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Sample records for acid spin probes

  1. Intra-albumin migration of bound fatty acid probed by spin label ESR

    SciTech Connect

    Gurachevsky, Andrey . E-mail: a.gurachevsky@medinnovation.de; Shimanovitch, Ekaterina; Gurachevskaya, Tatjana; Muravsky, Vladimir

    2007-09-07

    Conventional ESR spectra of 16-doxyl-stearic acid bound to bovine and human serum albumin were recorded at different temperatures in order to investigate the status of spin-labeled fatty acid in the interior of the protein globule. A computer spectrum simulation of measured spectra, performed by non-linear least-squares fits, clearly showed two components corresponding to strongly and weakly immobilized fatty acid molecules. The two-component model was verified on spectra measured at different pH. Thermodynamic parameters of the spin probe exchange between two spin probe states were analyzed. It was concluded that at physiological conditions, fatty acid molecules permanently migrate in the globule interior between the specific binding sites and a space among albumin domains.

  2. Development and Application of Spin Traps, Spin Probes, and Spin Labels.

    PubMed

    Bagryanskaya, Elena G; Krumkacheva, Olesya A; Fedin, Matvey V; Marque, Sylvain R A

    2015-01-01

    This chapter focuses on major achievements of the last decade in the synthesis and applications of spin traps, spin probes, and spin labels. Our discussion on spin trapping is mainly concerned with novel aspects of nitrones used as spin traps and with the kinetics caused by bioreductants. The second part of the chapter deals with recent developments in site-directed spin labeling (SDSL) for studying structure and functions of proteins and nucleic acids. We focus on SDSL EPR distance measurements using advanced trityl and nitroxide labels, on new approaches for incorporation of spin labels in biomolecules, and finally, on recent room/physiological temperature measurements made feasible by these novel spin labels. PMID:26478492

  3. Probing absolute spin polarization at the nanoscale.

    PubMed

    Eltschka, Matthias; Jäck, Berthold; Assig, Maximilian; Kondrashov, Oleg V; Skvortsov, Mikhail A; Etzkorn, Markus; Ast, Christian R; Kern, Klaus

    2014-12-10

    Probing absolute values of spin polarization at the nanoscale offers insight into the fundamental mechanisms of spin-dependent transport. Employing the Zeeman splitting in superconducting tips (Meservey-Tedrow-Fulde effect), we introduce a novel spin-polarized scanning tunneling microscopy that combines the probing capability of the absolute values of spin polarization with precise control at the atomic scale. We utilize our novel approach to measure the locally resolved spin polarization of magnetic Co nanoislands on Cu(111). We find that the spin polarization is enhanced by 65% when increasing the width of the tunnel barrier by only 2.3 Å due to the different decay of the electron orbitals into vacuum. PMID:25423049

  4. Electric probe for spin transition and fluctuation

    NASA Astrophysics Data System (ADS)

    Qiu, Zhiyong; Li, Jia; Hou, Dazhi; Arenholz, Elke; N'diaye, Alpha T.; Tan, Ali; Uchida, Ken-Ichi; Sato, Koji; Tserkovnyak, Yaroslov; Qiu, Z. Q.; Saitoh, Eiji

    Spin fluctuation and transition have always been one of central topics of magnetism and condense matter science. To probe them, neutron scatterings have been used as powerful tools. A part of neutrons injected into a sample is scattered by spin fluctuation inside the sample. This process transcribes the spin fluctuation onto scattering intensity, which is commonly represented by dynamical magnetic susceptibility of the sample and is maximized at magnetic phase transitions. Importantly, a neutron carries spin without electric charge, and it thus can bring spin into a sample without being disturbed by electric energy: an advantage of neutrons, although large facilities such as a nuclear reactor is necessary. Here we show that spin pumping, frequently used in nanoscale spintronic devices, provides a desktop micro probe for spin fluctuation and transition; not only a neutron beam, spin current is also a flux of spin without an electric charge and its transport reflects spin fluctuation in a sample. We demonstrate detection of anti-ferromagnetic transition in ultra-thin CoO films via frequency dependent spin-current transmission measurements.

  5. ESR spin probes in ionic liquids.

    PubMed

    Stoesser, Reinhard; Herrmann, Werner; Zehl, Andrea; Strehmel, Veronika; Laschewsky, André

    2006-05-12

    The spin probes 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO), 4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPOL), and 2,2,6,6-tetramethyl-4-trimethylammoniumpiperidine-1-oxylIodide (CAT-1) are examined in a number of ionic liquids based on substituted imidazolium cations and tetrafluoroborate and hexafluorophosphate anions, respectively. The reorientation correlation times tau(R) of the spin probes in these systems have been determined by complete spectra simulation and, for rapid reortientation, by analysis of the intensities of the hyperfine lines of the electron spin resonance (ESR) spectra. A comparison of the results with those from the model system glycerol/water and selected organic solvents is made. Additions of diamagnetic and paramagnetic ions allow the conclusion that salt effects and spin exchange are present, and that both are superimposed by motional effects. Specific interactions in the ionic liquids, as well as between the spin-probe molecules and the constituents of the ionic liquids are reflected in the spectra of the spin probes, depending on their molecular structure.

  6. A quantum spin-probe molecular microscope

    NASA Astrophysics Data System (ADS)

    Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L. C. L.

    2016-10-01

    Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy.

  7. A quantum spin-probe molecular microscope

    PubMed Central

    Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L.C.L.

    2016-01-01

    Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy. PMID:27725630

  8. Spin Polarized Electron Probes and Magnetic Nanostructures

    SciTech Connect

    D.L. Mills

    2003-10-15

    OAK B188 This report summarizes progress to date in our theoretical research program, for the period from July 1, 2002 to November 1, 2003. In addition, our research priorities for the coming year are set forth. The reporting period has been a most exciting and significant one. For the past several years, one of our principal thrust areas has been development of the theory of spin dynamics in magnetic nanostructures with emphasis on the use of spin polarized electrons as probes of short wavelength spin dynamics in such entities. Our program stimulated the first experiment which detected large wave vector spin waves in ultrathin films in 1999 through spin polarized electron loss spectroscopy (SPEELS); the publication which announced this discovery was a joint publication between a group in Halle (Germany) with our theory effort. The continued collaboration has led to the design and implementation of the new SPEELS spectrometer and we now have in hand the first detailed measurements of spin wave dispersion in an ultrathin film. A second such spectrometer is now operational in the laboratory of Prof. H. Hopster, at UC Irvine. We are thus entering a most exciting new era in the spectroscopy of spin excitations in magnetic nanostructures. During the reporting period, we have completed very important new analyses which predict key aspects of the spectra which will be uncovered by these new instruments, and the calculations continue to be developed and to expand our understanding. In addition, we have initiated a new series of theoretical studies directed toward spin dynamics of single magnetic adatoms on metal surfaces, with STM based studies of this area n mind. In the near future, these studies will continue, and we will expand our effort into new areas of spin dynamics in magnetic nanostructures.

  9. Electron spin echo study of doxyl spin probes in micellar systems of ammonium perfluorooctanoate

    SciTech Connect

    Romanelli, M.; Ristori, S.; Martini, G. ); Kang, Y.S.; Kevan, L. )

    1994-02-24

    The two-phase and three-pulse electron spin echo techniques were applied to investigate the behavior of doxyl stearic acid spin probes in micellar aqueous solutions of ammonium perfluorooctanoate. Three doxyl stearic acids with the nitroxide group in different positions on the alkyl chain were used as spin probes, and deuteriated water was used to study the deuterium modulation of the echo signals. The experimental patterns were interpreted by best-fit spectra calculated by taking into account both the echo decay and the nuclear modulation. The analysis determines the number of deuterium nuclei in the surroundings of the NO groups and the time constant for the electron spin reorientation causing spectral diffusion and echo decay. From these data we conclude that water molecules belonging to the NO solvation sphere were maintained in the micelles and that the long-chain nitroxide probes were tilted in the micelle core in order to occupy regions with relatively easy water accessibility which was slightly higher for 12-DXSA than for 5- and 16-DXSA. The modulation of the hyperfine couplings of the methyl protons due to their rotational motion was the main mechanism contributing to the echo decay. 44 refs., 4 figs., 2 tabs.

  10. Spin-current probe for phase transition in an insulator.

    PubMed

    Qiu, Zhiyong; Li, Jia; Hou, Dazhi; Arenholz, Elke; N'Diaye, Alpha T; Tan, Ali; Uchida, Ken-Ichi; Sato, Koji; Okamoto, Satoshi; Tserkovnyak, Yaroslav; Qiu, Z Q; Saitoh, Eiji

    2016-01-01

    Spin fluctuation and transition have always been one of the central topics of magnetism and condensed matter science. Experimentally, the spin fluctuation is found transcribed onto scattering intensity in the neutron-scattering process, which is represented by dynamical magnetic susceptibility and maximized at phase transitions. Importantly, a neutron carries spin without electric charge, and therefore it can bring spin into a sample without being disturbed by electric energy. However, large facilities such as a nuclear reactor are necessary. Here we show that spin pumping, frequently used in nanoscale spintronic devices, provides a desktop microprobe for spin transition; spin current is a flux of spin without an electric charge and its transport reflects spin excitation. We demonstrate detection of antiferromagnetic transition in ultra-thin CoO films via frequency-dependent spin-current transmission measurements, which provides a versatile probe for phase transition in an electric manner in minute devices. PMID:27573443

  11. Spin-current probe for phase transition in an insulator

    PubMed Central

    Qiu, Zhiyong; Li, Jia; Hou, Dazhi; Arenholz, Elke; N'Diaye, Alpha T.; Tan, Ali; Uchida, Ken-ichi; Sato, Koji; Okamoto, Satoshi; Tserkovnyak, Yaroslav; Qiu, Z. Q.; Saitoh, Eiji

    2016-01-01

    Spin fluctuation and transition have always been one of the central topics of magnetism and condensed matter science. Experimentally, the spin fluctuation is found transcribed onto scattering intensity in the neutron-scattering process, which is represented by dynamical magnetic susceptibility and maximized at phase transitions. Importantly, a neutron carries spin without electric charge, and therefore it can bring spin into a sample without being disturbed by electric energy. However, large facilities such as a nuclear reactor are necessary. Here we show that spin pumping, frequently used in nanoscale spintronic devices, provides a desktop microprobe for spin transition; spin current is a flux of spin without an electric charge and its transport reflects spin excitation. We demonstrate detection of antiferromagnetic transition in ultra-thin CoO films via frequency-dependent spin-current transmission measurements, which provides a versatile probe for phase transition in an electric manner in minute devices. PMID:27573443

  12. Spin-current probe for phase transition in an insulator

    DOE PAGES

    Qiu, Zhiyong; Li, Jia; Hou, Dazhi; Arenholz, Elke; N’Diaye, Alpha T.; Tan, Ali; Uchida, Ken-ichi; Sato, Koji; Okamoto, Satoshi; Tserkovnyak, Yaroslav; et al

    2016-08-30

    Spin fluctuation and transition have always been one of the central topics of magnetism and condensed matter science. Experimentally, the spin fluctuation is found transcribed onto scattering intensity in the neutron-scattering process, which is represented by dynamical magnetic susceptibility and maximized at phase transitions. Importantly, a neutron carries spin without electric charge, and therefore it can bring spin into a sample without being disturbed by electric energy. However, large facilities such as a nuclear reactor are necessary. Here we present that spin pumping, frequently used in nanoscale spintronic devices, provides a desktop microprobe for spin transition; spin current is amore » flux of spin without an electric charge and its transport reflects spin excitation. Additionally, we demonstrate detection of antiferromagnetic transition in ultra-thin CoO films via frequency-dependent spin-current transmission measurements, which provides a versatile probe for phase transition in an electric manner in minute devices.« less

  13. Spin-current probe for phase transition in an insulator.

    PubMed

    Qiu, Zhiyong; Li, Jia; Hou, Dazhi; Arenholz, Elke; N'Diaye, Alpha T; Tan, Ali; Uchida, Ken-Ichi; Sato, Koji; Okamoto, Satoshi; Tserkovnyak, Yaroslav; Qiu, Z Q; Saitoh, Eiji

    2016-01-01

    Spin fluctuation and transition have always been one of the central topics of magnetism and condensed matter science. Experimentally, the spin fluctuation is found transcribed onto scattering intensity in the neutron-scattering process, which is represented by dynamical magnetic susceptibility and maximized at phase transitions. Importantly, a neutron carries spin without electric charge, and therefore it can bring spin into a sample without being disturbed by electric energy. However, large facilities such as a nuclear reactor are necessary. Here we show that spin pumping, frequently used in nanoscale spintronic devices, provides a desktop microprobe for spin transition; spin current is a flux of spin without an electric charge and its transport reflects spin excitation. We demonstrate detection of antiferromagnetic transition in ultra-thin CoO films via frequency-dependent spin-current transmission measurements, which provides a versatile probe for phase transition in an electric manner in minute devices.

  14. Spin-current probe for phase transition in an insulator

    NASA Astrophysics Data System (ADS)

    Qiu, Zhiyong; Li, Jia; Hou, Dazhi; Arenholz, Elke; N'diaye, Alpha T.; Tan, Ali; Uchida, Ken-Ichi; Sato, Koji; Okamoto, Satoshi; Tserkovnyak, Yaroslav; Qiu, Z. Q.; Saitoh, Eiji

    2016-08-01

    Spin fluctuation and transition have always been one of the central topics of magnetism and condensed matter science. Experimentally, the spin fluctuation is found transcribed onto scattering intensity in the neutron-scattering process, which is represented by dynamical magnetic susceptibility and maximized at phase transitions. Importantly, a neutron carries spin without electric charge, and therefore it can bring spin into a sample without being disturbed by electric energy. However, large facilities such as a nuclear reactor are necessary. Here we show that spin pumping, frequently used in nanoscale spintronic devices, provides a desktop microprobe for spin transition; spin current is a flux of spin without an electric charge and its transport reflects spin excitation. We demonstrate detection of antiferromagnetic transition in ultra-thin CoO films via frequency-dependent spin-current transmission measurements, which provides a versatile probe for phase transition in an electric manner in minute devices.

  15. Polarized hyperons probe dynamics of quark spin

    SciTech Connect

    Daniel S. Carman; T. S. Harry Lee; Mac Mestayer; Reinhard Schumacher

    2007-08-01

    Researchers at Jefferson Laboratory demonstrate how two analyses of the same data provide two plausible models of spin transfer in exclusive hyperon production, yielding quite different pictures of quark spin dynamics and challenging existing theories.

  16. Probing spin flip scattering in ballistic nanosystems

    SciTech Connect

    Zeng, Z. M.; Feng, J. F.; Wang, Y.; Han, Prof. X. F.; Zhan, W. S.; Zhang, Xiaoguang; Zhang, Z.

    2006-01-01

    Because spin-flip scattering length is longer than the electron mean-free-path in a metal, past studies of spin-flip scattering are limited to the diffusive regime. Spin accumulation in the nanometer sized spacer layer of a magnetic double barrier tunnel junction allows the study of spin flip scattering near ballistic limit. We extract the spin-flip conductance $G_s$ of the spacer layer from magnetoresistance measurements. A linear temperature dependence of $G_s$ is found. The bias voltage dependence shows a quantum well resonance which explains the sharp reduction of the magnetoresistance. At 4.2K $G_s$ yields the mean-free-path (70nm) and the spin-flip length ($1.0$-$2.6\\mu$m).

  17. Perforated cenosphere-supported pH-sensitive spin probes

    SciTech Connect

    Fomenko, E.V.; Bobko, A.A.; Salanov, A.N.; Kirilyuk, I.A.; Grigor'ev, I.A.; Khramtsov, V.V.; Anshits, A.G.

    2008-03-15

    Porous supports with an accessible internal volume and a shell providing the diffusive migration of pH-sensitive spin probes were obtained for the first time from hollow aluminosilicate cenospheres isolated from the coal fly ash. Using the methods of scanning electron microscopy and electron spin resonance, the morphology of different porous cenosphere modifications and its influence on the diffusion of spin probes from the internal volume were studied. When supporting aqueous solutions of a radical, the characteristic diffusion time for the mesoporous structure of the support is longer by a factor of 3-5 than that for the macroporous structure. Ferrospinel in a content of 6 wt.% do not virtually affect the diffusion rate of spin probes. A constant rate of radical migration of similar to 1 {mu} mol min{sup -1}, determined by radical solubility in water, is achieved when a radical in the solid aggregate state is supported on the magnetic cenospheres.

  18. Using spin to probe hadronic structure

    SciTech Connect

    Ramsey, G.P. |

    1994-12-02

    The theoretical and experimental status of high energy spin phenomena is summarized, with emphasis on the spin properties of nucleons. It is stressed that crucial tests of the Standard Model can be made with polarization experiments. By performing the experiments discussed here, the authors will reveal important constituent and composite properties of protons and neutrons. The future prospects for planned polarization experiments are discussed.

  19. Functional nucleic acid probes and uses thereof

    DOEpatents

    Nilsen-Hamilton, Marit

    2006-10-03

    The present invention provides functional nucleic acid probes, and methods of using functional nucleic acid probes, for binding a target to carry out a desired function. The probes have at least one functional nucleic acid, at least one regulating nucleic acid, and at least one attenuator. The functional nucleic acid is maintained in an inactive state by the attenuator and activated by the regulating nucleic acid only in the presence of a regulating nucleic acid target. In its activated state the functional nucleic acid can bind to its target to carry out a desired function, such as generating a signal, cleaving a nucleic acid, or catalyzing a reaction.

  20. Microscopic understanding of spin current probed by shot noise

    NASA Astrophysics Data System (ADS)

    Arakawa, Tomonori

    much longer than the spin relaxation length. In other words, the spin currents in such a semiconducting material can be strongly out of equilibrium. In this invited talk, I will present a series of experimental work on the spin current in a (Ga,Mn)As/tunnel barrier/n-GaAs based lateral spin valve device, mainly probed by the current noise measurement. Finally I hope I will mention about our future plan to cool down the effective temperature of the spin current by using superconductivity. This work was partially supported by JSPS KAKENHI Grant Numbers 26220711, 25887037, 25103003, and 15K17680.

  1. Electron spin resonance (ESR) probe for interventional MRI instrument localization.

    PubMed

    Ehnholm, G J; Vahala, E T; Kinnunen, J; Nieminen, J E; Standertskjöld-Nordenstam, C; Uusitalo, M A

    1999-08-01

    This article presents a miniaturized electron spin resonance (ESR) probe for deducing the position of a surgical instrument on an MR image. The ESR probe constructed was small enough to fit inside a 14-G biopsy needle sheath, and position information of the sheath could be acquired using a simple gradient sequence. The position accuracy was estimated from needle trajectories as inferred from the needle artifact, the actual physical trajectory, and measured coordinates. The probe was able to track the tip of a biopsy needle quickly (10 samples/sec) and precisely with accuracy better than +/-2 mm. J. Magn. Reson. Imaging 1999;10:216-219.

  2. Nucleic acid probes in diagnostic medicine

    NASA Technical Reports Server (NTRS)

    Oberry, Phillip A.

    1991-01-01

    The need for improved diagnostic procedures is outlined and variations in probe technology are briefly reviewed. A discussion of the application of probe technology to the diagnosis of disease in animals and humans is presented. A comparison of probe versus nonprobe diagnostics and isotopic versus nonisotopic probes is made and the current state of sequence amplification is described. The current market status of nucleic acid probes is reviewed with respect to their diagnostic application in human and veterinary medicine. Representative product examples are described and information on probes being developed that offer promise as future products is discussed.

  3. Some implications of satellite spin effects in cylindrical probe measurements

    NASA Technical Reports Server (NTRS)

    Miller, N. J.

    1971-01-01

    In-situ measurements of ambient electron densities with satellite-borne cylindrical probes exhibit periodic variations synchronous with the satellite's spin cycle. Representing these fluctuations as a superposition of effects attributable to both the presence of the satellite wake and the geomagnetic field leads to a model of the modulations of accelerated electron current to cylindrical probes in which one modulation component displays current variations dependent upon the probe-velocity angle (psi) and the other displays variations dependent upon the angle between the probe axis and the geomagnetic field lines (beta). The modulations produce an electron current decrease whenever the probe axis rotates into the satellite wake or whenever the probe axis rotates toward alignment with the geomagnetic field lines. With increasing altitude, the modulation dependent upon psi decreases whereas the modulation dependent upon beta increases. The analysis results imply that the most accurate of atmospheric electron densities by satellite-borne cylindrical probes come from measurements taken out of the satellite's wake and when the probe axis is within 20 degrees of being perpendicular to the geomagnetic field lines.

  4. Nanometre-scale probing of spin waves using single-electron spins

    PubMed Central

    van der Sar, Toeno; Casola, Francesco; Walsworth, Ronald; Yacoby, Amir

    2015-01-01

    Pushing the frontiers of condensed-matter magnetism requires the development of tools that provide real-space, few-nanometre-scale probing of correlated-electron magnetic excitations under ambient conditions. Here we present a practical approach to meet this challenge, using magnetometry based on single nitrogen-vacancy centres in diamond. We focus on spin-wave excitations in a ferromagnetic microdisc, and demonstrate local, quantitative and phase-sensitive detection of the spin-wave magnetic field at ∼50 nm from the disc. We map the magnetic-field dependence of spin-wave excitations by detecting the associated local reduction in the disc's longitudinal magnetization. In addition, we characterize the spin–noise spectrum by nitrogen-vacancy spin relaxometry, finding excellent agreement with a general analytical description of the stray fields produced by spin–spin correlations in a 2D magnetic system. These complementary measurement modalities pave the way towards imaging the local excitations of systems such as ferromagnets and antiferromagnets, skyrmions, atomically assembled quantum magnets, and spin ice. PMID:26249673

  5. Application of electron spin resonance spectroscopy and spin probes to investigate the effect of ingredients on changes in wheat dough during heating.

    PubMed

    Robertson, J A; Sutcliffe, L H; Mills, E N C

    2006-02-22

    The change in microviscosity of the aqueous and lipid phases of wheat flour dough, during heating and subsequent cooling, has been measured using novel spin probes based on the isoindolin-yloxyl structure. The spin probes, water and/or lipid soluble, were used with combinations of dough ingredients: diacetyl tartaric acid ester of monoglycerides (DATEM), salt, yeast, and sodium ascorbate. The lipid soluble probe showed that DATEM does not produce a homogeneous phase with endogenous lipids but is found in a separate, less mobile phase. Also, the lipids were shown not to be involved in the baking process, although DATEM may be incorporated into the gelled starch matrix. The water soluble probe enabled starch gelatinization to be investigated in detail and showed that gelatinization produces a reduction of dielectric constant. The technique is appropriate for the detailed examination of the behavior of different ingredients during baking and also potentially to examine interactions between ingredients and flour components in dough.

  6. A general protocol for temperature calibration of MAS NMR probes at arbitrary spinning speeds.

    PubMed

    Guan, Xudong; Stark, Ruth E

    2010-01-01

    A protocol using (207)Pb NMR of solid lead nitrate was developed to determine the temperature of magic-angle spinning (MAS) NMR probes over a range of nominal set temperatures and spinning speeds. Using BioMAS and FastMAS probes with typical sample spinning rates of 8 and 35 kHz, respectively, empirical equations were devised to predict the respective sample temperatures. These procedures provide a straightforward recipe for temperature calibration of any MAS probe. PMID:21036557

  7. A General Protocol for Temperature Calibration of MAS NMR Probes at Arbitrary Spinning Speeds

    PubMed Central

    Guan, Xudong; Stark, Ruth E.

    2010-01-01

    A protocol using 207Pb NMR of solid lead nitrate was developed to determine the temperature of magic-angle spinning (MAS) NMR probes over a range of nominal set temperatures and spinning speeds. Using BioMAS and fastMAS probes with typical sample spinning rates of 8 and 35 kHz, respectively, empirical equations were devised to predict the respective sample temperatures. These procedures provide a straightforward recipe for temperature calibration of any MAS probe. PMID:21036557

  8. Probing Spin Excitations Using Magneto-Raman Spectroscopy

    NASA Astrophysics Data System (ADS)

    Thirunavukkuarasu, K.; Lu, Z.; Simpson, J.; Walker, A.; Sears, J.; Kim, Y.-J.; Burch, K.; Smirnov, D.

    The presence of a 2D quantum spin liquid state was recently suggested for the spin-orbit coupled Mott insulator α-RuCl3 with a honeycomb lattice.[Phys. Rev. 90, 041112 (2014)] Optical spectroscopy, Raman scattering, specific heat as well as magnetic susceptibility measurements on α-RuCl3 identified elementary excitations due to electronic correlations and spin-orbit coupling.[arXiv:1503.07593, Phys. Rev. Letters 114, 147201 (2015), and Phys. Rev. 91, 144420 (2015)] These observations appear to be consistent with theoretical expectations for Heisenberg-Kitaev model for QSL.[Phys. Rev. 91, 241110 (2015)] The underlying mechanism for the unconventional magnetism in α-RuCl3 was further investigated by probing the effect of external magnetic field on the Raman spectroscopic signatures. Raman scattering experiments were performed at temperatures down to 5 K and magnetic fields up to 10 T. The intensity of strongest A1g phonon was found to decrease with increasing magnetic field strength suggesting the presence of strong magnetic interactions. The experimental observations and its implications will be presented. Current Affiliation: Florida A and M University.

  9. ESR investigation of starch gelatinization using novel spin probes.

    PubMed

    Robertson, James A; Sutcliffe, Leslie H

    2005-06-01

    The spin probes 1,1,3,3-tetramethylisoindolin-2-yloxyl (TMIO) and the sodium salt of its sulfonate, 1,1,3,3-tetramethylisoindolin-2-yloxyl-5-sulfonate (NaTMIOS) were used to monitor the microviscosity changes of water during starch gelatinization. In cereal starch, which contains mainly A-type polymorphs, evidence was found for the amylopectin and amylose regions, the latter undergoing a transition at about 55 degrees C and a large increase in the microviscosity on cooling. Pea starch contains both A-and B-type polymorphs and this was also found to have two domains and the 55 degrees C transition was observed for the amylose phase: the less mobile amylopectin showed a reversible decrease in water microviscosity on heating.

  10. Sealed magic angle spinning nuclear magnetic resonance probe and process for spectroscopy of hazardous samples

    DOEpatents

    Cho, Herman M.; Washton, Nancy M.; Mueller, Karl T.; Sears, Jr., Jesse A.; Townsend, Mark R.; Ewing, James R.

    2016-06-14

    A magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) probe is described that includes double containment enclosures configured to seal and contain hazardous samples for analysis. The probe is of a modular design that ensures containment of hazardous samples during sample analysis while preserving spin speeds for superior NMR performance and convenience of operation.

  11. Arrays of nucleic acid probes on biological chips

    DOEpatents

    Chee, Mark; Cronin, Maureen T.; Fodor, Stephen P. A.; Huang, Xiaohua X.; Hubbell, Earl A.; Lipshutz, Robert J.; Lobban, Peter E.; Morris, MacDonald S.; Sheldon, Edward L.

    1998-11-17

    DNA chips containing arrays of oligonucleotide probes can be used to determine whether a target nucleic acid has a nucleotide sequence identical to or different from a specific reference sequence. The array of probes comprises probes exactly complementary to the reference sequence, as well as probes that differ by one or more bases from the exactly complementary probes.

  12. Probing Spatial Spin Correlations of Ultracold Gases by Quantum Noise Spectroscopy

    SciTech Connect

    Bruun, G. M.; Andersen, Brian M.; Demler, Eugene; Soerensen, Anders S.

    2009-01-23

    Spin noise spectroscopy with a single laser beam is demonstrated theoretically to provide a direct probe of the spatial correlations of cold fermionic gases. We show how the generic many-body phenomena of antibunching, pairing, antiferromagnetic, and algebraic spin liquid correlations can be revealed by measuring the spin noise as a function of laser width, temperature, and frequency.

  13. Vibrational Stark Effect Probes for Nucleic Acids

    PubMed Central

    Silverman, Lisa N.; Pitzer, Michael E.; Ankomah, Peter O.; Boxer, Steven G.; Fenlon, Edward E.

    2008-01-01

    The vibrational Stark effect (VSE) has proven to be an effective method for the study of electric fields in proteins via the use of infrared probes. In order to explore the use of VSE in nucleic acids, the Stark spectroscopy of nine structurally diverse nucleosides was investigated. These nucleosides contained nitrile or azide probes in positions that correspond to both the major and minor grooves of DNA. The nitrile probes showed better characteristics and exhibited absorption frequencies over a broad range; i.e., from 2253 cm−1 for 2′-O-cyanoethyl ribonucleosides 8 and 9 to 2102 cm−1 for a 13C-labeled 5-thiocyanatomethyl-2’-deoxyuridine 3c. The largest Stark tuning rate observed was |Δµ| = 1.1 cm−1/(MV/cm) for both 5-cyano-2′-deoxyuridine 1 and N2-nitrile-2′-deoxyguanosine 7. The latter is a particularly attractive probe because of its high extinction coefficient (ε = 412 M−1cm−1) and ease of incorporation into oligomers. PMID:17877390

  14. Probing protein stability with unnatural amino acids

    SciTech Connect

    Mendel, D.; Ellman, J.A.; Zhiyuh Chang; Veenstra, D.L.; Kollman, P.A.; Schultz, P.G. )

    1992-06-26

    Unnatural amino acid mutagenesis, in combination with molecular modeling and simulation techniques, was used to probe the effect of side chain structure on protein stability. Specific replacements at position 133 in T4 lysozyme included (1) leucine (wt), norvaline, ethylglycine, and alanine to measure the cost of stepwise removal of methyl groups from the hydrophobic core, (2) norvaline and O-methyl serine to evaluate the effects of side chain solvation, and (3) leucine, S,S-2-amino-4-methylhexanoic acid, and S-2-amino-3-cyclopentylpropanoic acid to measure the influence of packing density and side chain conformational entropy on protein stability. All of these factors (hydrophobicity, packing, conformational entropy, and cavity formation) significantly influence protein stability and must be considered when analyzing any structural change to proteins.

  15. Probing excitations in insulators via injection of spin currents

    NASA Astrophysics Data System (ADS)

    Chatterjee, Shubhayu; Sachdev, Subir

    2015-10-01

    We propose a spin transport experiment to measure the low-energy excitations in insulators with spin degrees of freedom, with a focus on detecting ground states that lack magnetic order. A general formalism to compute the spin current from a metal with a nonequilibrium distribution of spins to an insulator is developed. It is applied to insulating states with and without long range magnetic order, and salient features in the spin conductance are noted.

  16. Direct Detection of Pure ac Spin Current by X-Ray Pump-Probe Measurements.

    PubMed

    Li, J; Shelford, L R; Shafer, P; Tan, A; Deng, J X; Keatley, P S; Hwang, C; Arenholz, E; van der Laan, G; Hicken, R J; Qiu, Z Q

    2016-08-12

    Despite recent progress in spin-current research, the detection of spin current has mostly remained indirect. By synchronizing a microwave waveform with synchrotron x-ray pulses, we use the ferromagnetic resonance of the Py (Ni_{81}Fe_{19}) layer in a Py/Cu/Cu_{75}Mn_{25}/Cu/Co multilayer to pump a pure ac spin current into the Cu_{75}Mn_{25} and Co layers, and then directly probe the spin current within the Cu_{75}Mn_{25} layer and the spin dynamics of the Co layer by x-ray magnetic circular dichroism. This element-resolved pump-probe measurement unambiguously identifies the ac spin current in the Cu_{75}Mn_{25} layer. PMID:27563981

  17. Direct Detection of Pure ac Spin Current by X-Ray Pump-Probe Measurements

    NASA Astrophysics Data System (ADS)

    Li, J.; Shelford, L. R.; Shafer, P.; Tan, A.; Deng, J. X.; Keatley, P. S.; Hwang, C.; Arenholz, E.; van der Laan, G.; Hicken, R. J.; Qiu, Z. Q.

    2016-08-01

    Despite recent progress in spin-current research, the detection of spin current has mostly remained indirect. By synchronizing a microwave waveform with synchrotron x-ray pulses, we use the ferromagnetic resonance of the Py (Ni81Fe19 ) layer in a Py /Cu /Cu75Mn25/Cu /Co multilayer to pump a pure ac spin current into the Cu75Mn25 and Co layers, and then directly probe the spin current within the Cu75Mn25 layer and the spin dynamics of the Co layer by x-ray magnetic circular dichroism. This element-resolved pump-probe measurement unambiguously identifies the ac spin current in the Cu75Mn25 layer.

  18. Spin-label studies on rat liver and heart plasma membranes: do probe-probe interactions interfere with the measurement of membrane properties?

    PubMed

    Sauerheber, R D; Gordon, L M; Crosland, R D; Kuwahara, M D

    1977-02-24

    The structures of purified rat liver and heart plasma membranes were studied with the 5-nitroxide stearic acid spin probe, I(12,3). ESR spectra were recorded with a 50 gauss field sweep, and also with a new technique which "expands" the spectrum by (1) recording pairs of adjoining peaks with a smaller field sweep and (2) superposing the common peaks. The hyperfine splittings measured from the "expanded" spectra were significantly more precise than those obtained from the "unexpanded" spectra. Both procedures were used to study the effects of various I(12,3) probe concentrations on the spectra of liver and heart membranes, as well as the effects of temperature and CaCl2 additions on the spectra of liver membranes, and revealed the following: The polarity-corrected order parameters of liver (31 degrees) and heart (22 degrees) membranes were found to be independent of the probe concentration, if experimentally-determined low I(12,3)/lipid ratios were employed. The absence of obvious radical-interaction broadening in the unexpanded spectra indicated that "intrinsic" membrane properties may be measured at these low probe/lipid ratios. Here, "intrinsic" properties are defined as those which are measured when probe-probe interactions are negligible, and do not refer to membrane behavior in the absence of a perturbing spin label. At higher I(12,3)/lipid ratios, the order parameters of liver and heart membranes were found to substantially decrease with increasing probe concentration. The increase in the "apparent" fluidity of both membrane systems is attributed to enhanced radical interactions; however, an examination of these spectra (without reference to "low" probe concentration spectra) might incorrectly suggest that radical interactions were absent. For the membrane concentrations employed in these studies, the presence of "liquid-lines" (or "fluid components") in the unexpanded ESR spectra was a convenient marker of high probe concentrations. A thermotropic phase

  19. Probing spin-flip scattering in ballistic nanosystems.

    PubMed

    Zeng, Z M; Feng, J F; Wang, Y; Han, X F; Zhan, W S; Zhang, X-G; Zhang, Z

    2006-09-01

    Because spin-flip length is longer than the electron mean-free path in a metal, past studies of spin-flip scattering are limited to the diffusive regime. We propose to use a magnetic double barrier tunnel junction to study spin-flip scattering in the nanometer sized spacer layer near the ballistic limit. We extract the voltage and temperature dependence of the spin-flip conductance Gs in the spacer layer from magnetoresistance measurements. In addition to spin scattering information including the mean-free path (70 nm) and the spin-flip length (1.0-2.6 microm) at 4.2 K, this technique also yields information on the density of states and quantum well resonance in the spacer layer. PMID:17025839

  20. Reduction process of nitroxyl spin probes used in Overhauser-enhanced magnetic resonance imaging: An ESR study

    NASA Astrophysics Data System (ADS)

    Meenakumari, V.; Jawahar, A.; Premkumar, S.; Benial, A. Milton Franklin

    2016-05-01

    The Electron spin resonance studies on the reduction process of nitroxyl spin probes were carried out for 1mM 14N- labeled nitroxyl radicals in pure water and 1 mM concentration of ascorbic acid as a function of time. The electron spin resonance parameters, such as line width, hyperfine coupling constant, g-factor, signal intensity ratio and rotational correlation time were estimated. The 3-carbamoyl-PROXYL radical has narrowest line width and fast tumbling motion compared with 3-carboxy-PROXYL, 4-methoxy-TEMPO, and 4-acetamido-TEMPO radicals. The half life time and decay rate were estimated for 1mM concentration of 14N- labeled nitroxyl radicals in 1 mM concentration of ascorbic acid. From the results, the 3-carbamoyl-PROXYL has long half life time and high stability compared with 3-carboxy-PROXYL, 4-methoxy-TEMPO and 4-acetamido-TEMPO radicals. Therefore, this study reveals that the 3-carbamoyl-PROXYL radical can act as a good redox sensitive spin probe for Overhauser-enhanced Magnetic Resonance Imaging.

  1. Kit for detecting nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    2001-01-01

    A kit is provided for detecting a target nucleic acid sequence in a sample, the kit comprising: a first hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the first hybridization probe including a first complexing agent for forming a binding pair with a second complexing agent; and a second hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the first hybridization probe does not selectively hybridize, the second hybridization probe including a detectable marker; a third hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the third hybridization probe including the same detectable marker as the second hybridization probe; and a fourth hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the third hybridization probe does not selectively hybridize, the fourth hybridization probe including the first complexing agent for forming a binding pair with the second complexing agent; wherein the first and second hybridization probes are capable of simultaneously hybridizing to the target sequence and the third and fourth hybridization probes are capable of simultaneously hybridizing to the target sequence, the detectable marker is not present on the first or fourth hybridization probes and the first, second, third, and fourth hybridization probes each include a competitive nucleic acid sequence which is sufficiently complementary to a third portion of the target sequence that the competitive sequences of the first, second, third, and fourth hybridization probes compete with each other to hybridize to the third portion of the

  2. Probing variations of the Rashba spin-orbit coupling at the nanometre scale

    NASA Astrophysics Data System (ADS)

    Bindel, Jan Raphael; Pezzotta, Mike; Ulrich, Jascha; Liebmann, Marcus; Sherman, Eugene Ya.; Morgenstern, Markus

    2016-10-01

    As the Rashba effect is an electrically tunable spin-orbit interaction, it could form the basis for a multitude of applications, such as spin filters, spin transistors and quantum computing using Majorana states in nanowires. Moreover, this interaction can determine the spin dephasing and antilocalization phenomena in two dimensions. However, the real space pattern of the Rashba parameter, which critically influences spin transistors using the spin-helix state and the otherwise forbidden electron backscattering in topologically protected channels, is difficult to probe. Here, we map this pattern down to nanometre length scales by measuring the spin splitting of the lowest Landau level using scanning tunnelling spectroscopy. We reveal strong fluctuations correlated with the local electrostatic potential for an InSb inversion layer with a large Rashba coefficient (~1 eV Å). This type of Rashba field mapping enables a more comprehensive understanding of its fluctuations, which might be decisive towards robust semiconductor-based spintronic devices.

  3. Spin pumping through a topological insulator probed by x-ray detected ferromagnetic resonance

    NASA Astrophysics Data System (ADS)

    Figueroa, A. I.; Baker, A. A.; Collins-McIntyre, L. J.; Hesjedal, T.; van der Laan, G.

    2016-02-01

    In the field of spintronics, the generation of a pure spin current (without macroscopic charge flow) through spin pumping of a ferromagnetic (FM) layer opens up the perspective of a new generation of dissipation-less devices. Microwave driven ferromagnetic resonance (FMR) can generate a pure spin current that enters adjacent layers, allowing for both magnetization reversal (through spin-transfer torque) and to probe spin coherence in non-magnetic materials. However, standard FMR is unable to probe multilayer dynamics directly, since the measurement averages over the contributions from the whole system. The synchrotron radiation-based technique of x-ray detected FMR (XFMR) offers an elegant solution to this drawback, giving access to element-, site-, and layer-specific dynamical measurements in heterostructures. In this work, we show how XFMR has provided unique information to understand spin pumping and spin transfer torque effects through a topological insulator (TI) layer in a pseudo-spin valve heterostructure. We demonstrate that TIs function as efficient spin sinks, while also allowing a limited dynamic coupling between ferromagnetic layers. These results shed new light on the spin dynamics of this novel class of materials, and suggest future directions for the development of room temperature TI-based spintronics.

  4. SPIN POLARIZED PHOTOELECTRON SPECTROSCOPY AS A PROBE OF MAGNETIC SYSTEMS.

    SciTech Connect

    JOHNSON, P.D.; GUNTHERODT, G.

    2006-11-01

    Spin-polarized photoelectron spectroscopy has developed into a versatile tool for the study of surface and thin film magnetism. In this chapter, we examine the methodology of the technique and its recent application to a number of different problems. We first examine the photoemission process itself followed by a detailed review of spin-polarization measurement techniques and the related experimental requirements. We review studies of spin polarized surface states, interface states and quantum well states followed by studies of the technologically important oxide systems including half-metallic transition metal oxides, ferromagnet/oxide interfaces and the antiferromagnetic cuprates that exhibit high Tc Superconductivity. We also discuss the application of high-resolution photoemission with spin resolving capabilities to the study of spin dependent self energy effects.

  5. Emergence of robust gaps in two-dimensional antiferromagnets via additional spin-1/2 probes

    SciTech Connect

    Ferreira, Aires; Lopes, J. Viana; Lopes dos Santos, J. M. B.

    2010-08-15

    We study the capacity of antiferromagnetic lattices of varying geometries to entangle two additional spin-1/2 probes. Analytical modeling of the quantum Monte Carlo data shows the appearance of a robust gap, allowing a description of entanglement in terms of probe-only states, even in cases where the coupling to the probes is larger than the gap of the spin lattice and cannot be treated perturbatively. We find a considerable enhancement of the temperature at which probe entanglement disappears as we vary the geometry of the bus and the coupling to the probes. In particular, the square Heisenberg antiferromagnet exhibits the best thermal robustness of all systems, whereas the three-leg ladder chain shows the best performance in the natural quantum ground state.

  6. Probing Spin-Orbit Misalignment Processes Around Early-Type Stars

    NASA Astrophysics Data System (ADS)

    Ahlers, Johnathon; Barnes, Jason W.

    2016-10-01

    Planets in early-type systems seem to frequently misalign from their host star's spin axis. These spin-orbit misaligned systems challenge conventional planet-formation theories because planets probably do not form with initially misaligned orbits -- their angular momenta must be conserved with the stellar nursery in which they formed. In such a case, planets must migrate to their misaligned positions. However, very few transiting exoplanets have had their spin-orbit alignment angles measured. Our model constrains spin-orbit alignment angles via photometry and asteroseismology while accounting for the brightness effects of stellar variability and rapid rotation that commonly occur in early-type stars, making the analysis of hundreds of Kepler transit light curves possible for the first time. We will employ these techniques to probe spin-orbit misalignment theories by empirically testing the spin-orbit state of exoplanets orbiting early-type stars.

  7. Acid properties of solid acid catalysts characterized by solid-state 31P NMR of adsorbed phosphorous probe molecules.

    PubMed

    Zheng, Anmin; Huang, Shing-Jong; Liu, Shang-Bin; Deng, Feng

    2011-09-01

    A brief review is presented on acidity characterization of solid acid catalysts by means of solid-state phosphor-31 magic-angle-spinning nuclear magnetic resonance ((31)P MAS NMR) spectroscopy using phosphor-containing molecules as probes. It is emphasized that such a simple approach using (31)P MAS NMR of adsorbed phosphorous probe molecules, namely trimethylphosphine (TMP) and trialkylphosphine oxides (R(3)PO), represents a unique technique in providing detailed qualitative and quantitative features, viz. type, strength, distribution, and concentration of acid sites in solid acid catalysts. In particular, it will be shown that when applied with a proper choice of probe molecules with varied sizes and results obtained from elemental analysis, the amounts and locations (intracrystalline vs. extracrystalline) of different types (Brønsted vs. Lewis) of acid sites may be determined. In addition, by incorporating the NMR results with that obtained from theoretical density functional theory (DFT) calculations, correlations between the (31)P chemical shifts (δ(31)P) and acidic strengths of Brønsted and Lewis acid sites may also be derived, facilitating a suitable acidity scale for solid acid catalysts.

  8. Detection of atomic spin labels in a lipid bilayer using a single-spin nanodiamond probe

    PubMed Central

    Kaufmann, Stefan; Simpson, David A.; Hall, Liam T.; Perunicic, Viktor; Senn, Philipp; Steinert, Steffen; McGuinness, Liam P.; Johnson, Brett C.; Ohshima, Takeshi; Caruso, Frank; Wrachtrup, Jörg; Scholten, Robert E.; Mulvaney, Paul; Hollenberg, Lloyd

    2013-01-01

    Magnetic field fluctuations arising from fundamental spins are ubiquitous in nanoscale biology, and are a rich source of information about the processes that generate them. However, the ability to detect the few spins involved without averaging over large ensembles has remained elusive. Here, we demonstrate the detection of gadolinium spin labels in an artificial cell membrane under ambient conditions using a single-spin nanodiamond sensor. Changes in the spin relaxation time of the sensor located in the lipid bilayer were optically detected and found to be sensitive to near-individual (4 ± 2) proximal gadolinium atomic labels. The detection of such small numbers of spins in a model biological setting, with projected detection times of 1 s [corresponding to a sensitivity of ∼5 Gd spins per Hz1/2], opens a pathway for in situ nanoscale detection of dynamical processes in biology. PMID:23776230

  9. Determination of partition coefficient of spin probe between different lipid membrane phases.

    PubMed

    Arsov, Zoran; Strancar, Janez

    2005-01-01

    Model lipid membranes made from binary mixtures of dimyristoylphosphatidylcholine/dipalmitoylphosphatidylcholine (DMPC/DPPC) and dimyristoylphosphatidylcholine/cholesterol (DMPC/Chol) exhibit coexistence of diverse lipid phases at appropriate temperature and composition. Since lipids in different phases show different structural and motional properties, it is expected that the corresponding spin probe electron paramagnetic resonance (EPR) spectra will be superposition of several spectral components. From comparison of proportions of spectral components of the EPR spectrum with the fractions of the corresponding lipid phases obtained from known phase diagrams the partition coefficient of spin probe methyl ester of 5-doxyl palmitate between different lipid phases was determined. The results indicate that the used spin probe partitions approximately equally between different phases. PMID:16309270

  10. Diffusion studies on permeable nitroxyl spin probes through bilayer lipid membranes: A low frequency ESR study

    SciTech Connect

    Meenakumari, V.; Benial, A. Milton Franklin; Utsumi, Hideo; Ichikawa, Kazuhiro; Yamada, Ken-ichi; Hyodo, Fuminori; Jawahar, A.

    2015-06-24

    Electron spin resonance (ESR) studies were carried out for permeable 2mM {sup 14}N-labeled deutrated 3 Methoxy carbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl (MC-PROXYL) in pure water and 1mM, 2mM, 3mM, 4mM concentration of 14N-labeled deutrated MC-PROXYL in 400mM concentration of liposomal solution by using a 300 MHz ESR spectrometer. The ESR parameters such as linewidth, hyperfine coupling constant, g-factor, partition parameter and permeability were reported for these samples. The line broadening was observed for the nitroxyl spin probe in the liposomal solution. The line broadening indicates that the high viscous nature of the liposomal solution. The partition parameter and permeability values indicate the maximum diffusion of nitroxyl spin probes in the bilayer lipid membranes at 2 mM concentration of nitroxyl radical. This study illustrates that ESR can be used to differentiate between the intra and extra- membrane water by loading the liposome vesicles with a lipid-permeable nitroxyl spin probe. From the ESR results, the spin probe concentration was optimized as 2mM in liposomal solution for ESR phantom studies/imaging, invivo and invitro experiments.

  11. International conference on spin observables of nuclear probes: Summary talk

    SciTech Connect

    Garvey, G.T.

    1988-01-01

    A selected summary of the presentation and discussions at the 4th Telluride Conference is presented. The summary deals mainly with the effects of nuclear spin and isospin on the interaction between nucleons and their consequences in nuclear structure. 11 figs.

  12. Probing Spin Accumulation induced Magnetocapacitance in a Single Electron Transistor

    PubMed Central

    Lee, Teik-Hui; Chen, Chii-Dong

    2015-01-01

    The interplay between spin and charge in solids is currently among the most discussed topics in condensed matter physics. Such interplay gives rise to magneto-electric coupling, which in the case of solids was named magneto-electric effect, as predicted by Curie on the basis of symmetry considerations. This effect enables the manipulation of magnetization using electrical field or, conversely, the manipulation of electrical polarization by magnetic field. The latter is known as the magnetocapacitance effect. Here, we show that non-equilibrium spin accumulation can induce tunnel magnetocapacitance through the formation of a tiny charge dipole. This dipole can effectively give rise to an additional serial capacitance, which represents an extra charging energy that the tunneling electrons would encounter. In the sequential tunneling regime, this extra energy can be understood as the energy required for a single spin to flip. A ferromagnetic single-electron-transistor with tunable magnetic configuration is utilized to demonstrate the proposed mechanism. It is found that the extra threshold energy is experienced only by electrons entering the islands, bringing about asymmetry in the measured Coulomb diamond. This asymmetry is an unambiguous evidence of spin accumulation induced tunnel magnetocapacitance, and the measured magnetocapacitance value is as high as 40%. PMID:26348794

  13. Conformational dynamics of nucleic acid molecules studied by PELDOR spectroscopy with rigid spin labels

    NASA Astrophysics Data System (ADS)

    Prisner, T. F.; Marko, A.; Sigurdsson, S. Th.

    2015-03-01

    Nucleic acid molecules can adopt a variety of structures and exhibit a large degree of conformational flexibility to fulfill their various functions in cells. Here we describe the use of Pulsed Electron-Electron Double Resonance (PELDOR or DEER) to investigate nucleic acid molecules where two cytosine analogs have been incorporated as spin probes. Because these new types of spin labels are rigid and incorporated into double stranded DNA and RNA molecules, there is no additional flexibility of the spin label itself present. Therefore the magnetic dipole-dipole interaction between both spin labels encodes for the distance as well as for the mutual orientation between the spin labels. All of this information can be extracted by multi-frequency/multi-field PELDOR experiments, which gives very precise and valuable information about the structure and conformational flexibility of the nucleic acid molecules. We describe in detail our procedure to obtain the conformational ensembles and show the accuracy and limitations with test examples and application to double-stranded DNA.

  14. Probing dynamics of a spin ensemble of P1 centers in diamond using a superconducting resonator

    NASA Astrophysics Data System (ADS)

    de Lange, Gijs; Ranjan, Vishal; Schutjens, Ron; Debelhoir, Thibault; Groen, Joost; Szombati, Daniel; Thoen, David; Klapwijk, Teun; Hanson, Ronald; Dicarlo, Leonardo

    2013-03-01

    Solid-state spin ensembles are promising candidates for realizing a quantum memory for superconducting circuits. Understanding the dynamics of such ensembles is a necessary step towards achieving this goal. Here, we investigate the dynamics of an ensemble of nitrogen impurities (P1 centers) in diamond using magnetic-field controlled coupling to the first two modes of a superconducting (NbTiN) coplanar waveguide resonator. Three hyperfine-split spin sub-ensembles are clearly resolved in the 0.25-1.2 K temperature range, with a collective coupling strength extrapolating to 23 MHz at full polarization. The coupling to multiple modes allows us to distinguish the contributions of dipolar broadening and magnetic field inhomogeneity to the spin linewidth. We find the spin polarization recovery rate to be temperature independent below 1 K and conclude that spin out-diffusion across the resonator mode volume provides the mechanism for spin relaxation of the ensemble. Furthermore, by pumping spins in one sub-ensemble and probing the spins in the other sub-ensembles, we observe fast steady-state cross-relaxation (compared to spin repolarization) across the hyperfine transitions. These observations have important implications for using the three sub-ensembles as independent quantum memories. Research supported by NWO, FOM, and EU Project SOLID

  15. Zip nucleic acids are potent hydrolysis probes for quantitative PCR

    PubMed Central

    Paris, Clément; Moreau, Valérie; Deglane, Gaëlle; Voirin, Emilie; Erbacher, Patrick; Lenne-Samuel, Nathalie

    2010-01-01

    Zip nucleic acids (ZNAs) are oligonucleotides conjugated with cationic spermine units that increase affinity for their target. ZNAs were recently shown to enable specific and sensitive reactions when used as primers for polymerase chain reaction (PCR) and reverse-transcription. Here, we report their use as quantitative PCR hydrolysis probes. Ultraviolet duplex melting data demonstrate that attachment of cationic residues to the 3′ end of an oligonucleotide does not alter its ability to discriminate nucleotides nor the destabilization pattern relative to mismatch location in the oligonucleotide sequence. The stability increase provided by the cationic charges allows the use of short dual-labeled probes that significantly improve single-nucleotide polymorphism genotyping. Longer ZNA probes were shown to display reduced background fluorescence, therefore, generating greater sensitivity and signal level as compared to standard probes. ZNA probes thus provide broad flexibility in assay design and also represent an effective alternative to minor groove binder- and locked nucleic-acid-containing probes. PMID:20071749

  16. Highly selective detection of individual nuclear spins with rotary echo on an electron spin probe

    SciTech Connect

    Mkhitaryan, V. V.; Jelezko, F.; Dobrovitski, V. V.

    2015-10-26

    We consider an electronic spin, such as a nitrogen-vacancy center in diamond, weakly coupled to a large number of nuclear spins, and subjected to the Rabi driving with a periodically alternating phase. We show that by switching the driving phase synchronously with the precession of a given nuclear spin, the interaction to this spin is selectively enhanced, while the rest of the bath remains decoupled. The enhancement is of resonant character. The key feature of the suggested scheme is that the width of the resonance is adjustable, and can be greatly decreased by increasing the driving strength. Thus, the resonance can be significantly narrowed, by a factor of 10–100 in comparison with the existing detection methods. Significant improvement in selectivity is explained analytically and confirmed by direct numerical many-spin simulations. As a result, the method can be applied to a wide range of solid-state systems.

  17. Highly selective detection of individual nuclear spins with rotary echo on an electron spin probe

    DOE PAGES

    Mkhitaryan, V. V.; Jelezko, F.; Dobrovitski, V. V.

    2015-10-26

    We consider an electronic spin, such as a nitrogen-vacancy center in diamond, weakly coupled to a large number of nuclear spins, and subjected to the Rabi driving with a periodically alternating phase. We show that by switching the driving phase synchronously with the precession of a given nuclear spin, the interaction to this spin is selectively enhanced, while the rest of the bath remains decoupled. The enhancement is of resonant character. The key feature of the suggested scheme is that the width of the resonance is adjustable, and can be greatly decreased by increasing the driving strength. Thus, the resonancemore » can be significantly narrowed, by a factor of 10–100 in comparison with the existing detection methods. Significant improvement in selectivity is explained analytically and confirmed by direct numerical many-spin simulations. As a result, the method can be applied to a wide range of solid-state systems.« less

  18. Current-induced spin polarization on metal surfaces probed by spin-polarized positron beam

    PubMed Central

    Zhang, H. J.; Yamamoto, S.; Fukaya, Y.; Maekawa, M.; Li, H.; Kawasuso, A.; Seki, T.; Saitoh, E.; Takanashi, K.

    2014-01-01

    Current-induced spin polarization (CISP) on the outermost surfaces of Au, Cu, Pt, Pd, Ta, and W nanoscaled films were studied using a spin-polarized positron beam. The Au and Cu surfaces showed no significant CISP. In contrast, the Pt, Pd, Ta, and W films exhibited large CISP (3~15% per input charge current of 105 A/cm2) and the CISP of Ta and W were opposite to those of Pt and Pd. The sign of the CISP obeys the same rule in spin Hall effect suggesting that the spin-orbit coupling is mainly responsible for the CISP. The magnitude of the CISP is explained by the Rashba-Edelstein mechanism rather than the diffusive spin Hall effect. This settles a controversy, that which of these two mechanisms dominates the large CISP on metal surfaces. PMID:24776781

  19. Spectroscopy of spontaneous spin noise as a probe of spin dynamics and magnetic resonance.

    PubMed

    Crooker, S A; Rickel, D G; Balatsky, A V; Smith, D L

    2004-09-01

    Not all noise in experimental measurements is unwelcome. Certain fundamental noise sources contain valuable information about the system itself-a notable example being the inherent voltage fluctuations (Johnson noise) that exist across any resistor, which allow the temperature to be determined. In magnetic systems, fundamental noise can exist in the form of random spin fluctuations. For example, statistical fluctuations of N paramagnetic spins should generate measurable noise of order N spins, even in zero magnetic field. Here we exploit this effect to perform perturbation-free magnetic resonance. We use off-resonant Faraday rotation to passively detect the magnetization noise in an equilibrium ensemble of paramagnetic alkali atoms; the random fluctuations generate spontaneous spin coherences that precess and decay with the same characteristic energy and timescales as the macroscopic magnetization of an intentionally polarized or driven ensemble. Correlation spectra of the measured spin noise reveal g-factors, nuclear spin, isotope abundance ratios, hyperfine splittings, nuclear moments and spin coherence lifetimes-without having to excite, optically pump or otherwise drive the system away from thermal equilibrium. These noise signatures scale inversely with interaction volume, suggesting a possible route towards non-perturbative, sourceless magnetic resonance of small systems. PMID:15343328

  20. Probing quantum spin glass like system with a double quantum dot

    NASA Astrophysics Data System (ADS)

    Koh, C. Y.; Kwek, L. C.

    2016-06-01

    We study the ground state properties of a 4-qubit spin glass like (SGL) chain with probes at the end of the chain and compare our results with the non-spin glass like (NSGL) case. The SGL is modeled as a spin chain with nearest-neighbor couplings, taking on normal variates with mean J and variance Δ2. The entanglement between the probes is used to detect any discontinuity in the ground state energy spectrum. For the NSGL case, it was found that the concurrence of the probes exhibits sharp transitions whenever there are abrupt changes in the energy spectrum. In particular, for the 4-qubit case, there is a sudden change in the ground state energy at an external magnetic field B of around 0.66 (resulting in a drop in concurrence of the probes) and 1.7 (manifest as a spike). The latter spike persists for finite temperature case. For the SGL sample with sufficiently large Δ, however, the spike is absent. Thus, an absence in the spike could act as a possible signature of the presence of SGL effects. Moreover, the sudden drop in concurrence at B ≈ 0.66 does not disappear but gets smeared with increasing Δ. However, this drop can be accentuated with a smaller probe coupling. The finite temperature case is also briefly discussed.

  1. Electron paramagnetic resonance studies of slowly tumbling vanadyl spin probes in nematic liquid crystals

    NASA Technical Reports Server (NTRS)

    Bruno, G. V.; Harrington, J. K.; Eastman, M. P.

    1978-01-01

    The purposes of this vanadyl spin probe study are threefold: (1) to establish when the breakdown of motionally narrowed formulas occurs; (2) to analyze the experimental vanadyl EPR line shapes by the stochastic Lioville method as developed by Polnaszek et al. (1973) for slow tumbling in an anisotropic liquid; and (3) to compare the vanadyl probe study results with those of Polnaszek and Freed (1975). Spectral EPR line shapes are simulated for experimental spectra of vanadyl acetylacetonate (VOAA) in nematic liquid crystal butyl p-(p-ethoxyphenoxycarbonyl) phenyl carbonate (BEPC) and Phase V of EM laboratories. It is shown that the use of typical vanadyl complexes as spin probes for nematic liquid crystals simplifies the theoretical analysis and the subsequent interpretation. Guidelines for the breakdown of motionally narrowed formulas are established. Both the slow tumbling aspects and the effects of non-Brownian rotation should be resolved in order to extract quantitative information about molecular ordering and rotational mobility.

  2. Probing the thiol-gold planar interface by spin polarized tunneling

    SciTech Connect

    Zhang, Xiaohang; McGill, Stephen A.; Xiong, Peng; Wang, Xiaolei; Zhao, Jianhua

    2014-04-14

    Reports of induced magnetism at thiol-gold interface have generated considerable recent interest. In these studies, the sample magnetization was generally measured by superconducting quantum interference device magnetometry which has limitation in determining surface and interface magnetism. In this work, we have fabricated planar tunnel junctions incorporating a thiol-gold interface. An observed room temperature humidity effect together with low temperature inelastic electron tunneling spectroscopy confirmed the existence of a thiol-gold interface in the organic-inorganic hybrid heterostructure. Spin polarized tunneling measurements were performed to probe the spin polarization at the thiol-gold interface; however, the obtained spin polarized tunneling spectra indicate no measurable spin polarization at the thiol-gold interface.

  3. EPR spin probe investigation of irradiated wheat, rice and sunflower seeds

    NASA Astrophysics Data System (ADS)

    Paktaş, Dilek Dadaylι; Sünnetçiogˇlu, M. Maral

    2007-01-01

    TEMPO and 4-nitro-TEMPO spin probes were used to monitor dose-dependent changes in the EPR spectra of irradiated wheat and rice embryos and sunflower embryo parts. Rice embryos were studied in the 233-293 K temperature range using 4-nitro-TEMPO. TEMPAMINE, TEMPYO and DTBN spin probes were also studied for their applicability in the determination of irradiated seeds. All the recorded spectra were simulated, and spectral parameters and partition of the probes among various domains were determined. Despite the contribution of the signal from extracellular regions, it was possible to detect the changes in the water/lipid ratios with dose. The hydrophilic character of the probe alone was not sufficient to distinguish the different doses of irradiation. Line widths and rotational correlation times of various domains within embryo also play an important role. Partition after dehydration was another measure in the selection of the suitable probes for irradiation studies. Better results were obtained in dehydrated embryos for the probes preferring lipid bodies.

  4. Possible spin frustration in Nd2Ti2O7 probed by muon spin relaxation.

    PubMed

    Guo, Hanjie; Xing, Hui; Tong, Jun; Tao, Qian; Watanabe, Isao; Xu, Zhu-an

    2014-10-29

    Muon spin relaxation on Nd2Ti2O7 (NTO) and NdLaTi2O7 (NLTO) compounds are presented. The time spectra for both compounds are as expected for the paramagnetic state at high temperatures, but deviate from the exponential function below around 100 K. Firstly, the muon spin relaxation rate increases with decreasing temperature and then levels off below around 10 K, which is reminiscent of the frustrated systems. An enhancement of the relaxation rate by a longitudinal field in the paramagnetic state is observed for NTO and eliminated by a magnetic dilution for the NLTO sample. This suggests that the spectral density is modified by a magnetic dilution and thus indicates that the spins behave cooperatively rather than individually. The zero-field measurement at 0.3 K indicates that the magnetic ground state for NTO is ferromagnetic.

  5. Transport through a quantum spin Hall antidot as a spectroscopic probe of spin textures

    NASA Astrophysics Data System (ADS)

    Rod, Alexia; Dolcetto, Giacomo; Rachel, Stephan; Schmidt, Thomas L.

    2016-07-01

    We investigate electron transport through an antidot embedded in a narrow strip of a two-dimensional topological insulator. We focus on the most generic and experimentally relevant case with broken axial spin symmetry. Spin-nonconservation allows additional scattering processes, which change the transport properties profoundly. We start from an analytical model for noninteracting transport, which we also compare with a numerical tight-binding simulation. We then extend this model by including Coulomb repulsion on the antidot, and we study the transport in the Coulomb-blockade limit. We investigate sequential tunneling and cotunneling regimes, and we find that the current-voltage characteristic allows a spectroscopic measurement of the edge-state spin textures.

  6. Detection of nanoscale electron spin resonance spectra demonstrated using nitrogen-vacancy centre probes in diamond

    PubMed Central

    Hall, L. T.; Kehayias, P.; Simpson, D. A.; Jarmola, A.; Stacey, A.; Budker, D.; Hollenberg, L. C. L.

    2016-01-01

    Electron spin resonance (ESR) describes a suite of techniques for characterizing electronic systems with applications in physics, chemistry, and biology. However, the requirement for large electron spin ensembles in conventional ESR techniques limits their spatial resolution. Here we present a method for measuring ESR spectra of nanoscale electronic environments by measuring the longitudinal relaxation time of a single-spin probe as it is systematically tuned into resonance with the target electronic system. As a proof of concept, we extracted the spectral distribution for the P1 electronic spin bath in diamond by using an ensemble of nitrogen-vacancy centres, and demonstrated excellent agreement with theoretical expectations. As the response of each nitrogen-vacancy spin in this experiment is dominated by a single P1 spin at a mean distance of 2.7 nm, the application of this technique to the single nitrogen-vacancy case will enable nanoscale ESR spectroscopy of atomic and molecular spin systems. PMID:26728001

  7. Wet spinning of solid polyamic acid fibers

    NASA Technical Reports Server (NTRS)

    Dorogy, William E., Jr. (Inventor); St.clair, Anne K. (Inventor)

    1991-01-01

    The invention is a process for the production of solid aromatic polyamic acid and polyimide fibers from a wet gel or coagulation bath wet gel using N,N-dimethylacetamide (DMAc) solutions of the polyamic acid derived from aromatic dianhydrides such as 3,3',4,4' benzophenonetetra carboxylic dianhydride (BTDA) and aromatic diamines such as 4,4'-oxydianiline (4,4'-ODA). By utilizing the relationship among coagulation medium and concentration, resin inherent viscosity, resin percent solids, filament diameter, and fiber void content, it is possible to make improved polyamic acid fibers. Solid polyimide fibers, obtained by the thermal cyclization of the polyamic acid precursor, have increased tensile properties compared to fibers containing macropores from the same resin system.

  8. An EPR spin probe method for characterizing changes in the accessible regions of coal upon oxidation

    SciTech Connect

    Sady, W.; Kispert, L.D.; Spears, D.R.

    1992-01-01

    Eight Argonne Premium Coal Samples (APCS) were weathered in air and the structural and chemical changes that upon swelling with toluene and pyridine were, examined by an EPR spin probe method developed in this laboratory. Under mild oxidation conditions and swelling with toluene large structural changes were observed for lignite (Beulah-Zap) which suggested the collapse of the coal structure. This did not occur for higher rank coal. Upon oxidation and swelling with toluene and pyridine an increase occurred in the amino substituted spin probe concentration for coals with the carbon percent above 80%. A maximum was found for the creation of 5 {Angstrom} diameter pores upon swelling with pyridine at 85% C.

  9. An EPR spin probe method for characterizing changes in the accessible regions of coal upon oxidation

    SciTech Connect

    Sady, W.; Kispert, L.D.; Spears, D.R.

    1992-09-01

    Eight Argonne Premium Coal Samples (APCS) were weathered in air and the structural and chemical changes that upon swelling with toluene and pyridine were, examined by an EPR spin probe method developed in this laboratory. Under mild oxidation conditions and swelling with toluene large structural changes were observed for lignite (Beulah-Zap) which suggested the collapse of the coal structure. This did not occur for higher rank coal. Upon oxidation and swelling with toluene and pyridine an increase occurred in the amino substituted spin probe concentration for coals with the carbon percent above 80%. A maximum was found for the creation of 5 {Angstrom} diameter pores upon swelling with pyridine at 85% C.

  10. Swelling behavior of O-alkylated APCS coals as examined by the EPR spin probe method

    SciTech Connect

    Ding, Ruisong; Tucker, D.; Kispert, L.D.

    1995-12-31

    Known O-alkylation procedures have been used to derivatize the carboxyl and hydroxyl groups in the APCS coals Lewiston-Stockton, Wyodak-Anderson, Beulah-Zap, Illinois {number_sign}6, Upper Freeport, and Pittsburgh {number_sign}8. In general the resulting decrease in hydrogen bonding reduced the cyclical variation in nitroxide spin probe retention observed for nonalkylated coals when small amounts (<1%) of pyridine are present in the toluene swelling solvent. An increase in spin probe retention by the O-alkylated coals relative to the underivatized coals indicates a more open arrangement in the coal due to a decrease in attractive forces, confirming that microporosity increases with increasing rank.

  11. ESR studies of the slow tumbling of vanadyl spin probes in nematic liquid crystals

    NASA Technical Reports Server (NTRS)

    Eastman, M. P.; Bruno, G. V.; Lawson, J. O.

    1977-01-01

    ESR line shapes that are appropriate for slowly tumbling vanadyl spin probes in viscous nematic liquid crystals were calculated by the stochastic Liouville method. Because of the symmetry possessed by vanadyl, the analysis and interpretation of these line shapes was simplified considerably. Spectral line shapes agreed well with experimental spectra of VOAcAc in the nematic liquid crystal Phase V and BEPC. Deviations from Brownian rotational diffusion were noted. A slowly fluctuating torque analysis yielded good agreement with the experimental spectra.

  12. Electron spin resonance studies on intact cells and isolated lipid droplets from fatty acid-modified L1210 murine leukemia.

    PubMed

    Simon, I; Burns, C P; Spector, A A

    1982-07-01

    It has been suggested that the formation of cytoplasmic lipid droplets may produce an artifact and be responsible for the differences in membrane physical properties detected in lipid-modified cells using fluorescence polarization or spin label probes. To investigate this, the electron spin resonance spectra of lipid droplets isolated from the cytoplasm of L1210 leukemia cells were compared with spectra obtained from the intact cell. Mice bearing the L1210 leukemia were fed diets containing either 16% sunflower oil or 16% coconut oil in order to modify the fatty acid composition of the tumor. A microsome-rich fraction prepared from L1210 cells grown in animals fed the sunflower oil-rich diet contained more polyenoic fatty acids (52 versus 29%), while microsomes from L1210 cells grown in animals fed the coconut oil-rich diets contained more monoenoic fatty acids (37 versus 12%). The order parameter calculated for lipid droplets labeled with the 5-nitroxystearic acid spin probe was only about one-half that of intact cells, whereas it was similar to that obtained for pure triolein droplets suspended in buffer. Order parameters of the inner hyperfine splittings calculated from the spectra of cells grown in the sunflower oil-fed animals [0.543 +/- 0.001 (S.E.)] were lower than those from the cells grown in animals fed the coconut oil diets (0.555 +/- 0.002) (p less than 0.005). In contrast, the order parameters of the lipid droplets isolated from the cells grown in animals fed sunflower oil (0.303 +/- 0.029) or coconut oil (0.295 +/- 0.021) were not significantly different, indicating that motion of a spin label probe in the highly fluid cytoplasmic lipid droplets is not affected by these types of modifications in cellular fatty acid composition. Therefore, the electron spin resonance changes that are observed in the intact cells cannot be due to localization of the probe in cytoplasmic lipid droplets. These results support the conclusion that the electron spin

  13. Triplet excitons as sensitive spin probes for structure analysis of extended defects in microcrystalline silicon

    NASA Astrophysics Data System (ADS)

    Meier, Christoph; Teutloff, Christian; Behrends, Jan; Bittl, Robert; Astakhov, Oleksandr; Lips, Klaus

    2016-07-01

    Electrically detected magnetic resonance (EDMR) spectroscopy is employed to study the influence of triplet excitons on the photocurrent in state-of-the-art microcrystalline silicon thin-film solar cells. These triplet excitons are used as sensitive spin probes for the investigation of their electronic and nuclear environment in this mixed-phase material. According to low-temperature EDMR results obtained from solar cells with different spins in conduction band tail states nearby, and take part in a spin-dependent recombination process. Our study shows that extended defects such as grain boundaries or stacking faults in the crystalline part of the material act as charge carrier traps that can influence the material conductivity.

  14. Molecular dynamics in rod-like liquid crystals probed by muon spin resonance spectroscopy.

    PubMed

    McKenzie, Iain; Scheuermann, Robert; Sedlak, Kamil; Stoykov, Alexey

    2011-08-01

    Muoniated spin probes were produced by the addition of muonium (Mu) to two rod-like liquid crystals: N-(4-methoxybenzylidene)-4'-n-butylaniline (MBBA) and cholesteryl nonanoate (CN). Avoided level crossing muon spin resonance spectroscopy was used to characterize the muoniated spin probes and to probe dynamics at the molecular level. In MBBA Mu adds predominantly to the carbon of the bridging imine group and the muon and methylene proton hyperfine coupling constants (hfccs) of the resulting radical shift in the nematic phase due to the dipolar hyperfine coupling, the ordering of the molecules along the applied magnetic field and fluctuations about the local director. The amplitude of these fluctuations in in the nematic phase of MBBA is determined from the temperature dependence of the methylene proton hfcc. Mu adds to the double bond of the steroidal ring system of CN and the temperature dependence of the Δ(1) line width provides information about the amplitude of the fluctuations about the local director in the chiral nematic phase and the slow isotropic reorientation in the isotropic phase.

  15. Interaction of poly(ethylene oxide) with the sodium dodecyl sulfate micelle interface studied with nitroxide spin probes

    SciTech Connect

    Kang, Y.S.; Kevan, L. )

    1994-08-04

    Electron spin resonance (ESR) line widths of 5-, 7-, 12-, and 16-doxylstearic acid (x-DSA) and tempo nitroxides versus the concentration of poly(ethylene oxide) (PEO) in sodium dodecyl sulfate (SDS) micelles show different trends. The ESR line widths of 5-, 7-, and 16-DSA increase with increasing concentration of PEO, which is interpreted as due to increasing viscosity in the environment of the nitroxide spin probe. The tempo and 12-DSA line widths were independent of the concentration of PEO. The line width showed the highest value for 5-DSA and the lowest value of tempo. The line width of x-DSA decreases from 5-DSA to a minimum value for 12-DSA and then increases somewhat for 16-DSA. This is interpreted as bending of the alkyl chain to provide different locations for the nitroxide moiety relative to the micelle interface. The relative distances of the nitroxide moiety of [chi]-DSA from deuterated water at the SDS micelle interface was measured by deuterium electron spin echo modulation. The distances increased from 5-DSA to 12-DSA and then decreased for 16-DSA. The interpretation of the DSR line width trend is supported by the deuterium modulation depth trend. 28 refs., 5 figs., 2 tabs.

