Hybridization Assay by Time-Resolved Capillary Gel Electrophoresis with a Lanthanide Chelate

Capillary electrophoresis of crude biological samples with time-resolved fluorescence (TRF) detection enables elimination of interference from organic fluorophores and from light scattering. Because the fluorescence lifetime of biological substances and impurities overlaps the fluorescence lifetime of conventional labeling dyes, TRF detection with conventional organic labeling dyes suffers from background fluorescence. In this work, we synthesized a luminescent lanthanide chelating reagent to covalently bind the 5′-end of DNA through its dichroic functional group while retaining the unique luminescent properties of the lanthanide chelate, i.e. large Stokes shift, sharp emission, and a long luminescence lifetime in the microsecond to millisecond range. The luminescence of lanthanide chelates is inherently quenched by dissociation of the central metals in typical biological buffers containing a strong chelator, for example EDTA or phosphate; the synthesized Eu³⁺ chelate reagent, however, was stable even in EDTA solutions. In addition to stability in biological buffer solution, the synthesized Eu³⁺ chelate reagent enabled direct labeling of single-stranded oligonucleotides, and was used for DNA hybridization assay by time-resolved capillary gel electrophoresis. DNA hybridization assay in fetal bovine serum was also demonstrated.     

Femtosecond/picosecond time-resolved fluorescence study of hydrophilic polymer fine particles

Femtosecond/picosecond time-resolved fluorescence study of hydrophilic polymer fine particles (polyacrylamide, PAAm) was reported. Ultrafast fluorescence dynamics of polymer/water solution was monitored using a fluorescent probe molecule (C153). In the femtosecond time-resolved fluorescence measurement at 480 nm, slowly decay components having lifetimes of tau(1) approximately 53 ps and tau(2) approximately 5 ns were observed in addition to rapid fluorescence decay. Picosecond time-resolved fluorescence spectra of C153/PAAm/H2O solution were also measured. In the time-resolved fluorescence spectra of C153/PAAm/H2O, a peak shift from 490 to 515 nm was measured, which can be assigned to the solvation dynamics of polymer fine particles. The fluorescence peak shift was related to the solvation response function and two time constants were determined (tau(3) approximately 50 ps and tau(4) approximately 467 ps). Therefore, the tau(1) component observed in the femtosecond time-resolved fluorescence measurement was assigned to the solvation dynamics that was observed only in the presence of polymer fine particles. Rotational diffusion measurements were also carried out on the basis of the picosecond time-resolved fluorescence spectra. In the C153/PAAm/H2O solution, anisotropy decay having two different time constants was also derived (tau(6) approximately 76 ps and tau(7) approximately 676 ps), indicating the presence of two different microscopic molecular environments around the polymer surface. Using the Stokes-Einstein-Debye (SED) equation, microscopic viscosity around the polymer surface was evaluated. For the area that gave a rotational diffusion time of tau(6) approximately 76 ps, the calculated viscosity is approximately 1.1 cP and for tau(7) approximately 676 ps, it is approximately 10 cP. The calculated viscosity values clearly revealed that there are two different molecular environments around the polyacrylamide fine particles.     

Investigation of tetherable distilbazolium compounds as fluorescent probes in nanostructured silica sol-gel materials

Distibazolium dyes are investigated by steady-state and time-resolved fluorescence techniques in a series of low- and high-viscosity polar solvents and in a silica sol-gel matrix. In all solvents and the sol-gel matrix, an interplay of photoinduced switching between different cis-trans isomers and solvation dynamics is observed. Even in a viscous solution (glycerol) and in silica gel, cis-trans isomerization is solvent-controlled. Whereas in glycerol the solvation results in a time-dependent fluorescence Stokes shift, the solvation-induced spectral heterogeneity in silica gel is mostly static, possibly due to a close proximity of dye molecules to the silica surfaces of the nanopores. Compared to low-viscosity solvents, where the cis-trans isomerization process takes place with a solvent-dependent rate on the timescale of about 120-150 ps, it slows down to about 1100-1400 ps in glycerol and about 1500 ps in a sol-gel matrix. Additionally, fluorescence kinetics of the dyes in the sol-gel reveals the presence of a range of different "frozen-in" conformers exhibiting a broad spectrum of lifetimes from 20 to 300 ps.     

