Preparation of DNA Markers Based on E. Coli Plasmid DNA

DNA fragments of various length were produced by enzymatic restriction of plasmid DNA from various strains of E. coli. A molecular DNA marker was constructed based on the DNA restricts.     

大肠杆菌DNA和RNA中核苷的高效液相色谱分析

建立了用反相高效液相色谱法（RP-HPLC）测定大肠杆菌（E.coli）脱氧核糖核酸（DNA）和核糖核酸（RNA）水解产物中核苷的方法，色谱柱为Supelco Inc.c18反相柱，254nm和280nm紫外吸收波长同时检测，分析条件经选择在流速为1mL/min，流动相A（2.5%甲醇 0.01mol/L KH2PO4,PH4.6)28min，流动相B（8.0%甲醇 0.01mol/L KH2PO4，PH4.6)37min，柱温为20℃条件下65min可实现核苷的完全分离，回收率为80.19%-99.31%，相对标准偏差RSD为0.86%-2.62%，该方法具有高灵敏度、高选择性的特点，得到的结果与十分满意。     

Complexation and Transport of Alkali and Alkaline Earth Metal Cations by p-tert-Butyldihomooxacalix[4]arene Tetraketone Derivatives

The binding properties of three p-tert-butyldihomooxacalix[4]arene tetraketone derivatives (tert-butyl 2b, adamantyl 2c and phenyl 2d) in the cone conformation and one derivative (methyl 2a) in a partial cone conformation, towards alkali and alkaline earth metal cations have been established by extraction studies of metal picrates from water into dichloromethane, stability constant measurements in methanol and acetonitrile, and by ¹H NMR spectrometry. Transport experiments of metal picrates through a dichloromethane membrane were also performed. The results are compared to those obtained with closely-related calix[n]arene derivatives (n = 4 and 5) and discussed in terms of the substituents, size and conformational effects. Methylketone 2a is a poor binder for all the cations studied, due to its partial cone conformation. Ketones 2b, 2c and 2d show high extraction and complexation levels for the alkali cations, with similar profiles and preference for K⁺ and Na⁺ (plateau selectivity). Towards alkaline earth cations, these ketones show a strong peak selectivity for Ba²⁺ in extraction, but a plateau selectivity for Ca²⁺, Sr²⁺ and Ba²⁺ in complexation. The nature of the substituent attached to the ketone function has some influence on their binding properties, with phenylketone 2d being a slightly weaker binder than ketones 2b and 2c. ¹H NMR titrations confirm the formation of 1:1 complexes between the ketones and the cations studied, also indicating that they should be located inside the cavity defined by the phenoxy and carbonyl oxygen atoms. Ketones 2b, 2c and 2d show transport rates that do not follow, in general, the same trends observed in extraction and complexation.     

Anion Complexation by Meso-Octamethylcalix[4]pyrrole in Aqueous Solution

The ligand calix[4]pyrrole is quite insoluble in aqueous solution. In the presence of NaCl, KCl, CsCl, NH₄Cl, CaCl₂, and CdCl₂, the solubility of calix[4]pyrrole linearly increases with the salt concentration. The ligand calix[4]pyrrole forms stable complexes with the chloride anion. All other halogen anions do not form complexes. The measurement of the amount of dissolved ligand allows the determination of the complex stabilities in aqueous solution. This experimental method is discussed in detail due to its general suitability to study the complexation reactions with nearly insoluble ligands.     

Competitive Complexation of Lanthanide Cations by Xylitol and Nitrate Anion in Aqueous Solution: A Microcalorimetric Investigation

The apparent equilibrium constants and enthalpies of complexation of Nd³⁺, Sm³⁺, Eu³⁺, and Gd³⁺ by xylitol in aqueous solutions containing NaNO₃ at an ionic strength of 2.0 mol-kg^–1 have been determined by microcalorimetry at 25°C. Since nitrate anion weakly complexes the lanthanide cations, these values are analyzed in terms of competition between xylitol and NO ₃ ^- The method leads to the apparent equilibrium constants and enthalpies of complexation of the lanthanide cations by NO ₃ ^- at this particular ionic strength. Despite the difficulties encountered in characterizing rather weak associations, the results are, whenever comparison is possible, in good agreement with those obtained by direct microcalorimetry. The advantage of this competition method is that it can be used when the enthalpic effects are too weak and insufficiently concentration dependent for direct microcalorimetric determination. In the present case, it allows us to thermodynamically characterize the formation of SmNO ₃ ²⁺ and EuNO ₃ ²⁺ , processes we have not been able to study directly.     

