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.     

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     

Assessing genotypic variability of cowpea (Vigna unguiculata [L.] Walp.) to current and projected ultraviolet-B radiation

The current and projected terrestrial ultraviolet-B (UV-B) radiation affects growth and reproductive potential of many crops. Cowpea (Vigna unguiculata [L.] Walp.), mostly grown in tropical and sub-tropical regions may already be experiencing critical doses of UV-B radiation due to a thinner ozone column in those regions. Better understanding of genotypic variability to UV-B radiation is a prerequisite in developing genotypes tolerant to current and projected changes in UV-B radiation. An experiment was conducted in sunlit, controlled environment chambers to evaluate the sensitivity of cowpea genotypes to a range of UV-B radiation levels. Six cowpea genotypes [Prima, California Blackeye (CB)-5, CB-27, CB-46, Mississippi Pinkeye (MPE) and UCR-193], representing origin of different geographical locations, were grown at 30/22 degrees C day/night temperature from seeding to maturity. Four biologically effective ultraviolet-B radiation treatments of 0 (control), 5, 10, and 15 kJ m(-2)d(-1) were imposed from eight days after emergence to maturity. Significant genotypic variability was observed for UV-B responsiveness of eighteen plant attributes measured. The magnitude of the sensitivity to UV-B radiation also varied among cowpea genotypes. Plants from all genotypes grown in elevated UV-B radiation were significantly shorter in stem and flower lengths and exhibited lower seed yields compared to the plants grown under control conditions. Most of the vegetative parameters, in general, showed a positive response to UV-B, whereas the reproductive parameters exhibited a negative response showing the importance of reproductive characters in determining tolerance of cultivars to UV-B radiation. However, all cultivars, except MPE, behaved negatively to UV-B when a combined response index was derived across parameters and UV-B levels. Based on the combined total stress response index (C-TSRI) calculated as sum of individual vegetative, physiological and reproductive component responses over the UV-B treatments, the genotypes were classified as tolerant (MPE), intermediate (CB-5, CB-46 and UCR-193) and sensitive (CB-27 and Prima) to UV-B radiation. The differences in sensitivity among the cowpea genotypes emphasize the need for selecting or developing genotypes with tolerance to current and projected UV-B radiation.     

Dye Degradation and Sulfur Oxidation of Methyl Orange and Thiophenol via Newly Designed Nanocomposite GQDs/NiSe-NiO Photocatalyst Under Homemade LED Light

Photocatalytic processes triggered by graphene-based photocatalysts under solar light have sparked interest as a new sort of instrument for solar chemical synthesis. Herein we investigated self-assembled graphene quantum dots (GQDs)/NiSe-NiO composite photocatalyst for organic transformation as well as dye degradation. The synthesized GQDs/NiSe-NiO composite photocatalyst has an excellent suitable band gap, high molar extinction coefficient, low toxicity and chemical/thermal stability. The GQDs/NiSe-NiO composite photocatalyst emerges as a new standard for sulfur oxidation and dye degradation reactions under homemade LED light with high yield.     

α-Synuclein Spontaneously Adopts Stable and Reversible α-Helical Structure in Water-Less Environment

A highly stable, spontaneous, and reversible α-helical-structure formation in recombinant and chemically modified α-synuclein protein is demonstrated for the first time in a water-less (1.5 % w/w H₂O) polymer surfactant environment. Using a combination of circular dichroism and ATR-FTIR spectroscopy, we show that whilst native α-synuclein in aqueous solution shows a predominant unordered conformation (≈64 %), mixing with polyethylene glycol based anionic polymer surfactant (PS) and removing water reveals a 25 % unordered, 25 % α-helical, and 27 % β-sheet structure. Interestingly, bioconjugation of native α-synuclein with a diamine molecule, to increase the positive charge on the protein chain, and subsequent electrostatic coupling with the PS forms a conjugate with a retained unordered structure. Removal of water from this system provides a highly stable α-helical (≈74 %) water-less liquid system. Surprisingly, the α-helical-to-unordered state transition is completely reversible and is achieved at ≈25–30 w/w% of water in the system. Moreover, the α-helix shows an extraordinary temporal stability (>6 months) in a waterless environment.     

Pyridones as NNRTIs against HIV-1 mutants: 3D-QSAR and protein informatics

CoMFA and CoMSIA based 3D-QSAR of HIV-1 RT wild and mutant (K103, Y181C, and Y188L) inhibitory activities of 4-benzyl/benzoyl pyridin-2-ones followed by protein informatics of corresponding non-nucleoside inhibitors’ binding pockets from pdbs 2BAN, 3MED, 1JKH, and 2YNF were analysed to discover consensus features of the compounds for broad-spectrum activity. The CoMFA/CoMSIA models indicated that compounds with groups which lend steric-cum-electropositive fields in the vicinity of C5, hydrophobic field in the vicinity of C3 of pyridone region and steric field in aryl region produce broad-spectrum anti-HIV-1 RT activity. Also, a linker rendering electronegative field between pyridone and aryl moieties is common requirement for the activities. The protein informatics showed considerable alteration in residues 181 and 188 characteristics on mutation. Also, mutants’ isoelectric points shifted in acidic direction. The study offered fresh avenues for broad-spectrum anti-HIV-1 agents through designing new molecules seeded with groups satisfying common molecular fields and concerns of mutating residues.