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At least 541 records · Page 30Linked to original sources
PubMed2003

Clear distinction of purine bases on the complementary strand by a fluorescence change of a novel fluorescent nucleoside.

A new fluorescent nucleoside, benzopyridopyrimidine (BPP), which can sharply distinguish between A and G bases opposite BPP has been devised. The base-pairing degeneracy of BPP strongly contributes to the sharp fluorescence change that is dependent on the type of purine bases opposite BPP. The hybridization of an ODN probe containing BPP with a target DNA facilitates the judgment with the naked eye of the type of purine base located at a specific site on the target DNA. The BPP-containing ODN is a very effective probe for A/G SNP typing.

DNA↗
PubMed2005

Carboxy SNARF-4F as a fluorescent pH probe for ensemble and fluorescence correlation spectroscopies.

The optical spectroscopic properties of 1,4(and 5)-benzenedicarboxylic acid, 2-[10-(dimethylamino)-4-fluoro-3-oxo-3H-benzo[c]xanthen-7-yl] (carboxy SNARF-4F), a commercial promising fluorescent pH probe, are investigated in buffered aqueous solutions in the 5.6-8.2 pH range by steady-state and time-resolved spectroscopy. A multiexponential global analysis of the picosecond time-resolved data is performed. The nonprotonated A species decays monoexponentially (0.73 ns), while the protonated species AH decays following a biexponential law with time constants of 0.40 and 1.87 ns. A kinetic scheme is proposed to explain the observations, which involves AH in equilibrium with a species denoted Y. The nature of Y is discussed in terms of a possible structural change in the molecule producing the lactone form, although the formation of a hydrogen-bonded complex to the solvent cannot be ruled out. Finally, the ability of the dye to probe pH at the single-molecule level is explored using fluorescence correlation spectroscopy.

Absorption↗
PubMedDate not supplied

[Synthesis and fluorescent properties of oligonucleotides, containing a new fluorescent marker--n-(2-benzoxazolyl)tolane].

A functional (dihydroxybutyl) derivative of p-(2-benzoxazolyl)tolane, a fluorescent label novel for biopolymers, was synthesized. The functionalized solid support obtained on its basis was employed in the synthesis of oligodeoxynucleotides 3-terminally labeled with benzoxazolyltolane (these oligonucleotides also contained 1-phenylethynylpyrene residues). This fluorophore within its dihydroxybutyl derivative and the oligonucleotides modified with it displays an intensive fluorescence characterized by a high Stokes shift. The oligonucleotides labeled with this fluorophore are potential probes sensitive to the biopolymer microenvironment.

Fluorescence↗
PubMed2005

Imaging of the intracellular topography of copper with a fluorescent sensor and by synchrotron x-ray fluorescence microscopy.

Copper is an essential micronutrient that plays a central role for a broad range of biological processes. Although there is compelling evidence that the intracellular milieu does not contain any free copper ions, the rapid kinetics of copper uptake and release suggests the presence of a labile intracellular copper pool. To elucidate the subcellular localization of this pool, we have synthesized and characterized a membrane-permeable, copper-selective fluorescent sensor (CTAP-1). Upon addition of Cu(I), the sensor exhibits a 4.6-fold emission enhancement and reaches a quantum yield of 14%. The sensor exhibits excellent selectivity toward Cu(I), and its emission response is not compromised by the presence of millimolar concentrations of Ca(II) or Mg(II) ions. Variable temperature dynamic NMR studies revealed a rapid Cu(I) self-exchange equilibrium with a low activation barrier of deltaG++ = 44 kJ.mol(-1) and k(obs) approximately 10(5) s(-1) at room temperature. Mouse fibroblast cells (3T3) incubated with the sensor produced a copper-dependent perinuclear staining pattern, which colocalizes with the subcellular locations of mitochondria and the Golgi apparatus. To evaluate and confirm the sensor's copper-selectivity, we determined the subcellular topography of copper by synchrotron-based x-ray fluorescence microscopy. Furthermore, microprobe x-ray absorption measurements at various subcellular locations showed a near-edge feature that is characteristic for low-coordinate monovalent copper but does not resemble the published spectra for metallothionein or glutathione. The presented data provide a coherent picture with strong evidence for a kinetically labile copper pool, which is predominantly localized in the mitochondria and the Golgi apparatus.

Animals↗
PubMed1991

Fluorescent-labeled oligonucleotide probes: detection of hybrid formation in solution by fluorescence polarization spectroscopy.

