & Co.) to be tested for the presence of human papillomavirus (HPV) DNA because they suspected that residual recombinant HPV DNA left in the vaccine might have been a contributing factor leading to some of the unexplained post-vaccination side effects. A total of 16 packages of Gardasil were received from Australia, Bulgaria, France, India, New Zealand, Poland, Russia, Spain and the United States. A nested polymerase chain reaction (PCR) method using the MY09/MY11 degenerate primers for initial amplification and the GP5/GP6-based nested PCR primers for the second amplification were used to prepare the template for direct automated cycle DNA sequencing of a hypervariable segment of the HPV L1 gene which is used for manufacturing of the HPV L1 capsid protein by a DNA recombinant technology in vaccine production. Detection of HPV DNA and HPV genotyping of all positive samples were finally validated by BLAST (Basic Local Alignment Search Tool) analysis of a 45-60 bases sequence of the computer-generated electropherogram. The results showed that all 16 Gardasil samples, each with a different lot number, contained fragments of HPV-11 DNA, or HPV-18 DNA, or a DNA fragment mixture from both genotypes. The detected HPV DNA was found to be firmly bound to the insoluble, proteinase-resistant fraction, presumably of amorphous aluminum hydroxyphosphate sulfate (AAHS) nanoparticles used as adjuvant. The clinical significance of these residual HPV DNA fragments bound to a particulate mineral-based adjuvant is uncertain after intramuscular injection, and requires further investigation for vaccination safety. Copyright © 2012 Elsevier Inc. All rights reserved.

  13. Ion-driven instabilities of surface dust ion-acoustic waves in bounded plasma devices

    Science.gov (United States)

    Lee, Myoung-Jae; Jung, Young-Dae

    2018-02-01

    The growth rates of the dust ion-acoustic surface wave in the plasma slab device containing ion streaming passing through the stationary electrons and dusty grains at the speed of wave phase velocity are derived and numerically analyzed. We have found that the growth rates for the resonant symmetric and antisymmetric waves are similar to the case of semi-bounded plasma when we have a thick slab. However, in the case of the symmetric wave, the growth rate moves towards the bulk wave as the slab thickness reduces. In the case of the antisymmetric wave, the growth rate increases fast as the slab thickness decreases. The growth rates of surface waves in a plasma slab are compared with those of semi-bounded and bulk waves.

  14. Crystal Structures of SlyA Protein, a Master Virulence Regulator of Salmonella, in Free and DNA-bound States

    Energy Technology Data Exchange (ETDEWEB)

    Dolan, Kyle T.; Duguid, Erica M.; He, Chuan (UC)

    2011-11-17

    SlyA is a master virulence regulator that controls the transcription of numerous genes in Salmonella enterica. We present here crystal structures of SlyA by itself and bound to a high-affinity DNA operator sequence in the slyA gene. SlyA interacts with DNA through direct recognition of a guanine base by Arg-65, as well as interactions between conserved Arg-86 and the minor groove and a large network of non-base-specific contacts with the sugar phosphate backbone. Our structures, together with an unpublished structure of SlyA bound to the small molecule effector salicylate (Protein Data Bank code 3DEU), reveal that, unlike many other MarR family proteins, SlyA dissociates from DNA without large conformational changes when bound to this effector. We propose that SlyA and other MarR global regulators rely more on indirect readout of DNA sequence to exert control over many genes, in contrast to proteins (such as OhrR) that recognize a single operator.

  15. Bohm potential effect on the propagation of electrostatic surface wave in semi-bounded quantum plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Myoung-Jae [Department of Physics, Hanyang University, Seoul 04763 (Korea, Republic of); Research Institute for Natural Sciences, Hanyang University, Seoul 04763 (Korea, Republic of); Jung, Young-Dae, E-mail: ydjung@hanyang.ac.kr [Department of Applied Physics and Department of Bionanotechnology, Hanyang University, Ansan, Kyunggi-Do 15588 (Korea, Republic of); Department of Electrical and Computer Engineering, MC 0407, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0407 (United States)

    2017-02-12

    High frequency electrostatic wave propagation in a dense and semi-bounded electron quantum plasma is investigated with consideration of the Bohm potential. The dispersion relation for the surface mode of quantum plasma is derived and numerically analyzed. We found that the quantum effect enhances the frequency of the wave especially in the high wave number regime. However, the frequency of surface wave is found to be always lower than that of the bulk wave for the same quantum wave number. The group velocity of the surface wave for various quantum wave number is also obtained. - Highlights: • High frequency electrostatic wave propagation is investigated in a dense semi-bounded quantum plasma. • The dispersion relation for the surface mode of quantum plasma is derived and numerically analyzed. • The quantum effect enhances the frequency of the wave especially in the high wave number regime. • The frequency of surface wave is found to be always lower than that of the bulk wave. • The group velocity of the surface wave for various quantum wave number is also obtained.

  16. Mechanical splitting of microtubules into protofilament bundles by surface-bound kinesin-1.

    Science.gov (United States)

    VanDelinder, Virginia; Adams, Peter G; Bachand, George D

    2016-12-21

    The fundamental biophysics of gliding microtubule (MT) motility by surface-tethered kinesin-1 motor proteins has been widely studied, as well as applied to capture and transport analytes in bioanalytical microdevices. In these systems, phenomena such as molecular wear and fracture into shorter MTs have been reported due the mechanical forces applied on the MT during transport. In the present work, we show that MTs can be split longitudinally into protofilament bundles (PFBs) by the work performed by surface-bound kinesin motors. We examine the properties of these PFBs using several techniques (e.g., fluorescence microscopy, SEM, AFM), and show that the PFBs continue to be mobile on the surface and display very high curvature compared to MT. Further, higher surface density of kinesin motors and shorter kinesin-surface tethers promote PFB formation, whereas modifying MT with GMPCPP or higher paclitaxel concentrations did not affect PFB formation.

  17. Crystal Structure of the Dimeric Oct6 (Pou3fl) POU Domain Bound to Palindromic MORE DNA

    Energy Technology Data Exchange (ETDEWEB)

    R Jauch; S Choo; C Ng; P Kolatkar

    2011-12-31

    POU domains (named after their identification in Pit1, Oct1 unc86) are found in around 15 transcription factors encoded in mammalian genomes many of which feature prominently as key regulators at development bifurcations. For example, the POU III class Octamer binding protein 6 (Oct6) is expressed in embryonic stem cells and during neural development and drives the differentia5tion of myelinated cells in the central and peripheral nervous system. Defects in oct6 expression levels are linked to neurological disorders such as schizophrenia. POU proteins contain a bi-partite DNA binding domain that assembles on various DNA motifs with differentially configured subdomains. Intriguingly, alternative configurations of POU domains on different DNA sites were shown to affect the subsequent recruitment of transcriptional coactivators. Namely, binding of Oct1 to a Palindromic Oct-factor Recognition Element (PORE) was shown to facilitate the recruitment of the OBF1 coactivator whereas More of PORE (MORE) bound Oct1 does not. Moreover, Pit1 was shown to recruit the corepressor N-CoR only when bound to a variant MORE motif with a 2 bp half-site spacing. Therefore, POU proteins are seen as a paradigm for DNA induced allosteric effects on transcription factors modulating their regulatory potential. However, a big unresolved conundrum for the POU class and for most if not all other transcription factor classes is how highly similar proteins regulate different sets of genes causing fundamentally different biological responses. Ultimately, there must be subtle features enabling those factors to engage in contrasting molecular interactions in the cell. Thus, the dissection of the molecular details of the transcription-DNA recognition in general, and the formation of multimeric regulatory complexes, in particular, is highly desirable. To contribute to these efforts they solved the 2.05 {angstrom} crystal structure of Oct6 bound as a symmetrical homodimer to palindromic MORE DNA.

  18. Interference effects in laser-induced plasma emission from surface-bound metal micro-particles.

    Science.gov (United States)

    Feigenbaum, Eyal; Malik, Omer; Rubenchik, Alexander M; Matthews, Manyalibo J

    2017-05-01

    The light-matter interaction of an optical beam and metal micro-particulates at the vicinity of an optical substrate surface is critical to the many fields of applied optics. Examples of impacted fields are laser-induced damage in high power laser systems, sub-wavelength laser machining of transmissive materials, and laser-target interaction in directed energy applications. We present a full-wave-based model that predicts the laser-induced plasma pressure exerted on a substrate surface as a result of light absorption in surface-bound micron-scale metal particles. The model predictions agree with experimental observation of laser-induced shallow pits, formed by plasma emission and etching from surface-bound metal micro-particulates. It provides an explanation for the prototypical side lobes observed along the pit profile, as well as for the dependence of the pit shape on the incident laser and particle parameters. Furthermore, the model highlights the significance of the interference of the incident light in the open cavity geometry formed between the micro-particle and the substrate in the resulting pit shape.

  19. DNA Polymerase III, but Not Polymerase IV, Must Be Bound to a τ-Containing DnaX Complex to Enable Exchange into Replication Forks.

    Science.gov (United States)

    Yuan, Quan; Dohrmann, Paul R; Sutton, Mark D; McHenry, Charles S

    2016-05-27

    Examples of dynamic polymerase exchange have been previously characterized in model systems provided by coliphages T4 and T7. Using a dominant negative D403E polymerase (Pol) III α that can form initiation complexes and sequester primer termini but not elongate, we investigated the possibility of exchange at the Escherichia coli replication fork on a rolling circle template. Unlike other systems, addition of polymerase alone did not lead to exchange. Only when D403E Pol III was bound to a τ-containing DnaX complex did exchange occur. In contrast, addition of Pol IV led to rapid exchange in the absence of bound DnaX complex. Examination of Pol III* with varying composition of τ or the alternative shorter dnaX translation product γ showed that τ-, τ2-, or τ3-DnaX complexes supported equivalent levels of synthesis, identical Okazaki fragment size, and gaps between fragments, possessed the ability to challenge pre-established replication forks, and displayed equivalent susceptibility to challenge by exogenous D403E Pol III*. These findings reveal that redundant interactions at the replication fork must stabilize complexes containing only one τ. Previously, it was thought that at least two τs in the trimeric DnaX complex were required to couple the leading and lagging strand polymerases at the replication fork. Possible mechanisms of exchange are discussed. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. DNA stretching on functionalized gold surfaces.

    OpenAIRE

    Zimmermann, R M; Cox, E C

    1994-01-01

    We describe a method for anchoring bacteriophage lambda DNA by one end to gold by Au-biotin-streptavidin-biotin-DNA bonds. DNA anchored to a microfabricated Au line could be aligned and stretched in flow and electric fields. The anchor was shown to resist a force of at least 11 pN, a linkage strong enough to allow DNA molecules of chromosome size to be stretched and aligned.

  1. Structure of the Tetrameric p53 Tumor Suppressor Bound to DNA

    National Research Council Canada - National Science Library

    Marmorstein, Ronen

    2002-01-01

    The p53 tumor suppressor binds DNA as a tetramer to regulate the transcription of genes involved in cell cycle arrest and apoptosis, and alterations in the DNA-binding core domain of p53 are the most...

  2. Study of Auger effect in DNA when bound to molecules containing platinum. A possible application to hadrontherapy

    Science.gov (United States)

    Kobayashi, K.; Usami, N.; Sasaki, I.; Frohlich, H.; Le Sech, C.

    2003-01-01

    Complexes made of DNA and Cyclo-Pt bound to plasmid DNA, were placed in aqueous solution and irradiated with monochromatic X-rays in the range E=8.5-13 keV, including the resonant photoabsorption energy of the L III shell of the platinum atom. The number of single- and double-strand breaks (ssb and dsb) induced by irradiation on a supercoiled DNA plasmid was measured by the production of circular-nicked and linear forms. In order to disentangle the contribution of the direct effects imparted to ionization, and the indirect effects due to a free radical attack, experiments have been performed in the presence of a small concentration (64 mmol l -1) of hydroxyl free radical scavenger dimethyl sulfoxide (DMSO). An enhancement of the number of ssb and dsb is observed when the plasmids contain the Pt intercalating molecules. Even when off-resonant X-rays are used, the strand break efficiency remains higher than expected based upon the absorption cross-section, as if the Pt bound to DNA is increasing the yield of strand breaks. A mechanism is suggested, involving photoelectrons generated from the ionization of water which efficiently ionize Pt atoms. This observation may provide an insight to understanding the effects of new radiotherapy protocols, associated chemotherapeutic agents such as cisplatin and ordinary radiotherapy for tumoral treatments.

  3. Electrical potential-assisted DNA hybridization. How to mitigate electrostatics for surface DNA hybridization.

    Science.gov (United States)

    Tymoczko, Jakub; Schuhmann, Wolfgang; Gebala, Magdalena

    2014-12-24

    Surface-confined DNA hybridization reactions are sensitive to the number and identity of DNA capture probes and experimental conditions such as the nature and the ionic strength of the electrolyte solution. When the surface probe density is high or the concentration of bulk ions is much lower than the concentration of ions within the DNA layer, hybridization is significantly slowed down or does not proceed at all. However, high-density DNA monolayers are attractive for designing high-sensitivity DNA sensors. Thus, circumventing sluggish DNA hybridization on such interfaces allows a high surface concentration of target DNA and improved signal/noise ratio. We present potential-assisted hybridization as a strategy in which an external voltage is applied to the ssDNA-modified interface during the hybridization process. Results show that a significant enhancement of hybridization can be achieved using this approach.

  4. Adsorption of DNA binding proteins to functionalized carbon nanotube surfaces with and without DNA wrapping.

    Science.gov (United States)

    Ishibashi, Yu; Oura, Shusuke; Umemura, Kazuo

    2017-09-01

    We examined the adsorption of DNA binding proteins on functionalized, single-walled carbon nanotubes (SWNTs). When SWNTs were functionalized with polyethylene glycol (PEG-SWNT), moderate adsorption of protein molecules was observed. In contrast, nanotubes functionalized with CONH 2 groups (CONH 2 -SWNT) exhibited very strong interactions between the CONH 2 -SWNT and DNA binding proteins. Instead, when these SWNT surfaces were wrapped with DNA molecules (thymine 30-mers), protein binding was a little decreased. Our results revealed that DNA wrapped PEG-SWNT was one of the most promising candidates to realize DNA nanodevices involving protein reactions on DNA-SWNT surfaces. In addition, the DNA binding protein RecA was more adhesive than single-stranded DNA binding proteins to the functionalized SWNT surfaces.

  5. Crystal Structure of a CRISPR RNA-guided Surveillance Complex Bound to a ssDNA Target

    Energy Technology Data Exchange (ETDEWEB)

    Mulepati, Sabin [Johns Hopkins Univ., Baltimore, MD (United States); Heroux, Annie; Bailey, Scott [Johns Hopkins Univ., Baltimore, MD (United States)

    2014-09-19

    In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.

  6. In situ surface enhanced resonance Raman scattering analysis of a reactive dye covalently bound to cotton.

    Science.gov (United States)

    White, P C; Munro, C H; Smith, W E

    1996-06-01

    An in situ surface enhanced resonance Raman scattering (SERRS) procedure is described for the analysis of a reactive dye covalently bound to a single strand of a cotton fibre. This procedure can be completed in 5 h, whereas an alternative enzyme digestion method takes approximately 21 h. These two fibre preparation methods give similar spectra from picogram quantities of dye present on a 2-5 mm length of fibre. The in situ nature of the analysis and the small sample size make this method particularly suitable for forensic applications.

  7. DNA nanosensor surface grafting and salt dependence

    Science.gov (United States)

    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.

  8. A Polycomb complex remains bound through DNA replication in the absence of other eukaryotic proteins

    KAUST Repository

    Lengsfeld, Bettina M.

    2012-09-17

    Propagation of chromatin states through DNA replication is central to epigenetic regulation and can involve recruitment of chromatin proteins to replicating chromatin through interactions with replication fork components. Here we show using a fully reconstituted T7 bacteriophage system that eukaryotic proteins are not required to tether the Polycomb complex PRC1 to templates during DNA replication. Instead, DNA binding by PRC1 can withstand passage of a simple replication fork.

  9. The role of casein in supporting the operation of surface bound kinesin

    Directory of Open Access Journals (Sweden)

    Hancock William O

    2008-10-01

    Full Text Available Abstract Microtubules and associated motor proteins such as kinesin are envisioned for applications such as bioseparation and molecular sorting to powering hybrid synthetic mechanical devices. One of the challenges in realizing such systems is retaining motor functionality on device surfaces. Kinesin motors adsorbed onto glass surfaces lose their functionality or ability to interact with microtubules if not adsorbed with other supporting proteins. Casein, a milk protein, is commonly used in microtubule motility assays to preserve kinesin functionality. However, the mechanism responsible for this preservation of motor function is unknown. To study casein and kinesin interaction, a series of microtubule motility assays were performed where whole milk casein, or its αs1 and αs2, β or κ subunits, were introduced or omitted at various steps of the motility assay. In addition, a series of epifluorescence and total internal reflection microscopy (TIRF experiments were conducted where fluorescently labeled casein was introduced at various steps of the motility assay to assess casein-casein and casein-glass binding dynamics. From these experiments it is concluded that casein forms a bi-layer which supports the operation of kinesin. The first tightly bound layer of casein mainly performs the function of anchoring the kinesin while the second more loosely bound layer of casein positions the head domain of the kinesin to more optimally interact with microtubules. Studies on individual casein subunits indicate that β casein was most effective in supporting kinesin functionality while κ casein was found to be least effective.

  10. Surface-enhanced localized surface plasmon resonance biosensing of avian influenza DNA hybridization using subwavelength metallic nanoarrays

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Shin Ae; Jang, Sung Min; Kim, Sung June [School of Electrical Engineering and Computer Science, Seoul National University, Seoul 151-742 (Korea, Republic of); Byun, Kyung Min [Department of Biomedical Engineering, Kyung Hee University, Yongin 446-701 (Korea, Republic of); Kim, Kyujung; Kim, Donghyun [Program of Nanomedical Science and Technology, Yonsei University, Seoul 120-749 (Korea, Republic of); Ma, Kyungjae; Oh, Youngjin [School of Electrical and Electronic Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Kim, Sung Guk [College of Veterinary Medicine, Cornell University, Ithaca, New York 14853 (United States); Shuler, Michael L, E-mail: kmbyun@khu.ac.kr [Department of Biomedical Engineering, Cornell University, Ithaca, New York 14853 (United States)

    2010-09-03

    We demonstrated enhanced localized surface plasmon resonance (SPR) biosensing based on subwavelength gold nanoarrays built on a thin gold film. Arrays of nanogratings (1D) and nanoholes (2D) with a period of 200 nm were fabricated by electron-beam lithography and used for the detection of avian influenza DNA hybridization. Experimental results showed that both nanoarrays provided significant sensitivity improvement and, especially, 1D nanogratings exhibited higher SPR signal amplification compared with 2D nanohole arrays. The sensitivity enhancement is associated with changes in surface-limited reaction area and strong interactions between bound molecules and localized plasmon fields. Our approach is expected to improve both the sensitivity and sensing resolution and can be applicable to label-free detection of DNA without amplification by polymerase chain reaction.

  11. Proton surface charge determination in Spodosol horizons with organically bound aluminum

    Science.gov (United States)

    Skyllberg, Ulf; Borggaard, Ole K.

    1998-05-01

    Net proton surface charge densities were determined in O, E, Bh, and Bs horizons of a sandy till, Spodosol from Denmark, by means of acid-base titration combined with ion adsorption in 0.005 M Ca(NO 3) 2 and independent permanent charge determination. The release of organic anions exceeded the adsorption of NO 3-, resulting in a desorption of anions in all horizons. Data were found to obey the law of balance between surface charges and adsorbed ions only when charges pertaining to Al and organic anions released during the titration experiments were accounted for, in addition to charges pertaining the potential determining ions (PDI) H + and OH - and the index ions Ca 2+ and NO 3-. It was furthermore shown that the point of zero net proton charge (PZNPC) in soils highly depends on the concentration of organically bound Al. Approaches previously used in soils, in which adsorbed Al n+ has been ignored (i.e., considered equivalent to nH + as a PDI), resulted in a PZNPC of 4.1 in the Bs horizon. If instead organically bound Al was accounted for as a counter-ion similar to 3/2Ca 2+, a PZNPC of 2.9 was obtained for the same Bs horizon. Based on PZNPC values estimated by the latter approach, combined with a weak-acid analog, it was shown that organic proton surface charges buffered pH with a similar intensity in the O, E, Bh, and Bs horizons of this study. Because the acidity of Al adsorbed to conjugate bases of soil organic acids is substantially weaker than the acidity of the corresponding protonated form of the organic acids, the point of zero net proton charge (PZNPC) will increase if the concentration of organically adsorbed Al increases at the expense of adsorbed H. This means that PZNPC values determined for soils with unknown concentrations of organically adsorbed Al are highly operational and not very meaningful as references.

  12. Bacterial cell surface properties: role of loosely bound extracellular polymeric substances (LB-EPS).

    Science.gov (United States)

    Zhao, Wenqiang; Yang, Shanshan; Huang, Qiaoyun; Cai, Peng

    2015-04-01

    This study investigated the effect of loosely bound extracellular polymeric substances (LB-EPS) on the comprehensive surface properties of four bacteria (Bacillus subtilis, Streptococcus suis, Escherichia coli and Pseudomonas putida). The removal of LB-EPS from bacterial surfaces by high-speed centrifugation (12,000×g) was confirmed by SEM images. Viability tests showed that the percentages of viable cells ranged from 95.9% to 98.0%, and no significant difference was found after treatment (P>0.05). FTIR spectra revealed the presence of phosphodiester, carboxylic, phosphate, and amino functional groups on bacteria surfaces, and the removal of LB-EPS did not alter the types of cell surface functional groups. Potentiometric titration results suggested the total site concentrations on the intact bacteria were higher than those on LB-EPS free bacteria. Most of the acidity constants (pKa) were almost identical, except the increased pKa values of phosphodiester groups on LB-EPS free S. suis and E. coli surfaces. The electrophoretic mobilities and hydrodynamic diameters of the intact and LB-EPS free bacteria were statistically unchanged (P>0.05), indicating LB-EPS had no influence on the net surface charges and size distribution of bacteria. However, LB-ESP could enhance cell aggregation processes. The four LB-EPS free bacteria all exhibited fewer hydrophobicity values (26.1-65.0%) as compared to the intact cells (47.4-69.3%), suggesting the removal of uncharged nonpolar compounds (e.g., carbohydrates) in LB-EPS. These findings improve our understanding of the changes in cell surface characterizations induced by LB-EPS, and have important implications for assessing the role of LB-EPS in bacterial adhesion and transport behaviors. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Harnessing surface-bound enzymatic reactions to organize microcapsules in solution.

    Science.gov (United States)

    Shklyaev, Oleg E; Shum, Henry; Sen, Ayusman; Balazs, Anna C

    2016-03-01

    By developing new computational models, we examine how enzymatic reactions on an underlying surface can be harnessed to direct the motion and organization of reagent-laden microcapsules in a fluid-filled microchannel. In the presence of appropriate reagents, surface-bound enzymes can act as pumps, which drive large-scale fluid flows. When the reagents diffuse through the capsules' porous shells, they can react with enzymatic sites on the bottom surface. The ensuing reaction generates fluid density variations, which result in fluid flows. These flows carry the suspended microcapsules and drive them to aggregate into "colonies" on and near the enzyme-covered sites. This aggregation continues until the reagent has been depleted and the convection stops. We show that the shape of the assembled colonies can be tailored by patterning the distribution of enzymes on the surface. This fundamental physicochemical mechanism could have played a role in the self-organization of early biological cells (protocells) and can be used to regulate the autonomous motion and targeted delivery of microcarriers in microfluidic devices.

  14. Critical surface roughness for wall bounded flow of viscous fluids in an electric submersible pump

    Science.gov (United States)

    Deshmukh, Dhairyasheel; Siddique, Md Hamid; Kenyery, Frank; Samad, Abdus

    2017-11-01

    Surface roughness plays a vital role in the performance of an electric submersible pump (ESP). A 3-D numerical analysis has been carried out to find the roughness effect on ESP. The performance of pump for steady wall bounded turbulent flows is evaluated at different roughness values and compared with smooth surface considering a non-dimensional roughness factor K. The k- ω SST turbulence model with fine mesh at near wall region captures the rough wall effects accurately. Computational results are validated with experimental results of water (1 cP), at a design speed (3000 RPM). Maximum head is observed for a hydraulically smooth surface (K=0). When roughness factor is increased, the head decreases till critical roughness factor (K=0.1) due to frictional loss. Further increase in roughness factor (K>0.1) increases the head due to near wall turbulence. The performance of ESP is analyzed for turbulent kinetic energy and eddy viscosity at different roughness values. The wall disturbance over the rough surface affects the pressure distribution and velocity field. The roughness effect is predominant for high viscosity oil (43cP) as compared to water. Moreover, the study at off-design conditions showed that Reynolds number influences the overall roughness effect.

  15. A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle

    Czech Academy of Sciences Publication Activity Database

    Schneider, Bohdan; Bozikova, Paulina; Čech, P.; Svozil, D.; Černý, Jiří

    2017-01-01

    Roč. 8, č. 10 (2017), č. článku 278. ISSN 2073-4425 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0109 Grant - others:GA MŠk(CZ) EF16_013/0001777 Institutional support: RVO:86652036 Keywords : DNA * DNA-protein recognition * transcription factors Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8) Impact factor: 3.600, year: 2016

  16. Effectiveness of UV-C equipped vacuum at reducing culturable surface-bound microorganisms on carpets.

    Science.gov (United States)

    Lutz, Eric A; Sharma, Smita; Casto, Bruce; Needham, Glen; Buckley, Timothy J

    2010-12-15

    Carpets are both sinks and sources for exposure to chemicals, allergens, and microbes and consequently influence health, including asthma, allergies, and infectious diseases. Asthmatics, children, and the immune-compromised are particularly vulnerable to health risks resulting from exposure to carpet contaminants. To address this risk, a commercial upright vacuum cleaner with an ultraviolet germicidal lamp (λ=253.7 nm, UVC) has been developed for residential and commercial uses. However, its effectiveness in reducing microbial load on real-world carpets has not been previously demonstrated. Accordingly, the purpose of the current study was to evaluate the effectiveness of a UVC-equipped vacuum in reducing the carpet surface-bound microbial load. This was accomplished by comparing the carpet microbial surface load from pre- to post-treatment of 9 ft(2) in-use carpet sections under three treatment scenarios: 1) UVC alone (UV), 2) the beater-bar plus vacuum (BB+Vac), or 3) a combination of all three (COMB). Each treatment was two minutes in duration. Microbial surface loads were measured by pressing contact plates containing Sabourauds Dextrose agar onto the carpet surface. In-use carpets from three locations were tested in place. The treatment effect was evaluated at two levels. First, we considered the mean reduction in CFU from pre- to post-treatment for each 9 ft(2) carpet grid (n = 4 for each treatment). The second level considered each 1 ft(2) section using a paired analysis (n = 40 to 49 for each treatment). A total of 125 pre/post-sample pairs were collected across the three treatments. Results showed that all three treatments were associated with a reduction in carpet microbial load (p < 0.0001). The COMB yielded the largest reduction of 13 CFU/plate (87% reduction) and was approximately the sum of the individual effects of either UVC (6.6 CFU/plate, 60% reduction, p = 0.009) or BB+Vac (7.3 CFU/plate, 78% reduction, p < 0.0001). We therefore conclude that a

  17. Label-free quantitative proteome analysis of the surface-bound salivary pellicle.

    Science.gov (United States)

    Delius, Judith; Trautmann, Simone; Médard, Guillaume; Kuster, Bernhard; Hannig, Matthias; Hofmann, Thomas

    2017-04-01

    The salivary pellicle, covering natural as well as restored tooth surfaces in the oral cavity as an immobilized protein-rich layer, acts as an important physico-chemical and biological mediator at the tooth-saliva-interface. For the first time, the pellicle's proteome of individual volunteers were analyzed separately on three consecutive days and the relative protein abundance determined by a label-free quantitative nano-LC-MS/MS approach. A total of 72 major proteins were identified in the initial pellicles formed intraorally on dental ceramic specimens already after 3min with high inter-individual and inter-day consistency. In comparison, significant differences in protein abundance were evident between subjects, thus indicating unique individual pellicle profiles. Furthermore, the relative protein abundance in pellicles was compared to the proteome pattern in the corresponding saliva samples of the same individuals to provide first data on significantly enriched and depleted salivary proteins (p <0.05) within the surface-bound salivary pellicle. Our findings reveal the initial adsorption of salivary proteins at the solid-liquid interface to be a rapid, highly selective, and reproducible process leading to the immobilization of a broad range of protective proteins and enzymes on the substratum surface within a few minutes. This provides evidence that the pellicle layer might be physiologically functional even without further maturation. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Mechanism of action of pefloxacin on surface morphology, DNA ...

    African Journals Online (AJOL)

    It was observed that the site of pefloxacin action was intracellular and it caused surface alterations. The present investigation also showed the effect of Quinolone pefloxacin on DNA gyrase activity of K. aerogenes. DNA gyrase was purified by affinity chromatography and inhibition of pefloxacin on supercoiling activity of DNA ...

  19. Ancient microbes from halite fluid inclusions: optimized surface sterilization and DNA extraction.

    Directory of Open Access Journals (Sweden)

    Krithivasan Sankaranarayanan

    Full Text Available Fluid inclusions in evaporite minerals (halite, gypsum, etc. potentially preserve genetic records of microbial diversity and changing environmental conditions of Earth's hydrosphere for nearly one billion years. Here we describe a robust protocol for surface sterilization and retrieval of DNA from fluid inclusions in halite that, unlike previously published methods, guarantees removal of potentially contaminating surface-bound DNA. The protocol involves microscopic visualization of cell structures, deliberate surface contamination followed by surface sterilization with acid and bleach washes, and DNA extraction using Amicon centrifugal filters. Methods were verified on halite crystals of four different ages from Saline Valley, California (modern, 36 ka, 64 ka, and 150 ka, with retrieval of algal and archaeal DNA, and characterization of the algal community using ITS1 sequences. The protocol we developed opens up new avenues for study of ancient microbial ecosystems in fluid inclusions, understanding microbial evolution across geological time, and investigating the antiquity of life on earth and other parts of the solar system.

  20. Surface Andreev Bound States and Odd-Frequency Pairing in Topological Superconductor Junctions

    Science.gov (United States)

    Tanaka, Yukio; Tamura, Shun

    2018-04-01

    In this review, we summarize the achievement of the physics of surface Andreev bound states (SABS) up to now. The route of this activity has started from the physics of SABS of unconventional superconductors where the pair potential has a sign change on the Fermi surface. It has been established that SABS can be regarded as a topological edge state with topological invariant defined in the bulk Hamiltonian. On the other hand, SABS accompanies odd-frequency pairing like spin-triplet s-wave or spin-singlet p-wave. In a spin-triplet superconductor junction, induced odd-frequency pairing can penetrate into a diffusive normal metal (DN) attached to the superconductor. It causes so called anomalous proximity effect where the local density of states of quasiparticle in DN has a zero energy peak. When bulk pairing symmetry is spin-triplet px-wave, the anomalous proximity effect becomes prominent and the zero bias voltage conductance is always quantized independent of the resistance in DN and interface. Finally, we show that the present anomalous proximity effect is realized in an artificial topological superconducting system, where a nanowire with spin-orbit coupling and Zeeman field is put on the conventional spin-singlet s-wave superconductor.

  1. Surface-bound phosphatase activity in living hyphae of ectomycorrhizal fungi of Nothofagus obliqua.

    Science.gov (United States)

    Alvarez, Maricel; Godoy, Roberto; Heyser, Wolfgang; Härtel, Steffen

    2004-01-01

    We determined the location and the activity of surface-bound phosphomonoesterase (SBP) of five ectomycorrhizal (EM) fungi of Nothofagus oblique. EM fungal mycelium of Paxillus involutus, Austropaxillus boletinoides, Descolea antartica, Cenococcum geophilum and Pisolithus tinctorius was grown in media with varying concentrations of dissolved phosphorus. SBP activity was detected at different pH values (3-7) under each growth regimen. SBP activity was assessed using a colorimetric method based on the hydrolysis of p-nitrophenyl phosphate (pNPP) to p-nitrophenol phosphate (pNP) + P. A new technique involving confocal laser-scanning microscopy (LSM) was used to locate and quantify SBP activity on the hyphal surface. EM fungi showed two fundamentally different patterns of SBP activity in relation to varying environmental conditions (P-concentrations and pH). In the cases of D. antartica, A. boletinoides and C. geophilum, changes in SBP activity were induced primarily by changes in the number of SBP-active centers on the hyphae. In the cases of P. tinctorius and P. involutus, the number of SBP-active centers per μm hyphal length changed much less than the intensity of the SBP-active centers on the hyphae. Our findings not only contribute to the discussion about the role of SBP-active centers in EM fungi but also introduce LSM as a valuable method for studying EM fungi.

  2. Crystallization of a member of the recFOR DNA repair pathway, RecO, with and without bound oligonucleotide

    Energy Technology Data Exchange (ETDEWEB)

    Aono, Shelly; Hartsch, Thomas; Schulze-Gahmen, Ursula

    2003-01-22

    RecFOR proteins are important for DNA repair by homologous recombination in bacteria. The RecO protein from Thermus thermophilus was cloned, purified and characterized for its binding to oligonucleotides. The protein was crystallized alone and in complex with a 14-mer oligonucleotide. Both crystal forms grow under different crystallization conditions in the same space group, P3121 or P3221, with almost identical unit cell parameters. Complete data sets were collected to 2.8 Angstrom and 2.5 Angstrom for RecO alone and the RecO-oligonucleotide complex, respectively. Visual comparison of the diffraction patterns between the two crystal forms and calculation of an Rmerge of 33.9 percent on F indicate that one of the crystal forms is indeed a complex of RecO with bound oligonucleotide.

  3. Oxidation of DNA, proteins and lipids by DOPA, protein-bound DOPA, and related catechol(amine)s

    DEFF Research Database (Denmark)

    Pattison, David I; Dean, Roger T; Davies, Michael Jonathan

    2002-01-01

    , including semiquinone radicals, quinones, and metal ion-DOPA complexes have also been implicated in some cases. Non-radical reactions of DOPA with suitable nucleophiles (e.g. thiol groups) can also result in modification of the target, with this process being particularly prevalent with proteins......Incubation of free 3,4-dihydroxyphenylalanine (DOPA), protein-bound DOPA (PB-DOPA) and related catechols with DNA, proteins and lipids has been shown to result in oxidative damage to the target molecule. This article reviews these reactions with particular emphasis on those that occur...... in the presence of molecular O(2) and redox-active metal ions (e.g. Fe(3+), Cu(2+), Cr(6+)), which are known to increase the rate of DOPA oxidation. The majority of oxidative damage appears to be mediated by reactive oxygen species (ROS) such as superoxide and HO(.) radicals, though other DOPA oxidation products...

  4. Surface plasmon polaritons in a semi-bounded degenerate plasma: Role of spatial dispersion and collisions

    International Nuclear Information System (INIS)

    Tyshetskiy, Yu.; Kompaneets, R.; Vladimirov, S. V.

    2012-01-01

    Surface plasmon polaritons (SPPs) in a semi-bounded degenerate plasma (e.g., a metal) are studied using the quasiclassical mean-field kinetic model, taking into account the spatial dispersion of the plasma (due to quantum degeneracy of electrons) and electron-ion (electron-lattice, for metals) collisions. SPP dispersion and damping are obtained in both retarded (ω/k z ∼c) and non-retarded (ω/k z ≪c) regions, as well as in between. It is shown that the plasma spatial dispersion significantly affects the properties of SPPs, especially at short wavelengths (less than the collisionless skin depth, λ ≲ c/ω pe ). Namely, the collisionless (Landau) damping of SPPs (due to spatial dispersion) is comparable to the purely collisional (Ohmic) damping (due to electron-lattice collisions) in a wide range of SPP wavelengths, e.g., from λ∼20 nm to λ∼0.8 nm for SPP in gold at T = 293 K and from λ∼400 nm to λ∼0.7 nm for SPPs in gold at T = 100 K. The spatial dispersion is also shown to affect, in a qualitative way, the dispersion of SPPs at short wavelengths λ ≲ c/ω pe .

  5. Atomic force microscopy of the EcoKI Type I DNA restriction enzyme bound to DNA shows enzyme dimerization and DNA looping

    Science.gov (United States)

    Neaves, Kelly J.; Cooper, Laurie P.; White, John H.; Carnally, Stewart M.; Dryden, David T. F.; Edwardson, J. Michael; Henderson, Robert M.

    2009-01-01

    Atomic force microscopy (AFM) allows the study of single protein–DNA interactions such as those observed with the Type I Restriction–Modification systems. The mechanisms employed by these systems are complicated and understanding them has proved problematic. It has been known for years that these enzymes translocate DNA during the restriction reaction, but more recent AFM work suggested that the archetypal EcoKI protein went through an additional dimerization stage before the onset of translocation. The results presented here extend earlier findings confirming the dimerization. Dimerization is particularly common if the DNA molecule contains two EcoKI recognition sites. DNA loops with dimers at their apex form if the DNA is sufficiently long, and also form in the presence of ATPγS, a non-hydrolysable analogue of the ATP required for translocation, indicating that the looping is on the reaction pathway of the enzyme. Visualization of specific DNA loops in the protein–DNA constructs was achieved by improved sample preparation and analysis techniques. The reported dimerization and looping mechanism is unlikely to be exclusive to EcoKI, and offers greater insight into the detailed functioning of this and other higher order assemblies of proteins operating by bringing distant sites on DNA into close proximity via DNA looping. PMID:19223329

  6. Limits of RNA 2'-OH Mimicry by Fluorine: Crystal Structure of Bacillus halodurans RNase H Bound to a 2'-FRNA:DNA Hybrid.

    Science.gov (United States)

    Pallan, Pradeep S; Prakash, Thazha P; de Leon, Arnie R; Egli, Martin

    2016-09-27

    RNase H1 cleaves the RNA strand of RNA:DNA hybrids. Replacement of RNA 2'-hydroxyls by fluorine (FRNA) is commonly used to stabilize aptamers and siRNAs. However, FRNA:DNA hybrids fail to elicit RNase H activity. The underlying reasons are unclear, as 2'-OH groups are not directly involved in cleavage. We determined the crystal structure of Bacillus halodurans RNase H bound to a FRNA:DNA hybrid. The structure points to dynamic (slippage of the FRNA:DNA hybrid relative to the enzyme), geometric (different curvatures of FRNA:DNA and RNA:DNA hybrids), and electronic reasons (Mg(2+) absent from the active site of the FRNA:DNA complex) for the loss of RNaseH activity.

  7. Application of the rotating ring-disc-electrode technique to water oxidation by surface-bound molecular catalysts.

    Science.gov (United States)

    Concepcion, Javier J; Binstead, Robert A; Alibabaei, Leila; Meyer, Thomas J

    2013-10-07

    We report here the application of a simple hydrodynamic technique, linear sweep voltammetry with a modified rotating-ring-disc electrode, for the study of water oxidation catalysis. With this technique, we have been able to reliably obtain turnover frequencies, overpotentials, Faradaic conversion efficiencies, and mechanistic information from single samples of surface-bound metal complex catalysts.

  8. A Novel Supramolecular Assembly Film of Porphyrin Bound DNA: Characterization and Catalytic Behaviors Towards Nitric Oxide

    Directory of Open Access Journals (Sweden)

    Osamu Ikeda

    2005-04-01

    Full Text Available A stable Fe(4-TMPyP-DNA-PADDA (FePyDP film was characterized onpyrolytic graphite electrode (PGE or an indium-tin oxide (ITO electrode through thesupramolecular interaction between water-soluble iron porphyrin (Fe(4-TMPyP and DNAtemplate, where PADDA (poly(acrylamide-co-diallyldimethylammonium chloride isemployed as a co-immobilizing polymer. Cyclic voltammetry of FePyDP film showed a pairof reversible FeIII/FeII redox peaks and an irreversible FeIV/FeIII peak at –0.13 V and 0.89vs. Ag|AgCl in pH 7.4 PBS, respectively. An excellent catalytic reduction of NO wasdisplayed at –0.61 V vs. Ag|AgCl at a FePyDP film modified electrode.Chronoamperometric experiments demonstrated a rapid response to the reduction of NOwith a linear range from 0.1 to 90 μM and a detection limit of 30 nM at a signal-to-noiseratio of 3. On the other hand, it is the first time to apply high-valent iron porphyrin ascatalyst at modified electrode for NO catalytic oxidation at 0.89 vs. Ag|AgCl. The sensorshows a high selectivity of some endogenous electroactive substances in biological systems.The mechanism of response of the sensors to NO is preliminary studied.

  9. Controlling DNA Translocation Speed through Solid-State Nanopores by Surface Charge Modulation

    Science.gov (United States)

    Meller, Amit

    2013-03-01

    The Nanopore method is an emerging technique, which extends gel-electrophoresis to the single-molecule level and allows the analysis of DNAs, RNAs and DNA-protein complexes. The strength of the technique stems from two fundamental facts: First, nanopores due to their nanoscale size can be used to uncoil biopolymers, such as DNA or RNA and slide them in a single file manner that allows scanning their properties. Consequently, the method can be used to probe short as well as extremely long biopolymers, such as genomic DNA with high efficiency. Second, electrostatic focusing of charged biopolymers into the nanopore overcomes thermally driven diffusion, thus facilitating an extremely efficient end-threading (or capture) of DNA. Thus, nanopores can be used to detect minute DNA copy numbers, circumventing costly molecular amplification such as Polymerase Chain Reaction. A critical factor, which determines the ability of nanopore to distinguish fine properties within biopolymers, such as the location of bound small-molecules, proteins, or even the nucleic acid's sequence, is the speed at which molecules are translocated through the pore. When the translocation speed is too high the electrical noise masks the desired signal, thus limiting the utility of the method. Here I will discuss new experimental results showing that modulating the surface charge inside the pore can effectively reduce the translocation speed through solid-state nanopores fabricated in thin silicon nitride membranes. I will present a simple physical model to account for these results.

  10. Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands.

    Science.gov (United States)

    Krimmer, Stefan G; Cramer, Jonathan; Betz, Michael; Fridh, Veronica; Karlsson, Robert; Heine, Andreas; Klebe, Gerhard

    2016-12-08

    A previously studied congeneric series of thermolysin inhibitors addressing the solvent-accessible S 2 ' pocket with different hydrophobic substituents showed modulations of the surface water layers coating the protein-bound inhibitors. Increasing stabilization of water molecules resulted in an enthalpically more favorable binding signature, overall enhancing affinity. Based on this observation, we optimized the series by designing tailored P 2 ' substituents to improve and further stabilize the surface water network. MD simulations were applied to predict the putative water pattern around the bound ligands. Subsequently, the inhibitors were synthesized and characterized by high-resolution crystallography, microcalorimetry, and surface plasmon resonance. One of the designed inhibitors established the most pronounced water network of all inhibitors tested so far, composed of several fused water polygons, and showed 50-fold affinity enhancement with respect to the original methylated parent ligand. Notably, the inhibitor forming the most perfect water network also showed significantly prolonged residence time compared to the other tested inhibitors.

  11. DNA damage response to different surface chemistry of silver nanoparticles in mammalian cells

    International Nuclear Information System (INIS)

    Ahamed, Maqusood; Karns, Michael; Goodson, Michael; Rowe, John; Hussain, Saber M.; Schlager, John J.; Hong Yiling

    2008-01-01

    Silver nanoparticles (Ag NPs) have recently received much attention for their possible applications in biotechnology and life sciences. Ag NPs are of interest to defense and engineering programs for new material applications as well as for commercial purposes as an antimicrobial. However, little is known about the genotoxicity of Ag NPs following exposure to mammalian cells. This study was undertaken to examine the DNA damage response to polysaccharide surface functionalized (coated) and non-functionalized (uncoated) Ag NPs in two types of mammalian cells; mouse embryonic stem (mES) cells and mouse embryonic fibroblasts (MEF). Both types of Ag NPs up-regulated the cell cycle checkpoint protein p53 and DNA damage repair proteins Rad51 and phosphorylated-H2AX expression. Furthermore both of them induced cell death as measured by the annexin V protein expression and MTT assay. Our observations also suggested that the different surface chemistry of Ag NPs induce different DNA damage response: coated Ag NPs exhibited more severe damage than uncoated Ag NPs. The results suggest that polysaccharide coated particles are more individually distributed while agglomeration of the uncoated particles limits the surface area availability and access to membrane bound organelles

  12. Probing protein: DNA interactions using a uniform monolayer of DNA and surface plasmon resonance

    Science.gov (United States)

    Shumaker-Parry, Jennifer S.; Campbell, Charles T.; Stormo, Gary D.; Silbaq, Fauzi S.; Aebersold, Rudolf H.

    2000-04-01

    A method is described for immobilizing double-stranded DNAs to a planar gold surface with high density and uniform spacing. This is accomplished by adsorbing biotinylated DNAs onto a nearly close-packed monolayer of the protein streptavidin. This streptavidin monolayer, which offers approximately 5 X 1012 biotin sites per cm2, is prepared first by adsorbing it onto a mixed self-assembled monolayer on gold which contains biotin-terminated and oligo-terminated alkylthiolates in a 3/7 ratio. This DNA- functionalized surface resists non-specific protein adsorption and is useful for probing the kinetics and equilibrium binding of proteins to DNA with surface plasmon resonance. This is demonstrated with the Mnt protein, which is found to bind in 3.8:1 ratio to its immobilized DNA operator sequence. This is consistent with its behavior in homogeneous solution, where it binds as a tetramer to its DNA. A sequence with a single base-pair mutation shows nearly as much Mnt binding, but a completely random DNA sequence shows only 5 percent of this binding. This proves that DNA-binding proteins bind sequence-specifically to double-stranded DNAs which are immobilized to gold with this streptavidin linker layer.

  13. Cell-bound complement activation products in systemic lupus erythematosus: comparison with anti-double-stranded DNA and standard complement measurements

    OpenAIRE

    Putterman, Chaim; Furie, Richard; Ramsey-Goldman, Rosalind; Askanase, Anca; Buyon, Jill; Kalunian, Kenneth; Chatham, W Winn; Massarotti, Elena; Kirou, Kyriakos; Jordan, Nicole; Blanco, Irene; Weinstein, Arthur; Chitkara, Puja; Manzi, Susan; Ahearn, Joseph

    2014-01-01

    Objective To compare the performance characteristics of cell-bound complement (C4d) activation products (CBCAPS) on erythrocyte (EC4d) and B cells (BC4d) with antibodies to double-stranded DNA (anti-dsDNA) and complement C3 and C4 in systemic lupus erythematosus (SLE). Methods The study enrolled 794 subjects consisting of 304 SLE and a control group consisting of 285 patients with other rheumatic diseases and 205 normal individuals. Anti-dsDNA and other autoantibodies were measured using soli...

  14. Tracking the Interplay between Bound Peptide and the Lid Domain of DnaK, Using Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Yossi Tsfadia

    2013-06-01

    Full Text Available Hsp70 chaperones consist of two functional domains: the 44 kDa Nucleotide Binding Domain (NBD, that binds and hydrolyses ATP, and the 26 kDa Substrate Binding Domain (SBD, which binds unfolded proteins and reactivates them, utilizing energy obtained from nucleotide hydrolysis. The structure of the SBD of the bacterial Hsp70, DnaK, consists of two sub-domains: A β-sandwich part containing the hydrophobic cavity to which the hepta-peptide NRLLLTG (NR is bound, and a segment made of 5 α-helices, called the “lid” that caps the top of the β-sandwich domain. In the present study we used the Escherichia coli Hsp70, DnaK, as a model for Hsp70 proteins, focusing on its SBD domain, examining the changes in the lid conformation. We deliberately decoupled the NBD from the SBD, limiting the study to the structure of the SBD section, with an emphasis on the interaction between the charges of the peptide with the residues located in the lid. Molecular dynamics simulations of the complex revealed significant mobility within the lid structure; as the structure was released from the forces operating during the crystallization process, the two terminal helices established a contact with the positive charge at the tip of the peptide. This contact is manifested only in the presence of electrostatic attraction. The observed internal motions within the lid provide a molecular role for the function of this sub-domain during the reaction cycle of Hsp 70 chaperones.

  15. Trans and surface membrane bound zervamicin IIB: 13C-MAOSS-NMR at high spinning speed

    International Nuclear Information System (INIS)

    Raap, J.; Hollander, J.; Ovchinnikova, T. V.; Swischeva, N. V.; Skladnev, D.; Kiihne, S.

    2006-01-01

    Interactions between 15 N-labelled peptides or proteins and lipids can be investigated using membranes aligned on a thin polymer film, which is rolled into a cylinder and inserted into the MAS-NMR rotor. This can be spun at high speed, which is often useful at high field strengths. Unfortunately, substrate films like commercially available polycarbonate or PEEK produce severe overlap with peptide and protein signals in 13 C-MAOSS NMR spectra. We show that a simple house hold foil support allows clear observation of the carbonyl, aromatic and C α signals of peptides and proteins as well as the ester carbonyl and choline signals of phosphocholine lipids. The utility of the new substrate is validated in applications to the membrane active peptide zervamicin IIB. The stability and macroscopic ordering of thin PC10 bilayers was compared with that of thicker POPC bilayers, both supported on the household foil. Sidebands in the 31 P-spectra showed a high degree of alignment of both the supported POPC and PC10 lipid molecules. Compared with POPC, the PC10 lipids are slightly more disordered, most likely due to the increased mobilities of the shorter lipid molecules. This mobility prevents PC10 from forming stable vesicles for MAS studies. The 13 C-peptide peaks were selectively detected in a 13 C-detected 1 H-spin diffusion experiment. Qualitative analysis of build-up curves obtained for different mixing times allowed the transmembrane peptide in PC10 to be distinguished from the surface bound topology in POPC. The 13 C-MAOSS results thus independently confirms previous findings from 15 N spectroscopy [Bechinger, B., Skladnev, D.A., Ogrel, A., Li, X., Rogozhkina, E.V., Ovchinnikova, T.V., O'Neil, J.D.J. and Raap, J. (2001) Biochemistry, 40, 9428-9437]. In summary, application of house hold foil opens the possibility of measuring high resolution 13 C-NMR spectra of peptides and proteins in well ordered membranes, which are required to determine the secondary and

  16. Evaluating the Hydrologic Sensitivities of Three Land Surface Models to Bound Uncertainties in Runoff Projections

    Science.gov (United States)

    Chiao, T.; Nijssen, B.; Stickel, L.; Lettenmaier, D. P.

    2013-12-01

    Hydrologic modeling is often used to assess the potential impacts of climate change on water availability and quality. A common approach in these studies is to calibrate the selected model(s) to reproduce historic stream flows prior to the application of future climate projections. This approach relies on the implicit assumptions that the sensitivities of these models to meteorological fluctuations will remain relatively constant under climate change and that these sensitivities are similar among models if all models are calibrated to the same historic record. However, even if the models are able to capture the historic variability in hydrological variables, differences in model structure and parameter estimation contribute to the uncertainties in projected runoff, which confounds the incorporation of these results into water resource management decision-making. A better understanding of the variability in hydrologic sensitivities between different models can aid in bounding this uncertainty. In this research, we characterized the hydrologic sensitivities of three watershed-scale land surface models through a case study of the Bull Run watershed in Northern Oregon. The Distributed Hydrology Soil Vegetation Model (DHSVM), Precipitation-Runoff Modeling System (PRMS), and Variable Infiltration Capacity model (VIC) were implemented and calibrated individually to historic streamflow using a common set of long-term, gridded forcings. In addition to analyzing model performances for a historic period, we quantified the temperature sensitivity (defined as change in runoff in response to change in temperature) and precipitation elasticity (defined as change in runoff in response to change in precipitation) of these three models via perturbation of the historic climate record using synthetic experiments. By comparing how these three models respond to changes in climate forcings, this research aims to test the assumption of constant and similar hydrologic sensitivities. Our

  17. Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence.

    Science.gov (United States)

    Petukh, Marharyta; Zhang, Min; Alexov, Emil

    2015-12-15

    Ions are engaged in multiple biological processes in cells. By binding to the macromolecules or being mobile in the solvent, they maintain the integrity of the structure of macromolecules; participate in their enzymatic activity; or screen electrostatic interactions. While experimental methods are not always able to assign the exact location of ions, computational methods are in demand. Although the majority of computational methods are successful in predicting the position of ions buried inside macromolecules, they are less effective in deciphering positions of surface bound ions. Here, we propose the new BION algorithm (http://compbio.clemson.edu/bion_server_ph/) that predicts the location of the surface bound ions. It is more efficient and accurate compared to the previous version since it uses more advanced clustering algorithm in combination with pairing rules. In addition, the BION webserver allows specifying the pH and the salt concentration in predicting ions positions. © 2015 Wiley Periodicals, Inc.

  18. On the lipid head group hydration of floating surface monolayers bound to self-assembled molecular protein layers

    DEFF Research Database (Denmark)

    Lösche, M.; Erdelen, C.; Rump, E.

    1994-01-01

    The structure of monomolecular layers of the protein streptavidin, specifically bound to biotin-functionalized lipid monolayers at aqueous surfaces, has been characterized. Neutron and X-ray reflectivity measurements allowed an assessment of the organization of these self-assembled systems...... with molecular resolution. Emphasis here is placed on the hydration of the lipid head groups in the bound state. For three functionalized lipids with spacers of different lengths between the biotin and their chains it was observed that the head groups were dehydrated in monolayers of the pure lipids, which were...... kept at low surface pressure before protein adsorption. The introduction of dipole moments at the interface by the admixture of phospholipids or the application of lateral pressure on the lipid monolayer before protein adsorption were found to impose an extension of the spacer moieties. The biotin...

  19. Construction of yeast surface-displayed cDNA libraries.

    Science.gov (United States)

    Bidlingmaier, Scott; Liu, Bin

    2011-01-01

    Using yeast display, heterologous protein fragments can be efficiently displayed at high copy levels on the Saccharomyces cerevisiae cell wall. Yeast display can be used to screen large expressed protein libraries for proteins or protein fragments with specific binding properties. Recently, yeast surface-displayed cDNA libraries have been constructed and used to identify proteins that bind to various target molecules such as peptides, small molecules, and antibodies. Because yeast protein expression pathways are similar to those found in mammalian cells, human protein fragments displayed on the yeast cell wall are likely to be properly folded and functional. Coupled with fluorescence-activated cell sorting, yeast surface-displayed cDNA libraries potentially allow the selection of protein fragments or domains with affinity for any soluble molecule that can be fluorescently detected. In this report, we describe protocols for the construction and validation of yeast surface-displayed cDNA libraries using preexisting yeast two-hybrid cDNA libraries as a starting point.

  20. Immunological usefulness of semen manipulation for artificial insemination homologous (AIH) in subjects with antisperm antibodies bound to sperm surface.

    Science.gov (United States)

    Lenzi, A; Gandini, L; Claroni, F; Lombardo, F; Morrone, S; Dondero, F

    1988-01-01

    The authors report trials carried out in the preparation of semen for homologous artificial insemination in subjects with antisperm autoantibodies. The tests have demonstrated that swim-up is not able to select spermatozoa free of antibodies bound to the sperm surface. All the experiments of migration, dilution, antigenic competition and cryoconservation, carried out to evaluate the theoretical possibility of a better recovery of non "immunologically compromised" spermatozoa, have confirmed such negative results both with the Immunobead Test and Cytofluorimetric analysis.

  1. A Real-Time QCM-D Approach to Monitoring Mammalian DNA Damage Using DNA Adsorbed to a Polyelectrolyte Surface

    Science.gov (United States)

    Rawle, Robert J.; Johal, Malkiat S.; Selassie, Cynthia R. D.

    2008-01-01

    We have successfully demonstrated that the quartz crystal microbalance with dissipation monitoring (QCM-D) can be used to monitor real-time damage to genomic mammalian DNA adsorbed to a polyelectrolyte surface. To reveal the capabilities of this technique, we exposed DNA surfaces to quercetin, an agent that has been implicated in causing DNA strand breaks in a Cu(II)-dependent fashion in vitro. We show that the QCM-D frequency and dissipation patterns that result from exposure of the DNA surfaces to quercetin/Cu(II) are consistent with the induction of DNA strand scission. We use QCM-D to furthermore demonstrate that this process is dependent on Cu(II) and that the DNA damage induced by quercetin can still be detected if Cu(II) is in situ with the DNA surface and not in solution-phase. PMID:18076139

  2. Methods of DNA sequencing by hybridization based on optimizing concentration of matrix-bound oligonucleotide and device for carrying out same

    Science.gov (United States)

    Khrapko, Konstantin R.; Khorlin, Alexandr A.; Ivanov, Igor B.; Ershov, Gennady M.; Lysov, Jury P.; Florentiev, Vladimir L.; Mirzabekov, Andrei D.

    1996-09-03

    A method for sequencing DNA by hybridization that includes the following steps: forming an array of oligonucleotides at such concentrations that either ensure the same dissociation temperature for all fully complementary duplexes or allows hybridization and washing of such duplexes to be conducted at the same temperature; hybridizing said oligonucleotide array with labeled test DNA; washing in duplex dissociation conditions; identifying single-base substitutions in the test DNA by analyzing the distribution of the dissociation temperatures and reconstructing the DNA nucleotide sequence based on the above analysis. A device for carrying out the method comprises a solid substrate and a matrix rigidly bound to the substrate. The matrix contains the oligonucleotide array and consists of a multiplicity of gel portions. Each gel portion contains one oligonucleotide of desired length. The gel portions are separated from one another by interstices and have a thickness not exceeding 30 .mu.m.

  3. Study on the bound water of several high specific surface-area oxides (beryllia, alumina, silica-alumina)

    International Nuclear Information System (INIS)

    Rouquerol, J.

    1964-11-01

    This study is concerned with the bound water of several oxides (beryllia, alumina, silica-alumina) at different steps of their dehydration (heating temperatures between 150 and 1100 deg. C). The following techniques have been used simultaneously: Thermal analysis (a new method has been developed), nitrogen adsorption (study of the texture), Diborane hydrolysis (qualitative and quantitative analysis of surface water), Infra-red spectrography (in the absorption range of water), Nuclear magnetic resonance (in the resonance range of protons). Thanks to these different techniques, five kinds of bound water have been observed. Attention is called on the great influence of the thermal treatment conditions on the evolution of the products resulting from the decomposition of alumina α-trihydrate Al(OH) 3 and beryllium α-hydroxide, in the course of the dehydration. Moreover, the author emphasizes the peculiar properties of the two kinds of oxides (alumina and beryllia) prepared through a new method of treatment under low pressure and constant speed of decomposition. Such particular features concern mainly texture, bound water, and consequently, also catalytic activity. (author) [fr

  4. Simple surface modification of poly(dimethylsiloxane) for DNA hybridization

    Science.gov (United States)

    Zhou, Jinwen; Voelcker, Nicolas H.; Ellis, Amanda V.

    2010-01-01

    Here, we present a simple chemical modification of poly(dimethylsiloxane) (PDMS) by curing a mixture of 2 wt% undecylenic acid (UDA) in PDMS prepolymer on a gold-coated glass slide. This gold slide had been previously pretreated with a self-assembled hydrophilic monolayer of 3-mercaptopropionic acid (MPA). During curing of the UDA∕PDMS prepolymer, the hydrophilic UDA carboxyl moieties diffuses toward the hydrophilic MPA carboxyl moieties on the gold surface. This diffusion of the UDA within the PDMS prepolymer to the surface is a direct result of surface energy minimization. Once completely cured, the PDMS is peeled off the gold substrate, thereby exposing the interfacial carboxyl groups. These groups are then available for subsequent attachment of 5′-amino terminated DNA oligonucleotides via amide linkages. Our results show that the covalently tethered oligonucleotides can successfully capture fluorescein-labeled complementary oligonucleotides via hybridization, which are visualized using fluorescence microscopy. PMID:21264061

  5. High Efficiency Acetylcholinesterase Immobilization on DNA Aptamer Modified Surfaces

    Directory of Open Access Journals (Sweden)

    Orada Chumphukam

    2014-04-01

    Full Text Available We report here the in vitro selection of DNA aptamers for electric eel acetylcholinesterase (AChE. One selected aptamer sequence (R15/19 has a high affinity towards the enzyme (Kd = 157 ± 42 pM. Characterization of the aptamer showed its binding is not affected by low ionic strength (~20 mM, however significant reduction in affinity occurred at high ionic strength (~1.2 M. In addition, this aptamer does not inhibit the catalytic activity of AChE that we exploit through immobilization of the DNA on a streptavidin-coated surface. Subsequent immobilization of AChE by the aptamer results in a 4-fold higher catalytic activity when compared to adsorption directly on to plastic.

