Fluorescence Polarization Method Research Articles

Fluorescence Determination of Omethoate Based on a Dual Strategy for Improving Sensitivity.

Omethoate is a frequently used organophosphorus pesticide, and the establishment of a sensitive, selective, and simple method to determine omethoate is very important for food safety. In this paper, a dual strategy was applied to improve the detection sensitivity of omethoate. In the first strategy, graphene quantum dots (GQDs) were doped with nitrogen to increase the fluorescence quantum yield to 30%. By coupling N-GQDs with omethoate aptamer, an N-GQDs-aptamer probe was synthesized. The fluorescence of the N-GQDs-aptamer probe was turned off by graphene oxide (GO), but recovered by omethoate. Based on this principle, the fluorescence method for detecting omethoate was established with a detection limit of 0.041 nM. To further improve the detection sensitivity, the fluorescence polarization analysis method was applied as another strategy based on the polarization signal of GQDs. The detection limit was decreased to 0.029 pM by using the fluorescence polarization method. The detection limits in this paper were lower than those in other reports. The imaging of omethoate on plant leaves showed that the probe could be used for visual semiquantitative determination of omethoate.

Characterization of DNA Substrate Binding to the Phosphatase Domain of the DNA Repair Enzyme Polynucleotide Kinase/Phosphatase.

Polynucleotide kinase/phosphatase (PNKP) is a DNA strand break repair enzyme that uses separate 5' kinase and 3' phosphatase active sites to convert damaged 5'-hydroxyl/3'-phosphate strand termini to ligatable 5'-phosphate/3'-hydroxyl ends. The phosphatase active site has received particular attention as a target of inhibition in cancer therapy development. The phosphatase domain dephosphorylates a range of single- and double-stranded substrates; however, structural studies have shown that the phosphatase catalytic cleft can bind only single-stranded substrates. Here we use a catalytically inactive but structurally intact phosphatase mutant to probe interactions between PNKP and a variety of single- and double-stranded DNA substrates using an electrophoretic mobility shift assay. This work indicates that the phosphatase domain binds 3'-phosphorylated single-stranded DNAs in a manner that is highly dependent on the presence of the 3'-phosphate. Double-stranded substrate binding, in contrast, is not as dependent on the 3'-phosphate. Experiments comparing blunt-end, 3'-overhanging, and frayed-end substrates indicate that the predicted loss of energy due to base pair disruption upon binding of the phosphatase active site is likely balanced by favorable interactions between the liberated complementary strand and PNKP. Comparison of the effects on substrate binding of mutations within the phosphatase active site cleft with mutations in surrounding positively charged surfaces suggests that the surrounding surfaces are important for binding to double-stranded substrates. We further show that while fluorescence polarization methods can detect specific binding of single-stranded DNAs with the phosphatase domain, this method does not detect specific interactions between the PNKP phosphatase and double-stranded substrates.

迅速かつ簡便な微生物遺伝子情報計測の応用

In this research, it aims to measure promptly and handily the genetic information of microorganisms, which normally adhere to human's skin and mucous membrane. Additionally, we report the results of genetic information measurement for the microorganisms that exist in human's life environment. The specific DNA sequence for the gene of Pseudomonas aeruginosa, which exists widely in the environment, was detected with a fluorescence polarization method.

Kinetics of binding of fluorescent ligands to enzymes with engineered access tunnels.

Molecular recognition mechanisms and kinetics of binding of ligands to buried active sites via access tunnels are not well understood. Fluorescence polarization enables rapid and non-destructive real-time quantification of the association between small fluorescent ligands and large biomolecules. In this study, we describe analysis of binding kinetics of fluorescent ligands resembling linear halogenated alkanes to haloalkane dehalogenases. Dehalogenases possess buried active sites connected to the surrounding solvent by access tunnels. Modification of these tunnels by mutagenesis has emerged as a novel strategy to tailor the enzyme properties. We demonstrate that the fluorescence polarization method can sense differences in binding kinetics originating from even single mutations introduced to the tunnels. The results show, strikingly, that the rate constant of the dehalogenase variants varied across seven orders of magnitude, and the type of ligand used strongly affected the binding kinetics of the enzyme. Furthermore, fluorescence polarization could be applied to cell-free extracts instead of purified proteins, extending the method's application to medium-throughput screening of enzyme variant libraries generated in directed evolution experiments. The method can also provide in-depth kinetic information about the rate-determining step in binding kinetics and reveals the bottlenecks of enzyme accessibility. Assuming availability of appropriate fluorescent ligand, the method could be applied for analysis of accessibility of tunnels and buried active sites of enzymes forming a covalent alkyl-enzyme intermediate during their catalytic cycle, such as α/β-hydrolases containing >100000 protein sequences based on the Pfam database.

