Time gating improves sensitivity in energy transfer assays with terbium chelate/dark quencher oligonucleotide probes

Lanthanides are attractive as biolabels because their long luminescence decay rates allow time-gated detection, which separates background scattering and fluorescence from the lanthanide emission. A stable and highly luminescent terbium complex based on a tetraisophthalamide (TIAM) chelate is paired with a polyaromatic-azo dark quencher (referred to as a Black Hole Quencher or BHQ) to prepare a series of 5'TIAM(Tb)/3'BHQ dual-labeled oligonucleotide probes with no secondary structure. Luminescence quenching efficiency within terbium/BHQ probes is very dependent on the terbium-BHQ distance. In an intact probe, the average terbium-BHQ distance is short, and Tb --> BHQ energy transfer is efficient, decreasing both the terbium emission intensity and lifetime. Upon hybridization or nuclease digestion, which spatially separate the Tb and BHQ moieties, the Tb luminescence intensity and lifetime increase. As a result, time-gated detection increases the emission intensity ratio of the unquenched probe/quenched probe due to the shorter lifetime of the quenched species. A 40-mer probe that has a 3-fold increase in steady-state luminescence upon digestion has a 50-fold increase when gated detection is used. This study demonstrates that time gating with lanthanide/dark quencher probes in energy transfer assays is an effective means of improving sensitivity.     

Fluorescence resonance energy transfer by quencher adsorption into hydrogels containing fluorophores

We synthesized anionic hydrogels containing fluorophores and investigated the adsorption of a cationic quencher having an amino group into hydrogels by fluorescence resonance energy transfer (FRET). FRET from the fluorophore to the quencher in hydrogels was examined by fluorescence intensity and fluorescence decay using a fluorescence spectrophotometer and femtosecond laser spectroscopy. The fluorescence intensity of the fluorophore‐containing hydrogels decreased rapidly with increasing amounts of adsorbed cationic quencher. The fluorescence emission of the fluorophore in the quencher‐adsorbed hydrogels containing fluorophores decayed more rapidly than that of the original hydrogels. The aforementioned result indicates that the fluorescence of the fluorophore‐containing hydrogels is quenched due to FRET from the fluorophore to the quencher as the cationic quenchers can approach the fluorophores in hydrogels by electrostatic interactions. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 3245–3252, 2006     

Analysis of Phosphorescence Decay in Heterogeneous Systems: Consequences of Finite Excitation Flash Duration

Analysis of phosphorescence lifetimes using the Stern-Volmer equation is a reliable means of determining quencher concentration for a uniform sample. Methods of analysis for heterogeneous systems are based on the assumption that the excitation is produced by a momentary flash. This condition is an idealization because a real flash has a finite duration and a complex time profile. In the case of a heterogeneous quencher concentration, an excitation flash produces different initial intensities and different times of peak intensity from compartments having different concentrations of quencher. We formulated a model to explore the effects of flash duration on the shape of the emission curve obtained from systems in which the heterogeneity is continuous. We developed mathematical models that can be used to recover fitting parameters of continuous distributions of reciprocal lifetimes approximated as rectangular or Gaussian distributions, or an arbitrary histogram. We also formulated a procedure to convert the distribution of reciprocal lifetimes into a volume distribution of quencher concentration. We found that (1) the Stern-Volmer ratio of phosphorescence intensities cannot be employed for interpretation of pulse phosphorometric data in terms of a volume distribution of quencher; (2) shortening the flash duration decreases the difference of initial intensities between compartments having high and low quencher concentration; (3) the parameters of the volume distribution of quencher concentration can be recovered correctly only after taking account of the difference in initial intensities; and (4) calibration of the initial intensities for a given fitting delay and flash function is necessary.     

Ultrasensitive optical DNA biosensor based on surface immobilization of molecular beacon by a bridge structure.

A novel biotinylated molecular beacon (MB) probe was developed to prepare a DNA biosensor using a bridge structure. MB was biotinylated at the quencher side of the stem and linked on a biotinylated glass cover slip through streptavidin, which acted as a bridge between MB and glass matrix. An efficient fluorescence microscope system was constructed to detect the fluorescence change caused by the conformation change of MB in the presence of complementary DNA target. The proposed biosensor was used to directly detect, in real-time, the target DNA molecules. The bridge immobilization method caused the proposed DNA biosensor to have a faster and more stable response. Under the optimal conditions, the newly developed DNA biosensor showed a linear response toward ssDNA in the range of 5-100 nM with a detection limit of 2 nM. It was interesting to note that the described biosensor was reproducible after being regenerated by urea.     

