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.     

Chemical agents for binding post-translationally methylated lysines and arginines

Post-translational methylation, discovered more than half a century ago, encodes information in the form of a structural modification on a peptide or protein. The addition of a CH₃ group is one of the most subtle covalent modifications that exist in biology. In spite of this, recent years have revealed the many profound functional effects that arise from protein methylation in the cell. In an effort to open the doors to new assays and detection methods that would enable new basic and applied research into methylation pathways, chemical agents that can recognise and bind to methylated sites are now being pursued. In this review, we describe the supramolecular approaches to the recognition of methylated amino acids, peptides and proteins that have arisen in the last few years.     

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.     

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.     

Targeted Synthesis of Isomeric Naphthalene-Based 2D Kagome Covalent Organic Frameworks

Targeted synthesis of kagome ( kgm ) topologic 2D covalent organic frameworks remains challenging, presumably due to the severe dependence on building units and synthetic conditions. Herein, two isomeric “two-in-one” monomers with different lengths of substituted arms based on naphthalene core (p-Naph and m-Naph) are elaborately designed and utilized for the defined synthesis of isomeric kgm Naph-COFs. The two isomeric frameworks exhibit splendid crystallinity and showcase the same chemical composition and topologic structure with, however, different pore channels. Interestingly, C₆₀ is able to uniformly be encapsulated into the triangle channels of m-Naph-COF via in situ incorporation method, while not the isomeric p-Naph-COF, likely due to the different pore structures of the two isomeric COFs. The resulting stable C₆₀@m-Naph-COF composite exhibits much higher photoconductivity than the m-Naph-COF owing to charge transfer between the conjugated skeletons and C₆₀ guests.     

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.     

High-yield synthesis of a novel water-soluble macrocycle for selective recognition of naphthalene

A novel good water-soluble macrocycle containing two pyridinium moieties was synthesized in high yield.It could form 1:1 complexes with neutral guests containing naphthalene or phenyl units in water.The water-soluble macrocycle can selectively encapsulate naphthalene to form a 1:1 complex over a variety of polycyclic aromatic hydrocarbons.     

萘基相互连接的多孔碳纳米囊的制备及超电容性能

以萘为碳源, 采用MgO模板诱导耦合KOH裁剪技术制备了相互连接的多孔碳纳米囊(ICNC). 结果表明所制备的ICNC₂具有大的比表面积(1811 m²/g)、 高的压实密度(1.38 g/cm³)和微孔孔容含量(58.93%). 在对称的超级电容器(SC)中, ICNC₂电极的体积比容在不同电流密度下分别高达420.8 F/cm³(0.069 A/cm³)和315 F/cm³(27.6 A/cm³), 容量保持率为74.82%. 在38 W/L功率密度下, ICNC₂基SC的体积能量密度为14.6 W?h/L. 经过20000次循环后, 其体积比容仅衰减1.4%, 库伦效率为99.1%, 为从萘基小分子制备储能用功能碳材料提供了一种可行的方法.     

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.