  16. Antiferromagnetic Spin Coupling between Rare Earth Adatoms and Iron Islands Probed by Spin-Polarized Tunneling.

    PubMed

    Coffey, David; Diez-Ferrer, José Luis; Serrate, David; Ciria, Miguel; de la Fuente, César; Arnaudas, José Ignacio

    2015-01-01

    High-density magnetic storage or quantum computing could be achieved using small magnets with large magnetic anisotropy, a requirement that rare-earth iron alloys fulfill in bulk. This compelling property demands a thorough investigation of the magnetism in low dimensional rare-earth iron structures. Here, we report on the magnetic coupling between 4f single atoms and a 3d magnetic nanoisland. Thulium and lutetium adatoms deposited on iron monolayer islands pseudomorphically grown on W(110) have been investigated at low temperature with scanning tunneling microscopy and spectroscopy. The spin-polarized current indicates that both kind of adatoms have in-plane magnetic moments, which couple antiferromagnetically with their underlying iron islands. Our first-principles calculations explain the observed behavior, predicting an antiparallel coupling of the induced 5d electrons magnetic moment of the lanthanides with the 3d magnetic moment of iron, as well as their in-plane orientation, and pointing to a non-contribution of 4f electrons to the spin-polarized tunneling processes in rare earths. PMID:26333417

  17. Antiferromagnetic Spin Coupling between Rare Earth Adatoms and Iron Islands Probed by Spin-Polarized Tunneling.

    PubMed

    Coffey, David; Diez-Ferrer, José Luis; Serrate, David; Ciria, Miguel; de la Fuente, César; Arnaudas, José Ignacio

    2015-09-03

    High-density magnetic storage or quantum computing could be achieved using small magnets with large magnetic anisotropy, a requirement that rare-earth iron alloys fulfill in bulk. This compelling property demands a thorough investigation of the magnetism in low dimensional rare-earth iron structures. Here, we report on the magnetic coupling between 4f single atoms and a 3d magnetic nanoisland. Thulium and lutetium adatoms deposited on iron monolayer islands pseudomorphically grown on W(110) have been investigated at low temperature with scanning tunneling microscopy and spectroscopy. The spin-polarized current indicates that both kind of adatoms have in-plane magnetic moments, which couple antiferromagnetically with their underlying iron islands. Our first-principles calculations explain the observed behavior, predicting an antiparallel coupling of the induced 5d electrons magnetic moment of the lanthanides with the 3d magnetic moment of iron, as well as their in-plane orientation, and pointing to a non-contribution of 4f electrons to the spin-polarized tunneling processes in rare earths.

  18. Antiferromagnetic Spin Coupling between Rare Earth Adatoms and Iron Islands Probed by Spin-Polarized Tunneling

    PubMed Central

    Coffey, David; Diez-Ferrer, José Luis; Serrate, David; Ciria, Miguel; Fuente, César de la; Arnaudas, José Ignacio

    2015-01-01

    High-density magnetic storage or quantum computing could be achieved using small magnets with large magnetic anisotropy, a requirement that rare-earth iron alloys fulfill in bulk. This compelling property demands a thorough investigation of the magnetism in low dimensional rare-earth iron structures. Here, we report on the magnetic coupling between 4f single atoms and a 3d magnetic nanoisland. Thulium and lutetium adatoms deposited on iron monolayer islands pseudomorphically grown on W(110) have been investigated at low temperature with scanning tunneling microscopy and spectroscopy. The spin-polarized current indicates that both kind of adatoms have in-plane magnetic moments, which couple antiferromagnetically with their underlying iron islands. Our first-principles calculations explain the observed behavior, predicting an antiparallel coupling of the induced 5d electrons magnetic moment of the lanthanides with the 3d magnetic moment of iron, as well as their in-plane orientation, and pointing to a non-contribution of 4f electrons to the spin-polarized tunneling processes in rare earths. PMID:26333417

  19. Pneumatic switched angle spinning NMR probe with capacitively coupled double saddle coil.

    PubMed

    Litvak, Ilya M; Espinosa, Catalina A; Shapiro, Rebecca A; Oldham, Andrew N; Duong, Vincent V; Martin, Rachel W

    2010-10-01

    Switched angle spinning (SAS) experiments can be used for generating isotropic-anisotropic correlations in oriented samples in a single experiment. In order for these methods to become widespread, specialized hardware is required. Here we describe the electronic and mechanical design and performance of a double-resonance SAS probe. Unlike many previous SAS probe implementations, the focus here is on systems where the dipolar couplings are partially averaged by molecular motion. This probe has a moving double saddle coil capacitively coupled to the stationary circuit. Angle switching is accomplished by a steam engine-type pneumatic mechanism. The speed and stability of the switching hardware for SAS experiments are demonstrated using spectra of model compounds. PMID:20673643

  20. Pneumatic switched angle spinning NMR probe with capacitively coupled double saddle coil.

    PubMed

    Litvak, Ilya M; Espinosa, Catalina A; Shapiro, Rebecca A; Oldham, Andrew N; Duong, Vincent V; Martin, Rachel W

    2010-10-01

    Switched angle spinning (SAS) experiments can be used for generating isotropic-anisotropic correlations in oriented samples in a single experiment. In order for these methods to become widespread, specialized hardware is required. Here we describe the electronic and mechanical design and performance of a double-resonance SAS probe. Unlike many previous SAS probe implementations, the focus here is on systems where the dipolar couplings are partially averaged by molecular motion. This probe has a moving double saddle coil capacitively coupled to the stationary circuit. Angle switching is accomplished by a steam engine-type pneumatic mechanism. The speed and stability of the switching hardware for SAS experiments are demonstrated using spectra of model compounds.

  1. Pneumatic switched angle spinning NMR probe with capacitively coupled double saddle coil

    NASA Astrophysics Data System (ADS)

    Litvak, Ilya M.; Espinosa, Catalina A.; Shapiro, Rebecca A.; Oldham, Andrew N.; Duong, Vincent V.; Martin, Rachel W.

    2010-10-01

    Switched angle spinning (SAS) experiments can be used for generating isotropic-anisotropic correlations in oriented samples in a single experiment. In order for these methods to become widespread, specialized hardware is required. Here we describe the electronic and mechanical design and performance of a double-resonance SAS probe. Unlike many previous SAS probe implementations, the focus here is on systems where the dipolar couplings are partially averaged by molecular motion. This probe has a moving double saddle coil capacitively coupled to the stationary circuit. Angle switching is accomplished by a steam engine-type pneumatic mechanism. The speed and stability of the switching hardware for SAS experiments are demonstrated using spectra of model compounds.

  2. Spin-probe ESR study on the entrapment of organic solutes by the nanochannel of MCM-41 in benzene.

    PubMed

    Okazaki, Masaharu; Anandan, Sambandam; Seelan, Sindhu; Nishida, Masakazu; Toriyama, Kazumi

    2007-01-30

    An ESR study has been made on the adsorption of three types of aminoxyl radicals with different substituent groups in the nanochannel of MCM-41 in benzene. In the suspensions of MCM-41, all the aminoxyl radicals, usually called as spin probes, show the ESR spectra composed of two signals: the main broader one from the spin probes trapped in the nanochannel, and a sharp minor signal from those in the bulk. The spin probes adsorbed in the nanochannel retain considerable mobility especially at higher temperatures over 300 K. When fumed silica, having a surface structure similar to that of MCM-41, is employed, on the other hand, the relatively hydrophobic spin probe mainly remains in the bulk, but the hydrophilic one is mostly adsorbed and immobilized rigidly. From these results, the adsorption by the MCM-41 nanochannel in benzene is characterized by medium selectivity and considerable motional allowance to the adsorbate molecule. The mobility of the spin probe in the MCM-41 nanochannel increases and the adsorption efficiency decreases by either of the following changes made to the system: (a) increasing the channel diameter, (b) increasing the hydrophobicity of the spin probe, (c) adding a small amount of 2-propanol in the solution, (d) methylation of the surface OH groups of the nanochannel, and (e) elevating the system temperature. A model of this special type of adsorption has been proposed on the basis of the thermodynamic parameters and the ESR spectra for the modified systems including those with different solvents.

  3. Probing iron spin state by optical absorption in laser-heated diamond anvil cell

    NASA Astrophysics Data System (ADS)

    Lobanov, S.; Goncharov, A. F.; Holtgrewe, N.; Lin, J. F.

    2015-12-01

    Pressure-induced spin-pairing transitions in iron-bearing minerals have been in the focus of geophysical studies1. Modern consensus is that iron spin state in the lower mantle is a complex function of crystal structure, composition, pressure, and temperature. Discontinuities in physical properties of lower mantle minerals have been revealed over the spin transition pressure range, but at room temperature. In this work, we have used a supercontinuum laser source and an intensified CCD camera to probe optical properties of siderite, FeCO3, and post-perovskite, Mg0.9Fe0.1SiO3, across the spin transition in laser-heated diamond anvil cell. Synchronously gating the CCD with the supercontinuum pulses (Fig. 1A) allowed diminishing thermal background to ~8.3*10-4. Utilizing the experimental setup we infer the spin state of ferrous iron in siderite at high pressure and temperature conditions (Fig. 1B). Similar behavior is observed for low spin ferric iron in post-perovskite at 130 GPa indicating that all iron in post-perovskite is high spin at lower mantle conditions. Also, our experimental setup holds promise for measuring radiative thermal conductivity of mantle minerals at relevant mantle conditions. Figure 1. (A) Timing of the optical absorption measurements at high temperature. (B) High temperature siderite absorption spectra at 45 GPa. Before heating and quenched after 1300 K spectra are shown in light and dark blue, respectively. Green and red curves are absorption spectra at 1200 K and 1300 K, respectively. Spectra shown in black represent room temperature absorption data on HS (43 GPa) and LS (45.5 GPa) siderite after Lobanov et al., 2015, shown for comparison.

  4. Probing long-range carrier-pair spin–spin interactions in a conjugated polymer by detuning of electrically detected spin beating

    PubMed Central

    van Schooten, Kipp J.; Baird, Douglas L.; Limes, Mark E.; Lupton, John M.; Boehme, Christoph

    2015-01-01

    Weakly coupled electron spin pairs that experience weak spin–orbit interaction can control electronic transitions in molecular and solid-state systems. Known to determine radical pair reactions, they have been invoked to explain phenomena ranging from avian magnetoreception to spin-dependent charge-carrier recombination and transport. Spin pairs exhibit persistent spin coherence, allowing minute magnetic fields to perturb spin precession and thus recombination rates and photoreaction yields, giving rise to a range of magneto-optoelectronic effects in devices. Little is known, however, about interparticle magnetic interactions within such pairs. Here we present pulsed electrically detected electron spin resonance experiments on poly(styrene-sulfonate)-doped poly(3,4-ethylenedioxythiophene) (PEDOT:PSS) devices, which show how interparticle spin–spin interactions (magnetic-dipolar and spin-exchange) between charge-carrier spin pairs can be probed through the detuning of spin-Rabi oscillations. The deviation from uncoupled precession frequencies quantifies both the exchange (<30 neV) and dipolar (23.5±1.5 neV) interaction energies responsible for the pair's zero-field splitting, implying quantum mechanical entanglement of charge-carrier spins over distances of 2.1±0.1 nm. PMID:25868686

  5. Hybrid molecular probe for nucleic acid analysis in biological samples.

    PubMed

    Yang, Chaoyong James; Martinez, Karen; Lin, Hui; Tan, Weihong

    2006-08-01

    The ability to detect changes in gene expression, especially in real-time and with sensitivity sufficient enough to monitor small variations in a single-cell, will have considerable value in biomedical research and applications. Out of the many available molecular probes for intracellular monitoring of nucleic acids, molecular beacon (MB) is the most frequently used probe with the advantages of high sensitivity and selectivity. However, any processes in which the MB stem-loop structure is broken will result in a restoration of the fluorescence in MB. This brings in a few possibilities for false positive signal such as nuclease degradation, protein binding, thermodynamic fluctuation, solution composition variations (such as pH, salt concentration) and sticky-end pairing. These unwanted processes do exist inside living cells, making nucleic acid monitoring inside living cells difficult. We have designed and synthesized a hybrid molecular probe (HMP) for intracellular nucleic acid monitoring to overcome these problems. HMP has two DNA probes, one labeled with a donor and the other an acceptor. The two DNA probes are linked by a poly(ethylene glycol) (PEG) linker, with each DNA being complementary to adjacent areas of a target sequence. Target binding event brings the donor and acceptor in proximity, resulting in quenching of the donor fluorescence and enhancement of the acceptor emission. The newly designed HMP has high sensitivity, selectivity, and fast hybridization kinetics. The probe is easy to design and synthesize. HMP does not generate any false positive signal upon digestion by nuclease, binding by proteins, forming complexes by sticky-end pairing, or by other molecular interaction processes. HMP is capable of selectively detecting nucleic acid targets from cellular samples.

  6. Effects of azole treatments on the physical properties of Candida albicans plasma membrane: a spin probe EPR study.

    PubMed

    Sgherri, Cristina; Porta, Amalia; Castellano, Sabrina; Pinzino, Calogero; Quartacci, Mike F; Calucci, Lucia

    2014-01-01

    EPR spectroscopy was applied to investigate the effects of the treatment of Candida albicans cells with fluconazole (FLC) and two newly synthesized azoles (CPA18 and CPA109), in a concentration not altering yeast morphology, on the lipid organization and dynamics of the plasma membrane. Measurements were performed in the temperature range between 0°C and 40°C using 5-doxyl- (5-DSA) and 16-doxyl- (16-DSA) stearic acids as spin probes. 5-DSA spectra were typical of lipids in a highly ordered environment, whereas 16-DSA spectra consisted of two comparable components, one corresponding to a fluid bulk lipid domain in the membrane and the other to highly ordered and motionally restricted lipids interacting with integral membrane proteins. A line shape analysis allowed the relative proportion and the orientational order and dynamic parameters of the spin probes in the different environments to be determined. Smaller order parameters, corresponding to a looser lipid packing, were found for the treated samples with respect to the control one in the region close to the membrane surface probed by 5-DSA. On the other hand, data on 16-DSA indicated that azole treatments hamper the formation of ordered lipid domains hosting integral proteins and/or lead to a decrease in integral protein content in the membrane. The observed effects are mainly ascribable to the inhibition of ergosterol biosynthesis by the antifungal agents, although a direct interaction of the CPA compounds with the membrane bilayer in the region close to the lipid polar head groups cannot be excluded. PMID:24184423

  7. Localized excitation of magnetostatic surface spin waves in yttrium iron garnet by shorted coaxial probe detected via spin pumping and rectification effect

    SciTech Connect

    Soh, Wee Tee Ong, C. K.; Peng, Bin

    2015-04-21

    We demonstrate the localized excitation and dc electrical detection of magnetostatic surface spin waves (MSSWs) in yttrium iron garnet (YIG) by a shorted coaxial probe. Thin films of NiFe and Pt are patterned at different regions onto a common bulk YIG substrate. A shorted coaxial probe is used to excite spin precession locally near various patterned regions. The dc voltages across the corresponding regions are recorded. For excitation of the Pt regions, the dc voltage spectra are dominated by the spin pumping of MSSWs from YIG, where various modes can be clearly distinguished. For the NiFe region, it is also found that spin pumping from MSSWs generated in YIG dominated the spectra, indicating that the spin pumped currents are dissipated into charge currents via the inverse Spin Hall effect (ISHE) in NiFe. For all regions, dc signals from YIG MSSWs are observed to be much stronger than the ferromagnetic resonance (FMR) uniform mode, likely due to the nature of the microwave excitation. The results indicate the potential of this probe for microwave imaging via dc detection of spin dynamics in continuous and patterned films.

  8. Gyroscope spin axis direction control for the Gravity Probe B satellite

    NASA Astrophysics Data System (ADS)

    Bencze, William Joseph

    The Gravity Probe B Relativity Experiment (GP-B) is a joint NASA/Stanford University orbiting astrophysics experiment, under development, to test two predictions of Einstein's theory of general relativity, the geodetic and frame-dragging effects, using orbiting, ultra-precise, mechanical, electrically-suspended gyroscopes (ESVG) carefully isolated from Newtonian torques. General relativity predicts that the gyroscopes' spin axes will precess with respect to a distant inertial reference frame at a rate of 6.6 arc-sec/year for the geodetic effect, and 42 marc-sec/year due to frame-dragging in the planned orbit. To achieve the needed levels of measurement precision, the gyroscopes' axes must be aligned to within 10 arc-sec of the line-of-sight to a distant guide star. Presented is a technique by which the initial orientation of each gyroscope can be controlled through the use of residual torques generated by the gyroscope' s electrostatic suspension system. The electrostatic torques acting on the gyroscope depend on the rotor shape, which is nominally spherical but also contains small manufacturing asphericities and a spin-induced bulge. These torques are averaged by rotor spin to take on a simple form: they cause the gyroscope to precess about the suspension electrode axes. Orientation control torques are applied by introducing additional suspension voltages to the electrodes in combinations which do not exert a force on the gyroscope, but do generate a torque. A control system was developed to use these torques to drive the spin axis to a desired orientation in minimum-time using a bang-bang actuation scheme. A net torque identification scheme was also created to monitor polhode-induced modulations of the spin-averaged torques. This information was used by the orientation control system to keep the spin axis on a minimum-time trajectory. Laboratory experiments confirmed the validity of the spin-averaged torque models and gave a proof-of-principle of the

  9. Designer nucleic acids to probe and program the cell.

    PubMed

    Krishnan, Yamuna; Bathe, Mark

    2012-12-01

    Recent advances in nucleic acid sequencing, structural, and computational technologies have resulted in dramatic progress in our understanding of nucleic acid structure and function in the cell. This knowledge, together with the predictable base-pairing of nucleic acids and powerful synthesis and expression capabilities now offers the unique ability to program nucleic acids to form precise 3D architectures with diverse applications in synthetic and cell biology. The unique modularity of structural motifs that include aptamers, DNAzymes, and ribozymes, together with their well-defined construction rules, enables the synthesis of functional higher-order nucleic acid complexes from these subcomponents. As we illustrate here, these highly programmable, smart complexes are increasingly enabling researchers to probe and program the cell in a sophisticated manner that moves well beyond the use of nucleic acids for conventional genetic manipulation alone.

  10. Advanced slow-magic angle spinning probe for magnetic resonance imaging and spectroscopy

    DOEpatents

    Wind, Robert A.; Hu, Jian Zhi; Minard, Kevin R.; Rommereim, Donald N.

    2006-01-24

    The present invention relates to a probe and processes useful for magnetic resonance imaging and spectroscopy instruments. More particularly, the invention relates to a MR probe and processes for obtaining resolution enhancements of fluid objects, including live specimens, using an ultra-slow (magic angle) spinning (MAS) of the specimen combined with a modified phase-corrected magic angle turning (PHORMAT) pulse sequence. Proton NMR spectra were measured of the torso and the top part of the belly of a female BALBc mouse in a 2T field, while spinning the animal at a speed of 1.5 Hz. Results show that even in this relatively low field with PHORMAT, an isotropic spectrum is obtained with line widths that are a factor 4.6 smaller than those obtained in a stationary mouse. Resolution of 1H NMR metabolite spectra are thus significantly enhanced. Results indicate that PHORMAT has the potential to significantly increase the utility of 1H NMR spectroscopy for in vivo biochemical, biomedical and/or medical applications involving large-sized biological objects such as mice, rats and even humans within a hospital setting. For small-sized objects, including biological objects, such as excised tissues, organs, live bacterial cells, and biofilms, use of PASS at a spinning rate of 30 Hz and above is preferred.

  11. Optical probe of spin-orbit fields in metallic magnetic structures

    NASA Astrophysics Data System (ADS)

    Montazeri, Mohammad; Upadhyaya, Pramey; Yu, Guoqiang; Wong, Kin L.; Lang, Murong; Fan, Yabin; Khalili Amiri, Pedram; Schwartz, Robert N.; Wang, Kang L.

    2015-03-01

    We report a novel self-consistent optical approach based on magneto-optical Kerr effect to directly and quantitatively probe the spin-orbit fields of magnetic devices with 1um diffraction limited spatial resolution. The optical probe is exemplified by investigating the spin-orbit fields in a magnetic stack of Ta(5 nm)/CoFeB(1.1 nm)/MgO(2.0 nm)/TaOx with enhanced perpendicular anisotropy. Both field-like and damping-like contributions were measured independently and their coefficients are quantified at 3 . 3 ×10-6 and - 2 . 0 ×10-6 Oe / A . cm-2 respectively. A detailed comparison with standard transport technique is presented in which a very good agreement were found. Our results establish the relevance of the optical methods for studying spin-orbit torque related physics. We acknowledge the support from the National Science Foundation (DMR-1411085) and the FAME Center, one of the six centers of STARnet, a Semiconductor Research Corporation program sponsored by MARCO and DARPA.

  12. Probing ultrafast spin dynamics through a magnon resonance in the antiferromagnetic multiferroic HoMnO3

    NASA Astrophysics Data System (ADS)

    Bowlan, P.; Trugman, S. A.; Bowlan, J.; Zhu, J.-X.; Hur, N. J.; Taylor, A. J.; Yarotski, D. A.; Prasankumar, R. P.

    2016-09-01

    We demonstrate an approach for directly tracking antiferromagnetic (AFM) spin dynamics by measuring ultrafast changes in a magnon resonance. We test this idea on the multiferroic HoMnO3 by optically photoexciting electrons, after which changes in the spin order are probed with a THz pulse tuned to a magnon resonance. This reveals a photoinduced change in the magnon line shape that builds up over 5-12 picoseconds, which we show to be the spin-lattice thermalization time, indicating that electrons heat the spins via phonons. We compare our results to previous studies of spin-lattice thermalization in ferromagnetic manganites, giving insight into fundamental differences between the two systems. Our work sheds light on the microscopic mechanism governing spin-phonon interactions in AFMs and demonstrates a powerful approach for directly monitoring ultrafast spin dynamics.

  13. Probing the Migration Histories of Exoplanets Through Measurements of Their Spin-Orbit Alignments

    NASA Astrophysics Data System (ADS)

    Addison, Brett Christopher; Tinney, Chris; Wright, Duncan; Bayliss, Daniel

    2015-08-01

    The discovery of giant planets orbiting <0.1AU of their host star was one of the most unexpected results of early exoplanetary science. The widely accepted core-accretion model of planet formation predicts that giant planets should form several AU from their star (beyond the ice line) and on nearly coplanar orbits that are well aligned to the spin axis of their host star. However, a significant fraction of short period Jovian planets are found on substantially misaligned orbits, suggesting that the migration mechanisms producing Hot Jupiters are also misaligning their orbits.Therefore, to probe the processes involved in the formation and migration of exoplanets, we have measured the sky-projected spin-orbit angles (i.e., the angle, λ, between the spin angular momentum vector of a host star and the orbital angular momentum vector of its planet) of four Hot Jupiter systems using the Rossiter-McLaughlin effect. Our Exoplanetary Science at UNSW group is utilizing the new CYCLOPS2 fibre feed on the Anglo-Australian Telescope to carry out high precision Doppler observations of southern hemisphere transiting systems, including spin-orbit alignment data for these systems.We have found that WASP-79b is in a significantly misaligned, nearly polar orbit. HATS-3b and two additional systems we studied are consistent with being on aligned orbits. I will discuss how these spin-orbit alignment measurements are set to become even more critical for exoplanetary science in the years ahead, as K2 and TESS discover much larger numbers of transiting systems bright enough for Rossiter-McLaughlin observations on current telescopes. I will highlight the importance for carrying out additional spin-orbit measurements of suitable systems that belong to the least explored parameter space, which includes sub-Jovian, long-period, and multi-planet systems, to help to elucidate the complex formation and evolution mechanisms of exoplanets.

  14. Spectral functions in a magnetic field as a probe of spin-charge separation

    NASA Astrophysics Data System (ADS)

    Rabello, Silvio; Si, Qimiao

    2001-03-01

    We show that the single-particle spectral functions in a magnetic field can be used to probe spin-charge separation[1]. For concreteness our discussion will be focused on the Luttinger liquid, but our idea is applicable to spin-charge separated metals in general. We will show two types of manifestations of spin-charge separation. For the energy dispersion away from the Fermi momentum, the magnetic field splits both the spinon peak and holon peak; here the spin-charge separation nature is reflected in the different magnitude of the two splittings. For the energy dispersion at the Fermi momentum, the magnetic field splits the zero-field peak into FOUR peaks. The effect of a magnetic field on the momentum dispersion, on the other hand, is very different. Either at or away from the Fermi energy, the magnetic field splits the zero-field peak into only two peaks; the magnitude of the splittings of the spinon and holon peaks is always the same. The contrast between the energy dispersion and momentum dispersion reflects the generic physics that the magnetic field causes as main effect the splitting of the spinon Fermi momentum. Finally, we will discuss the feasibility of studying this effect using angle-resolved photoemission and momentum-resolved tunneling[2]. [1] S. Rabello and Q. Si, cond-mat/0008065. [2]S. A. Grigera, S. Rabello et al, in preparation; A. Altland et al. Phys. Rev. Lett. 83, 1203 (1999).

  15. Luminescent Probes for Ultrasensitive Detection of Nucleic Acids

    PubMed Central

    Krasnoperov, Lev N.; Marras, Salvatore A.E.; Kozlov, Maxim; Wirpsza, Laura; Mustaev, Arkady

    2010-01-01

    Novel amino-reactive derivatives of lanthanide-based luminescent labels of enhanced brightness and metal retention were synthesized and used for the detection of complementary DNA oligonucleotides by molecular beacons. Time-resolved acquisition of the luminescent signal that occurs upon hybridization of the probe to the target enabled the avoidance of short-lived background fluorescence, markedly enhancing the sensitivity of detection, which was less than 1 pM. This value is about 50 to 100 times more sensitive than the level achieved with conventional fluorescence-based molecular beacons, and is 10 to 60 times more sensitive than previously reported for other lanthanide-based hybridization probes. These novel luminescent labels should significantly enhance the sensitivity of all type of nucleic acid hybridization probes, and could dramatically improve the detection limit of other biopolymers and small compounds that are used in a variety of biological applications. PMID:20085336

  16. Probing dynamics of fusion reactions through cross-section and spin distribution measurement

    NASA Astrophysics Data System (ADS)

    Kaur, Maninder; Behera, B. R.; Singh, Gulzar; Singh, Varinderjit; Madhavan, N.; Muralithar, S.; Nath, S.; Gehlot, J.; Mohanto, G.; Mukul, Ish; Siwal, D.; Thakur, M.; Kapoor, K.; Sharma, P.; Banerjee, T.; Jhingan, A.; Varughese, T.; Bala, Indu; Nayak, B. K.; Saxena, A.; Chatterjee, M. B.; Stevenson, P. D.

    2016-05-01

    Present work aims to explicate the effect of entrance channel mass asymmetry on fusion dynamics for the Compound Nucleus 80Sr populated through two different channels, 16O+64Zn and 32S+48Ti, using cross-section and spin distribution measurements as probes. The evaporation spectra studies for these systems, reported earlier indicate the presence of dynamical effects for mass symmetric 32S+48Ti system.The CCDEF and TDHF calculations have been performed for both the systems and an attempt has been made to explain the reported deviations in the α-particle spectrum for the mass symmetric system.

  17. Nanoscale magnetic field mapping with a single spin scanning probe magnetometer

    SciTech Connect

    Rondin, L.; Tetienne, J.-P.; Spinicelli, P.; Roch, J.-F.; Jacques, V.; Dal Savio, C.; Karrai, K.; Dantelle, G.; Thiaville, A.; Rohart, S.

    2012-04-09

    We demonstrate quantitative magnetic field mapping with nanoscale resolution, by applying a lock-in technique on the electron spin resonance frequency of a single nitrogen-vacancy defect placed at the apex of an atomic force microscope tip. In addition, we report an all-optical magnetic imaging technique which is sensitive to large off-axis magnetic fields, thus extending the operation range of diamond-based magnetometry. Both techniques are illustrated by using a magnetic hard disk as a test sample. Owing to the non-perturbing and quantitative nature of the magnetic probe, this work should open up numerous perspectives in nanomagnetism and spintronics.

  18. Evaluation of glucose-linked nitroxide radicals for use as an in vivo spin-label probe.

    PubMed

    Sato, Shingo; Yamaguchi, Masaki; Nagai, Akio; Onuma, Ryo; Saito, Misaki; Sugawara, Rina; Shinohara, Sayaka; Okabe, Eriko; Ito, Tomohiro; Ogata, Tateaki

    2014-04-24

    In vivo incorporation and reduction abilities of 4-carboxy-2,2,6,6-tetramethylpiperidine-1-oxyl (4-carboxy-TEMPO) (1), 3-carboxy-2,2,5,5-tetramethylpyrroline-1-oxyl (3-carboxy-dehydro-PROXYL, 3-carboxy-DPRO) (2), 4-hydroxy-TEMPO and 3-hydroxymethyl-DPRO O-β-D-glucosides (3 and 5), and newly designed forms of 6-O-(TEMPO-4-carbonyl and DPRO-3-carbonyl)-D-glucose (4 and 6) were evaluated using white radish sprouts. For each of these compounds, electron spin resonance (ESR) spectrometry was used to measure two effects: the rate of in vitro reduction via the addition of ascorbic acid; and, the rate of successful incorporation into radish sprouts for a reduction to the corresponding hydroxyl amine. DPRO-radicals 2, 5, and 6 were detected significantly more than TEMPO-radicals 1, 3, and 4 in vitro and in vivo for both experiments. Four glucose-linked nitroxide radicals were reduced faster than the glucose-non-linked ones in the in vitro experiment, but were nonetheless detected more each time in radish sprouts due to the absorbability. Glucose ester-linked radicals 4 and 6 were detected more than glycosides 3 and 5, which suggests that glucose ester-linked DPRO-radical 6 is the best for use as a spin-label probe that a plant will incorporate.

  19. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids

    PubMed Central

    Tangprasertchai, Narin S.; Zhang, Xiaojun; Ding, Yuan; Tham, Kenneth; Rohs, Remo; Haworth, Ian S.; Qin, Peter Z.

    2015-01-01

    The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve “correct” all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements. PMID:26477260

  20. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids.

    PubMed

    Tangprasertchai, Narin S; Zhang, Xiaojun; Ding, Yuan; Tham, Kenneth; Rohs, Remo; Haworth, Ian S; Qin, Peter Z

    2015-01-01

    The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve "correct" all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements. PMID:26477260

  1. Parametric Harmonic Generation as a Probe of Unconstrained Spin Magnetization Precession in the Shallow Barrier Limit.

    PubMed

    Capua, Amir; Rettner, Charles; Parkin, Stuart S P

    2016-01-29

    We study the parametric excitation of high orders of magnetization precession in ultrathin films having perpendicular magnetic anisotropy. We observe that for a given driving field amplitude the harmonic generation can be increased by lowering the barrier with the application of an in-plane magnetic field in the manner of the Smit-Beljers effect. In this effect, the magnetic stiffness is reduced not by lowering the magnitude of the magnetic field upon which the spins precess, but rather by effectively releasing the field's "anchoring" point. This results in a shallow energy barrier where the electrons' spin is locally unconstrained. While the observation is unveiled in the form of nonlinear high harmonic generation, we believe that the physics whereby the barrier is suppressed by an external magnetic field may apply to other phenomena associated with ultrathin films. In these cases, such unconstrained motion may serve as a sensitive probe of the torques associated with proximate spin currents. Moreover, our approach may be used as a model system for the study of phase transitions in the field of nonlinear dynamics.

  2. Probing the spin of the central black hole in the Galactic Centre with secondary images

    NASA Astrophysics Data System (ADS)

    Jørgensen, Jonas Helboe; Bjælde, Ole Eggers; Hannestad, Steen

    2016-06-01

    This paper explores the possibility of determining the spin of the supermassive black hole (SMBH) in Sgr A* by using secondary images of stars orbiting the SMBH. The photons propagate close to the SMBH and their trajectories probe the space-time in a region where the spin of the SMBH is important. We find the appearance of spikes in the secondary image, which depends on the angular momentum and spin axis of the SMBH and study the specific case of the star S2 in detail. The spikes have a magnitude of ˜29 in the K band and the required angular resolution is of the order of 15-20 μas. The combination of these two requirements poses an extreme observational challenge, but might be possible with interferometric observations in the sub-mm regime. The next possible time frame for observing this effect on the star S2 is in the late 2017 and then it repeats with the period of the star.

  3. Diffusion studies on permeable nitroxyl spin probe through lipid bilayer membrane

    SciTech Connect

    Benial, A. Milton Franklin; Meenakumari, V.; Ichikawa, Kazuhiro; Yamada, Ken-ichi; Utsumi, Hideo; Hyodo, Fuminori; Jawahar, A.

    2014-04-24

    Electron spin resonance (ESR) studies were carried out for 2mM {sup 14}N labeled deutrated permeable 3- methoxycarbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl (MC-PROXYL) in pure water, 1 mM, 2 mM, 3 mM and 4 mM concentration of MC-PROXYL in 300 mM concentration of liposomal solution by using a L-band ESR spectrometer. The ESR parameters such as linewidth, hyperfine coupling constant, g-factor, partition parameter and permeability were reported. The partition parameter and permeability values indicate the maximum spin distribution in the lipid phase at 2 mM concentration. This study illustrates that ESR can be used to differentiate between the intra and extra-membrane water by loading the liposome vesicles with a lipid-permeable nitroxyl spin probe. From the ESR results, the radical concentration was optimized as 2 mM in liposomal solution for ESR phantom studies and experiments.

  4. Parametric Harmonic Generation as a Probe of Unconstrained Spin Magnetization Precession in the Shallow Barrier Limit.

    PubMed

    Capua, Amir; Rettner, Charles; Parkin, Stuart S P

    2016-01-29

    We study the parametric excitation of high orders of magnetization precession in ultrathin films having perpendicular magnetic anisotropy. We observe that for a given driving field amplitude the harmonic generation can be increased by lowering the barrier with the application of an in-plane magnetic field in the manner of the Smit-Beljers effect. In this effect, the magnetic stiffness is reduced not by lowering the magnitude of the magnetic field upon which the spins precess, but rather by effectively releasing the field's "anchoring" point. This results in a shallow energy barrier where the electrons' spin is locally unconstrained. While the observation is unveiled in the form of nonlinear high harmonic generation, we believe that the physics whereby the barrier is suppressed by an external magnetic field may apply to other phenomena associated with ultrathin films. In these cases, such unconstrained motion may serve as a sensitive probe of the torques associated with proximate spin currents. Moreover, our approach may be used as a model system for the study of phase transitions in the field of nonlinear dynamics. PMID:26871356

  5. Spin-probes designed for measuring the intrathylakoid pH in chloroplasts.

    PubMed

    Tikhonov, Alexander N; Agafonov, Roman V; Grigor'ev, Igor A; Kirilyuk, Igor A; Ptushenko, Vasilii V; Trubitsin, Boris V

    2008-03-01

    Nitroxide radicals are widely used as molecular probes in different fields of chemistry and biology. In this work, we describe pH-sensitive imidazoline- and imidazolidine-based nitroxides with pK values in the range 4.7-7.6 (2,2,3,4,5,5-hexamethylperhydroimidazol-1-oxyl, 4-amino-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-1-oxyl, 4-dimethylamino-2,2-diethyl-5,5-dimethyl-2,5-dihydro-1H-imidazol-1-oxyl, and 2,2-diethyl-5,5-dimethyl-4-pyrrolidyline-1-yl-2,5-dihydro-1H-imidazol-1-oxyl), which allow the pH-monitoring inside chloroplasts. We have demonstrated that EPR spectra of these spin-probes localized in the thylakoid lumen markedly change with the light-induced acidification of the thylakoid lumen in chloroplasts. Comparing EPR spectrum parameters of intrathylakoid spin-probes with relevant calibrating curves, we could estimate steady-state values of lumen pHin established during illumination of chloroplasts with continuous light. For isolated bean (Vicia faba) chloroplasts suspended in a medium with pHout=7.8, we found that pHin approximately 5.4-5.7 in the state of photosynthetic control, and pHin approximately 5.7-6.0 under photophosphorylation conditions. Thus, ATP synthesis occurs at a moderate acidification of the thylakoid lumen, corresponding to transthylakoid pH difference DeltapH approximately 1.8-2.1. These values of DeltapH are consistent with a point of view that under steady-state conditions the proton gradient DeltapH is the main contributor to the proton motive force driving the operation of ATP synthesis, provided that stoichiometric ratio H+/ATP is n> or =4-4.7.

  6. Synthesis of kojic acid derivatives as secondary binding site probes of D-amino acid oxidase

    PubMed Central

    Raje, Mithun; Hin, Niyada; Duvall, Bridget; Ferraris, Dana V.; Berry, James F.; Thomas, Ajit G.; Alt, Jesse; Rojas, Camilo; Slusher, Barbara S.; Tsukamoto, Takashi

    2013-01-01

    A series of kojic acid (5-hydroxy-2-hydroxymethyl-4H-pyran-4-one) derivatives were synthesized and tested for their ability to inhibit D-amino acid oxidase (DAAO). Various substituents were incorporated into kojic acid at its 2-hydroxymethyl group. These analogs serve as useful molecular probes to explore the secondary binding site, which can be exploited in designing more potent DAAO inhibitors. PMID:23683589

  7. Spin-exchange relaxation-free magnetometer with nearly parallel pump and probe beams

    DOE PAGES

    Karaulanov, Todor; Savukov, Igor; Kim, Young Jin

    2016-03-22

    We constructed a spin-exchange relaxation-free (SERF) magnetometer with a small angle between the pump and probe beams facilitating a multi-channel design with a flat pancake cell. This configuration provides almost complete overlap of the beams in the cell, and prevents the pump beam from entering the probe detection channel. By coupling the lasers in multi-mode fibers, without an optical isolator or field modulation, we demonstrate a sensitivity of 10 fTmore » $$/\\sqrt{\\text{Hz}}$$ for frequencies between 10 Hz and 100 Hz. In addition to the experimental study of sensitivity, we present a theoretical analysis of SERF magnetometer response to magnetic fields for small-angle and parallel-beam configurations, and show that at optimal DC offset fields the magnetometer response is comparable to that in the orthogonal-beam configuration. Based on the analysis, we also derive fundamental and probe-limited sensitivities for the arbitrary non-orthogonal geometry. The expected practical and fundamental sensitivities are of the same order as those in the orthogonal geometry. As a result, we anticipate that our design will be useful for magnetoencephalography (MEG) and magnetocardiography (MCG) applications.« less

  8. Cryogenic sample exchange NMR probe for magic angle spinning dynamic nuclear polarization

    PubMed Central

    Barnes, Alexander B.; Mak-Jurkauskas, Melody L.; Matsuki, Yoh; Bajaj, Vikram S.; van der Wel, Patrick C. A.; DeRocher, Ronald; Bryant, Jeffrey; Sirigiri, Jagadishwar R.; Temkin, Richard J.; Lugtenburg, Johan; Herzfeld, Judith; Griffin, Robert G.

    2009-01-01

    We describe a cryogenic sample exchange system that dramatically improves the efficiency of magic angle spinning (MAS) dynamic nuclear polarization (DNP) experiments by reducing the time required to change samples and by improving long-term instrument stability. Changing samples in conventional cryogenic MAS DNP/NMR experiments involves warming the probe to room temperature, detaching all cryogenic, RF, and microwave connections, removing the probe from the magnet, replacing the sample, and reversing all the previous steps, with the entire cycle requiring a few hours. The sample exchange system described here — which relies on an eject pipe attached to the front of the MAS stator and a vacuum jacketed dewar with a bellowed hole — circumvents these procedures. To demonstrate the excellent sensitivity, resolution, and stability achieved with this quadruple resonance sample exchange probe, we have performed high precision distance measurements on the active site of the membrane protein bacteriorhodopsin. We also include a spectrum of the tripeptide N-f-MLF-OH at 100 K which shows 30 Hz linewidths. PMID:19356957

  9. Spin-exchange relaxation-free magnetometer with nearly parallel pump and probe beams

    NASA Astrophysics Data System (ADS)

    Karaulanov, Todor; Savukov, Igor; Kim, Young Jin

    2016-05-01

    We constructed a spin-exchange relaxation-free (SERF) magnetometer with a small angle between the pump and probe beams facilitating a multi-channel design with a flat pancake cell. This configuration provides almost complete overlap of the beams in the cell, and prevents the pump beam from entering the probe detection channel. By coupling the lasers in multi-mode fibers, without an optical isolator or field modulation, we demonstrate a sensitivity of 10 f T/\\sqrt{\\text{Hz}} for frequencies between 10 Hz and 100 Hz. In addition to the experimental study of sensitivity, we present a theoretical analysis of SERF magnetometer response to magnetic fields for small-angle and parallel-beam configurations, and show that at optimal DC offset fields the magnetometer response is comparable to that in the orthogonal-beam configuration. Based on the analysis, we also derive fundamental and probe-limited sensitivities for the arbitrary non-orthogonal geometry. The expected practical and fundamental sensitivities are of the same order as those in the orthogonal geometry. We anticipate that our design will be useful for magnetoencephalography (MEG) and magnetocardiography (MCG) applications.

  10. Nitrogen nuclear spin flips in nitroxide spin probes of different sizes in glassy o-terphenyl: Possible relation with α- and β-relaxations

    NASA Astrophysics Data System (ADS)

    Isaev, N. P.; Dzuba, S. A.

    2011-09-01

    The pulsed electron-electron double resonance (ELDOR) technique was employed to study nitroxide spin probes of three different sizes dissolved in glassy o-terphenyl. A microwave pulse applied to the central hyperfine structure (hfs) component of the nitroxide electron paramagnetic resonance spectrum was followed by two echo-detecting pulses of different microwave frequency to probe the magnetization transfer (MT) to the low-field hfs component. The MT between hfs components is readily related to flips in the nitrogen nuclear spin, which in turn are induced by molecular motion. The MT on the time scale of tens of microseconds was observed over a wide temperature range, including temperatures near and well below the glass transition. For a bulky nitroxide, it was found that MT rates approach dielectric α (primary) relaxation frequencies reported for o-terphenyl in the literature. For small nitroxides, MT rates were found to match the frequencies of dielectric β (secondary) Johari-Goldstein relaxation. The most probable motional mechanism inducing the nitrogen nuclear spin flips is large-angle angular jumps, between some orientations of unequal occupation probabilities. The pulsed ELDOR of nitroxide spin probes may provide additional insight into the nature of Johari-Goldstein relaxation in glassy media and may serve as a tool for studying this relaxation in substances consisting of non-rigid molecules (such as branched polymers) and in heterogeneous and non-polar systems (such as a core of biological membranes).

  11. Inorganic-Organic Hybrid Luminescent Binary Probe for DNA Detection Based on Spin-Forbidden Resonance Energy Transfer

    PubMed Central

    Marti, Angel A.; Puckett, Cindy A.; Dyer, Joanne; Stevens, Nathan; Jockusch, Steffen; Ju, Jingyue; Barton, Jacqueline K.; Turro, Nicholas J.

    2009-01-01

    We describe the design of new fluorescent binary probe sensors for DNA detection based on spin-forbidden resonance energy transfer (SF-RET). Binary probes consist of a donor and acceptor fluorophores that are attached to two different oligonucleotides and serve as resonance energy transfer (RET) donor-acceptor pair when hybridized to adjacent sites of a target sequence. In the absence of target, excitation of the donor results in fluorescence only from the donor, but when the probes hybridize to target, the fluorophores are brought into close proximity favoring RET, yielding fluorescence mainly from the acceptor fluorophore. These new binary probes use the metal complex Ru(bpy′)(DIP)22+ as the energy donor and an organic fluorophore (Cy5) as the energy acceptor. Energy transfer from the MLCT state of the Ru complex to singlet Cy5 is spin forbidden and produces a delayed fluorescence of Cy5. This paper demonstrate that fluorescence delay of Cy5 can be used to time resolve the emission of the probe from the intense fluorescence background of a model system for cellular background; this provides the reported system to overcome intense autofluorescence, an important and general advantage over “classical” spin-allowed steady-state probes. PMID:17592843

  12. Scanned probe imaging of nanoscale magnetism at cryogenic temperatures with a single-spin quantum sensor

    NASA Astrophysics Data System (ADS)

    Pelliccione, Matthew; Jenkins, Alec; Ovartchaiyapong, Preeti; Reetz, Christopher; Emmanuelidu, Eve; Ni, Ni; Bleszynski Jayich, Ania

    The nitrogen vacancy (NV) defect in diamond has emerged as a promising candidate for high resolution magnetic imaging based on its atomic size and quantum-limited sensing capabilities afforded by long spin coherence times. Although the NV center has been successfully implemented as a nanoscale scanning magnetic probe at room temperature, it has remained an outstanding challenge to extend this capability to cryogenic temperatures, where many solid-state systems exhibit non-trivial magnetic order. In this talk, we present NV magnetic imaging at T = 6 K, first benchmarking the technique with a magnetic hard disk sample, then utilizing the technique to image vortices in the iron pnictide superconductor BaFe2(As0.7P0.3)2 with Tc = 30 K. In addition, we discuss other candidate solid-state systems that can benefit from the high spatial resolution and field sensitivity of the scanning NV magnetometer.

  13. 57 Fe Mössbauer probe of spin crossover thin films on a bio-membrane

    NASA Astrophysics Data System (ADS)

    Naik, Anil D.; Garcia, Yann

    2012-03-01

    An illustrious complex [Fe(ptz)6](BF4)2 (ptz = 1-propyl-tetrazole) ( 1) which was produced in the form of submicron crystals and thin film on Allium cepa membrane was probed by 57Fe Mossbauer spectroscopy in order to follow its intrinsic spin crossover. In addition to a weak signal that corresponds to neat SCO compound significant amount of other iron compounds are found that could have morphed from 1 due to specific host-guest interaction on the lipid-bilayer of bio-membrane. Further complimentary information about biogenic role of membrane, was obtained from variable temperature Mossbauer spectroscopy on a ~5% enriched [57Fe(H2O)6](BF4)2 salt on this membrane.

  14. Studies of osmoregulation in salt adaptation of cyanobacteria with ESR spin-probe techniques

    PubMed Central

    Blumwald, Eduardo; Mehlhorn, Rolf J.; Packer, Lester

    1983-01-01

    Sucrose is accumulated in response to NaCl-induced stress in the cyanobacterium Synechococcus 6311. Internal cell volume was measured by ESR spectra with 2,2,6,6-tetramethyl-4-oxopiperidinoxy free radical (TEMPONE) as a spin probe in order to calculate sucrose concentrations inside the cell. This method is rapid and reliable and provides an unambiguous measurement of absolute volumes in different osmotic environments. Because the osmolar concentration of sucrose does not counter-balance the osmolar concentrations of ions in the growth medium, we suggest that sucrose accumulation is one of the mechanisms involved in the process of adaptation to salt of Synechococcus 6311. The accumulation of sucrose in non-N2-fixing cyanobacteria such as Synechococcus 6311 and in N2-fixing cyanobacteria such as Nostoc muscorum suggests a common mechanism of osmoregulation of fresh water cyanobacteria in response to increasing NaCl concentrations in the growth medium. Images PMID:16593309

  15. Probing Johnson noise and ballistic transport in normal metals with a single-spin qubit

    NASA Astrophysics Data System (ADS)

    Kolkowitz, S.; Safira, A.; High, A. A.; Devlin, R. C.; Choi, S.; Unterreithmeier, Q. P.; Patterson, D.; Zibrov, A. S.; Manucharyan, V. E.; Park, H.; Lukin, M. D.

    2015-03-01

    Thermally induced electrical currents, known as Johnson noise, cause fluctuating electric and magnetic fields in proximity to a conductor. These fluctuations are intrinsically related to the conductivity of the metal. We use single-spin qubits associated with nitrogen-vacancy centers in diamond to probe Johnson noise in the vicinity of conductive silver films. Measurements of polycrystalline silver films over a range of distances (20 to 200 nanometers) and temperatures (10 to 300 kelvin) are consistent with the classically expected behavior of the magnetic fluctuations. However, we find that Johnson noise is markedly suppressed next to single-crystal films, indicative of a substantial deviation from Ohm’s law at length scales below the electron mean free path. Our results are consistent with a generalized model that accounts for the ballistic motion of electrons in the metal, indicating that under the appropriate conditions, nearby electrodes may be used for controlling nanoscale optoelectronic, atomic, and solid-state quantum systems.

  16. Electron spin resonance probed competing states in NiMnInSi Heusler alloy

    NASA Astrophysics Data System (ADS)

    Chen, Y. S.; Lin, J. G.; Titov, I. S.; Granovsky, A. B.

    2016-06-01

    Shape memory Heusler alloy Ni50Mn35In12Si3 is investigated with electron spin resonance (ESR) technique in a temperature range of 200-300 K. ESR is a dynamic probe allowing us to separate the responses from various magnetic phases, thus to study the complex phase transitions. The sample shows three transition temperatures: TcA (271 K), TM (247 K) and TcM (212 K), where TcA is the Curie temperature of austenitic phase, TM and TcM are the temperatures of magnetostructural martensitic transition and the Curie temperature of martensitic phase, respectively. Furthermore, ESR data reveals the coexistence of two magnetic modes in whole temperature range of 200-300 K. Particularly in martensitic phase, two magnetic modes are attributed to two different kinds of lattice deformation, the slip and twinning deformations.

  17. GDR as a Probe of the Collective Motion in Nuclei at High Spins, Temperatures or Isospins

    SciTech Connect

    Maj, Adam

    2008-11-11

    The gamma-decay of the Giant Dipole Resonance (GDR), the high-frequency collective vibration of protons against neutrons, has been proven to be a basic probe for the shapes of hot nuclei, especially to study the effective shape evolution caused by the collective rotation of a nucleus. In this context an interesting question arises: what is the nuclear shape at extreme values of spin or temperatures, close to the limit impose by another collective motion--fission, and how evolves the giant dipole collective vibrations as a function of isospin. Short overview of the results from the experiments aimed to answer these questions are presented and possible perspectives of these type of studies for exotic nuclei to be obtained with the novel gamma-calorimeter PARIS and soon available intense radioactive beams are discussed.

  18. Pyrene excimer signaling molecular beacons for probing nucleic acids.

    PubMed

    Conlon, Patrick; Yang, Chaoyong James; Wu, Yanrong; Chen, Yan; Martinez, Karen; Kim, Youngmi; Stevens, Nathan; Marti, Angel A; Jockusch, Steffen; Turro, Nicholas J; Tan, Weihong

    2008-01-01

    Molecular beacon DNA probes, containing 1-4 pyrene monomers on the 5' end and the quencher DABCYL on the 3' end, were engineered and employed for real-time probing of DNA sequences. In the absence of a target sequence, the multiple-pyrene labeled molecular beacons (MBs) assumed a stem-closed conformation resulting in quenching of the pyrene excimer fluorescence. In the presence of target, the beacons switched to a stem-open conformation, which separated the pyrene label from the quencher molecule and generated an excimer emission signal proportional to the target concentration. Steady-state fluorescence assays resulted in a subnanomolar limit of detection in buffer, whereas time-resolved signaling enabled low-nanomolar target detection in cell-growth media. It was found that the excimer emission intensity could be scaled by increasing the number of pyrene monomers conjugated to the 5' terminal. Each additional pyrene monomer resulted in substantial increases in the excimer emission intensities, quantum yields, and excited-state lifetimes of the hybridized MBs. The long fluorescence lifetime ( approximately 40 ns), large Stokes shift (130 nm), and tunable intensity of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling in nucleic acid probes.

  19. Pyrene Excimer Signaling Molecular Beacons for Probing Nucleic Acids

    PubMed Central

    Conlon, Patrick; Yang, Chaoyong James; Wu, Yanrong; Chen, Yan; Martinez, Karen; Kim, Youngmi; Stevens, Nathan; Marti, Angel A.; Jockusch, Steffen

    2008-01-01

    Molecular beacon DNA probes, containing one to four pyrene monomers on the 5′ end and the quencher DABCYL on the 3′ end, were engineered and employed for real-time probing of DNA sequences. In the absence of a target sequence, the multiple-pyrene labeled molecular beacons (MBs) assumed a stem-closed conformation resulting in quenching of the pyrene excimer fluorescence. In the presence of target, the beacons switched to a stem-open conformation which separated the pyrene label from the quencher molecule and generated an excimer emission signal proportional to the target concentration. Steady-state fluorescence assays resulted in a sub-nanomolar limit of detection in buffer, while time-resolved signaling enabled low-nanomolar target detection in cell growth media. It was found that the excimer emission intensity could be scaled by increasing the number of pyrene monomers conjugated to the 5′ terminal. Each additional pyrene monomer resulted in substantial increases in the excimer emission intensities, quantum yields, and excited-state lifetimes of the hybridized MBs. The long fluorescence lifetime (~40 ns), large Stokes shift (130 nm), and tunable intensity of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling in nucleic acid probes. In addition, this excimer complex serves as an efficient FRET donor for red-emitting fluorophores, such as TMR, for further extending the Stokes shift of the fluorescent complex. PMID:18078339

  20. Model membrane partition ESR study in the presence of alpha-tocopherol by a new spin probe

    SciTech Connect

    Severcan, F.; Cannistraro, S. )

    1989-08-01

    The effect of alpha-tocopherol (alpha T) on partitioning and fluidity changes occurring in phospholipid liposomes have been investigated by monitoring the X-band ESR spectrum of the high resolution amphiphilic spin probe perdeutero-di-t-butyl nitroxide (PDDTBN), which partitions in the lipid and water phase of liposomes, showing all the three resonances from each phase well resolved.

  1. A diamond-based scanning probe spin sensor operating at low temperature in ultra-high vacuum

    SciTech Connect

    Schaefer-Nolte, E.; Wrachtrup, J.; Reinhard, F.; Ternes, M.; Kern, K.

    2014-01-15

    We present the design and performance of an ultra-high vacuum (UHV) low temperature scanning probe microscope employing the nitrogen-vacancy color center in diamond as an ultrasensitive magnetic field sensor. Using this center as an atomic-size scanning probe has enabled imaging of nanoscale magnetic fields and single spins under ambient conditions. In this article we describe an experimental setup to operate this sensor in a cryogenic UHV environment. This will extend the applicability to a variety of molecular systems due to the enhanced target spin lifetimes at low temperature and the controlled sample preparation under UHV conditions. The instrument combines a tuning-fork based atomic force microscope (AFM) with a high numeric aperture confocal microscope and the facilities for application of radio-frequency (RF) fields for spin manipulation. We verify a sample temperature of <50 K even for strong laser and RF excitation and demonstrate magnetic resonance imaging with a magnetic AFM tip.

  2. Oligonucleotide-conjugated thiazole orange probes as "light-up" probes for messenger ribonucleic acid molecules in living cells.

    PubMed

    Privat, E; Melvin, T; Asseline, U; Vigny, P

    2001-10-01

    "Light-up" probes, icosa-alpha-thymidylate-thiazole orange conjugates, for the in situ time-resolved detection of messenger ribonucleic acid (mRNA) in living cells are evaluated. Upon annealing with polyA in aqueous solutions, the icosa-alpha-thymidylate-thiazole orange conjugates were shown to be up to 15 times more fluorescent. Microinjection of these probes into adherent fibroblasts resulted in high yields of hybridization and fluorescent signals. Incubation of cells in the presence of these probes resulted in facile internalization of the probe and similar painting of the messenger RNA in the nuclear and cytosolic regions.

  3. Probing the dynamics of a nuclear spin bath in diamond through time-resolved central spin magnetometry.

    PubMed

    Dréau, A; Jamonneau, P; Gazzano, O; Kosen, S; Roch, J-F; Maze, J R; Jacques, V

    2014-09-26

    Using fast electron spin resonance spectroscopy of a single nitrogen-vacancy defect in diamond, we demonstrate real-time readout of the Overhauser field produced by its nuclear spin environment under ambient conditions. These measurements enable narrowing the Overhauser field distribution by postselection, corresponding to a conditional preparation of the nuclear spin bath. Correlations of the Overhauser field fluctuations are quantitatively inferred by analyzing the Allan deviation over consecutive measurements. This method allows us to extract the dynamics of weakly coupled nuclear spins of the reservoir.

  4. Probing the Dynamics of a Nuclear Spin Bath in Diamond through Time-Resolved Central Spin Magnetometry

    NASA Astrophysics Data System (ADS)

    Dréau, A.; Jamonneau, P.; Gazzano, O.; Kosen, S.; Roch, J.-F.; Maze, J. R.; Jacques, V.

    2014-09-01

    Using fast electron spin resonance spectroscopy of a single nitrogen-vacancy defect in diamond, we demonstrate real-time readout of the Overhauser field produced by its nuclear spin environment under ambient conditions. These measurements enable narrowing the Overhauser field distribution by postselection, corresponding to a conditional preparation of the nuclear spin bath. Correlations of the Overhauser field fluctuations are quantitatively inferred by analyzing the Allan deviation over consecutive measurements. This method allows us to extract the dynamics of weakly coupled nuclear spins of the reservoir.

  5. Method for producing labeled single-stranded nucleic acid probes

    DOEpatents

    Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

    1999-10-19

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  6. In situ magnetic compensation for potassium spin-exchange relaxation-free magnetometer considering probe beam pumping effect

    SciTech Connect

    Fang, Jiancheng; Wang, Tao Quan, Wei; Yuan, Heng; Li, Yang; Zhang, Hong; Zou, Sheng

    2014-06-15

    A novel method to compensate the residual magnetic field for an atomic magnetometer consisting of two perpendicular beams of polarizations was demonstrated in this paper. The method can realize magnetic compensation in the case where the pumping rate of the probe beam cannot be ignored. In the experiment, the probe beam is always linearly polarized, whereas, the probe beam contains a residual circular component due to the imperfection of the polarizer, which leads to the pumping effect of the probe beam. A simulation of the probe beam's optical rotation and pumping rate was demonstrated. At the optimized points, the wavelength of the probe beam was optimized to achieve the largest optical rotation. Although, there is a small circular component in the linearly polarized probe beam, the pumping rate of the probe beam was non-negligible at the optimized wavelength which if ignored would lead to inaccuracies in the magnetic field compensation. Therefore, the dynamic equation of spin evolution was solved by considering the pumping effect of the probe beam. Based on the quasi-static solution, a novel magnetic compensation method was proposed, which contains two main steps: (1) the non-pumping compensation and (2) the sequence compensation with a very specific sequence. After these two main steps, a three-axis in situ magnetic compensation was achieved. The compensation method was suitable to design closed-loop spin-exchange relaxation-free magnetometer. By a combination of the magnetic compensation and the optimization, the magnetic field sensitivity was approximately 4 fT/Hz{sup 1/2}, which was mainly dominated by the noise of the magnetic shield.

  7. In situ magnetic compensation for potassium spin-exchange relaxation-free magnetometer considering probe beam pumping effect.

    PubMed

    Fang, Jiancheng; Wang, Tao; Quan, Wei; Yuan, Heng; Zhang, Hong; Li, Yang; Zou, Sheng

    2014-06-01

    A novel method to compensate the residual magnetic field for an atomic magnetometer consisting of two perpendicular beams of polarizations was demonstrated in this paper. The method can realize magnetic compensation in the case where the pumping rate of the probe beam cannot be ignored. In the experiment, the probe beam is always linearly polarized, whereas, the probe beam contains a residual circular component due to the imperfection of the polarizer, which leads to the pumping effect of the probe beam. A simulation of the probe beam's optical rotation and pumping rate was demonstrated. At the optimized points, the wavelength of the probe beam was optimized to achieve the largest optical rotation. Although, there is a small circular component in the linearly polarized probe beam, the pumping rate of the probe beam was non-negligible at the optimized wavelength which if ignored would lead to inaccuracies in the magnetic field compensation. Therefore, the dynamic equation of spin evolution was solved by considering the pumping effect of the probe beam. Based on the quasi-static solution, a novel magnetic compensation method was proposed, which contains two main steps: (1) the non-pumping compensation and (2) the sequence compensation with a very specific sequence. After these two main steps, a three-axis in situ magnetic compensation was achieved. The compensation method was suitable to design closed-loop spin-exchange relaxation-free magnetometer. By a combination of the magnetic compensation and the optimization, the magnetic field sensitivity was approximately 4 fT/Hz(1/2), which was mainly dominated by the noise of the magnetic shield.

  8. Microwave Field Distribution in a Magic Angle Spinning Dynamic Nuclear Polarization NMR Probe

    PubMed Central

    Nanni, Emilio A.; Barnes, Alexander B.; Matsuki, Yoh; Woskov, Paul P.; Corzilius, Björn; Griffin, Robert G.; Temkin, Richard J.

    2011-01-01

    We present a calculation of the microwave field distribution in a magic angle spinning (MAS) probe utilized in dynamic nuclear polarization (DNP) experiments. The microwave magnetic field (B1S) profile was obtained from simulations performed with the High Frequency Structure Simulator (HFSS) software suite, using a model that includes the launching antenna, the outer Kel-F stator housing coated with Ag, the RF coil, and the 4 mm diameter sapphire rotor containing the sample. The predicted average B1S field is 13µT/W1/2, where S denotes the electron spin. For a routinely achievable input power of 5 W the corresponding value is γ SB1S = 0.84 MHz. The calculations provide insights into the coupling of the microwave power to the sample, including reflections from the RF coil and diffraction of the power transmitted through the coil. The variation of enhancement with rotor wall thickness was also successfully simulated. A second, simplified calculation was performed using a single pass model based on Gaussian beam propagation and Fresnel diffraction. This model provided additional physical insight and was in good agreement with the full HFSS simulation. These calculations indicate approaches to increasing the coupling of the microwave power to the sample, including the use of a converging lens and fine adjustment of the spacing of the windings of the RF coil. The present results should prove useful in optimizing the coupling of microwave power to the sample in future DNP experiments. Finally, the results of the simulation were used to predict the cross effect DNP enhancement (ε) vs. ω1S/(2π) for a sample of 13C-urea dissolved in a 60:40 glycerol/water mixture containing the polarizing agent TOTAPOL; very good agreement was obtained between theory and experiment. PMID:21382733

  9. Probing the Specificity Determinants of Amino Acid Recognition by Arginase

    SciTech Connect

    Shishova, E.; Di Costanzo, L; Emig, F; Ash, D; Christianson, D

    2009-01-01

    Arginase is a binuclear manganese metalloenzyme that serves as a therapeutic target for the treatment of asthma, erectile dysfunction, and atherosclerosis. In order to better understand the molecular basis of inhibitor affinity, we have employed site-directed mutagenesis, enzyme kinetics, and X-ray crystallography to probe the molecular recognition of the amino acid moiety (i.e., the ?-amino and ?-carboxylate groups) of substrate l-arginine and inhibitors in the active site of arginase I. Specifically, we focus on (1) a water-mediated hydrogen bond between the substrate ?-carboxylate and T135, (2) a direct hydrogen bond between the substrate ?-carboxylate and N130, and (3) a direct charged hydrogen bond between the substrate ?-amino group and D183. Amino acid substitutions for T135, N130, and D183 generally compromise substrate affinity as reflected by increased KM values but have less pronounced effects on catalytic function as reflected by minimal variations of kcat. As with substrate KM values, inhibitor Kd values increase for binding to enzyme mutants and suggest that the relative contribution of intermolecular interactions to amino acid affinity in the arginase active site is water-mediated hydrogen bond < direct hydrogen bond < direct charged hydrogen bond. Structural comparisons of arginase with the related binuclear manganese metalloenzymes agmatinase and proclavaminic acid amidinohydrolase suggest that the evolution of substrate recognition in the arginase fold occurs by mutation of residues contained in specificity loops flanking the mouth of the active site (especially loops 4 and 5), thereby allowing diverse guanidinium substrates to be accommodated for catalysis.

  10. Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

    DOEpatents

    Ramsey, J. Michael; Foote, Robert S.

    2003-12-09

    A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

  11. Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

    DOEpatents

    Ramsey, J. Michael; Foote, Robert S.

    2002-01-01

    A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

  12. Probing the quantum ground state of a spin-1 Bose-Einstein condensate with cavity transmission spectra

    SciTech Connect

    Zhang, J. M.; Cui, S.; Jing, H.; Zhou, D. L.; Liu, W. M.

    2009-10-15

    We propose to probe the quantum ground state of a spin-1 Bose-Einstein condensate with the transmission spectra of an optical cavity. By choosing a circularly polarized cavity mode with an appropriate frequency, we can realize coupling between the cavity mode and the magnetization of the condensate. The cavity transmission spectra then contain information of the magnetization statistics of the condensate and thus can be used to distinguish the ferromagnetic and antiferromagnetic quantum ground states. This technique may also be useful for continuous observation of the spin dynamics of a spinor Bose-Einstein condensate.

  13. Spin current and inverse spin Hall effect in ferromagnetic metals probed by Y{sub 3}Fe{sub 5}O{sub 12}-based spin pumping

    SciTech Connect

    Wang, Hailong; Du, Chunhui; Chris Hammel, P. Yang, Fengyuan

    2014-05-19

    Using ferromagnetic (FM) resonance spin pumping, we observe injection of spin currents from Y{sub 3}Fe{sub 5}O{sub 12} (YIG) films to FM metals, including Ni{sub 81}Fe{sub 19} (Py), Fe, Co, and Ni, and detection of spin currents by inverse spin Hall effect (ISHE) in the FM metals. We obtain a high effective spin mixing conductance of 6.3 × 10{sup 18} m{sup −2} in a YIG/Cu/Py trilayer and a spin Hall angle of 0.020 for Py. The spin pumping signals in Fe, Co, and Ni confirm the mechanism of ISHE in FMs is the inverse process of the anomalous Hall effect.

  14. Method for replicating an array of nucleic acid probes

    DOEpatents

    Cantor, Charles R.; Przetakiewicz, Marek; Smith, Cassandra L.; Sano, Takeshi

    1998-01-01

    The invention relates to the replication of probe arrays and methods for replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5'- and/or 3'-overhangs.

  15. Method for replicating an array of nucleic acid probes

    DOEpatents

    Cantor, C.R.; Przetakiewicz, M.; Smith, C.L.; Sano, T.

    1998-08-18

    The invention relates to the replication of probe arrays and methods for replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5{prime}- and/or 3{prime}-overhangs. 16 figs.

  16. Muoniated spin probes in the discotic liquid crystal HHTT: rapid electron spin relaxation in the hexagonal columnar and isotropic phases.

    PubMed

    McKenzie, Iain; Cammidge, Andrew N; Gopee, Hemant; Dilger, Herbert; Scheuermann, Robert; Stoykov, Alexey; Jayasooriya, Upali A

    2013-01-01

    Avoided level crossing muon spin resonance (ALC-μSR) spectroscopy was used to study radicals produced by the addition of the light hydrogen isotope muonium (Mu) to the discotic liquid crystal (DLC) 2,3,6,7,10,11-hexahexylthiotriphenylene (HHTT). Mu adds to the secondary carbon atoms of HHTT to produce a substituted cyclohexadienyl radical, whose identity was confirmed by comparing the measured hyperfine coupling constants with values obtained from DFT calculations. ALC-μSR spectra were obtained in the isotropic (I), hexagonal columnar (Col(h)), helical (H), and crystalline (Cr) phases. In the I and Col(h) phases the radicals, which are incorporated within the stacks of HHTT molecules as isolated paramagnetic defects, undergo extremely rapid electron spin relaxation, on the order of a hundredfold faster than in the H or Cr phases. The electron spin relaxation rate increases significantly with increasing temperature and appears to be caused by the liquidlike motion within the columns, which modulates the overlap between the π system of the radical and the π systems of the neighboring HHTT molecules, and hence, the hyperfine coupling constants. Rapid electron spin relaxation should occur for any π radical incorporated within the columns of a DLC, which may limit the utility of DLCs for future spin-based technologies.

  17. Spin and Time-Reversal Symmetries of Superconducting Electron Pairs Probed by the Muon Spin Rotation and Relaxation Technique

    NASA Astrophysics Data System (ADS)

    Higemoto, Wataru; Aoki, Yuji; MacLaughlin, Douglas E.

    2016-09-01

    Unconventional superconductivity based on the strong correlation of electrons is one of the central issues of solid-state physics. Although many experimental techniques are appropriate for investigating unconventional superconductivity, a complete perspective has not been established yet. The symmetries of electron pairs are crucial properties for understanding the essential state of unconventional superconductivity. In this review, we discuss the investigation of the time-reversal and spin symmetries of superconducting electron pairs using the muon spin rotation and relaxation technique. By detecting a spontaneous magnetic field under zero field and/or the temperature dependence of the muon Knight shift in the superconducting phase, the time-reversal symmetry and spin parity of electron pairs have been determined for several unconventional superconductors.

  18. Cold shock hemolysis in human erythrocytes studied by spin probe method and freeze-fracture electron microscopy.

    PubMed Central

    Takahashi, T; Noji, S; Erbe, E F; Steere, R L; Kon, H

    1986-01-01

    When human erythrocytes are osmotically stressed or chemically treated, they hemolyze on cooling below 10 degrees C (called cold shock). We have studied the effects of osmotic stress and cooling on the state of membrane by the spin-probe method and freeze-fracture electron microscopy. At room temperature, the membrane fluidity detected by 12-doxyl stearate spin probe showed a steady decrease with osmolality in hypertonic NaCl solutions up to 900 mOsm/kg, above which it remained unchanged. In hypertonic sucrose solutions, the electron paramagnetic resonance spectra showed an additional pair of absorptions, indicating development of regions, in the membrane, further immobilized than in NaCl solutions. Mobility of a cholesterol analogue probe, androstane, did not show change by hypertonicity, but the spectral intensity dropped at 1,200 mOsm/kg, probably due to formation of loose aggregates in the cholesterol phase. On cooling the osmotically stressed cells in NaCl solution, the isotropic rotational correlation time vs. inverse temperature plot of 12-doxyl stearate probe exhibited a step-wise discontinuity at approximately 10 degrees C, suggestive of a drastic transition in the state of the membrane. At about the same temperature, the freeze-fracture pattern of osmotically stressed cells revealed the development of large wrinkles and aggregation of membrane particles, in contrast to the case of the cells in isotonicity. Significance of these findings in understanding cold shock hemolysis is discussed. Images FIGURE 3 PMID:3006813

  19. Probing the Spin Transfer Efficiency at Topological Insulator/Ferromagnetic Insulator Interfaces

    NASA Astrophysics Data System (ADS)

    Wang, Hailong; Kally, James; Lee, Joon Sue; Richardella, Anthony; Kempinger, Susan; Pan, Yu; Kamp, Eric; Samarth, Nitin; Liu, Tao; Chang, Houcheng; Wu, Mingzhong; Reifsnyder-Hickey, Danielle; Mkhoyan, Andre

    The development of next-generation spintronics devices has driven extensive studies of spin-charge conversion through measurement of the inverse spin Hall effect (ISHE) and ferromagnetic resonance (FMR) driven spin pumping of pure spin currents in ferromagnet/non-magnet bilayers. Topological insulators (TIs) such as the Bi-chalcogenides are naturally relevant in this context because the inherent spin-momentum ``locking'' in their surface states promises very efficient spin-charge conversion, although the first experimental studies have involved ferromagnetic metals that provide a shunting current path [e.g. Nature, 511,449 (2014)]. To circumvent the current shunting problem, we are growing and characterizing bilayers of TIs and the ferrimagnetic insulator Y3Fe5O12 (YIG). Here, we report measurements of FMR-driven spin pumping in TI/YIG bilayers, showing robust spin pumping signals at room temperature. Analysis of the ISHE voltages and FMR linewidth broadening show that, as in other studies of spin pumping into TIs [Nano Lett., 15 (10) (2015)], the interface condition presents a critical challenge for enhancing the spin conversion efficiency in these devices. Funded by C-SPIN/SRC/DARPA and ONR.

