Stabilization of the Triplet Biradical Intermediate of 5-Methylcytosine Enhances Cyclobutane Pyrimidine Dimer (CPD) Formation in DNA

Cyclobutane pyrimidine dimer (CPD) is a photoproduct formed by two stacked pyrimidine bases through a cycloaddition reaction upon irradiation. Owing to its close association with skin cancer, the mechanism of CPD formation has been studied thoroughly. Among many aspects of CPD, its formation involving 5-methylcytosine (5mC) has been of special interest because the CPD yield is known to increase with C5-methylation of cytosine. In this work, high-level quantum mechanics/molecular mechanics (QM/MM) calculations are used to examine a previously experimentally detected pathway for CPD formation in hetero (thymine-cytosine and thymine-5mC) dipyrimidines, which is facilitated through intersystem crossing in thymine and formation of a triplet biradical intermediate. A DNA duplex model system containing a core sequence TmCG or TCG is used. The stabilization of a radical center in the biradical intermediate by the methyl group of 5mC can lead to increased CPD yield in TmCG compared with its non-methylated counterpart, TCG, thereby suggesting the existence of a new pathway of CPD formation enhanced by 5mC.     

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.     

有机化学创新设计性实验“甲基化反应”的改进*

结合科研成果及实验教学经验,对有机化学实验中传统的甲基化反应实验进行改进。教材中涉及的传统甲基化试剂具有毒性大等缺点,不利于实验教学的实施。因此,提出使用三氟乙酸甲酯取代传统甲基化试剂,应用于本科有机化学实验教学中,加强学生对甲基化反应理论知识的理解。本实验结合新颖的科研内容,引入科研实验的设计思路,不仅有利于学生更好地掌握理论知识,而且有利于激发学生对科学研究的兴趣,提高学生的综合素养。     

The Deuterated “Magic Methyl” Group: A Guide to Site-Selective Trideuteromethyl Incorporation and Labeling by Using CD3 Reagents

In the field of medicinal chemistry, the precise installation of a trideuteromethyl group is gaining ever-increasing attention. Site-selective incorporation of the deuterated “magic methyl” group can provide profound pharmacological benefits and can be considered an important tool for drug optimization and development. This review provides a structured overview, according to trideuteromethylation reagent, of currently established methods for site-selective trideuteromethylation of carbon atoms. In addition to CD₃, the selective introduction of CD₂H and CDH₂ groups is also considered. For all methods, the corresponding mechanism and scope are discussed whenever reported. As such, this review can be a starting point for synthetic chemists to further advance trideuteromethylation methodologies. At the same time, this review aims to be a guide for medicinal chemists, offering them the available C−CD₃ formation strategies for the preparation of new or modified drugs.     

气相色谱-串联质谱检测烟草中15种苯氧羧酸类除草剂残留

建立了气相色谱-串联质谱技术对烟草中15种苯氧羧酸类除草剂农药残留量的分析方法。样品采用乙腈提取、Carbon TPT固相萃取柱净化、三甲基硅烷化重氮甲烷衍生化,采用气相色谱-串联质谱对15种苯氧羧酸类除草剂进行测定,通过保留时间、选择离子及相对丰度定性,外标法定量。结果表明,15种苯氧羧酸类除草剂在20~1 000μg/L浓度范围内均呈良好线性关系,相关系数大于0.992,检出限为0.9~3.3μg/kg,定量下限为3.2~10.8μg/kg。在20,100,200μg/kg 3个加标水平下的平均回收率为71.5%~105.6%,相对标准偏差(RSD)为4.5%~14.9%。该方法简便、快速、灵敏,适用于烟草中15种苯氧羧酸类除草剂的同时检测。     

Transition-Metal-Catalyzed Utilization of Methanol as a C1 Source in Organic Synthesis

Methanol is used as a common solvent, cost-effective reagent, and sustainable feedstock for value-added chemicals, pharmaceuticals, and materials. Among the various applications, the utilization of methanol as a C₁ source for the formation of carbon–carbon, carbon–nitrogen, and carbon–oxygen bonds continues to be important in organic synthesis and drug discovery. In particular, the synthesis of C-, N-, and O-methylated products is of central interest because these motifs are found in a large number of natural products as well as fine and bulk chemicals. In this Minireview, we summarize the utilization of methanol as a C₁ source in methylation, methoxylation, formylation, methoxycarbonylation, and oxidative methyl ester formation reactions.     

Discovering DNA methylation patterns for long non-coding RNAs associated with cancer subtypes

Despite growing evidence demonstrates that the long non-coding ribonucleic acids (lncRNAs) are critical modulators for cancers, the knowledge about the DNA methylation patterns of lncRNAs is quite limited. We develop a systematic analysis pipeline to discover DNA methylation patterns for lncRNAs across multiple cancer subtypes from probe, gene and network levels. By using The Cancer Genome Atlas (TCGA) breast cancer methylation data, the pipeline discovers various DNA methylation patterns for lncRNAs across four major subtypes such as luminal A, luminal B, her2-enriched as well as basal-like. On the probe and gene level, we find that both differentially methylated probes and lncRNAs are subtype specific, while the lncRNAs are not as specific as probes. On the network level, the pipeline constructs differential co-methylation lncRNA network for each subtype. Then, it identifies both subtype specific and common lncRNA modules by simultaneously analyzing multiple networks. We show that the lncRNAs in subtype specific and common modules differ greatly in terms of topological structure, sequence conservation as well as expression. Furthermore, the subtype specific lncRNA modules serve as biomarkers to improve significantly the accuracy of breast cancer subtypes prediction. Finally, the common lncRNA modules associate with survival time of patients, which is critical for cancer therapy.     

Methylation of Cyanidin-3-O-Glucoside with Dimethyl Carbonate

The approach presented in this study is the first for the hemisynthesis of methylated anthocyanins. It was possible to obtain cyanidin-3-O-glucoside derivatives with different degrees of methylation. Cautious identification of 4′-, 5-, and 7-OH monomethylated derivatives was also accomplished. The methylation agent used was the “green chemical” dimethyl carbonate (DMC), which is characterized by low human and ecological toxicity. The influence of the temperature, reaction time, and amount of the required diazabicyclo[5.4.0]undec-7-en (DBU) catalyst on the formation of the products was examined. Compared to conventional synthesis methods for methylated flavonoids using DMC and DBU, the conditions identified in this study result in a reduction of reaction time, and an important side reaction, so-called carboxymethylation, was minimized by using higher amounts of catalyst.