  6. Surface-assisted DNA self-assembly: An enzyme-free strategy towards formation of branched DNA lattice.

    Science.gov (United States)

    Bhanjadeo, Madhabi M; Nayak, Ashok K; Subudhi, Umakanta

    2017-04-01

    DNA based self-assembled nanostructures and DNA origami has proven useful for organizing nanomaterials with firm precision. However, for advanced applications like nanoelectronics and photonics, large-scale organization of self-assembled branched DNA (bDNA) into periodic lattices is desired. In this communication for the first time we report a facile method of self-assembly of Y-shaped bDNA nanostructures on the cationic surface of Aluminum (Al) foil to prepare periodic two dimensional (2D) bDNA lattice. Particularly those Y-shaped bDNA structures having smaller overhangs and unable to self-assemble in solution, they are easily assembled on the surface of Al foil in the absence of ligase. Field emission scanning electron microscopy (FESEM) analysis shows homogenous distribution of two-dimensional bDNA lattices across the Al foil. When the assembled bDNA structures were recovered from the Al foil and electrophoresed in nPAGE only higher order polymeric bDNA structures were observed without a trace of monomeric structures which confirms the stability and high yield of the bDNA lattices. Therefore, this enzyme-free economic and efficient strategy for developing bDNA lattices can be utilized in assembling various nanomaterials for functional molecular components towards development of DNA based self-assembled nanodevices. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Wear and roughness of the metal surface at polishing by bound abrasive

    International Nuclear Information System (INIS)

    Spasskij, M.R.; Lokhov, Yu.N.; Ashkerov, Yu.V.

    1987-01-01

    The model is proposed of the process of polishing of plastic metals by a resin polisher with the surface-saturated layer of abrasive. The model is based on the idea about a net independent effect of individual grains on the metal surface. A linear dependence of the wear rate on the applied pressure is substantiated. It is shown that a determining characteristic of metal in the process of polishing is elastic modulus rather than hardness or yield point. The dependence of a maximally attainable roughness of the metal surface on its plasticity, pressure, concentration and dimension of the abrasive is found

  8. DNA adsorption and desorption on mica surface studied by atomic force microscopy

    International Nuclear Information System (INIS)

    Sun Lanlan; Zhao Dongxu; Zhang Yue; Xu Fugang; Li Zhuang

    2011-01-01

    The adsorption of DNA molecules on mica surface and the following desorption of DNA molecules at ethanol-mica interface were studied using atomic force microscopy. By changing DNA concentration, different morphologies on mica surface have been observed. A very uniform and orderly monolayer of DNA molecules was constructed on the mica surface with a DNA concentration of 30 ng/μL. When the samples were immersed into ethanol for about 15 min, various desorption degree of DNA from mica (0-99%) was achieved. It was found that with the increase of DNA concentration, the desorption degree of DNA from the mica at ethanol-mica interface decreased. And when the uniform and orderly DNA monolayers were formed on the mica surface, almost no DNA molecule desorbed from the mica surface in this process. The results indicated that the uniform and orderly DNA monolayer is one of the most stable DNA structures formed on the mica surface. In addition, we have studied the structure change of DNA molecules after desorbed from the mica surface with atomic force microscopy, and found that the desorption might be ascribed to the ethanol-induced DNA condensation.

  9. Low-frequency surface waves on semi-bounded magnetized quantum plasma

    Energy Technology Data Exchange (ETDEWEB)

    Moradi, Afshin, E-mail: a.moradi@kut.ac.ir [Department of Engineering Physics, Kermanshah University of Technology, Kermanshah (Iran, Islamic Republic of)

    2016-08-15

    The propagation of low-frequency electrostatic surface waves on the interface between a vacuum and an electron-ion quantum plasma is studied in the direction perpendicular to an external static magnetic field which is parallel to the interface. A new dispersion equation is derived by employing both the quantum magnetohydrodynamic and Poisson equations. It is shown that the dispersion equations for forward and backward-going surface waves are different from each other.

  10. Crystal optimization and preliminary diffraction data analysis of the Smad1 MH1 domain bound to a palindromic SBE DNA element

    International Nuclear Information System (INIS)

    Baburajendran, Nithya; Palasingam, Paaventhan; Ng, Calista Keow Leng; Jauch, Ralf; Kolatkar, Prasanna R.

    2009-01-01

    Crystals of palindromic SBE DNA-bound Smad1 MH1 domain diffracting to 2.7 Å resolution have been obtained. The bone morphogenetic protein (BMP) signalling pathway regulates diverse processes such as cell differentiation, anterior/posterior axis specification, cell growth and the formation of extra-embryonic tissues. The transcription factor Smad1 relays the BMP signal from the cytoplasm to the nucleus, where it binds short DNA-sequence motifs and regulates gene expression. However, how Smad1 selectively targets particular genomic regions is poorly understood. In order to understand the physical basis of the specific interaction of Smad1 with DNA and to contrast it with the highly homologous but functionally distinct Smad3 protein, the DNA-binding Mad-homology 1 (MH1) domain of Smad1 was cocrystallized with a 17-mer palindromic Smad-binding element (SBE). The extensive optimizations of the length, binding-site spacing and terminal sequences of the DNA element in combination with the other crystallization parameters necessary for obtaining diffraction-quality crystals are described here. A 2.7 Å resolution native data set was collected at the National Synchrotron Radiation Research Centre, Taiwan, from crystals grown in a solution containing 0.2 M ammonium tartrate dibasic, 20% PEG 3350, 3% 2-propanol and 10% glycerol. The data set was indexed and merged in space group P222, with unit-cell parameters a = 73.94, b = 77.49, c = 83.78 Å, α = β = γ = 90°. The solvent content in the unit cell is consistent with the presence of two Smad1 MH1 molecules bound to the duplex DNA in the asymmetric unit

  11. Surface-Bound Ligands Modulate Chemoselectivity and Activity of a Bimetallic Nanoparticle Catalyst

    KAUST Repository

    Vu, Khanh B.

    2015-04-03

    "Naked" metal nanoparticles (NPs) are thermodynamically and kinetically unstable in solution. Ligands, surfactants, or polymers, which adsorb at a particle\\'s surface, can be used to stabilize NPs; however, such a mode of stabilization is undesirable for catalytic applications because the adsorbates block the surface active sites. The catalytic activity and the stability of NPs are usually inversely correlated. Here, we describe an example of a bimetallic (PtFe) NP catalyst stabilized by carboxylate surface ligands that bind preferentially to one of the metals (Fe). NPs stabilized by fluorous ligands were found to be remarkably competent in catalyzing the hydrogenation of cinnamaldehyde; NPs stabilized by hydrocarbon ligands were significantly less active. The chain length of the fluorous ligands played a key role in determining the chemoselectivity of the FePt NP catalysts. (Chemical Presented). © 2015 American Chemical Society.

  12. Major membrane surface proteins of Mycoplasma hyopneumoniae selectively modified by covalently bound lipid

    Energy Technology Data Exchange (ETDEWEB)

    Wise K.S.; Kim, M.F.

    1987-12-01

    Surface protein antigens of Mycoplasma hyopneumoniae were identified by direct antibody-surface binding or by radioimmunoprecipitation of surface /sup 125/I-labeled proteins with a series of monoclonal antibodies (MAbs). Radioimmunoprecipitation of TX-114-phase proteins from cells labeled with (/sup 35/S) methionine, /sup 14/C-amino acids, or (/sup 3/H) palmitic acid showed that proteins p65, p50, and p44 were abundant and (with one other hydrophobic protein, p60) were selectively labeled with lipid. Alkaline hydroxylamine treatment of labeled proteins indicated linkage of lipids by amide or stable O-linked ester bonds. Proteins p65, p50, and p44 were highly immunogenic in the natural host as measured by immunoblots of TX-114-phase proteins with antisera from swine inoculated with whole organisms. These proteins were antigenically and structurally unrelated, since hyperimmune mouse antibodies to individual gel-purified proteins were monospecific and gave distinct proteolytic epitope maps. Intraspecies size variants of one surface antigen of M. hyopneumoniae were revealed by a MAb to p70 (defined in strain J, ATCC 25934), which recognized a large p73 component on strain VPP11 (ATCC 25617). In addition, MAb to internal, aqueous-phase protein p82 of strain J failed to bind an analogous antigen in strain VPP11.

  13. Major membrane surface proteins of Mycoplasma hyopneumoniae selectively modified by covalently bound lipid

    International Nuclear Information System (INIS)

    Wise, K.S.; Kim, M.F.

    1987-01-01

    Surface protein antigens of Mycoplasma hyopneumoniae were identified by direct antibody-surface binding or by radioimmunoprecipitation of surface 125 I-labeled proteins with a series of monoclonal antibodies (MAbs). Radioimmunoprecipitation of TX-114-phase proteins from cells labeled with [ 35 S] methionine, 14 C-amino acids, or [ 3 H] palmitic acid showed that proteins p65, p50, and p44 were abundant and (with one other hydrophobic protein, p60) were selectively labeled with lipid. Alkaline hydroxylamine treatment of labeled proteins indicated linkage of lipids by amide or stable O-linked ester bonds. Proteins p65, p50, and p44 were highly immunogenic in the natural host as measured by immunoblots of TX-114-phase proteins with antisera from swine inoculated with whole organisms. These proteins were antigenically and structurally unrelated, since hyperimmune mouse antibodies to individual gel-purified proteins were monospecific and gave distinct proteolytic epitope maps. Intraspecies size variants of one surface antigen of M. hyopneumoniae were revealed by a MAb to p70 (defined in strain J, ATCC 25934), which recognized a large p73 component on strain VPP11 (ATCC 25617). In addition, MAb to internal, aqueous-phase protein p82 of strain J failed to bind an analogous antigen in strain VPP11

  14. A novel DNA restriction technology based on laser pulse energy conversion on sequence-specific bound metal nanoparticles

    Science.gov (United States)

    Csaki, Andrea; Maubach, Gunter; Garwe, Frank; Steinbrueck, Andrea; Koenig, Karsten; Fritzsche, Wolfgang

    2005-03-01

    DNA restriction is a basic method in today"s molecular biology. Besides application for DNA manipulation, this method is used in DNA analytics for 'restriction analysis'. Thereby DNA is digested by sequence specific restriction enzymes, and the length distribution of the resulting fragments is detected by gel electrophoresis. Differences in the sequence lead to different restriction patterns. A disadvantage of this standard method is the limitation to a small set of fixed sequences, so that the assay can not be adapted to any sequence of interest (e.g. SNP). We designed a scheme for DNA restriction in order to provide access to any desired sequence, based on laser light conversion on sequence-specific positioned metal nanoparticles. Especially gold nanoparticles are known for their interesting optical properties caused by plasmon resonance. The resulting absorption can be used to convert laser light pulses into heat, resulting in nanoparticle destruction. We work on the combination of this principle with DNA-modification of nanoparticles and the sequence-specific binding (hybridization) of these DNA-nanoparticle complexes along DNA molecules. Different mechanisms of light-conversion were studied, and the destructive effect of laser light on the nanoparticles and DNA is demonstrated.

  15. Effect of pullulan nanoparticle surface charges on HSA complexation and drug release behavior of HSA-bound nanoparticles.

    Directory of Open Access Journals (Sweden)

    Xiaojun Tao

    Full Text Available Nanoparticle (NP compositions such as hydrophobicity and surface charge are vital to determine the presence and amount of human serum albumin (HSA binding. The HSA binding influences drug release, biocompatibility, biodistribution, and intercellular trafficking of nanoparticles (NPs. Here, we prepared 2 kinds of nanomaterials to investigate HSA binding and evaluated drug release of HSA-bound NPs. Polysaccharides (pullulan carboxyethylated to provide ionic derivatives were then conjugated to cholesterol groups to obtain cholesterol-modified carboxyethyl pullulan (CHCP. Cholesterol-modified pullulan (CHP conjugate was synthesized with a similar degree of substitution of cholesterol moiety to CHCP. CHCP formed self-aggregated NPs in aqueous solution with a spherical structure and zeta potential of -19.9 ± 0.23 mV, in contrast to -1.21 ± 0.12 mV of CHP NPs. NPs could quench albumin fluorescence intensity with maximum emission intensity gradually decreasing up to a plateau at 9 to 12 h. Binding constants were 1.12 × 10(5 M(-1 and 0.70 × 10(5 M(-1 to CHP and CHCP, respectively, as determined by Stern-Volmer analysis. The complexation between HSA and NPs was a gradual process driven by hydrophobic force and inhibited by NP surface charge and shell-core structure. HSA conformation was altered by NPs with reduction of α-helical content, depending on interaction time and particle surface charges. These NPs could represent a sustained release carrier for mitoxantrone in vitro, and the bound HSA assisted in enhancing sustained drug release.

  16. Small, acid-soluble proteins bound to DNA protect Bacillus subtilis spores from killing by dry heat.

    OpenAIRE

    Setlow, B; Setlow, P

    1995-01-01

    Dry Bacillus subtilis spores lacking their two major DNA-binding proteins (small, acid-soluble proteins [SASP] alpha and beta) were much more sensitive to dry heat than were wild-type spores. Survivors of dry heat treatment of both wild-type and mutant spores exhibited a high frequency of mutations, and the DNA from the heated spores had increased numbers of single-strand breaks. These data indicate that SASP alpha and beta provide significant protection to spore DNA against the damaging effe...

  17. Surface-Bound Molecular Film Structure Effects on Electronic and Magnetic Properties

    Science.gov (United States)

    Pronschinske, Alex M.

    This thesis dissertation will discuss the importance of understanding the driving forces of molecular assembly on surfaces and the need to characterize the electronic and magnetic properties of the resulting organic films. Furthermore, experimental results on model organic molecular assemblies, benzoate on Cu(110) and Fe[(H2BPz2)2bpy] ("Fe-bpy") on Au(111), and their novel film properties will be presented. The primary experimental techniques used in this work are scanning tunneling microscopy and spectroscopy (STM, STS), and so a theoretical characterization of constant current distance-voltage STS (z(V)-STS) will also be developed. Deposition of benzoic acid (C6H5COOH) on to Cu(110) will be used to create a diverse molecular environment of benzoate molecules (C6H5COO+). In this film we will utilize structural phases consisting of co-existing orientation (alpha-phase) and uniform molecular orientation (c(8x2) phase) to probe electric potential variation across the surface of the film. Using z( V)-STS find that the electron affinity level of a molecule's near-neighbor will exert a substrate-mediated influence on the energy of the molecule's image potential state; which we describe using a 1-D dielectric continuum model. Motivated by the unique utility of z(V)-STS for gentle probing of molecular electronic structure and electric potential we perform a thorough theoretical characterize of z( V)-STS. We derive a differential equation for simulating z(V)-STS spectra under the standard approximation of a square tunneling barrier. Moreover, we derive an equation for sample density of states (DOS) that is applicable for all modes of STS. The central result of this work for interpretation of z(V)-STS results is a characterization of systematic error between state energy and z(V)-STS peak location, as well we show that empirical normalization procedure for removing background distortion from constant height current-voltage STS, (V/I)dI/dV, is also applicable to z(V)-STS is

  18. Structure of the DNA-bound BRCA1 C-terminal region from human replication factor C p140 and model of the protein-DNA complex

    NARCIS (Netherlands)

    Kobayashi, M.; AB, E.; Bonvin, A.M.J.J.; Siegal, G.

    2010-01-01

    BRCA1 C-terminal domain (BRCT)-containing proteins are found widely throughout the animal and bacteria kingdoms where they are exclusively involved in cell cycle regulation and DNA metabolism. Whereas most BRCT domains are involved in protein-protein interactions, a small subset has bona fide DNA

  19. Examination of Proteins Bound to Nascent DNA in Mammalian Cells Using BrdU-ChIP-Slot-Western Technique.

    Science.gov (United States)

    Bhaskara, Srividya

    2016-01-14

    Histone deacetylases 1 and 2 (HDAC1,2) localize to the sites of DNA replication. In the previous study, using a selective inhibitor and a genetic knockdown system, we showed novel functions for HDAC1,2 in replication fork progression and nascent chromatin maintenance in mammalian cells. Additionally, we used a BrdU-ChIP-Slot-Western technique that combines chromatin immunoprecipitation (ChIP) of bromo-deoxyuridine (BrdU)-labeled DNA with slot blot and Western analyses to quantitatively measure proteins or histone modification associated with nascent DNA. Actively dividing cells were treated with HDAC1,2 selective inhibitor or transfected with siRNAs against Hdac1 and Hdac2 and then newly synthesized DNA was labeled with the thymidine analog bromodeoxyuridine (BrdU). The BrdU labeling was done at a time point when there was no significant cell cycle arrest or apoptosis due to the loss of HDAC1,2 functions. Following labeling of cells with BrdU, chromatin immunoprecipitation (ChIP) of histone acetylation marks or the chromatin-remodeler was performed with specific antibodies. BrdU-labeled input DNA and the immunoprecipitated (or ChIPed) DNA was then spotted onto a membrane using the slot blot technique and immobilized using UV. The amount of nascent DNA in each slot was then quantitatively assessed using Western analysis with an anti-BrdU antibody. The effect of loss of HDAC1,2 functions on the levels of newly synthesized DNA-associated histone acetylation marks and chromatin remodeler was then determined by normalizing the BrdU-ChIP signal obtained from the treated samples to the control samples.

  20. On-Demand Final State Control of a Surface-Bound Bistable Single Molecule Switch.

    Science.gov (United States)

    Garrido Torres, José A; Simpson, Grant J; Adams, Christopher J; Früchtl, Herbert A; Schaub, Renald

    2018-04-12

    Modern electronic devices perform their defined action because of the complete reliability of their individual active components (transistors, switches, diodes, and so forth). For instance, to encode basic computer units (bits) an electrical switch can be used. The reliability of the switch ensures that the desired outcome (the component's final state, 0 or 1) can be selected with certainty. No practical data storage device would otherwise exist. This reliability criterion will necessarily need to hold true for future molecular electronics to have the opportunity to emerge as a viable miniaturization alternative to our current silicon-based technology. Molecular electronics target the use of single-molecules to perform the actions of individual electronic components. On-demand final state control over a bistable unimolecular component has therefore been one of the main challenges in the past decade (1-5) but has yet to be achieved. In this Letter, we demonstrate how control of the final state of a surface-supported bistable single molecule switch can be realized. On the basis of the observations and deductions presented here, we further suggest an alternative strategy to achieve final state control in unimolecular bistable switches.

  1. Investigating ozone-induced decomposition of surface-bound permethrin for conditions in aircraft cabins.

    Science.gov (United States)

    Coleman, B K; Wells, J R; Nazaroff, W W

    2010-02-01

    The reaction of ozone with permethrin can potentially form phosgene. Published evidence on ozone levels and permethrin surface concentrations in aircraft cabins indicated that significant phosgene formation might occur in this setting. A derivatization technique was developed to detect phosgene with a lower limit of detection of 2 ppb. Chamber experiments were conducted with permethrin-coated materials (glass, carpet, seat fabric, and plastic) exposed to ozone under cabin-relevant conditions (150 ppb O(3), 4.5/h air exchange rate, means of material-balance modeling indicates that the upper limit on the phosgene level in aircraft cabins resulting from this chemistry is approximately 1 microg/m(3) or approximately 0.3 ppb. It was thus determined that phosgene formation, if it occurs in aircraft cabins, is not likely to exceed relevant, health-based phosgene exposure guidelines. Phosgene formation from ozone-initiated oxidation of permethrin in the aircraft cabin environment, if it occurs, is estimated to generate levels below the California Office of Environmental Health Hazard Assessment acute reference exposure level of 4 microg/m(3) or approximately 1 ppb.

  2. Laser-based standoff detection of surface-bound explosive chemicals

    Science.gov (United States)

    Huestis, David L.; Smith, Gregory P.; Oser, Harald

    2010-04-01

    Avoiding or minimizing potential damage from improvised explosive devices (IEDs) such as suicide, roadside, or vehicle bombs requires that the explosive device be detected and neutralized outside its effective blast radius. Only a few seconds may be available to both identify the device as hazardous and implement a response. As discussed in a study by the National Research Council, current technology is still far from capable of meeting these objectives. Conventional nitrocarbon explosive chemicals have very low vapor pressures, and any vapors are easily dispersed in air. Many pointdetection approaches rely on collecting trace solid residues from dust particles or surfaces. Practical approaches for standoff detection are yet to be developed. For the past 5 years, SRI International has been working toward development of a novel scheme for standoff detection of explosive chemicals that uses infrared (IR) laser evaporation of surfacebound explosive followed by ultraviolet (UV) laser photofragmentation of the explosive chemical vapor, and then UV laser-induced fluorescence (LIF) of nitric oxide. This method offers the potential of long standoff range (up to 100 m or more), high sensitivity (vaporized solid), simplicity (no spectrometer or library of reference spectra), and selectivity (only nitrocompounds).

  3. Adsorption behavior of DNA-wrapped carbon nanotubes on self-assembled monolayer surfaces.

    Science.gov (United States)

    Zangmeister, Rebecca A; Maslar, James E; Opdahl, Aric; Tarlov, Michael J

    2007-05-22

    We have examined the adsorption of DNA-wrapped single-walled carbon nanotubes (DNA-SWNTs) on hydrophobic, hydrophilic, and charged surfaces of alkylthiol self-assembled monolayers (SAMs) on gold. Our goal is to understand how DNA-SWNTs interact with surfaces of varying chemical functionality. These samples were characterized using reflection absorption FTIR (RAIRS), X-ray photoelectron spectroscopy (XPS), and Raman spectroscopy. We have found that DNA-SWNTs preferentially adsorb to positively charged amine-terminated SAMs and to bare gold surfaces versus hydrophobic methyl-terminated or negatively charged carboxylic acid-terminated SAMs. Examination of the adsorption on gold of single-strand DNA (ssDNA) of the same sequence used to wrap the SWNTs suggests that the DNA wrapping plays a role in the adsorption behavior of DNA-SWNTs.

  4. Bacteriophage phi W-14: the contribution of covalently bound putrescine to DNA packing in the phage head.

    Science.gov (United States)

    Scraba, D G; Bradley, R D; Leyritz-Wills, M; Warren, R A

    1983-01-15

    Bacteriophage phi W-14 is unusual because its DNA contains 12 mol% of the hypermodified pyrimidine, alpha-putrescinylthymine. The phi W-14 virion is similar in morphology to T4, except that the phi W-14 head is isometric rather than prolate, there is no collar-whisker structure associated with the neck, the tail fibers are short (approximately 15 nm), and the base plate terminates in small plates or knobs rather than spikes. The contractile tail sheath of phi W-14 appears to have a right-handed helical arrangement of subunits with a pitch in the extended form of approximately 20 nm. The "stacked disk" appearance of the tail sheath visible on negatively stained particles has a periodicity of 3-4 nm. The protein shell of the head has a similar thickness (2-3 nm) to that of T4. The phi W-14 virion contains at least 17 different polypeptide species. Based on measurements from electron micrographs of negatively stained phage particles on the same grid square, the volume of the phi W-14 head was estimated to be approximately 72% that of the T4 head. Surprisingly, however, the lengths of the DNA molecules released from phi W-14 and T4 heads by osmotic shock were 59.6 +/- 1.9 and 62.1 +/- 2.4 microns, respectively. am42 is an amber mutant of phi W-14 in which there is only 5 mol% putThy in the DNA made in the nonpermissive host. am42 virions are morphologically normal, but the length of the DNA released from these virions is only 53.1 +/- 3.1 microns. We conclude that phi W-14 DNA is packed much more compactly than T4 DNA into a virion of similar morphology and comparable complexity and that the tight packing is a consequence of, and dependent upon, the presence of putThy in phi W-14 DNA.

  5. Chirality of weakly bound complexes: The potential energy surfaces for the hydrogen-peroxide−noble-gas interactions

    Energy Technology Data Exchange (ETDEWEB)

    Roncaratti, L. F., E-mail: lz@fis.unb.br; Leal, L. A.; Silva, G. M. de [Instituto de Física, Universidade de Brasília, 70910 Brasília (Brazil); Pirani, F. [Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia (Italy); Aquilanti, V. [Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia (Italy); Instituto de Física, Universidade Federal da Bahia, 40210 Salvador (Brazil); Gargano, R. [Instituto de Física, Universidade de Brasília, 70910 Brasília (Brazil); Departments of Chemistry and Physics, University of Florida, Quantum Theory Project, Gainesville, Florida 32611 (United States)

    2014-10-07

    We consider the analytical representation of the potential energy surfaces of relevance for the intermolecular dynamics of weakly bound complexes of chiral molecules. In this paper we study the H{sub 2}O{sub 2}−Ng (Ng=He, Ne, Ar, Kr, and Xe) systems providing the radial and the angular dependence of the potential energy surface on the relative position of the Ng atom. We accomplish this by introducing an analytical representation which is able to fit the ab initio energies of these complexes in a wide range of geometries. Our analysis sheds light on the role that the enantiomeric forms and the symmetry of the H{sub 2}O{sub 2} molecule play on the resulting barriers and equilibrium geometries. The proposed theoretical framework is useful to study the dynamics of the H{sub 2}O{sub 2} molecule, or other systems involving O–O and S–S bonds, interacting by non-covalent forces with atoms or molecules and to understand how the relative orientation of the O–H bonds changes along collisional events that may lead to a hydrogen bond formation or even to selectivity in chemical reactions.

  6. Catastrophic instabilities of modified DA-DC hybrid surface waves in a semi-bounded plasma system

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Myoung-Jae [Department of Physics and Research Institute for Natural Sciences, Hanyang University, Seoul 04763 (Korea, Republic of); Jung, Young-Dae, E-mail: ydjung@hanyang.ac.kr [Department of Applied Physics and Department of Bionanotechnology, Hanyang University, Ansan, Kyunggi-Do 15588, South Korea and Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180-3590 (United States)

    2016-06-15

    We find the catastrophic instabilities and derive the growth rates for the dust-cyclotron resonance (DCR) and dust-rotation resonance (DRR) modes of the modified dust-acoustic and dust-cyclotron (DA-DC) hybrid surface waves propagating at the plasma–vacuum interface where the plasma is semi-bounded and composed of electrons and rotating dust grains. The effects of magnetic field and dust rotation frequency on the DCR- and DDR-modes are also investigated. We find that the dust rotation frequency enhances the growth rate of DCR-mode and the effect of dust rotation on this resonance mode decreases with an increase of the wave number. We also find that an increase of magnetic field strength enhances the DCR growth rate, especially, for the short wavelength regime. In the case of DRR-mode, the growth rate is found to be decreased less sensitively with an increase of the wave number compared with the case of DCR, but much significantly enhanced by an increase of dust rotation frequency. The DRR growth rate also decreases with an increase of the magnetic field strength, especially in the long wavelength regime. Interestingly, we find that catastrophic instabilities occur for both DCR- and DRR-modes of the modified DA-DC hybrid surface waves when the rotational frequency is close to the dust-cyclotron frequency. Both modes can also be excited catastrophically due to the cooperative interaction between the DCR-mode and the DRR-mode.

  7. Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer.

    Science.gov (United States)

    Miller, Matthew T; Tuske, Steve; Das, Kalyan; DeStefano, Jeffrey J; Arnold, Eddy

    2016-01-01

    The development of a modified DNA aptamer that binds HIV-1 reverse transcriptase (RT) with ultra-high affinity has enabled the X-ray structure determination of an HIV-1 RT-DNA complex to 2.3 Å resolution without the need for an antibody Fab fragment or RT-DNA cross-linking. The 38-mer hairpin-DNA aptamer has a 15 base-pair duplex, a three-deoxythymidine hairpin loop, and a five-nucleotide 5'-overhang. The aptamer binds RT in a template-primer configuration with the 3'-end positioned at the polymerase active site and has 2'-O-methyl modifications at the second and fourth duplex template nucleotides that interact with the p66 fingers and palm subdomains. This structure represents the highest resolution RT-nucleic acid structure to date. The RT-aptamer complex is catalytically active and can serve as a platform for studying fundamental RT mechanisms and for development of anti-HIV inhibitors through fragment screening and other approaches. Additionally, the structure allows for a detailed look at a unique aptamer design and provides the molecular basis for its remarkably high affinity for RT. © 2015 The Protein Society.

  8. Crystal optimization and preliminary diffraction data analysis of the Smad1 MH1 domain bound to a palindromic SBE DNA element

    Science.gov (United States)

    Baburajendran, Nithya; Palasingam, Paaventhan; Ng, Calista Keow Leng; Jauch, Ralf; Kolatkar, Prasanna R.

    2009-01-01

    The bone morphogenetic protein (BMP) signalling pathway regulates diverse processes such as cell differentiation, anterior/posterior axis specification, cell growth and the formation of extra-embryonic tissues. The transcription factor Smad1 relays the BMP signal from the cytoplasm to the nucleus, where it binds short DNA-sequence motifs and regulates gene expression. However, how Smad1 selectively targets particular genomic regions is poorly understood. In order to understand the physical basis of the specific interaction of Smad1 with DNA and to contrast it with the highly homologous but functionally distinct Smad3 protein, the DNA-binding Mad-homology 1 (MH1) domain of Smad1 was cocrystallized with a 17-mer palindromic Smad-binding element (SBE). The extensive optimizations of the length, binding-site spacing and terminal sequences of the DNA element in combination with the other crystallization parameters necessary for obtaining diffraction-quality crystals are described here. A 2.7 Å resolution native data set was collected at the National Synchrotron Radiation Research Centre, Taiwan, from crystals grown in a solution containing 0.2 M ammonium tartrate dibasic, 20% PEG 3350, 3% 2-­propanol and 10% glycerol. The data set was indexed and merged in space group P222, with unit-cell parameters a = 73.94, b = 77.49, c = 83.78 Å, α = β = γ = 90°. The solvent content in the unit cell is consistent with the presence of two Smad1 MH1 molecules bound to the duplex DNA in the asymmetric unit. PMID:19923727

  9. N-(2-chloroethyl)-N-nitrosoureas covalently bound to nonionic and monocationic lexitropsin dipeptides. Synthesis, DNA affinity binding characteristics, and reactions with 32P-end-labeled DNA

    International Nuclear Information System (INIS)

    Church, K.M.; Wurdeman, R.L.; Zhang, Yi; Chen, Faxian; Gold, B.

    1990-01-01

    The synthesis and characterization of a series of compounds that contain an N-alkyl-N-nitrosourea functionality linked to DNA minor groove binding bi- and tripeptides (lexitropsins or information-reading peptides) based on methylpyrrole-2-carboxamide subunits are described. The lexitropsins (lex) synthesized have either a 3-(dimethylamino)propyl or propyl substituent on the carboxyl terminus. The preferred DNA affinity binding sequences of these compounds were footprinted in 32 P-end-labeled restriction fragments with methidiumpropyl-EDTA·Fe(II), and in common with other structural analogues, e.g., distamycin and netropsin, these nitrosoureas recognize A-T-rich runs. The affinity binding of the compound with the dimethylamino terminus, which is ionized at near-neutral pH, appeared stronger than that observed for the neutral dipeptide. The sequence specificity for DNA alkylation by (2-chloroethyl)nitrosourea-lex dipeptides (Cl-ENU-lex), with neutral and charged carboxyl termini, using 32 P-end-labeled restriction fragments, was determined by the conversion of the adducted sites into single-strand breaks by sequential heating at neutral pH and exposure to base. The DNA cleavage sites were visualized by polyacrylamide gel electrophoresis and autoradiography. Linking the Cl-ENU moiety to minor groove binders is a viable strategy to qualitatively and quantitatively control the delivery and release of the ultimate DNA alkylating agent in a sequence-dependent fashion

  10. DNA self-assembly on graphene surface studied by SERS mapping

    DEFF Research Database (Denmark)

    Botti, Sabina; Rufoloni, Alessandro; Laurenzi, Susanna

    2016-01-01

    The self-assembly of double-stranded DNA (dsDNA) segments on two variations of graphene surfaces having nano-platelets with different lateral sizes and thicknesses was investigated using surface enhanced Raman spectroscopy (SERS) and electrical impedance spectroscopy (EIS) techniques. Due...... nano-platelets. Results from the EIS analysis supported the SERS findings and confirmed that SERS mapping is a reliable method for a rapid monitoring of the procedures used to interface DNA with graphene surfaces. The present study, linking DNA anchoring morphology to the conductive properties of nano...

  11. Comment on “Propagation of surface waves on a semi-bounded quantum magnetized collisional plasma” [Phys. Plasmas 20, 122106 (2013)

    Energy Technology Data Exchange (ETDEWEB)

    Moradi, Afshin, E-mail: a.moradi@kut.ac.ir [Department of Engineering Physics, Kermanshah University of Technology, Kermanshah (Iran, Islamic Republic of)

    2016-04-15

    In a recent article [Niknam et al., Phys. Plasmas 20, 122106 (2013)], Niknam et al. investigated the propagation of TM surface waves on a semi-bounded quantum magnetized collisional plasma in the Faraday configuration (in this case, the magnetic field is parallel to the both of the plasma surface and direction of propagation). Here, we present a fresh look at the problem and show that TM surface waves cannot propagate on surface of the present system. We find in the Faraday configuration the surface waves acquire both TM and TE components due to the cyclotron motion of electrons. Therefore, the main result of the work by Niknam et al. is incorrect.

  12. Surface and bulk dissolution properties, and selectivity of DNA-linked nanoparticle assemblies

    NARCIS (Netherlands)

    Lukatsky, D.B.; Frenkel, D.

    2005-01-01

    Using a simple mean-field model, we analyze the surface and bulk dissolution properties of DNA-linked nanoparticle assemblies. We find that the dissolution temperature and the sharpness of the dissolution profiles increase with the grafting density of the single-stranded DNA "probes" on the surface

  13. Localized surface plasmon resonance (LSPR) study of DNA hybridization at single nanoparticle transducers

    International Nuclear Information System (INIS)

    Schneider, T.; Jahr, N.; Jatschka, J.; Csaki, A.; Stranik, O.; Fritzsche, W.

    2013-01-01

    The effect of DNA–DNA interaction on the localized surface plasmon resonance of single 80 nm gold nanoparticles is studied. Therefore, both the attachment of the capture DNA strands at the particle surface and the sequence-specific DNA binding (hybridization) of analyte DNA to the immobilized capture DNA is subject of investigations. The influence of substrate attachment chemistry, the packing density of DNA as controlled by an assisting layer of smaller molecules, and the distance as increased by a linker on the LSPR efficiency is investigated. The resulting changes in signal can be related to a higher hybridization efficiency of the analyte DNA to the immobilized capture DNA. The subsequent attachment of additional DNA strands to this system is studied, which allows for a multiple step detection of binding and an elucidation of the resulting resonance shifts. The detection limit was determined for the utilized DNA system by incubation with various concentration of analyte DNA. Although the method allows for a marker-free detection, we show that additional markers such as 20 nm gold particle labels increase the signal and thereby the sensitivity significantly. The study of resonance shift for various DNA lengths revealed that the resonance shift per base is stronger for shorter DNA molecules (20 bases) as compared to longer ones (46 bases).

  14. The persistence of human DNA in soil following surface decomposition.

    Science.gov (United States)

    Emmons, Alexandra L; DeBruyn, Jennifer M; Mundorff, Amy Z; Cobaugh, Kelly L; Cabana, Graciela S

    2017-09-01

    Though recent decades have seen a marked increase in research concerning the impact of human decomposition on the grave soil environment, the fate of human DNA in grave soil has been relatively understudied. With the purpose of supplementing the growing body of literature in forensic soil taphonomy, this study assessed the relative persistence of human DNA in soil over the course of decomposition. Endpoint PCR was used to assess the presence or absence of human nuclear and mitochondrial DNA, while qPCR was used to evaluate the quantity of human DNA recovered from the soil beneath four cadavers at the University of Tennessee's Anthropology Research Facility (ARF). Human nuclear DNA from the soil was largely unrecoverable, while human mitochondrial DNA was detectable in the soil throughout all decomposition stages. Mitochondrial DNA copy abundances were not significantly different between decomposition stages and were not significantly correlated to soil edaphic parameters tested. There was, however, a significant positive correlation between mitochondrial DNA copy abundances and the human associated bacteria, Bacteroides, as estimated by 16S rRNA gene abundances. These results show that human mitochondrial DNA can persist in grave soil and be consistently detected throughout decomposition. Copyright © 2017 The Chartered Society of Forensic Sciences. Published by Elsevier B.V. All rights reserved.

  15. Adsorption of DNA onto gold nanoparticles and graphene oxide: surface science and applications.

    Science.gov (United States)

    Liu, Juewen

    2012-08-14

    The interaction between DNA and inorganic surfaces has attracted intense research interest, as a detailed understanding of adsorption and desorption is required for DNA microarray optimization, biosensor development, and nanoparticle functionalization. One of the most commonly studied surfaces is gold due to its unique optical and electric properties. Through various surface science tools, it was found that thiolated DNA can interact with gold not only via the thiol group but also through the DNA bases. Most of the previous work has been performed with planar gold surfaces. However, knowledge gained from planar gold may not be directly applicable to gold nanoparticles (AuNPs) for several reasons. First, DNA adsorption affinity is a function of AuNP size. Second, DNA may interact with AuNPs differently due to the high curvature. Finally, the colloidal stability of AuNPs confines salt concentration, whereas there is no such limit for planar gold. In addition to gold, graphene oxide (GO) has emerged as a new material for interfacing with DNA. GO and AuNPs share many similar properties for DNA adsorption; both have negatively charged surfaces but can still strongly adsorb DNA, and both are excellent fluorescence quenchers. Similar analytical and biomedical applications have been demonstrated with these two surfaces. The nature of the attractive force however, is different for each of these. DNA adsorption on AuNPs occurs via specific chemical interactions but adsorption on GO occurs via aromatic stacking and hydrophobic interactions. Herein, we summarize the recent developments in studying non-thiolated DNA adsorption and desorption as a function of salt, pH, temperature and DNA secondary structures. Potential future directions and applications are also discussed.

  16. Crystallization and preliminary X-ray diffraction analysis of the Pax9 paired domain bound to a DC5 enhancer DNA element.

    Science.gov (United States)

    Narasimhan, Kamesh; Hilbig, Antonia; Udayasuryan, Barath; Jayabal, Sriram; Kolatkar, Prasanna R; Jauch, Ralf

    2014-10-01

    Pax genes belong to a family of metazoan transcription factors that are known to play a critical role in eye, ear, kidney and neural development. The mammalian Pax family of transcription factors is characterized by a ∼128-amino-acid DNA-binding paired domain that makes sequence-specific contacts with DNA. The diversity in Pax gene activities emerges from complex modes of interaction with enhancer regions and heterodimerization with multiple interaction partners. Based on in vitro optimal binding-site selection studies and enhancer identification assays, it has been suggested that Pax proteins may recognize and bind their target DNA elements with different binding modes/topologies, however this hypothesis has not yet been structurally explored. One of the most extensively studied DNA target elements of the Pax6 paired domain is the eye-lens specific DC5 (δ-crystallin) enhancer element. In order to shed light on Pax6-DC5 DNA interactions, the related paired-domain prototype Pax9 was crystallized with the minimal δ-crystallin DC5 enhancer element and preliminary X-ray diffraction analysis was attempted. A 3.0 Å resolution native data set was collected at the National Synchrotron Light Source (NSLS), Brookhaven from crystals grown in a solution consisting of 10%(w/v) PEG 20K, 20%(v/v) PEG 550 MME, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M NH2SO4, 0.1 M MES/imidazole pH 6.5. The data set was indexed and merged in space group C2221, with unit-cell parameters a = 75.74, b = 165.59, c = 70.14 Å, α = β = γ = 90°. The solvent content in the unit cell is consistent with the presence of one Pax9 paired domain bound to duplex DNA in the asymmetric unit.

  17. Crystallization and preliminary X-ray diffraction analysis of the Pax9 paired domain bound to a DC5 enhancer DNA element

    Science.gov (United States)

    Narasimhan, Kamesh; Hilbig, Antonia; Udayasuryan, Barath; Jayabal, Sriram; Kolatkar, Prasanna R.; Jauch, Ralf

    2014-01-01

    Pax genes belong to a family of metazoan transcription factors that are known to play a critical role in eye, ear, kidney and neural development. The mammalian Pax family of transcription factors is characterized by a ∼128-amino-acid DNA-binding paired domain that makes sequence-specific contacts with DNA. The diversity in Pax gene activities emerges from complex modes of interaction with enhancer regions and heterodimerization with multiple interaction partners. Based on in vitro optimal binding-site selection studies and enhancer identification assays, it has been suggested that Pax proteins may recognize and bind their target DNA elements with different binding modes/topologies, however this hypothesis has not yet been structurally explored. One of the most extensively studied DNA target elements of the Pax6 paired domain is the eye-lens specific DC5 (δ-crystallin) enhancer element. In order to shed light on Pax6–DC5 DNA interactions, the related paired-domain prototype Pax9 was crystallized with the minimal δ-crystallin DC5 enhancer element and preliminary X-ray diffraction analysis was attempted. A 3.0 Å resolution native data set was collected at the National Synchrotron Light Source (NSLS), Brookhaven from crystals grown in a solution consisting of 10%(w/v) PEG 20K, 20%(v/v) PEG 550 MME, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M NH2SO4, 0.1 M MES/imidazole pH 6.5. The data set was indexed and merged in space group C2221, with unit-cell parameters a = 75.74, b = 165.59, c = 70.14 Å, α = β = γ = 90°. The solvent content in the unit cell is consistent with the presence of one Pax9 paired domain bound to duplex DNA in the asymmetric unit. PMID:25286939

  18. Electron Transfer Mediator Effects in Water Oxidation Catalysis by Solution and Surface-Bound Ruthenium Bpy-Dicarboxylate Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Sheridan, Matthew V.; Sherman, Benjamin D.; Marquard, Seth L.; Fang, Zhen; Ashford, Dennis L.; Wee, Kyung-Ryang; Gold, Alexander S.; Alibabaei, Leila; Rudd, Jennifer A.; Coggins, Michael K.; Meyer, Thomas J.

    2015-11-12

    Electrocatalytic water oxidation by the catalyst, ruthenium 2,2'-bipyridine-6,6'-dicarboxylate (bda) bis-isoquinoline (isoq), [Ru(bda)(isoq)2], 1, was investigated at metal oxide electrodes surface-derivatized with electron transfer (ET) mediators. At indium-doped tin oxide (ITO) in pH 7.2 in H2PO4–/HPO42– buffers in 0.5 M NaClO4 with added acetonitrile (MeCN), the catalytic activity of 1 is enhanced by the surface-bound redox mediators [Ru (4,4'-PO3H2-bpy)(4,4'-R-bpy)2]2+ (RuPbpyR22+, R = Br, H, Me, or OMe, bpy = 2,2'-bipyridine). Rate-limiting ET between the Ru3+ form of the mediator and the RuIV(O) form in the [RuV/IV(O)]+/0 couple of 1 is observed at relatively high concentrations of HPO42– buffer base under conditions where O···O bond formation is facilitated by atom-proton transfer (APT). For the solution [Ru(bpy)3]3+/2+ mediator couple and 1 as the catalyst, catalytic currents vary systematically with the concentration of mediator and the HPO42– buffer base concentration. Electron transfer mediation of water oxidation catalysis was also investigated on nanoparticle TiO2 electrodes co-loaded with catalyst [Ru(bda)(py-4-O(CH2)3-PO3H2)2], 2, (py = pyridine) and RuPbpyR22+ (R = H, Me, or OMe) with an interplay between rate-limiting catalyst oxidation and rate-limiting O···O bond formation by APT. Lastly, the co-loaded assembly RuPbpyR22+ + 2 has been investigated in a dye-sensitized photoelectrosynthesis cell for water splitting.

  19. Direct Visualization of Dynamic Protein-DNA Interactions with a Dedicated Atomic Force Microscope

    NARCIS (Netherlands)

    van Noort, S.J.T.; van der Werf, Kees; Eker, Andre P.M.; Wyman, Claire; de Grooth, B.G.; van Hulst, N.F.; Greve, Jan

    1998-01-01

    Photolyase DNA interactions and the annealing of restriction fragment ends are directly visualized with the atomic force microscope (AFM). To be able to interact with proteins, DNA must be loosely bound to the surface. When MgCl2 is used to immobilize DNA to mica, DNA is attached to the surface at

  20. Dyes as bifunctional markers of DNA hybridization on surfaces and mutation detection.

    Science.gov (United States)

    García-Mendiola, Tania; Cerro, María Ramos; López-Moreno, José María; Pariente, Félix; Lorenzo, Encarnación

    2016-10-01

    The interaction of small molecules with DNA has found diagnostic and therapeutic applications. In this work, we propose the use of two different dyes, in particular Azure A and Safranine, as bifunctional markers of on-surface DNA hybridization and potent tools for screening of specific gene mutations directly in real DNA PCR amplicons extracted from blood cells. By combining spectroscopic and electrochemical methods we demonstrate that both dyes can interact with single and double stranded DNA to a different extent, allowing reliable hybridization detection. From these data, we have also elucidated the nature of the interaction. We conclude that the binding mode is fundamentally intercalative with an electrostatic component. The dye fluorescence allows their use as nucleic acid stains for the detection of on-surfaces DNA hybridization. Its redox activity is exploited in the development of selective electrochemical DNA biosensors. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Fabrication, characterization, and biological assessment of multilayer laminin γ2 DNA coatings on titanium surfaces

    Science.gov (United States)

    Yang, Guoli; Zhang, Jing; Dong, Wenjing; Liu, Li; Shi, Jue; Wang, Huiming

    2016-01-01

    The purpose of this work was to fabricate a multilayer laminin γ2 DNA coating on a titanium surface and evaluate its biological properties. A multilayer laminin γ2 DNA coating was fabricated on titanium using a layer-by-layer assembly technique. The rate of coating degradation was evaluated by detecting the amount of cDNA remaining. Surface analysis using X-ray photoelectron spectroscopy, atomic force microscopy, and surface contact angle measurements revealed the multilayer structure to consist of cationic lipid and confirmed that a laminin γ2 DNA layer could be fabricated on titanium via the layer-by-layer assembly process. The transfection efficiency was highest for five layers in the multilayer structure. HEK293 cells cultured on the multilayer films displayed significantly higher adhesion activity than the control group. The expression of laminin γ2 and the co-localization of integrin β4 and plectin were more obvious in HN4 cells cultured on the multilayer laminin γ2 DNA coating, while weak immunoreactivities were observed in the control group. We concluded that the DNA-loaded multilayer provided a surface with good biocompatibility and that the multilayer laminin γ2 DNA coating might be effective in improving cell adhesion and the formation of hemidesmosomes on titanium surfaces. PMID:26996815

  2. Immobilization, hybridization, and oxidation of synthetic DNA on gold surface: Electron transfer investigated by electrochemistry and scanning tunneling microscopy

    Energy Technology Data Exchange (ETDEWEB)

    McEwen, Gerald D.; Chen Fan [Biological Engineering Program, Department of Biological and Irrigation Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105 (United States); Zhou Anhong, E-mail: Anhong.Zhou@usu.edu [Biological Engineering Program, Department of Biological and Irrigation Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105 (United States)

    2009-06-08

    Fundamental understanding of interfacial electron transfer (ET) among electrolyte/DNA/solid-surface will facilitate the design for electrical detection of DNA molecules. In this report, the electron transfer characteristics of synthetic DNA (sequence from pathogenic Cryptosporidium parvum) self-assembled on a gold surface was electrochemically studied. The effects of immobilization order on the interface ET related parameters such as diffusion coefficient (D{sub 0}), surface coverage ({theta}{sub R}), and monolayer thickness (d{sub i}) were determined by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). DNA surface density ({Gamma}{sub DNA}) was determined by the integration of the charge of the electro-oxidation current peaks during the initial cyclic voltammetry scans. It was found that the DNA surface densities at different modifications followed the order: {Gamma}{sub DNA} (dsS-DNA/Au) > {Gamma}{sub DNA} (MCH/dsS-DNA/Au) > {Gamma}{sub DNA} (dsS-DNA/MCH/Au). It was also revealed that the electro-oxidation of the DNA modified gold surface would involve the oxidation of nucleotides (guanine and adenine) with a 5.51 electron transfer mechanism and the oxidative desorption of DNA and MCH molecules by a 3 electron transfer mechanism. STM topography and current image analysis indicated that the surface conductivity after each surface modification followed the order: dsS-DNA/Au < MCH/dsS-DNA/Au < oxidized MCH/dsS-DNA/Au < Hoechst/oxidized MCH/dsS-DNA/Au. The results from this study suggested a combination of variations in immobilization order may provide an alternative approach for the optimization of DNA hybridization and the further development for electrical detection of DNA.

  3. DNA origami as biocompatible surface to match single-molecule and ensemble experiments

    Science.gov (United States)

    Gietl, Andreas; Holzmeister, Phil; Grohmann, Dina; Tinnefeld, Philip

    2012-01-01

    Single-molecule experiments on immobilized molecules allow unique insights into the dynamics of molecular machines and enzymes as well as their interactions. The immobilization, however, can invoke perturbation to the activity of biomolecules causing incongruities between single molecule and ensemble measurements. Here we introduce the recently developed DNA origami as a platform to transfer ensemble assays to the immobilized single molecule level without changing the nano-environment of the biomolecules. The idea is a stepwise transfer of common functional assays first to the surface of a DNA origami, which can be checked at the ensemble level, and then to the microscope glass slide for single-molecule inquiry using the DNA origami as a transfer platform. We studied the structural flexibility of a DNA Holliday junction and the TATA-binding protein (TBP)-induced bending of DNA both on freely diffusing molecules and attached to the origami structure by fluorescence resonance energy transfer. This resulted in highly congruent data sets demonstrating that the DNA origami does not influence the functionality of the biomolecule. Single-molecule data collected from surface-immobilized biomolecule-loaded DNA origami are in very good agreement with data from solution measurements supporting the fact that the DNA origami can be used as biocompatible surface in many fluorescence-based measurements. PMID:22523083

  4. DNA motion induced by electrokinetic flow near an Au coated nanopore surface as voltage controlled gate.

    Science.gov (United States)

    Sugimoto, Manabu; Kato, Yuta; Ishida, Kentaro; Hyun, Changbae; Li, Jiali; Mitsui, Toshiyuki

    2015-02-13

    We used fluorescence microscopy to investigate the diffusion and drift motion of λ DNA molecules on an Au-coated membrane surface near nanopores, prior to their translocation through solid-state nanopores. With the capability of controlling electric potential at the Au surface as a gate voltage, Vgate, the motions of DNA molecules, which are presumably generated by electrokinetic flow, vary dramatically near the nanopores in our observations. We carefully investigate these DNA motions with different values of Vgate in order to alter the densities and polarities of the counterions, which are expected to change the flow speed or direction, respectively. Depending on Vgate, our observations have revealed the critical distance from a nanopore for DNA molecules to be attracted or repelled-DNA's anisotropic and unsteady drifting motions and accumulations of DNA molecules near the nanopore entrance. Further finite element method (FEM) numerical simulations indicate that the electrokinetic flow could qualitatively explain these unusual DNA motions near metal-collated gated nanopores. Finally, we demonstrate the possibility of controlling the speed and direction of DNA motion near or through a nanopore, as in the case of recapturing a single DNA molecule multiple times with alternating current voltages on the Vgate.

  5. Bounding the $\

    CERN Document Server

    Gutiérrez-Rodríguez, A

    2003-01-01

    A bound on the nu /sup tau / magnetic moment is calculated through the reaction e/sup +/e/sup -/ to nu nu gamma at the Z/sub 1/-pole, and in the framework of a left-right symmetric model at LEP energies. We find that the bound is almost independent of the mixing angle phi of the model in the allowed experimental range for this parameter. (31 refs).

  6. A study of double stranded DNA adsorption on aluminum surface by means of electrochemical impedance spectroscopy.

    Science.gov (United States)

    Heli, H

    2014-04-01

    Immobilization of DNA on the solid surfaces is one of the goals in bio- and nano-technologies. Adsorption of double stranded DNA on the surface of aluminum was electrochemically studied by means of impedance spectroscopy. Nyquist diagram of aluminum in a tris (hydroxymethyl) ammoniummethane-HCl (Tris-HCl) buffer solution, pH 7.4 consisted of two overlapped capacitive semicircles. The high-frequency semicircle was related to the passivity of Cl(-)-containing aluminum species in the oxide layer, and low-frequency semicircle was attributed to metal dissolution. When DNA was added to the Tris-HCl buffer solution, Nyquist diagrams represented an inductive loop at low frequencies due to the adsorption of DNA on the pre-covered aluminum surface by hydroxy-contained species. The DNA adsorption on the aluminum surface was also confirmed by X-ray photoelectron spectroscopy. Open circuit potential variation with time also indicated the chemical adsorption of DNA on the aluminum surface. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Cloning of a cDNA encoding a surface antigen of Schistosoma mansoni schistosomula recognized by sera of vassinated mice

    International Nuclear Information System (INIS)

    Dalton, J.P.; Tom, T.D.; Strand, M.

    1987-01-01

    Spleen cells of mice vaccinated with radiation-attenuated Schistosoma mansoni cercariae were used to produce monoclonal antibodies directed against newly transformed schistosomular surface antigens. One of these monoclonal antibodies recognized a polypeptide of 18 kDa. Binding was measured by radioimmunoassay. This glycoprotein was purified by monoclonal antibody immunoaffinity chromatography and a polyclonal antiserum was prepared against it. Immunofluorescence assays showed that the polyclonal antiserum bound to the surface of newly transformed schistosomula and lung-stage organisms but not to the surface of liver-stage and adult worms. Using this polyclonal antiserum we isolated recombinant clones from an adult worm cDNA expression library constructed in λgt11. Clone 654.2 contained an insert of 0.52 kilobase and hybridized to a 1.2-kilobase mRNA species from adult worms. Most importantly, clone 654.2 produced a fusion protein of 125 kDa that was reactive with sera of vaccinated mice that are capable of transferring resistance. This result encourages future vaccination trials with the fusion protein

  8. Surface-bound capsular polysaccharide of type Ia group B Streptococcus mediates C1 binding and activation of the classic complement pathway

    International Nuclear Information System (INIS)

    Levy, N.J.; Kasper, D.L.

    1986-01-01

    The role of surface-bound type Ia group B Streptococcus (GBS) capsular polysaccharide in anti-body-independent binding of C1 and activation of the classic component pathway was investigated. In a radiolabeled bacterial-polymorphonuclear leukocyte (PMN) association assay, a measure of bacterial opsonization, preincubation of 3 H-type Ia GBS with purified F(ab') 2 to the organism blocked the association of the bacteria with PMN', and the inhibitory effect was dose dependent. The specificity of F(ab') 2 blocking was shown after adsorption of F(ab') 2 with type Ia polysaccharide-sensitized erythrocytes. Polysaccharide-adsorbed F(ab') 2 had a 70% decrease in ability to block the association of bacteria with PMN. Neuraminidase digestion removed 80% of the terminal sialic acid residues from the native polysaccharide. These neuraminidase-digested organisms had a 72% decrease in binding and transfer of purified C1 compared with non-enzyme-treated organisms. Type Ia capsular polysaccharide bound to sheep erythrocytes promoted classic complement pathway-mediated hemolysis of the cells. The role of C1 inhibitor (INH) in modulation of C1 activation by the organisms was investigated. The possibility existed that the C1 INH could be bound by the bacteria, allowing C1 activation to occur in the fluid phase. The inhibitor was purified from human serum, and its activity was measured before and after incubation with type Ia GBS. The organisms had no effect on C1 INH activity. Thus surface-bound capsular polysacchardie of type Ia GBS mediates C1 binding and classic pathway activation, and this does not involve the C1 INH

  9. Hybrid surface platform for the simultaneous detection of proteins and DNA using a surface plasmon resonance (SPR) imaging sensor

    Czech Academy of Sciences Publication Activity Database

    Homola, Jiří; Piliarik, Marek; Ladd, J.; Taylor, A.; Shaoyi, J.

    2008-01-01

    Roč. 80, č. 11 (2008), s. 4231-4236 ISSN 0003-2700 R&D Projects: GA AV ČR KAN200670701 Institutional research plan: CEZ:AV0Z20670512 Keywords : Surface plasmon resonance imaging * DNA -directed immobilization * protein array Subject RIV: JB - Sensors, Measurment, Regulation Impact factor: 5.712, year: 2008

  10. Rapid outer-surface protein C DNA tattoo vaccination protects against Borrelia afzelii infection.

    Science.gov (United States)

    Wagemakers, A; Mason, L M K; Oei, A; de Wever, B; van der Poll, T; Bins, A D; Hovius, J W R

    2014-12-01

    Borrelia afzelii is the predominant Borrelia species causing Lyme borreliosis in Europe. Currently there is no human vaccine against Lyme borreliosis, and most research focuses on recombinant protein vaccines against Borrelia burgdorferi sensu stricto. DNA tattooing is a novel vaccination method that can be applied in a rapid vaccination schedule. We vaccinated C3H/HeN mice with B. afzelii strain PKo OspC (outer-surface protein C) using a codon-optimized DNA vaccine tattoo and compared this with recombinant protein vaccination in a 0-2-4 week vaccination schedule. We also assessed protection by DNA tattoo in a 0-3-6 day schedule. DNA tattoo and recombinant OspC vaccination induced comparable total IgG responses, with a lower IgG1/IgG2a ratio after DNA tattoo. Two weeks after syringe-challenge with 5 × 10(5) B. afzelii spirochetes most vaccinated mice had negative B. afzelii tissue DNA loads and all were culture negative. Furthermore, DNA tattoo vaccination in a 0-3-6 day regimen also resulted in negative Borrelia loads and cultures after challenge. To conclude, DNA vaccination by tattoo was fully protective against B. afzelii challenge in mice in a rapid vaccination protocol, and induces a favorable humoral immunity compared to recombinant protein vaccination. Rapid DNA tattoo is a promising vaccination strategy against spirochetes.

  11. Self-assembling of large ordered DNA arrays using superhydrophobic patterned surfaces

    International Nuclear Information System (INIS)

    Ciasca, G; Papi, M; Chiarpotto, M; Palmieri, V; De Spirito, M; Businaro, L; Notargiacomo, A; De Ninno, A; Carta, S; Giovine, E; Gerardino, A

    2013-01-01

    In this paper we present a simple and robust method to realize highly ordered arrays of stretched and suspended DNA molecules over the millimeter length scale. To this end we used an ad hoc designed superhydrophobic surface made of high aspect-ratio silicon pillars, where we deposited a droplet containing genomic DNA. A precise positioning of DNA strands was achieved by shaping the silicon pillars so that sharpened features resembling tips were included. Such features allowed us to accurately control the droplet de-wetting dynamics, pinning DNA strands in a well-defined position above pillars. The proposed technique has the potential to positively impact on the development of novel DNA chips for genetic analysis. (paper)

  12. Surface-enhanced Raman spectroscopy of DNA bases

    NARCIS (Netherlands)

    Otto, Cornelis; van den Tweel, T.J.J.; de Mul, F.F.M.; Greve, Jan

    1986-01-01

    A Raman microprobe has been used to measure the surface-enhanced Raman spectra of adenine, guanine, cytosine and thymine. Comparison of the SERS spectrum with solution spectra shows that some line positions are not influenced by the adsorption process while others show large shifts. In the SERS

  13. Evaluation of Skin Surface as an Alternative Source of Reference DNA Samples: A Pilot Study.

    Science.gov (United States)

    Albujja, Mohammed H; Bin Dukhyil, Abdul Aziz; Chaudhary, Abdul Rauf; Kassab, Ahmed Ch; Refaat, Ahmed M; Babu, Saranya Ramesh; Okla, Mohammad K; Kumar, Sachil

    2018-01-01

    An acceptable area for collecting DNA reference sample is a part of the forensic DNA analysis development. The aim of this study was to evaluate skin surface cells (SSC) as an alternate source of reference DNA sample. From each volunteer (n = 10), six samples from skin surface areas (forearm and fingertips) and two traditional samples (blood and buccal cells) were collected. Genomic DNA was extracted and quantified then genotyped using standard techniques. The highest DNA concentration of SSC samples was collected using the tape/forearm method of collection (2.1 ng/μL). Cotton swabs moistened with ethanol yielded higher quantities of DNA than swabs moistened with salicylic acid, and it gave the highest percentage of full STR profiles (97%). This study supports the use of SSC as a noninvasive sampling technique and as a extremely useful source of DNA reference samples among certain cultures where the use of buccal swabs can be considered socially unacceptable. © 2017 American Academy of Forensic Sciences.

  14. The effects of intracrystalline and surface-bound proteins on the attachment of calcium oxalate monohydrate crystals to renal cells in undiluted human urine.