  20. Coherent ultrafast spin-dynamics probed in three dimensional topological insulators.

    PubMed

    Boschini, F; Mansurova, M; Mussler, G; Kampmeier, J; Grützmacher, D; Braun, L; Katmis, F; Moodera, J S; Dallera, C; Carpene, E; Franz, C; Czerner, M; Heiliger, C; Kampfrath, T; Münzenberg, M

    2015-10-29

    Topological insulators are candidates to open up a novel route in spin based electronics. Different to traditional ferromagnetic materials, where the carrier spin-polarization and magnetization are based on the exchange interaction, the spin properties in topological insulators are based on the coupling of spin- and orbit interaction connected to its momentum. Specific ways to control the spin-polarization with light have been demonstrated: the energy momentum landscape of the Dirac cone provides spin-momentum locking of the charge current and its spin. We investigate a spin-related signal present only during the laser excitation studying real and imaginary part of the complex Kerr angle by disentangling spin and lattice contributions. This coherent signal is only present at the time of the pump-pulses' light field and can be described in terms of a Raman coherence time. The Raman transition involves states at the bottom edge of the conduction band. We demonstrate a coherent femtosecond control of spin-polarization for electronic states at around the Dirac cone.

  1. Coherent ultrafast spin-dynamics probed in three dimensional topological insulators

    PubMed Central

    Boschini, F.; Mansurova, M.; Mussler, G.; Kampmeier, J.; Grützmacher, D.; Braun, L.; Katmis, F.; Moodera, J. S.; Dallera, C.; Carpene, E.; Franz, C.; Czerner, M.; Heiliger, C.; Kampfrath, T.; Münzenberg, M.

    2015-01-01

    Topological insulators are candidates to open up a novel route in spin based electronics. Different to traditional ferromagnetic materials, where the carrier spin-polarization and magnetization are based on the exchange interaction, the spin properties in topological insulators are based on the coupling of spin- and orbit interaction connected to its momentum. Specific ways to control the spin-polarization with light have been demonstrated: the energy momentum landscape of the Dirac cone provides spin-momentum locking of the charge current and its spin. We investigate a spin-related signal present only during the laser excitation studying real and imaginary part of the complex Kerr angle by disentangling spin and lattice contributions. This coherent signal is only present at the time of the pump-pulses’ light field and can be described in terms of a Raman coherence time. The Raman transition involves states at the bottom edge of the conduction band. We demonstrate a coherent femtosecond control of spin-polarization for electronic states at around the Dirac cone. PMID:26510509

  2. Absence of a spin-signature from a single Ho adatom as probed by spin-sensitive tunneling

    PubMed Central

    Steinbrecher, M.; Sonntag, A.; Dias, M. dos Santos; Bouhassoune, M.; Lounis, S.; Wiebe, J.; Wiesendanger, R.; Khajetoorians, A. A.

    2016-01-01

    Whether rare-earth materials can be used as single-atom magnetic memory is an ongoing debate in recent literature. Here we show, by inelastic and spin-resolved scanning tunnelling-based methods, that we observe a strong magnetic signal and excitation from Fe atoms adsorbed on Pt(111), but see no signatures of magnetic excitation or spin-based telegraph noise for Ho atoms. Moreover, we observe that the indirect exchange field produced by a single Ho atom is negligible, as sensed by nearby Fe atoms. We demonstrate, using ab initio methods, that this stems from a comparatively weak coupling of the Ho 4f electrons with both tunnelling electrons and substrate-derived itinerant electrons, making both magnetic coupling and detection very difficult when compared to 3d elements. We discuss these results in the context of ongoing disputes and clarify important controversies. PMID:26838811

  3. Absence of a spin-signature from a single Ho adatom as probed by spin-sensitive tunneling.

    PubMed

    Steinbrecher, M; Sonntag, A; dos Santos Dias, M; Bouhassoune, M; Lounis, S; Wiebe, J; Wiesendanger, R; Khajetoorians, A A

    2016-01-01

    Whether rare-earth materials can be used as single-atom magnetic memory is an ongoing debate in recent literature. Here we show, by inelastic and spin-resolved scanning tunnelling-based methods, that we observe a strong magnetic signal and excitation from Fe atoms adsorbed on Pt(111), but see no signatures of magnetic excitation or spin-based telegraph noise for Ho atoms. Moreover, we observe that the indirect exchange field produced by a single Ho atom is negligible, as sensed by nearby Fe atoms. We demonstrate, using ab initio methods, that this stems from a comparatively weak coupling of the Ho 4f electrons with both tunnelling electrons and substrate-derived itinerant electrons, making both magnetic coupling and detection very difficult when compared to 3d elements. We discuss these results in the context of ongoing disputes and clarify important controversies. PMID:26838811

  4. Absence of a spin-signature from a single Ho adatom as probed by spin-sensitive tunneling

    NASA Astrophysics Data System (ADS)

    Steinbrecher, M.; Sonntag, A.; Dias, M. Dos Santos; Bouhassoune, M.; Lounis, S.; Wiebe, J.; Wiesendanger, R.; Khajetoorians, A. A.

    2016-02-01

    Whether rare-earth materials can be used as single-atom magnetic memory is an ongoing debate in recent literature. Here we show, by inelastic and spin-resolved scanning tunnelling-based methods, that we observe a strong magnetic signal and excitation from Fe atoms adsorbed on Pt(111), but see no signatures of magnetic excitation or spin-based telegraph noise for Ho atoms. Moreover, we observe that the indirect exchange field produced by a single Ho atom is negligible, as sensed by nearby Fe atoms. We demonstrate, using ab initio methods, that this stems from a comparatively weak coupling of the Ho 4f electrons with both tunnelling electrons and substrate-derived itinerant electrons, making both magnetic coupling and detection very difficult when compared to 3d elements. We discuss these results in the context of ongoing disputes and clarify important controversies.

  5. mtsslSuite: Probing Biomolecular Conformation by Spin-Labeling Studies.

    PubMed

    Hagelueken, Gregor; Abdullin, Dinar; Schiemann, Olav

    2015-01-01

    EPR long-range distance measurements on spin-labeled macromolecules have recently become a popular tool in structural biology. The method can be used to obtain coarse-grained structures of biomolecules, to track conformational changes and dynamics, to dock macromolecular complexes, or to localize spin centers within macromolecules using trilateration. Because the conformation of the spin label is usually unknown, it is often necessary to construct conformational models of the spin label on the macromolecules for data interpretation. For this purpose, so-called in silico spin-labeling approaches have been developed. In this chapter, a comprehensive summary of the mtsslSuite is provided, one of the in silico spin-labeling software packages. The package currently contains three programs: mtsslWizard, mtsslDock, and mtsslTrilaterate. Worked examples for the usage of all three programs during the planning- and interpretation stages of the EPR experiment are given. PMID:26478500

  6. Light-up probes: thiazole orange-conjugated peptide nucleic acid for detection of target nucleic acid in homogeneous solution.

    PubMed

    Svanvik, N; Westman, G; Wang, D; Kubista, M

    2000-05-15

    We have constructed light-up probes for nucleic acid detection. The light-up probe is a peptide nucleic acid (PNA) oligonucleotide to which the asymmetric cyanine dye thiazole orange (TO) is tethered. It combines the excellent hybridization properties of PNA and the large fluorescence enhancement of TO upon binding to DNA. When the PNA hybridizes to target DNA, the dye binds and becomes fluorescent. Free probes have low fluorescence, which may increase almost 50-fold upon hybridization to complementary nucleic acid. This makes the light-up probes particularly suitable for homogeneous hybridization assays, where separation of the bound and free probe is not necessary. We find that the fluorescence enhancement upon hybridization varies among different probes, which is mainly due to variations in free probe fluorescence. For eight probes studied the fluorescence quantum yield at 25 degrees C in the unbound state ranged from 0.0015 to 0.08 and seemed to depend mainly on the PNA sequence. The binding of the light-up probes to target DNA is highly sequence specific and a single mismatch in a 10-mer target sequence was readily identified.

  7. Spin excitations in ferromagnetic Ni: Electrons and neutrons as a probe

    SciTech Connect

    Hong, Jisang; Mills, D. L.

    2000-01-01

    We present theoretical calculations of the contribution to the spin polarized electron energy loss spectrum of ferromagnetic Ni. We find, save for the wave-vector transfer near the center of the Brillouin zone, the spin-wave loss feature is obscured by low-lying Stoner excitations, in contrast to Fe. Our calculations, and earlier work, show that in inelastic neutron-scattering studies of spin waves in Ni, the spin-wave loss peak dominates. The physical reason for this difference is discussed. (c) 2000 The American Physical Society.

  8. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes.

    PubMed

    Junager, Nina P L; Kongsted, Jacob; Astakhova, Kira

    2016-01-01

    Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells. PMID:27472344

  9. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes

    PubMed Central

    Junager, Nina P. L.; Kongsted, Jacob; Astakhova, Kira

    2016-01-01

    Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells. PMID:27472344

  10. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes.

    PubMed

    Junager, Nina P L; Kongsted, Jacob; Astakhova, Kira

    2016-01-01

    Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells.

  11. Cationic spin probe reporting on thermal denaturation and complexation-decomplexation of BSA with SDS. Potential applications in protein purification processes.

    PubMed

    Matei, Iulia; Ariciu, Ana Maria; Neacsu, Maria Victoria; Collauto, Alberto; Salifoglou, Athanasios; Ionita, Gabriela

    2014-09-25

    In this work, we present evidence on the suitability of spin probes to report on the thermal treatment of bovine serum albumin (BSA), in the temperature range 293-343 K, and indirectly monitor the release of sodium dodecyl sulfate (SDS) from its complex with BSA using a covalent gel with β-cyclodextrin (β-CD) in the network. The spin probes used, 5- and 7-doxyl-stearic acids (5-DSA, 7-DSA) or 4-(N,N'-dimethyl-N-hexadecyl)ammonium-2,2',6,6'-tetramethylpiperidine-1-oxyl iodide (CAT16), present similar, fatty acid-like structural features. Their continuous wave electron paramagnetic resonance (CW-EPR) spectra, however, reflect different dynamics when complexed with BSA: a restricted motion for 5-DSA, almost nonsensitive to the heating/cooling cycle, and a faster temperature-dependent dynamic motion for CAT16. Molecular docking allows us to rationalize these results by revealing the different binding modes of 5-DSA and CAT16. The EPR data on the temperature effect on BSA are supported by circular dichroism results projecting recovery, upon cooling, of the initial binding ability of BSA for samples heated to 323 K. The interactions occurring in BSA/SDS/β-CD systems are investigated by CW-EPR and FT-ESEEM spectroscopies. It is found that the covalent gel containing β-CD can efficiently remove SDS from the BSA/SDS complex. The gel is not permeable to BSA but it can encapsulate SDS, thus yielding the free protein in solution and allowing recovery of the native protein conformation. Collectively, the accrued knowledge supports potential applications in protein purification biotechnological processes.

  12. Permeability studies of redox-sensitive nitroxyl spin probes in corn oil using an L-band ESR spectrometer

    NASA Astrophysics Data System (ADS)

    Jebaraj, D. David; Utsumi, Hideo; Asath, R. Mohamed; Benial, A. Milton Franklin

    2016-05-01

    Electron spin resonance (ESR) studies were carried out for 2mM 14N labeled 2H enriched 3-methoxycarbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl (MC-PROXYL) and 3-carboxy-2,2,5,5,-tetramethyl-1-pyrrolidinyloxy (carboxy-PROXYL) in pure water and various concentrations of corn oil. The ESR parameters, such as the line width, hyperfine coupling constant, g-factor, rotational correlation time, partition parameter and permeability were reported for the samples. The line width broadening was observed for both nitroxyl radicals in corn oil solutions. The partition parameter for permeable MC-PROXYL in corn oil increases with increasing concentration of corn oil, which reveals that the nitroxyl spin probe permeates into the oil phase. From the results, the corn oil concentration was optimized as 50 % for phantom studies. The rotational correlation time also increases with increasing concentration of corn oil. The permeable and impermeable nature of nitroxyl spin probes was demonstrated. These results will be useful for the development of ESR/OMR imaging modalities in in vivo and in vitro studies.

  13. Measuring small compartment dimensions by probing diffusion dynamics via Non-uniform Oscillating-Gradient Spin-Echo (NOGSE) NMR

    NASA Astrophysics Data System (ADS)

    Shemesh, Noam; Álvarez, Gonzalo A.; Frydman, Lucio

    2013-12-01

    Noninvasive measurements of microstructure in materials, cells, and in biological tissues, constitute a unique capability of gradient-assisted NMR. Diffusion-diffraction MR approaches pioneered by Callaghan demonstrated this ability; Oscillating-Gradient Spin-Echo (OGSE) methodologies tackle the demanding gradient amplitudes required for observing diffraction patterns by utilizing constant-frequency oscillating gradient pairs that probe the diffusion spectrum, D(ω). Here we present a new class of diffusion MR experiments, termed Non-uniform Oscillating-Gradient Spin-Echo (NOGSE), which dynamically probe multiple frequencies of the diffusion spectral density at once, thus affording direct microstructural information on the compartment's dimension. The NOGSE methodology applies N constant-amplitude gradient oscillations; N - 1 of these oscillations are spaced by a characteristic time x, followed by a single gradient oscillation characterized by a time y, such that the diffusion dynamics is probed while keeping (N - 1)x + y ≡ TNOGSE constant. These constant-time, fixed-gradient-amplitude, multi-frequency attributes render NOGSE particularly useful for probing small compartment dimensions with relatively weak gradients - alleviating difficulties associated with probing D(ω) frequency-by-frequency or with varying relaxation weightings, as in other diffusion-monitoring experiments. Analytical descriptions of the NOGSE signal are given, and the sequence's ability to extract small compartment sizes with a sensitivity towards length to the sixth power, is demonstrated using a microstructural phantom. Excellent agreement between theory and experiments was evidenced even upon applying weak gradient amplitudes. An MR imaging version of NOGSE was also implemented in ex vivo pig spinal cords and mouse brains, affording maps based on compartment sizes. The effects of size distributions on NOGSE are also briefly analyzed.

  14. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    1997-01-01

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided.

  15. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1997-04-01

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided. 7 figs.

  16. Spin-distribution measurement: A sensitive probe for incomplete fusion dynamics

    SciTech Connect

    Singh, Pushpendra P.; Singh, B. P.; Sharma, Manoj Kumar; Unnati,; Singh, D.; Ansari, M. A.; Prasad, R.; Kumar, R.; Golda, K. S.; Singh, R. P.; Muralithar, S.; Bhowmik, R. K.

    2008-07-15

    Spin distributions of various reaction products populated via complete and/or incomplete fusion of {sup 16}O with {sup 169}Tm have been measured at projectile energy {approx_equal}5.6 MeV/nucleon. Particle (Z=1,2) {gamma}-coincidences have been employed to achieve the information about involved reaction modes on the basis of their entry state spin populations. The experimentally measured spin distributions for incomplete fusion products have been found to be distinctly different than those observed for complete fusion products. The driving input angular momenta associated with incomplete fusion products have been found to be relatively higher than complete fusion products, and increases with direct {alpha}-multiplicity. It has also been observed that incomplete fusion products are less fed and/or the population of lower spin states are strongly hindered, while complete fusion products indicating strong feeding over a broad spin range.

  17. Fluorescence probe for the convenient and sensitive detection of ascorbic acid.

    PubMed

    Matsuoka, Yuta; Yamato, Mayumi; Yamada, Ken-Ichi

    2016-01-01

    Ascorbic acid is an important antioxidant that plays an essential role in the biosynthesis of numerous bioactive substances. The detection of ascorbic acid has traditionally been achieved using high-performance liquid chromatography and absorption spectrophotometry assays. However, the development of fluorescence probes for this purpose is highly desired because they provide a much more convenient and highly sensitive technique for the detection of this material. OFF-ON-type fluorescent probes have been developed for the detection of non-fluorescent compounds. Photo-induced electron transfer and fluorescence resonance energy transfer are the two main fluorescence quenching mechanisms for the detection of ascorbic acid, and several fluorescence probes have been reported based on redox-responsive metals and quantum dots. Profluorescent nitroxide compounds have also been developed as non-metal organic fluorescence probes for ascorbic acid. These nitroxide systems have a stable unpaired electron and can therefore react with ascorbic acid and a strong fluorescence quencher. Furthermore, recent synthetic advances have allowed for the synthesis of α-substituted nitroxides with varying levels of reactivity towards ascorbic acid. In this review, we have discussed the design strategies used for the preparation of fluorescent probes for ascorbic acid, with particular emphasis on profluorescent nitroxides, which are unique radical-based redox-active fluorescent probes.

  18. Fluorescence probe for the convenient and sensitive detection of ascorbic acid

    PubMed Central

    Matsuoka, Yuta; Yamato, Mayumi; Yamada, Ken-ichi

    2016-01-01

    Ascorbic acid is an important antioxidant that plays an essential role in the biosynthesis of numerous bioactive substances. The detection of ascorbic acid has traditionally been achieved using high-performance liquid chromatography and absorption spectrophotometry assays. However, the development of fluorescence probes for this purpose is highly desired because they provide a much more convenient and highly sensitive technique for the detection of this material. OFF-ON-type fluorescent probes have been developed for the detection of non-fluorescent compounds. Photo-induced electron transfer and fluorescence resonance energy transfer are the two main fluorescence quenching mechanisms for the detection of ascorbic acid, and several fluorescence probes have been reported based on redox-responsive metals and quantum dots. Profluorescent nitroxide compounds have also been developed as non-metal organic fluorescence probes for ascorbic acid. These nitroxide systems have a stable unpaired electron and can therefore react with ascorbic acid and a strong fluorescence quencher. Furthermore, recent synthetic advances have allowed for the synthesis of α-substituted nitroxides with varying levels of reactivity towards ascorbic acid. In this review, we have discussed the design strategies used for the preparation of fluorescent probes for ascorbic acid, with particular emphasis on profluorescent nitroxides, which are unique radical-based redox-active fluorescent probes. PMID:26798193

  19. Probing the flexibility of internal rotation in silylated phenols with the NMR scalar spin-spin coupling constants.

    PubMed

    Sychrovský, Vladimír; Benda, Ladislav; Prokop, Alexandr; Blechta, Vratislav; Schraml, Jan; Spirko, Vladimír

    2008-06-12

    The rotation of a trimethylsiloxy (TMSO) group in three silylated phenols (with three different ortho substituents -H, -CH3, and -C(CH3)3) was studied with the NMR (n)J(Si,C), n = 2, 3, 4, 5, scalar spin-spin coupling between the (29)Si nucleus of the TMSO group and the (13)C nuclei of the phenyl ring. The internal rotation potential calculated with the B3LYP and MP2 calculation methods including the effect of a solvent environment (gas phase, chloroform, and water) was used for the calculation of the dynamical averages of the scalar coupling constants in the framework of the rigid-bender formalism. Solvent effects, the quality of the rotational potential, and the applicability of the classical molecular dynamic to the problem is discussed. Quantum effects have a sizable impact on scalar couplings, particularly for the internal rotational states well localized within the wells of the potential surfaces for the TMSO group. The overall difference between the experimental and theoretical scalar couplings calculated for the global energy-minima structures (static model) decreases substantially for both model potentials (B3LYP, MP2) when the molecular motion of the TMSO group is taken into account. The calculated data indicate that the inclusion of molecular motion is necessary for the accurate calculation of the scalar coupling constants and their reliable structural interpretation for any system which possesses a large-amplitude motion. PMID:18491850

  20. A phosphomolybdic acid anion probe-based label-free, stable and simple electrochemical biosensing platform.

    PubMed

    Wei, Tianxiang; Chen, Yuyun; Tu, Wenwen; Lan, Yaqian; Dai, Zhihui

    2014-08-25

    A versatile label-free, stable, low-cost and simple electrochemical biosensing platform has been developed based on a phosphomolybdic acid anion probe by jointly taking advantages of its native electronegativity, electrochemical activity and chemisorption with graphene oxide.

  1. Multi-walled carbon nanotubes and poly(lactic acid) nanocomposite fibrous membranes prepared by solution blow spinning.

    PubMed

    Oliveira, Juliano E; Zucolotto, Valtencir; Mattoso, Luiz H C; Medeiros, Eliton S

    2012-03-01

    Nanocomposite fibers based on multi-walled carbon nanotubes (MWCNT) and poly(lactic acid) (PLA) were prepared by solution blow spinning (SBS). Fiber morphology was characterized by scanning electron microscopy (SEM) and optical microscopy (OM). Electrical, thermal, surface and crystalline properties of the spun fibers were evaluated, respectively, by conductivity measurements (4-point probe), thermogravimetric analyses (TGA), differential scanning calorimetry (DSC), contact angle and X-ray diffraction (XRD). OM analysis of the spun mats showed a poor dispersion of MWCNT in the matrix, however dispersion in solution was increased during spinning where droplets of PLA in solution loaded with MWCNT were pulled by the pressure drop at the nozzle, producing PLA fibers filled with MWCNT. Good electrical conductivity and hydrophobicity can be achieved at low carbon nanotube contents. When only 1 wt% MWCNT was added to low-crystalline PLA, surface conductivity of the composites increased from 5 x 10(-8) to 0.46 S/cm. Addition of MWCNT can slightly influence the degree of crystallinity of PLA fibers as studied by XRD and DSC. Thermogravimetric analyses showed that MWCNT loading can decrease the onset degradation temperature of the composites which was attributed to the catalytic effect of metallic residues in MWCNT. Moreover, it was demonstrated that hydrophilicity slightly increased with an increase in MWCNT content. These results show that solution blow spinning can also be used to produce nanocomposite fibers with many potential applications such as in sensors and biosensors. PMID:22755116

  2. Probe kit for identifying a base in a nucleic acid

    DOEpatents

    Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

    2001-01-01

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  3. Detection and isolation of nucleic acid sequences using a bifunctional hybridization probe

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    2000-01-01

    A method for detecting and isolating a target sequence in a sample of nucleic acids is provided using a bifunctional hybridization probe capable of hybridizing to the target sequence that includes a detectable marker and a first complexing agent capable of forming a binding pair with a second complexing agent. A kit is also provided for detecting a target sequence in a sample of nucleic acids using a bifunctional hybridization probe according to this method.

  4. Probing the Nuclear Spin-Lattice Relaxation Time at the Nanoscale

    NASA Astrophysics Data System (ADS)

    Wagenaar, J. J. T.; den Haan, A. M. J.; de Voogd, J. M.; Bossoni, L.; de Jong, T. A.; de Wit, M.; Bastiaans, K. M.; Thoen, D. J.; Endo, A.; Klapwijk, T. M.; Zaanen, J.; Oosterkamp, T. H.

    2016-07-01

    Nuclear spin-lattice relaxation times are measured on copper using magnetic-resonance force microscopy performed at temperatures down to 42 mK. The low temperature is verified by comparison with the Korringa relation. Measuring spin-lattice relaxation times locally at very low temperatures opens up the possibility to measure the magnetic properties of inhomogeneous electron systems realized in oxide interfaces, topological insulators, and other strongly correlated electron systems such as high-Tc superconductors.

  5. The use of election paramagnetic resonance spectroscopy in early preformulation experiments: the impact of different experimental formulations on the release of a lipophilic spin probe into gastric juice.

    PubMed

    Bittner, B; Isel, H; Mountfield, R J

    2001-03-01

    The lipophilic spin probe TEMPOL-benzoate was dissolved in different experimental formulations, including polyethylene glycol 400 (PEG 400), Miglyol, glycerol monooleate (GMO), and Cremophor RH-40. Samples were measured by electron paramagnetic resonance (EPR) spectroscopy before and after addition to human gastric juice. The distance between the first and the third peak in the EPR spectrum (2a(N)) was measured to monitor the polarity of the spin probe's microenvironment. Moreover, the ratio between the signal amplitudes of the second and the third peak (a/b ratio) was used to monitor the mobility of the spin probe in a certain formulation. Thus, by calculating 2a(N) and the a/b ratio of the EPR spectra it was possible to determine a potential release of the spin probe from different formulations into gastric juice. It was found that oily and surface-active vehicles (Miglyol, Cremophor RH-40, and GMO) were more suitable to protect a lipophilic compound from being released within a gastric environment than PEG 400. Our results demonstrate that EPR spectroscopy seems to be a promising tool in early preformulation experiments to monitor the release of spin probes from formulations of different nature. This kind of experiment can be of value for the optimization of exploratory formulations.

  6. GIAO-DFT isotropic magnetic shielding constants and spin-spin coupling of tartaric acid in water solution

    NASA Astrophysics Data System (ADS)

    Fideles, Bruna; Oliveira, Leonardo B. A.; Colherinhas, Guilherme

    2016-01-01

    We investigate the nuclear isotropic shielding constants and spin-spin coupling for oxygen and carbons atoms of isomers of tartaric acid in gas phase and in water solutions by Monte Carlo simulation and quantum mechanics calculations using the GIAO-B3LYP approach. Solute polarization effects are included iteratively and play an important role in the quantitative determination of shielding constants. Our MP2/aug-cc-pVTZ results show substantial increases of the dipole moment in solution as compared with the gas phase results (61-221%). The solvent effects on the σ(13O) values are in general small. More appreciable solvent effects can be seen on the σ(17O) and J(Csbnd O).

  7. Spin excitations in the quasi-two-dimensional charge-ordered insulator α -(BEDT-TTF ) 2I3 probed via 13C NMR

    NASA Astrophysics Data System (ADS)

    Ishikawa, Kyohei; Hirata, Michihiro; Liu, Dong; Miyagawa, Kazuya; Tamura, Masafumi; Kanoda, Kazushi

    2016-08-01

    The spin excitations from the nonmagnetic charge-ordered insulating state of α -(BEDT-TTF ) 2I3 at ambient pressure have been investigated by probing the static and low-frequency dynamic spin susceptibilities via site-selective nuclear magnetic resonance at 13C sites. The site-dependent values of the shift and the spin-lattice relaxation rate 1 /T1 below the charge-ordering transition temperature (TCO≈135 K ) demonstrate a spin density imbalance in the unit cell, in accord with the charge-density ratio reported earlier. The shift and 1 /T1 show activated temperature dependence with a static (shift) gap ΔS≈47 -52 meV and a dynamic (1 /T1 ) gap ΔR≈40 meV . The sizes of the gaps are well described in terms of a localized spin model, where spin-1/2 antiferromagnetic dimer chains are weakly coupled with each other.

  8. Synthesis of nucleic acid probes on membrane supports: a procedure for the removal of unincorporated precursors.

    PubMed

    Bhat, S P

    1990-01-01

    We have used DNA bound to small pieces of nylon membrane for the synthesis of radioactive probes. The DNA to be used for generating the probe(s) is first bound to nylon membranes and then introduced into the reaction mix. The labeling reaction takes place on the membrane and therefore allows easy removal of unincorporated precursors by simple washing for 1-2 min. The clean labeled probe is eluted from the membrane in formamide or in water and is ready for use. This DNA-membrane can be stored for reuse. Synthesis of probes on a solid support such as nylon membrane thus circumvents problems associated with chromatographic manipulations needed for the separation of labeled DNA from unicorporated precursors. Probes synthesized in this manner are as efficient in detecting nucleic acid sequences as those synthesized in solution. PMID:2321760

  9. Methods of staining target chromosomal DNA employing high complexity nucleic acid probes

    DOEpatents

    Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Ol'li-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

    2006-10-03

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

  10. Genetic Incorporation of the Unnatural Amino Acid p-Acetyl Phenylalanine into Proteins for Site-Directed Spin Labeling

    PubMed Central

    Evans, Eric G.B.; Millhauser, Glenn L.

    2016-01-01

    Site-directed spin labeling (SDSL) is a powerful tool for the characterization of protein structure and dynamics; however, its application in many systems is hampered by the reliance on unique and benign cysteine substitutions for the site-specific attachment of the spin label. An elegant solution to this problem involves the use of genetically encoded unnatural amino acids (UAAs) containing reactive functional groups that are chemically orthogonal to those of the 20 amino acids found naturally in proteins. These unique functional groups can then be selectively reacted with an appropriately functionalized spin probe. In this chapter, we detail the genetic incorporation of the ketone-bearing amino acid p-acetyl phenylalanine (pAcPhe) into recombinant proteins expressed in E. coli. Incorporation of pAcPhe is followed by chemoselective reaction of the ketone side chain with a hydroxylamine-functionalized nitroxide to afford the spin-labeled side chain “K1,” and we present two protocols for successful K1 labeling of proteins bearing site-specific pAcPhe. We outline the basic requirements for pAcPhe incorporation and labeling, with an emphasis on practical aspects that must be considered by the researcher if high yields of UAA incorporation and efficient labeling reactions are to be achieved. To this end, we highlight recent advances that have led to increased yields of pAcPhe incorporation, and discuss the use of aniline-based catalysts allowing for facile conjugation of the hydroxylamine spin label under mild reaction conditions. To illustrate the utility of K1 labeling in proteins where traditional cysteine-based SDSL methods are problematic, we site-specifically K1 label the cellular prion protein at two positions in the C-terminal domain and determine the interspin distance using double electron–electron resonance EPR. Recent advances in UAA incorporation and ketone-based bioconjugation, in combination with the commercial availability of all requisite

  11. Genetic Incorporation of the Unnatural Amino Acid p-Acetyl Phenylalanine into Proteins for Site-Directed Spin Labeling.

    PubMed

    Evans, Eric G B; Millhauser, Glenn L

    2015-01-01

    Site-directed spin labeling (SDSL) is a powerful tool for the characterization of protein structure and dynamics; however, its application in many systems is hampered by the reliance on unique and benign cysteine substitutions for the site-specific attachment of the spin label. An elegant solution to this problem involves the use of genetically encoded unnatural amino acids (UAAs) containing reactive functional groups that are chemically orthogonal to those of the 20 amino acids found naturally in proteins. These unique functional groups can then be selectively reacted with an appropriately functionalized spin probe. In this chapter, we detail the genetic incorporation of the ketone-bearing amino acid p-acetyl phenylalanine (pAcPhe) into recombinant proteins expressed in E. coli. Incorporation of pAcPhe is followed by chemoselective reaction of the ketone side chain with a hydroxylamine-functionalized nitroxide to afford the spin-labeled side chain "K1," and we present two protocols for successful K1 labeling of proteins bearing site-specific pAcPhe. We outline the basic requirements for pAcPhe incorporation and labeling, with an emphasis on practical aspects that must be considered by the researcher if high yields of UAA incorporation and efficient labeling reactions are to be achieved. To this end, we highlight recent advances that have led to increased yields of pAcPhe incorporation, and discuss the use of aniline-based catalysts allowing for facile conjugation of the hydroxylamine spin label under mild reaction conditions. To illustrate the utility of K1 labeling in proteins where traditional cysteine-based SDSL methods are problematic, we site-specifically K1 label the cellular prion protein at two positions in the C-terminal domain and determine the interspin distance using double electron-electron resonance EPR. Recent advances in UAA incorporation and ketone-based bioconjugation, in combination with the commercial availability of all requisite reagents

  12. Genetic Incorporation of the Unnatural Amino Acid p-Acetyl Phenylalanine into Proteins for Site-Directed Spin Labeling.

    PubMed

    Evans, Eric G B; Millhauser, Glenn L

    2015-01-01

    Site-directed spin labeling (SDSL) is a powerful tool for the characterization of protein structure and dynamics; however, its application in many systems is hampered by the reliance on unique and benign cysteine substitutions for the site-specific attachment of the spin label. An elegant solution to this problem involves the use of genetically encoded unnatural amino acids (UAAs) containing reactive functional groups that are chemically orthogonal to those of the 20 amino acids found naturally in proteins. These unique functional groups can then be selectively reacted with an appropriately functionalized spin probe. In this chapter, we detail the genetic incorporation of the ketone-bearing amino acid p-acetyl phenylalanine (pAcPhe) into recombinant proteins expressed in E. coli. Incorporation of pAcPhe is followed by chemoselective reaction of the ketone side chain with a hydroxylamine-functionalized nitroxide to afford the spin-labeled side chain "K1," and we present two protocols for successful K1 labeling of proteins bearing site-specific pAcPhe. We outline the basic requirements for pAcPhe incorporation and labeling, with an emphasis on practical aspects that must be considered by the researcher if high yields of UAA incorporation and efficient labeling reactions are to be achieved. To this end, we highlight recent advances that have led to increased yields of pAcPhe incorporation, and discuss the use of aniline-based catalysts allowing for facile conjugation of the hydroxylamine spin label under mild reaction conditions. To illustrate the utility of K1 labeling in proteins where traditional cysteine-based SDSL methods are problematic, we site-specifically K1 label the cellular prion protein at two positions in the C-terminal domain and determine the interspin distance using double electron-electron resonance EPR. Recent advances in UAA incorporation and ketone-based bioconjugation, in combination with the commercial availability of all requisite reagents

  13. Oxidation of tertiary amines by cytochrome p450-kinetic isotope effect as a spin-state reactivity probe.

    PubMed

    Li, Chunsen; Wu, Wei; Cho, Kyung-Bin; Shaik, Sason

    2009-08-24

    Two types of tertiary amine oxidation processes, namely, N-dealkylation and N-oxygenation, by compound I (Cpd I) of cytochrome P450 are studied theoretically using hybrid DFT calculations. All the calculations show that both N-dealkylation and N-oxygenation of trimethylamine (TMA) proceed preferentially from the low-spin (LS) state of Cpd I. Indeed, the computed kinetic isotope effects (KIEs) for the rate-controlling hydrogen abstraction step of dealkylation show that only the KIE(LS) fits the experimental datum, whereas the corresponding value for the high-spin (HS) process is much higher. These results second those published before for N,N-dimethylaniline (DMA), and as such, they further confirm the conclusion drawn then that KIEs can be a sensitive probe of spin state reactivity. The ferric-carbinolamine of TMA decomposes most likely in a non-enzymatic reaction since the Fe-O bond dissociation energy (BDE) is negative. The computational results reveal that in the reverse reaction of N-oxygenation, the N-oxide of aromatic amine can serve as a better oxygen donor than that of aliphatic amine to generate Cpd I. This capability of the N-oxo derivatives of aromatic amines to transfer oxygen to the heme, and thereby generate Cpd I, is in good accord with experimental data previously reported. PMID:19322770

  14. Terahertz probes of magnetic field induced spin reorientation in YFeO{sub 3} single crystal

    SciTech Connect

    Lin, Xian; Jiang, Junjie; Ma, Guohong; Jin, Zuanming; Wang, Dongyang; Tian, Zhen; Han, Jiaguang; Cheng, Zhenxiang

    2015-03-02

    Using the terahertz time-domain spectroscopy, we demonstrate the spin reorientation of a canted antiferromagnetic YFeO{sub 3} single crystal, by evaluating the temperature and magnetic field dependence of resonant frequency and amplitude for the quasi-ferromagnetic (FM) and quasi-antiferromagnetic modes (AFM), a deeper insight into the dynamics of spin reorientation in rare-earth orthoferrites is established. Due to the absence of 4f-electrons in Y ion, the spin reorientation of Fe sublattices can only be induced by the applied magnetic field, rather than temperature. In agreement with the theoretical predication, the frequency of FM mode decreases with magnetic field. In addition, an obvious step of spin reorientation phase transition occurs with a relatively large applied magnetic field of 4 T. By comparison with the family members of RFeO{sub 3} (R = Y{sup 3+} or rare-earth ions), our results suggest that the chosen of R would tailor the dynamical rotation properties of Fe ions, leading to the designable spin switching in the orthoferrite antiferromagnetic systems.

  15. Probing the population of the spin-orbit split levels in the actinide 5f states.

    PubMed

    Moore, K T; van der Laan, G; Tobin, J G; Chung, B W; Wall, M A; Schwartz, A J

    2006-03-01

    Spin-orbit interaction in the 5f states is believed to strongly influence exotic behaviors observed in actinide metals and compounds. Understanding these interactions and how they relate to the actinide series is of considerable importance. To address this issue, the branching ratio of the white-line peaks of the N4,5 edge for the light actinide metals, alpha-Th, alpha-U, and alpha-Pu were recorded using electron energy-loss spectroscopy (EELS) in a transmission electron microscope (TEM) and synchrotron-radiation-based X-ray absorption spectroscopy (XAS). Using the spin-orbit sum rule and the branching ratios from both experimental spectra and many-electron atomic spectral calculations, accurate values of the spin-orbit interaction, and thus the relative occupation of the j = 5/2 and 7/2 levels, are determined for the actinide 5f states. Results show that the spin-orbit sum rule works very well with both EELS and XAS spectra, needing little or no correction. This is important, since the high spatial resolution of a TEM can be used to overcome the problems of single-crystal growth often encountered with actinide metals, allowing acquisition of EELS spectra, and subsequent spin-orbit analysis, from nm-sized regions. The relative occupation numbers obtained by our method have been compared with recent theoretical results and they show a good agreement in their trend.

  16. Spin-wave thermal population as temperature probe in magnetic tunnel junctions

    NASA Astrophysics Data System (ADS)

    Le Goff, A.; Nikitin, V.; Devolder, T.

    2016-07-01

    We study whether a direct measurement of the absolute temperature of a Magnetic Tunnel Junction (MTJ) can be performed using the high frequency electrical noise that it delivers under a finite voltage bias. Our method includes quasi-static hysteresis loop measurements of the MTJ, together with the field-dependence of its spin wave noise spectra. We rely on an analytical modeling of the spectra by assuming independent fluctuations of the different sub-systems of the tunnel junction that are described as macrospin fluctuators. We illustrate our method on perpendicularly magnetized MgO-based MTJs patterned in 50 × 100 nm2 nanopillars. We apply hard axis (in-plane) fields to let the magnetic thermal fluctuations yield finite conductance fluctuations of the MTJ. Instead of the free layer fluctuations that are observed to be affected by both spin-torque and temperature, we use the magnetization fluctuations of the sole reference layers. Their much stronger anisotropy and their much heavier damping render them essentially immune to spin-torque. We illustrate our method by determining current-induced heating of the perpendicularly magnetized tunnel junction at voltages similar to those used in spin-torque memory applications. The absolute temperature can be deduced with a precision of ±60 K, and we can exclude any substantial heating at the spin-torque switching voltage.

  17. Probing the C₆₀ triplet state coupling to nuclear spins inside and out.

    PubMed

    Filidou, Vasileia; Mamone, Salvatore; Simmons, Stephanie; Karlen, Steven D; Anderson, Harry L; Kay, Christopher W M; Bagno, Alessandro; Rastrelli, Federico; Murata, Yasujiro; Komatsu, Koichi; Lei, Xuegong; Li, Yongjun; Turro, Nicholas J; Levitt, Malcolm H; Morton, John J L

    2013-09-13

    The photoexcitation of functionalized fullerenes to their paramagnetic triplet electronic state can be studied by pulsed electron paramagnetic resonance (EPR) spectroscopy, whereas the interactions of this state with the surrounding nuclear spins can be observed by a related technique: electron nuclear double resonance (ENDOR). In this study, we present EPR and ENDOR studies on a functionalized exohedral fullerene system, dimethyl[9-hydro (C60-Ih)[5,6]fulleren-1(9H)-yl]phosphonate (DMHFP), where the triplet electron spin has been used to hyperpolarize, couple and measure two nuclear spins. We go on to discuss the extension of these methods to study a new class of endohedral fullerenes filled with small molecules, such as H₂@C₆₀, and we relate the results to density functional calculations. PMID:23918718

  18. Combining of neutron spin echo and reflectivity: a new technique for probing surface and interface order

    NASA Astrophysics Data System (ADS)

    Major, J.; Dosch, H.; Felcher, G. P.; Habicht, K.; Keller, T.; te Velthuis, S. G. E.; Vorobiev, A.; Wahl, M.

    2003-08-01

    The recently proposed spin-echo resolved grazing-incidence scattering (SERGIS) uses the well-known neutron spin echo effect for encoding the momentum transfer in reflectometry. By the application of tilted magnetic-field borders, SERGIS measures the scattering angle in grazing incidence experiments in absence of any geometrical beam-defining tool, such as slits. The main difficulty in such set-ups is the realization of geometrically flat field borders. The possibility of the application of neutron resonance spin echo (NRSE) for such a purpose is discussed, where the field borders are defined by current sheets. Prototype SERGIS experiments performed on holographically made optical gratings at a NRSE triple-axis spectrometer are shown.

  19. Meissner effect probing of odd-frequency triplet pairing in superconducting spin valves

    NASA Astrophysics Data System (ADS)

    Alidoust, Mohammad; Halterman, Klaus; Linder, Jacob

    2014-02-01

    Superconducting correlations which are long ranged in magnetic systems have attracted much attention due to their spin-polarization properties and potential use in spintronic devices. Whereas experiments have demonstrated the slow decay of such correlations, it has proven more difficult to obtain a smoking gun signature of their odd-frequency character which is responsible, e.g., for their gapless behavior. Here we demonstrate that the magnetic susceptibility response of a normal metal in contact with a superconducting spin valve provides precisely this signature, namely, in the form of an anomalous positive Meissner effect, which may be tuned back to a conventional negative Meissner response simply by altering the magnetization configuration of the spin valve.

  20. Measurement of the proton $A_1$ and $A_2$ spin asymmetries. Probing Color Forces

    SciTech Connect

    Armstrong, Whitney

    2015-05-01

    The Spin Asymmetries of the Nucleon Experiment (SANE) measured the proton spin structure function $g_2$ in a range of Bjorken x, 0.3 < x < 0.8, where extraction of the twist-3 matrix element $d_2^p$ (an integral of $g_2$ weighted by $x^2$) is most sensitive. The data was taken from $Q^2$ equal to 2.5 $GeV^2$ up to 6.5 $GeV^2$. In this polarized electron scattering off a polarized hydrogen target experiment, two double spin asymmetries, A∥ and A⊥ were measured using the BETA (Big Electron Telescope Array) Detector. BETA consisted of a scintillator hodoscope, gas Cerenkov counter, lucite hodoscope and a large lead glass electromagnetic calorimeter. With a unique open geometry, a threshold gas Cerenkov detector allowed BETA to cleanly identify electrons for this inclusive experiment. A measurement of $d_2^p$ is compared to lattice QCD calculations.

  1. Terbium fluorescence as a sensitive, inexpensive probe for UV-induced damage in nucleic acids.

    PubMed

    El-Yazbi, Amira F; Loppnow, Glen R

    2013-07-01

    Much effort has been focused on developing methods for detecting damaged nucleic acids. However, almost all of the proposed methods consist of multi-step procedures, are limited, require expensive instruments, or suffer from a high level of interferences. In this paper, we present a novel simple, inexpensive, mix-and-read assay that is generally applicable to nucleic acid damage and uses the enhanced luminescence due to energy transfer from nucleic acids to terbium(III) (Tb(3+)). Single-stranded oligonucleotides greatly enhance the Tb(3+) emission, but duplex DNA does not. With the use of a DNA hairpin probe complementary to the oligonucleotide of interest, the Tb(3+)/hairpin probe is applied to detect ultraviolet (UV)-induced DNA damage. The hairpin probe hybridizes only with the undamaged DNA. However, the damaged DNA remains single-stranded and enhances the intrinsic fluorescence of Tb(3+), producing a detectable signal directly proportional to the amount of DNA damage. This allows the Tb(3+)/hairpin probe to be used for sensitive quantification of UV-induced DNA damage. The Tb(3+)/hairpin probe showed superior selectivity to DNA damage compared to conventional molecular beacons probes (MBs) and its sensitivity is more than 2.5 times higher than MBs with a limit of detection of 4.36±1.2 nM. In addition, this probe is easier to synthesize and more than eight times cheaper than MBs, which makes its use recommended for high-throughput, quantitative analysis of DNA damage.

  2. Long-Lived Hole Spin/Valley Polarization Probed by Kerr Rotation in Monolayer WSe2.

    PubMed

    Song, Xinlin; Xie, Saien; Kang, Kibum; Park, Jiwoong; Sih, Vanessa

    2016-08-10

    Time-resolved Kerr rotation and photoluminescence measurements are performed on MOCVD-grown monolayer tungsten diselenide (WSe2). We observe a surprisingly long-lived Kerr rotation signal (∼80 ns) at 10 K, which is attributed to spin/valley polarization of the resident holes. This polarization is robust to transverse magnetic field (up to 0.3 T). Wavelength-dependent measurements reveal that only excitation near the free exciton energy generates this long-lived spin/valley polarization. PMID:27466727

  3. Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids.

    PubMed

    Nguyen, Camha; Grimes, Jeffrey; Gerasimova, Yulia V; Kolpashchikov, Dmitry M

    2011-11-11

    Hybridization probes are often inefficient in the analysis of single-stranded DNA or RNA that are folded in stable secondary structures. A molecular beacon (MB) probe is a short DNA hairpin with a fluorophore and a quencher attached to opposite sides of the oligonucleotide. The probe is widely used in real-time analysis of specific DNA and RNA sequences. This study demonstrates how a conventional MB probe can be used for the analysis of nucleic acids that form very stable (T(m) > 80 °C) hairpin structures. Here we demonstrate that the MB probe is not efficient in direct analysis of secondary structure-folded analytes, whereas a MB-based tricomponent probe is suitable for these purposes. The tricomponent probe takes advantage of two oligonucleotide adaptor strands f and m. Each adaptor strand contains a fragment complementary to the analyte and a fragment complementary to a MB probe. In the presence of a specific analyte, the two adaptor strands hybridize to the analyte and the MB probe, thus forming a quadripartite complex. DNA strand f binds to the analyte with high affinity and unwinds its secondary structure. Strand m forms a stable complex only with the fully complementary analyte. The MB probe fluorescently reports the formation of the quadripartite associate. It was demonstrated that the DNA analytes folded in hairpin structures with stems containing 5, 6, 7, 8, 9, 11, or 13 base pairs can be detected in real time with the limit of detection (LOD) lying in the nanomolar range. The stability of the stem region in the DNA analyte did not affect the LOD. Analytes containing single base substitutions in the stem or in the loop positions were discriminated from the fully complementary DNA at room temperature. The tricomponent probe promises to simplify nucleic acid analysis at ambient temperatures in such applications as in vivo RNA monitoring, detection of pathogens, and single nucleotide polymorphism (SNP) genotyping by DNA microarrays.

  4. Membrane-Sugar Interactions Probed by Pulsed Electron Paramagnetic Resonance of Spin Labels.

    PubMed

    Konov, Konstantin B; Leonov, Dmitry V; Isaev, Nikolay P; Fedotov, Kirill Yu; Voronkova, Violeta K; Dzuba, Sergei A

    2015-08-13

    Sugars can stabilize biological systems under extreme desiccation and freezing conditions. Hypothetical molecular mechanisms suggest that the stabilization effect may be determined either by specific interactions of sugars with biological molecules or by the influence of sugars on the solvating shell of the biomolecule. To explore membrane-sugar interactions, we applied electron spin echo envelope modulation (ESEEM) spectroscopy, a pulsed version of electron paramagnetic resonance (EPR), to phospholipid bilayers with spin-labeled lipids added and solvated by aqueous deuterated sucrose and trehalose solutions. The phospholipids were 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). The spin-labeled lipids were 1,2-dipalmitoyl-sn-glycero-3-phospho(TEMPO)choline (T-PCSL), with spin-label TEMPO at the lipid polar headgroup. The deuterium ESEEM amplitude was calibrated using known concentrations of glassy deuterated sugar solvents. The data obtained indicated that the sugar concentration near the membrane surface obeyed a simple Langmuir model of monolayer adsorption, which assumes direct sugar-molecule bonding to the bilayer surface. PMID:26214261

  5. Diradicals acting through diamagnetic phenylene vinylene bridges: Raman spectroscopy as a probe to characterize spin delocalization

    SciTech Connect

    González, Sandra Rodríguez; Nieto-Ortega, Belén; González Cano, Rafael C.; López Navarrete, Juan T. E-mail: teodomiro@uma.es Casado, Juan E-mail: teodomiro@uma.es; Novoa, Juan J.; Mota, Fernando; Corro, Elena del; Taravillo, Mercedes; Baonza, Valentín G.

    2014-04-28

    We present a complete Raman spectroscopic study in two structurally well-defined diradical species of different lengths incorporating oligo p-phenylene vinylene bridges between two polychlorinated triphenylmethyl radical units, a disposition that allows sizeable conjugation between the two radicals through and with the bridge. The spectroscopic data are interpreted and supported by quantum chemical calculations. We focus the attention on the Raman frequency changes, interpretable in terms of: (i) bridge length (conjugation length); (ii) bridge conformational structure; and (iii) electronic coupling between the terminal radical units with the bridge and through the bridge, which could delineate through-bond spin polarization, or spin delocalization. These items are addressed by using the “oligomer approach” in conjunction with pressure and temperature dependent Raman spectroscopic data. In summary, we have attempted to translate the well-known strategy to study the electron (charge) structure of π−conjugated molecules by Raman spectroscopy to the case of electron (spin) interactions via the spin delocalization mechanism.

  6. Probing Spin-Orbit Coupling and Interlayer Coupling in Atomically Thin Molybdenum Disulfide Using Hydrostatic Pressure.

    PubMed

    Dou, Xiuming; Ding, Kun; Jiang, Desheng; Fan, Xiaofeng; Sun, Baoquan

    2016-01-26

    In two-dimensional transition-metal dichalcogenides, both spin-orbit coupling and interlayer coupling play critical roles in the electronic band structure and are desirable for the potential applications in spin electronics. Here, we demonstrate the pressure characteristics of the exciton absorption peaks (so-called excitons A, B and C) in monolayer, bilayer, and trilayer molybdenum disulfide (MoS2) by studying the reflectance spectra under hydrostatic pressure and performing the electronic band structure calculations based on density functional theory to account for the experimental observations. We find that the valence band maximum splitting at the K point in monolayer MoS2, induced by spin-orbit coupling, remains almost unchanged with increasing pressure applied up to 3.98 GPa, indicating that the spin-orbit coupling is insensitive to the pressure. For bilayer and trilayer MoS2, however, the splitting shows an increase with increasing pressure due to the pressure-induced strengthening of the interlayer coupling. The experimental results are in good agreement with the theoretical calculations. Moreover, the exciton C is identified to be the interband transition related to the van Hove singularity located at a special point which is approximately 1/4 of the total length of Γ-K away from the Γ point in the Brillouin zone. PMID:26745440

  7. Full spin polarization of complex ferrimagnetic bismuth iron garnet probed by magneto-optical Faraday spectroscopy

    NASA Astrophysics Data System (ADS)

    Deb, Marwan; Popova, Elena; Fouchet, Arnaud; Keller, Niels

    2013-06-01

    We investigate the spin-dependent electronic density of states near and above the Fermi level in bismuth iron garnet (BIG), Bi3Fe5O12, by magnetic circular dichroism and magneto-optical Faraday spectroscopy. BIG is a recently synthesized material, as its preparation requires special nonequilibrium conditions. Its scientific and applicative interest resides in huge specific Faraday rotation of the incident light, useful for magneto-optic applications. We show experimentally the presence of spin gaps in the conduction band as recently predicted theoretically by Oikawa [T. Oikawa, S. Suzuki, and K. Nakao, J. Phys. Soc. Jpn.JUPSAU0031-901510.1143/JPSJ.74.401 74, 401 (2005)]. In the range of photon energies, where full spin polarization is expected, completely asymmetric Faraday hysteresis loops were observed, similar to those observed in half-metals such as (Pr,La)0.7Ca0.3MnO3 and Fe3O4. These results were modeled using even and odd (with respect to magnetization) contributions into hysteresis loops. The odd contribution appears only in the energy ranges where the density of states is fully spin polarized and vanishes at the Curie temperature. These results open a new perspective for the use of bismuth iron garnet in optic spintronics at room temperature and above.

  8. A single molecular beacon probe is sufficient for the analysis of multiple nucleic acid sequences.

    PubMed

    Gerasimova, Yulia V; Hayson, Aaron; Ballantyne, Jack; Kolpashchikov, Dmitry M

    2010-08-16

    Molecular beacon (MB) probes are dual-labeled hairpin-shaped oligodeoxyribonucleotides that are extensively used for real-time detection of specific RNA/DNA analytes. In the MB probe, the loop fragment is complementary to the analyte: therefore, a unique probe is required for the analysis of each new analyte sequence. The conjugation of an oligonucleotide with two dyes and subsequent purification procedures add to the cost of MB probes, thus reducing their application in multiplex formats. Here we demonstrate how one MB probe can be used for the analysis of an arbitrary nucleic acid. The approach takes advantage of two oligonucleotide adaptor strands, each of which contains a fragment complementary to the analyte and a fragment complementary to an MB probe. The presence of the analyte leads to association of MB probe and the two DNA strands in quadripartite complex. The MB probe fluorescently reports the formation of this complex. In this design, the MB does not bind the analyte directly; therefore, the MB sequence is independent of the analyte. In this study one universal MB probe was used to genotype three human polymorphic sites. This approach promises to reduce the cost of multiplex real-time assays and improve the accuracy of single-nucleotide polymorphism genotyping.

  9. Design and synthesis of an activity-based protein profiling probe derived from cinnamic hydroxamic acid.

    PubMed

    Ai, Teng; Qiu, Li; Xie, Jiashu; Geraghty, Robert J; Chen, Liqiang

    2016-02-15

    In our continued effort to discover new anti-hepatitis C virus (HCV) agents, we validated the anti-replicon activity of compound 1, a potent and selective anti-HCV hydroxamic acid recently reported by us. Generally favorable physicochemical and in vitro absorption, distribution, metabolism, and excretion (ADME) properties exhibited by 1 made it an ideal parent compound from which activity-based protein profiling (ABPP) probe 3 was designed and synthesized. Evaluation of probe 3 revealed that it possessed necessary anti-HCV activity and selectivity. Therefore, we have successfully obtained compound 3 as a suitable ABPP probe to identify potential molecular targets of compound 1. Probe 3 and its improved analogs are expected to join a growing list of ABPP probes that have made important contributions to not only the studies of biochemical and cellular functions but also discovery of selective inhibitors of protein targets.

  10. Development of Peptide Nucleic Acid Probes for Detection of the HER2 Oncogene

    PubMed Central

    Song, Young K.; Evangelista, Jennifer; Aschenbach, Konrad; Johansson, Peter; Wen, Xinyu; Chen, Qingrong; Lee, Albert; Hempel, Heidi; Gheeya, Jinesh S.; Getty, Stephanie; Gomez, Romel; Khan, Javed

    2013-01-01

    Peptide nucleic acids (PNAs) have gained much interest as molecular recognition tools in biology, medicine and chemistry. This is due to high hybridization efficiency to complimentary oligonucleotides and stability of the duplexes with RNA or DNA. We have synthesized 15/16-mer PNA probes to detect the HER2 mRNA. The performance of these probes to detect the HER2 target was evaluated by fluorescence imaging and fluorescence bead assays. The PNA probes have sufficiently discriminated between the wild type HER2 target and the mutant target with single base mismatches. Furthermore, the probes exhibited excellent linear concentration dependence between 0.4 to 400 fmol for the target gene. The results demonstrate potential application of PNAs as diagnostic probes with high specificity for quantitative measurements of amplifications or over-expressions of oncogenes. PMID:23593123

  11. Error analyses for the delivery of a spinning probe to Jupiter

    NASA Technical Reports Server (NTRS)

    Hintz, G. R.; Longuski, J. M.

    1985-01-01

    The task of delivering the Galileo Probe to specified atmospheric entry conditions at Jupiter is especially challenging because tracking, trajectory corrections, and attitude adjustments are not possible after release of the Probe from the carrier vehicle. Statistical analysis of the spacecraft dynamics mapped into Probe dispersions in atmosphere-relative and relay-geometry parameters show that attitude stability, heating, and relay performance requirements can be satisfied. Reconstruction techniques are used to enhance estimates of the delivery parameters to permit correct interpretation of the scientific data for the Jovian atmosphere. A tradeoff which sacrifices some delivery accuracy and propellant is shown to guarantee satisfaction of a very tight reconstruction requirement for the trajectory considered in this report.

  12. Signal-on electrochemical Y or junction probe detection of nucleic acid.

    PubMed

    Shen, Zuliang; Nakayama, Shizuka; Semancik, Steve; Sintim, Herman O

    2012-08-01

    A methylene-blue (MB)-labeled molecular beacon junction probe allows for a signal-on electrochemical detection of nucleic acids via target recycling using endonucleases. Electron transfer is reduced when the MB is intercalated in the stem of the molecular beacon, but then electron transfer from MB to a gold electrode is enhanced upon cleavage of the junction probe due to increased probability of MB approaching the electrode when attached to the more flexible ssDNA.

  13. Negative spin polarization of Mn2VGa probed by tunnel magnetoresistance.

    PubMed

    Klewe, Christoph; Meinert, Markus; Schmalhorst, Jan; Reiss, Günter

    2013-02-20

    The ferrimagnetic Heusler compound Mn(2)VGa is predicted to have a pseudogap in the majority spin channel, which should lead to a negative tunnel magnetoresistance (TMR). We synthesized epitaxial Mn(2)VGa thin films on MgO(001) substrates by dc and rf magnetron co-sputtering, resulting in nearly stoichiometric films. XRD analysis revealed a mostly B2 ordered structure for the films deposited at substrate temperatures of 350, 450, and 550 °C. Magnetic tunnel junctions with MgO barriers and CoFe counter-electrodes were fabricated. After post-annealing at up to T(a) = 425 °C negative TMR was obtained around zero bias, providing evidence for inverted spin polarization. The band structures of both electrodes were computed within the coherent potential approximation and used to calculate the TMR(V) characteristics, which were in good agreement with our experimental findings.

  14. Theoretical probing of inelastic spin-excitations in adatoms on surfaces

    NASA Astrophysics Data System (ADS)

    Lounis, Samir; Schweflinghaus, Benedikt; Dias, Manuel dos Santos; Bouhassoune, Mohammed; Muniz, Roberto B.; Costa, Antonio T.

    2014-12-01

    We review our recent work on the simulation, description and prediction of spin-excitations in adatoms and dimers deposited on metallic surfaces. This work done together with Douglas L. Mills, is an extension of his seminal contribution (with Pascal Lederer) published 50 years ago on the spin-dynamics of transition metal impurities embedded in transition metal hosts [Lederer et al. (1967)]. The main predictions of his model were verified experimentally with state of the art inelastic scanning tunneling spectroscopy on adatoms. Our formalism, presented in this review, is based on time-dependent density functional theory, combined with the Korringa-Kohn-Rostoker Green function method. Comparison to experiments is shown and discussed in detail. Our scheme enables the description and prediction of the main characteristics of these excitations, i.e. their resonance frequency, their lifetime and their behavior upon application of external perturbations such as a magnetic field.

  15. Negative spin polarization of Mn2VGa probed by tunnel magnetoresistance.

    PubMed

    Klewe, Christoph; Meinert, Markus; Schmalhorst, Jan; Reiss, Günter

    2013-02-20

    The ferrimagnetic Heusler compound Mn(2)VGa is predicted to have a pseudogap in the majority spin channel, which should lead to a negative tunnel magnetoresistance (TMR). We synthesized epitaxial Mn(2)VGa thin films on MgO(001) substrates by dc and rf magnetron co-sputtering, resulting in nearly stoichiometric films. XRD analysis revealed a mostly B2 ordered structure for the films deposited at substrate temperatures of 350, 450, and 550 °C. Magnetic tunnel junctions with MgO barriers and CoFe counter-electrodes were fabricated. After post-annealing at up to T(a) = 425 °C negative TMR was obtained around zero bias, providing evidence for inverted spin polarization. The band structures of both electrodes were computed within the coherent potential approximation and used to calculate the TMR(V) characteristics, which were in good agreement with our experimental findings. PMID:23327939

  16. Probing the antiferromagnetic long-range order with Glauber spin states

    NASA Technical Reports Server (NTRS)

    Cabrera, Guillermo G.

    1994-01-01

    It is well known that the ground state of low-dimensional antiferromagnets deviates from Neel states due to strong quantum fluctuations. Even in the presence of long-range order, those fluctuations produce a substantial reduction of the magnetic moment from its saturation value. Numerical simulations in anisotropic antiferromagnetic chains suggest that quantum fluctuations over Neel order appear in the form of localized reversal of pairs of neighboring spins. In this paper, we propose a coherent state representation for the ground state to describe the above situation. In the one-dimensional case, our wave function corresponds to a two-mode Glauber state, when the Neel state is used as a reference, while the boson fields are associated to coherent flip of spin pairs. The coherence manifests itself through the antiferromagnetic long-range order that survives the action of quantum fluctuations. The present representation is different from the standard zero-point spin wave state, and is asymptotically exact in the limit of strong anisotropy. The fermionic version of the theory, obtained through the Jordan-Wigner transformation, is also investigated.

  17. Quantum electronics. Probing Johnson noise and ballistic transport in normal metals with a single-spin qubit.

    PubMed

    Kolkowitz, S; Safira, A; High, A A; Devlin, R C; Choi, S; Unterreithmeier, Q P; Patterson, D; Zibrov, A S; Manucharyan, V E; Park, H; Lukin, M D

    2015-03-01

    Thermally induced electrical currents, known as Johnson noise, cause fluctuating electric and magnetic fields in proximity to a conductor. These fluctuations are intrinsically related to the conductivity of the metal. We use single-spin qubits associated with nitrogen-vacancy centers in diamond to probe Johnson noise in the vicinity of conductive silver films. Measurements of polycrystalline silver films over a range of distances (20 to 200 nanometers) and temperatures (10 to 300 kelvin) are consistent with the classically expected behavior of the magnetic fluctuations. However, we find that Johnson noise is markedly suppressed next to single-crystal films, indicative of a substantial deviation from Ohm's law at length scales below the electron mean free path. Our results are consistent with a generalized model that accounts for the ballistic motion of electrons in the metal, indicating that under the appropriate conditions, nearby electrodes may be used for controlling nanoscale optoelectronic, atomic, and solid-state quantum systems.

  18. Short-range, spin-dependent interactions of electrons: a sensitive probe for exotic pseudo-Goldstone bosons

    NASA Astrophysics Data System (ADS)

    Terrano, William; Adelberger, Eric; Lee, John; Heckel, Blayne

    2016-03-01

    We used a torsion pendulum and rotating attractor with 20-pole electron-spin distributions to probe dipole-dipole interactions mediated by exotic pseudo-Goldstone bosons with mbc2 <= 500 μ eV and coupling strengths up to 14 orders of magnitude weaker than electromagnetism. Our 95% confidence result indicates that any hidden global symmetry involving electrons must have a symmetry-breaking scale F >= 70 TeV, the highest reached in any laboratory experiment. We used an attractor with a 20-pole unpolarized mass distribution to improve laboratory bounds on CP -violating monopole-dipole forces with 1 . 5 μ eV

  19. Acidity characterization of heterogeneous catalysts by solid-state NMR spectroscopy using probe molecules.

    PubMed

    Zheng, Anmin; Liu, Shang-Bin; Deng, Feng

    2013-01-01

    Characterization of the surface acidic properties of solid acid catalysts is a key issue in heterogeneous catalysis. Important acid features of solid acids, such as their type (Brønsted vs. Lewis acid), distribution and accessibility (internal vs. external sites), concentration (amount), and strength of acid sites are crucial factors dictating their reactivity and selectivity. This short review provides information on different solid-state NMR techniques used for acidity characterization of solid acid catalysts. In particular, different approaches using probe molecules containing a specific nucleus of interest, such as pyridine-d5, 2-(13)C-acetone, trimethylphosphine, and trimethylphosphine oxide, are compared. Incorporation of valuable information (such as the adsorption structure, deprotonation energy, and NMR parameters) from density functional theory (DFT) calculations can yield explicit correlations between the chemical shift of adsorbed probe molecules and the intrinsic acid strength of solid acids. Methods that combine experimental NMR data with DFT calculations can therefore provide both qualitative and quantitative information on acid sites.

  20. High-resolution probing of local conformational changes in proteins by the use of multiple labeling: unfolding and self-assembly of human carbonic anhydrase II monitored by spin, fluorescent, and chemical reactivity probes.

    PubMed

    Hammarström, P; Owenius, R; Mårtensson, L G; Carlsson, U; Lindgren, M

    2001-06-01

    Two different spin labels, N-(1-oxyl-2,2,5,5-tetramethyl-3-pyrrolidinyl)iodoacetamide (IPSL) and (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate (MTSSL), and two different fluorescent labels 5-((((2-iodoacetyl)amino)-ethyl)amino)naphtalene-1-sulfonic acid (IAEDANS) and 6-bromoacetyl-2-dimetylaminonaphtalene (BADAN), were attached to the introduced C79 in human carbonic anhydrase (HCA II) to probe local structural changes upon unfolding and aggregation. HCA II unfolds in a multi-step manner with an intermediate state populated between the native and unfolded states. The spin label IPSL and the fluorescent label IAEDANS reported on a substantial change in mobility and polarity at both unfolding transitions at a distance of 7.4-11.2 A from the backbone of position 79. The shorter and less flexible labels BADAN and MTSSL revealed less pronounced spectroscopic changes in the native-to-intermediate transition, 6.6-9.0 A from the backbone. At intermediate guanidine (Gu)-HCl concentrations the occurrence of soluble but irreversibly aggregated oligomeric protein was identified from refolding experiments. At approximately 1 M Gu-HCl the aggregation was found to be essentially complete. The size and structure of the aggregates could be varied by changing the protein concentration. EPR measurements and line-shape simulations together with fluorescence lifetime and anisotropy measurements provided a picture of the self-assembled protein as a disordered protein structure with a representation of both compact as well as dynamic and polar environments at the site of the molecular labels. This suggests that a partially folded intermediate of HCA II self-assembles by both local unfolding and intermolecular docking of the intermediates vicinal to position 79. The aggregates were determined to be 40-90 A in diameter depending on the experimental conditions and spectroscopic technique used.

  1. Probing fatty acid metabolism in bacteria, cyanobacteria, green microalgae and diatoms with natural and unnatural fatty acids.

    PubMed

    Beld, Joris; Abbriano, Raffaela; Finzel, Kara; Hildebrand, Mark; Burkart, Michael D

    2016-04-01

    In both eukaryotes and prokaryotes, fatty acid synthases are responsible for the biosynthesis of fatty acids in an iterative process, extending the fatty acid by two carbon units every cycle. Thus, odd numbered fatty acids are rarely found in nature. We tested whether representatives of diverse microbial phyla have the ability to incorporate odd-chain fatty acids as substrates for their fatty acid synthases and their downstream enzymes. We fed various odd and short chain fatty acids to the bacterium Escherichia coli, cyanobacterium Synechocystis sp. PCC 6803, green microalga Chlamydomonas reinhardtii and diatom Thalassiosira pseudonana. Major differences were observed, specifically in the ability among species to incorporate and elongate short chain fatty acids. We demonstrate that E. coli, C. reinhardtii, and T. pseudonana can produce longer fatty acid products from short chain precursors (C3 and C5), while Synechocystis sp. PCC 6803 lacks this ability. However, Synechocystis can incorporate and elongate longer chain fatty acids due to acyl-acyl carrier protein synthetase (AasS) activity, and knockout of this protein eliminates the ability to incorporate these fatty acids. In addition, expression of a characterized AasS from Vibrio harveyii confers a similar capability to E. coli. The ability to desaturate exogenously added fatty acids was only observed in Synechocystis and C. reinhardtii. We further probed fatty acid metabolism of these organisms by feeding desaturase inhibitors to test the specificity of long-chain fatty acid desaturases. In particular, supplementation with thia fatty acids can alter fatty acid profiles based on the location of the sulfur in the chain. We show that coupling sensitive gas chromatography mass spectrometry to supplementation of unnatural fatty acids can reveal major differences between fatty acid metabolism in various organisms. Often unnatural fatty acids have antibacterial or even therapeutic properties. Feeding of short

  2. Probing fatty acid metabolism in bacteria, cyanobacteria, green microalgae and diatoms with natural and unnatural fatty acids.

    PubMed

    Beld, Joris; Abbriano, Raffaela; Finzel, Kara; Hildebrand, Mark; Burkart, Michael D

    2016-04-01

    In both eukaryotes and prokaryotes, fatty acid synthases are responsible for the biosynthesis of fatty acids in an iterative process, extending the fatty acid by two carbon units every cycle. Thus, odd numbered fatty acids are rarely found in nature. We tested whether representatives of diverse microbial phyla have the ability to incorporate odd-chain fatty acids as substrates for their fatty acid synthases and their downstream enzymes. We fed various odd and short chain fatty acids to the bacterium Escherichia coli, cyanobacterium Synechocystis sp. PCC 6803, green microalga Chlamydomonas reinhardtii and diatom Thalassiosira pseudonana. Major differences were observed, specifically in the ability among species to incorporate and elongate short chain fatty acids. We demonstrate that E. coli, C. reinhardtii, and T. pseudonana can produce longer fatty acid products from short chain precursors (C3 and C5), while Synechocystis sp. PCC 6803 lacks this ability. However, Synechocystis can incorporate and elongate longer chain fatty acids due to acyl-acyl carrier protein synthetase (AasS) activity, and knockout of this protein eliminates the ability to incorporate these fatty acids. In addition, expression of a characterized AasS from Vibrio harveyii confers a similar capability to E. coli. The ability to desaturate exogenously added fatty acids was only observed in Synechocystis and C. reinhardtii. We further probed fatty acid metabolism of these organisms by feeding desaturase inhibitors to test the specificity of long-chain fatty acid desaturases. In particular, supplementation with thia fatty acids can alter fatty acid profiles based on the location of the sulfur in the chain. We show that coupling sensitive gas chromatography mass spectrometry to supplementation of unnatural fatty acids can reveal major differences between fatty acid metabolism in various organisms. Often unnatural fatty acids have antibacterial or even therapeutic properties. Feeding of short

  3. Domain wall spin structures in mesoscopic Fe rings probed by high resolution SEMPA

    NASA Astrophysics Data System (ADS)

    Krautscheid, Pascal; Reeve, Robert M.; Lauf, Maike; Krüger, Benjamin; Kläui, Mathias

    2016-10-01

    We present a combined theoretical and experimental study of the energetic stability and accessibility of different domain wall spin configurations in mesoscopic magnetic iron rings. The evolution is investigated as a function of the width and thickness in a regime of relevance to devices, while Fe is chosen as a material due to its simple growth in combination with attractive magnetic properties including high saturation magnetization and low intrinsic anisotropy. Micromagnetic simulations are performed to predict the lowest energy states of the domain walls, which can be either the transverse or vortex wall spin structure, in good agreement with analytical models, with further simulations revealing the expected low temperature configurations observable on relaxation of the magnetic structure from saturation in an external field. In the latter case, following the domain wall nucleation process, transverse domain walls are found at larger widths and thicknesses than would be expected by just comparing the competing energy terms demonstrating the importance of metastability of the states. The simulations are compared to high spatial resolution experimental images of the magnetization using scanning electron microscopy with polarization analysis to provide a phase diagram of the various spin configurations. In addition to the vortex and simple symmetric transverse domain wall, a significant range of geometries are found to exhibit highly asymmetric transverse domain walls with properties distinct from the symmetric transverse wall. Simulations of the asymmetric walls reveal an evolution of the domain wall tilting angle with ring thickness which can be understood from the thickness dependencies of the contributing energy terms. Analysis of all the data reveals that in addition to the geometry, the influence of materials properties, defects and thermal activation all need to be taken into account in order to understand and reliably control the experimentally accessible

  4. Spin transport in intermediate-energy heavy-ion collisions as a probe of in-medium spin-orbit interactions

    NASA Astrophysics Data System (ADS)

    Xia, Yin; Xu, Jun; Li, Bao-An; Shen, Wen-Qing

    2016-11-01

    The spin up-down splitting of collective flows in intermediate-energy heavy-ion collisions as a result of the nuclear spin-orbit interaction is investigated within a spin- and isospin-dependent Boltzmann-Uehling-Uhlenbeck transport model SIBUU12. Using a Skyrme-type spin-orbit coupling quadratic in momentum, we found that the spin splittings of the directed flow and elliptic flow are largest in peripheral Au+Au collisions at beam energies of about 100-200 MeV/nucleon, and the effect is considerable even in smaller systems especially for nucleons with high transverse momenta. The collective flows of light clusters of different spin states are also investigated using an improved dynamical coalescence model with spin. Our study can be important in understanding the properties of in-medium nuclear spin-orbit interactions once the spin-dependent observables proposed in this work can be measured.

  5. Spin-Ml and El responses of nuclei probed by proton inelastic scattering

    NASA Astrophysics Data System (ADS)

    Tamii, Atsushi; Matsubara, Hiroaki

    2014-12-01

    We pick up two studies on the nuclear responses from the recent experiments of high-resolution proton inelastic scattering at the Research Center for Nuclear Physics, Osaka University; 1) study of the nuclear symmetry and the neutron skin thickness by the measurement of energy electric dipole (El) response of 208Pb, and 2) study of the tensor correlation in the ground state by the measurement of the spin-Ml responses of even-even self-conjugate nuclei in the sd-shell nuclei.

