Sensitive detection of hydroxymethylcytosine levels in normal and neoplastic cells and tissues

A new sensitive analytical method using capillary electrophoresis with laser induced fluorescence (CE‐LIF) was applied for the simultaneous detection of DNA methylation and hydroxymethylation levels in human cancers of different origin. DNA hydroxymethylation, measured as 5‐hydroxymethylcytosine (5hmC) levels, was decreased in gliomas with mutation in the isocitrate dehydrogenase 1 (IDH1) gene when compared to IDH1‐wildtype gliomas. Independent from IDH1 mutation, 5hmC levels were decreased in lung carcinomas when compared to normal lung tissue. Reduced DNA hydroxymethylation was also observed upon dedifferentiation in cultured murine embryonic fibroblasts. Our data show that reduced DNA hydroxymethylation is related to cellular dedifferentiation and can be detected in various types of cancers, independent from the IDH1 mutation status. Quantitative determination of altered 5hmC levels may therefore have potential as a biomarker linked to cellular differentiation and tumorigenesis.     

A fully portable microchip real‐time polymerase chain reaction for rapid detection of pathogen

Point‐of‐care detection for pathogen is of critical need for wide epidemic warning and medical diagnosis. In this work, we have designed and developed a fully portable and integrated microchip based real‐time polymerase chain reaction machine for rapid pathogen detection. The instrument consists of three functional components including heating, optical, and electrical modules, which are integrated into a portable compact box. The microchip is consumable material replaceable to meet various detection needs. Consequently, we demonstrated the outstanding performance of this portable machine for rapid detection of Salmonella and Escherichia coli O157:H7 with the advantage of time‐saving (～25 min), less samples consumption, portability, and user‐friendly operation.     

Ideal‐filter capillary electrophoresis: A highly efficient partitioning method for selection of protein binders from oligonucleotide libraries

Selection of affinity ligands for protein targets from oligonucleotide libraries currently involves multiple rounds of alternating steps of partitioning of protein‐bound oligonucleotides (binders) from protein‐unbound oligonucleotides (nonbinders). We have recently introduced ideal‐filter capillary electrophoresis (IFCE) for binder selection in a single step of partitioning. In IFCE, protein‐binder complexes and nonbinders move inside the capillary in the opposite directions, and the efficiency of their partitioning reaches 10⁹, i.e., only one of a billion molecules of nonbinders leaks through IFCE while all binders pass through. The condition of IFCE can be satisfied when the magnitude of the mobility of EOF is smaller than that of the protein‐binder complexes and larger than that of nonbinders. The efficiency of partitioning in IFCE is 10 million times higher than those of solid‐phase‐based methods of partitioning typically used in selection of affinity ligands for protein targets from oligonucleotide libraries. Here, we provide additional details on our justification for IFCE development. We elaborate on electrophoretic aspects of the method and define the theoretical range of EOF mobilities that support IFCE. Based on these theoretical results, we identify an experimental range of background electrolyte's ionic strength that supports IFCE. We also extend our interpretation of the results and discuss in‐depth IFCE's prospective in practical applications and fundamental studies.     

Optimization of DNA extraction from dental remains

Efficient DNA extraction procedures is a critical step involved in the process of successful DNA analysis of such samples. Various protocols have been devised for the genomic DNA extraction from human tissues and forensic stains, such as dental tissue that is the skeletal part that better preserves DNA over time. However DNA recovery is low and protocols require labor‐intensive and time‐consuming step prior to isolating genetic material. Herein, we describe an extremely fast procedure of DNA extraction from teeth compared to classical method. Sixteen teeth of 100‐year‐old human remains were divided into two groups of 8 teeth and we compared DNA yield, in term of quantity and quality, starting from two different sample preparation steps. Specifically, teeth of group 1 were treated with a classic technique based on several steps of pulverization and decalcification, while teeth of group 2 were processed following a new procedure to withdraw dental pulp. In the next phase, the samples of both group underwent the same procedure of extraction, quantification and DNA profile analysis. Our findings provide an alternative protocol to obtain a higher amount of good quality DNA in a fast time procedure, helpful for forensic and anthropological studies.     

