Thiazole orange as an everyday replacement for ethidium bromide and costly DNA dyes for electrophoresis

DNA gel electrophoresis is a standard tool of biochemistry and molecular biology laboratories. The common dye ethidium bromide suffers from toxicity concerns and requires the use of damaging ultraviolet light. We observe that exposing plasmid DNA to a UV transilluminator for only 1 s results in detectable loss of colonies following transformation, suggesting rapid accumulation of DNA damage. SYBR Safe, a commercial product, is marketed as a safe alternative to ethidium bromide and has excellent sensitivity with nondamaging blue light, but suffers from prohibitively high costs. We show that thiazole orange, the parent compound of SYBR Safe, is an excellent, simple, and inexpensive alternative to these dyes. It is excitable with safe blue light or UV light, with DNA detection limits in agarose gels similar to ethidium bromide and SYBR Safe (1–2 ng/lane). Thiazole orange safely allows the use of nondamaging blue light at the same cost as ethidium bromide.     

Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges

Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform–water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER‐99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld‐I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld‐I method related to the unstable isolated anionic nitrogen pro‐atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. © 2018 Wiley Periodicals, Inc.     

单核锇配合物的合成、晶体结构及其与DNA的作用

使用溶剂热合成法,以p-bitmb配体(1,4-二(1-咪唑基-亚甲基)-2,3,5,6-四甲基苯)与[(η6-cymene)Os(μ-Cl)Cl]2或[(η6-bip)Os(μ-Cl)Cl]2为原料,合成了2种单核芳基锇配合物,并利用核磁、质谱、元素分析和X射线单晶衍射等手段对配合物进行了表征。配合物1属于单斜晶系,P21/c空间群,为一个单核锇的结构。中心锇原子与2个配体p-bitmb上的氮原子以及氯原子进行配位,2个配体的另一个咪唑基团通过一个亚甲基碳原子进行连接形成咪唑嗡离子,形成一个类似"碗"状的结构。一个氯离子通过氢键装载在结构的空腔内。利用核磁共振氢谱研究了结构中亚甲基的来源,并研究了配合物在缓冲溶液中的稳定性。用紫外吸收光谱、圆二色谱以及粘度法研究了配合物与DNA的相互作用,结果表明,配合物中的亚甲基来自于溶剂二氯甲烷。配合物以嵌入的方式与CT-DNA相互作用,结合常数分别为3.222×10~4 L·mol-1 (1)和1.53×10~4 L·mol-1 (2),同时配合物会减弱DNA的碱基堆积作用并可以使DNA发生解旋。     

Biocomputing for Portable,Resettable, and Quantitative Point‐of‐Care Diagnostics: Making the Glucose Meter a Logic‐Gate Responsive Device for Measuring Many Clinically Relevant Targets

It is recognized that biocomputing can provide intelligent solutions to complex biosensing projects. However, it remains challenging to transform biomolecular logic gates into convenient, portable, resettable and quantitative sensing systems for point‐of‐care (POC) diagnostics in a low‐resource setting. To overcome these limitations, the first design of biocomputing on personal glucose meters (PGMs) is reported, which utilizes glucose and the reduced form of nicotinamide adenine dinucleotide as signal outputs, DNAzymes and protein enzymes as building blocks, and demonstrates a general platform for installing logic‐gate responses (YES, NOT, INHIBIT, NOR, NAND, and OR) to a variety of biological species, such as cations (Na⁺), anions (citrate), organic metabolites (adenosine diphosphate and adenosine triphosphate) and enzymes (pyruvate kinase, alkaline phosphatase, and alcohol dehydrogenases). A concatenated logical gate platform that is resettable is also demonstrated. The system is highly modular and can be generally applied to POC diagnostics of many diseases, such as hyponatremia, hypernatremia, and hemolytic anemia. In addition to broadening the clinical applications of the PGM, the method reported opens a new avenue in biomolecular logic gates for the development of intelligent POC devices for on‐site applications.     

Synthesis,crystal structures and DNA/human serum albumin binding of ternary Cu(II) complexes containing amino acids and 6‐(pyrazin‐2‐yl)‐1,3,5‐triazine‐2,4‐diamino

Two water‐soluble 6‐(pyrazin‐2‐yl)‐1,3,5‐triazine‐2,4‐diamino (pzta)‐based Cu(II) complexes, namely [Cu(l ‐Val)(pzta)(H₂O)]ClO₄ ( 1 ) and [Cu(l ‐Thr)(pzta)(H₂O)]ClO₄ ( 2 ) (l ‐Val: l ‐valinate; l ‐Thr: l ‐threoninate), were synthesized and characterized using elemental analyses, molar conductance measurements, spectroscopic methods and single‐crystal X‐ray diffraction. The results indicated that the molecular structures of the complexes are five‐coordinated and show a distorted square‐pyramidal geometry, in which the central copper ions are coordinated to N,N atoms of pzta and N,O atoms of amino acids. The interactions of the complexes with DNA were investigated using electronic absorption, competitive fluorescence titration, circular dichroism and viscosity measurements. These studies confirmed that the complexes bind to DNA through a groove binding mode with certain affinities (K_b = 4.71 × 10³ and 1.98 × 10³ M^?1 for 1 and 2 , respectively). The human serum albumin (HSA) binding properties of the complexes were also evaluated using fluorescence and synchronous fluorescence spectroscopies, indicating that the complexes could quench the intrinsic fluorescence of HSA in a static quenching process. The relevant thermodynamic parameters revealed the involvement of van der Waals forces and hydrogen bonds in the formation of complex–HSA systems. Finally, molecular docking technology was also used to further verify the interactions of the complexes with DNA/HSA.     