  6. Probing the spin state of a single electron trap by random telegraph signal.

    PubMed

    Xiao, M; Martin, I; Jiang, H W

    2003-08-15

    We have studied the random telegraph signal (RTS) generated by a single paramagnetic spin center adjacent to a submicrometer silicon metal-oxide-semiconductor field-effect transistor. An in-plane magnetic field induces a substantial change in the statistics of the RTS. We show that a model using the grand partition theorem can qualitatively explain the change in statistics of the RTS as a function of the applied magnetic field. While the data at high temperatures can be well described by this simple model, quantitative discrepancy increases as the temperature is lowered. PMID:12935055

  7. Dynamical instability of a spin spiral in an interacting Fermi gas as a probe of the Stoner transition

    SciTech Connect

    Conduit, G. J.; Altman, E.

    2010-10-15

    We propose an experiment to probe ferromagnetic phenomena in an ultracold Fermi gas, while alleviating the sensitivity to three-body loss and competing many-body instabilities. The system is initialized in a small pitch spin spiral, which becomes unstable in the presence of repulsive interactions. To linear order the exponentially growing collective modes exhibit critical slowing down close to the Stoner transition point. Also, to this order, the dynamics are identical on the paramagnetic and ferromagnetic sides of the transition. However, we show that scattering off the exponentially growing modes qualitatively alters the collective mode structure. The critical slowing down is eliminated and in its place a new unstable branch develops at large wave vectors. Furthermore, long-wavelength instabilities are quenched on the paramagnetic side of the transition. We study the experimental observation of the instabilities, specifically addressing the trapping geometry and how phase-contrast imaging will reveal the emerging domain structure. These probes of the dynamical phenomena could allow experiments to detect the transition point and distinguish between the paramagnetic and ferromagnetic regimes.

  8. Few-second-long correlation times in a quantum dot nuclear spin bath probed by frequency-comb nuclear magnetic resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Waeber, A. M.; Hopkinson, M.; Farrer, I.; Ritchie, D. A.; Nilsson, J.; Stevenson, R. M.; Bennett, A. J.; Shields, A. J.; Burkard, G.; Tartakovskii, A. I.; Skolnick, M. S.; Chekhovich, E. A.

    2016-07-01

    One of the key challenges in spectroscopy is the inhomogeneous broadening that masks the homogeneous spectral lineshape and the underlying coherent dynamics. Techniques such as four-wave mixing and spectral hole-burning are used in optical spectroscopy, and spin-echo in nuclear magnetic resonance (NMR). However, the high-power pulses used in spin-echo and other sequences often create spurious dynamics obscuring the subtle spin correlations important for quantum technologies. Here we develop NMR techniques to probe the correlation times of the fluctuations in a nuclear spin bath of individual quantum dots, using frequency-comb excitation, allowing for the homogeneous NMR lineshapes to be measured without high-power pulses. We find nuclear spin correlation times exceeding one second in self-assembled InGaAs quantum dots--four orders of magnitude longer than in strain-free III-V semiconductors. This observed freezing of the nuclear spin fluctuations suggests ways of designing quantum dot spin qubits with a well-understood, highly stable nuclear spin bath.

  9. Design and Evaluation of Peptide Nucleic Acid Probes for Specific Identification of Candida albicans

    PubMed Central

    Kim, Hyun-Joong

    2014-01-01

    Candida albicans is an important cause of systemic fungal infections, and rapid diagnostics for identifying and differentiating C. albicans from other Candida species are critical for the timely application of appropriate antimicrobial therapy, improved patient outcomes, and pharmaceutical cost savings. In this work, two 28S rRNA-directed peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) probes, P-Ca726 (targeting a novel region of the ribosome) and P-CalB2208 (targeting a previously reported region), were evaluated. Hybridization conditions were optimized by using both fluorescence microscopy (FM) and flow cytometry (FCM), and probes were screened for specificity and discriminative ability against a panel of C. albicans and various nontarget Candida spp. The performance of these PNA probes was compared quantitatively against that of DNA probes or DNA probe/helper combinations directed against the same target regions. Ratiometric analyses of FCM results indicated that both the hybridization quality and yield of the PNA probes were higher than those of the DNA probes. In FCM-based comparisons of the PNA probes, P-Ca726 was found to be highly specific, showing 2.5- to 5.5-fold-higher discriminatory power for C. albicans than P-CalB2208. The use of formamide further improved the performance of the new probe. Our results reinforce the significant practical and diagnostic advantages of PNA probes over their DNA counterparts for FISH and indicate that P-Ca726 may be used advantageously for the rapid and specific identification of C. albicans in clinical and related applications, especially when combined with FCM. PMID:25428160

  10. Unconventional superconductivity in Y5Rh6Sn18 probed by muon spin relaxation.

    PubMed

    Bhattacharyya, Amitava; Adroja, Devashibhai; Kase, Naoki; Hillier, Adrian; Akimitsu, Jun; Strydom, Andre

    2015-01-01

    Conventional superconductors are robust diamagnets that expel magnetic fields through the Meissner effect. It would therefore be unexpected if a superconducting ground state would support spontaneous magnetics fields. Such broken time-reversal symmetry states have been suggested for the high-temperature superconductors, but their identification remains experimentally controversial. We present magnetization, heat capacity, zero field and transverse field muon spin relaxation experiments on the recently discovered caged type superconductor Y5Rh6Sn18 ( TC= 3.0 K). The electronic heat capacity of Y5Rh6Sn18 shows a T(3) dependence below Tc indicating an anisotropic superconducting gap with a point node. This result is in sharp contrast to that observed in the isostructural Lu5Rh6Sn18 which is a strong coupling s-wave superconductor. The temperature dependence of the deduced superfluid in density Y5Rh6Sn18 is consistent with a BCS s-wave gap function, while the zero-field muon spin relaxation measurements strongly evidences unconventional superconductivity through a spontaneous appearance of an internal magnetic field below the superconducting transition temperature, signifying that the superconducting state is categorized by the broken time-reversal symmetry. PMID:26286229

  11. Unconventional superconductivity in Y5Rh6Sn18 probed by muon spin relaxation

    PubMed Central

    Bhattacharyya, Amitava; Adroja, Devashibhai; Kase, Naoki; Hillier, Adrian; Akimitsu, Jun; Strydom, Andre

    2015-01-01

    Conventional superconductors are robust diamagnets that expel magnetic fields through the Meissner effect. It would therefore be unexpected if a superconducting ground state would support spontaneous magnetics fields. Such broken time-reversal symmetry states have been suggested for the high—temperature superconductors, but their identification remains experimentally controversial. We present magnetization, heat capacity, zero field and transverse field muon spin relaxation experiments on the recently discovered caged type superconductor Y5Rh6Sn18 ( TC= 3.0 K). The electronic heat capacity of Y5Rh6Sn18 shows a T3 dependence below Tc indicating an anisotropic superconducting gap with a point node. This result is in sharp contrast to that observed in the isostructural Lu5Rh6Sn18 which is a strong coupling s—wave superconductor. The temperature dependence of the deduced superfluid in density Y5Rh6Sn18 is consistent with a BCS s—wave gap function, while the zero-field muon spin relaxation measurements strongly evidences unconventional superconductivity through a spontaneous appearance of an internal magnetic field below the superconducting transition temperature, signifying that the superconducting state is categorized by the broken time-reversal symmetry. PMID:26286229

  12. Unconventional superconductivity in Y5Rh6Sn18 probed by muon spin relaxation.

    PubMed

    Bhattacharyya, Amitava; Adroja, Devashibhai; Kase, Naoki; Hillier, Adrian; Akimitsu, Jun; Strydom, Andre

    2015-08-19

    Conventional superconductors are robust diamagnets that expel magnetic fields through the Meissner effect. It would therefore be unexpected if a superconducting ground state would support spontaneous magnetics fields. Such broken time-reversal symmetry states have been suggested for the high-temperature superconductors, but their identification remains experimentally controversial. We present magnetization, heat capacity, zero field and transverse field muon spin relaxation experiments on the recently discovered caged type superconductor Y5Rh6Sn18 ( TC= 3.0 K). The electronic heat capacity of Y5Rh6Sn18 shows a T(3) dependence below Tc indicating an anisotropic superconducting gap with a point node. This result is in sharp contrast to that observed in the isostructural Lu5Rh6Sn18 which is a strong coupling s-wave superconductor. The temperature dependence of the deduced superfluid in density Y5Rh6Sn18 is consistent with a BCS s-wave gap function, while the zero-field muon spin relaxation measurements strongly evidences unconventional superconductivity through a spontaneous appearance of an internal magnetic field below the superconducting transition temperature, signifying that the superconducting state is categorized by the broken time-reversal symmetry.

  13. Signal turn-on probe for nucleic acid detection based on (19)F nuclear magnetic resonance.

    PubMed

    Sakamoto, Takashi; Shimizu, Yu-ki; Sasaki, Jun; Hayakawa, Hikaru; Fujimoto, Kenzo

    2011-01-01

    To image gene expression in vivo, we designed and synthesized a novel signal turn-on probe for (19)F nuclear magnetic resonance (MR) imaging based on paramagnetic relaxation enhancement. The stem-loop structured oligodeoxyribonucleotide (ODN) having a molecular beacon sequence for point mutated K-ras mRNA was doubly labeled with bis(trifluoromethyl)benzene moiety and Gd-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid chelate moiety at the each termini of the ODN probe, respectively. We found that the (19)F MR signal of the bis(trifluoromethyl)benzene moiety tethered at the 5' termini of the probe turned on by the addition of complementary ODN. The probe has the potential to image gene expressions in vivo.

  14. Probing the Binding Site of Bile Acids in TGR5.

    PubMed

    Macchiarulo, Antonio; Gioiello, Antimo; Thomas, Charles; Pols, Thijs W H; Nuti, Roberto; Ferrari, Cristina; Giacchè, Nicola; De Franco, Francesca; Pruzanski, Mark; Auwerx, Johan; Schoonjans, Kristina; Pellicciari, Roberto

    2013-12-12

    TGR5 is a G-protein-coupled receptor (GPCR) mediating cellular responses to bile acids (BAs). Although some efforts have been devoted to generate homology models of TGR5 and draw structure-activity relationships of BAs, none of these studies has hitherto described how BAs bind to TGR5. Here, we present an integrated computational, chemical, and biological approach that has been instrumental to determine the binding mode of BAs to TGR5. As a result, key residues have been identified that are involved in mediating the binding of BAs to the receptor. Collectively, these results provide new hints to design potent and selective TGR5 agonists. PMID:24900622

  15. Probing the Binding Site of Bile Acids in TGR5

    PubMed Central

    2013-01-01

    TGR5 is a G-protein-coupled receptor (GPCR) mediating cellular responses to bile acids (BAs). Although some efforts have been devoted to generate homology models of TGR5 and draw structure–activity relationships of BAs, none of these studies has hitherto described how BAs bind to TGR5. Here, we present an integrated computational, chemical, and biological approach that has been instrumental to determine the binding mode of BAs to TGR5. As a result, key residues have been identified that are involved in mediating the binding of BAs to the receptor. Collectively, these results provide new hints to design potent and selective TGR5 agonists. PMID:24900622

  16. [Study on recovery and its influencing factors of ferulic acid and tetramethylpyrazine in cerebral microdialysis probe].

    PubMed

    Liao, Wei-guo; Wang, Li-sheng; Fan, Wen-tao; Li, Zhou; Yu, Jian-ye; Liao, Feng-yun; Wu, Yin-ai; Ba, Wen-qiang; Wang, Ding

    2015-11-01

    To establish a method for detecting microdialysis recovery of tetramethylpyrazine (TMP) and ferulic acid (FA) and investigating the influencing factors, providing the basis for further in vivo microdialysis experiments. The concentration of FA and TMP in dialysates were determined by high pressure liquid chromatography ( HPLC) and probe recovery were calculated respectively. The influence of the flow rates, medium concentration, temperature and in vivo probe stability on the recovery of FA and TMP were investigated by using concentration difference method (incremental method and decrement method). The recovery obtained by incremental method were similar to by decrement method. The in vitro recovery rate of FA and TMP decreased with the increase of 1-2.5 μL min(-1), and increased obviously with the temperature of 25-42 degrees C under the same conditions. The concentration of FA and TMP had no obvious effect on the probe recovery under the same flow rate. In addition, the recovery of TMP and FA remained stable and showed similar trends under the condition of four concentration cycles, indicating that the intra day reproducibility of the concentration difference method was good. The recovery of brain microdialysis probes in vivo 8 h maintained a relatively stable, but certain differences existed between different brain microdialysis probes, demonstrating that each probe was required for recovery correction in vivo experiment. Microdialysis sampling can be used for the local brain pharmacokinetic study of FA and TMP, and retrodialysis method can be used in probe recovery of FA and TMP in vivo. PMID:27071270

  17. Ratiometric emission fluorescent pH probe for imaging of living cells in extreme acidity.

    PubMed

    Niu, Weifen; Fan, Li; Nan, Ming; Li, Zengbo; Lu, Dongtao; Wong, Man Shing; Shuang, Shaomin; Dong, Chuan

    2015-03-01

    A novel ratiometric emission fluorescent probe, 1,1-dimethyl-2-[2-(quinolin-4-yl)vinyl]-1H-benzo[e]indole (QVBI), is facilely synthesized via ethylene bridging of benzoindole and quinoline. The probe exhibits ratiometric fluorescence emission (F(522nm)/F(630nm)) characteristics with pKa 3.27 and linear response to extreme-acidity range of 3.8-2.0. Also, its high fluorescence quantum yield (Φ = 0.89) and large Stokes shift (110 nm) are favorable. Moreover, QVBI possesses highly selective response to H(+) over metal ions and some bioactive molecules, good photostability, and excellent reversibility. The probe has excellent cell membrane permeability and is further applied successfully to monitor pH fluctuations in live cells and imaging extreme acidity in Escherichia coli cells without influence of autofluorescence and native cellular species in biological systems. PMID:25664606

  18. Measurements of d2n and A1n : Probing the neutron spin structure

    NASA Astrophysics Data System (ADS)

    Flay, D.; Posik, M.; Parno, D. S.; Allada, K.; Armstrong, W. R.; Averett, T.; Benmokhtar, F.; Bertozzi, W.; Camsonne, A.; Canan, M.; Cates, G. D.; Chen, C.; Chen, J.-P.; Choi, S.; Chudakov, E.; Cusanno, F.; Dalton, M. M.; Deconinck, W.; de Jager, C. W.; Deng, X.; Deur, A.; Dutta, C.; Fassi, L. El; Franklin, G. B.; Friend, M.; Gao, H.; Garibaldi, F.; Gilad, S.; Gilman, R.; Glamazdin, O.; Golge, S.; Gomez, J.; Guo, L.; Hansen, O.; Higinbotham, D. W.; Holmstrom, T.; Huang, J.; Hyde, C.; Ibrahim, H. F.; Jiang, X.; Jin, G.; Katich, J.; Kelleher, A.; Kolarkar, A.; Korsch, W.; Kumbartzki, G.; LeRose, J. J.; Lindgren, R.; Liyanage, N.; Long, E.; Lukhanin, A.; Mamyan, V.; McNulty, D.; Meziani, Z.-E.; Michaels, R.; Mihovilovič, M.; Moffit, B.; Muangma, N.; Nanda, S.; Narayan, A.; Nelyubin, V.; Norum, B.; Nuruzzaman, Oh, Y.; Peng, J. C.; Qian, X.; Qiang, Y.; Rakhman, A.; Ransome, R. D.; Riordan, S.; Saha, A.; Sawatzky, B.; Shabestari, M. H.; Shahinyan, A.; Širca, S.; Solvignon, P.; Subedi, R.; Sulkosky, V.; Tobias, W. A.; Troth, W.; Wang, D.; Wang, Y.; Wojtsekhowski, B.; Yan, X.; Yao, H.; Ye, Y.; Ye, Z.; Yuan, L.; Zhan, X.; Zhang, Y.; Zhang, Y.-W.; Zhao, B.; Zheng, X.; Jefferson Lab Hall A Collaboration

    2016-09-01

    We report on the results of the E06-014 experiment performed at Jefferson Lab in Hall A, where a precision measurement of the twist-3 matrix element d2 of the neutron (d2n) was conducted. The quantity d2n represents the average color Lorentz force a struck quark experiences in a deep inelastic electron scattering event off a neutron due to its interaction with the hadronizing remnants. This color force was determined from a linear combination of the third moments of the 3He spin structure functions, g1 and g2, after nuclear corrections had been applied to these moments. The structure functions were obtained from a measurement of the unpolarized cross section and of double-spin asymmetries in the scattering of a longitudinally polarized electron beam from a transversely and a longitudinally polarized 3He target. The measurement kinematics included two average Q2 bins of 3.2 GeV2 and 4.3 GeV2 , and Bjorken-x 0.25 ≤x ≤0.90 covering the deep inelastic and resonance regions. We have found that d2n is small and negative for ⟨Q2⟩ =3.2 GeV2 , and even smaller for ⟨Q2⟩ =4.3 GeV2 , consistent with the results of a lattice QCD calculation. The twist-4 matrix element f2n was extracted by combining our measured d2n with the world data on the first moment in x of g1n, Γ1n. We found f2n to be roughly an order of magnitude larger than d2n. Utilizing the extracted d2n and f2n data, we separated the Lorentz color force into its electric and magnetic components, FEy ,n and FBy ,n, and found them to be equal and opposite in magnitude, in agreement with the predictions from an instanton model but not with those from QCD sum rules. Furthermore, using the measured double-spin asymmetries, we have extracted the virtual photon-nucleon asymmetry on the neutron A1n, the structure function ratio g1n/F1n, and the quark ratios (Δ u +Δ u ¯)/(u +u ¯) and (Δ d +Δ d ¯)/(d +d ¯). These results were found to be consistent with deep-inelastic scattering world data and with the

  19. Bioavailability of xenobiotics in unsaturated soils – implications for nucleic acid based stable isotope probing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The use of stable isotopes to label phylogenetically informative biomolecules (phospholipid fatty acids, DNA, or RNA), typically referred to as stable isotope probing (SIP) has the potential of providing definitive evidence that a detected population is active in a specific process, if that process ...

  20. Discovery of boronic acid-based fluorescent probes targeting amyloid-beta plaques in Alzheimer's disease.

    PubMed

    Jung, Seung-Jin; Lee, Jun Young; Kim, Tae Ho; Lee, Dong-Eun; Jeon, Jongho; Yang, Seung Dae; Hur, Min Goo; Min, Jung-Joon; Park, Yong Dae

    2016-04-01

    A boronic acid-based fluorescent probe was developed for diagnosis of amyloid-β (Aβ) plaques from Alzheimer's disease (AD). Probe 4c, which included boronic acid as a functional group, exhibited a significant increase (64.37-fold, FAβ/F0) in fluorescence intensity as a response to Aβ aggregates, with a blue shift (105nm) in the maximum emission wavelength. We found that boronic acid as a functional group improved the binding affinity (KD value=0.79±0.05μM for 4c) for Aβ aggregates and confirmed that 4c selectively stained Aβ plaques in brain sections from APP/PS1 mice. Ex vivo fluorescence imaging using mice (normal and APP/PS1) also revealed that 4c was able to penetrate the blood-brain barrier (BBB) and to stain Aβ plaques in the brain. From these results, we believe that 4c will be useful as a fluorescent probe in preclinical research related to AD. Furthermore, we believe that our results with boronic acid also provide valuable information for the development of a probe for Aβ plaques. PMID:26927427

  1. Non-Gilbert-damping Mechanism in a Ferromagnetic Heusler Compound Probed by Nonlinear Spin Dynamics.

    PubMed

    Pirro, P; Sebastian, T; Brächer, T; Serga, A A; Kubota, T; Naganuma, H; Oogane, M; Ando, Y; Hillebrands, B

    2014-11-28

    The nonlinear decay of propagating spin waves in the low-Gilbert-damping Heusler film Co_{2}Mn_{0.6}Fe_{0.4}Si is reported. Here, two initial magnons with frequency f_{0} scatter into two secondary magnons with frequencies f_{1} and f_{2}. The most remarkable observation is that f_{1} stays fixed if f_{0} is changed. This indicates, that the f_{1} magnon mode has the lowest instability threshold, which, however, cannot be understood if only Gilbert damping is present. We show that the observed behavior is caused by interaction of the magnon modes f_{1} and f_{2} with the thermal magnon bath. This evidences a significant contribution of the intrinsic magnon-magnon scattering mechanisms to the magnetic damping in high-quality Heusler compounds.

  2. Probing Structure and Dynamics of Protein Assemblies by Magic Angle Spinning NMR Spectroscopy

    PubMed Central

    Yan, Si; Suiter, Christopher L.; Hou, Guangjin; Zhang, Huilan; Polenova, Tatyana

    2013-01-01

    CONSPECTUS In living organisms, biological molecules often organize into multi-component complexes. Such assemblies consist of various proteins and carry out essential functions, ranging from cell division, transport, and energy transduction to catalysis, signaling, and viral infectivity. To understand the biological functions of these assemblies, in both healthy and disease states, researchers need to study their three-dimensional architecture and molecular dynamics. To date, the large size, the lack of inherent long-range order, and insolubility have made atomic-resolution studies of many protein assemblies challenging or impractical using traditional structural biology methods such as X-ray diffraction and solution NMR spectroscopy. In the past ten years, we have focused our work on the development and application of magic angle spinning solid-state NMR (MAS NMR) methods to characterize large protein assemblies at atomic-level resolution. In this Account, we discuss the rapid progress in the field of MAS NMR spectroscopy, citing work from our laboratory and others on methodological developments that have facilitated the in-depth analysis of biologically important protein assemblies. We emphasize techniques that yield enhanced sensitivity and resolution, such as fast MAS (spinning frequencies of 40 kHz and above) and non-uniform sampling protocols for data acquisition and processing. We also discuss the experiments for gaining distance restraints and for recoupling anisotropic tensorial interactions under fast MAS conditions. We give an overview of sample preparation approaches when working with protein assemblies. Following the overview of contemporary MAS NMR methods, we present case studies into the structure and dynamics of two classes of biological systems under investigation in our laboratory. We will first turn our attention to cytoskeletal microtubule motor proteins including mammalian dynactin and dynein light chain 8. We will then discuss protein

  3. Probing the enhanced superconductivity and chiral edge current in spin-triplet superconductor strontium ruthenate

    NASA Astrophysics Data System (ADS)

    Ying, Yiqun Alex

    This dissertation aims at providing insight into the mechanism of spin-triplet superconductivity in Sr2RuO4, the only Cu-free layered perovskite material found to be superconducting. The work starts by looking at the Sr2RuO4-Ru eutectic phase featuring Ru islands embedded in a bulk crystal of Sr2RuO 4. The Sr2RuO4-Ru interface was found to be atomically smooth. Surprisingly, even such a clean interface appears not to allow the proximity effect of spin-triplet superconducting gap to enter the Ru islands. The previously observed 3 K-phase superconductivity in this eutectic phase seems to occur away from the interface where dislocations are present. To pinpoint the enhanced superconductivity to dislocations, micrometer sized flakes of Sr2RuO4 were studied, in which the effect of dislocations on Tc can be studied without the influence of Ru islands. The origin of the 3 K-phase was shown to be the presence of dislocations, near which the crystalline symmetry is lowered. The reduced symmetry leads naturally to an enhanced Tc, as revealed by a phenomenologically theory. After that, a different experiment is presented. Unconventional Josephson coupling was shown to occur in ramp-type junctions on Sr2RuO 4 flakes. The chiral edge current was measured using Josephson interferometry. An upper limit of the edge current was obtained to be as small as 0.1 percent of the theoretically predicted value. Such an upper limit was found to be similar to the measured transport critical current density of the Sr 2RuO4 flakes. The results suggest that the interlayer coupling and the multiband nature of the electronic structure are important to the mechanism of superconductivity.

  4. Spin probe dynamics in relation to free volume in crystalline organics from ESR and PALS: Cyclohexane

    NASA Astrophysics Data System (ADS)

    Švajdlenková, H.; Zgardzinska, B.; Lukešová, M.; Bartoš, J.

    2016-01-01

    A joint external probe ESR and PALS study on cyclohexane (CHX) using stable free radical 2,2,6,6-tetra-methyl-1-piperidinyloxy (TEMPO) or ortho-positronium (o-Ps), respectively, is reported. The slow to fast transition of TEMPO occurs at the characteristic ESR temperature T50G coinciding with the solid to solid transition temperature, TSS. Moreover, o-Ps lifetime τ3(T50G) = 2.0 ns is close to an empirical rule τ3(T50G) = 2.17 ± 0.15 ns found for a series of amorphous glass-formers indicating that main transition of the TEMPO connected with the 'rigid' to plastic crystalline state transition in CHX occurs under the similar local free volume condition as in amorphous media.

  5. Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe

    PubMed Central

    Qin, Peter Z; Haworth, Ian S; Cai, Qi; Kusnetzow, Ana K; Grant, Gian Paola G; Price, Eric A; Sowa, Glenna Z; Popova, Anna; Herreros, Bruno; He, Honghang

    2008-01-01

    This protocol describes the procedures for measuring nanometer distances in nucleic acids using a nitroxide probe that can be attached to any nucleotide within a given sequence. Two nitroxides are attached to phosphorothioates that are chemically substituted at specific sites of DNA or RNA. Inter-nitroxide distances are measured using a four-pulse double electron–electron resonance technique, and the measured distances are correlated to the parent structures using a Web-accessible computer program. Four to five days are needed for sample labeling, purification and distance measurement. The procedures described herein provide a method for probing global structures and studying conformational changes of nucleic acids and protein/nucleic acid complexes. PMID:17947978

  6. Probing the structure of nucleic acids with Ni(II) complexes

    SciTech Connect

    Chen, Xiaoying.

    1992-01-01

    The structure of nucleic acids determines their biological function. Interest in the development of novel probes from structures of nucleic acid has led to the discovery of conformation-specific oxidation of guanine sites in DNA and RNA using Ni(II) complexes. The reaction is highly dependent upon the nature of Ni(II) complexes with the most important feature of a strong in-plane ligand field. The unique properties of Ni(II) complexes combining redox and coordination features provide sensitive probes for nucleic acid conformation. One of these nickel complexes, NiCR, has been shown to selectively promote cleavage of DNA at guanine sites held accessible through the formation of unusual secondary structures such as ends, mismatches, bulges and loops. An unique mechanism for the base and conformation-specific oxidation of DNA promoted by Ni(II) complexes is proposed, involving direct ligation of nickel to N-7 of guanine delivering a non-diffusible oxidizing species. NiCR has been proved to be a sensitive and predictable probe for the tertiary structure of RNAs. The specific sites of oxidation of tRNS[sup phe] promoted by NiCR correspond to the most accessible guanine residues determined by theoretic calculations. NiCR has also been successfully applied to probe the tertiary structure of self-splicing Tetrahymena pre-rRNA intron, and has provided important information about the folding of this intron, especially in the region of the catalytic core.

  7. Superior structure stability and selectivity of hairpin nucleic acid probes with an L-DNA stem.

    PubMed

    Kim, Youngmi; Yang, Chaoyong James; Tan, Weihong

    2007-01-01

    Hairpin nucleic acid probes have been highly useful in many areas, especially for intracellular and in vitro nucleic acid detection. The success of these probes can be attributed to the ease with which their conformational change upon target binding can be coupled to a variety of signal transduction mechanisms. However, false-positive signals arise from the opening of the hairpin due mainly to thermal fluctuations and stem invasions. Stem invasions occur when the stem interacts with its complementary sequence and are especially problematic in complex biological samples. To address the problem of stem invasions in hairpin probes, we have created a modified molecular beacon that incorporates unnatural enantiomeric l-DNA in the stem and natural d-DNA or 2'-O-Me-modified RNA in the loop. l-DNA has the same physical characteristics as d-DNA except that l-DNA cannot form stable duplexes with d-DNA. Here we show that incorporating l-DNA into the stem region of a molecular beacon reduces intra- and intermolecular stem invasions, increases the melting temperature, improves selectivity to its target, and leads to enhanced bio-stability. Our results suggest that l-DNA is useful for designing functional nucleic acid probes especially for biological applications.

  8. Ultrafast high harmonics for probing the fastest spin and charge dynamics in magnetic materials

    NASA Astrophysics Data System (ADS)

    Grychtol, Patrick

    2015-03-01

    Ultrafast light based on the high-harmonic up-conversion of femtosecond laser pulses have been successfully employed to access resonantly enhanced magnetic contrast at the Mabsorption edges of the 3d ferromagnets Fe, Co and Ni in a table-top setup. Thus, it has been possible to study element-specific dynamics in magnetic materials at femtosecond time scales in a laboratory environment, providing a wealth of opportunities for a greater fundamental understanding of correlated phenomena in solid-state matter. However, these investigations have so far been limited to linear polarized harmonics, since most techniques by which circular soft x-rays can be generated are highly inefficient reducing the photon flux to a level unfit for scientific applications. Besides presenting key findings of our ultrafast studies on charge and spin dynamics, we introduce a simple setup which allows for the efficient generation of circular harmonics bright enough for XMCD experiments. Our work thus represents a critical advance that enables element-specific imaging and spectroscopy of multiple elements simultaneously in magnetic and other chiral media with very high spatial and temporal resolution on the tabletop. In collboration with Ronny Knut, Emrah Turgut, Dmitriy Zusin, Christian Gentry, Henry Kapteyn, Margaret Murnane, JILA, University of Colorado, Boulder; Justin Shaw, Hans Nembach, Tom Silva, Electromagnetics Division, NIST, Boulder, CO; and Ofer Kfir, Avner Fleischer, Oren Cohen, Extreme Nonlinear Optics Group, Solid State Institute, Technion, Israel.

  9. Probing the holographic principle using dynamical gauge effects from open spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Zhao, Jianshi; Price, Craig; Liu, Qi; Gemelke, Nathan

    2016-05-01

    Dynamical gauge fields result from locally defined symmetries and an effective over-labeling of quantum states. Coupling atoms weakly to a reservoir of laser modes can create an effective dynamical gauge field purely due to the disregard of information in the optical states. Here we report measurements revealing effects of open spin-orbit coupling in a system where an effective model can be formed from a non-abelian SU(2) × U(1) field theory following the Yang-Mills construct. Forming a close analogy to dynamical gauge effects in quantum chromodynamics, we extract a measure of atomic motion which reveals the analog of a closing mass gap for the relevant gauge boson, shedding insight on long standing open problems in gauge-fixing scale anomalies. Using arguments following the holographic principle, we measure scaling relations which can be understood by quantifying information present in the local potential. New prospects using these techniques for developing fractionalization of multi-particle and macroscopic systems using dissipative and non-abelian gauge fields will also be discussed. We acknowledge support from NSF Award No. 1068570, and the Charles E. Kaufman Foundation.

  10. Electronic Structure of Hydrogen Donors in Semiconductors and Insulators Probed by Muon Spin Rotation

    NASA Astrophysics Data System (ADS)

    Shimomura, Koichiro; Ito, Takashi U.

    2016-09-01

    Hydrogen in semiconductors and insulators plays a crucial role in their electric conductivity. Substantial experimental and theoretical efforts have been made to establish this hypothesis in the last decade, and the muon spin rotation technique has played a pioneering role. Positive muons implanted into such low-carrier systems often form a muonium (an analogue of hydrogen, the bound state of a positive muon and an electron). Although its dynamical aspect may be different from the heavier hydrogen, the electronic structure of the muonium is expected to be identical to that of hydrogen after a small correction of the reduced mass (˜0.4%). Since the discovery of a shallow muonium in CdS, its properties have been intensively studied in many semiconductors and insulators, and then it was interpreted as a possible origin of n-type conductivity under the context of a classical shallow donor model. In this article, we will describe the principle of muonium experiments and survey recent achievements in this field.

  11. Magnetostatic spin wave modes in trilayer nanowire arrays probed using ferromagnetic resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhou, X.; Adeyeye, A. O.

    2016-08-01

    We investigate the spin wave modes in asymmetric trilayer [N i80F e20(10 nm ) /Cu (tCu) /N i80F e20(30 nm ) ] nanowire structures as a function of the Cu thickness (tCu) in the range from 0 to 20 nm using perpendicular ferromagnetic resonance (pFMR) spectroscopy. For tCu=0 nm , corresponding to the 40 nm thick single layer N i80F e20 nanowires, both the fundamental and first order modes are observed in the saturation region. However, for the trilayer structures, two additional modes, which are the fundamental and first order optical modes, are observed. We also found that the resonance fields of these modes are markedly sensitive to the Cu thickness due to the competing effects of interlayer exchange coupling and magnetostatic dipolar coupling. When the tCu≥10 nm , the fundamental optical mode is more pronounced. Our experimental results are in quantitative agreement with the dynamic micromagnetic simulations.

  12. Nucleon transverse spin structure in the valence quark region: Probing color forces

    NASA Astrophysics Data System (ADS)

    Meziani, Zein-Eddine

    2016-03-01

    The first direct observation that protons are not elementary objects and the discovery that their constituents, dubbed ``partons'', are point-like particles made use of elastic and deep inelastic (DIS) scattering of electrons off protons, respectively. With the advent of quantum chromodynamics (QCD), the modern theory of strong interactions, partons were identified as quarks and gluons and an intensive theoretical effort is still underway to grasp the full consequences of this theory. Recently scattering experiments at Jefferson Lab using a 6 GeV polarized electron beam and polarized targets at high luminosity have allowed us to delve deeper into the role of partons dynamics in the nucleon (proton and neutron). These studies of dynamics in the valence quark region are helping us unravel the rich but elusive structure of the confined building blocks of matter and impacting our understanding of the non-perturbative aspects of QCD through comparisons with lattice QCD and models. I will present recent results of measurements of the average color electric and magnetic forces acting on the struck quark in a proton, due to the remnant ``di-quark'' as it start its journey to emerge as a hadron. A flavor separation of the color force acting on the up and down quarks is carried out by combining measurements on polarized protons and neutrons. I will conclude by describing the planned measurements with the 12 GeV upgrade of Jefferson Lab to complete our picture of nucleon transverse spin structure in the valence region.

  13. Oxidation of freestanding silicon nanocrystals probed with electron spin resonance of interfacial dangling bonds

    NASA Astrophysics Data System (ADS)

    Pereira, R. N.; Rowe, D. J.; Anthony, R. J.; Kortshagen, U.

    2011-04-01

    The oxidation of freestanding silicon nanocrystals (Si-NCs) passivated with Si-H bonds has been investigated for a wide range of oxidation times (from a few minutes to several months) by means of electron spin resonance (ESR) of dangling bonds (DBs) naturally incorporated at the interface between the NC core and the developing oxide shell. These measurements are complemented with surface chemistry analysis from Fourier transform infrared spectroscopy. Two surface phenomena with initiation time thresholds of 15 min and 30 h are inferred from the dependence of ESR spectra on oxidation time. The first initiates before oxidation of surface Si-Si bonds and destruction of the NC hydrogen termination takes place (induction period) and results in a decrease of the DB density and a localization of the DB orbital at the central Si atom. Within the Cabrera-Mott oxidation mechanism, we associate this process with the formation of intermediate interfacial configurations, resulting from surface adsorption of water and oxygen molecules. The second surface phenomenon leads to a steep increase of the defect density and correlates with the formation of surface Si-O-Si bridges, lending experimental support to theoretically proposed mechanisms for interfacial defect formation involving the emission of Si interstitials at the interface between crystalline Si and the growing oxide.

  14. A Comparison of NMR Spectra Obtained for Solid-Phase-Synthesis Resins Using Conventional High-Resolution, Magic-Angle-Spinning, and High-Resolution Magic-Angle-Spinning Probes

    NASA Astrophysics Data System (ADS)

    Keifer, Paul A.; Baltusis, Laima; Rice, David M.; Tymiak, Adrienne A.; Shoolery, James N.

    It has recently been shown that high-resolution 1H NMR spectra can be obtained for samples covalently bound to polystyrene-based (Tentagel) solid-phase-synthesis resins by the use of magic-angle spinning (MAS) combined with high-resolution-probe technology. The attainable spectral resolution in the 1H and 13C NMR spectra of these resins is affected by molecular mobility and magnetic-susceptibility mismatches, both within the sample and in the probe itself. Using new high-resolution MAS probes called Nano·nmr probes, the importance of magnetic-susceptibility matching in the construction of these probes is demonstrated, and the limitations of using MAS alone to generate line narrowing in both 1H and 13C NMR are explored using a solvent-swollen functionalized Wang resin. The effects of presaturation, temperature, spin rate, and different solvents upon spectral quality have also been investigated, and advanced 1D- and 2D-experimental capability is demonstrated. This ability to generate high-resolution NMR spectra of samples still bound to the resins is expected to be of extreme interest in not only solid-phase synthesis, but also in the rapidly growing field of combinatorial chemistry.

  15. Electron spin resonance probing of fundamental point defects in nanometer-sized silica particles

    NASA Astrophysics Data System (ADS)

    Stesmans, A.; Clémer, K.; Afanas'Ev, V. V.

    2005-10-01

    Point defects in fumed ˜7-nm -sized silica nanoparticles have been studied by K - and Q -band electron spin resonance (ESR) following 10-eV irradiation used to photodissociate H from passivated defects. Various types of ESR-active point defects are revealed, including the familiar E' center (generic entity •SiO3 ), EX, the peroxy radical (POR), the methyl radical, and an unknown closely axially symmetric center ( g‖=2.0041 , g⊥=2.0027 ). The possible atomic nature of the latter is addressed. The E' defects, occurring in a maximum density of ˜1×10-3 per nanoparticle, are monitored as a function of thermal treatment in vacuum in the range 850-1115°C in order to assess specific physicochemical structural aspects of the particles. Experimental evidence is presented for the presence of two different systems of E' centers. The specific ESR parameters of the E' centers of one bath are found to be very similar to those of the E'γ center in bulk fused silica, while the second bath exhibits a different zero crossing g value and line shape, attributed to variations in local structure. It is inferred that the latter E' system pertains to the outer SiO2 layers, exposing a structural nature different from bulk glassy SiO2 . Besides PORs, large numbers of other oxygen-hole type defects appear to be present also. The exhaustive number of all oxygen-hole centers, including the PORs, is determined at ˜0.07 defects/nanoparticle, making this kind of defect highly unlikely as playing a substantial role in narrowing of the optical bandgap, in contrast with previous suggestion.

  16. STM probe on the surface electronic states of spin-orbit coupled materials

    NASA Astrophysics Data System (ADS)

    Zhou, Wenwen

    Spin-orbit coupling (SOC) is the interaction of an electron's intrinsic angular momentum (spin) with its orbital momentum. The strength of this interaction is proportional to Z4 where Z is the atomic number, so generally it is stronger in atoms with higher atomic number, such as bismuth (Z=83) and iridium (Z=77). In materials composed of such heavy elements, the prominent SOC can be sufficient to modify the band structure of the system and lead to distinct phase of matter. In recent years, SOC has been demonstrated to play a critical role in determining the unusual properties of a variety of compounds. SOC associated materials with exotic electronic states have also provided a fertile platform for studying emergent phenomena as well as new physics. As a consequence, the research on these interesting materials with any insight into understanding the microscopic origin of their unique properties and complex phases is of great importance. In this context, we implement scanning tunneling microscopy (STM) and spectroscopy (STS) to explore the surface states (SS) of the two major categories of SOC involved materials, Bi-based topological insulators (TI) and Ir-based transition metal oxides (TMO). As a powerful tool in surface science which has achieved great success in wide variety of material fields, STM/STS is ideal to study the local density of states of the subject material with nanometer length scales and is able to offer detailed information about the surface electronic structure. In the first part of this thesis, we report on the electronic band structures of three-dimensional TIs Bi2Te3 and Bi2Se 3. Topological insulators are distinct quantum states of matter that have been intensely studied nowadays. Although they behave like ordinary insulators in showing fully gapped bulk bands, they host a topologically protected surface state consisting of two-dimensional massless Dirac fermions which exhibits metallic behavior. Indeed, this unique gapless surface state is a

  17. Imaging thermal conductivity with nanoscale resolution using a scanning spin probe

    DOE PAGES

    Laraoui, Abdelghani; Aycock-Rizzo, Halley; Gao, Yang; Lu, Xi; Riedo, Elisa; Meriles, Carlos A.

    2015-11-20

    The ability to probe nanoscale heat flow in a material is often limited by lack of spatial resolution. Here, we use a diamond-nanocrystal-hosted nitrogen-vacancy centre attached to the apex of a silicon thermal tip as a local temperature sensor. We apply an electrical current to heat up the tip and rely on the nitrogen vacancy to monitor the thermal changes the tip experiences as it is brought into contact with surfaces of varying thermal conductivity. By combining atomic force and confocal microscopy, we image phantom microstructures with nanoscale resolution, and attain excellent agreement between the thermal conductivity and topographic maps.more » The small mass and high thermal conductivity of the diamond host make the time response of our technique short, which we demonstrate by monitoring the tip temperature upon application of a heat pulse. Our approach promises multiple applications, from the investigation of phonon dynamics in nanostructures to the characterization of heterogeneous phase transitions and chemical reactions in various solid-state systems.« less

  18. Imaging thermal conductivity with nanoscale resolution using a scanning spin probe

    SciTech Connect

    Laraoui, Abdelghani; Aycock-Rizzo, Halley; Gao, Yang; Lu, Xi; Riedo, Elisa; Meriles, Carlos A.

    2015-11-20

    The ability to probe nanoscale heat flow in a material is often limited by lack of spatial resolution. Here, we use a diamond-nanocrystal-hosted nitrogen-vacancy centre attached to the apex of a silicon thermal tip as a local temperature sensor. We apply an electrical current to heat up the tip and rely on the nitrogen vacancy to monitor the thermal changes the tip experiences as it is brought into contact with surfaces of varying thermal conductivity. By combining atomic force and confocal microscopy, we image phantom microstructures with nanoscale resolution, and attain excellent agreement between the thermal conductivity and topographic maps. The small mass and high thermal conductivity of the diamond host make the time response of our technique short, which we demonstrate by monitoring the tip temperature upon application of a heat pulse. Our approach promises multiple applications, from the investigation of phonon dynamics in nanostructures to the characterization of heterogeneous phase transitions and chemical reactions in various solid-state systems.

  19. Scanned probe imaging of nanoscale magnetism at cryogenic temperatures with a single-spin quantum sensor

    NASA Astrophysics Data System (ADS)

    Pelliccione, Matthew; Jenkins, Alec; Ovartchaiyapong, Preeti; Reetz, Christopher; Emmanouilidou, Eve; Ni, Ni; Bleszynski Jayich, Ania C.

    2016-08-01

    High-spatial-resolution magnetic imaging has driven important developments in fields ranging from materials science to biology. However, to uncover finer details approaching the nanoscale with greater sensitivity requires the development of a radically new sensor technology. The nitrogen-vacancy (NV) defect in diamond has emerged as a promising candidate for such a sensor on the basis of its atomic size and quantum-limited sensing capabilities. It has remained an outstanding challenge to implement the NV centre as a nanoscale scanning magnetic probe at cryogenic temperatures, however, where many solid-state systems exhibit non-trivial magnetic order. Here, we present NV magnetic imaging down to 6 K with 3 μT Hz-1/2 field sensitivity, and use the technique to image vortices in the iron pnictide superconductor BaFe2(As0.7P0.3)2 with critical temperature Tc = 30 K. The expansion of NV-based magnetic imaging to cryogenic temperatures will enable future studies of previously inaccessible nanoscale magnetism in condensed-matter systems.

  20. Imaging thermal conductivity with nanoscale resolution using a scanning spin probe

    PubMed Central

    Laraoui, Abdelghani; Aycock-Rizzo, Halley; Gao, Yang; Lu, Xi; Riedo, Elisa; Meriles, Carlos A.

    2015-01-01

    The ability to probe nanoscale heat flow in a material is often limited by lack of spatial resolution. Here, we use a diamond-nanocrystal-hosted nitrogen-vacancy centre attached to the apex of a silicon thermal tip as a local temperature sensor. We apply an electrical current to heat up the tip and rely on the nitrogen vacancy to monitor the thermal changes the tip experiences as it is brought into contact with surfaces of varying thermal conductivity. By combining atomic force and confocal microscopy, we image phantom microstructures with nanoscale resolution, and attain excellent agreement between the thermal conductivity and topographic maps. The small mass and high thermal conductivity of the diamond host make the time response of our technique short, which we demonstrate by monitoring the tip temperature upon application of a heat pulse. Our approach promises multiple applications, from the investigation of phonon dynamics in nanostructures to the characterization of heterogeneous phase transitions and chemical reactions in various solid-state systems. PMID:26584676

  1. Scanned probe imaging of nanoscale magnetism at cryogenic temperatures with a single-spin quantum sensor

    NASA Astrophysics Data System (ADS)

    Pelliccione, Matthew; Jenkins, Alec; Ovartchaiyapong, Preeti; Reetz, Christopher; Emmanouilidou, Eve; Ni, Ni; Bleszynski Jayich, Ania C.

    2016-08-01

    High-spatial-resolution magnetic imaging has driven important developments in fields ranging from materials science to biology. However, to uncover finer details approaching the nanoscale with greater sensitivity requires the development of a radically new sensor technology. The nitrogen–vacancy (NV) defect in diamond has emerged as a promising candidate for such a sensor on the basis of its atomic size and quantum-limited sensing capabilities. It has remained an outstanding challenge to implement the NV centre as a nanoscale scanning magnetic probe at cryogenic temperatures, however, where many solid-state systems exhibit non-trivial magnetic order. Here, we present NV magnetic imaging down to 6 K with 3 μT Hz–1/2 field sensitivity, and use the technique to image vortices in the iron pnictide superconductor BaFe2(As0.7P0.3)2 with critical temperature Tc = 30 K. The expansion of NV-based magnetic imaging to cryogenic temperatures will enable future studies of previously inaccessible nanoscale magnetism in condensed-matter systems.

  2. Scanned probe imaging of nanoscale magnetism at cryogenic temperatures with a single-spin quantum sensor.

    PubMed

    Pelliccione, Matthew; Jenkins, Alec; Ovartchaiyapong, Preeti; Reetz, Christopher; Emmanouilidou, Eve; Ni, Ni; Bleszynski Jayich, Ania C

    2016-08-01

    High-spatial-resolution magnetic imaging has driven important developments in fields ranging from materials science to biology. However, to uncover finer details approaching the nanoscale with greater sensitivity requires the development of a radically new sensor technology. The nitrogen-vacancy (NV) defect in diamond has emerged as a promising candidate for such a sensor on the basis of its atomic size and quantum-limited sensing capabilities. It has remained an outstanding challenge to implement the NV centre as a nanoscale scanning magnetic probe at cryogenic temperatures, however, where many solid-state systems exhibit non-trivial magnetic order. Here, we present NV magnetic imaging down to 6 K with 3 μT Hz(-1/2) field sensitivity, and use the technique to image vortices in the iron pnictide superconductor BaFe2(As0.7P0.3)2 with critical temperature Tc = 30 K. The expansion of NV-based magnetic imaging to cryogenic temperatures will enable future studies of previously inaccessible nanoscale magnetism in condensed-matter systems.

  3. Ultramild protein-mediated click chemistry creates efficient oligonucleotide probes for targeting and detecting nucleic acids.

    PubMed

    Nåbo, Lina J; Madsen, Charlotte S; Jensen, Knud J; Kongsted, Jacob; Astakhova, Kira

    2015-05-26

    Functionalized synthetic oligonucleotides are finding growing applications in research, clinical studies, and therapy. However, it is not easy to prepare them in a biocompatible and highly efficient manner. We report a new strategy to synthesize oligonucleotides with promising nucleic acid targeting and detection properties. We focus in particular on the pH sensitivity of these new probes and their high target specificity. For the first time, human copper(I)-binding chaperon Cox17 was applied to effectively catalyze click labeling of oligonucleotides. This was performed under ultramild conditions with fluorophore, peptide, and carbohydrate azide derivatives. In thermal denaturation studies, the modified probes showed specific binding to complementary DNA and RNA targets. Finally, we demonstrated the pH sensitivity of the new rhodamine-based fluorescent probes in vitro and rationalize our results by electronic structure calculations.

  4. Forced intercalation probes (FIT Probes): thiazole orange as a fluorescent base in peptide nucleic acids for homogeneous single-nucleotide-polymorphism detection.

    PubMed

    Köhler, Olaf; Jarikote, Dilip Venkatrao; Seitz, Oliver

    2005-01-01

    Fluorescent base analogues in DNA are versatile probes of nucleic acid-nucleic acid and nucleic acid-protein interactions. New peptide nucleic acid (PNA) based probes are described in which the intercalator dye thiazole orange (TO) serves as a base surrogate. The investigation of six TO derivatives revealed that the linker length and the conjugation site decided whether a base surrogate conveys sequence-selective DNA binding and whether fluorescence is increased or decreased upon single-mismatched hybridization. One TO derivative conferred universal PNA-DNA base pairing while maintaining duplex stability and hybridization selectivity. TO fluorescence increased up to 26-fold upon hybridization. In contrast to most other probes, in which fluorescence is invariant once hybridization had occurred, the emission of TO-containing PNA probes is attenuated when forced to intercalate next to a mismatched base pair. The specificity of DNA detection is therefore not limited by the selectivity of probe-target binding and a DNA target can be distinguished from its single-base mutant under nonstringent hybridization conditions. This property should be of advantage for real-time quantitative PCR and nucleic acid detection within living cells.

  5. Slow Domain Motions of an Oligomeric Protein from Deep-Sea Hyperthermophile probed by Neutron Spin Echo

    NASA Astrophysics Data System (ADS)

    Bhowmik, Debsindhu; Shrestha, Utsab; Dhindsa, Gurpreet; Sharp, Melissa; Stingaciu, Laura R.; Chu, Xiang-Qiang; Xiang-Qiang Chu Team

    Deep-sea microorganisms have the ability to survive under extreme conditions, such as high pressure and high temperature. In this work, we used the combination of the neutron spin-echo (NSE) and the small angle neutron scattering (SANS) techniques to study the inter-domain motions of the inorganic pyrophosphate (IPPase) enzyme derived from thermostable microorganisms Thermococcus thioreducens. The IPPase has hexameric quaternary structure with molecular mass of approx. 120kDa (each subunit of 20kDa), which is a large oligomeric structure. The understanding of its slow inter-domain motions can be the key to explain how they are able to perform catalytic activity at higher temperature compared to mesophilic enzymes, thus leading to adapt to extreme environment present at the seabed. The NSE can probe these slow motions directly in the time domain up to several tens of nanoseconds at the nanometers length scales, while the corresponding structural change can be explored by the SANS. Our results provide a better picture of the local flexibility and conformational substates unique to these types of proteins, which will help us better understandthe relation between protein dynamics and their biological activities

  6. Measurements of d2n and A1n: Probing the neutron spin structure

    DOE PAGES

    Flay, D.; Posik, M.; Parno, D. S.; Allada, K.; Armstrong, W. R.; Averett, T.; Benmokhtar, F.; Bertozzi, W.; Camsonne, A.; Canan, M.; et al

    2016-09-06

    We report on the results of the E06-014 experiment performed at Jefferson Lab in Hall A, where a precision measurement of the twist-3 matrix elementmore » $d_2$ of the neutron ($$d_{2}^{n}$$) was conducted. This quantity represents the average color Lorentz force a struck quark experiences in a deep inelastic electron scattering event off a neutron due to its interaction with the hadronizing remnants. This color force was determined from a linear combination of the third moments of the spin structure functions $g_1$ and $g_2$ on $$^{3}$$He after nuclear corrections had been applied to these moments. The kinematics included two average $$Q^{2}$$ bins of $3.2$ GeV$$^{2}$$ and $4.3$ GeV$$^{2}$$, and Bjorken-$x$ $$0.25 \\leq x \\leq 0.90$$ covering the DIS and resonance regions. We found $d_2^n$ to be small and negative for $ = 3.2$ GeV$$^{2}$$, and smaller for $ = 4.3$ GeV$$^{2}$$, consistent with a lattice QCD calculation. The twist-4 matrix element $$f_{2}^{n}$$ was extracted by combining our $$d_{2}^{n}$$ with the world data on $$\\Gamma_{1}^{n} = \\int_{0}^{1} g_{1}^{n} dx$$. We found $$f_{2}^{n}$$ to be roughly an order of magnitude larger than $$d_{2}^{n}$$. Utilizing the extracted $$d_{2}^{n}$$ and $$f_{2}^{n}$$ data, we separated the color force into its electric and magnetic components, $$F_{E}^{y,n}$$ and $$F_{B}^{y,n}$$, and found them to be equal and opposite in magnitude, in agreement with instanton model predictions but not with those from QCD sum rules. Additionally, we have extracted the neutron virtual photon-nucleon asymmetry $$A_{1}^{n}$$, the structure function ratio $$g_{1}^{n}/F_{1}^{n}$$, and the quark ratios $$(\\Delta u + \\Delta \\bar{u})/(u + \\bar{u})$$ and $$(\\Delta d + \\Delta \\bar{d})/(d + \\bar{d})$$. Lastly, these results were found to be consistent with DIS world data and with the prediction of the constituent quark model but at odds with those of perturbative QCD at large $x$.« less

  7. Spin-probe ESR study on the dynamics of liquid molecules in the MCM-41 nanochannel: temperature dependence on 2-propanol and water.

    PubMed

    Okazaki, Masaharu; Toriyama, Kazumi

    2005-07-14

    A spin-probe ESR study has been made on the dynamics of 2-propanol and water molecules in the nanochannel of MCM-41 at various temperatures. In the former system, 2-propanol is separated into two phases: one with molecules immobilized in the ESR time scale and the other with mobile ones, even at temperatures more than 40 degrees higher than the bulk melting point. In the case of water, on the other hand, only the "immobilized" water was detected at a temperature as high as 313 K. At higher temperature, spin-probe molecule undergoes anisotropic rotational diffusion to reduce resistance from the solvent molecules in the nanochannel. These results are explained in relation to the intermolecular network intensified in the nanochannel. Static as well as dynamic structures of these solutions have been discussed.

  8. Label-free potentiometry for detecting DNA hybridization using peptide nucleic acid and DNA probes.

    PubMed

    Goda, Tatsuro; Singi, Ankit Balram; Maeda, Yasuhiro; Matsumoto, Akira; Torimura, Masaki; Aoki, Hiroshi; Miyahara, Yuji

    2013-02-07

    Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry.

  9. Docosahexaenoic acid conjugated near infrared flourescence probe for in vivo early tumor diagnosis

    NASA Astrophysics Data System (ADS)

    Li, Siwen; Cao, Jie; Qin, Jingyi; Zhang, Xin; Achilefu, Samuel; Qian, Zhiyu; Gu, Yueqing

    2013-02-01

    Docosahexaenoic acid(DHA) is an omega-3 C22 natural fatty acid with six cis double bonds and as a constituent of membranes used as a precursor for metabolic and biochemical path ways. In this manuscript,we describe the synthesis of near-infrared(NIR) flourescence ICG-Der-01 labeled DHA for in vitro and vivo tumor targeting.The structure of the probe was intensively characterized by UV and MS. The in vitro and vivo tumor targeting abilities of the DHA-based NIR probes were investigeted in MCF-7 cells and MCF-7 xenograft mice model differently by confocal microscopy and CCD camera. The cell cytotoxicity were tested in tumor cells MCF-7 .The results shows that the DHA-based NIR probes have high affinity with the tumor both in vitro and vivo.In addition ,we also found that the DHA-based NIR probes have the apparent cytotoxicity on MCF-7 cells .which demonstrated that DHA was conjugated with other antitumor drug could increase the abilities of antirumor efficacy .So DHA-ICG-Der-01 is a promising optical agent for diagnosis of tumors especially in their early stage.

  10. A Locked Nucleic Acid Probe Based on Selective Salt-Induced Effect Detects Single Nucleotide Polymorphisms

    PubMed Central

    Zhang, Jing; Wu, Huizhe; Chen, Qiuchen; Zhao, Pengfei; Zhao, Haishan; Yao, Weifan; Wei, Minjie

    2015-01-01

    Detection of single based genetic mutation by using oligonucleotide probes is one of the common methods of detecting single nucleotide polymorphisms at known loci. In this paper, we demonstrated a hybridization system which included a buffer solution that produced selective salt-induced effect and a locked nucleic acid modified 12 nt oligonucleotide probe. The hybridization system is suitable for hybridization under room temperature. By using magnetic nanoparticles as carriers for PCR products, the SNPs (MDR1 C3435T/A) from 45 volunteers were analyzed, and the results were consistent with the results from pyrophosphoric acid sequencing. The method presented in this paper differs from the traditional method of using molecular beacons to detect SNPs in that it is suitable for research institutions lacking real-time quantitative PCR detecting systems, to detect PCR products at room temperature. PMID:26347880

  11. Structural Changes of a Doubly Spin-Labeled Chemically Driven Molecular Shuttle Probed by PELDOR Spectroscopy.

    PubMed

    Franchi, Paola; Bleve, Valentina; Mezzina, Elisabetta; Schäfer, Christian; Ragazzon, Giulio; Albertini, Marco; Carbonera, Donatella; Credi, Alberto; Di Valentin, Marilena; Lucarini, Marco

    2016-06-20

    Gaining detailed information on the structural rearrangements associated with stimuli-induced molecular movements is of utmost importance for understanding the operation of molecular machines. Pulsed electron-electron double resonance (PELDOR) was employed to monitor the geometrical changes arising upon chemical switching of a [2]rotaxane that behaves as an acid-base-controlled molecular shuttle. To this aim, the rotaxane was endowed with stable nitroxide radical units in both the ring and axle components. The combination of PELDOR data and molecular dynamic calculations indicates that in the investigated rotaxane, the ring displacement along the axle, caused by the addition of a base, does not alter significantly the distance between the nitroxide labels, but it is accompanied by a profound change in the geometry adopted by the macrocycle. PMID:27123774

  12. Photo-Induced Spin-State Conversion in Solvated Transition Metal Complexes Probed via Time-Resolved Soft X-ray Spectroscopy

    SciTech Connect

    Huse, Nils; Kim, Tae Kyu; Jamula, Lindsey; McCusker, James K.; de Groot, Frank M. F.; Schoenlein, Robert W.

    2010-04-30

    Solution-phase photoinduced low-spin to high-spin conversion in the FeII polypyridyl complex [Fe(tren(py)3)]2+ (where tren(py)3 is tris(2-pyridylmethyliminoethyl)amine) has been studied via picosecond soft X-ray spectroscopy. Following 1A1 --> 1MLCT (metal-to-ligand charge transfer) excitation at 560 nm, changes in the iron L2- and L3-edges were observed concomitant with formation of the transient high-spin 5T2 state. Charge-transfer multiplet calculations coupled with data acquired on low-spin and high-spin model complexes revealed a reduction in ligand field splitting of 1 eV in the high-spin state relative to the singlet ground state. A significant reduction in orbital overlap between the central Fe-3d and the ligand N-2p orbitals was directly observed, consistent with the expected ca. 0.2 Angstrom increase in Fe-N bond length upon formation of the high-spin state. The overall occupancy of the Fe-3d orbitals remains constant upon spin crossover, suggesting that the reduction in sigma-donation is compensated by significant attenuation of pi-back-bonding in the metal-ligand interactions. These results demonstrate the feasibility and unique potential of time-resolved soft X-ray absorption spectroscopy to study ultrafast reactions in the liquid phase by directly probing the valence orbitals of first-row metals as well as lighter elements during the course of photochemical transformations.

  13. Visible sensing of nucleic acid sequences using a genetically encodable unmodified mRNA probe.

    PubMed

    Narita, Atsushi; Ogawa, Kazumasa; Sando, Shinsuke; Aoyama, Yasuhiro

    2006-01-01

    We previously reported a molecular beacon-mRNA (MB-mRNA) strategy for nucleic acid detection/sensing in a cell-free translation system using unmodified RNA as a probe. Here in this presentation, we report that a combination with RNase H activity, which induces an additional process of irreversible cleavage of MB-domain, achieves an improved sequence selectivity (one nucleotide selectivity) and an enhanced sensitivity. This improved system finally enabled visible sensing of target nucleic acid sequence at a single nucleotide resolution under isothermal conditions.

  14. A novel spin probe with long life in vivo for ESR imaging.

    PubMed

    Yoshioka, H; Tanizawa, H; Ogata, T; Kazama, S

    1995-11-01

    A dextran-bonded nitroxide radical (TEMPO-DX) was synthesized to obtain a radical with long life in vivo for ESR imaging. TEMPO-DX was injected intravenously into a rat tail vein and the decrease in ESR intensity in the collected, circulating blood was followed. The result showed that the half life of TEMPO-DX in vivo was 30 min, the longest value reported so far and more than 30 times longer than the corresponding radicals of the six-membered piperidine ring, which means that the bonding of a radical to the polymer greatly prolonged life. The stabilities of TEMPO-DX against the reduction with L-ascorbic acid and the rat liver homogenate were also examined and compared with those of the 3-carbamoyl-2,2,5,5-tetramethylpyrolidin-1-yloxy (CPROXYL) known as a radical stable in vivo. TEMPO-DX was shown not to be as stable as CPROXYL, thus in vivo stability of TEMPO-DX arises from the fact that it is slowly absorbed into the tissues where the radicals are quenched. An ESR image of the mouse head domain was obtained only by an intravenous injection of TEMPO-DX solution into the tail vein.

  15. Electron density dependence of the spin Hall effect in GaAs probed by scanning Kerr rotation microscopy

    NASA Astrophysics Data System (ADS)

    Matsuzaka, S.; Ohno, Y.; Ohno, H.

    2009-12-01

    We studied electron density (n) dependence of the extrinsic spin Hall effect in n -doped GaAs with n raging from 1.8×1016 to 3.3×1017cm-3 . By scanning Kerr microscopy measurements, we observed spin accumulation near the channel edges in all the samples due to the extrinsic spin Hall effect. The spin Hall conductivity σSH is obtained for each sample by comparing the Kerr rotation induced by optically injected spins. σSH is found to increase with n , and it is shown that a theoretical model reported earlier agrees well with the experimental n dependence of σSH .

  16. Spin dynamics in the La1.85Sr0.15Cu1-xFexO4 system probed by ESR

    NASA Astrophysics Data System (ADS)

    Cieplak, Marta Z.; Sienkiewicz, A.; Mila, F.; Guha, S.; Xiao, Gang; Xiao, J. Q.; Chien, C. L.

    1993-08-01

    We study the magnetic properties of the La1.85Sr0.15Cu1-xFexO4 system (x=0-0.1) in the vicinity of the metal-insulator (MI) transition using static-susceptibility measurements and the electron-spin resonance (ESR) of the Fe ions. Spin-glass (SG) freezing is present for all nonsuperconducting specimens. The iron ESR line broadens on approaching the freezing temperature, similarly to the effect observed in canonical spin glasses. This broadening can be attributed to the influence of the slowing down of spin fluctuations on the spin-spin relaxation rate. It depends differently on x on the two different sides of the MI transition suggesting the existence of two different SG phases: insulating (ISG) where the Fe spins couple to the Cu-spin array by superexchange interactions, and metallic (MSG), where there exists, in addition, Ruderman-Kittel-Kasuya-Yosida-like coupling mediated by the free carriers. The proximity of the MI transition suppresses this coulping, giving rise to the observed dependence of the paramagnet -SG phase boundary on x. In the MSG phase, at high temperatures, the spin-lattice relaxation mechanism is also mediated by the free carriers. It differs from the analogous process observed in conventional metals in that the ESR linewidth increases with increasing T faster than linearly. We explain this behavior by assuming that the effective magnetic field felt by the Fe moments originates mainly from the spins of holes located on the nearest-neighbor oxygen ions. The linewidth divided by T which probes the dynamical susceptibility at the Fe site varies as a+bT. Here a goes to zero as the MI transition is approached and so plays the role of the Pauli susceptibility of the free carriers, whereas b is independent of x in the vicinity of the MI transition but decreases for small Fe dopings away from the MI transition and may be identified as originating from the antiferromagnetic spin fluctuations in the system.

  17. Probing the formation and evolution of comets via nuclear spin temperatures of C_2H_6, CH_3OH, CH_4, NH_3, and H_2O

    NASA Astrophysics Data System (ADS)

    Villanueva, G.; Mumma, M.; Bonev, B.; DiSanti, M.; Paganini, L.; Magee-Sauer, K.; Gibb, E.

    2014-07-01

    Comets are true remnants of our primordial Solar System, and provide unique clues to its formation and evolution, including the delivery of organics and water to our planet. A key indicator stored in the molecular structure of the nuclear ices is the spin temperature (T_{spin}), derived from spin-isomeric ratios (R_{spin}, e.g., ortho/para). At the time when cometary ices formed, the prevailing temperature defined the relative abundance of the different spin-isomeric species, and herewith R_{spin} and T_{spin} are normally treated as ''remnant thermometers'' probing the formation environments of cometary molecules. Radiative and collisional transitions between the ortho and para states are strongly forbidden and herewith this indicator is preserved over time. Most of our knowledge of this indicator comes from the measurements of the ortho-para ratios in water and NH_2 (a proxy for ammonia), suggesting a common T_{spin} near 30 K. This information is based on a restricted sample of comets, and the measurements are particularly sensitive to the molecular modeling technique and adopted spectral database. Here, we present new methodologies for extracting spin temperatures from ethane (C_2H_6), methane (CH_4), and methanol (CH_3OH), and advanced new models for ortho/para water (H_2O) and ammonia (NH_3). Our H_2O analysis is based on the most complete fluorescence radiative-transfer model to date, which incorporates 1,200 million transitions including those originating from high-energy levels that are activated in comets via a non-resonant cascade. In a similar fashion, we developed non-resonant fluorescence models for NH_3 and HCN, and quantum-band models for the ν_7 band of C_2H_6 and ν_3 band of CH_3OH. All models respect spin-symmetry non-conversion radiative rules, and make use of a realistic solar spectrum for the computation of fluorescence pumps. We applied these new methods to derive spin-isomeric ratios for H_2O, CH_4, C_2H_6, CH_3OH, and NH_3 from three high

  18. Immobilization-free electrochemical DNA detection with anthraquinone-labeled pyrrolidinyl peptide nucleic acid probe.

    PubMed

    Kongpeth, Jutatip; Jampasa, Sakda; Chaumpluk, Piyasak; Chailapakul, Orawon; Vilaivan, Tirayut

    2016-01-01

    Electrochemical detection provides a simple, rapid, sensitive and inexpensive method for DNA detection. In traditional electrochemical DNA biosensors, the probe is immobilized onto the electrode. Hybridization with the DNA target causes a change in electrochemical signal, either from the intrinsic signal of the probe/target or through a label or a redox indicator. The major drawback of this approach is the requirement for probe immobilization in a controlled fashion. In this research, we take the advantage of different electrostatic properties between PNA and DNA to develop an immobilization-free approach for highly sequence-specific electrochemical DNA sensing on a screen-printed carbon electrode (SPCE) using a square-wave voltammetric (SWV) technique. Anthraquinone-labeled pyrrolidinyl peptide nucleic acid (AQ-PNA) was employed as a probe together with an SPCE that was modified with a positively-charged polymer (poly quaternized-(dimethylamino-ethyl)methacrylate, PQDMAEMA). The electrostatic attraction between the negatively-charged PNA-DNA duplex and the positively-charged modified SPCE attributes to the higher signal of PNA-DNA duplex than that of the electrostatically neutral PNA probe, resulting in a signal change. The calibration curve of this proposed method exhibited a linear range between 0.35 and 50 nM of DNA target with a limit of detection of 0.13 nM (3SD(blank)/Slope). The sub-nanomolar detection limit together with a small sample volume required (20 μL) allowed detection of <10 fmol (<1 ng) of DNA. With the high specificity of the pyrrolidinyl PNA probe used, excellent discrimination between complementary and various single-mismatched DNA targets was obtained. An application of this new platform for a sensitive and specific detection of isothermally-amplified shrimp's white spot syndrome virus (WSSV) DNA was successfully demonstrated. PMID:26695270

  19. Immobilization-free electrochemical DNA detection with anthraquinone-labeled pyrrolidinyl peptide nucleic acid probe.

    PubMed

    Kongpeth, Jutatip; Jampasa, Sakda; Chaumpluk, Piyasak; Chailapakul, Orawon; Vilaivan, Tirayut

    2016-01-01

    Electrochemical detection provides a simple, rapid, sensitive and inexpensive method for DNA detection. In traditional electrochemical DNA biosensors, the probe is immobilized onto the electrode. Hybridization with the DNA target causes a change in electrochemical signal, either from the intrinsic signal of the probe/target or through a label or a redox indicator. The major drawback of this approach is the requirement for probe immobilization in a controlled fashion. In this research, we take the advantage of different electrostatic properties between PNA and DNA to develop an immobilization-free approach for highly sequence-specific electrochemical DNA sensing on a screen-printed carbon electrode (SPCE) using a square-wave voltammetric (SWV) technique. Anthraquinone-labeled pyrrolidinyl peptide nucleic acid (AQ-PNA) was employed as a probe together with an SPCE that was modified with a positively-charged polymer (poly quaternized-(dimethylamino-ethyl)methacrylate, PQDMAEMA). The electrostatic attraction between the negatively-charged PNA-DNA duplex and the positively-charged modified SPCE attributes to the higher signal of PNA-DNA duplex than that of the electrostatically neutral PNA probe, resulting in a signal change. The calibration curve of this proposed method exhibited a linear range between 0.35 and 50 nM of DNA target with a limit of detection of 0.13 nM (3SD(blank)/Slope). The sub-nanomolar detection limit together with a small sample volume required (20 μL) allowed detection of <10 fmol (<1 ng) of DNA. With the high specificity of the pyrrolidinyl PNA probe used, excellent discrimination between complementary and various single-mismatched DNA targets was obtained. An application of this new platform for a sensitive and specific detection of isothermally-amplified shrimp's white spot syndrome virus (WSSV) DNA was successfully demonstrated.

  20. A Large Sample Volume Magic Angle Spinning Nuclear Magnetic Resonance Probe for In-Situ Investigations with Constant Flow of Reactants

    SciTech Connect

    Hu, Jian Z.; Sears, Jesse A.; Mehta, Hardeep S.; Ford, Joseph J.; Kwak, Ja Hun; Zhu, Kake; Wang, Yong; Liu, Jun; Hoyt, David W.; Peden, Charles HF

    2012-02-21

    A large-sample-volume constant-flow magic angle sample spinning (CF-MAS) NMR probe is reported for in-situ studies of the reaction dynamics, stable intermediates/transition states, and mechanisms of catalytic reactions. In our approach, the reactants are introduced into the catalyst bed using a fixed tube at one end of the MAS rotor while a second fixed tube, linked to a vacuum pump, is attached at the other end of the rotor. The pressure difference between both ends of the catalyst bed inside the sample cell space forces the reactants flowing through the catalyst bed, which improves the diffusion of the reactants and products. This design allows the use of a large sample volume for enhanced sensitivity and thus permitting in-situ 13C CF-MAS studies at natural abundance. As an example of application, we show that reactants, products and reaction transition states associated with the 2-butanol dehydration reaction over a mesoporous silicalite supported heteropoly acid catalyst (HPA/meso-silicalite-1) can all be detected in a single 13C CF-MAS NMR spectrum at natural abundance. Coke products can also be detected at natural 13C abundance and under the stopped flow condition. Furthermore, 1H CF-MAS NMR is used to identify the surface functional groups of HPA/meso-silicalite-1 under the condition of in-situ drying . We also show that the reaction dynamics of 2-butanol dehydration using HPA/meso-silicalite-1 as a catalyst can be explored using 1H CF-MAS NMR.

  1. X-ray emission spectroscopy with a laser-heated diamond anvil cell: a new experimental probe of the spin state of iron in the Earth's interior

    SciTech Connect

    Lin, J.-F.; Struzhkin, V.V.; Jacobsen, S.D.; Shen, G.; Prakapenka, V.B.; Mao, H.-K.; Hemley, R.J.

    2010-07-19

    Synchrotron-based X-ray emission spectroscopy (XES) is well suited to probing the local electronic structure of 3d transition metals such as Fe and Mn in their host phases. The laser-heated diamond anvil cell technique is uniquely capable of generating ultra-high static pressures and temperatures in excess of 100 GPa and 3000 K. Here X-ray emission spectroscopy and X-ray diffraction have been interfaced with the laser-heated diamond cell for studying the electronic spin states of iron in magnesiowuestite-(Mg{sub 0.75},Fe{sub 0.25})O and its crystal structure under lower-mantle conditions. X-ray emission spectra of the ferrous iron in a single crystal of magnesiowuestite-(Mg{sub 0.75},Fe{sub 0.25})O indicate that a high-spin to low-spin transition of ferrous iron occurs at 54 to 67 GPa and 300 K and the ferrous iron remains in the high-spin state up to 47 GPa and 1300 K. This pilot study points to the unique capability of the synchrotron-based XES and X-ray diffraction techniques for addressing the issue of electronic spin transition or crossover in 3d transition metals and compounds under extreme high-P-T conditions.