A computational foray into the mechanism and catalysis of the adduct formation reaction of guanine with crotonaldehyde

Crotonaldehyde, a common environmental pollutant and product of endogenous lipid peroxidation, reacts with guanine to form DNA adducts with pronounced genotoxicity and mutagenicity. Here, we explore the molecular mechanism of this adduct formation using double-hybrid density functional theory methods. The reaction can be envisaged to occur in a two-step fashion via an aza-Michael addition leading to an intermediate ring-open adduct followed by a cyclization reaction giving the mutagenic ring-closed adduct. We find that (i) a 1,2-type addition is favored over a 1,4-type addition for the aza-Michael addition, and (ii) an initial tautomerization of the guanine moiety in the resulting ring-open adduct significantly reduces the barrier toward cyclization compared to the direct cyclization of the ring-open adduct in its keto-form. Overall, the aza-Michael addition is found to be rate-determining. We further find that participation of a catalytic water molecule significantly reduces the energy barriers of both the addition and cyclization reaction. © 2018 Wiley Periodicals, Inc.     

DNA依赖的蛋白激酶抑制剂STL127705的合成工艺研究

DNA依赖的蛋白激酶（DNA-PK）是肿瘤治疗的一个潜在靶点,其抑制剂具有增强放化疗敏感性的作用。STL127705是一种有效的DNA-PK抑制剂,本文采用逆合成分析,以2-甲硫醚-4-氯嘧啶-5-基甲酸乙酯为起始原料,先后经过氨化、水解、酰胺缩合、合环、氧化、取代等6步反应制备得到目标化合物,总收率为36.8%,纯度达到95.5%,产物结构通过1H-NMR、13C-NMR、MS等表征。     

Synthesis of 5-Alkyl- and 5-Phenylamino-Substituted Azothiazole Dyes with Solvatochromic and DNA-Binding Properties

A series of new 5-mono- and 5,5′-bisamino-substituted azothiazole derivatives was synthesized from the readily available diethyl azothiazole-4,4′-dicarboxylate. This reaction most likely comprises an initial Michael-type addition by the respective primary alkyl and aromatic amines at the carbon atom C5 of the substrate. Subsequently, the resulting intermediates are readily oxidized by molecular oxygen to afford the amino-substituted azothiazole derivatives. The latter exhibit remarkably red-shifted absorption bands (λ_abs=507–661 nm) with high molar extinction coefficients and show a strong positive solvatochromism. As revealed by spectrometric titrations and circular and linear dichroism studies, the water-soluble, bis-(dimethylaminopropylamino)-substituted azo dye associates with duplex DNA by formation of aggregates along the phosphate backbone at high ligand–DNA ratios (LDR) and by intercalation at low LDR, which also leads to a significant increase of the otherwise low emission intensity at 671 nm.     

DNA-二维纳米片层材料传感平台的构建及其应用

DNA-二维纳米片层材料传感平台结合DNA分子特异性识别能力与二维纳米片层材料优越的物理、化学特性,已成为化学/生物传感器领域重要的研究方向之一.鉴于二维纳米片层材料领域的快速发展,首先介绍了DNA-二维纳米片层材料传感平台的构筑机理,随后重点综述了该传感平台在化学、生物目标物分析检测中的应用研究,并对该类传感平台的应用前景做了展望.     

A simple visual method for DNA detection based on the formation of gold nanoparticles

A simple visual method for DNA detection during the formation of gold nanoparticles (AuNPs) was developed based on different electrostatic properties of single strand DNA (ssDNA) and double strand DNA (dsDNA). Since the ssDNA is easy to bind to AuNPs due to its exposed bases which could prevent salt-induced aggregation of AuNPs. The dsDNA always present negative charge because its negatively charged phosphate backbone is exposed. In this case, the dsDNA could disturb the adsorption between dsDNA and AuNPs and result in non-aggregation of AuNPs. After hybridization, chloroauric acid and ascorbic acid were added to the mixture solution, and the solution changed to red immediately and turned to purple in 10 min in the present of target DNA. TEM results confirmed that the change of color stemed from aggregation of AuNPs. In order to obtain accurate results by naked eye, the DNA detection assay should be conducted under pH 7.0.     

Nanostructured DNA Microarrays for Dual SERS and Electrochemical Read‐out

We present a strategy to fabricate nanostructured microarrays ready to perform a dual read‐out, namely electrochemical (EC) as well as surface‐enhanced Raman spectroscopy (SERS) based detection of DNA hydridization. A polystyrene nanobeads monolayer assembly, obtained by means of a Langmuir Blodgett type technique, followed by electrochemical Au deposition, was employed to construct homogeneous nanostructures in the form of inverse‐opal nanovoids on a 32‐electrode Au microarray chip. Characterization of the obtained nanostructured electrodes of the array by means of cyclic voltammetry demonstrated high reproducibility of the surface modification process. The performance of the obtained array platform was investigated by modifying the microarray electrodes with three different oligonucleotide capture probes using a previously developed potential‐assisted surface modification protocol. Two ferrocene‐labeled target DNA sequences and one target RNA sequence with a Texas red label were detected electrochemically and via SERS, respectively.