Determining PPARγ-ligand binding affinity using fluorescent assay with cis-parinaric acid as a probe

Upon the study of small-molecules binding to proteins, the traditional methods for calculating dissociation constants (Kd and Ki) have shortcomings in dealing with the single binding site models. In this paper, two equations have been derived to solve this problem. These two equations are independent of the total concentration or initial degree of saturation of receptor and the activity of the competitive molecule. Through nonlinear fitting against these two equations, Kd value of a probe can be obtained by binding assay, and Ki value of a ligand can be obtained by competitive assay. Moreover, only the total concentrations of receptor([R]t), ligand([L]t) and probe([P]t) are required for the data fitting. In this work, Ki values of some typical ligands of PPARγ were successfully determined by use of our equations, among which the Ki value of PPARγ-LY171883 was reported for the first time.     

新型酰腙类荧光探针的合成及其对Al(Ⅲ)的传感性质

合成了两个酰腙类荧光探针1和2,在DMSO-H_2O(7∶3,体积比)体系中,两者分别在478 nm和460 nm处对Al~(3+)具有较好的荧光选择识别作用。Job's法、核磁滴定、质谱分析表明,探针1和2与Al~(3+)的配位比均为1∶2,且对Al~(3+)的检出限分别为9.58×10~(-8) mol/L和6.52×10~(-8) mol/L。同时提出了探针1和2对Al~(3+)的荧光传感机理。实际应用研究表明,探针1和2可用于河水和自来水中一定浓度范围内Al~(3+)的检测。     

Effect of DNA and bivalent metal ions on the interaction of thermostable DNA polymerase <Emphasis Type="Italic">Tte</Emphasis> with dNTPs

The interaction of DNA polymerase Tte from Thermus thermophilus B35 with dUTP analog containing a fluorescein residue bound to C(5) of the base (Flu-dUTP) was studied by fluorescence titration. The dissociation constants of the enzyme—substrate complexes in the absence and in the presence of a DNA duplex containing an extended template and bivalent metal ions and the kinetic parameters of polymerization by DNA polymerase Tte in the presence of Flu-dUTP were determined. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1268–1272, May, 2005.     

Siderophore production by a marine Pseudomonas aeruginosa and its antagonistic action against phytopathogenic fungi

A marine isolate of fluorescent Pseudomonas sp. having the ability to produce the pyoverdine type of siderophores under low iron stress (up to 10 μM iron in the succinate medium) was identified as Pseudomonas aeruginosa by using BIOLOG Breathprint and siderotyping. Pyoverdine production was optimum at 0.2% (w/v) succinate, pH 6.0, in an iron-deficient medium. Studies carried out in vitro revealed that purified siderophores and Pseudomonas culture have good antifungal activity against the plant deleterious fungi, namely, Aspergillus niger, Aspergillus flavus, Aspergillus oryzae, Fusarium oxysporum, and Sclerotium rolfsii. Siderophore-based maximum inhibition was observed against A. niger. These in vitro antagonistic actions of marine Pseudomonas against phytopathogens suggest the potential of the organism to serve as a biocontrol agent.     

Positron annihilation studies of poly(N‐isopropyl acrylamide) gel in mixed solvents

Positron annihilation lifetime spectroscopy was used to characterize the reentrant volume‐phase‐transition behavior of poly(N‐isopropyl acrylamide) hydrogel in an ethanol/water mixed solvent. The polymer gel was synthesized with γ irradiation. The ortho‐positronium lifetime (τ₃) in the gel slowly increased with an increase in the ethanol content in the mixed solvent. τ₃ was not influenced by the volume phase transition. The ortho‐positronium intensity decreased with the collapse of the gel in an approximately 10% ethanol/water mixture. When swelled in pure ethanol, τ₃ initially increased with the solvent amount in the gel, showing the destruction of intramolecular hydrogen bonding and the relaxation of polymer chains. The lower critical solution temperature of the gel in the 10% ethanol/water mixture was lower than that in pure water, and τ₃ for various solvent contents showed behavior similar to that seen in pure solvent. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1028–1036, 2002     

Permeation associated with three-phase-partitioning method on release of green fluorescent protein

