Genomic organization, nucleotide sequence analysis of the core histone genes cluster in Chlamys farreri and molecular evolution assessment of the H2A and H2B

This work represents the nucleotide sequence of the core histone gene cluster from scallop Chlamys farreri. The tandemly repeated unit of 5671 bp containing a copy of the four core histone genes H4, H2B, H2A and H3 was amplified and identified by the techniques of homology cloning and genomic DNA walking. All the histone genes in the cluster had the structures in their 3' flanking region which related to the evolution of histone gene expression patterns throughout the cell cycle, including two different termination signals, the hairpin structure and at least one AATAAA polyadenylation signal. In their 5' region, the transcription initiation sites with a conserved sequence of 5'-PyATTCPu-3' known as the CAP site were present in all genes except to H2B, generally 37-45 bp upstream of the start code. Canonical TATA and CAAT boxes were identified only in certain histone genes. In the case of the promoters of H2B and H2A genes, there was a 5'-GATCC-3' element, which had been found to be essential to start transcription at the appropriate site. After this element, in the promoter of H2B, there was another sequence, 5'-GGATCGAAACGTTC-3', which was similar to the consensus sequence of 5'-GGAATAAACGTATTC-3' corresponding to the H2B-specific promoter element. The presence of enhancer sequences (5'-TGATATATG-3') was identified from the H4 and H3 genes, matching perfectly with the consensus sequence defined for histone genes. There were several slightly more complex repetitive DNA in the intergene regions. The presence of the series of conserved sequences and reiterated sequences was consistent with the view that mollusc histone gene cluster arose by duplicating of an ancestral precursor histone gene, the birth-and-death evolution model with strong purifying selection enabled the histone cluster less variation and more conserved function. Meanwhile, the H2A and the H2B were demonstrated to be potential good marks for phylogenetic analysis. All the results will be contributed to the characterization of repeating histone gene families in molluscs.

Molecular dynamics study on the phase diagrams of linear and branched chain molecules

The particle transfer molecular dynamics is used to study the phase equilibria of linear and branched chain molecules. The scaling of the critical temperature versus chain length is obtained and the critical densities are found to decrease with increasing chain length, which are in agreement with the results of experiment and theory. The phase diagrams of the linear and the branched chain molecules nearly overlap with each other. Moreover, the radial distribution functions of linear and branched chain molecules in gas phase are very similar, but in the liquid phase, they are different for different kinds of chains.

The electrochemical behavior of a system with a limited number of molecules

In this paper, based on Einstein relationship between diffusion and random walk, the electrochemical behavior of a system with a limited number of molecules was simulated and explored theoretically. The transition of the current vs time responses from discrete to continuous was clearly obtained as the number of redox molecules increased from 10 to 10(6).

Single-walled carbon nanotubes binding to human telomeric i-motif DNA under molecular-crowding conditions: More water molecules released

The natural occurrence of the human telomeric G-quadruplex or i-motif in vivo has not been demonstrated and the biological effects of the induction of these structures need to be clarified. Intracellular environments are highly crowded with various biomolecules and in vitro studies under molecular-crowding conditions will provide important information on how biomolecules behave in cells. Here we report that cell-mimic crowding can increase i-motif stability at acid pH and cause dehydration.

Real-Time Study of Genomic DNA Structural Changes upon Interaction with Small Molecules Using Dual-Polarization Interferometry

The structural changes of genomic DNA upon interaction with small molecules have been studied in real time using dual-polarization interferometry (DPI). Native or thermally denatured DNA was immobilized on the silicon oxynitride surface via a preadsorbed poly(ethylenimine) (PEI) layer. The mass loading was similar for both types of DNA, however, native DNA formed a looser and thicker layer due to its rigidity, unlike the more flexible denatured DNA, which mixed with PEI to form a denser and thinner layer. Ethidium bromide (EtBr), a classical intercalator, induced the large thickness decrease and density increase of native DNA (double-stranded), but a slight increase in both the thickness and density of denatured DNA (partial single-stranded).

Interweaving of single-helical and equal double-helical chains with the same helical axis in a 3D metal-organic framework

A novel metal-organic framework with unprecedented interweaving of coaxial single-helical and equal double-helical chains of opposite chirality, which features a super-connective helix simultaneously tangling with eight helices, was reported.

