Sequence-dependent clustering properties of nucleotides fragments in an ionic solution

The chemical nature of the DNA bases is an important factor in sequence-mediated association of DNA molecules. Nucleotides are the fundamental DNA elements and the base identity impacts the molecular properties of nucleotide fragments. It is interesting to study the fundamental nature of nucleotides in DNA, on the basis of base-specific interactions, association, and modes of standard atomic or molecular interactions. With all-atom molecular dynamics simulations of model dinucleotide and tetranucleotide systems having single-stranded dinucleotide or tetranucleotide fragments of varying sequences, we show how the base identity and interactions between the different bases as well as water may affect the clustering properties of nucleotides fragments in an ionic solution. Sequence-dependent differential interactions between the nucleotide fragments, ionic concentration, and elevated temperature are found to influence the clustering properties and dynamics of association. Well-known epigenetic modification of DNA, that is, cytosine methylation also promotes dinucleotide clustering in solution. These observations point to one possible chemical nature of the DNA bases, as well as the importance of the base pairing, base stacking, and ionic interactions in DNA structure formation, and DNA sequence-mediated association. Sequence- and the ionic environment-mediated self-association properties of the dinucleotides indicate its great potential to develop biological nanomaterials for desired applications.     

The influence of ions on the structure of water

Journal of Structural Chemistry - The main features of the changes produced by ions in water may be summarized as follows. The influence of ions on the structure of the “free” water...     

The porous structure of pulp fibres with different yields and its influence on paper strength

The porous structure of the interior of papermaking fibres is a well-known important property of the fibres. Changes of this structure will influence tensile and burst strength of paper formed from the fibres and a change in pore size of the pores within the fibre wall is also important for the ability of molecules to diffuse in and out of the fibre wall. Relevant examples of this latter effect are the removal of lignin during cooking and the addition of performance chemicals during papermaking. In this paper, pore sizes and the pore size distribution of unbleached softwood fibres have been studied. A well-characterised fibre material consisting of laboratory cooked spruce and pine pulp of various lignin contents was used. Pore size and pore size distribution were measured by studies of the relaxation behaviour of ²H in fibres saturated with ²H₂O. Beside this the total and surface charge of the fibres were also measured together with strength properties of papers from unbeaten fibres. For both pulps, there is a maximum in pore radius at a yield around 46%. Calculations of fibre wall volume from water retention values and yield levels show that there is a discontinuity in pore radius as a function of the fibre wall volume around a yield of 51%. It is suggested that this discontinuity is caused by the breakdown of the hemicellulose/lignin matrix within the fibre wall at this yield level. The strength of the papers formed from the fibres shows a correlation with the surface charge of the fibres. Based on the change in surface charge with yield and the change in total charge with yield, this correlation is suggested to be due to an opening up of the external part of the fibre wall. This stresses the importance of the chemical composition and physical structure of the outer layer of the fibre wall.     

RNA secondary structure alignment based on an extended binary coding method

Recently, we proposed a three‐dimensional cube representation of RNA secondary structure. An efficient method for mutation analysis has been proposed based on the introduced representation. According to the proposed three‐dimensional cube representations, we will introduce an extended binary coding method for RNA secondary structure alignment by converting the structure alignment to sequence alignment. Using our method, the result of structure alignment can be obtained quickly. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

The influence of hydrogen bonds on the globular structure of HP-copolymers

We present the results of computer modeling of coil-globule transition of HP-copolymer which can form hydrogen bonds between some specific monomer units (hydrogen bond units). Langevin dynamics approach is used for the simulation of coil-globule transition. We study the influence of the number and distribution of hydrogen bond units along primary sequence on the formation of globular conformations.     

The influence of a radical structure on the kinetics of photopolymerization

A radical initiation ability of new initiating systems in photopolymerization of 2‐ethyl‐2‐(hydroxymethyl)‐1,3‐propanediol triacrylate has been investigated and presented. The evaluation of alkyltriphenyl‐ and tetraalkylborates, iodonium salts, N‐alkoxypyridinium salts, maleimides, phthalimides, 1,3,5‐triazine derivatives and others as a free radical source in combination with suitable photosensitizer for radical polymerization of triacrylate is described. It is assumed that the photochemical decomposition of a coinitiator molecule results in formation of free radicals, which further initiate polymerization. The order of activity of free radical sources on kinetic of photopolymerization was also presented. Different initiator activity can be explained by the difference in the decomposition rate constant and the reactivity of radicals formed toward the double bond of monomer. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 1575–1589     