Fluorescein-labeled oligonucleotides as DNA-probes were synthesized and used to monitor hybrid formation, namely to detect DNA or oligonucleotide sequence in solution. The introduction of fluorescein to oligonucleotides was carried out by oxidation of a hydrogen phosphonate linkage with ethylenediamine or hexamethylenediamine as a tether and by a subsequent labeling of the primary amine moiety by FITC. Fluorescence anisotropy, r, was adopted as an index to monitor the behavior of F-probe in solution. An increase in the anisotropy was observed upon an increase in the chain-length of F-probe. When F-Probe formed a hybrid with its complementary oligonucleotide in solution, the r value increased compared to that of F-Probe itself. These observations clearly indicate that measurements of r in solution will readily lead to the monitoring of the presence of a hybrid in solution. Consequently, it is promising to detect a certain nucleic acid sequence in solution using fluorescent-labeled oligonucleotides.

Chromatography, High Pressure Liquid↗
PubMed1994

Internal fluorescence labeling with fluorescent deoxynucleotides in two-label peak-height encoded DNA sequencing by capillary electrophoresis.

Fluorescently labeled deoxynucleotides were used for internal labeling of DNA sequencing fragments generated in a two-color peak-height encoded protocol. Sequenase and a manganese-containing buffer were used to generate uniform peak heights. Tetramethyl rhodamine - dATP was used in a labeling step, followed by termination with ddATP and ddCTP in a 3:1 ratio. Fluorescein - dATP was used in a second reaction, followed by termination with ddGTP and ddTTP in a 3:1 ratio. The fragments were pooled and separated by capillary gel electrophoresis. The results were compared with peak-height encoded sequencing based on fluorescently labeled primers. The dye-labeled primers produced higher resolution separations for shorter fragments. However, dye-labeled primer fragments suffered from an earlier onset of biased reptation and produced shorter sequencing reads. Fragments from 50 to at least 500 bases in length could be sequenced with the internal labels.

Capillary Action↗
PubMed1998

DNA binding and oligomerization of NtrC studied by fluorescence anisotropy and fluorescence correlation spectroscopy.

Fluorescence anisotropy and fluorescence correlation spectroscopy measurements of rhodamine-labeled DNA oligonucleotide duplexes have been used to determine equilibrium binding constants for DNA binding of the prokaryotic transcription activator protein NtrC. Measurements were made with wild-type NtrC from Escherichia coli and the constitutively active mutant NtrCS160Ffrom Salmonella using DNA duplexes with one or two binding sites. The following results were obtained: (i) the dissociation constant K d for binding of one NtrC dimer to a single binding site was the same for the wild-type and mutant proteins within the error of measurement. (ii) The value of K d decreased from 1.4 +/- 0.7 x 10(-11) M at 15 mM K acetate to 5.8 +/- 2.6 x 10(-9) M at 600 mM K acetate. From the salt dependence of the dissociation constant we calculated that two ion pairs form upon binding of one dimeric protein to the DNA. (iii) Binding of two NtrC dimers to the DNA duplex with two binding sites occured with essentially no cooperativity. Titration curves of NtrCS160Fbinding to the same duplex demonstrated that more than two protein dimers of the mutant protein could bind to the DNA.

Amino Acid Sequence↗
PubMed2003

Clear distinction of pyrimidine bases on the complementary strand by fluorescence change of novel fluorescent nucleosides.

New fluorescent nucleosides, methoxybenzodeazaadenine ((MD)A) and methoxybenzodeazainosine ((MD)I) which can sharply distinguish between C and T bases, respectably. The hybridization of an ODN probe containing (MD)A and (MD)I with a target DNA facilitates the judgment with the fluorescence spectra of the type of pyrimidine bases located at a specific site on the target DNA. The (MD)A- and (MD)I containing ODN are very effective probes for pyrimidine SNP typing.

Adenine↗
PubMed2006

Synthesis of fluorescent cyclic cytosine nucleosides and their fluorescent properties upon incorporation into oligonucleotides.

We report here the synthesis and spectroscopic characterization of a new fluorescent pyrimidopyrimidoindole nucleoside derivative (dC(PPI)) modified at the cytosine base. The photophysical properties of dC(PPI) were examined by fluorescent spectroscopy and quantum chemical calculations. It was found that dC(PPI)-labeled oligonucleotides gave almost the same thermal stability as that of the corresponding unmodified sequences. In addition, the quantum yield of dC(PPI) in the double-stranded state was significantly higher than that in the single-stranded state.

DNA Probes↗
PubMed2000

Evidence for downregulation of the endothelin-B-receptor by the use of fluorescent endothelin-1 and a fusion protein consisting of the endothelin-B-receptor and the green fluorescent protein.

