A fluorescent high-throughput assay for double-stranded DNA: the RediPlate PicoGreen assay

The fluorescent PicoGreen reagent for detection and quantitation of double-stranded DNA has been adapted for high-throughput screening: the RediPlate PicoGreen double-stranded DNA assay format. In the RediPlate PicoGreen assay format, the PicoGreen reagent is predistributed and co-dried into either 96- or 384-well microplates with the excipient trehalose. The user resuspends the dried reagents upon adding DNA, and measures the resulting fluorescence after a five minute incubation. Replicate fluorescence measurements on nominally identical wells have less than a 5% coefficient of variation. The assay is linear from 5 to 500 ng/ml DNA in a 200 micro l volume. The RediPlate PicoGreen assay format retains the advantages of the original PicoGreen reagent - sensitivity, speed, and specificity - but in a high-throughput format.     

Direct determination of single-to-double stranded DNA ratio in solution using steady-state fluorescence measurements

We report a simple and rapid method for quantitation of single-to-double stranded (ss : ds) DNA ratios in solution, using steady-state measurements of fluorescence from two simultaneously excited intercalated dyes; the ratio of fluorescence intensities from PicoGreen (525 nm) and ethidium bromide (610 nm) is directly proportional to the ss : ds DNA ratio.     

Laser-Induced fluorescence detection in conventional-size liquid chromatography with a frequency-doubled argon-ion laser

Laser-induced fluorescence (LIF) detection in conventional-size column liquid chromatography is achieved at 257 nm with a frequency-doubled argon-ion laser. Short-wavelength excitation offers two important advantages: firstly, a wide variety of analytes can be excited, and secondly, the Raman scatter of the eluent does not interfere with the fluorescence of the analytes. A standard mixture of polynuclear aromatic hydrocarbons was studied, both with LIF detection and with a commercially available sensitive conventional fluorescence detector. The improvement in the detection limits ranges from about a factory of 4 to 30; the LIF detection limits are typically at the 50 ng l^?1 level, which corresponds to an injected amount of 0.5 pg.     

Immunoassays using capillary electrophoresis laser induced fluorescence detection for DNA adducts

Human DNA is exposed to a variety of endogenous and environmental agents that may induce a wide range of damage. The critical role of DNA damage in cancer development makes it essential to develop highly sensitive and specific assays for DNA lesions. We describe here ultrasensitive assays for DNA damage, which incorporate immuno-affinity with capillary electrophoresis (CE) separation and laser induced fluorescence (LIF) detection. Both competitive and non-competitive assays using CE/LIF were developed for the determination of DNA adducts of benzo[a]pyrene diol epoxide (BPDE). A fluorescently labeled oligonucleotide containing a single BPDE adduct was synthesized and used as a fluorescent probe for competitive assay. Binding between this synthetic oligonucleotide and a monoclonal antibody (MAb) showed both 1:1 and 1:2 complexes between the MAb and the oligonucleotide. The 1:1 and 1:2 complexes were separated by CE and detected with LIF, revealing binding stoichiometry information consistent with the bidentate nature of the immunoglobulin G antibody. For non-competitive assay, a fluorescently labeled secondary antibody fragment F(ab′)₂ was used as an affinity probe to recognize a primary antibody that was specific for the BPDE-DNA adducts. The ternary complex of BPDE-DNA adducts with the bound antibodies was separated from the unbound antibodies using CE and detected with LIF for quantitation of the DNA adducts. The assay was used for the determination of trace levels of BPDE-DNA adducts in human cells. Analysis of cellular DNA from A549 human lung carcinoma cells that were incubated with low doses of BPDE (32 nM–1 μM) showed a clear dose–response relationship. BPDE is a potent environmental carcinogen, and the ultrasensitive assays for BPDE-DNA adducts are potentially useful for monitoring human exposure to this carcinogen and for studying cellular repair of DNA damage.     