Thiacalix[4]arene-Supported Planar Ln(4) (Ln = Tb-III, Dy-III) Clusters: Toward Luminescent and Magnetic Bifunctional Materials

This paper reports the syntheses, crystal structures, and luminescent and magnetic properties of four tetranuclear Tb-III (1 and 3) and Dy-III (2 and 4) complexes supported by p-phenylthiacalix[4]arene (H(4)PTC4A) and p-tert-butylthiacalix-[4]arene (H(4)TC4A). All four frameworks can be formulated as [Ln(4)(III)(PTC4A/TC4A)(2)(mu(4)-OH)Cl-3(CH3OH)(2)(H2O)(3)], and some methanol and water solvent molecules are occupied in the interstices. The compounds are featured with a sandwichlike unit constructed by two tail-to-tail calixarene molecules and a planar tetragonal (mu(4)-OH)Ln(4) cluster. The photoluminescent analyses suggest that there is an efficient ligand-to-Ln(III) energy transfer for compounds 1-3 and H(4)PTC4A is a more efficient "antenna" than H(4)TC4A.

Assembly of 'discrete' (H2O)(16) water clusters within a supramolecular compound of calixarene

A 'discrete' (H2O)(16) cluster, featuring four basic cyclic nine-membered rings and a twelve-membered ring, illustrates a new mode of supramolecular association of water molecules.

Monitoring catalytic degradation of dye molecules on silver-coated ZnO nanowire arrays by surface-enhanced Raman spectroscopy

Catalytic degradation of organic dye molecules has attracted extensive attention due to their high toxicity to water resources. In this paper, we propose a novel method for the fabrication of uniform silver-coated ZnO nanowire arrays. The degradation of typical dye molecule rhodamine 6G (R6G), as an example, is investigated in the presence of the as-prepared silver-coated ZnO nanowire arrays. The experimental results show that such composite nanostructures exhibit high catalytic activity, and the reaction follows pseudo-first-order kinetics. Furthermore, these nanowire arrays are desirable SERS substrates for monitoring the catalytic degradation of dye molecules. Compared with traditional UV-visible spectroscopy, SERS technology can reflect more truly the catalytic degradation process occurring on the surface of the catalysts.

Chemical Bonding and Electronic Structure of 4d-Metal Monosulfides

Bond distances, vibrational frequencies, dissociation energies, electron affinities, ionization potentials and dipole moments of the title molecules in neutral and charged ions were studied by use of density functional method. Ground states for each molecule were assigned. The calculated bond distance decreases with the increasing of atomic number of 4d metals, reaches minimum at RhS, then increases. For cationic molecules, the calculated bond distance decreases to the minimum at MoS+, then increases. The calculated vibrational frequency decreases from YS(YS+) to PdS(PdS+) for both neutral and cationic molecules. The bond ionic character decreases from YS(YS+) to PdS(PdS+) for neutral and cationic molecules. The bonding patterns are discussed and compared with the available studies.

Magnetic Coupling between Copper(II) Ions Mediated by Hydrogen-Bonded (Neutral) Water Molecules

A new hydrogen-bonded dinuclear copper(II) coordination compound has been synthesized from the Schiff-base ligand 6-(pyridine-2-ylhydrazonomethyl)phenol (Hphp). The molecular structure of [Cu-2(php)(2)(H2O2)(2)(ClO4)](ClO4)- (H2O) (1), determined by single-crystal X-ray diffraction, reveals the presence of two copper(II) centers held together by means of two strong hydrogen bonds, with O center dot O contacts of only 2.60-2.68 angstrom. Temperature-dependent magnetic susceptibility measurements down to 3 K show that the two metal ions are antiferromagnetically coupled (J = -19.8(2) cm(-1)). This exchange is most likely through two hydrogen-bonding pathways, where a coordinated water on the first Cu, donates a H bond to the O atoms of the coordinated php at the other Cu. This strong O center dot H (water) bonding interaction has been clearly evidenced by theoretical calculations. In the relatively few related cases from the literature, this exchange path, mediated by a (neutral) coordinated water molecule, was not recognized.

Adaptive recognition of small molecules by nucleic acid aptamers through a label-free approach

We report a novel label-free method for the investigation of the adaptive recognition of small molecules by nucleic acid aptamers using capillary electrophoresis analysis. Cocaine and argininamide were chosen as model molecules, and the two corresponding DNA aptamers were used. These single-strand DNAs folded into their specific secondary structures, which were mainly responsible for the binding of the target molecules with high affinity and specificity. For molecular recognition, the nucleic acid structures then underwent additional conformational changes, while keeping the target molecules stabilized by intermolecular hydrogen bonds. The intrinsic chemical and physical properties of the target molecules enabled them to act as indicators for adaptive binding. Thus any labeling or modification of the aptamers or target molecules were made obsolete. This label-free method for aptamer-based molecular recognition was also successfully applied to biological fluids and therefore indicates that this approach is a promising tool for bioanalysis.

Reusable, label-free electrochemical aptasensor for sensitive detection of small molecules

We report a sensitive electrochemical aptasensor for adenosine based on electrochemical impedance spectroscopy measurement, which gives not only a label-free but also a reusable platform to make the detection of small molecules simple and convenient.