Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations

Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.     

Thermodynamics of water entry in hydrophobic channels of carbon nanotubes

Experiments and computer simulations demonstrate that water spontaneously fills the hydrophobic cavity of a carbon nanotube. To gain a quantitative thermodynamic understanding of this phenomenon, we use the recently developed two phase thermodynamics method to compute translational and rotational entropies of confined water molecules inside single-walled carbon nanotubes and show that the increase in energy of a water molecule inside the nanotube is compensated by the gain in its rotational entropy. The confined water is in equilibrium with the bulk water and the Helmholtz free energy per water molecule of confined water is the same as that in the bulk within the accuracy of the simulation results. A comparison of translational and rotational spectra of water molecules confined in carbon nanotubes with that of bulk water shows significant shifts in the positions of the spectral peaks that are directly related to the tube radius.     

2-(2-Pyridyl) benzimidazole based Co(II) complex as an efficient fluorescent probe for trace level determination of aspartic and glutamic acid in aqueous solution: a displacement approach

A weakly fluorescent cobalt(II) complex is synthesized using 2-(2-pyridyl)-benzimidazole (PBI) as a chelating fluorescent ligand and characterized by single crystal X-ray structure. This complex serves as an efficient fluorescent probe for trace level determination of aspartic acid (AspA) and glutamic acid (GluA) in aqueous solution. Rest of the naturally occurring amino acids did not interfere. Both aspartic acid and glutamic acid replaces PBI from the coordination sphere of Co(II)-PBI complex resulting appearance of strong fluorescence signal for the released free PBI. The signal response is very fast and the interaction of both the AspA and GluA with the Co(II) is strong enough as evident from their displacement equilibrium constant values, viz. 4357.8 M(-1) and 8333.33 M(-1) respectively.     

Chitosan nanoparticles of 5-fluorouracil for ophthalmic delivery: characterization, in-vitro and in-vivo study

The aim of this investigation was to develop 5-fluorouracil (5-FU) loaded chitosan nanoparticles (CH-DNPs) for ophthalmic delivery. CH-DNPs were fabricated by ionotropic gelation mechanism using chitosan (CH) and a polyanion (TPP). The nanoparticles were smooth and spherical, confirmed by scanning electron microscopy (SEM) and atomic force microscope (AFM). CH/TPP mass ratio and TPP significantly changed the particles size morphology and encapsulation efficiency. The nanoparticles size ranged from approximately 114 to 192 nm and had a positive zeta potential (30±4 mV). The encapsulation efficiency, loading capacity and recovery of DNPs were 8.12-34.32%, 3.14-15.24% and 24.22 to 67% respectively. Physical characterization was done by Fourier transform infrared (FT-IR) and X-ray diffraction (XRD). No interaction was observed in between drug and polymer and crystallinity of drug was not changed in drug loaded nanoparticles. In-vitro release study of DNPs showed diffusion controlled release. Bioavailability study of batch CS9 was studied in rabbit eye and compare to 5-FU solution. 5-FU level was significantly higher in aqueous humor of rabbit eye. Ocular tolerance was studied in the eye of New Zealand rabbits and tested formulation was non-irritant with no sign of inflammation.     

Multiplex cancer cell detection by SERS nanotags with cyanine and triphenylmethine Raman reporters

SERS nanotags have been prepared to accomplish the multiplex detection of cancer cells. Herein we evaluated the adequacy of lipoic acid-containing cyanine derivatives (Cy3LA and Cy5LA) to function as multiplex partners with a triphenylmethine Raman reporter (B2LA) under a single excitation wavelength. SERS experiments enabled the multiplex recognition of two different cancer cells with antibody-conjugated nanotags that were derivatized with optimized cyanine and triphenylmethine reporters.     

Surfactant mediated oxygen reuptake in water for green aerobic oxidation: mass-spectrometric determination of discrete intermediates to correlate oxygen uptake with oxidation efficiency

A novel strategy of catalytic green aerobic oxidation by surfactant-mediated oxygen reuptake in water offers a new dimension to the applications of surfactants to look beyond as solubility aids and a conceptual advancement in understanding the role of surfactants in aquatic organic reactions through mass spectrometry guided identification of discrete intermediates.     

Chemoselectivity in the Cu-catalyzed O-arylation of phenols and aliphatic alcohols

An orthogonal set of Cu-catalysts for the selective mono-arylation of alkyl aryl diols using aryl iodides is presented. Picolinic acid ligated copper catalyst provided phenol O-arylation only, while alkyl aryl ethers are generated by ligand-free copper catalyst in the presence of 2 equivalents NaOt-Bu.     

PEGylated inorganic nanoparticles

Application of inorganic nanoparticles in diagnosis and therapy has become a critical component in the targeted treatment of diseases. The surface modification of inorganic oxides is important for providing diversity in size, shape, solubility, long-term stability, and attachment of selective functional groups. This Minireview describes the role of polyethylene glycol (PEG) in the surface modification of oxides and focuses on their biomedical applications. Such a PEGylation of surfaces provides "stealth" characteristics to nanomaterials otherwise identified as foreign materials by human body. The role of PEG as structure-directing agent in synthesis of oxides is also presented.     

Two storage inventory model in a mixed environment

Multi-item inventory models with two storage facility and bulk release pattern are developed with linearly time dependent demand in a finite time horizon under crisp, stochastic and fuzzy-stochastic environments. Here different inventory parameters—holding costs, ordering costs, purchase costs, etc.—are assumed as probabilistic or fuzzy in nature. In particular cases stochastic and crisp models are derived. Models are formulated as profit maximization principle and three different approaches are proposed for solution. In the first approach, fuzzy extension principle is used to find membership function of the objective function and then it’s Graded Mean Integration Value (GMIV) for different optimistic levels are taken as equivalent stochastic objectives. Then the stochastic model is transformed to a constraint multi-objective programming problem using Stochastic Non-linear Programming (SNLP) technique. The multi-objective problems are transferred to single objective problems using Interactive Fuzzy Satisfising (IFS) technique. Finally, a Region Reducing Genetic Algorithm (RRGA) based on entropy has been developed and implemented to solve the single objective problems. In the second approach, the above GMIV (which is stochastic in nature) is optimized with some degree of probability and using SNLP technique model is transferred to an equivalent single objective crisp problem and solved using RRGA. In the third approach, objective function is optimized with some degree of possibility/necessity and following this approach model is transformed to an equivalent constrained stochastic programming problem. Then it is transformed to an equivalent single objective crisp problem using SNLP technique and solved via RRGA. The models are illustrated with some numerical examples and some sensitivity analyses have been presented.