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.     

Molecular structure and dynamics in the low temperature (orthorhombic) phase of NH3BH3

Variable temperature 2H NMR experiments on the orthorhombic phase of selectively deuterated NH3BH3 spanning the static to fast exchange limits of the borane and amine motions are reported. New values of the electric field gradient (EFG) tensor parameters have been obtained from the static 2H spectra of V(zz) = 1.652 (+/-0.082) x 10(21) V/m(2) and eta = 0.00 +/- 0.05 for the borane hydrogens and V(zz) = 2.883 (+/-0.144) x 10(21) V/m(2) and eta = 0.00 +/- 0.05 for the amine hydrogens. The molecular symmetry inferred from the observation of equal EFG tensors for the three borane hydrogens and likewise for the three amine hydrogens is in sharp contrast with the C(s) symmetry derived from diffraction studies. The origin of the apparent discrepancy has been investigated using molecular dynamics methods in combination with electronic structure calculations of NMR parameters, bond lengths, and bond angles. The computation of parameters from a statistical ensemble rather than from a single set of atomic Cartesian coordinates gives values that are in close quantitative agreement with the 2H NMR electric field gradient tensor measurements and are more consistent with the molecular symmetry revealed by the NMR spectra.     

Antiaromatic spacer-bridged bisfluorenyl dications generated by superacid induced ionization

Derivatives of the dication of tetrabenzo[5.5]fulvalene were prepared with phenyl and ethynyl spacers through ionization of the appropriate bis-methylethers. The antiaromaticity shown by the parent dication was demonstrated for these dications with spacers, although it was attenuated by the presence of the spacer. It was substantially greater than that of fluorenyl monocations with similar substituents. Antiaromaticity was evaluated through comparison of (1)H NMR shifts with those of acyclic analogues, through nucleus independent chemical shifts, and through magnetic susceptibility exaltation. Although the fluorenyl systems are separated by spacers, the antiaromaticity of one system is affected by the other remote fluorenyl system. An explanation for this interaction may lie in the ability of a remote cationic substituent to attenuate delocalization in the spacer. The use of spacers is designed to prevent side reactions in less stable antiaromatic dications, allowing exploration of a number of species that have previously been inaccessible.     

Convergent assembly of highly potent analogues of bryostatin 1 via pyran annulation: bryostatin look-alikes that mimic phorbol ester function

Highly potent bryostatin analogues which contain the complete bryostatin core structure have been synthesized using a pyran annulation approach as a key strategic element. The A ring pyran was assembled using a pyran annulation reaction between a C1-C8 hydroxy allylsilane and an aldehyde comprising C9-C13. This pyran was transformed to a new hydroxy allylsilane and then coupled with a preformed C ring aldehyde subunit in a second pyran annulation, with concomitant formation of the B ring. This tricyclic intermediate was elaborated to bryostatin analogues which displayed nanomolar to subnanomolar affinity for PKC, but displayed properties indistinguishable from a phorbol ester in a proliferation/attachment assay.     

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...     

Near infrared spectroscopic imaging assessment of cartilage composition: Validation with mid infrared imaging spectroscopy

Disease or injury to articular cartilage results in loss of extracellular matrix components which can lead to the development of osteoarthritis (OA). To better understand the process of disease development, there is a need for evaluation of changes in cartilage composition without the requirement of extensive sample preparation. Near infrared (NIR) spectroscopy is a chemical investigative technique based on molecular vibrations that is increasingly used as an assessment tool for studying cartilage composition. However, the assignment of specific molecular vibrations to absorbance bands in the NIR spectrum of cartilage, which arise from overtones and combinations of primary absorbances in the mid infrared (MIR) spectral region, has been challenging. In contrast, MIR spectroscopic assessment of cartilage is well-established, with many studies validating the assignment of specific bands present in MIR spectra to specific molecular vibrations. In the current study, NIR imaging spectroscopic data were obtained for compositional analysis of tissues that served as an in vitro model of OA. MIR spectroscopic data obtained from the identical tissue regions were used as the gold-standard for collagen and proteoglycan (PG) content. MIR spectroscopy in transmittance mode typically requires a much shorter pathlength through the sample (≤10 microns thick) compared to NIR spectroscopy (millimeters). Thus, this study first addressed the linearity of small absorbance bands in the MIR region with increasing tissue thickness, suitable for obtaining a signal in both the MIR and NIR regions. It was found that the linearity of specific, small MIR absorbance bands attributable to the collagen and PG components of cartilage (at 1336 and 856 cm⁻¹, respectively) are maintained through a thickness of 60 μm, which was also suitable for NIR data collection. MIR and NIR spectral data were then collected from 60 μm thick samples of cartilage degraded with chondroitinase ABC as a model of OA. Partial least squares (PLS) regression using NIR spectra as input predicted the MIR-determined compositional parameters of PG/collagen within 6% of actual values. These results indicate that NIR spectral data can be used to assess molecular changes that occur with cartilage degradation, and further, the data provide a foundation for future clinical studies where NIR fiber optic probes can be used to assess the progression of cartilage degradation.     

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.     

Carbon nanotubes for electrochemical biosensing

The aim of this review is to summarize the most relevant contributions in the development of electrochemical (bio)sensors based on carbon nanotubes in the last years.Since the first application of carbon nanotubes in the preparation of an electrochemical sensor, an increasing number of publications involving carbon nanotubes-based sensors have been reported, demonstrating that the particular structure of carbon nanotubes and their unique properties make them a very attractive material for the design of electrochemical biosensors.The advantages of carbon nanotubes to promote different electron transfer reactions, in special those related to biomolecules; the different strategies for constructing carbon nanotubes-based electrochemical sensors, their analytical performance and future prospects are discussed in this article.     

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.