A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein

The structure and properties of the double-helical form of the alternating copolymer poly(dA-dT) are considered. Different lines of evidence are interpreted in terms of a structure in which every second phosphate-diester linkage has a conformation different from that of the normal B form. A rationale for this “alternating-B” structure is given which provides an explanation for the effects of chemical modifications of the T residues on the binding of the poly(dA-dT)· poly(dA-dT) to the lac repressor of Escherichia coli.

Accommodating Unwelcome Guests in Inorganic Layered Hosts: Inclusion of Chloranil in a Layered Double Hydroxide

The host-guest chemistry of most inorganic layered solids is limited to ion-exchange reactions. The guest species are either cations or anions to compensate for the charge deficit, either positive or negative, of the inorganic layers. Here, we outline a strategy to include neutral molecules like ortho- and para-chloranil, that are known to be good acceptors in donor-acceptor or charge-transfer complexes, within the galleries of a layered solid. We have succeeded in including neutral ortho- and para-chloranil molecules within the galleries of an Mg-Al layered double hydroxide (LDH) by using charge-transfer interactions with preintercalated p-aminobenzoate ions as the driving force. The p-aminobenzoate ions are introduced in the Mg-Al LDH via ion exchange. The intercalated LDH can adsorb ortho- and para-chloranil from chloroform solutions by forming charge-transfer complexes with the p-aminobenzoate anions present in the galleries. We use X-ray diffraction, spectroscopy, and molecular dynamics simulations to establish the nature of interactions and arrangement of the charge-transfer complex within the galleries of the layered double hydroxide.

Glassy dielectric response in Tb2NiMnO6 double perovskite with similarities to a Griffiths phase

Results of frequency-dependent and temperature-dependent dielectric measurements performed on the double-perovskite Tb2NiMnO6 are presented. The real (epsilon(1)(f,T)) and imaginary (epsilon(2)(f,T)) parts of dielectric permittivity show three plateaus suggesting dielectric relaxation originating from the bulk, grain boundaries and the sample-electrode interfaces, respectively. The epsilon(1)(f,T) and epsilon(2)(f,T) are successfully simulated by a RC circuit model. The complex plane of impedance, Z'-Z `', is simulated using a series network with a resistor R and a constant phase element. Through the analysis of epsilon(f,T) using the modified Debye model, two different relaxation time regimes separated by a characteristic temperature, T*, are identified. The temperature variation of R and C corresponding to the bulk and the parameter alpha from modified Debye fit lend support to this hypothesis. Interestingly, the T* compares with the Griffiths temperature for this compound observed in magnetic measurements. Though these results cannot be interpreted as magnetoelectric coupling, the relationship between lattice and magnetism is markedly clear. We assume that the observed features have their origin in the polar nanoregions which originate from the inherent cationic defect structure of double perovskites. Copyright (C) EPLA, 2013

Modeling of Channel Potential and Subthreshold Slope of Symmetric Double-Gate Transistor

A new physically based classical continuous potential distribution model, particularly considering the channel center, is proposed for a short-channel undoped body symmetrical double-gate transistor. It involves a novel technique for solving the 2-D nonlinear Poisson's equation in a rectangular coordinate system, which makes the model valid from weak to strong inversion regimes and from the channel center to the surface. We demonstrated, using the proposed model, that the channel potential versus gate voltage characteristics for the devices having equal channel lengths but different thicknesses pass through a single common point (termed ``crossover point''). Based on the potential model, a new compact model for the subthreshold swing is formulated. It is shown that for the devices having very high short-channel effects (SCE), the effective subthreshold slope factor is mainly dictated by the potential close to the channel center rather than the surface. SCEs and drain-induced barrier lowering are also assessed using the proposed model and validated against a professional numerical device simulator.

