A glossary of DNA structures from A to Z

The right-handed double-helical Watson-Crick model for B-form DNA is the most commonly known DNA structure. In addition to this classic structure, several other forms of DNA have been observed and it is clear that the DNA molecule can assume different structures depending on the base sequence and environment. The various forms of DNA have been identified as A, B, C etc. In fact, a detailed inspection of the literature reveals that only the letters F, Q, U, V and Y are now available to describe any new DNA structure that may appear in the future. It is also apparent that it may be more relevant to talk about the A, B or C type dinucleotide steps, since several recent structures show mixtures of various different geometries and a careful analysis is essential before identifying it as a 'new structure'. This review provides a glossary of currently identified DNA structures and is quite timely as it outlines the present understanding of DNA structure exactly 50 years after the original discovery of DNA structure by Watson and Crick

Generation of Flat and Curved Membranes by Inverse-BAR Domain Proteins

Biological membranes are tightly linked to the evolution of life, because they provide a way to concentrate molecules into partially closed compartments. The dynamic shaping of cellular membranes is essential for many physiological processes, including cell morphogenesis, motility, cytokinesis, endocytosis, and secretion. It is therefore essential to understand the structure of the membrane and recognize the players that directly sculpt the membrane and enable it to adopt different shapes. The actin cytoskeleton provides the force to push eukaryotic plasma membrane in order to form different protrusions or/and invaginations. It has now became evident that actin directly co-operates with many membrane sculptors, including BAR domain proteins, in these important events. However, the molecular mechanisms behind BAR domain function and the differences between the members of this large protein family remain largely unresolved. In this thesis, the structure and functions of the I-BAR domain family members IRSp53 and MIM were thoroughly analyzed. By using several methods such as electron microscopy and systematic mutagenesis, we showed that these I-BAR domain proteins bind to PI(4,5)P2-rich membranes, generate negative membrane curvature and are involved in the formation of plasma membrane protrusions in cells e.g. filopodia. Importantly, we characterized a novel member of the BAR-domain superfamily which we named Pinkbar. We revealed that Pinkbar is specifically expressed in kidney and epithelial cells, and it localizes to Rab13-positive vesicles in intestinal epithelial cells. Remarkably, we learned that the I-BAR domain of Pinkbar does not generate membrane curvature but instead stabilizes planar membranes. Based on structural, mutagenesis and biochemical work we present a model for the mechanism of the novel membrane deforming activity of Pinkbar. Collectively, this work describes the mechanism by which I-BAR domain proteins deform membranes and provides new information about the biological roles of these proteins. Intriguingly, this work also gives evidence that significant functional plasticity exists within the I-BAR domain family. I-BAR proteins can either generate negative membrane curvature or stabilize planar membrane sheets, depending on the specific structural properties of their I-BAR domains. The results presented in this thesis expand our knowledge on membrane sculpting mechanisms and shows for the first time how flat membranes can be generated in cells.

Quinoxaline: Z `=1 form

A new Z' = 1 crystal structure of quinoxaline (or 1,4-diazanaphthalene), C8H6N2, with one-fifth the volume of the earlier known Z' = 5 structure was obtained by means of an in situ cryocrystallization technique.

Application of a modified z-cosy experiment for the analysis of spectra of oriented molecules - the spectrum of cis,cis-mucanonitrile

NMR spectra of cis,cis-mucanonitrile oriented in a liquid crystal have been analysed using the connectivity information obtained from a modified Z-COSY experiment which provided crucial clues for the starting parameters for the iterative analysis. The proton spectra with and without C-13 satellites and the C-13 spectra have thus been interpreted. The indirect spin-spin couplings required for the analyses have been obtained from the corresponding isotropic spectra. The H-1-H-1 and C-13-H-1 dipolar couplings so obtained have been utilized to determine the relative internuclear distances. The results indicate that the molecule is planar. (C) 1994 Academic Press, Inc.

