Comparison of sieving matrices for on-the-fly fluorescence lifetime detection of dye-labeled DNA fragments

Commercially available, replaceable sieving matrices and their solvent modulated forms were evaluated for use in on-the-fly fluorescence lifetime detection of dye-labeled DNA fragments in capillary electrophoresis. The fragments were labeled with dyes that can be excited by the 488 nm line of an argon ion laser and have lifetimes in the range of 0.8 ns to 3.8 ns. The sieving matrices and buffer systems included poly(vinylpyrrolidone) (PVP), poly(ethyleneoxide) (PEO), hydroxyethylcellulose (HEC), Tris-borate-EDTA (TBE) and Tris-TAPS-EDTA buffers modified with DMSO and formamide. Selection of the optimal sieving matrix is based on the separation efficiency and the enhancement of lifetime resolution of DNA fragments. Best results for both electrophoretic resolution and lifetime detection were obtained using a poly(ethyleneoxide)/TBE gel buffer in the presence of 10% formamide.     

Comparison of sieving matrices for on-the-fly fluorescence lifetime detection of dye-labeled DNA fragments

Commercially available, replaceable sieving matrices and their solvent modulated forms were evaluated for use in on-the-fly fluorescence lifetime detection of dye-labeled DNA fragments in capillary electrophoresis. The fragments were labeled with dyes that can be excited by the 488 nm line of an argon ion laser and have lifetimes in the range of 0.8 ns to 3.8 ns. The sieving matrices and buffer systems included poly(vinylpyrrolidone) (PVP), poly(ethyleneoxide) (PEO), hydroxyethylcellulose (HEC), Tris-borate-EDTA (TBE) and Tris-TAPS-EDTA buffers modified with DMSO and formamide. Selection of the optimal sieving matrix is based on the separation efficiency and the enhancement of lifetime resolution of DNA fragments. Best results for both electrophoretic resolution and lifetime detection were obtained using a poly(ethyleneoxide)/TBE gel buffer in the presence of 10% formamide. Received: 25 August 2000 / Revised: 7 November 2000 / Accepted: 14 November 2000     

新型水溶性不对称五甲川菁染料的合成、光稳定性及蛋白质的荧光标记

合成并表征了系列水溶性五甲川菁染料, 研究了其在不同溶剂中的光谱性能. 结果表明, 染料在水中的最大吸收和荧光光谱在647~665 nm波长范围内, 荧光量子产率达到0.1左右. 考察了N位取代基对染料水溶液光稳定性的影响, 结果表明, 在N原子上引入带有苯环结构和大体积的磺酸基, 可以提高染料的光稳定性. 高效液相色谱(HPLC)分析结果表明, 染料4a的N-羟基琥珀酰亚胺(NHS)活性酯标记牛血清白蛋白(BSA)的检测限为1.2×10^-8 mol/L, 与紫外检测相比, 检测灵敏度提高了近2个数量级.     

Truncated fragments in polymerase chain reaction-based DNA sequencing

Reconstitution experiments were performed by using an ordinary dye-primer protocol of a template spiked with known amounts of truncated fragments. We observed that as little as 0.2 mole-percentage of the truncated fragment caused sequence interpretation problems. Two protocols were developed for sequencing with dye-labeled terminators; this eliminates the problems with truncated fragments, which are adapted to a one-dye chemistry. One was designed for single extension sequencing using T7 DNA polymerase and one for cycle sequencing. To avoid precipitation and centrifugation and to facilitate automation, the dye-terminator protocols included the use of a biotinylated sequencing primer. Thus, the Sanger fragments were recovered and, by magnetic separation, washed and released by formamide, EDTA, and heat treatment before loading on the electrophoresis gel. Integrated procedures for sequencing PCR products using one-dye-labeled terminators suitable for automation are described. High quality data in terms of long reads and detection of polymorphisms is obtained. The protocols serve as attractive alternatives to internal labeling and dye-primer approaches.     