The influence of chemical structure on the antimicrobial activities of thiosemicarbazone-chitosan

We have previously reported the preparation of acetyl and benzoyl phenyl-thiosemicarbazone derivatives of chitosan and their antimicrobial activities. The purpose of this study was to further assess the relationship between chemical structure and antimicrobial activity of chloracetyl phenyl-thiosemicarbazone-chitosan. Ten new chloracetyl phenyl-thiosemicarbazone-chitosans were prepared, and their structures were characterized using FT-IR and elemental analysis. The synthesized compounds were tested against four species of bacteria and four crop-threatening pathogenic fungi. Different molecular weights and concentrations were evaluated. The antifungal activities of the synthesized compounds were related to the positive polarity of the N₄ atom and the distribution of the electron atmosphere in the C=S group. All chitosan compounds had inhibitory effects when tested with bacteria. The minimum MIC and MBC with Escherichia coli were 7.03 and 56.25 μg mL^?1, respectively.     

The influence of water structure on the rotational depolarization of fluorescence

A method based on the rotational depolarization of fluorescence of dye molecules acting as luminescent sonds is proposed to study the temperature changes in the structure of water. A visible discrepancy of the experimental points from the linear Perrin formula was found for erythrosine B in water. From the emission anisotropy and the mean fluorescence lifetime, the effective Volume V of erythrosine B in water was determined. It was shown that the temperature changes in the effective volume can be associated with those in the water structure.     

硫化对聚乙炔结构和性能的影响

本文利用DSC, FT-IR光谱对聚乙炔硫化产物进行了表征, 研究了聚乙炔硫化前后结构和性能的变化。采用量子化学CNDO/2晶体轨道方法, 首次对硫化聚乙炔的分子结构及电子性质进行理论计算, 探讨了硫化对聚乙炔结构和性能的影响。     

The influence of fullerene additives on the structure of polystyrene films

It was shown by electron microscopy and X-ray diffraction that a polystyrene solid with a three-level hierarchical structure was formed when the solvent was evaporated from a solution of polystyrene in o-xylene (polystyrene molecules stuck together united to form a framework). The kinetics of the transformation of formerly dissolved molecules into aggregates could be described by a Fokker-Planck-type equation. Fullerenes introduced into a solution of polystyrene in amounts less than 0.1 wt % transformed aggregated polystyrene molecules into nanocrystals and accelerated the formation of aggregates. The influence of fullerenes on the kinetics of the processes could be correctly described in the continuum approximation taking into account aggregation rate fluctuations. Original Russian Text ? O.V. Alekseeva, N.A. Bagrovskaya, S.M. Kuz’min, A.V. Noskov, I.V. Melikhov, V.N. Rudin, 2009, published in Zhurnal Fizicheskoi Khimii, 2009, Vol. 83, No. 7, pp. 1320–1326.     

The influence of surfactants on the structure of transparent gelatin films

The interference image of cold-dried transparent gelatin films containing different surfactants was determined in the conoscopic ray of monochromatic light. From the results obtained the order of the structure of gelatin in the film was characterized. Unlike the ionic surfactants (sodium dodecyl sulfate and hexadecyltrimethyl ammonium bromide), which lead to a reduction of the ordered structure, the addition of nonionic and amphoteric surfactants [ethoxylized octylphenole and a technical C₁₂/C₁₄-dipoly(oxyethylene)ammoniopropane sulfonate] causes an increase of the ordered structure of gelatin. The results quantitatively agree with those found for the influence of surfactants on the secondary structure of gelatin in diluted gelatin solutions. The influence is independent of the gelatin/surfactant ratio and has been explained by gelatin/gelatin interaction competing with the gelatin/surfactant interaction if the gelatin concentration becomes sufficiently high.     

Retrospective analysis of an experimental high-throughput screening data set by recursive partitioning

With the emergence of combinatorial chemistry, whether based on parallel, mixture, solution, or solid phase chemistry, it is now possible to generate large numbers of diverse or focused compound libraries. In this paper we aim to demonstrate that it is possible to design targeted libraries by applying nonparametric statistical methods, recursive partitioning in particular, to large data sets containing thousands of compounds and their associated biological data. Moreover, when applied to an experimental high-throughput screening (HTS) data set, our data strongly suggest that this method can improve the hit rate of our primary screens (about 4- to 5-fold) while increasing screening efficiency: less than one-fifth of the complete selection needs to be screened in order to identify about 75% of all actives present.