Construction of energy-level diagram of oriented benzene using connectivity information obtained by modified z-cosy experiment

Experiments involving selective perturbation of a transition yield information about the directly connected transitions, which in turn yield information for deriving the parameters of the spin Hamiltonian of oriented molecules. Problems involved with selective perturbation are removed by the use of a two-dimensional experiment, namely, the modified Z-COSY-experiment, The use of this experiment is demonstrated for obtaining the connectivity information and for determining the parameters of the spin Hamiltonian of oriented benzene, a strongly coupled six-spin system

Signals of additional Z ` boson in e(+)e(-) -> W+W- at the ILC with polarized beams

We consider the possibility of fingerprinting the presence of heavy additional Z' bosons that arise naturally in extensions of the standard model such as E-6 models and left-right symmetric models, through their mixing with the standard model Z boson. By considering a class of observables including total cross sections, energy distributions and angular distributions of decay leptons we find significant deviation from the standard model predictions for these quantities with right-handed electrons and left-handed positrons at root s= 800GeV. The deviations being less pronounced at smaller centre of mass energies as the models are already tightly constrained. Our work suggests that the ILC should have a strong beam polarization physics program particularly with these configurations. On the other hand, a forward backward asymmetry and lepton fraction in the backward direction are more sensitive to new physics with realistic polarization due to interesting interplay with the neutrino t-channel diagram. This process complements the study of fermion pair production processes that have been considered for discrimination between these models.

Edge-sharing bioctahedral diruthenium(III) complexes containing methoxy and carboxylate bridges:x-ray structures, redox behavior, and core stability

Edge-sharing bioctahedral (ESBO) complexes [Ru-2(OMe)(O2CC6H4-p-X)3(1-MeIm)(4)](ClO4)2 (X = OMe (1a), Me (1b)) and [Ru-2(O2CC6H4-P-X)(4)(1-MeIm)(4)](ClO4)(2) (X = OMe (2a), Me (2b)) are prepared by reacting Ru2Cl(O(2)CR)(4) with 1-methylimidazole (1-MeIm) in methanol followed by treatment with NaClO4. Complex 2a and the PF6- salt (1a') of 1a have been structurally characterized. Crystal data for 1a.1.5MeCN. 0.5Et(2)O: triclinic, P (1) over bar, a = 13.125(2) Angstrom, b = 15.529(3) Angstrom, c 17.314(5) Angstrom, a; 67.03(2)degrees, beta 68.05(2)degrees, gamma = 81.38(1)degrees, V 3014(1) Angstrom(3), Z = 2. Crystal data for 2a: triclinic, P (1) over bar, a 8.950(1) Angstrom, b = 12.089(3) Angstrom, c = 13.735(3) Angstrom, alpha 81.09(2)degrees, beta = 72.27(1)degrees, gamma = 83.15(2)degrees, V = 1394(1) Angstrom(3), Z = 1. The complexes consist of a diruthenium(III) unit held by two monoatomic and two three-atom bridging ligands. The 1-MeIm ligands are at the terminal sites of the [Ru-2(mu-L)(eta(1):mu-O(2)CR)(eta(1):eta(1):mu-O(2)CR)(2)](2+) core having a Ru-Ru single bond (L = OMe or eta(1)-O(2)CR). The Ru-Ru distance and the Ru-O-Ru angle in the core of 1a' and 2a are 2.49 Angstrom and similar to 76 degrees. The complexes undergo one-electron oxidation and reduction processes in MeCN-0.1 M TBAP to form mixed-valence diruthenium species with Ru-Ru bonds of orders 1.5 and 0.5, respectively.

3-D Warping in Four-Bar Laminated Linkages

This paper deals with the evaluation of the component-laminate load-carrying capacity, i.e., to calculate the loads that cause the failure of the individual layers and the component-laminate as a whole in four-bar mechanism. The component-laminate load-carrying capacity is evaluated using the Tsai-Wu-Hahn failure criterion for various layups. The reserve factor of each ply in the component-laminate is calculated by using the maximum resultant force and the maximum resultant moment occurring at different time steps at the joints of the mechanism. Here, all component bars of the mechanism are made of fiber reinforced laminates and have thin rectangular cross-sections. They could, in general, be pre-twisted and/or possess initial curvature, either by design or by defect. They are linked to each other by means of revolute joints. We restrict ourselves to linear materials with small strains within each elastic body (beam). Each component of the mechanism is modeled as a beam based on geometrically nonlinear 3-D elasticity theory. The component problems are thus split into 2-D analyses of reference beam cross-sections and nonlinear 1-D analyses along the three beam reference curves. For the thin rectangular cross-sections considered here, the 2-D cross-sectional nonlinearity is also overwhelming. This can be perceived from the fact that such sections constitute a limiting case between thin-walled open and closed sections, thus inviting the nonlinear phenomena observed in both. The strong elastic couplings of anisotropic composite laminates complicate the model further. However, a powerful mathematical tool called the Variational Asymptotic Method (VAM) not only enables such a dimensional reduction, but also provides asymptotically correct analytical solutions to the nonlinear cross-sectional analysis. Such closed-form solutions are used here in conjunction with numerical techniques for the rest of the problem to predict more quickly and accurately than would otherwise be possible. Local 3-D stress, strain and displacement fields for representative sections in the component-bars are recovered, based on the stress resultants from the 1-D global beam analysis. A numerical example is presented which illustrates the failure of each component-laminate and the mechanism as a whole.

