Identification of methylated regions with peak search based on Poisson model from massively parallel methylated DNA immunoprecipitation-sequencing data

DNA methylation is one of the most important epigenetic modification types, which plays a critical role in gene expression. High efficient surveying of whole genome DNA methylation has been aims of many researchers for long. Recently, the rapidly developed massively parallel DNA‐sequencing technologies open the floodgates to vast volumes of sequence data, enabling a paradigm shift in profiling the whole genome methylation. Here, we describe a strategy, combining methylated DNA immunoprecipitation sequencing with peak search to identify methylated regions on a whole‐genome scale. Massively parallel methylated DNA immunoprecipitation sequencing combined with methylation DNA immunoprecipitation was adopted to obtain methylated DNA sequence data from human leukemia cell line K562, and the methylated regions were identified by peak search based on Poison model. From our result, 140 958 non‐overlapping methylated regions have been identified in the whole genome. Also, the credibility of result has been proved by its strong correlation with bisulfite‐sequencing data (Pearson R²=0.92). It suggests that this method provides a reliable and high‐throughput strategy for whole genome methylation identification.     

对叔丁基杯[8]芳烃酯类衍生物的合成方法改进及其对酯型儿茶素的萃取性能

以酰氯为酰基化试剂,用三乙胺作缚酸剂和催化剂,制备了一系列对叔丁基杯[8]芳烃酯类衍生物(2a～2e),其结构经1H NMR, IR和元素分析表征.以2为萃取剂,考察了酯型儿茶素单体在二氯甲烷-水两相体系中的萃取分配行为.结果表明:2e的萃取效果最佳.     

Density Functional Theory Study of the Interaction between Guanine and Catechin

The interacting patterns and mechanism of the catechin and guanine have been investigated with the density functional theory B3LYP method by 6‐31G* basis set. Fourteen stable structures for the catechin‐guanine complexes have been found which form two hydrogen bonds at least. The results indicate that the complexes are mainly stabilized by the hydrogen bonding interactions. At the same time, the number and strength of hydrogen bond play a co‐determinant parts in the stability of the complexes which can form two or more hydrogen bonds. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) have been adopted to investigate the hydrogen bonds involved in all systems. The interaction energies of all complexes have been corrected for basis set superposition error (BSSE), ranging from ?38.86 to ?14.56 kJ/mol. The results showed that the hydrogen bonding contributes to the interaction energies dominantly. The corresponding bonds stretching motions in all complexes are red‐shifted relative to that of the monomer, which is in agreement with experimental results.     

Substituent and solvent effects on the structural bioactivity and anticancer characteristic of catechin as a bioactive constituent of green tea

In this study, quantum chemical calculations using density functional theory and 6‐311G (d) basis set have been applied to analyze the substituent effect on the electronic structural properties including thermochemical parameters as well as anticancer characteristics of catechin as a bioactive constituent of green tea. It has been found out that different substituents with two kinds of electron donating and electron withdrawing groups including ? NO₂, ? NH₂, ? Cl, ? OCH₃, and ? CH₃ leaded to different structural stabilities. The catechin with chloro substituents has been referred to the most stable catechin derivatives based on the minimum energy of investigated compounds. In this study, the calculated values have been compared in gas phase and different solvent media with a wide range of solvent dielectrics using the self‐consistent reaction field method with polarizable continuum model. Relative interaction energies between solute and solvent as well as dipole moment values have been analyzed. The results of solvent effect study revealed that the formation of hydrogen bonds accounts for the stabilization of catechin. These calculated data were found to be a logical way in predicting the relative stability of catechin derivatives and can be useful for drug design of anticancer drugs and would open a new door for the researchers who are interested in natural products. The results presented in this article will be helpful to improve existing model and will open up a whole new arena of study to understand the anticancer characteristic of these antioxidant drugs derived from natural products against the photosensitizing DNA damage induce by catechin extracts and enable a much clearer understanding of how anticancer drugs mediate their effects on the specific spot. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Methylated Azopyridine as a New Electron Transfer Mediator for the Electrocatalytic Oxidation of NADH

Carbon ionic liquid electrode (CILE) has been modified with a new synthesized mediator i.e. N,N′‐dimethyl‐4,4′‐azopyridinium hexafluorophosphate (MAZPHP) via sol process and the electron transfer mediating characteristics of this mediator has been evaluated. 4,4′‐Azopyridine (AZP) did not show any electrocatalytic activity toward the selected probe, NADH, while its synthesized methylated derivative, MAZPHP, is a very efficient mediator for the electrocatalytic NADH oxidation. Cyclic voltammetry of MAZPHP/Sol/CILE exhibited a pair of reversible peaks corresponding to incorporated mediator with a formal potential of about 221 mV vs. Ag/AgCl. MAZPHP/Sol/CILE is free from fouling effects by the oxidation products of NADH which generally give hindrance to amperometric detection of NADH. Using amperometric technique, NADH can be determined in the range of 1.0×10^?5 M to 1.4×10^?3 M with a detection limit of 2.0×10^?6 M.     