Enhanced sensitivity in detection of Kerr rotation by double modulation and time averaging based on Allan variance

Experiments in spintronics necessarily involve the detection of spin polarization. The sensitivity of this detection becomes an important factor to consider when extending the low temperature studies on semiconductor spintronic devices to room temperature, where the spin signal is weaker. In pump-probe experiments, which optically inject and detect spins, the sensitivity is often improved by using a photoelastic modulator (PEM) for lock-in detection. However, spurious signals can arise if diode lasers are used as optical sources in such experiments, along with a PEM. In this work, we eliminated the spurious electromagnetic coupling of the PEM onto the probe diode laser, by the double modulation technique. We also developed a test for spurious modulated interference in the pump-probe signal, due to the PEM. Besides, an order of magnitude enhancement in the sensitivity of detection of spin polarization by Kerr rotation, to 3x10(-8) rad was obtained by using the concept of Allan variance to optimally average the time series data over a period of 416 s. With these improvements, we are able to experimentally demonstrate at room temperature, photoinduced steady-state spin polarization in bulk GaAs. Thus, the advances reported here facilitate the use of diode lasers with a PEM for sensitive pump-probe experiments. They also constitute a step toward detection of spin-injection in Si at room temperature.

Dynamic initiation toughness measu~ment using double Grooved discs

Among the multitude of test specimen geometries used for dynamic fiacture toughness evaluation, the most widely uscd specimen is lhc Chavpy specimen due its simple geomclry and availability of testing machines. The standard Chatpy specimen dimensions may llOl always give plane st~ain condilions and hence, it may be necessary Io coilduct lcs/s using specimens of dillEvcnt thicknesses to establish the plane strain K~a. An axisymmct/ic specimen, on the otlaev hand would always give flow constraints l~n a nominal specimen thickness i~rcspcctive of the test matctial. The notched disk specimen pVOl)oscd by Bcrn:ud ctal. [1] for static and dynamic initiation toughness measurement although p~ovicles plain-strain conditions, the crack plopagatcs at an angle to the direction of applied load. This makes inteq~retation of the test results difficult us it ~Ccluivcs ~actial slices to be cut fiom the fractured specimen to ascertain the angle o1 crack growth and a linite element model l~)r tl);t{ pa~ticulat ctack o~icntalion.

Local structure of Sr2FeMoxW1-xO6 double perovskites across the composition-driven metal to insulator transition

Sr2FeMoO6 oxides exhibit a half-metallic ferromagnetic (HM-FM) ground state and peculiar magnetic and magnetotransport properties, which are interesting for applications in the emerging field of spintronics and attractive for fundamental research in the field of heavily correlated electron systems. Sr2FeWO6 is an insulator with an antiferromagnetic (I-AFM) ground state. The solid solutions Sr2FeMoxW1-xO6 also have peculiar properties-W doping enhances chemical order which allows stabilization of the HM-FM state; as the W content exceeds a certain value a metal to insulator transition (MIT) occurs. The role of W in determining the physical properties of Sr2FeMoxW1-xO6 systems has been a matter of intense investigation. This work deals with the problem of the structural and electronic changes related to the MIT from a local perspective by means of x-ray absorption spectroscopy (XAS). This technique allows one to probe in detail the local structure and electronic modifications around selected absorber ions (W, Mo, Fe and Sr in our case). The results of XAS analysis in the whole composition range (0 <= x <= 1), in the near edge (XANES) and extended (EXAFS) regions, demonstrate an abrupt change of the local structure around the Fe and Mo sites at the critical composition, x(c). This change represents the microstructural counterpart associated with the MIT. Conversely, the local structure and electronic configuration of W ions remain unaltered in the whole composition range, suggesting indirect participation of W in the MIT.

Base specific binding of deoxyguanylate and deoxycytidylate antibodies to double stranded DNA

Antibodies raised in rabbits against daoxyguanylate and daoxycytidylate bind to 3H-(lambda) double stranded DNA and the binding is base specific. The concentrations of antibody populations that bind to double stranded DNA are much less than those binding to denatured DNA. Due to their low concentrations, these antibodies ware not detected in earlier studies. These antibodies are expected to be useful to probe the conformational flexibilities of double stranded DNAs.

ESR Studies of Phase Transitions in Double Propionates: Dicalcium Barium Propionate Ca2Ba(C2H5COO)6

Single crystal [(111) and (100) planes], and powder ESR of Mn2+ (substituting for Ca2+) in Ca2Ba(C2H5COO)6 in the temperature range 220°C to -160°C shows (i) a doubling of both the physically and chemically inequivalent sites, and a change in the magnitude (150 G at -6°C to 170 G at -8°C) as well as the orientation of the D tensor across the -6°C transition and (ii) an inflection point in the D vs T plot across the -75°C transition. The oxygen octahedra around the Ca2+ sites are inferred to undergo alternate rotations, showing the participation of the carboxyl oxygens in the -6°C transition. A relation of the type D=D0(1+αT+βT2) seems to fit the D variation satisfactorily.

