7-methylpterin in methanogenic bacteria

Abstract A blue fluorescent compound was extracted and purified from cells of Methanobacterium thermoautotrophicum . The compound was identified as 7-methylpterin on the basis of its (physico-) chemical properties and by comparison with 7-methylpterin prepared by organic synthesis. The compound is present in all methanogenic bacteria studied so far and it provides methanogenic bacteria the characteristic blue fluorescence observed upon fluorescence microscopy.     

The Synthesis of a Coumarin Carbohydrazide Dinuclear Copper Complex Based Fluorescence Probe and Its Detection of Thiols

Small-molecule thiols, such as cysteine (CYS) and glutathione (GSH), are essential for maintaining the cellular redox environment and play important roles in regulating various cellular physiological functions. A fluorescence probe (compound 1-Cu²⁺) for thiols based on coumarin carbohydrazide dinuclear copper complex was developed. Compound 1 was synthesized from the reaction of 7-(diethylamino)-2-oxo-2H-chromene-3-carbohydrazide with 4-tert-butyl-2,6- diformylphenol. Accordingly, the copper complex (compound 1-Cu²⁺) was prepared by mixing compound 1 with 2 equivalents copper ions. Compound 1 had strong fluorescence while compound 1-Cu²⁺ hardly possessed fluorescence owing to the quenching nature of paramagnetism Cu²⁺ to the fluorescence molecule excited state. However, the fluorescence intensity of compound 1-Cu²⁺ was increased dramatically after the addition of thiol-containing amino acids, but not the other non-sulfhydryl amino acids. UV-vis absorption and fluorescence spectra indicated that compound 1-Cu²⁺ had good selectivity and sensitivity for thiols such as glutathione in CH₃CN:H₂O (3:2, v/v) PBS solution. The fluorescence imaging experiments implied that compound 1-Cu²⁺ has potential application in thiol-containing amino acids detection in living cells.     

Formation of the intermediate nitronyl nitroxide-anthracene dyad sensing saccharides

We design a new saccharides sensor based on the ensemble of compound 2 with a boronic group and compound 3 with two phenolic -OH groups, taking advantage of the fluorescence quenching ability of nitronyl nitroxides and reversible boronate formation between boronic acid and diol. The results show that the fluorescence of compound 2 was largely quenched upon addition of compound 3 due to the formation of the intermediate nitronyl nitroxide-anthracene dyad 1. Sequential addition of saccharides such as fructose to the ensemble of compounds 2 and 3 together with dyad 1 induced the fluorescence enhancement. These results clearly demonstrate the possibility to employ the ensemble of compounds 2 and 3 (with dyad 1) to sense saccharides.     

Detection of silver(I) ions based on the controlled self-assembly of a perylene fluorescence probe

In the current work, we report a label-free fluorescence turn-on approach for the sensitive and selective sensing of Ag(+). A cationic perylene derivative, compound A, was used as the fluorescence probe. Compound A monomer is strongly fluorescent, and the fluorescence can be efficiently quenched through self-aggregation (self-assembly). A cytosine (C)-rich oligonucleotide, oligo-C, was employed. In the absence of Ag(+), oligo-C induced strong compound A aggregation due to electrostatic interactions in aqueous media, and very weak fluorescence signal was detected. However, in the presence of Ag(+), the specific interactions between oligo-C and Ag(+) induced hairpin structure formation of oligo-C through C-Ag(+)-C bonding interactions. Oligo-C binding to compound A aggregates was weakened; therefore, compound A monomer could be released and detected. The intensity of the fluorescence signal was directly related to the amount of Ag(+) added to the assay solution. Our method is highly sensitive-a limit of detection of 5nM was obtained-and also very selective. Ag(+) detection in complex sample mixtures was also demonstrated.     