  2. The use of variable temperature and magic-angle sample spinning in studies of fulvic acids

    USGS Publications Warehouse

    Earl, W.L.; Wershaw, R. L.; Thorn, K.A.

    1987-01-01

    Intensity distortions and poor signal to noise in the cross-polarization magic-angle sample spinning NMR of fulvic acids were investigated and attributed to molecular mobility in these ostensibly "solid" materials. We have shown that inefficiencies in cross polarization can be overcome by lowering the sample temperature to about -60??C. These difficulties can be generalized to many other synthetic and natural products. The use of variable temperature and cross-polarization intensity as a function of contact time can yield valuable qualitative information which can aid in the characterization of many materials. ?? 1987.

  3. Proton transfer in benzoic acid crystals: A chemical spin-boson problem. Theoretical analysis of nuclear magnetic resonance, neutron scattering, and optical experiments

    NASA Astrophysics Data System (ADS)

    Skinner, J. L.; Trommsdorff, H. P.

    1988-07-01

    The double proton transfer in benzoic acid crystals can be described by a double-minimum potential. At low temperatures one need consider only the two lowest energy eigenstates, which must be coupled to the crystalline phonons in order to obtain relaxation. Thus the benzoic acid system provides a well-defined chemical example of the spin-boson Hamiltonian. Within this model the tunneling relaxation between localized states occurs by one-phonon emission or absorption. Alternatively, at high temperatures the proton transfer is thermally activated. With this simple picture in mind we analyze NMR T1 relaxation experiments. The temperature-dependent proton transfer rate that emerges from the NMR analysis is in good agreement with inelastic neutron scattering experiments. Optical transitions of a dye probe have also been used to determine proton transfer rates in crystalline benzoic acid. Our model allows us to discuss both doped and pure crystal experiments within a unified framework. Thus, we find that all three different experimental probes yield results that are consistent with our simple theoretical picture. From our results we can determine the proton-phonon coupling constant.

  4. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

    DOEpatents

    Weier, Heinz-Ulrich G.; Gray, Joe W.

    1995-01-01

    A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers ard probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity.

  5. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

    DOEpatents

    Weier, H.U.G.; Gray, J.W.

    1995-06-27

    A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers and probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity. 18 figs.

  6. Fluorescence imaging of siRNA delivery by peptide nucleic acid-based probe.

    PubMed

    Sato, Takaya; Sato, Yusuke; Iwai, Kenta; Kuge, Shusuke; Teramae, Norio; Nishizawa, Seiichi

    2015-01-01

    We report on the use of a peptide nucleic acid (PNA)-based fluorescent probe for the analysis of siRNA delivery to living cells. The probe, Py-AA-TO, possesses thiazole orange (TO) and pyrene moieties in the C- and N-termini of PNA, and can function as a light-up probe capable of selective binding to 3'-overhanging nucleotides of target siRNAs. The affinity-labeling of the siRNAs with Py-AA-TO facilitates fluorescence imaging of cellular uptake of polymer-based carriers encapsulating the siRNAs (polyplexes) through endocytosis and subsequent sequestration into lysosome. In addition, flow cytometric measurements reveal that the monitoring of Py-AA-TO fluorescence inside the cells is successfully applicable to the analysis of the polyplex disassembly. These promising functions of Py-AA-TO are presented and discussed as a basis for the design of molecular probes for fluorescent imaging and quantitative analysis of the siRNA delivery process. PMID:25864675

  7. Spin dynamics of the ordered dipolar-octupolar pseudospin-1/2 pyrochlore Nd2Zr2O7 probed by muon spin relaxation

    NASA Astrophysics Data System (ADS)

    Xu, J.; Balz, C.; Baines, C.; Luetkens, H.; Lake, B.

    2016-08-01

    We present a muon spin relaxation study on the Ising pyrochlore Nd2Zr2O7 which develops an "all-in-all-out" magnetic order below 0.4 K. At 20 mK, far below the ordering transition temperature, the zero-field muon spin relaxation spectra show no static features and can be well described by a dynamical Gaussian-broadened Gaussian Kubo-Toyabe function indicating strong fluctuations of the ordered state. The spectra of the paramagnetic state (below 4.2 K) reveal anomalously slow paramagnetic spin dynamics and show only a small difference with the spectra of the ordered state. We find that the fluctuation rate decreases with decreasing temperature and becomes nearly temperature independent below the transition temperature, indicating persistent slow spin dynamics in the ground state. The field distribution width shows a small but sudden increase at the transition temperature and then becomes almost constant. The spectra in applied longitudinal fields are well fitted by the conventional dynamical Gaussian Kubo-Toyabe function, which further supports the dynamical nature of the ground state. The fluctuation rate shows a peak as a function of external field which is associated with a field-induced spin-flip transition. The strong dynamics in the ordered state is attributed to the transverse coupling of the Ising spins introduced by the multipole interactions.

  8. Probing the structural dynamics of proteins and nucleic acids with optical tweezers.

    PubMed

    Ritchie, Dustin B; Woodside, Michael T

    2015-10-01

    Conformational changes are an essential feature of most molecular processes in biology. Optical tweezers have emerged as a powerful tool for probing conformational dynamics at the single-molecule level because of their high resolution and sensitivity, opening new windows on phenomena ranging from folding and ligand binding to enzyme function, molecular machines, and protein aggregation. By measuring conformational changes induced in a molecule by forces applied by optical tweezers, new insight has been gained into the relationship between dynamics and function. We discuss recent advances from studies of how structure forms in proteins and RNA, including non-native structures, fluctuations in disordered proteins, and interactions with chaperones assisting native folding. We also review the development of assays probing the dynamics of complex protein-nucleic acid and protein-protein assemblies that reveal the dynamic interactions between biomolecular machines and their substrates.

  9. Ascorbic acid-functionalized Ag NPs as a probe for colorimetric sensing of glutathione

    NASA Astrophysics Data System (ADS)

    D'souza, Stephanie L.; Pati, Ranjan; Kailasa, Suresh Kumar

    2015-08-01

    In this work, we report the use of ascorbic acid-capped silver nanoparticles (AA-Ag NPs) as a probe for selective colorimetric detection of glutathione (GSH) in aqueous solution. This detection system was based on the GSH-induced aggregation of AA-Ag NPs, resulting in drastic changes in the absorption spectra and color of the AA-Ag NPs system. The GSH-induced AA-Ag NPs aggregation was confirmed by UV-visible spectrometry, dynamic light scattering (DLS) and transmission electron microscopic (TEM) techniques. Under optimal conditions, this method exhibited good linearity over the concentration ranges from 5.0 to 50 µM, with the limit of detection 2.4 × 10-7 M. This method was successfully applied to detect GSH in the presence of other biomolecules, which confirms that this probe can be used for the detection of GSH in real samples.

  10. Development of a Radioiodinated Triazolopyrimidine Probe for Nuclear Medical Imaging of Fatty Acid Binding Protein 4

    PubMed Central

    Onoe, Satoru; Sampei, Sotaro; Kimura, Ikuo; Ono, Masahiro; Saji, Hideo

    2014-01-01

    Fatty acid binding protein 4 (FABP4) is the most well-characterized FABP isoform. FABP4 regulates inflammatory pathways in adipocytes and macrophages and is involved in both inflammatory diseases and tumor formation. FABP4 expression was recently reported for glioblastoma, where it may participate in disease malignancy. While FABP4 is a potential molecular imaging target, with the exception of a tritium labeled probe there are no reports of other nuclear imaging probes that target this protein. Here we designed and synthesized a nuclear imaging probe, [123I]TAP1, and evaluated its potential as a FABP4 targeting probe in in vitro and in vivo assays. We focused on the unique structure of a triazolopyrimidine scaffold that lacks a carboxylic acid to design the TAP1 probe that can undergo facilitated delivery across cell membranes. The affinity of synthesized TAP1 was measured using FABP4 and 8-anilino-1-naphthalene sulfonic acid. [125I]TAP1 was synthesized by iododestannylation of a precursor, followed by affinity and selectivity measurements using immobilized FABPs. Biodistributions in normal and C6 glioblastoma-bearing mice were evaluated, and excised tumors were subjected to autoradiography and immunohistochemistry. TAP1 and [125I]TAP1 showed high affinity for FABP4 (Ki = 44.5±9.8 nM, Kd = 69.1±12.3 nM). The FABP4 binding affinity of [125I]TAP1 was 11.5- and 35.5-fold higher than for FABP3 and FABP5, respectively. In an in vivo study [125I]TAP1 displayed high stability against deiodination and degradation, and moderate radioactivity accumulation in C6 tumors (1.37±0.24% dose/g 3 hr after injection). The radioactivity distribution profile in tumors partially corresponded to the FABP4 positive area and was also affected by perfusion. The results indicate that [125I]TAP1 could detect FABP4 in vitro and partly in vivo. As such, [125I]TAP1 is a promising lead compound for further refinement for use in in vivo FABP4 imaging. PMID:24732569

  11. (1) Majorana fermions in pinned vortices; (2) Manipulating and probing Majorana fermions using superconducting circuits; and (3) Controlling a nanowire spin-orbit qubit via electric-dipole spin resonance

    NASA Astrophysics Data System (ADS)

    Nori, Franco

    2014-03-01

    We study a heterostructure which consists of a topological insulator and a superconductor with a hole. This system supports a robust Majorana fermion state bound to the vortex core. We study the possibility of using scanning tunneling spectroscopy (i) to detect the Majorana fermion in this setup and (ii) to study excited states bound to the vortex core. The Majorana fermion manifests itself as an H-dependent zero-bias anomaly of the tunneling conductance. The excited states spectrum differs from the spectrum of a typical Abrikosov vortex, providing additional indirect confirmation of the Majorana state observation. We also study how to manipulate and probe Majorana fermions using super-conducting circuits. In we consider a semiconductor nanowire quantum dot with strong spin-orbit coupling (SOC), which can be used to achieve a spin-orbit qubit. In contrast to a spin qubit, the spin-orbit qubit can respond to an external ac electric field, i.e., electric-dipole spin resonance. We develop a theory that can apply in the strong SOC regime. We find that there is an optimal SOC strength ηopt = √ 2/2, where the Rabi frequency induced by the ac electric field becomes maximal. Also, we show that both the level spacing and the Rabi frequency of the spin-orbit qubit have periodic responses to the direction of the external static magnetic field. These responses can be used to determine the SOC in the nanowire. FN is partly supported by the RIKEN CEMS, iTHES Project, MURI Center for Dynamic Magneto-Optics, JSPS-RFBR Contract No. 12-02-92100, Grant-in-Aid for Scientific Research (S), MEXT Kakenhi on Quantum Cybernetics, and the JSPS via its FIRST program.

  12. Acidic-pH-activatable fluorescence probes for visualizing exocytosis dynamics.

    PubMed

    Asanuma, Daisuke; Takaoka, Yousuke; Namiki, Shigeyuki; Takikawa, Kenji; Kamiya, Mako; Nagano, Tetsuo; Urano, Yasuteru; Hirose, Kenzo

    2014-06-10

    Live imaging of exocytosis dynamics is crucial for a precise spatiotemporal understanding of secretion phenomena, but current approaches have serious limitations. We designed and synthesized small-molecular fluorescent probes that were chemically optimized for sensing acidic intravesicular pH values, and established that they can be used to sensitively and reliably visualize vesicular dynamics following stimulation. This straightforward technique for the visualization of exocytosis as well as endocytosis/reacidification processes with high spatiotemporal precision is expected to be a powerful tool for investigating dynamic cellular phenomena involving changes in the pH value.

  13. Spin-lattice coupling in uranium dioxide probed by magnetostriction measurements at high magnetic fields (P08358-E001-PF)

    SciTech Connect

    Gofryk, K.; Jaime, M.

    2014-12-01

    Our preliminary magnetostriction measurements have already shown a strong interplay of lattice dynamic and magnetism in both antiferromagnetic and paramagnetic states, and give unambiguous evidence of strong spin- phonon coupling in uranium dioxide. Further studies are planned to address the puzzling behavior of UO2 in magnetic and paramagnetic states and details of the spin-phonon coupling.

  14. Excited States of Nucleic Acids Probed by Proton Relaxation Dispersion NMR Spectroscopy.

    PubMed

    Juen, Michael Andreas; Wunderlich, Christoph Hermann; Nußbaumer, Felix; Tollinger, Martin; Kontaxis, Georg; Konrat, Robert; Hansen, D Flemming; Kreutz, Christoph

    2016-09-19

    In this work an improved stable isotope labeling protocol for nucleic acids is introduced. The novel building blocks eliminate/minimize homonuclear (13) C and (1) H scalar couplings thus allowing proton relaxation dispersion (RD) experiments to report accurately on the chemical exchange of nucleic acids. Using site-specific (2) H and (13) C labeling, spin topologies are introduced into DNA and RNA that make (1) H relaxation dispersion experiments applicable in a straightforward manner. The novel RNA/DNA building blocks were successfully incorporated into two nucleic acids. The A-site RNA was previously shown to undergo a two site exchange process in the micro- to millisecond time regime. Using proton relaxation dispersion experiments the exchange parameters determined earlier could be recapitulated, thus validating the proposed approach. We further investigated the dynamics of the cTAR DNA, a DNA transcript that is involved in the viral replication cycle of HIV-1. Again, an exchange process could be characterized and quantified. This shows the general applicablility of the novel labeling scheme for (1) H RD experiments of nucleic acids.

  15. Excited States of Nucleic Acids Probed by Proton Relaxation Dispersion NMR Spectroscopy.

    PubMed

    Juen, Michael Andreas; Wunderlich, Christoph Hermann; Nußbaumer, Felix; Tollinger, Martin; Kontaxis, Georg; Konrat, Robert; Hansen, D Flemming; Kreutz, Christoph

    2016-09-19

    In this work an improved stable isotope labeling protocol for nucleic acids is introduced. The novel building blocks eliminate/minimize homonuclear (13) C and (1) H scalar couplings thus allowing proton relaxation dispersion (RD) experiments to report accurately on the chemical exchange of nucleic acids. Using site-specific (2) H and (13) C labeling, spin topologies are introduced into DNA and RNA that make (1) H relaxation dispersion experiments applicable in a straightforward manner. The novel RNA/DNA building blocks were successfully incorporated into two nucleic acids. The A-site RNA was previously shown to undergo a two site exchange process in the micro- to millisecond time regime. Using proton relaxation dispersion experiments the exchange parameters determined earlier could be recapitulated, thus validating the proposed approach. We further investigated the dynamics of the cTAR DNA, a DNA transcript that is involved in the viral replication cycle of HIV-1. Again, an exchange process could be characterized and quantified. This shows the general applicablility of the novel labeling scheme for (1) H RD experiments of nucleic acids. PMID:27533469

  16. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    1998-01-01

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration.

  17. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOEpatents

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1998-03-24

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration. 14 figs.

  18. Folic acid-conjugated europium complexes as luminescent probes for selective targeting of cancer cells.

    PubMed

    Quici, Silvio; Casoni, Alessandro; Foschi, Francesca; Armelao, Lidia; Bottaro, Gregorio; Seraglia, Roberta; Bolzati, Cristina; Salvarese, Nicola; Carpanese, Debora; Rosato, Antonio

    2015-02-26

    We report the synthesis of three optical probes (Eu(3+)⊂1, Eu(3+)⊂2, and Eu(3+)⊂3) having a luminescent Eu complex (signaling unit) bonded in different positions to folic acid (FA), the folate receptor (FR) targeting unit. The structures of the two regioisomers Eu(3+)⊂1 and Eu(3+)⊂2 were assigned by mass spectrometric experiments. The optical properties and stability of these probes were assessed in phosphate-buffered saline, cell culture medium, rat serum, and cellular lysate, and results indicated that they are chemically and photophysically stable. Cytotoxicity was studied with ovarian cancer cells having high (SKOV-3), intermediate (OVCAR-3), low (IGROV-1), or null (A2780) expression of FRs. The internalized probe, evaluated in SKOV-3, IGROV-1, and A2780 cells, was in the order Eu(3+)⊂2 > Eu(3+)⊂1 > Eu(3+)⊂3. No internalization was observed for A2780 cells. Such results, together with those obtained in competition experiments of FA versus Eu(3+)⊂2 and FA or Eu(3+)⊂2 versus (3)H-FA, indicate that internalization is receptor-mediated and that Eu(3+)⊂2 shows high selectivity and specificity for FR.

  19. Translational and rotational diffusion of flexible PEG and rigid dendrimer probes in sodium caseinate dispersions and acid gels.

    PubMed

    Salami, Souad; Rondeau-Mouro, Corinne; Barhoum, Myriam; van Duynhoven, John; Mariette, François

    2014-09-01

    The dynamics of rigid dendrimer and flexible PEG probes in sodium caseinate dispersions and acid gels, including both translational diffusion and rotational diffusion, were studied by NMR. Above the onset of the close-packing limit (C ∼ 10 g/100 g H2 O), translational diffusion of the probe depended on its flexibility and on the fluctuations of the matrix chains. The PEG probe diffused more rapidly than the spherical dendrimer probe of corresponding hydrodynamic radius. The greater conformational flexibility of PEG facilitated its motion through the crowded casein matrix. Rotational diffusion was, however, substantially less hindered than the translational diffusion and depended on the local protein-probe friction which became high when the casein concentration increased. The coagulation of the matrix led to the formation of large voids, which resulted in an increase in the translational diffusion of the probes, whereas the rotational diffusion of the probes was retarded in the gel, which could be attributed to the immobilized environment surrounding the probe. Quantitative information from PFG-NMR and SEM micrographs have been combined for characterizing microstructural details in SC acid gels.

  20. Boronic Acid: A Bio-Inspired Strategy To Increase the Sensitivity and Selectivity of Fluorescent NADH Probe.

    PubMed

    Wang, Lu; Zhang, Jingye; Kim, Beomsue; Peng, Juanjuan; Berry, Stuart N; Ni, Yong; Su, Dongdong; Lee, Jungyeol; Yuan, Lin; Chang, Young-Tae

    2016-08-24

    Fluorescent probes have emerged as an essential tool in the molecular recognition events in biological systems; however, due to the complex structures of certain biomolecules, it remains a challenge to design small-molecule fluorescent probes with high sensitivity and selectivity. Inspired by the enzyme-catalyzed reaction between biomolecule and probe, we present a novel combination-reaction two-step sensing strategy to improve sensitivity and selectivity. Based on this strategy, we successfully prepared a turn-on fluorescent reduced nicotinamide adenine dinucleotide (NADH) probe, in which boronic acid was introduced to bind with NADH and subsequently accelerate the sensing process. This probe shows remarkably improved sensitivity (detection limit: 0.084 μM) and selectivity to NADH in the absence of any enzymes. In order to improve the practicality, the boronic acid was further modified to change the measurement conditions from alkalescent (pH 9.5) to physiological environment (pH 7.4). Utilizing these probes, we not only accurately quantified the NADH weight in a health care product but also evaluated intracellular NADH levels in live cell imaging. Thus, these bio-inspired fluorescent probes offer excellent tools for elucidating the roles of NADH in biological systems as well as a practical strategy to develop future sensitive and selective probes for complicated biomolecules. PMID:27500425

  1. Probing the effective nuclear-spin magnetic field in a single quantum dot via full counting statistics

    SciTech Connect

    Xue, Hai-Bin; Nie, Yi-Hang; Chen, Jingzhe; Ren, Wei

    2015-03-15

    We study theoretically the full counting statistics of electron transport through a quantum dot weakly coupled to two ferromagnetic leads, in which an effective nuclear-spin magnetic field originating from the configuration of nuclear spins is considered. We demonstrate that the quantum coherence between the two singly-occupied eigenstates and the spin polarization of two ferromagnetic leads play an important role in the formation of super-Poissonian noise. In particular, the orientation and magnitude of the effective field have a significant influence on the variations of the values of high-order cumulants, and the variations of the skewness and kurtosis values are more sensitive to the orientation and magnitude of the effective field than the shot noise. Thus, the high-order cumulants of transport current can be used to qualitatively extract information on the orientation and magnitude of the effective nuclear-spin magnetic field in a single quantum dot. - Highlights: • The effective nuclear-spin magnetic field gives rise to the off-diagonal elements of the reduced density matrix of single QD. • The off-diagonal elements of reduced density matrix of the QD have a significant impact on the high-order current cumulants. • The high-order current cumulants are sensitive to the orientation and magnitude of the effective nuclear-spin magnetic field. • The FCS can be used to detect the orientation and magnitude of the effective nuclear-spin magnetic field in a single QD.

  2. Selective local lysis and sampling of live cells for nucleic acid analysis using a microfluidic probe

    PubMed Central

    Kashyap, Aditya; Autebert, Julien; Delamarche, Emmanuel; Kaigala, Govind V.

    2016-01-01

    Heterogeneity is inherent to biology, thus it is imperative to realize methods capable of obtaining spatially-resolved genomic and transcriptomic profiles of heterogeneous biological samples. Here, we present a new method for local lysis of live adherent cells for nucleic acid analyses. This method addresses bottlenecks in current approaches, such as dilution of analytes, one-sample-one-test, and incompatibility to adherent cells. We make use of a scanning probe technology - a microfluidic probe - and implement hierarchical hydrodynamic flow confinement (hHFC) to localize multiple biochemicals on a biological substrate in a non-contact, non-destructive manner. hHFC enables rapid recovery of nucleic acids by coupling cell lysis and lysate collection. We locally lysed ~300 cells with chemical systems adapted for DNA or RNA and obtained lysates of ~70 cells/μL for DNA analysis and ~15 cells/μL for mRNA analysis. The lysates were introduced into PCR-based workflows for genomic and transcriptomic analysis. This strategy further enabled selective local lysis of subpopulations in a co-culture of MCF7 and MDA-MB-231 cells, validated by characteristic E-cadherin gene expression in individually extracted cell types. The developed strategy can be applied to study cell-cell, cell-matrix interactions locally, with implications in understanding growth, progression and drug response of a tumor. PMID:27411740

  3. Electron spin resonance studies on reduction process of nitroxyl spin radicals used in molecular imaging

    SciTech Connect

    Dhas, M. Kumara; Benial, A. Milton Franklin; Jawahar, A.

    2014-04-24

    The Electron spin resonance studies on the reduction process of nitroxyl spin probes were carried out for 1mM {sup 14}N labeled nitroxyl radicals in pure water and 1 mM concentration of ascorbic acid as a function of time. The electron spin resonance parameters such as signal intensity ratio, line width, g-value, hyperfine coupling constant and rotational correlation time were determined. The half life time was estimated for 1mM {sup 14}N labeled nitroxyl radicals in 1 mM concentration of ascorbic acid. The ESR study reveals that the TEMPONE has narrowest line width and fast tumbling motion compared with TEMPO and TEMPOL. From the results, TEMPONE has long half life time and high stability compared with TEMPO and TEMPOL radical. Therefore, this study reveals that the TEMPONE radical can act as a good redox sensitive spin probe for molecular imaging.

  4. Use of spin-labelling techniques to probe the dynamics of He(2 3S) deexcitation at solid surfaces

    NASA Astrophysics Data System (ADS)

    Dunning, F. B.; Oró, D. M.; Soletsky, P. A.; Zhang, X.; Nordlander, P.; Walters, G. K.

    1994-06-01

    Spin labelling techniques, specifically the use of electron-spin-polarized He(23 S) metastable atoms coupled with energy-resolved spin analysis of the ejected electrons, are used to investigate the dynamics of He(23 S) deexcitation at solid surfaces. Data for a clean Au(100) surface are presented that show that deexcitation occurs exclusively through resonance ionization followed by Auger neutralization. The electrons involved in Auger neutralization are observed to be correlated in spin and possible reasons for this are discussed. Results obtained at Xe and NO films adsorbed on cooled Au(100) and Cu(100) substrates, respectively, show that He(23 S) metastable atom deexcitation is analogous to gas-phase Penning ionization. Detailed differences are apparent that can be attributed to effects associated with the underlying substrate and interactions involving neighboring atoms in the film.

  5. Matter-wave interferometry of a levitated thermal nano-oscillator induced and probed by a spin.

    PubMed

    Scala, M; Kim, M S; Morley, G W; Barker, P F; Bose, S

    2013-11-01

    We show how the interference between spatially separated states of the center of mass (c.m.) of a mesoscopic harmonic oscillator can be evidenced by coupling it to a spin and performing solely spin manipulations and measurements (Ramsey interferometry). We propose to use an optically levitated diamond bead containing a nitrogen-vacancy center spin. The nanoscale size of the bead makes the motional decoherence due to levitation negligible. The form of the spin-motion coupling ensures that the scheme works for thermal states so that moderate feedback cooling suffices. No separate control or observation of the c.m. state is required and thereby one dispenses with cavities, spatially resolved detection, and low-mass-dispersion ensembles. The controllable relative phase in the Ramsey interferometry stems from a gravitational potential difference so that it uniquely evidences coherence between states which involve the whole nanocrystal being in spatially distinct locations. PMID:24237492

  6. Matter-Wave Interferometry of a Levitated Thermal Nano-Oscillator Induced and Probed by a Spin

    NASA Astrophysics Data System (ADS)

    Scala, M.; Kim, M. S.; Morley, G. W.; Barker, P. F.; Bose, S.

    2013-11-01

    We show how the interference between spatially separated states of the center of mass (c.m.) of a mesoscopic harmonic oscillator can be evidenced by coupling it to a spin and performing solely spin manipulations and measurements (Ramsey interferometry). We propose to use an optically levitated diamond bead containing a nitrogen-vacancy center spin. The nanoscale size of the bead makes the motional decoherence due to levitation negligible. The form of the spin-motion coupling ensures that the scheme works for thermal states so that moderate feedback cooling suffices. No separate control or observation of the c.m. state is required and thereby one dispenses with cavities, spatially resolved detection, and low-mass-dispersion ensembles. The controllable relative phase in the Ramsey interferometry stems from a gravitational potential difference so that it uniquely evidences coherence between states which involve the whole nanocrystal being in spatially distinct locations.

  7. Matter-wave interferometry of a levitated thermal nano-oscillator induced and probed by a spin.

    PubMed

    Scala, M; Kim, M S; Morley, G W; Barker, P F; Bose, S

    2013-11-01

    We show how the interference between spatially separated states of the center of mass (c.m.) of a mesoscopic harmonic oscillator can be evidenced by coupling it to a spin and performing solely spin manipulations and measurements (Ramsey interferometry). We propose to use an optically levitated diamond bead containing a nitrogen-vacancy center spin. The nanoscale size of the bead makes the motional decoherence due to levitation negligible. The form of the spin-motion coupling ensures that the scheme works for thermal states so that moderate feedback cooling suffices. No separate control or observation of the c.m. state is required and thereby one dispenses with cavities, spatially resolved detection, and low-mass-dispersion ensembles. The controllable relative phase in the Ramsey interferometry stems from a gravitational potential difference so that it uniquely evidences coherence between states which involve the whole nanocrystal being in spatially distinct locations.

  8. Magic-angle-spinning NMR studies of acid sites in zeolite H-ZSM-5

    SciTech Connect

    Brunner, E.; Ernst, H.; Freude, D.; Froehlich, T.; Hunger, M.; Pfeifer, H. )

    1991-01-01

    {sup 1}H, {sup 13}C, {sup 27}Al, and {sup 29}Si magic-angle-spinning (MAS) NMR was used to elucidate the nature of the catalytic activity of zeolite H-ZSM-5. {sup 1}H MAS NMR of sealed samples after mild hydrothermal dealumination shows that the enhanced activity for n-hexane cracking is not due to an enhanced Bronstead acidity. The concentrations of the various OH groups and aluminous species suggest that the reason for the enhanced catalytic activity is the interaction of the n-hexane molecule with a bridging hydroxyl group and with extra-framework aluminium species, which give rise to the enhanced activity, cannot be easily removed from their positions, and are therefore immobilized by the zeolitic framework.

  9. An aldehyde group-based P-acid probe for selective fluorescence turn-on sensing of cysteine and homocysteine.

    PubMed

    Yang, Chunlei; Wang, Xiu; Shen, Lei; Deng, Wenping; Liu, Haiyun; Ge, Shenguang; Yan, Mei; Song, Xianrang

    2016-06-15

    A highly sensitive and selective turn on fluorescent probe P-acid-aldehyde (P-CHO) is developed for the determination of cysteine (Cys) and homocysteine (Hcy). The probe is designed and synthesized by incorporating the specific functional group aldehyde group for thiols into a stable π-conjugated material 4,4'-(2,5-dimethoxy-1,4-phenylene) bis(ethyne-2,1-diyl) dibenzoic acid (P-acid). The probe fluorescence is quenched through donor photoinduced electron transfer (d-PET) between the fluorophore (P-acid) and the recognition group (aldehyde group). In the presence of thiols, Cys and Hcy can selectively react with aldehyde group of the probe because the inhibition of d-PET between fluorophore and recognition group. Therefore, a turn-on fluorescent sensor was established for the fluorescence recovery. Under the optimized conditions, the fluorescence response of probe is directly proportional to the concentration of Cys in the range of 4-95 NM L(-1), with a detection limit 3.0 nM. In addition, the sensing system exhibits good selectively toward Cys and Hcy in the presence of other amino acids. It has been successfully applied for bioimaging of Cys and Hcy in living cells with low cell toxicity.

  10. Probe design rules and effective enzymes for endonuclease-based detection of nucleic acids.

    PubMed

    Yan, Lei; Nakayama, Shizuka; Sintim, Herman O

    2013-10-15

    Junction probe (JP) platform is an isothermal endonuclease-based detection assay for both RNA and DNA. Herein, we screen 31 REAse and identify effective restriction endonucleases that can be used for JP detection. Secondly, we investigate how different probe architectures affect JP cleavage rates and conclude that although molecular beacon (MB) JP probes give less background noise than linear JP probes, the cleavage of MB JP probes are slower than linear JP probes.

  11. Exploring the Hybridization Thermodynamics of Spherical Nucleic Acids to Tailor Probes for Diagnostic and Therapeutic Applications

    NASA Astrophysics Data System (ADS)

    Randeria, Pratik Shailesh

    Spherical nucleic acids (SNAs), three-dimensional nanoparticle conjugates composed of densely packed and highly oriented oligonucleotides around organic or inorganic nanoparticles, are an emergent class of nanostructures that show promise as single-entity agents for intracellular messenger RNA (mRNA) detection and gene regulation. SNAs exhibit superior biocompatibility and biological properties compared to linear oligonucleotides, enabling them to overcome many of the limitations of linear oligonucleotides for use in biomedical applications. However, the origins of these biologically attractive properties are not well understood. In this dissertation, the chemistry underlying one such property is studied in detail, and the findings are applied towards the rational design of more effective SNAs for diagnostic and therapeutic applications. Chapter 1 introduces the synthesis of SNAs, the unique properties that make them superior to linear nucleic acids for biomedicine, and previously studied applications of these structures. Chapter 2 focuses on quantitatively studying the impact of the chemical structure of the SNA on its ability to hybridize multiple complementary nucleic acids. This chapter lays the groundwork for understanding the factors that govern SNA hybridization thermodynamics and how to tailor SNAs to increase their binding affinity to target mRNA strands. Chapters 3 and 4 capitalize on this knowledge to engineer probes for intracellular mRNA detection and gene regulation applications. Chapter 3 reports the development of an SNA-based probe that can simultaneously report the expression level of two different mRNA transcripts in live cells and differentiate diseased cells from non-diseased cells. Chapter 4 investigates the use of topically-applied SNAs to down-regulate a critical mediator of impaired wound healing in diabetic mice to accelerate wound closure. This study represents the first topical therapeutic application of SNA nanotechnology to treat open

  12. Local Probe Study of S=1 Spin Liquid Candidate Ba3NiSb2O9

    NASA Astrophysics Data System (ADS)

    Quilliam, Jeffrey; Bert, Fabrice; Mendels, Philippe; Orain, Jean-Christophe; Manseau, Anthoni; Darie, Céline; Payen, Christophe; Guillot-Deudon, Catherine

    2015-03-01

    The family of hexagonal perovskites, Ba3 M Sb2O9, has attracted a considerable amount of attention in recent years, with the discovery of several spin liquid candidates. For M = Cu, the material is fairly disordered and likely exhibits a honeycomb-like lattice whereas in other cases the structure consists of triangular planes of spins. Three different structural phases of Ba3NiSb2O9 have been discovered, depending on synthesis pressure. Two of these phases (6HA and 6HB) consist of triangular planes of S = 1 moments, and differ primarily by the stacking of these planes. Here, we present muon spin rotation (μSR) and 121Sb nuclear magnetic resonance (NMR) results on a high-pressure synthesis of this material, 6HB-Ba3NiSb2O9. Most importantly, we demonstrate that there are no signs of magnetic ordering or spin freezing down to temperatures as low as 20 mK, making this material a plausible spin liquid candidate. Furthermore our NMR results are indicative of gapless excitations, consistent with previous specific heat and magnetic susceptibility results.

  13. Spin Labeling ESR Investigation of a Role of Humic Acids at Covalent Binding of Xenobiotics to Soil

    NASA Astrophysics Data System (ADS)

    Aleksandrova, Olga

    2014-05-01

    The environmental risk of organic xenobiotic chemicals released into soils is controlled by their sorption and binding processes. However, the molecular mechanisms of reversible and irreversible interactions of xenobiotics with soil constituents and an influence of humic substances on this interaction are only partly understood. New methods and approaches aimed at understanding of molecular mechanisms in the soil environment and a role of humic substances in the sorption and binding processes are today required to manage and keep the quality of soil used and fertilized in agricultural industry. The paper presents a new approach of using stable ESR spin labels to investigate a role of humic substances in the interactions of organic xenobiotic chemicals with constituents of natural soil via the typical functional groups of xenobiotics, such as Amines. At the experiment, the nitroxide spin labels, such as TEMPO (2,2,6,6-Tetramethylpiperidin-1-oxyl), Amino-TEMPO (4-amino-2,2,6,6-Tetramethylpiperidin-1-oxyl) and Aniline spin labels (2,5,5-Trimethyl-2-(3-aminophenyl)pyrrolidin-1-oxyl), were added to samples of different natural soils, such luvisol, cambisol and chernozem. Amino-TEMPO and Aniline spin labels include the aliphatic amino and aromatic amino functional groups, respectively. A significant broadening of the ESR spectrum of Aniline spin labels incubated in different soils indicated a stable effect of covalent binding of the spin labels to soil constituents via the aromatic amino, whereas the ESR spectra of the other two spin labels were not broadened that pointed at the absence of covalent binding of spin labels via the aliphatic amino. As shown, a part of bound spin labels via the aromatic amino increased with increasing of the concentration of humic acids in soil. The same broadened signals were also be detected with the humic acids extracted from the investigated soils. A strong covalent binding of spin labels to humic substances via the aromatic amines was

  14. A Sensitive Peptide Nucleic Acid Probe Assay for Detection of BRAF V600 Mutations in Melanoma.

    PubMed

    Chen, Tai-Long; Chang, John Wen-Cheng; Hsieh, Jia-Juan; Cheng, Hsin-Yi; Chiou, Chiuan-Chian

    Mutated v-Raf murine sarcoma viral oncogene homolog B (BRAF) is an important biomarker for the prediction of therapeutic efficacy of several anticancer drugs. The detection of BRAF mutation faces two challenges: Firstly, there are multiple types of mutations, and secondly, tumor samples usually contain various amounts of wild-type, normal tissues. Here, we describe a newly established method for sensitive detection of multiple types of BRAF V600 mutations in excess wild-type background. The method introduced a fluorophore-tagged peptide nucleic acid (PNA) to serve as both polymerase chain reaction (PCR) clamp and sensor probe, which inhibited the amplification of wild-type templates during PCR and revealed multiple types of mutant signals during melting analysis. We demonstrated the design and optimization process of the method, and applied it in the detection of BRAF mutations in 49 melanoma samples. This PNA probe assay method detected three types of mutations in 17 samples, and was much more sensitive than conventional PCR plus Sanger sequencing. PMID:27566656

  15. Peptide nucleic acid probe detection of mutations in Mycobacterium tuberculosis genes associated with drug resistance.

    PubMed

    Bockstahler, L E; Li, Z; Nguyen, N Y; Van Houten, K A; Brennan, M J; Langone, J J; Morris, S L

    2002-03-01

    The emergence of drug-resistant strains of Mycobacterium tuberculosis is a serious public health problem. Many of the specific gene mutations that cause drug resistance in M. tuberculosis are point mutations. We are developing a PCR-peptide nucleic acid (PNA)-based ELISA as a diagnostic method to recognize point mutations in genes associated with isoniazid and rifampin resistance in M. tuberculosis. Specific point mutation-containing sequences and wild-type sequences of cloned mycobacterial genes were PCR-amplified, denatured, and hybridized with PNA probes bound to microplate wells. Using 15-base PNA probes, we established the hybridization temperatures (50 degrees C-55 degrees C) and other experimental conditions suitable for detecting clinically relevant point mutations in the katG and rpoB genes. Hybridization of PCR-amplified sequences that contained these point mutations with complementary mutation-specific PNAs resulted in significant increases in ELISA response compared with hybridization using wild-type-specific PNAs. Conversely, PCR-amplified wild-type sequences hybridized much more efficiently with wild-type PNAs than with the mutation-specific PNAs. Using the M. tuberculosis cloned genes and PCR-PNA-ELISA format developed here, M. tuberculosis sequences containing point mutations associated with drug resistance can be identified in less than 24 h. PMID:11926172

  16. Neutrophil chemotaxis and arachidonic acid metabolism are not linked: evidence from metal ion probe studies

    SciTech Connect

    Turner, S.R.; Turner, R.A.; Smith, D.M.; Johnson, J.A.

    1986-03-05

    Heavy metal ions can inhibit arachidonic acid (AA) metabolism protect against ionophore cytotoxicity (ibid) and inhibit neutrophil chemotaxis. In this study they used Au/sup 3 +/, Zn/sup 2 +/, Cr/sup 3 +/, Mn/sup 2 +/ and Cu/sup 2 +/ as probes of the interrelationships among AA metabolism, ionophore-mediated cytotoxicity, and chemotaxis. Phospholipid deacylation was measured in ionophore-treated cells prelabeled with /sup 3/H-AA. Eicosanoid release from ionophore-treated cells was monitored by radioimmunoassay. Cytoprotection was quantitated as ability to exclude trypan blue. Chemotaxis toward f-met-leu-phe was measured by leading front analysis. The results imply that metal ions attenuate ionophore cytotoxicity by blocking phospholipid deacylation and eicosanoid release. In contrast to previous reports, no correlation between AA metabolism and chemotaxis was demonstrated, suggesting that these 2 processes are not linked.

  17. DNA detection using water-soluble conjugated polymers and peptide nucleic acid probes

    NASA Astrophysics Data System (ADS)

    Gaylord, Brent S.; Heeger, Alan J.; Bazan, Guillermo C.

    2002-08-01

    The light-harvesting properties of cationic conjugated polymers are used to sensitize the emission of a dye on a specific peptide nucleic acid (PNA) sequence for the purpose of homogeneous, "real-time" DNA detection. Signal transduction is controlled by hybridization of the neutral PNA probe and the negative DNA target. Electrostatic interactions bring the hybrid complex and cationic polymer within distances required for Förster energy transfer. Conjugated polymer excitation provides fluorescein emission >25 times higher than that obtained by exciting the dye, allowing detection of target DNA at concentrations of 10 pM with a standard fluorometer. A simple and highly sensitive assay with optical amplification that uses the improved hybridization behavior of PNA/DNA complexes is thus demonstrated.

  18. Infrared probe of spin-phonon coupling in antiferromagnetic honeycomb lattice compound Li2MnO3

    NASA Astrophysics Data System (ADS)

    Song, Seungjae; Lee, Sanghyun; Jeon, Seyoung; Park, Je-Geun; Moon, S. J.

    2015-12-01

    We investigated temperature-dependent infrared-active phonon modes of honeycomb Li2MnO3 which shows an antiferromagnetic transition at T N  =  36 K. In the far-infrared frequency region, we observed fourteen phonon modes. We obtained the temperature dependence of each phonon mode from the analysis of optical conductivity spectra by using the Lorentz and the Fano-type oscillator models. We found that the resonance frequencies of nine phonon modes showed an anomalous behavior near T N that should be attributed to the spin-phonon coupling. We calculated the magnitude of the spin-phonon coupling constant from the shift in the resonance frequencies of the phonon modes below T N. Our results suggest that Li2MnO3 is weakly frustrated and that spin-phonon coupling plays a role in antiferromagnetic ordering.

  19. Probing the spin polarization of current by soft x-ray imaging of current-induced magnetic vortex dynamics

    SciTech Connect

    Kasai, Shinya; Fischer, Peter; Im, Mi-Young; Yamada, Keisuke; Nakatani, Yoshinobu; Kobayashi, Kensuke; Kohno, Hiroshi; Ono, Teruo

    2008-12-09

    Time-resolved soft X-ray transmission microscopy is applied to image the current-induced resonant dynamics of the magnetic vortex core realized in a micron-sized Permalloy disk. The high spatial resolution better than 25 nm enables us to observe the resonant motion of the vortex core. The result also provides the spin polarization of the current to be 0.67 {+-} 0.16 for Permalloy by fitting the experimental results with an analytical model in the framework of the spin-transfer torque.

  20. Probing the Specificity Determinants of Amino Acid Recognition by Arginase†,‡

    PubMed Central

    Shishova, Ekaterina Y.; Di Costanzo, Luigi; Emig, Francis A.; Ash, David E.; Christianson, David W.

    2009-01-01

    Arginase is a binuclear manganese metalloenzyme that serves as a therapeutic target for the treatment of asthma, erectile dysfunction, and atherosclerosis. In order to better understand the molecular basis of inhibitor affinity, we have employed site-directed mutagenesis, enzyme kinetics, and X-ray crystallography to probe the molecular recognition of the amino acid moiety (i.e., the α-amino and α-carboxylate groups) of substrate l-arginine and inhibitors in the active site of human arginase I. Specifically, we focus on: (1) a water-mediated hydrogen bond between the substrate α-carboxylate and T135, (2) a direct hydrogen bond between the substrate α-carboxylate and N130, and (3) a direct charged hydrogen bond between the substrate α-amino group and D183. Amino acid substitutions for T135, N130, and D183 generally compromise substrate affinity as reflected by increased KM values, but have less pronounced effects on catalytic function as reflected by minimal variations of kcat. As with substrate KM values, inhibitor Kd values increase for binding to enzyme mutants and suggest that the relative contribution of intermolecular interactions to amino acid affinity in the arginase active site is: water-mediated hydrogen bond < direct hydrogen bond < direct charged hydrogen bond. Structural comparisons of arginase with the related binuclear manganese metalloenzymes agmatinase and proclavaminic acid amidinohydrolase suggest that the evolution of substrate recognition in the arginase fold occurs by mutation of residues contained in specificity loops flanking the mouth of the active site (especially loops 4 and 5), thereby allowing diverse guanidinium substrates to be accommodated for catalysis. PMID:19093830

  1. Extraordinary adhesion of phenylboronic acid derivatives of polyvinylamine to wet cellulose: a colloidal probe microscopy investigation.

    PubMed

    Notley, Shannon M; Chen, Wei; Pelton, Robert

    2009-06-16

    Typically, the adhesion between cellulose surfaces under aqueous conditions is very poor. Often, adsorbed polymers such as polyvinylamine (PVAm) are used to increase the wet strength; however, this provides only a minimal increase in the adhesion energy. Here, the adhesion between cellulose surfaces with adsorbed layers of phenylboronic acid derivatized polyvinylamine has been studied using colloidal probe microscopy as a function of pH. The adhesion due to the phenylboronic acid (PBA) groups grafted on the polyvinylamine backbone is almost 30 times greater, providing a new, exciting class of polymers using covalent linkages to improve the strength of the joint between cellulose surfaces. The measured surface forces on approach provided key information on the molecular conformation of the polymers at the cellulose-solution interface. At low pH, the three polymers tested, PVAm, PVAm-Ph (with pendant phenol groups), and PVAm-PBA (with phenylboronic acid groups) all had a relatively flat conformation at the interface, which is in agreement with the predictions based upon theory for highly charged polyelectrolytes adsorbing to an oppositely charged interface. With increasing pH, the charge on the polymers is reduced, eventually resulting in a more expansive conformation at the interface at pH 10 and above with the development of a steric interaction force. The onset of this steric force correlates well with the observed significant increase in the pull-off force upon separation of the cellulose surfaces. Furthermore, a greater increase in the adhesion was observed for PVAm-PBA in agreement with previous studies using macroscopic cellulose surfaces. This is attributed to the formation of boronic acid esters between the polymer and the cis diol groups on the cellulose surface.

  2. pH-Controllable bioelectrocatalysis based on "on-off" switching redox property of electroactive probes for spin-assembled layer-by-layer films containing branched poly(ethyleneimine).

    PubMed

    Song, Shaoling; Hu, Naifei

    2010-03-18

    Weak polybase branched poly(ethyleneimine) (BPEI) and strong polyacid poly(styrenesulfonate) (PSS) were assembled into BPEI/{PSS/BPEI}(n) layer-by-layer (LBL) films on electrodes by electrostatic interaction between them with spin-coating approach. The cyclic voltammetric (CV) response of ferrocenedicarboxylic acid (Fc(COOH)(2)) at BPEI/{PSS/BPEI}(n) film electrodes was very sensitive to the pH of the testing solutions. At pH 4.0, the probe showed a well-defined CV peak pair with relatively large peak currents for the films, while, at pH 7.0, the CV response was significantly depressed. By switching the film electrodes in buffers between pH 4.0 and 7.0, the CV peak currents changed periodically between a relatively high value at the "on" state and a very low value at the "off" state, indicating that the pH-sensitive "on-off" switching function of the films toward the probe is reversible. A series of comparative experiments indicates that the electrostatic interaction between the films and the probe plays a predominant role in deciding the pH-sensitive behavior of the films. This pH-dependent property of the films could be used to control or modulate the bioelectrocatalysis of glucose by glucose oxidase (GOD) with Fc(COOH)(2) as the mediator by changing the surrounding pH. This "smart" bioelectrocatalytic film system may establish a foundation for fabricating novel pH-controllable electrochemical biosensors.

  3. Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions.

    PubMed

    Vavřinská, Andrea; Zelinka, Jiří; Šebera, Jakub; Sychrovský, Vladimír; Fiala, Radovan; Boelens, Rolf; Sklenář, Vladimír; Trantírek, Lukáš

    2016-01-01

    Heteronuclear and homonuclear direct (D) and indirect (J) spin-spin interactions are important sources of structural information about nucleic acids (NAs). The Hamiltonians for the D and J interactions have the same functional form; thus, the experimentally measured apparent spin-spin coupling constant corresponds to a sum of J and D. In biomolecular NMR studies, it is commonly presumed that the dipolar contributions to Js are effectively canceled due to random molecular tumbling. However, in strong magnetic fields, such as those employed for NMR analysis, the tumbling of NA fragments is anisotropic because the inherent magnetic susceptibility of NAs causes an interaction with the external magnetic field. This motional anisotropy is responsible for non-zero D contributions to Js. Here, we calculated the field-induced D contributions to 33 structurally relevant scalar coupling constants as a function of magnetic field strength, temperature and NA fragment size. We identified two classes of Js, namely (1)JCH and (3)JHH couplings, whose quantitative interpretation is notably biased by NA motional anisotropy. For these couplings, the magnetic field-induced dipolar contributions were found to exceed the typical experimental error in J-coupling determinations by a factor of two or more and to produce considerable over- or under-estimations of the J coupling-related torsion angles, especially at magnetic field strengths >12 T and for NA fragments longer than 12 bp. We show that if the non-zero D contributions to J are not properly accounted for, they might cause structural artifacts/bias in NA studies that use solution NMR spectroscopy. PMID:26685997

  4. Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions.

    PubMed

    Vavřinská, Andrea; Zelinka, Jiří; Šebera, Jakub; Sychrovský, Vladimír; Fiala, Radovan; Boelens, Rolf; Sklenář, Vladimír; Trantírek, Lukáš

    2016-01-01

    Heteronuclear and homonuclear direct (D) and indirect (J) spin-spin interactions are important sources of structural information about nucleic acids (NAs). The Hamiltonians for the D and J interactions have the same functional form; thus, the experimentally measured apparent spin-spin coupling constant corresponds to a sum of J and D. In biomolecular NMR studies, it is commonly presumed that the dipolar contributions to Js are effectively canceled due to random molecular tumbling. However, in strong magnetic fields, such as those employed for NMR analysis, the tumbling of NA fragments is anisotropic because the inherent magnetic susceptibility of NAs causes an interaction with the external magnetic field. This motional anisotropy is responsible for non-zero D contributions to Js. Here, we calculated the field-induced D contributions to 33 structurally relevant scalar coupling constants as a function of magnetic field strength, temperature and NA fragment size. We identified two classes of Js, namely (1)JCH and (3)JHH couplings, whose quantitative interpretation is notably biased by NA motional anisotropy. For these couplings, the magnetic field-induced dipolar contributions were found to exceed the typical experimental error in J-coupling determinations by a factor of two or more and to produce considerable over- or under-estimations of the J coupling-related torsion angles, especially at magnetic field strengths >12 T and for NA fragments longer than 12 bp. We show that if the non-zero D contributions to J are not properly accounted for, they might cause structural artifacts/bias in NA studies that use solution NMR spectroscopy.

  5. A highly specific ferrocene-based fluorescent probe for hypochlorous acid and its application to cell imaging.

    PubMed

    Chen, Suming; Lu, Jinxin; Sun, Chengdong; Ma, Huimin

    2010-03-01

    A highly specific ferrocene-based fluorescent probe, (9-anthryl)ethenylferrocene, has been designed, synthesized and characterized for fluorescence imaging of hypochlorous acid (HOCl) in live cells. The design strategy for the probe is based on the strong quenching effect of electron-donor ferrocene on anthracene fluorescence via an intramolecular charge transfer process, and is accomplished through constructing the conjugated molecule by using a cleavable double bond as a linker. The double bond in the probe reacts selectively with HOCl rather than the other reactive oxygen species (e.g., *OH, *O(2)(-), (1)O(2), and H(2)O(2)) in pH 7.4, accompanied by more than 100-fold fluorescence enhancement. Moreover, the probe is cell membrane permeable, and its applicability has been successfully demonstrated for fluorescence imaging of HOCl in HeLa cells.

  6. Real time RNA transcription monitoring by Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes: norovirus detection.

    PubMed

    Tonelli, Alessandro; Tedeschi, Tullia; Germini, Andrea; Sforza, Stefano; Corradini, Roberto; Medici, Maria Cristina; Chezzi, Carlo; Marchelli, Rosangela

    2011-05-01

    Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes have been reported as a valuable strategy for DNA analysis; however, no investigations targeting RNA molecules and no comparisons between different derivatization approaches have been reported so far. In this work, two TO-conjugated PNAs for genogroup II noroviruses (NoV GII) detection were designed and synthesized. Both the probes target the most conserved stretch of nucleotides identified in the open reading frame 1-2 (ORF1-ORF2) junction region and differ for the dye conjugation strategy: one PNA is end-labelled with the TO molecule tethered by a linker; the other probe bears the TO molecule directly linked to the PNA backbone, replacing a conventional nucleobase. The spectroscopic properties of the two PNA probes were studied and their applicability to NoVs detection, using an isothermal assay, was investigated. Both probes showed good specificity and high fluorescence enhancement upon hybridization, especially targeting RNA molecules. Moreover, the two probes were successfully employed for NoVs detection from stool specimens in an isothermal-based amplification assay targeting RNA 'amplicons'. The probes showed to be specific even in the presence of high concentrations of non-target RNA.

  7. A colorimetric and near-infrared fluorescent probe with high sensitivity and selectivity for acid phosphatase and inhibitor screening.

    PubMed

    Xu, Yongqian; Li, Benhao; Xiao, Liangliang; Ouyang, Jia; Sun, Shiguo; Pang, Yi

    2014-08-14

    A dual-channel including a colorimetric and fluorescent probe based on the aggregation-caused quenching (ACQ) and enzymolysis approach has been presented to screen acid phosphatase (ACP) and its inhibitor. Moreover, the ACP activity was determined by real time assay. PMID:24957006

  8. First observation of high-spin states in {sup 214}Po: Probing the valence space beyond {sup 208}Pb

    SciTech Connect

    Astier, Alain; Porquet, Marie-Genevieve

    2011-01-15

    Excited states in {sup 214}Po have been populated using the {sup 18}O + {sup 208}Pb reaction at 85-MeV beam energy and studied with the Euroball IV {gamma}-multidetector array. The level scheme has been built up to {approx}2.7-MeV excitation energy and spin I=12({h_bar}/2{pi}) from the triple-{gamma} coincidence data. Spin and parity values of most of the observed states have been assigned from the {gamma}-angular properties. The configurations of the yrast states are discussed using results of empirical shell-model calculations and by analogy with the neighboring nuclei. The {sup 214}Po level scheme established in this work constitutes an important step for the determination of the effective nucleon-nucleon interactions beyond N=126.

  9. Probe depth matters in dermal microdialysis sampling of benzoic acid after topical application: an ex vivo study in human skin.

    PubMed

    Holmgaard, R; Benfeldt, E; Bangsgaard, N; Sorensen, J A; Brosen, K; Nielsen, F; Nielsen, J B

    2012-01-01

    Microdialysis (MD) in the skin - dermal microdialysis (DMD) - is a unique technique for sampling of topically as well as systemically administered drugs at the site of action, e.g. sampling of dermatological drug concentrations in the dermis. Debate has concerned the existence of a correlation between the depth of the sampling device - the probe - in the dermis and the amount of drug sampled following topical drug administration. This study evaluates the relation between probe depth and drug sampling using dermal DMD sampling ex vivo in human skin. We used superficial (<1 mm), intermediate (1-2 mm) and deep (>2 mm) positioning of the linear MD probe in the dermis of human abdominal skin, followed by topical application of 4 mg/ml of benzoic acid (BA) in skin chambers overlying the probes. Dialysate was sampled every hour for 12 h and analysed for BA content by high-performance liquid chromatography. Probe depth was measured by 20-MHz ultrasound scanning. The area under the time-versus-concentration curve (AUC) describes the drug exposure in the tissue during the experiment and is a relevant parameter to compare for the 3 dermal probe depths investigated. The AUC(0-12) were: superficial probes: 3,335 ± 1,094 μg·h/ml (mean ± SD); intermediate probes: 2,178 ± 1,068 μg·h/ml, and deep probes: 1,159 ± 306 μg·h/ml. AUC(0-12) sampled by the superficial probes was significantly higher than that of samples from the intermediate and deeply positioned probes (p value <0.05). There was a significant inverse correlation between probe depth and AUC(0-12) sampled by the same probe (p value <0.001, r(2) value = 0.5). The mean extrapolated lag-times (±SD) for the superficial probes were 0.8 ± 0.1 h, for the intermediate probes 1.7 ± 0.5 h, and for the deep probes 2.7 ± 0.5 h, which were all significantly different from each other (p value <0.05). In conclusion, this paper demonstrates that there is an inverse relationship between the depth of the probe in the dermis

  10. Probe depth matters in dermal microdialysis sampling of benzoic acid after topical application: an ex vivo study in human skin.

    PubMed

    Holmgaard, R; Benfeldt, E; Bangsgaard, N; Sorensen, J A; Brosen, K; Nielsen, F; Nielsen, J B

    2012-01-01

    Microdialysis (MD) in the skin - dermal microdialysis (DMD) - is a unique technique for sampling of topically as well as systemically administered drugs at the site of action, e.g. sampling of dermatological drug concentrations in the dermis. Debate has concerned the existence of a correlation between the depth of the sampling device - the probe - in the dermis and the amount of drug sampled following topical drug administration. This study evaluates the relation between probe depth and drug sampling using dermal DMD sampling ex vivo in human skin. We used superficial (<1 mm), intermediate (1-2 mm) and deep (>2 mm) positioning of the linear MD probe in the dermis of human abdominal skin, followed by topical application of 4 mg/ml of benzoic acid (BA) in skin chambers overlying the probes. Dialysate was sampled every hour for 12 h and analysed for BA content by high-performance liquid chromatography. Probe depth was measured by 20-MHz ultrasound scanning. The area under the time-versus-concentration curve (AUC) describes the drug exposure in the tissue during the experiment and is a relevant parameter to compare for the 3 dermal probe depths investigated. The AUC(0-12) were: superficial probes: 3,335 ± 1,094 μg·h/ml (mean ± SD); intermediate probes: 2,178 ± 1,068 μg·h/ml, and deep probes: 1,159 ± 306 μg·h/ml. AUC(0-12) sampled by the superficial probes was significantly higher than that of samples from the intermediate and deeply positioned probes (p value <0.05). There was a significant inverse correlation between probe depth and AUC(0-12) sampled by the same probe (p value <0.001, r(2) value = 0.5). The mean extrapolated lag-times (±SD) for the superficial probes were 0.8 ± 0.1 h, for the intermediate probes 1.7 ± 0.5 h, and for the deep probes 2.7 ± 0.5 h, which were all significantly different from each other (p value <0.05). In conclusion, this paper demonstrates that there is an inverse relationship between the depth of the probe in the dermis

  11. Antiferromagnetic spin structure and lithium ion diffusion in Li2MnO3 probed by μ+SR

    NASA Astrophysics Data System (ADS)

    Sugiyama, Jun; Mukai, Kazuhiko; Nozaki, Hiroshi; Harada, Masashi; Månsson, Martin; Kamazawa, Kazuya; Andreica, Daniel; Amato, Alex; Hillier, Adrian D.

    2013-01-01

    In order to elucidate the antiferromagnetic (AF) spin structure below TN˜35 K and to clarify the diffusive behavior of Li+ ions in the layered compound Li2MnO3, we have performed a muon-spin rotation and relaxation (μ+SR) experiment using a powder sample in the temperature range between 2 and 500 K. Below TN, the zero-field (ZF-) μ+SR spectrum showed a clear oscillation that consists of two muon-spin precession signals with different frequencies. Combining with the dipole field calculations, it was found that the most probable spin structure for Li2MnO3 is the Cx-type AF order in which Mn moments align parallel or antiparallel to the a axis in the [Li1/3Mn2/3]O2 layer, and a ferromagnetic chain along the a axis aligns antiferromagnetically along both the b and c axes. The ordered Mn moment was estimated as 2.62μB at 2 K. In the paramagnetic state, ZF- and longitudinal-field μ+SR spectra exhibited a dynamic nuclear field relaxation. From the temperature dependence of the field distribution width, the Li+ ions were found to diffuse mainly along the c axis through the Li ion in the [Li1/3Mn2/3]O2 layer. Also, based on the field fluctuation rate, a self-diffusion coefficient of Li+ ions (DLi) at 300 K was estimated as 4.7(4)×10-11 cm2/s with the thermal activation energy Ea=0.156(3) eV.

  12. Jet drifts and flips in radio galaxies as probes of the historical evolution of spin axis in supermassive black holes

    NASA Astrophysics Data System (ADS)

    Saripalli, Lakshmi; Subrahmanyan, Ravi; Hall Roberts, David

    2015-08-01

    Jets in radio galaxies create twin lobes of synchrotron plasma on opposite sides of the host elliptical. The jets are believed to emerge along the spin axis of the central supermassive black hole. The history of evolution in spin axis is traced in the off axis distortions in the radio structure. We have analyzed the radio structures in a large sample of distorted radio galaxies to examine black hole spin axis behavior. These sources are selected specifically to have low axial-ratio structures and hence off-axis distortions that are, however, unbiased with respect to the nature of the distortions.We have imaged 52 radio galaxies having length to width ratio less than 1 to obtain detailed radio structures that enable a tracing of the origin of the off-axis radio emission. The unique sample consists of radio sources where the off axis radio emission originates from strategic locations - regions closer to the host galaxy and from the outer ends of the jets. A third category consists of sources where there is only a swathe of radio emission nearly orthogonal to the radio axis and passing through the central radio core.Our study has highlighted the potential of radio galaxies in tracing black hole spin axis changes over time; we use the occurrence rates of the different categories of sources to derive occurrence rates of drifts and flips in black hole axis. Since the host galaxies are an unbiased sampling of luminous elliptical galaxies, the rates derived are relevant to this parent population (Roberts, Cohen, Lu, Saripalli and Subrahmanyan, 2015, arXiv150203954; Roberts, Saripalli, Subrahmanyan, 2015, arXiv150302021).

  13. Antimicrobial Poly(lactic acid)-Based Nanofibres Developed by Solution Blow Spinning.

    PubMed

    Martínez-Sanz, Marta; Bilbao-Sainz, Cristina; Du, Wen-Xian; Chiou, Bor-Sen; Williams, Tina G; Wood, Delilah F; Imam, Syed H; Orts, William J; Lopez-Rubio, Amparo; Lagaron, Jose M

    2015-01-01

    The present study reports on the development of hybrid poly(lactic acid) (PLA) fibres loaded with highly crystalline bacterial cellulose nanowhiskers (BCNW) by the novel solution blow spinning method. Furthermore, fibres with antimicrobial properties were generated by incorporating carvacrol and THC as antimicrobial agents and the biocide effect against Listeria monocytogenes was studied. Initially, PLA blow spun fibres containing BCNW were optimized in terms of morphology and thermal properties. The addition of BCNW was seen to significantly increase the viscosity and surface tension of solutions, restricting the capacity to form fibres for concentrations greater than 30 wt.-% BCNW. 15 wt.-% BCNW was selected as the optimum nanofiller loading as it led to the most uniform fibres morphology, with BCNW homogeneously distributed along the fibres' axis. Subsequently, carvacrol and THC were incorporated into the fibres to confer them with antimicrobial properties, although the hydrophobic PLA matrix did not provide an efficient release of the antimicrobials. Thus, hydrophilic substances were added in order to trigger the antimicrobials release through water sorption mechanisms. The addition of the BCNW filler was not seen to significantly increase the antimicrobial capacity of the fibres by itself and, hence, gelatin was added to help promoting further the hydrophylicity and biocide performance of the fibres. Nevertheless, for the more hydrophilic THC, the biocide capacity of the fibres with gelatin was accentuated further by the presence of the BCNW.

  14. Antimicrobial Poly(lactic acid)-Based Nanofibres Developed by Solution Blow Spinning.

    PubMed

    Martínez-Sanz, Marta; Bilbao-Sainz, Cristina; Du, Wen-Xian; Chiou, Bor-Sen; Williams, Tina G; Wood, Delilah F; Imam, Syed H; Orts, William J; Lopez-Rubio, Amparo; Lagaron, Jose M

    2015-01-01

    The present study reports on the development of hybrid poly(lactic acid) (PLA) fibres loaded with highly crystalline bacterial cellulose nanowhiskers (BCNW) by the novel solution blow spinning method. Furthermore, fibres with antimicrobial properties were generated by incorporating carvacrol and THC as antimicrobial agents and the biocide effect against Listeria monocytogenes was studied. Initially, PLA blow spun fibres containing BCNW were optimized in terms of morphology and thermal properties. The addition of BCNW was seen to significantly increase the viscosity and surface tension of solutions, restricting the capacity to form fibres for concentrations greater than 30 wt.-% BCNW. 15 wt.-% BCNW was selected as the optimum nanofiller loading as it led to the most uniform fibres morphology, with BCNW homogeneously distributed along the fibres' axis. Subsequently, carvacrol and THC were incorporated into the fibres to confer them with antimicrobial properties, although the hydrophobic PLA matrix did not provide an efficient release of the antimicrobials. Thus, hydrophilic substances were added in order to trigger the antimicrobials release through water sorption mechanisms. The addition of the BCNW filler was not seen to significantly increase the antimicrobial capacity of the fibres by itself and, hence, gelatin was added to help promoting further the hydrophylicity and biocide performance of the fibres. Nevertheless, for the more hydrophilic THC, the biocide capacity of the fibres with gelatin was accentuated further by the presence of the BCNW. PMID:26328414

  15. Difference between ²JC2H3 and ²JC3H2 spin-spin couplings in heterocyclic five- and six-membered rings as a probe for studying σ-ring currents: a quantum chemical analysis.

    PubMed

    Contreras, Rubén H; dos Santos, Francisco P; Ducati, Lucas C; Tormena, Cláudio F

    2010-12-01

    Adequate analyses of canonical molecular orbitals (CMOs) can provide rather detailed information on the importance of different σ-Fermi contact (FC) coupling pathways (FC term transmitted through the σ-skeleton). Knowledge of the spatial distribution of CMOs is obtained by expanding them in terms of natural bond orbitals (NBOs). Their relative importance for transmitting the σ-FC contribution to a given spin-spin coupling constants (SSCCs) is estimated by resorting to the expression of the FC term given by the polarisation propagator formalism. In this way, it is possible to classify the effects affecting such couplings in two different ways: delocalisation interactions taking place in the neighbourhood of the coupling nuclei and 'round the ring' effects. The latter, associated with σ-ring currents, are observed to yield significant differences between the FC terms of (2)J(C2H3) and (2)J(C3H2) SSCCs which, consequently, are taken as probes to gauge the differences in σ-ring currents for the five-membered rings (furan, thiophene, selenophene and pyrrol) and also for the six-membered rings (benzene, pyridine, protonated pyridine and N-oxide pyridine) used in the present study.

  16. Wavelength-ratiometric near-physiological pH sensors based on 6-aminoquinolinium boronic acid probes.

    PubMed

    Badugu, Ramachandram; Lakowicz, Joseph R; Geddes, Chris D

    2005-04-30

    We describe the pH response of a set of isomeric water-soluble fluorescent probes based on both the 6-aminoquinolinium and boronic acid moieties. These probes show spectral shifts and intensity changes with pH, in a wavelength-ratiometric and colorimetric manner. Subsequently, changes in pH can readily be determined around the physiological level. Although boronic acid containing probes are known to exhibit pH sensitivity along with an ability for saccharide binding/chelating, the new probes reported here are considered to be unique and show an unperturbed pH response, even in the presence of high concentrations of background saccharide, such as with glucose and fructose, allowing for the predominant pH sensitivity. The response of the probes is based on the ability of the boronic acid group to interact with strong bases like OH(-), changing from the neutral form of the boronic acid group, R-B(OH)(2), to the anionic ester, R-B(-)(OH)(3), form, which is an electron donating group. The presence of an electron deficient quaternary heterocyclic nitrogen center and a strong electron donating amino group in the 6-position of the quinolinium backbone, provides for the spectral changes observed upon OH(-) complexation. In addition, by comparing the results obtained with systems separately incorporating 6-methoxy or 6-methyl substituents, the suppressed response towards monosaccharides, such as with glucose and fructose, can clearly be observed for these systems. Finally we compare our results to those of a control compound, BAQ, which does not contain the boronic acid group, allowing a rationale of the spectral changes to be made.

  17. Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm

    PubMed Central

    Öhrmalm, Christina; Jobs, Magnus; Eriksson, Ronnie; Golbob, Sultan; Elfaitouri, Amal; Benachenhou, Farid; Strømme, Maria; Blomberg, Jonas

    2010-01-01

    One of the main problems in nucleic acid-based techniques for detection of infectious agents, such as influenza viruses, is that of nucleic acid sequence variation. DNA probes, 70-nt long, some including the nucleotide analog deoxyribose-Inosine (dInosine), were analyzed for hybridization tolerance to different amounts and distributions of mismatching bases, e.g. synonymous mutations, in target DNA. Microsphere-linked 70-mer probes were hybridized in 3M TMAC buffer to biotinylated single-stranded (ss) DNA for subsequent analysis in a Luminex® system. When mismatches interrupted contiguous matching stretches of 6 nt or longer, it had a strong impact on hybridization. Contiguous matching stretches are more important than the same number of matching nucleotides separated by mismatches into several regions. dInosine, but not 5-nitroindole, substitutions at mismatching positions stabilized hybridization remarkably well, comparable to N (4-fold) wobbles in the same positions. In contrast to shorter probes, 70-nt probes with judiciously placed dInosine substitutions and/or wobble positions were remarkably mismatch tolerant, with preserved specificity. An algorithm, NucZip, was constructed to model the nucleation and zipping phases of hybridization, integrating both local and distant binding contributions. It predicted hybridization more exactly than previous algorithms, and has the potential to guide the design of variation-tolerant yet specific probes. PMID:20864443

  18. Contributions of the electronic spin and orbital current to the CoCl{sub 4}{sup 2-} magnetic field probed in polarised neutron diffraction experiments

    SciTech Connect

    Cassam-Chenaie, Patrick; Jayatilaka, Dylan

    2012-08-14

    Polarised neutron diffraction experiments conducted at 4.2 K on Cs{sub 3}CoCl{sub 5} crystals have been analysed by using a four-dimensional model Hilbert space made of ab initio n-electron wave functions of the CoCl{sub 4}{sup 2-} molecular ion. Two spin-orbit mixing coefficients and several configuration interaction coefficients have been optimized by fitting calculated magnetic structure factors to experimental ones, to obtain the best ensemble density operator that is representable in the model space. A goodness of fit, {chi}{sup 2}, less then 1 has been obtained for the first time for the two experimental data sets available. In the present article, the optimized density operators are used to calculate the magnetic field densities that are the genuine observables probed in neutron diffraction experiments. Density maps of such observables are presented for the first time and numerical details are provided. The respective contributions of spin density and orbital current to the magnetic field density are analyzed.

  19. Local pharmacokinetic analysis of a stable spin probe in mice by in vivo L-band ESR with surface-coil-type resonators.

    PubMed

    Kamataria, Masayuki; Yasui, Hiroyuki; Ogata, Tateaki; Sakurai, Hiromu

    2002-10-01

    In vivo ESR spectroscopy using a low frequency microwave of approximately 1 GHz has been developed to measure non-invasive ESR spectra in animals given paramagnetic compounds, in which a loop-gap-type resonator was used and ESR spectra were measured at the animal's head or abdomen. Therefore, the concentrations of paramagnetic species in both the blood and organs were compositely contributed to the spectra. When we understand the kinetics of paramagnetic species in detail, it is essentially important to know how these kinetics are expressed in each organ. For this purpose, a surface-coil-type resonator, which enabled local ESR measurement in specific organs, has been developed. By using this method, we studied the real-time pharmacokinetics of spin clearance curves detected in the organs of mice given 4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl (4-hydroxy-TEMPO) intravenously (i.v.), by monitoring the inferior vena cava, liver and kidney. Quantified dearance curves in the organs were analyzed on the basis of a two-compartment model, and pharmacokinetic parameters were estimated based on the curve-fitting. The obtained pharmacokinetic parameters were found to depend on the measurement site, and the distribution and elimination processes of the spin probe were successfully separated between the blood and organs of mice.

  20. Polymer dynamics near the surface and in the bulk of poly(tetrafluoroethylene) probed by zero-field muon-spin-relaxation spectroscopy.

    PubMed

    McKenzie, Iain; Salman, Zaher; Giblin, Sean R; Han, Yun Yu; Leach, Gary W; Morenzoni, Elvezio; Prokscha, Thomas; Suter, Andreas

    2014-02-01

    The results of many experiments on polymers such as polystyrene indicate that the polymer chains near a free surface exhibit enhanced dynamics when compared with the bulk. We have investigated whether this is the case for poly(tetrafluoroethylene) (PTFE) by using zero-field muon-spin-relaxation spectroscopy to characterize a local probe, the F-Mu(+)-F state, which forms when spin-polarized positive muons are implanted in PTFE. Low-energy muons (implantation energies from 2.0 to 23.0 keV) were used to study the F-Mu(+)-F state between ∼ 23 and 191 nm from the free surface of PTFE. Measurements were also made with surface muons (4.1 MeV) where the mean implantation depth is on the order of ∼ 0.6 mm. The relaxation rate of the F-Mu(+)-F state up to ∼ 150 K was found to be significantly higher for muons implanted at 2.0 keV than for higher implantation energies, which suggests that the polymer chains in a region on the order of a few tens of nanometers from the free surface are more mobile than those in the bulk.

  1. Polymer dynamics near the surface and in the bulk of poly(tetrafluoroethylene) probed by zero-field muon-spin-relaxation spectroscopy.