Opposed steric constraints in human DNA polymerase beta and E. coli DNA polymerase I

DNA polymerase selectivity is crucial for the survival of any living species, yet varies significantly among different DNA polymerases. Errors within DNA polymerase-catalyzed DNA synthesis result from the insertion of noncanonical nucleotides and extension of misaligned DNA substrates. The substrate binding characteristics among DNA polymerases are believed to vary in properties such as shape and tightness of the binding pocket, which might account for the observed differences in fidelity. Here, we employed 4'-alkylated nucleotides and primer strands bearing 4'-alkylated nucleotides at the 3'-terminal position as steric probes to investigate differential active site properties of human DNA polymerase beta (Pol beta) and the 3'-->5'-exonuclease-deficient Klenow fragment of E. coli DNA polymerase I (KF(exo-)). Transient kinetic measurements indicate that both enzymes vary significantly in active site tightness at both positions. While small 4'-methyl and -ethyl modifications of the nucleoside triphosphate perturb Pol beta catalysis, extension of modified primer strands is only marginally affected. Just the opposite was observed for KF(exo-). Here, incorporation of the modified nucleotides is only slightly reduced, whereas size augmentation of the 3'-terminal nucleotide in the primer reduces the catalytic efficiency by more than 7000- and 260,000-fold, respectively. NMR studies support the notion that the observed effects derive from enzyme substrate interactions rather than inherent properties of the modified substrates. These findings are consistent with the observed differential capability of the investigated DNA polymerases in fidelity such as processing misaligned DNA substrates. The results presented provide direct evidence for the involvement of varied steric effects among different DNA polymerases on their fidelity.     

Near-U.V. photolysis of pyrimidine heteroadducts in E. coli DNA

Abstract— The cytosine-thymine precursor of the U–T adduct is not subject to enzymatic photoreactivation, but can be eliminated directly from u.v.-irradiated E. coli DNA by exposure to wavelengths around 313 nm.     

N-硝基脲类的合成及其阴离子识别研究

合成了两种新型的阴离子识别受体N-硝基-N-(2,6-二硝基-4-三氟甲基苯基)-N'-(4-氯苯基)脲(受体1)和N-硝基-N-(2,6-二硝基-4-三氟甲基苯基)-N'-(4-甲基苯基)脲(受体2).利用紫外-可见吸收光谱考察了其与F-、Cl-、Br-、I-、H2PO4-、HPO42-、PO43-阴离子客体的识别作用.结果表明:在受体分子中加入F-、H2PO4-、HPO42-阴离子,其紫外-可见吸收光谱发生明显变化且溶液颜色由黄色变为紫色,而加入其他离子时无此现象.从而实现对这3种阴离子的裸眼检测.测定了结合物的结合比及结合常数.Job工作曲线表明受体与阴离子客体形成了1:1结合物.结合常数表明:同一受体对不同阴离子的选择性不同,受体分子1选择性HPO42- > H2PO4 > F-,受体分子2选择性HPO42- > F- > H2PO4;受体分子与同一阴离子客体的结合能力呈现规律性,1>2.提出了可能的结合模式.     

Synthesis of Computationally Designed 2,5(6)-Benzimidazole Derivatives via Pd-Catalyzed Reactions for Potential E. coli DNA Gyrase B Inhibition

A pharmacophore model for inhibitors of Escherichia coli’s DNA Gyrase B was developed, using computer-aided drug design. Subsequently, docking studies showed that 2,5(6)-substituted benzimidazole derivatives are promising molecules, as they possess key hydrogen bond donor/acceptor groups for an efficient interaction with this bacterial target. Furthermore, 5(6)-bromo-2-(2-nitrophenyl)-1H-benzimidazole, selected as a core molecule, was prepared on a multi-gram scale through condensation of 4-bromo-1,2-diaminobenzene with 2-nitrobenzaldehyde using a sustainable approach. The challenging functionalization of the 5(6)-position was carried out via palladium-catalyzed Suzuki–Miyaura and Buchwald-Hartwig amination cross-coupling reactions between N-protected-5-bromo-2-nitrophenyl-benzimidazole and aryl boronic acids or sulfonylanilines, with yields up to 81%. The final designed molecules (2-(aminophen-2-yl)-5(6)-substituted-1H-benzimidazoles), which encompass the appropriate functional groups in the 5(6)-position according to the pharmacophore model, were obtained in yields up to 91% after acid-mediated N-boc deprotection followed by Pd-catalyzed hydrogenation. These groups are predicted to favor interactions with DNA gyrase B residues Asn46, Asp73, and Asp173, aiming to promote an inhibitory effect.     

