用于HBV病毒快速诊断的分子信标探针设计

分子信标是一种高灵敏度、高特异性的新型荧光核酸探针.它在与互补DNA或RNA靶序列杂交时放出荧光.利用Genebank中调出已知HBV病毒ayr亚型基因组信息,通过BeaconDesigner4.0软件进行分子信标探针设计,共设计出6条分子信标探针,以便于为目前HBV病毒快速诊断提供参考.     

银染增强的纳米金标记探针对微量核酸的检测

本研究利用银染增强的纳米金技术建立了一种简单快速的核酸定量方法.该方法基于纳米金与烷巯基修饰的寡核苷酸分子共价键合作用,将纳米微粒报告基团标记在与靶核酸一端序列互补的寡核苷酸上,同时生物素化修饰另一端互补序列.靶核酸与两段寡核苷酸探针杂交后,借亲和素固定在酶标板孔内,通过纳米金催化的银染放大效应产生高灵敏的识别信号,适时记录其吸光度值从而实现核酸分子的定量.该检测方法检测单链核酸分子的灵敏度达0.1 fM,双链分子为10 fM.     

以分子信标为报告分子的凝血酶检测新方法

以分子信标为报告分子,核酸适体为识别分子,发展了一种新的凝血酶检测方法.含有分子信标互补序列的核酸适体探针与凝血酶结合后,分子信标的荧光信号下降,从而得到凝血酶的浓度信息.该方法快速、灵敏,核酸适体探针无需荧光标记、设计简单,检测限达到0.83nmol/L.     

分子灯塔设计核酸测定原理及应用

分子灯塔是一种在分子杂交基础上发展的一种荧光探针。这种探针５′端标记荧光物质,３′端连接荧光淬灭剂,而且在５′端和３′端设计互补碱基序列,使探针形成茎环结构。在检测核酸时具有快速、重复性好、灵敏度和特异性高、结果明确等优点。本文就分子灯塔的设计原则、分子特点和在核酸测定中的应用前景简要综述。     

用序列比对设计的茎环结构探针检测金黄色葡萄球菌

基于金黄色葡萄球菌16S rRNA基因序列,采用序列比对设计了一种茎环结构的寡聚核苷酸探针。探针的环序列即为金黄色葡萄球菌16S rRNA基因序列的其中一个片段,同其他菌种的16S rRNA基因序列误配2个以上的核苷酸,因此能高度专一、灵敏的检测金黄色葡萄球菌16S rRNA。根据分子信标技术和酶联免疫分析的原理,评估一个实验方法,即利用能构象转换的、固定化的茎环结构探针酶联检测靶核酸。由于探针的特异性加强,这个检测系统能有效的排除假阳性即不会出现误配一个核苷酸的情况。采用微量浓度测定分析,最低下限可检测出大约4ng的金葡球菌16SrRNA。这种方法的灵敏度比其他常规检测方法高出了至少一个数量级。     

分子信标检测限制性内切酶活性的新型荧光分析方法

利用分子信标被切割后荧光信号的变化.发展了一种简便的检测限制性内切酶活性的新型荧光分析方法.以限制性内切酶Xsp I为例.将其识别位点嵌入具有茎环结构的分子信标探针(Molecular Beacon,MB)的环状部分,利用这种分子信标在溶液中形成的瞬时二聚体结构,实现了限制性内切酶对分子信标的切割.在优化的条件下,反应初速度与酶的浓度成正比,线性范围为0.05～50 U/mL,检测限为0.05 U/mL.通过改变分子信标环部的识别位点的序列.还可以检测其他限制性内切酶如Alu I的活性.     

HRP化学发光体系在基因检测中的应用

随着分子生物学及其相关学科的飞速发展,基因检测技术不断得到创新并且日趋完善,核酸探针是检测特异、互补序列的有力工具,是基因检测技术中一项重要内容。核酸探针不仅对胎儿性别、亲子关系和个体差异从分子水平上进行准确的分析判别,而且对内源基因突变引起的各种先天性遗传病和癌症、对各种病毒、细菌和寄生虫等入侵人体所致的各种传染病进行可靠的基因诊断。     

