Synthesis, characterization, and applications of a fluorescent probe of DNA damage

Capillary electrophoresis-based immunoassay and aptamer assay: A review

Over the last two decades, the group of techniques called affinity probe CE has been widely used for the detection and the determination of several types of biomolecules with high sensitivity. These techniques combine the low sample consumption and high separation power of CE with the selectivity of the probe to the target molecule. The assays can be defined according to the type of probe used: CE immunoassays, with an antibody as the probe, or aptamer-based CE, with an aptamer as the probe. Immunoassays are generally divided into homogeneous and heterogeneous groups, and homogeneous variant can be further performed in competitive or noncompetitive formats. Interacting partners are free in solution at homogeneous assay, as opposed to heterogeneous analyses, where one of them is immobilized onto a solid support. Highly sensitive fluorescence, chemiluminescence or electrochemical detections were typically used in this type of study. The use of the aptamers as probes has several advantages over antibodies such as shorter generation time, higher thermal stability, lower price, and lower variability. The aptamer-based CE technique was in practice utilized for the determination of proteins in biological fluids and environmentally or clinically important small molecules. Both techniques were also transferred to microchip. This review is focused on theoretical principles of these techniques and a summary of their applications in research.

Clinical applications of capillary electrophoresis based immunoassays

Immunoassays have long been an important set of tools in clinical laboratories for the detection, diagnosis, and treatment of disease. Over the last two decades, there has been growing interest in utilizing CE as a means for conducting immunoassays with clinical samples. The resulting method is known as a CE immunoassay. This approach makes use of the selective and strong binding of antibodies for their targets, as is employed in a traditional immunoassay, and combines this with the speed, efficiency, and small sample requirements of CE. This review discusses the variety of ways in which CE immunoassays have been employed with clinical samples. An overview of the formats and detection modes that have been employed in these applications is first presented. A more detailed discussion is then given on the type of clinical targets and samples that have been measured or studied by using CE immunoassays. Particular attention is given to the use of this method in the fields of endocrinology, pharmaceutical measurements, protein and peptide analysis, immunology, infectious disease detection, and oncology. Representative applications in each of these areas are described, with these examples involving work with both traditional and microanalytical CE systems.

DNA wrapping is required for DNA damage recognition in the Escherichia coli DNA nucleotide excision repair pathway

Localized DNA melting may provide a general strategy for recognition of the wide array of chemically and structurally diverse DNA lesions repaired by the nucleotide excision repair (NER) pathway. However, it is not clear what causes such DNA melting and how it is driven. Here, we show a DNA wrapping-melting model supported by results from dynamic monitoring of the key DNA-protein and protein-protein interactions involved in the early stages of the Escherichia coli NER process. Using an analytical technique involving capillary electrophoresis coupled with laser-induced fluorescence polarization, which combines a mobility shift assay with conformational analysis, we demonstrate that DNA wrapping around UvrB, mediated by UvrA, is an early event in the damage-recognition process during E. coli NER. DNA wrapping of UvrB was confirmed by Förster resonance energy transfer and fluorescence lifetime measurements. This wrapping did not occur with readily denaturable damaged DNA substrates ("bubble" DNA), suggesting that DNA wrapping of UvrB plays an important role in the induction of DNA melting around the damage site. Analysis of DNA wrapping of mutant UvrB Y96A further suggests that a cooperative interaction between DNA wrapping of UvrA(2)B and contact of the beta-hairpin of UvrB with the bulky damage moiety may be involved in the local DNA melting at the damage site.

Capillary electrophoresis-based immunoassays: principles and quantitative applications

The use of CE as a tool to conduct immunoassays has been an area of increasing interest over the last decade. This approach combines the efficiency, small sample requirements, and relatively high speed of CE with the selectivity of antibodies as binding agents. This review examines the various assay formats and detection modes that have been reported for these assays, along with some representative applications. Most CE immunoassays in the past have employed homogeneous methods in which the sample and reagents are allowed to react in solution. These homogeneous methods have been conducted as both competitive binding immunoassays and as noncompetitive binding immunoassays. Fluorescent labels are most commonly used for detection in these assays, but enzyme labels have also been utilized for such work. Some additional work has been performed in CE immunoassays with heterogeneous methods in which either antibodies or an analog of the analyte is immobilized to a solid support. These heterogeneous methods can be used for the selective isolation of analytes prior to their separation by CE or to remove a given species from a sample/reagent mixture prior to analysis by CE. These CE immunoassays can be used with a variety of detection modes, such as fluorescence, UV/Vis absorbance, chemiluminescence, electrochemical measurements, MS, and surface plasmon resonance.