    Science.gov (United States)

    Grover, Phulwinder K; Thurgood, Lauren A; Wang, Tingting; Ryall, Rosemary L

    2010-03-01

    To compare the binding to Madin-Darby canine kidney (MDCK)-II cells of: (i) inorganic calcium oxalate monohydrate (iCOM) crystals and COM crystals precipitated from urine containing different concentrations of protein; and (ii) urinary COM crystals containing intracrystalline and intracrystalline + surface-bound protein. Urinary COM crystals were generated in sieved (sCOM), centrifuged and filtered (cfCOM), and ultrafiltered (ufCOM) portions of a pooled human urine and their adhesion to MDCK-II cells was compared using six different ultrafiltered urine samples as the binding medium. Crystal matrix extract (CME) was prepared by demineralizing calcium oxalate crystals precipitated from human urine and used to prepare COM crystals with intracrystalline, and intracrystalline + surface-bound CME at protein concentrations of 0, 0.05, 0.1, 0.5 and 5.0 mg/L. The amount of protein associated with the crystals was qualitatively assessed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and Western blotting, using prothrombin fragment 1 (PTF1) as a marker. Protein concentration was determined in sieved, centrifuged and filtered, and ultrafiltered fractions of 10 additional urine samples. The median crystal attachment in the six urine types decreased in the order iCOM > ufCOM > cfCOM = sCOM, in inverse proportion to the concentration of protein in the solution or urine from which they were precipitated. sCOM and cfCOM crystals bound approximately 23% less than iCOM crystals. The attachment of COM crystals generated in the presence of increasing concentrations of CME proteins was unaffected up to a concentration of 5 mg/L, but binding of crystals containing the same concentrations of intracrystalline + surface-bound proteins decreased proportionally at protein concentrations from 0 to 5.0 mg/L. Inorganic COM crystals bind significantly more strongly to MDCK-II cells than urinary crystals precipitated from sieved, centrifuged and filtered, and ultrafiltered urine

  15. Efficient self-assembly of DNA-functionalized fluorophores and gold nanoparticles with DNA functionalized silicon surfaces: the effect of oligomer spacers

    Science.gov (United States)

    Milton, James A.; Patole, Samson; Yin, Huabing; Xiao, Qiang; Brown, Tom; Melvin, Tracy

    2013-01-01

    Although strategies for the immobilization of DNA oligonucleotides onto surfaces for bioanalytical and top-down bio-inspired nanobiofabrication approaches are well developed, the effect of introducing spacer molecules between the surface and the DNA oligonucleotide for the hybridization of nanoparticle–DNA conjugates has not been previously assessed in a quantitative manner. The hybridization efficiency of DNA oligonucleotides end-labelled with gold nanoparticles (1.4 or 10 nm diameter) with DNA sequences conjugated to silicon surfaces via hexaethylene glycol phosphate diester oligomer spacers (0, 1, 2, 6 oligomers) was found to be independent of spacer length. To quantify both the density of DNA strands attached to the surfaces and hybridization with the surface-attached DNA, new methodologies have been developed. Firstly, a simple approach based on fluorescence has been developed for determination of the immobilization density of DNA oligonucleotides. Secondly, an approach using mass spectrometry has been created to establish (i) the mean number of DNA oligonucleotides attached to the gold nanoparticles and (ii) the hybridization density of nanoparticle–oligonucleotide conjugates with the silicon surface–attached complementary sequence. These methods and results will be useful for application with nanosensors, the self-assembly of nanoelectronic devices and the attachment of nanoparticles to biomolecules for single-molecule biophysical studies. PMID:23361467

  16. Structural Changes of Zn(IIbleomycin Complexes When Bound to DNA Hairpins Containing the 5′-GT-3′ and 5′-GC-3′ Binding Sites, Studied through NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Shelby E. Follett

    2017-12-01

    Full Text Available We have previously investigated the diverse levels of disruption caused by Zn(IIBLMs with different C-termini to DNA hairpins containing 5′-GC-3′ and 5′-GT-3′ binding sites. The results of this investigation indicated that both the DNA-binding site and the bleomycin C-termini have an impact on the final conformation of the aforementioned hairpins in the drug-target complexes, as suggested by the different sets of intramolecular NOEs displayed by both oligonucleotides when bound to each Zn(IIBLM. The NMR signals elicited by 1H nuclei in the oligonucleotide bases and sugar moieties were also affected differently (shifted upfield or downfield in various patterns depending on the BLM C-termini and the binding site in the oligonucleotides. The overall conclusion derived from the precedent research is that the spatial conformation of target DNA segments in DNA-Zn(IIBLM complexes could be forged by interactions between drug and DNA that are guided by the DNA binding site and the BLM C-termini. The present study focuses on the structural alterations exhibited by Zn(IIbleomycin-A2, -B2, -A5 and Zn(IIpeplomycin molecules upon binding to the previously studied hairpins. Our main goal is to determine if different spatial conformations of the drugs in their DNA-bound forms are found in drug-DNA complexes that differ in the oligonucleotide binding site and BLM C-termini. Evidence that suggest that each Zn(IIbleomycin is structurally affected depending these two factors, as indicated by different sets of intramolecular NOE connectivities between drug protons and diverse patterns of shifting of their 1H-NMR signals, is provided.

  17. A Simple, Cleated DNA Walker That Hangs on to Surfaces.

    Science.gov (United States)

    Jung, Cheulhee; Allen, Peter B; Ellington, Andrew D

    2017-08-22

    We designed and demonstrated a single-legged or unipedal walker that has a "cleat" that allows it to persistently associate with a track and make autonomous decisions about movement. The walker is highly processive over long periods of time, as shown by its movement over a microparticle surface suffused with substrate. The simple design can be readily optimized on the basis of simple energetic considerations. The walker can be used for signal amplification and should prove especially valuable for programming amorphous computations within chemical reaction networks.

  18. Molecular dynamics simulations of the DNA interaction with metallic nanoparticles and TiO2 surfaces

    International Nuclear Information System (INIS)

    Kholmurodov, Kh.T.; Krasavin, E.A.; Dushanov, E.B.; Hassan, H.K.; Galal, A.; ElHabashy, H.A.; Sweilam, N.H.; Yasuoka, K.

    2013-01-01

    The understanding of the mechanism of DNA interactions and binding with metallic nanoparticles (NPs) and surfaces represents a great interest in today's medicine applications due to diagnostic and treatment of oncology diseases. Recent experimental and simulation studies involve the DNA interaction with highly localized proton beams or metallic NPs (such as Ag, Au, etc.), aimed at targeted cancer therapy through the injection of metal micro- or nanoparticles into the tumor tissue with consequent local microwave or laser heating. The effects of mutational structure changes in DNA and protein structures could result in destroying of native chemical (hydrogen) bonds or, on the contrary, creating of new bonds that do not normally exist there. The cause of such changes might be the alteration of one or several nucleotides (in DNA) or the substitution of specific amino acid residues (in proteins) that can lead to the essential structural destabilization or unfolding. At the atomic or molecular level, the replacement of one nucleotide by another (in DNA double helices) or replacement of one amino acid residue by another (in proteins) cause essential modifications of the molecular force fields of the environment that break locally important hydrogen bonds underlying the structural stability of the biological molecules. In this work, the molecular dynamics(MD) simulations were performed for four DNA models and the flexibilities of the purine and pyrimidine nucleotides during the interaction process with the metallic NPs and TiO 2 surface were clarified

  19. The Spatiotemporal Oscillations of Order Parameter for Isothermal Model of the Surface-Directed Spinodal Decomposition in Bounded Binary Mixtures

    Directory of Open Access Journals (Sweden)

    Igor B. Krasnyuk

    2009-01-01

    Full Text Available The asymptotical behavior of order parameter in confined binary mixture is considered in one-dimensional geometry. The interaction between bulk and surface forces in the mixture is investigated. Its established conditions are when the bulk spinodal decomposition may be ignored and when the main role in the process of formation of the oscillating asymptotic periodic spatiotemporal structures plays the surface-directed spinodal decomposition which is modelled by nonlinear dynamical boundary conditions.

  20. Adsorption and combing of DNA on HOPG surfaces of bulk crystals and nanosheets: application to the bridging of DNA between HOPG/Si heterostructures

    International Nuclear Information System (INIS)

    Rose, F; Martin, P; Fujita, H; Kawakatsu, H

    2006-01-01

    Controlled and reproducible combing of λ-phage DNA molecules can be realized in predetermined orientations on highly oriented pyrolitic graphite (HOPG) surfaces. Observations by atomic force microscopy (AFM) show that DNA adsorption onto HOPG surfaces leads to different hierarchical organizations such as balls, networks, films, and fractal structures. HOPG nanosheets (3.5-100 nm thick) were created by simply rubbing a HOPG crystal onto a silicon oxide surface, and then patterned with a focused ion beam (FIB) to fabricate HOPG/Si heterostructures (arrays of silicon micropillars and microtracks decorated on their top surface with HOPG nanosheets). The surface reactivity of HOPG nanosheets toward DNA is found to be the same as of HOPG bulk crystals. Finally, combing is used to attach and suspend bundles of approximately 20-50 DNA molecules between HOPG/Si heterostructures

  1. A Polymethyl Methacrylate-Based Acrylic Dental Resin Surface Bound with a Photoreactive Polymer Inhibits Accumulation of Bacterial Plaque.

    Science.gov (United States)

    Fukunishi, Miya; Inoue, Yuuki; Morisaki, Hirobumi; Kuwata, Hirotaka; Ishihara, Kazuhiko; Baba, Kazuyoshi

    The aim of this study was to examine the ability of a poly(2-methacryloyloxyethyl phosphorylcholine-co-n-butylmethacrylate-co-2-methacryloyloxyethyloxy-p-azidobenzoate) (PMBPAz) coating on polymethyl methacrylate (PMMA)-based dental resin to inhibit bacterial plaque formation, as well as the polymer's durability against water soaking and chemical exposure. Successful application of PMBPAz on PMMA surfaces was confirmed by x-ray photoelectron spectroscopy (XPS) and measuring the static air contact angle in water. The anti-adhesive effects to bacterial plaque were evaluated using Streptococcus mutans biofilm formation assay. The mechanical and chemical durabilities of the PMBPAz coating on the PMMA surfaces were examined using soaking and immersion tests, respectively. XPS signals for phosphorus and nitrogen atoms and hydrophilic status on PMMA surfaces treated with PMBPAz were observed, indicating the presence of the polymer on the substrates. The treated PMMA surfaces showed significant inhibition of S mutans biofilm formation compared to untreated surfaces. The PMBPAz coating was preserved after water soaking and chemical exposure. In addition, water soaking did not decrease the ability of treated PMMA to inhibit biofilm formation compared to treated PMMA specimens not subjected to water soaking. This study suggests that PMBPAz coating may represent a useful modification to PMMA surfaces for inhibiting denture plaque accumulation.

  2. Impact of Donor Age, Gender and Handling Time on the DNA Concentration Left on Different Surfaces

    Directory of Open Access Journals (Sweden)

    Branka Gršković

    2014-09-01

    Full Text Available Background: We analyzed the correlation between several factors (donor age and gender, and handling time and trace DNA concentration that participants left on different surfaces (paper, plastic, plastic coated metal while holding items in their hands or rubbing them with their fingers, their palms, and the side of the palm of the dominant hand. Material and Methods: Sixty participants took part in the study. Items were swabbed with a moistened cotton swab. DNA was isolated using the Chelex procedure and quantified by real-time PCR. Results: We found that DNA concentration transferred to an item was independent of the handling time. On the contrary, it was dependent on the item’s texture; the greatest concentration was left on plastic coated metal (PCM and the least on paper. The greatest concentration of trace DNA was left by participants from 35 to 44 years of age. Results of the study showed that men deposit a higher DNA concentration than do women. Conclusion: Item texture, donor age, and gender influence trace DNA concentration. Further investigations are necessary to fully understand the process of DNA transfer from donors to handled items.

  3. Anatomy of the primase-alpha DNA polymerase reaction accomplished by nucleoprotein complexes harboring an exrachromosomal DNA identical with avian myeloblastosis virus core-bound DNA: influencing by carbonyldiphosphonate, mimosine and butylphenil deoxyguanosine-5-triphosphate

    Czech Academy of Sciences Publication Activity Database

    Říman, Josef

    2001-01-01

    Roč. 45, č. 1 (2001), s. 109-124 ISSN 0001-723X Institutional research plan: CEZ:AV0Z5052915 Keywords : primase * alpha DNA-polymerase * enzyme complex Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.644, year: 2001

  4. Silanization of quartz, silicon and mica surfaces with light-driven molecular motors : construction of surface-bound photo-active nanolayers

    NARCIS (Netherlands)

    London, Gabor; Carroll, Gregory T.; Feringa, Ben L.

    2013-01-01

    The attachment of molecular rotary motors containing triethoxysilane functional groups to quartz, silicon and mica surfaces is described. Motors containing silane coupling agents in their structure form stable molecular layers on quartz and silicon surfaces. Motors attached to these surfaces were

  5. Acid-base properties and the chemical imaging of surface-bound functional groups studied with scanning force microscopy

    NARCIS (Netherlands)

    van der Vegte, E.W.; Hadziioannou, G

    1997-01-01

    In this paper we present a scanning force microscopy (SFM) study on electrostatic and hydrogen-bonding interactions between chemically modified SFM probes and surface functional groups. pH-dependent adhesion force measurements in aqueous media between various ionizable functional groups showed a

  6. Controlled amino-functionalization by electrochemical reduction of bromo and nitro azobenzene layers bound to Si(111) surfaces

    NARCIS (Netherlands)

    Ullien, D.; Thüne, P.C.; Jager, W.F.; Sudhölter, E.J.R.; De Smet, L.C.P.M.

    2014-01-01

    4-Nitrobenzenediazonium (4-NBD) and 4-bromobenzenediazonium (4-BBD) salts were grafted electrochemically onto H-terminated, p-doped silicon (Si) surfaces. Atomic force microscopy (AFM) and ellipsometry experiments clearly showed layer thicknesses of 2–7 nm, which indicate multilayer formation.

  7. Molecular-scale model for the mass density of electrolyte solutions bound by clay surfaces: application to bentonites.

    Science.gov (United States)

    Gonçalvès, J; Rousseau-Gueutin, P

    2008-04-15

    A model to simulate the density of solutions adsorbed onto clay mineral surfaces is proposed. In this model, the alteration of the ionic distribution caused by the electric field associated with the surface charge of clay platelets is accounted for using an electrical triple-layer model with an overlapping diffuse layer. The combined effects of ion hydration and the electric field on the structure of water are introduced through their influence on the partial molar volume of water. This model, applied to Na-montmorillonite, simulates the distribution of the interplatelet solution density as a function of the distance to the mineral surface. High densities in the direct vicinity of the surface and slightly lower density (a few percent) than the normal density in the diffuse layer are obtained. These results show good consistency with the available data on bentonite and with the densities that can be inferred from molecular dynamics simulations. This model shows that the interplatelet distance plays an important role in the distribution of the mass density of the solution in the pore space of clay rocks.

  8. Photogeneration of singlet oxygen by the phenothiazine derivatives covalently bound to the surface-modified glassy carbon

    Energy Technology Data Exchange (ETDEWEB)

    Blacha-Grzechnik, Agata, E-mail: agata.blacha@polsl.pl [Faculty of Chemistry, Silesian University of Technology, Strzody 9, 44-100 Gliwice (Poland); Piwowar, Katarzyna; Krukiewicz, Katarzyna [Faculty of Chemistry, Silesian University of Technology, Strzody 9, 44-100 Gliwice (Poland); Koscielniak, Piotr; Szuber, Jacek [Institute of Electronics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice (Poland); Zak, Jerzy K. [Faculty of Chemistry, Silesian University of Technology, Strzody 9, 44-100 Gliwice (Poland)

    2016-05-15

    Highlights: • The selected group of four NH{sub 2}-derivatives of phenothiazine was grafted to Glassy Carbon (GC) surface. • The grafted phenothiazines are able to generate {sup 1}O{sub 2} when activated by the radiation. • Such modified solid surfaces may find their application in the wastewater treatment. - Abstract: The selected group of four amine-derivatives of phenothiazine was covalently grafted to the glassy carbon surface in the four-step procedure consisting of the electrochemical reduction of the diazonium salt followed by the electrochemical and chemical post-modification steps. The proposed strategy involves the bonding of linker molecule to which the photosensitizer is attached. The synthesized organic layers were characterized by means of cyclic voltammetry, XPS and Raman Spectroscopy. It was shown that the phenothiazines immobilized via proposed strategy retain their photochemical properties and are able to generate {sup 1}O{sub 2} when activated by the laser radiation. The effectiveness of in situ singlet oxygen generation by those new solid photoactive materials was determined by means of UVVis spectroscopy. The reported, covalently modified solid surfaces may find their application as the singlet oxygen photogenerators in the fine chemicals’ synthesis or in the wastewater treatment.

  9. Characterization of grafting density and binding efficiency of DNA and proteins on gold surfaces.

    Science.gov (United States)

    Castelino, Kenneth; Kannan, Balaji; Majumdar, Arun

    2005-03-01

    The surface grafting density of biomolecules is an important factor for quantitative assays using a wide range of biological sensors. We use a fluorescent measurement technique to characterize the immobilization density of thiolated probe DNA on gold and hybridization efficiency of target DNA as a function of oligonucleotide length and salt concentration. The results indicate the dominance of osmotic and hydration forces in different regimes of salt concentration, which was used to validate previous simulations and to optimize the performance of surface-stress based microcantilever biosensors. The difference in hybridization density between complementary and mismatched target sequences was also measured to understand the response of these sensors in base-pair mismatch detection experiments. Finally, two different techniques for immobilizing proteins on gold were considered and the surface densities obtained in both cases were compared.

  10. Interaction of metal ions and DNA films on gold surfaces: an electrochemical impedance study.

    Science.gov (United States)

    Bin, Xiaomin; Kraatz, Heinz-Bernhard

    2009-07-01

    Electrochemical impedance spectroscopy (EIS) has been used to investigate the effects of a number of metal ions with DNA films on gold surfaces exploiting [Fe(CN)6](3-/4-) as a solution-based redox probe. Alkaline earth metal ions Mg2+, Ca2+, trivalent Al3+, La3+ and divalent transition metal ions Ni2+, Cu2+, Cd2+ and Hg2+ have been selected in this study and the results are compared with previous studies on the effects of Zn2+ on the EIS of DNA films. All experimental results were evaluated with the help of equivalent circuits which allowed the extraction of resistive and capacitive components. For all metal ions studied here, addition of the metal ions causes a decrease in the charge transfer resistance. The difference of charge transfer resistance (DeltaR(ct)) of ds-DNA films in the presence and absence of the various metal ions is different and particular to any given metal ion. In addition, we studied the EIS of ds-DNA films containing a single A-C mismatch in the presence and absence of Ca2+, Zn2+, Cd2+ and Hg2+. DeltaR(ct) values for ds-DNA films with a single A-C mismatch is smaller than those of fully matched ds-DNA films.

  11. Enhanced immunogenicity of DNA fusion vaccine encoding secreted hepatitis B surface antigen and chemokine RANTES

    International Nuclear Information System (INIS)

    Kim, Seung Jo; Suh, Dongchul; Park, Sang Eun; Park, Jeong-Sook; Byun, Hyang-Min; Lee, Chan; Lee, Sun Young; Kim, Inho; Oh, Yu-Kyoung

    2003-01-01

    To increase the potency of DNA vaccines, we constructed genetic fusion vaccines encoding antigen, secretion signal, and/or chemokine RANTES. The DNA vaccines encoding secreted hepatitis B surface antigen (HBsAg) were constructed by inserting HBsAg gene into an expression vector with an endoplasmic reticulum (ER)-targeting secretory signal sequence. The plasmid encoding secretory HBsAg (pER/HBs) was fused to cDNA of RANTES, generating pER/HBs/R. For comparison, HBsAg genes were cloned into pVAX1 vector with no signal sequence (pHBs), and further linked to the N-terminus of RANTES (pHBs/R). Immunofluorescence study showed the cytoplasmic localization of HBsAg protein expressed from pHBs and pHBs/R, but not from pER/HBs and pER/HBs/R at 48 h after transfection. In mice, RANTES-fused DNA vaccines more effectively elicited the levels of HBsAg-specific IgG antibodies than pHBs. All the DNA vaccines induced higher levels of IgG 2a rather than IgG 1 antibodies. Of RANTES-fused vaccines, pER/HBs/R encoding the secreted fusion protein revealed much higher humoral and CD8 + T cell-stimulating responses compared to pHBs/R. These results suggest that the immunogenicity of DNA vaccines could be enhanced by genetic fusion to a secretory signal peptide sequence and RANTES

  12. Surface-assisted large-scale ordering of DNA origami tiles.

    Science.gov (United States)

    Aghebat Rafat, Ali; Pirzer, Tobias; Scheible, Max B; Kostina, Anna; Simmel, Friedrich C

    2014-07-14

    The arrangement of DNA-based nanostructures into extended higher order assemblies is an important step towards their utilization as functional molecular materials. We herein demonstrate that by electrostatically controlling the adhesion and mobility of DNA origami structures on mica surfaces by the simple addition of monovalent cations, large ordered 2D arrays of origami tiles can be generated. The lattices can be formed either by close-packing of symmetric, non-interacting DNA origami structures, or by utilizing blunt-end stacking interactions between the origami units. The resulting crystalline lattices can be readily utilized as templates for the ordered arrangement of proteins. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Mycobacterium tuberculosis DNA detection using surface plasmon resonance modulated by telecommunication wavelength.

    Science.gov (United States)

    Hsu, Shih-Hsiang; Lin, Yan-Yu; Lu, Shao-Hsi; Tsai, I-Fang; Lu, Yen-Ta; Ho, Hsin-Tsung

    2013-12-27

    A surface plasmon resonance sensor for Mycobacterium tuberculosis (MTB) deoxyribonucleic acid (DNA) is developed using repeatable telecommunication wavelength modulation based on optical fiber communications laser wavelength and stability. MTB DNA concentrations of 1 μg/mL and 10 μg/mL were successfully demonstrated to have the same spectral half-width in the dip for optimum coupling. The sensitivity was shown to be -0.087 dB/(μg/mL) at all applied telecommunication wavelengths and the highest sensitivity achieved was 115 ng/mL without thiolated DNA immobilization onto a gold plate, which is better than the sensor limit of 400 ng/mL possible with commercial biosensor equipment.

  14. Nanoparticular surface-bound PCBs, PCDDs, and PCDFs-a novel class of potentially higher toxic POPs.

    Science.gov (United States)

    Schön, Peter; Ctistis, Georgios; Bakker, Wouter; Luthe, Gregor

    2017-05-01

    In a previous study, Env Sci Poll Res:1-7, 2015 showed that polychlorinated biphenyls (PCBs), polychlorinated dibenzo dioxins (PCDDs), and polychlorinated dibenzo furanes (PCDFs) are found in commercially available (nano) particular titanium dioxide as a result of the fabrication. Here, we give a brief perspective and reason the toxicity of these new classes of persistent organic pollutants (POPs) by reviewing also their nanoparticular properties, such as surface-to-volume ratio, photocatalytic activity, polarity shifts, and stealth effect. These insights point towards a new class of POPs and toxicologic effects, which are related to the size but not a result of nanotechnology itself. We pave the way to the understanding of until now unresolved very complex phenomena, such as the indoor exposure, formation, and transformation of POP and sick-building syndrome. This is a fundamental message for nanotoxicology and kinetics and should be taken into account when determining the toxicity of nanomaterials and POPs separately and as a combination.

  15. Controlled amino-functionalization by electrochemical reduction of bromo and nitro azobenzene layers bound to Si(111) surfaces.

    Science.gov (United States)

    Ullien, Daniela; Thüne, Peter C; Jager, Wolter F; Sudhölter, Ernst J R; de Smet, Louis C P M

    2014-09-28

    4-Nitrobenzenediazonium (4-NBD) and 4-bromobenzenediazonium (4-BBD) salts were grafted electrochemically onto H-terminated, p-doped silicon (Si) surfaces. Atomic force microscopy (AFM) and ellipsometry experiments clearly showed layer thicknesses of 2-7 nm, which indicate multilayer formation. Decreasing the diazonium salt concentration and the reaction time resulted in a smaller layer thickness, but did not prevent the formation of multilayers. It was demonstrated, mainly by X-ray photoelectron spectroscopy (XPS), that the diazonium salts not only react with the H-terminated Si surface, but also with electrografted phenyl groups via azo-bond formation. These azo bonds can be electrochemically reduced at Ered = -1.5 V, leading to the corresponding amino groups. This reduction resulted in a modest decrease in layer thickness, and did not yield monolayers. This indicates that other coupling reactions, notably a biphenyl coupling, induced by electrochemically produced phenyl radicals, take place as well. In addition to the azo functionalities, the nitro functionalities in electrografted layers of 4-NBD were independently reduced to amino functionalities at a lower potential (Ered = -2.1 V). The presence of amino functionalities on fully reduced layers, both from 4-NBD- and 4-BBD-modified Si, was shown by the presence of fluorine after reaction with trifluoroacetic anhydride (TFAA). This study shows that the electrochemical reduction of azo bonds generates amino functionalities on layers produced by electrografting of aryldiazonium derivatives. In this way multifunctional layers can be formed by employing functional aryldiazonium salts, which is believed to be very practical in the fabrication of sensor platforms, including those made of multi-array silicon nanowires.

  16. Monocyte proliferation and differentiation to osteoclasts is affected by density of collagen covalently bound to a poly(dimethyl siloxane) culture surface.

    Science.gov (United States)

    Shafieyan, Yousef; Tiedemann, Kerstin; Goulet, Andrew; Komarova, Svetlana; Quinn, Thomas M

    2012-06-01

    Osteoclast differentiation is affected by substrate characteristics and environmental conditions; these parameters are therefore of interest for understanding bone remodeling. As a step toward osteoclast mechanotransduction experiments, we aimed to optimize conditions for osteoclast differentiation on extendable poly(dimethylsiloxane) (PDMS) substrates. Because cells attach poorly on PDMS alone, chemical modification by covalent attachment of collagen type I was performed. Effects of collagen surface concentrations on monocyte fusion and osteoclast differentiation were examined. Osteoclasts differentiated on modified PDMS were fewer in number (by ∼50%) than controls on polystyrene physically modified by nonspecific attachment of collagen, and exhibited somewhat different morphologies. Nevertheless, for certain choices of the chemical modification procedures, appropriate differentiation on PDMS was still evident by qRT-PCR analysis for tartrate-resistant acid phosphate (TRAP) and cathepsin K (CTSK) gene expression, positive TRAP staining, fluorescent phalloidin staining showing actin ring formation and bone resorption assays. At relatively high collagen surface densities, monocyte clumps appeared on PDMS suggesting substrate-induced alterations to monocyte fusion. Covalently bound collagen can therefore be used to promote osteoclast differentiation on extendable PDMS substrates. Under appropriate conditions osteoclasts retain similar functionality as on polystyrene, which will enable future studies of osteoclast interactions with microstructured surfaces and mechanostimulation. Copyright © 2012 Wiley Periodicals, Inc.

  17. DNA of Dientamoeba fragilis detected within surface-sterilized eggs of Enterobius vermicularis.

    Science.gov (United States)

    Röser, Dennis; Nejsum, Peter; Carlsgart, Anne Josefine; Nielsen, Henrik Vedel; Stensvold, Christen Rune

    2013-01-01

    With no evidence of a cyst stage, the mode of transmission of Dientamoeba fragilis, an intestinal protozoon of common occurrence and suggested pathogenicity, is incompletely known. Numerous studies have suggested that eggs of intestinal nematodes, primarily Enterobius vermicularis (pinworm), can serve as vectors for D. fragilis, although attempts to culture D. fragilis from pinworm eggs have been unsuccessful and data from epidemiological studies on D. fragilis/pinworm co-infection have been conflicting. The aim of this study was to investigate whether we could detect D. fragilis DNA from pinworm eggs collected from routine diagnostic samples (cellophane tape) and surface-sterilised by hypochlorite. DNA was extracted from individual eggs and tested by PCR using D. fragilis- and E. vermicularis-specific primers; amplicons were sequenced for confirmation. In cellophane tape samples from 64 patients with unknown D. fragilis status we detected D. fragilis DNA in 12/238 (5%) eggs, and in a patient known to harbour D. fragilis we detected D. fragilis DNA in 39/99 (39%) eggs. The finding of D. fragilis DNA within eggs of E. vermicularis strongly supports the hypothesis of D. fragilis-transmission by pinworm and has implications for antimicrobial intervention as well as control and public health measures. Copyright © 2012 Elsevier Inc. All rights reserved.

  18. Fabrication of endothelial progenitor cell capture surface via DNA aptamer modifying dopamine/polyethyleneimine copolymer film

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xin; Deng, Jinchuan; Yuan, Shuheng; Wang, Juan; Luo, Rifang; Chen, Si [Key Lab. of Advanced Technology for Materials of Education Ministry, Southwest Jiaotong University, Chengdu 610031 (China); School of Material Science and Engineering, Southwest Jiaotong University, Chengdu 610031 (China); Wang, Jin, E-mail: jinxxwang@263.net [Key Lab. of Advanced Technology for Materials of Education Ministry, Southwest Jiaotong University, Chengdu 610031 (China); Huang, Nan [Key Lab. of Advanced Technology for Materials of Education Ministry, Southwest Jiaotong University, Chengdu 610031 (China); School of Material Science and Engineering, Southwest Jiaotong University, Chengdu 610031 (China)

    2016-11-15

    Highlights: • The dopamine/PEI film with controlled amine density was successfully prepared. • The DNA aptamer was assembled onto the film via electrostatic incorporation. • The A@DPfilmscanspecificallyandeffectivelycaptureEPCs. • The A@DP film can support the survival of ECs, control the hyperplasia of SMCs. • The dynamic/co-culture models are useful for studying cells competitive adhesion. - Abstract: Endothelial progenitor cells (EPCs) are mainly located in bone marrow and circulate, and play a crucial role in repairmen of injury endothelium. One of the most promising strategies of stents designs were considered to make in-situ endothelialization in vivo via EPC-capture biomolecules on a vascular graft to capture EPCs directly from circulatory blood. In this work, an EPC specific aptamer with a 34 bases single strand DNA sequence was conjugated onto the stent surface via dopamine/polyethyleneimine copolymer film as a platform and linker. The assembled density of DNA aptamer could be regulated by controlling dopamine percentage in this copolymer film. X-ray photoelectron spectroscopy (XPS), water contact angle (WCA) and fluorescence test confirmed the successful immobilization of DNA aptamer. To confirm its biofunctionality and cytocompatibility, the capturing cells ability of the aptamer modified surface and the effects on the growth behavior of human umbilical vein endothelial cells (HUVECs), smooth muscle cells (SMCs) were investigated. The aptamer functionalized sample revealed a good EPC-capture ability, and had a cellular friendly feature for both EPC and EC growth, while not stimulated the hyperplasia of SMCs. And, the co-culture experiment of three types of cells confirmed the specificity capturing of EPCs to aptamer modified surface, rather than ECs and SMCs. These data suggested that this aptamer functionalized surface may have a large potentiality for the application of vascular grafts with targeted endothelialization.

  19. Fabrication of endothelial progenitor cell capture surface via DNA aptamer modifying dopamine/polyethyleneimine copolymer film

    International Nuclear Information System (INIS)

    Li, Xin; Deng, Jinchuan; Yuan, Shuheng; Wang, Juan; Luo, Rifang; Chen, Si; Wang, Jin; Huang, Nan

    2016-01-01

    Highlights: • The dopamine/PEI film with controlled amine density was successfully prepared. • The DNA aptamer was assembled onto the film via electrostatic incorporation. • The A@DPfilmscanspecificallyandeffectivelycaptureEPCs. • The A@DP film can support the survival of ECs, control the hyperplasia of SMCs. • The dynamic/co-culture models are useful for studying cells competitive adhesion. - Abstract: Endothelial progenitor cells (EPCs) are mainly located in bone marrow and circulate, and play a crucial role in repairmen of injury endothelium. One of the most promising strategies of stents designs were considered to make in-situ endothelialization in vivo via EPC-capture biomolecules on a vascular graft to capture EPCs directly from circulatory blood. In this work, an EPC specific aptamer with a 34 bases single strand DNA sequence was conjugated onto the stent surface via dopamine/polyethyleneimine copolymer film as a platform and linker. The assembled density of DNA aptamer could be regulated by controlling dopamine percentage in this copolymer film. X-ray photoelectron spectroscopy (XPS), water contact angle (WCA) and fluorescence test confirmed the successful immobilization of DNA aptamer. To confirm its biofunctionality and cytocompatibility, the capturing cells ability of the aptamer modified surface and the effects on the growth behavior of human umbilical vein endothelial cells (HUVECs), smooth muscle cells (SMCs) were investigated. The aptamer functionalized sample revealed a good EPC-capture ability, and had a cellular friendly feature for both EPC and EC growth, while not stimulated the hyperplasia of SMCs. And, the co-culture experiment of three types of cells confirmed the specificity capturing of EPCs to aptamer modified surface, rather than ECs and SMCs. These data suggested that this aptamer functionalized surface may have a large potentiality for the application of vascular grafts with targeted endothelialization.

  20. EPR Studies of Spin Labels Bound to Ceramic Surfaces, and Simulation of Magnetic Resonance Spectra by Molecular Trajectory.

    Science.gov (United States)

    Auteri, Francesco Paul

    Electron paramagnetic resonance (EPR) spectroscopy is sensitive to molecular rotational correlation times in the range of 10^{-6} to 10^{-11} seconds. EPR spin labels are often attached or incorporated into molecular structures as probes of local viscosities and dynamics. In part I of this work, methods of covalently attaching a variety of spin labels to silica and alumina ceramic surfaces are developed in an attempt to study local viscosities at varying distances from about 5 A^circ to 25 A^circ from the ceramic/liquid interface. Three solvents, diethyl ether, benzene, and cyclohexane, are chosen for detailed study in combination with the spin labels, TEMPOL, 5-DOXYL, and 12-DOXYL. EPR spectra of each system are taken over the range of temperatures from -140 ^circC to 50^circ C (or just below the solvent boiling point). Spectra show good sensitivity to solvent, temperature, and probe. The effect of adding 3% (w/o) poly-(octadecyl-methacrylate) (PODM) to benzene and cyclohexane on spin label mobility is also studied in this work. Rotational correlation times from lineshapes are analyzed assuming isotropic rotation using spectral splitting, line width, and simulation methods. These approaches are often inadequate for the more complex spectral line shapes observed for tethered spin labels, especially in the intermediate motional regime where sensitivity to anisotropic dynamics is greatest. In part II of this work, a novel approach to the prediction of spectral line shapes is developed. It is shown that EPR spectra may be computed directly from molecular trajectories using classical approximations to describe the time evolution of the magnetization vector under fluctuating effective interaction tensor values. Line shape simulations using molecular trajectories generated by Brownian dynamics theory are less time intensive than existing methods. Simulation of magnetic resonance line shapes by molecular trajectories as generated by programs such as CHARMM promises to be

  1. On-chip magnetic bead-based DNA melting curve analysis using a magnetoresistive sensor

    DEFF Research Database (Denmark)

    Rizzi, Giovanni; Østerberg, Frederik Westergaard; Henriksen, Anders Dahl

    2014-01-01

    We present real-time measurements of DNA melting curves in a chip-based system that detects the amount of surface-bound magnetic beads using magnetoresistive magnetic field sensors. The sensors detect the difference between the amount of beads bound to the top and bottom sensor branches of the di......We present real-time measurements of DNA melting curves in a chip-based system that detects the amount of surface-bound magnetic beads using magnetoresistive magnetic field sensors. The sensors detect the difference between the amount of beads bound to the top and bottom sensor branches...

  2. Bacterial surface-displayed GII.4 human norovirus capsid proteins bound to surface of Romaine lettuce through HBGA-like molecules

    Science.gov (United States)

    Human Noroviruses (HuNoVs) are the main cause of nonbacterial gastroenteritis. Contaminated produce is a main vehicle for dissemination of HuNoVs. In this study, we used an ice nucleation protein (INP) mediated surface display system to present the protruding domain of GII.4 HuNoV capsid protein (G...

  3. Real-time sensing of surface-bound fibrinogen and fibrin interactions using spectroscopy of guided modes in optical waveguide structures, surface plasmon resonance, and monoclonal antibodies

    Czech Academy of Sciences Publication Activity Database

    Dyr, J. E.; Tichý, Ivo; Jiroušková, M.; Tobiška, Petr; Slavík, Radan; Homola, Jiří; Suttnar, J.

    1998-01-01

    Roč. 9, č. 7 (1998), s. 675 ISSN 0957-5235 R&D Projects: GA ČR GA303/96/1358 Institutional research plan: CEZ:AV0Z2067918 Keywords : surface plasmons * biosensors * biomedical engineering Subject RIV: CE - Biochemistry

  4. Cell surface-bound heat shock protein 70 (Hsp70) mediates perforin-independent apoptosis by specific binding and uptake of granzyme B.

    Science.gov (United States)

    Gross, Catharina; Koelch, Walter; DeMaio, Antonio; Arispe, Nelson; Multhoff, Gabriele

    2003-10-17

    Cell surface-bound heat shock protein 70 (Hsp70) renders tumor cells more sensitive to the cytolytic attack mediated by natural killer (NK) cells. A 14-amino acid Hsp70 sequence, termed TKD (TKDNNLLGRFELSG, aa450-463) could be identified as the extracellular localized recognition site for NK cells. Here, we show by affinity chromatography that both, full-length Hsp70-protein and Hsp70-peptide TKD, specifically bind a 32-kDa protein derived from NK cell lysates. The serine protease granzyme B was uncovered as the 32-kDa Hsp70-interacting protein using matrix-assisted laser desorption ionization time-of-flight mass peptide fingerprinting. Incubation of tumor cells with increasing concentrations of perforin-free, isolated granzyme B shows specific binding and uptake in a dose-dependent manner and results in initiation of apoptosis selectively in tumor cells presenting Hsp70 on the cell surface. Remarkably, Hsp70 cation channel activity was also determined selectively in purified phospholipid membranes of Hsp70 membrane-positive but not in membrane-negative tumor cells. The physiological role of our findings was demonstrated in primary NK cells showing elevated cytoplasmic granzyme B levels following contact with TKD. Furthermore, an increased lytic activity of Hsp70 membrane-positive tumor cells could be associated with granzyme B release by NK cells. Taken together we propose a novel perforin-independent, granzyme B-mediated apoptosis pathway for Hsp70 membrane-positive tumor cells.

  5. The extracellular membrane-proximal domain of membrane-bound IgE restricts B cell activation by limiting B cell antigen receptor surface expression.

    Science.gov (United States)

    Vanshylla, Kanika; Opazo, Felipe; Gronke, Konrad; Wienands, Jürgen; Engels, Niklas

    2018-03-01

    Immunoglobulin E (IgE) antibodies are key mediators of allergic reactions. Due to their potentially harmful anaphylactic properties, their production is tightly regulated. The membrane-bound isoform of IgE (mIgE), which is an integral component of the B cell antigen receptor, has been shown to be critical for the regulation of IgE responses in mice. In primate species including humans, mIgE can be expressed in two isoforms that are produced by alternative splicing of the primary ε Ig heavy chain transcript, and differ in the absence or presence of an extracellular membrane-proximal domain (EMPD) consisting of 52 amino acids. However, the function of the EMPD remains unclear. Here, we demonstrate that the EMPD restricts surface expression of mIgE-containing BCRs in human and murine B cells. The EMPD does not interfere with BCR assembly but acts as an autonomous endoplasmic reticulum retention domain. Limited surface expression of EMPD-containing mIgE-BCRs caused impaired activation of intracellular signaling cascades and hence represents a regulatory mechanism that may control the production of potentially anaphylactic IgE antibodies in primate species. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. A portable pulmonary delivery system for nano engineered DNA vaccines driven by surface acoustic wave devices

    International Nuclear Information System (INIS)

    Rajapaksa, A.E.; Qi, Aisha; Yeo, L.; Friend, J.

    2010-01-01

    Full text: The increase in the need for effective delivery of potelll vaccines against infectious diseases, require robust yet straightforward pro duction of encapsulated DNA-laden aerosols. Aerosol delivery of drugs represents the next generation of vaccine delivery where the drug is deposited into the lung, which provides an ideal, non-invasive route. Moreover, several features of D A vaccines make them more attractive than conventional vaccines; thus, DNA vaccines have gained global interest for a variety of applications. However, several limitations such as ineffective cellular uptake and intracellular delivery, and degradation of DNA need to be overcome before clin ical applications. In this study, a novel and scalable engineered technique has been developed to create a biodegradable polymer system, which enables controlled delivery of a well designed DNA vaccine for immuno-therapeutics. Surface Acoustic Wave (SAW) atomisation has been found as useful mechanism for atomising fluid samples for medical and industrial devices. It is a straightforward method for synthesising un-agglomerated biodegradable nanoparti cles (<250 nm) in the absence of organic solvents which would represent a major breakthrough for biopharmaceutical encapsulation and delivery. Nano-scale polymer particles for DNA vaccines deliv ery were obtained through an evaporative process of the initial aerosol created by surface acoustic waves at 8-150 MHz, the final size of which could be controlled by modifying the initial polymer concen tration and solid contents. Thus, SAW atomiser represents a promising alternative for the development of a low power device for producing nano-engineered vaccines with a controlled and narrow size distribution as delivery system for genetic immuno-therapeutics.

  7. Highly sensitive surface plasmon resonance biosensor for the detection of HIV-related DNA based on dynamic and structural DNA nanodevices.

    Science.gov (United States)

    Diao, Wei; Tang, Min; Ding, Shijia; Li, Xinmin; Cheng, Wenbin; Mo, Fei; Yan, Xiaoyu; Ma, Hongmin; Yan, Yurong

    2018-02-15

    Early detection, diagnosis and treatment of human immune deficiency virus (HIV) infection is the key to reduce acquired immunodeficiency syndrome (AIDS) mortality. In our research, an innovative surface plasmon resonance (SPR) biosensing strategy has been developed for highly sensitive detection of HIV-related DNA based on entropy-driven strand displacement reactions (ESDRs) and double-layer DNA tetrahedrons (DDTs). ESDRs as enzyme-free and label-free signal amplification circuit can be specifically triggered by target DNA, leading to the cyclic utilization of target DNA and the formation of plentiful double-stranded DNA (dsDNA) products. Subsequently, the dsDNA products bind to the immobilized hairpin capture probes and further combine with DDTs nanostructures. Due to the high efficiency of ESDRs and large molecular weight of DDTs, the SPR response signal was enhanced dramatically. The proposed SPR biosensor could detect target DNA sensitively and specifically in a linear range from 1pM to 150nM with a detection limit of 48fM. In addition, the whole detecting process can be accomplished in 60min with high accuracy and duplicability. In particular, the developed SPR biosensor was successfully used to analyze target DNA in complex biological sample, indicating that the developed strategy is promising for rapid and early clinical diagnosis of HIV infection. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. A chelating dendritic ligand capped quantum dot: preparation, surface passivation, bioconjugation and specific DNA detection

    Science.gov (United States)

    Zhou, Dejian; Li, Yang; Hall, Elizabeth A. H.; Abell, Chris; Klenerman, David

    2011-01-01

    Herein we report the synthesis of a new chelating dendritic ligand (CDL) and its use in the preparation a compact, stable and water-soluble quantum dot (QD), and further development of specific DNA sensor. The CDL, which contains a chelative dihydrolipoic acid moiety for strong QD surface anchoring and four dendritic carboxylic acidgroups, provides a stable, compact and entangled hydrophilic coating around the QD that significantly increases the stability of the resulting water-soluble QD. A CDL-capped CdSe/ZnS core/shell QD (CDL-QD) has stronger fluorescence than that capped by a monodendate single-chain thiol, 3-mercapto-propionic acid (MPA-QD). In addition, the fluorescence of the CDL-QD can be enhanced by 2.5-fold by treatments with Zn2+ or S2- ions, presumably due to effective passivation of the surface defects. This level of fluorescence enhancement obtained for the CDL-QD is much greater than that for the MPA-QD. Further, by coupling a short single-stranded DNA target to the QD via the CDL carboxylic acidgroup, a functional QD-DNA conjugate that can resist non-specific adsorption and hybridize quickly to its complementary DNAprobe has been obtained. This functional QD-DNA conjugate is suitable for specific quantification of short, labelled complementary probes at the low DNAprobe:QD copy numbers via a QD-sensitised dyefluorescence resonance energy transfer (FRET) response with 500 pM sensitivity on a conventional fluorimeter.Herein we report the synthesis of a new chelating dendritic ligand (CDL) and its use in the preparation a compact, stable and water-soluble quantum dot (QD), and further development of specific DNA sensor. The CDL, which contains a chelative dihydrolipoic acid moiety for strong QD surface anchoring and four dendritic carboxylic acidgroups, provides a stable, compact and entangled hydrophilic coating around the QD that significantly increases the stability of the resulting water-soluble QD. A CDL-capped CdSe/ZnS core/shell QD (CDL-QD) has

  9. The Photochemistry of Unprotected DNA and DNA inside Bacillus subtilis Spores Exposed to Simulated Martian Surface Conditions of Atmospheric Composition, Temperature, Pressure, and Solar Radiation.

    Science.gov (United States)

    Nicholson, Wayne L; Schuerger, Andrew C; Douki, Thierry

    2018-03-28

    DNA is considered a potential biomarker for life-detection experiments destined for Mars. Experiments were conducted to examine the photochemistry of bacterial DNA, either unprotected or within Bacillus subtilis spores, in response to exposure to simulated martian surface conditions consisting of the following: temperature (-10°C), pressure (0.7 kPa), atmospheric composition [CO 2 (95.54%), N 2 (2.7%), Ar (1.6%), O 2 (0.13%), and H 2 O (0.03%)], and UV-visible-near IR solar radiation spectrum (200-1100 nm) calibrated to 4 W/m 2 of UVC (200-280 nm). While the majority (99.9%) of viable spores deposited in multiple layers on spacecraft-qualified aluminum coupons were inactivated within 5 min, a detectable fraction survived for up to the equivalent of ∼115 martian sols. Spore photoproduct (SP) was the major lesion detected in spore DNA, with minor amounts of cyclobutane pyrimidine dimers (CPD), in the order TT CPD > TC CPD > CT CPD. In addition, the (6-4)TC, but not the (6-4)TT, photoproduct was detected in spore DNA. When unprotected DNA was exposed to simulated martian conditions, all photoproducts were detected. Surprisingly, the (6-4)TC photoproduct was the major photoproduct, followed by SP ∼ TT CPD > TC CPD > (6-4)TT > CT CPD > CC CPD. Differences in the photochemistry of unprotected DNA and spore DNA in response to simulated martian surface conditions versus laboratory conditions are reviewed and discussed. The results have implications for the planning of future life-detection experiments that use DNA as the target, and for the long-term persistence on Mars of forward contaminants or their DNA. Key Words: Bacillus subtilis-DNA-Mars-Photochemistry-Spore-Ultraviolet. Astrobiology 18, xxx-xxx.

  10. Cell surface-bound TIMP3 induces apoptosis in mesenchymal Cal78 cells through ligand-independent activation of death receptor signaling and blockade of survival pathways.

    Directory of Open Access Journals (Sweden)

    Christina Koers-Wunrau

    Full Text Available BACKGROUND: The matrix metalloproteinases (MMPs and their endogenous regulators, the tissue inhibitor of metalloproteinases (TIMPs 1-4 are responsible for the physiological remodeling of the extracellular matrix (ECM. Among all TIMPs, TIMP3 appears to play a unique role since TIMP3 is a secreted protein and, unlike the other TIMP family members, is tightly bound to the ECM. Moreover TIMP3 has been shown to be able to induce apoptotic cell death. As little is known about the underlying mechanisms, we set out to investigate the pro-apoptotic effect of TIMP3 in human mesenchymal cells. METHODOLOGY/PRINCIPAL FINDINGS: Lentiviral overexpression of TIMP3 in mesenchymal cells led to a strong dose-dependent induction of ligand-independent apoptosis as reflected by a five-fold increase in caspase 3 and 7 activity compared to control (pLenti6/V5-GW/lacZ or uninfected cells, whereas exogenous TIMP3 failed to induce apoptosis. Concordantly, increased cleavage of death substrate PARP and the caspases 3 and 7 was observed in TIMP3 overexpressing cultures. Notably, activation of caspase-8 but not caspase-9 was observed in TIMP3-overexpressing cells, indicating a death receptor-dependent mechanism. Moreover, overexpression of TIMP3 led to a further induction of apoptosis after stimulation with TNF-alpha, FasL and TRAIL. Most interestingly, TIMP3-overexpression was associated with a decrease in phosphorylation of cRaf, extracellular signal-regulated protein kinase (Erk1/2, ribosomal S6 kinase (RSK1 and Akt and serum deprivation of TIMP3-overexpressing cells resulted in a distinct enhancement of apoptosis, pointing to an impaired signaling of serum-derived survival factors. Finally, heparinase treatment of heparan sulfate proteoglycans led to the release of TIMP3 from the surface of overexpressing cells and to a significant decrease in apoptosis indicating that the binding of TIMP3 is necessary for apoptosis induction. CONCLUSION: The results demonstrate that

  11. The Generation of Surface-bound Exospheres via Electron-Stimulated Desorption (and Related Phenomena): Results from Apollo samples and Hermian Regolith Simulants

    Science.gov (United States)

    Bennett, C.; Poston, M.; McLain, J. L.; Orlando, T. M.

    2014-12-01

    The generation of surface-bound exospheres present around the Moon, Mercury and other airless rocky bodies are produced primarily by the interaction of micrometeoroid impacts and charged particles from the solar wind, and magnetospheres with those surfaces. While the study of the interactions of both micrometeoroids and ion sputtering are well investigated, the contributions arising from energetic electron interactions are typically less-well established. Observations from the Fast Imaging Plasma Spectrometer (FIPS), taken < 400 km from the surface, have shown a plasma cusp with energetic heavy ions (i.e. Na+- and O+-groups) for which the source has not been determined. However, the precipitation of keV electrons onto the surfaces of Mercury has recently been inferred from measurements using the X-Ray Spectrometer (XRS) instrument onboard the MESSENGER spacecraft observations of the night-side of Mercury. A newly developed global kinetic transport model suggests that electron-stimulated desorption (ESD), and possibly light ion stimulated desorption (ISD), can directly yield ions that can be transported and dynamically accelerated to the plasma cusp regions observed by FIPS. In addition, keV electrons and ions from the solar wind and Earth's magnetosphere frequently bombard with the lunar surface. Here, we present some of the most recent results from our ongoing work studying the effects of photon-stimulated desorption (PSD), ion-stimulated desorption (ISD) and implantation, as well as electron-stimulated desorption (ESD). Apollo samples collected from both the lunar highland and Mare regions, as well as simulants of the Mercury Regolith have been investigated. The temperature- (100-600 K) and energy-dependence (threshold - 2 keV) of ESD time-of-flight (ToF) results will be presented for these materials along with some preliminary results from our group based on photon-desorption studies of water on lunar material, temperature-programmed desorption (TPD) studies of

  12. Mesenchymal stromal cells induce epithelial-to-mesenchymal transition in human colorectal cancer cells through the expression of surface-bound TGF-β.

    Science.gov (United States)

    Mele, Valentina; Muraro, Manuele G; Calabrese, Diego; Pfaff, Dennis; Amatruda, Nunzia; Amicarella, Francesca; Kvinlaug, Brynn; Bocelli-Tyndall, Chiara; Martin, Ivan; Resink, Therese J; Heberer, Michael; Oertli, Daniel; Terracciano, Luigi; Spagnoli, Giulio C; Iezzi, Giandomenica

    2014-06-01

    Mesenchymal stem/stromal cells (MSC) are multipotent precursors endowed with the ability to home to primary and metastatic tumor sites, where they can integrate into the tumor-associated stroma. However, molecular mechanisms and outcome of their interaction with cancer cells have not been fully clarified. In this study, we investigated the effects mediated by bone marrow-derived MSC on human colorectal cancer (CRC) cells in vitro and in vivo. We found that MSC triggered epithelial-to-mesenchymal transition (EMT) in tumor cells in vitro, as indicated by upregulation of EMT-related genes, downregulation of E-cadherin and acquisition of mesenchymal morphology. These effects required cell-to-cell contact and were mediated by surface-bound TGF-β newly expressed on MSC upon coculture with tumor cells. In vivo tumor masses formed by MSC-conditioned CRC cells were larger and characterized by higher vessel density, decreased E-cadherin expression and increased expression of mesenchymal markers. Furthermore, MSC-conditioned tumor cells displayed increased invasiveness in vitro and enhanced capacity to invade peripheral tissues in vivo. Thus, by promoting EMT-related phenomena, MSC appear to favor the acquisition of an aggressive phenotype by CRC cells. © 2013 The Authors. Published by Wiley Periodicals, Inc. on behalf of UICC.

  13. Characteristics of depositional sequences, systems tracts and bounding surfaces in Early Ordovician greenhouse passive margin carbonates to Late Ordovician glacio-eustatic influenced foreland basin facies

    Energy Technology Data Exchange (ETDEWEB)

    Pope, M.C.; Read, J.F. (Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Geology)

    1994-03-01

    Passive margin, cyclic carbonates of the Early Ordovician Knox Group, Appalachians are dominated by meter scale dolomitized carbonate cycles. These are stacked into 1 to 5 m.y. depositional sequences that appear to be relatively conformable. The sequences are defined by stacking patterns on Fischer plots that graph long term changes in accommodation with thick less dolomitized cycles in the TST, and thin, highly dolomitized cycles in the HST, becoming quartzose in the late HST and LST. Sequence and systems tract boundaries are subtle and typically marked by zones of cycles rather than single discrete surfaces. In contrast, sequences in the later Ordovician foreland basin fill locally show: (1) sequence bounding unconformities on the Knox, the Camp Nelson and on top of the Ordovician, (2) well defined low stand deposits as in the subaerial breccias and detrital dolomite muds veneering the Knox unconformity; redbeds and associated quartz sands and conglomerates with intercalated peritidal carbonate layers and their distal equivalent peritidal laminites; (3) TST's in the lower part of the Middle Ordovician limestones include regionally traceable cyclic peritidal carbonates or in the lower Lexington Limestone, transgressive high energy grainstones; (4) HST's consist of poorly cyclic deeper water up into shallow water grainstone bank and northward prograding peritidal carbonate facies; The ongoing study of detailed logs of outcrop and core should help refine the understanding of the fine scale makeup of sequences developed in these contrasting tectonic and global climatic settings.

  14. A silica nanoparticle-based sensor for selective fluorescent detection of homocysteine via interaction differences between thiols and particle-surface-bound polymers

    Science.gov (United States)

    Yu, Changmin; Zeng, Fang; Luo, Ming; Wu, Shuizhu

    2012-08-01

    Biothiols play crucial roles in maintaining biological systems; among them, homocysteine (Hcy) has received increasing attention since elevated levels of Hcy have been implicated as an independent risk factor for cardiovascular disease. Hence, the selective detection of this specific biothiol, which is a disease-associated biomarker, is very important. In this paper, we demonstrate a new mesoporous silica nanoparticle-based sensor for selective detection of homocysteine from biothiols and other common amino acids. In this fluorescent sensing system, an anthracene nitroolefin compound was placed inside the mesopores of mesoporous silica nanoparticles (MSNs) and used as a probe for thiols. The hydrophilic polyethylene glycol (PEG 5000) molecules were covalently bound to the MSN surface and used as a selective barrier for Hcy detection via different interactions between biothiols and the PEG polymer chains. The sensor can discriminate Hcy from the two low-molecular mass biothiols (GSH and Cys) and other common amino acids in totally aqueous media as well as in serum, with a detection limit of 0.1 μM. This strategy may offer an approach for designing other MSN-based sensing systems by using polymers as diffusion regulators in sensing assays for other analytes.

  15. Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5' flap DNA: basis of interstrand cross-link repair by FAN1

    Energy Technology Data Exchange (ETDEWEB)

    Gwon, Gwang Hyeon; Kim, Youngran; Liu, Yaqi; Watson, Adam T.; Jo, Aera; Etheridge, Thomas J.; Yuan, Fenghua; Zhang, Yanbin; Kim, YoungChang; Carr, Anthony M.; Cho, Yunje

    2014-10-15

    Fanconi anemia (FA) is an autosomal recessive genetic disorder caused by defects in any of 15 FA genes responsible for processing DNA interstrand cross-links (ICLs). The ultimate outcome of the FA pathway is resolution of cross-links, which requires structure-selective nucleases. FA-associated nuclease 1 (FAN1) is believed to be recruited to lesions by a monoubiquitinated FANCI–FANCD2 (ID) complex and participates in ICL repair. Here, we determined the crystal structure of Pseudomonas aeruginosa FAN1 (PaFAN1) lacking the UBZ (ubiquitin-binding zinc) domain in complex with 5' flap DNA. All four domains of the right-hand-shaped PaFAN1 are involved in DNA recognition, with each domain playing a specific role in bending DNA at the nick. The six-helix bundle that binds the junction connects to the catalytic viral replication and repair (VRR) nuclease (VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction. The six-helix bundle also inhibits the cleavage of intact Holliday junctions. PaFAN1 shares several conserved features with other flap structure-selective nucleases despite structural differences. A clamping motion of the domains around the wedge helix, which acts as a pivot, facilitates nucleolytic cleavage. The PaFAN1 structure provides insights into how archaeal Holliday junction resolvases evolved to incise 5' flap substrates and how FAN1 integrates with the FA complex to participate in ICL repair.

  16. Immobilization mechanisms of deoxyribonucleic acid (DNA) to hafnium dioxide (HfO2) surfaces for biosensing applications.

    Science.gov (United States)

    Fahrenkopf, Nicholas M; Rice, P Zachary; Bergkvist, Magnus; Deskins, N Aaron; Cady, Nathaniel C

    2012-10-24

    Immobilization of biomolecular probes to the sensing substrate is a critical step for biosensor fabrication. In this work we investigated the phosphate-dependent, oriented immobilization of DNA to hafnium dioxide surfaces for biosensing applications. Phosphate-dependent immobilization was confirmed on a wide range of hafnium oxide surfaces; however, a second interaction mode was observed on monoclinic hafnium dioxide. On the basis of previous materials studies on these films, DNA immobilization studies, and density functional theory (DFT) modeling, we propose that this secondary interaction is between the exposed nucleobases of single stranded DNA and the surface. The lattice spacing of monoclinic hafnium dioxide matches the base-to-base pitch of DNA. Monoclinic hafnium dioxide is advantageous for nanoelectronic applications, yet because of this secondary DNA immobilization mechanism, it could impede DNA hybridization or cause nonspecific surface intereactions. Nonetheless, DNA immobilization on polycrystalline and amorphous hafnium dioxide is predominately mediated by the terminal phosphate in an oriented manner which is desirable for biosensing applications.

  17. DNA sequencing using fluorescence background electroblotting membrane

    Science.gov (United States)

    Caldwell, K.D.; Chu, T.J.; Pitt, W.G.

    1992-05-12

    A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through amino groups contained on the surface. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to the target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membranes may be reprobed numerous times. No Drawings

  18. DNA sequencing using fluorescence background electroblotting membrane

    Science.gov (United States)

    Caldwell, Karin D.; Chu, Tun-Jen; Pitt, William G.

    1992-01-01

    A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through said smino groups contained on the surface thereof. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to said target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membrances may be reprobed numerous times.

  19. Formation of copper nanoparticles on poly(thymine) through surface-initiated enzymatic polymerization and its application for DNA detection.

    Science.gov (United States)

    Hu, Weiwen; Ning, Yong; Kong, Jinming; Zhang, Xueji

    2015-08-21

    Poly(thymine) (polyT) and double-stranded DNA (dsDNA) can act as efficient templates for the formation of copper nanoparticles (CuNPs) at a low concentration of CuSO4, and the formed CuNPs emit excellent fluorescence. In this work, we demonstrated a new and facile strategy for the highly sensitive and selective detection of DNA on streptavidin-functionalized magnetic beads (SA-MB) using DNA-templated CuNPs as the fluorescent probe. Target DNA (tDNA) was hybridized with the capture DNA that was immobilized on the surface of SA-MB. Surface initiated enzymatic polymerization (SIEP) was employed as the signal amplification method to generate the polyT at the 3' end of tDNA for the formation of CuNPs. The incorporation of polyT by SIEP resulted in ∼35.7 fold signal amplification compared to the dsDNA after hybridization without SIEP. A dose-response curve for detection of DNA was obtained, with a linear dynamic range of 0.1 nM to 10 nM. We showed that this method has a low pM limit of detection (LOD 98.2 pM) and it is also very sensitive to the mismatch type in a specific DNA sequence. In addition, it avoids rigorously controlled temperature, complex synthesis of the fluorescent probe and prelabeling of DNA strands and eliminates the use of sophisticated experimental techniques and equipment. Armed with these intriguing properties, the proposed system could provide an efficient tool for early diagnosis and risk assessment of malignancy.