SARS冠状病毒实时荧光RT-PCR定量检测

为建立一种快速、准确、特异的SARS病毒RNA定量检测方法,根据复合探针荧光定量分析原理,对SARS病毒核酸进行实时荧光定量RT-PCR检测.借助计算机辅助,对SARS病毒基因靶序列以及检测引物和探针进行了优化筛选;利用体外转录SARS病毒RNA靶序列,对RT-PCR反应的镁离子浓度参数进行了优化;比较Trizol法、磁珠法、Qiagen法、煮沸法等4种方法提取RNA的检测效果,建立了样本处理方法;通过对构建的体外转录靶序列模型的检测,对本方法的灵敏度、特异性、定量线性关系、精确度等进行了评价,并通过对42例临床标本的检测对本方法的检测效果进行了评估. 通过克隆SARS病毒核酸靶序列并进行体外转录,获得了长度约1.2 kb的体外转录RNA靶序列;经优化,荧光RT-PCR反应液中的Mg²⁺浓度以4.0 mmol/L为最好;RNA提取方法采用磁珠法效果较好;本方法的检测灵敏度最低可达5个拷贝的体外转录RNA分子,特异性100%,C_t值的CV值小于5%.对临床确诊的42份SARS病人血清和漱口水标本的检测结果表明,该方法的检出率为79%,与荧光抗体检测法的符合率为70%.上述结果表明,该方法建立的荧光定量RT-PCR技术能够快速准确、特异、敏感地对SARS病毒核酸进行定量分析,为临床SARS冠状病毒RNA的检测提供了新的,更为有效的检测方法.     

新型分子信标技术的研究进展

分子信标是一种设计巧妙的新型荧光标记核酸探针。特殊的发夹结构使分子信标具有很强的特异性识别靶标序列的能力,目前已成为生物学中一种强有力的研究工具。本文介绍了近年来出现的各种新型的分子信标(MB)的结构及工作原理。简要概述了MB技术在生命科学领域中的应用,展望了MB技术的发展趋势。     

分子信标及其应用研究进展

分子信标作为一种核酸荧光探针,其最初的设计目的是用来检测核酸,特别是用作实时荧光PCR反应的探针。由于其特殊的发夹结构,决定的其具有多种的用途。不仅能在液相或固相对核酸进行定性、定量分析,还能用于多种DNA－蛋白质、DNA－DNA损伤试剂之间相互作用等的研究。     

Discovery of novel 2-(3-phenylpiperazin-1-yl)-pyrimidin-4-ones as glycogen synthase kinase-3β inhibitors

We herein describe the results of further evolution of glycogen synthase kinase (GSK)-3β inhibitors from our promising compounds containing a 2-phenylmorpholine moiety. Transformation of the morpholine moiety into a piperazine moiety resulted in potent GSK-3β inhibitors. SAR studies focused on the phenyl moiety revealed that a 4-fluoro-2-methoxy group afforded potent inhibitory activity toward GSK-3β. Based on docking studies, new hydrogen bonding between the nitrogen atom of the piperazine moiety and the oxygen atom of the main chain of Gln185 has been indicated, which may contribute to increased activity compared with that of the corresponding phenylmorpholine analogues. Effect of the stereochemistry of the phenylpiperazine moiety is also discussed.     

The subunits of Chlorobium flavocytochrome c.

The subunits of cytochrome c-553 (Chlorobium thiosulfatophilum) were studied. The cytochrome is split into a cytochrome moiety and a flavoprotein moiety by treatment with 2% trichloroacetic acid. The molecular weights of the cytochrome and flavoprotein moieties are 11,000 and 47,000, respectively. The cytochrome moiety seems to have only one cysteine residue in the molecule, although its heme appears to be quite similar to the usual heme c. The flavoprotein moiety shows absorption peaks at 350 and 452nm and is insoluble at neutral pH. When the two moieties are mixed at alkaline pH, and the pH of the mixture is then brought to neutral, the flavoprotein moiety remains soluble. However, the preparation thus obtained is different from the original cytochrome c-553.     

Organization of the synthesis of glycolipid oligosaccharides in the Golgi complex

Glycolipids constitute a complex family of amphipathic molecules structurally characterized by a hydrophilic mono- or oligo-saccharide moiety linked to a hydrophobic ceramide moiety. Due to their asymmetric distribution in cell membranes, exposing the saccharide moiety to the extracytoplasmic side of the cell, glycolipids participate in a variety of cell-cell and cell-ligand interactions. Here we summarize aspects of the cell biology of the stepwise synthesis of the saccharide moiety in the Golgi complex of cells from vertebrates. In particular we refer to the participant glycosyltransferases, with emphasis on their trafficking along the secretory pathway, their retention and organization in the Golgi complex membranes and their dependence on the Golgi complex ultra structural organization for proper function.     