    PubMed

    McKenzie, Iain; Salman, Zaher; Giblin, Sean R; Han, Yun Yu; Leach, Gary W; Morenzoni, Elvezio; Prokscha, Thomas; Suter, Andreas

    2014-02-01

    The results of many experiments on polymers such as polystyrene indicate that the polymer chains near a free surface exhibit enhanced dynamics when compared with the bulk. We have investigated whether this is the case for poly(tetrafluoroethylene) (PTFE) by using zero-field muon-spin-relaxation spectroscopy to characterize a local probe, the F-Mu(+)-F state, which forms when spin-polarized positive muons are implanted in PTFE. Low-energy muons (implantation energies from 2.0 to 23.0 keV) were used to study the F-Mu(+)-F state between ∼ 23 and 191 nm from the free surface of PTFE. Measurements were also made with surface muons (4.1 MeV) where the mean implantation depth is on the order of ∼ 0.6 mm. The relaxation rate of the F-Mu(+)-F state up to ∼ 150 K was found to be significantly higher for muons implanted at 2.0 keV than for higher implantation energies, which suggests that the polymer chains in a region on the order of a few tens of nanometers from the free surface are more mobile than those in the bulk. PMID:25353500

  2. Quantification of syntrophic fatty acid-{beta}-oxidizing bacteria in a mesophilic biogas reactor by oligonucleotide probe hybridization

    SciTech Connect

    Hansen, K.H.; Ahring, B.K.; Raskin, L.

    1999-11-01

    Small-subunit rRNA sequences were obtained for two saturated fatty acid-{beta}-oxidizing syntrophic bacteria, Syntrophomonas sapovorans and Syntrophomonas wolfei LYB, and sequence analysis confirmed their classification as members of the family Syntrophomonadaceae. S.wolfei LYB was closely related to S.wolfei subsp. solfei, but S. sapovorans did not cluster with the other members of the genus Syntrophomonas. Five oligonucleotide probes targeting the small-subunit rRNA of different groups within the family Syntrophomonadaceae, which contains all currently known saturated fatty acid-{beta}-oxidizing syntrophic bacteria, were developed and characterized. The probes were designed to be specific at the family, genus, and species levels and were characterized by temperature-of-dissociation and specificity studies. To demonstrate the usefulness of the probes for the detection and quantification of saturated fatty acid-{beta}-oxidizing syntrophic bacteria in methanogenic environments, the microbial community structure of a sample from a full-scale biogas plant was determined. Hybridization results with probes for syntrophic bacteria and methanogens were compared to specific methanogenic activities and microbial numbers determined with most-probable-number estimates. Most of the methanogenic rRNA was comprised of Methanomicrobiales rRNA, suggesting that members of this order served as the main hydrogen-utilizing microorganisms. Between 0.2 and 1% of the rRNA was attributed to the Syntrophomonadaceae, or which the majority was accounted for by the genus Syntrophomonas.

  3. Benzimidazole-based ratiometric two-photon fluorescent probes for acidic pH in live cells and tissues.

    PubMed

    Kim, Hyung Joong; Heo, Cheol Ho; Kim, Hwan Myung

    2013-11-27

    Many aspects of cell metabolism are controlled by acidic pH. We report a new family of small molecule and ratiometric two photon (TP) probes derived from benzimidazole (BH1-3 and BH1L) for monitoring acidic pH values. These probes are characterized by a strong two-photon excited fluorescence, a marked blue-to-green emission color change in response to pH, pKa values ranging from 4.9 to 6.1, a distinctive isoemissive point, negligible cytotoxicity, and high photostability, thereby allowing quantitative analysis of acidic pH. Moreover, we show that BH1L optimized as a lysosomal-targeted probe allows for direct, real-time estimation of the pH values inside lysosomal compartments in live cells as well as in living mouse brain tissues through the use of two-photon microscopy. These findings demonstrate that these probes will find useful applications in biomedical research.

  4. Ultrafast supercontinuum fiber-laser based pump-probe scanning magneto-optical Kerr effect microscope for the investigation of electron spin dynamics in semiconductors at cryogenic temperatures with picosecond time and micrometer spatial resolution.

    PubMed

    Henn, T; Kiessling, T; Ossau, W; Molenkamp, L W; Biermann, K; Santos, P V

    2013-12-01

    We describe a two-color pump-probe scanning magneto-optical Kerr effect microscope which we have developed to investigate electron spin phenomena in semiconductors at cryogenic temperatures with picosecond time and micrometer spatial resolution. The key innovation of our microscope is the usage of an ultrafast "white light" supercontinuum fiber-laser source which provides access to the whole visible and near-infrared spectral range. Our Kerr microscope allows for the independent selection of the excitation and detection energy while avoiding the necessity to synchronize the pulse trains of two separate picosecond laser systems. The ability to independently tune the pump and probe wavelength enables the investigation of the influence of excitation energy on the optically induced electron spin dynamics in semiconductors. We demonstrate picosecond real-space imaging of the diffusive expansion of optically excited electron spin packets in a (110) GaAs quantum well sample to illustrate the capabilities of the instrument.

  5. Ultrafast supercontinuum fiber-laser based pump-probe scanning magneto-optical Kerr effect microscope for the investigation of electron spin dynamics in semiconductors at cryogenic temperatures with picosecond time and micrometer spatial resolution

    SciTech Connect

    Henn, T.; Kiessling, T. Ossau, W.; Molenkamp, L. W.; Biermann, K.; Santos, P. V.

    2013-12-15

    We describe a two-color pump-probe scanning magneto-optical Kerr effect microscope which we have developed to investigate electron spin phenomena in semiconductors at cryogenic temperatures with picosecond time and micrometer spatial resolution. The key innovation of our microscope is the usage of an ultrafast “white light” supercontinuum fiber-laser source which provides access to the whole visible and near-infrared spectral range. Our Kerr microscope allows for the independent selection of the excitation and detection energy while avoiding the necessity to synchronize the pulse trains of two separate picosecond laser systems. The ability to independently tune the pump and probe wavelength enables the investigation of the influence of excitation energy on the optically induced electron spin dynamics in semiconductors. We demonstrate picosecond real-space imaging of the diffusive expansion of optically excited electron spin packets in a (110) GaAs quantum well sample to illustrate the capabilities of the instrument.

  6. Characterization of Aqueous Oleic Acid/Oleate Dispersions by Fluorescent Probes and Raman Spectroscopy.

    PubMed

    Suga, Keishi; Kondo, Dai; Otsuka, Yoko; Okamoto, Yukihiro; Umakoshi, Hiroshi

    2016-08-01

    Oleic acid (OA) and oleates form self-assembled structures dispersible in aqueous media. Herein, the physicochemical properties of OA/oleate assemblies were characterized using fluorescent probes and Raman spectroscopy, under relatively high dilution (<100 mM of total amphiphile) at 25 °C. Anisotropy analysis using 1,6-diphenyl-1,3,5-hexatriene showed that the microviscosity of the OA/oleate assembly was highest at pH 7.5 (the pH range of 6.9-10.6 was investigated). The fluorescence spectra of 6-lauroyl-2-dimethylaminonaphthalene revealed the dehydrated environments on membrane surfaces at pH < 7.7. The pH-dependent Raman peak intensity ratios, chain torsion (S = I1124/I1096) and chain packing (R = I2850/I2930), showed local maxima, indicating the occurrence of metastable phases, such as dispersed cubic phase (pH = 7.5), vesicle (pH = 8.5), and dispersed cylindrical micelle (pH = 9.7). These results suggest that large-scale OA/oleate assemblies could possess particular membrane properties in a narrow pH region, e.g., at pH 7.5, and 9.7.

  7. Two-photon probes for intracellular free metal ions, acidic vesicles, and lipid rafts in live tissues.

    PubMed

    Kim, Hwan Myung; Cho, Bong Rae

    2009-07-21

    Optical imaging with fluorescence microscopy is a vital tool in the study of living systems. The most common method for cell imaging, one-photon microscopy (OPM), uses a single photon of higher energy to excite the fluorophore. However, two-photon microscopy (TPM), which uses two photons of lower energy as the excitation source, is growing in popularity among biologists because of several distinct advantages. Using TPM, researchers can image intact tissue for a long period of time with minimum interference from tissue preparation artifacts, self-absorption, autofluorescence, photobleaching, and photodamage. However, to make TPM a more versatile tool in biology, researchers need a wider variety of two-photon probes for specific applications. In this Account, we describe a series of two-photon probes that we developed that can visualize the distribution of intracellular metal ions, acidic vesicles, and lipid rafts in living cells and tissues. The development of these probes requires a significant two-photon cross section for the bright image and receptors (sensing moieties) that triggers the emission of the two-photon excited fluorescence upon binding with the ions or membrane in the living system. These probes also must be sensitive to the polarity of the environment to allow selective detection of cytosolic and membrane-bound probes. In addition, they need to be cell-permeable, water-soluble for the staining of cells and tissues, and highly photostable for long-term imaging. The resulting probes-AMg1 (Mg(2+)), ACa1-ACa3 (Ca(2+)), AZn1 and AZn2 (Zn(2+)), AH1, AH2, and AL1 (acidic vesicles), and CL2 (membrane)-use 2-acetyl-6-aminonaphthalene as the fluorophore and receptors for the target ions or membrane. All of these two-photon turn-on probes can detect the intracellular free metal ions, acidic vesicles, and lipid rafts at 100-300 microm depth in live tissues. Moreover, with ACa1-AM, we could simultaneously visualize the spontaneous Ca(2+) waves in the somas of

  8. Probing temperature-driven spin reorientation transition of GdFeCo film by Kerr loops and ferromagnetic resonance

    SciTech Connect

    He, Wei Liu, Hao-Liang; Cai, Jian-Wang; Cheng, Zhao-Hua; Wu, Hong-Ye

    2015-01-26

    The magnetic anisotropy is of both scientific and technological interest for magneto-optical material GdFeCo film. We characterize the magnetic anisotropy of a 20 nm GdFeCo film from 265 K to 320 K via Kerr loops and ferromagnetic resonance. With increasing temperature, both of the first-order uniaxial magnetic anisotropy and shape anisotropy increase. However, the competition between them causes a temperature-driven spin reorientation transition (SRT) and the effective perpendicular magnetic anisotropy decrease from 2.22 × 10{sup 4 }ergs/cm{sup 3} (288 K) to −1.56 × 10{sup 4 }ergs/cm{sup 3} (317 K). The positive second-order uniaxial magnetic anisotropy determines an easy-cone state as the mediated state during SRT.

  9. Probing the neutron star spin evolution in the young Small Magellanic Cloud Be/X-ray binary SXP 1062

    NASA Astrophysics Data System (ADS)

    Popov, S. B.; Turolla, R.

    2012-03-01

    The newly discovered Be/X-ray binary in the Small Magellanic Cloud, SXP 1062, provides the first example of a robust association with a supernova remnant (SNR). The short age estimated for the SNR qualifies SXP 1062 as the youngest known source in its class, ?. As such, it allows us to test current models of magnetorotational evolution of neutron stars in a still unexplored regime. Here we discuss possible evolutionary scenarios for SXP 1062 in an attempt to reconcile its long spin period, ?, and short age. Although several options can be considered, like an anomalously long initial period or the presence of a fossil disc, our results indicate that SXP 1062 may host a neutron star born with a large initial magnetic field, typically in excess of ˜ 1014 G, which then decayed to ˜ 1013 G.

  10. Acid-Activatable Michael-Type Fluorescent Probes for Thiols and for Labeling Lysosomes in Live Cells.

    PubMed

    Dai, Chun-Guang; Du, Xiao-Jiao; Song, Qin-Hua

    2015-12-18

    A Michael addition is usually taken as a base-catalyzed reaction. Most fluorescent probes have been designed to detect thiols in slightly alkaline solutions (pH 7-9). The sensing reactions of almost all Michael-type fluorescent probes for thiols are faster in a high pH solution than in a low pH solution. In this work, we synthesized a series of 7-substituted 2-(quinolin-2-ylmethylene)malonic acids (QMAs, substituents: NEt2, OH, H, Cl, or NO2) and their ethyl esters (QMEs) as Michael-type fluorescent probes for thiols. The sensing reactions of QMAs and QMEs occur in distinct pH ranges, pH < 7 for QMAs and pH > 7 for QMEs. On the basis of experimental and theoretic studies, we have clarified the distinct pH effects on the sensing reactivity between QMAs and QMEs and demonstrated that two QMAs (NEt2, OH) are highly sensitive and selective fluorescent probes for thiols in acidic solutions (pH < 7) and promising dyes that can label lysosomes in live cells.

  11. Intracellular surface-enhanced Raman scattering probe based on gold nanorods functionalized with mercaptohexadecanoic acid with reduced cytotoxicity.

    PubMed

    Liu, Min; Wang, Zhuyuan; Zong, Shenfei; Zhang, Ruohu; Yang, Jing; Cui, Yiping

    2012-01-01

    A surface-enhanced Raman scattering (SERS) probe for intracellular detection was demonstrated by utilizing gold nanorods (GNRs) coated with p-aminothiophenol as the Raman reporters. In this probe, to reduce the cytotoxicity of GNRs, cetyltrimethylammonium bromide (CTAB) molecules adsorbed on the surfaces of GNRs as ligands were replaced by mercaptohexadecanoic acid via a "round-trip" phase change method. Such a ligand exchange can reduce the toxicity of the probe compared to the original CTAB-stabilized GNRs, which were confirmed by both 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and bright field view of HeLa cells. Meanwhile, the transmission electron microscopy images indicated that there is no significant morphologic change of GNRs before and after the ligand exchange. Moreover, its SERS performance was adequately retained after the incorporation of the probe into living HeLa cells. This new type of SERS probe is expected to have great potential in intracellular imaging or sensing applications.

  12. Detection and quantification of genetically modified organisms using very short, locked nucleic acid TaqMan probes.

    PubMed

    Salvi, Sergio; D'Orso, Fabio; Morelli, Giorgio

    2008-06-25

    Many countries have introduced mandatory labeling requirements on foods derived from genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (PCR) based upon the TaqMan probe chemistry has become the method mostly used to support these regulations; moreover, event-specific PCR is the preferred method in GMO detection because of its high specificity based on the flanking sequence of the exogenous integrant. The aim of this study was to evaluate the use of very short (eight-nucleotide long), locked nucleic acid (LNA) TaqMan probes in 5'-nuclease PCR assays for the detection and quantification of GMOs. Classic TaqMan and LNA TaqMan probes were compared for the analysis of the maize MON810 transgene. The performance of the two types of probes was tested on the maize endogenous reference gene hmga, the CaMV 35S promoter, and the hsp70/cryIA(b) construct as well as for the event-specific 5'-integration junction of MON810, using plasmids as standard reference molecules. The results of our study demonstrate that the LNA 5'-nuclease PCR assays represent a valid and reliable analytical system for the detection and quantification of transgenes. Application of very short LNA TaqMan probes to GMO quantification can simplify the design of 5'-nuclease assays. PMID:18494480

  13. Detection and quantification of genetically modified organisms using very short, locked nucleic acid TaqMan probes.

    PubMed

    Salvi, Sergio; D'Orso, Fabio; Morelli, Giorgio

    2008-06-25

    Many countries have introduced mandatory labeling requirements on foods derived from genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (PCR) based upon the TaqMan probe chemistry has become the method mostly used to support these regulations; moreover, event-specific PCR is the preferred method in GMO detection because of its high specificity based on the flanking sequence of the exogenous integrant. The aim of this study was to evaluate the use of very short (eight-nucleotide long), locked nucleic acid (LNA) TaqMan probes in 5'-nuclease PCR assays for the detection and quantification of GMOs. Classic TaqMan and LNA TaqMan probes were compared for the analysis of the maize MON810 transgene. The performance of the two types of probes was tested on the maize endogenous reference gene hmga, the CaMV 35S promoter, and the hsp70/cryIA(b) construct as well as for the event-specific 5'-integration junction of MON810, using plasmids as standard reference molecules. The results of our study demonstrate that the LNA 5'-nuclease PCR assays represent a valid and reliable analytical system for the detection and quantification of transgenes. Application of very short LNA TaqMan probes to GMO quantification can simplify the design of 5'-nuclease assays.

  14. Efficient detection of secondary structure folded nucleic acids related to Alzheimer's disease based on junction probes.

    PubMed

    Li, Juan; Qi, Xiu-Juan; Du, Yan-Yan; Fu, Hua-E; Chen, Guo-Nan; Yang, Huang-Hao

    2012-01-01

    Single stranded DNA often forms stable secondary structures under physiological conditions. These DNA secondary structures play important physiological roles. However, the analysis of such secondary structure folded DNA is often complicated because of its high thermodynamic stability and slow hybridization kinetics. In this article, we demonstrate that Y-shaped junction probes could be used for rapid and highly efficient detection of secondary structure folded DNA. Our approach contained a molecular beacon (MB) probe and an assistant probe. In the absence of target, the MB probe failed to hybridize with the assistant probe. Whereas, the MB probe and the assistant probe could cooperatively unwind the secondary structure folded DNA target to form a ternary Y-shaped junction structure. In this condition, the MB probe was also opened, resulting in separating the fluorophores from the quenching moiety and emitting the fluorescence signal. This approach allowed for the highly sensitive detection of secondary structure folded DNA target, such as a tau specific DNA fragment related to Alzheimer's disease in this case. Additionally, this approach showed strong SNPs identifying capability. Furthermore, it was noteworthy that this newly proposed approach was capable of detecting secondary structure folded DNA target in cell lysate samples.

  15. A high-resolution mitochondria-targeting ratiometric fluorescent probe for detection of the endogenous hypochlorous acid

    NASA Astrophysics Data System (ADS)

    Zhou, Liyi; Lu, Dan-Qing; Wang, Qianqian; Hu, Shunqin; Wang, Haifei; Sun, Hongyan; Zhang, Xiaobing

    2016-09-01

    Hypochlorite anion, one of the biologically important reactive oxygen species, plays an essential role in diverse normal biochemical functions and abnormal pathological processes. Herein, an efficient high-resolution mitochondria-targeting ratiometric fluorescent probe for hypochlorous acid detection has been designed, synthesized and characterized. It is easily synthesized by the condensation reaction (Cdbnd C) of a 2-(2-hydroxyphenyl) quinazolin-4(3H)-one fluorophore and a cyanine group (mitochondria-targeting), which made the whole molecular a large Stokes shift (210 nm) and the two well-resolved emission peaks separated by 140 nm. As a result, it is considered as a good candidate for high resolution hypochlorous acid imaging in live cells. The ratiometric fluorescent probe exhibited outstanding features of high sensitivity, high selectivity, rapid response time (within 50 s), and excellent mitochondria-targeting ability. Moreover, the probe can also be successfully applied to imaging endogenously hypochlorous acid in the mitochondria of living cells with low cytotoxicity, and high resolution.

  16. pH-Sensitive Polymeric Micelle-based pH Probe for Detecting and Imaging Acidic Biological Environments

    PubMed Central

    Lee, Young Ju; Kang, Han Chang; Hu, Jun; Nichols, Joseph W.; Jeon, Yong Sun; Bae, You Han

    2012-01-01

    To overcome the limitations of monomeric pH probes for acidic tumor environments, this study designed a mixed micelle pH probe composed of polyethylene glycol (PEG)-b- poly(L-histidine) (PHis) and PEG-b-poly(L-lactic acid) (PLLA), which is well-known as an effective antitumor drug carrier. Unlike monomeric histidine and PHis derivatives, the mixed micelles can be structurally destabilized by changes in pH, leading to a better pH sensing system in nuclear magnetic resonance (NMR) techniques. The acidic pH-induced transformation of the mixed micelles allowed pH detection and pH mapping of 0.2–0.3 pH unit differences by pH-induced “on/off”-like sensing of NMR and magnetic resonance spectroscopy (MRS). The micellar pH probes sensed pH differences in non-biological phosphate buffer and biological buffers such as cell culture medium and rat whole blood. In addition, the pH-sensing ability of the mixed micelles was not compromised by loaded doxorubicin. In conclusion, PHis-based micelles could have potential as a tool to simultaneously treat and map the pH of solid tumors in vivo. PMID:22861824

  17. Probing Ground and Excited States of Phospholamban in Model and Native Lipid Membranes by Magic Angle Spinning NMR Spectroscopy

    PubMed Central

    Gustavsson, Martin; Traaseth, Nathaniel J.; Veglia, Gianluigi

    2013-01-01

    In this paper, we analyzed the ground and excited states of phospholamban (PLN), a membrane protein that regulates sarcoplasmic reticulum calcium ATPase (SERCA), in different membrane mimetic environments. Previously, we proposed that the conformational equilibria of PLN are central to SERCA regulation. Here, we show that these equilibria detected in micelles and bicelles are also present in native sarcoplasmic reticulum lipid membranes as probed by MAS solid-state NMR. Importantly, we found that the kinetics of conformational exchange and the extent of ground and excited states in detergent micelles and lipid bilayers are different, revealing a possible regulatory role of the membrane composition on the allosteric regulation of SERCA. Since the extent of excited states is directly correlated to SERCA inhibition, these findings open up the exciting possibility that calcium transport in the heart can be controlled by the lipid bilayer composition. PMID:21839724

  18. Physical characterization of the state of motion of the phenalenyl spin probe in cation-exchanged faujasite zeolite supercages with pulsed EPR

    NASA Astrophysics Data System (ADS)

    Doetschman, D. C.; Dwyer, D. W.; Fox, J. D.; Frederick, C. K.; Scull, S.; Thomas, G. D.; Utterback, S. G.; Wei, J.

    1994-08-01

    The molecular motion of the phenalenyl (PNL) spin probe in the supercages of cation-exchanged X and Y zeolites (faujasites) has been physically characterized by pulsed and continuous wave (CW) electron paramagnetic resonance (EPR). Both X and Y zeolites, whose cation sites were exchanged with the alkali metal ions, Li +, Na +, K +, Rb + and Cs + were examined. There is a good correspondence between the temperature dependences of the PNL electron spin phase memory time and the CW EPR spectra. Both display evidence of a thermal activation from a stationary, non-rotating molecular state to a low-temperature state of in-plane rotation (Das et al., Chem Phys. 143 (1990) 253). The rate of in-plane rotation is an activated process, with E* | / R=1289 |+- 35 K and 1462 ± 47 K in NaX and KX zeolites, respectively. The rotation appears to be about an axis along which the half-filled, non-bonding π orbital interacts with the exchanged cation in the supercage. Both CW and pulsed EPR also show a higher temperature activation from the in-plane rotating state to an effectively isoptropic state of rotation of PNL in which the PNL-cation bond is thought to be broken, with E* ⊥ / R=2050 ± 110 K, 1956 ± 46K, 1335 ± 97 K in LiX, NaX and KX zeolites, respectively. The strength of the PNL-cation bonding decreases with increasing cation atomic number as indicated by E* ⊥ and the peripheral repulsion (crowding) of PNL increases with cation size as indicated E* |. There are qualitative indications that the binding of PNL to the cations in the Y zeolite is stronger than in the X zeolite.

  19. Slow dynamics of water molecules in an aqueous solution of lithium chloride probed by neutron spin-echo.

    PubMed

    Mamontov, E; Ohl, M

    2013-07-14

    Aqueous solutions of lithium chloride are uniquely similar to pure water in the parameters such as glass transition temperature, Tg, yet they could be supercooled without freezing down to below 200 K even in the bulk state. This provides advantageous opportunity to study low-temperature dynamics of water molecules in water-like environment in the bulk rather than nano-confined state. Using high-resolution neutron spin-echo data, we argue that the critical temperature, Tc, which is also common between lithium chloride aqueous solutions and pure water, is associated with the split of a secondary relaxation from the main structural relaxation on cooling down. Our results do not allow distinguishing between a well-defined separate secondary relaxation process and the "excess wing" scenario, in which the temperature dependence of the secondary relaxation follows the main relaxation. Importantly, however, in either of these scenarios the secondary relaxation is associated with density-density fluctuations, measurable in a neutron scattering experiment. Neutron scattering could be the only experimental technique with the capability of providing information on the spatial characteristics of the secondary relaxation through the dependence of the signal on the scattering momentum transfer. We propose a simple method for such analysis. PMID:23689686

  20. Detection of Sialic Acid-Utilising Bacteria in a Caecal Community Batch Culture Using RNA-Based Stable Isotope Probing

    PubMed Central

    Young, Wayne; Egert, Markus; Bassett, Shalome A.; Bibiloni, Rodrigo

    2015-01-01

    Sialic acids are monosaccharides typically found on cell surfaces and attached to soluble proteins, or as essential components of ganglioside structures that play a critical role in brain development and neural transmission. Human milk also contains sialic acid conjugated to oligosaccharides, glycolipids, and glycoproteins. These nutrients can reach the large bowel where they may be metabolised by the microbiota. However, little is known about the members of the microbiota involved in this function. To identify intestinal bacteria that utilise sialic acid within a complex intestinal community, we cultured the caecal microbiota from piglets in the presence of 13C-labelled sialic acid. Using RNA-based stable isotope probing, we identified bacteria that consumed 13C-sialic acid by fractionating total RNA in isopycnic buoyant density gradients followed by 16S rRNA gene analysis. Addition of sialic acid caused significant microbial community changes. A relative rise in Prevotella and Lactobacillus species was accompanied by a corresponding reduction in the genera Escherichia/Shigella, Ruminococcus and Eubacterium. Inspection of isotopically labelled RNA sequences suggests that the labelled sialic acid was consumed by a wide range of bacteria. However, species affiliated with the genus Prevotella were clearly identified as the most prolific users, as solely their RNA showed significantly higher relative shares among the most labelled RNA species. Given the relevance of sialic acid in nutrition, this study contributes to a better understanding of their microbial transformation in the intestinal tract with potential implications for human health. PMID:25816158

  1. Detection of sialic acid-utilising bacteria in a caecal community batch culture using RNA-based stable isotope probing.

    PubMed

    Young, Wayne; Egert, Markus; Bassett, Shalome A; Bibiloni, Rodrigo

    2015-03-25

    Sialic acids are monosaccharides typically found on cell surfaces and attached to soluble proteins, or as essential components of ganglioside structures that play a critical role in brain development and neural transmission. Human milk also contains sialic acid conjugated to oligosaccharides, glycolipids, and glycoproteins. These nutrients can reach the large bowel where they may be metabolised by the microbiota. However, little is known about the members of the microbiota involved in this function. To identify intestinal bacteria that utilise sialic acid within a complex intestinal community, we cultured the caecal microbiota from piglets in the presence of 13C-labelled sialic acid. Using RNA-based stable isotope probing, we identified bacteria that consumed 13C-sialic acid by fractionating total RNA in isopycnic buoyant density gradients followed by 16S rRNA gene analysis. Addition of sialic acid caused significant microbial community changes. A relative rise in Prevotella and Lactobacillus species was accompanied by a corresponding reduction in the genera Escherichia/Shigella, Ruminococcus and Eubacterium. Inspection of isotopically labelled RNA sequences suggests that the labelled sialic acid was consumed by a wide range of bacteria. However, species affiliated with the genus Prevotella were clearly identified as the most prolific users, as solely their RNA showed significantly higher relative shares among the most labelled RNA species. Given the relevance of sialic acid in nutrition, this study contributes to a better understanding of their microbial transformation in the intestinal tract with potential implications for human health.

  2. Detection of Chromosomal Inversions Using Non-Repetitive Nucleic Acid Probes

    NASA Technical Reports Server (NTRS)

    Bailey, Susan M. (Inventor); Ray, F. Andrew (Inventor); Goodwin, Edwin H. (Inventor); Bedford, Joel S. (Inventor); Cornforth, Michael N. (Inventor)

    2014-01-01

    A method and a kit for the identification of chromosomal inversions are described. Single-stranded sister chromatids are generated, for example by CO-FISH. A plurality of non-repetitive, labeled probes of relatively small size are hybridized to portions of only one of a pair of single-stranded sister chromatids. If no inversion exists, all of the probes will hybridize to a first chromatid. If an inversion has occurred, these marker probes will be detected on the sister chromatid at the same location as the inversion on the first chromatid.

  3. Detection of chromosomal inversions using non-repetitive nucleic acid probes

    NASA Technical Reports Server (NTRS)

    Bailey, Susan M. (Inventor); Ray, F. Andrew (Inventor); Goodwin, Edwin H. (Inventor); Bedford, Joel S. (Inventor); Cornforth, Michael N. (Inventor)

    2012-01-01

    A method for the identification of chromosomal inversions is described. Single-stranded sister chromatids are generated, for example by CO-FISH. A plurality of non-repetitive, labeled probes of relatively small size are hybridized to portions of only one of a pair of single-stranded sister chromatids. If no inversion exists, all of the probes will hybridize to a first chromatid. If an inversion has occurred, these marker probes will be detected on the sister chromatid at the same location as the inversion on the first chromatid.

  4. Colorimetric and fluorescence detection of G-quadruplex nucleic acids with a coumarin-benzothiazole probe.

    PubMed

    Yan, Jin-wu; Tian, Yi-guang; Tan, Jia-heng; Huang, Zhi-shu

    2015-11-01

    A colorimetric and red-emitting fluorescent dual probe for G-quadruplexes was devised with a conjugated coumarin-benzothiazole scaffold. Its significant and distinct changes in both color and fluorescence enable the label-free and visual detection of G-quadruplex structures. In addition, this probe gives a distinct strong emission response to the nucleoli in fixed cells imaging, which might be attributed to the interaction between the probe and rDNA G-quadruplex based on the chromatin immunoprecipitation assay. All these results suggest its promising application prospects in the G-quadruplex research field.

  5. Diffusive behavior in LiMPO4 with M=Fe, Co, Ni probed by muon-spin relaxation

    NASA Astrophysics Data System (ADS)

    Sugiyama, Jun; Nozaki, Hiroshi; Harada, Masashi; Kamazawa, Kazuya; Ikedo, Yutaka; Miyake, Yasuhiro; Ofer, Oren; Månsson, Martin; Ansaldo, Eduardo J.; Chow, Kim H.; Kobayashi, Genki; Kanno, Ryoji

    2012-02-01

    In order to study the diffusive nature of lithium transition-metal phospho-olivines, we measured muon-spin relaxation (μ+SR) spectra for the polycrystalline LiMPO4 samples with M=Mn, Fe, Co, or Ni in the temperature range between 50 and 500 K. The μ+SR spectra under zero applied field are strongly affected by the magnetic moments of the 3d electrons in the M2+ ions so that, for LiMnPO4, it was difficult to detect the relaxation change caused by the diffusion due to the large Mn2+(S=5/2) moments. However, diffusive behavior was clearly observed via the relaxation due to nuclear dipolar fields above ˜150 K for LiFePO4, LiCoPO4, and LiNiPO4 as S decreased from 2 to 1. From the temperature dependence of the nuclear field fluctuation rate, self-diffusion coefficients of Li+ ions (DLi) at 300 K and its activation energy (Ea) were estimated, respectively, as ˜3.6(2)×10-10 cm2/s and Ea=0.10(2) eV for LiFePO4, ˜1.6(1)×10-10 cm2/s and Ea=0.10(1) eV for LiCoPO4, and ˜2.7(4)×10-10 cm2/s and Ea=0.17(2) eV for LiNiPO4, assuming that the diffusing Li+ ions jump between the regular site and interstitial sites.

  6. Human papillomavirus 35 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorincz, A.T.

    1989-07-18

    This patent describes an HPV 35 hybridization probe comprising a member selected from the group consisting of (i) HPV 35 DNA or fragments thereof labelled with a marker and (ii) HPV 35 RNA or fragments thereof labelled with a marker.

  7. Human papillomavirus 43 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorincz, A.T.

    1989-07-18

    This patent describes an HPV 43 hybridization probe comprising a member selected from the group consisting of (i) HPV 43 DNA or fragments thereof labelled with a marker and (ii) HPV 43 RNA or fragments thereof labelled with a marker.

  8. Human papillomavirus 44 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorincz, A.T.

    1989-07-18

    This patent describes an HPV 44 hybridization probe comprising a member selected from the group consisting of (1) HPV 44 DNA or fragments thereof labelled with a marker and (ii) HPV 44 RNA or fragments thereof labelled with a marker.

  9. Human papillomavirus 56 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorinez, A.T.

    1990-03-13

    This patent describes an HPV 56 hybridization probe. It comprises: a member selected from the group consisting of HPV 56 DNA or fragments thereof labelled with a marker and HPV 56 RNA or fragments thereof labelled with a marker.

  10. Structural transitions in full-length human prion protein detected by xenon as probe and spin labeling of the N-terminal domain

    PubMed Central

    Narayanan, Sunilkumar Puthenpurackal; Nair, Divya Gopalakrishnan; Schaal, Daniel; Barbosa de Aguiar, Marisa; Wenzel, Sabine; Kremer, Werner; Schwarzinger, Stephan; Kalbitzer, Hans Robert

    2016-01-01

    Fatal neurodegenerative disorders termed transmissible spongiform encephalopathies (TSEs) are associated with the accumulation of fibrils of misfolded prion protein PrP. The noble gas xenon accommodates into four transiently enlarged hydrophobic cavities located in the well-folded core of human PrP(23–230) as detected by [1H, 15N]-HSQC spectroscopy. In thermal equilibrium a fifth xenon binding site is formed transiently by amino acids A120 to L125 of the presumably disordered N-terminal domain and by amino acids K185 to T193 of the well-folded domain. Xenon bound PrP was modelled by restraint molecular dynamics. The individual microscopic and macroscopic dissociation constants could be derived by fitting the data to a model including a dynamic opening and closing of the cavities. As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain. This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn2+-binding to the octarepeat motif. PMID:27341298

  11. Structural transitions in full-length human prion protein detected by xenon as probe and spin labeling of the N-terminal domain.

    PubMed

    Narayanan, Sunilkumar Puthenpurackal; Nair, Divya Gopalakrishnan; Schaal, Daniel; Barbosa de Aguiar, Marisa; Wenzel, Sabine; Kremer, Werner; Schwarzinger, Stephan; Kalbitzer, Hans Robert

    2016-01-01

    Fatal neurodegenerative disorders termed transmissible spongiform encephalopathies (TSEs) are associated with the accumulation of fibrils of misfolded prion protein PrP. The noble gas xenon accommodates into four transiently enlarged hydrophobic cavities located in the well-folded core of human PrP(23-230) as detected by [(1)H, (15)N]-HSQC spectroscopy. In thermal equilibrium a fifth xenon binding site is formed transiently by amino acids A120 to L125 of the presumably disordered N-terminal domain and by amino acids K185 to T193 of the well-folded domain. Xenon bound PrP was modelled by restraint molecular dynamics. The individual microscopic and macroscopic dissociation constants could be derived by fitting the data to a model including a dynamic opening and closing of the cavities. As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain. This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn(2+)-binding to the octarepeat motif. PMID:27341298

  12. Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ

    DOEpatents

    Gray, J.W.; Weier, H.U.

    1998-11-24

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences. 9 figs.

  13. Y chromosome specific nucleic acid probe and method for identifying the Y chromosome in SITU

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich

    1999-01-01

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences.

  14. Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich

    1998-01-01

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences.

  15. Y chromosome specific nucleic acid probe and method for identifying the Y chromosome in SITU

    DOEpatents

    Gray, J.W.; Weier, H.U.

    1999-03-30

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences. 9 figs.

  16. Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich

    2001-01-01

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences.

  17. Sensitivity and specificity of nucleic acid probes for potato leafroll luteovirus detection.

    PubMed

    Robinson, D J; Romero, J

    1991-01-01

    Complementary DNA (cDNA) probes, prepared by nick-translation or by oligolabelling of a 520 bp fragment representing residues 4741 to 5261 in the potato leafroll luteovirus (PLRV) sequence, were equally sensitive, with a detection limit equivalent to sap from about 600 micrograms of infected potato or Nicotiana clevelandii leaf tissue and to RNA from about 120 micrograms tissue. Increasing the concentration of oligolabelled probe gave similar results with shorter autoradiographic exposures, but also resulted in positive signals with sap extracts from healthy plants. In contrast, a complementary RNA (cRNA) probe made by in vitro transcription of the cDNA insert could be used at higher concentration without giving rise to reactions with healthy plant extracts, and had a detection limit equivalent to 5 micrograms tissue/spot. Five oligolabelled probes representing different regions of the PLRV genome detected PLRV equally well. A probe that represented a portion of the particle protein gene also detected beet western yellows luteovirus (BWYV), with which it has 69% nucleotide sequence homology, and an English strain of the RPV form of barley yellow dwarf luteovirus, and reacted weakly with extracts from plants infected with groundnut rosette assistor luteovirus or carrot red leaf luteovirus. Probes for regions on either side of the particle protein gene also detected RPV, but not any of the other luteoviruses tested, in agreement with earlier suggestions that RPV is more closely related to PLRV than are BWYV or the other luteoviruses tested. An attempt to improve the detection of weak heterologous reactions by using a cRNA probe was unsuccessful, perhaps because tests using cRNA are more affected by mismatching than tests using cDNA probes. PMID:1804851

  18. Regeneration of high-quality silk fibroin fiber by wet spinning from CaCl2-formic acid solvent.

    PubMed

    Zhang, Feng; Lu, Qiang; Yue, Xiaoxiao; Zuo, Baoqi; Qin, Mingde; Li, Fang; Kaplan, David L; Zhang, Xueguang

    2015-01-01

    Silks spun by silkworms and spiders feature outstanding mechanical properties despite being spun under benign conditions. The superior physical properties of silk are closely related to its complicated hierarchical structures constructed from nanoscale building blocks, such as nanocrystals and nanofibrils. Here, we report a novel silk dissolution behavior, which preserved nanofibrils in CaCl2-formic acid solution, that enables spinning of high-quality fibers with a hierarchical structure. This process is characterized by simplicity, high efficiency, low cost, environmental compatibility and large-scale industrialization potential, as well as having utility and potential for the recycling of silk waste and the production of silk-based functional materials.

  19. ESR Study of Electron-Nuclear Dipolar Relaxation for AsO 44-Spin Probe in the Paraelectric Phase of KH 2AsO 4

    NASA Astrophysics Data System (ADS)

    Rakvin, B.; Merunka, D.

    1997-05-01

    Saturation behavior of allowed and forbidden ESR transition of AsO44-paramagnetic probe in KH2AsO4was studied in the wide temperature interval around the paraelectric-ferroelectric phase transition,Tc. The ratios between forbidden and allowed line intensities were employed to deduce information on the electron-nuclear dipolar (END) relaxation mechanism. It was shown that a proton END relaxation mechanism exhibits an extremal temperature behavior in the paraelectric phase around 230 K. The extremal temperature behavior was described by employing a model of proton hopping along the O-H···O bonds around the paramagnetic centers, and the correlation time of this hopping was estimated in the wide temperature range in the paraelectric phase (150-330 K). The temperature dependence of effective proton distance from the neighbor oxygens was obtained, and it was discussed in terms of a localization of the spin density on these oxygens caused by charge inbalance in the As-O bonds in the ferroelectric phase.

  20. Pulsed Electron Double Resonance in Structural Studies of Spin-Labeled Nucleic Acids

    PubMed Central

    Fedorova, O. S.; Tsvetkov, Yu. D.

    2013-01-01

    This review deals with the application of the pulsed electron double resonance (PELDOR) method to studies of spin-labeled DNA and RNA with complicated spatial structures, such as tetramers, aptamers, riboswitches, and three- and four-way junctions. The use of this method for studying DNA damage sites is also described. PMID:23556128

  1. A Far-Red Emitting Probe for Unambiguous Detection of Mobile Zinc in Acidic Vesicles and Deep Tissue†

    PubMed Central

    Rivera-Fuentes, Pablo; Wrobel, Alexandra T.; Zastrow, Melissa L.; Khan, Mustafa; Georgiou, John; Luyben, Thomas T.; Roder, John C.; Okamoto, Kenichi

    2015-01-01

    Imaging mobile zinc in acidic environments remains challenging because most small-molecule optical probes display pH-dependent fluorescence. Here we report a reaction-based sensor that detects mobile zinc unambiguously at low pH. The sensor responds reversibly and with a large dynamic range to exogenously applied Zn2+ in lysosomes of HeLa cells, endogenous Zn2+ in insulin granules of MIN6 cells, and zinc-rich mossy fiber boutons in hippocampal tissue from mice. This long-wavelength probe is compatible with the green-fluorescent protein, enabling multicolor imaging, and facilitates visualization of mossy fiber boutons at depths of >100 µm, as demonstrated by studies in live tissue employing two-photon microscopy. PMID:25815162

  2. Distance measurements across randomly distributed nitroxide probes from the temperature dependence of the electron spin phase memory time at 240 GHz

    NASA Astrophysics Data System (ADS)

    Edwards, Devin T.; Takahashi, Susumu; Sherwin, Mark S.; Han, Songi

    2012-10-01

    At 8.5 T, the polarization of an ensemble of electron spins is essentially 100% at 2 K, and decreases to 30% at 20 K. The strong temperature dependence of the electron spin polarization between 2 and 20 K leads to the phenomenon of spin bath quenching: temporal fluctuations of the dipolar magnetic fields associated with the energy-conserving spin "flip-flop" process are quenched as the temperature of the spin bath is lowered to the point of nearly complete spin polarization. This work uses pulsed electron paramagnetic resonance (EPR) at 240 GHz to investigate the effects of spin bath quenching on the phase memory times (TM) of randomly-distributed ensembles of nitroxide molecules below 20 K at 8.5 T. For a given electron spin concentration, a characteristic, dipolar flip-flop rate (W) is extracted by fitting the temperature dependence of TM to a simple model of decoherence driven by the spin flip-flop process. In frozen solutions of 4-Amino-TEMPO, a stable nitroxide radical in a deuterated water-glass, a calibration is used to quantify average spin-spin distances as large as r¯=6.6 nm from the dipolar flip-flop rate. For longer distances, nuclear spin fluctuations, which are not frozen out, begin to dominate over the electron spin flip-flop processes, placing an effective ceiling on this method for nitroxide molecules. For a bulk solution with a three-dimensional distribution of nitroxide molecules at concentration n, we find W∝n∝1/r, which is consistent with magnetic dipolar spin interactions. Alternatively, we observe W∝n for nitroxides tethered to a quasi two-dimensional surface of large (Ø ˜ 200 nm), unilamellar, lipid vesicles, demonstrating that the quantification of spin bath quenching can also be used to discern the geometry of molecular assembly or organization.

  3. Distance measurements across randomly distributed nitroxide probes from the temperature dependence of the electron spin phase memory time at 240 GHz.

    PubMed

    Edwards, Devin T; Takahashi, Susumu; Sherwin, Mark S; Han, Songi

    2012-10-01

    At 8.5 T, the polarization of an ensemble of electron spins is essentially 100% at 2 K, and decreases to 30% at 20 K. The strong temperature dependence of the electron spin polarization between 2 and 20 K leads to the phenomenon of spin bath quenching: temporal fluctuations of the dipolar magnetic fields associated with the energy-conserving spin "flip-flop" process are quenched as the temperature of the spin bath is lowered to the point of nearly complete spin polarization. This work uses pulsed electron paramagnetic resonance (EPR) at 240 GHz to investigate the effects of spin bath quenching on the phase memory times (T(M)) of randomly-distributed ensembles of nitroxide molecules below 20 K at 8.5 T. For a given electron spin concentration, a characteristic, dipolar flip-flop rate (W) is extracted by fitting the temperature dependence of T(M) to a simple model of decoherence driven by the spin flip-flop process. In frozen solutions of 4-Amino-TEMPO, a stable nitroxide radical in a deuterated water-glass, a calibration is used to quantify average spin-spin distances as large as r=6.6 nm from the dipolar flip-flop rate. For longer distances, nuclear spin fluctuations, which are not frozen out, begin to dominate over the electron spin flip-flop processes, placing an effective ceiling on this method for nitroxide molecules. For a bulk solution with a three-dimensional distribution of nitroxide molecules at concentration n, we find W∝n∝1/r(3), which is consistent with magnetic dipolar spin interactions. Alternatively, we observe W∝n(32) for nitroxides tethered to a quasi two-dimensional surface of large (Ø∼200 nm), unilamellar, lipid vesicles, demonstrating that the quantification of spin bath quenching can also be used to discern the geometry of molecular assembly or organization.

  4. Fast Li ion dynamics in the solid electrolyte Li7 P3 S11 as probed by (6,7) Li NMR spin-lattice relaxation.

    PubMed

    Wohlmuth, Dominik; Epp, Viktor; Wilkening, Martin

    2015-08-24

    The development of safe and long-lasting all-solid-state batteries with high energy density requires a thorough characterization of ion dynamics in solid electrolytes. Commonly, conductivity spectroscopy is used to study ion transport; much less frequently, however, atomic-scale methods such as nuclear magnetic resonance (NMR) are employed. Here, we studied long-range as well as short-range Li ion dynamics in the glass-ceramic Li7 P3 S11 . Li(+) diffusivity was probed by using a combination of different NMR techniques; the results are compared with those obtained from electrical conductivity measurements. Our NMR relaxometry data clearly reveal a very high Li(+) diffusivity, which is reflected in a so-called diffusion-induced (6) Li NMR spin-lattice relaxation peak showing up at temperatures as low as 313 K. At this temperature, the mean residence time between two successful Li jumps is in the order of 3×10(8) s(-1) , which corresponds to a Li(+) ion conductivity in the order of 10(-4) to 10(-3) S cm(-1) . Such a value is in perfect agreement with expectations for the crystalline but metastable glass ceramic Li7 P3 S11 . In contrast to conductivity measurements, NMR analysis reveals a range of activation energies with values ranging from 0.17 to 0.26 eV, characterizing Li diffusivity in the bulk. In our case, through-going Li ion transport, when probed by using macroscopic conductivity spectroscopy, however, seems to be influenced by blocking grain boundaries including, for example, amorphous regions surrounding the Li7 P3 S11 crystallites. As a result of this, long-range ion transport as seen by impedance spectroscopy is governed by an activation energy of approximately 0.38 eV. The findings emphasize how surface and grain boundary effects can drastically affect long-range ionic conduction. If we are to succeed in solid-state battery technology, such effects have to be brought under control by, for example, sophisticated densification or through the preparation

  5. Spin structure functions

    SciTech Connect

    Jian-ping Chen, Alexandre Deur, Sebastian Kuhn, Zein-eddine Meziani

    2011-06-01

    Spin-dependent observables have been a powerful tool to probe the internal structure of the nucleon and to understand the dynamics of the strong interaction. Experiments involving spin degrees of freedom have often brought out surprises and puzzles. The so-called "spin crisis" in the 1980s revealed the limitation of naive quark-parton models and led to intensive worldwide efforts, both experimental and theoretical, to understand the nucleon spin structure. With high intensity and high polarization of both the electron beam and targets, Jefferson Lab has the world's highest polarized luminosity and the best figure-of-merit for precision spin structure measurements. It has made a strong impact in this subfield of research. This chapter will highlight Jefferson Lab's unique contributions in the measurements of valence quark spin distributions, in the moments of spin structure functions at low to intermediate Q2, and in the transverse spin structure.

  6. Probing the Active Center of Benzaldehyde Lyase with Substitutions and the Pseudosubstrate Analogue Benzoylphosphonic Acid Methyl Ester

    SciTech Connect

    Brandt, Gabriel S.; Nemeria, Natalia; Chakraborty, Sumit; McLeish, Michael J.; Yep, Alejandra; Kenyon, George L.; Petsko, Gregory A.; Jordan, Frank; Ringe, Dagmar

    2008-07-28

    Benzaldehyde lyase (BAL) catalyzes the reversible cleavage of (R)-benzoin to benzaldehyde utilizing thiamin diphosphate and Mg{sup 2+} as cofactors. The enzyme is important for the chemoenzymatic synthesis of a wide range of compounds via its carboligation reaction mechanism. In addition to its principal functions, BAL can slowly decarboxylate aromatic amino acids such as benzoylformic acid. It is also intriguing mechanistically due to the paucity of acid-base residues at the active center that can participate in proton transfer steps thought to be necessary for these types of reactions. Here methyl benzoylphosphonate, an excellent electrostatic analogue of benzoylformic acid, is used to probe the mechanism of benzaldehyde lyase. The structure of benzaldehyde lyase in its covalent complex with methyl benzoylphosphonate was determined to 2.49 {angstrom} (Protein Data Bank entry 3D7K) and represents the first structure of this enzyme with a compound bound in the active site. No large structural reorganization was detected compared to the complex of the enzyme with thiamin diphosphate. The configuration of the predecarboxylation thiamin-bound intermediate was clarified by the structure. Both spectroscopic and X-ray structural studies are consistent with inhibition resulting from the binding of MBP to the thiamin diphosphate in the active centers. We also delineated the role of His29 (the sole potential acid-base catalyst in the active site other than the highly conserved Glu50) and Trp163 in cofactor activation and catalysis by benzaldehyde lyase.

  7. Proteomic-based stable isotope probing reveals taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton

    DOE PAGES

    Bryson, Samuel; Li, Zhou; Pett-Ridge, Jennifer; Robert L. Hettich; Mayali, Xavier; Pan, Chongle; Mueller, Ryan S.

    2016-04-26

    Heterotrophic marine bacterioplankton are a critical component of the carbon cycle, processing nearly a quarter of annual global primary production, yet defining how substrate utilization preferences and resource partitioning structure these microbial communities remains a challenge. In this study, we utilized proteomics-based stable isotope probing (proteomic SIP) to characterize the assimilation of amino acids by coastal marine bacterioplankton populations. We incubated microcosms of seawater collected from Newport, OR and Monterey Bay, CA with 1 M 13C-amino acids for 15 and 32 hours. Subsequent analysis of 13C incorporation into protein biomass quantified the frequency and extent of isotope enrichment for identifiedmore » proteins. Using these metrics we tested whether amino acid assimilation patterns were different for specific bacterioplankton populations. Proteins associated with Rhodobacterales and Alteromonadales tended to have a significantly high number of tandem mass spectra from 13C-enriched peptides, while Flavobacteriales and SAR11 proteins generally had significantly low numbers of 13C-enriched spectra. Rhodobacterales proteins associated with amino acid transport and metabolism had an increased frequency of 13C-enriched spectra at time-point 2, while Alteromonadales ribosomal proteins were 13C- enriched across time-points. Overall, proteomic SIP facilitated quantitative comparisons of dissolved free amino acids assimilation by specific taxa, both between sympatric populations and between protein functional groups within discrete populations, allowing an unprecedented examination of population-level metabolic responses to resource acquisition in complex microbial communities.« less

  8. Probing the active center of benzaldehyde lyase with substitutions and the pseudosubstrate analogue benzoylphosphonic acid methyl ester.

    PubMed

    Brandt, Gabriel S; Nemeria, Natalia; Chakraborty, Sumit; McLeish, Michael J; Yep, Alejandra; Kenyon, George L; Petsko, Gregory A; Jordan, Frank; Ringe, Dagmar

    2008-07-22

    Benzaldehyde lyase (BAL) catalyzes the reversible cleavage of ( R)-benzoin to benzaldehyde utilizing thiamin diphosphate and Mg (2+) as cofactors. The enzyme is important for the chemoenzymatic synthesis of a wide range of compounds via its carboligation reaction mechanism. In addition to its principal functions, BAL can slowly decarboxylate aromatic amino acids such as benzoylformic acid. It is also intriguing mechanistically due to the paucity of acid-base residues at the active center that can participate in proton transfer steps thought to be necessary for these types of reactions. Here methyl benzoylphosphonate, an excellent electrostatic analogue of benzoylformic acid, is used to probe the mechanism of benzaldehyde lyase. The structure of benzaldehyde lyase in its covalent complex with methyl benzoylphosphonate was determined to 2.49 A (Protein Data Bank entry 3D7K ) and represents the first structure of this enzyme with a compound bound in the active site. No large structural reorganization was detected compared to the complex of the enzyme with thiamin diphosphate. The configuration of the predecarboxylation thiamin-bound intermediate was clarified by the structure. Both spectroscopic and X-ray structural studies are consistent with inhibition resulting from the binding of MBP to the thiamin diphosphate in the active centers. We also delineated the role of His29 (the sole potential acid-base catalyst in the active site other than the highly conserved Glu50) and Trp163 in cofactor activation and catalysis by benzaldehyde lyase.

  9. Detection of glyceraldehyde 3-phosphate dehydrogenase messenger RNA using a peptide nucleic acid probe in paraffin-embedded archival specimens.

    PubMed

    Hiroyasu, Makoto; Akatsuka, Shinya; Shirase, Tomoyuki; Toda, Yoshinobu; Hiai, Hiroshi; Toyokuni, Shinya

    2004-04-01

    Although the human genome project has been completed, the functions of many genes remain undetermined. In situ hybridization (ISH) is a key method for identifying cells in which a given messenger RNA is transcribed. Paraffin-embedded specimens remain precious materials for research, but preservation of high-quality RNA in these specimens is not expected unless ample caution was taken during fixation. Peptide nucleic acid (PNA) is a recently developed hybrid molecule with genetic information that has high stability and high affinity to the complementary DNA or RNA. We applied a PNA probe to mRNA ISH of liver specimens obtained by autopsy and embedded in paraffin 28-48 years ago. An 18-mer PNA probe for glyceraldehyde 3-phosphate dehydrogenase was used. Staining was then analyzed in association with morphology by hematoxylin and eosin staining, and with the time between death of the patient and tissue fixation. Notably, specimens fixed with formalin and embedded in paraffin 48 years ago yielded excellent results if the time before fixation was short enough (<8 h). There was a significant inverse correlation between the intensity of ISH staining and the time before fixation. Oligonucleotide PNA probe, albeit at high cost, would increase the value of paraffin-embedded specimens in storage for use in human medical research.

  10. Mercaptopropionic acid-capped CdTe quantum dots as fluorescence probe for the determination of salicylic acid in pharmaceutical products.

    PubMed

    Bunkoed, Opas; Kanatharana, Proespichaya

    2015-11-01

    Mercaptopropionic acid (MPA)-capped cadmium telluride (CdTe) quantum dot (QDs) fluorescent probes were synthesized in aqueous solution and used for the determination of salicylic acid. The interaction between the MPA-capped CdTe QDs and salicylic acid was studied using fluorescence spectroscopy and some parameters that could modify the fluorescence were investigated to optimize the measurements. Under optimum conditions, the quenched fluorescence intensity of MPA-capped CdTe QDs was linearly proportional to the concentration of salicylic acid in the range of 0.5-40 µg mL(-1) with a coefficient of determination of 0.998, and the limit of detection was 0.15 µg mL(-1). The method was successfully applied to the determination of salicylic acid in pharmaceutical products, and satisfactory results were obtained that were in agreement with both the high pressure liquid chromatography (HPLC) method and the claimed values. The recovery of the method was in the range 99 ± 3% to 105 ± 9%. The proposed method is simple, rapid, cost effective, highly sensitivity and eminently suitable for the quality control of pharmaceutical preparation. The possible mechanisms for the observed quenching reaction was also discussed.

  11. Fluorescence in situ Hybridization method using Peptide Nucleic Acid probes for rapid detection of Lactobacillus and Gardnerella spp.

    PubMed Central

    2013-01-01

    Background Bacterial vaginosis (BV) is a common vaginal infection occurring in women of reproductive age. It is widely accepted that the microbial switch from normal microflora to BV is characterized by a decrease in vaginal colonization by Lactobacillus species together with an increase of Gardnerella vaginalis and other anaerobes. Our goal was to develop and optimize a novel Peptide Nucleic Acid (PNA) Fluorescence in situ Hybridization assay (PNA FISH) for the detection of Lactobacillus spp. and G. vaginalis in mixed samples. Results Therefore, we evaluated and validated two specific PNA probes by using 36 representative Lactobacillus strains, 22 representative G. vaginalis strains and 27 other taxonomically related or pathogenic bacterial strains commonly found in vaginal samples. The probes were also tested at different concentrations of G. vaginalis and Lactobacillus species in vitro, in the presence of a HeLa cell line. Specificity and sensitivity of the PNA probes were found to be 98.0% (95% confidence interval (CI), from 87.8 to 99.9%) and 100% (95% CI, from 88.0 to 100.0%), for Lactobacillus spp.; and 100% (95% CI, from 92.8 to 100%) and 100% (95% CI, from 81.5 to 100.0%) for G. vaginalis. Moreover, the probes were evaluated in mixed samples mimicking women with BV or normal vaginal microflora, demonstrating efficiency and applicability of our PNA FISH. Conclusions This quick method accurately detects Lactobacillus spp. and G. vaginalis species in mixed samples, thus enabling efficient evaluation of the two bacterial groups, most frequently encountered in the vagina. PMID:23586331

  12. Double-stem Hairpin Probe and Ultrasensitive Colorimetric Detection of Cancer-related Nucleic Acids.

    PubMed

    Xu, Jianguo; Li, Hongling; Wu, Zai-Sheng; Qian, Jun; Xue, Chang; Jia, Lee

    2016-01-01

    The development of a versatile biosensing platform to screen specific DNA sequences is still an essential issue of molecular biology research and clinic diagnosis of genetic disease. In this work, we for the first time reported a double-stem hairpin probe (DHP) that was simultaneously engineered to incorporate a DNAzyme, DNAzyme's complementary fragment and nicking enzyme recognition site. The important aspect of this hairpin probe is that, although it is designed to have a long ds DNA fragment, no intermolecular interaction occurs, circumventing the sticky-end pairing-determined disadvantages encountered by classic molecular beacon. For the DHP-based colorimetric sensing system, as a model analyte, cancer-related DNA sequence can trigger a cascade polymerization/nicking cycle on only one oligonucleotide probe. This led to the dramatic accumulation of G-quadruplexes directly responsible for colorimetric signal conversion without any loss. As a result, the target DNA is capable of being detected to 1 fM (six to eight orders of magnitude lower than that of catalytic molecular beacons) and point mutations are distinguished by the naked eye. The described DHP as a-proof-of-concept would not only promote the design of colorimetric biosensors but also open a good way to promote the diagnosis and treatment of genetic diseases. PMID:26909108

  13. Double-stem Hairpin Probe and Ultrasensitive Colorimetric Detection of Cancer-related Nucleic Acids

    PubMed Central

    Xu, Jianguo; Li, Hongling; Wu, Zai-Sheng; Qian, Jun; Xue, Chang; Jia, Lee

    2016-01-01

    The development of a versatile biosensing platform to screen specific DNA sequences is still an essential issue of molecular biology research and clinic diagnosis of genetic disease. In this work, we for the first time reported a double-stem hairpin probe (DHP) that was simultaneously engineered to incorporate a DNAzyme, DNAzyme's complementary fragment and nicking enzyme recognition site. The important aspect of this hairpin probe is that, although it is designed to have a long ds DNA fragment, no intermolecular interaction occurs, circumventing the sticky-end pairing-determined disadvantages encountered by classic molecular beacon. For the DHP-based colorimetric sensing system, as a model analyte, cancer-related DNA sequence can trigger a cascade polymerization/nicking cycle on only one oligonucleotide probe. This led to the dramatic accumulation of G-quadruplexes directly responsible for colorimetric signal conversion without any loss. As a result, the target DNA is capable of being detected to 1 fM (six to eight orders of magnitude lower than that of catalytic molecular beacons) and point mutations are distinguished by the naked eye. The described DHP as a-proof-of-concept would not only promote the design of colorimetric biosensors but also open a good way to promote the diagnosis and treatment of genetic diseases. PMID:26909108

  14. Double-stem Hairpin Probe and Ultrasensitive Colorimetric Detection of Cancer-related Nucleic Acids.

    PubMed

    Xu, Jianguo; Li, Hongling; Wu, Zai-Sheng; Qian, Jun; Xue, Chang; Jia, Lee

    2016-01-01

    The development of a versatile biosensing platform to screen specific DNA sequences is still an essential issue of molecular biology research and clinic diagnosis of genetic disease. In this work, we for the first time reported a double-stem hairpin probe (DHP) that was simultaneously engineered to incorporate a DNAzyme, DNAzyme's complementary fragment and nicking enzyme recognition site. The important aspect of this hairpin probe is that, although it is designed to have a long ds DNA fragment, no intermolecular interaction occurs, circumventing the sticky-end pairing-determined disadvantages encountered by classic molecular beacon. For the DHP-based colorimetric sensing system, as a model analyte, cancer-related DNA sequence can trigger a cascade polymerization/nicking cycle on only one oligonucleotide probe. This led to the dramatic accumulation of G-quadruplexes directly responsible for colorimetric signal conversion without any loss. As a result, the target DNA is capable of being detected to 1 fM (six to eight orders of magnitude lower than that of catalytic molecular beacons) and point mutations are distinguished by the naked eye. The described DHP as a-proof-of-concept would not only promote the design of colorimetric biosensors but also open a good way to promote the diagnosis and treatment of genetic diseases.

  15. Carboxylic Acid Ionophores as Probes of the Role of Calcium in Biological Systems

    NASA Technical Reports Server (NTRS)

    Reed, P. W.

    1983-01-01

    The biological effects of calcium ionophores are described, focusing on arachidonic acid oxygenation, and the formation of a number of oxygenated metabolites of arachidonic acid. These metabolites are involved in a number of bodily functions, and their production may be regulated by calcium.

  16. Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Chaudhari, Sachin Rama; Suryaprakash, N.

    2012-05-01

    Benzene carboxylic acids and benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by 1H, 13C and 15N NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations.

  17. Probing the Sophisticated Synergistic Allosteric Regulation of Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis Using ᴅ-Amino Acids

    PubMed Central

    Reichau, Sebastian; Blackmore, Nicola J.; Jiao, Wanting; Parker, Emily J.

    2016-01-01

    Chirality plays a major role in recognition and interaction of biologically important molecules. The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) is the first enzyme of the shikimate pathway, which is responsible for the synthesis of aromatic amino acids in bacteria and plants, and a potential target for the development of antibiotics and herbicides. DAH7PS from Mycobacterium tuberculosis (MtuDAH7PS) displays an unprecedented complexity of allosteric regulation, with three interdependent allosteric binding sites and a ternary allosteric response to combinations of the aromatic amino acids l-Trp, l-Phe and l-Tyr. In order to further investigate the intricacies of this system and identify key residues in the allosteric network of MtuDAH7PS, we studied the interaction of MtuDAH7PS with aromatic amino acids that bear the non-natural d-configuration, and showed that the d-amino acids do not elicit an allosteric response. We investigated the binding mode of d-amino acids using X-ray crystallography, site directed mutagenesis and isothermal titration calorimetry. Key differences in the binding mode were identified: in the Phe site, a hydrogen bond between the amino group of the allosteric ligands to the side chain of Asn175 is not established due to the inverted configuration of the ligands. In the Trp site, d-Trp forms no interaction with the main chain carbonyl group of Thr240 and less favourable interactions with Asn237 when compared to the l-Trp binding mode. Investigation of the MtuDAH7PSN175A variant further supports the hypothesis that the lack of key interactions in the binding mode of the aromatic d-amino acids are responsible for the absence of an allosteric response, which gives further insight into which residues of MtuDAH7PS play a key role in the transduction of the allosteric signal. PMID:27128682

  18. Long-lived frequency shifts observed in a magnetic resonance force microscope experiment following microwave irradiation of a nitroxide spin probe

    SciTech Connect

    Chen, Lei; Longenecker, Jonilyn G.; Moore, Eric W.; Marohn, John A.

    2013-04-01

    We introduce a spin-modulation protocol for force-gradient detection of magnetic resonance that enables the real-time readout of longitudinal magnetization in an electron spin resonance experiment involving fast-relaxing spins. We applied this method to observe a prompt change in longitudinal magnetization following the microwave irradiation of a nitroxide-doped perdeuterated polystyrene film having an electron spin-lattice relaxation time of T{sub 1}{approx}1ms. The protocol allowed us to discover a large, long-lived cantilever frequency shift. Based on its magnitude, lifetime, and field dependence, we tentatively attribute this persistent signal to deuteron spin magnetization created via transfer of polarization from nitroxide spins.

  19. Molecular recognition of α-cyclodextrin (CD) to choral amino acids based on methyl orange as a molecular probe

    NASA Astrophysics Data System (ADS)

    Yuexian, Fan; Yu, Yang; Shaomin, Shuang; Chuan, Dong

    2005-03-01

    The molecular recognition interaction of α-CD to chiral amino acids was investigated by using spectrophotometry based on methyl orange as a molecular probe. The molecular recognition ability depended on the inclusion formation constants. The molecular recognition of α-CD to aromatic amino acids was the order: DL-tryptophan > L-tryptophan > L-phenylalanine > L-tyrosine ≈ DL-β-3,4-dihydroxy-phenylalanine; whereas for aliphatic amino acids, the order was: L- iso-leucine > L-leucine ≈ L-methionine ≈ DL-mehtionine > D-leucine. The effect of temperature on the inclusion interaction was examined and the thermodynamic parameters of inclusion process, Δ G, Δ H, Δ S, were determined. The experimental results indicated that the inclusion process was an exothermic and enthalpy-driven process accompanied with a negative or minor positive entropic contribution. The inclusion interaction between α-CD and amino acids satisfied the law of enthalpy-entropy compensation. The compensation temperature was 291 K.

  20. ω-Azido fatty acids as probes to detect fatty acid biosynthesis, degradation, and modification[S

    PubMed Central

    Pérez, Alexander J.; Bode, Helge B.

    2014-01-01

    FAs play a central role in the metabolism of almost all known cellular life forms. Although GC-MS is regarded as a standard method for FA analysis, other methods, such as HPLC/MS, are nowadays widespread but are rarely applied to FA analysis. Here we present azido-FAs as probes that can be used to study FA biosynthesis (elongation, desaturation) or degradation (β-oxidation) upon their uptake, activation, and metabolic conversion. These azido-FAs are readily accessible by chemical synthesis and their metabolic products can be easily detected after click-chemistry based derivatization with high sensitivity by HPLC/MS, contributing a powerful tool to FA analysis, and hence, lipid analysis in general. PMID:25013232

  1. Kinetics of rapid covalent bond formation of aniline with humic acid: ESR investigations with nitroxide spin labels

    NASA Astrophysics Data System (ADS)

    Glinka, Kevin; Matthies, Michael; Theiling, Marius; Hideg, Kalman; Steinhoff, Heinz-Jürgen

    2016-04-01

    Sulfonamide antibiotics used in livestock farming are distributed to farmland by application of slurry as fertilizer. Previous work suggests rapid covalent binding of the aniline moiety to humic acids found in soil. In the current work, kinetics of this binding were measured in X-band EPR spectroscopy by incubating Leonardite humic acid (LHA) with a paramagnetic aniline spin label (anilino-NO (2,5,5-Trimethyl-2-(3-aminophenyl)pyrrolidin-1-oxyl)). Binding was detected by a pronounced broadening of the spectral lines after incubation of LHA with anilino-NO. The time evolution of the amplitude of this feature was used for determining the reaction kinetics. Single- and double-exponential models were fitted to the data obtained for modelling one or two first-order reactions. Reaction rates of 0.16 min-1 and 0.012 min-1, were found respectively. Addition of laccase peroxidase did not change the kinetics but significantly enhanced the reacting fraction of anilino-NO. This EPR-based method provides a technically simple and effective method for following rapid binding processes of a xenobiotic substance to humic acids.

  2. Probing the interaction of individual amino acids with inorganic surfaces using atomic force spectroscopy.

    PubMed

    Razvag, Yair; Gutkin, Vitaly; Reches, Meital

    2013-08-13

    This article describes single-molecule force spectroscopy measurements of the interaction between individual amino acid residues and inorganic surfaces in an aqueous solution. In each measurement, there is an amino acid residue, lysine, glutamate, phenylalanine, leucine, or glutamine, and each represents a class of amino acids (positively or negatively charged, aromatic, nonpolar, and polar). Force-distance curves measured the interaction of the individual amino acid bound to a silicon atomic force microscope (AFM) tip with a silcon substrate, cut from a single-crystal wafer, or mica. Using this method, we were able to measure low adhesion forces (below 300 pN) and could clearly determine the strength of interactions between the individual amino acid residues and the inorganic substrate. In addition, we observed how changes in the pH and ionic strength of the solution affected the adsorption of the residues to the substrates. Our results pinpoint the important role of hydrophobic interactions among the amino acids and the substrate, where hydrophobic phenylalanine exhibited the strongest adhesion to a silicon substrate. Additionally, electrostatic interactions also contributed to the adsorption of amino acid residues to inorganic substrates. A change in the pH or ionic strength values of the buffer altered the strength of interactions among the amino acids and the substrate. We concluded that the interplay between the hydrophobic forces and electrostatic interactions will determine the strength of adsorption among the amino acids and the surface. Overall, these results contribute to our understanding of the interaction at the organic-inorganic interface. These results may have implications for our perception of the specificity of peptide binding to inorganic surfaces. Consequently, it would possibly lead to a better design of composite materials and devices.

  3. Spin pumping and inverse spin Hall effects—Insights for future spin-orbitronics (invited)

    SciTech Connect

    Zhang, Wei Jungfleisch, Matthias B.; Jiang, Wanjun; Fradin, Frank Y.; Pearson, John E.; Hoffmann, Axel; Sklenar, Joseph; Ketterson, John B.

    2015-05-07

    Quantification of spin-charge interconversion has become increasingly important in the fast-developing field of spin-orbitronics. Pure spin current generated by spin pumping acts as a sensitive probe for many bulk and interface spin-orbit effects, which has been indispensable for the discovery of many promising new spin-orbit materials. We apply spin pumping and inverse spin Hall effect experiments, as a useful metrology, and study spin-orbit effects in a variety of metals and metal interfaces. We quantify the spin Hall effects in Ir and W using the conventional bilayer structures and discuss the self-induced voltage in a single layer of ferromagnetic permalloy. Finally, we extend our discussions to multilayer structures and quantitatively reveal the spin current flow in two consecutive normal metal layers.

  4. Probing Protein Structure by Amino Acid-Specific Covalent Labeling and Mass Spectrometry

    PubMed Central

    Mendoza, Vanessa Leah; Vachet, Richard W.

    2009-01-01

    For many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. These covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. The reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label and the reactivity of the amino acid side chain. Peptide mass mapping with ESI- or MALDI-MS and peptide sequencing with tandem MS are typically employed to identify modification sites to provide site-specific structural information. In this review, we describe the reagents that are most commonly used in these residue-specific modification reactions, details about the proper use of these covalent labeling reagents, and information about the specific biochemical problems that have been addressed with covalent labeling strategies. PMID:19016300

  5. Fabrication and characterization of polylactic acid and polylactic acid/multi-walled carbon nanotube nanofibers through centrifugal spinning

    NASA Astrophysics Data System (ADS)

    Patlan, Richard

    Biocompatible polymer nanofibers hold great potential in the biomedical engineering field. Their biodegradable nature and enhanced properties could help solve a wide array of health related problems, particularly in the areas of tissue regeneration, drug delivery, and biosensor design. The novel Forcespinning™ method allows the production of submicron fibers without many of the drawbacks found in electrospinning, while also providing a substantial increase in fiber production. The aim of the study was to utilize this method to fabricate non-woven nanofibrous mats composed of polylactic acid (PLA) and polylactic acid/multi-walled carbon nanotube composite fibers. The morphology, thermal properties, and crystalline structure of the resulting nanofibers were then characterized using Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), Thermogravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC), and X-Ray Diffraction (XRD).

  6. Probing Phosphorus Efficient Low Phytic Acid Content Soybean Genotypes with Phosphorus Starvation in Hydroponics Growth System.

    PubMed

    Kumar, Varun; Singh, Tiratha Raj; Hada, Alkesh; Jolly, Monica; Ganapathi, Andy; Sachdev, Archana

    2015-10-01

    Phosphorus is an essential nutrient required for soybean growth but is bound in phytic acid which causes negative effects on both the environment as well as the animal nutrition. Lowering of phytic acid levels is associated with reduced agronomic characteristics, and relatively little information is available on the response of soybean plants to phosphorus (P) starvation. In this study, we evaluated the effects of different P starvation concentrations on the phytic acid content, growth, and yield of seven mutant genotypes along with the unirradiated control, JS-335, in a hydroponics growth system. The low phytic acid containing mutant genotypes, IR-JS-101, IR-DS-118, and IR-V-101, showed a relatively high growth rate in low P concentration containing nutrient solution (2 μM), whereas the high P concentration (50 μM) favored the growth of IR-DS-111 and IR-DS-115 mutant genotypes containing moderate phytate levels. The mutant genotypes with high phytic acid content, IR-DS-122, IR-DS-114, and JS-335, responded well under P starvation and did not have any significant effect on the growth and yield of plants. Moreover, the reduction of P concentration in nutrient solution from 50 to 2 μM also reduced the phytic acid content in the seeds of all the soybean genotypes under study. The desirable agronomic performance of low phytic acid containing mutant genotype IR-DS-118 reported in this study suggested it to be a P-efficient genotype which could be considered for agricultural practices under P limiting soils. PMID:26239443

  7. Probing Phosphorus Efficient Low Phytic Acid Content Soybean Genotypes with Phosphorus Starvation in Hydroponics Growth System.

