Hybridization and enzymatic extension of au nanoparticle-bound oligonucleotides

We have investigated the impact of steric effects on the hybridization and enzymatic extension of oligonucleotides bound to 12-nm colloidal Au particles. In these experiments, a nanoparticle-bound 12-mer sequence is hybridized either to its solution phase 12-mer complement or to an 88-mer template sequence. The particle-bound oligonucleotide serves as a primer for enzymatic extension reactions, in which covalent incorporation of nucleotides to form the complement of the template is achieved by the action of DNA polymerase. Primers were attached via-C(6)H(12)SH, -C(12)H(24)SH, and -TTACAATC(6)H(12)SH linkers attached at the 5' end. Primer coverage on the nanoparticles was varied by dilution with (5')HSC(6)H(12)AAA AAA(3'). Hybridization efficiencies were determined as a function of linker length, primer coverage, complement length (12-mer vs 88-mer), and primer:complement concentration ratio. In all cases, hybridization for the 88-mer was less efficient than for the 12-mer. Low primer surface coverage, greater particle-primer separation, and higher primer:complement ratios led to optimal hybridization. Hybridization efficiencies as high as 98% and 75% were observed for the 12-mer and 88-mer, respectively. Enzymatic extension of particle-bound primers was observed under all conditions tested; however, the efficiency of the reaction was strongly affected by linker length and primer coverage. Extension of primers attached by the longest linker was as efficient as the solution-phase reaction.     

Deoxygenation of tertiary amine N-oxides under metal free condition using phenylboronic acid

A simple and efficient method for the deoxygenation of amine N-oxides to corresponding amines is reported using the green and economical reagent phenylboronic acid. Deoxygenation of N,N-dialkylaniline N-oxides, trialkylamine N-oxides and pyridine N-oxides were achieved in good to excellent yields. The reduction susceptible functional groups such as ketone, amide, ester and nitro groups are well tolerated with phenylboronic acid during the deoxygenation process even at high temperature. In addition, an indirect method for identification and quantification of tert-amine N-oxide is demonstrated using UV–Vis spectrometry which may be useful for drug metabolism studies.     

Molar extinction coefficients of some carbohydrates in aqueous solutions

Molar extinction coefficients of some carbohydrates viz. l-arabinose (C₅H₁₀O₅), d-glucose (C₆H₁₂O₆), d-mannose (C₆H₁₂O₆), d-galactose (C₆H₁₂O₆), d(-) fructose (C₆H₁₂O₆) and maltose (C₁₂H₂₄O₁₂) in aqueous solutions have been determined at 81, 356, 511, 662, 1173 and 1332 keV by gamma ray transmission method in a narrow beam good geometry set-up. These coefficients have been found to depend upon the photon energy following a 4-parameter polynomial. These extinction coefficients for different sugars having the same molecular formula have same values varying within experimental uncertainty. Within concentration ranges studied, Beer-Lambert law is obeyed very well.     

Measurement of temperature of a dusty plasma from its configuration

A new concept called “configurational temperature” is introduced in the context of dusty plasma, where the temperature of the dust particles submerged in the plasma can be measured directly from the positional information of the individual dust particles and the interaction potential between the dust grains. This method does not require the velocity information of individual particles, which is a key parameter to measure the dust temperature in the conventional method. The technique is initially tested using two-dimensional (2D) OpenMP parallel molecular dynamics and Monte Carlo simulation and then compared with the temperature evaluated from experimental data. The experiment have been carried out in the Dusty Plasma Experimental (DPEx) device, where a 2D stationary plasma crystal of melamine formaldehyde particles is formed in the cathode sheath of a DC glow discharge argon plasma. The kinetic temperature of the dust is calculated using the standard particle image velocimetry technique at different pressures. An extended simulation result for the three-dimensional case is also presented, which can be employed for the temperature measurement of a three-dimensional dust crystal in laboratory devices.     

Cytotoxic Oligomers and Fibrils Trapped in a Gel‐like State of α‐Synuclein Assemblies

α‐Synuclein (α‐Syn) aggregation is associated with Parkinson's disease (PD) pathogenesis. In PD, the role of oligomers versus fibrils in neuronal cell death is debatable, but recent studies suggest oligomers are a proximate neurotoxin. Herein, we show that soluble α‐Syn monomers undergo a transformation from a solution to a gel state on incubation at high concentration. Detailed characterization of the gel showed the coexistence of monomers, oligomers, and short fibrils. In vitro, the gel was highly cytotoxic to human neuroblastoma cells. The individual constituents of the gel are short‐lived species but toxic to the cells. They comprise a structurally heterogeneous population of α‐helical and β‐sheet‐rich oligomers and short fibrils with the cross‐β motif. Given the recent evidence of the gel‐like state of the protein associated with neurodegenerative diseases, the gel state of α‐Syn in this study represents a mechanistic and structural model for the in vivo toxicity of α‐Syn in PD.     

Vibrational spectra, normal coordinate analysis and thermodynamics of 2, 5-difluorobenzonitrile

The FTIR spectrum of 2, 5-difluorobenzonitrile has been recorded in the region 200–4000 cm⁻¹ (in liquid phase). The laser Raman spectrum in the range of 0–3500 cm⁻¹ (in liquid phase) has also been recorded. The spectra have been analyzed assuming C _s point group symmetry for the molecule. A zero-order normal coordinate analysis has been made for the molecule using force constants derived earlier. On the basis of potential energy distributions and eigen vectors unambiguous vibrational assignments have been made for all the fundamentals of the molecule. Thermodynamic functions have also been computed in the temperature range 200–1000 K by utilizing the observed fundamental frequencies assuming rigid-rotor harmonic oscillator approximation.     

Geometrical parameters,vibrational wavenumbers,and relationships established with six difluorobenzonitriles

The geometry, vibrational wavenumbers, and thermodynamical parameters have been calculated using density functional methods (DFT) for benzonitrile (BN) and the six difluorobenzonitriles (DFBNs) of the series. The results were compared with the available experimental data, and correlations were established for the ? C?N and C? F moieties between the natural atomic charges and the geometrical parameters of the compounds. These relations were found as linear or slightly parabolic in most cases. Investigations were carried out to examine the effect of substituents on structural deformations and other properties. Correlations were also determined with the stretching vibrations. Other general conclusions have also been drawn. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

离子液体作为溶剂/催化剂用于卤代烃对胺的选择性烷基化反应

在三乙胺存在下,在离子液体([bmim]I和[bmim]PF6)中进行了各种卤代烃对胺类化合物中氨基的选择性烷基化反应.反应在相对温和的条件下进行,转化率和选择性优异.离子液体可以回收并重复使用.     

Homoconjugation in the adamantane cage: DFT/IGLO studies of the 1, 3-dehydro-5-adamantyl cation, its isoelectronic boron analogue 1, 3-dehydro-5-boraadamantane, and related systems(1)(,)

The structure of 1,3-dehydro-5-adamantyl cation and its isoelectronic boron analogue 1,3-dehydro-5-boraadamantane as well as some related adamantane systems, hitherto unknown as persistent long-lived species, were investigated by using the density functional theory (DFT) method. (13)C and (11)B NMR chemical shifts of the compounds were also calculated using the IGLO method. Stabilization of the systems due to homoconjugation is discussed.     

Theoretical study of relative width of photonic band gap for the 3-D dielectric structure

Calculations for the relative width (Δω/ω₀) as a function of refractive index and relative radius of the photonic band gap for the fcc closed packed 3-D dielectric microstructure are reported and comparison of experimental observations and theoretical predictions are given. This work is useful for the understanding of photonic crystals and occurrence of the photonic band gap.