Anion Recognition by Urea Derivatives of Anthraquinone: Dihydrogen Phosphate Ion Selective Neutral Receptors

Three urea derivatives of anthraquinone were synthesized and they showed a high selectivity for dihydrogen phosphate ions.     

Using molecular beacon to monitor activity of E. coli DNA ligase

NAD(+)-dependent DNA ligase has been widely used in gene diagnostics for disease-associated mutation detection and has proved to be necessary for screening bactericidal drugs targeted to DNA ligases. However, further research has been restricted since conventional ligase assay technology is limited to gel electrophoresis, which is discontinuous, time-consuming and laborious. An innovative approach is developed for monitoring the activity of E. coli DNA ligase catalyzing nucleic acid ligation in the report. This approach utilizes a molecular beacon hybridized with two single-stranded DNA (ssDNA) segments to be ligated to form a hybrid with a nick, and could therefore be recognized by the enzyme. Ligation of the two ssDNA segments would cause conformation changes of the molecular beacon, leading to significant fluorescence enhancement. Compared to gel electrophoresis, this approach can provide real time information about ligase, is more time efficient, and is easier to use. The effect of quinacrine, a drug for malaria, on the activity of the ligase is detected, thereby certifying the capability of the method for developing novel antibacterial drugs targeted at NAD(+)-dependent ligase. The fidelity of strand joining by the ligase is examined based on this approach. The effects of external factors on activity of the ligase are analyzed, and then an assay of E. coli DNA ligase is performed with a broad linear range of 4.0 x 10(-4) Weiss Unit mL(-1) to 0.4 Weiss Unit mL(-1) and the detection limit of 4.0 x 10(-4) Weiss Unit mL(-1).     

基于分子信标实时监测大肠杆菌DNA连接酶催化的DNA连接过程

报道了一种对DNA连接过程进行实时监测的方法,利用分子信标核酸探针作为DNA连接反应的模板和检测探针,实时监测了 E.coli DNA连接酶催化的DNA连接反应,克服了传统的凝胶电泳技术操作复杂、周期长及无法实时监测DNA连接过程的缺点,为核酸连接过程的实时监测和连接酶催化机理的研究提供了更为丰富的信息.在此基础上,发展了一种快速、准确测定 E.coli DNA连接酶的方法,线性响应范围为4.0×10^-6～2.0×10^-4U/μL,检测下限为4.0×10^-6U/μL.     

Electrochemical detection of nicotinamide adenine dinucleotide based on molecular beacon-like DNA and E. coli DNA ligase

An electrochemical method for nicotinamide adenine dinucleotide (NAD⁺) detection with high sensitivity and selectivity has been developed by using molecular beacon (MB)-like DNA and Escherichia coli DNA ligase. In this method, MB-like DNA labeled with 5′-SH and 3′-biotin was self-assembled onto a gold electrode in its duplex form by means of facile gold-thiol chemistry, which resulted in blockage of electronic transmission. It was eT OFF state. In the presence of NAD⁺, E. coli DNA ligase was activated, and the two nucleotide fragments which were complementary to the loop of the MB-like DNA could be ligated by the NAD⁺-dependent E. coli DNA ligase. Hybridization of the ligated DNA with the MB-like DNA induced a large conformational change in this surface-confined DNA structure, which in turn pushed the biotin away from the electrode surface and made the electrons exchange freely with the electrode. Then the generated electrochemical signals can be measured by differential pulse voltammetry (DPV). Under optimized conditions, a linear response to logarithmic concentration of NAD⁺ range from 3 nM to 5 μM and a detection limit of 1.8 nM were obtained. Furthermore, the proposed strategy had sufficient selectivity to discriminate NAD⁺ from its analogues.     