Evaluation of fluorescent compound interference in 4 fluorescence polarization assays: 2 kinases, 1 protease,and 1 phosphatase

With the increasing use of fluorescence-based assays in high-throughput screening (HTS), the possibility of interference by fluorescent compounds needs to be considered. To investigate compound interference, a well-defined sample set of biologically active compounds, LOPAC, was evaluated using 4 fluorescein-based fluorescence polarization (FP) assays. Two kinase assays, a protease assay, and a phosphatase assay were studied. Fluorescent compound interference and light scattering were observed in both mixture- and single-compound testing under certain circumstances. In the kinase assays, which used low levels (1-3 nM) of fluorophore, an increase in total fluorescence, an abnormal decrease in mP readings, and negative inhibition values were attributed to compound fluorescence. Light scattering was observed by an increase in total fluorescence and minimal reduction in mP, leading to false positives. The protease and phosphatase assays, which used a higher concentration of fluorophore (20-1200 nM) than the kinase assays, showed minimal interference from fluorescent compounds, demonstrating that an increase in the concentration of the fluorophore minimized potential fluorescent compound interference. The data also suggests that mixtures containing fluorescent compounds can result in either false negatives that can mask a potential "hit" or false positives, depending on the assay format. Cy dyes (e.g., Cy3B and Cy5 ) excite and emit further into the red region than fluorescein and, when used in place of fluorescein in kinase 1, eliminate fluorescence interference and light scattering by LOPAC compounds. This work demonstrates that fluorescent compound and light scattering interferences can be overcome by increasing the fluorophore concentration in an assay or by using longer wavelength dyes.     

Effects of intrinsic fluorescence and quenching on fluorescence-based screening of natural products

To evaluate the effects of intrinsic (natural) fluorescence and quenching as confounding variables in fluorescence-based enzyme inhibition assays of natural products, we measured the fluorescence and quenching properties of 25 components of popular herbal products. The analyses were performed under conditions typically employed in drug-drug interaction studies that use c-DNA-derived P450 isoforms and surrogate fluorogenic substrates. Four of the 25 compounds tested (isorhamnetin, quercetin, vitexin, and yangonin) fluoresced or quenched sufficiently to interfere with these assays. Intrinsic fluorescence had a greater effect on these assays than quenching and for one compound, yangonin, was sufficient to mask inhibition and potentially produce a false negative result. Quenching had less of an effect on these assays, but was significant enough for one compound, quercetin, to mimic "weak" inhibition. Therefore, because intrinsic fluorescence or quenching could render some natural products unsuitable for testing in certain fluorometric assays, it would be prudent to include an evaluation of these properties in experimental protocols.     

Design and synthesis of ICT-based fluorescent probe for high-sensitivity protein detection and application to rapid protein staining for SDS-PAGE

A novel fluorescent molecular probe possessing styryl, sulfonyl, and cyanopyranyl moieties that was termed compound 1 was designed and synthesized to detect proteins through noncovalent bonding. Compound 1 did not produce fluorescence emission in the absence of proteins. However, its fluorescence spectrum showed a dramatic increase in the fluorescence intensity and strong orange emission after the addition of BSA. These changes were caused by intramolecular charge transfer (ICT). The fluorescence intensities of compound 1 were plotted as a function of the protein concentrations. A good linear relationship was observed up to a protein concentration of 325 mug/mL, and the detection limit was 70 ng/mL under the given assay conditions; this detection limit was higher than that of previously reported compounds. To demonstrate the application of compound 1, proteins in an SDS-PAGE gel were stained with compound 1 and were successfully imaged with a higher sensitivity and shorter staining operation time as compared to those of the silver staining method and SYPRO Ruby staining method. Thus, easy and high-sensitivity protein detection can be performed with the fluorescent probe, and this probe is ideally suited to proteomic applications.     