    PubMed

    Kumar, Varun; Singh, Tiratha Raj; Hada, Alkesh; Jolly, Monica; Ganapathi, Andy; Sachdev, Archana

    2015-10-01

    Phosphorus is an essential nutrient required for soybean growth but is bound in phytic acid which causes negative effects on both the environment as well as the animal nutrition. Lowering of phytic acid levels is associated with reduced agronomic characteristics, and relatively little information is available on the response of soybean plants to phosphorus (P) starvation. In this study, we evaluated the effects of different P starvation concentrations on the phytic acid content, growth, and yield of seven mutant genotypes along with the unirradiated control, JS-335, in a hydroponics growth system. The low phytic acid containing mutant genotypes, IR-JS-101, IR-DS-118, and IR-V-101, showed a relatively high growth rate in low P concentration containing nutrient solution (2 μM), whereas the high P concentration (50 μM) favored the growth of IR-DS-111 and IR-DS-115 mutant genotypes containing moderate phytate levels. The mutant genotypes with high phytic acid content, IR-DS-122, IR-DS-114, and JS-335, responded well under P starvation and did not have any significant effect on the growth and yield of plants. Moreover, the reduction of P concentration in nutrient solution from 50 to 2 μM also reduced the phytic acid content in the seeds of all the soybean genotypes under study. The desirable agronomic performance of low phytic acid containing mutant genotype IR-DS-118 reported in this study suggested it to be a P-efficient genotype which could be considered for agricultural practices under P limiting soils.

  8. Orbital elementary excitations as probes of entanglement and quantum phase transitions of collective spins in an entangled Bose-Einstein condensate

    SciTech Connect

    Wu Rukuan; Shi Yu

    2011-02-15

    A mixture of two species of pseudospin-(1/2) Bose gases exhibits interesting interplay between spin and orbital degrees of freedom. Expectation values of various quantities of the collective spins of the two species play crucial roles in the Gross-Pitaevskii-like equations governing the four orbital wave functions in which Bose-Einstein condensation occurs. Consequently, the elementary excitations of these orbital wave functions reflect properties of the collective spins. When the coupling between the two collective spins is isotropic, the energy gap of the gapped orbital excitation peaks. There is a quantum phase transition in the ground state of the effective Hamiltonian of the two collective spins, which have previously been found to be maximally entangled.

  9. Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same

    DOEpatents

    Chee, Mark; Gingeras, Thomas R.; Fodor, Stephen P. A.; Hubble, Earl A.; Morris, MacDonald S.

    1999-01-19

    The invention provides an array of oligonucleotide probes immobilized on a solid support for analysis of a target sequence from a human immunodeficiency virus. The array comprises at least four sets of oligonucleotide probes 9 to 21 nucleotides in length. A first probe set has a probe corresponding to each nucleotide in a reference sequence from a human immunodeficiency virus. A probe is related to its corresponding nucleotide by being exactly complementary to a subsequence of the reference sequence that includes the corresponding nucleotide. Thus, each probe has a position, designated an interrogation position, that is occupied by a complementary nucleotide to the corresponding nucleotide. The three additional probe sets each have a corresponding probe for each probe in the first probe set. Thus, for each nucleotide in the reference sequence, there are four corresponding probes, one from each of the probe sets. The three corresponding probes in the three additional probe sets are identical to the corresponding probe from the first probe or a subsequence thereof that includes the interrogation position, except that the interrogation position is occupied by a different nucleotide in each of the four corresponding probes.

  10. Soft x-ray resonant magneto-optical kerr effect as a depth-sensitive probe of magnetic heterogeneity: its application to resolve helical spin structures using linear p polarization

    SciTech Connect

    Lee, Ki-Suk; Kim, Sang-Koog; Kortright, J.B.

    2004-06-01

    We have calculated the soft x-ray resonant Kerr intensities as a function of the incident grazing angle of linearly p-polarized waves from the model spin structures, where the chirality (handedness) of the spin spirals (twist in depth) in a magnetic layer and the periodicity of a unit spiral are designed to vary. Variations in the chirality and the periodicity lead to noticeable changes in the Kerr intensity versus the grazing angle, which is due not only to a large sensitivity of the Kerr intensity of the linear p polarization to both the magnitude and direction of the transverse components of magnetizations, but also to a large dependence of the depth sensitivity on the grazing angle at the resonance regions. The measurement and analysis of the specular Kerr intensity are relatively straightforward in determining the inhomogeneous spin structures in depth, compared to those of the Kerr rotation and ellipticity. This is proven to be a convenient and useful probe to determine the handedness of spin spiral structures, as well as to resolve the detailed magnetic heterostructures in depth in ultrathin-layered films.

  11. Functionalized ZnS quantum dots as luminescent probes for detection of amino acids.

    PubMed

    Mobarraz, Mahsa; Ganjali, Mohammad Reza; Chaichi, Mohammad Javad; Norouzi, Parviz

    2012-10-01

    In this work, L-cysteine capped-ZnS quantum dots were synthesized in aqueous medium, and their interaction with some of the amino acids was studied with fluorescence spectra. The results demonstrated that histidine could effectively quench the Quantum dots emission more than other amino acids. Electron transfer process between the capping ligands and histidine was mainly responsible for the remarkable quenching effect of histidine, because according to the structure of histidine, it is the strongest acceptor among essential amino acids. Under optimum conditions, the quenched fluorescence intensity increased linearly with the concentration of histidine ranging from 1.33×10(-6) to 1.49×10(-4) mol L(-1). The limit of detection for histidine was 0.05×10(-7) mol L(-1). PMID:22925905

  12. Facilitating unambiguous NMR assignments and enabling higher probe density through selective labeling of all methyl containing amino acids.

    PubMed

    Proudfoot, Andrew; Frank, Andreas O; Ruggiu, Fiorella; Mamo, Mulugeta; Lingel, Andreas

    2016-05-01

    The deuteration of proteins and selective labeling of side chain methyl groups has greatly enhanced the molecular weight range of proteins and protein complexes which can be studied using solution NMR spectroscopy. Protocols for the selective labeling of all six methyl group containing amino acids individually are available, however to date, only a maximum of five amino acids have been labeled simultaneously. Here, we describe a new methodology for the simultaneous, selective labeling of all six methyl containing amino acids using the 115 kDa homohexameric enzyme CoaD from E. coli as a model system. The utility of the labeling protocol is demonstrated by efficiently and unambiguously assigning all methyl groups in the enzymatic active site using a single 4D (13)C-resolved HMQC-NOESY-HMQC experiment, in conjunction with a crystal structure. Furthermore, the six fold labeled protein was employed to characterize the interaction between the substrate analogue (R)-pantetheine and CoaD by chemical shift perturbations, demonstrating the benefit of the increased probe density. PMID:27130242

  13. Interplay of magnetism and superconductivity in EuFe2(As1-xPx)2 single crystals probed by muon spin rotation and 57Fe Mössbauer spectroscopy

    NASA Astrophysics Data System (ADS)

    Goltz, T.; Kamusella, S.; Jeevan, H. S.; Gegenwart, P.; Luetkens, H.; Materne, P.; Spehling, J.; Sarkar, R.; Klauss, H.-H.

    2014-12-01

    We present our results of a local probe study on EuFe2(As1-xPx)2 single crystals with x=0.13, 0.19 and 0.28 by means of muon spin rotation and 57Fe Mössbauer spectroscopy. We focus our discussion on the sample with x=0.19 viz. at the optimal substitution level, where bulk superconductivity (TSC = 28 K) sets in above static europium order (TEu = 20 K) but well below the onset of the iron antiferromagnetic (AFM) transition (~100 K). We find enhanced spin dynamics in the Fe sublattice closely above TSC and propose that these are related to enhanced Eu fluctuations due to the evident coupling of both sublattices observed in our experiments.

  14. Adaptation and Validation of E-Probe Diagnostic Nucleic Acid Analysis for Detection of Escherichia coli O157:H7 in Metagenomic Data from Complex Food Matrices.

    PubMed

    Blagden, Trenna; Schneider, William; Melcher, Ulrich; Daniels, Jon; Fletcher, Jacqueline

    2016-04-01

    The Centers for Disease Control and Prevention recently emphasized the need for enhanced technologies to use in investigations of outbreaks of foodborne illnesses. To address this need, e-probe diagnostic nucleic acid analysis (EDNA) was adapted and validated as a tool for the rapid, effective identification and characterization of multiple pathogens in a food matrix. In EDNA, unassembled next generation sequencing data sets from food sample metagenomes are queried using pathogen-specific sequences known as electronic probes (e-probes). In this study, the query of mock sequence databases demonstrated the potential of EDNA for the detection of foodborne pathogens. The method was then validated using next generation sequencing data sets created by sequencing the metagenome of alfalfa sprouts inoculated with Escherichia coli O157:H7. Nonspecific hits in the negative control sample indicated the need for additional filtration of the e-probes to enhance specificity. There was no significant difference in the ability of an e-probe to detect the target pathogen based upon the length of the probe set oligonucleotides. The results from the queries of the sample database using E. coli e-probe sets were significantly different from those obtained using random decoy probe sets and exhibited 100% precision. The results support the use of EDNA as a rapid response methodology in foodborne outbreaks and investigations for establishing comprehensive microbial profiles of complex food samples. PMID:27052861

  15. Identification and quantification of acetic acid bacteria in wine and vinegar by TaqMan-MGB probes.

    PubMed

    Torija, M J; Mateo, E; Guillamón, J M; Mas, A

    2010-04-01

    A Real-Time PCR (RT-PCR) assay was developed using TaqMan minor groove binder (MGB) probes for the specific detection and quantification of five acetic acid bacteria (AAB) species (Acetobacter pasteurianus, Acetobacter aceti, Gluconacetobacter hansenii, Gluconacetobacter europaeus and Gluconobacter oxydans) in wine and vinegar. The primers and probes, designed from the 16S rRNA gene, showed good specificity with the target AAB species. The technique was tested on AAB grown in glucose medium (GY) and inoculated samples of red wine and wine vinegar. Standard curves were constructed with the five target species in all these matrices. Quantification was linear over at least 5 log units using both serial dilution of purified DNA and cells. When this technique was tested in GY medium and inoculated matrices, at least 10(2)-10(3) cells/ml were detected. To quantify low populations of AAB in microbiologically complex samples, a PCR enrichment including part of the 16S-23S rRNA gene ITS region was needed to increase the amount of target DNA compared to non-target DNA. The RT-PCR assay used in this study is a reliable, specific and fast method for quantifying these five AAB species in wine and vinegar.

  16. Water uptake of internally mixed ammonium sulfate and dicarboxylic acid particles probed by infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Miñambres, Lorena; Méndez, Estíbaliz; Sánchez, María N.; Castaño, Fernando; Basterretxea, Francisco J.

    2013-05-01

    Tropospheric aerosols are usually mixtures of inorganic and organic compounds in variable proportions, and the relative amount of organic fraction can influence the hygroscopic properties of the particles. Infrared spectra of submicrometer internally mixed dry particles of ammonium sulfate (AS) with various dicarboxylic acids (oxalic, malonic, maleic, glutaric and pimelic) have been measured in an aerosol flow tube at several solute mass ratios. The spectra show a notable broadening in the bandwidth of sulfate ion ν3 vibrational band near 1115 cm-1 with respect to pure AS. We attribute these perturbations, that are biggest at AS/organic acid mass ratio near unity, to intermolecular interactions between inorganic ions and organic acid molecules in the internally mixed solids. The water uptake behavior of internally mixed particles has been measured by recording the infrared integrated absorbance of liquid water as a function of relative humidity (RH). The amount of water present in the particles prior to deliquescence correlates partially with the water solubilities of the dicarboxylic acids, and also with the relative magnitudes of intermolecular interactions in the internally mixed dry solids. Phase change of ammonium sulfate in the internally mixed particles with RH has been spectrally monitored, and it is shown that water uptaken before full deliquescence produces structural changes in the particles that are revealed by their vibrational spectra.

  17. Vibrational probes and determinants of the S = 0 ⇌ S = 2 spin crossover in five-coordinate [Fe(TPP)(CN)]-.

    PubMed

    Li, Jianfeng; Peng, Qian; Barabanschikov, Alexander; Pavlik, Jeffrey W; Alp, E Ercan; Sturhahn, Wolfgang; Zhao, Jiyong; Sage, J Timothy; Scheidt, W Robert

    2012-11-01

    The low-frequency vibrational characterization of the spin-crossover complex, five-coordinate cyano(tetraphenylporphyrinato)iron(II), [Fe(TPP)(CN)](-), is reported. Nuclear resonance vibrational spectroscopy has been used to measure all low-frequency vibrations involving iron at several temperatures; this yields vibrational spectra of both the low- (S = 0) and high-spin (S = 2) states. Multitemperature oriented single-crystal measurements facilitate assignments of the vibrational character of all modes and are consistent with the DFT-predicted spectra. The availability of the entire iron vibrational spectrum allows for the complete correlation of the modes between the two spin states. These data demonstrate that not only do the frequencies of the vibrations shift to lower values for the high-spin species as would be expected owing to the weaker bonds in the high-spin state, but also the mixing of iron modes with ligand modes changes substantially. Diagrams illustrating the changing character of the modes and their correlation are given. The reduced iron-ligand frequencies are the primary factor in the entropic stabilization of the high-spin state responsible for the spin crossover.

  18. Probing inclusion complexes of cyclodextrins with amino acids by physicochemical approach.

    PubMed

    Roy, Mahendra Nath; Roy, Aditi; Saha, Subhadeep

    2016-10-20

    Formations of host-guest inclusion complexes of two natural amino acids, viz., l-Leucine and l-Isoleucine as guests with α and β-cyclodextrins have been investigated which include diverse applications in modern science such as controlled delivery in the field of pharmaceuticals, food processing etc. Surface tension and conductivity studies establish the formation of inclusion complexes with 1:1 stoichiometry. The interactions of cyclodextrins with amino acids have been supported by density, viscosity, refractive index, hydration and solvation number measurements indicating higher degree of inclusion in case of α-cyclodextrin. l-Leucine interacts more with the hydrophobic cavity of cyclodextrin than its isomer. With the help of stability constant by NMR titration, hydrophobic effect, H-bonds and structural effects the formations of inclusion complexes have been explained. PMID:27474589

  19. Energetics of side-chain snorkeling in transmembrane helices probed by nonproteinogenic amino acids

    PubMed Central

    Öjemalm, Karin; Higuchi, Takashi; Lara, Patricia; Lindahl, Erik; Suga, Hiroaki

    2016-01-01

    Cotranslational translocon-mediated insertion of membrane proteins into the endoplasmic reticulum is a key process in membrane protein biogenesis. Although the mechanism is understood in outline, quantitative data on the energetics of the process is scarce. Here, we have measured the effect on membrane integration efficiency of nonproteinogenic analogs of the positively charged amino acids arginine and lysine incorporated into model transmembrane segments. We provide estimates of the influence on the apparent free energy of membrane integration (ΔGapp) of “snorkeling” of charged amino acids toward the lipid–water interface, and of charge neutralization. We further determine the effect of fluorine atoms and backbone hydrogen bonds (H-bonds) on ΔGapp. These results help establish a quantitative basis for our understanding of membrane protein assembly in eukaryotic cells. PMID:27601675

  20. Energetics of side-chain snorkeling in transmembrane helices probed by nonproteinogenic amino acids.

    PubMed

    Öjemalm, Karin; Higuchi, Takashi; Lara, Patricia; Lindahl, Erik; Suga, Hiroaki; von Heijne, Gunnar

    2016-09-20

    Cotranslational translocon-mediated insertion of membrane proteins into the endoplasmic reticulum is a key process in membrane protein biogenesis. Although the mechanism is understood in outline, quantitative data on the energetics of the process is scarce. Here, we have measured the effect on membrane integration efficiency of nonproteinogenic analogs of the positively charged amino acids arginine and lysine incorporated into model transmembrane segments. We provide estimates of the influence on the apparent free energy of membrane integration (ΔGapp) of "snorkeling" of charged amino acids toward the lipid-water interface, and of charge neutralization. We further determine the effect of fluorine atoms and backbone hydrogen bonds (H-bonds) on ΔGapp These results help establish a quantitative basis for our understanding of membrane protein assembly in eukaryotic cells. PMID:27601675

  1. Using modern tools to probe the structure-function relationship of fatty acid synthases

    PubMed Central

    Burkart, Michael D.

    2015-01-01

    Fatty acid biosynthesis is essential to life and represents one of the most conserved pathways in Nature, preserving the same handful of chemical reactions over all species. Recent interest in the molecular details of the de novo fatty acid synthase (FAS) has been heightened by demand for renewable fuels and the emergence of multidrug resistant bacterial strains. Central to FAS is the acyl carrier protein (ACP), a protein chaperone that shuttles the growing acyl chain between catalytic enzymes within the FAS. Human efforts to alter fatty acid biosynthesis for oil production, chemical feedstock or antimicrobial purposes has been met with limited success in part due to a lack of detailed molecular information behind the ACP-partner protein interactions inherent to the pathway. This review will focus on recently developed tools for the modification of ACP and analysis of protein-protein interactions, such as mechanism-based crosslinking, and the studies exploiting them. Discussion specific to each enzymatic domain focuses first on mechanism and known inhibitors, followed by available structures and known interactions with ACP. While significant unknowns remain, new understandings into the intricacies of FAS point to future advances in manipulating this complex molecular factory. PMID:25676190

  2. Re-engineering of CYP2C9 to probe acid-base substrate selectivity.

    PubMed

    Tai, Guoying; Dickmann, Leslie J; Matovic, Nicholas; DeVoss, James J; Gillam, Elizabeth M J; Rettie, Allan E

    2008-10-01

    A common feature of many CYP2C9 ligands is their weak acidity. As revealed by crystallography, the structural basis for this behavior involves a charge-pairing interaction between an anionic moiety on the substrate and an active site R108 residue. In the present study we attempted to re-engineer CYP2C9 to better accept basic ligands by charge reversal at this key residue. We expressed and purified the R108E and R108E/D293N mutants and compared their ability with that of native CYP2C9 to interact with (S)-warfarin, diclofenac, pyrene, propranolol, and ibuprofen amine. As expected, the R108E mutant maintained all the native enzyme's pyrene 1-hydroxylation activity, but catalytic activity toward diclofenac and (S)-warfarin was abrogated. In contrast, the double mutant displayed much less selectivity in its behavior toward these control ligands. Neither of the mutants displayed significant enhancement of propranolol metabolism, and all three preparations exhibited a type II (inhibitor) rather than type I (substrate) spectrum with ibuprofen amine, although binding became progressively weaker with the single and double mutants. Collectively, these data underscore the importance of the amino acid at position 108 in the acid substrate selectivity of CYP2C9, highlight the accommodating nature of the CYP2C9 active site, and provide a cautionary note regarding facile re-engineering of these complex cytochrome P450 active sites.

  3. Mitochondrial, acidic, and cytosolic pHs determination by ³¹P NMR spectroscopy: design of new sensitive targeted pH probes.

    PubMed

    Culcasi, Marcel; Thétiot-Laurent, Sophie; Atteia, Ariane; Pietri, Sylvia

    2015-01-01

    (31)P nuclear magnetic resonance (NMR) is a unique technique to monitor noninvasively the energetics of living systems at real time through the detection of a variety of phosphorylated metabolites. Using adequately designed α-aminophosphonates as external probes, we have shown earlier that (31)P NMR can also give access simultaneously to the accurate pH of cytosolic and acidic compartments in normal and stressed cultured cells or isolated perfused organs, a feature that was not possible using endogenous inorganic phosphate as the probe. More recently, we obtained a series of derivatives of these new pH probes that incorporate a triphenylphosphonium cation as a specific vector to the mitochondrion. Here, we describe the synthesis, (31)P NMR pH titrating properties in buffers, and application in cultures of the green alga Chlamydomonas reinhardtii of two of these mitochondria-targeted pH probes in comparison with one nonvectorized, yet still informative α-aminophosphonate.

  4. Mitochondrial, acidic, and cytosolic pHs determination by ³¹P NMR spectroscopy: design of new sensitive targeted pH probes.

    PubMed

    Culcasi, Marcel; Thétiot-Laurent, Sophie; Atteia, Ariane; Pietri, Sylvia

    2015-01-01

    (31)P nuclear magnetic resonance (NMR) is a unique technique to monitor noninvasively the energetics of living systems at real time through the detection of a variety of phosphorylated metabolites. Using adequately designed α-aminophosphonates as external probes, we have shown earlier that (31)P NMR can also give access simultaneously to the accurate pH of cytosolic and acidic compartments in normal and stressed cultured cells or isolated perfused organs, a feature that was not possible using endogenous inorganic phosphate as the probe. More recently, we obtained a series of derivatives of these new pH probes that incorporate a triphenylphosphonium cation as a specific vector to the mitochondrion. Here, we describe the synthesis, (31)P NMR pH titrating properties in buffers, and application in cultures of the green alga Chlamydomonas reinhardtii of two of these mitochondria-targeted pH probes in comparison with one nonvectorized, yet still informative α-aminophosphonate. PMID:25634273

  5. Primers and a specific DNA probe for detecting lactic acid bacteria producing 3-hydroxypropionaldehyde from glycerol in spoiled ciders.

    PubMed

    Claisse, O; Lonvaud-Funel, A

    2001-06-01

    Of the 40 strains isolated from several spoiled ciders where glycerol was degraded, 36 were identified as Lactobacillus collinoides, three were Lactobacillus hilgardii, and one was Lactobacillus mali. However, only 30 L. collinoides and two L. hilgardii could degrade glycerol. The glycerol dehydratase activity was shown. The main product of the transformation was 1.3 propanediol. Two DNA primers GD1 and GD2 were chosen in the region encoding one of the subunits of glycerol dehydratase of Citrobacter freundii, Klebsiella pneumoniae, Klebsiella oxytoca, Salmonella Typhimurium, and Clostridium pasteurianum. A 279-bp amplicon in polymerase chain reaction amplification was obtained with the genomic L. collinoides IOEB 9527 DNA as template. The amino acid sequence deduced from the amplicon DNA sequence showed a very high similarity and identity with the gene of gram-negative and C. pasteurianum species. After labeling, the amplicon was used as DNA probe in dot-blot hybridization with the genomic DNA of all the tested strains. Only strains that could degrade glycerol hybridized. Moreover, polymerase chain reactions using GDI and GD2 revealed only glycerol dehydratase genes of positive L. collinoides and L. hilgardii strains. The primers and the amplicon proved to be suitable and reliable tools to detect the lactic acid bacteria involved in the deterioration of cider. PMID:11403134

  6. Molecular beacons: a novel DNA probe for nucleic acid and protein studies.

    PubMed

    Tan, W; Fang, X; Li, J; Liu, X

    2000-04-01

    A new concept has been introduced for molecular beacon DNA molecules. Molecular beacons are a new class of oligonucleotides that can report the presence of specific nucleic acids in both homogeneous solutions and at the liquid-solid interface. They emit an intense fluorescent signal only when hybridized to their target DNA or RNA molecules. Biotinylated molecular beacons have been designed and used for the development of ultrasensitive DNA sensors and for DNA molecular interaction studies at a solid-liquid interface. Molecular beacons have also been used to study protein-DNA interactions. They have provided a variety of exciting opportunities in DNA/RNA/protein studies.

  7. On the use of 16-iodohexadecanoic acid (IHDA) as a probe for myocardial beta-oxidation of fatty acids

    SciTech Connect

    De Grado, T.R.; Gatley, S.J.; Ng, C.K.; Holden, J.E.; Bernstein, D.R.

    1984-01-01

    The rate of myocardial clearance of label IHDA was compared with the beta-oxidation rate by coinjection of 125-IHDA and 3-H-Palmitic Acid (THDA) into isolated rat hearts. I-125 residue curves and efflux I-125 and H-3 curves were obtained. Three groups of hearts were studied, control, ischemic and those from rats previously treated with the beta-oxidation inhibitor Ethyl 2(5(4-chlorophenyl)pentyl)-oxiran-2-carboxylate (POCA). Both labels were found to exit ischemic and POCA treated hearts more slowly than controls. In all cases, the clearance of label from IHDA was significantly slower than that of the labelled water from beta-oxidation of THDA, consistent with previous work indicating the efflux of iodide from the mitochondria to be rate-limiting. Assay of heart homogenates showed 60% of the extracted label to be iodide at 1 minute. Thus, iodide is pooled within the mitochondria and diffuses out with a characteristic rate governed by electrochemical and lemmal properties. By assuming parallel utilization of IHDA and THDA and transient clearance of both labelled metabolites from the cytosol, the H-3 curves were interpreted ad equivalent with the production of free iodide in the mitochondria. A rate constant describing the flux of iodide across the mitochondrial membrane was calculated by fitting the I-125 curve (I/sup -/ output) to the H-3 curve (I/sup -/ input) convolved with a single exponential. The rate constant (k/sub I/=2.25 +- .35 x 10/sup -3/ s/sup -1/ for normals) was similar to the largest rate constant from fitted residue curves (k=2.08 +- .05 x 10/sup -3/ s/sup -1/).

  8. Effects of acid catalyst type on structural, morphological, and optoelectrical properties of spin-coated TiO2 thin film

    NASA Astrophysics Data System (ADS)

    Golobostanfard, Mohammad Reza; Abdizadeh, Hossein

    2013-03-01

    The effects of different acid catalysts of nitric acid, hydrochloric acid, sulfuric acid, phosphoric acid, boric acid, acetic acid, and citric acid on structural, morphological, and optoelectrical properties of nanocrystalline spin-coated TiO2 thin films synthesized via alkoxide sol-gel route were investigated. It was found that only the sols with HNO3 and HCl are suitable for film preparation. The X-ray diffractometry and Raman analysis showed that crystalline phases could be controlled by the type of acid catalyst. Although the H2SO4 sol shows good stability, it causes extremely different morphology to form due to its different sol nature and high contact angle. Fourier transformed infrared spectra confirmed the presence of acid anion species in all samples even after calcination. Furthermore, it was inferred from UV-visable absorption spectra that although the band gap and thickness of the films are independent of acid catalyst type, the refractive index and porosity of the films are strongly affected by the type of acids.

  9. Spin-current emission governed by nonlinear spin dynamics

    PubMed Central

    Tashiro, Takaharu; Matsuura, Saki; Nomura, Akiyo; Watanabe, Shun; Kang, Keehoon; Sirringhaus, Henning; Ando, Kazuya

    2015-01-01

    Coupling between conduction electrons and localized magnetization is responsible for a variety of phenomena in spintronic devices. This coupling enables to generate spin currents from dynamical magnetization. Due to the nonlinearity of magnetization dynamics, the spin-current emission through the dynamical spin-exchange coupling offers a route for nonlinear generation of spin currents. Here, we demonstrate spin-current emission governed by nonlinear magnetization dynamics in a metal/magnetic insulator bilayer. The spin-current emission from the magnetic insulator is probed by the inverse spin Hall effect, which demonstrates nontrivial temperature and excitation power dependences of the voltage generation. The experimental results reveal that nonlinear magnetization dynamics and enhanced spin-current emission due to magnon scatterings are triggered by decreasing temperature. This result illustrates the crucial role of the nonlinear magnon interactions in the spin-current emission driven by dynamical magnetization, or nonequilibrium magnons, from magnetic insulators. PMID:26472712

  10. Probing determinants of cyclopiazonic acid sensitivity of bacterial Ca2+-ATPases.

    PubMed

    Kotšubei, Aljona; Gorgel, Manuela; Morth, Jens P; Nissen, Poul; Andersen, Jacob L

    2013-11-01

    Cyclopiazonic acid (CPA) is a specific and potent inhibitor of the sarcoplasmic reticulum Ca(2+)-ATPase 1a (SERCA1a). Despite high sequence similarity to SERCA1a, Listeria monocytogenes Ca(2+)-ATPase 1 (LMCA1) is not inhibited by CPA. To test whether a CPA binding site could be created while maintaining the functionality of the ATPase we targeted four amino acid positions in LMCA1 for mutational studies based on a multiple sequence alignment of SERCA-like Ca(2+)-ATPases and structural analysis of the CPA site. The identification of CPA-sensitive gain-of-function mutants pinpointed key determinants of the CPA binding site. The importance of these determinants was further underscored by the characterization of the CPA sensitivity of two additional bacterial Ca(2+)-ATPases from Lactococcus lactis and Bacillus cereus. The CPA sensitivity was predicted from their sequence compared with the LMCA1 results, and this was experimentally confirmed. Interestingly, a cluster of Lactococcus bacteria applied in the production of fermented cheese display Ca(2+)-ATPases that are predictably CPA insensitive and may originate from their coexistence with CPA-producing Penicillum and Aspergillus fungi in the cheese. The differences between bacterial and mammalian binding pockets encompassing the CPA site suggest that CPA derivatives that are specific for bacteria or other pathogens can be developed. PMID:23621633

  11. Locked Nucleic Acid Probe-Based Real-Time PCR Assay for the Rapid Detection of Rifampin-Resistant Mycobacterium tuberculosis.

    PubMed

    Zhao, Yong; Li, Guilian; Sun, Chongyun; Li, Chao; Wang, Xiaochen; Liu, Haican; Zhang, Pingping; Zhao, Xiuqin; Wang, Xinrui; Jiang, Yi; Yang, Ruifu; Wan, Kanglin; Zhou, Lei

    2015-01-01

    Drug-resistant Mycobacterium tuberculosis can be rapidly diagnosed through nucleic acid amplification techniques by analyzing the variations in the associated gene sequences. In the present study, a locked nucleic acid (LNA) probe-based real-time PCR assay was developed to identify the mutations in the rpoB gene associated with rifampin (RFP) resistance in M. tuberculosis. Six LNA probes with the discrimination capability of one-base mismatch were designed to monitor the 23 most frequent rpoB mutations. The target mutations were identified using the probes in a "probe dropout" manner (quantification cycle = 0); thus, the proposed technique exhibited superiority in mutation detection. The LNA probe-based real-time PCR assay was developed in a two-tube format with three LNA probes and one internal amplification control probe in each tube. The assay showed excellent specificity to M. tuberculosis with or without RFP resistance by evaluating 12 strains of common non-tuberculosis mycobacteria. The limit of detection of M. tuberculosis was 10 genomic equivalents (GE)/reaction by further introducing a nested PCR method. In a blind validation of 154 clinical mycobacterium isolates, 142/142 (100%) were correctly detected through the assay. Of these isolates, 88/88 (100%) were determined as RFP susceptible and 52/54 (96.3%) were characterized as RFP resistant. Two unrecognized RFP-resistant strains were sequenced and were found to contain mutations outside the range of the 23 mutation targets. In conclusion, this study established a sensitive, accurate, and low-cost LNA probe-based assay suitable for a four-multiplexing real-time PCR instrument. The proposed method can be used to diagnose RFP-resistant tuberculosis in clinical laboratories.

  12. New Real-Time PCR Assay Using Locked Nucleic Acid Probes To Assess Prevalence of ParC Mutations in Fluoroquinolone-Susceptible Streptococcus pneumoniae Isolates from France

    PubMed Central

    Decousser, Jean-Winoc; Methlouthi, Imen; Pina, Patrick; Collignon, Anne; Allouch, Pierre

    2006-01-01

    A real-time PCR assay with locked nucleic acid probes was developed to screen mutations at codons 79 and 83 of the Streptococcus pneumoniae parC gene. Only silent mutations were detected among 236 French invasive fluoroquinolone-susceptible strains. This test could be useful for some high-risk patients or in national surveys. PMID:16569894

  13. ESTIMATION OF BACTERIAL CELL NUMBERS IN HUMIC ACID-RICH SALT MARSH SEDIMENTS WITH PROBES DIRECTED TO 16S RIBOSOMAL DNA

    EPA Science Inventory

    The feasibility of using probes directed towards ribosomal DNAs (rDNAs) as a quantitative approach to estimating cell numbers was examined and applied to study the structure of a bacterial community in humic acid-rich salt marsh sediments. Hybridizations were performed with membr...

  14. Highly water-soluble monoboronic acid probes that show optical sensitivity to glucose based on 4-sulfo-1,8-naphthalic anhydride.

    PubMed

    Cao, Zhi; Nandhikonda, Premchendar; Heagy, Michael D

    2009-05-01

    Two highly water-soluble monoboronic acid probes that display the more desirable off-on fluorescence response were synthesized based on 4-sulfo-1,8-naphthalic anhydride and a remarkable sensitivity for glucose rather than fructose and galactose was also observed.

  15. Adaptation and validation of E-probe diagnostic nucleic acid analysis for detection of Escherichia coli O157:H7 in metagenomic data of complex food matrices

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Foodborne pathogens are an increasing problem threatening the US food supply. The need for rapid sensitive diagnostic tools that can address multiple types and taxonomic classes of foodbourne pathogens is growing. This paper describes the adaptation of E-probe Diagnostic Nucleic acid Analysis (EDNA)...

  16. ESA Mission ROSETTA Will Probe for Chirality of Cometary Amino Acids

    NASA Astrophysics Data System (ADS)

    Thiemann, Wolfram H.-P.; Meierhenrich, Uwe

    2001-02-01

    New crucial theoretical investigations on the origin of biomolecular chirality are reviewed briefly. With the goal to investigate these theories our team is going to perform the `chirality-experiment' in the near future with cometary matter. In 2012 the robotical lander RoLand will detach from the orbiter of the ROSETTA spacecraft and set down on the surface of comet 46P/Wirtanen in order to separate and identify cometary organic compounds via GC-MS in situ. Chiral organics will be separated into their enantiomers by application of 3 capillary columns coated with different kinds of stationary phases. Non-volatile compounds like amino acids will be derivatized in especially developed gas phase alkylation steps avoiding reactions in the liquid phase. The results of these preliminary gas phase reactions are presented in this article.

  17. Label-free and selective sensing of uric acid with gold nanoclusters as optical probe.

    PubMed

    Wang, Jian; Chang, Yong; Wu, Wen Bi; Zhang, Pu; Lie, Shao Qing; Huang, Cheng Zhi

    2016-05-15

    Clinically, the amount of uric acid (UA) in biological fluids is closely related to some diseases such as hyperuricemia and gout, thus it is of great significance to sense UA in clinical samples. In this work, red gold nanoclusters (AuNCs) with relatively high fluorescence quantum yield and strong fluorescence emission were facilely available using bovine serum albumin (BSA) as template. The fluorescence of BSA-protected AuNCs can be sensitively quenched by H2O2, which is further capable of sensing UA through the specific catalytic oxidation with uricase, since it generates stoichiometric quantity of H2O2 by-product. The proposed assay allows for the selective detection of UA in the range of 10-800 μM with a detection limit of 6.6 μM, which is applicable to sense UA in clinical samples with satisfactory results, suggesting its great potential for diagnostic purposes. PMID:26992526

  18. Probing 3D Collective Cancer Invasion Using Double-Stranded Locked Nucleic Acid Biosensors.

    PubMed

    Dean, Zachary S; Elias, Paul; Jamilpour, Nima; Utzinger, Urs; Wong, Pak Kin

    2016-09-01

    Cancer is a leading cause of death worldwide and metastases are responsible for over 90% of human cancer deaths. There is an urgent need to develop novel therapeutics for suppressing cancer invasion, the initial step of metastasis. Nevertheless, the regulation of cancer invasion is poorly understood due to a paucity of tools for monitoring the invasion process in 3D microenvironments. Here, we report a double-stranded locked nucleic acid (dsLNA) biosensor for investigating 3D collective cancer invasion. By incorporating multiphoton microscopy and the dsLNA biosensor, we perform dynamic single cell gene expression analysis while simultaneously characterizing the biomechanical interaction between the invading sprouts and the extracellular matrix. Gene profiling of invasive leader cells and detached cells suggest distinctive signaling mechanisms involved in collective and individual invasion in the 3D microenvironment. Our results underscore the involvement of Notch signaling in 3D collective cancer invasion, which warrants further investigation toward antimetastasis therapy in the future.

  19. Picosecond Spin Caloritronics

    NASA Astrophysics Data System (ADS)

    Cahill, David G.

    The coupling of spin and heat, i.e., spin caloritronics, gives rise to new physical phenomena in nanoscale spin devices and new ways to manipulate local magnetization. Our work in this field takes advantage of recent advances in the measurement and understanding of heat transport at the nanoscale using ultrafast lasers. We use a picosecond duration pump laser pulses as a source of heat and picosecond duration probe laser pulses to detect changes in temperature, spin accumulation, and spin transfer torque using a combination of time-domain thermoreflectance and time-resolved magneto-optic Kerr effect Our pump-probe optical methods enable us to change the temperature of ferromagnetic layers on a picosecond time-scale and generate enormous heat fluxes on the order of 100 GW m-2 that persist for ~ 30 ps. Thermally-driven ultrafast demagnetization of a perpendicular ferromagnet leads to spin accumulation in a normal metal and spin transfer torque in an in-plane ferromagnet. The data are well described by models of spin generation and transport based on differences and gradients of thermodynamic parameters. The spin-dependent Seebeck effect of a perpendicular ferromagnetic layer converts a heat current into spin current, which in turn can be used to exert a spin transfer torque (STT) on a second ferromagnetic layer with in-plane magnetization. Using a [Co,Ni] multilayer as the source of spin, an energy fluence of ~ 4 J m-2 creates thermal STT sufficient to induce ~ 1 % tilting of the magnetization of a 2 nm-thick CoFeB layer.

  20. Styrene oligomerization as a molecular probe reaction for Brønsted acidity at the nanoscale.

    PubMed

    Aramburo, Luis R; Wirick, Sue; Miedema, Piter S; Buurmans, Inge L C; de Groot, Frank M F; Weckhuysen, Bert M

    2012-05-21

    The Brønsted acid-catalyzed oligomerization of 4-fluorostyrene has been studied on a series of H-ZSM-5 zeolite powders, steamed under different conditions, with a combination of UV-Vis micro-spectroscopy and Scanning Transmission X-ray Microscopy (STXM). UV-Vis micro-spectroscopy and STXM have been used to monitor the relative formation of cyclic and linear dimeric carbocations as a function of the steaming post-treatment (i.e., parent vs. steaming at 600, 700 and 800 °C). It was found that the UV-Vis band intensity ratios of linear to cyclic dimeric species increase from 0.79 (parent H-ZSM-5) over 1.41 (H-ZSM-5 steamed at 600 °C) and 1.88 (H-ZSM-5 steamed at 700 °C) to 2.33 (H-ZSM-5 steamed at 800 °C). STXM confirms this trend in reaction product selectivity, as the relative intensities of the transitions attributed to the presence of the cyclic dimer in the carbon K-edge spectra decrease with increasing severity of the steaming post-treatment. Furthermore, STXM reveals spatial heterogeneities in reaction product formation within the H-ZSM-5 zeolite powders at the nanoscale. More specifically, a shrinking carbon core-shell distribution was detected within the zeolite aggregates, in which the relative amount of cyclic dimeric species is higher in the core relative to the shell of the zeolite aggregate and the relative amount of cyclic dimeric species in the zeolite core gradually decreases with increasing severity of the steaming post-treatment. These differences are rationalized in terms of spatial differences in Brønsted acidity within H-ZSM-5 zeolite powders as well as by changes in the formation process of linear and dimeric carbocations within H-ZSM-5 micro- and mesopores.

  1. Alkali-Metal Spin Maser.

    PubMed

    Chalupczak, W; Josephs-Franks, P

    2015-07-17

    Quantum measurement is a combination of a read-out and a perturbation of the quantum system. We explore the nonlinear spin dynamics generated by a linearly polarized probe beam in a continuous measurement of the collective spin state in a thermal alkali-metal atomic sample. We demonstrate that the probe-beam-driven perturbation leads, in the presence of indirect pumping, to complete polarization of the sample and macroscopic coherent spin oscillations. As a consequence of the former we report observation of spectral profiles free from collisional broadening. Nonlinear dynamics is studied through exploring its effect on radio frequency as well as spin noise spectra. PMID:26230788

  2. Alkali-Metal Spin Maser

    NASA Astrophysics Data System (ADS)

    Chalupczak, W.; Josephs-Franks, P.

    2015-07-01

    Quantum measurement is a combination of a read-out and a perturbation of the quantum system. We explore the nonlinear spin dynamics generated by a linearly polarized probe beam in a continuous measurement of the collective spin state in a thermal alkali-metal atomic sample. We demonstrate that the probe-beam-driven perturbation leads, in the presence of indirect pumping, to complete polarization of the sample and macroscopic coherent spin oscillations. As a consequence of the former we report observation of spectral profiles free from collisional broadening. Nonlinear dynamics is studied through exploring its effect on radio frequency as well as spin noise spectra.

  3. Reversible two-photon fluorescent probe for imaging of hypochlorous acid in live cells and in vivo.

    PubMed

    Zhang, Wei; Liu, Wei; Li, Ping; kang, Junqing; Wang, Jiaoyang; Wang, Hui; Tang, Bo

    2015-06-25

    Herein, we have developed a novel reversible two-photon fluorescent probe that is well suited for monitoring HOCl levels selectively and instantaneously. Results showed the reversible and instantaneous responses of the probe towards intracellular HOCl. Moreover, the probe was successfully applied to the imaging of the HOCl levels in zebrafish and mice via two-photon imaging.

  4. Microscopic studies of nonlocal spin dynamics and spin transport (invited)

    SciTech Connect

    Adur, Rohan; Du, Chunhui; Cardellino, Jeremy; Scozzaro, Nicolas; Wolfe, Christopher S.; Wang, Hailong; Herman, Michael; Bhallamudi, Vidya P.; Pelekhov, Denis V.; Yang, Fengyuan; Hammel, P. Chris

    2015-05-07

    Understanding the behavior of spins coupling across interfaces in the study of spin current generation and transport is a fundamental challenge that is important for spintronics applications. The transfer of spin angular momentum from a ferromagnet into an adjacent normal material as a consequence of the precession of the magnetization of the ferromagnet is a process known as spin pumping. We find that, in certain circumstances, the insertion of an intervening normal metal can enhance spin pumping between an excited ferromagnetic magnetization and a normal metal layer as a consequence of improved spin conductance matching. We have studied this using inverse spin Hall effect and enhanced damping measurements. Scanned probe magnetic resonance techniques are a complementary tool in this context offering high resolution magnetic resonance imaging, localized spin excitation, and direct measurement of spin lifetimes or damping. Localized magnetic resonance studies of size-dependent spin dynamics in the absence of lithographic confinement in both ferromagnets and paramagnets reveal the close relationship between spin transport and spin lifetime at microscopic length scales. Finally, detection of ferromagnetic resonance of a ferromagnetic film using the photoluminescence of nitrogen vacancy spins in neighboring nanodiamonds demonstrates long-range spin transport between insulating materials, indicating the complexity and generality of spin transport in diverse, spatially separated, material systems.

  5. Probing the interaction of the amino acid alanine with the surface of ZnO(1010).

    PubMed

    Gao, Y K; Traeger, F; Shekhah, O; Idriss, H; Wöll, C

    2009-10-01

    The adsorption modes and stability of the amino acid alanine (NH(2)-CH(CH(3))-COOH) have been studied on the nonpolar single crystal surface of zinc oxide, ZnO(1010), experimentally by X-ray photoelectron spectroscopy (XPS) and computationally using density functional theory (DFT). Deposition at 200 K was found to lead to the formation of multilayers identified by an XPS N1s peak at 401.7 eV assigned to the NH(3)(+) group, a fingerprint of the zwitterionic structure of alanine in the solid state. Heating to 300 K resulted in the removal of most of the multilayers with the remaining surface coverage estimated to 0.4 with respect to Zn cations. At this temperature most of the alanine molecules are found to be deprotonated (dissociated), yielding a carboxylate species (NH(2)-CH(CH(3))-COO(-) (a) + OH (s); where O is surface oxygen, (a) for adsorbed and (s) for surface species). Further heating of the surface resulted in a gradual decrease of the surface coverage and by 500 K a large fraction of adsorbed alanine molecules have desorbed from the surface. Total energy DFT computations of different adsorbate species identified two stable dissociative adsorption modes: bidentate and monodentate. The bidentate species with adsorption energy of 1.75 eV was found to be more stable than the monodentate species by about 0.7 eV.

  6. Probing 3D Collective Cancer Invasion Using Double-Stranded Locked Nucleic Acid Biosensors.

    PubMed

    Dean, Zachary S; Elias, Paul; Jamilpour, Nima; Utzinger, Urs; Wong, Pak Kin

    2016-09-01

    Cancer is a leading cause of death worldwide and metastases are responsible for over 90% of human cancer deaths. There is an urgent need to develop novel therapeutics for suppressing cancer invasion, the initial step of metastasis. Nevertheless, the regulation of cancer invasion is poorly understood due to a paucity of tools for monitoring the invasion process in 3D microenvironments. Here, we report a double-stranded locked nucleic acid (dsLNA) biosensor for investigating 3D collective cancer invasion. By incorporating multiphoton microscopy and the dsLNA biosensor, we perform dynamic single cell gene expression analysis while simultaneously characterizing the biomechanical interaction between the invading sprouts and the extracellular matrix. Gene profiling of invasive leader cells and detached cells suggest distinctive signaling mechanisms involved in collective and individual invasion in the 3D microenvironment. Our results underscore the involvement of Notch signaling in 3D collective cancer invasion, which warrants further investigation toward antimetastasis therapy in the future. PMID:27529634

  7. Probing the affinity of polyanions for acidic fibroblast growth factor by unfolding kinetics.

    PubMed

    Mach, H; Middaugh, C R

    1994-02-15

    The relationship between ligand-protein affinity and the extent of protein stabilization induced by such interactions has been investigated using the binding of polyanions to acidic fibroblast growth factor (aFGF) as a model system. It was found that the experimentally observed unfolding rate constant of aFGF consists of two components: one equal to the unfolding rate constant of the aFGF-ligand complex and the other the product of the unfolding rate constant of free aFGF, the aFGF-ligand dissociation constant (Kd), and the reciprocal of the molar ligand concentration. This reflects the presence of two possible unfolding pathways: at high ligand excess dissociation is suppressed and slow unfolding of the aFGF-ligand complex itself prevails. When lower concentrations of ligand allows equilibrium-driven appearance of free aFGF, a more rapid unfolding of dissociated protein predominates. Existence of a steady state of dissociated aFGF undergoing unfolding was demonstrated by computer simulation of the elementary events, using experimentally determined rate constants. The potential applications of such simulations are outlined. An equation allowing estimation of dissociation constants from equilibrium denaturation curves obtained in the presence of a varying amount of ligand is also proposed. In addition, determination of initial unfolding rates in the presence of excess protein permits the the stoichiometry of the interaction to be determined.

  8. Probing Gαi1 Protein Activation at Single Amino Acid Resolution

    PubMed Central

    Sun, Dawei; Maeda, Shoji; Matkovic, Milos; Mendieta, Sandro; Mayer, Daniel; Dawson, Roger; Schertler, Gebhard F.X.; Madan Babu, M.; Veprintsev, Dmitry B.

    2016-01-01

    We present comprehensive single amino acid resolution maps of the residues stabilising the human Gαi1 subunit in nucleotide- and receptor-bound states. We generated these maps by measuring the effects of alanine mutations on the stability of Gαi1 and of the rhodopsin-Gαi1 complex. We identified stabilization clusters in the GTPase and helical domains responsible for structural integrity and the conformational changes associated with activation. In activation cluster I, helices α1 and α5 pack against strands β1-3 to stabilize the nucleotide-bound states. In the receptor-bound state, these interactions are replaced by interactions between α5 and strands β4-6. Key residues in this cluster are Y320, crucial for the stabilization of the receptor-bound state, and F336, which stabilizes nucleotide-bound states. Destabilization of helix α1, caused by rearrangement of this activation cluster, leads to the weakening of the inter-domain interface and release of GDP. PMID:26258638

  9. DNAzyme molecular beacon probes for target-induced signal-amplifying colorimetric detection of nucleic acids.

    PubMed

    Fu, Rongzhan; Li, Taihua; Lee, Soo Suk; Park, Hyun Gyu

    2011-01-15

    A novel DNAzyme molecular beacon (DNAzymeMB) strategy was developed for target-induced signal-amplifying colorimetric detection of target nucleic acids. The DNAzymeMB, which exhibits peroxidase activity in its free hairpin structure, was engineered to form a catalytically inactive hybrid through hybridization with a blocker DNA. The presence of target DNA leads to dissociation of the DNAzymeMB from the inactive hybrid through hybridization with the blocker DNA. This process results in recovery of the catalytically active DNAzymeMB, which can catalyze a colorimetric reaction that signals the presence of the target DNA. In addition, a primer was rationally designed to anneal to the blocker DNA of the blocker/target DNA duplex and displace the bound target DNA during the extension reaction. The released target DNA triggers the next cycle involving hybridization with blocker DNA, DNAzymeMB dissociation, primer extension, and target displacement. This unique amplifying strategy leads to the generation of multiple numbers of active DNAzymeMB molecules from a single target molecule and gives a detection limit down to 1 pM, a value that is nearly 3 or 5 orders of magnitude lower than those of previously reported DNAzyme molecular beacon-based DNA detection methods.

  10. Probing the interaction of the amino acid alanine with the surface of ZnO(1010).

    PubMed

    Gao, Y K; Traeger, F; Shekhah, O; Idriss, H; Wöll, C

    2009-10-01

    The adsorption modes and stability of the amino acid alanine (NH(2)-CH(CH(3))-COOH) have been studied on the nonpolar single crystal surface of zinc oxide, ZnO(1010), experimentally by X-ray photoelectron spectroscopy (XPS) and computationally using density functional theory (DFT). Deposition at 200 K was found to lead to the formation of multilayers identified by an XPS N1s peak at 401.7 eV assigned to the NH(3)(+) group, a fingerprint of the zwitterionic structure of alanine in the solid state. Heating to 300 K resulted in the removal of most of the multilayers with the remaining surface coverage estimated to 0.4 with respect to Zn cations. At this temperature most of the alanine molecules are found to be deprotonated (dissociated), yielding a carboxylate species (NH(2)-CH(CH(3))-COO(-) (a) + OH (s); where O is surface oxygen, (a) for adsorbed and (s) for surface species). Further heating of the surface resulted in a gradual decrease of the surface coverage and by 500 K a large fraction of adsorbed alanine molecules have desorbed from the surface. Total energy DFT computations of different adsorbate species identified two stable dissociative adsorption modes: bidentate and monodentate. The bidentate species with adsorption energy of 1.75 eV was found to be more stable than the monodentate species by about 0.7 eV. PMID:19596338

  11. Design and Performance of rRNA Targeted Oligonucleotide Probes for in Situ Detection and Phylogenetic Identification of Microorganisms Inhabiting Acid Mine Drainage Environments.

    PubMed

    Bond, P.L.; Banfield, J.F.

    2001-02-01

    At Iron Mountain, CA, there is an extreme occurrence of acid mine drainage (AMD). This is a result of past mining activity that has exposed a sulfide ore body to weathering and microbial activity. This study presents seven new oligonucleotide probes for the detection of microorganisms at this AMD site by fluorescent in situ hybridization. In the design of these probes we have accounted for a large body of 16S rRNA sequence data recently compiled by us. This was obtained by PCR and cloning directly from environmental DNA and was mostly represented by novel sequences. The probes were developed to include detection of novel and uncultivated organisms. This includes detection for the Thermoplasmales group, a new group of Leptospirillum, the genus Sulfobacillus, the Acidiphilium genus, Acidimicrobium and relatives, and for organisms within the delta Proteobacteria. These probes have been used to examine the abundance and distribution of organisms, including novel and uncultivated taxa, and to clarify their potential contributions to AMD production at the site. We anticipate that these probes will be useful tools for exploration of the microbiology of other natural acidic environments and bioleaching systems. PMID:12032620

  12. Adsorption of 4-picoline and piperidine to the hydrated SiO2 surface: probing the surface acidity with vibrational sum frequency generation spectroscopy.

    PubMed

    Liu, Dingfang; Ma, Gang; Allen, Heather C

    2005-04-01

    Vapor adsorption is an important process influencing the migration and the fate of many organic pollutants in the environment. In this study, vibrational sum frequency generation (SFG) spectroscopy was used to study the adsorption of two surface acidity probe molecules, 4-picoline (pKa = 5.94) and piperidine (pKa = 11.24), onto the amorphous SiO2 surface. The adsorption of 4-picoline onto the silica surface occurs by forming weak hydrogen bonds between the nitrogen atoms of 4-picoline molecules and the hydrogen atoms of surface silanol OH groups. Piperidine molecules are strongly chemisorbed onto the SiO2 surface through the protonation of piperidine molecules by surface silanol OH groups. The SFG results indicate that the surface acidity constant of silanol OH groups (pKa-(HOSi triple bond)) is in the range of 5.94-11.24 at the air/solid interface. Although this range of surface acidity constants is quite wide, it is possible to narrow it by choosing probe molecules with a smaller pKa range. Together with theoretical prediction methods, adsorption studies using vibrational SFG spectroscopy are capable of quantifying the surface acidity of mineral oxides by carefully choosing the acidity probe molecules.

  13. A streptavidin paramagnetic-particle based competition assay for the evaluation of the optical selectivity of quadruplex nucleic acid fluorescent probes.

    PubMed

    Largy, Eric; Hamon, Florian; Teulade-Fichou, Marie-Paule

    2012-05-01

    Although quadruplex nucleic acids are thought to be involved in many biological processes, they are massively overwhelmed by duplex DNA in the cell. Small molecules, able to probe quadruplex nucleic acids with high optical selectivity, could possibly achieve the visualization of these processes. The aim of the method described herein is to evaluate quickly the optical selectivity of quadruplex nucleic acid probes, in isothermal conditions, using widely available materials, small quantities of oligonucleotides and virtually any kind and quantity of biological competitor. The assay relies on the use of streptavidin-coated paramagnetic particles and biotinylated quadruplex forming oligonucleotides, allowing a quick and easy separation of the quadruplex target from the competitor. In the present study, two quadruplex nucleic acids (the DNA and RNA human telomeric repeats) have been used as targets while a duplex DNA oligonucleotide, total DNA, total RNA, another quadruplex nucleic acid and a protein have been used as competitors. The optical selectivity of various probes, displaying different photophysical properties and binding selectivities, has been successfully examined, allowing the identification of a best candidate for further cell microscopy experiments. This assay allows a quick and reliable assessment of the labeling properties of a quadruplex binder in cellular environment conditions. It is an interesting alternative to gel electrophoresis experiments since it is performed in solution, has a well-resolved separation system and allows easy quantifications.

  14. pH at the micellar interface: synthesis of pH probes derived from salicylic acid, acid-base dissociation in sodium dodecyl sulfate micelles, and Poisson-Boltzmann simulation.

    PubMed

    Souza, T P; Zanette, D; Kawanami, A E; de Rezende, L; Ishiki, H M; do Amaral, A T; Chaimovich, H; Agostinho-Neto, A; Cuccovia, I M

    2006-05-01

    The study of the H+ concentration at the micellar interface is a convenient system for modeling the distribution of H+ at interfaces. We have synthesized salicylic acid derivatives to analyze the proton dissociation of both the carboxylic and phenol groups of the probes, determining spectrophotometrically the apparent pK(a)'s (pK(ap)) in sodium dodecyl sulfate, SDS, micelles with and without added salt. The synthesized probes were 2-hydroxy-5-(2-trimethylammoniumacetyl)benzoate; 2-hydroxy-5-(2-dimethylhexadecylammoniumacetyl)benzoate; 2-hydroxy-5-(2-dimethylhexadecylammoniumhexanoyl)benzoate; 2-hydroxy-5-(2-dimethylhexadecylammoniumundecanoyl)benzoate; 2-hydroxy-5-acetylbenzoic acid; and 2-hydroxy-5-dodecanoylbenzoic acid. Upon incorporation into SDS micelles the pK(ap)'s of both carboxylic and phenol groups increased by ca. 3 pH units and NaCl addition caused a decrease in the probe-incorporated pK(ap). The experimental results were fitted with a cell model Poisson-Boltzmann (P-B) equation taking in consideration the effect of salt on the aggregation number of SDS and using the distance of the dissociating group as a parameter. The conformations of the probes were analyzed theoretically using two dielectric constants, e.g., 2 and 78. Both the P-B analysis and conformation calculations can be interpreted by assuming that the acid groups dissociate very close to, or at, the interface. Our results are consistent with the assumption that the intrinsic pK(a)'s of both carboxylic and phenol groups of the salicylic acid probes used here can be taken as those in water. Using this assumption the micellar and salt effects on the pK(ap)'s of the (trialkylammonium)benzoate probes were described accurately using a cell model P-B analysis.

  15. Triplex-Forming Peptide Nucleic Acid Probe Having Thiazole Orange as a Base Surrogate for Fluorescence Sensing of Double-stranded RNA.

    PubMed

    Sato, Takaya; Sato, Yusuke; Nishizawa, Seiichi

    2016-08-01

    We have developed a new fluorescent sensing probe for double-stranded RNA (dsRNA) by integrating thiazole orange (TO) as a base surrogate into triplex-forming PNA. Our probe forms the thermally stable triplex with the target dsRNA at acidic pH; and the triplex formation is accompanied by the remarkable light-up response of the TO unit. The binding of our probe to the target dsRNA proceeds very rapidly, allowing real-time monitoring of the triplex formation. Importantly, we found the TO base surrogate in our probe functions as a universal base for the base pair opposite the TO unit in the triplex formation. Furthermore, the TO unit is significantly more responsive for the fully matched dsRNA sequence compared to the mismatch-containing sequences, which enables the analysis of the target dsRNA sequence at the single-base pair resolution. The binding and sensing functions of our probe are described for the development of fluorescent probes applicable to sensing biologically relevant dsRNA. PMID:27442229

  16. Association of fluorescent probes 1-anilinonaphthalene-8-sulfonate and 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid with T7 RNA polymerase.

    PubMed

    Ghosh, Utpal; Das, Mili; Dasgupta, Dipak

    2003-01-01

    T7 RNA polymerase is an enzyme that carries out transcription using DNA as the template and ribonucleotides as the substrates. Here we report the association of the polymerase with 1-anilinonaphthalene-8-sulfonate (ANS) and 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS), which are two fluorescent hydrophobic probes that are frequently used to study structural perturbations in proteins and intermediate states of proteins during folding and unfolding. Our results from the fluorescence titration data show that these two molecules bind to the enzyme with dissociation constants on the micromolar order. The results from the tryptic digestion of the enzyme in the absence and presence of the probes show that they inhibit the rate of tryptic digestion. Circular dichroism spectroscopic studies of the protein in the near UV region indicate that both probes induce tertiary structural changes in the polymerase. There is also a probe (ANS or bis-ANS) induced inhibition of the enzymatic activity. All these results are attributed to association of the probes with the enzyme, leading to an alteration in the conformation of T7 RNA polymerase. This limits the use of these extrinisic probes to the study of the folding properties of the enzyme.

  17. Triplex-Forming Peptide Nucleic Acid Probe Having Thiazole Orange as a Base Surrogate for Fluorescence Sensing of Double-stranded RNA.

    PubMed

    Sato, Takaya; Sato, Yusuke; Nishizawa, Seiichi

    2016-08-01

    We have developed a new fluorescent sensing probe for double-stranded RNA (dsRNA) by integrating thiazole orange (TO) as a base surrogate into triplex-forming PNA. Our probe forms the thermally stable triplex with the target dsRNA at acidic pH; and the triplex formation is accompanied by the remarkable light-up response of the TO unit. The binding of our probe to the target dsRNA proceeds very rapidly, allowing real-time monitoring of the triplex formation. Importantly, we found the TO base surrogate in our probe functions as a universal base for the base pair opposite the TO unit in the triplex formation. Furthermore, the TO unit is significantly more responsive for the fully matched dsRNA sequence compared to the mismatch-containing sequences, which enables the analysis of the target dsRNA sequence at the single-base pair resolution. The binding and sensing functions of our probe are described for the development of fluorescent probes applicable to sensing biologically relevant dsRNA.

  18. Synthesis of fluorescent D-amino acids (FDAAs) and their use for probing peptidoglycan synthesis and bacterial growth in situ

    PubMed Central

    Kuru, Erkin; Tekkam, Srinivas; Hall, Edward

    2015-01-01

    Fluorescent D-amino acids (FDAAs) are efficiently incorporated into the peptidoglycan of diverse bacterial species at the sites of active peptidoglycan biosynthesis, allowing specific and covalent probing of bacterial growth with minimal perturbation. Here, we provide a protocol for the synthesis of four FDAAs emitting light in blue, green or red and for their use in peptidoglycan labeling of live bacteria. Our modular synthesis protocol gives easy access to a library of different FDAAs made with commercially available fluorophores. FDAAs can be synthesized in a typical chemistry laboratory in 2–3 days. The simple labeling procedure involves addition of the FDAAs to the bacterial sample for the desired labeling duration and stopping further label incorporation by fixation or by washing away excess dye. We discuss several scenarios for the use of these labels including short or long labeling durations, and the combination of different labels in pure culture or complex environmental samples. Depending on the experiment, FDAA labeling can take as little as 30 s for a rapidly growing species such as Escherichia coli. PMID:25474031

  19. Denaturant effects on HbGp hemoglobin as monitored by 8-anilino-1-naphtalene-sulfonic acid (ANS) probe.

    PubMed

    Barros, Ana E B; Carvalho, Francisco A O; Alves, Fernanda R; Carvalho, José W P; Tabak, Marcel

    2015-03-01

    Glossoscolex paulistus extracellular hemoglobin (HbGp) stability has been monitored in the presence of denaturant agents. 8-Anilino-1-naphtalene-sulfonic acid (ANS) was used, and spectroscopic and hydrodynamic studies were developed. Dodecyltrimethylammonium bromide (DTAB) induces an increase in ANS fluorescence emission intensity, with maximum emission wavelength blue-shifted from 517 to 493 nm. Two transitions are noticed, at 2.50 and 9.50 mmol/L of DTAB, assigned to ANS interaction with pre-micellar aggregates and micelles, respectively. In oxy-HbGp, ANS binds to protein sites less exposed to solvent, as compared to DTAB micelles. In DTAB-HbGp-ANS ternary system, at pH 7.0, protein aggregation, oligomeric dissociation and unfolding were observed, while, at pH 5.0, aggregation is absent. DTAB induced unfolding process displays two transitions, one due to oligomeric dissociation and the second one, probably, to the denaturation of dissociated subunits. Moreover, guanidine hydrochloride and urea concentrations above 1.5 and 4.0 mol/L, respectively, induce the full HbGp denaturation, with reduction of ANS-bound oxy-HbGp hydrophobic patches, as noticed by fluorescence quenching up to 1.0 and 5.0 mol/L of denaturants. Our results show clearly the differences in probe sensitivity to the surfactant, in the presence and absence of protein, and new insights into the denaturant effects on HbGp unfolding.

  20. Spin foams without spins

    NASA Astrophysics Data System (ADS)

    Hnybida, Jeff

    2016-10-01

    We formulate the spin foam representation of discrete SU(2) gauge theory as a product of vertex amplitudes each of which is the spin network generating function of the boundary graph dual to the vertex. In doing so the sums over spins have been carried out. The boundary data of each n-valent node is explicitly reduced with respect to the local gauge invariance and has a manifest geometrical interpretation as a framed polyhedron of fixed total area. Ultimately, sums over spins are traded for contour integrals over simple poles and recoupling theory is avoided using generating functions.

  1. Air jet spinning of hydroxyapatite/poly(lactic acid) hybrid nanocomposite membrane mats for bone tissue engineering.

    PubMed

    Abdal-hay, Abdalla; Sheikh, Faheem A; Lim, Jae Kyoo

    2013-02-01

    The technique for the production of multifunctional scaffolds from bioactive ceramics and biodegradable polymers for use in tissue scaffolds remains challenging. Here, the goal was to fabricate 3D nanocomposite nanofiber scaffolds of nanohydroxyapatite/poly(lactic acid) (nHA/PLA) prepared by air jet spinning (AJS) as a novel and facile composite fabrication process. The characteristics of the fabricated 3D scaffolds were investigated using SEM, water contact angle, DSC, FTIR, XRD analyses and tensile tests. The surface morphology exhibited highly interconnected bonded fibers due to the high fabrication rates. It was also found that the nHA particles were effectively embedded in the fibers' surface due to the difference in the kinetic energies between the nHA particles and polymer molecules. The as-received PLA film showed a low crystallinity value of about 19%, which was expected with the casting process. The crystallinities of the plain PLA and nHA/PLA membrane scaffolds were about 31.78% and 32.21%, respectively. This reveals that HA nanoparticles could engage in a beneficial interaction with the PLA chain molecules during the AJS process. The tensile strength of the membrane PLA mats, particularly the hybrid nanocomposite samples with low nHA contents, was considerably improved compared to that of the PLA casted film. Biological in vitro cell cultures of MC3T3-E1 osteoblast-like cells on the fabricated scaffolds were studied for up to seven days. The nanocomposite membrane mats of nHA/PLA, fabricated by AJS, had highly interconnected fibers. This facile technique has a high production rate and is a new concept of potential interest for bone tissue engineering applications.

  2. Air jet spinning of hydroxyapatite/poly(lactic acid) hybrid nanocomposite membrane mats for bone tissue engineering.

    PubMed

    Abdal-hay, Abdalla; Sheikh, Faheem A; Lim, Jae Kyoo

    2013-02-01

    The technique for the production of multifunctional scaffolds from bioactive ceramics and biodegradable polymers for use in tissue scaffolds remains challenging. Here, the goal was to fabricate 3D nanocomposite nanofiber scaffolds of nanohydroxyapatite/poly(lactic acid) (nHA/PLA) prepared by air jet spinning (AJS) as a novel and facile composite fabrication process. The characteristics of the fabricated 3D scaffolds were investigated using SEM, water contact angle, DSC, FTIR, XRD analyses and tensile tests. The surface morphology exhibited highly interconnected bonded fibers due to the high fabrication rates. It was also found that the nHA particles were effectively embedded in the fibers' surface due to the difference in the kinetic energies between the nHA particles and polymer molecules. The as-received PLA film showed a low crystallinity value of about 19%, which was expected with the casting process. The crystallinities of the plain PLA and nHA/PLA membrane scaffolds were about 31.78% and 32.21%, respectively. This reveals that HA nanoparticles could engage in a beneficial interaction with the PLA chain molecules during the AJS process. The tensile strength of the membrane PLA mats, particularly the hybrid nanocomposite samples with low nHA contents, was considerably improved compared to that of the PLA casted film. Biological in vitro cell cultures of MC3T3-E1 osteoblast-like cells on the fabricated scaffolds were studied for up to seven days. The nanocomposite membrane mats of nHA/PLA, fabricated by AJS, had highly interconnected fibers. This facile technique has a high production rate and is a new concept of potential interest for bone tissue engineering applications. PMID:23107942

  3. Tensor spin observables and spin stucture at low Q2

    SciTech Connect

    Slifer, Karl J.

    2015-04-01

    We discuss recent spin structure results from Jefferson Lab, and outline an emerging program to study tensor spin observables using solid deuteron targets. These new experiments open the potential to study hidden color, the tensor nature of short range correlations, and to probe for exotic gluonic states.

  4. The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns.

    PubMed

    Naccache, Samia N; Greninger, Alexander L; Lee, Deanna; Coffey, Lark L; Phan, Tung; Rein-Weston, Annie; Aronsohn, Andrew; Hackett, John; Delwart, Eric L; Chiu, Charles Y

    2013-11-01

    Next-generation sequencing was used for discovery and de novo assembly of a novel, highly divergent DNA virus at the interface between the Parvoviridae and Circoviridae. The virus, provisionally named parvovirus-like hybrid virus (PHV), is nearly identical by sequence to another DNA virus, NIH-CQV, previously detected in Chinese patients with seronegative (non-A-E) hepatitis. Although we initially detected PHV in a wide range of clinical samples, with all strains sharing ∼99% nucleotide and amino acid identity with each other and with NIH-CQV, the exact origin of the virus was eventually traced to contaminated silica-binding spin columns used for nucleic acid extraction. Definitive confirmation of the origin of PHV, and presumably NIH-CQV, was obtained by in-depth analyses of water eluted through contaminated spin columns. Analysis of environmental metagenome libraries detected PHV sequences in coastal marine waters of North America, suggesting that a potential association between PHV and diatoms (algae) that generate the silica matrix used in the spin columns may have resulted in inadvertent viral contamination during manufacture. The confirmation of PHV/NIH-CQV as laboratory reagent contaminants and not bona fide infectious agents of humans underscores the rigorous approach needed to establish the validity of new viral genomes discovered by next-generation sequencing.

  5. The kinetic isotope effect as a probe of spin crossover in the C-H activation of methane by the FeO(+) cation.

    PubMed

    Mai, Binh Khanh; Kim, Yongho

    2015-03-23

    Two-state reactivity (TSR) is often used to explain the reaction of transition-metal-oxo reagents in the bare form or in the complex form. The evidence of the TSR model typically comes from quantum-mechanical calculations for energy profiles with a spin crossover in the rate-limiting step. To prove the TSR concept, kinetic profiles for CH activation by the FeO(+) cation were explored. A direct dynamics approach was used to generate potential energy surfaces of the sextet and quartet H-transfers and rate constants and kinetic isotope effects (KIEs) were calculated using variational transition-state theory including multidimensional tunneling. The minimum energy crossing point with very large spin-orbit coupling matrix element was very close to the intrinsic reaction paths of both sextet and quartet H-transfers. Excellent agreement with experiments were obtained when the sextet reactant and quartet transition state were used with a spin crossover, which strongly support the TSR model.

  6. Simultaneous detection and differentiation of human rhino- and enteroviruses in clinical specimens by real-time PCR with locked nucleic Acid probes.

    PubMed

    Osterback, Riikka; Tevaluoto, Tuire; Ylinen, Tiina; Peltola, Ville; Susi, Petri; Hyypiä, Timo; Waris, Matti

    2013-12-01

    Human rhinoviruses (HRVs) and human enteroviruses (HEVs) are significant respiratory pathogens. While HRV infections are restricted to the respiratory tract, HEV infections may spread to secondary target organs. The method of choice for sensitive specific detection of these viruses is reverse transcription (RT)-PCR with primers targeting the conserved 5' noncoding region of the viral RNA. On the other hand, sequence similarities between HRVs and HEVs complicate their differential detection. In this study, we describe the use of locked nucleic acid (LNA) analogues in short double-dye probes which contained only two selectively HRV- or HEV-specific bases. The double-stranded DNA dye BOXTO (4-[6-(benzoxazole-2-yl-(3-methyl-)-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene)]-1-methyl-quinolinium chloride) was used with the LNA probes in a tricolor real-time PCR assay to allow specific detection of HRVs (probes labeled with 6-carboxyfluorescein [FAM] [green]) and HEVs (Cy5 [red]) with additional melting curve analysis (BOXTO [yellow]). The functionality of the probes was validated in PCR and RT-PCR assays using plasmids containing viral cDNA, quantified viral RNA transcripts, cultivated rhino- and enterovirus prototypes, and clinical specimens. Of 100 HRV and 63 HEV prototypes, the probes correctly identified all HEVs except one that produced only a BOXTO signal. Among 118 clinical specimens with sequencing results, concordant results were obtained for 116 specimens. Two specimens were reactive with both probes, but sequencing yielded only a single virus. Real-time PCR with LNA probes allowed sensitive group-specific identification of HRVs and HEVs and would enable relative copy number determination. The assay is suitable for rapid and accurate differential detection of HRVs and HEVs in a diagnostic laboratory setting.

  7. A unique "turn-on" fluorescence signalling strategy for highly specific detection of ascorbic acid using carbon dots as sensing probe.

