Efficient preparation of amine-modified oligodeoxynucleotide using modified H-phosphonate chemistry for DNA microarray fabrication

Amine-modified oligodeoxynucleotides (AMO) are commonly used probe oligodeoxynucleotides for DNA microarray preparation. Two methods are currently used for AMO preparation—use of amine phosphoramidites protected by acid-labile monomethoxytrityl (MMT) groups or alkali-labile trifluoroacetyl (TFA) groups. Because conventional AMO preparation procedures have defects, for example stringent acidic conditions are required for deprotection of MMT and hydrophobic purification cannot be used for TFA-protected amino groups, conventional preparation of AMO is unlikely to result in the expected outcome. In this paper a method of AMO synthesis using modified H-phosphonate chemistry is suggested. An aliphatic diamine is coupled with a phosphonate group forming a phosphoramidate linkage to the last internucleotide phosphate of oligodeoxynucleotides. In this method dimethoxytrityl (DMT) purification steps are used and stringent acid deprotection is not required to obtain the AMO. Although the method could lead to formation of AMO diastereomers, melting-temperature and CD analysis showed for two AMO that DNA duplex formation was the same as when normal oligodeoxynucleotides were used. Also, when these AMO were used as probes for DNA microarrays the immobilization efficiency was similar to that for AMO probes prepared by conventional means using an amino-modifier unit. The hybridization performance of these AMO was better than for those prepared conventionally. The procedures suggested would be useful for preparation of efficient AMO for fabrication of DNA microarrays and DNA-based nanoparticle systems. Nagendra Kumar Kamisetty and Seung Pil Pack have equally contributed to this work.     

Magnesium ion selective two-photon fluorescent probe based on a benzo[h]chromene derivative for in vivo imaging

A novel, two-photon probe for the detection of free Mg2+ ions in living cells and live tissues has been developed. The probe can be excited by 880 nm laser photons, emits strong two-photon excited fluorescence in response to Mg2+ ions, can be easily loaded into the cell and tissue, shows high photostability, and can measure the Mg2+ ion concentration without interference by Ca2+ ions in living cells. The intracellular dissociation constant (Kdi) for Mg2+ determined by the two-photon process is 2.5 mM, which is suitable for dynamic Mg2+ concentration measurement. In addition, the probe is capable of imaging endogenous stores of free Mg2+ at a few hundred micrometers depth in live tissues using two-photon microscopy (TPM).     

Effect of the Linking Structure of Nonlinear Optical Side Groups on the Phase Behavior of an Aromatic Polyester Backbone

Summary: The phase behavior of poly(p‐phenylene terephthalate)s (PPT) with pendant side groups, N‐(4‐nitrophenyl)ethylaminoethanol (NPE) and N‐(4‐nitrophenyl)‐L ‐prolinol (NPP) has been studied by using differential scanning calorimetry (DSC), wide‐angle X‐ray scattering (WAXS), and second harmonic generation (SHG). PPT‐NPE showed a layered liquid crystalline morphology while PPT‐NPP showed a completely amorphous structure. Compressive or shear stress applied on the polymer melt surface at 210 °C induced a more prominent layered structure of PPT‐NPE whereas the amorphous structure of PPT‐NPP remained unchanged under the stress. In order to understand this phase difference in terms of the repeat structure, we attempted theoretical ab initio Hartree‐Fock, and DFT calculations for the monomers and molecular dynamics for the bulk state. The results indicated that molecular configurations are a good way of microscopically understanding the phases of rigid backbone polymers with functional side groups: The NPT (constant particle number, pressure, and temperature) simulation data at 210 °C agree qualitatively with the experimental data and the difference between PPT‐NPE and PPT‐NPP could be understood using rotational energy barrier, steric hindrance and inter‐chain interactions. X‐ray diffractometer (XRD) simulation patterns for the oligomers are also in qualitative agreement with the experimental WAXS data and the structural parameters of stacks of PPT‐NPE chains are estimated to be layer distance (4.6 Å), backbone distance (21.5 Å), and side distance (12 Å).