Use of fluorescence lifetime technology to provide efficient protection from false hits in screening applications

This article describes novel data analysis of fluorescence lifetime-based protein kinase assays to identify and correct for compound interference in several practical cases. This ability, together with inherent advantages of fluorescence lifetime technology (FLT) as a homogeneous, antibody-free format independent of sample concentration, volume, excitation intensity, and geometry, makes fluorescence lifetime a practical alternative to the established “gold standards” of radiometric and mobility shift (Caliper) assays. The analysis is based on a photochemical model that sets constraints on the values of fluorescence lifetimes in the time responses of the assay. The addition of an exponential component with free floating lifetime to the constrained model, in which the lifetimes are constants predetermined from control measurements and the preexponential coefficients are “floating” parameters, allows the relative concentration of phosphorylated and nonphosphorylated substrates to be calculated even in the presence of compound fluorescence. The method is exemplified using both simulated data and experimental results measured from mixtures of dye-labeled phosphorylated and nonphosphorylated kinase substrates. A change of the fluorescence lifetime is achieved by the phosphorylated substrate-specific interaction with a bifunctional ligand, where one binding site interacts with the phosphate group and the other interacts with the dye.     

Antibiotic Y: biosynthesis by Fusarium avenaceum (Corda ex Fries) Sacc., isolation, and some physicochemical and biological properties.

A compound very similar to the mycotoxin citrinin was observed on thin-layer chromatographic plates during the screening analysis of grain extracts. This compound was produced by 22 of the tested Fusarium avenaceum (Corda ex Fries) Sacc. strains isolated from wheat, triticale, barley, corn, and potatoes. A chemical test confirmed the presence of an unknown compound, which was given the preliminary name of antibiotic Y (indicating yellow fluorescence). The following properties of the new metabolite are described: spectroscopic (UV, infrared, proton nuclear magnetic resonance, fluorescence, and mass spectrometry), phytotoxic, antibiotic (inhibitory effect of bacterial growth), and toxic (toxicity to Artemia salina, chicken embryos, and mouse fibroblasts). Elemental analysis of the compound showed that it had the general formula C15H10O8, in agreement with the mass spectrometric finding that the molecular ion had a molecular weight of 318. The structure of the compound is presently under study.     

Antibiotic Y: biosynthesis by Fusarium avenaceum (Corda ex Fries) Sacc., isolation, and some physicochemical and biological properties

A compound very similar to the mycotoxin citrinin was observed on thin-layer chromatographic plates during the screening analysis of grain extracts. This compound was produced by 22 of the tested Fusarium avenaceum (Corda ex Fries) Sacc. strains isolated from wheat, triticale, barley, corn, and potatoes. A chemical test confirmed the presence of an unknown compound, which was given the preliminary name of antibiotic Y (indicating yellow fluorescence). The following properties of the new metabolite are described: spectroscopic (UV, infrared, proton nuclear magnetic resonance, fluorescence, and mass spectrometry), phytotoxic, antibiotic (inhibitory effect of bacterial growth), and toxic (toxicity to Artemia salina, chicken embryos, and mouse fibroblasts). Elemental analysis of the compound showed that it had the general formula C15H10O8, in agreement with the mass spectrometric finding that the molecular ion had a molecular weight of 318. The structure of the compound is presently under study.     

A reduction-triggered fluorescence probe for sensing nucleic acids

We have developed a reduction-triggered fluorescence probe with a new fluorogenic compound derivatized from Rhodamine for sensing oligonucleotides. The chemistry to activate the compound involves the reaction between the azide group of rhodamine derivatives and the reducing reagents, with the fluorescence signal appearing after reduction of the azide group. The signal/background ratio of this fluorogenic compound reached 2100-fold enhancement in fluorescence intensity. Dithio-1,4-threitol or triphenylphosphine as reducing reagents were successfully utilized for this chemistry to be introduced into the DNA probe. The genetic detection requires that two strands of DNA bind onto target oligonucleotides, one probe carrying a reducible fluorogenic compound while the other carries the reducing reagents. The reaction proceeds automatically without any enzymes or reagents under biological conditions to produce a fluorescence signal within 10-20 min in the presence of target DNA or RNA. In addition, the probe was very stable under biological conditions, even such extreme conditions as pH 5 solution, pH 10 solution, or high temperature (90 degrees C) with no undesirable background signal. The probes were successfully applied to the detection of oligonucleotides at the single nucleotide level in solution and endogenous RNA in bacterial cells.     

