Interaction between 14mer DNA oligonucleotide and cationic surfactants of various chain lengths

In the recent genomic era, a novel gene silencing approach has been introduced based on the use of small synthetic oligonucleotides, such as antisense RNAs, siRNAs, to inhibit the expression of a specific target gene. Successful implementation of this methodology calls for the development of efficient systems to deliver small oligonucleotides into the cells using various natural and synthetic cationic agents. While extensive studies have focused on the interaction of various natural and synthetic cationic surfactants with long DNA, less attention has been paid to surfactant interaction with small oligonucleotides. In this study, the interaction between 14mer double stranded DNA and alkyltrimethylammonium bromides of C16 (cetyl, CTAB), C14 (tetradecyl, TTAB), and C12 (dodecyl, DTAB) chain lengths was investigated at different charge ratios by gel electrophoresis, ethidium bromide exclusion, circular dichroism, and UV melting. Our gel studies at 1 microM oligonucleotide concentration showed that CTAB, TTAB, and DTAB neutralize the oligonucleotides at a charge ratio (Z+/-) of 1, 14, and 50, respectively. At lower charge ratios, CTAB and TTAB interact with oligonucleotides, and the complexes show electrophoretic mobility shifts in the gel, while such mobility shifts were completely absent in the case of DTAB. UV melting experiments revealed that interaction with all three surfactants increased the thermostability of the oligonucleotide. The extent of thermal stabilization was highest in the case of CTAB, moderate in the case of TTAB, and extremely low in the case of DTAB. Oligonucleotides within fully neutralized complexes denatured at further higher temperatures, and again, stabilization was the highest in the case of CTAB followed by TTAB and DTAB, hence revealing that the oligonucleotides interacted more strongly with CTAB than with the other two surfactants. Ethidium bromide exclusion studies also supported our UV melting studies, confirming that CTAB binds most strongly to the oligonucleotide. CD titrations of oligonucleotides with increasing amounts of surfactants revealed common spectral patterns consisting of the progressive loss of CD signals for native helical DNA conformations. Overall, our results demonstrate that interaction between oligonucleotides and cationic surfactants, although qualitatively similar to long double stranded DNA, shows subtle differences that need to be understood to improve small oligonucleotide delivery into the cells by using common delivery agents that have been used to deliver long pieces of DNA.     

Functional group dependent dissociative electron attachment to simple organic molecules

Dissociative electron attachment (DEA) cross sections for simple organic molecules, namely, acetic acid, propanoic acid, methanol, ethanol, and n-propyl amine are measured in a crossed beam experiment. We find that the H(-) ion formation is the dominant channel of DEA for these molecules and takes place at relatively higher energies (>4 eV) through the core excited resonances. Comparison of the cross sections of the H(-) channel from these molecules with those from NH(3), H(2)O, and CH(4) shows the presence of functional group dependence in the DEA process. We analyze this new phenomenon in the context of the results reported on other organic molecules. This discovery of functional group dependence has important implications such as control in electron induced chemistry and understanding radiation induced damage in biological systems.     

An expeditious route toward pyrazine-containing nucleoside analogues

An improved and convenient methodology for the synthesis of asymmetrically substituted pyrazines starting from 3,5-dichloropyrazin-2(1H)-ones has been elaborated. Several nucleoside analogues have been synthesized containing the pyrazine core as the organic base coupled with the sugar via a triazole linkage. The beneficial effect of microwave irradiation throughout the sequence has been demonstrated.     

Microwave-assisted C-C bond forming cross-coupling reactions: an overview

Among the fundamental transformations in the field of synthetic organic chemistry, transition-metal-catalyzed reactions provide some of the most attractive methodologies for the formation of C-C and C-heteroatom bonds. As a result, the application of these reactions has increased tremendously during the past decades and cross-coupling reactions became a standard tool for synthetic organic chemists. Furthermore, a tremendous upsurge in the development of new catalysts and ligands, as well as an increased understanding of the mechanisms, has contributed substantially to recent advances in the field. Traditionally, organic reactions are carried out by conductive heating with an external heat source (for example, an oil bath). However, the application of microwave irradiation is a steadily gaining field as an alternative heating mode since its dawn at the end of the last century. This tutorial review focuses on some of the recent developments in the field of cross-coupling reactions assisted by microwave irradiation.     

Characterization of collagen thin films for von Willebrand factor binding and platelet adhesion