  20. Molecular investigation of evaporation of biodroplets containing single-strand DNA on graphene surface.

    Science.gov (United States)

    Akbari, Fahimeh; Foroutan, Masumeh

    2018-02-14

    In this study, the water droplet behaviour of four different types of single-strand DNA with homogeneous base sequence on a graphene substrate during evaporation of the droplet was investigated using molecular dynamics (MD) simulation. The simulation results indicated that the evaporation depended on the DNA sequence. The observed changes can be divided into four parts: (i) vaporization mode, (ii) evaporation flux, (iii) mechanism of single-strand placement on the surface, and (iv) consideration of remaining single strands after evaporation. Our simulation observations indicated different evaporation modes for thymine biodroplets as compared to those for other biodroplets. The evaporation of the thymine biodroplets occurred with an increase in the contact angle, while that of the other biodroplets occur in a constant contact angle mode. Moreover, thymine biodroplets generate the lowest contact line compared to other single strands, and it is always placed far away from the centre of the droplets during evaporation. Investigating variations in the evaporation flux shows that thymine has the highest evaporation flux and guanine has the lowest. Moreover, during initial evaporation, the flux of evaporation increases at the triple point of the biodroplets containing thymine single strands, while it decreases in the other biodroplets. The following observation was obtained from the study of the placement of single strands on the substrate: guanine and thymine interacted slower than other single strands during evaporation with graphene, adenine single strand had a higher folding during evaporation, and guanine single strand showed the lowest end-to-end distance. The investigation of single-strand DNA after evaporation shows that adenine produces the most stable structure at the end of evaporation. In addition, cytosine is the most stretched single-strand DNA due to its lack of internal π-π stacking and hydrogen bonding. Therefore, cytosine single strand is more

  1. DNA microarrays on ultraviolet-modified surfaces for speciation of bacteria.

    Science.gov (United States)

    Liu, Yanyang; He, Jianzhong; Yang, Kun-Lin

    2014-02-15

    In this study, we report an approach to activate inert hydrocarbon monolayers with ultraviolet (UV) light to fabricate DNA microarrays. Unlike traditional microarrays that require reactive functional groups on the surface, our DNA microarray is built on an inert layer of N,N-dimethyl-N-octadecyl(3-aminopropyl)trimethoxysilyl chloride silane (DMOAP). This layer is activated by UV (254 nm) just prior to the immobilization of oligonucleotide probes. Our X-ray photoelectron spectroscopy (XPS) results show that new functional groups such as alcohol (C--O), aldehyde (C=O), and carboxylic acid (O--C=O) form on the surface after the UV exposure. Among them, aldehyde groups are responsible for the immobilization of amine-label oligonucleotides. By using this approach, we further optimize UV exposure time and oligonucleotide concentration and also reduce agent concentration to achieve a high density of immobilized oligonucleotides up to 0.16 pmol/mm². As a proof of concept, we demonstrate that this microarray can be used for differentiation of different Clostridium species such as Clostridium acetobutylicum, Clostridium butylicum, and Clostridium beijerinkii. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Ferrocene-terminated monolayers covalently bound to hydrogen-terminated silicon surfaces. Toward the development of charge storage and communication devices.

    Science.gov (United States)

    Fabre, Bruno

    2010-12-21

    The combination of monocrystalline silicon's well-defined structure and the ability to prepare hydrogen-terminated surfaces (Si-H) easily and reproducibly has made this material a very attractive substrate for immobilizing functional molecules. The functionalization of Si-H using the covalent attachment of organic monolayers has received intense attention due to the numerous potential applications of controlled and robust organic/Si interfaces. Researchers have investigated these materials in diverse fields such as molecular electronics, chemistry, and bioanalytical chemistry. Applications include the preparation of surface insulators, the incorporation of chemical or biochemical functionality at interfaces for use in photovoltaic conversion, and the development of new chemical and biological sensing devices. Unlike those of gold, silicon's electronic properties are tunable, and researchers can directly integrate silicon-based devices within electronic circuitry. Moreover, the technological processes used for the micro- and nanopatterning of silicon are numerous and mature enough for producing highly miniaturized functional electronic components. In this Account, we describe a powerful approach that integrates redox-active molecules, such as ferrocene, onto silicon toward electrically addressable systems devoted to information storage or transfer. Ferrocene exhibits attractive electrochemical characteristics: fast electron-transfer rate, low oxidation potential, and two stable redox states (neutral ferrocene and oxidized ferrocenium). Accordingly, ferrocene-modified silicon surfaces could be used as charge storage components with the bound ferrocene center as the memory element. Upon application of a positive potential to silicon, ferrocene is oxidized to its corresponding ferrocenium form. This redox change is equivalent to the change of a bit of information from the "0" to "1" state. To erase the stored charge and return the device to its initial state, a low

  3. Study on the bound water of several high specific surface-area oxides (beryllia, alumina, silica-alumina); Etude de l'eau de constitution de plusieurs oxydes a grande surface specifique (glucine, alumine, silice-alumine)

    Energy Technology Data Exchange (ETDEWEB)

    Rouquerol, J. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1964-11-01

    This study is concerned with the bound water of several oxides (beryllia, alumina, silica-alumina) at different steps of their dehydration (heating temperatures between 150 and 1100 deg. C). The following techniques have been used simultaneously: Thermal analysis (a new method has been developed), nitrogen adsorption (study of the texture), Diborane hydrolysis (qualitative and quantitative analysis of surface water), Infra-red spectrography (in the absorption range of water), Nuclear magnetic resonance (in the resonance range of protons). Thanks to these different techniques, five kinds of bound water have been observed. Attention is called on the great influence of the thermal treatment conditions on the evolution of the products resulting from the decomposition of alumina {alpha}-trihydrate Al(OH){sub 3} and beryllium {alpha}-hydroxide, in the course of the dehydration. Moreover, the author emphasizes the peculiar properties of the two kinds of oxides (alumina and beryllia) prepared through a new method of treatment under low pressure and constant speed of decomposition. Such particular features concern mainly texture, bound water, and consequently, also catalytic activity. (author) [French] Ce travail porte sur l'eau de constitution de plusieurs oxydes (glucine, alumine, silice-alumine) aux differents degres de leur deshydratation (temperatures de traitement comprises entre 150 et 1100 deg. C). Cette etude met simultanement en oeuvre: l'analyse thermique (proposition d'une nouvelle methode), l'adsorption d'azote (etude de texture), l'hydrolyse du diborane (analyse qualitative et quantitative de l'eau de surface), la spectrographie infra-rouge (dans le domaine d'absorption de l'eau), la resonance magnetique nucleaire (dans le domaine de resonance des protons). A l'aide de ces differentes techniques, cinq formes d'eau de constitution ont ete observees. L'attention est attiree sur la tres grande influence

  4. Azide photochemistry for facile modification of graphitic surfaces: preparation of DNA-coated carbon nanotubes for biosensing

    International Nuclear Information System (INIS)

    Moghaddam, Minoo J; Yang Wenrong; Bojarski, Barbara; Gengenbach, Thomas R; Gao Mei; Zareie, Hadi; McCall, Maxine J

    2012-01-01

    A facile, two-step method for chemically attaching single-stranded DNA to graphitic surfaces, represented here by carbon nanotubes, is reported. In the first step, an azide-containing compound, N-5-azido-nitrobenzoyloxy succinimide (ANB-NOS), is used to form photo-adducts on the graphitic surfaces in a solid-state photochemical reaction, resulting in active ester groups being oriented for the subsequent reactions. In the second step, pre-synthesized DNA strands bearing a terminal amine group are coupled in an aqueous solution with the active esters on the photo-adducts. The versatility of the method is demonstrated by attaching pre-synthesized DNA to surfaces of carbon nanotubes in two platforms—as vertically-aligned multi-walled carbon nanotubes on a solid support and as tangled single-walled carbon nanotubes in mats. The reaction products at various stages were characterized by x-ray photoelectron spectroscopy. Two different assays were used to check that the DNA strands attached to the carbon nanotubes were able to bind their partner strands with complementary base sequences. The first assay, using partner DNA strands tethered to gold nanoparticles, enabled the sites of DNA attachment to the carbon nanotubes to be identified in TEM images. The second assay, using radioactively labelled partner DNA strands, quantified the density of functional DNA strands attached to the carbon nanotubes. The diversity of potential applications for these DNA-modified carbon-nanotube platforms is exemplified here by the successful use of a DNA-modified single-walled carbon-nanotube mat as an electrode for the specific detection of metal ions. (paper)

  5. [Enhancing effect of irradiation on carcinoma of the uterine cervix by administering the protein-bound polysaccharide kureha (PSK)--quantitative nuclear DNA analysis following irradiation].

    Science.gov (United States)

    Hayashi, Y

    1988-02-01

    The combined effect of PSK and radiation therapy has been studied in 34 patients with squamous cell carcinoma of the uterine cervix by noting the tumor cell kinetics change following irradiation. The DNA content of Pararosanillin-Feulgen stained tumor cells was measured by cytofluorometry to elucidate tumor cell kinetics. Twenty-one cases (PSK group) were administrated 3g. or 6g. of PSK daily until at least 30Gy. Thirteen cases (control group) were treated with external cobalt-60 irradiation without PSK. In radiosensitive cases (n = 29; PSK group: 19, control group: 10), the PSK group had a smaller Over 4C Cell population in the DNA histogram after 14Gy than the control group, and the population at 20 Gy in the PSK group was significantly smaller (p less than 0.05). At 20Gy, the PSK group showed better histopathological response than the control group according to the Ooboshi-Shimosato classification, and the PSK group showed a smaller giant cell formation and more colliquative necrosis. These findings indicated that Over 4C cell (giant cell) formation due to endomitosis was decreased because of the increase in lethal damage to tumor cells following PSK administration with irradiation. In radioresistant cases (n = 5) also, there seemed to be an advantage.

  6. The Influence of Selected Fingerprint Enhancement Techniques on Forensic DNA Typing of Epithelial Cells Deposited on Porous Surfaces.

    Science.gov (United States)

    Tsai, Li-Chin; Lee, Cheng-Chang; Chen, Chun-Chieh; Lee, James Chun-I; Wang, Sheng-Meng; Huang, Nu-En; Linacre, Adrian; Hsieh, Hsing-Mei

    2016-01-01

    Fingerprints deposited at crime scene can be a source of DNA. Previous reports on the effects of fingerprint enhancement methods have focused mainly on fingermarks deposited in blood or saliva. Here, we evaluate the effects of fingerprint enhancement methods on fingerprints deposited on porous surfaces. We performed real-time quantification and STR typing, the results of which indicated that two methods (iodine fuming and 1,2-indanedione in ethyl acetate enhancement) had no effect on the quantity of DNA isolated and resultant STR alleles when compared to control samples. DNA quantities and allele numbers were lower for samples enhanced with silver nitrate and 1,2-indanedione in acetic acid when compared to control samples. Based on DNA quantity, quality, and observable stochastic effects, our data indicated that iodine fuming and 1,2-indanedione in ethyl acetate were the preferred options for the enhancement of fingerprints on porous surfaces. © 2015 American Academy of Forensic Sciences.

  7. Strand breaks in plasmid DNA following positional changes of Auger-electron-emitting radionuclides

    International Nuclear Information System (INIS)

    Adelstein, S.J.; Kassis, A.I.

    1996-01-01

    The purpose of our studies is to elucidate the kinetics of DNA strand breaks caused by low-energy Auger electron emitters in close proximity to DNA. Previously we have studied the DNA break yields in plasmids after the decay of indium-111 bound to DNA or free in solution. In this work, we compare the DNA break yields in supercoiled DNA of iodine-125 decaying close to DNA following DNA intercalation, minor-groove binding, or surface binding, and at a distance form DNA. Supercoiled DNA, stored at 4 C to accumulate radiation dose from the decay of 125 I, was then resolved by gel electrophoresis into supercoiled, nicked circular, and linear forms, representing undamaged DNA, single-strand breaks, and double-strand breaks respectively. DNA-intercalated or groove-bound 125 I is more effective than surface-bound radionuclide or 125 I free in solution. The hydroxyl radical scavenger DMSO protects against damage by 125 I free in solution but has minimal effect on damage by groove-bound 125 I. (orig.)

  8. Perceptron Mistake Bounds

    OpenAIRE

    Mohri, Mehryar; Rostamizadeh, Afshin

    2013-01-01

    We present a brief survey of existing mistake bounds and introduce novel bounds for the Perceptron or the kernel Perceptron algorithm. Our novel bounds generalize beyond standard margin-loss type bounds, allow for any convex and Lipschitz loss function, and admit a very simple proof.

  9. cDNA cloning of glucose-6-phosphate isomerase from crucian carp (Carassius carassius) and expression of the active region as myofibril-bound serine proteinase inhibitor in Escherichia coli.

    Science.gov (United States)

    Han, Long; Cao, Min-Jie; Shi, Chao-lan; Wei, Xiao-Nan; Li, Huan; Du, Cui-Hong

    2014-02-01

    Glucose-6-phosphate isomerase (GPI) (EC 5.3.1.9) can act as a myofibril-bound serine proteinase (MBSP) inhibitor (MBSPI) in fish. In order to better understand the biological information of the GPI and its functional domain for inhibiting MBSP, the cDNA of GPI was cloned from crucian carp (Carassius carassius) with RT-PCR, nested-PCR and 3'-RACE. The result of sequencing showed that the GPI cDNA had an open reading frame of 1662bp encoding 553 amino acid residues. After constructing and comparing the three-dimensional structures of GPI and MBSP, the middle fragment of crucian carp GPI (GPI-M) was predicted as a functional domain for inhibiting MBSP. Then the crucian carp GPI-M gene was cloned and expressed in Escherichia coli. SDS-polyacrylamide gel electrophoresis (SDS-PAGE) showed that the recombinant GPI-M (rGPI-M) with molecular mass of approximately 21kDa in the form of inclusion bodies. The rGPI-M was obtained at an electrophoresis level purity of approximately 95% after denaturation and dialysis renaturation. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. A molecular exploration of human DNA/RNA co-extracted from the palmar surface of the hands and fingers.

    Science.gov (United States)

    Lacerenza, D; Aneli, S; Omedei, M; Gino, S; Pasino, S; Berchialla, P; Robino, C

    2016-05-01

    "Touch DNA" refers to the DNA that is left behind when a person touches or comes into contact with an item. However, the source of touch DNA is still debated and the large variability in DNA yield from casework samples suggests that, besides skin, various body fluids can be transferred through contact. Another important issue concerning touch DNA is the possible occurrence of secondary transfer, but the data published in the literature in relation to the background levels of foreign DNA present on the hand surfaces of the general population are very limited. As the present study aimed at better understanding the nature and characteristics of touch DNA, samples were collected from the palmar surface of the hands and fingers ("PHF" samples) of 30 male and 30 female donors by tape-lifting/swabbing and subjected to DNA/RNA co-extraction. Multiplex mRNA profiling showed that cellular material different from skin could be observed in 15% of the PHF samples. The total amount of DNA recovered from these samples (median 5.1 ng) was significantly higher than that obtained from samples containing skin cells only (median 1.6 ng). The integrity of the DNA isolated from the donors' hands and fingers as well as the prevalence of DNA mixtures were evaluated by STR typing and compared with reference STR profiles from buccal swabs. DNA integrity appeared significantly higher in the male rather than in the female subsample, as the average percentage of the donors' alleles effectively detected in PHF profiles was 75.1% and 60.1%, respectively. The prevalence of mixtures with a foreign DNA contribution ≥20% was 19.2% (30.0% in the female PHF samples and 8.3% in the male PHF samples). The obtained results support the hypothesis that transfer of cellular material different from skin may underlie the occasional recovery of quality STR profiles from handled items. These results also suggest that gender may represent an important factor influencing the propensity of individuals to carry

  11. Exogenous and Cell Surface Glycosaminoglycans Alter DNA Delivery Efficiency of Arginine and Lysine Homopeptides in Distinctly Different Ways*

    Science.gov (United States)

    Naik, Rangeetha J.; Chandra, Pallavi; Mann, Anita; Ganguli, Munia

    2011-01-01

    Glycosaminoglycans (GAGs) expressed ubiquitously on the cell surface are known to interact with a variety of ligands to mediate different cellular processes. However, their role in the internalization of cationic gene delivery vectors such as liposomes, polymers, and peptides is still ambiguous and seems to be controlled by multiple factors. In this report, taking peptides as model systems, we show that peptide chemistry is one of the key factors that determine the dependence on cell surface glycosaminoglycans for cellular internalization and gene delivery. Arginine peptides and their complexes with plasmid DNA show efficient uptake and functional gene transfer independent of the cell surface GAGs. On the other hand, lysine peptides and complexes primarily enter through a GAG-dependent pathway. The peptide-DNA complexes also show differential interaction with soluble GAGs. In the presence of exogenous GAGs under certain conditions, arginine peptide-DNA complexes show increased transfection efficiency that is not observed with lysine. This is attributed to a change in the complex nature that ensures better protection of the compacted DNA in the case of arginine complexes, whereas the lysine complexes get destabilized under these conditions. The presence of a GAG coating also ensures better cell association of arginine complexes, resulting in increased uptake. Our results indicate that the role of both the cell surface and exogenous glycosaminoglycans in gene delivery is controlled by the nature of the peptide and its complex with DNA. PMID:21471199

  12. Exogenous and cell surface glycosaminoglycans alter DNA delivery efficiency of arginine and lysine homopeptides in distinctly different ways.

    Science.gov (United States)

    Naik, Rangeetha J; Chandra, Pallavi; Mann, Anita; Ganguli, Munia

    2011-05-27

    Glycosaminoglycans (GAGs) expressed ubiquitously on the cell surface are known to interact with a variety of ligands to mediate different cellular processes. However, their role in the internalization of cationic gene delivery vectors such as liposomes, polymers, and peptides is still ambiguous and seems to be controlled by multiple factors. In this report, taking peptides as model systems, we show that peptide chemistry is one of the key factors that determine the dependence on cell surface glycosaminoglycans for cellular internalization and gene delivery. Arginine peptides and their complexes with plasmid DNA show efficient uptake and functional gene transfer independent of the cell surface GAGs. On the other hand, lysine peptides and complexes primarily enter through a GAG-dependent pathway. The peptide-DNA complexes also show differential interaction with soluble GAGs. In the presence of exogenous GAGs under certain conditions, arginine peptide-DNA complexes show increased transfection efficiency that is not observed with lysine. This is attributed to a change in the complex nature that ensures better protection of the compacted DNA in the case of arginine complexes, whereas the lysine complexes get destabilized under these conditions. The presence of a GAG coating also ensures better cell association of arginine complexes, resulting in increased uptake. Our results indicate that the role of both the cell surface and exogenous glycosaminoglycans in gene delivery is controlled by the nature of the peptide and its complex with DNA.

  13. Nanopore detection of DNA molecules in magnesium chloride solutions

    Science.gov (United States)

    Zhang, Yin; Liu, Lei; Sha, Jingjie; Ni, Zhonghua; Yi, Hong; Chen, Yunfei

    2013-05-01

    High translocation speed of a DNA strand through a nanopore is a major bottleneck for nanopore detection of DNA molecules. Here, we choose MgCl2 electrolyte as salt solution to control DNA mobility. Experimental results demonstrate that the duration time for straight state translocation events in 1 M MgCl2 solution is about 1.3 ms which is about three times longer than that for the same DNA in 1 M KCl solution. This is because Mg2+ ions can effectively reduce the surface charge density of the negative DNA strands and then lead to the decrease of the DNA electrophoretic speed. It is also found that the Mg2+ ions can induce the DNA molecules binding together and reduce the probability of straight DNA translocation events. The nanopore with small diameter can break off the bound DNA strands and increase the occurrence probability of straight DNA translocation events.

  14. Circuit lower bounds in bounded arithmetics

    Czech Academy of Sciences Publication Activity Database

    Pich, Ján

    2015-01-01

    Roč. 166, č. 1 (2015), s. 29-45 ISSN 0168-0072 R&D Projects: GA AV ČR IAA100190902 Keywords : bounded arithmetic * circuit lower bounds Subject RIV: BA - General Mathematics Impact factor: 0.582, year: 2015 http://www.sciencedirect.com/science/article/pii/S0168007214000888

  15. mtSSB may sequester UNG1 at mitochondrial ssDNA and delay uracil processing until the dsDNA conformation is restored

    DEFF Research Database (Denmark)

    Wollen Steen, Kristian; Doseth, Berit; westbye, Marianne

    2012-01-01

    identified a putative surface motif in mtSSB that may recruit UNG1 to DNA-bound mtSSB. We suggest that the massive amount of mtSSB in mitochondria effectively prevents processing of uracil and other types of damaged bases to avoid introduction of nicks in single-stranded mtDNA formed during replication....... Local enrichment of UNG1 at DNA-bound mtSSB may furthermore facilitate rapid access to- and processing of the damage once the dsDNA conformation is restored. This could be of potential biological importance, since mitochondria have no or limited capacity for homologous recombination to process nicks...

  16. A new insight into the interaction of ZnO with calf thymus DNA through surface defects.

    Science.gov (United States)

    Das, Sumita; Chatterjee, Sabyasachi; Pramanik, Srikrishna; Devi, Parukuttyamma Sujatha; Kumar, Gopinatha Suresh

    2018-01-01

    Experimental evidences on the binding interaction of ZnO and Calf Thymus (CT) DNA using several biophysical techniques are the centre of interest of the present study. The interaction of ZnO with CT DNA has been investigated in detail by absorption spectral study, fluorescence titration, Raman analysis, zeta potential measurement, viscometric experiment along with thermal melting study and microscopic analysis. Steady-state fluorescence study revealed the quenching (48%) of the surface defect related peak intensity of ZnO on interaction with DNA. The optimized concentration of ZnO and DNA to obtain this level of quenching has been found to be 0.049mM and 1.027μM, respectively. Additional fluorescence study with 8-hydroxy-5-quinoline (HQ) as a fluorescence probe for Zn 2+ ruled out the dissolution effect of ZnO under the experimental conditions. DNA conjugation on the surface of ZnO was also supported by Raman study. The quantitative variation in conductivity as well as electrophoretic mobility indicated significant interaction of ZnO with the DNA molecule. Circular dichroism (CD) and viscometry titrations provided clear evidence in support of the conformational retention of the DNA on interaction with ZnO. The binding interaction was found to be predominantly entropy driven in nature. The bio-physical studies presented in this paper exploring ZnO-CT DNA interaction could add a new horizon to understand the interaction between metal oxide and DNA. Copyright © 2017. Published by Elsevier B.V.

  17. cDNA sequence analysis of a 29-kDa cysteine-rich surface antigen of pathogenic Entamoeba histolytica

    International Nuclear Information System (INIS)

    Torian, B.E.; Stroeher, V.L.; Stamm, W.E.; Flores, B.M.; Hagen, F.S.

    1990-01-01

    A λgt11 cDNA library was constructed from poly(U)-Spharose-selected Entamoeba histolytica trophozoite RNA in order to clone and identify surface antigens. The library was screened with rabbit polyclonal anti-E. histolytica serum. A 700-base-pair cDNA insert was isolated and the nucleotide sequence was determined. The deduced amino acid sequence of the cDNA revealed a cysteine-rich protein. DNA hybridizations showed that the gene was specific to E. histolytica since the cDNA probe reacted with DNA from four axenic strains of E. histolytica but did not react with DNA from Entamoeba invadens, Acanthamoeba castellanii, or Trichomonas vaginalis. The insert was subcloned into the expression vector pGEX-1 and the protein was expressed as a fusion with the C terminus of glutathione S-transferase. Purified fusion protein was used to generate 22 monoclonal antibodies (mAbs) and a mouse polyclonal antiserum specific for the E. histolytica portion of the fusion protein. A 29-kDa protein was identified as a surface antigen when mAbs were used to immunoprecipitate the antigen from metabolically 35 S-labeled live trophozoites. The surface location of the antigen was corroborated by mAb immunoprecipitation of a 29-kDa protein from surface- 125 I-labeled whole trophozoites as well as by the reaction of mAbs with live trophozoites in an indirect immunofluorescence assay performed at 4 degree C. Immunoblotting with mAbs demonstrated that the antigen was present on four axenic isolates tested. mAbs recognized epitopes on the 29-kDa native antigen on some but not all clinical isolates tested

  18. cDNA sequence analysis of a 29-kDa cysteine-rich surface antigen of pathogenic Entamoeba histolytica

    Energy Technology Data Exchange (ETDEWEB)

    Torian, B.E.; Stroeher, V.L.; Stamm, W.E. (Univ. of Washington, Seattle (USA)); Flores, B.M. (Louisiana State Univ. Medical Center, New Orleans (USA)); Hagen, F.S. (Zymogenetics Incorporated, Seattle, WA (USA))

    1990-08-01

    A {lambda}gt11 cDNA library was constructed from poly(U)-Spharose-selected Entamoeba histolytica trophozoite RNA in order to clone and identify surface antigens. The library was screened with rabbit polyclonal anti-E. histolytica serum. A 700-base-pair cDNA insert was isolated and the nucleotide sequence was determined. The deduced amino acid sequence of the cDNA revealed a cysteine-rich protein. DNA hybridizations showed that the gene was specific to E. histolytica since the cDNA probe reacted with DNA from four axenic strains of E. histolytica but did not react with DNA from Entamoeba invadens, Acanthamoeba castellanii, or Trichomonas vaginalis. The insert was subcloned into the expression vector pGEX-1 and the protein was expressed as a fusion with the C terminus of glutathione S-transferase. Purified fusion protein was used to generate 22 monoclonal antibodies (mAbs) and a mouse polyclonal antiserum specific for the E. histolytica portion of the fusion protein. A 29-kDa protein was identified as a surface antigen when mAbs were used to immunoprecipitate the antigen from metabolically {sup 35}S-labeled live trophozoites. The surface location of the antigen was corroborated by mAb immunoprecipitation of a 29-kDa protein from surface-{sup 125}I-labeled whole trophozoites as well as by the reaction of mAbs with live trophozoites in an indirect immunofluorescence assay performed at 4{degree}C. Immunoblotting with mAbs demonstrated that the antigen was present on four axenic isolates tested. mAbs recognized epitopes on the 29-kDa native antigen on some but not all clinical isolates tested.

  19. Surface science of DNA adsorption onto citrate-capped gold nanoparticles.

    Science.gov (United States)

    Zhang, Xu; Servos, Mark R; Liu, Juewen

    2012-02-28

    Single-stranded DNA can be adsorbed by citrate capped gold nanoparticles (AuNPs), resulting in increased AuNP stability, which forms the basis of a number of biochemical and analytical applications, but the fundamental interaction of this adsorption reaction remains unclear. In this study, we measured DNA adsorption kinetics, capacity, and isotherms, demonstrating that the adsorption process is governed by electrostatic forces. The charge repulsion among DNA strands and between DNA and AuNPs can be reduced by adding salt, reducing pH or by using noncharged peptide nucleic acid (PNA). Langmuir adsorption isotherms are obtained, indicating the presence of both adsorption and desorption of DNA from AuNPs. While increasing salt concentration facilitates DNA adsorption, the desorption rate is also enhanced in higher salt due to DNA compaction. DNA adsorption capacity is determined by DNA oligomer length, DNA concentration, and salt. Previous studies indicated faster adsorption of short DNA oligomers by AuNPs, we find that once adsorbed, longer DNAs are much more effective in protecting AuNPs from aggregation. DNA adsorption is also facilitated by using low pH buffers and high alcohol concentrations. A model based on electrostatic repulsion on AuNPs is proposed to rationalize the DNA adsorption/desorption behavior. © 2012 American Chemical Society

  20. An inexpensive and simple method for thermally stable immobilization of DNA on an unmodified glass surface: UV linking of poly(T)10-poly(C)10-tagged DNA probes

    DEFF Research Database (Denmark)

    Guðnason, Haukur; Dufva, Hans Martin; Bang, Dang Duong

    2008-01-01

    the hybridization performance of the immobilized probes on the amino-silane surface, indicating a general benefit of adding a TC tag to DNA probes. In conclusion, our results show that using TC-tagged DNA probes immobilized on an unmodified glass surface is a robust, heat-stable, very simple, and inexpensive method...

  1. D-glucose derived novel gemini surfactants: synthesis and study of their surface properties, interaction with DNA, and cytotoxicity.

    Science.gov (United States)

    Kumar, Vikash; Chatterjee, Amrita; Kumar, Nupur; Ganguly, Anasuya; Chakraborty, Indranil; Banerjee, Mainak

    2014-10-09

    Four new D-glucose derived m-s-m type gemini surfactants with variable spacer and tail length have been synthesized by a simple and efficient synthetic methodology utilizing the free C-3 hydroxy group of diisopropylidene glucose. The synthetic route to these gemini surfactants with a quaternary ammonium group as polar head group involves a sequence of simple reactions including alkylation, imine formation, quaternization of amine etc. The surface properties of the new geminis were evaluated by surface tension and conductivity measurements. These gemini surfactants showed low cytotoxicity by MTT assay on HeLa cell line. The DNA binding capabilities of these surfactants were determined by agarose gel electrophoresis, fluorescence titration, and DLS experiments. The preliminary studies by agarose gel electrophoresis indicated chain length dependent DNA binding abilities, further supported by ethidium bromide exclusion experiments. Two of the D-glucose derived gemini surfactants showed effective binding with pET-28a plasmid DNA (pDNA) at relatively low N/P ratio (i.e., cationic nitrogen/DNA phosphate molar ratio). Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. A matrix lower bound

    Energy Technology Data Exchange (ETDEWEB)

    Grcar, Joseph F.

    2002-02-04

    A matrix lower bound is defined that generalizes ideas apparently due to S. Banach and J. von Neumann. The matrix lower bound has a natural interpretation in functional analysis, and it satisfies many of the properties that von Neumann stated for it in a restricted case. Applications for the matrix lower bound are demonstrated in several areas. In linear algebra, the matrix lower bound of a full rank matrix equals the distance to the set of rank-deficient matrices. In numerical analysis, the ratio of the matrix norm to the matrix lower bound is a condition number for all consistent systems of linear equations. In optimization theory, the matrix lower bound suggests an identity for a class of min-max problems. In real analysis, a recursive construction that depends on the matrix lower bound shows that the level sets of continuously differential functions lie asymptotically near those of their tangents.

  3. Extracellular DNA is essential for maintaining Bordetella biofilm integrity on abiotic surfaces and in the upper respiratory tract of mice.

    Directory of Open Access Journals (Sweden)

    Matt S Conover

    2011-02-01

    Full Text Available Bacteria form complex and highly elaborate surface adherent communities known as biofilms which are held together by a self-produced extracellular matrix. We have previously shown that by adopting a biofilm mode of existence in vivo, the gram negative bacterial pathogens Bordetella bronchiseptica and Bordetella pertussis are able to efficiently colonize and persist in the mammalian respiratory tract. In general, the bacterial biofilm matrix includes polysaccharides, proteins and extracellular DNA (eDNA. In this report, we investigated the function of DNA in Bordetella biofilm development. We show that DNA is a significant component of Bordetella biofilm matrix. Addition of DNase I at the initiation of biofilm growth inhibited biofilm formation. Treatment of pre-established mature biofilms formed under both static and flow conditions with DNase I led to a disruption of the biofilm biomass. We next investigated whether eDNA played a role in biofilms formed in the mouse respiratory tract. DNase I treatment of nasal biofilms caused considerable dissolution of the biofilm biomass. In conclusion, these results suggest that eDNA is a crucial structural matrix component of both in vitro and in vivo formed Bordetella biofilms. This is the first evidence for the ability of DNase I to disrupt bacterial biofilms formed on host organs.

  4. A novel graphene coated surface plasmon resonance biosensor with tungsten disulfide (WS2) for sensing DNA hybridization

    Science.gov (United States)

    Rahman, M. Saifur; Hasan, Md. Rabiul; Rikta, Khaleda Akter; Anower, M. S.

    2018-01-01

    In this paper, we propose a rigorous configuration of graphene coated surface plasmon resonance (SPR) sensor with Tungsten Disulfide (WS2) for sensing DNA hybridization. The present configuration is consisted of prism (SF10 glass), Gold (Au), WS2- graphene and sensing medium. We perform the performance parameters of the proposed sensor in terms of sensitivity, detection accuracy and quality factor. Here we report a dramatic enhancement of the overall performance. Addition of graphene layers increase the sensitivity but decrease the other performance parameters. To increase the all performance parameters we add WS2 between metal and graphene layer. Furthermore in this paper, the thickness effect of Gold (Au) is also analyzed. Numerical analysis shows that the variation of SPR angle for mismatched DNA strands is quiet negligible whereas that for complementary DNA strands is considerably countable. Therefore, the proposed biosensor opens a new window towards detection for biomolecular interactions.

  5. Surface plasmon resonator using high sensitive resonance telecommunication wavelengths for DNA sensors of Mycobacterium tuberculosis with thiol-modified probes.

    Science.gov (United States)

    Hsu, Shih-Hsiang; Hung, Shao-Chiang; Chen, Yu-Kun; Jian, Zhi-Hao

    2014-12-25

    Various analytes can be verified by surface plasmon resonance, thus continuous improvement of this sensing technology is crucial for better sensing selection and higher sensitivity. The SPR sensitivity on the wavelength modulation is enhanced with increasing wavelengths. The telecommunication wavelength range was then utilized to detect Mycobacterium tuberculosis (MTB) deoxyribonucleic acid (DNA) under two situations, without immobilization and with 5'-thiol end labeled IS6100 DNA probes, for SPR sensitivity comparison. The experimental data demonstrated that the SPR sensitivity increased more than 13 times with the wavelength modulation after immobilization. Since the operating wavelength accuracy of a tunable laser source can be controlled within 0.001 nm, the sensitivity and resolution on immobilized MTB DNA were determined as 1.04 nm/(μg/mL) and 0.9 ng/mL, respectively.

  6. Polarized DNA Ejection from the Herpesvirus Capsid

    Science.gov (United States)

    Newcomb, William W.; Cockrell, Shelley K.; Homa, Fred L.; Brown, Jay C.

    2009-01-01

    Ejection of DNA from the capsid is an early step in infection by all herpesviruses. Ejection or DNA uncoating occurs after a parental capsid has entered the host cell cytoplasm, migrated to the nucleus and bound to a nuclear pore. DNA exits the capsid through the portal vertex and proceeds by way of the nuclear pore complex into the nucleoplasm where it is transcribed and replicated. Here we describe use of an in vitro uncoating system to determine which genome end exits first from the herpes simplex virus (HSV-1) capsid. Purified DNA-containing capsids were bound to a solid surface and warmed under conditions in which some, but not all, of the DNA was ejected. Restriction endonuclease digestion was then used to identify the genomic origin of the ejected DNA. The results support the view that the S segment end exits the capsid first. Preferential release at the S end demonstrates that herpesvirus DNA uncoating conforms to the paradigm in dsDNA bacteriophage where the last end packaged is the first to be ejected. Release of HSV-1 DNA beginning at the S end causes the first gene to enter the host cell nucleus to be α4, a transcription factor required for expression of early genes. PMID:19631662

  7. Assessment of DNA damages caused by exposure of bacterial cells and spores to the Mars surface environment

    Science.gov (United States)

    Fajardo-Cavazos, Patricia; Schuerger, Andrew; Robles-Martinez, Jose; Douki, Thierry; Nicholson, Wayne

    Joint NASA and ESA missions are planned for the next decade to investigate the possibility of present or past life on Mars [1]. Evidence of extraterrestrial life will likely rely on the de-tection of biomarkers, highlighting the importance of preventing forward contamination not only with viable microorganisms, but also with biomolecules that could compromise the valid-ity of life-detection experiments [2-4]. The designation of DNA as a high-priority biomarker makes it necessary to evaluate its persistence in extraterrestrial environments, and the effects of exposure on its biological activity. To accomplish this, we deposited naked DNA, cells and spores of Bacillus subtilis 168 or B. pumilus SAFR-032, or cells of Acinetobacter radioresistens 50v1 onto spacecraft-qualified aluminum coupons. Samples were exposed to a simulated Mars surface environment as described in detail previously [4, 5] for various periods of time, and DNA damage was assessed by a number of measurements. Double-and single-strand breaks were measured by neutral and alkaline agarose gel electrophoresis, and DNA bipyrimidine pho-toproducts were measured by HPLC-mass spectrometry, as described previously [6, 7]. Loss of functionality of DNA to serve as a template for replication by DNA polymerase was measured using a quantitative polymerase chain reaction (qPCR) assay [8]. In all cases, DNA damage was directly correlated with time of exposure to simulated martian solar radiation (UV, visible, and infrared wavelengths). Exposure of samples to Mars surface conditions, but shielded from solar radiation, did not result in appreciable damage over the time periods tested, relative to controls. DNA contained within cells or spores was much less susceptible to damage than was naked DNA. Using the qPCR assay, we found that inactivation of naked DNA or DNA extracted from exposed spores of B. subtilis followed a multiphasic dose-response, and that a fraction of DNA molecules retained functionality after

  8. Physical Uncertainty Bounds (PUB)

    Energy Technology Data Exchange (ETDEWEB)

    Vaughan, Diane Elizabeth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Preston, Dean L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-03-19

    This paper introduces and motivates the need for a new methodology for determining upper bounds on the uncertainties in simulations of engineered systems due to limited fidelity in the composite continuum-level physics models needed to simulate the systems. We show that traditional uncertainty quantification methods provide, at best, a lower bound on this uncertainty. We propose to obtain bounds on the simulation uncertainties by first determining bounds on the physical quantities or processes relevant to system performance. By bounding these physics processes, as opposed to carrying out statistical analyses of the parameter sets of specific physics models or simply switching out the available physics models, one can obtain upper bounds on the uncertainties in simulated quantities of interest.

  9. DNA self-assembly-driven positioning of molecular components on nanopatterned surfaces

    Science.gov (United States)

    Szymonik, M.; Davies, A. G.; Wälti, C.

    2016-09-01

    We present a method for the specific, spatially targeted attachment of DNA molecules to lithographically patterned gold surfaces—demonstrated by bridging DNA strands across nanogap electrode structures. An alkanethiol self-assembled monolayer was employed as a molecular resist, which could be selectively removed via electrochemical desorption, allowing the binding of thiolated DNA anchoring oligonucleotides to each electrode. After introducing a bridging DNA molecule with single-stranded ends complementary to the electrode-tethered anchoring oligonucleotides, the positioning of the DNA molecule across the electrode gap, driven by self-assembly, occurred autonomously. This demonstrates control of molecule positioning with resolution limited only by the underlying patterned structure, does not require any alignment, is carried out entirely under biologically compatible conditions, and is scalable.

  10. The Adsorption of Short Single-Stranded DNA Oligomers on Mineral Surfaces

    Science.gov (United States)

    Kopstein, M.; Sverjensky, D. A.; Hazen, R. M.; Cleaves, H. J.

    2009-12-01

    Previous studies have described feasible pathways for the synthesis of simple organic building blocks such as formaldehyde and hydrogen cyanide, and their reaction to form more complex biomolecules such as nucleotide bases, amino acids and sugars (Miller and Orgel 1974, Miller and Cleaves 2006). However, the polymerization of monomers into a useful genetic material remains problematic (Orgel 2004). Organic building blocks were unlikely to polymerize from very dilute aqueous solution in the primitive oceans. Mineral surface adsorption has been suggested as a possible mechanism for concentrating the necessary building blocks (Bernal 1951). This study focused on the adsorption behavior of single-stranded DNA homo-oligomers of adenine and thymine (including the monomers, dimers, tetramers, hexamers, octomers, and decamers) with five different mineral surfaces (pyrite, rutile, hematite, olivine and calcite). Adsorption was studied in 0.1 M pH 8.1 KHCO3 with0.05 M NaCl as background electrolyte. Solutions were mixed for 24 hours at room temperature, centrifuged and the supernatants analyzed by UV/visible spectrophotometry. Equilibrium solution concentrations were measured and used to determine the number of moles adsorbed per square meter. Langmuir isotherms were constructed using the experimental data. It was found that adenine-containing molecules tend to bind much more strongly than thymine-containing molecules. It was also found that the number of moles adsorbed at saturation tends to fall with increasing chain length, while adsorption affinity tends to rise. Oligomer length appears to affect adsorption more than the mineral type. These results may have implications for the primordial organization of the first nucleic acid molecules as the persistence of extra-cellular nucleic acids in the environment. References Bernal, J. D. (1951) The Physical Basis of Life (Routledge, London). Miller S.L. and Cleaves, H.J. (2006) Prebiotic chemistry on the primitive Earth. In

  11. Photon virtual bound state

    International Nuclear Information System (INIS)

    Inoue, J.; Ohtaka, K.

    2004-01-01

    We study virtual bound states in photonics, which are a vectorial extension of electron virtual bound states. The condition for these states is derived. It is found that the Mie resonant state which satisfies the condition that the size parameter is less than the angular momentum should be interpreted as a photon virtual bound state. In order to confirm the validity of the concept, we compare the photonic density of states, the width of which represents the lifetime of the photon virtual bound states, with numerical results

  12. Crystal structure of the gamma-2 herpesvirus LANA DNA binding domain identifies charged surface residues which impact viral latency.

    Directory of Open Access Journals (Sweden)

    Bruno Correia

    Full Text Available Latency-associated nuclear antigen (LANA mediates γ2-herpesvirus genome persistence and regulates transcription. We describe the crystal structure of the murine gammaherpesvirus-68 LANA C-terminal domain at 2.2 Å resolution. The structure reveals an alpha-beta fold that assembles as a dimer, reminiscent of Epstein-Barr virus EBNA1. A predicted DNA binding surface is present and opposite this interface is a positive electrostatic patch. Targeted DNA recognition substitutions eliminated DNA binding, while certain charged patch mutations reduced bromodomain protein, BRD4, binding. Virus containing LANA abolished for DNA binding was incapable of viable latent infection in mice. Virus with mutations at the charged patch periphery exhibited substantial deficiency in expansion of latent infection, while central region substitutions had little effect. This deficiency was independent of BRD4. These results elucidate the LANA DNA binding domain structure and reveal a unique charged region that exerts a critical role in viral latent infection, likely acting through a host cell protein(s.

  13. Colloidal Au-enhanced surface plasmon resonance imaging: application in a DNA hybridization process

    International Nuclear Information System (INIS)

    Manera, M G; Spadavecchia, J; Taurino, A; Rella, R

    2010-01-01

    The detection of the DNA hybridization mechanism using monodispersed gold nanoparticles as labels is an interesting alternative to increase the sensitivity of the SPR imaging technique. DNA-modified Au nanoparticles (DNA-Au NPs) containing single-stranded (ss) portions of DNA were prepared by monitoring their monolayer formation by UV–vis spectroscopy. The hybridization process between specific thio-oligonucleotides immobilized on the DNA–Au NPs and the corresponding complementary strands is reported and compared with the traditional hybridization process on properly self-assembled thin gold films deposited on glass substrates. A remarkable signal amplification is observed, following the incorporation of colloidal Au into a SPR biosensing experiment, resulting in an increased SPR response to DNA–DNA interactions. In particular Fusarium thiolated DNA (5'HS poly(T) 15 ATC CCT CAA AAA CTG CCG CT-3) and trichothecenes complementary DNA (5'-AGC GGC AGT TTT TGA GGG AT-3') sequences have been explored due to their possible application to agro-industry for the control of food quality

  14. Au nanoparticle-modified DNA sensor based on simultaneous electrochemical impedance spectroscopy and localized surface plasmon resonance.

    Science.gov (United States)

    Cheng, Xin R; Hau, Ben Y H; Endo, Tatsuro; Kerman, Kagan

    2014-03-15

    Electrochemical impedance spectroscopy (EIS) and localized surface plasmon resonance (LSPR) were performed on the same Au nanoparticle (AuNP)-modified indium tin oxide (ITO) coated glass surfaces. Cyclic voltammetry was applied to electrodeposit AuNPs on ITO surface directly. The surface plasmon band characterization of AuNPs was initially studied by controlling the electrodeposition conditions. It was found that the size of AuNP clusters was significantly affected by the applied potential and KCl concentration in solution. The dual-detection platform was applied to detect DNA hybridization related to a specific point mutation in apolipoprotein E gene (ApoE), which was related to the progression of Alzheimer's disease. The preliminary results facilitate the development of a versatile biosensor that can be easily miniaturized and integrated into a high-throughput diagnostic device. © 2013 Elsevier B.V. All rights reserved.

  15. The DMM Bound

    DEFF Research Database (Denmark)

    Emiris, Ioannis Z.; Mourrain, Bernard; Tsigaridas, Elias

    2010-01-01

    In this paper we derive aggregate separation bounds, named after Davenport-Mahler-Mignotte (DMM), on the isolated roots of polynomial systems, specifically on the minimum distance between any two such roots. The bounds exploit the structure of the system and the height of the sparse (or toric) re...

  16. Bounded Gaussian process regression

    DEFF Research Database (Denmark)

    Jensen, Bjørn Sand; Nielsen, Jens Brehm; Larsen, Jan

    2013-01-01

    We extend the Gaussian process (GP) framework for bounded regression by introducing two bounded likelihood functions that model the noise on the dependent variable explicitly. This is fundamentally different from the implicit noise assumption in the previously suggested warped GP framework. We...

  17. Uniqueness of bounded observables

    Energy Technology Data Exchange (ETDEWEB)

    Navara, M. [Czech Technical Univ., Praha (Czech Republic). Dept. of Math.

    1995-09-01

    By an application of a new construction technique we construct a {sigma}-orthomodular lattice with a strongly order-determining set of states and two bounded observables whose expectations are equal at each state. This answers negatively the uniqueness problem for bounded observables, formulated by S. Gudder. (orig.).

  18. Quantum Bounded Symmetric Domains

    OpenAIRE

    Vaksman, L. L.

    2008-01-01

    This is Leonid Vaksman's monograph "Quantum bounded symmetric domains" (in Russian), preceded with an English translation of the table of contents and (a part) of the introduction. Quantum bounded symmetric domains are interesting from several points of view. In particular, they provide interesting examples for noncommutative complex analysis (i.e., the theory of subalgebras of C^*-algebars) initiated by W. Arveson.

  19. Surface-attached molecular beacons light the way for DNA sequencing

    Czech Academy of Sciences Publication Activity Database

    Paleček, Emil

    2004-01-01

    Roč. 22, č. 2 (2004), s. 55-58 ISSN 0167-7799 R&D Projects: GA AV ČR IBS5004355; GA ČR GA204/03/0566 Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular beacon * DNA stem-loop structure * DNA sensors Subject RIV: BO - Biophysics Impact factor: 8.606, year: 2004

  20. Bounding species distribution models

    Directory of Open Access Journals (Sweden)

    Thomas J. STOHLGREN, Catherine S. JARNEVICH, Wayne E. ESAIAS,Jeffrey T. MORISETTE

    2011-10-01

    Full Text Available Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for “clamping” model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART and maximum entropy (Maxent models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5: 642–647, 2011].

  1. Bounding Species Distribution Models

    Science.gov (United States)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  2. Optical and surface analysis of DNA microarrays to assess printed spot heterogeneity

    Science.gov (United States)

    Nagaraja Rao, Archana

    DNA microarrays have been plagued with analytical problems with quantitation, metrics, figures of merit, and reliability and reproducibility issues, hindering their acceptance in clinical and diagnostic settings. The main deficiency in the printed DNA format is the microspot heterogeneity occurring during array fabrication and further amplified during target hybridization. Work described in this dissertation focuses on assessment of DNA microarray spots generated with conventional pin-type contact printing of fluorescently labeled DNA probes, on industry-standard commercial polymer-coated array slides and their hybridization with complementary oligomer DNA target. Printing of probe DNA microspots shares many features of commonly reported droplet evaporation dynamics that lead to different drying patterns and spot morphologies. This study directly identifies and analyzes different DNA probe chemical and spatial microenvironments within spots, analyzed with high-resolution time-of-flight secondary ion mass spectrometry (TOF-SIMS) chemical imaging, confocal epifluorescence, and probe microscopy force imaging methods. Drying of DNA probe spots shows Marangoni flow effects with high densities of probe DNA-Cy3 located in spot centers and nonhomogeneous DNA distributed radially within printed spots with both TOF-SIMS imaging and epifluorescence microscopy. Target hybridization kinetics and duplex formation were assessed using real-time in situ confocal imaging, and confirmed radial hemispherical diffusion-mediated distribution of target capture from spot edge to its interior. Kinetic modeling indicates pseudo-first order kinetics due to transport limitations and local density-dependent probe interactions with diffusing target. Fluorescence resonance energy transfer (FRET) and photobleaching results show that the high- density probe overcrowding in spots facilitates a broad range of target binding interactions regardless of dye orientations. Moreover, lateral probe density

  3. Induction of Boosted Immune Response in Mice by Leptospiral Surface Proteins Expressed in Fusion with DnaK

    Directory of Open Access Journals (Sweden)

    Marina V. Atzingen

    2014-01-01

    Full Text Available Leptospirosis is an important global disease of human and veterinary concern. Caused by pathogenic Leptospira, the illness was recently classified as an emerging infectious disease. Currently available veterinarian vaccines do not induce long-term protection against infection and do not provide cross-protective immunity. Several studies have suggested the use of DnaK as an antigen in vaccine formulation, due to an exceptional degree of immunogenicity. We focused on four surface proteins: rLIC10368 (Lsa21, rLIC10494, rLIC12690 (Lp95, and rLIC12730, previously shown to be involved in host-pathogen interactions. Our goal was to evaluate the immunogenicity of the proteins genetically fused with DnaK in animal model. The chosen genes were amplified by PCR methodology and cloned into pAE, an E. coli vector. The recombinant proteins were expressed alone or in fusion with DnaK at the N-terminus. Our results demonstrate that leptospiral proteins fused with DnaK have elicited an enhanced immune response in mice when compared to the effect promoted by the individual proteins. The boosted immune effect was demonstrated by the production of total IgG, lymphocyte proliferation, and significant amounts of IL-10 in supernatant of splenocyte cell cultures. We believe that this approach could be employed in vaccines to enhance presentation of antigens of Leptospira to professional immune cells.

  4. Morphology dependent catalysis and surface enhanced Raman scattering (SERS) studies using Pd nanostructures in DNA, CTAB and PVA scaffolds.

    Science.gov (United States)

    Kundu, Subrata; Yi, Su-In; Ma, Lian; Chen, Yunyun; Dai, Wei; Sinyukov, Alexander M; Liang, Hong

    2017-07-25

    Palladium nanoparticles (Pd NPs) of three different morphologies viz., nanocubes with cetyltrimethylammonium bromide (CTAB), nanowires with polyvinyl alcohol (PVA) and Pd NPs with deoxyribonucleic acid (DNA) scaffolds were synthesized by UV-irradiation. Catalysis and surface enhanced Raman scattering (SERS) studies were done with the synthesized morphologically distinct Pd nanostructures for the very first time. The catalytic rate was extremely high with Pd nanowires templated with PVA and the order of the catalytic rate was Pd nanowires in PVA > Pd nanocubes in CTAB > DNA-Pd wire-like assemblies. The highest catalytic rate was observed for PVA capped Pd nanowires which is a few hundred fold higher than other metal NP catalysts. Methylene blue (MB) was used as a Raman analyte for the SERS study and the largest EF of 1.9 × 10 5 at a peak position of 1391 cm -1 was observed with Pd nanowires in the DNA scaffold as a SERS substrate. The order of the SERS EF values was DNA-Pd wire-like assemblies > Pd nanocubes in CTAB > Pd nanowires in PVA. Beyond everything, the present synthesis route is easy, faster, candid, highly reproducible and cost-effective. In the near future, the same protocol could be applied to synthesize other materials for various applications.

  5. Structure and Function of the PriC DNA Replication Restart Protein.

    Science.gov (United States)

    Wessel, Sarah R; Cornilescu, Claudia C; Cornilescu, Gabriel; Metz, Alice; Leroux, Maxime; Hu, Kaifeng; Sandler, Steven J; Markley, John L; Keck, James L

    2016-08-26

    Collisions between DNA replication complexes (replisomes) and barriers such as damaged DNA or tightly bound protein complexes can dissociate replisomes from chromosomes prematurely. Replisomes must be reloaded under these circumstances to avoid incomplete replication and cell death. Bacteria have evolved multiple pathways that initiate DNA replication restart by recognizing and remodeling abandoned replication forks and reloading the replicative helicase. In vitro, the simplest of these pathways is mediated by the single-domain PriC protein, which, along with the DnaC helicase loader, can load the DnaB replicative helicase onto DNA bound by the single-stranded DNA (ssDNA)-binding protein (SSB). Previous biochemical studies have identified PriC residues that mediate interactions with ssDNA and SSB. However, the mechanisms by which PriC drives DNA replication restart have remained poorly defined due to the limited structural information available for PriC. Here, we report the NMR structure of full-length PriC from Cronobacter sakazakii PriC forms a compact bundle of α-helices that brings together residues involved in ssDNA and SSB binding at adjacent sites on the protein surface. Disruption of these interaction sites and of other conserved residues leads to decreased DnaB helicase loading onto SSB-bound DNA. We also demonstrate that PriC can directly interact with DnaB and the DnaB·DnaC complex. These data lead to a model in which PriC acts as a scaffold for recruiting DnaB·DnaC to SSB/ssDNA sites present at stalled replication forks. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Micropatterned Ferrocenyl Monolayers Covalently Bound to Hydrogen-Terminated Silicon Surfaces: Effects of Pattern Size on the Cyclic Voltammetry and Capacitance Characteristics

    NARCIS (Netherlands)

    Fabre, B.; Pujari, S.P.; Scheres, L.M.W.; Zuilhof, H.

    2014-01-01

    The effect of the size of patterns of micropatterned ferrocene (Fc)-functionalized, oxide-free n-type Si(111) surfaces was systematically investigated by electrochemical methods. Microcontact printing with amine-functionalized Fc derivatives was performed on a homogeneous acid fluoride-terminated

  7. Terahertz response of DNA oligonucleotides on the surface of silicon nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Bagraev, N. T., E-mail: bagraev@mail.ioffe.ru [Peter the Great Saint-Petersburg Polytechnic University (Russian Federation); Chernev, A. L. [Russian Academy of Sciences, Saint Petersburg Academic University—Nanotechnology Research and Education Center (Russian Federation); Klyachkin, L. E.; Malyarenko, A. M. [Russian Academy of Sciences, Ioffe Physical–Technical Institute (Russian Federation); Emel’yanov, A. K.; Dubina, M. V. [Russian Academy of Sciences, Saint Petersburg Academic University—Nanotechnology Research and Education Center (Russian Federation)

    2016-09-15

    The possibility of identifying DNA oligonucleotides deposited onto the region of the edge channels of silicon nanostructures is considered. The role of various THz (terahertz) radiation harmonics of silicon nanostructures in the resonance response of oligonucleotides is analyzed. In particular, this makes it possible to compare single-stranded 100- and 50-mer DNA oligonucleotides. A technique for the rapid identification of different oligonucleotides by measuring changes in the conductance and transverse potential difference of silicon nanostructures with microcavities, embedded in the edge channels for selecting THz radiation characteristics, is proposed.

  8. Electrostatic control by lipids upon the membrane-bound (Na+ + K+)-ATPase. II. The influence of surface potential upon the activating ion equilibria.

    Science.gov (United States)

    Ahrens, M L

    1983-07-13

    Electrostatic influences upon the enzymatic activity of the (Na+ + K+)-ATPase from ox brain (EC 3.6.1.3) have been studied. (1) The characteristics of the temperature dependence of the activity - the slopes and inflection temperature, Ti, of the Arrhenius plots - have been shown to depend on the total concentration, but not on the specific properties of added monovalent ions. (2) The enzymatic activity has been shown to be subject simultaneously to unspecific and specific influences of alkali-metal ions or NH+4. Ion-specific effects result from different binding constants of complexation between activating ions and enzyme. These stability constants are affected by the formation of an electrical double layer at the membrane surface. With increasing electrostatic screening, the complex formation is destabilized and, as a consequence, the enzymatic activity decreases. (3) This interaction between ion binding and surface electrostatics enables the enzyme to adapt its activity to the actual ionic conditions. This gives rise to a complex net dependence of the enzymatic activity upon the concentrations of activating ions. Such dependencies are analyzed, and an 'activity surface' has been constructed which represents the enzymatic activity as a function of simultaneously varying concentrations of sodium and potassium. The shape of this activity surface is determined by the relations between ion concentrations, surface potential and the resulting stability of the complexation between the activating ions and the enzyme. By means of three-dimensional representation it is demonstrated that the adaptability of the stability constants is of great importance with respect to the maintenance of the optimal ionic concentrations within the living cell. Therefore, by means of the surrounding membrane, the ATPase is provided with a quality, in addition to its substrate specificity and catalytic ability, which is necessary for its function as a transport enzyme.

  9. Crystal structure, Hirshfeld surfaces and DNA cleavage investigation of two copper(II) complexes containing polypyridine and salicylide ligands.

    Science.gov (United States)

    Luo, Yang-Hui; Sun, Bai-Wang

    2014-05-21

    Two copper complexes 1 [Cu2(phen)2(salicylaldehyde)2(ClO4)2] and 2 [Cu2 (2,2'-dipyridyl)2(salicylaldehyde)2(ClO4)2] have been synthesized and characterized by elemental analysis and single-crystal X-ray diffraction. These two complexes were display binuclear structure with Cu(II) ions in distorted octahedral environment but antipodal orientation of the binuclear units between them. Molecular Hirshfeld surfaces revealed that the crystal structures of 1 and 2 were supported mainly by H-H, C-H⋯π, π⋯π (C-C), and C-H⋯O intermolecular interactions. DNA cleavage experiments of complexes 1 and 2 revealed that these complexes can intercalation with DNA. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Surface-Enhanced Raman Spectroscopy forStaphylococcus aureusDNA Detection by Using Surface-Enhanced Raman Scattering Tag on Au Film Over Nanosphere Substrate.

    Science.gov (United States)

    Chen, Jian; Wang, Jun-Feng; Wu, Xue-Zhong; Rong, Zhen; Dong, Pei-Tao; Xiao, Rui

    2018-06-01

    We developed a high-performance surface-enhanced Raman scattering (SERS) sensing platform that can be used for specific and sensitive DNA detection. The SERS platform combines the advantages of Au film over nanosphere (AuFON) substrate and Ag@PATP@SiO2 SERS tag. SERS tag-on-AuFON is a sensing system that operates by the self-assembly of SERS tag onto an AuFON substrate in the presence of target DNAs. The SERS signals can be dramatically enhanced by the formation of "hot spots" in the interstices between the assembled nanostructures, as confirmed by finite-difference time-domain (FDTD) simulation. As a new sensing platform, SERS tag-on-AuFON was utilized to detect Staphylococcus aureus (S. aureus) DNA with a limit of detection at 1 nM. A linear relationship was also observed between the SERS intensity at Raman peak 1439 cm-1 and the logarithm of target DNA concentrations ranging from 1 μM to 1 nM. Besides, the sensing platform showed good homogeneity, with a relative standard deviation of about 1%. The sensitive SERS platform created in this study is a promising tool for detecting trace biochemical molecules because of its relatively simple and effective fabrication procedure, high sensitivity, and high reproducibility of the SERS effect.

  11. Ultra-small rhenium nanoparticles immobilized on DNA scaffolds: An excellent material for surface enhanced Raman scattering and catalysis studies.

    Science.gov (United States)

    Anantharaj, S; Sakthikumar, K; Elangovan, Ayyapan; Ravi, G; Karthik, T; Kundu, Subrata

    2016-12-01

    Highly Sensitive and ultra-small Rhenium (Re) metal nanoparticles (NPs) were successfully stabilized in water by the staging and fencing action of the versatile biomolecule DNA that resulted in two distinct aggregated chain-like morphologies with average grain sizes of 1.1±0.1nm and 0.7±0.1nm for the very first time within a minute of reaction time. Re NPs are formed by the borohydride reduction of ammonium perrhenate (NH4ReO4) in the presence of DNA at room temperature (RT) under stirring. The morphologies were controlled by carefully monitoring the molar ratio of NH4ReO4 and DNA. The synthesized material was employed in two potential applications: as a substrate for surface enhanced Raman scattering (SERS) studies and as a catalyst for the reduction of aromatic nitro compounds. SERS study was carried out by taking methylene blue (MB) as the probe and the highest SERS enhancement factor (EF) of 2.07×10(7) was found for the aggregated chain-like having average grain size of 0.7±0.1nm. Catalytic reduction of 4-nitro phenol (4-NP), 2-nitro phenol (2-NP) and 4-nitroaniline (4-NA) with a rate constant value of 6×10(-2)min(-1), 33.83×10(-2)min(-1) and 37.4×10(-2)min(-1) have testified the excellent catalytic performance of our Re NPs immobilized on DNA. The overall study have revealed the capability of DNA in stabilizing the highly reactive Re metal at nanoscale and made them applicable in practice. The present route can also be extended to prepare one dimensional (1-D), self-assembled NPs of other reactive metals, mixed metals or even metal oxides for specific applications in water based solutions. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Epitaxy of the bound water phase on hydrophilic surfaces of biopolymers as key mechanism of microwave radiation effects on living objects.