     

Preparation of Ag‐Embedded Polystyrene Nanospheres and Nanocapsules by Miniemulsion Polymerization

An isopropyl myristate (IPM) biocompatible oil and an IPM solution of dodecanethiol‐capped Ag nanoparticles (NPs, 4.5 nm) were used as hydrophobes to suppress the Ostwald ripening of monomer/hydrophobe miniemulsified droplets in a surfactant‐stabilized water phase. The formation of non‐IPM‐encapsulated nanospheres (48 nm) and IPM‐encapsulated nanocapsules (90 nm) were precisely controlled by using a water‐soluble and an oil‐soluble initiator, respectively, in the presence of a pure IPM as a hydrophobe in miniemulsion polymerization. Well‐defined PS nanospheres, on which surfaces were coated with Ag NPs (Ag/PS nanospheres, 65 nm), and nanocapsules encapsulating both NPs and IPM liquid phase (Ag‐IPM/PS nanocapsules, 115 nm) were made by replacing the hydrophobe from pure IPM with Ag/IPM solution. These nanostructures were characterized by transmission and scanning electron microscopes.

     

On-line arbitrarily vertex decomposable suns

We give a complete characterization of on-line arbitrarily vertex decomposable graphs in the family of unicycle graphs called suns. A sun is a graph with maximum degree three, such that deleting vertices of degree one results in a cycle. This result has already been used in another paper to prove some Ore-type conditions for on-line arbitrarily decomposable graphs.     

Downward self‐polarization of lead‐free (K0.5Na0.5)(Mn0.005Nb0.995)O3 ferroelectric thin films on Nb:SrTiO3 substrate

Spontaneously appearing macroscopic polarization (self‐polarization) in ferroelectrics without an electrode or an external electric field would enable the freedom to design many ferroelectric heterostructures and devices. The (K_0.5Na_0.5)(Mn_0.005Nb_0.995)O₃ (KNMN) thin film was grown on Nb:SrTiO₃ single‐crystal substrate and the resultant self‐polarization behavior due to strain relaxation was investigated. The lattice mismatch and difference in TEC between the KNMN thin film and the Nb:SrTiO₃ substrate creates a compressive strain. The compressive strain gradient may be the main cause for the observed downward self‐polarization. The downward self‐polarization of the KNMN thin film can be explained by the strong inhomogeneous compressive strain caused by strain relaxation. (© 2016 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

An electron paramagnetic resonance study of Cu(II) sorbed on quartz

The nature of the interaction among Cu(II), adsorbed water, and quartz surface was studied using electron paramagnetic resonance (EPR) spectroscopy. The EPR lineshape gave information concerning the motional status of sorbed Cu(II) that revealed its binding strength at the surface. Two distinct absorption lines of sorbed Cu(II), namely, the liquid-type and the solid-type signal, were simultaneously observed at the fully hydrated surface at room temperature. The absorption lines and the variation of their intensity with experimental and measurement conditions such as degree of hydration, pH, ionic strength, and surface coverage indicated that there exist three kinds of Cu(II) entities, the inner-sphere surface complex, the outer-sphere surface complex, and the surface precipitate on the quartz surface, and that their concentrations change with experimental conditions. The reversible conversion of the liquid-type signal to the solid-type one during the drying-wetting or freezing-melting of the surface suggested the development of multiple layers of adsorbed water molecules on the quartz surface. It is assumed that the innermost layer of the water layers contains the inner-sphere Cu(II) surface complexes, while the outer layers contain the outer-sphere complexes whose binding strength decreases outward with increasing distance from the surface. The result of this work suggests that the sorption mechanism of a metal cation on a given mineral surface; hence its mobility in the environment may change significantly with the solution pH, the ionic strength, and the surface coverage.