New 2-(2-Phenylethyl)chromone Derivatives and Inhibitors of Phosphodiesterase (PDE) 3A from Agarwood

The MeOH extract of agarwood showed inhibitory activity against phosphodiesterase (PDE) 3A. Fractionation of the extract led to the isolation of two new 2-(2-phenylethyl)chromones, 6,8-dihydroxy-2-[2-(4'-methoxyphenyl)ethyl]chromone (6), and 6,7-dihydroxy-2-(2-phenylethyl)chromone (8), together with six known compounds. All isolated compounds were tested for their PDE 3A inhibitory activity using fluorescence polarization method. Compound 7 showed PDE 3A inhibitory activity with IC50 of 4.83 μM.

Investigation of β-lactam antibacterial drugs, β-lactamases, and penicillin-binding proteins with fluorescence polarization and anisotropy: a review

This review covers the uses of fluorescence polarization and anisotropy for the investigation of bacterial penicillin binding proteins (PBPs), which are the targets of β-lactam antibacterial drugs (penicillins, cephalosporins, carbapenems, and monobactams), and of the β-lactamase enzymes that destroy these drugs and help to render bacterial pathogens resistant to them. Fluorescence polarization and anisotropy-based methods for quantitation of β-lactam drugs are also reviewed. A particular emphasis is on methods for quantitative measurement of the interactions of β-lactams and other inhibitors with PBPs and β-lactamases.

Effect of CYP2C19 polymorphism on Voriconazole Cmin in children with hematological malignancies complicated with invasive fungal infection

Objective To explore the effect of CYP2C19 polymorphism on plasma minimum concentration of Voriconazole in children with hematological malignancies complicated with invasive fungal infection. Methods Twenty children with hematological malignancies complicated with invasive fungal infection were selected from the Department of Pediatrics, the First Affiliated Hospital of Zhengzhou University were selected, and 5 mL venous blood for each was extracted.CYP2C19 genotypes of the whole blood of all patients were detected by using the method of polymerase chainreaction restriction-fragment length polymorphism(PCR-RFLP). All the patients were treated with Voriconazole at the same time and by the same way.Plasma concentration of Voriconazole was measured by the method of fluo rescence polarization immunoassay.The impact of CYP2C19 genotypes on plasma minimum concentration of voriconazole was analyzed by using the rank sum test. Results Typing results showed that the incidence of iuhomozygous extensive metabolizers (EM) genotype (CYP2C19* 1/*1) was 30%(6/20 cases); the incidence of mixed sub extensive metabolizers (IM) genotype (CYP2C19*1/*2 or CYP2C19*1/*3) was 45%(9/20 cases), among which , CYP2C19*1/*2 was in 4 cases, CYP2C19*1/*3 was in 5 cases; and that of poor metabolizer (PM) genotype (CYP2C19*2/*2 or CYP2C19*2/*3 or CYP2C19*3/*3) was 25%(5/20 cases), among which, CYP2C19*2/*2 was in 3 cases, CYP2C19*2/*3 was in 1 case, and CYP2C19*3/*3 was in 1 case.The serum trough concentration of Voriconazole in EM group, IM group and PM group was(2.30±0.50) mg/L, (3.23±0.71) mg/L, (4.84±0.29) mg/L, respectively.There was a statistically significant relationship between CYP2C19 genotype and plasma minimum concentration of Voriconazole (F=26.99, P=0.032). Conclusions CYP2C19 polymorphism has a significant effect on the minimum concentration of Voriconazole in children with hematological malignancies complicated with invasive fungal infection, which indicates that administration of Voriconazole for clinical treatment should be based on individual CYP2C19 genotype. Key words: Voriconazole; CYP2C19; Gene polymorphism; Plasma drug concentration; Invasive fungal infection

Development and Application of a High-Throughput Fluorescence Polarization Assay to Target Pim Kinases.