USE OF A PULSED LASER DIODE TO MEASURE PICOSECOND FLUORESCENCE LIFETIMES

Abstract— The use of an inexpensive pulsed laser diode (Hamamatsu picosecond light pulser PLP-01) as the excitation source for a single photon timing spectrolluorimeter with microchannel plate photomultiplier detection was dem-onstrated. The performance of the instrument was tested with two very short-lived fluorescent dyes and two pho-tosynthetic systems with wcll-defined decay characteristics. Individual fluorescence decays were analyzed by modeling with a convolution of the instrument response function to a sum of exponential decay components. Accurate fluorcscence lifetimcs of the dyes cryptocyanine (55 ps in acetone and 83 ps in ethanol) and 1,1'-diethyl-2,2'-dicarbocyanine iodide (13 ps in acetone and 26 ps in ethanol) were obtained by analysis of the decay kinetics with a single exponential component. Fits to the fluorescence decay kinetics of isolated photosystem I particles and intact cyanobacterial cells required three and four decay components. respectively. The decay kinetics of the isolated photosystem I preparation were dominated (99%) by a very fast 9 ps lifetime, reflecting the preparation's small antenna size of approximately 30 chlorophyll a . The cyanobackria showed decay components of 35 ps, 160 ps, 400 ps and 1.95 ns similar to those described previously by Mullincaux and Holzwarth ( Rinchim. Biophys. Acfa 1098 , 68–78, 1991). The performance of the pulsed laser diode as an excitation source for single photon timing is discussed in comparison with conventional sources of picosecond light pulses.     

Multiplexed DNA sizing by capillary electrophoresis using entangled polymer solutions and diode array detection

We developed a method for the analysis of multiplexed double-stranded DNA (dsDNA) samples complexed to various intercalating dyes using entangled polymer solution. A commercial single-column capillary electrophoresis (CE) instrument with diode array detection was used for multiplexed detection of DNA samples by addition of intercalating fluorescent molecules. A Phi X174HinfI and a pGEM DNA ladder (1 mg/mL) were used for the electrophoretic separation of dsDNA fragments ranging in size from 24 to 726 and 36 to 2645 bp, respectively. The results suggested that simultaneous electrophoretic separation of different DNA ladders multiplexed with different dyes could be performed in the same capillary yielding fast DNA sizing separations. CE analysis, which is often overpowered by slab gel in sample throughput, could now overcome this disadvantage by allowing multiplexed sample analysis in a fraction of the time needed for slab gel analysis. The separation efficiency of stained DNA molecules with both dyes were dramatically improved with buffers containing a large cation such as tetrapentylammonium ion (Npe(4) (+)) as the only cation in the buffer.     

Amplified quenching of a conjugated polyelectrolyte by cyanine dyes

The conjugated polyelectrolyte PPESO3 features a poly(phenylene ethynylene) backbone substituted with anionic 3-sulfonatopropyloxy groups. PPESO3 is quenched very efficiently (KSV > 10(6) M(-1)) by cationic energy transfer quenchers in an amplified quenching process. In the present investigation, steady-state and picosecond time-resolved fluorescence spectroscopy are used to examine amplified quenching of PPESO3 by a series of cyanine dyes via singlet-singlet energy transfer. The goal of this work is to understand the mechanism of amplified quenching and to characterize important parameters that govern the amplification process. Steady-state fluorescence quenching of PPESO3 by three cationic oxacarbocyanine dyes in methanol solution shows that the quenching efficiency does not correlate with the Forster radius computed from spectral overlap of the PPESO3 fluorescence with the cyanines' absorption. The quenching efficiency is controlled by the stability of the polymer-dye association complex. When quenching studies are carried out in water where PPESO3 is aggregated, changes observed in the absorption and fluorescence spectra of 1,1',3,3,3',3'-hexamethylindotricarbocyanine iodide (HMIDC) indicate that the polymer templates the formation of a J-aggregate of the dye. The fluorescence dynamics in the PPESO3/HMIDC system were probed by time-resolved upconversion and the results show that PPESO3 to HMIDC energy transfer occurs on two distinctive time scales. At low HMIDC concentration, the dynamics are dominated by an energy transfer pathway with a time scale faster than 4 ps. With increasing HMIDC concentration, an energy pathway with a time scale of 0.1-1 ns is active. The prompt pathway (tau < 4 ps) is attributed to quenching of delocalized PPESO3 excitons created near the HMIDC association site, whereas the slow phase is attributed to intra- and interchain exciton diffusion to the HMIDC.     