    Science.gov (United States)

    Kuznetsov, Denis B; Orlova, Ekaterina V; Neschislyaev, Valery A; Volkhin, Igor L; Izmestiev, Igor V; Lunegov, Igor V; Balandina, Alevtina V; Dianova, Dina G

    2017-06-01

    The research investigates the mechanism of microwave radiation effects on biological characteristics and structural-dynamic parameters of a sensor bioluminescence system. The research objects are a sterile growth medium (fish meal hydrolisate) and a bacterial culture. It has been established that irradiation causes changes of the growth medium spectral properties within the range of 200-350nm. Changes take place in the intensity and character of luminescence, as well as in relaxation parameters of nuclear magnetic resonance, growth characteristics of the bacterial culture, its cellular morphology and surface topology. The research results enabled us to establish the mechanisms of primary molecular processes that occur when the bacterial culture is exposed to microwave radiation. Transformation of the dynamic-structural state of adsorbed water phases on biopolymer surfaces has been found to be the key factor in the mechanism of microwave effects on living and water-containing objects. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Rapid outer-surface protein C DNA tattoo vaccination protects against Borrelia afzelii infection

    NARCIS (Netherlands)

    Wagemakers, A.; Mason, L. M. K.; Oei, A.; de Wever, B.; van der Poll, T.; Bins, A. D.; Hovius, J. W. R.

    2014-01-01

    Borrelia afzelii is the predominant Borrelia species causing Lyme borreliosis in Europe. Currently there is no human vaccine against Lyme borreliosis, and most research focuses on recombinant protein vaccines against Borrelia burgdorferi sensu stricto. DNA tattooing is a novel vaccination method

  14. DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families

    DEFF Research Database (Denmark)

    Sander, Adam F.; Lavstsen, Thomas; Rask, Thomas Salhøj

    2014-01-01

    -erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers...

  15. Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere

    Science.gov (United States)

    Whon, Tae Woong; Kim, Min-Soo; Roh, Seong Woon; Shin, Na-Ri; Lee, Hae-Won

    2012-01-01

    Airborne viruses are expected to be ubiquitous in the atmosphere but they still remain poorly understood. This study investigated the temporal and spatial dynamics of airborne viruses and their genotypic characteristics in air samples collected from three distinct land use types (a residential district [RD], a forest [FR], and an industrial complex [IC]) and from rainwater samples freshly precipitated at the RD site (RD-rain). Viral abundance exhibited a seasonal fluctuation in the range between 1.7 × 106 and 4.0 × 107 viruses m−3, which increased from autumn to winter and decreased toward spring, but no significant spatial differences were observed. Temporal variations in viral abundance were inversely correlated with seasonal changes in temperature and absolute humidity. Metagenomic analysis of air viromes amplified by rolling-circle phi29 polymerase-based random hexamer priming indicated the dominance of plant-associated single-stranded DNA (ssDNA) geminivirus-related viruses, followed by animal-infecting circovirus-related sequences, with low numbers of nanoviruses and microphages-related genomes. Particularly, the majority of the geminivirus-related viruses were closely related to ssDNA mycoviruses that infect plant-pathogenic fungi. Phylogenetic analysis based on the replication initiator protein sequence indicated that the airborne ssDNA viruses were distantly related to known ssDNA viruses, suggesting that a high diversity of viruses were newly discovered. This research is the first to report the seasonality of airborne viruses and their genetic diversity, which enhances our understanding of viral ecology in temperate regions. PMID:22623790

  16. Supported organoactinides. Surface chemistry and catalytic properties of alumina-bound (Cyclopentadienyl)- and (Pentamethylcyclopentadienyl)thorium and -uranium hydrocarbyls and hydrides

    International Nuclear Information System (INIS)

    He, M.Y.; Xiong, G.; Toscano, P.J.; Burwell, R.L. Jr.; Marks, T.J.

    1985-01-01

    Results of a detailed, quantitative investigation are reported of surface chemistry and catalysis involving selected organoactinides and partially dehydroxylated (PDA) or dehydroxylated (DA) alumina supports. For the complexes Cp' 2 M(CH 3 ) 2 and Cp' 2 M(CD 3 ) 2 (Cp' = eta 5 - (CH 3 ) 5 ; M = Th, U), methane-evolving surface reaction pathways are identified as M-CH 3 protonolysis via surface OH (especially on PDA), Cp' H atom abstraction, and intramolecular elimination of methane within M(CH 3 ) 2 units. This latter process is proposed on the basis of methylene transfer to acetone and some olefin metathesis activity to result in Al 3+ -stabilized alkylidenes. Hydogenolysis studies indicate that ca. 25% of the Cp' 2 M(CH 3 ) 2 /DA surface M-CH 3 groups are removable as methane; reduction of methyl chloride to methane confirms the presence of surface M-H groups produced by hydrogenolysis. The Cp' 2 M(CH 3 ) 2 /DA complexes are active catalysts for propylene hydrogenation following a variety of pretreatment conditions, with N/sub t/ approx. = 0.5 s -1 in a flow reactor at -63 0 C (about 10 times more active than typical Pt/SiO 2 catalysts under the same conditions). M = Th and U are comparable in hydrogenation activity, and CO poisoning experiments indicate that ca. 3% of the adsorbed molecules are catalytically active. Cp' 2 M(CH 3 ) 2 complexes on PDA and silica gel are considerably less active catalysts. The Cp' 2 M(CH 3 ) 2 /DA systems are also active catalysts for ethylene polymerization and weakly active for butene isomerization. Experiments with Cp' 2 Th[CH 2 C(CH 3 ) 3 ] 2 and [Cp' 2 Th(μ-H)H] 2 on DA reveal activity for propylene hydrogenation comparable to the Cp' 2 M(CH 3 ) 2 systems. In contrast, more coordinatively saturated Cp 3 UCH 3 and Cp 3 Th(n-C 4 H 9 ) (Cp = eta 5 -C 5 H 5 ) are far less active, while Cp'Th(CH 2 C 6 H 5 ) 3 is far more active (N/sub t/ approx. = 10 s -1 )

  17. Stepwise bending of DNA by a single TATA box binding protein

    DEFF Research Database (Denmark)

    Tolic-Nørrelykke, Simon F; Rasmussen, Mette B; Pavone, Francesco S

    2006-01-01

    The TATA-box binding protein (TBP) is required by all three eucaryotic RNA polymerases for the initiation of transcription from most promoters. TBP recognizes, binds to, and bends promoter sequences called "TATA-boxes" in the DNA. We present results from the study of individual Saccharomyces...... cerevisiae TBPs interacting with single DNA molecules containing a TATA-box. Using video microscopy, we observed the Brownian motion of the beads tethered by short surface-bound DNA. When TBP binds to and bends the DNA, the conformation of the DNA changes and the amplitude of Brownian motion of the tehtered...

  18. Integration of Multiplexed Microfluidic Electrokinetic Concentrators with a Morpholino Microarray via Reversible Surface Bonding for Enhanced DNA Hybridization.

    Science.gov (United States)

    Martins, Diogo; Wei, Xi; Levicky, Rastislav; Song, Yong-Ak

    2016-04-05

    We describe a microfluidic concentration device to accelerate the surface hybridization reaction between DNA and morpholinos (MOs) for enhanced detection. The microfluidic concentrator comprises a single polydimethylsiloxane (PDMS) microchannel onto which an ion-selective layer of conductive polymer poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) ( PSS) was directly printed and then reversibly surface bonded onto a morpholino microarray for hybridization. Using this electrokinetic trapping concentrator, we could achieve a maximum concentration factor of ∼800 for DNA and a limit of detection of 10 nM within 15 min. In terms of the detection speed, it enabled faster hybridization by around 10-fold when compared to conventional diffusion-based hybridization. A significant advantage of our approach is that the fabrication of the microfluidic concentrator is completely decoupled from the microarray; by eliminating the need to deposit an ion-selective layer on the microarray surface prior to device integration, interfacing between both modules, the PDMS chip for electrokinetic concentration and the substrate for DNA sensing are easier and applicable to any microarray platform. Furthermore, this fabrication strategy facilitates a multiplexing of concentrators. We have demonstrated the proof-of-concept for multiplexing by building a device with 5 parallel concentrators connected to a single inlet/outlet and applying it to parallel concentration and hybridization. Such device yielded similar concentration and hybridization efficiency compared to that of a single-channel device without adding any complexity to the fabrication and setup. These results demonstrate that our concentrator concept can be applied to the development of a highly multiplexed concentrator-enhanced microarray detection system for either genetic analysis or other diagnostic assays.

  19. Hepatitis B Virus DNA in Blood Samples Positive for Antibodies to Core Antigen and Negative for Surface Antigen

    Science.gov (United States)

    Gutiérrez, C.; León, G.; Loureiro, C. L.; Uzcátegui, N.; Liprandi, F.; Pujol, F. H.

    1999-01-01

    Anti-hepatitis B core antigen (HBcAg)-positive hepatitis B surface antigen (HBsAg)-negative plasma samples from blood donors were tested by nested PCR. DNA positivity was more significantly associated with high levels of anti-HBcAg than with low levels of anti-HBsAg antibodies. Analysis of a dilution of anti-HBcAg antibodies might result in a more rational exclusion of anti-HBcAg-positive HBsAg-negative samples, reducing the number of donations discarded and enabling more countries to incorporate anti-HBcAg testing. PMID:10473534

  20. The flexible structure of the K24S28 region of Leucine-Rich Amelogenin Protein (LRAP bound to apatites as a function of surface type, calcium, mutation, and ionic strength

    Directory of Open Access Journals (Sweden)

    Junxia eLu

    2014-07-01

    Full Text Available Leucine-Rich Amelogenin Protein (LRAP is a member of the amelogenin family of biomineralization proteins, proteins which play a critical role in enamel formation. Recent studies have revealed the structure and orientation of the N- and C-terminus of LRAP bound to hydroxyapatite (HAP, a surface used as an analog of enamel. The structure of one region, K24 to S28, was found to be sensitive to phosphorylation of S16, the only naturally observed site of serine phosphorylation in LRAP, suggesting that K24S28 may sit at a key region of structural flexibility and play a role in the protein’s function. In this work, we investigated the sensitivity of the structure and orientation of this region when bound to HAP as a function of several factors which may vary during enamel formation to influence structure: the ionic strength (0.05 M, 0.15 M, 0.2 M, the calcium concentration (0.07 mM and 0.4 mM, and the surface to which it is binding (HAP and carbonated apatite (CAP, a more direct mimic of enamel. A naturally occurring mutation found in amelogenin (T21I was also investigated. The structure in the K24S28 region of the protein was found to be sensitive to these conditions, with the CAP surface and excess Ca2+ (8:1 [Ca2+]:[LRAP-K24S28(+P] resulting in a tighter helix, while low ionic strength relaxed the helical structure. Higher ionic strength and the point mutation did not result in any structural change in this region. The distance of the backbone of K24 from the surface was most sensitive to excess Ca2+ and in the T21I-mutation. Collectively, these data suggest that phosphorylated LRAP is able to accommodate structural changes while maintaining its interaction with the surface, and provides further evidence of the structural sensitivity of the K24S28 region, a sensitivity that may contribute to function in biomineralization.

  1. A single-surface electrochemical biosensor for the detection of DNA triplet repeat expansion

    Czech Academy of Sciences Publication Activity Database

    Fojta, Miroslav; Horáková Brázdilová, Petra; Cahová, Kateřina; Pečinka, Petr

    2006-01-01

    Roč. 18, č. 2 (2006), s. 141-151 ISSN 1040-0397 R&D Projects: GA MPO(CZ) 1H-PK/42; GA AV ČR(CZ) IAA4004402 Institutional research plan: CEZ:AV0Z50040507 Keywords : DNA hybridization * electrochemical biosensor * enzyme-linked assay Subject RIV: BO - Biophysics Impact factor: 2.444, year: 2006

  2. DNA Origami Directed Au Nanostar Dimers for Single-Molecule Surface-Enhanced Raman Scattering.

    Science.gov (United States)

    Tanwar, Swati; Haldar, Krishna Kanta; Sen, Tapasi

    2017-12-06

    We demonstrate the synthesis of Au nanostar dimers with tunable interparticle gap and controlled stoichiometry assembled on DNA origami. Au nanostars with uniform and sharp tips were immobilized on rectangular DNA origami dimerized structures to create nanoantennas containing monomeric and dimeric Au nanostars. Single Texas red (TR) dye was specifically attached in the junction of the dimerized origami to act as a Raman reporter molecule. The SERS enhancement factors of single TR dye molecules located in the conjunction region in dimer structures having interparticle gaps of 7 and 13 nm are 2 × 10 10 and 8 × 10 9 , respectively, which are strong enough for single analyte detection. The highly enhanced electromagnetic field generated by the plasmon coupling between sharp tips and cores of two Au nanostars in the wide conjunction region allows the accommodation and specific detection of large biomolecules. Such DNA-directed assembled nanoantennas with controlled interparticle separation distance and stoichiometry, and well-defined geometry, can be used as excellent substrates in single-molecule SERS spectroscopy and will have potential applications as a reproducible platform in single-molecule sensing.

  3. Mutations on the DNA binding surface of TBP discriminate between yeast TATA and TATA-less gene transcription.

    Science.gov (United States)

    Kamenova, Ivanka; Warfield, Linda; Hahn, Steven

    2014-08-01

    Most RNA polymerase (Pol) II promoters lack a TATA element, yet nearly all Pol II transcription requires TATA binding protein (TBP). While the TBP-TATA interaction is critical for transcription at TATA-containing promoters, it has been unclear whether TBP sequence-specific DNA contacts are required for transcription at TATA-less genes. Transcription factor IID (TFIID), the TBP-containing coactivator that functions at most TATA-less genes, recognizes short sequence-specific promoter elements in metazoans, but analogous promoter elements have not been identified in Saccharomyces cerevisiae. We generated a set of mutations in the yeast TBP DNA binding surface and found that most support growth of yeast. Both in vivo and in vitro, many of these mutations are specifically defective for transcription of two TATA-containing genes with only minor defects in transcription of two TATA-less, TFIID-dependent genes. TBP binds several TATA-less promoters with apparent high affinity, but our results suggest that this binding is not important for transcription activity. Our results are consistent with the model that sequence-specific TBP-DNA contacts are not important at yeast TATA-less genes and suggest that other general transcription factors or coactivator subunits are responsible for recognition of TATA-less promoters. Our results also explain why yeast TBP derivatives defective for TATA binding appear defective in activated transcription. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  4. Feasibility of using DNA-immobilized nanocellulose-based immunoadsorbent for systemic lupus erythematosus plasmapheresis.

    Science.gov (United States)

    Xu, Changgang; Carlsson, Daniel O; Mihranyan, Albert

    2016-07-01

    The goal of this project was to study the feasibility of using a DNA-immobilized nanocellulose-based immunoadsorbent for possible application in medical apheresis such as systemic lupus erythematosus (SLE) treatment. Calf thymus DNA was bound to high surface area nanocellulose membrane at varying concentrations using UV-irradiation. The DNA-immobilized samples were characterized with scanning electron microscopy, atomic force microscopy, and phosphorus elemental analysis. The anti-ds-DNA IgG binding was tested in vitro using ELISA. The produced sample showed high affinity in vitro to bind anti-ds-DNA-antibodies from mice, as much as 80% of added IgG was bound by the membrane. Furthermore, the binding efficiency was quantitatively dependent on the amount of immobilized DNA onto nanocellulose membrane. The described nanocellulose membranes are interesting immunoadsorbents for continued clinical studies. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Trapping and manipulating single molecules of DNA

    Science.gov (United States)

    Shon, Min Ju

    This thesis presents the development and application of nanoscale techniques to trap and manipulate biomolecules, with a focus on DNA. These methods combine single-molecule microscopy and nano- and micro-fabrication to study biophysical properties of DNA and proteins. The Dimple Machine is a lab-on-a-chip device that can isolate and confine a small number of molecules from a bulk solution. It traps molecules in nanofabricated chambers, or "dimples", and the trapped molecules are then studied on a fluorescence microscope at the single-molecule level. The sampling of bulk solution by dimples is representative, reproducible, and automated, enabling highthroughput single-molecule experiments. The device was applied to study hybridization of oligonucleotides, particularly in the context of reaction thermodynamics and kinetics in nanoconfinement. The DNA Pulley is a system to study protein binding and the local mechanical properties of DNA. A molecule of DNA is tethered to a surface on one end, and a superparamagnetic bead is attached to the other. A magnet pulls the DNA taut, and a silicon nitride knife with a nanoscale blade scans the DNA along its contour. Information on the local properties of the DNA is extracted by tracking the bead with nanometer precision in a white-light microscope. The system can detect proteins bound to DNA and localize their recognition sites, as shown with a model protein, EcoRI restriction enzyme. Progress on the measurements of nano-mechanical properties of DNA is included.

  6. Validation of EMP bounds

    Energy Technology Data Exchange (ETDEWEB)

    Warne, L.K.; Merewether, K.O.; Chen, K.C.; Jorgenson, R.E.; Morris, M.E.; Solberg, J.E.; Lewis, J.G. [Sandia National Labs., Albuquerque, NM (United States); Derr, W. [Derr Enterprises, Albuquerque, NM (United States)

    1996-07-01

    Test data on canonical weapon-like fixtures are used to validate previously developed analytical bounding results. The test fixtures were constructed to simulate (but be slightly worse than) weapon ports of entry but have known geometries (and electrical points of contact). The exterior of the test fixtures exhibited exterior resonant enhancement of the incident fields at the ports of entry with magnitudes equal to those of weapon geometries. The interior consisted of loaded transmission lines adjusted to maximize received energy or voltage but incorporating practical weapon geometrical constraints. New analytical results are also presented for bounding the energies associated with multiple bolt joints and for bounding the exterior resonant enhancement of the exciting fields.

  7. Massive Galileon positivity bounds

    Science.gov (United States)

    de Rham, Claudia; Melville, Scott; Tolley, Andrew J.; Zhou, Shuang-Yong

    2017-09-01

    The EFT coefficients in any gapped, scalar, Lorentz invariant field theory must satisfy positivity requirements if there is to exist a local, analytic Wilsonian UV completion. We apply these bounds to the tree level scattering amplitudes for a massive Galileon. The addition of a mass term, which does not spoil the non-renormalization theorem of the Galileon and preserves the Galileon symmetry at loop level, is necessary to satisfy the lowest order positivity bound. We further show that a careful choice of successively higher derivative corrections are necessary to satisfy the higher order positivity bounds. There is then no obstruction to a local UV completion from considerations of tree level 2-to-2 scattering alone. To demonstrate this we give an explicit example of such a UV completion.

  8. A Conserved DNA Repeat Promotes Selection of a Diverse Repertoire of Trypanosoma brucei Surface Antigens from the Genomic Archive.

    Directory of Open Access Journals (Sweden)

    Galadriel Hovel-Miner

    2016-05-01

    Full Text Available African trypanosomes are mammalian pathogens that must regularly change their protein coat to survive in the host bloodstream. Chronic trypanosome infections are potentiated by their ability to access a deep genomic repertoire of Variant Surface Glycoprotein (VSG genes and switch from the expression of one VSG to another. Switching VSG expression is largely based in DNA recombination events that result in chromosome translocations between an acceptor site, which houses the actively transcribed VSG, and a donor gene, drawn from an archive of more than 2,000 silent VSGs. One element implicated in these duplicative gene conversion events is a DNA repeat of approximately 70 bp that is found in long regions within each BES and short iterations proximal to VSGs within the silent archive. Early observations showing that 70-bp repeats can be recombination boundaries during VSG switching led to the prediction that VSG-proximal 70-bp repeats provide recombinatorial homology. Yet, this long held assumption had not been tested and no specific function for the conserved 70-bp repeats had been demonstrated. In the present study, the 70-bp repeats were genetically manipulated under conditions that induce gene conversion. In this manner, we demonstrated that 70-bp repeats promote access to archival VSGs. Synthetic repeat DNA sequences were then employed to identify the length, sequence, and directionality of repeat regions required for this activity. In addition, manipulation of the 70-bp repeats allowed us to observe a link between VSG switching and the cell cycle that had not been appreciated. Together these data provide definitive support for the long-standing hypothesis that 70-bp repeats provide recombinatorial homology during switching. Yet, the fact that silent archival VSGs are selected under these conditions suggests the 70-bp repeats also direct DNA pairing and recombination machinery away from the closest homologs (silent BESs and toward the rest of

  9. Effect of water-surface discharge on the inactivation of Bacillus subtilis due to protein lysis and DNA damage.

    Science.gov (United States)

    Kadowaki, Kazunori; Sone, Toshifumi; Kamikozawa, Takashi; Takasu, Hiroyuki; Suzuki, Satoru

    2009-09-01

    The effect of water-surface discharge on the inactivation of Bacillus subtilis ATCC6633 in water was examined by using a very short high-voltage pulse generator. The surviving number of spore cells at 10(4) CFU/ml in initial concentration exponentially decreased with increasing discharge-treatment time. The input energy into the water-surface discharge under an O(2) gas flow for reduction in the survival number to 10% was lower than that under an air flow because many oxidation agents such as ozone and OH radical were produced under the O(2) gas flow. The input energy density for the one-tenth reduction depended not only on the spore state but also on the initial cell concentration. The input energy for the high-concentration spore cells (10(7) CFU/ml) was much higher than that for the low-concentration spore cells (10(4) CFU/ml). Cellular proteins and DNA were degraded by a 30-min discharge treatment of vegetative cells, whereas DNA of the high-concentration spore cells was relatively resistant.

  10. DNA Condensation by Partially Acetylated Poly(amido amine Dendrimers: Effects of Dendrimer Charge Density on Complex Formation

    Directory of Open Access Journals (Sweden)

    Ronald G. Larson

    2013-09-01

    Full Text Available The ability of poly(amido amine (or PAMAM dendrimers to condense semiflexible dsDNA and penetrate cell membranes gives them great potential in gene therapy and drug delivery but their high positive surface charge makes them cytotoxic. Here, we describe the effects of partial neutralization by acetylation on DNA condensation using light scattering, circular dichroism, and single molecule imaging of dendrimer-DNA complexes combed onto surfaces and tethered to those surfaces under flow. We find that DNA can be condensed by generation-five (G5 dendrimers even when the surface charges are more than 65% neutralized, but that such dendrimers bind negligibly when an end-tethered DNA is stretched in flow. We also find that when fully charged dendrimers are introduced by flow to end-tethered DNA, all DNA molecules become equally highly coated with dendrimers at a rate that becomes very fast at high dendrimer concentration, and that dendrimers remain bound during subsequent flow of dendrimer-free buffer. These results suggest that the presence of dendrimer-free DNA coexisting with dendrimer-bound DNA after bulk mixing of the two in solution may result from diffusion-limited irreversible dendrimer-DNA binding, rather than, or in addition to, the previously proposed cooperative binding mechanism of dendrimers to DNA.

  11. The binding parameters of radiolabelled monoclonal F (ab')2 and Fab' fragments relative to immunoglobulin G in reactions with surface-bound antigens

    International Nuclear Information System (INIS)

    Fjeld, J.G.; Nustad, K.; Michaelsen, T.E.

    1992-01-01

    The binding parameters of iodine-125-labelled intact monoclonal immunoglobulin G (IgG), F(ab') 2 and Fab' fragments were compared. The study was carried out with the two monoclonal antibodies (MoAbs) K13 and K16 specific for human Ig light chains κ and λ, respectively. When testing the 125 I-MoAbs against monodisperse polymer particles coated with the specific antigens, the K a for the F(ab') 2 fragments were similar to that for IgG, while the K a for the Fab' fragments were reduced to 10%-20% of that for IgG. The number N of effective target sites revealed with Fab' was higher than with F(ab') and IgG, presumably because less surface area is occupied by the small Fab' molecules. The immunoreactive fraction F ranged according to IgG>F(ab') 2 >Fab'. The explanation of the moderate difference between the K a of the monoclonal Fab' and the divalent IgG and F(ab') 2 was that the divalent molecules were not divalently attached to the particles. When testing the same antibody preparations against humanlymphoma cells producing Ig with light chains κ or λ, the binding results were less reliable than when particles were utilised, presumably due to antigen shedding. Different MoAbs vary in their loss of immunoreactivity due to enzymatic degradation and the radiolabelling procedure. The preparation of the radiolabelled fragments should therefore be optimized for each MoAb, and evaluation is necessary before injection. Artificial targets with a low leakage of antigen, like the monodisperse polymer particles here applied, are recommended for the in vitro evaluation of the immunoreactivity of labelled MoAb preparations. (orig.)

  12. Bounded variation and around

    CERN Document Server

    Appell, Jürgen; Merentes Díaz, Nelson José

    2013-01-01

    This monographis a self-contained exposition of the definition and properties of functionsof bounded variation and their various generalizations; the analytical properties of nonlinear composition operators in spaces of such functions; applications to Fourier analysis, nonlinear integral equations, and boundary value problems. The book is written for non-specialists. Every chapter closes with a list of exercises and open problems.

  13. Born Level Bound States

    Science.gov (United States)

    Hoyer, Paul

    2017-05-01

    Bound state poles in the S-matrix of perturbative QED are generated by the divergence of the expansion in α . The perturbative corrections are necessarily singular when expanding around free, {O}( α ^0 ) in and out states that have no overlap with finite-sized atomic wave functions. Nevertheless, measurables such as binding energies do have well-behaved expansions in powers of α (and log α ). It is desirable to formulate the concept of "lowest order" for gauge theory bound states such that higher order corrections vanish in the α → 0 limit. This may allow to determine a lowest order term for QCD hadrons which incorporates essential features such as confinement and chiral symmetry breaking, and thus can serve as the starting point of a useful perturbative expansion. I discuss a "Born" (no loop, lowest order in \\hbar ) approximation. Born level states are bound by gauge fields which satisfy the classical field equations. Gauss' law determines a distinct field A^0({\\varvec{x}}) for each instantaneous position of the charges. A Poincaré covariant boundary condition for the gluon field leads to a confining potential for q\\bar{q} and qqq states. In frames where the bound state is in motion the classical gauge field is obtained by a Lorentz boost of the rest frame field.

  14. Bounded Brownian Motion

    Directory of Open Access Journals (Sweden)

    Peter Carr

    2017-11-01

    Full Text Available Diffusions are widely used in finance due to their tractability. Driftless diffusions are needed to describe ratios of asset prices under a martingale measure. We provide a simple example of a tractable driftless diffusion which also has a bounded state space.

  15. Bound anionic states of adenine

    Energy Technology Data Exchange (ETDEWEB)

    Haranczyk, Maciej; Gutowski, Maciej S; Li, Xiang; Bowen, Kit H

    2007-03-20

    Anionic states of nucleic acid bases are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated nucleic acid base parent anions probed only dipole-bound states, which are not present in condensed phase environments, but did not observe valence anionic states, which for purine bases, are thought to be adiabatically unbound. Contrary to this expectation, we have demonstrated that some thus far ignored tautomers of adenine, which result from enamine-imine transformations, support valence anionic states with electron vertical detachment energies as large as 2.2 eV, and at least one of these anionic tautomers is adiabatically bound. Moreover, we predict that the new anionic tautomers should also dominate in solutions and should be characterized by larger values of electron vertical detachment energy than the canonical valence anion. All of the new-found anionic tautomers might be formed in the course of dissociative electron attachment followed by a hydrogen atom attachment to a carbon atom, and they might affect the structure and properties of DNA and RNA exposed to low-energy electrons. The discovery of these valence anionic states of adenine was facilitated by the development of: (i) a new experimental method for preparing parent anions of nucleic acid bases for photoelectron experiments, and (ii) a new combinatorial/ quantum chemical approach for identification of the most stable tautomers of organic molecules. The computational portion of this work was supported by the: (i) Polish State Committee for Scientific Research (KBN) Grants: DS/8000-4-0140-7 (M.G.) and N204 127 31/2963 (M.H.), (ii) European Social Funds (EFS) ZPORR/2.22/II/2.6/ARP/U/2/05 (M.H.), and (iii) US DOE Office of Biological and Environmental Research, Low Dose Radiation Research Program (M.G.). M.H. holds the Foundation for Polish Science (FNP) award for young scientists. The calculations were performed at the Academic

  16. Whole genome expression profiling using DNA microarray for determining biocompatibility of polymeric surfaces

    DEFF Research Database (Denmark)

    Stangegaard, Michael; Wang, Zhenyu; Kutter, Jörg Peter

    2006-01-01

    conventional methods to determine biocompatibility such as cellular growth rate, morphology and the hydrophobicity of the surfaces. HeLa cells grown on polymethylmethacrylate (PMMA) or a SU-8 surface treated with HNO3-ceric ammonium nitrate (HNO3-CAN) and ethanolamine showed no differences in growth rate......, morphology or gene expression profiles as compared to HeLa cells grown in cell culture flasks. Cells grown on SU-8 treated with only HNO3-CAN showed almost the same growth rate (36 ¡ 1 h) and similar morphology as cells grown in cell culture flasks (32 ¡ 1 h), indicating good biocompatibility. However, more...... than 200 genes showed different expression levels in cells grown on SU-8 treated with HNO3-CAN compared to cells grown in cell culture flasks. This shows that gene expression profiling is a simple and precise method for determining differences in cells grown on different surfaces that are otherwise...

  17. Surface-enhanced Raman scattering biosensor for DNA detection on nanoparticle island substrates

    DEFF Research Database (Denmark)

    Yuan, Scott Wu; Ho, Ho Pui; Lee, Rebecca K.Y.

    2009-01-01

    We present a study on the surface-enhanced Raman scattering (SERS) properties of Ag nanoparticle island substrates (NIS) and their applications for target oligonucleotide (OND) detection. It has been found that the surface nanostructure of NIS samples can be controlled with a good degree...... on the use of the detection OND with or without the gold nanoparticle (Au-NP). Our results confirm that, when the detection OND is coupled to the Au-NP, a better sensitivity for the target OND detection, in terms of a wider dynamic range and a lower detection limit (0:4 fM versus 1nM without Au-NP), would...

  18. Electronic properties and assambly of DNA-based molecules on gold surfaces

    DEFF Research Database (Denmark)

    Salvatore, Princia

    evidenced by such AQMS-intercalated systems inspired further studies of the double helical structures in the presence of polycationic compounds, such as hexamine cobalt(III) chloride, magnesium chloride, and spermidine trihydrochloride. The larger multivalent cations are expected to give a more rigid ds....... The spontaneous insertion of AQMS into the DNA double helix, and the chelating geometry of the triply dentate terpy coordinated to several transition metals offered a route to study electronic properties and charge transfer kinetics of the ONs confined at the electrochemical gold/electrolyte interface...... and addressing metal coordination of ONs with the terpyridine ligand in the highly flexible structure ofthe new synthetic unlocked nucleic acid (UNA). Composite voltammetric behaviour for each of the metal-functionalized ONbased monolayers was observed and supported by in situscanning tunnelling microscopy...

  19. One-step polymer surface modification for minimizing drug, protein, and DNA adsorption in microanalytical systems

    DEFF Research Database (Denmark)

    Larsen, Esben Kjær Unmack; Larsen, Niels Bent

    2013-01-01

    The non-specific adsorption of dissolved analytes strongly reduces the sensitivity and reliability in polymer microanalytical systems. Here, a one-step aqueous phase procedure modifies polymer material surfaces to strongly reduce their non-specific adsorption of a broad range of organic analytes ...... systems, including polystyrene (PS), cyclic olefin copolymer (COC), liquid crystalline polymer (LCP), and polyimide (PI)....

  20. Surface-immobilized DNAzyme-type biocatalysis

    Science.gov (United States)

    Stefan, Loic; Lavergne, Thomas; Spinelli, Nicolas; Defrancq, Eric; Monchaud, David

    2014-02-01

    The structure of the double helix of deoxyribonucleic acid (DNA, also called duplex-DNA) was elucidated sixty years ago by Watson, Crick, Wilkins and Franklin. Since then, DNA has continued to hold a fascination for researchers in diverse fields including medicine and nanobiotechnology. Nature has indeed excelled in diversifying the use of DNA: beyond its canonical role of repository of genetic information, DNA could also act as a nanofactory able to perform some complex catalytic tasks in an enzyme-mimicking manner. The catalytic capability of DNA was termed DNAzyme; in this context, a peculiar DNA structure, a quadruple helix also named quadruplex-DNA, has recently garnered considerable interest since its autonomous catalytic proficiency relies on its higher-order folding that makes it suitable to interact efficiently with hemin, a natural cofactor of many enzymes. Quadruplexes have thus been widely studied for their hemoprotein-like properties, chiefly peroxidase-like activity, i.e., their ability to perform hemin-mediated catalytic oxidation reactions. Recent literature is replete with applications of quadruplex-based peroxidase-mimicking DNAzyme systems. Herein, we take a further leap along the road to biochemical applications, assessing the actual efficiency of catalytic quadruplexes for the detection of picomolar levels of surface-bound analytes in an enzyme-linked immunosorbent (ELISA)-type assay. To this end, we exploit an innovative strategy based on the functionalization of DNA by a multitasking platform named RAFT (for regioselectivity addressable functionalized template), whose versatility enables the grafting of DNA whatever its nature (duplex-DNA, quadruplex-DNA, etc.). We demonstrate that the resulting biotinylated RAFT/quadruplex systems indeed acquire catalytic properties that allow for efficient luminescent detection of picomoles of surface-bound streptavidin. We also highlight some of the pitfalls that have to be faced during optimization

  1. Charge-controlled fixation of DNA molecules on silicon surface and electro-physical properties of Au–DNA–Si interface

    Energy Technology Data Exchange (ETDEWEB)

    Bazlov, N.V., E-mail: nikolay.bazlov@gmail.com [V.A. Fok Institute of Physics, Saint-Petersburg State University, Ulyanovskaya 1, 198504 Saint-Petersburg (Russian Federation); Vyvenko, O.F.; Sokolov, P.A.; Kas’yanenko, N.A.; Petrov, Yu V. [V.A. Fok Institute of Physics, Saint-Petersburg State University, Ulyanovskaya 1, 198504 Saint-Petersburg (Russian Federation)

    2013-02-15

    Light-induced fixation of DNA molecules on silicon surface was done and electro-physical properties of Schottky diodes with DNA on interfaces were investigated. Thymus DNA molecules were deposited on silicon from a water solution. Fixed molecular structures were observed with helium ionic microscopy and atomic force microscopy and then they were covered with thermal sputtered gold film. Obtained structures Au–DNA–(n-Si) were examined with current–voltage and frequency dependent admittance measurements. In darkness immobilizing of molecules leaded to form DNA ropes with thickness up to 10 nm and distances between them about 1 mkm. Fixation under illumination resulted in forming of single DNA mesh with thickness about 1 nm and cell size about 100 nm. Presence of molecular mesh on interface leaded to increasing of charge density controlled by metal Fermi level and improved diode quality. Presence of molecular ropes resulted in increasing of charge density controlled by semiconductor. From the estimation of interface state density values the origin of the states at the interface between DNA and silicon substrate is suggested to be DNA phosphate groups contacting or being close to the substrate surface.

  2. Preparation and phase behaviour of surface-active pharmaceuticals: self-assembly of DNA and surfactants with membranes. Differential adiabatic scanning microcalorimetric study.

    Science.gov (United States)

    Süleymanoğlu, Erhan

    2005-08-01

    Some energetics issues relevant to preparation and surface characterization of zwitterionic phospholipid-DNA self-assemblies, as alternative models of the currently used problematic lipoplexes are presented. Nucleic acid compaction capacities of Mg(2+) and N-alkyl-N,N,N-trimetylammonium ions (C(n)TMA, n=12) were compared, with regard to surface interaction with unilamellar vesicles. Differential adiabatic scanning microcalorimetric measurements of synthetic phosphatidylcholine liposomes and calf thymus DNA and their ternary complexes with Mg(2+) and C(12)TMA, were employed for deduction of the thermodynamic model describing their structural transitions. Small monodisperce and highly stable complexes are established after precompaction of DNA with detergent, followed by addition of liposomes. In contrast, divalent metal cation-mediated aggregation of vesicles either leads to heterogeneous multilamellar DNA-lipid arrangements, or to DNA-induced bilayer destabilization and lipid fusion. Possible dependence of the cellular internalization and gene transfection efficiency on the structure and physicochemical properties of DNA-Mg(2+)-liposomes or DNA-cationic surfactant-liposome systems is emphasized by proposing the structure of their molecular self-organizations with further implications in gene transfer research.

  3. Inverse-scattering-theory approach to the exact n→∞ solutions of O(n) ϕ⁴ models on films and semi-infinite systems bounded by free surfaces.

    Science.gov (United States)

    Rutkevich, Sergei B; Diehl, H W

    2015-06-01

    The O(n) ϕ(4) model on a strip bounded by a pair of planar free surfaces at separation L can be solved exactly in the large-n limit in terms of the eigenvalues and eigenfunctions of a self-consistent one-dimensional Schrödinger equation. The scaling limit of a continuum version of this model is considered. It is shown that the self-consistent potential can be eliminated in favor of scattering data by means of appropriately extended methods of inverse scattering theory. The scattering data (Jost function) associated with the self-consistent potential are determined for the L=∞ semi-infinite case in the scaling regime for all values of the temperature scaling field t=(T-T(c))/T(c) above and below the bulk critical temperature T(c). These results are used in conjunction with semiclassical and boundary-operator expansions and a trace formula to derive exact analytical results for a number of quantities such as two-point functions, universal amplitudes of two excess surface quantities, the universal amplitude difference associated with the thermal singularity of the surface free energy, and potential coefficients. The asymptotic behaviors of the scaled eigenenergies and eigenfunctions of the self-consistent Schrödinger equation as function of x=t(L/ξ(+))(1/ν) are determined for x→-∞. In addition, the asymptotic x→-∞ forms of the universal finite-size scaling functions Θ(x) and ϑ(x) of the residual free energy and the Casimir force are computed exactly to order 1/x, including their x(-1)ln|x| anomalies.

  4. Bounded Tamper Resilience

    DEFF Research Database (Denmark)

    Damgård, Ivan Bjerre; Faust, Sebastian; Mukherjee, Pratyay

    2013-01-01

    -free information) which can be used to refresh the secret key. We believe that bounded tampering is a meaningful and interesting alternative to avoid known impossibility results and can provide important insights into the security of existing standard cryptographic schemes.......Related key attacks (RKAs) are powerful cryptanalytic attacks where an adversary can change the secret key and observe the effect of such changes at the output. The state of the art in RKA security protects against an a-priori unbounded number of certain algebraic induced key relations, e.......g., affine functions or polynomials of bounded degree. In this work, we show that it is possible to go beyond the algebraic barrier and achieve security against arbitrary key relations, by restricting the number of tampering queries the adversary is allowed to ask for. The latter restriction is necessary...

  5. Bound Exciton Complexes

    Science.gov (United States)

    Meyer, B. K.

    In the preceding chapter, we concentrated on the properties of free excitons. These free excitons may move through the sample and hit a trap, a nonradiative or a radiative recombination center. At low temperatures, the latter case gives rise to either deep center luminescence, mentioned in Sect. 7.1 and discussed in detail in Chap. 9, or to the luminescence of bound exciton complexes (BE or BEC). The chapter continues with the most prominent of these BECs, namely A-excitons bound to neutral donors. The next aspects are the more weakly BEs at ionized donors. The Sect. 7.4 treats the binding or localization energies of BEC from a theoretical point of view, while Sect. 7.5 is dedicated to excited states of BECs, which contain either holes from deeper valence bands or an envelope function with higher quantum numbers. The last section is devoted to donor-acceptor pair transitions. There is no section devoted specifically to excitons bound to neutral acceptors, because this topic is still partly controversially discussed. Instead, information on these A0X complexes is scattered over the whole chapter, however, with some special emphasis seen in Sects. 7.1, 7.4, and 7.5.

  6. Surface-enhanced Raman spectroscopy of genomic DNA from in vitro grown tomato (Lycopersicon esculentum Mill.) cultivars before and after plant cryopreservation.

    Science.gov (United States)

    Muntean, Cristina M; Leopold, Nicolae; Tripon, Carmen; Coste, Ana; Halmagyi, Adela

    2015-06-05

    In this work the surface-enhanced Raman scattering (SERS) spectra of five genomic DNAs from non-cryopreserved control tomato plants (Lycopersicon esculentum Mill. cultivars Siriana, Darsirius, Kristin, Pontica and Capriciu) respectively, have been analyzed in the wavenumber range 400-1800 cm(-1). Structural changes induced in genomic DNAs upon cryopreservation were discussed in detail for four of the above mentioned tomato cultivars. The surface-enhanced Raman vibrational modes for each of these cases, spectroscopic band assignments and structural interpretations of genomic DNAs are reported. We have found, that DNA isolated from Siriana cultivar leaf tissues suffers the weakest structural changes upon cryogenic storage of tomato shoot apices. On the contrary, genomic DNA extracted from Pontica cultivar is the most responsive system to cryopreservation process. Particularly, both C2'-endo-anti and C3'-endo-anti conformations have been detected. As a general observation, the wavenumber range 1511-1652 cm(-1), being due to dA, dG and dT residues seems to be influenced by cryopreservation process. These changes could reflect unstacking of DNA bases. However, not significant structural changes of genomic DNAs from Siriana, Darsirius and Kristin have been found upon cryopreservation process of tomato cultivars. Based on this work, specific plant DNA-ligand interactions or accurate local structure of DNA in the proximity of a metallic surface, might be further investigated using surface-enhanced Raman spectroscopy. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Surface-enhanced Raman spectroscopy of genomic DNA from in vitro grown tomato (Lycopersicon esculentum Mill.) cultivars before and after plant cryopreservation

    Science.gov (United States)

    Muntean, Cristina M.; Leopold, Nicolae; Tripon, Carmen; Coste, Ana; Halmagyi, Adela

    2015-06-01

    In this work the surface-enhanced Raman scattering (SERS) spectra of five genomic DNAs from non-cryopreserved control tomato plants (Lycopersicon esculentum Mill. cultivars Siriana, Darsirius, Kristin, Pontica and Capriciu) respectively, have been analyzed in the wavenumber range 400-1800 cm-1. Structural changes induced in genomic DNAs upon cryopreservation were discussed in detail for four of the above mentioned tomato cultivars. The surface-enhanced Raman vibrational modes for each of these cases, spectroscopic band assignments and structural interpretations of genomic DNAs are reported. We have found, that DNA isolated from Siriana cultivar leaf tissues suffers the weakest structural changes upon cryogenic storage of tomato shoot apices. On the contrary, genomic DNA extracted from Pontica cultivar is the most responsive system to cryopreservation process. Particularly, both C2‧-endo-anti and C3'-endo-anti conformations have been detected. As a general observation, the wavenumber range 1511-1652 cm-1, being due to dA, dG and dT residues seems to be influenced by cryopreservation process. These changes could reflect unstacking of DNA bases. However, not significant structural changes of genomic DNAs from Siriana, Darsirius and Kristin have been found upon cryopreservation process of tomato cultivars. Based on this work, specific plant DNA-ligand interactions or accurate local structure of DNA in the proximity of a metallic surface, might be further investigated using surface-enhanced Raman spectroscopy.

  8. Plasmid DNA binds to the core oligosaccharide domain of LPS molecules of E. coli cell surface in the CaCl2-mediated transformation process.

    Science.gov (United States)

    Panja, Subrata; Aich, Pulakesh; Jana, Bimal; Basu, Tarakdas

    2008-09-01

    In the standard procedure for artificial transformation of E. coli by plasmid DNA, cellular competence for DNA uptake is developed by suspending the cells in ice-cold CaCl2 (50-100 mM). It is believed that CaCl2 helps DNA adsorption to the lipopolysaccharide (LPS) molecules on E. coli cell surface; however, the binding mechanism is mostly obscure. In this report, we present our findings of an in-depth study on in vitro interaction between plasmid DNA and E. coli LPS, using different techniques like absorption and circular dichroism spectroscopy, isothermal titration calorimetry, electron and atomic force microscopy, and so on. The results suggest that the Ca(II) ions, forming coordination complexes with the phosphates of DNA and LPS, facilitate the binding between them. The binding interaction appears to be cooperative, reversible, exothermic, and enthalpy-driven in nature. Binding of LPS causes a partial transition of DNA from B- to A-form. Finer study with the hydrolyzed products of LPS shows that only the core oligosaccharide domain of LPS is responsible for the interaction with DNA. Moreover, the biological significance of this interaction becomes evident from the observation that E. coli cells, from which the LPS have been leached out considerably, show higher efficiency of transformation, when transformed with plasmid-LPS complex rather than plasmid DNA alone.

  9. A method to estimate the elastic energy stored in braided DNA molecules using hydrodynamic equations

    Science.gov (United States)

    Fernández-Sierra, Mónica; Delgado-Martí, Violeta; Colón-García, Jorge E.; Quiñones, Edwin

    2011-01-01

    We present a single-molecule method for measuring the torque exerted by braided DNA molecules undergoing spontaneous unbraiding while attached to a paramagnetic dumbbell in the absence of external manipulation. A magnetic tweezers setup is employed to braid pairs of lambda DNA molecules covalently bound to a surface. Upon removing the magnetic field, the braided DNA molecules undergo spontaneous unbraiding, efficiently transforming the stored elastic energy into enough mechanical energy to rotate the tethered dumbbells for periods as long as 30 minutes. Using hydrodynamic equations we estimate the torque exerted on the dumbbells by the DNA braids, yielding values ranging from 47 to 166 pN nm. PMID:21765578

  10. Analysis of the role of PCNA-DNA contacts during clamp loading

    Directory of Open Access Journals (Sweden)

    Goedken Eric R

    2010-01-01

    Full Text Available Abstract Background Sliding clamps, such as Proliferating Cell Nuclear Antigen (PCNA in eukaryotes, are ring-shaped protein complexes that encircle DNA and enable highly processive DNA replication by serving as docking sites for DNA polymerases. In an ATP-dependent reaction, clamp loader complexes, such as the Replication Factor-C (RFC complex in eukaryotes, open the clamp and load it around primer-template DNA. Results We built a model of RFC bound to PCNA and DNA based on existing crystal structures of clamp loaders. This model suggests that DNA would enter the clamp at an angle during clamp loading, thereby interacting with positively charged residues in the center of PCNA. We show that simultaneous mutation of Lys 20, Lys 77, Arg 80, and Arg 149, which interact with DNA in the RFC-PCNA-DNA model, compromises the ability of yeast PCNA to stimulate the DNA-dependent ATPase activity of RFC when the DNA is long enough to extend through the clamp. Fluorescence anisotropy binding experiments show that the inability of the mutant clamp proteins to stimulate RFC ATPase activity is likely caused by reduction in the affinity of the RFC-PCNA complex for DNA. We obtained several crystal forms of yeast PCNA-DNA complexes, measuring X-ray diffraction data to 3.0 Å resolution for one such complex. The resulting electron density maps show that DNA is bound in a tilted orientation relative to PCNA, but makes different contacts than those implicated in clamp loading. Because of apparent partial disorder in the DNA, we restricted refinement of the DNA to a rigid body model. This result contrasts with previous analysis of a bacterial clamp bound to DNA, where the DNA was well resolved. Conclusion Mutational analysis of PCNA suggests that positively charged residues in the center of the clamp create a binding surface that makes contact with DNA. Disruption of this positive surface, which had not previously been implicated in clamp loading function, reduces RFC

  11. Nano-patterning of a stainless steel microneedle surface to improve the dip-coating efficiency of a DNA vaccine and its immune response.

    Science.gov (United States)

    Jung, Daeyoon; Rejinold, N Sanoj; Kwak, Jeong-Eun; Park, Su-Hyung; Kim, Yeu-Chun

    2017-11-01

    DNA vaccination with microneedles (MNs) into the skin represents a potential therapeutic approach for the clinical treatment of viral diseases as well as for intradermal genetic immunization. In this study, we investigated a DNA vaccination against the severe fever with thrombocytopenia syndrome virus (SFTSV) delivered by nano-patterned microneedles (nMNs) to improve the efficiency compared to a conventional MN vaccination. Because DNA vaccinations delivered by coated MNs have major disadvantages such as a poor coating efficiency and immunogenicity, additional excipients are necessary. Therefore, we developed nMNs to improve the affinity of stainless steel for plasmid DNA vaccinations. The results show that the nMNs have an improved DNA vaccine loading capacity because their surfaces have an increased hydrophilicity from the high surface/volume ratio. The cytocompatibility analysis also showed a higher cell proliferation when using the nMNs. Finally, the in vivo experiments with balb/c mice vaccinated with the SFTSV DNA vaccine-coated nMNs generated a higher level of cellular immune responses than that of the unmodified MNs. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Blog life: Entropy Bound

    Science.gov (United States)

    Steinberg, Peter

    2008-06-01

    Who is the blog written by? Peter Steinberg is a nuclear physicist at the Brookhaven National Laboratory in New York, US. He is acting project manager of the PHOBOS experiment, which used Brookhaven's Relativistic Heavy Ion Collider (RHIC) to search for unusual events produced during collisions between gold nuclei. He is also involved with the PHENIX experiment, which seeks to discover a new state of matter known as the quark-gluon plasma. In addition to his own blog Entropy Bound, Steinberg is currently blogging on a website that was set up last year to publicize the involvement of US scientists with the Large Hadron Collider (LHC) at CERN.

  13. Regularity of Bound States

    DEFF Research Database (Denmark)

    Faupin, Jeremy; Møller, Jacob Schach; Skibsted, Erik

    2011-01-01

    We study regularity of bound states pertaining to embedded eigenvalues of a self-adjoint operator H, with respect to an auxiliary operator A that is conjugate to H in the sense of Mourre. We work within the framework of singular Mourre theory which enables us to deal with confined massless Pauli–......–Fierz models, our primary example, and many-body AC-Stark Hamiltonians. In the simpler context of regular Mourre theory, our results boil down to an improvement of results obtained recently in [8, 9]....

  14. A surface plasmon resonance study of the intermolecular interaction between Escherichia coli topoisomerase I and pBAD/Thio supercoiled plasmid DNA

    Science.gov (United States)

    Tiwari, Purushottam Babu; Annamalai, Thirunavukkarasu; Cheng, Bokun; Narula, Gagandeep; Wang, Xuewen; Tse-Dinh, Yuk-Ching; He, Jin; Darici, Yesim

    2014-01-01

    To date, the bacterial DNA topoisomerases are one of the major target biomolecules for the discovery of new antibacterial drugs. DNA topoisomerase regulates the topological state of DNA, which is very important for replication, transcription and recombination. The relaxation of negatively supercoiled DNA is catalyzed by bacterial DNA topoisomerase I (topoI) and this reaction requires Mg2+. In this report, we first quantitatively studied the intermolecular interactions between Escherichia coli topoisomerase I (EctopoI) and pBAD/Thio supercoiled plasmid DNA using surface plasmon resonance (SPR) technique. The equilibrium dissociation constant (Kd) for EctopoI-pBAD/Thio interactions is determined to be about 8 nM. We then studied the effect of Mg2+ on the catalysis of EctopoI-pBAD/Thio reaction. A slightly higher equilibrium dissociation constant (~15 nM) was obtained for Mg2+ coordinated EctopoI (Mg2+EctopoI)-pBAD/Thio interactions. In addition, we observed a larger dissociation rate constant (kd) for Mg2+EctopoI-pBAD/Thio interactions (~0.043 s−1), compared to EctopoI-pBAD/Thio interactions (~0.017 s−1). These results suggest that enzyme turnover during plasmid DNA relaxation is enhanced due to the presence of Mg2+ and furthers the understanding of importance of the Mg2+ ion for bacterial topoisomerase I catalytic activity. PMID:24530905

  15. A surface plasmon resonance study of the intermolecular interaction between Escherichia coli topoisomerase I and pBAD/Thio supercoiled plasmid DNA.

    Science.gov (United States)

    Tiwari, Purushottam Babu; Annamalai, Thirunavukkarasu; Cheng, Bokun; Narula, Gagandeep; Wang, Xuewen; Tse-Dinh, Yuk-Ching; He, Jin; Darici, Yesim

    2014-03-07

    To date, the bacterial DNA topoisomerases are one of the major target biomolecules for the discovery of new antibacterial drugs. DNA topoisomerase regulates the topological state of DNA, which is very important for replication, transcription and recombination. The relaxation of negatively supercoiled DNA is catalyzed by bacterial DNA topoisomerase I (topoI) and this reaction requires Mg(2+). In this report, we first quantitatively studied the intermolecular interactions between Escherichia coli topoisomerase I (EctopoI) and pBAD/Thio supercoiled plasmid DNA using surface plasmon resonance (SPR) technique. The equilibrium dissociation constant (Kd) for EctopoI-pBAD/Thio interactions was determined to be about 8 nM. We then studied the effect of Mg(2+) on the catalysis of EctopoI-pBAD/Thio reaction. A slightly higher equilibrium dissociation constant (~15 nM) was obtained for Mg(2+) coordinated EctopoI (Mg(2+)EctopoI)-pBAD/Thio interactions. In addition, we observed a larger dissociation rate constant (kd) for Mg(2+)EctopoI-pBAD/Thio interactions (~0.043 s(-1)), compared to EctopoI-pBAD/Thio interactions (~0.017 s(-1)). These results suggest that enzyme turnover during plasmid DNA relaxation is enhanced due to the presence of Mg(2+) and furthers the understanding of importance of the Mg(2+) ion for bacterial topoisomerase I catalytic activity. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Surface-enhanced Raman scattering detection of DNA derived from the West Nile virus genome using magnetic capture of Raman-active gold nanoparticles

    Science.gov (United States)

    A model paramagnetic nanoparticle (MNP) assay is demonstrated for surface-enhanced Raman scattering (SERS) detection of DNA oligonucleotides derived from the West Nile virus (WNV) genome. Detection is based on the capture of WNV target sequences by hybridization with complementary oligonucleotide pr...

  17. Electrochemistry and in situ scanning tunnelling microscopy of pure and redox-marked DNA- and UNA-based oligonucleotides on Au(111)-electrode surfaces

    DEFF Research Database (Denmark)

    Hansen, Allan Glargaard; Salvatore, Princia; Karlsen, K.

    2013-01-01

    We have studied adsorption and electrochemical electron transfer of several 13- and 15-base DNA and UNA (unlocked nucleic acids) oligonucleotides (ONs) linked to Au(111)-electrode surfaces via a 50-C6-SH group using cyclic voltammetry (CV) and scanning tunnelling microscopy in aqueous buffer under...

  18. Recent Development of Nano-Materials Used in DNA Biosensors

    Directory of Open Access Journals (Sweden)

    Yibin Ying

    2009-07-01

    Full Text Available As knowledge of the structure and function of nucleic acid molecules has increased, sequence-specific DNA detection has gained increased importance. DNA biosensors based on nucleic acid hybridization have been actively developed because of their specificity, speed, portability, and low cost. Recently, there has been considerable interest in using nano-materials for DNA biosensors. Because of their high surface-to-volume ratios and excellent biological compatibilities, nano-materials could be used to increase the amount of DNA immobilization; moreover, DNA bound to nano-materials can maintain its biological activity. Alternatively, signal amplification by labeling a targeted analyte with nano-materials has also been reported for DNA biosensors in many papers. This review summarizes the applications of various nano-materials for DNA biosensors during past five years. We found that nano-materials of small sizes were advantageous as substrates for DNA attachment or as labels for signal amplification; and use of two or more types of nano-materials in the biosensors could improve their overall quality and to overcome the deficiencies of the individual nano-components. Most current DNA biosensors require the use of polymerase chain reaction (PCR in their protocols. However, further development of nano-materials with smaller size and/or with improved biological and chemical properties would substantially enhance the accuracy, selectivity and sensitivity of DNA biosensors. Thus, DNA biosensors without PCR amplification may become a reality in the foreseeable future.

  19. RNA binding to APOBEC3G induces the disassembly of functional deaminase complexes by displacing single-stranded DNA substrates

    Science.gov (United States)

    Polevoda, Bogdan; McDougall, William M.; Tun, Bradley N.; Cheung, Michael; Salter, Jason D.; Friedman, Alan E.; Smith, Harold C.

    2015-01-01

    APOBEC3G (A3G) DNA deaminase activity requires a holoenzyme complex whose assembly on nascent viral reverse transcripts initiates with A3G dimers binding to ssDNA followed by formation of higher-order A3G homo oligomers. Catalytic activity is inhibited when A3G binds to RNA. Our prior studies suggested that RNA inhibited A3G binding to ssDNA. In this report, near equilibrium binding and gel shift analyses showed that A3G assembly and disassembly on ssDNA was an ordered process involving A3G dimers and multimers thereof. Although, fluorescence anisotropy showed that A3G had similar nanomolar affinity for RNA and ssDNA, RNA stochastically dissociated A3G dimers and higher-order oligomers from ssDNA, suggesting a different modality for RNA binding. Mass spectrometry mapping of A3G peptides cross-linked to nucleic acid suggested ssDNA only bound to three peptides, amino acids (aa) 181–194 in the N-terminus and aa 314–320 and 345–374 in the C-terminus that were part of a continuous exposed surface. RNA bound to these peptides and uniquely associated with three additional peptides in the N- terminus, aa 15–29, 41–52 and 83–99, that formed a continuous surface area adjacent to the ssDNA binding surface. The data predict a mechanistic model of RNA inhibition of ssDNA binding to A3G in which competitive and allosteric interactions determine RNA-bound versus ssDNA-bound conformational states. PMID:26424853

  20. Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA.

    Science.gov (United States)

    Burmeister, Wim P; Tarbouriech, Nicolas; Fender, Pascal; Contesto-Richefeu, Céline; Peyrefitte, Christophe N; Iseni, Frédéric

    2015-07-17

    Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase catalytic subunit E9 associated with its heterodimeric co-factor A20·D4 required for processive genome synthesis. Although A20 has no known enzymatic activity, D4 is an active uracil-DNA glycosylase (UNG). The presence of a repair enzyme as a component of the viral replication machinery suggests that, for poxviruses, DNA synthesis and base excision repair is coupled. We present the 2.7 Å crystal structure of the complex formed by D4 and the first 50 amino acids of A20 (D4·A201-50) bound to a 10-mer DNA duplex containing an abasic site resulting from the cleavage of a uracil base. Comparison of the viral complex with its human counterpart revealed major divergences in the contacts between protein and DNA and in the enzyme orientation on the DNA. However, the conformation of the dsDNA within both structures is very similar, suggesting a dominant role of the DNA conformation for UNG function. In contrast to human UNG, D4 appears rigid, and we do not observe a conformational change upon DNA binding. We also studied the interaction of D4·A201-50 with different DNA oligomers by surface plasmon resonance. D4 binds weakly to nonspecific DNA and to uracil-containing substrates but binds abasic sites with a Kd of DNA complex structure of a family I UNG gives new insight into the role of D4 as a co-factor of vaccinia virus DNA polymerase and allows a better understanding of the structural determinants required for UNG action. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA*

    Science.gov (United States)

    Burmeister, Wim P.; Tarbouriech, Nicolas; Fender, Pascal; Contesto-Richefeu, Céline; Peyrefitte, Christophe N.; Iseni, Frédéric

    2015-01-01

    Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase catalytic subunit E9 associated with its heterodimeric co-factor A20·D4 required for processive genome synthesis. Although A20 has no known enzymatic activity, D4 is an active uracil-DNA glycosylase (UNG). The presence of a repair enzyme as a component of the viral replication machinery suggests that, for poxviruses, DNA synthesis and base excision repair is coupled. We present the 2.7 Å crystal structure of the complex formed by D4 and the first 50 amino acids of A20 (D4·A201–50) bound to a 10-mer DNA duplex containing an abasic site resulting from the cleavage of a uracil base. Comparison of the viral complex with its human counterpart revealed major divergences in the contacts between protein and DNA and in the enzyme orientation on the DNA. However, the conformation of the dsDNA within both structures is very similar, suggesting a dominant role of the DNA conformation for UNG function. In contrast to human UNG, D4 appears rigid, and we do not observe a conformational change upon DNA binding. We also studied the interaction of D4·A201–50 with different DNA oligomers by surface plasmon resonance. D4 binds weakly to nonspecific DNA and to uracil-containing substrates but binds abasic sites with a Kd of DNA complex structure of a family I UNG gives new insight into the role of D4 as a co-factor of vaccinia virus DNA polymerase and allows a better understanding of the structural determinants required for UNG action. PMID:26045555

  2. Werner helicase wings DNA binding

    OpenAIRE

    Hoadley, Kelly A.; Keck, James L.