Synthesis and evaluation of a new non-fluorescent quencher in fluorogenic oligonucleotide probes for real-time PCR

A non-fluorescent quencher, based on the diaminoanthraquinone Disperse Blue 3, has been incorporated into oligonucleotides at the 5'-end, the 3'-end and internally as a thymidine derivative. Fluorimetry and fluorogenic real-time PCR experiments demonstrate that the quencher is effective with a wide range of fluorescent dyes. The anthraquinone moiety increases the melting temperature of DNA duplexes, thus allowing shorter, more discriminatory probes to be used. The quencher has been used in Scorpion primers and TaqMan probes for human DNA sequence recognition and mutation detection.     

Molecular assembly of superquenchers in signaling molecular interactions

We have designed a novel molecular assembly of quencher molecules to form superquenchers with excellent quenching efficiency. The superquencher can be engineered as desired by assembling different types and different numbers of quencher molecules. By labeling a superquencher to a molecular beacon, a 320-fold enhancement of fluorescent signal was achieved, compared to about 14-fold from a molecular beacon prepared with the same monomer quencher. Our molecular assembly approach can effectively improve the sensitivity of a variety of fluorescent assays and can be widely useful for molecular interaction studies.     

Kinetics of quenching of luminescent probes in polyelectrolyte solutions

Rate equations are derived for the quenching of luminescent polyelectrolyte-pendant probes by quencher counterions following pulsed excitation. The polyelectrolyte solution is considered to be divided into a bound and a solution phase and modified Poisson statistics are used to describe the distribution of quencher ions among the polyelectrolytes.     

Enhancement in fluorescence response by a quencher for amiloride upon binding to thymine opposite an abasic site in a DNA duplex

By using iodide (I⁻) as a quencher, we successfully improve the fluorescence response of amiloride when binding to thymine opposite an AP site in a 21-meric DNA duplex. From fluorescence measurements, as compared to the NaCl solutions, the addition of NaI as a quencher as well as salt to adjust the ionic strength effectively suppresses the background fluorescence from unbound amiloride in a solution. The Stern-Volmer analysis shows that the bound amiloride to the nucleobase at the AP site is unexposed to NaI quencher. Therefore the high signal-to-background fluorescence response of amiloride is obtained. Such enhancement in fluorescence response of amiloride by using the quencher can provide the significant improvement of the detection limit for DNA duplexes carrying T target base. The method presented in this study is simple and effective. The present method could be applicable to other detection system where microenvironment of fluorophores changes at a recognition event.     

Intramolecular dimers: a new strategy to fluorescence quenching in dual-labeled oligonucleotide probes

Many genomics assays use profluorescent oligonucleotide probes that are covalently labeled at the 5' end with a fluorophore and at the 3' end with a quencher. It is generally accepted that quenching in such probes without a stem structure occurs through F?rster resonance energy transfer (FRET or FET) and that the fluorophore and quencher should be chosen to maximize their spectral overlap. We have studied two dual-labeled probes with two different fluorophores, the same sequence and quencher, and with no stem structure: 5'Cy3.5-beta-actin-3'BHQ1 and 5'FAM-beta-actin-3'BHQ1. Analysis of their absorption spectra, relative fluorescence quantum yields, and fluorescence lifetimes shows that static quenching occurs in both of these dual-labeled probes and that it is the dominant quenching mechanism in the Cy3.5-BHQ1 probe. Absorption spectra are consistent with the formation of an excitonic dimer, an intramolecular heterodimer between the Cy3.5 fluorophore and the BHQ1 quencher.     