Pim proteins consisting of three isoforms (Pim-1, Pim-2, and Pim-3) are a family of serine/threonine kinases that regulate fundamental cellular responses such as cell growth, differentiation, and apoptosis. Overexpression of the Pim kinases has been linked to a wide variety of hematological and solid tumors. Thus, all three Pim kinases have been studied as promising targets for anticancer therapy. Here, we report on the development and optimization of an immobilized metal ion affinity partitioning (IMAP) fluorescence polarization (FP) method for Pim kinases. In this homogeneous 384-well assay method, fluorescein-labeled phosphopeptides are captured on cationic nanoparticles through interactions with immobilized trivalent metals, resulting in high polarization values. The apparent Km values for adenosine triphosphate (ATP) were determined to be 45 ± 7, 6.4 ± 2, and 29 ± 5 μM for Pim-1, Pim-2, and Pim-3, respectively. The assay yielded robustness with Z'-factors of >0.75 and low day-to-day variability (CV <5%) for all three Pim kinases. The IMAP FP assay was further validated by determining IC50 values for staurosporine and a known Pim inhibitor. We have also used an IMAP FP assay to examine whether compound 1, an ATP mimetic inhibitor designed through structure-based drug design, is indeed an ATP-competitive inhibitor of Pim kinases. Kinetic analysis based on Lineweaver-Burk plots showed that the inhibition mechanism of compound 1 is ATP competitive against all three Pim isoforms. The optimized IMAP assay for Pim kinases not only allows for high-throughput screening but also facilitates the characterization of novel Pim inhibitors for drug development.

Affinity-Based Fluorescence Polarization Assay for High-Throughput Screening of Prolyl Hydroxylase 2 Inhibitors.

Prolyl hydroxylase domain 2 (PHD2) enzyme, a Fe(II) and 2-oxoglutarate (2-OG) dependent oxygenase, mediates key physiological responses to hypoxia by modulating the levels of hypoxia inducible factor 1-α (HIF1α). PHD2 has been shown to have the therapeutic potentials for conditions including anemia and ischemic disease. Currently, many activity-based assays have been developed for identifying PHD2 inhibitors. Here we report an affinity-based fluorescence polarization method using FITC-labeled HIF1α (556-574) peptide as a probe for quantitative and site-specific screening of small molecule PHD2 inhibitors.

Modeling Interactions of Erythromycin Derivatives with Ribosomes.

Using a method of static simulation, a series of erythromycin A analogs was designed with aldehyde functions introduced instead of one of the methyl substituents in the 3'-N-position of the antibiotic that was potentially capable of forming a covalent bond with an amino group of one of the nucleotide residues of the 23S rRNA in the ribosomal exit tunnel. Similar interaction is observed for antibiotics of the tylosin series, which bind tightly to the large ribosomal subunit and demonstrate high antibacterial activity. Binding of novel erythromycin derivatives with the bacterial ribosome was investigated with the method of fluorescence polarization. It was found that the erythromycin analog containing a 1-methyl-3-oxopropyl group in the 3'-N-position demonstrates the best binding. Based on the ability to inhibit protein biosynthesis, it is on the same level as erythromycin, and it is significantly better than desmethyl-erythromycin. Molecular dynamic modeling of complexes of the derivatives with ribosomes was conducted to explain the observed effects.

Development of a Nonradioactive Steroid Receptor Ligand Binding Assay Using Fluorescence Polarization for Studying Hsp90‐Mediated Chaperone Protein Activity

While glucocorticoid receptor (GR) ligand binding has historically been measured using radiolabeled agonists, such as [3H]dexamethasone, new methods have sought to use fluorescently conjugated ligands, such as dexamethasone‐fluorescein (Dex‐Fl), as more sustainable alternatives. The molecular chaperone protein hsp90 has been shown to be essential for facilitating GR ligand binding, and structurally unrelated hsp90 inhibitors are currently in various phases of clinical investigation. The purpose of our study was to develop a fluorescence polarization (FP)‐based assay for measuring GR binding activity suitable for use in undergraduate research environments, and then apply this method to evaluating the extent to which specific agonists and antagonists of the GR and hsp90 chaperone machinery affect ligand binding. We constructed a versatile FP assay with comparable results to the previously used radiation‐based method. Interestingly, GR agonists dexamethasone and cortisol produced equivalent Dex‐Fl competition to the GR antagonist RU486, and did so in a concentration‐dependent manner. Data from hsp90 and hsp70 inhibitors showed mixed results, with hsp90 antagonists radicicol, NVP‐AUY922, and BIIB012 having limited effects, while the hsp70 antagonist novobiocin showed a potentiation of FP‐detectable steroid binding. Using the described FP method to evaluate steroid binding can be applied to broader studies examining clinically relevant GR and hsp90‐based drug therapies.

