An Improved Protocol for DNA Extraction from Alkaline Soil and Sediment Samples for Constructing Metagenomic Libraries

An improved single-step protocol has been developed for extracting pure community humic substance-free DNA from alkaline soils and sediments. The method is based on direct cell lysis in the presence of powdered activated charcoal and polyvinylpolypyrrolidone followed by precipitation with polyethyleneglycol and isopropanol. The strategy allows simultaneous isolation and purification of DNA while minimizing the loss of DNA with respect to other available protocols for metagenomic DNA extraction. Moreover, the purity levels are significant, which are difficult to attain with any of the methods reported in the literature for DNA extraction from soils. The DNA thus extracted was free from humic substances and, therefore, could be processed for restriction digestion, PCR amplification as well as for the construction of metagenomic libraries.     

meso-meso-Linked corrole dimers with modified cores: synthesis, characterization, and properties

The synthesis and characterization of the first examples of core-modified corrole dimers linked through the meso positions are described. The dimers are obtained by a simple Ag(I)- or Fe(III)-catalyzed coupling reaction in near-quantitative yields. The corroles obtained are metalated with metal ions, such as Cu(II) and Ni(II). The electronic-absorption spectral studies reveal weak electronic interaction between the two subunits and the exciton coupling observed for the free-base corrole dimer (1717 cm(-1)) is lower than that for the corresponding protonated derivative (4081 cm(-1)). The solution-state structure derived from (1)H and two-dimensional NMR spectral studies reveals a noncoplanar arrangement of two corrole units. Geometry optimization at the B3LYP-631G level also confirms the noncoplanar arrangement of corroles with a dihedral angle of 64.8 degrees between two corrole planes. The electron paramagnetic resonance (EPR) and magnetic characterization studies on the paramagnetic copper-metalated dimer indicate that both copper ions behave as independent spins without any noticeable interaction. Results of fluorescence studies reveal a bathochromic shift of about 60 nm upon dimerization. The first hyperpolarizability (beta) measured by using the hyper Rayleigh scattering (HRS) method reveals doubling of the beta values on progressing from monomer to dimer, attributed to enhanced pi conjugation. The use of copper dimers in the photocleavage of DNA is also explored. It is shown that the bimetallic copper dimer selectively cleaves the nucleic acids without affecting the proteins, suggesting a possible application of the copper complex in the removal of nucleic acid contaminants from protein extracts through a simple photolytic pathway.     

Barrel- and crown-shaped dodecanuclear copper(II) cages built from phosphonate, pyrazole, and hydroxide ligands

The reaction of Cu(ClO4)2. 6H2O with t-BuP(O)(OH)2 and 3,5-(CF3)2PzH in the presence of triethylamine afforded the dodecanuclear cage ([Et3NH]2[Cu12(mu-3,5-(CF3)2Pz)6(mu3-OH)6(mu-OH)3(mu3-t-BuPO3)2(mu6-t-BuPO3)3][t-BuPO2OH][C6H5CH3]2) (2). The molecular structure of this cage revealed that it possesses a barrel-shaped architechture. The cage structure is built by the cumulative coordination action of phosphonate, hydroxide, and pyrazolyl ligands. A similar reaction involving Cu(NO3)2. 3H2O, t-BuP(O)(OH)2, 3,5-dimethylpyrazole, and triethylamine afforded another dodecanuclear cage [Cu12(mu-DMPz)8(eta1-DMPzH)2(mu4-O)2(mu3-OH)4(mu3- t-BuPO3)4].3MeOH (3). The latter is crown-shaped and is built by the coordination of pyrazole, pyrazolyl, phosphonate, hydroxide, oxide, and methanol ligands. Both of the dodecanuclear cages are efficient nucleases in the presence of magnesium monoperoxyphthalate.     

Reactivity of a sterically hindered Fe(II) thiolate dimer with amines and hydrazines

The sterically hindered Fe(II) thiolate dimer Fe(2)(mu-STriph)(2)(STriph)(2) (1; [STriph](-) = 2,4,6-triphenylbenzenethiolate) reacts with primary amines ((t)BuNH(2), aniline) and N(2)H(4) to form the structurally characterized addition complexes Fe(STriph)(2)(NH(2)(t)Bu)(2), Fe(2)(mu-STriph)(2)(STriph)(2)(NH(2)Ph)(2), and Fe(2)(mu-eta(1):eta(1)-N(2)H(4))(2)(N(2)H(4))(4)(STriph)(4) in high yield. Chemical and NMR spectroscopic evidence indicate that the binding of these nitrogen donors is labile in solution and multispecies equilibria are likely. With arylhydrazines, 1 catalytically disproportionates 1,2-diphenylhydrazine to aniline and azobenzene, and it rearranges 1-methyl-1,2-diarylhydrazines to give, after treatment with alumina, mononuclear, trigonal bipyramidal Fe(III) complexes of composition Fe(ISQ)(2)(STriph), where [ISQ](-) denotes an appropriately substituted bidentate o-diiminobenzosemiquinonate ligand. Complex 1 shows no reaction with hindered 1,2-dialkylhydrazines (isopropyl or tert-butyl) or tetrasubstituted 1,2-dimethyl-1,2-diphenylhydrazine.     