Focusing and stabilization of bis‐intercalating dye–DNA complexes for high‐sensitive CE‐LIF DNA analysis

Multiple labeling of nucleic acids by intercalative dyes is a promising method for ultrasensitive nucleic acid assays. The properties of the fast dissociation and instability of dye–DNA complexes may prevent from their wide applications in CE‐LIF nucleic acid analysis. Here, we describe an optimum CE focusing method by using appropriately paired sample and separation buffers, Tris‐glycine buffer and Tris‐glycine‐acetic acid buffer. The developed method was applied in both uncoated and polyacrylamide coated fused‐silica capillary‐based CE‐LIF analysis while the sample and separation buffers were conversely used. The complexes of intercalative dye benzoxazolium‐4‐pyridinium dimer and dsDNA were greatly focused (separation efficiency: 1.8 million theoretical plates per meter) by transient isotachophoresis mechanism in uncoated capillary, and moderately focused by transient isotachophoresis in combination of field amplified sample stacking and further stabilized by the paired buffer in polyacrylamide coated capillary. Based on the developed focusing strategy, an ultrasensitive DNA assay was developed for quantitation of calf thymus dsDNA (from 0.02 to 2.14 pM). By the use of an excitation laser power as low as 1 mW, the detection limits of calf thymus dsDNA (3.5 kb) are 7.9 fM in concentration and 2.4×10^?22 mol (150 molecules) in mass. We further demonstrate that the non‐gel sieving CE‐LIF analysis of DNA fragments can be enhanced by the same strategy. Since the presented strategy can be applied to uncoated and coated capillaries and does not require special device, it is also reasonable to extend to the applications in chip‐based CE DNA analysis.     

Synthesis of fluorescently labeled alkylated DNA adduct standards and separation by capillary electrophoresis

DNA adducts are regarded as individual internal dosimeters for the exposure to chemical carcinogens. To date, the most sensitive method for DNA adduct analysis is the radioactive 32P-postlabeling method, which allows the detection of one adduct in 10(10) unmodified nucleotides in microg amounts of DNA. However, this technique suffers from disadvantages such as working with radioactive phosphorus and time-consuming chromatographic separation procedures. In addition, the simultaneous detection of adducts from different classes of carcinogens in a DNA sample is difficult. In order to overcome these drawbacks, we are developing a new detection method, comprising fluorescence labeling of DNA adducts, capillary electrophoretic (CE) separation, and on-line detection by monitoring laser-induced fluorescence (LIF). So far, we have evaluated the separation power and the detection limit of CE with fluorescently labeled standard compounds such as unmodified nucleotides or alkylated thymidines. For this purpose, we developed a universal method for labeling 5'-OH-mononucleosid-3'-dicyanoethyl-phosphates with fluorescent dyes based on the phosphoramidite technology for DNA synthesis. The separation of N3-methylated, N3-, O2- and O4-butylated thymidines from the unmodified nucleotide within a few minutes recommends CE-LIF as a powerful method for DNA adduct analysis.     

Label-Free Fluorescent Kinase and Phosphatase Enzyme Assays with Supramolecular Host-Dye Pairs

The combination of the macrocyclic hosts p-sulfonatocalix[4]arene and cucurbit[7]uril with the fluorescent dyes lucigenin and berberine affords two label-free enzyme assays for the detection of kinase and phosphatase activity by fluorescence monitoring. In contrast to established assays, no substrate labeling is required. Since phosphorylation is one of the most important regulatory mechanisms in biological signal transduction, the assays should be useful for identification of inhibitors and activators in high-throughput screening (HTS) format for drug discovery.     

Handling and detection of 0.8 amol of a near-infrared cyanine dye by capillary electrophoresis with laser-induced fluorescence detection

We are interested in the detection of DNA adducts and other trace analytes by labeling them with a fluorescent tag followed by use of capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) for high resolution and sensitivity. Towards this goal, here we report the following: (1) synthesis and handling properties of a near-IR, carboxyl-substituted heptamethine cyanine dye; (2) modification of an existing ball lens LIF detector to provide near-LIF detection with excitation at 785 nm for CE; and (3) corresponding handling and detection of as little as 0.8 amol of the dye by enrich-injection of 4.7 microl of 1 x 10(-13) mol/l dye in methanol from an 8-microl volume into a corresponding CE-LIF system. The electrolyte for the separation was methanol-40 mmol/l aqueous sodium borate (98:2, v/v). This finding encourages further exploration of the dye by functionalization of its carboxyl group for chemical labeling purposes.     