Ion Complexation Properties of Calix[6]Arene Derivatives: I. 1,4-Calix[6]Crown-4 Derivatives

Abstract

A series of 1,4-p-tert-butyl-calix[6]crown-4 tetraesters, tetraamides, tetraacids with defined conformation have been synthesized, and their complexation properties towards metal ions and alkyl ammonium ions were investigated systematically. It was found that 1,4-p-tert-butyl-calix[6]crown-4 tetraethylester (3a) and 1,4-p-tert-butyl-calix[6]benzocrown-4 tetramethyl-ester (4b) show high selectivity towards Na⁺, Li⁺, respectively and all of them exhibit high complexation abilities towards Et₂NH₂ ⁺ cation.     

Enumeration of total coliforms and E. coli in foods by the SimPlate coliform and E. coli color indicator method and conventional culture methods: collaborative study

The relative effectiveness of the SimPlate Coliform and E. coli Color Indicator (CEc-CI) method was compared to the AOAC 3-tube Most Probable Number (MPN) methods for enumerating and confirming coliforms and Escherichia coli in foods (966.23 and 966.24). In this study, test portions were prepared and analyzed according to the conditions stated in both the AOAC methods and SimPlate directions for use. Six food types were artificially contaminated with coliform bacteria and E. coli: frozen burritos, frozen broccoli, fluid pasteurized milk, whole almond nut meats, cheese, and powdered cake mix. Method comparisons were conducted. Overall, the SimPlate method demonstrated <0.3 log difference for total coliform and E. coli counts compared to the AOAC reference methods for the majority of food types and levels analyzed. In all cases, the repeatability and reproducibility of the SimPlate CEc-CI method were not different from those of the reference methods and in certain cases, were statistically better than those of the AOAC 3-tube MPN methods. These results indicate that the SimPlate CEc-CI method and the reference culture methods are comparable for enumeration of both total coliforms and E. coli in foods.     

壳聚糖及其衍生物对金属离子的吸附研究(下)

壳聚糖是一种天然高分子,在其分子结构的重复单元中有-NH2和-OH,因而对金属离子有较好地吸附和配位能力。本文较全面的综述了壳聚糖及其衍生物对金属离子的吸附性能,简述了它们与金属离子形成配合物的结构及吸附机理。其中下篇主要讲述了壳聚糖及其衍生物与金属离子形成配合物后的结构以及吸附机理,并对其发展前景作了展望。     

Binding Characteristics Study of DNA based Aptamers for E. coli O157:H7

E. coli O157:H7 is a pathogenic bacterium producing verotoxins that could lead to serious complications such as hemolytic uremia syndrome. Fast detection of such pathogens is important. For rapid detection, aptamers are quickly gaining traction as alternative biorecognition molecules besides conventional antibodies. Several DNA aptamers have been selected for E. coli O157:H7. Nonetheless, there has not been a comparative study of the binding characteristics of these aptamers. In this work, we present a comprehensive analysis of binding characteristics including binding affinity (K_d) and binding capacity (B_max) of DNA-based aptamers for E. coli O157:H7 using qPCR. Our results show that aptamer E18R has the highest binding capacity to E. coli 157:H7 and the highest specificity over non-pathogenic E. coli strains K12 and DH5α. Our study also finds that the common biotin-tag modification at 5′ end typically changes the binding capacity significantly. For most of the selected aptamers, the binding capacity after a biotin-tag modification decreases. There exists a discrepancy in the binding capability between the selected aptamer and the aptamer used for detection. Our study also shows that a lower concentration of Mg²⁺ ions in the binding buffer leads to a decrease in the binding capacity of E17F and E18R, while it does not affect the binding capacity of S1 and EcoR1.     

壳聚糖及其衍生物对金属离子的吸附研究(上)

壳聚糖是一种天然高分子,在其分子结构的重复单元中有-NH2和-OH,因而对金属离子有较好地吸附和配位能力.本文较全面地综述了壳聚糖及其衍生物对金属离子的吸附性能,简述了它们与金属离子形成配合物的结构及吸附机理,并对其发展前景作了展望.其中上篇主要讲述了壳聚糖及其衍生物对金属离子吸附性能的研究进展.