Monovalent cation localization in DNA A-tracts with different sequences

The free solution mobilities of 26-base pair (bp) DNA oligomers containing A-tracts with and without internal ApT steps have been measured by capillary electrophoresis, using the mobility of a 26-bp random-sequence oligomer as a reference. The background electrolytes (BGEs) contained mixtures of Li⁺ and tetrapropylammonium (TPA⁺) ions, keeping the total cation concentration constant at 0.3 M. The mobility ratios equaled 1.00 in 0.3 M TPA⁺, indicating that the A-tract and reference oligomers had the same B-form conformation in this BGE. With increasing [Li⁺], the mobility ratio decreased as Li⁺ ions became localized in the A-tract minor groove, suggesting that the A-tract was now in the B* conformation. If the A-tract contained an internal ApT step and the oligomer contained less than ∼50% A + T, the mobility ratio reached a reduced plateau value that remained constant as the [Li⁺] increased to 0.3 M. However, for A-tracts without an internal ApT step and for A-tracts embedded in oligomers containing more than 50% A + T, the mobility ratios increased again at high [Li⁺], eventually reaching a plateau value of 1.00. Hence, DNA A-tracts in solution appear to exist as mixtures of the B and B* conformations, with the fractional concentration of each conformer depending on the [Li⁺], the A-tract sequence, and the total A + T content of the oligomer.     

Poly(diiododiacetylene): preparation, isolation, and full characterization of a very simple poly(diacetylene)

Poly(diiodiacetylene), or PIDA, is a conjugated polymer containing the poly(diacetylene) (PDA) backbone but with only iodine atom substituents. The monomer diiodobutadiyne (1) can be aligned in the solid state with bis(nitrile) oxalamide hosts by hydrogen bonds between oxalamide groups and weak Lewis acid-base interactions (halogen bonds) between nitriles and iodoalkynes. The resulting cocrystals start out pale blue but turn shiny and copper-colored as the polymerization progresses. The development of a crystallization methodology that greatly improves the yield of PIDA to about 50% now allows the full characterization of the polymer by X-ray diffraction, solid-state (13)C MAS NMR, Raman, and electron absorption spectroscopy. Comparison of a series of hosts reveals an odd-even effect in the topochemical polymerization, based on the alkyl chain length of the host. In the cocrystals formed with bis(pentanenitrile) oxalamide (4) and bis(heptanenitrile) oxalamide (6), the host/guest ratio is 1:2 and the monomer polymerizes spontaneously at room temperature, while in the case of bis(butanenitrile) oxalamide (3) and bis(hexanenitrile) oxalamide (5), where the host and guest form cocrystals in a 1:1 ratio, the polymerization is disfavored and does not go to completion. The topochemical polymerization can also be observed in water suspensions of micrometer-sized 6.1 cocrystals; the size distribution of these microcrystals, and the resulting polymer chains, can be controlled by sonication. Completely polymerized PIDA cocrystals show a highly resolved vibronic progression in their UV/vis absorption spectra. Extensive rinsing of the crystals in organic solvents such as methanol, THF, and chloroform separates the polymer from the soluble host. Once isolated, PIDA forms blue suspensions in a variety of solvents. The UV/vis absorption spectra of these suspensions match the cocrystal spectrum, without the vibronic resolution. However, they also include a new longer-wavelength absorption peak, associated with aggregation of the polymer chains.     

Genetic Diversity in Chemically Diverse Accessions of Bacopa monnieri

JPC – Journal of Planar Chromatography – Modern TLC - Bacopa monnieri (L.) Pennell, commonly known as Brahmi, is an important medicinal plant of the Ayurvedic System of Medicine and is...     

Sulfonate salts of the therapeutic agent dapsone: 4‐[(4‐aminophenyl)sulfonyl]anilinium benzenesulfonate monohydrate and 4‐[(4‐aminophenyl)sulfonyl]anilinium methanesulfonate monohydrate

Dapsone, formerly used to treat leprosy, now has wider therapeutic applications. As is the case for many therapeutic agents, low aqueous solubility and high toxicity are the main problems associated with its use. Derivatization of its amino groups has been widely explored but shows no significant therapeutic improvements. Cocrystals have been prepared to understand not only its structural properties, but also its solubility and dissolution rate. Few salts of dapsone have been described. The title salts, C₁₂H₁₃N₂O₂S⁺·C₆H₅O₃S⁻·H₂O and C₁₂H₁₃N₂O₂S⁺·CH₃SO₃⁻·H₂O, crystallize as hydrates and both compounds exhibit the same space group (monoclinic, P2₁/n). The asymmetric unit of each salt consists of a 4‐[(4‐aminophenyl)sulfonyl]anilinium monocation, the corresponding sulfonate anion and a water molecule. The cation, anion and water molecule form hydrogen‐bonded networks through N—H…O=S, N—H…O_water and O_water—H…O=S hydrogen bonds. For both salts, the water molecules interact with one sulfonate anion and two anilinium cations. The benzenesulfonate salt forms a two‐dimensional network, while the hydrogen bonding within the methanesulfonate salt results in a three‐dimensional network.     