Surface modification of poly(methyl methacrylate) microfluidic devices for high-resolution separations of single-stranded DNA

While polymer-based microfluidic devices offer some unique opportunities in developing low-cost systems for a variety of application areas, the ability to sort electrophoretically with high efficiency a number of different targets has remained somewhat elusive with an example consisting of achieving single base resolution as required for DNA sequencing. While the reasons for this are many-fold, it is clear that some type of coating is required on the polymer substrate to suppress the EOF and/or minimize potential solute/wall interactions. To this end, we report on a simple grafting procedure to allow the formation of polymer coats, which in this example used linear polyarcylamides (LPAs), onto a poly(methyl methacrylate) (PMMA) microfluidic device. The procedure involved creating an amine-terminated PMMA surface by appropriately functionalizing the PMMA through either a chemical or photochemical process. The aminated surface could then be used to covalently anchor methacrylic acid, which was used as a scaffold to produce LPAs on the surface through radical polymerization of acrylamide. The resulting surfaces demonstrated EOFs that were nearly an order of magnitude smaller than native PMMA. In addition, these LPA-coated devices could produce highly reproducible migration times of over approximately 20 runs with plate numbers exceeding 10(5) m(-1). Using gel electrophoretic analysis of a single base track generated from an M13mp18 template using Sanger cycle sequencing and dye-primer chemistry, the resolution value obtained for bases 199 and 200 was 0.18 while for bases 208 and 209 it was 0.21. For the native PMMA, these bands were found to comigrate.     

Near-infrared time-resolved fluorescence lifetime determinations in poly(methylmethacrylate) microchip electrophoresis devices

High aspect-ratio microstructures were hot-embossed in polymer substrates with a molding tool fabricated using lithography/electroplating/forming (LIGA). The resulting devices were used for the electrophoretic separation of oligonucleotides labeled with near-infrared (near-IR) dyes. Near-IR time-resolved fluorescence was used as an identification method for the labeling dyes. The detection apparatus consisted of a pulsed laser diode operating at 680 nm, a single-photon avalanche diode, an integrated microscope, and a PC-board incorporating time-correlated single photon counting electronics. Investigation of the optical quality and amount of autofluorescence generated from different polymer substrates was carried out in the near-IR region for determining compatibility with time-resolved fluorescence. Our results revealed that of several poly(methylmethacrylate)(PMMA) substrates, brand Plexiglas offered minimal replication errors in the embossed features using appropriate embossing conditions with low background fluorescence contributions to the observed decay. Near-IR dye-labeled oligonucleotides were separated to determine the applicability of fluorescence lifetime discrimination between Cy5.5 (tauf = 930 ps) and IRD700 (tauf = 851 ps) labeling dyes during the microchip separation. These dyes were used to label T-fragments (thymine) of an M13mp18 ssDNA template. The DNA ladders were electrophoresed at 130 V/cm in a 4% linear polyacrylamide gel (LPA) gel matrix in a 9.5 cm long serpentine channel heated to 50 degrees C. The electropherogram revealed that the lifetimes could be accurately read well beyond 450 bases, although single-base pair resolution in the electropherogram was difficult to achieve due to potential solute-wall interactions in the polymer microdevice or the electroosmotic flow (EOF) properties of the device. The relative standard deviations secured for individual bands in the electropherogram were similar to those obtained using capillary gel electrophoresis, in spite of the lower load volume.     