Studies On Thermal-Decomposition Of Double-Base Propellants

The scanning thermogram of a block sample of a double-base propellant shows a shoulder around 200°C which is not observed in a powder sample of the sample propellant. The heat of decomposition was also found to be different In the two cases. Product analysis and activation energy calculations show that nitroglycerine un dergoes decomposition in the block sample, whereas it vaporizes in the powder sample.

Photo-induced double-strand DNA and site-specific protein cleavage activity of L-histidine (mu-oxo)diiron(III) complexes of heterocyclic bases

Three oxo-bridged diiron(III) complexes of L-histidine and heterocyclic bases [Fe-2(mu-O)(L-his)(2)(B)(2)](ClO4)(2) (1-3), where B is 2,2'-bipyridine (bpy),1,10-phenanthroline (phen), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq), were prepared and characterized. The bpy complex 1 was structurally characterized by X-ray crystallography. The molecular structure showed a {Fe-2(mu-O)} core in which iron(III) in a FeN4O2 coordination is bound to tridentate monoanionic L-histidine and bidentate bpy ligands. The Fe center dot center dot center dot Fe distance is similar to 3.5 angstrom. The Fe-O-Fe unit is essentially linear, giving a bond angle of similar to 172 degrees. The complexes showed irreversible cyclic voltammetric cathodic response near -0.1 V vs. SCE in H2O-0.1 M KCl. The binuclear units displayed antiferromagnetic interaction between two high-spin (S = 5/2) iron(III) centers giving a -J value of -110 cm(-1). The complexes showed good DNA binding propensity giving a binding constant value of similar to 10(5) M-1. Isothermal titration calorimetric data indicated single binding mode to the DNA. The binding was found to be driven by negative free energy change and enthalpy. The dpq complex 3 showed oxidative double-strand DNA cleavage on exposure to UV-A and visible light. The phen complex 2 displayed single-strand photocleavage of DNA. The DNA double-strand breaks were rationalized from theoretical molecular docking calculations. Mechanistic investigations showed formation of hydroxyl radicals as the reactive species through photodecarboxylation of the L-histidine ligand. The complexes exhibited good binding propensity to bovine serum albumin (BSA) protein in Tris-HCl/NaCl buffer medium. The dpq complex 3 showed UV-A light-induced site-specific oxidative BSA cleavage forming fragments of similar to 45 kDa and similar to 20 kDa molecular weights via SOH pathway.

Sequence-dependent conformation of an A-DNA double helix: The crystal structure of the octamer d(G-G-T-A-T-A-C-C)

The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1·8 and 2·25 Å, respectively. The molecules adopt an A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions.

On prequantization to reduce errors in double phase holograms

Prequantization has been forwarded as a means to improve the performance of double phase holograms (DPHs). We show here that any improvement (even under the best of conditions) is not large enough to help the DPH to compete favourably with other holograms.

Topochemical dimerization of non-parallel double bonds: 7-methoxycoumarin

X-ray crystal structure analysis of 7-methoxycoumarin reveals that the reactive double bonds are rotated by about 65° with respect to each other, the centre-to-centre distance between the double bonds being 3.83 Å. In spite of this unfavourable arrangement, photodimerization occurs in the crystalline state yielding the syn-head-tail dimer as the only product. Lattice energy calculations on ground-state molecules in crystals throw light on the mechanism of the reaction.

Sex Determination - A Hypothesis Based On Noncoding Dna

Certain recent models of sex determination in mammals, Drosophila melanogaster, Caenorhabditis elegans, and snakes are examined in the light of the hypothesis that the relevant genetic regulatory mechanisms are similar and interrelated. The proposed key element in each of these instances is a noncoding DNA sequence, which serves as a high-affinity binding site for a repressor-like molecule regulating the activity of a major "sex-determining" gene. On this basis it is argued that, in several eukaryotes, (i) certain DNA sequences that are sex-determining are noncoding, in the sense that they are not the structural genes of a sex-determining protein; (ii) in some species these noncoding sequences are present in one sex and absent in the other, while in others their copy number or accessibility to regulatory molecules is significantly unequal between the two sexes; and (iii) this inequality determines whether the embryo develops into a male or a female.