End-labeled free-solution electrophoresis of DNA

DNA is a free-draining polymer. This subtle but "unfortunate" property of highly charged polyelectrolytes makes it impossible to separate nucleic acids by free-flow electrophoresis. This is why one must typically use a sieving matrix, such as a gel or an entangled polymer solution, in order to obtain some electrophoretic size separation. An alternative approach consists of breaking the charge to friction balance of free-draining DNA molecules. This can be achieved by labeling the DNA with a large, uncharged molecule (essentially a hydrodynamic parachute, which we also call a drag-tag) prior to electrophoresis; the resulting methodology is called end-labeled free-solution electrophoresis (ELFSE). In this article, we review the development of ELFSE over the last decade. In particular, we examine the theoretical concepts used to predict the ultimate performance of ELFSE for single-stranded (ssDNA) sequencing, the experimental results showing that ELFSE can indeed overcome the free-draining issue raised above, and the technological advances that are needed to speed the development of competitive ELFSE-based sequencing and separation technologies. Finally, we also review the reverse process, called free-solution conjugate electrophoresis (FSCE), wherein uncharged polymers of different sizes can be analyzed using a short DNA molecule as an electrophoretic engine.     

Modeling of Thin-Layer Chromatographic Separation of Androstane Isomers

JPC – Journal of Planar Chromatography – Modern TLC - Modeling of thin-layer chromatographic separation of androstane isomers to find the optimum mobile phase is described in this...     

Adduct formation properties of mono- and bidentate phosphine oxide compounds in the liquid—liquid extraction of some divalent metals with 1-phenyl-3-methyl-4-benzoyl-5-pyrazolone

The bidentate phosphine oxide compounds bis(diphenylphosphinyl)methane (BDPPM) and bis(diphenylphosphinyl)ethane (BDPPE) were synthesized and the liquid—liquid extraction equilibria of some divalent metal ions such as Co(II), Ni(II), Zn(II) and Cd(II) with 1-phenyl-3-methyl-4-benzoyl-5-pyrazolone (HPMBP) and the neutral phosphine oxide compounds were investigated. BDPPM was found to be much more powerful than BDPPE and the monodentate neutral ligand trioctylphosphine oxide (TOPO). The composition of the extracted species were determined by a graphical method to be M(PMBP)₂(TOPO)_s (s = 2 for Co, Ni, Cd and s = 1 for Zn), M(PMBP)₂(BDPPM) and M(PMBP)₂(BDPPE). The adduct formation constants between the acylpyrazolone chelates and the neutral ligands were determined and are discussed in terms of the molecular structure.     

Plasma-mediated grafting of poly(ethylene glycol) on polyamide and polyester surfaces and evaluation of antifouling ability of modified substrates

A simple cold plasma technique was developed to functionalize the surfaces of polyamide (PA) and polyester (PET) for the grafting of polyethylene glycol (PEG) with the aim of reducing biofilm formation. The surfaces of PA and PET were treated with silicon tetrachloride (SiCl4) plasma, and PEG was grafted onto plasma-functionalized substrates (PA-PEG, PET-PEG). Different molecular weights of PEG and grafting times were tested to obtain optimal surface coverage by PEG as monitored by electron spectroscopy for chemical analysis (ESCA). The presence of a predominant C-O peak on the PEG-modified substrates indicated that the grafting was successful. Data from hydroxyl group derivatization and water contact angle measurement also indicated the presence of PEG after grafting. The PEG-grafted PA and PET under optimal conditions had similar chemical composition and hydrophilicity; however, different morphology changes were observed after grafting. Both PA-PEG and PET-PEG surfaces developed under optimal plasma conditions showed about 96% reduction in biofilm formation by Listeria monocytogenes compared with that of the corresponding unmodified substrates. This plasma functionalization method provided an efficient way to graft PEG onto PA and PET surfaces. Because of the high reactivity of Si-Cl species, this method could potentially be applied to other polymeric materials.     

Stereoselective adduct formation of α-acylcamphorato-copper(II) chelates with some chiral Lewis bases

The formation constants of the mono-adducts of α-acylcamphorato-copper(II) chelates such as (+)-Cu(facam)₂, (?)-Cu(facam)₂, (+)-Cu(hfbc)₂ and (?)-Cu(hfbc)₂ with some chiral Lewis bases were determined spectrophotometrically in benzene. In order to compare the adduct formation constants obtained with the (+)- and (?)-forms, some pairs of chiral Lewis bases such as 1-amino-2-propanol [(R)(?), (S)(+)], 1-(α-naphthyl)ethylamine [(R)(+), (S)(?)], α-phenyl ethylamine [(R)(+), (S)(?)] and also quinine and quinidine were examined as neutral ligands. Although not very pronounced, the effects of combinations obtained for (+)- or (?)-Cu(II) chelates and (+)- or (?)-ligands indicate that formation constants obtained by the formation of adducts with the ligands having different directions of the optical rotation seems to be superior to those with the same direction.     

The B-factor index for the binding site (BFIbs) to prioritize crystal protein structures for docking

Structural Chemistry - In cheminformatics, protein-ligand docking is a powerful tool applied for virtual screening, pose prediction, and binding affinity estimation. However, docking results depend...     

Metal-Free Arylation of Benzothiophenes at C4 by Activation as their Benzothiophene S-Oxides

Benzothiophenes, activated by oxidation to the corresponding S-oxides, undergo C−H/C−H-type coupling with phenols to give C4 arylation products. While an electron-withdrawing group at C3 of the benzothiophene is important, the process operates without a directing group and a metal catalyst, thus rendering it compatible with sensitive functionalities—e.g. halides and formyl groups. Quantum chemical calculations suggest a formal stepwise mechanism involving heterolytic cleavage of an aryloxysulfur species to give a π-complex of the corresponding benzothiophene and a phenoxonium cation. Subsequent addition of the phenoxonium cation to the C4 position of the benzothiophene is favored over the addition to C3; Fukui functions predict that the major regioisomer is formed at the more electron-rich position between C3 and C4. Varied selective manipulation of the benzothiophene products showcase the synthetic utility of the metal-free arylation process.     

Approximation by complex szász-durrmeyer operators in compact disks

In the present paper, we deal with the complex Szász-Durrmeyer operators and study Voronovskaja type results with quantitative estimates for these operators attached to analytic functions of exponential growth on compact disks. Also, the exact order of approximation is found.     

APPROXIMATION BY COMPLEX SZASZ-DURRMEYER OPERATORS IN COMPACT DISKS

In the present paper, we deal with the complex Szasz-Durrmeyer operators and study Voronovskaja type results with quantitative estimates for these operators attached to analytic functions of exponential growth on compact disks. Also, the exact order of approximation is found.