Visualization of large elongated DNA molecules

Long and linear DNA molecules are the mainstream single‐molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA‐protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.     

A Modular Synthesis of Modified Phosphoanhydrides

Phosphoanhydrides (P‐anhydrides) are ubiquitously occurring modifications in nature. Nucleotides and their conjugates, for example, are among the most important building blocks and signaling molecules in cell biology. To study and manipulate their biological functions, a diverse range of analogues have been developed. Phosphate‐modified analogues have been successfully applied to study proteins that depend on these abundant cellular building blocks, but very often both the preparation and purification of these molecules are challenging. This study discloses a general access to P‐anhydrides, including different nucleotide probes, that greatly facilitates their preparation and isolation. The convenient and scalable synthesis of, for example, ¹⁸O labeled nucleoside triphosphates holds promise for future applications in phosphoproteomics.     

Electrochemical bromination of late stage intermediates and drug molecules

Aromatic CH bromination is one of the applications of late stage functionalization that provides precursors for generation of radio-labelled compounds to support drug metabolism and pharmacokinetic (DMPK) studies or provide a “handle” for further functionalization to expand SAR studies without having to resort to de novo synthesis. Electrochemical aromatic bromination was attempted on late stage intermediates and drug molecules such as cytidine, uridine, Tenofovir, MK-4618, Sch48973 and MK-8457. The reactions were conducted under mild galvanostatic electrolysis condition in aqueous NaBr solution. The brominated products were obtained and converted to the corresponding tritium labelled products. Electrochemical methodology provides an alternative way to quickly generate aryl bromides of late stage intermediates or drug molecules that are very useful in drug discovery.     

Site-Specific Fluorescent Labeling of RNA Interior Positions

The introduction of fluorophores into RNA for both in vitro and in cellulo studies of RNA function and cellular distribution is a subject of great current interest. Here I briefly review methods, some well-established and others newly developed, which have been successfully exploited to site-specifically fluorescently label interior positions of RNAs, as a guide to investigators seeking to apply this approach to their studies. Most of these methods can be applied directly to intact RNAs, including (1) the exploitation of natural posttranslational modifications, (2) the repurposing of enzymatic transferase reactions, and (3) the nucleic acid-assisted labeling of intact RNAs. In addition, several methods are described in which specifically labeled RNAs are prepared de novo.     

13C辅助的超高效液相色谱-三重四极杆质谱联用方法精确分析毕赤酵母胞内代谢物浓度

毕赤酵母作为一种高效的外源蛋白表达平台,其蛋白表达水平与胞内代谢物浓度紧密相关.但胞内代谢物种类多、物化性质差异大、浓度低、周转快,对其绝对浓度的精确检测一直难于实现.本研究将超高效液相色谱-三重四极杆质谱联用分析方法与13C同位素标记技术相结合,探索解决该难题的方法.首先,优化了超高效液相色谱的操作条件,利用3种色谱柱实现了64种常见中间代谢物的分离;对三重四极杆质谱仪的检测离子对和碰撞电压等操作条件进行优化,找到了对各种物质具有专一性的检测离子对.然后,利用全标记13C标记底物培养细胞,收集胞内的全标记代谢物用作定量内标物,建立了53种中间代谢物的标准曲线.实验结果表明,本方法不但精确性高,标准曲线相关系数达到0.99以上,而且重现性好,受实验条件和仪器操作条件的影响很小.将本方法应用于毕赤酵母胞内代谢物浓度的绝对定量分析,成功获得了胞内各种代谢物的浓度水平,为后续深入研究毕赤酵母代谢调控机理,实现外源蛋白的高效生产奠定了基础.     

List‐Coloring the Squares of Planar Graphs without 4‐Cycles and 5‐Cycles

Let G be a planar graph without 4‐cycles and 5‐cycles and with maximum degree . We prove that . For arbitrarily large maximum degree Δ, there exist planar graphs of girth 6 with . Thus, our bound is within 1 of being optimal. Further, our bound comes from coloring greedily in a good order, so the bound immediately extends to online list‐coloring. In addition, we prove bounds for ‐labeling. Specifically, and, more generally, , for positive integers p and q with . Again, these bounds come from a greedy coloring, so they immediately extend to the list‐coloring and online list‐coloring variants of this problem.     

消费者异质特征下的碳标签产品供应链决策模型

考虑消费者对标示碳标签产品的异质性消费偏好,建立不同消费群体支付意愿下的碳标签产品需求模型,研究供应商和零售商分别主导供应链情景下的最优决策.结果表明,在供应商或零售商主导供应链中,碳标签产品的定价相同.但供应链主导者通过身份力量影响批发价,从而在供应链总利润分享中获益.消费者群体中的普通顾客比例及普通顾客对碳标签产品的接受程度都影响供应链决策,但是普通顾客对碳标签产品的接受程度更具敏感性.     

Dual Fluorescent- and Isotopic-Labelled Self-Assembling Vancomycin for in vivo Imaging of Bacterial Infections

The increase of bacterial resistance demands rapid and accurate diagnosis of bacterial infections. Biosurface-induced supramolecular assembly for diagnosis and therapy has received little attention in detecting bacterial infections. Herein we present a dual fluorescent-nuclear probe based on self-assembly of vancomycin (Van) on Gram-positive bacteria for imaging bacterial infection. A Van- and rhodamine-modified peptide derivative (Rho-FF-Van), as the imaging agent, binds to the terminal peptide of the methicillin-resistant staphylococcus aureus (MRSA) and self-assembles to form nanoaggregates on the surface of MRSA. In an in vivo myositis model, Rho-FF-Van results in a significant increased fluorescence signal at the MRSA infected site. Radiolabeled with iodine-125, Rho-FF-Van shows strong radioactive signal in the MRSA-infected lungs in a murine model. This novel dual fluorescent and nuclear probe promises a new way for in vivo imaging of bacterial infections.     

Long‐Chain Alkyl Cyanides: Unprecedented Volatile Compounds Released by Pseudomonas and Micromonospora Bacteria

The analysis of volatiles from bacterial cultures revealed long‐chain aliphatic nitriles, a new class of natural products. Such nitriles are produced by both Gram‐positive Micromonospora echinospora and Gram‐negative Pseudomonas veronii bacteria, although the structures differ. A variable sequence of chain elongation and dehydration in the fatty acid biosynthesis leads to either unbranched saturated or unsaturated nitriles with an ω−7 double bond, such as (Z )‐11‐octadecenenitrile, or methyl‐branched unsaturated nitriles with the double bond located at C‐3, such as (Z )‐13‐methyltetradec‐3‐enenitrile. The nitrile biosynthesis starts from fatty acids, which are converted into their amides and finally dehydrated. The structures and biosyntheses of the 19 naturally occurring compounds were elucidated by mass spectrometry, synthesis, and feeding experiments with deuterium‐labeled precursors. Some of the nitriles showed antimicrobial activity, for example, against multiresistant Staphylococcus aureus strains.     

Dehydrogenation of the NH−NH Bond Triggered by Potassium tert-Butoxide in Liquid Ammonia

A novel strategy for the dehydrogenation of the NH−NH bond is disclosed using potassium tert-butoxide (tBuOK) in liquid ammonia (NH₃) under air at room temperature. Its synthetic value is well demonstrated by the highly efficient synthesis of aromatic azo compounds (up to 100 % yield, 3 min), heterocyclic azo compounds, and dehydrazination of phenylhydrazine. The broad application of this strategy and its benefit to chemical biology is proved by a novel, convenient, one-pot synthesis of aliphatic diazirines, which are important photoreactive agents for photoaffinity labeling.