Syntheses and reactivity of novel unsaturated cyclic compounds containing phosphorus atoms

Kinetic stabilization of compounds containing heavy main-group elements through the use of bulky substituents is of current interest. The widely used 2,4,6-tri-t-butylphenyl group (Mes*) is recognized as a powerful bulky protecting group and has enabled us to successfully prepare various types of phosphorus compounds with unusual structures. When a phosphaalkyne carrying Mes* was treated with tBuLi and then quenched with MeOH, a 1,3-diphosphacyclobutene was obtained, whereas, when MeI was used as a quencher, a 1,3-diphosphacyclobutane-2,4-diyl was formed almost quantitatively as a stable biradical compound. The reaction mechanism for the formation of both compounds can be explained by a phosphide intermediate, which can be formed via dimerization of the phosphaalkyne promoted by tBuLi. Some other diphosphacyclobutane-2,4-diyls with various substituents were prepared in a similar fashion and showed interesting reactivities including ring expansion, oxidation, isomerization and so on.     

Optical glucose detection across the visible spectrum using anionic fluorescent dyes and a viologen quencher in a two-component saccharide sensing system

A very general system is described in which anionic fluorescent dyes possessing a wide range of absorbance and emission wavelengths are used in combination with a boronic acid-modified viologen quencher to sense glucose at pH 7.4 in buffered aqueous solution. The present study demonstrates this capability with the use of eleven anionic fluorescent dyes of various structural types. Signal modulation occurs as the monosaccharide binds to the viologen quencher and alters its efficiency in quenching the fluorescence of the anionic dyes. The degree of quenching and the magnitude of the glucose signal were found to correlate roughly with the number of anionic groups on the dye. Optimal quencher : dye ratios were determined for each dye to provide a fairly linear signal in response to changes in glucose concentration across the physiological range.     

Quencher as leaving group: efficient detection of DNA-joining reactions

We describe a new fluorescence reporting strategy in which dabsyl, a well-known quencher, activates a hydroxyl group in a probe to convert it to a leaving group. When a nucleophilic phosphorothioate probe binds adjacent to a dabsyl quenched probe, autoligation occurs, releasing the quencher, and lighting up the probes, This signal change can be used to detect single nucleotide differences in DNA without enzymes or reagents.     

Capillary electrophoresis and fluorescence studies on molecular beacon-based variable length oligonucleotide target discrimination

Molecular beacons (MBs) are oligonucleotide probes having a compact hairpin structure, with a fluorophore attached to one end and a quencher molecule attached to the other end. In its native state, the fluorophore is quenched by virtue of its proximity to the quencher molecule. Upon hybridization with its complementary oligonucleotide target, fluorescence is elicited due to a conformational change that results in separation of the fluorophore and quencher molecule. The present study describes the hybridization interaction of an MB to various complementary target sequences. The effects of temperature and length of complementary target sequences on hybridization were investigated using capillary electrophoresis and solution-based fluorescence techniques. Hybridization efficiency was dependent on the ability of the target sequences to destabilize the stem region by binding directly to the stem region. Optimal hybridization occurred between 40 and 50 degrees C for all targets tested, with the true target forming a more stable hybrid complex.     

Partitioning of unsaturated hydrophilic monomer in microemulsion media monitored by pyrene fluorescence method

The extent of intra‐ and interchain associations of (un)charged water‐soluble monomers in the homogeneous and micellar solutions was studied with steady‐state fluorescence spectroscopy. Fluorescence spectroscopic experiments were performed on uncharged (acryl amide) and charged hydrophilic monomers [zwitterionic 3‐dimethyl(methacryloyloxyethyl)ammonium propane sulfonate (DMAPS), etc.] with pyrene as a probe. In both the homogeneous and micellar solutions, linear Stern–Volmer plots were obtained that implied that the quenching process can be considered as totally dynamic. The Stern–Volmer constant (K_SV) for DMAPS decreased with an increasing dielectric constant of solvent and the concentration of simple electrolyte. An abrupt decrease in K_SV was observed in the presence of a small amount of anionic emulsifier [below the critical micelle concentration (cmc)]. The dependence of K_SV on pH for DMAPS was described by a curve with a maximum at about pH = 7. This was interpreted in terms of segregation of DMAPS and the variation of a optimal microenvironment for the probe and quencher with pH. The quenching rate in the micellar solutions strongly increased above the cmc but was lower than that in the homogeneous solutions. In the micellar solutions (above the cmc), the microenvironment for an interaction between the probe and quencher was suggested to be the whole microdroplet. The dependence of K_SV on pH for DMAPS is described by a curve with a maximum at about pH = 9.3. The synergistic effect arises from the segregation of charged quencher molecules within the microdroplets. The complex (or strong interaction) between quencher and additive(s) is supposed to increase the dynamic nature of microdroplets that provides an optimal microenvironment for probe and quencher. A good coemulsifier, however, removes quencher from the interface and creates a barrier for entering monomer (quencher) into the core of micelles; therefore, quenching is depressed. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 571–581, 2003     