Protein labeling with red squarylium dyes for analysis by capillary electrophoresis with laser-induced fluorescence detection

Two new red luminescent asymmetric squarylium dyes (designated "Red-1c and Red-3") have been shown to exhibit absorbance shifts to longer wavelengths upon the addition of protein, along with a concomitant increase in fluorescence emission. Specifically, the absorbance maxima for Red-1c and Red-3 dyes are 607 and 622 nm, respectively, in the absence of HSA, and 642 and 640 nm in the presence of HSA, making the excitation of their protein complexes feasible with inexpensive and robust diode lasers. Fluorescence emission maxima, in the presence of HSA, are 656 and 644 nm for Red-1c and Red-3, respectively. Because of the inherently low fluorescence of the dyes in their free state, Red-1c and Red-3 were used as on-column labels (that is, with the dye incorporated into the separation buffer), thus eliminating the need for sample derivatization prior to injection and separation. A comparison of precolumn and on-column labeling of proteins with these squarylium dyes revealed higher efficiencies and greater sensitivities for on-column labeling, which, when conducted with a basic, high-salt content buffer, permitted baseline resolution of a mixture of five model proteins. LOD for model proteins, such as transferrin, alpha-lactalbumin, BSA, and beta-lactoglobulin A and B, labeled with these dyes and analyzed by CE with LIF detection (CE-LIF) were found to be dependent upon dye concentration and solution pH, and are as low as 5 nM for BSA. Satisfactory linear relationships between peak height (or peak area) and protein concentration were obtained by CE-LIF for this on-column labeling method with Red-3 and Red-1c.     

Fluorimetric characterization of single-walled carbon nanotubes

Single-walled carbon nanotubes (SWCNTs) are a family of structurally related artificial nanomaterials with unusual properties and many potential applications. Most SWCNTs can emit spectrally narrow near-IR fluorescence at wavelengths that are characteristic of their precise diameter and chiral angle. Near-IR fluorimetry therefore offers a powerful approach for identifying the structural species present in SWCNT samples. Such characterization is increasingly important for nanotube production, study, separation, and applications. General-purpose and specialized instruments suitable for SWCNT fluorimetric analysis are described, and methods for interpreting fluorimetric data to deduce the presence and relative abundances of different SWCNT species are presented. Fluorescence methods are highly effective for detecting SWCNTs in challenging samples such as complex environmental or biological specimens because of the methods’ high sensitivity and selectivity and the near absence of interfering background emission at near-IR wavelengths. Current limitations and future prospects for fluorimetric characterization of SWCNTs are discussed.     

Charge resonance character in the charge transfer state of bianthryls: effect of symmetry breaking on time-resolved near-IR absorption spectra

We study the effects of symmetry breaking on the photogenerated intramolecular charge transfer (CT) state of 9,9'-bianthryl (BA) with femtosecond time-resolved near-IR spectroscopy. The time-resolved near-IR spectra are measured in acetonitrile for a symmetric substituted derivative of 10,10'-dicyano-9,9'-bianthryl (DCBA) and asymmetric substituted derivatives of 10-cyano-9,9'-bianthryl (CBA) and 9-(N-carbazolyl)anthracene (C9A), as well as nonsubstituted BA. The transient near-IR absorption spectrum of each compound at 0 ps has a locally excited (LE) absorption band, which agrees with the transient absorption band of the corresponding monomer unit. At 3 ps after the photoexcitation, the symmetric compounds show a broad charge transfer (CT) absorption band, whereas no absorption peak appears in the spectra of the asymmetric compounds. The broad CT absorption at 1250 nm only observed for the symmetric compounds can be attributed to the charge resonance transition associated with two equivalent charge separated states.     