Conjectures about phase turbulence in the complex Ginzburg-Landau equation

In the complex Ginzburg-Landau equation, we consider possible ''phase turbulent'' regimes, where asymptotic correlations are controlled by phase fluctuations rather than by topological defects. Conjecturing that the decay of such correlations is governed by the Kardar-Parisi-Zhang (KPZ) model of growing interfaces, we derive the following results: (1) A scaling ansatz implies that equal-time spatial correlations in 1d, 2d, and 3d decay like e(-Ax2 zeta), where A is a nonuniversal constant, and zeta=1/2 in 1d. (2) Temporal correlations decay as exp(-t(2 beta)h(t/L(z))), with the scaling law <(beta)over bar> = <(zeta)over bar>/z, where z = 3/2, 1.58..., and 1.66..., for d = 1,2, and 3 respectively. The scaling function h(y) approaches a constant as y --> 0, and behaves like y(2(beta-<(beta)over bar>)), for large y. If in 3d the associated KPZ model turns out to be in its weak-coupling (''smooth'') phase, then, instead of the above behavior, the CGLE exhibits rotating long-range order whose connected correlations decay like 1/x in space or 1/t(1/2) in time. (3) For system sizes, L, and times t respectively less than a crossover length, L(c), and time, t(c), correlations are governed by the free-field or Edwards-Wilkinson (EW) equation, rather than the KPZ model. In 1d, we find that L(c) is large: L(c) similar to 35,000; for L < L(c) we show numerical evidence for stretched exponential decay of temporal correlations with an exponent consistent with the EW value beta(EW)= 1/4.

Giant magnetoresistance in lanthanum strontium yttrium manganese oxides (La(1-x)Sr(x-z)YuMnO(3))

Electron transport and magnetic properties of several compositions of the La1-xSx-zYzMnO3 system have been investigated in order to explore the effect of yttrium substitution on the magnetoresistance and related properties of these manganates. Yttrium substitution lowers the T-c and the insulator-metal transition temperature, while increasing the peak resistivity. A comparison of the properties of La1-xSrx-zYzMnO3 with the corresponding La1-xCax-zYzMnO3 compositions shows that the observed properties can be related to the average size of the A-site cations.

The crystal structure of hydrated barium copper oxalate

BaCu(C2O4)(2) . 6H2O is triclinic, P (1) over bar, with a = 6.5405(9), b = 9.202(3), c = 10.939(1) Angstrom, alpha = 85.46(2), beta = 79.22(1), gamma = 80.45(2), V = 636.99(1) Angstrom(3), Z = 2, D-0 = 2.14, D-c = 2.465 g . cm(-3), R = 0.074, wR = 0.0746 for 2219 significant reflections \F-0\ greater than or equal to 6.0 sigma F-0. The barium has eleven coordinations and the coordination polyhedra is a capped antiprism. Six water oxygen atoms are coordinated whereas the other five are coming from the oxalate group. In the unit cell the molecule's form a polymeric network. One lattice water molecule belongs to the coordinating water. The barium oxygen distances vary from 2.75 Angstrom to 3.15 Angstrom.

Organometallic Chemistry of Diphosphazanes. 11. Reactions of fac-[Mo(CO)3(MeCN){.eta.2-Ph2PN(Pri)PPh(DMP)}] (DMP = 3,5-Dimethyl-1-Pyrazolyl) with Diphosphazanes and Diphosphinoalkanes and Oxidative Addition with Iodine

