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.     

具高耐热性多芳烃结构环氧树脂的研究

综述了近年来具耐热性多芳烃结构环氧树脂的发展概况,包括萘系、蒽系和芘系环氧树脂,着重介绍了其合成途径、反应活性及结构与性能的关系.认为多芳烃结构环氧树脂具有良好的耐热耐湿性,颇具发展潜力.其中,萘系环氧树脂与蒽、芘系环氧树脂相比 ,具有较高的反应活性和耐热性,具有较高的实际应用价值.因此,近年来萘基环氧树脂受到研究人员和厂商的关注,并且一些萘系环氧树脂已经应用于生产.     

2-溴-3-(1H-吲哚-3)-N-甲基马来酰亚胺的合成

以琥珀酰亚胺为起始原料,经过溴化、甲基化后再与吲哚溴化镁加成反应合成了2-溴-3-(1H-吲哚-3)-N-甲基马来酰亚胺,总收率44.8%,其结构经1H NMR和IR确证.     

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.     

The pH effect on the naphthoquinone-photosensitized oxidation of 5-methylcytosine

The pH effect on the one-electron photooxidation of 5-methyl-2'-deoxycytidine (d(m)C) by sensitization with 2-methyl-1,4-naphthoquinone (NQ) was investigated. Photoirradiation of an aqueous solution containing d(m)C and NQ under slightly acidic conditions of pH 5.0 efficiently produced 5-formyl-2'-deoxycytidine, whereas similar NQ-photosensitized oxidation of d(m)C proceeded to a lesser extent under more acidic or basic conditions. Fluorescence-quenching experiments revealed that the less-efficient photooxidation at pH values below 4.5 is attributed to the decreased rate of one-electron oxidation of d(m)C owing to protonation at the N(3)-position. The NQ-photosensitized oxidation of an N(4)-dimethyl-substituted d(m)C derivative under various pH conditions also suggests that the pH change in the range of 5.0 to 8.0 may be responsible for a reversible deprotonation-protonation equilibrium at the N(4)-exocyclic amino group of the d(m)C radical cation. In accord with the photochemical reactivity of monomeric d(m)C, the 5-methylcytosine residue in oligodeoxynucleotides was oxidized efficiently by photoexcited NQ-tethered oligodeoxynucleotides under slightly acidic conditions to form an alkali-labile 5-formylcytosine residue.     

Phenyltrimethylammonium Salts as Methylation Reagents in the Nickel‐Catalyzed Methylation of C−H Bonds

Methylation of C(sp²)?H bonds was achieved through the Ni^II‐catalyzed reaction of benzamides with phenyltrimethylammonium bromide or iodide as the source of the methyl group. The reaction has a broad scope and shows high functional‐group compatibility. The reaction is also applicable to the methylation of C(sp³)?H bonds in aliphatic amides.     

Modified Nucleotides for Discrimination between Cytosine and the Epigenetic Marker 5‐Methylcytosine

5‐Methyl‐2′‐deoxycytosine, the most common epigenetic marker of DNA in eukaryotic cells, plays a key role in gene regulation and affects various cellular processes such as development and carcinogenesis. Therefore, the detection of 5mC can serve as an important biomarker for diagnostics. Here we describe that modified dGTP analogues as well as modified primers are able to sense the presence or absence of a single methylation of C, even though this modification does not interfere directly with Watson–Crick nucleobase pairing. By screening several modified nucleotide scaffolds, O⁶‐modified 2′‐deoxyguanosine analogues were identified as discriminating between C and 5mC. These modified nucleotides might find application in site‐specific 5mC detection, for example, through real‐time PCR approaches.     

Fine-tuning the molecular energy levels by incorporating thiophene units onto the π-backbone of core-expanded naphthalene diimides

A series of core-expanded naphthalene diimides (NDI-DTYM) and thiophene-based derivatives (1a-c) were designed and synthesized to investigate the relationship between molecular structures and the highest occupied molecular orbital (HOMO) energy levels but has little impact on the lowest unoccupied molecular orbital (LUMO) energy levels. The results demonstrated that increasing the number of thiophene units can gradually elevate the HOMO energy levels but had little impact on the LUMO energy levels. The n-channel organic field-effect transistors (OFETs) based on 1b and 1c have demonstrated that these almost unchanged LUMO energy levels are proper to transport electrons.     

Self‐Sufficient Formaldehyde‐to‐Methanol Conversion by Organometallic Formaldehyde Dismutase Mimic

The catalytic networks of methylotrophic organisms, featuring redox enzymes for the activation of one‐carbon moieties, can serve as great inspiration in the development of novel homogeneously catalyzed pathways for the interconversion of C₁ molecules at ambient conditions. An imidazolium‐tagged arene–ruthenium complex was identified as an effective functional mimic of the bacterial formaldehyde dismutase, which provides a new and highly selective route for the conversion of formaldehyde to methanol in absence of any external reducing agents. Moreover, secondary amines are reductively methylated by the organometallic dismutase mimic in a redox self‐sufficient manner with formaldehyde acting both as carbon source and reducing agent.     

BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data

Cytosine methylation is one of the most important RNA epigenetic modifications. With the development of experimental technology, scientists attach more importance to RNA cytosine methylation and find bisulfite sequencing is an effective experimental method for RNA cytosine methylation study. However, there are only a few tools can directly deal with RNA bisulfite sequencing data efficiently. Herein, we developed a specialized tool BS-RNA, which can analyze cytosine methylation of RNA based on bisulfite sequencing data and support both paired-end and single-end sequencing reads from directional bisulfite libraries. For paired-end reads, simply removing the biased positions from the 5′ end may result in “dovetailing” reads, where one or both reads seem to extend past the start of the mate read. BS-RNA could map “dovetailing” reads successfully. The annotation result of BS-RNA is exported in BED (.bed) format, including locations, sequence context types (CG/CHG/CHH, H = A, T, or C), reference sequencing depths, cytosine sequencing depths, and methylation levels of covered cytosine sites on both Watson and Crick strands. BS-RNA is an efficient, specialized and highly automated mapping and annotation tool for RNA bisulfite sequencing data. It performs better than the existing program in terms of accuracy and efficiency. BS-RNA is developed by Perl language and the source code of this tool is freely available from the website: http://bs-rna.big.ac.cn.