Synthesis,characterization and biological screening studies of mixed ligand complexes using flavonoids as precursors

Flavonoids are a group of plant phenolics that provide various health benefits through cell signalling pathways and antioxidant effects. In the present study, a new series of mixed ligand complexes of Co(II), Ni(II), Cu(II) and Zn(II) were synthesized by incorporating curcumin and quercetin flavonoid precursors. The structural features of the synthesized complexes were explored using elemental analysis, thermogravimetric analysis, UV–visible, infrared, NMR, mass and electron paramagnetic resonance spectral analyses and conductivity measurements. These data support an octahedral geometry of the synthesized complexes. In silico biological activity score for the ligand was predicted using PASS online software. ADMET properties were studied using VLS3D online software. Anti‐inflammatory and antioxidant activities were experimentally validated which prove that theoretical predictions are in agreement with the experimental results. Interestingly the synthesized complexes interact with calf thymus DNA through groove binding mode. Moreover, they have good potential to cleave pUC19 DNA. Minimum inhibitory concentration values of the synthesized complexes reveal that they have better antimicrobial efficacy than the ligands.     

Thiazonaphthalimide derivatives: Synthesis and interaction with DNA

The synthesis of several thiazonaphthalimide derivatives is described. The exclusive formation of angular rather than linear isomers was unequivocally demonstrated by NMR and single crystal X-ray diffraction. Their photophysical properties and ability to bind calf-Thymus DNA with affinities in the range of 10⁴ makes them interesting candidates to probe DNA by fluorescence.     

Quantitative Detection of Gene Methylated Level of Stool Samples Based on Invader Assay Coupled with Real-time Polymerase Chain Reaction and Its Application in Non-invasive Screening of Colorectal Cancer

Methylation of bone morphogenetic protein 3 (BMP3) in stool DNA is an effective biomarker for non-invasive screening of colorectal cancer. However, a highly sensitive and specific detection method is required. Here, a quantification method for BMP3 methylation was developed by combining real-time polymerase chain reaction (PCR) with invader assay using Beta-actin (ACTB) as a reference. Amplification efficiencies of BMP3 and ACTB were close to 100% after optimizing the concentration of detection probes, FEN1 enzyme and Taq polymerase, and the relative quantification of BMP3 methylation was achieved accurately by ΔCT algorithms. Ten copies and 0.01% of BMP3 methylation level could be successfully detected and non-specific signal was generated from non-methylated template, indicating that the method was highly sensitive and specific. The method was successfully applied to detect BMP3 methylation in fecal DNA from 16 colorectal cancer patients, 7 adenoma patients and 19 healthy volunteers. The results indicated that BMP3 methylation occurred in 5 of 16 cancer patients and 2 of 7 adenoma patients, but was not observed in 19 of healthy volunteers. Therefore, this method could be used to quantify methylation of gene in stool samples, providing an effective technique for non-invasive screening of colorectal cancer.     

Michael addition of 1,3-dicarbonyl compounds catalyzed by iron oxide nanoparticles

Several iron oxides nanoparticles (Fe₂O₃@Fe₂O₃, Fe°@Fe₂O₃, GO@Fe₂O₃ and calcinated Fe₂O₃) have been assessed as catalysts in the 1,4-addition of a cyclic β-ketoester onto methyl vinyl ketone under neat conditions. It appeared that calcinated Fe₂O₃NP are efficient catalysts at 1?mol% loading for the Michael addition of 1,3-dicarbonyl compounds onto various enones.     

Design,synthesis, characterization,and biological evaluation of pyrido[1,2-a]pyrimidinone coumarins as promising anti-inflammatory agents

Pursuing our recent interest regarding antimicrobial and anti-inflammatory activities of coumarin derivatives, we have synthesized a series of coumarin-linked pyridopyrimidinones by using Baylis Hillman adduct in aqueous condition with high purity. Pyrido[1,2-a]pyrimidin-2-ones are important class of heterocyclic compounds because of their use in medicinal and agro chemistry as active agents. All these newly synthesized compounds were evaluated for their antimicrobial and anti-inflammatory activity. Coumarin pyridopyrimidinones showed excellent anti-inflammatory activity against both MMP-2 and MMP-9 gelatinase zymography, whereas considerable good activity against Gram-positive and Gram-negative bacterial strains; however, antifungal activity observed in these series is more or less inactive. The active compounds of these series would be promising structural templates for the development of novel and more efficient anti-inflammatory agent.