Thermodynamic Modeling of Aqueous Aluminum Chemistry and Solid-Liquid Equilibria to High Solution Concentration and Temperature. I. The Acidic H-Al-Na-K-Cl-H2O System from 0 to 100 °C

In this paper, we describe the development of a thermodynamic model that calculates solute/solvent activities and solid-liquid equilibria in the acidic aluminum system, H-Al³⁺-Na-K-Cl-H₂O, to high molality from 0?° to ≈100?°C. The model incorporates the concentration-dependent, specific interaction equations for aqueous solutions of Pitzer (Activity Coefficients in Electrolyte Solutions, 2nd edn., pp. 75–153, CRC Press, Boca Raton, 1991). Parameterization of this model adds Al³⁺ specific interactions in the binary Al-Cl-H₂O and ternary Al-H-Cl-H₂O, Al-Na-Cl-H₂O and Al-K-Cl-H₂O systems as well as the standard chemical potentials of AlCl₃?6H₂O(s) and Al(OH)₃(s) (gibbsite) in the 0?° to 100?°C range to our variable temperature (0–250?°C) model of acid-base reactions in the H-Na-K-OH-Cl-HSO₄-SO₄-H₂O system (Christov and Moller in Geochim. Cosmochim. Acta 68:1309, 2004). In constructing our aluminum model, we used Emf, osmotic, equilibrium constant and solubility data. New Emf measurements using the cell Pt|H₂(g, 101.325 kPa)|HCl(m ₁), AlCl₃(m ₂)|AgCl(s)|Ag|Pt at temperatures ranging from 0 to 45?°C and at total ionic strength ranging from 0.1 to 3 mol?kg^?1 are presented. Gibbsite and boehmite, AlOOH(s), solubility data are used in testing the model. Limitations of the model due to data insufficiencies are discussed.     

Imidization and interdiffusion of poly(amic ethyl ester) precursors of PMDA/3,4′-ODA

Para-, meta-, and mixed isomeric poly(amic ethyl ester) precursors of the polyimide based on pyromellitic dianhydride (PMDA) and 3,4′-oxydianiline (3,4′-ODA) were synthesized. The intrinsic viscosity of each of the isomers was measured in an NMP solution and found to be less than corresponding isomers derived from PMDA and 4,4′-oxydianiline (4,4′-ODA) precursors with comparable molecular weight. The imidization and solvent retention were measured as a function of imidization temperatures, T_i using forward recoil spectrometry (FRES). For samples cast from a single solvent, either N-methyl pyrrolidone (NMP) or dimethyl sulfoxide (DMSO), no difference was observed in the temperature-dependent imidization behavior between the isomers. In all cases the imide fraction f increased as T_i increased, and reached a value of unity, i.e., full conversion at 400°C. At the same T_i, samples cast from DMSO showed a slightly higher f than samples cast from NMP. FRES and time of flight FRES (TOF-FRES) were used to measure the interdiffusion distance, w, of deuterium-labeled tracers into nondeuterated base layers of the polyimide of PMDA/3,4′-ODA treated at various T_i. The primary determinant of w for all isomers was T_i, and the particular isomer used as either the base or the tracer molecule did not seem to affect w. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 2247–2258, 1998     

Microstructural model for prediction of stress–strain curves of amorphous and semicrystalline elastomers

A fundamental microstructural model was developed to calculate the stress–strain curves of rubbery amorphous polymers and of semicrystalline polymers with a rubbery amorphous phase by numerical simulations. The rubbery amorphous phase was treated by using a version of the theory of rubber elasticity with finite extensibility. Physical entanglements and chemical crosslinks were both allowed. Slippage was implemented by a Monte Carlo algorithm controlled by kinetic parameters such as the activation energy and activation volume for slippage. The crystalline phase was treated in a very idealized manner, including a crude representation of tie chains but not taking the internal structure of the crystallites into account. A two-dimensional embodiment of the model was implemented into software. For amorphous polymers, while lacking truly quantitative accuracy, the model showed sufficiently good agreement with the experimental trends to be used as a qualitative or semiquantitative predictive tool, and it is currently being used in this manner. The more complex semicrystalline version was less accurate and will need to be improved in future work. Most of the limitations of the semicrystalline version could be ascribed unambiguously to specific simplifications made in the software implementation to reduce the amount of computer time required for the calculations. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 2715–2739, 1997     

Australian Synchrotron User Meeting 2014

Synchrotron users and experts from Australia, New Zealand, and further afield congregated in November for the Australian Synchrotron User Meeting 2014. Around 200 members of the synchrotron community attended the highly anticipated meeting held, in conjunction with the New User Symposium, at the Australian Synchrotron's National Centre for Synchrotron Science. Early career researchers played a prominent role at the meeting. Their achievements highlighted the promising capabilities of the region's next generation of synchrotron scientists.     

Effect of the matrix on DNA electrophoretic mobility

DNA electrophoretic mobilities are highly dependent on the nature of the matrix in which the separation takes place. This review describes the effect of the matrix on DNA separations in agarose gels, polyacrylamide gels and solutions containing entangled linear polymers, correlating the electrophoretic mobilities with information obtained from other types of studies. DNA mobilities in various sieving media are determined by the interplay of three factors: the relative size of the DNA molecule with respect to the effective pore size of the matrix, the effect of the electric field on the matrix, and specific interactions of DNA with the matrix during electrophoresis.