Transformed cells of Escherichia coli expressing recombinant green fluorescent protein (GFPuv) were subjected to two methods of extraction: (1) freezing/thawing/sonication (FTS) cycles prior to the three-phase partitioning (TPP) method, or (2) directly to TPP extraction. The amount of GFPuv released by the FTS plus TPP method varied: 374μg/mL (first cycle), 93–442 μg/mL (second cycle), 32–359 μg/mL (third cycle), 18–115 μg/mL (fourth cycle). The GFPuv yields by the second method (TPP only) were, 23–54 μg/mL for the first extract and 33–91 μg/mL for the second. The FTS plus TPP method released similar amounts of GFPuv to that extracted by TPP; and provided a better mixture elution through the hydrophobic interaction column: 13–63 μg/mL for FTS plus TPP methods, and 2.5–13 μg/mL for TPP. The results showed that although selective permeation is a more laborious methodology, it was more efficient for obtaining of GFPuv in relation to the direct extraction of the cells for TPP.     

SNAP-tag蛋白标签技术与荧光分析法在蛋白原位分析中的联合应用

为将生物体内微观的蛋白行为可视化并以宏观信号呈现出来对蛋白进行实时、动态分析，借助SNAP-tag蛋白标签技术与有机小分子荧光染料，构建了一系列用于活细胞内实时监测目标蛋白的免洗荧光探针。标签蛋白SNAP-tag能够特异性识别探针中的苄基鸟嘌呤，从而使目标蛋白共价连接上荧光团（萘酰亚胺），携带上荧光信使。此外，由于萘酰亚胺从水环境中被牵引至SNAP-tag蛋白的疏水空腔，其荧光信号呈现出2~13倍的增强。通过SNAP-tag标签蛋白与目标蛋白的融合，该荧光探针实现了对活细胞内线粒体蛋白CoX8A及核内蛋白H2B特异性识别，在免洗条件下完成了对目标蛋白的实时追踪及原位分析。     

5-氨基-1,10-菲咯啉：可异构化杂环螯合荧光载体作为比例计量型锌离子荧光探针的一种原型

5-amino-l,10-phenanthroline （5-AP）, as a tautomeric heterocyclic aromatic chelating fluorophore （THACF）, can sense Zn^2＋ selectively by shifting emission from 495 to 564 nm upon Zn^2＋ addition in ethanol. The ratiometric fluorescent sensing behavior has been correlated to the tautomerization of 5-AP affected by solvents and metal chelation. The strategy using THACF as ratiometric fluorescent sensor for Zn^2＋ not only simplifies the synthetic procedure but also gives a promising alternative for Zn^2＋ ratiometric fluorescent sensor design.     

Real-time measurement of nitric oxide using a bio-imaging and an electrochemical technique

Nitric oxide (NO) is an important mediator responsible for numerous physiological phenomena. Transient levels of NO in biological systems usually range from nanomolar to micromolar concentrations, with a rapid return to basal levels normally seen following these increases. Because NO can diffuse only over a local area in limited time due to such low levels of production and due to its short life-time prior to degradation, high spatial and temporal resolutions are required for direct and continuous NO measurement if the physiological role of NO is to be investigated in any system. For such purposes, analytical methods based on bio-imaging and electrochemical techniques for the measurement of NO are useful. In this paper, we describe the successful application of these methods to a number of biological systems. Specifically, complementary application of these methods demonstrate that it is possible to detect real-time NO production from nervous tissue with high spatial and temporal resolutions.     

Fluorescent Molecular Recognition and Sensing System of Bis-Dansyl Modified γ-Cyclodextrins

Flexible hosts, 6A,6B-; 6A,6C-; 6A,6D-; and 6A,6E-bis dansylglycine-modified -cyclodextrins (-1, -2, -3, and -4, respectively) have been synthesized as a sensing molecule for organic guests including terpenoids and bile acids. These host compounds show a pure monomer fluorescence whose intensity is decreased or enhanced upon addition of guest species. The value I/I₀, where I and I₀ are fluorescence intensities in the presence and absence of a guest and I is I₀- I, was used as a parameter of sensitivity. These hosts exhibit highly sensitive and selective molecular recognition ability, particularly, for lithochoic acid, chenodeoxycholic acid, and ursodeoxycholic acid. The behaviors of the appended moieties of these hosts when host–guest complexation occurs are studied by induced circular dichroism (ICD) spectra and fluorescence spectral change on accommodation of a guest. The ICD pattern of these hosts alone or on accommodation of a guest is very similar, indicating that the behavior of the appended moieties are very similar. The guest-induced variations in the fluorescence or ICD intensity suggest that the appended moieties act as a hydrophobic cap that enables the cyclodextrin to form 1 : 1 host–guest complexes.