We generated fusion proteins consisting of the endothelin-B (ET(B))-receptor and the enhanced green fluorescent protein (EGFP) to visualize receptor internalization. In Madin Darby canine kidney (MDCK) clones expressing ET(B)/EGFP fusion proteins, single class high affinity binding sites for [125I]endothelin-1 (ET-1) were found (for two different clones apparent K(D) values were 31 +/- 15 pM and 30 +/- 7 pM). Pretreatment of membranes with GTPgammaS prior to saturation analysis did not alter these values. We also labelled ET-1 with cyanine-dyes (Cy3/ET-1, Cy5/ET-1). In displacement analyses with membranes of MDCK ET(B)/EGFP clones using [125I]ET-1, we found reduced affinity for Cy3/ET-1 and Cy5/ET-1 (about 5- to 10-fold, respectively), but normal efficacy when compared to unlabelled ET-1. Both fluorescent ligands and the ET(B)/EGFP fusion protein were suitable for analysis of receptor trafficking in living cells and cells fixed at different timepoints. Laser scanning microscopy of MDCK ET(B)/EGFP clones incubated with Cy3/ET-1 or Cy5/ET-1 revealed rapid internalization of ligand/receptor complexes, which clustered in large, perinuclear structures (most probably late endosomes). Our data argue against recycling of the ET(B) receptor and favour its targeting to the lysosomal pathway.

Animals↗
PubMed2002

Noninvasive measurement of bacterial intracellular pH on a single-cell level with green fluorescent protein and fluorescence ratio imaging microscopy.

We show that a pH-sensitive derivative of the green fluorescent protein, designated ratiometric GFP, can be used to measure intracellular pH (pHi) in both gram-positive and gram-negative bacterial cells. In cells expressing ratiometric GFP, the excitation ratio (fluorescence intensity at 410 and 430 nm) is correlated to the pHi, allowing fast and noninvasive determination of pHi that is ideally suited for direct analysis of individual bacterial cells present in complex environments.

Escherichia coli↗
PubMedDate not supplied

Detection of early interproximal caries in vitro using laser fluorescence, dye-enhanced laser fluorescence and direct visual examination.

This in vitro study evaluated the use of laser fluorescence (LF) for the detection of early interproximal carious lesions and whether the detection could be enhanced using a fluorescent dye (DELF). Direct visual examination (DV) was used for comparison. Eighty extracted teeth were used, arranged in 20 blocks, each block having 2 premolars and 2 molars, lined up in a simulated sextant situation. After cleaning with a microabrasion kit, a subcontact window on half of the surfaces (60) was exposed to Carbopol white-spot solution for 5 days. The teeth were remounted in stone and examined by three independent examiners. For LF and DELF an argon laser was used (mixed wavelength of 488 and 514 nm) viewed through glasses (excluding wavelength <520 nm). For DELF a sodium fluorescein dye (0. 075%) was applied before examination. A clinical examination light was used for DV. The approximal surfaces were scored for lesion presence or absence. To verify lesion presence, the subcontact area was cut perpendicularly to the surface, stained with rhodamine B, and images were taken using a confocal microscope. The images were analyzed using a histogram program for lesion depth and image area. Lesions were present in 62 out of 120 approximal surfaces, with an average depth of 60 microm (range 17-190 microm). Sensitivity ranges for LF, DELF and DV were 56-74, 61-79 and 58-74%, and specificity ranges 67-78, 86-98 and 83-97%, respectively. With this model DELF compared favorably with DV and LF in sensitivity, but specificity was better for DELF and DV than for LF.

Bicuspid↗
PubMed1996

Improved localization of fluorescent tyramides for fluorescence in situ hybridization using dextran sulfate and polyvinyl alcohol.

Recently, a peroxidase-mediated amplification system has been described for immunofluorescence and fluorescence in situ hybridization studies. It is based on the deposition of hapten- or fluorochrome-labeled tyramide molecules. Although providing a significantly increased detection sensitivity compared to conventional procedures, its localization properties are inferior because of free diffusion of intermediate reaction products before they are immobilized. In enzyme cytochemistry, it is well established that improved localization of enzyme activity can be achieved through the addition of viscosity-increasing polymers to the incubation media. In this study we analyzed the effect of different polymers on the localization sharpness and sensitivity of the tyramide-peroxidase reaction in FISH applications. Significantly improved localization of the fluorescent endproduct was observed using dextran sulfate or polyvinylalcohol (PVA) with, respectively, no or little loss of sensitivity.

Dextran Sulfate↗
PubMed1976

Extrinsic signals for monitoring the association reaction of proteins as introduced by fluorescent and non-fluorescent labels.