    2010-01-01

    In this issue of Structure, Kitano et al. describe the structure of the DNA-bound winged-helix domain from the Werner helicase. This structure of a RecQ/DNA complex offers insights into the DNA unwinding mechanisms of RecQ family helicases.

  3. Multi-step surface functionalization of polyimide based evanescent wave photonic biosensors and application for DNA hybridization by Mach-Zehnder interferometer

    Energy Technology Data Exchange (ETDEWEB)

    Melnik, Eva [Health and Environment Department, Nano Systems, AIT Austrian Institute of Technology GmbH, Donau-City-Strasse 1, 1220 Vienna (Austria); Department of Analytical Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna (Austria); Bruck, Roman [Health and Environment Department, Nano Systems, AIT Austrian Institute of Technology GmbH, Donau-City-Strasse 1, 1220 Vienna (Austria); Hainberger, Rainer, E-mail: rainer.hainberger@ait.ac.at [Health and Environment Department, Nano Systems, AIT Austrian Institute of Technology GmbH, Donau-City-Strasse 1, 1220 Vienna (Austria); Laemmerhofer, Michael, E-mail: michael.laemmerhofer@univie.ac.at [Department of Analytical Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna (Austria)

    2011-08-12

    Highlights: {yields} We realize a biosensing platform for polyimide evanescent photonic wave sensors. {yields} We show that the surface functionalization via silanisation and biotinylation followed by streptavidin immobilization do not destroy or damage the thin polyimide film. {yields} A highly dense streptavidin layer enables the immobilisation of biotinylated ligands such as biotinylated ssDNA for the selective measurement of DNA hybridization. - Abstract: The process of surface functionalization involving silanization, biotinylation and streptavidin bonding as platform for biospecific ligand immobilization was optimized for thin film polyimide spin-coated silicon wafers, of which the polyimide film serves as a wave guiding layer in evanescent wave photonic biosensors. This type of optical sensors make great demands on the materials involved as well as on the layer properties, such as the optical quality, the layer thickness and the surface roughness. In this work we realized the binding of a 3-mercaptopropyl trimethoxysilane on an oxygen plasma activated polyimide surface followed by subsequent derivatization of the reactive thiol groups with maleimide-PEG{sub 2}-biotin and immobilization of streptavidin. The progress of the functionalization was monitored by using different fluorescence labels for optimization of the chemical derivatization steps. Further, X-ray photoelectron spectroscopy and atomic force microscopy were utilized for the characterization of the modified surface. These established analytical methods allowed to derive information like chemical composition of the surface, surface coverage with immobilized streptavidin, as well as parameters of the surface roughness. The proposed functionalization protocol furnished a surface density of 144 fmol mm{sup -2} streptavidin with good reproducibility (13.9% RSD, n = 10) and without inflicted damage to the surface. This surface modification was applied to polyimide based Mach-Zehnder interferometer

  4. Are the SSB-Interacting Proteins RecO, RecG, PriA and the DnaB-Interacting Protein Rep Bound to Progressing Replication Forks in Escherichia coli?

    Science.gov (United States)

    Bentchikou, Esma; Chagneau, Carine; Long, Emilie; Matelot, Mélody; Allemand, Jean-François; Michel, Bénédicte

    2015-01-01

    In all organisms several enzymes that are needed upon replication impediment are targeted to replication forks by interaction with a replication protein. In most cases these proteins interact with the polymerase clamp or with single-stranded DNA binding proteins (SSB). In Escherichia coli an accessory replicative helicase was also shown to interact with the DnaB replicative helicase. Here we have used cytological observation of Venus fluorescent fusion proteins expressed from their endogenous loci in live E. coli cells to determine whether DNA repair and replication restart proteins that interact with a replication protein travel with replication forks. A custom-made microscope that detects active replisome molecules provided that they are present in at least three copies was used. Neither the recombination proteins RecO and RecG, nor the replication accessory helicase Rep are detected specifically in replicating cells in our assay, indicating that either they are not present at progressing replication forks or they are present in less than three copies. The Venus-PriA fusion protein formed foci even in the absence of replication forks, which prevented us from reaching a conclusion.

  5. The effect of the shape of single, sub-ms voltage pulses on the rates of surface immobilization and hybridization of DNA

    International Nuclear Information System (INIS)

    Cabeca, R; Rodrigues, M; Chu, V; Conde, J P; Prazeres, D M F

    2009-01-01

    Electric fields generated by single square and sinusoidal voltage pulses with amplitudes below 2 V were used to assist the covalent immobilization of single-stranded, thiolated DNA probes, onto a chemically functionalized SiO 2 surface and to assist the specific hybridization of single-stranded DNA targets with immobilized complementary probes. The single-stranded immobilized DNA probes were either covalently immobilized (chemisorption) or electrostatically adsorbed (physisorption) to a chemically functionalized surface. Comparing the speed of electric field assisted immobilization and hybridization with the corresponding control reactions (without electric field), an increase of several orders of magnitude is observed, with the reaction timescaled down from 1 to 2 h to a range between 100 ns and 1 ms. The influence of the shape of the voltage pulse (square versus sinusoidal) and its duration were studied for both immobilization and hybridization reactions. The results show that pulsed electric fields are a useful tool to achieve temporal and spatial control of surface immobilization and hybridization reactions of DNA.

  6. Surface treatment on amorphous InGaZnO4 thin film for single-stranded DNA biosensing

    Science.gov (United States)

    Sun, Dali; Matsui, Hiroaki; Wu, Chun-Nan; Tabata, Hitoshi

    2015-01-01

    Amorphous InGaZnO4 (aIGZO) has been widely used as a transparent semiconductor. However, no research has been found yet applying aIGZO to biosensing. This paper examined the single strand DNA (ssDNA) immobilization on aIGZO by absorption with a comparison to ITO, which is the first step for many biosensing schemas. The DNA quantification by florescence intensity shows that the absorption capacity of aIGZO film to ssDNA is 6.7 times greater than that of ITO. XPS and contact angle analysis proved the high DNA absorption affinity on aIGZO film is related to its high effectiveness to OH- attachment. A feasible method to immobilized ssDNA on aIGZO thin film is evaluated in this paper, and consequently, enables a possible approach to apply aIGZO in biosensing.

  7. Gel Electrophoresis of Gold-DNA Nanoconjugates

    Directory of Open Access Journals (Sweden)

    T. Pellegrino

    2007-01-01

    Full Text Available Gold-DNA conjugates were investigated in detail by a comprehensive gel electrophoresis study based on 1200 gels. A controlled number of single-stranded DNA of different length was attached specifically via thiol-Au bonds to phosphine-stabilized colloidal gold nanoparticles. Alternatively, the surface of the gold particles was saturated with single stranded DNA of different length either specifically via thiol-Au bonds or by nonspecific adsorption. From the experimentally determined electrophoretic mobilities, estimates for the effective diameters of the gold-DNA conjugates were derived by applying two different data treatment approaches. The first method is based on making a calibration curve for the relation between effective diameters and mobilities with gold nanoparticles of known diameter. The second method is based on Ferguson analysis which uses gold nanoparticles of known diameter as reference database. Our study shows that effective diameters derived from gel electrophoresis measurements are affected with a high error bar as the determined values strongly depend on the method of evaluation, though relative changes in size upon binding of molecules can be detected with high precision. Furthermore, in this study, the specific attachment of DNA via gold-thiol bonds to Au nanoparticles is compared to nonspecific adsorption of DNA. Also, the maximum number of DNA molecules that can be bound per particle was determined.

  8. Disruption and formation of surface salt bridges are coupled to DNA binding by integration host factor: a computational analysis

    OpenAIRE

    Ma, L.; Sundlass, N. K.; Raines, R. T.; Cui, Q.

    2010-01-01

    Revealing the thermodynamic driving force of protein/DNA interactions is crucial to the understanding of factors that dictate the properties and function of protein-DNA complexes. For the binding of DNA to DNA-wrapping proteins, such as the integration host factor (IHF), Record and co-workers have proposed that the disruption of a large number of pre-existing salt-bridges is coupled with the binding process (J. Mol. Biol., 310, 2001, 379). To test this proposal, we have carried out explicit s...

  9. Bounding approaches to system identification

    CERN Document Server

    Norton, John; Piet-Lahanier, Hélène; Walter, Éric

    1996-01-01

    In response to the growing interest in bounding error approaches, the editors of this volume offer the first collection of papers to describe advances in techniques and applications of bounding of the parameters, or state variables, of uncertain dynamical systems. Contributors explore the application of the bounding approach as an alternative to the probabilistic analysis of such systems, relating its importance to robust control-system design.

  10. Changing serum levels of quantitative hepatitis B surface antigen and hepatitis B virus DNA in hepatitis B virus surface antigen carriers: A follow-up study of an elderly cohort

    Directory of Open Access Journals (Sweden)

    Yuan-Hung Kuo

    2015-02-01

    Full Text Available This study was to elucidate longitudinally quantitative changes of hepatitis B virus (HBV surface antigen (HBsAg and HBV DNA in elder HBsAg carriers in a community. Among 1002 residents screened for HBsAg in 2005, 405 responded to this follow-up study in 2010. Fifty-nine (14.6% were HBsAg carriers in 2005; HBsAg quantification and HBV DNA were measured. HBsAg quantification (cutoff 1600 IU/mL and HBV DNA (cutoff 2000 IU/mL were combined to stratify the participants between two screens. A total of 30 men and 29 women with a mean age of 63.9 ± 7.9 years were enrolled. Quantitative levels of HBsAg and HBV DNA were significantly correlated in 2005 (r = 0.509, p < 0.001 and 2010 (r = 0.777, p < 0.001. Concentrations of HBsAg (IU/mL significantly decreased from 2.2 ± 1.0 log in 2005 to 1.7 ± 1.5 log in 2010 (p < 0.001. The level of HBsAg was decreased in 48 (81.4% individuals and HBsAg was undetectable in eight (13.6%. The annual incidence of HBsAg clearance was 2.7%. These 59 HBsAg carriers in 2005 were divided into four groups: low HBsAg low HBV DNA (n = 32, high HBsAg low HBV DNA (n = 5, low HBsAg high HBV DNA (n = 12 and high HBsAg high HBV DNA (n = 10. All 32 individuals in the low HBsAg low HBV DNA group were still in that group in 2010, whereas only two of the high HBsAg high HBV DNA group became inactive. As with a younger cohort in hospital, HBsAg quantification was still well correlated with HBV DNA in elderly HBsAg carriers in the community. Lower levels of both HBsAg and HBV DNA might represent an inactive HBV infection.

  11. In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces.

    Science.gov (United States)

    Wu, Zhonghua; Hu, Gang; Yang, Jianyi; Peng, Zhenling; Uversky, Vladimir N; Kurgan, Lukasz

    2015-09-14

    We provide first large scale analysis of the peculiarities of surface areas of 5658 dissimilar (below 50% sequence similarity) proteins with known 3D-structures that bind to proteins, DNA or RNAs. We show here that area of the protein surface is highly correlated with the protein length. The size of the interface surface is only modestly correlated with the protein size, except for RNA-binding proteins where larger proteins are characterized by larger interfaces. Disordered proteins with disordered interfaces are characterized by significantly larger per-residue areas of their surfaces and interfaces when compared to the structured proteins. These result are applicable for proteins involved in interaction with DNA, RNA, and proteins and suggest that disordered proteins and binding regions are less compact and more likely to assume extended shape. We demonstrate that disordered protein binding residues in the interfaces of disordered proteins drive the increase in the per residue area of these interfaces. Our results can be used to predict in silico whether a given protomer from the DNA, RNA or protein complex is likely to be disordered in its unbound form. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  12. Ultrasensitive Direct Quantification of Nucleobase Modifications in DNA by Surface-Enhanced Raman Scattering: The Case of Cytosine.

    Science.gov (United States)

    Morla-Folch, Judit; Xie, Hai-nan; Gisbert-Quilis, Patricia; Gómez-de Pedro, Sara; Pazos-Perez, Nicolas; Alvarez-Puebla, Ramon A; Guerrini, Luca

    2015-11-09

    Recognition of chemical modifications in canonical nucleobases of nucleic acids is of key importance since such modified variants act as different genetic encoders, introducing variability in the biological information contained in DNA. Herein, we demonstrate the feasibility of direct SERS in combination with chemometrics and microfluidics for the identification and relative quantification of 4 different cytosine modifications in both single- and double-stranded DNA. The minute amount of DNA required per measurement, in the sub-nanogram regime, removes the necessity of pre-amplification or enrichment steps (which are also potential sources of artificial DNA damages). These findings show great potentials for the development of fast, low-cost and high-throughput screening analytical devices capable of detecting known and unknown modifications in nucleic acids (DNA and RNA) opening new windows of activity in several fields such as biology, medicine and forensic sciences. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. A sensitive DNA biosensor fabricated from gold nanoparticles, carbon nanotubes, and zinc oxide nanowires on a glassy carbon electrode

    International Nuclear Information System (INIS)

    Wang Jie; Li Shuping; Zhang Yuzhong

    2010-01-01

    We outline here the fabrication of a sensitive electrochemical DNA biosensor for the detection of sequence-specific target DNA. Zinc oxide nanowires (ZnONWs) were first immobilized on the surface of a glassy carbon electrode. Multi-walled carbon nanotubes (MWCNTs) with carboxyl groups were then dropped onto the surface of the ZnONWs. Gold nanoparticles (AuNPs) were subsequently introduced to the surface of the MWNTs/ZnONWs by electrochemical deposition. A single-stranded DNA probe with a thiol group at the end (HS-ssDNA) was covalently immobilized on the surface of the AuNPs by forming an Au-S bond. Scanning electron microscopy (SEM) and cyclic voltammetry (CV) were used to investigate the film assembly process. Differential pulse voltammetry (DPV) was used to monitor DNA hybridization by measuring the electrochemical signals of [Ru(NH 3 ) 6 ] 3+ bounding to double-stranded DNA (dsDNA). The incorporation of ZnONWs and MWCNTs in this sensor design significantly enhances the sensitivity and the selectivity. This DNA biosensor can detect the target DNA quantitatively in the range of 1.0 x 10 -13 to 1.0 x 10 -7 M, with a detection limit of 3.5 x 10 -14 M (S/N = 3). In addition, the DNA biosensor exhibits excellent selectivity, even for single-mismatched DNA detection.

  14. Cooperative assembly of Co-Smad4 MH1 with R-Smad1/3 MH1 on DNA: a molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Guihong Wang

    Full Text Available BACKGROUND: Smads, the homologs of Sma and MAD proteins, play a key role in gene expression regulation in the transforming growth factor-β (TGF-β signaling pathway. Recent experimental studies have revealed that Smad4/R-Smad heterodimers bound on DNA are energetically more favorable than homodimeric R-Smad/R-Smad complexes bound on DNA, which indicates that Smad4 might act as binding vehicle to cooperatively assemble with activated R-Smads on DNA in the nucleus. However, the details of interaction mechanism for cooperative recruitment of Smad4 protein to R-Smad proteins on DNA, and allosteric communication between the Smad4-DNA and R-Smad-DNA interfaces via DNA mediating are not yet clear so far. METHODOLOGY: In the present work, we have constructed a series of Smadn+DNA+Smadn (n = 1, 3, 4 models and carried out molecular dynamics simulations, free energy calculations and DNA dynamics analysis for them to study the interaction properties of Smadn (n = 1, 3, 4 with DNA molecule. RESULTS: The results revealed that the binding of Smad4 protein to DNA molecule facilitates energetically the formation of the heteromeric Smad4+DNA+Smad1/3 complex by increasing the affinity of Smad1/3 with DNA molecule. Further investigations through the residue/base motion correlation and DNA dynamics analyses predicted that the binding of Smad4 protein to DNA molecule in the heteromeric Smad4+DNA+Smad1/3 model induces an allosteric communication from the Smad4-DNA interface to Smad1/Smad3-DNA interface via DNA base-pair helical motions, surface conformation changes and new hydrogen bond formations. The present work theoretically explains the mechanism of cooperative recruitment of Smad4 protein to Smad1/3 protein via DNA-mediated indirect readout mode in the nucleus.

  15. Low upper bounds of ideals

    OpenAIRE

    Kucera, Antonin; Slaman, Theodore A.

    2007-01-01

    We show that there is a low T-upper bound for the class of K-trivial sets, namely those which are weak from the point of view of algorithmic randomness. This result is a special case of a more general characterization of ideals in Δ02 T-degrees for which there is a low T-upper bound.

  16. Bounds for Asian basket options

    Science.gov (United States)

    Deelstra, Griselda; Diallo, Ibrahima; Vanmaele, Michèle

    2008-09-01

    In this paper we propose pricing bounds for European-style discrete arithmetic Asian basket options in a Black and Scholes framework. We start from methods used for basket options and Asian options. First, we use the general approach for deriving upper and lower bounds for stop-loss premia of sums of non-independent random variables as in Kaas et al. [Upper and lower bounds for sums of random variables, Insurance Math. Econom. 27 (2000) 151-168] or Dhaene et al. [The concept of comonotonicity in actuarial science and finance: theory, Insurance Math. Econom. 31(1) (2002) 3-33]. We generalize the methods in Deelstra et al. [Pricing of arithmetic basket options by conditioning, Insurance Math. Econom. 34 (2004) 55-57] and Vanmaele et al. [Bounds for the price of discrete sampled arithmetic Asian options, J. Comput. Appl. Math. 185(1) (2006) 51-90]. Afterwards we show how to derive an analytical closed-form expression for a lower bound in the non-comonotonic case. Finally, we derive upper bounds for Asian basket options by applying techniques as in Thompson [Fast narrow bounds on the value of Asian options, Working Paper, University of Cambridge, 1999] and Lord [Partially exact and bounded approximations for arithmetic Asian options, J. Comput. Finance 10 (2) (2006) 1-52]. Numerical results are included and on the basis of our numerical tests, we explain which method we recommend depending on moneyness and time-to-maturity.

  17. Tight bounds for break minimization

    NARCIS (Netherlands)

    Brouwer, Andries E.; Post, Gerhard F.; Woeginger, Gerhard

    We consider round-robin sports tournaments with n teams and n − 1 rounds. We construct an infinite family of opponent schedules for which every home-away assignment induces at least 1/4 n(n−2) breaks. This construction establishes a matching lower bound for a corresponding upper bound from the

  18. Market Access through Bound Tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal

    on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive...... margin of trade. We find that bound tariffs are more effective with higher risk destination markets, that a large binding overhang may still command substantial market access, and that reductions in bound tariffs generate effective market access even when bound rates are above current and long......WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings...

  19. Metabolism of organically bound tritium

    International Nuclear Information System (INIS)

    Travis, C.C.

    1984-01-01

    The classic methodology for estimating dose to man from environmental tritium ignores the fact that organically bound tritium in foodstuffs may be directly assimilated in the bound compartment of tissues without previous oxidation. We propose a four-compartment model consisting of a free body water compartment, two organic compartments, and a small, rapidly metabolizing compartment. The utility of this model lies in the ability to input organically bound tritium in foodstuffs directly into the organic compartments of the model. We found that organically bound tritium in foodstuffs can increase cumulative total body dose by a factor of 1.7 to 4.5 times the free body water dose alone, depending on the bound-to-loose ratio of tritium in the diet. Model predictions are compared with empirical measurements of tritium in human urine and tissue samples, and appear to be in close agreement. 10 references, 4 figures, 3 tables

  20. Excited state dependent electron transfer of a rhenium-dipyridophenazine complex intercalated between the base pairs of DNA: a time-resolved UV-visible and IR absorption investigation into the photophysics of fac-[Re(CO)3(F2dppz)(py)]+ bound to either [poly(dA-dT)]2 or [poly(dG-dC)]2.

    Science.gov (United States)

    Cao, Qian; Creely, Caitriona M; Davies, E Stephen; Dyer, Joanne; Easun, Timothy L; Grills, David C; McGovern, David A; McMaster, Jonathan; Pitchford, Jonathan; Smith, Jayden A; Sun, Xue-Zhong; Kelly, John M; George, Michael W

    2011-08-01

    The transient species formed following excitation of fac-[Re(CO)(3)(F(2)dppz)(py)](+) (F(2)dppz = 11,12-difluorodipyrido[3,2-a:2',3'-c]phenazine) bound to double-stranded polynucleotides [poly(dA-dT)](2) or [poly(dG-dC)](2) have been studied by transient visible and infra-red spectroscopy in both the picosecond and nanosecond time domains. The latter technique has been used to monitor both the metal complex and the DNA by monitoring the regions 1900-2100 and 1500-1750 cm(-1) respectively. These data provide direct evidence for electron transfer from guanine to the excited state of the metal complex, which proceeds both on a sub-picosecond time scale and with a lifetime of 35 ps, possibly due to the involvement of two excited states. No electron transfer is found for the [poly(dA-dT)](2) complex, although characteristic changes are seen in the DNA-region TRIR consistent with changes in the binding of the bases in the intercalation site upon excitation of the dppz-complex. This journal is © The Royal Society of Chemistry and Owner Societies 2011

  1. Fischer carbene mediated covalent grafting of a peptide nucleic acid on gold surfaces and IR optical detection of DNA hybridization with a transition metalcarbonyl label

    Science.gov (United States)

    Srivastava, Pratima; Ghasemi, Mahsa; Ray, Namrata; Sarkar, Amitabha; Kocabova, Jana; Lachmanova, Stepanka; Hromadova, Magdalena; Boujday, Souhir; Cauteruccio, Silvia; Thakare, Pramod; Licandro, Emanuela; Fosse, Céline; Salmain, Michèle

    2016-11-01

    Amine-reactive surfaces comprising N-hydroxysuccinimide ester groups as well as much more unusual Fischer alkoxymetallocarbene groups were generated on gold-coated surfaces via self-assembled monolayers of carboxy- and azido-terminated thiolates, respectively. These functions were further used to immobilize homothymine peptide nucleic acid (PNA) decamer in a covalent fashion involving the primary amine located at its N-terminus. These stepwise processes were monitored by polarization modulation reflection - absorption infrared spectroscopy (PM-RAIRS) that gave useful information on the molecular composition of the organic layers. PNA grafting and hybridization with complementary DNA strand were successfully transduced by quartz crystal microbalance (QCM) measurements. Unfortunately, attempts to transduce the hybridization optically by IR in a label-free fashion were inconclusive. Therefore we undertook to introduce an IR reporter group, namely a transition metalcarbonyl (TMC) entity at the 5‧ terminus of complementary DNA. Evidence for the formation of PNA-DNA heteroduplex was brought by the presence of ν(Ctbnd O) bands in the 2000 cm-1 region of the IR spectrum of the gold surface owing to the metalcarbonyl label.

  2. Probing the dynamics of restriction endonuclease NgoMIV-DNA interaction by single-molecule FRET.

    Science.gov (United States)

    Tutkus, Marijonas; Sasnauskas, Giedrius; Rutkauskas, Danielis

    2017-12-01

    Many type II restriction endonucleases require two copies of their recognition sequence for optimal activity. Concomitant binding of two DNA sites by such an enzyme produces a DNA loop. Here we exploit single-molecule Förster resonance energy transfer (smFRET) of surface-immobilized DNA fragments to study the dynamics of DNA looping induced by tetrameric endonuclease NgoMIV. We have employed a DNA fragment with two NgoMIV recognition sites and a FRET dye pair such that upon protein-induced DNA looping the dyes are brought to close proximity resulting in a FRET signal. The dynamics of DNA-NgoMIV interactions proved to be heterogeneous, with individual smFRET trajectories exhibiting broadly different average looped state durations. Distinct types of the dynamics were attributed to different types of DNA-protein complexes, mediated either by one NgoMIV tetramer simultaneously bound to two specific sites ("slow" trajectories) or by semi-specific interactions of two DNA-bound NgoMIV tetramers ("fast" trajectories), as well as to conformational heterogeneity of individual NgoMIV molecules. © 2017 Wiley Periodicals, Inc.

  3. Coupling carbon nanotubes through DNA linker using a biological recognition complex

    Science.gov (United States)

    Goux-Capes, L.; Filoramo, A.; Cote, D.; Bourgoin, J.-Ph.; Patillon, J.-N.

    2006-05-01

    We present a simple and versatile method for linking single wall carbon nanotubes (SWNT) together through DNA by non-covalent chemistry using streptavidin-biotin recognition complex. Streptavidin coated SWNTs are reacted with biotin or bis-biotin ended DNA double strands leading to SWNT-DNA and SWNT-DNA-SWNT adducts in high yield. This method avoids strong acidic treatment of SWNTs prior to functionalization as usually required in covalent routes. Complementary characterizations by gel electrophoresis and AFM demonstrated the efficiency of the present binding method. In addition, SWNTs bound to DNA can be aligned on a substrate using the combing properties of DNA strands, bringing a new tool into the toolkit for self-assembling SWNTs onto surfaces.

  4. On the Holographic Bound in Newtonian Cosmology

    Directory of Open Access Journals (Sweden)

    José M. Isidro

    2018-01-01

    Full Text Available The holographic principle sets an upper bound on the total (Boltzmann entropy content of the Universe at around 10 123 k B ( k B being Boltzmann’s constant. In this work we point out the existence of a remarkable duality between nonrelativistic quantum mechanics on the one hand, and Newtonian cosmology on the other. Specifically, nonrelativistic quantum mechanics has a quantum probability fluid that exactly mimics the behaviour of the cosmological fluid, the latter considered in the Newtonian approximation. One proves that the equations governing the cosmological fluid (the Euler equation and the continuity equation become the very equations that govern the quantum probability fluid after applying the Madelung transformation to the Schroedinger wavefunction. Under the assumption that gravitational equipotential surfaces can be identified with isoentropic surfaces, this model allows for a simple computation of the gravitational entropy of a Newtonian Universe. In a first approximation, we model the cosmological fluid as the quantum probability fluid of free Schroedinger waves. We find that this model Universe saturates the holographic bound. As a second approximation, we include the Hubble expansion of the galaxies. The corresponding Schroedinger waves lead to a value of the entropy lying three orders of magnitude below the holographic bound. Current work on a fully relativistic extension of our present model can be expected to yield results in even better agreement with empirical estimates of the entropy of the Universe.

  5. DNA Diagnostics: Optical or by Electronics?

    KAUST Repository

    Khan, Hadayat Ullah

    2016-01-15

    In this paper, we very briefly review DNA biosensors based on optical and electrical detection principles, referring mainly to our past work applying both techniques but here using nearly identical sensor chip surface architectures, i.e., capture probe layers that were prepared based on a pulsed plasma deposition protocol for maleic anhydride and subsequent wet-chemical attachment of the amine-functionalized peptide nucleic acid (PNA) probe oligonucleotides. 15 mer DNA target strands, labeled with Cy5-chromophores that were attached at the 5’ end were used for surface plasmon optical detection and the same target DNA but without label was used in OTFT sensor-based detection where the mere charge density of the bound (hybridized) DNA molecules modulate the source-drain current. The sensing mechanisms and the detection limits of the devices are described in some detail. Both techniques allow for the monitoring of surface hybridization reactions, and offer the capacity to quantitatively discriminate between targets with different degrees of mismatched sequences.

  6. Structure-function relationships in human testis-determining factor SRY: an aromatic buttress underlies the specific DNA-bending surface of a high mobility group (HMG) box.

    Science.gov (United States)

    Racca, Joseph D; Chen, Yen-Shan; Maloy, James D; Wickramasinghe, Nalinda; Phillips, Nelson B; Weiss, Michael A

    2014-11-21

    Human testis determination is initiated by SRY, a Y-encoded architectural transcription factor. Mutations in SRY cause 46 XY gonadal dysgenesis with female somatic phenotype (Swyer syndrome) and confer a high risk of malignancy (gonadoblastoma). Such mutations cluster in the SRY high mobility group (HMG) box, a conserved motif of specific DNA binding and bending. To explore structure-function relationships, we constructed all possible substitutions at a site of clinical mutation (W70L). Our studies thus focused on a core aromatic residue (position 15 of the consensus HMG box) that is invariant among SRY-related HMG box transcription factors (the SOX family) and conserved as aromatic (Phe or Tyr) among other sequence-specific boxes. In a yeast one-hybrid system sensitive to specific SRY-DNA binding, the variant domains exhibited reduced (Phe and Tyr) or absent activity (the remaining 17 substitutions). Representative nonpolar variants with partial or absent activity (Tyr, Phe, Leu, and Ala in order of decreasing side-chain volume) were chosen for study in vitro and in mammalian cell culture. The clinical mutation (Leu) was found to markedly impair multiple biochemical and cellular activities as respectively probed through the following: (i) in vitro assays of specific DNA binding and protein stability, and (ii) cell culture-based assays of proteosomal degradation, nuclear import, enhancer DNA occupancy, and SRY-dependent transcriptional activation. Surprisingly, however, DNA bending is robust to this or the related Ala substitution that profoundly impairs box stability. Together, our findings demonstrate that the folding, trafficking, and gene-regulatory function of SRY requires an invariant aromatic "buttress" beneath its specific DNA-bending surface. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Combining Alphas via Bounded Regression

    Directory of Open Access Journals (Sweden)

    Zura Kakushadze

    2015-11-01

    Full Text Available We give an explicit algorithm and source code for combining alpha streams via bounded regression. In practical applications, typically, there is insufficient history to compute a sample covariance matrix (SCM for a large number of alphas. To compute alpha allocation weights, one then resorts to (weighted regression over SCM principal components. Regression often produces alpha weights with insufficient diversification and/or skewed distribution against, e.g., turnover. This can be rectified by imposing bounds on alpha weights within the regression procedure. Bounded regression can also be applied to stock and other asset portfolio construction. We discuss illustrative examples.

  8. On functions of bounded semivariation

    Czech Academy of Sciences Publication Activity Database

    Monteiro, Giselle Antunes

    2015-01-01

    Roč. 40, č. 2 (2015), s. 233-276 ISSN 0147-1937 Institutional support: RVO:67985840 Keywords : semivariation * functions of bounded variation * regulated functions Subject RIV: BA - General Mathematics http://projecteuclid.org/euclid. rae /1491271216

  9. Computational Lower Bounds Using Diagonalization

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 7. Computational Lower Bounds Using Diagonalization - Languages, Turing Machines and Complexity Classes. M V Panduranga Rao. General Article Volume 14 Issue 7 July 2009 pp 682-690 ...

  10. Construction and modeling of concatemeric DNA multilayers on a planar surface as monitored by QCM-D and SPR.

    Science.gov (United States)

    Sun, Lu; Svedhem, Sofia; Akerman, Björn

    2014-07-22

    The sequential hybridization of a 534 base pair DNA concatemer layer was monitored by QCM-D and SPR, and the QCM-D data were analyzed by Voigt viscoelastic models. The results show that Voigt-based modeling gives a good description of the experimental data but only if shear viscosity and elasticity are allowed to depend on the shear frequency. The derived layer thickness, shear viscosity and elasticity of the growing film give a representation of the DNA film in agreement with known bulk properties of DNA, and reveal a maximum in film viscosity when the molecules in the layer contain 75 base pairs. The experimental data during construction of a 3084 bp DNA concatemer layer were compared to predictions of the QCM-D response of a 1 μm thick film of rod-like polymers. A predicted nonmonotonous variation of dissipation with frequency (added mass) is in qualitative agreement with the experiments, but with a quantitative disagreement which likely reflects that the flexibility of such long DNA molecules is not included in the model.

  11. Structural basis for DNA strand separation by a hexameric replicative helicase

    Science.gov (United States)

    Chaban, Yuriy; Stead, Jonathan A.; Ryzhenkova, Ksenia; Whelan, Fiona; Lamber, Ekaterina P.; Antson, Alfred; Sanders, Cyril M.; Orlova, Elena V.

    2015-01-01

    Hexameric helicases are processive DNA unwinding machines but how they engage with a replication fork during unwinding is unknown. Using electron microscopy and single particle analysis we determined structures of the intact hexameric helicase E1 from papillomavirus and two complexes of E1 bound to a DNA replication fork end-labelled with protein tags. By labelling a DNA replication fork with streptavidin (dsDNA end) and Fab (5′ ssDNA) we located the positions of these labels on the helicase surface, showing that at least 10 bp of dsDNA enter the E1 helicase via a side tunnel. In the currently accepted ‘steric exclusion’ model for dsDNA unwinding, the active 3′ ssDNA strand is pulled through a central tunnel of the helicase motor domain as the dsDNA strands are wedged apart outside the protein assembly. Our structural observations together with nuclease footprinting assays indicate otherwise: strand separation is taking place inside E1 in a chamber above the helicase domain and the 5′ passive ssDNA strands exits the assembly through a separate tunnel opposite to the dsDNA entry point. Our data therefore suggest an alternative to the current general model for DNA unwinding by hexameric helicases. PMID:26240379

  12. Meis1 and pKnox1 bind DNA cooperatively with Pbx1 utilizing an interaction surface disrupted in oncoprotein E2a-Pbx1

    Science.gov (United States)

    Knoepfler, Paul S.; Calvo, Katherine R.; Chen, Haiming; Antonarakis, Stylianos E.; Kamps, Mark P.

    1997-01-01

    E2a-Pbx1 is a chimeric transcription factor oncoprotein produced by the t(1;19) translocation in human pre-B cell leukemia. Class I Hox proteins bind DNA cooperatively with both Pbx proteins and oncoprotein E2a-Pbx1, suggesting that leukemogenesis by E2a-Pbx1 and Hox proteins may alter transcription of cellular genes regulated by Pbx–Hox motifs. Likewise, in murine myeloid leukemia, transcriptional coactivation of Meis1 with HoxA7/A9 suggests that Meis1–HoxA7/9 heterodimers may evoke aberrant gene transcription. Here, we demonstrate that both Meis1 and its relative, pKnox1, dimerize with Pbx1 on the same TGATTGAC motif selected by dimers of Pbx proteins and unidentified partner(s) in nuclear extracts, including those from t(1;19) pre-B cells. Outside their homeodomains, Meis1 and pKnox1 were highly conserved only in two motifs required for cooperativity with Pbx1. Like the unidentified endogenous partner(s), both Meis1 and pKnox1 failed to dimerize significantly with E2a-Pbx1. The Meis1/pKnox1-interaction domain in Pbx1 resided predominantly in a conserved N-terminal Pbx domain deleted in E2a-Pbx1. Thus, the leukemic potential of E2a-Pbx1 may require abrogation of its interaction with members of the Meis and pKnox families of transcription factors, permitting selective targeting of genes regulated by Pbx–Hox complexes. In addition, because most motifs bound by Pbx–Meis1/pKnox1 were not bound by Pbx1–Hox complexes, the leukemic potential of Meis1 in myeloid leukemias may involve shifting Pbx proteins from promoters containing Pbx–Hox motifs to those containing Pbx–Meis motifs. PMID:9405651

  13. Meis1 and pKnox1 bind DNA cooperatively with Pbx1 utilizing an interaction surface disrupted in oncoprotein E2a-Pbx1.

    Science.gov (United States)

    Knoepfler, P S; Calvo, K R; Chen, H; Antonarakis, S E; Kamps, M P

    1997-12-23

    E2a-Pbx1 is a chimeric transcription factor oncoprotein produced by the t(1;19) translocation in human pre-B cell leukemia. Class I Hox proteins bind DNA cooperatively with both Pbx proteins and oncoprotein E2a-Pbx1, suggesting that leukemogenesis by E2a-Pbx1 and Hox proteins may alter transcription of cellular genes regulated by Pbx-Hox motifs. Likewise, in murine myeloid leukemia, transcriptional coactivation of Meis1 with HoxA7/A9 suggests that Meis1-HoxA7/9 heterodimers may evoke aberrant gene transcription. Here, we demonstrate that both Meis1 and its relative, pKnox1, dimerize with Pbx1 on the same TGATTGAC motif selected by dimers of Pbx proteins and unidentified partner(s) in nuclear extracts, including those from t(1;19) pre-B cells. Outside their homeodomains, Meis1 and pKnox1 were highly conserved only in two motifs required for cooperativity with Pbx1. Like the unidentified endogenous partner(s), both Meis1 and pKnox1 failed to dimerize significantly with E2a-Pbx1. The Meis1/pKnox1-interaction domain in Pbx1 resided predominantly in a conserved N-terminal Pbx domain deleted in E2a-Pbx1. Thus, the leukemic potential of E2a-Pbx1 may require abrogation of its interaction with members of the Meis and pKnox families of transcription factors, permitting selective targeting of genes regulated by Pbx-Hox complexes. In addition, because most motifs bound by Pbx-Meis1/pKnox1 were not bound by Pbx1-Hox complexes, the leukemic potential of Meis1 in myeloid leukemias may involve shifting Pbx proteins from promoters containing Pbx-Hox motifs to those containing Pbx-Meis motifs.

  14. Presence of antibodies against a cell-surface protein, cross-reactive with DNA, in systemic lupus erythrematosus: a marker of the disease

    International Nuclear Information System (INIS)

    Jacob, L.; Lety, M.A.; Choquette, D.; Viard, J.P.; Jacob, F.; Louvard, D.; Bach, J.F.

    1987-01-01

    Antibodies against a cell-surface protein, cross-reactive with double-stranded DNA, were detected in the serum of 25 patients with active human systemic lupus erythematosus (SLE), defined on the basis of the revised American Rheumatism Association classification. Among these sera, two did not display anti-DNA antibodies, as shown by Farr assay, solid-phase radioimmunoassay, and Crithidia luciliae test. Five other SLE patients were consecutively studied in active and remission states. Antibodies against the protein were detected in the serum of the 5 SLE patients when they were in active phase but not in the serum of the same patients in inactive phase of the disease. The anti-protein antibodies were not found in the serum of 10 inactive SLE patients or in the sera of 10 normal human controls, 10 patients with rheumatoid arthritis, 5 patients with scleroderma, and 4 patients with primary sicca syndrome. Taken together, these results strongly suggest that antibodies against this cell-surface protein could provide a better diagnosis marker and activity index than anti-DNA antibodies in SLE

  15. Presence of antibodies against a cell-surface protein, cross-reactive with DNA, in systemic lupus erythrematosus: a marker of the disease

    Energy Technology Data Exchange (ETDEWEB)

    Jacob, L.; Lety, M.A.; Choquette, D.; Viard, J.P.; Jacob, F.; Louvard, D.; Bach, J.F.

    1987-05-01

    Antibodies against a cell-surface protein, cross-reactive with double-stranded DNA, were detected in the serum of 25 patients with active human systemic lupus erythematosus (SLE), defined on the basis of the revised American Rheumatism Association classification. Among these sera, two did not display anti-DNA antibodies, as shown by Farr assay, solid-phase radioimmunoassay, and Crithidia luciliae test. Five other SLE patients were consecutively studied in active and remission states. Antibodies against the protein were detected in the serum of the 5 SLE patients when they were in active phase but not in the serum of the same patients in inactive phase of the disease. The anti-protein antibodies were not found in the serum of 10 inactive SLE patients or in the sera of 10 normal human controls, 10 patients with rheumatoid arthritis, 5 patients with scleroderma, and 4 patients with primary sicca syndrome. Taken together, these results strongly suggest that antibodies against this cell-surface protein could provide a better diagnosis marker and activity index than anti-DNA antibodies in SLE.

  16. Multiple DNA-binding modes for the ETS family transcription factor PU.1.

    Science.gov (United States)

    Esaki, Shingo; Evich, Marina G; Erlitzki, Noa; Germann, Markus W; Poon, Gregory M K

    2017-09-29

    The eponymous DNA-binding domain of ETS ( E 26 t ransformation- s pecific) transcription factors binds a single sequence-specific site as a monomer over a single helical turn. Following our previous observation by titration calorimetry that the ETS member PU.1 dimerizes sequentially at a single sequence-specific DNA-binding site to form a 2:1 complex, we have carried out an extensive spectroscopic and biochemical characterization of site-specific PU.1 ETS complexes. Whereas 10 bp of DNA was sufficient to support PU.1 binding as a monomer, additional flanking bases were required to invoke sequential dimerization of the bound protein. NMR spectroscopy revealed a marked loss of signal intensity in the 2:1 complex, and mutational analysis implicated the distal surface away from the bound DNA as the dimerization interface. Hydroxyl radical DNA footprinting indicated that the site-specifically bound PU.1 dimers occupied an extended DNA interface downstream from the 5'-GGAA-3' core consensus relative to its 1:1 counterpart, thus explaining the apparent site size requirement for sequential dimerization. The site-specifically bound PU.1 dimer resisted competition from nonspecific DNA and showed affinities similar to other functionally significant PU.1 interactions. As sequential dimerization did not occur with the ETS domain of Ets-1, a close structural homolog of PU.1, 2:1 complex formation may represent an alternative autoinhibitory mechanism in the ETS family at the protein-DNA level. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Impact of nanosilver on various DNA lesions and HPRT gene mutations - effects of charge and surface coating

    Czech Academy of Sciences Publication Activity Database

    Huk, A.; Izak-Nau, E.; el Yamani, N.; Uggerud, H.; Vadset, M.; Zasońska, Beata Anna; Duschl, A.; Dusinska, M.

    2015-01-01

    Roč. 12, 24 July (2015), 25_1-25_20 ISSN 1743-8977 Institutional support: RVO:61389013 Keywords : silver nanomaterials * surface charge * surface coating Subject RIV: CD - Macromolecular Chemistry Impact factor: 8.649, year: 2015

  18. DNA of Dientamoeba fragilis detected within surface-sterilized eggs of Enterobius vermicularis

    DEFF Research Database (Denmark)

    Röser, Dennis; Nejsum, Peter; Carlsgart, Anne Josefine

    2013-01-01

    With no evidence of a cyst stage, the mode of transmission of Dientamoeba fragilis, an intestinal protozoon of common occurrence and suggested pathogenicity, is incompletely known. Numerous studies have suggested that eggs of intestinal nematodes, primarily Enterobius vermicularis (pinworm), can...... serve as vectors for D. fragilis, although attempts to culture D. fragilis from pinworm eggs have been unsuccessful and data from epidemiological studies on D. fragilis/pinworm co-infection have been conflicting. The aim of this study was to investigate whether we could detect D. fragilis DNA from...... pinworm eggs collected from routine diagnostic samples (cellophane tape) and surface-sterilised by hypochlorite. DNA was extracted from individual eggs and tested by PCR using D. fragilis- and E. vermicularis-specific primers; amplicons were sequenced for confirmation. In cellophane tape samples from 64...

  19. Time Course of Detection of Human Male DNA from Stained Blood Sample on Various Surfaces by Loop Mediated Isothermal Amplification and Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Panan Kanchanaphum

    2018-01-01

    Full Text Available This study explores determining the sex of humans from blood stains taken from different surfaces and compares the time course of detection with the conventional PCR, Conventional Loop Mediated Isothermal Amplification (LAMP, and LAMP-Lateral Flow Dipstick (LFD. For the DNA templates, 7 male and 7 female blood stained samples were extracted and added to LAMP and PCR reaction solution to amplify the SRY gene. The DNA samples were extracted from the following blood stained materials: cloth, wood, clay, and tile. Then, the samples were stored at room temperature for 1, 7, 30, and 60 day(s. After the DNA amplification, the gel electrophoresis process was applied to detect LAMP product. The LFD was combined with the LAMP to detect LAMP product on the male cloth samples. For the male samples, the time course of detection on the first and seventh days indicated positive for both LAMP and PCR products on all the surfaces while no DNA amplification was found on any of the female samples. On day 30, positive LAMP product was still found on all the male samples. However, it had faded on the tiles. Moreover, all the male samples, which had tested positive for PCR product, were blurred and unclear. On day 60, LAMP product was still found on all the male samples. Conversely, the PCR method resulted in no bands showing for any of the male samples. However, the LAMP-LFD method detected product on all the male samples of cloth. The results show that the LAMP is an effective, practical, and reliable molecular-biological method. Moreover, the LFD can increase the efficiency and sensitivity of the LAMP, making it more suitable for field studies because gel electrophoresis apparatus is not required.

  20. Surface-enhanced Raman spectroscopic study of DNA and 6-mercapto-1-hexanol interactions using large area mapping

    DEFF Research Database (Denmark)

    Frøhling, Kasper Bayer; Alstrøm, Tommy Sonne; Bache, Michael

    2016-01-01

    intensities and peak positions it is possible to directly inspect the interplay between DNA and 6-mercapto-1-hexanol on gold covered nanopillars. It is demonstrated that optimised functionalization parameters can be extracted from the Raman spectra directly. Using the peak-fitting approach it is possible...

  1. Effect of the immobilisation of DNA aptamers on the detection of thrombin by means of surface plasmon resonance

    Czech Academy of Sciences Publication Activity Database

    Hianik, T.; Ostatná, V.; Vaisocherová, Hana; Homola, Jiří

    2008-01-01

    Roč. 391, č. 5 (2008), s. 1861-1869 ISSN 1618-2642 R&D Projects: GA AV ČR KAN200670701 Institutional research plan: CEZ:AV0Z20670512 Keywords : DNA aptamer * thrombin * dendrimers Subject RIV: EI - Biotechnology ; Bionics Impact factor: 3.328, year: 2008

  2. Surface-enhanced Raman Scattering Study of the Binding Modes of a Dibenzotetraaza[14]annulene Derivative with DNA/RNA Polynucleotides

    OpenAIRE

    Miljanić, Snežana; Dijanošić, Adriana; Kalac, Matea; Radić Stojković, Marijana; Piantanida, Ivo; Pawlica, Dariusz; Eilmes, Julita

    2012-01-01

    Binding modes of a dibenzotetraaza14annulene (DBTAA) derivative with synthetic nucleic acids were studied using surface-enhanced Raman spectroscopy (SERS). Changes in SERS intensity and appearance of new bands in spectra were attributed to different complexes formed between the DBTAA molecules and DNA/RNA polynucleotides. A decrease in intensity pointed to intercalation as the dominant binding mode of the annulene derivative with poly dGdC-poly dGdC and poly rA-poly rU, whereas new bands in...

  3. Simulation bounds for system availability

    International Nuclear Information System (INIS)

    Tietjen, G.L.; Waller, R.A.

    1976-01-01

    System availability is a dominant factor in the practicality of nuclear power electrical generating plants. A proposed model for obtaining either lower bounds or interval estimates on availability uses observed data on ''n'' failure-to-repair cycles of the system to estimate the parameters in the time-to-failure and time-to-repair models. These estimates are then used in simulating failure/repair cycles of the system. The availability estimate is obtained for each of 5000 samples of ''n'' failure/repair cycles to form a distribution of estimates. Specific percentile points of those simulated distributions are selected as lower simulation bounds or simulation interval bounds for the system availability. The method is illustrated with operational data from two nuclear plants for which an exponential time-to-failure and a lognormal time-to-repair are assumed

  4. Unitarity bound for gluon shadowing

    International Nuclear Information System (INIS)

    Kopeliovich, B. Z.; Levin, E.; Potashnikova, I. K.; Schmidt, Ivan

    2009-01-01

    Although at small Bjorken x gluons originated from different nucleons in a nucleus overlap in the longitudinal direction, most of them are still well separated in the transverse plane and therefore cannot fuse. For this reason the gluon density in nuclei cannot drop at small x below a certain bottom bound, which we evaluated in a model independent manner assuming the maximal strength of gluon fusion. We also calculated gluon shadowing in the saturated regime using the Balitsky-Kovchegov equation and found the nuclear ratio to be well above the unitarity bound. The recently updated analysis of parton distributions in nuclei, including BNL Relativistic Heavy Ion Collider (RHIC) data on high-p T hadron production at forward rapidities, led to strong gluon shadowing. Such strong shadowing and therefore the interpretation of the nuclear modification of the p T spectra in dA collisions at RHIC seem to be inconsistent with this unitarity bound.

  5. Bounds for nonlocality distillation protocols

    International Nuclear Information System (INIS)

    Forster, Manuel

    2011-01-01

    Nonlocality can be quantified by the violation of a Bell inequality. Since this violation may be amplified by local operations, an alternative measure has been proposed--distillable nonlocality. The alternative measure is difficult to calculate exactly due to the double exponential growth of the parameter space. In this paper, we give a way to bound the distillable nonlocality of a resource by the solutions to a related optimization problem. Our upper bounds are exponentially easier to compute than the exact value and are shown to be meaningful in general and tight in some cases.

  6. Space-bounded communication complexity

    DEFF Research Database (Denmark)

    Brody, Joshua Eric; Chen, Shiteng; Papakonstantinou, Periklis A.

    2013-01-01

    In the past thirty years, Communication Complexity has emerged as a foundational tool to proving lower bounds in many areas of computer science. Its power comes from its generality, but this generality comes at a price---no superlinear communication lower bound is possible, since a player may...... communicate his entire input. However, what if the players are limited in their ability to recall parts of their interaction? We introduce memory models for 2-party communication complexity. Our general model is as follows: two computationally unrestricted players, Alice and Bob, each have s(n) bits of memory...

  7. Bound entanglement and local realism

    International Nuclear Information System (INIS)

    Kaszlikowski, Dagomir; Zukowski, Marek; Gnacinski, Piotr

    2002-01-01

    We show using a numerical approach, which gives necessary and sufficient conditions for the existence of local realism, that the bound entangled state presented in Bennett et al. [Phys. Rev. Lett. 82, 5385 (1999)] admits a local and realistic description. We also find the lowest possible amount of some appropriate entangled state that must be ad-mixed to the bound entangled state so that the resulting density operator has no local and realistic description and as such can be useful in quantum communication and quantum computation

  8. Market access through bound tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Yalcin, Erdal; Schröder, Philipp

    2010-01-01

    WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings...... on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive...

  9. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  10. Surface functionalized Cu{sub 2}Zn{sub 1-x}Cd{sub x}SnS{sub 4} quinternary alloyed nanostructure for DNA sensing

    Energy Technology Data Exchange (ETDEWEB)

    Ibraheam, A.S.; Voon, C.H.; Foo, K.L.; Azizah, N. [University Malaysia Perlis, Institute of Nano Electronic Engineering, Kangar, Perlis (Malaysia); Al-Douri, Y. [University of Sidi-Bel-Abbes, Physics Department, Faculty of Science, Sidi Bel-Abbes (Algeria); Gopinath, S.C.B. [University Malaysia Perlis, Institute of Nano Electronic Engineering, Kangar, Perlis (Malaysia); Universiti Malaysia Perlis, School of Bioprocess Engineering, Arau, Perlis (Malaysia); Ameri, M. [Universite Djilali Liabes de Sidi Bel-Abbes, Laboratoire Physico-Chimie des Materiaux Avances (LPCMA), Sidi Bel-Abbes (Algeria); Ibrahim, Sattar S. [University of Anbar, Chemisty Department, College of Science, Al Rumadi (Iraq)

    2017-03-15

    A sensing plate of extended Cu{sub 2}Zn{sub 1-x}Cd{sub x}SnS{sub 4} quinternary alloy nanostructures, fabricated on an oxidized silicon substrate by the sol-gel method, is reported in this paper. The fabricated device was characterized and analyzed via field emission-scanning electron microscopy, X-ray diffraction (XRD), and photoluminescence (PL). The XRD peaks shifted towards the lower angle side alongside increasing concentration of cadmium. The average diameter of the Cu{sub 2}Zn{sub 1-x}Cd{sub x}SnS{sub 4} quinternary alloy nanostructures falls between 21.55 and 43.12 nm, while the shift of the PL bandgap was from 1.81 eV (x = 0) to 1.72 eV (x = 1). The resulting Cu{sub 2}Zn{sub 1-x}Cd{sub x}SnS{sub 4} quinternary alloy nanostructures components were functionalized with oligonucleotides probe DNA molecules and interacted with the target, exhibiting good sensing capabilities due to its large surface-to-volume ratio. The fabrication, immobilization, and hybridization processes were analyzed via representative current-voltage (I-V) plots. Its electrical profile shows that the device is capable to distinguish biomolecules. Its high performance was evident from the linear relationship between the probe DNA from cervical cancer and the target DNA, showing its applicability for medical applications. (orig.)

  11. Zinc fixation preserves flow cytometry scatter and fluorescence parameters and allows simultaneous analysis of DNA content and synthesis, and intracellular and surface epitopes

    DEFF Research Database (Denmark)

    Jensen, Uffe Birk; Owens, David; Pedersen, Søren

    2010-01-01

    Zinc salt-based fixation (ZBF) has proved advantageous in histochemical analyses conducted on intact tissues but has not been exploited in flow cytometry procedures that focus on quantitative analysis of individual cells. Here, we show that ZBF performs equally well to paraformaldehyde in the pre......Zinc salt-based fixation (ZBF) has proved advantageous in histochemical analyses conducted on intact tissues but has not been exploited in flow cytometry procedures that focus on quantitative analysis of individual cells. Here, we show that ZBF performs equally well to paraformaldehyde...... allowing subsequent quantitative PCR analysis or labeling for incorporation of the thymidine analog EdU following surface and intracellular epitope staining. Finally, ZBF treatment allows for long-term storage of labeled cells with little change in these parameters. Thus, we present a protocol for zinc...... salt fixation of cells that allows for the simultaneous analysis of DNA and intracellular and cell surface proteins by flow cytometry....

  12. New optimized DNA extraction protocol for fingerprints deposited on a special self-adhesive security seal and other latent samples used for human identification.

    Science.gov (United States)

    Kopka, Julieta; Leder, Monika; Jaureguiberry, Stella M; Brem, Gottfried; Boselli, Gabriel O

    2011-09-01

    Obtaining complete short tandem repeat (STR) profiles from fingerprints containing minimal amounts of DNA, using standard extraction techniques, can be difficult. The aim of this study was to evaluate a new kit, Fingerprint DNA Finder (FDF Kit), recently launched for the extraction of DNA and STR profiling from fingerprints placed on a special device known as Self-Adhesive Security Seal Sticker(®) and other latent fingerprints on forensic evidentiary material like metallic guns. The DNA extraction system is based on a reversal of the silica principle, and all the potential inhibiting substances are retained on the surface of a special adsorbent, while nucleic acids are not bound and remain in solution dramatically improving DNA recovery. DNA yield was quite variable among the samples tested, rendering in most of the cases (>90%) complete STR profiles, free of PCR inhibitors, and devoid of artifacts. Even samples with DNA amount below 100 pg could be successfully analyzed. © 2011 American Academy of Forensic Sciences.

  13. Transient response in granular bounded heap flows

    Science.gov (United States)

    Xiao, Hongyi; Ottino, Julio M.; Lueptow, Richard M.; Umbanhowar, Paul B.

    2017-11-01

    Heap formation, a canonical granular flow, is common in industry and is also found in nature. Here, we study the transition between steady flow states in quasi-2D bounded heaps by suddenly changing the feed rate from one fixed value to another. During the transition, in both experiments and discrete element method simulations, an additional wedge of flowing particles propagates over the rising free surface. The downstream edge of the wedge - the wedge front - moves downstream with velocity inversely proportional to the square root of time. An additional longer duration transient process continues after the wedge front reaches the downstream wall. The transient flux profile during the entire transition is well modeled by a diffusion-like equation derived from local mass balance and a local linear relation between the flux and the surface slope. Scalings for the transient kinematics during the flow transitions are developed based on the flux profiles. Funded by NSF Grant CBET-1511450.

  14. Entropy Bounds and Field Equations

    Directory of Open Access Journals (Sweden)

    Alessandro Pesci

    2015-08-01

    Full Text Available For general metric theories of gravity, we compare the approach that describes/derives the field equations of gravity as a thermodynamic identity with the one which looks at them from entropy bounds. The comparison is made through the consideration of the matter entropy flux across (Rindler horizons, studied by making use of the notion of a limiting thermodynamic scale l* of matter, previously introduced in the context of entropy bounds. In doing this: (i a bound for the entropy of any lump of matter with a given energy-momentum tensor Tab is considered, in terms of a quantity, which is independent of the theory of gravity that we use; this quantity is the variation of the Clausius entropy of a suitable horizon when the element of matter crosses it; (ii by making use of the equations of motion of the theory, the same quantity is then expressed as the variation of Wald’s entropy of that horizon (and this leads to a generalized form of the generalized covariant entropy bound, applicable to general diffeomorphism-invariant theories of gravity; and (iii a notion of l* for horizons, as well as an expression for it, is given.

  15. Bounded Densities and Their Derivatives

    DEFF Research Database (Denmark)

    Kozine, Igor; Krymsky, V.

    2009-01-01

    This paper describes how one can compute interval-valued statistical measures given limited information about the underlying distribution. The particular focus is on a bounded derivative of a probability density function and its combination with other available statistical evidence for computing ...

  16. Semiclassical bounds in magnetic bottles

    Czech Academy of Sciences Publication Activity Database

    Barseghyan, Diana; Exner, Pavel; Kovařík, H.; Weidl, T.

    2016-01-01

    Roč. 28, č. 1 (2016), s. 1650002 ISSN 0129-055X R&D Projects: GA ČR(CZ) GA14-06818S Institutional support: RVO:61389005 Keywords : magnetic Laplacian * discrete spectrum * eigenvalue bounds Subject RIV: BE - Theoretical Physics Impact factor: 1.426, year: 2016

  17. Positivity bounds for Sivers functions

    International Nuclear Information System (INIS)

    Kang Zhongbo; Soffer, Jacques

    2011-01-01

    We generalize a positivity constraint derived initially for parity-conserving processes to the parity-violating ones, and use it to derive non-trivial bounds on several Sivers functions, entering in the theoretical description of single spin asymmetry for various processes.

  18. Moderate deviations for bounded subsequences

    Directory of Open Access Journals (Sweden)

    George Stoica

    2006-01-01

    Full Text Available We study Davis' series of moderate deviations probabilities for Lp-bounded sequences of random variables (p>2. A certain subseries therein is convergent for the same range of parameters as in the case of martingale difference or i.i.d. sequences.

  19. Pieter Paul Rubens, "Prometheus Bound."

    Science.gov (United States)

    Shoemaker, Marla K.

    1986-01-01

    Provides a full-color reproduction of Pieter Paul Rubens' painting, "Prometheus Bound," and a lesson plan for using it with students in grades 10 through 12. The goal of the lesson is to introduce students to the techniques of design and execution used by Rubens. (JDH)

  20. Upward Bound: In the Beginning.

    Science.gov (United States)

    Groutt, John; Hill, Calvin

    2001-01-01

    Describes the early history of the Upward Bound program, including the role of President Johnson's vision, the Task Force on Poverty, the Office of Economic Opportunity, and Community Action Programs; influences on the development of the program; establishment of the program's administrative structure; pilot programs; and early problems leading to…

  1. A Functional Calculus for Quotient Bounded Operators

    Directory of Open Access Journals (Sweden)

    Sorin Mirel Stoian

    2006-12-01

    Full Text Available If (X, P is a sequentially locally convex space, then a quotient bounded operator T beloging to QP is regular (in the sense of Waelbroeck if and only if it is a bounded element (in the sense of Allan of algebra QP. The classic functional calculus for bounded operators on Banach space is generalized for bounded elements of algebra QP.

  2. Interaction of DNA with echinomycin at the mercury electrode surface as detected by impedance and chronopotentiometric measurements

    Czech Academy of Sciences Publication Activity Database

    Hasoň, Stanislav; Dvořák, Jakub; Jelen, František; Vetterl, Vladimír

    2002-01-01

    Roč. 56, č. 5 (2002), s. 905-913 ISSN 0039-9140 R&D Projects: GA AV ČR IAA4004901; GA AV ČR IAA4004002; GA AV ČR IBS5004107; GA ČR GV204/97/K084 Grant - others:GA FRVŠ(XC) G40583; GA FRVŠ(XC) F40564 Institutional research plan: CEZ:AV0Z5004920 Keywords : electrochemical impedance spectroscopy * DNA * echinomycin Subject RIV: BO - Biophysics Impact factor: 2.054, year: 2002

  3. The nucleotide-binding site of the Escherichia coli DnaC protein: molecular topography of DnaC protein-nucleotide cofactor complexes.

    Science.gov (United States)

    Galletto, Roberto; Jezewska, Maria J; Maillard, Rodrigo; Bujalowski, Wlodzimierz

    2005-01-01

    The structure of the nucleotide-binding site of the Escherichia coli replication factor DnaC protein and the effect of the nucleotide cofactor on the protein structure have been examined using ultraviolet, steady-state, and time-dependent fluorescence spectroscopy. Emission spectra and quenching studies of the fluorescent nucleotide analogs, 3'-O-(N-methylantraniloyl)-5'-triphosphate (MANT-ATP) and 3'-O-(N-methylantraniloyl)-5'-diphosphate (MANT-ADP), bound to the DnaC protein indicate that the nucleotide-binding site forms a hydrophobic cleft on the surface of the protein. Fluorescence decays of free and bound MANT-ATP and MANT-ADP indicate that cofactors exist in two different conformations both, free and bound to the protein. However, the two conformations of the bound nucleotides differ in their solvent accessibilities. Moreover, there are significant differences in the solvent accessibility between ATP and ADP complexes. Specific binding of magnesium to the protein controls the structure of the binding site, particularly, in the case of the ATP complex, leading to additional opening of the binding site cleft. Both tyrosine and tryptophan residues are located on the surface of the protein. The tryptophans are clustered at a large distance from the nucleotide-binding site. However, in spite of a large spatial separation, binding of both cofactors induces significant and different changes in the structure of the environment of tryptophans, indicating long-range structural effects through the DnaC molecule. Moreover, only ATP induces changes in the distribution of the tyrosine residues on the surface of the protein. The data reveal that the nucleotide-DnaC protein complex is a sophisticated allosteric system, responding differently to the ATP and ADP binding.