Photochemistry of 5-phenyl-1-pentene in the gas phase

The photochemistry of the title compound has been studied in the gas phase using 254-nm irradiation. In addition to meta cycloadducts analogous to those observed in solution, population of S1(vib) in the gas phase gives several products, the relative amounts of which depend on quencher gas pressure but not on excitation wavelength. For example, in the absence of butane, the major photoproduct is compound 5. This product is formed by a [1,5] hydrogen shift in the primary photoproduct, compound 4. Compound 4 is an intramolecular meta cycloadduct that is generated in the gas phase with sufficient excess vibrational energy to undergo rearrangement unless quencher gas is present. Likewise, there is evidence that two other meta cycloadducts (2 and 3) are also formed with appreciable vibrational energy in the absence of a quencher gas. A unique intramolecular ortho cycloadduct is also formed from 1 but only within a narrow range of quencher gas pressures. This is a two-photon product, with the initial cycloadduct (11) ring opening to a cyclooctatriene (12) that photochemically closes to 6. The pressure dependence of this ortho cycloaddition may be due to a requirement for vibrational deactivation of 11 (Scheme 5) or a precursor species (Scheme 6). The overall chemistry is outlined in Scheme 7.     

Graphene Oxide as an Enhancer of Fluorescence

Solvent‐dependent switching of graphene oxide (GO) as fluorescence quencher or enhancer was observed. In some solvents, GO increases the fluorescence yield of a hydrophilic molecule 7‐(diethylamino)‐coumarin‐3‐carboxylic acid (7‐DCA), and in some solvents GO act as a quencher of fluorescence.     

A new dark quencher for use in genetic analysis

A novel, long-wavelength, non-fluorescent quencher (LQ), based on 1,4-diaminoanthraquinone, has been incorporated at the 3' and 5'-termini of oligonucleotides. The quencher has been used in Molecular beacons, efficiently quenching the long wavelength fluorophore, Cy5.     

INTRAMOLECULAR FLUORESCENCE QUENCHING IN COVALENT ACRYLAMIDE-INDOLE ADDUCTS

Abstract— Indole derivatives have been prepared which have a covalently linked quencher, acrylamide. One of these adducts, N-acrylyltryptamine, has a flexible linkage and the other, N-acrylyl-1,2,3,4-tetrahydropyridoindole, has a rigid bridge between indole and the quencher. The intensity decays of these adducts were obtained using multi-frequency phase and modulation fluorometry. The fluorescence of these adducts appears to be dynamically quenched; dominant lifetimes of 64 ps and 31 ps are found for the flexible and rigid adducts. This indicates that very rapid intramolecular quenching occurs, even when the quencher and fluorophore cannot collide. Quenching in the rigid molecule probably involves electron transfer through two sigma bonds. Anisotropy decay data were also collected and rotational correlation times of 62 ps and 163 ps are reported for the flexibile and rigid adducts, respectively.     

INCLUSION AND FLUORESCENE QUENCHING OF 2, 3-DIMETHYLNAPHTHALENE IN β-CYCLODEXTRIN CAVITIES

Abstract— The fluorescence quenching of 2,3-dimethylnaphthalene (DMN) incorporated to β-cyclodextrin (β-CD) cavities by different olefins (fumaronitrile, acrylonitrile, acrylamide and 2-hydroxyethylmethacrylate) has been measured as a function of the β-CD concentration. The quenching efficiency decreases when the β-CD concentration increases, but extrapolation of the data to infinite cavities concentration does not indicate complete protection. These results are interpreted in terms of two quenching processes, one of them taking place between 2,3-dimethylnaphthalene associated to a β-CD cavity and free quencher, and the other between the DMN and the quencher molecule, both associated with a different cavity. The rate constants of both quenching processes and the β-CD quencher association constant are obtained from the dependence of the quenching efficiency with β-CD concentration.