Two known dansyl labels (I, II) and 5-[2-(iodoacetamido)ethylamino]-1-naphthalene-sulfonic acid (III) and three new azo-dyes (IV - VI) were covalently attached to alpha-chymotrypsin and to basic pancreatic trypsin inhibitor by four different reactive groups. In order to protect the contact region of the proteins the complex of the two proteins was labeled. Advantage was taken of the fact that a group which is buried in the complex reacts about (see article) times slower than a group which is always exposed (K = dissociation equilibrium constant, [C] = concentration of the complex). The complex was dissociated at pH 3 and the labeled proteins were isolated by column chromatography. They were fully active. The dansyl label was immobilized when introduced by dansyl chloride but highly mobile when attached via the longer imidoester group (II). Changes of absorption and of fluorescence which occur when differently labeled reaction partners recombine were studied. Changes in absorption (up to 18%) were mainly due to interactions of the label of one protein with the other protein. Fluorescence changes of up to 480% could be obtained. They were interpreted in terms of a Förster type energy transfer between donor and acceptor labels and changes of absorption and quantum yield due to interactions of the labels with the proteins. The kinetic constants of complex formation are not seriously altered by the labels (Bösterling, B & Engel, J. (1976) this J. 357, 1297-1307, succeeding). It is concluded that the labeling technique may be of general value for kinetic and equilibrium studies of protein associations.

Affinity Labels↗
PubMedDate not supplied

The fluorescent antibody and indirect fluorescent antibody assays for diagnosing stunting syndrome of turkeys.

The fluorescent antibody (FA) assay was developed for detecting the stunting syndrome agent (SSA) from intestinal tissue. Similarly, the indirect fluorescent antibody (IFA) assay was developed for detecting serum antibodies to SSA. Convalescent antiserum from turkeys orally immunized with SSA was found to be the primary antibody of choice for the FA assay. Intestinal jejunal samples from poults inoculated 3-4 days postinoculation (DPI) was found to be the best antigen source for the IFA assay. SSA was detected from the intestinal tracts of experimentally inoculated birds at 2 DPI with highest level of reactivity at 3 DPI by the FA assay. After 4 DPI the level of SSA infectivity of the intestines waned to low levels. Serum antibody was detected from experimentally inoculated birds as early as 7 DPI with all birds tested seroconverting by 12 DPI. These assays should prove useful for future studies concerning stunting syndrome.

Animals↗
PubMed2003

Monitoring of microbial diversity by fluorescence in situ hybridization and fluorescence spectrometry.

The goal of the research was the development of a simple method to quantify microbial groups in environmental samples. Fluorescence intensity was measured in the sample before and after whole cell fluorescence in situ hybridization with rRNA-targeted, fluorochrome-labeled oligonucleotide probes. To determine specific and non-specific binding of different oligonucleotide probes the following approaches have been used: (1) incubation of the sample with probes at two different temperatures; (2) hybridization of labeled probe in the presence of unlabeled probe; (3) incubation of the sample with labeled specific probe or labeled nonsense probe. Specific binding (hybridization) of the probe was calculated as the difference between total binding and non-specific binding of the probe. Specific binding was 40-50% of total binding in the environmental samples tested. The ratio of the specific binding of different probes may be used to quantify the ratio of different microbial groups in the environmental samples. This quantification is suitable for the microbiological monitoring of microbial aggregates because it is a simple technique and the results can be measured by a portable fluorometer.

Bacteria↗
PubMed2004

Simultaneous liquid chromatography-fluorescence analysis of type A and type B trichothecenes as fluorescent derivatives via reaction with coumarin-3-carbonyl chloride.

A method for the simultaneous LC-fluorescence detection (FLD) determination of eight trichothecenes A and B by pre-column derivatization with coumarin-3-carbonyl chloride, a highly fluorescent fluorophore, has been developed. The reaction conditions (temperature, reaction time, reactant ratios) were optimized to give a reproducible quantitative conversion. All derivatives were characterized by LC-MS. The chromatographic parameters were optimized (column, eluent) to give a very good separation of three type A (diacetoxyscirpenol, T-2 toxin, HT-2 toxin) and five type B trichothecenes [deoxynivalenol (DON), nivalenol, fusarenon-X, 3-acetyldeoxynivalenol, 15-acetyldeoxynivalenol]. The best conditions were obtained on a narrow-bore C18 column with a water-methanol gradient. The detection limits (S/N = 3:1) in grain samples, with an injected volume of 5 microl, were 0.2-1 ng/g for all trichothecenes. These values are more than one order of magnitude lower than those of other LC-FLD and LC-MS methods and are similar to those obtained by GC-MS. The calibration curves were linear between 100 and 2500 ng/g. The method was successfully applied to the analysis of a certified wheat reference material, after solvent extraction and clean-up on a Mycosep column, obtaining a good recovery (89% for DON) and a high accuracy (z-score value: 0.67).

Calibration↗