1504 A study on fluorescence polarization method for analyzing diffusional movement of abrasive grain in CMP slurry

1504 A study on fluorescence polarization method for analyzing diffusional movement of abrasive grain in CMP slurry

Methods for analysis of protein-protein and protein-ligand interactions

In order to maintain cellular homeostasis, cellular proteins coexist in complex and variable molecular assemblies. Therefore, understanding of major physiological processes at molecular level is based on analysis of protein-protein interaction networks. Firstly, composition of the molecular assembly has to be qualitatively analyzed. In the next step, quantitative bio-chemical properties of the identified protein-protein interactions are determined. Detailed information about the protein-protein interaction interface can be obtained by crystallographic methods. Accordingly, the insight into the molecular architecture of these protein-protein complexes allows us to rationally design new synthetic compounds that specifically influence various physiological or pathological processes by targeted modulation of protein interactions. This review is focused on description of the most used methods applied in both qualitative and quantitative analysis of protein-protein interactions. Co- immunoprecipitation and affinity co- precipitation are basic methods designed for qualitative analysis of protein binding partners. Further bio-chemical analysis of the interaction requires definition of kinetic and thermodynamic parameters. Surface plasmon resonance (SPR) is used for description of affinity and kinetic profile of the interaction, fluorescence polarization (FP) method for fast determination of inhibition potential of inhibitors and isothermal titration calorimetry (ITC) for definition of thermodynamic parameters of the interaction (G, H and S). Besides the importance of uncovering the molecular basis of protein interactions for basic research, the same methodological approaches open new possibilities in rational design of novel therapeutic agents.

High-Throughput Screening Assays for Estrogen Receptor by Using Coumestrol, a Natural Fluorescence Compound

Estrogen receptor (ER) is a ligand-inducible transcriptional factor involving in cell growth, differentiation, and diseases, so detection and identification of compounds having estrogenic effects are of great importance in the drug discovery industry. We have developed and validated a rapid, simple, and homogeneous method that can detect estrogenic compounds. This human ERα/β binding assay uses fluorescence polarization (FP) by applying an autofluorescent phytoestrogen, coumestrol (CS). A nonspecific adsorption assay shows that no obvious nonspecific adsorption is detected between CS and ERs. In the Scatchard plot analysis, the convex curve exhibits a positive cooperative binding, indicating that the binding of CS induces a conformational change of the ER to form a dimer and increases the affinity for the additional CS. In the Hill plot analysis, CS shows moderate binding affinity with both ERα and ERβ, and the measured Kd of CS is 32.66 µM and 36.14 µM, respectively, indicating that CS is applicable to the ER binding assay for determination of potent ligands of moderate binding affinity. Four typical ligands are selected to verify the ER binding assays, and the results are consistent with the reported data. All of above make the FP method based on CS suitable for high-throughput screening.

The rapid detection of microRNA based on p19-enhanced fluorescence polarization.

Via a molecular caliper p19 protein, we have developed an amplified fluorescence polarization method for rapid microRNA detection. This proposed assay has several intrinsic features including rapidity, simplicity, and accuracy.

Conformational Changes in the β Subunits of F1-Atpase Revealed by Fret Measurements During the Rotation of the γ Subunit

To uncover conformational changes in biomolecules accompanied with biochemical events remains challenging, even though the atomic structures and the kinetics of the biomolecules are revealed. F1-ATPase is a rotary molecular motor in which a central γ subunit rotates against hexagonally arranged subunits α3β3, hydrolyzing ATP sequentially in three β subunits. Previous study using a single-molecule fluorescence polarization method has proposed sets of the β subunit conformations during the rotation (Masaike et al., Nat. Struct. Mol. Biol. 2008). However, further information is indispensable for identifying the ATP-waiting form of which the atomic structure has not been revealed. Here we performed single-pair FRET measurement to detect distance changes between two β subunits. Time trajectories of FRET efficiency showed two-state transitions between high (0.8) and low (0.5). Given the crystal structures, low FRET efficiency indicates one β subunit in the open form but another in the closed form. On the other hand, high FRET efficiency indicates both of the β subunits in the closed form. Next, we performed a simultaneous measurement of FRET between two fluorescently labeled β subunits and the rotation of the γ subunit. High FRET efficiency was occurred in one of the three catalytic dwells. In the remaining five dwells, other two catalytic dwells and three ATP-waiting dwells, FRET efficiency was lower. These results suggest that in the ATP-waiting dwell two of three β subunits would not take the closed form as in the catalytic dwell. We are performing further experiments with a magnetic tweezers.