Direct interactions in the recognition between the environmental estrogen bisphenol AF and human serum albumin

Bisphenol AF (BPAF) was used as a model compound to investigate the binding mechanism between the endocrine disrupting compound and human serum albumin (HSA) using multispectroscopic techniques and molecular modeling method at the protein level. The results indicated that BPAF was indeed bound to HSA and located in the hydrophobic pocket of HSA on subdomain IIA through hydrogen bond and van der Waals interactions. The fluorescence quenching data showed that the binding of BPAF and HSA quenched the intrinsic fluorescence of HSA, and the static quenching constants were acquired. Copyright © 2015 John Wiley & Sons, Ltd.     

Mg-2,4-divinyl pheoporphyrin a5: the product of a reaction catalyzed in vitro by developing chloroplasts

The major product of an aerobic reaction mixture containing developing chloroplasts, Mg-protoporphyrin IX, S-adenosylmethionine, and other cofactors was isolated and purified. Structural studies using nuclear magnetic resonance confirmed earlier reports, based on fluorescence and absorption spectra, that this compound is Mg-2,4-divinyl pheoporphyrin a5. The molecular weight determined by secondary-ion mass spectroscopy further confirmed the assigned structure. Absorption and fluorescence spectra indicate that this compound is identical to that reported previously by various workers in less-purified biological extracts. The nuclear magnetic resonance spectrum of the Mg-free base also supports the assigned structure.     

A competitive co-cultivation assay for cancer drug specificity evaluation

The identification of compounds that specifically inhibit or kill cancer cells without affecting cells from healthy tissues is very challenging but very important for reducing the side effects of current cancer therapies. Hence, there is an urgent need for improved assays allowing the selectivity of a given compound to be monitored directly. The authors present an assay system based on the competitive co-cultivation of an excess of cancer cells with a small fraction of noncancer human indicator cells generating a fluorescence signal. In the absence of a specific anticancer compound, the cancer cells outgrow the indicator cells and abolish the fluorescence signal. In contrast, the presence of specific anticancer drugs (such as Tyrphostin-AG1478 or PLX4720) results in the selective growth of the indicator cells, giving rise to a strong fluorescence signal. Furthermore, the authors show that the nonspecific cytotoxic compound sodium azide kills both cancer and noncancer cells, and no fluorescence signal is obtained. Hence, this assay system favors the selection of compounds that specifically target cancer cells and decreases the probability of selecting nonspecific cytotoxic molecules. Z factors of up to 0.85 were obtained, indicating an excellent assay that can be used for high-throughput screening.     

Single-molecule detection technologies in miniaturized high-throughput screening: fluorescence intensity distribution analysis

Single-molecule detection technologies are becoming a powerful readout format to support ultra-high-throughput screening. These methods are based on the analysis of fluorescence intensity fluctuations detected from a small confocal volume element. The fluctuating signal contains information about the mass and brightness of the different species in a mixture. The authors demonstrate a number of applications of fluorescence intensity distribution analysis (FIDA), which discriminates molecules by their specific brightness. Examples for assays based on brightness changes induced by quenching/dequenching of fluorescence, fluorescence energy transfer, and multiple-binding stoichiometry are given for important drug targets such as kinases and proteases. FIDA also provides a powerful method to extract correct biological data in the presence of compound fluorescence.     

Ryodipine--a new fluorescent probe in the determination of differences between lymphocytes

Ryodipine (foridon ), a fluorescent compound possessing hypotensive activity, can be useful as fluorescence probe to distinguish between lymphocyte populations. The heterogeneity of cells revealed by the intensity of ryodipine fluorescence is mainly due to differences in the amount of membranous material in the cells. The use of ryodipine for lymphocyte identification has certain advantages over MBA, a known fluorescence probe generally employed for this purpose. Ryodipine is less prone to photodegradation and its fluorescence intensity shows no dependence on cell concentration over a much wider dye/cell ratio range.     