    PubMed

    Fong, Jessica Fung Yee; Chin, Suk Fun; Ng, Sing Muk

    2016-11-15

    Carbon dots (CDs) that showed strong blue fluorescence were successfully synthesised from sodium alginate via furnace pyrolysis. The single step pyrolytic synthesis was simple to perform while yielded CDs with high photostability, good water solubility and minimum by-products. In order to design the probe with "turn-on" sensing capability, the CDs were screened against a series of metal cations to first "turn-off" the fluorescence. It was found that ferric ions (Fe(3+)) were most responsive and effective in quenching the fluorescence of CDs. Based on this observation, the conditioning of the probe was performed to ensure the fluorescence was completely quenched, while not overloading the system with Fe(3+). At the optimised condition, the CDs-Fe(3+) mixture served as a highly specific detection probe for ascorbic acid (AA). The analytical potential of the probe was evaluated and showed a good linear range of response for AA concentration of 24-40μg/mL. The selectivity study against other possible co-existing species was carried out and proved that our unique "turn-on" fluorescence signalling strategy was highly effective and selective towards AA as the target analyte. The probe was demonstrated for quantification of AA in real samples, which was the commercially available vitamin C supplement. The result showed good accuracy with minimum deviation from standard method adopted for validation purpose. PMID:27290666

  8. Unravelling the Bacterial Vaginosis-Associated Biofilm: A Multiplex Gardnerella vaginalis and Atopobium vaginae Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes

    PubMed Central

    Hardy, Liselotte; Jespers, Vicky; Dahchour, Nassira; Mwambarangwe, Lambert; Musengamana, Viateur; Vaneechoutte, Mario; Crucitti, Tania

    2015-01-01

    Bacterial vaginosis (BV), a condition defined by increased vaginal discharge without significant inflammation, is characterized by a change in the bacterial composition of the vagina. Lactobacillus spp., associated with a healthy vaginal microbiome, are outnumbered by BV-associated organisms. These bacteria could form a polymicrobial biofilm which allows them to persist in spite of antibiotic treatment. In this study, we examined the presence of Gardnerella vaginalis and Atopobium vaginae in vaginal biofilms using Peptide Nucleic Acid (PNA) probes targeting these bacteria. For this purpose, we developed three new PNA probes for A. vaginae. The most specific A. vaginae probe, AtoITM1, was selected and then used in an assay with two existing probes, Gard162 and BacUni-1, to evaluate multiplex FISH on clinical samples. Using quantitative polymerase chain reaction (qPCR) as the gold standard, we demonstrated a sensitivity of 66.7% (95% confidence interval: 54.5% - 77.1%) and a specificity of 89.4% (95% confidence interval: 76.1% - 96%) of the new AtoITM1 probe. FISH enabled us to show the presence of a polymicrobial biofilm in bacterial vaginosis, in which Atopobium vaginae is part of a Gardnerella vaginalis-dominated biofilm. We showed that the presence of this biofilm is associated with high bacterial loads of A. vaginae and G. vaginalis. PMID:26305575

  9. Fluorescence determination of DNA with 1-pyrenebutyric acid nanoparticles coated with β-cyclodextrin as a fluorescence probe

    NASA Astrophysics Data System (ADS)

    Wang, Lun; Bian, Guirong; Wang, Leyu; Dong, Ling; Chen, Hongqi; Xia, Tingting

    2005-04-01

    A novel ultrasonication method has been successfully developed for the preparation of 1-pyrenebutyric acid (PBAC)/β-cyclodextrin(β-CD) complex nanoparticles. The as-prepared nanoparticles are characterized by transmission electron microscopy (TEM), fluorescence excitation and emission spectroscopy. Complex nanoparticles prepared with ultrasonication are smaller and better dispersed than single PBAC nanoparticles. At pH 3.0, the relative fluorescence intensity of complex nanoparticles of PBAC/β-CD can be quenched by the concentration of DNA. Based on this, a novel fluorimetric method has been developed for rapid determination of DNA. In comparison with single organic fluorophores, these nanoparticle probes are better water-solubility, more stable and do not suffer from blinking. Under optimum conditions, the calibration graphs are linear over the range 0.2-15 μg mL -1 for calf thymus DNA (ct-DNA) and 0.3-12 μg mL -1 for fish sperm DNA (fs-DNA). The corresponding detection limit is 0.01 μg mL -1 for ct-DNA and 0.02 μg mL -1 for fs-DNA. The relative standard deviation of seven replicate measurements is 1.2% for 2.0 μg mL -1 ct-DNA and 1.4% for 2.0 μg mL -1 fs-DNA, respectively. The method is simple and sensitive. The recovery and relative standard deviation are very satisfactory. A mechanism proposed to explain the process also has been studied.

  10. Analysis of Protein–Protein Interactions in MCF-7 and MDA-MB-231 Cell Lines Using Phthalic Acid Chemical Probes

    PubMed Central

    Liang, Shih-Shin; Wang, Tsu-Nai; Tsai, Eing-Mei

    2014-01-01

    Phthalates are a class of plasticizers that have been characterized as endocrine disrupters, and are associated with genital diseases, cardiotoxicity, hepatotoxicity, and nephrotoxicity in the GeneOntology gene/protein database. In this study, we synthesized phthalic acid chemical probes and demonstrated differing protein–protein interactions between MCF-7 cells and MDA-MB-231 breast cancer cell lines. Phthalic acid chemical probes were synthesized using silicon dioxide particle carriers, which were modified using the silanized linker 3-aminopropyl triethoxyslane (APTES). Incubation with cell lysates from breast cancer cell lines revealed interactions between phthalic acid and cellular proteins in MCF-7 and MDA-MB-231 cells. Subsequent proteomics analyses indicated 22 phthalic acid-binding proteins in both cell types, including heat shock cognate 71-kDa protein, ATP synthase subunit beta, and heat shock protein HSP 90-beta. In addition, 21 MCF-7-specific and 32 MDA-MB-231 specific phthalic acid-binding proteins were identified, including related proteasome proteins, heat shock 70-kDa protein, and NADPH dehydrogenase and ribosomal correlated proteins, ras-related proteins, and members of the heat shock protein family, respectively. PMID:25402641

  11. Electron Spin Density on the N-Donor Atoms of Cu(II)-(Bis)oxamidato Complexes As Probed by a Pulse ELDOR Detected NMR.

    PubMed

    Aliabadi, Azar; Zaripov, Ruslan; Salikhov, Kev; Voronkova, Violeta; Vavilova, Evgeniya; Abdulmalic, Mohammad A; Rüffer, Tobias; Büchner, Bernd; Kataev, Vladislav

    2015-10-29

    We have applied the pulse ELDOR detected NMR (EDNMR) technique to determine the tensors of the transferred Cu (S = 1/2) - (14)N (I = 1) hyperfine (HF) interaction in single crystals of diamagnetically diluted mononuclear o-phenylenebis(N(R)-oxamide) complexes of [(n)Bu4N]2[Cu(opboR2)] (R = Et 1, (n)Pr 2) (1%) in a host lattice of [(n)Bu4N]2[Ni(opboR2)] (R = Et 3, (n)Pr 4) (99%) (1@3 and 2@4)). To facilitate the analysis of our EDNMR data and to analyze possible manifestations of the nuclear quadrupole interaction in the EDNMR spectra, we have treated a model electron-nuclear system of the coupled S = 1/2 and I = 1 spins using the spin density matrix formalism. It appears that this interaction yields a peculiar asymmetry of the EDMR spectra that manifests not only in the shift of the positions of the EDNMR lines that correspond to the forbidden EPR transitions, as expected, but also in the intensities of the EDNMR lines. The symmetric shape of the experimental spectra suggests the conclusion that, in the studied complexes, the quadrupole interaction is negligible. This has simplified the analysis of the spectra. The HF tensors of all four N donor atoms could be accurately determined. On the basis of the HF tensors, an estimate of the spin density transferred from the central paramagnetic Cu(II) ion to the N donor atoms reveals its unequal distribution. We discuss possible implications of our estimates for the magnetic exchange paths and interaction strengths in respective trinuclear complexes [Cu3(opboR2) (pmdta)2](NO3)2 (R = Et 6, (n)Pr 7).

  12. Spin-phonon and magnetostriction phenomena in CaMn{sub 7}O{sub 12} helimagnet probed by Raman spectroscopy

    SciTech Connect

    Nonato, A.; Araujo, B. S.; Ayala, A. P.; Maciel, A. P.; Yanez-Vilar, S.; Sanchez-Andujar, M.; Senaris-Rodriguez, M. A.; Paschoal, C. W. A.

    2014-12-01

    In this letter, we investigated the temperature-dependent Raman spectra of CaMn{sub 7}O{sub 12} helimagnet from room temperature down to 10 K. The temperature dependence of the Raman mode parameters shows remarkable anomalies for both antiferromagnetic and incommensurate transitions that this compound undergoes at low temperatures. The anomalies observed at the magnetic ordering transition indicate a spin-phonon coupling at higher-temperature magnetic transition in this material, while a magnetostriction effect at the lower-temperature magnetic transition.

  13. Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation.

    PubMed

    Kellersberger, Katherine A; Yu, Eizadora; Kruppa, Gary H; Young, Malin M; Fabris, Daniele

    2004-05-01

    A top-down approach based on sustained off-resonance irradiation collision-induced dissociation (SORI-CID) has been implemented on an electrospray ionization (ESI) Fourier transform mass spectrometer (FTMS) to characterize nucleic acid substrates modified by structural probes. Solvent accessibility reagents, such as dimethyl sulfate (DMS), 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT), and beta-ethoxy-alpha-ketobutyraldehyde (kethoxal, KT) are widely employed to reveal the position of single- vs double-stranded regions and obtain the footprint of bound proteins onto nucleic acids structures. Established methods require end-labeling of the nucleic acid constructs, probe-specific chemistry to produce strand cleavage at the modified nucleotides, and analysis by polyacrylamide gel electrophoresis to determine the position of the susceptible sites. However, these labor-intensive procedures can be avoided when mass spectrometry is used to identify the probe-induced modifications from their characteristic mass signatures. In particular, ESI-FTMS can be directly employed to monitor the conditions of probe application to avoid excessive alkylation, which could induce unwanted distortion or defolding of the substrate of interest. The sequence position of the covalent modifications can be subsequently obtained from classic tandem techniques, which allow for the analysis of individual target adducts present in complex reaction mixtures with no need for separation techniques. Selection and activation by SORI-CID has been employed to reveal the position of adducts in nucleic acid substrates in excess of 6 kDa. The stability of the different covalent modifications under SORI-CID conditions was investigated. Multiple stages of isolation and activation were employed in MS(n)() experiments to obtain the desired sequence information whenever the adduct stability was not particularly favorable, and SORI-CID induced the facile loss of the modified base

  14. Targeting Acidity in Pancreatic Adenocarcinoma: Multispectral Optoacoustic Tomography Detects pH-low Insertion Peptide Probes in vivo

    PubMed Central

    Kimbrough, Charles W; Khanal, Anil; Zeiderman, Matthew; Khanal, Bigya R.; Burton, Neal C; McMasters, Kelly M; Vickers, Selwyn; Grizzle, William E; McNally, Lacey R

    2015-01-01

    Background pH-low Insertion Peptides (pHLIPs) can serve as a targeting moiety that enables pH-sensitive probes to detect solid tumors. Using these probes in conjunction with multispectral optoacoustic tomography (MSOT) is a promising approach to improve imaging for pancreatic cancer. Methods A pH-sensitive pHLIP (V7) was conjugated to 750 NIR fluorescent dye and evaluated as a targeted probe for pancreatic adenocarcinoma. The pH-insensitive K7 pHLIP served as an untargeted control. Probe binding was assessed in vitro at pH 7.4, 6.8, and 6.6 using human pancreatic cell lines S2VP10 and S2013. Using MSOT, semi-quantitative probe accumulation was then assessed in vivo with a murine orthotopic pancreatic adenocarcinoma model. Results In vitro, the V7–750 probe demonstrated significantly higher fluorescence at pH 6.6 compared to pH 7.4 (S2VP10, p=0.0119; S2013, p=0.0160), while no difference was observed with the K7–750 control (S2VP10, p=0.8783; S2013, p=0.921). In the in vivo S2VP10 model, V7–750 probe resulted in 782.5 MSOT a.u. signal compared to 5.3 MSOT a.u. in K7–750 control in tumor (p= 0.0001). Similarly, V7–750 probe signal was 578.3 MSOT a.u. in the S2013 model compared to K7–750 signal at 5.1 MSOT a.u. (p=0.0005). There was minimal off-target accumulation of the V7–750 probe within the liver or kidney, and probe distribution was confirmed with ex vivo imaging. Conclusion Compared to pH-insensitive controls, V7–750 pH-sensitive probe specifically targets pancreatic adenocarcinoma, and has minimal off-target accumulation. The non-invasive detection of pH-targeted probes by means of MSOT represents a promising modality to improve the detection and monitoring of pancreatic cancer. PMID:26124201

  15. Design, Synthesis, EPR-Studies and Conformational Bias of Novel Spin-Labeled DCC-Analogues for the Highly Regioselective Labeling of Aliphatic and Aromatic Carboxylic Acids.

    PubMed

    Gölz, Jan Philipp; NejatyJahromy, Yaser; Bauer, Mirko; Muhammad, Ashraf; Schnakenburg, Gregor; Grimme, Stefan; Schiemann, Olav; Menche, Dirk

    2016-07-01

    Novel types of spin-labeled N,N'-dicyclohexylcarbodiimides (DCC) are reported that bear a 2,2,6,6-tetramethylpiperidinyloxyl (TEMPO) residue on one side and different aromatic and aliphatic cyclohexyl analogues on the other side of the diimide core. These readily available novel reagents add efficiently to aliphatic and aromatic carboxylic acids, forming two possible spin-labeled amide derivatives with different radical distances of the resulting amide. The addition of aromatic DCC analogues proceeds with excellent selectivity, giving amides where the carboxylic acid is exclusively connected to the aromatic residue, while little or no selectivity was observed for the aliphatic congeners. The usefulness of these adducts in structural studies was demonstrated by EPR (electron paramagnetic resonance) measurements of biradical adducts of biphenyl-4,4'-dicarboxylic acids. These analyses also reveal high degrees of conformational bias for aromatic DCC derivatives, which further underlines the powerfulness of these novel reagents. This observation was further corroborated by quantum chemical calculations, giving a detailed understanding of the structural dynamics, while detailed information on the solid state structure of all novel reagents was obtained by X-ray structure analyses.

  16. Design, Synthesis, EPR-Studies and Conformational Bias of Novel Spin-Labeled DCC-Analogues for the Highly Regioselective Labeling of Aliphatic and Aromatic Carboxylic Acids.

    PubMed

    Gölz, Jan Philipp; NejatyJahromy, Yaser; Bauer, Mirko; Muhammad, Ashraf; Schnakenburg, Gregor; Grimme, Stefan; Schiemann, Olav; Menche, Dirk

    2016-07-01

    Novel types of spin-labeled N,N'-dicyclohexylcarbodiimides (DCC) are reported that bear a 2,2,6,6-tetramethylpiperidinyloxyl (TEMPO) residue on one side and different aromatic and aliphatic cyclohexyl analogues on the other side of the diimide core. These readily available novel reagents add efficiently to aliphatic and aromatic carboxylic acids, forming two possible spin-labeled amide derivatives with different radical distances of the resulting amide. The addition of aromatic DCC analogues proceeds with excellent selectivity, giving amides where the carboxylic acid is exclusively connected to the aromatic residue, while little or no selectivity was observed for the aliphatic congeners. The usefulness of these adducts in structural studies was demonstrated by EPR (electron paramagnetic resonance) measurements of biradical adducts of biphenyl-4,4'-dicarboxylic acids. These analyses also reveal high degrees of conformational bias for aromatic DCC derivatives, which further underlines the powerfulness of these novel reagents. This observation was further corroborated by quantum chemical calculations, giving a detailed understanding of the structural dynamics, while detailed information on the solid state structure of all novel reagents was obtained by X-ray structure analyses. PMID:27272435

  17. La-doping effect on spin-orbit coupled Sr2IrO4 probed by x-ray absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Cheng, Jie; Sun, Xuanyong; Liu, Shengli; Li, Bin; Wang, Haiyun; Dong, Peng; Wang, Yu; Xu, Wei

    2016-09-01

    Sr2IrO4 was predicted to be an unconventional superconductor upon carrier doping since it highly resembles the high-temperature cuprates. Here, to understand carrier doping effect on spin-orbit coupled Mott insulator Sr2IrO4, the electronic structure and local structure distortion for Sr2 - x La x IrO4 system have been investigated by x-ray absorption spectroscopy. By comparing the intensity of white-line features at the Ir L 2,3 absorption edges, we observe remarkably large branching ratios in La-doped compounds, greater than that of the parent material Sr2IrO4, suggesting a strong spin-orbit interaction for Sr2IrO4-based system. Moreover, extended x-ray absorption fine structure spectra demonstrate more regular IrO6 octahedra, i.e. the weakened crystal electric field versus La-doping. By theoretical calculations, the synergistic effect of regular IrO6 octahedra and electron doping is established, which accounts for the transition from a Mott insulator to a conductive state in Sr2 - x La x IrO4-based system.

  18. Probing many body effects using Fourier Transform Scanning Tunneling Spectroscopy: Can spin-orbit splitting in dispersion be observed in q-space?

    NASA Astrophysics Data System (ADS)

    Farahi, Gelareh; UBC Labortory for Atomic Imaging Research (LAIR)) Team

    Well studied surface systems such as Ag and Cu provide a safe platform to test novel spectroscopy methods that can have extended applications in near future. Our current focus is given to Fourier Transform Scanning Tunneling Spectroscopy (FT-STS) that allows us to study scattering effects (quasiparticle interactions - namely QPI) of CO and Co on Cu(111) surface. Magnetic Co adatoms are expected to generate a spin-orbit split in dispersion in QPI(q) space, the existence of which is confirmed by the k-space angle-resolved photo-emission spectroscopy (ARPES) of Cu(111) surface in the recent years. Hence the previously observed electron-phonon kink and spin-orbit splitting of the dispersion, as well as the scattering properties of CO molecules and Co adatoms, should also be observable in QPI space via FT-STS of Cu(111), and compatible with previous studies on similar systems. We are using a low temperature (4.2 K) commercial Scanning Tunneling Microscope (CREATEC STM) that operates using Nanonis electronic controllers and software which allows us to perform FT-STS as well as topological imaging.

  19. A rapid microwave synthesis of nitrogen-sulfur co-doped carbon nanodots as highly sensitive and selective fluorescence probes for ascorbic acid.

    PubMed

    Duan, Junxia; Yu, Jie; Feng, Suling; Su, Li

    2016-06-01

    A ultrafast one-step microwave-assisted method was developed for the synthesis of nitrogen-sulfur co-doped carbon nanodots (N,S-CDs) by using ethylenediamine as the carbon source and sulfamic acid as the surface passivation reagent. The morphology and the properties of N,S-CDs were explored by a series of techniques, such as high-resolution transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, UV-vis absorption and fluorescence spectroscopy. The prepared N,S-CDs exhibit bright blue photoluminescence with a high fluorescence quantum yield (FLQY) up to 28%, and high stability and excellent water solubility. A N,S-CDs-based fluorescent probe was developed for sensitive detection ascorbic acid (AA) in the presence of Cu(2+), based on the mechanism that AA reduces Cu(2+) to Cu(+), then Cu(+) quenches the fluorescence of N,S-CDs through electron or energy transfer due to the interaction between Cu(+) and thiol ligand on the N,S-CDs surface. The observed linear response concentration range was from 0.057 to 4.0μM to AA with a detection limit as low as 18nM. The probe exhibited a highly selective response toward AA even in the presence of possible interfering substances, such as uric acid and citric acid. Moreover, these promising features made the sensing system used for the analysis of human serum and urine samples. PMID:27130124

  20. A peptide nucleic acid-functionalized carbon nitride nanosheet as a probe for in situ monitoring of intracellular microRNA.

    PubMed

    Liao, Xianjiu; Wang, Quanbo; Ju, Huangxian

    2015-06-21

    A novel probe for recognition of both cancer cells and intracellular microRNA (miRNA) is designed by functionalizing a carbon nitride nanosheet (f-CNNS) with a Cy5-labeled peptide nucleic acid (Cy5-PNA) and folate. The interaction between Cy5-PNA and CNNS quenches the fluorescence of Cy5, and the presence of folate endows the probe with good specificity to folate acceptor overexpressed cells. The probe can be specifically taken up by cancer cells with an incubation step. Upon the recognition of the PNA to complementary miRNA, the hybridization product is released from the CNNS surface, which leads to the fluorescence recovery and provides a specific method for sensing of miRNA. Thus, this probe can be used for cell-specific intracellular miRNA sensing with a confocal microscope. Using miRNA-18a as a target model, the dynamic changes of its expression level inside living cells can be monitored with the proposed method. This method possesses promising applications in the study of miRNA related bioprocesses and biomedicine.

  1. Simultaneous brain and blood microdialysis study with a new removable venous probe. Serotonin and 5-hydroxyindolacetic acid changes after D-norfenfluramine or fluoxetine.

    PubMed

    Páez, X; Hernández, L

    1996-01-01

    A removable intravenous microdialysis probe was developed and simultaneously used with a removable microdialysis probe placed in the lateral hypothalamus (LH). Serotonin (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) changes in blood and brain dialysates were measured by HPLC-EC after an i.p. injection of 5 mg/kg d-norfenfluramine (dNF) or 10 mg/kg fluoxetine (FLU) in freely moving rats. 5-HT in the LH significantly increased after both drugs, but the rise was larger and faster with dNF [F(7,28)=4.0 p<0.05] than with FLU [F(5,20)=5.0 p<0.01]. By contrast, in venous blood 5-HT increased after FLU [F(5,20)=2.96 p<0.05] but not after dNF. 5-HIAA after both drugs continued decreasing significantly in the LH [dNF F(7,28)=11.4 p<0.01; FLU F(5,20)=22.8 p<0.01], but it did not change in blood. Simultaneous dialysis in brain and blood allowed evaluation of the differential effects of dNF and FLU on 5-HT and 5-HIAA in the two places. Removable venous probes prevented the inflammatory reaction that may occur around permanently implanted probes, and the dialysis could be more efficient and with less risk of clogging.

  2. A label-free fluorescent probe based on DNA-templated silver nanoclusters and exonuclease III-assisted recycling amplification detection of nucleic acid.

    PubMed

    Yang, Wen; Tian, Jianniao; Ma, Yefei; Wang, Lijun; Zhao, Yanchun; Zhao, Shulin

    2015-11-01

    A number of specific nucleic acids are closely related with many serious diseases, in the current research, a platform taking advantage of exonuclease III (Exo III) to realize double recycling amplification and label-free fluorescent DNA-templated silver nanoclusters (DNA-AgNCs) for detecting of nucleic acid had been developed. In this method, a molecular beacon (MB) with 3'-protruding termini and a single-stranded cytosine-rich (C-rich) probe were designed that coexist stably with Exo III. Once the target DNA appeared, portion of the MB could hybridize with target DNA and was digested by Exo III, which allowed the release of target DNA and a residual sequence. Subsequently, the residual sequence could trigger the Exo III to digest C-rich probe, and the DNA-AgNCs was not able to be synthesized because of the C-rich probe was destroyed; finally the fluorescent of solution was quenched. This assay enables to monitor human hemochromatosis gene (as a model) with high sensitivity, the detection limit is as low as 120 pM compared with other fluorescence DNA-AgNCs methods, this assay also exhibits superior specificity even against single base mismatch. The strategy is applied to detect human hemochromatosis gene in real human serum samples successfully. PMID:26572843

  3. A label-free fluorescent probe based on DNA-templated silver nanoclusters and exonuclease III-assisted recycling amplification detection of nucleic acid.

    PubMed

    Yang, Wen; Tian, Jianniao; Ma, Yefei; Wang, Lijun; Zhao, Yanchun; Zhao, Shulin

    2015-11-01

    A number of specific nucleic acids are closely related with many serious diseases, in the current research, a platform taking advantage of exonuclease III (Exo III) to realize double recycling amplification and label-free fluorescent DNA-templated silver nanoclusters (DNA-AgNCs) for detecting of nucleic acid had been developed. In this method, a molecular beacon (MB) with 3'-protruding termini and a single-stranded cytosine-rich (C-rich) probe were designed that coexist stably with Exo III. Once the target DNA appeared, portion of the MB could hybridize with target DNA and was digested by Exo III, which allowed the release of target DNA and a residual sequence. Subsequently, the residual sequence could trigger the Exo III to digest C-rich probe, and the DNA-AgNCs was not able to be synthesized because of the C-rich probe was destroyed; finally the fluorescent of solution was quenched. This assay enables to monitor human hemochromatosis gene (as a model) with high sensitivity, the detection limit is as low as 120 pM compared with other fluorescence DNA-AgNCs methods, this assay also exhibits superior specificity even against single base mismatch. The strategy is applied to detect human hemochromatosis gene in real human serum samples successfully.

  4. Effects of urea and acetic acid on the heme axial ligation structure of ferric myoglobin at very acidic pH.

    PubMed

    Droghetti, Enrica; Sumithran, Suganya; Sono, Masanori; Antalík, Marián; Fedurco, Milan; Dawson, John H; Smulevich, Giulietta

    2009-09-01

    The heme iron coordination of ferric myoglobin (Mb) in the presence of 9.0M urea and 8.0M acetic acid at acidic pH values has been probed by electronic absorption, magnetic circular dichroism and resonance Raman spectroscopic techniques. Unlike Mb at pH 2.0, where heme is not released from the protein despite the acid denaturation and the loss of the axial ligand, upon increasing the concentration of either urea or acetic acid, a spin state change is observed, and a novel, non-native six-coordinated high-spin species prevails, where heme is released from the protein.

  5. Effects of urea and acetic acid on the heme axial ligation structure of ferric myoglobin at very acidic pH

    PubMed Central

    Droghetti, Enrica; Sumithran, Suganya; Sono, Masanori; Antalík, Marián; Fedurco, Milan; Dawson, John H.; Smulevich, Giulietta

    2009-01-01

    The heme iron coordination of ferric myoglobin (Mb) in the presence of 9.0 M urea and 8.0 M acetic acid at acidic pH values has been probed by electronic absorption, magnetic circular dichroism and resonance Raman spectroscopic techniques. Unlike Mb at pH 2.0, where heme is not released from the protein despite the acid denaturation and the loss of the axial ligand, upon increasing the concentration of either urea or acetic acid, a spin state change is observed, and a novel, non-native six-coordinated high spin species prevails, where heme is released from the protein. PMID:19622342

  6. Assessing the acidity of high silica chabazite H-SSZ-13 by FTIR using CO as molecular probe: Comparison with H-SAPO-34.

    PubMed

    Bordiga, Silvia; Regli, Laura; Cocina, Donato; Lamberti, Carlo; Bjørgen, Morten; Lillerud, Karl Petter

    2005-02-24

    Zeolitic materials based on the chabazite topology, such as H-SAPO-34, possess unique shape-selectivity properties for converting methanol into light olefins. In addition to the topology, zeolite acidity is inherently linked to catalyst activity and selectivity. The acidic properties of high silica chabazite (H-SSZ-13) have attracted much attention in the past decade because the material represents an idealized model system having one acidic site per cage. Conclusions drawn so far have essentially been founded on quantum chemical methods. An experimentally based benchmark of the acidity of H-SSZ-13 has hitherto not been available. In this work, transmission FTIR spectroscopy provides a description of the different acidic sites of H-SSZ-13 by using CO as molecular probe at 70 K. The results demonstrate that H-SSZ-13 is a strongly Brønsted acidic material, essentially having two distinct families of acidic sites. In contrast to numerous preceding reports, we find it fundamental to consider proton distributions among all four possible sites, and do not delimit the interpretations to only two sites. The present data consistently suggest the most abundant family of protons to have three members being located on different crystalline positions on the eight-membered-ring window giving access to the chabazite cage. Consequently, these protons are exposed to two neighboring cages. The second, and less abundant family, is constituted by only one site that is situated on the six-membered ring defining the top/bottom of the barrel-shaped chabazite cage. This proton is therefore only exposed to one cage and requires a higher CO pressure to form adducts. Toward CO, both families of sites possess the same acidity. Parallel experiments were also carried out for the isostructural and commercially important H-SAPO-34 having an equal density of acidic sites. This is the first attempt to directly compare, on an experimental basis, the acidity of these two materials.

  7. Assessing the acidity of high silica chabazite H-SSZ-13 by FTIR using CO as molecular probe: Comparison with H-SAPO-34.

    PubMed

    Bordiga, Silvia; Regli, Laura; Cocina, Donato; Lamberti, Carlo; Bjørgen, Morten; Lillerud, Karl Petter

    2005-02-24

    Zeolitic materials based on the chabazite topology, such as H-SAPO-34, possess unique shape-selectivity properties for converting methanol into light olefins. In addition to the topology, zeolite acidity is inherently linked to catalyst activity and selectivity. The acidic properties of high silica chabazite (H-SSZ-13) have attracted much attention in the past decade because the material represents an idealized model system having one acidic site per cage. Conclusions drawn so far have essentially been founded on quantum chemical methods. An experimentally based benchmark of the acidity of H-SSZ-13 has hitherto not been available. In this work, transmission FTIR spectroscopy provides a description of the different acidic sites of H-SSZ-13 by using CO as molecular probe at 70 K. The results demonstrate that H-SSZ-13 is a strongly Brønsted acidic material, essentially having two distinct families of acidic sites. In contrast to numerous preceding reports, we find it fundamental to consider proton distributions among all four possible sites, and do not delimit the interpretations to only two sites. The present data consistently suggest the most abundant family of protons to have three members being located on different crystalline positions on the eight-membered-ring window giving access to the chabazite cage. Consequently, these protons are exposed to two neighboring cages. The second, and less abundant family, is constituted by only one site that is situated on the six-membered ring defining the top/bottom of the barrel-shaped chabazite cage. This proton is therefore only exposed to one cage and requires a higher CO pressure to form adducts. Toward CO, both families of sites possess the same acidity. Parallel experiments were also carried out for the isostructural and commercially important H-SAPO-34 having an equal density of acidic sites. This is the first attempt to directly compare, on an experimental basis, the acidity of these two materials. PMID:16851287

  8. Effect of solvent on the physical and morphological properties of poly(lactic acid) nanofibers obtained by solution blow spinning

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Solution blow spinning (SBS) is a simple, safe, and inexpensive alternative to electrospinning for making nanofibers from polymer solutions. However, since SBS is a relatively new technique, there is a general lack of information on polymer solutions and properties that affect fiber morphology and i...

  9. Identification of PCR-amplified genetically modified organisms (GMOs) DNA by peptide nucleic acid (PNA) probes in anion-exchange chromatographic analysis.

    PubMed

    Rossi, Stefano; Lesignoli, Francesca; Germini, Andrea; Faccini, Andrea; Sforza, Stefano; Corradini, Roberto; Marchelli, Rosangela

    2007-04-01

    PCR products obtained by selective amplification of transgenic DNA derived from food samples containing Roundup Ready soybean or Bt-176 maize have been analyzed by anion-exchange HPLC. Peptide nucleic acids (PNAs), oligonucleotide analogues known to bind to complementary single-stranded DNA with high affinity and specificity, have been used as specific probes in order to assess the identity of the peaks observed. Two different protocols were adopted in order to obtain single-stranded DNA: amplification with an excess of one primer or digestion of one DNA strand. The single-stranded DNA was mixed with the PNA probe, and the presence of a specific sequence was revealed through detection of the corresponding PNA:DNA peak with significantly different retention time. Advantages and limits of this approach are discussed. The method was tested with reference materials and subsequently applied to commercial samples.

  10. Interactions of /sup 14/N:/sup 15/N stearic acid spin-label pairs: effects of host lipid alkyl chain length and unsaturation

    SciTech Connect

    Feix, J.B.; Yin, J.J.; Hyde, J.S.

    1987-06-30

    Electron-electron double resonance (ELDOR) and saturation recovery electron paramagnetic resonance (EPR) spectroscopy have been employed to examine the interactions of /sup 14/N:/sup 15/N stearic acid spin-label pairs in fluid-phase model membrane bilayers composed of a variety of phospholipids. The (/sup 14/N)-16-doxylstearate:(/sup 15/N)-16-doxylstearate (16:16) pair was utilized to measure lateral diffusion of the spin-labels, while the (/sup 14/N)-16-doxylstearate:(/sup 15/N)-5-doxylstearate (16:5) pair provided information on vertical fluctuations of the 16-doxylstearate nitroxide moiety toward the membrane surface. Three saturated host lipids of varying alkyl chain length (dimyristoylphosphatidylcholine (DMPC), dipalmitoylphosphatidylcholine (DPPC), and distearoylphosphatidylcholine (DSPC)), an ..cap alpha..-saturated, ..beta..-unsaturated lipid (1-palmitoyl-2-oleoylphosphatidylcholine (POPC)), and phosphatidylcholine from a natural source (egg yolk phosphatidylcholine (egg PC)) were utilized as host lipids. Lateral diffusion of the stearic acid spin-labels was only slightly affected by alkyl chain length at a given reduced temperature (T/sub r/) in the saturated host lipids but was significantly decreased in POPC at the same T/sub r/. Lateral diffusion in DMPC, POPC, and egg PC was quite similar at 37/sup 0/C. A strong correlation was noted between lateral diffusion constants and rotational mobility of (/sup 14/N)-16-doxylstearate. Vertical fluctuations were likewise only slightly influenced by alklyl chain length but were strongly diminished in POPC and egg PC relative to the saturated systems. This diminution of the 16:5 interaction was observed even under conditions where no differences were discernible by conventional EPR.

  11. Cellular delivery of quantum dot-bound hybridization probe for detection of intracellular pre-microRNA using chitosan/poly(γ-glutamic acid) complex as a carrier.

    PubMed

    Geng, Yao; Lin, Dajie; Shao, Lijia; Yan, Feng; Ju, Huangxian

    2013-01-01

    A quantum dot (QD)-bound hybridization probe was designed for detection of intracellular pre-miRNA using chitosan (CS)/poly(γ-glutamic acid) (γ-PGA) complex as a gene vector. The probe was prepared by assembling thiolated RNA to gold nanoparticle (Au NP) via Au-S bond and then binding 3'-end amine of the RNA to the carboxy group capped on quantum dot surface. The QD-RNA-Au NP probe was assembled on the vector by mixing with aqueous γ-PGA solution and then CS solution to construct a gene delivery system for highly effective cellular uptake and delivery. After the probe was released from CS/γ-PGA complex to the cytoplasm by electrostatic repulsion at intracellular pH, it hybridized with pre-miRNA precursor as target. The formed product was then cleaved by RNase III Dicer, leading to the separation of QDs from Au NPs and fluorescence emission of QDs, which could be detected by confocal microscopic imaging to monitor the amount of the intracellular pre-miRNA precursor. The in vitro assays revealed that the QD-RNA-Au NP was a robust, sensitive and selective probe for quantitative detection of target pre-miRNA. Using MDA-MB231 and MCF-7 breast cancer cells as models, the relative amount of pre-miRNA let-7a could be successfully compared. Since the amount of miRNA is related to the progress and prognosis of cancer, this strategy could be expected to hold promising application potential in medical research and clinical diagnostics.

  12. A naphthalene-based two-photon fluorescent probe for selective and sensitive detection of endogenous hypochlorous acid.

    PubMed

    Zhou, Xiao-Hong; Jiang, Yu-Ren; Zhao, Xiong-Jie; Guo, Dong

    2016-11-01

    An efficient naphthalene-based two-photon fluorescent probe for endogenous HClO has been reported in the present study, which consists of a 6-(2-benzothiazolyl)-2-naphthalenol fluorophore connected with a 4-aminophenol (the fluorescence quenching and response group). This probe exhibits a high selectivity and excellent sensitivity with a detection limit of 7.6nM over other reactive oxygen species and analyte species, and the fluorescence intensity enhanced 103-fold when responsed. Furthermore, it was successfully used for two-photon imaging of endogenous HClO in live cells with high-resolution. PMID:27591640

  13. A naphthalene-based two-photon fluorescent probe for selective and sensitive detection of endogenous hypochlorous acid.

    PubMed

    Zhou, Xiao-Hong; Jiang, Yu-Ren; Zhao, Xiong-Jie; Guo, Dong

    2016-11-01

    An efficient naphthalene-based two-photon fluorescent probe for endogenous HClO has been reported in the present study, which consists of a 6-(2-benzothiazolyl)-2-naphthalenol fluorophore connected with a 4-aminophenol (the fluorescence quenching and response group). This probe exhibits a high selectivity and excellent sensitivity with a detection limit of 7.6nM over other reactive oxygen species and analyte species, and the fluorescence intensity enhanced 103-fold when responsed. Furthermore, it was successfully used for two-photon imaging of endogenous HClO in live cells with high-resolution.

  14. Probing Structural Dynamics and Topology of the KCNE1 Membrane Protein in Lipid Bilayers via Site-Directed Spin Labeling and Electron Paramagnetic Resonance Spectroscopy.

    PubMed

    Sahu, Indra D; Craig, Andrew F; Dunagan, Megan M; Troxel, Kaylee R; Zhang, Rongfu; Meiberg, Andrew G; Harmon, Corrinne N; McCarrick, Robert M; Kroncke, Brett M; Sanders, Charles R; Lorigan, Gary A

    2015-10-20

    KCNE1 is a single transmembrane protein that modulates the function of voltage-gated potassium channels, including KCNQ1. Hereditary mutations in the genes encoding either protein can result in diseases such as congenital deafness, long QT syndrome, ventricular tachyarrhythmia, syncope, and sudden cardiac death. Despite the biological significance of KCNE1, the structure and dynamic properties of its physiologically relevant native membrane-bound state are not fully understood. In this study, the structural dynamics and topology of KCNE1 in bilayered lipid vesicles was investigated using site-directed spin labeling (SDSL) and electron paramagnetic resonance (EPR) spectroscopy. A 53-residue nitroxide EPR scan of the KCNE1 protein sequence including all 27 residues of the transmembrane domain (45-71) and 26 residues of the N- and C-termini of KCNE1 in lipid bilayered vesicles was analyzed in terms of nitroxide side-chain motion. Continuous wave-EPR spectral line shape analysis indicated the nitroxide spin label side-chains located in the KCNE1 TMD are less mobile when compared to the extracellular region of KCNE1. The EPR data also revealed that the C-terminus of KCNE1 is more mobile when compared to the N-terminus. EPR power saturation experiments were performed on 41 sites including 18 residues previously proposed to reside in the transmembrane domain (TMD) and 23 residues of the N- and C-termini to determine the topology of KCNE1 with respect to the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG) lipid bilayers. The results indicated that the transmembrane domain is indeed buried within the membrane, spanning the width of the lipid bilayer. Power saturation data also revealed that the extracellular region of KCNE1 is solvent-exposed with some of the portions partially or weakly interacting with the membrane surface. These results are consistent with the previously published solution NMR

  15. Sensitivity enhanced (14)N/(14)N correlations to probe inter-beta-sheet interactions using fast magic angle spinning solid-state NMR in biological solids.

    PubMed

    Pandey, Manoj Kumar; Amoureux, Jean-Paul; Asakura, Tetsuo; Nishiyama, Yusuke

    2016-08-10

    (14)N/(14)N correlations are vital for structural studies of solid samples, especially those in which (15)N isotopic enrichment is challenging, time-consuming and expensive. Although (14)N nuclei have high isotopic abundance (99.6%), there are inherent difficulties in observing (14)N/(14)N correlations due to limited resolution and sensitivity related to: (i) low (14)N gyromagnetic ratio (γ), (ii) large (14)N quadrupolar couplings, (iii) integer (14)N spin quantum number (I = 1), and (iv) very weak (14)N-(14)N dipolar couplings. Previously, we demonstrated a proton-detected 3D (14)N/(14)N/(1)H correlation experiment at fast magic angle spinning (MAS) on l-histidine·HCl·H2O utilizing a through-bond (J) and residual dipolar-splitting (RDS) based heteronuclear multiple quantum correlation (J-HMQC) sequence mediated through (1)H/(1)H radio-frequency driven recoupling (RFDR). As an extension of our previous work, in this study we show the utility of dipolar-based HMQC (D-HMQC) in combination with (1)H/(1)H RFDR mixing to obtain sensitivity enhanced (14)N/(14)N correlations in more complex biological solids such as a glycyl-l-alanine (Gly-l-Ala) dipeptide, and parallel (P) and antiparallel (AP) β-strand alanine tripeptides (P-(Ala)3 and AP-(Ala)3, respectively). These systems highlight the mandatory necessity of 3D (14)N/(14)N/(1)H measurements to get (14)N/(14)N correlations when the amide proton resonances are overlapped. Moreover, the application of long selective (14)N pulses, instead of short hard ones, is shown to improve the sensitivity. Globally, we demonstrate that replacing J-scalar with dipolar interaction and hard- with selective-(14)N pulses allows gaining a factor of ca. 360 in experimental time. On the basis of intermolecular NH/NH distances and (14)N quadrupolar tensor orientations, (14)N/(14)N correlations are effectively utilized to make a clear distinction between the parallel and antiparallel arrangements of the β-strands in (Ala)3 through the

  16. Sensitivity enhanced (14)N/(14)N correlations to probe inter-beta-sheet interactions using fast magic angle spinning solid-state NMR in biological solids.

    PubMed

    Pandey, Manoj Kumar; Amoureux, Jean-Paul; Asakura, Tetsuo; Nishiyama, Yusuke

    2016-08-10

    (14)N/(14)N correlations are vital for structural studies of solid samples, especially those in which (15)N isotopic enrichment is challenging, time-consuming and expensive. Although (14)N nuclei have high isotopic abundance (99.6%), there are inherent difficulties in observing (14)N/(14)N correlations due to limited resolution and sensitivity related to: (i) low (14)N gyromagnetic ratio (γ), (ii) large (14)N quadrupolar couplings, (iii) integer (14)N spin quantum number (I = 1), and (iv) very weak (14)N-(14)N dipolar couplings. Previously, we demonstrated a proton-detected 3D (14)N/(14)N/(1)H correlation experiment at fast magic angle spinning (MAS) on l-histidine·HCl·H2O utilizing a through-bond (J) and residual dipolar-splitting (RDS) based heteronuclear multiple quantum correlation (J-HMQC) sequence mediated through (1)H/(1)H radio-frequency driven recoupling (RFDR). As an extension of our previous work, in this study we show the utility of dipolar-based HMQC (D-HMQC) in combination with (1)H/(1)H RFDR mixing to obtain sensitivity enhanced (14)N/(14)N correlations in more complex biological solids such as a glycyl-l-alanine (Gly-l-Ala) dipeptide, and parallel (P) and antiparallel (AP) β-strand alanine tripeptides (P-(Ala)3 and AP-(Ala)3, respectively). These systems highlight the mandatory necessity of 3D (14)N/(14)N/(1)H measurements to get (14)N/(14)N correlations when the amide proton resonances are overlapped. Moreover, the application of long selective (14)N pulses, instead of short hard ones, is shown to improve the sensitivity. Globally, we demonstrate that replacing J-scalar with dipolar interaction and hard- with selective-(14)N pulses allows gaining a factor of ca. 360 in experimental time. On the basis of intermolecular NH/NH distances and (14)N quadrupolar tensor orientations, (14)N/(14)N correlations are effectively utilized to make a clear distinction between the parallel and antiparallel arrangements of the β-strands in (Ala)3 through the

  17. Long-range Li+ dynamics in the lithium argyrodite Li7PSe6 as probed by rotating-frame spin-lattice relaxation NMR.

    PubMed

    Epp, V; Gün, O; Deiseroth, H-J; Wilkening, M

    2013-05-21

    Lithium-rich argyrodites belong to a relatively new group of fast ion conducting solids. They might serve as powerful electrolytes in all-solid-state lithium-ion batteries being, from a medium-term point of view, the key technology when safe energy storage systems have to be developed. Spin-lattice relaxation (SLR) nuclear magnetic resonance (NMR) measurements carried out in the rotating frame of reference turned out to be the method of choice to study Li dynamics in argyrodites. When plotted as a function of the inverse temperature, the SLR rates log10(R1ρ) reveal an asymmetric diffusion-induced rate peak. The rate peak contains information on the Li jump rate, the activation energy of the hopping process as well as correlation effects. In particular, considering the high-temperature flank of the SLR NMR rate peak recorded in the rotating frame of reference, an activation energy of approximately 0.49 eV is found. This value represents long-range lithium jump diffusion in crystalline Li7PSe6. As an example, at 325 K the Li jump rate determined from SLR NMR is in the order of 1.4 × 10(5) s(-1). The pronounced asymmetry of the rate peak R1ρ(1/T) points to correlated Li motion. It is comparable to that which is typically found for structurally disordered materials showing a broad range of correlation times.

  18. Oxidation and aging in U and Pu probed by spin-orbit sum rule analysis: indications for covalent metal-oxide bonds

    SciTech Connect

    Moore, K; der Laan, G v; Haire, R; Wall, M; Schwartz, A

    2005-10-07

    Transmission electron microscopy is used to acquire electron energy-loss spectra from phase-specific regions of Pu and U metal, PuO{sub 2} and UO{sub 2}, and aged, self-irradiated Pu metal. The N{sub 4,5} (4d {yields} 5f) spectra are analyzed using the spin-orbit sum rule. Our results show that the technique is sensitive enough to detect changes in the branching ratio of the white-line peaks between the metal and dioxide of both U and Pu. There is a small change in the branching ratio between different Pu metals, and the data trends as would be expected for varying f electron localization, i.e., {alpha}-Pu, {delta}-Pu, aged {delta}-Pu. Moreover, our results suggest that the metal-oxide bonds in UO{sub 2} and PuO{sub 2} are strongly covalent in nature and do not exhibit an integer valence change as would be expected from purely ionic bonding.

  19. The reduced [2Fe-2S] clusters in adrenodoxin and Arthrospira platensis ferredoxin share spin density with protein nitrogens, probed using 2D ESEEM†

    PubMed Central

    Dikanov, Sergei A.; Samoilova, Rimma I.; Kappl, Reinhard; Crofts, Antony R.; Hüttermann, Jürgen

    2009-01-01

    Summary We have used X-band ESEEM to study the reduced [2Fe-2S] cluster in adrenodoxin and Arthrospira platensis ferredoxin. By use of a 2D approach (HYSCORE), we have shown that the cluster is involved in weak magnetic interactions with several nitrogens in each protein. Despite substantial difference in the shape and orientational dependence of individual crosspeaks, the major spectral features in both proteins are attributable to two peptide nitrogens (N1 and N2) with similar hyperfine couplings ∼1.1 and ∼0.70 MHz. The couplings determined represent to a small fraction (0.0003–0.0005) of the unpaired spin density of the reduced cluster transferred to these nitrogens over H-bond bridges or the covalent bonds of cysteine ligands. Simulation of the HYSCORE spectra has allowed us to estimate the orientation of the nuclear quadrupole tensors of N1 and N2 in the g-tensor coordinate system. The most likely candidates for the role of N1 and N2 have been identified in the protein environment by comparing magnetic-resonance data with crystallographic structures of the oxidized proteins. A possible influence of redox-linked structural changes on ESEEM data is analyzed using available structures for related proteins in two redox states. PMID:19639155

  20. Spin-labeled polyribonucleotides.

    PubMed Central

    Petrov, A I; Sukhorukov, B I

    1980-01-01

    Poly (U), poly (C) and poly (A) were spin labeled with N-(2,2,5,5-tetramethyl-3-carbonylpyrroline-1-oxyl)-imidazole. This spin label interacts selectively with 2' OH ribose groups of polynucleotides and does not modify the nucleic acid bases. The extent of spin labeling is not dependent upon the nature of the base and is entirely determined by rigidity of the secondary structure of the polynucleotide. The extent of modification for poly (U), poly (C) and poly (A) was 4.2, 1.7 and 1.5 per cent, respectively, the secondary structure of the polynucleotides being practically unchanged. Some physico-chemical properties of the spin-labeled polynucleotides were investigated by ESR spectroscopy. Rotational correlation times of the spin label and activation energy of its motion were calculated. PMID:6253911

  1. Sensing of a nucleic acid binding protein via a label-free perylene probe fluorescence recovery assay.

    PubMed

    Liao, Dongli; Li, Wenying; Chen, Jian; Jiao, Huping; Zhou, Huipeng; Wang, Bin; Yu, Cong

    2013-10-01

    A novel label-free fluorescence recovery assay for the sensing of a DNA binding protein has been developed. A transcription factor c-Jun protein, and a 21 base pair duplex DNA containing the c-Jun protein binding site (J-DNA) were selected. J-DNA was mixed with a cationic fluorescent perylene probe (compound 1), and induced aggregation of the probe. Quenching of the probe's fluorescence was observed. However, when c-Jun protein was mixed with the J-DNA, c-Jun bound to the duplex DNA, which reduced the degree of the induced perylene probe aggregation, and a turn on fluorescence signal was observed. The recovered fluorescence intensity was directly related to the amount of c-Jun added. The method is highly selective, six non-DNA binding proteins and one randomly selected 21 base pair duplex DNA (con-1) were tested. No noticeable compound 1 fluorescence recovery was observed. Mutations were also introduced to the c-Jun recognition sequence and much reduced fluorescence recovery was observed. Our assay is label-free, convenient, inexpensive, and fast. It can be used in biomedical research such as high throughput screening of drugs targeted at DNA-binding proteins.

  2. Observation of an organic acid mediated spin state transition in a Co(II)-Schiff base complex: an EPR, HYSCORE, and DFT study.

    PubMed

    Vinck, Evi; Carter, Emma; Murphy, Damien M; Van Doorslaer, Sabine

    2012-08-01

    The interactions of a weak organic acid (acetic acid, HOAc) with a toluene solution of the Co(II)-Schiff base type complex, (R,R')-N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexane-diamino Co(II) (labeled [Co(1)]), was investigated using EPR, HYSCORE, and DFT computations. This activated [Co(II)(1)] system is extremely important within the context of asymmetric catalysts (notably the hydrolytic kinetic resolution of epoxides) despite the lack of detailed structural information about the nature of the paramagnetic species present. Under anaerobic conditions, the LS [Co(II)(1)] complex with a |yz, (2)A(2)〉 ground state is converted into a low-spin (LS) and a high-spin (HS) complex in the presence of the acid. The newly formed LS state is assigned to the coordinated [Co(II)(1)]-(HOAc) complex, possessing a |z(2), (2)A(1)〉 ground state (species A; g(x) = 2.42, g(y) = 2.28, g(z) = 2.02, A(x) = 100, A(y) = 120, A(z) = 310 MHz). The newly formed HS state is assigned to an acetate coordinated [Co(II)(1)]-(OAc(-)) complex, possessing an S = 3/2 spin ground state (species B, responsible for a broad EPR signal with g ≈ 4.6). These spin ground states were confirmed with DFT calculations using the hybrid BP86 and B3LYP functionals. Under aerobic conditions, the LS and HS complexes (species A and B) are not observed; instead, a new HS complex (species C) is formed. This complex is tentatively assigned to a paramagnetic superoxo bridged dimer (AcO(-))[Co(II)(1)···O(2)(-)Co(III)(1)](HOAc), as distinct from the more common diamagnetic peroxo bridged dimers. Species C is characterized by a very broad HS EPR signal (g(x) = 5.1, g(y) = 3.9, g(z) = 2.1) and is reversibly formed by oxygenation of the LS [Co(II)(1)]-(HOAc) complex to the superoxo complex [Co(III)(1)O(2)(-)](HOAc), which subsequently forms the association complex C by interaction with the HS [Co(II)(1)](OAc(-)) species. The LS and HS complexes were also identified using other organic acids (benzoic and

  3. Observation of an organic acid mediated spin state transition in a Co(II)-Schiff base complex: an EPR, HYSCORE, and DFT study.

    PubMed

    Vinck, Evi; Carter, Emma; Murphy, Damien M; Van Doorslaer, Sabine

    2012-08-01

    The interactions of a weak organic acid (acetic acid, HOAc) with a toluene solution of the Co(II)-Schiff base type complex, (R,R')-N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexane-diamino Co(II) (labeled [Co(1)]), was investigated using EPR, HYSCORE, and DFT computations. This activated [Co(II)(1)] system is extremely important within the context of asymmetric catalysts (notably the hydrolytic kinetic resolution of epoxides) despite the lack of detailed structural information about the nature of the paramagnetic species present. Under anaerobic conditions, the LS [Co(II)(1)] complex with a |yz, (2)A(2)〉 ground state is converted into a low-spin (LS) and a high-spin (HS) complex in the presence of the acid. The newly formed LS state is assigned to the coordinated [Co(II)(1)]-(HOAc) complex, possessing a |z(2), (2)A(1)〉 ground state (species A; g(x) = 2.42, g(y) = 2.28, g(z) = 2.02, A(x) = 100, A(y) = 120, A(z) = 310 MHz). The newly formed HS state is assigned to an acetate coordinated [Co(II)(1)]-(OAc(-)) complex, possessing an S = 3/2 spin ground state (species B, responsible for a broad EPR signal with g ≈ 4.6). These spin ground states were confirmed with DFT calculations using the hybrid BP86 and B3LYP functionals. Under aerobic conditions, the LS and HS complexes (species A and B) are not observed; instead, a new HS complex (species C) is formed. This complex is tentatively assigned to a paramagnetic superoxo bridged dimer (AcO(-))[Co(II)(1)···O(2)(-)Co(III)(1)](HOAc), as distinct from the more common diamagnetic peroxo bridged dimers. Species C is characterized by a very broad HS EPR signal (g(x) = 5.1, g(y) = 3.9, g(z) = 2.1) and is reversibly formed by oxygenation of the LS [Co(II)(1)]-(HOAc) complex to the superoxo complex [Co(III)(1)O(2)(-)](HOAc), which subsequently forms the association complex C by interaction with the HS [Co(II)(1)](OAc(-)) species. The LS and HS complexes were also identified using other organic acids (benzoic and

  4. Sensitive, Efficient Quantitation of 13C-Enriched Nucleic Acids via Ultrahigh-Performance Liquid Chromatography–Tandem Mass Spectrometry for Applications in Stable Isotope Probing

    PubMed Central

    Wilhelm, Roland; Szeitz, András; Klassen, Tara L.

    2014-01-01

    Stable isotope probing (SIP) of nucleic acids is a powerful tool for studying the functional traits of microbial populations within complex communities, but SIP involves a number of technical challenges. Many of the difficulties in DNA-SIP and RNA-SIP experiments can be effectively overcome with an efficient, sensitive method for quantitating the isotopic enrichment of nucleic acids. Here, we present a sensitive method for quantitating 13C enrichment of nucleic acids, requiring a few nanograms of sample, and we demonstrate its utility in typical DNA-SIP and RNA-SIP experiments. All five nucleobases (adenine, guanine, cytosine, thymine, and uracil) were separated and detected by using ultrahigh-performance liquid chromatography–tandem mass spectrometry. We detected all isotopic species in samples with as low as 1.5 atom% 13C above natural abundance, using 1-ng loadings. Quantitation was used to characterize the isotopic enrichment kinetics of cellulose- and lignin-based microcosm experiments and to optimize the recovery of enriched nucleic acids. Application of our method will minimize the quantity of expensive isotopically labeled substrates required and reduce the risk of failed experiments due to insufficient recovery of labeled nucleic acids for sequencing library preparation. PMID:25217022

  5. Sensitive, Efficient Quantitation of 13C-Enriched Nucleic Acids via Ultrahigh-Performance Liquid Chromatography-Tandem Mass Spectrometry for Applications in Stable Isotope Probing.

    PubMed

    Wilhelm, Roland; Szeitz, András; Klassen, Tara L; Mohn, William W

    2014-12-01

    Stable isotope probing (SIP) of nucleic acids is a powerful tool for studying the functional traits of microbial populations within complex communities, but SIP involves a number of technical challenges. Many of the difficulties in DNA-SIP and RNA-SIP experiments can be effectively overcome with an efficient, sensitive method for quantitating the isotopic enrichment of nucleic acids. Here, we present a sensitive method for quantitating (13)C enrichment of nucleic acids, requiring a few nanograms of sample, and we demonstrate its utility in typical DNA-SIP and RNA-SIP experiments. All five nucleobases (adenine, guanine, cytosine, thymine, and uracil) were separated and detected by using ultrahigh-performance liquid chromatography-tandem mass spectrometry. We detected all isotopic species in samples with as low as 1.5 atom% (13)C above natural abundance, using 1-ng loadings. Quantitation was used to characterize the isotopic enrichment kinetics of cellulose- and lignin-based microcosm experiments and to optimize the recovery of enriched nucleic acids. Application of our method will minimize the quantity of expensive isotopically labeled substrates required and reduce the risk of failed experiments due to insufficient recovery of labeled nucleic acids for sequencing library preparation.

  6. Geometrical spin symmetry and spin

    SciTech Connect

    Pestov, I. B.

    2011-07-15

    Unification of General Theory of Relativity and Quantum Mechanics leads to General Quantum Mechanics which includes into itself spindynamics as a theory of spin phenomena. The key concepts of spindynamics are geometrical spin symmetry and the spin field (space of defining representation of spin symmetry). The essence of spin is the bipolar structure of geometrical spin symmetry induced by the gravitational potential. The bipolar structure provides a natural derivation of the equations of spindynamics. Spindynamics involves all phenomena connected with spin and provides new understanding of the strong interaction.

  7. Detection of hydrofluoric acid by a SiO2 sol-gel coating fiber-optic probe based on reflection-based localized surface plasmon resonance.

    PubMed

    Chen, I-Cherng; Lin, Shiu-Shiung; Lin, Tsao-Jen; Du, Je-Kang

    2011-01-01

    A novel fiber-optic probe based on reflection-based localized surface plasmon resonance (LSPR) was developed to quantify the concentration of hydrofluoric acid (HF) in aqueous solutions. The LSPR sensor was constructed with a gold nanoparticle-modified PMMA fiber, integrated with a SiO(2) sol-gel coating. This fiber-sensor was utilized to assess the relationship between HF concentration and SiO(2) sol-gel layer etching reduction. The results demonstrated the LSPR sensor was capable of detecting HF-related erosion of hydrofluoric acid solutions of concentrations ranging from 1% to 5% using Relative RI Change Rates. The development of the LSPR sensor constitutes the basis of a detector with significant sensitivity for practical use in monitoring HF solution concentrations.

  8. Detection of Hydrofluoric Acid by a SiO2 Sol-Gel Coating Fiber-Optic Probe Based on Reflection-Based Localized Surface Plasmon Resonance

    PubMed Central

    Chen, I-Cherng; Lin, Shiu-Shiung; Lin, Tsao-Jen; Du, Je-Kang

    2011-01-01

    A novel fiber-optic probe based on reflection-based localized surface plasmon resonance (LSPR) was developed to quantify the concentration of hydrofluoric acid (HF) in aqueous solutions. The LSPR sensor was constructed with a gold nanoparticle-modified PMMA fiber, integrated with a SiO2 sol-gel coating. This fiber-sensor was utilized to assess the relationship between HF concentration and SiO2 sol-gel layer etching reduction. The results demonstrated the LSPR sensor was capable of detecting HF-related erosion of hydrofluoric acid solutions of concentrations ranging from 1% to 5% using Relative RI Change Rates. The development of the LSPR sensor constitutes the basis of a detector with significant sensitivity for practical use in monitoring HF solution concentrations. PMID:22319388

  9. Assay of the human liver citric acid cycle probe phenylacetylglutamine and of phenylacetate in plasma by gas chromatography-mass spectrometry.

    PubMed

    Yang, D; Beylot, M; Agarwal, K C; Soloviev, M V; Brunengraber, H

    1993-07-01

    Phenylacetate, derived from phenylalanine, is converted in human and primate liver to phenylacetylglutamine. The latter has been used to assess the labeling pattern of liver citric acid cycle intermediates. We present gas chromatographic-mass spectrometric assays of phenylacetylglutamine, phenylacetate, and phenylalanine in biological fluids. The compounds are derivatized with dimethylformamide dimethyl acetal. Limits of detection are 0.1 nmol for phenylacetylglutamine and phenylacetate and 2 nmol for phenylalanine. Baseline plasma concentrations of phenylacetate and phenylacetylglutamine and 1 and 3 microM, respectively. The 24-h urinary excretions of phenylacetate and phenylacetylglutamine are about 4 mumol and 1 mmol, respectively. Ingestion of phenylalanine (in the form of aspartame) by a human is followed by sequential increases in phenylacetate and phenylacetylglutamine concentrations in plasma and urine. This assay opens the way to noninvasive probing of the 13C-labeling pattern of liver citric acid cycle intermediates in humans.

  10. Isolation of a human anti-haemophilic factor IX cDNA clone using a unique 52-base synthetic oligonucleotide probe deduced from the amino acid sequence of bovine factor IX.

    PubMed

    Jaye, M; de la Salle, H; Schamber, F; Balland, A; Kohli, V; Findeli, A; Tolstoshev, P; Lecocq, J P

    1983-04-25

    A unique 52mer oligonucleotide deduced from the amino acid sequence of bovine Factor IX was synthesized and used as a probe to screen a human liver cDNA bank. The Factor IX clone isolated shows 5 differences in nucleotide and deduced amino acid sequence as compared to a previously isolated clone. In addition, precisely one codon has been deleted.Images

  11. Enhanced Atomic-Scale Spin Contrast due to Spin Friction

    NASA Astrophysics Data System (ADS)

    Ouazi, S.; Kubetzka, A.; von Bergmann, K.; Wiesendanger, R.

    2014-02-01

    Atom manipulation with the magnetic tip of a scanning tunneling microscope is a versatile technique to construct and investigate well-defined atomic spin arrangements. Here we explore the possibility of using a magnetic adatom as a local probe to image surface spin textures. As a model system we choose a Néel state with 120° between neighboring magnetic moments. Close to the threshold of manipulation, the adatom resides in the threefold, magnetically frustrated hollow sites, and consequently no magnetic signal is detected in manipulation images. At smaller tip-adatom distances, however, the adatom is moved towards the magnetically active bridge sites and due to the exchange force of the tip the manipulation process becomes spin dependent. In this way the adatom can be used as an amplifying probe for the surface spin texture.

  12. Spin noise in the anisotropic central spin model

    NASA Astrophysics Data System (ADS)

    Hackmann, Johannes; Anders, Frithjof B.

    2014-01-01

    Spin-noise measurements can serve as a direct probe for the microscopic decoherence mechanism of an electronic spin in semiconductor quantum dots (QDs). We have calculated the spin-noise spectrum in the anisotropic central spin model using a Chebyshev expansion technique which exactly accounts for the dynamics up to an arbitrary long but fixed time in a finite-size system. In the isotropic case, describing QD charge with a single electron, the short-time dynamics is in good agreement with quasistatic approximations for the thermodynamic limit. The spin-noise spectrum, however, shows strong deviations at low frequencies with a power-law behavior of ω-3/4 corresponding to a t-1/4 decay at intermediate and long times. In the Ising limit, applicable to QDs with heavy-hole spins, the spin-noise spectrum exhibits a threshold behavior of (ω-ωL)-1/2 above the Larmor frequency ωL=gμBB. In the generic anisotropic central spin model we have found a crossover from a Gaussian type of spin-noise spectrum to a more Ising-type spectrum with increasing anisotropy in a finite magnetic field. In order to make contact with experiments, we present ensemble averaged spin-noise spectra for QD ensembles charged with single electrons or holes. The Gaussian-type noise spectrum evolves to a more Lorentzian shape spectrum with increasing spread of characteristic time scales and g factors of the individual QDs.

  13. Analysis of cytochrome P450 metabolites of arachidonic acid by stable isotope probe labeling coupled with ultra high-performance liquid chromatography/mass spectrometry.

    PubMed

    Zhu, Quan-Fei; Hao, Yan-Hong; Liu, Ming-Zhou; Yue, Jiang; Ni, Jian; Yuan, Bi-Feng; Feng, Yu-Qi

    2015-09-01

    Cytochrome P450 metabolites of arachidonic acid (AA) belong to eicosanoids and are potent lipid mediators of inflammation. It is well-known that eicosanoids play an important role in numerous pathophysiological processes. Therefore, quantitative analysis of cytochrome P450 metabolites of AA, including hydroxyeicosatetraenoic acids (HETEs), epoxyeicosatreinoic acids (EETs), and dihydroxyeicosatrienoic acids (DHETs) can provide crucial information to uncover underlying mechanisms of cytochrome P450 metabolites of AA related diseases. Herein, we developed a highly sensitive method to identify and quantify HETEs, EETs, and DHETs in lipid extracts of biological samples based on stable isotope probe labeling coupled with ultra high-performance liquid chromatography/mass spectrometry. To this end, a pair of stable isotope probes, 2-dimethylaminoethylamine (DMED) and d4-2-dimethylaminoethylamine (d4-DMED), were utilized to facilely label eicosanoids. The heavy labeled eicosanoid standards were prepared and used as internal standards for quantification to minimize the matrix and ion suppression effects in mass spectrometry analysis. In addition, the detection sensitivities of DMED labeled eicosanoids improved by 3-104 folds in standard solution and 5-138 folds in serum matrix compared with unlabeled analytes. Moreover, a good separation of eicosanoids isomers was achieved upon DMED labeling. The established method provided substantial sensitivity (limit of quantification at sub-picogram), high specificity, and broad linear dynamics range (3 orders of magnitude). We further quantified cytochrome P450 metabolites of AA in rat liver, heart, brain tissues and human serum using the developed method. The results showed that 19 eicosanoids could be distinctly detected and the contents of 11-, 15-, 16-, 20-HETE, 5,6-EET, and 14,15-EET in type 2 diabetes mellitus patients and 5-, 11-, 12-, 15-, 16-, 20-HETE, 8,9-EET, and 5,6-DHET in myeloid leukemia patients had significant changes

  14. Current-induced spin-wave Doppler shift.

    PubMed

    Vlaminck, Vincent; Bailleul, Matthieu

    2008-10-17

    Spin transfer appears to be a promising tool for improving spintronics devices. Experiments that quantitatively access the magnitude of the spin transfer are required for a fundamental understanding of this phenomenon. By inductively measuring spin waves propagating along a permalloy strip subjected to a large electrical current, we observed a current-induced spin wave Doppler shift that we relate to the adiabatic spin transfer torque. Because spin waves provide a well-defined system for performing spin transfer, we anticipate that they could be used as an accurate probe of spin-polarized transport in various itinerant ferromagnets. PMID:18927387

  15. Incorporation of extra amino acids in peptide recognition probe to improve specificity and selectivity of an electrochemical peptide-based sensor.

    PubMed

    Zaitouna, Anita J; Maben, Alex J; Lai, Rebecca Y

    2015-07-30

    We investigated the effect of incorporating extra amino acids (AA) at the n-terminus of the thiolated and methylene blue-modified peptide probe on both specificity and selectivity of an electrochemical peptide-based (E-PB) HIV sensor. The addition of a flexible (SG)3 hexapeptide is, in particular, useful in improving sensor selectivity, whereas the addition of a highly hydrophilic (EK)3 hexapeptide has shown to be effective in enhancing sensor specificity. Overall, both E-PB sensors fabricated using peptide probes with the added AA (SG-EAA and EK-EAA) showed better specificity and selectivity, especially when compared to the sensor fabricated using a peptide probe without the extra AA (EAA). For example, the selectivity factor recorded in the 50% saliva was ∼2.5 for the EAA sensor, whereas the selectivity factor was 7.8 for both the SG-EAA and EK-EAA sensors. Other sensor properties such as the limit of detection and dynamic range were minimally affected by the addition of the six AA sequence. The limit of detection was 0.5 nM for the EAA sensor and 1 nM for both SG-EAA and EK-EAA sensors. The saturation target concentration was ∼200 nM for all three sensors. Unlike previously reported E-PB HIV sensors, the peptide probe functions as both the recognition element and antifouling passivating agent; this modification eliminates the need to include an additional antifouling diluent, which simplifies the sensor design and fabrication protocol.

  16. Optical manipulation of a multilevel nuclear spin in ZnO: Master equation and experiment

    NASA Astrophysics Data System (ADS)

    Buß, J. H.; Rudolph, J.; Wassner, T. A.; Eickhoff, M.; Hägele, D.

    2016-04-01

    We demonstrate the dynamics and optical control of a large quantum mechanical solid state spin system consisting of a donor electron spin strongly coupled to the 9/2 nuclear spin of 115In in the semiconductor ZnO. Comparison of electron spin dynamics observed by time-resolved pump-probe spectroscopy with density matrix theory reveals nuclear spin pumping via optically oriented electron spins, coherent spin-spin interaction, and quantization effects of the ten nuclear spin levels. Modulation of the optical electron spin orientation at frequencies above 1 MHz gives evidence for fast optical manipulation of the nuclear spin state.

  17. Fluorescence sensing of phosdrin pesticide by the luminescent Eu(III)- and Tb(III)-bis(coumarin-3-carboxylic acid) probes

    NASA Astrophysics Data System (ADS)

    Hussein, Belal H. M.; Khairy, Gasser M.; Kamel, Rasha M.

    2016-04-01

    Luminescence quenching of the Eu(III)- and Tb(III)-bis (coumarin-3-carboxylic acid) (Ln(III)-(CCA)2) probes has been studied in the presence of organophosphorus or organochlorine pesticides; Phosdrin (P1), Malathion (P2), Profenofos (P3), Formothion (P4), Heptachlor (P5), and Endosulfan (P6). The luminescence intensity of lanthanide complex probes Ln(III)-(CCA)2 decreases as the concentration of the Phosdrin pesticide increases, while the other investigated pesticides have no significant influence on the lanthanide fluorescent intensities. It is observed that the quenching of Eu(III) and Tb(III)-coumarin-3-carboxylic acid by Phosdrin proceeds via static quenching processes according to Stern-Volmer plot. The binding constants (K) and the thermodynamic parameters of the interaction of Ln(III)-(CCA)2 with Phosdrin have been determined. A direct method for the determination of the Phosdrin in ethanol has been developed based on the luminescence changes of the Ln(III)-(CCA)2-phosdrin ternary complexes. The detection limits of P1 were 6.28 and 1.07 μM in case of Eu(III) and Tb(III)-complex, respectively. The influence of various interfering species on the detection of P1 has been investigated to assess the analytical applicability of the method. The new method was applied to determine the Phosdrin pesticide in different types of water samples.

  18. Fluorescence sensing of phosdrin pesticide by the luminescent Eu(III)- and Tb(III)-bis(coumarin-3-carboxylic acid) probes.

    PubMed

    Hussein, Belal H M; Khairy, Gasser M; Kamel, Rasha M

    2016-04-01

    Luminescence quenching of the Eu(III)- and Tb(III)-bis (coumarin-3-carboxylic acid) (Ln(III)-(CCA)2) probes has been studied in the presence of organophosphorus or organochlorine pesticides; Phosdrin (P1), Malathion (P2), Profenofos (P3), Formothion (P4), Heptachlor (P5), and Endosulfan (P6). The luminescence intensity of lanthanide complex probes Ln(III)-(CCA)2 decreases as the concentration of the Phosdrin pesticide increases, while the other investigated pesticides have no significant influence on the lanthanide fluorescent intensities. It is observed that the quenching of Eu(III) and Tb(III)-coumarin-3-carboxylic acid by Phosdrin proceeds via static quenching processes according to Stern-Volmer plot. The binding constants (K) and the thermodynamic parameters of the interaction of Ln(III)-(CCA)2 with Phosdrin have been determined. A direct method for the determination of the Phosdrin in ethanol has been developed based on the luminescence changes of the Ln(III)-(CCA)2-phosdrin ternary complexes. The detection limits of P1 were 6.28 and 1.07 μM in case of Eu(III) and Tb(III)-complex, respectively. The influence of various interfering species on the detection of P1 has been investigated to assess the analytical applicability of the method. The new method was applied to determine the Phosdrin pesticide in different types of water samples.

  19. A novel adenosine-based molecular beacon probe for room temperature nucleic acid rapid detection in cotton thread device.

    PubMed

    Du, Ting-E; Wang, Yiyun; Zhang, Yi; Zhang, Tian; Mao, Xun

    2015-02-25

    We used cotton thread as substrate to develop a novel room temperature DNA detection device for low-cost, sensitive and rapid detection of a human genetic disease, hereditary tyrosinemia type I related DNA sequences. A novel adenosine based molecular beacon (ABMB) probe modified on gold nanoparticle was used as reporter probe. In the presence of coralyne, a small molecule which can react with adenosines, the ABMB would form a hairpin structure just like traditional molecular beacon used extensively. In the presence of target DNA sequences, the hairpin structure of ABMB modified on gold nanoparticles will be opened and the biotin group modified at one end of the DNA probes will be released and react with the streptavidin immobilized on the test zone of the cotton thread. The response of the thread based DNA test device is linear over the range of 2.5-100 nM complementary DNA. The ability of our developed device for discriminating the single base mismatched DNA related to a human genetic disease, hereditary tyrosinemia type I, was improved comparing with previous report. It is worth mentioning that the whole assay procedure for DNA test is performed under room temperature which simplified the assay procedures greatly.

  20. Probing the general time scale question of boronic acid binding with sugars in aqueous solution at physiological pH.

    PubMed

    Ni, Nanting; Laughlin, Sarah; Wang, Yingji; Feng, You; Zheng, Yujun; Wang, Binghe

    2012-05-01

    The boronic acid group is widely used in chemosensor design due to its ability to reversibly bind diol-containing compounds. The thermodynamic properties of the boronic acid-diol binding process have been investigated extensively. However, there are few studies of the kinetic properties of such binding processes. In this report, stopped-flow method was used for the first time to study the kinetic properties of the binding between three model arylboronic acids, 4-, 5-, and 8-isoquinolinylboronic acids, and various sugars. With all the boronic acid-diol pairs examined, reactions were complete within seconds. The k(on) values with various sugars follow the order of D-fructose>D-tagatose>D-mannose>D-glucose. This trend tracks the thermodynamic binding affinities for these sugars and demonstrates that the 'on' rate is the key factor determining the binding constant.