Preparation and kinetic properties of 5-ethylphenazine-lactate-dehydrogenase-NAD+ conjugate, a semisynthetic lactate oxidase showing a hide-and-seek effect.

5-Ethylphenazine-lactate-dehydrogenase-NAD+ conjugate (EP(+)-LDH-NAD+) was prepared by linking poly(ethylene glycol)-bound 5-ethylphenazine and poly(ethylene glycol)-bound NAD+ to lactate dehydrogenase. The average number of the ethylphenazine moieties bound per molecule of enzyme subunit was 0.46, and that of the NAD+ moieties was 0.32. This conjugate is a semisynthetic enzyme having lactate oxidase activity using oxygen or 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) as an electron acceptor; to make such conjugates seems to be a general method for artificially converting a dehydrogenase into an oxidase. When the concentration of oxygen or MTT is varied, the oxidase activity fits the Michaelis-Menten equation with the following kinetic constants: for the reaction system with oxygen, the turnover number per subunit is 2.3 min-1 and Km for oxygen is 1.91 mM; and for the system with MTT, the turnover number is 0.25 min-1 and Km for MTT is 0.076 mM. At the initial steady state of the oxidase reaction, only 2.1% of the NAD+ moieties of the conjugate are in the free state (i.e. not bound in the coenzyme-binding site of the lactate dehydrogenase moiety) and the rest are hidden in the coenzyme site; almost all the NAD+ moieties are in the reduced state. The apparent intramolecular rate constant for the reaction between a free NADH moiety and an oxidized ethylphenazine moiety is 2.3 s-1 and 2.1 s-1 for the systems with oxygen and with MTT, respectively. The apparent effective concentration of the free NADH moiety for the ethylphenazine moiety is 5.5 microM and is much smaller than that (0.34 mM) of the ethylphenazine moiety for the free NADH moiety; this difference is due to the effect of hiding the NADH moiety in the binding site, as the hidden NADH moiety cannot react with the ethylphenazine moiety.     

The use of a proteinaceous “cushion” with a polystyrene‐binding peptide tag to control the orientation and function of a target peptide adsorbed to a hydrophilic polystyrene surface

In immobilizing target biomolecules on a solid surface, it is essential (i) to orient the target moiety in a preferred direction and (ii) to avoid unwanted interactions of the target moiety including with the solid surface. The preferred orientation of the target moiety can be achieved by genetic conjugation of an affinity peptide tag specific to the immobilization surface. Herein, we report on a strategy for reducing the extent of direct interaction between the target moiety and surface in the immobilization of hexahistidine peptide (6His) and green fluorescent protein (GFP) on a hydrophilic polystyrene (PS) surface: Ribonuclease HII from Thermococcus kodakaraensis (cHII) was genetically inserted as a “cushion” between the PS‐affinity peptide tag and target moiety. The insertion of a cushion protein resulted in a considerably stronger immobilization of target biomolecules compared to conjugation with only a PS affinity peptide tag, resulting in a substantially enhanced accessibility of the detection antibody to the target 6His peptide. The fluorescent intensity of the GFP moiety was decreased by approximately 30% as the result of fusion with cHII and the PS‐affinity peptide tag but was fully retained in the immobilization on the PS surface irrespective of the increased binding force. Furthermore, the fusion of cHII did not impair the stability of the target GFP moiety. Accordingly, the use of a proteinaceous cushion appears to be promising for the immobilization of functional biomolecules on a solid surface. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:527–534, 2016     

Ideamine N-Oxides: Pyrrolizidine Alkaloids Sequestered by the Danaine Butterfly,Idea leuconoe

Two new pyrrolizidine alkaloids, ideamines A and B, together with other analogs (lycopsamine and parsonsine) were isolated in the N-oxide forms from adult bodies of the Apocynaceae-feeding danaine butterfly, Idea leuconoe. Ideamine A was characterized as a homolog of lycopsamine, in which the viridifloric acid moiety was replaced by a 2-ethyl-2,3-dihydroxybutanoic moiety. Likewise, ideamine B was identified as a nor-derivative of parsonsine, in which the trachelanthic acid moiety was replaced by a 2-ethyl-2,3-dihydroxybutanoic moiety diastereomeric to the necic acid from ideamine A.     