Von Willebrand factor (VWF) binding and platelet adhesion to subendothelial collagens are initial events in thrombus formation at sites of vascular injury. These events are often studied in vitro using flow assays designed to mimic vascular hemodynamics. Flow assays commonly employ collagen-functionalized substrates, but a lack of standardized methods of surface ligation limits their widespread use as a clinical diagnostic. Here, we report the use of collagen thin films (CTF) in flow assays. Thin films were grown on hydrophobic substrates from type I collagen solutions of increasing concentration (10, 100, and 1000 μg/mL). We found that the corresponding increase in fiber surface area determined the amount of VWF binding and platelet adhesion. The association rate constant (k(a)) of plasma VWF binding at a wall shear stress of 45 dyn/cm(2) was 0.3 × 10(5), 1.8 × 10(5), and 1.6 × 10(5) M(-1) s(-1) for CTF grown from 10, 100, and 1000 μg/mL solutions, respectively. We observed a 5-fold increase in VWF binding capacity with each 10-fold increase in collagen solution concentration. The association rates of Ser1731Thr and His1786Asp VWF mutants with collagen binding deficiencies were 9% and 22%, respectively, of wild-type rates. Using microfluidic devices for blood flow assays, we observed that CTF supported platelet adhesion at a wall shear rate of 1000 s(-1). CTF grown from 10 and 100 μg/mL solutions had variable levels of platelet surface coverage between multiple normal donors. However, CTF substrates grown from 1000 μg/mL solutions had reproducible surface coverage levels (74 ± 17%) between normal donors, and there was significantly diminished surface coverage from two type 1 von Willebrand disease patients (8.0% and 24%). These results demonstrate that collagen thin films are homogeneous and reproducible substrates that can measure dysfunctions in VWF binding and platelet adhesion under flow in a clinical microfluidic assay format.     

Conformational polymorphism in bicalutamide: a quantum chemical study

Bicalutamide is an anti-neoplastic drug widely used for the treatment of prostate cancer and it exhibits conformational polymorphism. Three crystal structures of bicalutamide are reported as racemic mixtures, two of which are polymorphs. In addition, three co-crystals are also reported—two with organic coformers and one with adrenoreceptor (the macromolecular target). All the reported structures show significant conformational differences. Quantum chemical B3LYP/6-31+G(d,p) analysis has been carried out to understand the interplay of intra- and intermolecular interactions leading to the conformational preferences in this molecule. The difference between the two polymorphic forms has been traced to the C5–S8–C11–C12 torsional angle. Inside the cavity of androgen receptor, a completely different conformation is found but it does not correspond to any local minima on the potential energy surface of the drug. A relatively rigid torsional angle C11–C12–C15–N17 is also expected due to a strong five-membered ring intramolecular hydrogen bond (H–O13–C12–C15–O16), which has been reported to be desirable; quantum chemical analysis revealed that this rigidity is of the order of 11 kcal/mol. Ab initio calculations demonstrate that polymorphs and polymorphic co-crystals differ in the extent of intra- and intermolecular hydrogen bonding interactions. The strength of the intermolecular interactions associated with these structures is analyzed in terms of energy release due to dimerization.     

Swift heavy ion induced effects at Mo/Si interface and silicide formation

Swift heavy ion (SHI) induced modification at metal/Si interfaces has emerged as an interesting field of research due to its large applications. In this study, we investigate SHI‐induced mixed molybdenum silicide film with ion fluences. The molybdenum thin films were deposited on silicon substrates using e‐beam evaporation at 10^?8 torr vacuum. Thin films were irradiated with Au ions of energy 120 MeV to form molybdenum silicide. The samples were characterized by grazing incidence X‐ray diffraction (GIXRD) technique for the identification of phase formation at the interface. Rutherford backscattering spectrometry (RBS) was used to investigate the elemental distribution in the films. The mixing rate calculations were made and the diffusivity values obtained lead to a transient melt phase formation at the interface according to thermal spike model. Irradiation‐induced effects at surface have been observed and roughness variations at the surface were calculated using atomic force microscopy (AFM) technique. Copyright © 2009 John Wiley & Sons, Ltd.     

Additive-free Aqueous Dispersions of Two-Dimensional Materials with Glial Cell Compatibility and Enzymatic Degradability

Water-dispersible two-dimensional (2D) materials are desirable for diverse applications. Aqueous dispersions make processing safer and greener and enable evaluation of these materials on biological and environmental fronts. To evaluate the effects of 2D materials with biological systems, obtaining dispersions without additives is critical and has been a challenge. Herein, a method was developed for obtaining additive-free aqueous dispersions of 2D materials like transition metal dichalcogenides and hexagonal boron nitride (h-BN). The nanosheet dispersions were investigated through spectroscopic and microscopic methods, along with the role of size on stability. The aqueous media enabled investigations on cytocompatibility and enzymatic degradation of molybdenum disulphide (MoS₂) and h-BN. Cytocompatibility with mixed glial cells was observed up to concentrations of 100 μg mL⁻¹, suggesting their plausible usage in bioelectronics. Besides, biodegradation using human myeloperoxidase (hMPO) mediated catalysis was investigated through Raman spectroscopy and electron microscopy. The findings suggested that additive-free 2H-MoS₂ and h-BN were degradable by hMPO, with 2H-phase exhibiting better resistance to degradation than the 1T-phase, while h-BN exhibited slower degradation. The findings pave a path for incorporating 2D materials in the burgeoning field of transient bioelectronics.     

Preparation and characterization of Pr2NiO4+δ infiltrated into Gd-doped ceria as SOFC cathode

Journal of Solid State Electrochemistry - Composite electrodes of Pr2NiO4+δ and Gd-doped ceria (Ce0.8Gd0.2O1.90 so-called GDC) have been prepared starting from a Pr-Ni nitrate solution (2:1...