  4. DNA-cell conjugates

    Science.gov (United States)

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2016-05-03

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  5. Rapid, highly sensitive and highly specific gene detection by combining enzymatic amplification and DNA chip detection simultaneously

    Directory of Open Access Journals (Sweden)

    Koji Hashimoto

    2016-05-01

    Full Text Available We have developed a novel gene detection method based on the loop-mediated isothermal amplification (LAMP reaction and the DNA dissociation reaction on the same DNA chip surface to achieve a lower detection limit, broader dynamic range and faster detection time than are attainable with a conventional DNA chip. Both FAM- and thiol-labeled DNA probe bound to the complementary sequence accompanying Dabcyl was immobilized on the gold surface via Au/thiol bond. The LAMP reaction was carried out on the DNA probe fixed gold surface. At first, Dabcyl molecules quenched the FAM fluorescence. According to the LAMP reaction, the complementary sequence with Dabcyl was competitively reacted with the amplified targeted sequence. As a result, the FAM fluorescence increased owing to dissociation of the complementary sequence from the DNA probe. The simultaneous reaction of LAMP and DNA chip detection was achieved, and 103 copies of the targeted gene were detected within an hour by measuring fluorescence intensity of the DNA probe. Keywords: Biosensor, DNA chip, Loop-mediated isothermal amplification (LAMP, Fluorescence detection, Gold substrate, Au/thiol bond

  6. Single-molecule mechanics of protein-labelled DNA handles

    Directory of Open Access Journals (Sweden)

    Vivek S. Jadhav

    2016-01-01

    Full Text Available DNA handles are often used as spacers and linkers in single-molecule experiments to isolate and tether RNAs, proteins, enzymes and ribozymes, amongst other biomolecules, between surface-modified beads for nanomechanical investigations. Custom DNA handles with varying lengths and chemical end-modifications are readily and reliably synthesized en masse, enabling force spectroscopic measurements with well-defined and long-lasting mechanical characteristics under physiological conditions over a large range of applied forces. Although these chemically tagged DNA handles are widely used, their further individual modification with protein receptors is less common and would allow for additional flexibility in grabbing biomolecules for mechanical measurements. In-depth information on reliable protocols for the synthesis of these DNA–protein hybrids and on their mechanical characteristics under varying physiological conditions are lacking in literature. Here, optical tweezers are used to investigate different protein-labelled DNA handles in a microfluidic environment under different physiological conditions. Digoxigenin (DIG-dsDNA-biotin handles of varying sizes (1000, 3034 and 4056 bp were conjugated with streptavidin or neutravidin proteins. The DIG-modified ends of these hybrids were bound to surface-modified polystyrene (anti-DIG beads. Using different physiological buffers, optical force measurements showed consistent mechanical characteristics with long dissociation times. These protein-modified DNA hybrids were also interconnected in situ with other tethered biotinylated DNA molecules. Electron-multiplying CCD (EMCCD imaging control experiments revealed that quantum dot–streptavidin conjugates at the end of DNA handles remain freely accessible. The experiments presented here demonstrate that handles produced with our protein–DNA labelling procedure are excellent candidates for grasping single molecules exposing tags suitable for molecular

  7. Computer simulation of bounded plasmas

    International Nuclear Information System (INIS)

    Lawson, W.S.

    1987-01-01

    The problems of simulating a one-dimensional bounded plasma system using particles in a gridded space are systematically explored and solutions to them are given. Such problems include the injection of particles at the boundaries, the solution of Poisson's equation, and the inclusion of an external circuit between the confining boundaries. A recently discovered artificial cooling effect is explained as being a side-effect of quiet injection, and its potential for causing serious but subtle errors in bounded simulation is noted. The methods described in the first part of the thesis are then applied to the simulation of an extension of the Pierce diode problem, specifically a Pierce diode modified by an external circuit between the electrodes. The results of these simulations agree to high accuracy with theory when a theory exists, and also show some interesting chaotic behavior in certain parameter regimes. The chaotic behavior is described in detail

  8. Bounded Rationality in Transposition Processes

    DEFF Research Database (Denmark)

    Vollaard, Hans; Martinsen, Dorte Sindbjerg

    2014-01-01

    Studies explaining the timeliness and correctness of the transposition of EU directives into national legislation have provided rather inconclusive findings. They do not offer a clear-cut prediction concerning the transposition of the patients’ rights directive, which is one of the first that con......Studies explaining the timeliness and correctness of the transposition of EU directives into national legislation have provided rather inconclusive findings. They do not offer a clear-cut prediction concerning the transposition of the patients’ rights directive, which is one of the first...... that concerns the organisation and financing of national healthcare systems. This article applies the perspective of bounded rationality to explain (irregularities in) the timely and correct transposition of EU directives. The cognitive and organisational constraints long posited by the bounded rationality...

  9. 78 FR 18326 - Agency Information Collection Activities; Comment Request; Upward Bound and Upward Bound Math...

    Science.gov (United States)

    2013-03-26

    ...; Comment Request; Upward Bound and Upward Bound Math Science Annual Performance Report AGENCY: The Office... considered public records. Title of Collection: Upward Bound and Upward Bound Math Science Annual Performance...) and Upward Bound Math and Science (UBMS) Programs. The Department is requesting a new APR because of...

  10. The highest affinity DNA element bound by Pbx complexes in t(1;19) leukemic cells fails to mediate cooperative DNA-binding or cooperative transactivation by E2a-Pbx1 and class I Hox proteins - evidence for selective targetting of E2a-Pbx1 to a subset of Pbx-recognition elements.

    Science.gov (United States)

    Knoepfler, P S; Kamps, M P

    1997-05-29

    Oncoprotein E2a-Pbx1 contains the N-terminal transactivation domains of E2a and the majority of the homeodomain protein, Pbx1. Using recombinant proteins, both Pbx1 and E2a-Pbx1 heterodimerize with Hox proteins on bipartite elements, Pbx1 binding a 5' TGAT core and Class I Hox proteins binding adjacent 3' TAAT, TTAT, or TGAT cores. In contrast to these in vitro results, nuclear extracts from E2a-Pbx1-transformed cells assemble an abundant Pbx-containing complex on TGATTGAT that excludes E2a-Pbx1, suggesting that an uncharacterized in vivo partner discriminates between E2a-Pbx1 and Pbx proteins, distinguishing it from Hox proteins. Here, we describe the DNA-binding properties of this complex, and identify TGATTGAC (PCE; Pbx Consensus Element) as its optimal recognition motif. In vitro, the PCE fails to bind heterodimers of Class I Hox proteins plus either Pbx1 or E2a-Pbx1. Likewise, in vivo, the PCE fails to mediate cooperative transactivation by E2a-Pbx1 plus Class I Hox proteins. Thus, the PCE binds a Pbx dimer partner that behaves unlike Class I Hox proteins. Competition analysis indicates that the Pbx-containing complex that binds the PCE also binds the TGATTGAT Pbx-Hox element and binds promoter elements required for tissue-specific expression of a number of cellular genes. Thus, different Pbx partners dictate targetting of Pbx heterodimers to related DNA motifs that differ in the sequence of their 3' half-sites, and E2a-Pbx1 heterodimerizes with only a subset of Pbx partners, restricting its potential DNA targets.

  11. Complexity Bounds for Quantum Computation

    Science.gov (United States)

    2007-06-22

    iently thanin lassi al omputation, onstru tion of small ir uits whi h an arry out phase estimation, show-ing that the quantum ontent of strong...on lower bounds for omputing parity or fanout using onstant or log depth quantum ir uits, quantum simulations of lassi al ir uit elements and...lasses, su h as thresh-old and mod fun tions, and the general relationships between quantum omplexity lasses and orre-sponding lassi al lasses

  12. Peptide Synthesis on a Next-Generation DNA Sequencing Platform.

    Science.gov (United States)

    Svensen, Nina; Peersen, Olve B; Jaffrey, Samie R

    2016-09-02

    Methods for displaying large numbers of peptides on solid surfaces are essential for high-throughput characterization of peptide function and binding properties. Here we describe a method for converting the >10(7) flow cell-bound clusters of identical DNA strands generated by the Illumina DNA sequencing technology into clusters of complementary RNA, and subsequently peptide clusters. We modified the flow-cell-bound primers with ribonucleotides thus enabling them to be used by poliovirus polymerase 3D(pol) . The primers hybridize to the clustered DNA thus leading to RNA clusters. The RNAs fold into functional protein- or small molecule-binding aptamers. We used the mRNA-display approach to synthesize flow-cell-tethered peptides from these RNA clusters. The peptides showed selective binding to cognate antibodies. The methods described here provide an approach for using DNA clusters to template peptide synthesis on an Illumina flow cell, thus providing new opportunities for massively parallel peptide-based assays. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. The effect of pH and DNA concentration on organic thin-film transistor biosensors

    KAUST Repository

    Khan, Hadayat Ullah

    2012-03-01

    Organic electronics are beginning to attract more interest for biosensor technology as they provide an amenable interface between biology and electronics. Stable biosensor based on electronic detection platform would represent a significant advancement in technology as costs and analysis time would decrease immensely. Organic materials provide a route toward that goal due to their compatibility with electronic applications and biological molecules. In this report, we detail the effects of experimental parameters, such as pH and concentration, toward the selective detection of DNA via surface-bound peptide nucleic acid (PNA) sequences on organic transistor biosensors. The OTFT biosensors are fabricated with thin-films of the organic semiconductor, 5,5′-bis-(7-dodecyl-9H-fluoren-2-yl)-2,2′-bithiophene (DDFTTF), in which they exhibit a stable mobility of 0.2 cm 2 V -1 s -1 in buffer solutions (phosphate-buffer saline, pH 7.4 or sodium acetate, pH 7). Device performance were optimized to minimize the deleterious effects of pH on gate-bias stress such that the sensitivity toward DNA detection can be improved. In titration experiments, the surface-bound PNA probes were saturated with 50 nM of complementary target DNA, which required a 10-fold increase in concentration of single-base mismatched target DNA to achieve a similar surface saturation. The binding constant of DNA on the surface-bound PNA probes was determined from the concentration-dependent response (titration measurements) of our organic transistor biosensors. © 2011 Elsevier B.V. All rights reserved.

  14. On resonances and bound states of Smilansky Hamiltonian

    Czech Academy of Sciences Publication Activity Database

    Exner, Pavel; Lotoreichik, Vladimir; Tater, Miloš

    2016-01-01

    Roč. 7, č. 5 (2016), s. 789-802 ISSN 2220-8054 R&D Projects: GA ČR(CZ) GA14-06818S Institutional support: RVO:61389005 Keywords : Smilansky Hamiltonian * resonances * resonance free region * weak coupling asymptotics * Riemann surface * bound states Subject RIV: BE - Theoretical Physics

  15. Stenostomum cf. leucops (Platyhelminthes in Thailand: a surface observation using scanning electron microscopy and phylogenetic analysis based on 18S ribosomal DNA sequences

    Directory of Open Access Journals (Sweden)

    Arin Ngamniyom

    2016-02-01

    Full Text Available The genus Stenostomum contains small turbellaria that are widely distributed in freshwater environments worldwide. However, there are only rare reports or studies of this genus from Thailand. Therefore, the objective of this study was to report S. cf. leucops in Thailand collected from Pathum Thani Province. The worm morphology and surface topography using scanning electron microscopy were determined. Moreover, the phylogenetic tree of S. cf. leucops was analysed with 17 flatworms based on the 18S ribosomal DNA sequences. The phylogenetic relationship shared a common ancestry of Catenulida species, and S. cf. leucops displayed a monophyletic pattern within Stenostomum spp. The results of the morphological and molecular data are discussed. These results may increase the knowledge of freshwater microturbellarians in Thailand.

  16. Fluorescence resonance energy transfer between green fluorescent protein and doxorubicin enabled by DNA nanotechnology.

    Science.gov (United States)

    Heger, Zbynek; Kominkova, Marketa; Cernei, Natalia; Krejcova, Ludmila; Kopel, Pavel; Zitka, Ondrej; Adam, Vojtech; Kizek, Rene

    2014-12-01

    DNA nanotechnology is a rapidly growing research area, where DNA may be used for wide range of applications such as construction of nanodevices serving for large scale of diverse purposes. Likewise a panel of various purified fluorescent proteins is investigated for their ability to emit their typical fluorescence spectra under influence of particular excitation. Hence these proteins may form ideal donor molecules for assembly of fluorescence resonance emission transfer (FRET) constructions. To extend the application possibilities of fluorescent proteins, while using DNA nanotechnology, we developed nanoconstruction comprising green fluorescent protein (GFP) bound onto surface of surface active nanomaghemite and functionalized with gold nanoparticles. We took advantage of natural affinity between gold and thiol moieties, which were modified to bind DNA fragment. Finally we enclosed doxorubicin into fullerene cages. Doxorubicin intercalated in DNA fragment bound on the particles and thus we were able to connect these parts together. Because GFP behaved as a donor and doxorubicin as an acceptor using excitation wavelength for GFP (395 nm) in emission wavelength of doxorubicin (590 nm) FRET was observed. This nanoconstruction may serve as a double-labeled transporter of doxorubicin guided by force of external magnetic force owing to the presence of nanomaghemite. Further nanomaghemite offers the possibility of using this technology for thermotherapy. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Dilation volumes of sets of bounded perimeter

    DEFF Research Database (Denmark)

    Kiderlen, Markus; Rataj, Jan

    , this derivative coincides up to sign with the directional derivative of the covariogram of A in direction u. By known results for the covariogram, this derivative can therefore be expressed by the cosine transform of the surface area measure of A. We extend this result to sets Q that are at most countable and use...... it to determine the derivative of the contact distribution function of a stationary random closed set at zero. A variant for uncountable Q is given, too. The proofs are based on approximation of the characteristic function of A by smooth functions of bounded variation and showing corresponding formulas for them....

  18. The algebras of bounded and essentially bounded Lebesgue measurable functions

    Directory of Open Access Journals (Sweden)

    Mortini Raymond

    2017-04-01

    Full Text Available Let X be a set in ℝn with positive Lebesgue measure. It is well known that the spectrum of the algebra L∞(X of (equivalence classes of essentially bounded, complex-valued, measurable functions on X is an extremely disconnected compact Hausdorff space.We show, by elementary methods, that the spectrum M of the algebra ℒb(X, ℂ of all bounded measurable functions on X is not extremely disconnected, though totally disconnected. Let ∆ = { δx : x ∈ X} be the set of point evaluations and let g be the Gelfand topology on M. Then (∆, g is homeomorphic to (X, Τdis,where Tdis is the discrete topology. Moreover, ∆ is a dense subset of the spectrum M of ℒb(X, ℂ. Finally, the hull h(I, (which is homeomorphic to M(L∞(X, of the ideal of all functions in ℒb(X, ℂ vanishing almost everywhere on X is a nowhere dense and extremely disconnected subset of the Corona M \\ ∆ of ℒb(X, ℂ.

  19. Bounds on dissipation in stress-driven flow

    Science.gov (United States)

    Tang, W.; Caulfield, C. P.; Young, W. R.

    2004-07-01

    We calculate the optimal upper and lower bounds, subject to the assumption of streamwise invariance, on the long-time-averaged mechanical energy dissipation rate varepsilon within the flow of an incompressible viscous fluid of constant kinematic viscosity nu and depth h driven by a constant surface stress tau=rho u(2_star) , where u_star is the friction velocity. We show that varepsilon ≤ varepsilon_{max}=tau(2/(rho^2nu)) , i.e. the dissipation is bounded above by the dissipation associated with the laminar solution bu=tau(z+h)/(rhonu) xvec, where xvec is the unit vector in the streamwise x-direction.

  20. Voronoi Diagrams Without Bounding Boxes

    Science.gov (United States)

    Sang, E. T. K.

    2015-10-01

    We present a technique for presenting geographic data in Voronoi diagrams without having to specify a bounding box. The method restricts Voronoi cells to points within a user-defined distance of the data points. The mathematical foundation of the approach is presented as well. The cell clipping method is particularly useful for presenting geographic data that is spread in an irregular way over a map, as for example the Dutch dialect data displayed in Figure 2. The automatic generation of reasonable cell boundaries also makes redundant a frequently used solution to this problem that requires data owners to specify region boundaries, as in Goebl (2010) and Nerbonne et al (2011).

  1. Sensitivity analysis using probability bounding

    International Nuclear Information System (INIS)

    Ferson, Scott; Troy Tucker, W.

    2006-01-01

    Probability bounds analysis (PBA) provides analysts a convenient means to characterize the neighborhood of possible results that would be obtained from plausible alternative inputs in probabilistic calculations. We show the relationship between PBA and the methods of interval analysis and probabilistic uncertainty analysis from which it is jointly derived, and indicate how the method can be used to assess the quality of probabilistic models such as those developed in Monte Carlo simulations for risk analyses. We also illustrate how a sensitivity analysis can be conducted within a PBA by pinching inputs to precise distributions or real values

  2. [Role of layered double hydroxide (LDH) in the protection of herring testis DNA from heavy metals].

    Science.gov (United States)

    Tang, Yi-Ni; Wu, Ping-Xiao; Zhu, Neng-Wu

    2012-10-01

    The role of layered double hydroxide (LDH) in the protection of herring testis DNA from heavy metals Cd2+ and Pb2+ was studied by X-ray diffraction ( XRD) spectra, Fourier transform infrared (FTIR) spectra, Scanning Electron Microscopy (SEM), Cyclic Voltammetry and Ultraviolet Spectrometry. Size expansion of the basal spacing (003) from 0. 76 nm in LDH to 2. 30 nm was observed in the resulting DNA-LDH nanohybrids and it gave peaks corresponding to C=O (1 534 cm(-1) and 1488 cm(-1)) in skeleton and bases, C-O stretching vibration (1228 cm(-1)), and P-O symmetrical stretching vibration (1096 cm(-1)) in functional groups of DNA, indicating that DNA were intercalated into the LDH by the ion exchange. However, the displacement of NO3(-) was not fully complete (partial intercalation of DNA). The DNA outside LDH interlayers was absorbed on the surface of LDH. The cyclic voltammetric curves showed that DNA in the composites exhibited a very similar peaks, which corresponded to the two reduction current peaks (E(P) = - 1.2 mV and E(P) = -2.4 mV) of free DNA. Also there was no cathode sag emerging in cyclic voltammetric curves, suggesting that both Cd2+ and Pb2+ cannot insert into the groove of DNA to associate with base pairs or other groups when DNA was bound on LDH. The results showed that, on the one hand, both Cd2+ and Pb2+ were absorbed on the external surface of LDH for immobilization, on the other hand, the layer of LDH provided ideal space for DNA by the action of protecting DNA molecules from Cd2+ and Pb2+.

  3. Rhodium catalysts bound to functionalized mesoporous silica

    Energy Technology Data Exchange (ETDEWEB)

    Bitterwolf, Thomas E.; Newell, J D.; Carver, Colin T.; Addleman, Raymond S.; Linehan, John C.; Fryxell, Glen E.

    2004-07-20

    Phosphine and amine functionalized mesoporous silica materials were metallated with Rh(CO)2(i-Pr2NH)Cl or Rh2(CO)4Cl2, respectively, to yield catalysts containing the Rh(PPh2R)2(CO)Cl or Rh(CO)2(NH2R)Cl, where R is a propyl chain bonded to the silica surface, reactive centers. In order to ascertain the effect of pore size on rates of hydroformylation catalysis both 35 and 45 ? pore size materials were used. Using the hydroformylation of octene as a reference reaction, the phosphine based, 45 ? catalysts were 1.5-1.3 times faster than the amine based, 45 ? materials were 2.6-2.1 times faster than the 35 ? catalysts, and the 45 ? materials. The orientation of the catalyst relative to the functionalized surface, and the steric environment around the catalyst active site appear to be significant in determining rate of reaction. The ability of the surface bound phosphine catalysts to affect hydroformylation was strongly influenced by the steric constraints of the substrate. Terminal alkenes were readily hydroformylated and norbornene was slowly hydroformylated, but pinene, trans-cyclododecene, cyclohexene and cholesterol were nonreactive to the catalytic center.

  4. Biomimetic DNA emulsions: specific, thermo-reversible and adjustable binding from a liquid-like DNA layer

    Science.gov (United States)

    Pontani, Lea-Laetitia; Feng, Lang; Dreyfus, Remi; Seeman, Nadrian; Chaikin, Paul; Brujic, Jasna

    2013-03-01

    We develop micron-sized emulsions coated with specific DNA sequences and complementary sticky ends. The emulsions are stabilized with phospholipids on which the DNA strands are grafted through biotin-streptavidin interactions, which allows the DNA to diffuse freely on the surface. We produce two complementary emulsions: one is functionalized with S sticky ends and dyed with red streptavidin, the other displays the complementary S' sticky ends and green streptavidin. Mixing those emulsions reveals specific adhesion between them due to the short-range S-S' hybridization. As expected this interaction is thermo-reversible: the red-green adhesive droplets dissociate upon heating and reassemble after cooling. Here the fluid phospholipids layer also leads to diffusive adhesion patches, which allows the bound droplets to rearrange throughout the packing structure. We quantify the adhesion strength between two droplets and build a theoretical framework that captures the observed trends through parameters such as the size of the droplets, the DNA surface density, the various DNA constructs or the temperature. This colloidal-scale, specific, thermo-reversible biomimetic emulsion offers a new versatile and powerful tool for the development of complex self-assembled materials.

  5. Substrate-Bound Protein Gradients to Study Haptotaxis

    Directory of Open Access Journals (Sweden)

    Sebastien G. Ricoult

    2015-03-01

    Full Text Available Cells navigate in response to inhomogeneous distributions of extracellular guidance cues. The cellular and molecular mechanisms underlying migration in response to gradients of chemical cues have been investigated for over a century. Following the introduction of micropipettes and more recently microfluidics for gradient generation, much attention and effort was devoted to study cellular chemotaxis, which is defined as guidance by gradients of chemical cues in solution. Haptotaxis, directional migration in response to gradients of substrate-bound cues, has received comparatively less attention; however it is increasingly clear that in vivo many physiologically relevant guidance proteins – including many secreted cues – are bound to cellular surfaces or incorporated into extracellular matrix and likely function via a haptotactic mechanism. Here, we review the history of haptotaxis. We examine the importance of the reference surface, the surface in contact with the cell that is not covered by the cue, which forms a gradient opposing the gradient of the protein cue and must be considered in experimental designs and interpretation of results. We review and compare microfluidics, contact-printing, light patterning and 3D fabrication to pattern substrate-bound protein gradients in vitro, and focus on their application to study axon guidance. The range of methods to create substrate-bound gradients discussed herein make possible systematic analyses of haptotactic mechanisms. Furthermore, understanding the fundamental mechanisms underlying cell motility will inform bioengineering approaches to program cell navigation and recover lost function.

  6. Determining Normal-Distribution Tolerance Bounds Graphically

    Science.gov (United States)

    Mezzacappa, M. A.

    1983-01-01

    Graphical method requires calculations and table lookup. Distribution established from only three points: mean upper and lower confidence bounds and lower confidence bound of standard deviation. Method requires only few calculations with simple equations. Graphical procedure establishes best-fit line for measured data and bounds for selected confidence level and any distribution percentile.

  7. QCM-based rupture force measurement as a tool to study DNA dehybridization and duplex stability.

    Science.gov (United States)

    Dultsev, Fedor N; Kolosovsky, Eugeny A; Lomzov, Alexander A; Pyshnyi, Dmitrii V

    2017-02-01

    The stability of double-stranded DNA (dsDNA) was assessed on the basis of unwinding force measurement. Unwinding force was measured directly with a quartz crystal microbalance (QCM). The amplitude of its surface oscillations was controlled by supplying variable alternate voltage. Under smoothly increasing amplitude of QCM surface oscillations, dsDNA fixed on QCM surface through one of its ends got unwound. This procedure allows reliable measurement of rupture force as small as 5-10 pN. It was demonstrated that oscillations of the surface, with dsDNA bound through one of its ends to this surface, at a frequency of 14 MHz, cause helix unwinding to form two complementary parts due to viscous forces of the liquid medium. Unwinding starts at the upper end. This was proven using oligonucleotide duplexes containing mismatches in different positions. For duplexes containing complementary 20 base pairs, the helix unwinding force is equal to 30-40 pN, which is in agreement with the data obtained by means of atomic-force microscopy (AFM) for the case of unzipping mode. Graphical Abstract Rupture force depending on mismatch position in dsDNA.

  8. Observational Bounds on Cosmic Doomsday

    Energy Technology Data Exchange (ETDEWEB)

    Shmakova, Marina

    2003-07-11

    Recently it was found, in a broad class of models, that the dark energy density may change its sign during the evolution of the universe. This may lead to a global collapse of the universe within the time t{sub c} {approx} 10{sup 10}-10{sup 11} years. Our goal is to find what bounds on the future lifetime of the universe can be placed by the next generation of cosmological observations. As an example, we investigate the simplest model of dark energy with a linear potential V({phi}) = V{sub 0}(1 + {alpha}{phi}). This model can describe the present stage of acceleration of the universe if {alpha} is small enough. However, eventually the field {phi} rolls down, V({phi}) becomes negative, and the universe collapses. The existing observational data indicate that the universe described by this model will collapse not earlier than t{sub c} {approx_equal} 10 billion years from the present moment. We show that the data from SNAP and Planck satellites may extend the bound on the ''doomsday'' time to tc 40 billion years at the 95% confidence level.

  9. Quantum bounds on Bell inequalities

    Science.gov (United States)

    Pál, Károly F.; Vértesi, Tamás

    2009-02-01

    We have determined the maximum quantum violation of 241 tight bipartite Bell inequalities with up to five two-outcome measurement settings per party by constructing the appropriate measurement operators in up to six-dimensional complex and eight-dimensional real-component Hilbert spaces using numerical optimization. Out of these inequalities 129 have been introduced here. In 43 cases higher-dimensional component spaces gave larger violation than qubits, and in three occasions the maximum was achieved with six-dimensional spaces. We have also calculated upper bounds on these Bell inequalities using a method proposed recently. For all but 20 inequalities the best solution found matched the upper bound. Surprisingly, the simplest inequality of the set examined, with only three measurement settings per party, was not among them, despite the high dimensionality of the Hilbert space considered. We also computed detection threshold efficiencies for the maximally entangled qubit pair. These could be lowered in several instances if degenerate measurements were also allowed.

  10. Evaluation of hepatitis B surface antigen and hepatitis B virus-DNA results in postmortem plasma specimens

    Directory of Open Access Journals (Sweden)

    Nihan Ziyade

    2015-03-01

    Full Text Available Objective: To assess the presence of hepatitis B surface antigen, one of the serologic markers of hepatitis B virus (HBV infection, in postmortem blood samples from autopsy cases using ELISA, and to compare the results with those obtained by PCR, which is the gold standard method in assessing HBV infection. Methods: The HBV test results of the blood samples from 880 autopsy cases determined in our laboratory, were retrospectively studied. Results: When compared with the gold standard method PCR, the sensitivity and specificity of postmortem ELISA were 100% and 84.1%, respectively. Conclusions: The increasingly used molecular diagnostic methods, such as PCR, should be used in cases where serological tests remain insufficient.We think that prospective studies on the comparison of ELISA and PCR assessment of postmortem blood samples with larger material should be carried out.

  11. Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations.

    Science.gov (United States)

    Ishida, Hisashi; Matsumoto, Atsushi

    2016-09-01

    In order to understand how MutS recognizes mismatched DNA and induces the reaction of DNA repair using ATP, the dynamics of the complexes of MutS (bound to the ADP and ATP nucleotides, or not) and DNA (with mismatched and matched base-pairs) were investigated using molecular dynamics simulations. As for DNA, the structure of the base-pairs of the homoduplex DNA which interacted with the DNA recognition site of MutS was intermittently disturbed, indicating that the homoduplex DNA was unstable. As for MutS, the disordered loops in the ATPase domains, which are considered to be necessary for the induction of DNA repair, were close to (away from) the nucleotide-binding sites in the ATPase domains when the nucleotides were (not) bound to MutS. This indicates that the ATPase domains changed their structural stability upon ATP binding using the disordered loop. Conformational analysis by principal component analysis showed that the nucleotide binding changed modes which have structurally solid ATPase domains and the large bending motion of the DNA from higher to lower frequencies. In the MutS-mismatched DNA complex bound to two nucleotides, the bending motion of the DNA at low frequency modes may play a role in triggering the formation of the sliding clamp for the following DNA-repair reaction step. Moreover, MM-PBSA/GBSA showed that the MutS-homoduplex DNA complex bound to two nucleotides was unstable because of the unfavorable interactions between MutS and DNA. This would trigger the ATP hydrolysis or separation of MutS and DNA to continue searching for mismatch base-pairs. Proteins 2016; 84:1287-1303. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  12. Normalization constraint for variational bounds on fluid permeability

    International Nuclear Information System (INIS)

    Berryman, J.G.; Milton, G.W.

    1985-01-01

    A careful reexamination of the formulation of Prager's original variational principle for viscous flow through porous media has uncovered a subtle error in the normalization constraint on the trial functions. Although a certain surface integral of the true pressure field over the internal surface area always vanishes for isotropic materials, the corresponding surface integral for a given trial pressure field does not necessarily vanish but has nevertheless been previously neglected in the normalization. When this error is corrected, the form of the variational estimate is actually simpler than before and furthermore the resulting bounds have been shown to improve when the constant trial functions are used in either the two-point or three-point bounds

  13. Holography, Dimensional Reduction and the Bekenstein Bound

    Science.gov (United States)

    Bak, Dongsu; Yee, Ho-Ung

    2004-04-01

    We consider dimensional reduction of the lightlike holography of the covariant entropy bound from D+1 dimensional geometry of M × S1 to the D dimensional geometry M. With a warping factor, the local Bekenstein bound in D+1 dimensions leads to a more refined form of the bound from the D dimensional view point. With this new local Bekenstein bound, it is quite possible to saturate the lightlike holography even with nonvanishing expansion rate. With a Kaluza-Klein gauge field, the dimensional reduction implies a stronger bound where the energy momentum tensor contribution is replaced by the energy momentum tensor with the electromagnetic contribution subtracted.

  14. Extending Quantum Chemistry of Bound States to Electronic Resonances

    Science.gov (United States)

    Jagau, Thomas-C.; Bravaya, Ksenia B.; Krylov, Anna I.

    2017-05-01

    Electronic resonances are metastable states with finite lifetime embedded in the ionization or detachment continuum. They are ubiquitous in chemistry, physics, and biology. Resonances play a central role in processes as diverse as DNA radiolysis, plasmonic catalysis, and attosecond spectroscopy. This review describes novel equation-of-motion coupled-cluster (EOM-CC) methods designed to treat resonances and bound states on an equal footing. Built on complex-variable techniques such as complex scaling and complex absorbing potentials that allow resonances to be associated with a single eigenstate of the molecular Hamiltonian rather than several continuum eigenstates, these methods extend electronic-structure tools developed for bound states to electronic resonances. Selected examples emphasize the formal advantages as well as the numerical accuracy of EOM-CC in the treatment of electronic resonances. Connections to experimental observables such as spectra and cross sections, as well as practical aspects of implementing complex-valued approaches, are also discussed.

  15. Capacity Bounds for Parallel Optical Wireless Channels

    KAUST Repository

    Chaaban, Anas

    2016-01-01

    A system consisting of parallel optical wireless channels with a total average intensity constraint is studied. Capacity upper and lower bounds for this system are derived. Under perfect channel-state information at the transmitter (CSIT), the bounds have to be optimized with respect to the power allocation over the parallel channels. The optimization of the lower bound is non-convex, however, the KKT conditions can be used to find a list of possible solutions one of which is optimal. The optimal solution can then be found by an exhaustive search algorithm, which is computationally expensive. To overcome this, we propose low-complexity power allocation algorithms which are nearly optimal. The optimized capacity lower bound nearly coincides with the capacity at high SNR. Without CSIT, our capacity bounds lead to upper and lower bounds on the outage probability. The outage probability bounds meet at high SNR. The system with average and peak intensity constraints is also discussed.

  16. On order bounded subsets of locally solid Riesz spaces | Hong ...

    African Journals Online (AJOL)

    In a topological Riesz space there are two types of bounded subsets: order bounded subsets and topologically bounded subsets. It is natural to ask (1) whether an order bounded subset is topologically bounded and (2) whether a topologically bounded subset is order bounded. A classical result gives a partial answer to (1) ...

  17. Surface-enhanced Raman detection of RNA and DNA bases following flow-injection analysis or HPLC separation

    Science.gov (United States)

    Cotton, Therese M.; Sheng, Rong-Sheng; Ni, Fan

    1990-11-01

    The goal of this study is to develop Surface-enhanced Raman scattering (SERS) detection methods for flow injection analysis (FIA) and high performance liquid chromatography (HPLC). Nucleic acid bases have been chosen for analysis because of their importance in life processes. The advantages to the use of SERS-based detection include its sensitivity, specificity and versatility. With the development of improved methodology, the detection limits should be comparable to UV spectroscopy. However, the specificity is considerably superior to that obtained with electronic spectroscopy in that the Raman spectrum provides a molecular fingerprint of the individual analytes. Raman spectroscopy is very versatile: aqueous samples, gases and solids can be analyzed with equal facility. The results presented here demonstrate that SERS can be used as a detection method for both FIA and HPLC detection. In the following experiments Ag sols have been used as the active substrate. The effect of various parameters such as temperature, pH, flow rate, and the nature of the interface between the HPLC system and the Raman spectrometer have been examined. One of the most significant findings is that the temperature of the Ag sol/HPLC effluent mixture has a dramatic effect on the SERS intensities. This effect is a result of increased colloid aggregation at higher temperatures. Aggregation is known to produce greater enhancement in SERS and proceeds much more rapidly at elevated temperatures. An increase in the temperature of the Ag sol enables SERS detection under flowing conditions and in real time. This is a substantial improvement over many of the previous attempts to interface SERS detection to FIA or HPLC. In most of the previous studies, it was necessary to stop the flow as the analyte eluted from the chromatogram and measure the SERS spectra under static conditions.

  18. VORONOI DIAGRAMS WITHOUT BOUNDING BOXES

    Directory of Open Access Journals (Sweden)

    E. T. K. Sang

    2015-10-01

    Full Text Available We present a technique for presenting geographic data in Voronoi diagrams without having to specify a bounding box. The method restricts Voronoi cells to points within a user-defined distance of the data points. The mathematical foundation of the approach is presented as well. The cell clipping method is particularly useful for presenting geographic data that is spread in an irregular way over a map, as for example the Dutch dialect data displayed in Figure 2. The automatic generation of reasonable cell boundaries also makes redundant a frequently used solution to this problem that requires data owners to specify region boundaries, as in Goebl (2010 and Nerbonne et al (2011.

  19. Cosmological bounds on neutrino statistics

    Science.gov (United States)

    de Salas, P. F.; Gariazzo, S.; Laveder, M.; Pastor, S.; Pisanti, O.; Truong, N.

    2018-03-01

    We consider the phenomenological implications of the violation of the Pauli exclusion principle for neutrinos, focusing on cosmological observables such as the spectrum of Cosmic Microwave Background anisotropies, Baryon Acoustic Oscillations and the primordial abundances of light elements. Neutrinos that behave (at least partly) as bosonic particles have a modified equilibrium distribution function that implies a different influence on the evolution of the Universe that, in the case of massive neutrinos, can not be simply parametrized by a change in the effective number of neutrinos. Our results show that, despite the precision of the available cosmological data, only very weak bounds can be obtained on neutrino statistics, disfavouring a more bosonic behaviour at less than 2σ.

  20. Fundamental Bounds on MIMO Antennas

    Science.gov (United States)

    Ehrenborg, Casimir; Gustafsson, Mats

    2018-01-01

    Antenna current optimization is often used to analyze the optimal performance of antennas. Antenna performance can be quantified in e.g., minimum Q-factor and efficiency. The performance of MIMO antennas is more involved and, in general, a single parameter is not sufficient to quantify it. Here, the capacity of an idealized channel is used as the main performance quantity. An optimization problem in the current distribution for optimal capacity, measured in spectral efficiency, given a fixed Q-factor and efficiency is formulated as a semi-definite optimization problem. A model order reduction based on characteristic and energy modes is employed to improve the computational efficiency. The performance bound is illustrated by solving the optimization problem numerically for rectangular plates and spherical shells.

  1. Spectral computations for bounded operators

    CERN Document Server

    Ahues, Mario; Limaye, Balmohan

    2001-01-01

    Exact eigenvalues, eigenvectors, and principal vectors of operators with infinite dimensional ranges can rarely be found. Therefore, one must approximate such operators by finite rank operators, then solve the original eigenvalue problem approximately. Serving as both an outstanding text for graduate students and as a source of current results for research scientists, Spectral Computations for Bounded Operators addresses the issue of solving eigenvalue problems for operators on infinite dimensional spaces. From a review of classical spectral theory through concrete approximation techniques to finite dimensional situations that can be implemented on a computer, this volume illustrates the marriage of pure and applied mathematics. It contains a variety of recent developments, including a new type of approximation that encompasses a variety of approximation methods but is simple to verify in practice. It also suggests a new stopping criterion for the QR Method and outlines advances in both the iterative refineme...

  2. Microbial interactions chapter: binding and entry of DNA in bacterial transformation

    Energy Technology Data Exchange (ETDEWEB)

    Lacks, S.A.

    1977-01-01

    Genetic transformation of bacteria by DNA released from cells of a related strain is discussed. The mechanism by which the giant information-bearing molecules of DNA are transported into the bacterial cell was investigated. It was concluded that the overall process of DNA uptake consists of two main steps, binding of donor DNA to the outside of the cell and entry of the bound DNA into the cell. Each step is discussed in detail. Inasmuch as these phenomena occur at the cell surface, they are related to structures and functions of the cell wall and membrane. In addition, the development of competence, that is the formation of cell surface structures allowing DNA uptake, is examined from both a physiological and evolutionary point of view. Genetic transfer mediated by free DNA is an obvious and important form of cellular interaction. The development of competence involves another, quite distinct system of interaction between bacterial cells. Streptococcus pneumoniae, Bacillus subtilis, and Hemophilus influenzae were used as the test organisms. 259 references.

  3. Disposable electrochemical DNA biosensor for environmental ...

    Indian Academy of Sciences (India)

    A simple procedure for the voltammetric detection of the DNA damage using a disposable electrochemical DNA biosensor is reported. The DNA biosensor is assembled by immobilizing the double stranded calf thymus DNA (dsDNA) on the surface of a disposable carbon screen-printed electrode. The interaction of ...

  4. Quantitive DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  5. Cationic Lipid-Formulated DNA Vaccine against Hepatitis B Virus : Immunogenicity of MIDGE-Th1 Vectors Encoding Small and Large Surface Antigen in Comparison to a Licensed Protein Vaccine

    NARCIS (Netherlands)

    Endmann, Anne; Klunder, Katharina; Kapp, Kerstin; Riede, Oliver; Oswald, Detlef; Talman, Eduard G.; Schroff, Matthias; Kleuss, Christiane; Ruiters, Marcel H. J.; Juhls, Christiane

    2014-01-01

    Currently marketed vaccines against hepatitis B virus (HBV) based on the small (S) hepatitis B surface antigen (HBsAg) fail to induce a protective immune response in about 10% of vaccinees. DNA vaccination and the inclusion of PreS1 and PreS2 domains of HBsAg have been reported to represent feasible

  6. Mechanisms of DNA binding and regulation of Bacillus anthracis DNA primase.

    Science.gov (United States)

    Biswas, Subhasis B; Wydra, Eric; Biswas, Esther E

    2009-08-11

    DNA primases are pivotal enzymes in chromosomal DNA replication in all organisms. In this article, we report unique mechanistic characteristics of recombinant DNA primase from Bacillus anthracis. The mechanism of action of B. anthracis DNA primase (DnaG(BA)) may be described in several distinct steps as follows. Its mechanism of action is initiated when it binds to single-stranded DNA (ssDNA) in the form of a trimer. Although DnaG(BA) binds to different DNA sequences with moderate affinity (as expected of a mobile DNA binding protein), we found that DnaG(BA) bound to the origin of bacteriophage G4 (G4ori) with approximately 8-fold higher affinity. DnaG(BA) was strongly stimulated (>or=75-fold) by its cognate helicase, DnaB(BA), during RNA primer synthesis. With the G4ori ssDNA template, DnaG(BA) formed short (primers in the absence of DnaB(BA). The presence of DnaB(BA) increased the rate of primer synthesis. The observed stimulation of primer synthesis by cognate DnaB(BA) is thus indicative of a positive effector role for DnaB(BA). By contrast, Escherichia coli DnaB helicase (DnaB(EC)) did not stimulate DnaG(BA) and inhibited primer synthesis to near completion. This observed effect of E. coli DnaB(EC) is indicative of a strong negative effector role for heterologous DnaB(EC). We conclude that DnaG(BA) is capable of interacting with DnaB proteins from both B. anthracis and E. coli; however, between DnaB proteins derived from these two organisms, only the homologous DNA helicase (DnaB(BA)) acted as a positive effector of primer synthesis.

  7. DNA-based hybrid catalysis.

    Science.gov (United States)

    Rioz-Martínez, Ana; Roelfes, Gerard

    2015-04-01

    In the past decade, DNA-based hybrid catalysis has merged as a promising novel approach to homogeneous (asymmetric) catalysis. A DNA hybrid catalysts comprises a transition metal complex that is covalently or supramolecularly bound to DNA. The chiral microenvironment and the second coordination sphere interactions provided by the DNA are key to achieve high enantioselectivities and, often, additional rate accelerations in catalysis. Nowadays, current efforts are focused on improved designs, understanding the origin of the enantioselectivity and DNA-induced rate accelerations, expanding the catalytic scope of the concept and further increasing the practicality of the method for applications in synthesis. Herein, the recent developments will be reviewed and the perspectives for the emerging field of DNA-based hybrid catalysis will be discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Gold and gold-silver core-shell nanoparticle constructs with defined size based on DNA hybridization

    International Nuclear Information System (INIS)

    Steinbrueck, Andrea; Csaki, Andrea; Ritter, Kathrin; Leich, Martin; Koehler, J. Michael; Fritzsche, Wolfgang

    2009-01-01

    Nanoparticles represent versatile building blocks in material science and nanotechnology. Thereby, the defined assembly of nanostructures (13 and 56 nm in diameter, respectively) is of significant importance. Short DNA sequences can be bound to the nanoparticle surface thus enabling highly specific DNA hybridization-driven events that direct the formation of nanoparticle constructs.In this paper, examples for the defined formation of gold nanoparticle constructs are demonstrated. In addition, gold-silver core-shell nanoparticles are introduced as further building blocks for the hybridization-controlled formation of nanoparticle constructs.

  9. Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates

    Science.gov (United States)

    Biller, Steven J; McDaniel, Lauren D; Breitbart, Mya; Rogers, Everett; Paul, John H; Chisholm, Sallie W

    2017-01-01

    Diverse microbes release membrane-bound extracellular vesicles from their outer surfaces into the surrounding environment. Vesicles are found in numerous habitats including the oceans, where they likely have a variety of functional roles in microbial ecosystems. Extracellular vesicles are known to contain a range of biomolecules including DNA, but the frequency with which DNA is packaged in vesicles is unknown. Here, we examine the quantity and distribution of DNA associated with vesicles released from five different bacteria. The average quantity of double-stranded DNA and size distribution of DNA fragments released within vesicles varies among different taxa. Although some vesicles contain sufficient DNA to be visible following staining with the SYBR fluorescent DNA dyes typically used to enumerate viruses, this represents only a small proportion (vesicles. Thus DNA is packaged heterogeneously within vesicle populations, and it appears that vesicles are likely to be a minor component of SYBR-visible particles in natural sea water compared with viruses. Consistent with this hypothesis, chloroform treatment of coastal and offshore seawater samples reveals that vesicles increase epifluorescence-based particle (viral) counts by less than an order of magnitude and their impact is variable in space and time. PMID:27824343

  10. Instanton bound states in ABJM theory

    Energy Technology Data Exchange (ETDEWEB)

    Hatsuda, Yasuyuki [DESY Hamburg (Germany). Theory Group; Tokyo Institute of Technology (Japan). Dept. of Physics; Moriyama, Sanefumi [Nagoya Univ. (Japan). Kobayashi Maskawa Inst. and Graduate School of Mathematics; Okuyama, Kazumi [Shinshu Univ., Matsumoto, Nagano (Japan). Dept. of Physics

    2013-06-15

    The partition function of the ABJM theory receives non-perturbative corrections due to instanton effects. We study these non-perturbative corrections, including bound states of worldsheet instantons and membrane instantons, in the Fermi-gas approach. We require that the total non-perturbative correction should be always finite for arbitrary Chern-Simons level. This finiteness is realized quite non-trivially because each bound state contribution naively diverges at some levels. The poles of each contribution should be canceled out in total. We use this pole cancellation mechanism to find unknown bound state corrections from known ones. We conjecture a general expression of the bound state contribution. Summing up all the bound state contributions, we find that the effect of bound states is simply incorporated into the worldsheet instanton correction by a redefinition of the chemical potential in the Fermi-gas system. Analytic expressions of the 3- and 4-membrane instanton corrections are also proposed.

  11. Improved yield of high molecular weight DNA coincides with increased microbial diversity access from iron oxide cemented sub-surface clay environments.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

    Full Text Available Despite over three decades of progress, extraction of high molecular weight (HMW DNA from high clay soils or iron oxide cemented clay has remained challenging. HMW DNA is desirable for next generation sequencing as it yields the most comprehensive coverage. Several DNA extraction procedures were compared from samples that exhibit strong nucleic acid adsorption. pH manipulation or use of alternative ion solutions offered no improvement in nucleic acid recovery. Lysis by liquid N2 grinding in concentrated guanidine followed by concentrated sodium phosphate extraction supported HMW DNA recovery from clays high in iron oxides. DNA recovered using 1 M sodium phosphate buffer (PB as a competitive desorptive wash was 15.22±2.33 µg DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46±0.25 µg DNA/g clay with the Powerlyzer system (MoBio. Increasing PB concentration in the lysis reagent coincided with increasing DNA fragment length during initial extraction. Rarefaction plots of 16S rRNA (V1-V3 region pyrosequencing from A-horizon and clay soils showed an ∼80% and ∼400% larger accessed diversity compared to the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more operational taxonomic units (OTU recovered.

  12. Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments

    Science.gov (United States)

    Hurt, Richard A.; Robeson, Michael S.; Shakya, Migun; Moberly, James G.; Vishnivetskaya, Tatiana A.; Gu, Baohua; Elias, Dwayne A.

    2014-01-01

    Despite over three decades of progress, extraction of high molecular weight (HMW) DNA from high clay soils or iron oxide cemented clay has remained challenging. HMW DNA is desirable for next generation sequencing as it yields the most comprehensive coverage. Several DNA extraction procedures were compared from samples that exhibit strong nucleic acid adsorption. pH manipulation or use of alternative ion solutions offered no improvement in nucleic acid recovery. Lysis by liquid N2 grinding in concentrated guanidine followed by concentrated sodium phosphate extraction supported HMW DNA recovery from clays high in iron oxides. DNA recovered using 1 M sodium phosphate buffer (PB) as a competitive desorptive wash was 15.22±2.33 µg DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46±0.25 µg DNA/g clay with the Powerlyzer system (MoBio). Increasing PB concentration in the lysis reagent coincided with increasing DNA fragment length during initial extraction. Rarefaction plots of 16S rRNA (V1–V3 region) pyrosequencing from A-horizon and clay soils showed an ∼80% and ∼400% larger accessed diversity compared to the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more operational taxonomic units (OTU) recovered. PMID:25033199

  13. Isolated HeLa cell nuclei synthesize meaningful DNA.

    OpenAIRE

    Kristensen, T; Prydz, H

    1985-01-01

    DNA replicated at the beginning of S phase was labelled by incubating nuclei isolated from cells arrested at the G/S border with radioactive deoxyribonucleoside triphosphate in a reaction mixture sustaining DNA synthesis. By hybridization against ribosomal RNA bound to nitrocellulose, the fraction of the labelled DNA which was complementary to rRNA could be quantified, and the stability of the RNA-DNA hybrids could be estimated by sequential elution of DNA at increasing temperatures. The resu...

  14. Bounded elements in Locally C*-algebras

    International Nuclear Information System (INIS)

    El Harti, Rachid

    2001-09-01

    In order to get more useful information about Locally C*-algebras, we introduce in this paper the notion of bounded elements. First, we study the connection between bounded elements and spectrally bounded elements. Some structural results of Locally C*-algebras are established in Theorems 1 , 2 and 3. As an immediate consequence of Theorem 3, we give a characterization of the connected component of the identity in the group of unitary elements for a Locally C*-algebra. (author)

  15. Boundedly UC spaces: characterisations and preservation | Jain ...

    African Journals Online (AJOL)

    A metric space (X, d) is called a boundedly UC space if every closed and bounded subset of X is a UC space. A metric space (X, d) is called a UC space if each real-valued continuous function on (X, d) is uniformly continuous. In this paper, we study twenty-two equivalent conditions for a metric space to be a boundedly UC ...

  16. Human RAD52 Captures and Holds DNA Strands, Increases DNA Flexibility, and Prevents Melting of Duplex DNA: Implications for DNA Recombination

    Directory of Open Access Journals (Sweden)

    Ineke Brouwer

    2017-03-01

    Full Text Available Human RAD52 promotes annealing of complementary single-stranded DNA (ssDNA. In-depth knowledge of RAD52-DNA interaction is required to understand how its activity is integrated in DNA repair processes. Here, we visualize individual fluorescent RAD52 complexes interacting with single DNA molecules. The interaction with ssDNA is rapid, static, and tight, where ssDNA appears to wrap around RAD52 complexes that promote intra-molecular bridging. With double-stranded DNA (dsDNA, interaction is slower, weaker, and often diffusive. Interestingly, force spectroscopy experiments show that RAD52 alters the mechanics dsDNA by enhancing DNA flexibility and increasing DNA contour length, suggesting intercalation. RAD52 binding changes the nature of the overstretching transition of dsDNA and prevents DNA melting, which is advantageous for strand clamping during or after annealing. DNA-bound RAD52 is efficient at capturing ssDNA in trans. Together, these effects may help key steps in DNA repair, such as second-end capture during homologous recombination or strand annealing during RAD51-independent recombination reactions.

  17. Bounded cohomology of discrete groups

    CERN Document Server

    Frigerio, Roberto

    2017-01-01

    The author manages a near perfect equilibrium between necessary technicalities (always well motivated) and geometric intuition, leading the readers from the first simple definition to the most striking applications of the theory in 13 very pleasant chapters. This book can serve as an ideal textbook for a graduate topics course on the subject and become the much-needed standard reference on Gromov's beautiful theory. -Michelle Bucher The theory of bounded cohomology, introduced by Gromov in the late 1980s, has had powerful applications in geometric group theory and the geometry and topology of manifolds, and has been the topic of active research continuing to this day. This monograph provides a unified, self-contained introduction to the theory and its applications, making it accessible to a student who has completed a first course in algebraic topology and manifold theory. The book can be used as a source for research projects for master's students, as a thorough introduction to the field for graduate student...

  18. Some Improved Nonperturbative Bounds for Fermionic Expansions

    Energy Technology Data Exchange (ETDEWEB)

    Lohmann, Martin, E-mail: marlohmann@gmail.com [Universita di Roma Tre, Dipartimento di Matematica (Italy)

    2016-06-15

    We reconsider the Gram-Hadamard bound as it is used in constructive quantum field theory and many body physics to prove convergence of Fermionic perturbative expansions. Our approach uses a recursion for the amplitudes of the expansion, discovered in a model problem by Djokic (2013). It explains the standard way to bound the expansion from a new point of view, and for some of the amplitudes provides new bounds, which avoid the use of Fourier transform, and are therefore superior to the standard bounds for models like the cold interacting Fermi gas.

  19. Vulnerable Derivatives and Good Deal Bounds

    DEFF Research Database (Denmark)

    Murgoci, Agatha

    2013-01-01

    a new restriction in the arbitrage free model by setting upper bounds on the Sharpe ratios (SRs) of the assets. The potential prices that are eliminated represent unreasonably good deals. The constraint on the SR translates into a constraint on the stochastic discount factor. Thus, tight pricing bounds......We price vulnerable derivatives – i.e. derivatives where the counterparty may default. These are basically the derivatives traded on the over-the-counter (OTC) markets. Default is modelled in a structural framework. The technique employed for pricing is good deal bounds (GDBs). The method imposes...... in a consistent way. Finally, we numerically analyse the behaviour of the good deal pricing bounds....

  20. Generating substrate bound functional chemokine gradients in vitro

    DEFF Research Database (Denmark)

    Hjortø, Gertrud Malene; Hansen, Morten; Larsen, Niels Bent

    2009-01-01

    Microcontact printing (mCP) is employed to generate discontinuous microscale gradients of active fractalkine, a chemokine expressed by endothelial cells near sites of inflammation where it is believed to form concentration gradients descending away from the inflamed area. In vivo, fractalkine is ...... surface-bound chemokines (haptotactic gradients). The use of a capture antibody facilitates control of the orientation of tagged molecules, thereby ensuring a high degree of bio-functionality through correct presentation and reduced protein denaturation....

  1. Electrochemical DNA sensor-based strategy for sensitive detection of DNA demethylation and DNA demethylase activity.

    Science.gov (United States)

    Shen, Qingming; Fan, Mengxing; Yang, Yin; Zhang, Hui

    2016-08-31

    DNA demethylation and demethylase activity play important roles in DNA self-repair, and their detection is key to early diagnosis of fatal diseases. Herein, a facile electrochemical DNA (E-DNA) sensor was developed for the sensitive detection of DNA demethylation and demethylase activity based on an enzyme cleavage strategy. The thiol modified hemi-methylated hairpin probe DNA (pDNA) was self-assembled on a Au electrode surface through the formation of AuS bonds. The hemi-methylated pDNA served as the substrate of DNA demethylase (using methyl-CpG-binding domain protein 2 (MBD2) as an example). Following demethylation, the hairpin stem was then recognized and cleaved by BstUI endonuclease. The ferrocene carboxylic acid (FcA)-tagged pDNA strands were released into the buffer solution from the electrode surface, resulting in a significant decrease of electrochemical signal and providing a means to observe DNA demethylation. The activity of DNA demethylase was analyzed in the concentration ranging from 0.5 to 500 ng mL(-1) with a limit of detection as low as 0.17 ng mL(-1). With high specificity and sensitivity, rapid response, and low cost, this simple E-DNA sensor provides a unique platform for the sensitive detection of DNA demethylation, DNA demethylase activity, and related molecular diagnostics and drug screening. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Modifications of the Bekenstein Bound from Dimensional Reduction of Covariant Entropy Bound

    Science.gov (United States)

    Yee, Ho-Ung

    2005-12-01

    We consider dimensional reduction of the covariant entropy bound from D + 1 dimensional geometry of M × S1 to the D dimensional geometry M. With a warping factor, the local Bekenstein bound in D + 1 dimensions leads to a more refined form of the local Bekenstein bound from the D dimensional view point. With this new local Bekenstein bound, it is possible to saturate the lightlike holography bound even with nonvanishing expansion rate. With a Kaluza-Klein gauge field, the dimensional reduction implies a stronger bound where the energy momentum tensor contribution is replaced by the energy momentum tensor with the electromagnetic contribution subtracted.

  3. DNA-PK dependent targeting of DNA-ends to a protein complex assembled on matrix attachment region DNA sequences

    International Nuclear Information System (INIS)

    Mauldin, S.K.; Getts, R.C.; Perez, M.L.; DiRienzo, S.; Stamato, T.D.

    2003-01-01

    Full text: We find that nuclear protein extracts from mammalian cells contain an activity that allows DNA ends to associate with circular pUC18 plasmid DNA. This activity requires the catalytic subunit of DNA-PK (DNA-PKcs) and Ku since it was not observed in mutants lacking Ku or DNA-PKcs but was observed when purified Ku/DNA-PKcs was added to these mutant extracts. Competition experiments between pUC18 and pUC18 plasmids containing various nuclear matrix attachment region (MAR) sequences suggest that DNA ends preferentially associate with plasmids containing MAR DNA sequences. At a 1:5 mass ratio of MAR to pUC18, approximately equal amounts of DNA end binding to the two plasmids were observed, while at a 1:1 ratio no pUC18 end-binding was observed. Calculation of relative binding activities indicates that DNA-end binding activities to MAR sequences was 7 to 21 fold higher than pUC18. Western analysis of proteins bound to pUC18 and MAR plasmids indicates that XRCC4, DNA ligase IV, scaffold attachment factor A, topoisomerase II, and poly(ADP-ribose) polymerase preferentially associate with the MAR plasmid in the absence or presence of DNA ends. In contrast, Ku and DNA-PKcs were found on the MAR plasmid only in the presence of DNA ends. After electroporation of a 32P-labeled DNA probe into human cells and cell fractionation, 87% of the total intercellular radioactivity remained in nuclei after a 0.5M NaCl extraction suggesting the probe was strongly bound in the nucleus. The above observations raise the possibility that DNA-PK targets DNA-ends to a repair and/or DNA damage signaling complex which is assembled on MAR sites in the nucleus

  4. Evaluation of protective immune responses induced by DNA vaccines encoding Toxoplasma gondii surface antigen 1 (SAG1) and 14-3-3 protein in BALB/c mice.

    Science.gov (United States)

    Meng, Min; He, Shenyi; Zhao, Guanghui; Bai, Yang; Zhou, Huaiyu; Cong, Hua; Lu, Gang; Zhao, Qunli; Zhu, Xing-Quan

    2012-11-26

    Toxoplasmosis, caused by an obligate intracellular protozoan parasite Toxoplasma gondii, has been a serious clinical and veterinary problem. Effective DNA vaccines against T. gondii can prevent and control the spread of toxoplasmosis, which is important for both human health and the farming industry. The T. gondii 14-3-3 protein has been proved to be antigenic and immunogenic and was a potential vaccine candidate against toxoplasmosis. In this study, we evaluated the immune responses induced by recombinant plasmids encoding T. gondii surface antigen 1 (SAG1) and 14-3-3 protein by immunizing BALB/c mice intramuscularly. In the present study, BALB/c mice were randomly divided into five groups, including three experimental groups (pSAG1, p14-3-3 and pSAG1/14-3-3) and two control groups (PBS and pBudCE4.1), and were immunized intramuscularly three times. The levels of IgG antibodies and cytokine production in mouse sera were determined by enzyme-linked immunosorbent assays (ELISA). Two weeks after the last immunization, all mice were challenged intraperitoneally (i.p.) with 1×10(4) tachyzoites of T. gondii and the survival time of mice was observed and recorded every day. Mice vaccinated with pSAG1, p14-3-3 or pSAG1/14-3-3 developed high levels of IgG2a and gamma interferon (IFN-γ) and low levels of interleukin-4 (IL-4) and interleukin-10 (IL-10) compared to control groups (PBS or pBudCE4.1), which suggested a modulated Th1 type immune response (Pmice in experimental groups was longer than control groups (Pmice and was a novel DNA vaccine candidate against toxoplasmosis, and the immune protective efficacy elicited by SAG1 gene was also demonstrated. Our results also showed multi-gene vaccine significantly enhanced immune responses and protective efficacy and was superior to the single-gene vaccine.