Fluorescent and photoaffinity labeling derivatives of rhizoxin

A fluorescent probe (D-RZX) and a photoreactive fluorescent probe (AD-RZX) for studying the rhizoxin binding site on tubulin were prepared by the derivatization of rhizoxin (RZX). D-RZX consists of a rhizoxin moiety and a dansyl moiety. AD-RZX has a 5-azidonaphthalene-1-sulfonyl moiety instead of the dansyl moiety of D-RZX. Both D-RZX and AD-RZX bound tubulin in a mutually competitive manner with rhizoxin, indicating their binding to the rhizoxin site on tubulin. AD-RZX bound the rhizoxin site covalently after UV-irradiation, thus showing its usefulness as a photo-affinity probe for labeling of the rhizoxin site.     

Novel prodrug approach to amprenavir-based HIV-1 protease inhibitors via O-->N acyloxy migration of P1 moiety

We have developed a new approach to prodrugs, which utilizes a pH-induced intramolecular O-->N migration of an acyloxy group in carbonate moiety to a free amino moiety at neutral pH. This method is exemplified by facile rearrangement of highly water-soluble prodrug 3 to carbamate 4, a close analogue of HIV-1 protease inhibitor Amprenavir. The O-->N acyloxy migration is unprecedented in the context of prodrugs and it enables a high atom economy due to recycling of the 'pro' moiety.     

Pharmacological evaluation of a novel series of urea,thiourea and guanidine derivatives as P2X7 receptor antagonists

We report on P2X₇ receptor antagonists based on a lead adamantly-cyanoguanidine-aryl moiety. We have investigated the importance of the central cyanoguanidine moiety by replacing it with urea, thiourea or guanidine moieties. We have also investigated the linker length between the central moiety and the aryl portion. All compounds were assessed for their inhibitory potency in a pore-formation dye uptake assay at the P2X₇ receptor. None of the compounds resulted in an improved potency illustrating the importance of the cyanoguanidine moiety in this chemotype.     

NMR analysis of the fibronectin cell-adhesive sequence, Arg-Gly-Asp, in a recombinant silk-like protein and a model peptide

It is well established that by introducing the cell-adhesive sequence Arg-Gly-Asp (RGD) from fibronectin into Bombyx mori silk fibroin by covalent coupling or bioengineering techniques, excellent biomaterials have been developed with the modified silk fibroin. However, there is no report about the structure and dynamics of the RGD moiety in the silk fibroin. To clarify the origin of such a high cell adhesion character and to design new recombinant silk protein with higher cell adhesion ability, it is necessary to characterize the structure and dynamics of the RGD moiety introduced into silk fibroin. In this study, the structure and dynamics of the RGD moiety in a recombinant silk-like protein, SLPF(10), consisting of the repeated silk fibroin sequence (AGSGAG)(3) and the sequence ASTGRGDSPA including the RGD moiety, were studied using solution NMR. The (1)H, (15)N, and (13)C chemical shifts indicate that the RGD moiety, as well as the silk fibroin sequence, takes a random coil form with high mobility in aqueous solution. Next, a (13)C solid-state NMR study was performed on a (13)C selectively labeled model peptide, AGSGAG[3-(13)C]A(7)GSGAGAGSGGT[2-(13)C]G(19)R[1-(13)C]G(21)DSPAGGGAGAGSGAG. After formic acid treatment, an increase in the β-sheet fraction for the AGSGAG sequence and peak narrowing of the residues around the RGD moiety were observed in the dry state. The latter indicates a decrease in the chemical shift distribution although the RGD moiety is still in random coil. A decrease in the peak intensities of the RGD moiety in the swollen state after immersing it in distilled water was observed, indicating high mobility of the RGD sequence in the peptide in the swollen state. Thus, the random coil state of the RGD moiety in the recombinant silk-like protein is maintained in aqueous solution and also in both dry and swollen state. This is similar to the case of the RGD moiety in fibronectin. The presence of the linker ASTG at the N-terminus and SPAGG at the C-terminus seems important to maintain the random coil form and the flexible state of the RGD sequence in order to permit access for binding to various integrins.