Unexpected highly selective fluorescence ‘turn-on’ and ratiometric detection of Hg based on fluorescein platform

Methylated fluorescein 1 was explored for fluorescence ‘turn-on’ and ratiometric detection of Hg²⁺ in THF and CH₂Cl₂/MeOH (v/v=9:1), respectively, with unexpected high selectivity. In the presence of Hg²⁺, characteristic structured absorption band of 1 diminished and a new sharp band appeared at 445 nm. Meanwhile a blue shifted and enhanced emission was observed. The ratio of the fluorescence intensity at 559 and 478 nm increased linearly with [Hg²⁺], and solution color changing from yellow to cyan under irradiation at 365 nm in CH₂Cl₂/MeOH. Job plot indicated a 1:1 stoichiometry for 1-Hg²⁺ complex in solution. ¹H NMR titration and IR spectra suggested the coordination of carbonyl group in xanthene moiety to Hg²⁺, affording its spectral behavior. Compound 2 bearing two triazolyl amino esters in place of methyl group showed quite similar behavior to Hg²⁺, which indicated that substituents did not interfere with the specific binding behavior of fluorescein platform. Our work presents a new way to explore xanthene dyes as new chemosensors by modulating electron density on the xanthene ring through non-covalent interactions with carbonyl group.     

儿茶素-胞嘧啶分子间相互作用的密度泛函研究

采用密度泛函理论的B3LYP方法,在6-31+G*基组水平上研究了儿茶素-胞嘧啶分子间相互作用机制,得到稳定的儿茶素-胞嘧啶复合物11个.计算结果表明氢键对于复合物的稳定性起着重要的作用,并且当复合物形成2个或更多的氢键时,氢键的类型及强度共同决定着复合物的稳定性.我们还应用了分子中的原子(AIM)理论和自然键轨道(NBO)理论对这11种复合物中氢键的性质和特征进行了分析.通过研究发现,所有的氢键复合物进行基组重叠误差(BSSE)校正后的相互作用能为-17.35～-43.27kJ/mol,相互作用能主要由氢键所贡献.振动分析显示,氢键的形成使相对应键的对称伸缩振动频率减小,说明这些复合物中形成的氢键都是正常的红移型氢键,与实验结果相一致.     

Synthesis and Characterization of a Biologically Active Lanthanum(III)–Catechin Complex and DNA Binding Spectroscopic Studies

A lanthanum(III) complex of catechin has been synthesized and characterized by elemental analysis, molar conductance, UV-Vis spectra, infrared spectra, thermal analysis, and ¹H NMR. The complex behaves as a nonelectrolyte in methanol solvent. The spectral and thermal properties of the complex are examined. A thermogravimetric (TGA) study showed the hydrated nature of the complex. ¹H NMR spectra of the lanthanum and the catechin (CT) ligands measured in CD₃OD-d₄ also show metal ligand coordination. The lanthanum–catechin complex shows bright luminescence in methanol solution. The interaction of the complex with calf thymus DNA has been investigated by absorption and emission spectroscopic measurements. Experimental spectral results suggest CT–DNA binding with catechin complex via an intercalative mode.     

Chemical composition and antioxidant activity of Borago officinalis L. leaf extract growing in Algeria

The aqueous and hydroalcoholic extracts of borage (Borago officinalis) leaves from Annaba region (Algeria) were preliminary analyzed for their phenolic profile (total phenolics, total flavonoids, total flavonols, total tannins and total anthocyanins). These extracts were evaluated for their antioxidant properties by different methods such as DPPH radical scavenging, test NBT and total antioxidant activity. The two extracts have exhibited a high antiradical capacity. Indeed, the ethanolic extract showed the lower IC50 values and the highest amount of phenolics (94.09 ± 1.72 mg gallic acid/g dry extract). Using LC-MS/MS analysis, it was possible to identify phenolic acids, flavonoids, sterol and for the first time oleuropein was identified in the aqueous extract of the plant. The obtained results have demonstrated that phenolic compounds are the major contributor to the antioxidant activity of plants.     

精确计算化学键解离能的ONIOM-G3B3方法及其在抗氧化剂研究中的应用

通过对179个有机化合物C—H, N—H, O—H键离解能的理论计算, 系统评估了高精度组合从头算方法(ONIOM-G3B3)和密度泛函理论方法(B3LYP)在预测键离解能上的可靠性. 研究发现ONIOM-G3B3方法可以准确预测各类有机化合物的键解离能, 精度达到5.9 kJ/mol. 运用ONIOM-G3B3方法成功预测了两类重要的天然抗氧化剂维生素E族和茶多酚族的键解离能, 并进一步讨论了抗氧化活性、自由基清除机理及其构效关系.