Optimization of sequencing conditions using near-infrared lifetime identification methods in capillary gel electrophoresis

We have investigated the sample preparation and electrophoresis conditions necessary to prepare DNA sequencing samples appropriate for use with near-infrared (IR) fluorescent labels with dye identification accomplished via lifetime techniques. It was found that several sample preparation protocols required attention to maximize the fluorescence yields of the labeling dyes, such as thermal cycling conditions, choice of counter ion used for the ethanol precipitation step and also, dye-primer versus dye-terminator chemistries. In addition, several different sieving matrices were investigated for their effects on both the fluorescence properties of the labeling dyes and electrophoretic resolution. Extended times used for the high temperature denaturing of duplexed DNA fragments during cycle sequencing produced cleavage products, in which the covalently attached dye to the sequencing primer was released through attack by dithiothreitol (DTT). Even under optimized thermal cycling conditions, free dye was generated that masked readable data from the sequencing traces. Ethanol precipitation was necessary to remove this free dye with the proper choice of counter ion (sodium). The results using different sieving matrices indicated that linear polyacrylamides (LPAs) were appropriate for any fluorescence measurement, since they could readily be replaced between runs minimizing deleterious memory effects associated with cross-linked polyacrylamide gels. After investigation of several different sieving LPAs, the commercially available POP6 was found to be particularly attractive, since it produced good electrophoretic resolution, single exponential behavior for the near-IR dye series investigated herein, and also, discernible lifetime differences within the dye set. Finally, dye-terminator chemistry was also found to minimize bleeding in the gel matrix produced by large amounts of unextended dye-primer within the gel lane.     

Characterization of acridone dyes for use in four-decay detection in DNA sequencing

Four acridone dyes and dye-labeled primers were characterized for use in four-decay DNA sequencing. In the four-decay scheme, fluorescence lifetime replaces spectral ("color") selectivity for distinguishing between four base-specific labels in a single-lane capillary electrophoresis (CE) separation of the DNA fragments. Prior to the introduction of the acridone dyes, a major obstacle to four-decay detection was the lack of four suitable dyes with resolvable lifetimes. The four acridone dyes, whether free in solution or tethered to DNA primer, exhibit significant differences among their lifetimes and are well-suited to use together in four-decay sequencing. The lifetimes of the four dye-labeled DNA primers that were sequentially injected and detected on-the-fly in a 2% POP6 sequencing gel were 4, 6, 11 and 14 ns. A 405 nm violet laser diode provides optimal excitation of the four dyes.     

Dye distribution in fluorescent-labeled latex prepared by emulsion polymerization

Emulsion polymerizations were used for preparing fluorescent-labeled polymers. The labeled polymers were analyzed by gel permeation chromatography (GPC) using both fluorescence (FL) and refractive index (RI) as detectors. The uniformity of polymer labeling was measured by the ratio between FL and RI signals, calculated by a computer software, on the basis of each GPC chromatogram. It was found that in emulsion polymerizations, the semicontinuous process can produce a more homogenous dye distribution in the host polymer molecules than the batch method. Uniform labeling of a polymer with various dyes can be achieved by the semi-continuous process. However, experimental conditions for polymerization, such as initiator concentration and the presence of surfactant or chain transfer agent, may influence the uniformity of dye distribution. © 1994 John Wiley & Sons, Inc.     

Stable incorporation of gold nanorods into N-isopropylacrylamide hydrogels and their rapid shrinkage induced by near-infrared laser irradiation

In this study, we prepared gold nanorod (NR)-embedded N-isopropylacrylamide (NIPAM) hydrogels and studied their volume phase transition behavior induced by near-infrared (near-IR) laser irradiation utilizing the photothermal conversion characteristics of the NRs. When poly(ethylene glycol)-modified NRs were used for the preparation of composite gels, the NRs showed marked dispersion stability in the gel. Near-IR laser irradiation of the gel (cylindrical shape, diameter = 140 microm) under the following conditions, NR concentrations in the gel > or =100 microM and laser irradiation power > or =490 mW, resulted in shrinkage of the gel in the following manner: (1) waist formation around the irradiation spot and (2) growth of the waist along the axial directions of the gel. The gel shrinking induced by near-IR irradiation occurred much more rapidly than that afforded by a temperature jump, because the former was not accompanied by the skin layer formation, which disturbs the rapid shrinking of the gels. When a composite gel containing the model drug (rhodamine-labeled dextran) was irradiated with a near-IR laser, the rapid release of the drug was observed. Taking advantage of the high spatial resolution of the irradiation point, we further achieved the irradiation-point-specific release of the drug from one such gel.     