High-sensitivity detection of biological amines using fast Hadamard transform CE coupled with photolytic optical gating

Here, we report the first utilization of Hadamard transform CE (HTCE), a high-sensitivity, multiplexed CE technique, with photolytic optical gating sample injection of caged fluorescent labels for the detection of biologically important amines. Previous implementations of HTCE have relied upon photobleaching optical gating sample injection of fluorescent dyes. Photolysis of caged fluorescent labels reduces the fluorescence background, providing marked enhancements in sensitivity compared to photobleaching. Application of fast Hadamard transform CE (fHTCE) for fluorescein-based dyes yields a ten-fold higher sensitivity for photolytic injections compared to photobleaching injections, due primarily to the reduced fluorescent background provided by caged fluorescent dyes. Detection limits as low as 5 pM (ca. 18 molecules per injection event) were obtained with on-column LIF detection using fHTCE in less than 25 s, with the capacity for continuous, online separations. Detection limits for glutamate and aspartate below 150 pM (1-2 amol/injection event) were obtained using photolytic sample injection, with separation efficiencies exceeding 1 x 10(6) plates/m and total multiplexed separation times as low as 8 s. These results strongly support the feasibility of this approach for high-sensitivity dynamic chemical monitoring applications.     

Determination of multiple drugs of abuse in human urine using capillary electrophoresis with fluorescence detection

Methods for separation and determination of multiple drugs of abuse in biological fluids using capillary electrophoresis (CE) with native fluorescence and laser-induced fluorescence (LIF) detection are described herein. Using native fluorescence, normorphine, morphine, 6-acetyl morphine (6-AM), and codeine were analyzed by CE without any derivatization procedure and detected at an excitation wavelength of 245 nm with a cut-off emission filter of 320 nm, providing a rapid and simple analysis. The detection limits were in the range of 200 ng/mL. For a highly sensitive analysis, LIF detection was also examined using a two-step precolumn derivatization procedure. In this case, drugs extracted from human urine were first subjected to an N-demethylation reaction involving the use of 1-chloroethyl chloroformate (ACE-Cl) and then derivatized using fluorescein isothiocyanate isomer I (FITC) and analyzed by CE coupled to a LIF detector. Variables affecting this derivatization: yield of demethylation reaction, FITC concentration, reaction time and temperature, were studied. The estimated instrumental detection limits of the FITC derivatives were in the range of 50-100 pg/mL, using LIF detection with excitation and emission wavelengths of 488 nm and 520 nm, respectively. The linearity, reproducibility and reliability of the methods were evaluated. In addition, a comparison of the characteristics for both native fluorescence and LIF detections was also discussed.     

Determination of nicotinyl pesticide residues in vegetables by micellar electrokinetic capillary chromatography with quantum dot indirect laser-induced fluorescence

A new assay was developed by use of micellar electrokinetic capillary chromatography with indirect LIF fluorescence for the determination of thiamethoxam, acetamiprid, and imidacloprid residues in vegetables, in which the cadmium telluride quantum dots (QDs) synthesized in aqueous phase were used as fluorescent background substance and their excitation and emission wavelengths matched with LIF detector by engineering their size. The factors that affected the peak height and the resolution were optimized. The running buffer was composed of 4.4 μM cadmium telluride QDs as fluorescent background substance, 40 mM borate and 60 mM SDS, and its pH was adjusted to 8.0. The separation voltage was 25 kV. Under the optimum conditions, the detection limits were 0.05, 0.01, and 0.009 mg/kg; the linear dynamic ranges were 0.5-30, 0.1-30, and 0.1-30 mg/L; and the average recoveries of spiked samples were 72.0-101.2, 74.0-106.7, and 77.8-105.1% for thiamethoxam, acetamiprid, and imidacloprid, respectively. The assay can meet the requirement of maximum residue limits to these three pesticides in the regulations of European Union and Japan, and has been applied for determining their residues in vegetables.     

Part-per-trillion level detection of estradiol by competitive fluorescence immunoassay using DNA/dye conjugate as antibody multiple labels

Fluorescent organic dyes are currently the standard signal-generating labels used in microarray quantification. However, new labeling strategies are needed to meet the demand for high sensitivity in the detection of low-abundance proteins and small molecules. In this report, a long-chain DNA/dye conjugate was used to attach multiple fluorescence labels on antibodies to improve signal intensity and immunoassay sensitivity. Compared with the 30 base-pair (bp) oligonucleotide used in our previous work [Q. Zhang, L.-H. Guo, Bioconjugate Chem. 18 (2007) 1668-1672], conjugation of a 219 bp DNA in solution with a fluorescent DNA binder SYBR Green I resulted in more than sixfold increase in signal intensity, consistent with the increase in bp number. In a direct immunoassay for the detection of goat anti-mouse IgG in a mouse IgG-coated 96-well plate, the long DNA conjugate label also produced higher fluorescence than the short one, accompanied by about 15-fold improvement in the detection limit. To demonstrate its advantage in real applications, the DNA/dye conjugate was employed in the competitive immunoassay of 17β-estradiol, a clinically and environmentally important analyte. The biotin-terminated DNA was attached to biotinylated anti-estradiol antibody through the biotin/streptavidin/biotin bridge after the immuno-reaction was completed, followed by conjugation with SYBR Green I. The limit of detection for 17β-estradiol is 1.9 pg mL⁻¹, which is 200-fold lower than the assay using fluorescein-labeled antibodies. The new multiple labeling strategy uses readily available reagents, and is also compatible with current biochip platform. It has great potential in the sensitive detection of protein and antibody microarrays.     