DBD Dyes as Fluorescence Lifetime Probes to Study Conformational Changes in Proteins

Previously, [1,3]dioxolo[4,5‐f][1,3]benzodioxole (DBD)‐based fluorophores used as highly sensitive fluorescence lifetime probes reporting on their microenvironmental polarity have been described. Now, a new generation of DBD dyes has been developed. Although they are still sensitive to polarity, in contrast to the former DBD dyes, they have extraordinary spectroscopic properties even in aqueous surroundings. They are characterized by long fluorescence lifetimes (10–20 ns), large Stokes shifts (≈100 nm), high photostabilities, and high quantum yields (>0.56). Here, the spectroscopic properties and synthesis of functionalized derivatives for labeling biological targets are described. Furthermore, thio‐reactive maleimido derivatives of both DBD generations show strong intramolecular fluorescence quenching. This mechanism has been investigated and is found to undergo a photoelectron transfer (PET) process. After reaction with a thiol group, this fluorescence quenching is prevented, indicating successful bonding. Being sensitive to their environmental polarity, these compounds have been used as powerful fluorescence lifetime probes for the investigation of conformational changes in the maltose ATP‐binding cassette transporter through fluorescence lifetime spectroscopy. The differing tendencies of the fluorescence lifetime change for both DBD dye generations promote their combination as a powerful toolkit for studying microenvironments in proteins.     

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.     

Electrophoretic studies of polygalacturonate oligomers and their interactions with metal ions

Polygalacturonic acid, a linear homopolysaccharide, was investigated by capillary electrophoresis (CE) using linear polyacrylamide-coated capillaries and laser-induced fluorescence (LIF) detection. A successful separation of its fluorescently labeled oligomers was achieved through sieving in polyacrylamide entangled matrices. The reaction conditions for the derivatization of polygalacturonic acid were optimized. In studying the interactions between polygalacturonic acid and various metal ions, the end-label, free-solution electrophoretic (ELFSE) technique, developed earlier in our laboratory (Sudor, J., Novotny, M. V., Anal. Chem. 1995, 67, 4205-4209) was found preferable to the sieving method. ELFSE is fast and convenient in that no polymer solutions are needed for the separation. The investigation showed that for the moderately large oligomers, the strongest binding occurred with calcium and cadmium ions, while the smallest interaction was observed with magnesium ions.     

Near-infrared tetra-substituted aluminum 2, 3-naphthalocyanine dyes for optical fiber applications

The synthesis and spectral characterization of several tetra-substituted aluminum 2, 3-naphthalocyanine dyes for the determination of metal ions is reported. The synthesis is done by means of a homogeneous phase reaction, replacing the previously used heterogeneous method. The new scheme allows for improved product yields, higher purity, better product reproducibility and can be monitored at different stages using UV-Vis-near-infrared spectroscopy. The incorporation of electron-donating or -withdrawing groups was found to influence the product yield and to cause a shift in the absorbance maximum. The typical shift in the excitation maximum (of up to 27 nm) enables the dye to match the output of semiconductor laser diodes. In addition the tetra-substituted groups were capable of undergoing an ion-exchange process with the metal ions which produced a change in the fluorescence signal of the dye. Similar results were achieved using an optical fiber metal probe. The detection of metal ions using the near-infrared dyes was accomplished via steady-state fluorescence using both a commerically available instrument and a fiber optic system and also via the fluorescence lifetime technique.     

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.     

Isolation of Xis Gen Fragment of λ Phage from Agarose Gel Using Magnetic Particles for Subsequent Enzymatic DNA Sequencing

Gel electrophoresis is one of the most important methods used in biochemistry and molecular biology. The recovery of analytes from the gel required for subsequent analysis including amplification by polymerase chain reaction (PCR) or DNA sequencing is an issue due to the gel contamination. Among the other methods used for sample recovery, the application of nanomaterials is also being investigated. In this study, the applicability of magnetic particles (1 μm) for isolation of DNA fragment from agarose gel with subsequent DNA sequencing was investigated. Electrochemical analysis and DNA sequencing was used to investigate the recovery yield. The influence of dilution of the gel prior to the purification was investigated and the linear dependence with regression coefficient R ² = 0.9972 was obtained using square wave voltammetry. Moreover, bioinformatic analysis was used for comparison of obtained sequences, and simple and easy identification of non-systematic errors caused by both fluorescence labeling reaction and electrophoretic separation. It was found that magnetic nanoparticles based isolation markedly lowered the errors occurring during sequencing of the isolated DNA fragment from 7 to 1 %.     