The use of fac-[Mo(CO)(3)(MeCN)(eta(2)-L(1))] (1a) {L(1) = Ph(2)PN(Pr-i)PPh(DMP)}(2) as a precursor to metalloligands and bimetallic, heterotrimetallic, and heptacoordinated complexes is reported. The reaction of 1a with diphosphazane, dppa, or a diphosphinoalkane such as dppm or dppe yields the fac-eta(1)-diphosphine substituted metalloligands, fac-[Mo(CO)(3)(eta(2)-L(1))(eta(1)-PXP)] {PXP = dppa (2), dppm (3), and dppe (4)}. These undergo isomerization to yield the corresponding mer-diphosphine complexes (5-7). Oxidation of the uncoordinated phosphorus atom of the mer-eta(1)-dppm-substituted complex eventually provides mer-[Mo(CO)(3)-(eta(2)-L(1)){eta(1)-Ph(2)PCH(2)P(O)Ph(2)}](8). The structure of the latter complex has been confirmed by single crystal X-ray diffraction {triclinic system, P ($) over bar 1; a = 11.994(3), b = 14.807(2), c = 15.855(3) Angstrom; alpha = 114.24(1), beta = 91.35(2), and gamma = 98.95(1)degrees; Z = 2, 4014 data (F-0 > 5 sigma(F-0)), R = 0.066, R(W) = 0.069}. Treatment of the dppe metalloligand 7 with [PtCl2(COD)] yields the heterotrimetallic complex cis-[PtCl2{mer-[Mo(CO)(3)(eta(2)-L(1))(eta(1)-dppe]}(2)] (9). Attempts to prepare a related trimetallic complex with the dppm-containing metalloligand were unsuccessful; only the tetracarbonyl complex cis-[Mo(CO)(4)(eta(2)-L(1))] (1b) and cis-[PtCl2(eta(2)-dppm)] were obtained. Reaction of la with dppe in the ratio 2:1 yields the mer-mer dinuclear complex [{mer-[Mo(CO)(3)(eta(2)-L(1))]}(2)(mu-dppe)] (10) bridged by dppe. Oxidation of 1a with iodine yields the Mo(II) heptacoordinated complex [MoI2(CO)(2)(eta(3)-L(1))] (11) with tridentate PPN coordination. The same Mo(II) complex 11 is also obtained by the direct oxidation of the tetracarbonyl complex cis-[Mo(CO)(4)(eta(2)-L(1))] (1b) with iodine. The structure of 11 has been confirmed by X-ray diffraction studies {monoclinic system, Cc; a = 10.471(2), b = 19.305(3), c = 17.325(3) Angstrom; beta = 95.47(2)degrees; Z = 4, 3153 data (F-0 > 5 sigma(F-0)), R = 0.049, R(W) = 0.051}. This complex exhibits an unusual capped-trigonal prismatic geometry around the metal. A similar heptacoordinated complex 12 with a chiral diphosphazane ligand {L(3) = (S,R)-P(h)2PN-(*CHMePh)*PPh(DMP)} has also been synthesized.

Uniform algebras generated by holomorphic and close-to-harmonic functions

The initial motivation for this paper is to discuss a more concrete approach to an approximation theorem of Axler and Shields, which says that the uniform algebra on the closed unit disc (D) over bar generated by z and h, where h is a nowhere-holomorphic harmonic function on D that is continuous up to partial derivative D, equals C((D) over bar). The abstract tools used by Axler and Shields make harmonicity of h an essential condition for their result. We use the concepts of plurisubharmonicity and polynomial convexity to show that, in fact, the same conclusion is reached if h is replaced by h + R, where R is a non-harmonic perturbation whose Laplacian is ``small'' in a certain sense.

Mo3O5(OH)(2)(AsO4)2: A new solid with a structure related to beta VOPO4

Mo3O5(OH)(2)(AsO4)(2) was prepared at 100 degrees C from an aqueous solution of MoO3 containing arsenic and nitric acids. It crystallises in the monoclinic system, a = 13.024(1)Angstrom, b = 7.2974 (2) Angstrom, c = 13.281(1) Angstrom, beta = 121.124(8)degrees, Z = 4, space group C2/c. The structure was determined by Rietveld refinement from X-ray powder diffraction data. The three-dimensional structure is built up from MoO6 and MoO5OH octahedra and AsO4 tetrahedra sharing corners. The octahedra share two opposite vertices forming zigzag chains that run parallel to [10(1) over bar]. Each AsO4 tetrahedron is connected to four octahedra, two of which belong to the same chain, thus linking three chains. The resulting covalent framework is similar to that of beta VOPO4 in which one tetrahedral P site for every three is empty. The two protons are likely to be bonded to two (out of four) unshared oxygen atoms surrounding this empty site. All the Mo atoms are strongly off-centred in the octahedra; and the off-centring is disordered. The disorder is discussed in terms of Mo shifts perturbed by a disordered hydrogen bonding scheme.

Coherence of the real symmetric Hardy algebra

Let D denote the open unit disk in C centered at 0. Let H-R(infinity) denote the set of all bounded and holomorphic functions defined in D that also satisfy f(z) = <(f <(z)over bar>)over bar> for all z is an element of D. It is shown that H-R(infinity) is a coherent ring.