Investigations of the solvent polarity effect on the photophysical properties of coumarin-7 dye

Photophysical investigations of coumarin-7 (C7) dye in different solvents using absorption, steady-state fluorescence and time-resolved fluorescence measurements reveal the behavioral changes of the dye in nonpolar and other solvents. In moderate to higher polarity solvents, the experimental parameters such as fluorescence quantum yield (Phif), fluorescence lifetime (tauf), radiative rate constant (k(f)), nonradiative rate constant (k(nr)) and Stokes' shift (Deltav) follow almost linear correlations with the Lippert-Mataga solvent polarity parameter Deltaf but show unusual deviations in nonpolar solvents. From the observed results, it is inferred that the dye exists in a planar intramolecular charge transfer structure in moderate to higher polarity solvents, but in nonpolar solvents, the dye exists in a nonplanar structure with its 7-NEt2 group adopting a pyramidal type of configuration. Unlike some of the other coumarin dyes, namely coumarin-120 (C120) (4-CH3-7-NH2-1,2-benzopyrone) and coumarin-151 (C151) 4-CF3-7-NH2-1,2-benzopyrone), which also show similar structural changes in nonpolar and other solvents, the C7 dye does not show any activation-controlled deexcitation process in nonpolar solvents. This is attributed to the very slow flip-flop motion of the 7-NEt2 group of the C7 dye in comparison with the very fast flip-flop motion of the 7-NH2 group in the C120 and C151 dyes. Qualitative potential energy diagrams are presented to rationalize the observed results of C7 dye and to compare these with those of the other dyes such as C120 and C151. A support for the observed results and interpretation has also been obtained from quantum chemical calculations on the structures of the C7 dye.     

Near-infrared spectroscopy of stitchtite, iowaite, desautelsite and arsenate exchanged takovite and hydrotalcite

The hydrotalcite minerals stitchtite, iowaite and desautelsite together with the arsenate exchanged takovite and arsenate exchanged hydrotalcite have been studied using near-IR reflectance spectroscopy. Each mineral has its own characteristic NIR spectrum enabling recognition of the particular hydrotalcite. As such the technique has application in the field for the analysis and identification of hydrotalcites. Hydrotalcites have proven useful as an anion exchange material. Takovite and hydrotalcite were used to exchange carbonate anions by arsenate. Three Near-IR spectral regions are identified: (a) the high wavenumber region between 6400 and 7400 cm(-1) attributed to the first overtone of the fundamental hydroxyl stretching mode, (b) the 4800-5400 cm(-1) region attributed to water combination modes of the hydroxyl fundamentals of water, and (c) the 4000-4800 cm(-1) region attributed to the combination of the stretching and deformation modes of the MOH units of the hydrotalcites. NIR spectroscopy enables the separation of the hydroxyl bands of the water and M-OH units for the hydrotalcites. Compared with the NIR spectroscopy of the structural units of the hydrotalcites namely gibbsite and brucite, the bands are broad.     

Fluorescence lifetime imaging microscope consisting of a compact picosecond dye laser and a gated charge-coupled device camera for applications to living cells.

An inverted microscope was combined with a compact dye laser with a pulse width of <190 ps and an intensified charge-coupled device (ICCD) camera with a minimum gate width of 200 ps. The resulting fluorescence lifetime imaging microscope, which has a temporal resolution of 340 ps, was used to measure the fluorescence lifetime of polymer microspherers. The results indicated a fluorescence lifetime of 0.9 ns. The present analytical instrument was also employed in an evaluation of biological cells after labeling them with SYTO 13, a fluorescent dye.     