Comparison of benzothiazole-based dyes for sensitive DNA detection

For efficient and quantitative DNA detection, fluorescence staining is the most often explored approach, which relies on non-covalent binding of dyes with double stranded DNA (dsDNA). Ethidium bromide (EB) is the most classic DNA stain, but suffers from its high carcinogenicity. A series of less toxic alternatives were developed, many of which contain the core structure of the benzothiazole ring. However, the relationship between the structure and the DNA detection performance was not illustrated. Herein, five benzothiazole dyes, namely thiazole orange, SYBR Green I, PicoGreen, SYBR Safe, and thioflavine-T, were compared for DNA detection through direct fluorescence and gel electrophoresis, with particular focus on the structure-performance relationship. It turned out that SYBR Green I is currently the best choice for DNA detection. The results in this work may be useful for future DNA-staining dye developments.     

The Combination of Laser-Induced Fluorescence and Intensified Linear Diode Array Detection in Column Liquid Chromatography

Abstract

The frequency-doubled 514-nm argon-ion laser line providing excitation at 257 nm is combined with an intensified linear diode array (ILDA) detector to enable on-the-fly identification by laser-induced fluorescence (LIF) in conventional-size column liquid chromatography (LC). The potential of this detection system is demonstrated for the analysis of a standard mixture of polynuclear aromatic hydrocarbons (PAHs). Detection limits are at the 1.5 μg 1^?1 level (15 pg injected); the identitication limits are about one order of magnitude higher.     

Comparison of benzothiazole-based dyes for sensitive DNA detection

For efficient and quantitative DNA detection, fluorescence staining is the most often explored approach, which relies on non-covalent binding of dyes with double stranded DNA (dsDNA). Ethidium bromide (EB) is the most classic DNA stain, but suffers from its high carcinogenicity. A series of less toxic alternatives were developed, many of which contain the core structure of the benzothiazole ring. However, the relationship between the structure and the DNA detection performance was not illustrated. Herein, five benzothiazole dyes, namely thiazole orange, SYBR Green I, PicoGreen, SYBR Safe, and thioflavine-T, were compared for DNA detection through direct fluorescence and gel electrophoresis, with particular focus on the structure-performance relationship. It turned out that SYBR Green I is currently the best choice for DNA detection. The results in this work may be useful for future DNA-staining dye developments.     

Capillary electrophoresis coupled with laser-induced fluorescence polarization as a hybrid approach to ultrasensitive immunoassays.

Immunoassays using capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) is a powerful approach to the determination of trace amounts of analytes in a complex biological matrix. However, its applicability is limited by the requirement that the free and bound tracer (fluorescently labeled compound) be resolved for their identification and quantitation. Here we show that replacing LIF with laser-induced fluorescence polarization (LIFP) permits ultrasensitive immunoassays to be performed with or without the separation of the free and bound tracer. A binding system involving cyclosporin A (CyA) and monoclonal antibody to CyA was chosen to demonstrate both homogeneous and heterogeneous immunoassay approaches. In the homogeneous scheme where the free and bound tracer were not separated, the fluorescence polarization of the mixture was a quantitative measure of the antibody-bound tracer. The concentration and mass detection limits for CyA using the homogeneous competitive assay were found to be 1 nM and 1 amol (10(-18) mol), respectively. The heterogeneous assay involved a nearly baseline separation of the free and bound tracer using CE with a phosphate running buffer of pH 7.0. The complex of the tracer with the antibody had a fluorescence polarization of approximately 0.24 whereas the free tracer had negligible polarization. The fluorescence polarization was independent of analyte concentration, and the fluorescence intensity of either the free or bound tracer was used for quantitation. Results from both assays suggest that the CE-LIFP approaches may have a wider application than the immunoassays based on either CE-LIF or fluorescence polarization alone.     