Carbon nanotube-nucleobase hybrids: nanorings from uracil-modified single-walled carbon nanotubes

Single‐walled carbon nanotubes (SWCNTs) have been covalently functionalized with uracil nucleobase. The hybrids have been characterized by using complementary spectroscopic and microscopic techniques including solid‐state NMR spectroscopy. The uracil‐functionalized SWCNTs are able to self‐assemble into regular nanorings with a diameter of 50–70 nm, as observed by AFM and TEM. AFM shows that the rings do not have a consistent height and thickness, which indicates that they may be formed by separate bundles of CNTs. The simplest model for the nanoring formation likely involves two bundles of CNTs interacting with each other via uracil–uracil base‐pairing at both CNT ends. These nanorings can be envisaged for the development of advanced electronic circuits.     

A simple and reliable semipreparative high-performance liquid chromatography technique for the isolation of marker-grade hyperforin from Hypericum perforatum L extract

The present work describes isolation of bioactive lipophilic constituent [namely, hyperforin from St. John's wort (Hypericum perforatum L.)], of approximately 98% purity by semipreparative high-performance liquid chromatography (LC). The extraction, isolation, and analysis of the collected compound is performed without the use of antioxidants and inert gas atmospheres at all the stages. Hyperforin, separated isocratically on a 12microm semiprep column, is obtained in high purity, lyophilized after the removal of the organic phase, and preserved at a low temperature. The purity of the collected marker compound is estimated by the use of LC-mass spectrometry and spectroscopic techniques.     

Conformational landscape of the HIV-V3 hairpin loop from all-atom free-energy simulations

Small beta hairpins have many distinct biological functions, including their involvement in chemokine and viral receptor recognition. The relevance of structural similarities between different hairpin loops with near homologous sequences is not yet understood, calling for the development of methods for de novo hairpin structure prediction and simulation. De novo folding of beta strands is more difficult than that of helical proteins because of nonlocal hydrogen bonding patterns that connect amino acids that are distant in the amino acid sequence and there is a large variety of possible hydrogen bond patterns. Here we use a greedy version of the basin hopping technique with our free-energy forcefield PFF02 to reproducibly and predictively fold the hairpin structure of a HIV-V3 loop. We performed 20 independent basin hopping runs for 500 cycles corresponding to 7.4 x 10(7) energy evaluations each. The lowest energy structure found in the simulation has a backbone root mean square deviation (bRMSD) of only 2.04 A to the native conformation. The lowest 9 out of the 20 simulations converged to conformations deviating less than 2.5 A bRMSD from native.     

Templated growth of hybrid structures at the peptide-peptide interface

This study describes the use of peptide vesicular platforms for the templated growth of fibrillar structures to craft hybrids that retain the gross morphological features of two discreet self-assembled peptides. A synthetic triskelion peptide, which results in the rapid emergence of self-assembled spherical structures, was employed as a template. Addition of either one of two different peptides, both of which form long filamentous structures when co-incubated with the triskelion solution, affords hybrids that retain the gross morphology of both the spherical and filamentous structures. It is surmised that this process is aided by hydrogen bonding and the interdigitation of aromatic residues, which leads to the growth of hybrid structures. We believe that observations concerning the surface-assisted growth of peptide fibrils and tubular structures from vesicular platforms may have ramifications for the design and development of peptide-based hybrid materials with controlled hierarchical structures.     

（E）—2—甲基—1,3—戊二烯的振动光谱及其稳定构象的研究

记录了（Ｅ）－２－二甲基－１，３－戊二烯的固，液，气态ＦＴＩＲ光谱（４００～４０００ｃｍ＾－１）和固、液态Ｒａｍａｎ光谱（５０～４０００ｃｍ＾－１），观测了６８５及６５８ｃｍ＾－１谱线的变温ＦＴＩＲ光谱（－７３～１０℃），对所得谱图进行了指认分析发现，该化合物存在两种单键旋构象异构体ｓ－ｔｒａｎｓ和ｓ－ｃｉｓ，由变温ＦＴＩＲ光谱峰强度随温度的变化得到了这两种构象互变的△Ｈ＾０和△Ｓ＾０。