A reusable and sensitive biosensor for total mercury in canned fish based on fluorescence polarization

In this work, we developed a sensitive and selective sensor technique for total mercury (Hg) detection in canned fish samples based on the fluorescence polarization (FP) method. The detection principle was that ssDNA containing thymine (T) bases was modified on magnetic nanoparticles (MNPs), which were used as enhancement probe. In the presence of Hg(2+), the ssDNA on MNPs can hybridize with the fluorophore labeled aptamer owing to the specific interaction between T bases and Hg(2+). The formation of thymine-Hg(2+)-thymine (T-Hg(2+)-T) complexes leads to the molar mass increase of fluorophore molecules, resulting in the enhancement of FP signal. The increase of FP was in a good linearity with the concentration of Hg(2+) in range of 2.0 nM-1.0 mM and the limit of detection was 0.49 nM (3.29 SB/m, according to the recent recommendation of IUPAC). Moreover, the proposed biosensor can be reused for 6 cycling times and was successfully applied in monitoring Hg(2+) in real samples.

Studies on Insecticidal Activities and Action Mechanism of Novel Benzoylphenylurea Candidate NK-17

Insecticidal activity of NK-17 was evaluated both in laboratory and in field. It was found that the toxicity of NK-17 against S. exigua was 1.93 times and 2.69 times those of hexaflumuron and chlorfluazuron respectively, and the toxicity of NK-17 against P. xylostella was 1.36 times and 1.90 times those of hexaflumuron and chlorfluazuron respectively, and the toxicity of NK-17 against M. separate was 18.24 times those of hexaflumuron in laboratory, and 5% NK-17 EC at 60 g a.i ha−1 can control S. exigua and P. xylostella with the best control efficiency of about 89% and over 88% respectively in Changsha and Tianjin in field. The insecticidal mechanism of NK-17 was explored for the first time by utilizing the fluorescence polarization method. NK-17 could bind to sulfonylurea receptor (SUR) of B. germanica with stronger affinity comparing to diflubenzuron and glibenclamide, which suggested that NK-17 may also act on the site of SUR to inhibit the chitin synthesis in insect body and the result can well explain that NK-17 exhibited stronger toxicity against B. germanica than diflubenzuron and glibenclamide in vivo.

Fluorescence Polarization Immunoassay for Rapid, Accurate and Sensitive Determination of Ochratoxin A in Wheat

A sensitive and accurate fluorescence polarization (FP) immunoassay has been developed for the determination of ochratoxin A (OTA) in naturally contaminated wheat samples. A fluorescein-labeled OTA tracer was synthesized, and its binding response with three monoclonal antibodies was tested. The most sensitive competitive FP immunoassay showed an IC50 value of 0.48 ng/mL with a negligible cross-reactivity for ochratoxin B (1.7 %) and no cross-reactivity with other mycotoxins commonly occurring in wheat. The wheat sample was extracted with acetonitrile/water (60:40, v/v) and purified by a rapid solid-phase extraction procedure using an aminopropyl column prior to the FP immunoassay. The overall time of analysis was less than 20 min. The average recovery from spiked wheat samples (3 to 10 μg/kg) was 87 %, with relative standard deviations generally lower than 6 %. Limits of detection and quantification were 0.8 and 2.0 μg/kg, respectively. The trueness of the method was assessed by using two reference materials for OTA showing good accuracy and precision. A good correlation (r = 0.995) was observed between OTA contamination of 19 naturally contaminated wheat samples analyzed by both FP immunoassay and high-performance liquid chromatography/immunoaffinity clean-up used as reference method. These results show that the developed FP method is suitable for high-throughput screening, as well as for reliable quantitative determination of OTA in wheat at level far below the EU regulatory limits.

Membrane Damage Induced by Supercritical Carbon Dioxide in Rhodotorula mucilaginosa

To clarify the mechanism of microbial inactivation by supercritical carbon dioxide (SCCO2), membrane damage of Rhodotorula mucilaginosa was investigated within specific pressure (10Mpa), temperature (37°C), and treatment time (10-70min) ranges, including cell morphological structure, membrane permeability and fluidity. SEM and TEM observations showed morphological changes in the cell envelope and intracellular organization after SCCO2 treatment. Increase of membrane permeability was measured as increased uptake of the trypan blue dye with microscopy, and leakage of intracellular substances such as UV-absorbing materials and ions by determining the change of protein and electrical conductivity. The SCCO2 mediated reduction in CFUml(-1) was 0.5-1 log higher at 37°C and 10MPa for 60min in Rose Bengal Medium containing 4% sodium than a similar treatment in Rose Bengal Medium. Membrane fluidity analyzed by fluorescence polarization method using 1,6-diphenyl-1,3,5-hexatriene showed that the florescence polarization and florescence anisotropy of the SCCO2-treated cells were increased slightly and gently compared with the untreated cells. The correlation between membrane damage and death of cells under SCCO2 was clear, and the membrane damage was a key factor induced the inactivation of cells.