Novel wavelength-resolved fluorescence detection for a high-throughput capillary electrophoresis system under a diascopic configuration

This paper presents a novel method regarding a wavelength-resolved fluorescence detection scheme for high-throughput analysis of bio-samples in a micro-CE chip. Instead of using the conventional laser-induced fluorescence (LIF) microscope equipped with delicate spatial filters and complex control systems, this study adopts a hollow cone illumination generated using a dark-field condenser for exciting fluorescence in the microchannel and an ultraviolet-visible-near-infrared (UV-Vis-NIR) spectrometer for detecting the emission signals. Experimental results show that the proposed system is feasible for simultaneously detecting a mixed sample composed of Atto 610, Rhodamine B and fluorescein isothiocyanate (FITC) fluorescent dyes in a single test run. Furthermore, a mixed bio-sample composed of two mixed 16-mer single-stranded DNAs labeled with Cy3 and FITC fluorescent dyes is also successfully detected with the proposed system. The measured limit of detection (LOD) for detecting FITC of the proposed system can be as low as 5.4x10(-6)M (S/N=3). This proposed detection method has shown its potential on RNA identification and DNA sequencing applications.     

高效液相色谱-柱后在线光化学衍生荧光检测法测定辣椒油中4种苏丹红染料

建立了在线光化学衍生、荧光检测、高效液相色谱(HPLC)测定辣椒油中苏丹红I、II、III和B的方法。以乙腈-水为流动相,采用梯度洗脱方式在SB-C18色谱柱上分离。用实验室自制的程序控制时间/光强光化学反应器作为在线衍生装置,优化了光衍生反应的条件和荧光检测条件。3种不同加标浓度下,辣椒油样品中4种苏丹红染料的加标回收率为81.3%～100.4%。加标水平为0.8 mg/kg下荧光信号强度的相对标准偏差(RSD,n=6)为2.6%～3.8%。苏丹红I、II、III和B的检出限(LOD)和定量限(LOQ)范围分别为0.009～0.054 mg/kg和0.030～0.181 mg/kg,优于传统的HPLC分离、二极管阵列检测器检测方法。该方法具有简单、灵敏、选择性好的特点,适用于食品样品中苏丹红的常规分析。     

Characterization of organotin species using microbore and capillary liquid chromatographic techniques with an epifluorescence microscope as a novel imaging detector

The novel application of a UV epifluorescence microscope as an imaging detector for microbore and capillary high-performance liquid chromatography (HPLC) is reported. The microscope is focused on an in-line quartz flow cell incorporated down stream of a microbore HPLC column or directly on an optically clear portion of fused-silica capillary columns for analyte detection. The effect of different fluorescent ligand to analyte ratios on detection limits is also reported, as well as the effect of different image volume sizes produced by changes in microscope objective lens magnification power. Determination of relative sensitivities an detection limits for methyl- and butyltin compounds, complexed with fluorescent dyes, reveals that the organotins show decreasing sensitivity as the number of alkyl substituents on the tin atom increases, with minimum detectable amounts of 6-160 pg of analyte-ligand complex.     

Detection of duck hepatitis B virus DNA fragments using on-column intercalating dye labeling with capillary electrophoresis-laser-induced fluorescence.

A rapid on-column DNA labeling technique is used to detect viral restriction DNA fragments by capillary electrophoresis-laser induced fluorescence detection. Intercalating dyes such as POPO3 or ethidium homodimer-2 are incorporated into the detection buffer. The cationic dyes migrate into the capillary during electrophoresis and bind to the oppositely migrating DNA fragments. A post-column sheath-flow fluorescence detector is used in the experiment. Excellent labeling efficiency is achieved at minimal background fluorescence by diluting the dyes to between 1 x 10(-7) M and 5 x 10(-7) M in a buffer with low ionic strength relative to the running buffer within the capillary. This dilute sheath-flow buffer allows stacking of dye molecules inside the capillary when an electric field is applied. Calibration curves using a series of DNA size markers (between 72 and 1353 base pairs) were linear over an order of magnitude in DNA concentration. Sensitivity also increased linearly with fragment length, and detection limits ranged from 4 x 10(-14) M to 5 x 10(-13) M for the size-standards. Analysis of cloned viral DNA using duck hepatitis B virus demonstrated a concentration detection limit of 3.9 x 10(-16) M. Last, the technique produced very high separation efficiency, 14 x 10(6) theoretical plates which is greater than 47 x 10(6) plates m-1, for the duck hepatitis B viral genome.