Intramolecular exciplexes based on benzoxazole: photophysics and applications as fluorescent cation sensors.

Exciplex behaviour of three benzoxazole derivatives has been detected and intensively investigated by means of steady-state and time-resolved fluorescence techniques and transient absorption spectroscopy. The fluorescence of these compounds shows the properties which are typical for the excited state charge transfer complexes (exciplexes). Besides of the short wavelength fluorescence, which is similar in spectral distribution to the fluorescence of the electron acceptor (2-p-tolyl-benzoxazole), the red shifted, broad and structureless emission band is observed in solvents of low and medium polarity. The detailed analysis of the fluorescence data shows that the ratio of the CT and LE fluorescence initially increases with increasing solvent polarity, achieves a maximum, and drops for more polar solvents (epsilon(s) = 7). Similar behaviour is observed for the exciplex fluorescence lifetimes. The overall fluorescence and the relative intersystem crossing quantum yields show the decrease of these values with increasing solvent polarity. These observations have been explained on the basis of Marcus-type theory for nonradiative charge transfer rate constants. Increasing solvent polarity strongly accelerates the back electron transfer process which recovers the whole molecule in the ground state. The probability of the compact exciplex formation (i.e. sandwich-type structures) depends on solvent viscosity and degree of freedom of the bending of the saturated linker. The compound containing crown ether as a donor subunit may be used as a fluorescent indicator of inorganic cations (barium and lithium). We found an effective complexation of the compound in the ground state with barium and lithium cations. The complex is also stable in the excited state which manifests itself in strong increase of the fluorescence intensity.     

Novel bisbenzimide-nitroxides for nuclear redox imaging in living cells

Nuclear oxidative stress damages genomic DNA and may lead to cell death, leading to aging and aging-related disorders. Though it is important to measure the nuclear oxidative stress separately, there are still little examples that applicable to living cells. We have designed and synthesized three bisbenzimide-nitroxides as probes to selectively visualize nuclear redox changes in terms of fluorescence. Compound 3, containing two radical moieties, showed the largest reduction-induced fluorescence change, with good localization in nuclei. RAW264.7 murine macrophage cells were loaded with compound 3 and then treated with 100μM hydrogen peroxide for 5min to show the fluorescence increase. This fluorescence increase was inhibited by pretreatment of 1mM ascorbic acid. These results show that compound 3 was suitable for nuclear-specific redox imaging in murine macrophages.     

Fluorescence decrease of conjugated polymers by the catalytic activity of horseradish peroxidase and its application in phenolic compounds detection

We report the fluorescence decrease of the water-soluble π-π-conjugated polymer poly(2-methoxy-5-propyloxy sulfonate phenylene vinylene, MPS-PPV) by the catalytic activity of horseradish peroxidase in the presence of H(2)O(2). MPS-PPV acts as a donor substrate in the catalytic cycle of horseradish peroxidase where the electron-deficient enzymatic intermediates compounds I and II can subtract electrons from the polymer leading to its fluorescence decrease. The addition of phenolic drug acetaminophen to the former solution favors the decrease of the polymer fluorescence, which indicates the peroxidase-catalyzed co-oxidation of MPS-PPV and acetaminophen. The encapsulation of horseradish peroxidase within polyacrylamide microgels allows the isolation of intermediates compound I and compound II from the polymer, leading to a fluorescence decrease that is only due to the product of biocatalytic acetaminophen oxidation. This system could be used to develop a new device for phenolic compounds detection.     

Interaction of DNA with a novel photoactive platinum diimine complex

Interaction of DNA with a novel photoactive platinum diimine compound has been studied by electronic absorption spectra, fluorescence spectra and viscosity measurements. The red light-induced DNA cleavage activity of the platinum compound has also been studied by agarose gel electrophoresis. The results suggest that the platinum compound may interact with DNA by intercalation mode. When irradiated with red light, the platinum compound can generate singlet oxygen, resulting in cleavage of DNA.