  5. Sensing Conformational Changes in DNA upon Ligand Binding Using QCM-D. Polyamine Condensation and Rad51 Extension of DNA Layers

    KAUST Repository

    Sun, Lu

    2014-10-16

    © 2014 American Chemical Society. Biosensors, in which binding of ligands is detected through changes in the optical or electrochemical properties of a DNA layer confined to the sensor surface, are important tools for investigating DNA interactions. Here, we investigate if conformational changes induced in surface-attached DNA molecules upon ligand binding can be monitored by the quartz crystal microbalance with dissipation (QCM-D) technique. DNA duplexes containing 59-184 base pairs were formed on QCM-D crystals by stepwise assembly of synthetic oligonucleotides of designed base sequences. The DNA films were exposed to the cationic polyamines spermidine and spermine, known to condense DNA molecules in bulk experiments, or to the recombination protein Rad51, known to extend the DNA helix. The binding and dissociation of the ligands to the DNA films were monitored in real time by measurements of the shifts in resonance frequency (Δf) and in dissipation (ΔD). The QCM-D data were analyzed using a Voigt-based model for the viscoelastic properties of polymer films in order to evaluate how the ligands affect thickness and shear viscosity of the DNA layer. Binding of spermine shrinks all DNA layers and increases their viscosity in a reversible fashion, and so does spermidine, but to a smaller extent, in agreement with its lower positive charge. SPR was used to measure the amount of bound polyamines, and when combined with QCM-D, the data indicate that the layer condensation leads to a small release of water from the highly hydrated DNA films. The binding of Rad51 increases the effective layer thickness of a 59bp film, more than expected from the know 50% DNA helix extension. The combined results provide guidelines for a QCM-D biosensor based on ligand-induced structural changes in DNA films. The QCM-D approach provides high discrimination between ligands affecting the thickness and the structural properties of the DNA layer differently. The reversibility of the film

  6. Sensing conformational changes in DNA upon ligand binding using QCM-D. Polyamine condensation and Rad51 extension of DNA layers.

    Science.gov (United States)

    Sun, Lu; Frykholm, Karolin; Fornander, Louise H; Svedhem, Sofia; Westerlund, Fredrik; Akerman, Björn

    2014-10-16

    Biosensors, in which binding of ligands is detected through changes in the optical or electrochemical properties of a DNA layer confined to the sensor surface, are important tools for investigating DNA interactions. Here, we investigate if conformational changes induced in surface-attached DNA molecules upon ligand binding can be monitored by the quartz crystal microbalance with dissipation (QCM-D) technique. DNA duplexes containing 59-184 base pairs were formed on QCM-D crystals by stepwise assembly of synthetic oligonucleotides of designed base sequences. The DNA films were exposed to the cationic polyamines spermidine and spermine, known to condense DNA molecules in bulk experiments, or to the recombination protein Rad51, known to extend the DNA helix. The binding and dissociation of the ligands to the DNA films were monitored in real time by measurements of the shifts in resonance frequency (Δf) and in dissipation (ΔD). The QCM-D data were analyzed using a Voigt-based model for the viscoelastic properties of polymer films in order to evaluate how the ligands affect thickness and shear viscosity of the DNA layer. Binding of spermine shrinks all DNA layers and increases their viscosity in a reversible fashion, and so does spermidine, but to a smaller extent, in agreement with its lower positive charge. SPR was used to measure the amount of bound polyamines, and when combined with QCM-D, the data indicate that the layer condensation leads to a small release of water from the highly hydrated DNA films. The binding of Rad51 increases the effective layer thickness of a 59 bp film, more than expected from the know 50% DNA helix extension. The combined results provide guidelines for a QCM-D biosensor based on ligand-induced structural changes in DNA films. The QCM-D approach provides high discrimination between ligands affecting the thickness and the structural properties of the DNA layer differently. The reversibility of the film deformation allows comparative

  7. Atomic Force Microscopy of Biochemically Tagged DNA

    Science.gov (United States)

    Murray, Matthew N.; Hansma, Helen G.; Bezanilla, Magdalena; Sano, Takeshi; Ogletree, D. Frank; Kolbe, William; Smith, Casandra L.; Cantor, Charles R.; Spengler, Sylvia; Hansma, Paul K.; Salmeron, Miquel

    1993-05-01

    Small fragments of DNA of known length were made with the polymerase chain reaction. These fragments had biotin molecules covalently attached at their ends. They were subsequently labeled with a chimeric protein fusion between streptavidin and two immunoglobulin G-binding domains of staphyloccocal protein A. This tetrameric species was expected to bind up to four DNA molecules via their attached biotin moieties. The DNA-protein complex was deposited on mica and imaged with an atomic force microscope. The images revealed the protein chimera at the expected location at the ends of the strands of DNA as well as the expected dimers, trimers, and tetramers of DNA bound to a single protein.

  8. Dynamics of water bound to crystalline cellulose

    Energy Technology Data Exchange (ETDEWEB)

    O’Neill, Hugh; Pingali, Sai Venkatesh; Petridis, Loukas; He, Junhong; Mamontov, Eugene; Hong, Liang; Urban, Volker; Evans, Barbara; Langan, Paul; Smith, Jeremy C.; Davison, Brian H.

    2017-09-19

    Interactions of water with cellulose are of both fundamental and technological importance. Here, we characterize the properties of water associated with cellulose using deuterium labeling, neutron scattering and molecular dynamics simulation. Quasi-elastic neutron scattering provided quantitative details about the dynamical relaxation processes that occur and was supported by structural characterization using small-angle neutron scattering and X-ray diffraction. We can unambiguously detect two populations of water associated with cellulose. The first is “non-freezing bound” water that gradually becomes mobile with increasing temperature and can be related to surface water. The second population is consistent with confined water that abruptly becomes mobile at ~260 K, and can be attributed to water that accumulates in the narrow spaces between the microfibrils. Quantitative analysis of the QENS data showed that, at 250 K, the water diffusion coefficient was 0.85 ± 0.04 × 10-10 m2sec-1 and increased to 1.77 ± 0.09 × 10-10 m2sec-1 at 265 K. MD simulations are in excellent agreement with the experiments and support the interpretation that water associated with cellulose exists in two dynamical populations. Our results provide clarity to previous work investigating the states of bound water and provide a new approach for probing water interactions with lignocellulose materials.

  9. DNA interactions with a Methylene Blue redox indicator depend on the DNA length and are sequence specific.

    Science.gov (United States)

    Farjami, Elaheh; Clima, Lilia; Gothelf, Kurt V; Ferapontova, Elena E

    2010-06-01

    A DNA molecular beacon approach was used for the analysis of interactions between DNA and Methylene Blue (MB) as a redox indicator of a hybridization event. DNA hairpin structures of different length and guanine (G) content were immobilized onto gold electrodes in their folded states through the alkanethiol linker at the 5'-end. Binding of MB to the folded hairpin DNA was electrochemically studied and compared with binding to the duplex structure formed by hybridization of the hairpin DNA to a complementary DNA strand. Variation of the electrochemical signal from the DNA-MB complex was shown to depend primarily on the DNA length and sequence used: the G-C base pairs were the preferential sites of MB binding in the duplex. For short 20 nts long DNA sequences, the increased electrochemical response from MB bound to the duplex structure was consistent with the increased amount of bound and electrochemically readable MB molecules (i.e. MB molecules that are available for the electron transfer (ET) reaction with the electrode). With longer DNA sequences, the balance between the amounts of the electrochemically readable MB molecules bound to the hairpin DNA and to the hybrid was opposite: a part of the MB molecules bound to the long-sequence DNA duplex seem to be electrochemically mute due to long ET distance. The increasing electrochemical response from MB bound to the short-length DNA hybrid contrasts with the decreasing signal from MB bound to the long-length DNA hybrid and allows an "off"-"on" genosensor development.

  10. Isoperimetric upper bounds for the first eigenvalue

    Indian Academy of Sciences (India)

    [5] Buser P and Karcher H, Gromov's almost flat manifolds, Société mathématique de. France (1981). [6] Grosjean J F, Upper bounds for the first eigenvalue of the Laplacian on compact submanifolds, Pacific. J. Math. 206 (2002) 93–112. [7] Heintze Ernst, Extinsic upper bounds for λ1, Math. Ann. 280 (1988) 389–402.

  11. No-arbitrage bounds for financial scenarios

    DEFF Research Database (Denmark)

    Geyer, Alois; Hanke, Michael; Weissensteiner, Alex

    2014-01-01

    We derive no-arbitrage bounds for expected excess returns to generate scenarios used in financial applications. The bounds allow to distinguish three regions: one where arbitrage opportunities will never exist, a second where arbitrage may be present, and a third, where arbitrage opportunities...

  12. On the range of completely bounded maps

    Directory of Open Access Journals (Sweden)

    Richard I. Loebl

    1978-01-01

    Full Text Available It is shown that if every bounded linear map from a C*-algebra α to a von Neumann algebra β is completely bounded, then either α is finite-dimensional or β⫅⊗Mn, where is a commutative von Neumann algebra and Mn is the algebra of n×n complex matrices.

  13. Bound constrained quadratic programming via piecewise

    DEFF Research Database (Denmark)

    Madsen, Kaj; Nielsen, Hans Bruun; Pinar, M. C.

    1999-01-01

    We consider the strictly convex quadratic programming problem with bounded variables. A dual problem is derived using Lagrange duality. The dual problem is the minimization of an unconstrained, piecewise quadratic function. It involves a lower bound of lambda/sub 1/ , the smallest eigenvalue...

  14. Stacked spheres and lower bound theorem

    Indian Academy of Sciences (India)

    BASUDEB DATTA

    2011-11-20

    Nov 20, 2011 ... Preliminaries. Lower bound theorem. On going work. Definitions. An n-simplex is a convex hull of n + 1 affinely independent points. (called vertices) in some Euclidean space R. N . Stacked spheres and lower bound theorem. Basudeb Datta. Indian Institute of Science. 2 / 27 ...

  15. Exponential Lower Bounds For Policy Iteration

    OpenAIRE

    Fearnley, John

    2010-01-01

    We study policy iteration for infinite-horizon Markov decision processes. It has recently been shown policy iteration style algorithms have exponential lower bounds in a two player game setting. We extend these lower bounds to Markov decision processes with the total reward and average-reward optimality criteria.

  16. Upper Bounds on Numerical Approximation Errors

    DEFF Research Database (Denmark)

    Raahauge, Peter

    2004-01-01

    This paper suggests a method for determining rigorous upper bounds on approximationerrors of numerical solutions to infinite horizon dynamic programming models.Bounds are provided for approximations of the value function and the policyfunction as well as the derivatives of the value function...

  17. Bounds in the location-allocation problem

    DEFF Research Database (Denmark)

    Juel, Henrik

    1981-01-01

    Develops a family of stronger lower bounds on the objective function value of the location-allocation problem. Solution methods proposed to solve problems in location-allocation; Efforts to develop a more efficient bound solution procedure; Determination of the locations of the sources....

  18. New bounds for multi-dimensional packing

    NARCIS (Netherlands)

    S. Seiden; R. van Stee (Rob)

    2001-01-01

    textabstractNew upper and lower bounds are presented for a multi-dimensional generalization of bin packing called box packing. Several variants of this problem, including bounded space box packing, square packing, variable sized box packing and resource augmented box packing are also studied. The

  19. Impedance, zero energy wavefunction, and bound states

    CERN Document Server

    Martin, A

    1977-01-01

    The authors show that for the three-dimensional Schrodinger equation without spherical symmetry the existence of a bound state is related to the impossibility of solving a certain equation; it is further shown that some general conditions for the absence of bound states are readily obtained from this property. (13 refs).

  20. Conductivity bound from dirty black holes

    Energy Technology Data Exchange (ETDEWEB)

    Bitaghsir Fadafan, Kazem, E-mail: bitaghsir@shahroodut.ac.ir

    2016-11-10

    We propose a lower bound of the dc electrical conductivity in strongly disordered, strongly interacting quantum field theories using holography. We study linear response of black holes with broken translational symmetry in Einstein–Maxwell-dilaton theories of gravity. Using the generalized Stokes equations at the horizon, we derive the lower bound of the electrical conductivity for the dual two dimensional disordered field theory.

  1. Specific mutations in the C-terminus domain of HBV surface antigen significantly correlate with low level of serum HBV-DNA in patients with chronic HBV infection

    NARCIS (Netherlands)

    Mirabelli, Carmen; Surdo, Matteo; van Hemert, Formijn; Lian, Zhichao; Salpini, Romina; Cento, Valeria; Cortese, Maria Francesca; Aragri, Marianna; Pollicita, Michela; Alteri, Claudia; Bertoli, Ada; Berkhout, Ben; Micheli, Valeria; Gubertini, Guido; Santoro, Maria Mercedes; Romano, Sara; Visca, Michela; Bernassola, Martina; Longo, Roberta; de Sanctis, Giuseppe Maria; Trimoulet, Pascal; Fleury, Hervè; Marino, Nicoletta; Mazzotta, Francesco; Cappiello, Giuseppina; Spanò, Alberto; Sarrecchia, Cesare; Zhang, Jing Maria; Andreoni, Massimo; Angelico, Mario; Verheyen, Jens; Perno, Carlo Federico; Svicher, Valentina

    2015-01-01

    Background: To define HBsAg-mutations correlated with different serum HBV-DNA levels in HBV chronically-infected drug-naive patients. Methods: This study included 187 patients stratified into the following ranges of serum HBV-DNA: 12-2000 IU/ml, 2000-100,000 IU/ml, and > 100,000 IU/ml.

  2. New bounds on isotropic Lorentz violation

    International Nuclear Information System (INIS)

    Carone, Christopher D.; Sher, Marc; Vanderhaeghen, Marc

    2006-01-01

    Violations of Lorentz invariance that appear via operators of dimension four or less are completely parametrized in the Standard Model Extension (SME). In the pure photonic sector of the SME, there are 19 dimensionless, Lorentz-violating parameters. Eighteen of these have experimental upper bounds ranging between 10 -11 and 10 -32 ; the remaining parameter, k-tilde tr , is isotropic and has a much weaker bound of order 10 -4 . In this Brief Report, we point out that k-tilde tr gives a significant contribution to the anomalous magnetic moment of the electron and find a new upper bound of order 10 -8 . With reasonable assumptions, we further show that this bound may be improved to 10 -14 by considering the renormalization of other Lorentz-violating parameters that are more tightly constrained. Using similar renormalization arguments, we also estimate bounds on Lorentz-violating parameters in the pure gluonic sector of QCD

  3. How adsorption influences DNA denaturation

    NARCIS (Netherlands)

    Allahverdyan, A.E.; Gevorkian, Z.S.; Hu, C.-K.; Nieuwenhuizen, T.M.

    2009-01-01

    The thermally induced denaturation of DNA in the presence of an attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the surface, the denaturation phase transition disappears. Instead,

  4. Bound-free Spectra for Diatomic Molecules

    Science.gov (United States)

    Schwenke, David W.

    2012-01-01

    It is now recognized that prediction of radiative heating of entering space craft requires explicit treatment of the radiation field from the infrared (IR) to the vacuum ultra violet (VUV). While at low temperatures and longer wavelengths, molecular radiation is well described by bound-bound transitions, in the short wavelength, high temperature regime, bound-free transitions can play an important role. In this work we describe first principles calculations we have carried out for bound-bound and bound-free transitions in N2, O2, C2, CO, CN, NO, and N2+. Compared to bound ]bound transitions, bound-free transitions have several particularities that make them different to deal with. These include more complicated line shapes and a dependence of emission intensity on both bound state diatomic and atomic concentrations. These will be discussed in detail below. The general procedure we used was the same for all species. The first step is to generate potential energy curves, transition moments, and coupling matrix elements by carrying out ab initio electronic structure calculations. These calculations are expensive, and thus approximations need to be made in order to make the calculations tractable. The only practical method we have to carry out these calculations is the internally contracted multi-reference configuration interaction (icMRCI) method as implemented in the program suite Molpro. This is a widely used method for these kinds of calculations, and is capable of generating very accurate results. With this method, we must first of choose which electrons to correlate, the one-electron basis to use, and then how to generate the molecular orbitals.

  5. Surface-bounded growth modeling applied to human mandibles

    DEFF Research Database (Denmark)

    Andresen, Per Rønsholt; Brookstein, F. L.; Conradsen, Knut

    2000-01-01

    automatically using shape features and a new algorithm called geometry-constrained diffusion. The semilandmarks are mapped into Procrustes space. Principal component analysis extracts a one-dimensional subspace, which is used to construct a linear growth model. The worst case mean modeling error in a cross...

  6. DNA-based Artificial Nanostructures: Fabrication, Properties, and Applications

    OpenAIRE

    Sun, Young; Kiang, Ching-Hwa

    2005-01-01

    Table of Content 1. Introduction 2. DNA fundamentals 3. Attachment of DNA to surface 4. Fabrication of nanostructures using DNA 4.1 Nanostructures of pure DNA 4.2 DNA-based assembly of metal nanoparticles 4.3 Construction of semiconductor particle arrays using DNA 4.4 DNA-directed nanowires 4.5 DNA-functionalized carbon nanotubes 4.6 Field-transistor based on DNA 4.7 Nanofabrication using artificial DNA 5. DNA-based nanostructures as biosensors 6. Properties of DNA-linked gold nanoparticles 6...

  7. Pluto's Paleoglaciation: Processes and Bounds.

    Science.gov (United States)

    Umurhan, O. M.; Howard, A. D.; White, O. L.; Moore, J. M.; Grundy, W. M.; Schenk, P.; Beyer, R. A.; McKinnon, W. B.; Singer, K. N.; Lauer, T.; Cheng, A. F.; Stern, A.; Weaver, H. A., Jr.; Young, L. A.; Ennico Smith, K.; Olkin, C.

    2017-12-01

    New Horizons imaging of Pluto's surface shows eroded landscapes reminiscent of assorted glaciated terrains found on the Earth such as alpine valleys, dendritic networks and others. For example, LORRI imaging of fluted craters show radially oriented ridging which also resembles Pluto's washboard terrain. Digital elevation modeling indicates that these down-gradient oriented ridges are about 3-4 km spaced apart with depths ranging from 0.2-0.5 km. Present day glaciation on Pluto is characterized by moving N2 ice blocks presumably riding over a H2O ice bedrock substrate. Assuming Pluto's ancient surface was sculpted by N2 glaciation, what remains a mystery is the specific nature of the glacial erosion mechanism(s) responsible for the observed features. To better resolve this puzzle, we perform landform evolution modeling of several glacial erosion processes known from terrestrial H2O ice glaciation studies. These terrestrial processes, which depend upon whether or not the glacier's base is wet or dry, include quarrying/plucking and fluvial erosion. We also consider new erosional processes (to be described in this presentation) which are unique to the highly insulating character of solid N2 including both phase change induced hydrofracture and geothermally driven basal melt. Until improvements in our knowledge of solid N2's rheology are made available (including its mechanical behavior as a binary/trinary mixture of CH4 and CO), it is difficult to assess with high precision which of the aforementioned erosion mechanisms are responsible for the observed surface etchings. Nevertheless, we consider a model crater surface and examine its erosional development due to flowing N2 glacial ice as built up over time according to N2 deposition rates based on GCM modeling of Pluto's ancient atmosphere. For given erosional mechanism our aim is to determine the permissible ranges of model input parameters (e.g., ice strength, flow rates, grain sizes, quarrying rates, etc.) that best

  8. Ecotin-Like ISP of L. major Promastigotes Fine-Tunes Macrophage Phagocytosis by Limiting the Pericellular Release of Bradykinin from Surface-Bound Kininogens: A Survival Strategy Based on the Silencing of Proinflammatory G-Protein Coupled Kinin B2 and B1 Receptors

    Directory of Open Access Journals (Sweden)

    Erik Svensjö

    2014-01-01

    Full Text Available Inhibitors of serine peptidases (ISPs expressed by Leishmania major enhance intracellular parasitism in macrophages by targeting neutrophil elastase (NE, a serine protease that couples phagocytosis to the prooxidative TLR4/PKR pathway. Here we investigated the functional interplay between ISP-expressing L. major and the kallikrein-kinin system (KKS. Enzymatic assays showed that NE inhibitor or recombinant ISP-2 inhibited KKS activation in human plasma activated by dextran sulfate. Intravital microscopy in the hamster cheek pouch showed that topically applied L. major promastigotes (WT and Δisp2/3 mutants potently induced plasma leakage through the activation of bradykinin B2 receptors (B2R. Next, using mAbs against kininogen domains, we showed that these BK-precursor proteins are sequestered by L. major promastigotes, being expressed at higher % in the Δisp2/3 mutant population. Strikingly, analysis of the role of kinin pathway in the phagocytic uptake of L. major revealed that antagonists of B2R or B1R reversed the upregulated uptake of Δisp2/3 mutants without inhibiting macrophage internalization of WT L. major. Collectively, our results suggest that L. major ISP-2 fine-tunes macrophage phagocytosis by inhibiting the pericellular release of proinflammatory kinins from surface bound kininogens. Ongoing studies should clarify whether L. major ISP-2 subverts TLR4/PKR-dependent prooxidative responses of macrophages by preventing activation of G-protein coupled B2R/B1R.

  9. Ecotin-like ISP of L. major promastigotes fine-tunes macrophage phagocytosis by limiting the pericellular release of bradykinin from surface-bound kininogens: a survival strategy based on the silencing of proinflammatory G-protein coupled kinin B2 and B1 receptors.

    Science.gov (United States)

    Svensjö, Erik; Nogueira de Almeida, Larissa; Vellasco, Lucas; Juliano, Luiz; Scharfstein, Julio

    2014-01-01

    Inhibitors of serine peptidases (ISPs) expressed by Leishmania major enhance intracellular parasitism in macrophages by targeting neutrophil elastase (NE), a serine protease that couples phagocytosis to the prooxidative TLR4/PKR pathway. Here we investigated the functional interplay between ISP-expressing L. major and the kallikrein-kinin system (KKS). Enzymatic assays showed that NE inhibitor or recombinant ISP-2 inhibited KKS activation in human plasma activated by dextran sulfate. Intravital microscopy in the hamster cheek pouch showed that topically applied L. major promastigotes (WT and Δisp2/3 mutants) potently induced plasma leakage through the activation of bradykinin B2 receptors (B2R). Next, using mAbs against kininogen domains, we showed that these BK-precursor proteins are sequestered by L. major promastigotes, being expressed at higher % in the Δisp2/3 mutant population. Strikingly, analysis of the role of kinin pathway in the phagocytic uptake of L. major revealed that antagonists of B2R or B1R reversed the upregulated uptake of Δisp2/3 mutants without inhibiting macrophage internalization of WT L. major. Collectively, our results suggest that L. major ISP-2 fine-tunes macrophage phagocytosis by inhibiting the pericellular release of proinflammatory kinins from surface bound kininogens. Ongoing studies should clarify whether L. major ISP-2 subverts TLR4/PKR-dependent prooxidative responses of macrophages by preventing activation of G-protein coupled B2R/B1R.

  10. Process interpretation of current entropic bounds

    Science.gov (United States)

    Nardini, Cesare; Touchette, Hugo

    2018-01-01

    We show for Markov diffusion processes that the quadratic entropic bound, recently derived for the rate functions of nonequilibrium currents, can be seen as being produced by an effective process that creates current fluctuations in a sub-optimal way by modifying only the non-reversible part of the drift or force of the process considered while keeping its reversible part constant. This provides a clear interpretation of the bound in terms of a physical process, which explains, among other things, its relation to the fluctuation relation, linear response, and reversible limits. The existence of more general quadratic bounds, and related uncertainty relations, for physical quantities other than currents is also discussed.

  11. Lower bound for the nuclear kinetic energy

    Energy Technology Data Exchange (ETDEWEB)

    Dehesa, J.S. (Granada Univ. (Spain). Dept. de Fisica Nuclear); Galvez, F.J. (Granada Univ. (Spain). Dept. de Fisica Teorica)

    1985-06-27

    We argue that the kinetic energy of a many-fermion system is bounded from below by Kqsup(-2/3)A sup(5/3) / , with K = 0.565 where q is the number of spin states available to each particle and sup(1/2) is the root mean square radius of the single-particle density. A simple lower bound for the nuclear kinetic energy is found. Numerical values of the bound for several nuclei are shown, and a comparison with some self-consistent calculations and some pseudo-empirical values is made.

  12. Remarks on Bousso's covariant entropy bound

    CERN Document Server

    Mayo, A E

    2002-01-01

    Bousso's covariant entropy bound is put to the test in the context of a non-singular cosmological solution of general relativity found by Bekenstein. Although the model complies with every assumption made in Bousso's original conjecture, the entropy bound is violated due to the occurrence of negative energy density associated with the interaction of some the matter components in the model. We demonstrate how this property allows for the test model to 'elude' a proof of Bousso's conjecture which was given recently by Flanagan, Marolf and Wald. This corroborates the view that the covariant entropy bound should be applied only to stable systems for which every matter component carries positive energy density.

  13. Quasi-bound states in continuum

    International Nuclear Information System (INIS)

    Nakamura, Hiroaki; Hatano, Naomichi; Garmon, Sterling; Petrosky, Tomio

    2007-08-01

    We report the prediction of quasi-bound states (resonant states with very long lifetimes) that occur in the eigenvalue continuum of propagating states for a wide region of parameter space. These quasi-bound states are generated in a quantum wire with two channels and an adatom, when the energy bands of the two channels overlap. A would-be bound state that lays just below the upper energy band is slightly destabilized by the lower energy band and thereby becomes a resonant state with a very long lifetime (a second QBIC lays above the lower energy band). (author)

  14. DNA-based machines.

    Science.gov (United States)

    Wang, Fuan; Willner, Bilha; Willner, Itamar

    2014-01-01

    The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications.

  15. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

    Science.gov (United States)

    Rao, Archana N.; Grainger, David W.

    2014-01-01

    Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA’s persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools. PMID:24765522

  16. Tight Bounds for Distributed Functional Monitoring

    DEFF Research Database (Denmark)

    Woodruff, David P.; Zhang, Qin

    2011-01-01

    $, our bound resolves their main open question. Our lower bounds are based on new direct sum theorems for approximate majority, and yield significant improvements to problems in the data stream model, improving the bound for estimating $F_p, p > 2,$ in $t$ passes from $\\tilde{\\Omega}(n^{1-2/p}/(\\eps^{2/p......} t))$ to $\\tilde{\\Omega}(n^{1-2/p}/(\\eps^{4/p} t))$, giving the first bound for estimating $F_0$ in $t$ passes of $\\Omega(1/(\\eps^2 t))$ bits of space that does not use the gap-hamming problem, and showing a distribution for the gap-hamming problem with high external information cost or super-polynomial......We resolve several fundamental questions in the area of distributed functional monitoring, initiated by Cormode, Muthukrishnan, and Yi (SODA, 2008). In this model there are $k$ sites each tracking their input and communicating with a central coordinator that continuously maintain an approximate...

  17. Numerical Bounds on the Price of Anarchy

    Directory of Open Access Journals (Sweden)

    Louis de Grange

    2017-01-01

    Full Text Available Theoretical upper bounds for price of anarchy have been calculated in previous studies. We present an empirical analysis for the price of anarchy for congested transportation networks; different network sizes and demand levels are considered for each network. We obtain a maximum price of anarchy for the cases studied, which is notably lower than the theoretical bounds reported in the literature. This result should be carefully considered in the design and implementation of road pricing mechanisms for cities.

  18. Learning Intelligent Dialogs for Bounding Box Annotation

    OpenAIRE

    Konyushkova, Ksenia; Uijlings, Jasper; Lampert, Christoph; Ferrari, Vittorio

    2017-01-01

    We introduce Intelligent Annotation Dialogs for bounding box annotation. We train an agent to automatically choose a sequence of actions for a human annotator to produce a bounding box in a minimal amount of time. Specifically, we consider two actions: box verification [37], where the annotator verifies a box generated by an object detector, and manual box drawing. We explore two kinds of agents, one based on predicting the probability that a box will be positively verified, and the other bas...

  19. New Spectral Features from Bound Dark Matter

    DEFF Research Database (Denmark)

    Catena, Riccardo; Kouvaris, Chris

    2016-01-01

    We demonstrate that dark matter particles gravitationally bound to the Earth can induce a characteristic nuclear recoil signal at low energies in direct detection experiments. The new spectral feature we predict can provide the ultimate smoking gun for dark matter discovery for experiments...... with positive signal but unclear background. The new feature is universal, in that the ratio of bound over halo dark matter event rates at detectors is independent of the dark matter-nucleon cross section....

  20. Error Bounds: Necessary and Sufficient Conditions

    Czech Academy of Sciences Publication Activity Database

    Outrata, Jiří; Kruger, A.Y.; Fabian, Marián; Henrion, R.

    2010-01-01

    Roč. 18, č. 2 (2010), s. 121-149 ISSN 1877-0533 R&D Projects: GA AV ČR IAA100750802 Institutional research plan: CEZ:AV0Z10750506; CEZ:AV0Z10190503 Keywords : Error bounds * Calmness * Subdifferential * Slope Subject RIV: BA - General Mathematics Impact factor: 0.333, year: 2010 http://library.utia.cas.cz/separaty/2010/MTR/outrata-error bounds necessary and sufficient conditions.pdf

  1. Torsional regulation of hRPA-induced unwinding of double-stranded DNA

    NARCIS (Netherlands)

    De Vlaminck, I.; Vidic, I.; Van Loenhout, M.T.J.; Kanaar, R.; Lebbink, J.H.G.; Dekker, C.

    2010-01-01

    All cellular single-stranded (ss) DNA is rapidly bound and stabilized by single stranded DNA-binding proteins (SSBs). Replication protein A, the main eukaryotic SSB, is able to unwind double-stranded (ds) DNA by binding and stabilizing transiently forming bubbles of ssDNA. Here, we study the

  2. Suppressors of Hyperinitiation in Escherichia coli Couple DNA Replication to Precursor Biosynthesis and Energy Metabolism

    DEFF Research Database (Denmark)

    Bjørn, Louise

    The Hda protein plays an essential role in inactivation of the initiator protein DnaA from its active, ATP bound form to the inactive DnaA-ADP in E. coli. Cells deficient in Hda suffer from overinitiation, asynchronous initiation and cell death as a consequence of an increased DnaAATP/ DnaA-ADP r...

  3. How a DNA polymerase clamp loader opens a sliding clamp

    OpenAIRE

    Kelch, Brian A.; Makino, Debora L.; O’Donnell, Mike; Kuriyan, John

    2011-01-01

    Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of ATPases. We present structures for the ATP-bound state of the clamp loader complex from bacteriophage T4, bound to an open clamp and primer-template DNA. The clamp loader traps a spiral conformation of the open clamp so that both the loader and the clamp match the helical symmetry of DNA. One structure reveals that ATP has been hydroly...

  4. Covalently bound conjugates of albumin and heparin: Synthesis, fractionation and characterization

    NARCIS (Netherlands)

    Hennink, Wim E.; Feijen, Jan; Ebert, Charles D.; Kim, Sung Wan

    1983-01-01

    Covalently bound conjugates of human serum albumin and heparin were prepared as compounds which could improve the blood-compatibility of polymer surfaces either by preadsorption or by covalent coupling of the conjugates onto blood contacting surfaces. The conjugates (10–16 weight % of heparin) were

  5. Lower Bounds on Q for Finite Size Antennas of Arbitrary Shape

    DEFF Research Database (Denmark)

    Kim, Oleksiy S.

    2016-01-01

    The problem of the lower bound on the radiation Q for an arbitrarily shaped finite size antenna of non-zero volume is formulated in terms of equivalent electric and magnetic currents densities distributed on a closed surface coinciding with antenna exterior surface. When these equivalent currents...

  6. Proximity Hybridization-Regulated Immunoassay for Cell Surface Protein and Protein-Overexpressing Cancer Cells via Electrochemiluminescence.

    Science.gov (United States)

    Wang, Xiaofei; Gao, Hongfang; Qi, Honglan; Gao, Qiang; Zhang, Chengxiao

    2018-03-06

    A simple electrochemiluminescence (ECL) immunoassay based on a proximity hybridization-regulated strategy was developed for highly sensitive and specific detection of cell surface protein and protein-overexpressing cancer cells. A biosensor was fabricated by self-assembling a thiolated capture ss-DNA3 (partially hybridize with ss-DNA1 and ss-DNA2) and blocking with 6-mercapto-1-hexanol on a gold electrode surface. Target protein was simultaneously bound by two ss-DNA-tagged antibody probes (DNA1-Ab1 and DNA2-Ab2), while DNA1 and DNA2 were brought in sufficient proximity and hybridized with capture DNA3 on the surface of the biosensor. After ECL signal reagent Ru(phen) 3 2+ was intercalated into the hybridized ds-DNAs, ECL measurement was performed in the coreactant solution. A "signal on" proximity hybridization-regulated ECL immunoassay for alpha-fetoprotein (AFP) was developed. The ECL intensity increased with the increase of AFP concentration in the range of 0.05-20.0 ng/mL with a detection limit of 6.2 pg/mL. Moreover, the developed ECL method was successfully used to detect AFP-overexpressing cancer cells (MCF-7 cancer cells as model) with a detection limit of 620 cells/mL (∼60 MCF-7 cells in 100 μL of cell suspension) and discriminate AFP expression on different types of the living cell surface. This work for the first time reports a proximity hybridization-regulated ECL immunoassay for the detection of the cell surface protein on a living cell surface with good specificity and sensitivity. This simple, specific, and sensitive strategy is greatly promising for the detection of proteins and specific cells.

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

    Energy Technology Data Exchange (ETDEWEB)

    Netzel, T.L.

    1997-03-01

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

  8. Mitochondrial DNA.

    Science.gov (United States)

    Wright, Russell G.; Bottino, Paul J.

    1986-01-01

    Provides background information for teachers on mitochondrial DNA, pointing out that it may have once been a free-living organism. Includes a ready-to-duplicate exercise titled "Using Microchondrial DNA to Measure Evolutionary Distance." (JN)

  9. Comparisons of DNA-mediated immunization procedures directed against surface glycoproteins of human immunodeficiency virus type-1 and hepatitis B virus

    DEFF Research Database (Denmark)

    Fomsgaard, A; Nielsen, H V; Nielsen, C

    1998-01-01

    DNA vaccination methods were compared to examine the in vivo expression of HIV-1 gp160 and beta-galactosidase, and the resulting immune response. Beta-galactosidase plasmid showed expression rates of 2-5% of muscle fibers with or without pretreatments using bupivacaine or cardiotoxin facilitators 1...... expressed rather than the DNA vaccination method. It is proposed that gene gun or i.m. injection be used without pretreatment in the case of DNA vaccination with plasmid encoding HIV MN gp160....... or 5 days earlier, respectively. In contrast, HIV gp160 expression was lower in untreated or bupivacaine-treated muscles, but was improved by pretreatment with cardiotoxin. Equal expression of beta-galactosidase and HIV gp160 was obtained using gene gun delivery to the epidermis. Unlike the i...

  10. Error bounds from extra precise iterative refinement

    Energy Technology Data Exchange (ETDEWEB)

    Demmel, James; Hida, Yozo; Kahan, William; Li, Xiaoye S.; Mukherjee, Soni; Riedy, E. Jason

    2005-02-07

    We present the design and testing of an algorithm for iterative refinement of the solution of linear equations, where the residual is computed with extra precision. This algorithm was originally proposed in the 1960s [6, 22] as a means to compute very accurate solutions to all but the most ill-conditioned linear systems of equations. However two obstacles have until now prevented its adoption in standard subroutine libraries like LAPACK: (1) There was no standard way to access the higher precision arithmetic needed to compute residuals, and (2) it was unclear how to compute a reliable error bound for the computed solution. The completion of the new BLAS Technical Forum Standard [5] has recently removed the first obstacle. To overcome the second obstacle, we show how a single application of iterative refinement can be used to compute an error bound in any norm at small cost, and use this to compute both an error bound in the usual infinity norm, and a componentwise relative error bound. We report extensive test results on over 6.2 million matrices of dimension 5, 10, 100, and 1000. As long as a normwise (resp. componentwise) condition number computed by the algorithm is less than 1/max{l_brace}10,{radical}n{r_brace} {var_epsilon}{sub w}, the computed normwise (resp. componentwise) error bound is at most 2 max{l_brace}10,{radical}n{r_brace} {center_dot} {var_epsilon}{sub w}, and indeed bounds the true error. Here, n is the matrix dimension and w is single precision roundoff error. For worse conditioned problems, we get similarly small correct error bounds in over 89.4% of cases.

  11. Upper bounds on superpartner masses from upper bounds on the Higgs boson mass.

    Science.gov (United States)

    Cabrera, M E; Casas, J A; Delgado, A

    2012-01-13

    The LHC is putting bounds on the Higgs boson mass. In this Letter we use those bounds to constrain the minimal supersymmetric standard model (MSSM) parameter space using the fact that, in supersymmetry, the Higgs mass is a function of the masses of sparticles, and therefore an upper bound on the Higgs mass translates into an upper bound for the masses for superpartners. We show that, although current bounds do not constrain the MSSM parameter space from above, once the Higgs mass bound improves big regions of this parameter space will be excluded, putting upper bounds on supersymmetry (SUSY) masses. On the other hand, for the case of split-SUSY we show that, for moderate or large tanβ, the present bounds on the Higgs mass imply that the common mass for scalars cannot be greater than 10(11)  GeV. We show how these bounds will evolve as LHC continues to improve the limits on the Higgs mass.

  12. Modeling DNA

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  13. Bounds on poloidal kinetic energy in plane layer convection

    Science.gov (United States)

    Tilgner, A.

    2017-12-01

    A numerical method is presented that conveniently computes upper bounds on heat transport and poloidal energy in plane layer convection for infinite and finite Prandtl numbers. The bounds obtained for the heat transport coincide with earlier results. These bounds imply upper bounds for the poloidal energy, which follow directly from the definitions of dissipation and energy. The same constraints used for computing upper bounds on the heat transport lead to improved bounds for the poloidal energy.

  14. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  15. Comparisons of DNA-mediated immunization procedures directed against surface glycoproteins of human immunodeficiency virus type-1 and hepatitis B virus

    DEFF Research Database (Denmark)

    Fomsgaard, Anders; Nielsen, Henrik Vedel; Nielsen, Claus

    1998-01-01

    DNA vaccination methods were compared to examine the in vivo expression of HIV-1 gp160 and beta-galactosidase, and the resulting immune response. beta-galactosidase plasmid showed expression rates of 2-5% of muscle fibers with or without pretreatments using bupivacaine or cardiotoxin facilitators...

  16. Selection and Characterization of Single-Stranded DNA Aptamers Binding Human B-Cell Surface Protein CD20 by Cell-SELEX

    Directory of Open Access Journals (Sweden)

    Mansoureh Haghighi

    2018-03-01

    Full Text Available The B-lymphocyte antigen (CD20 is a suitable target for single-stranded (ss nucleic acid oligomer (aptamers. The aim of study was selection and characterization of a ssDNA aptamer against CD20 using Cell-Systematic Evolution of Ligands by Exponential Enrichment (Cell-SELEX. The cDNA clone of CD20 (pcDNA-CD20 was transfected to human embryonic kidney (HEK293T cells. Ten rounds of Cell-SELEX was performed on recombinant HEK-CD20 cells. The final eluted ssDNA pool was amplified and ligated in T/A vector for cloning. The plasmids of positive clones were extracted, sequenced and the secondary structures of the aptamers predicted using DNAMAN® software. The sequencing results revealed 10 different types; three of them had the highest thermodynamic stability, named AP-1, AP-2 and AP-3. The AP-1 aptamer was the most thermodynamically stable one (ΔGAP-1 = −10.87 kcal/mol with the highest binding affinity to CD20 (96.91 ± 4.5 nM. Since, the CD20 is a suitable target for recognition of B-Cell. The selected aptamers could be comparable to antibodies with many advantages. The AP-1, AP-2 and AP-3 could be candidate instead of antibodies for diagnostic and therapeutic applications in immune deficiency, autoimmune diseases, leukemia and lymphoma.

  17. Light-Triggered Release of DNA from Plasmon-Resonant Nanoparticles

    Science.gov (United States)

    Huschka, Ryan

    Plasmon-resonant nanoparticle complexes show promising potential for lighttriggered, controllable delivery of deoxyribonucleic acids (DNA) for research and therapeutic purposes. For example, the approach of RNA interference (RNAi) . using antisense DNA or RNA oligonucleotides to silence activity of a specific pathogenic gene transcript and reduce expression of the encoded protein . is very useful in dissecting genetic function and holds promise as a molecular therapeutic. Herein, we investigate the mechanism and probe the in vitro therapeutic potential of DNA light-triggered release from plasmonic nanoparticles. First, we investigate the mechanism of light-triggered release by dehybridizing double-stranded (dsDNA) via laser illumination from two types of nanoparticle substrates: gold (Au) nanoshells and Au nanorods. Both light-triggered and thermally induced releases are distinctly observable from nanoshell-based complexes. Surprisingly, no analogous measurable light-triggered release was observable from nanorod-based complexes below the DNA melting temperature. These results suggest that a nonthermal mechanism may play a role in light-triggered DNA release. Second, we demonstrate the in vitro light-triggered release of molecules noncovalently attached within dsDNA bound to the Au nanoshell surface. DAPI (4',6- diamidino-2-phenylindole), a bright blue fluorescent molecule that binds reversibly to double-stranded DNA, was chosen to visualize this intracellular light-induced release process. Illumination through the cell membrane of the nanoshell-dsDNA-DAPI complexes dehybridizes the DNA and releases the DAPI molecules within living cells. The DAPI molecules diffuse to the nucleus and associate with the cell's endogenous DNA. This work could have future applications towards drug delivery of molecules that associate with dsDNA. Finally, we demonstrate an engineered Au nanoshell (AuNS)-based therapeutic oligonucleotide delivery vehicle, designed to release its cargo on

  18. Better Bounds on Online Unit Clustering

    Science.gov (United States)

    Ehmsen, Martin R.; Larsen, Kim S.

    Unit Clustering is the problem of dividing a set of points from a metric space into a minimal number of subsets such that the points in each subset are enclosable by a unit ball. We continue work initiated by Chan and Zarrabi-Zadeh on determining the competitive ratio of the online version of this problem. For the one-dimensional case, we develop a deterministic algorithm, improving the best known upper bound of 7/4 by Epstein and van Stee to 5/3. This narrows the gap to the best known lower bound of 8/5 to only 1/15. Our algorithm automatically leads to improvements in all higher dimensions as well. Finally, we strengthen the deterministic lower bound in two dimensions and higher from 2 to 13/6.

  19. Experimental bounds on sterile neutrino mixing angles

    CERN Document Server

    Ruchayskiy, Oleg

    2012-01-01

    We derive bounds on the mixing between the left-chiral ("active") and the right-chiral ("sterile") neutrinos, provided from the combination of neutrino oscillation data and direct experimental searches for sterile neutrinos. We demonstrate that the mixing of sterile neutrinos with any flavour can be significantly suppressed, provided that the angle theta_13 is non-zero. This means that the lower bounds on sterile neutrino lifetime, coming from the negative results of direct experimental searches can be relaxed (by as much as the order of magnitude at some masses). We also demonstrate that the results of the negative searches of sterile neutrinos with PS191 and CHARM experiments are not applicable directly to the see-saw models. The reinterpretation of these results provides up to the order of magnitude stronger bounds on sterile neutrino lifetime than previously discussed in the literature. We discuss the implications of our results for the Neutrino Minimal Standard Model (the NuMSM).

  20. Bounded Gaps between Products of Special Primes

    Directory of Open Access Journals (Sweden)

    Ping Ngai Chung

    2014-03-01

    Full Text Available In their breakthrough paper in 2006, Goldston, Graham, Pintz and Yıldırım proved several results about bounded gaps between products of two distinct primes. Frank Thorne expanded on this result, proving bounded gaps in the set of square-free numbers with r prime factors for any r ≥ 2, all of which are in a given set of primes. His results yield applications to the divisibility of class numbers and the triviality of ranks of elliptic curves. In this paper, we relax the condition on the number of prime factors and prove an analogous result using a modified approach. We then revisit Thorne’s applications and give a better bound in each case.

  1. Properties of Water Bound in Hydrogels

    Directory of Open Access Journals (Sweden)

    Vladimir M. Gun’ko

    2017-10-01

    Full Text Available In this review, the importance of water in hydrogel (HG properties and structure is analyzed. A variety of methods such as 1H NMR (nuclear magnetic resonance, DSC (differential scanning calorimetry, XRD (X-ray powder diffraction, dielectric relaxation spectroscopy, thermally stimulated depolarization current, quasi-elastic neutron scattering, rheometry, diffusion, adsorption, infrared spectroscopy are used to study water in HG. The state of HG water is rather non-uniform. According to thermodynamic features of water in HG, some of it is non-freezing and strongly bound, another fraction is freezing and weakly bound, and the third fraction is non-bound, free water freezing at 0 °C. According to structural features of water in HG, it can be divided into two fractions with strongly associated and weakly associated waters. The properties of the water in HG depend also on the amounts and types of solutes, pH, salinity, structural features of HG functionalities.

  2. Yukawa Bound States and Their LHC Phenomenology

    Directory of Open Access Journals (Sweden)

    Enkhbat Tsedenbaljir

    2013-01-01

    Full Text Available We present the current status on the possible bound states of extra generation quarks. These include phenomenology and search strategy at the LHC. If chiral fourth-generation quarks do exist their strong Yukawa couplings, implied by current experimental lower bound on their masses, may lead to formation of bound states. Due to nearly degenerate 4G masses suggested by Precision Electroweak Test one can employ “heavy isospin” symmetry to classify possible spectrum. Among these states, the color-octet isosinglet vector ω 8 is the easiest to be produced at the LHC. The discovery potential and corresponding decay channels are covered in this paper. With possible light Higgs at ~125 GeV two-Higgs doublet version is briefly discussed.

  3. Prevalence of Serologic Hepatitis B Markers in Blood Donors From Puebla, Mexico: The Association of Relatively High Levels of Anti-Core Antibodies With the Detection of Surface Antigen and Genomic DNA.

    Science.gov (United States)

    Sosa-Jurado, Francisca; Hilda Rosas-Murrieta, Nora; Guzman-Flores, Belinda; Perez Zempoaltecalt, Cintia; Patricia Sanchez Torres, Ana; Ramirez Rosete, Leticia; Bernal-Soto, Maribel; Marquez-Dominguez, Luis; Melendez-Mena, Daniel; Angel Mendoza Torres, Miguel; Teresa Lopez Delgado, Maria; Reyes-Leyva, Julio; Vallejo-Ruiz, Veronica; Santos-Lopez, Gerardo

    2016-06-01

    The hepatitis B virus (HBV) causes chronic hepatitis, hepatic cirrhosis, and hepatocellular carcinoma. Surface antigen (HBsAg) detection is a definitive test that can confirm HBV infection, while the presence of antibodies against the core protein (anti-HBc) suggests either a previous or ongoing infection or occult hepatitis B infection (OBI). The aim of the present study was to determine the prevalence of anti-HBc and HBsAg in blood donors. Further, the study aimed to estimate the anti-HBc level at which HBV DNA is detected in putative OBI cases, as well as to search for mutations in the "a" determinant associated with the non-detection of HBsAg in serum. We conducted a cross-sectional study from 2003-2009. The study included 120,552 blood donors from the state of Puebla, Mexico. Different commercial systems based on microparticles (enzymatic (MEIA) or chemiluminescent (CMIA)) were used to determine the HBsAg and anti-HBc levels. For the detection of HBV DNA, a nested polymerase chain reaction (nested PCR) was used and the genotypes were determined using Sanger sequencing. Of the 120,552 blood donors, 1437 (1.19%, 95% CI: 1.12 - 1.26) were reactive to anti-HBc, while 82 (0.066%, 95% CI: 0.053 - 0.079) were reactive to HBsAg. Some 156 plasma samples collected in 2009 from anti-HBc-positive/HBsAg-negative blood donors were submitted for HBV DNA detection in a search for probable OBI. Viral DNA was detected in 27/156 (17.3%, 95% CI: 11.5 - 23.1). Our results show an association between HBV DNA or HBsAg and anti-HBc S/CO levels ≥ 4.0. All DNA samples were identified as genotype H and some "a" determinant mutations were identified, although none corresponded to mutations previously reported to hinder the detection of HBsAg by commercial immunoassays. We observed that as the anti-HBc levels increase, there is a higher prevalence of the viral protein HBsAg in blood donors. Samples testing positive for HBV-DNA were seen to exhibit a ten-fold higher presence of anti

  4. Prevalence of Serologic Hepatitis B Markers in Blood Donors From Puebla, Mexico: The Association of Relatively High Levels of Anti-Core Antibodies With the Detection of Surface Antigen and Genomic DNA

    Science.gov (United States)

    Sosa-Jurado, Francisca; Hilda Rosas-Murrieta, Nora; Guzman-Flores, Belinda; Perez Zempoaltecalt, Cintia; Patricia Sanchez Torres, Ana; Ramirez Rosete, Leticia; Bernal-Soto, Maribel; Marquez-Dominguez, Luis; Melendez-Mena, Daniel; Angel Mendoza Torres, Miguel; Teresa Lopez Delgado, Maria; Reyes-Leyva, Julio; Vallejo-Ruiz, Veronica; Santos-Lopez, Gerardo

    2016-01-01

    Background The hepatitis B virus (HBV) causes chronic hepatitis, hepatic cirrhosis, and hepatocellular carcinoma. Surface antigen (HBsAg) detection is a definitive test that can confirm HBV infection, while the presence of antibodies against the core protein (anti-HBc) suggests either a previous or ongoing infection or occult hepatitis B infection (OBI). Objectives The aim of the present study was to determine the prevalence of anti-HBc and HBsAg in blood donors. Further, the study aimed to estimate the anti-HBc level at which HBV DNA is detected in putative OBI cases, as well as to search for mutations in the “a” determinant associated with the non-detection of HBsAg in serum. Patients and Methods We conducted a cross-sectional study from 2003–2009. The study included 120,552 blood donors from the state of Puebla, Mexico. Different commercial systems based on microparticles (enzymatic (MEIA) or chemiluminescent (CMIA)) were used to determine the HBsAg and anti-HBc levels. For the detection of HBV DNA, a nested polymerase chain reaction (nested PCR) was used and the genotypes were determined using Sanger sequencing. Results Of the 120,552 blood donors, 1437 (1.19%, 95% CI: 1.12 - 1.26) were reactive to anti-HBc, while 82 (0.066%, 95% CI: 0.053 - 0.079) were reactive to HBsAg. Some 156 plasma samples collected in 2009 from anti-HBc-positive/HBsAg-negative blood donors were submitted for HBV DNA detection in a search for probable OBI. Viral DNA was detected in 27/156 (17.3%, 95% CI: 11.5 - 23.1). Our results show an association between HBV DNA or HBsAg and anti-HBc S/CO levels ≥ 4.0. All DNA samples were identified as genotype H and some “a” determinant mutations were identified, although none corresponded to mutations previously reported to hinder the detection of HBsAg by commercial immunoassays. Conclusions We observed that as the anti-HBc levels increase, there is a higher prevalence of the viral protein HBsAg in blood donors. Samples testing positive

  5. Career Development and Personal Functioning Differences between Work-Bound and Non-Work Bound Students

    Science.gov (United States)

    Creed, Peter A.; Patton, Wendy; Hood, Michelle

    2010-01-01

    We surveyed 506 Australian high school students on career development (exploration, planning, job-knowledge, decision-making, indecision), personal functioning (well-being, self-esteem, life satisfaction, school satisfaction) and control variables (parent education, school achievement), and tested differences among work-bound, college-bound and…

  6. Causality, joint measurement and Tsirelson's bound

    International Nuclear Information System (INIS)

    Choudhary, Sujit K.; Kar, Guruprasad; Kunkri, Samir; Rahaman, Ramij

    2007-01-01

    Tsirelson showed that 2√(2) is the maximum value that CHSH expression can take for quantum correlations [B.S. Tsirelson, Lett. Math. Phys. 4 (1980) 93]. This bound simply follows from the algebra of observables. Recently by exploiting the physical structure of quantum mechanics like unitarity and linearity, Buhrman and Massar [H. Buhrman, S. Massar, Phys. Rev. A 72 (2005) 052103] have established that violation of Tsirelson's bound in quantum mechanics will imply signalling. We prove the same with the help of realistic joint measurement in quantum mechanics and a Bell's inequality which has been derived under the assumption of existence of joint measurement and no signalling condition

  7. G-frames with bounded linear operators

    OpenAIRE

    Xiao, Xiang-chun; Zhu, Yu-can; Shu, Zhi-biao; Ding, Ming-ling

    2015-01-01

    In this paper, we introduce the more general g-frame which is called a $K$-g-frame by combining a g-frame with a bounded linear operator $K$ in a Hilbert space. We give several equivalent characterizations for $K$-g-frames and discuss the stability of perturbation for $K$-g-frames. We also investigate the relationship between a $K$-g-frame and the range of the bounded linear operator $K$. In the end, we give two sufficient conditions for the remainder of a $K$-g-frame after an erasure to stil...

  8. Quantum Kolmogorov complexity and bounded quantum memory

    Science.gov (United States)

    Miyadera, Takayuki

    2011-04-01

    The effect of bounded quantum memory in a primitive information protocol has been examined using the quantum Kolmogorov complexity as a measure of information. We employed a toy two-party protocol in which Bob, by using a bounded quantum memory and an unbounded classical memory, estimates a message that was encoded in qubits by Alice in one of the bases X or Z. Our theorem gave a nontrivial effect of the memory boundedness. In addition, a generalization of the uncertainty principle in the presence of quantum memory has been obtained.

  9. Quantum Kolmogorov complexity and bounded quantum memory

    International Nuclear Information System (INIS)

    Miyadera, Takayuki

    2011-01-01

    The effect of bounded quantum memory in a primitive information protocol has been examined using the quantum Kolmogorov complexity as a measure of information. We employed a toy two-party protocol in which Bob, by using a bounded quantum memory and an unbounded classical memory, estimates a message that was encoded in qubits by Alice in one of the bases X or Z. Our theorem gave a nontrivial effect of the memory boundedness. In addition, a generalization of the uncertainty principle in the presence of quantum memory has been obtained.

  10. Learning within bounds and dream sleep

    Science.gov (United States)

    Geszti, T.; Pazmandi, F.

    1987-12-01

    In a bounded-synapses version of Hopfield's model (1984) for neural networks the quasienergy of a given memory, which is approximately equal to the depth of the corresponding energy well is calculated exactly by treating the change of a synaptic strength on learning as a random walk within bounds. Attractors corresponding to stored memories are found to be considerably flattened before serious retrieval errors arise. This allows dream sleep to be interpreted as random recall and relearning of fresh strong memories, in order to stack them on top of weak incidental memory imprints of a day.

  11. Quantum Kolmogorov Complexity and Bounded Quantum Memory

    OpenAIRE

    Miyadera, Takayuki

    2011-01-01

    In this study, the effect of bounded quantum memory in a primitive information protocol has been examined using the quantum Kolmogorov complexity as a measure of information. We employed a toy two-party protocol in which Bob by using a bounded quantum memory and an unbounded classical memory estimates a message that was encoded in qubits by Alice in one of the bases X or Z. Our theorem gave a nontrivial effect of the memory boundedness. In addition, a generalization of the uncertainty princip...

  12. Violation of Energy Bounds in Designer Gravity

    CERN Document Server

    Hertog, T

    2007-01-01

    We continue our study of the stability of designer gravity theories, where one considers anti-de Sitter gravity coupled to certain tachyonic scalars with boundary conditions defined by a smooth function W. It has recently been argued there is a lower bound on the conserved energy in terms of the global minimum of W, if the scalar potential arises from a superpotential P and the scalar reaches an extremum of P at infinity. We show, however, there are superpotentials for which these bounds do not hold.

  13. Bound states in curved quantum waveguides

    International Nuclear Information System (INIS)

    Exner, P.; Seba, P.

    1987-01-01

    We study free quantum particle living on a curved planar strip Ω of a fixed width d with Dirichlet boundary conditions. It can serve as a model for electrons in thin films on a cylindrical-type substrate, or in a curved quantum wire. Assuming that the boundary of Ω is infinitely smooth and its curvature decays fast enough at infinity, we prove that a bound state with energy below the first transversal mode exists for all sufficiently small d. A lower bound on the critical width is obtained using the Birman-Schwinger technique. (orig.)

  14. Finding Maximal Pairs with Bounded Gap

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Lyngsø, Rune B.; Pedersen, Christian N. S.

    1999-01-01

    . In this paper we present methods for finding all maximal pairs under various constraints on the gap. In a string of length n we can find all maximal pairs with gap in an upper and lower bounded interval in time O(n log n+z) where z is the number of reported pairs. If the upper bound is removed the time reduces...... to O(n+z). Since a tandem repeat is a pair where the gap is zero, our methods can be seen as a generalization of finding tandem repeats. The running time of our methods equals the running time of well known methods for finding tandem repeats....

  15. Plasmid DNA is released from nanosized acicular material surface by low molecular weight oligonucleotides: exogenous plasmid acquisition mechanism for penetration intermediates based on the Yoshida effect.

    Science.gov (United States)

    Yoshida, N; Ide, K

    2008-10-01

    When a colloidal solution consisting of nanosized acicular material and bacterial cells is stimulated with sliding friction at the interface between the hydrogel and interface-forming material where the frictional coefficient increases rapidly, the nanosized acicular material accompanying the bacterial cells forms a penetration intermediate. This effect is known as the Yoshida effect in honor of its discoverer. Through the Yoshida effect, a novel property in which penetration intermediates incorporate exogenous plasmid DNA has been identified. This report proposes a possible mechanism for exogenous plasmid acquisition by penetration intermediates in the Yoshida effect. Escherichia coli cells, pUC18, and chrysotile were used as recipient cells, plasmid DNA, and nanosized acicular material, respectively. Even when repeatedly washing the mixture consisting of pUC18 and chrysotile, transformation efficiency by pUC18 was stable. Accordingly, pUC18 adsorbed onto chrysotile was introduced into recipient E. coli cells. At saturation, the amount of pUC18 adsorbed onto chrysotile was 0.8-1.2 microg/mg. To investigate whether pUC18 adsorbed on chrysotile is replicated by polymerase, polymerase chain reaction (PCR) was carried out with the chrysotile. Amplification of the beta-lactamase gene coded in pUC18, which was adsorbed onto chrysotile, was strongly inhibited. This suggests that DNA adsorbed onto chrysotile is not replicated in vivo. When we searched for substances to release pUC18 adsorbed onto chrysotile, we found that a 300-bp single- or double-stranded segment of DNA releases pUC18 from chrysotile. Competitive adsorption onto chrysotile between double-stranded DNA and pUC18 was then examined through the Yoshida effect. The 310- and 603-bp double-stranded nucleotides caused 50% competitive inhibition at the same molar ratio with pUC18. Hence, the adsorbed region of pUC18 is about 300 bp in length. As the culture period for recipient cells increases, transformation

  16. Scattering theory methods for bound state problems

    International Nuclear Information System (INIS)

    Raphael, R.B.; Tobocman, W.

    1978-01-01

    For the analysis of the properties of a bound state system one may use in place of the Schroedinger equation the Lippmann-Schwinger (LS) equation for the wave function or the LS equation for the reactance operator. Use of the LS equation for the reactance operator constrains the solution to have correct asymptotic behaviour, so this approach would appear to be desirable when the bound state wave function is to be used to calculate particle transfer form factors. The Schroedinger equation based N-level analysis of the s-wave bound states of a square well is compared to the ones based on the LS equation. It is found that the LS equation methods work better than the Schroedinger equation method. The method that uses the LS equation for the wave function gives the best results for the wave functions while the method that uses the LS equation for the reactance operator gives the best results for the binding energies. The accuracy of the reactance operator based method is remarkably insensitive to changes in the oscillator constant used for the harmonic oscillator function basis set. It is also remarkably insensitive to the number of nodes in the bound state wave function. (Auth.)

  17. Computational Lower Bounds Using Diagonalization-II

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 4. Computational Lower Bounds Using Diagonalization - II. M V Panduranga Rao. General Article Volume 15 Issue 4 April 2010 pp 337-346 ... Keywords. Diagonalization; time–hierarchy theorem; relativization; Baker–Gill–Solovay theorem.

  18. Bounds on Gromov hyperbolicity constant in graphs

    Indian Academy of Sciences (India)

    Home; Journals; Proceedings – Mathematical Sciences; Volume 122; Issue 1. Bounds on Gromov Hyperbolicity Constant in Graphs. José M Rodríguez José M Sigarreta. Volume 122 ... Spain; Facultad de Matemáticas, Universidad Autónoma de Guerrero, Carlos E. Adame No. 54 Col. Garita, 39650 Acalpulco Gro., Mexico ...

  19. Bogomol'nyi bounds for cosmic strings

    International Nuclear Information System (INIS)

    Comtet, A.; Gibbons, G.W.; Cambridge Univ.

    1987-09-01

    We establish Bogomol'nyi inequalities for the deficit angle of some cylindrically symmetric asymptotically local flat (CALF) spacetimes containing cosmic strings. These results prove the stability against arbitrary cylindrical deformations of those configurations which saturate the bound. Such configurations satisfy first order equations which can, in some cases, be solved exactly

  20. Bounded Rationality of Generalized Abstract Fuzzy Economies

    Directory of Open Access Journals (Sweden)

    Lei Wang

    2014-01-01

    Full Text Available By using a nonlinear scalarization technique, the bounded rationality model M for generalized abstract fuzzy economies in finite continuous spaces is established. Furthermore, by using the model M, some new theorems for structural stability and robustness to (λ,ϵ-equilibria of generalized abstract fuzzy economies are proved.