New indolium and quinolinium dyes sensitive to aqueous halide ions at physiological concentrations

Twelve new highly fluorescent dyes have been produced by the reaction of two heterocyclic nitrogen bases with 8-bromooctanoic acid, 11-bromoundecanoic acid and 15-bromopentadecanoic acid. The bromide counter ions of the first six dyes have been replaced with the tetraphenylborate ion. Unlike the bases themselves, the quaternary salts are water soluble and have fluorescence characteristics independent of pH in the pH range 7–11. Both the fluorescence intensity and fluorescence lifetime of dyes 1–12 are reduced in the presence of aqueous halide ions allowing halide concentrations to be determined accurately at physiological levels. All the dyes have been characterised in terms of steady state fluorescence spectra and steady-state Stern-Volmer analysis.     

Thiol-reactive dyes for fluorescence labeling of proteomic samples

Covalent derivatization of proteins with fluorescent dyes prior to separation is increasingly used in proteomic research. This paper examines the properties of several commercially available iodoacetamide and maleimide dyes and discusses the conditions and caveats for their use in labeling of proteomic samples. The iodoacetamide dyes BODIPY TMR cadaverine IA and BODIPY Fl C(1)-IA were highly specific for cysteine residues and showed little or no nonspecific labeling even at very high dye:thiol ratios. These dyes also showed minimal effects on pI's of standard proteins. Some iodoacetamide dyes, (5-TMRIA and eosin-5-iodoacetamide) and some maleimide dyes (ThioGlo I and Rhodamine Red C(2) maleimide) exhibited nonspecific labeling at high dye:thiol ratios. Labeling by both iodoacetamide and maleimide dyes was inhibited by tris(2-carboxyethyl)phosphine (TCEP); interactions between TCEP and dye were also observed. Thiourea, an important component of sample solubilization cocktails, inhibited labeling of proteins with iodoacetamide dyes but not with maleimide dyes. Maleimide dyes may serve as an alternative for labeling proteins where it is essential to have thiourea in the solubilization buffer. Covalent derivatization by BODIPY TMR cadaverine IA, BODIPY Fl C(1)-IA or Rhodamine Red C(2) maleimide was also demonstrated to be compatible with in-gel digestion and peptide mass fingerprinting by matrix assisted laser desorption/ionization-mass spectrometry and allowed successful protein identification.     

Ultrafast dynamics of Auramine O in composite films

Ultrafast excited-state dynamics of Auramine O, a diphenylmethane dye, in polymethylmethacrylate (PMMA) and in hybrid organic/inorganic sol–gel based films have been studied by means of femtosecond fluorescence upconversion experiments. The fluorescence transients of the samples showed a fast decay (few picoseconds) and a long decay (hundreds of picoseconds) representing a rapid cooling of the excess excitation energy to the matrices and the excited-state lifetime of the dye molecules, respectively. Different dynamic Stokes shifts in PMMA and hybrid glasses have been observed, which is argued to be ascribed to the different couplings between the emissive and nonemissive excited states for the two types of matrices.     

Effect of TiO2 colloids on the fluorescence behavior of two cyanine dyes

The photophysical properties of two typical cyanine dyes [3,3'-diethyl-9-methyl-thiacarbocyanine iodide (dye A) and anhydro-3,3'-disulfopropyl-5,5'-diphenyl-9-ethyloxacarbocyanine hydroxide (dye B)] in the absence and presence of TiO(2) colloids have been investigated by UV-visible spectroscopy, (1)H-NMR spectroscopy, fluorescence spectroscopy, fluorescence lifetime measurements, and ESR measurements. It was found from the absorption spectra and NMR results that there are two isomers in the ground state of these dyes. Steady-state fluorescence spectra show that the fluorescence intensities of dye A and dye B are enhanced and quenched by TiO(2) colloids, respectively. Time-resolved fluorescence lifetime measurements indicate that the lifetimes of dye A and dye B in the presence of TiO(2) colloids are longer and shorter than those obtained in the absence of TiO(2) colloids, respectively. ESR measurements demonstrate that the electron transfer efficiency from (1)dye B* to the conduction band of TiO(2) is much larger than that from (1)dye A* to the conduction band of TiO(2). The different fluorescence behavior of dye A and dye B can be intepreted in terms of whether phi(Tr,nr)(0)-phi(Tr,nr) (the reduction of the quantum yield for radiationless transition in the excited singlet state (1)dye* caused by the TiO(2) colloids) is larger or smaller than phi(ET) (the quantum yield of electron transfer from (1)dye* to the conduction band of TiO(2) colloids).     