Non-radiative deactivation pathways of subphthalocyanine and subnaphthalocyanine dyes and of their mixture

Subphthalocyanine and subnaphthalocyanine dyes and their mixture were investigated by means of the spectroscopic and photoelectric methods. Absorption, fluorescence, steady-state and time-resolved photothermal measurements for the dyes and their mixture were done in order to get information about the radiative and non-radiative deactivation processes as competetive processes to charge separation. It was shown that energy transfer between the dyes improved the photocurrent generation in photoelectrochemical cells (PEC) based on In(2)O(3) and SnO(2) as an electrode. The possible participation of the dye triplet states in non-radiative processes was discussed.     

Oligonucleotide-stabilized Ag nanocluster fluorophores

Single-stranded oligonucleotides stabilize highly fluorescent Ag nanoclusters, with emission colors tunable via DNA sequence. We utilized DNA microarrays to optimize these scaffold sequences for creating nearly spectrally pure Ag nanocluster fluorophores that are highly photostable and exhibit great buffer stability. Five different nanocluster emitters have been created with tunable emission from the blue to the near-IR and excellent photophysical properties. Ensemble and single molecule fluorescence studies show that oligonucleotide encapsulated Ag nanoclusters exhibit significantly greater photostability and higher emission rates than commonly used cyanine dyes.     

Fluorescent nanocrystals grown in sol–gel thin films for generic stable and sensitive sensors

Through the sol–gel route, we have well-controlled the preparation of fluorescent organic nanocrystals grown in silicate thin films. This process is based on the confined nucleation and growth of dyes in the pores of wet gels. The resulting nanocomposite sol–gel thin films, coated onto low-cost substrates, exhibit coupled properties: transparency, stability, easy shaping of sol–gel thin films and high fluorescence intensity coming from organic nanocrystals. The sensitivity of the fluorescence intensity of nanocrystals to their environments can be exploited for the development of optical sensors. Indeed, Förster Resonance Energy Transfer can inhibit nanocrystal fluorescence when probe molecules are adsorbed or grafted on the nanocrystal surface after their diffusion through the pores of the sol–gel matrix. We investigated by time-resolved fluorescence spectroscopy the effect of nanocrystal size and probe concentration on the fluorescence quenching in presence of Methylene Blue used in this study as molecular probe. As strong fluorescence quenchings can be achieved, even for low probe concentrations, these hybrid organic–inorganic nanocoposites are promising for the development of sensor devices by increasing their fluorescence contrasts under specific chemical or biological environments.     

Rapid and sensitive determination of phosphorus-containing amino acid herbicides in soil samples by capillary zone electrophoresis with diode laser-induced fluorescence detection

A straightforward and sensitive method has been developed for the analysis of phosphorus-containing amino acid herbicides (glufosinate and aminomethylphosphonic acid, the major metabolite of glyphosate) in soil samples. For this purpose, the analytical features of two indocyanine fluorescent dyes, sulfoindocyanine succinimidyl ester (Cy5) and 1-ethyl-1-[5-(N-succinimidyl-oxycarbonyl)pentyl]-3,3,3,3-tetramethyl-indodicarbocyanine chloride, as labeling reagents for the determination of these herbicides by CZE with diode LIF detection were investigated. Practical aspects related to the labeling chemistry and CZE separation showed that the two probes behave similarly, Cy5 being the best choice for the determination of these herbicides on account of its higher sensitivity. The optimum procedure includes a derivatization step of the pesticides at 25 degrees C for 30 min and direct injection to CZE analysis, which is conducted within about 14 min using ACN in the running buffer. The lowest detectable analyte concentration ranged from 0.025 to 0.18 microg/L with a precision of 3.6-5.4%. These results indicate that indocyanine fluorescence dyes are useful as rapid and sensitive labels for the determination of these herbicides when compared with typical fluorescein dyes such as FITC and 5-(4,6-dichloro-s-triazin-2-ylamino) fluorescein, because they provide faster labeling reactions even at room temperature and the excess of reagent practically does not interfere the determination. Finally, the Cy5 method was successfully applied to soil samples without a preliminary clean-up procedure, and the herbicides were measured without any interference from coexisting substances. The recoveries of these compounds in these samples at fortification levels of 100-500 ng/g were 90-93%.