阴阳离子菁染料超快荧光动力学特性研究

采用飞秒荧光上转换技术,研究了阴阳离子菁染料及对应的阴离子和阳离子菁染料吸附在立方型和T型溴碘化银表面上形成J-聚集体的荧光衰减时间分辨特性,分析了几种菁染料增感体系的超快电子转移动力学过程及其对增感效率的影响.通过比较几种菁染料增感体系的荧光衰减特性,两种阴阳离子染料要明显快于阴离子染料、阳离子染料及二者的加合,说明阴阳离子染料聚集体到溴碘化银的电子注入速率较快,增感效果更好.对两种阴阳离子染料聚集体荧光衰减特性的比较,可以看出染料在T型颗粒溴碘化银上形成聚集体的荧光寿命更短,因而对T型颗粒的增感效果更好.染料Dye2的荧光衰减要快于染料Dye1,说明染料Dye2到溴碘化银的电子注入速率更快,增感效率更高.     

Mono- and bis-intercalating dyes for multiplex fluorescence lifetime detection of DNA restriction fragments in capillary electrophoresis

The use of novel intercalating dyes as labels in DNA restriction fragment analysis by capillary electrophoresis with frequency-domain fluorescence lifetime detection is described. The dyes, including one mono-intercalating dye with three positive charges and three bis-intercalating, homodimeric dyes with four positive charges, were excited by the 488 nm line of an argon ion laser and exhibited lifetimes in the range of 1-3 ns. The separations were performed using a gel containing 1% high-molecular-weight (HMW) hydroxyethylcellulose (HEC) (90,000-105,000) and 0.3% low-molecular-weight (LMW) HEC (24,000-27,000) in Tris-borate-EDTA buffer (TBE). Multiplex lifetime detection of mixtures of dye-labeled DNA restriction fragment digests and size standard fragments was achieved. Compared to previous results obtained with several mono-intercalating dyes of lesser charge (McIntosh, S. L., Nunnally, B. K., Nesbit, A. R., Deligeorgiev, T. G., Gadjev, N. I., McGown, L. B., Anal. Chem. 2000, 72, 5444-5449), the present dyes provided a wider range of lifetimes and better lifetime discrimination in multiplex detection. There was no evidence of dye exchange during the capillary electrophoresis experiment.     

THE PHOTOPHYSICAL CONSTANTS OF SEVERAL FLUORESCENT DYES PERTAINING TO ULTRASENSITIVE FLUORESCENCE SPECTROSCOPY

Abstract— The successful implementation of ultrasensitive fluorescence spectroscopy of biological and chemical species depends upon certain photophysical parameters associated with the fluorescent dye used in the investigation. These parameters include the fluorescence quantum efficiency, photodestruction quantum efficiency, absorption cross section and fluorescence lifetime. These photophysical constants were measured for several fluorescent dyes that are used for the tagging of biological species. Three different solvents, ethanol, water and a cationic surfactant used above its critical micelle concentration, were studied. The effective photon yield (ratio of the fluorescence quantum yield to the photodestruction quantum efficiency) for the dyes is nearly 100 times greater in ethanol than it is in water because of the superior photostabilities of these dyes in ethanol solvents. The implications of these parameters for the design of an ultrasensitive fluorescence experiment are discussed.     

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.