Simultaneous analysis of four stereoisomers of anti-benzo[a]pyrene diol epoxide-deoxyguanosine adducts in short oligodeoxynucleotides using reversed-phase high-performance liquid chromatography

anti-Benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (anti-BPDE), a reactive metabolite of the environmental carcinogen benzo[a]pyrene, predominantly binds to deoxyguanine in DNA and forms four stereoisomeric adducts. Here we developed an improved method for simultaneous analysis and purification of four stereoisomeric adducts in short oligonucleotides using reversed-phase high-performance liquid chromatography, providing a selection strategy of stationary phase for analysis and separation of polyaromatic hydrocarbon-DNA adducts. This work demonstrates that secondary retention of oligonucleotides on C18 stationary phases induced by exposed silanol heavily affects the separation of four stereoisomeric adducts on C18 stationary phases, and the silicone polymer monolayer coating for completely capping exposed silica or silanol greatly reduces such secondary retention, thereby displaying a much better resolution of the four stereoisomeric adducts. We further demonstrate that aromatic group (phenyl)-based stationary phase can significantly improve stereoisomeric separation of four anti-BPDE-deoxyguanosine (dG) adducts in short oligonucleotides over nonaromatic C18 stationary phase due to enhancement of the selective interaction with aromatic anti-BPDE moiety in oligonucleotides. The developed method was also used for purification and preparation of anti-BPDE-oligonucleotide adducts.

DNA-driven focusing for protein-DNA binding assays using capillary electrophoresis

A DNA-driven focusing technique is reported for protein-DNA binding assays using capillary electrophoresis. A fluorescent DNA aptamer of 84 nucleotides (RT12) was used to bind to a specific protein, human immunodeficiency virus type 1 reverse transcriptase. The aptamer-protein complexes were effectively focused, separated by capillary electrophoresis, and detected by laser-induced fluorescence (LIF). With this DNA-driven focusing, the separation efficiency of the aptamer-protein complex reached 5 million theoretical plates/m, and the sensitivity for the detection of this complex was improved by 70-120-fold. The DNA-driven focusing technique was further applied to protein-DNA binding assays and to enhance the detection of DNA adducts. DNA adducts present in short oligonucleotides or genomic DNA were recognized by and bound to specific antibodies, and the complexes were focused electrophoretically and detected by LIF. The results demonstrate that the DNA-driven focusing can improve separation, sensitivity, and speed of analysis. The focusing is tolerant to high-salt medium, which is usually necessary to support physiological protein-DNA binding. This technique may be applied to nucleic acid analysis, aptamer affinity analysis, immunoassays for DNA damage, and DNA/RNA based binding assays.

Selective immunoclean-up followed by liquid chromatography for the monitoring of a biomarker of exposure to polycyclic aromatic hydrocarbons in urine at the ngl−1 level

A selective clean-up procedure using an immunosorbent (IS) was developed for the trace-level determination, in water and urine samples, of 3-benzo(a)pyrene-glucuronide (3-BP-G), a biomarker of exposure to carcinogenic polycyclic aromatic hydrocarbons (PAHs). First, three sorbents used for the immobilization of antibodies were evaluated for their ability to limit the risk of non-specific interactions and to provide a high bonding density. The best sorbent, i.e. sepharose, was used for the immobilization of two different monoclonal antibodies. The most specific antibody for 3-BP-G was applied to the selective extraction from urine providing a clean extract, an easy and reliable quantification by comparison with a classical SPE process. The sensitivity of the fluorescence associated with the selectivity of the IS provides a limit of detection up to 1.2 ng l(-1) in urine for 3-BP-G.

Capillary electrophoresis immunoassay chemiluminescence detection of zeptomoles of bone morphogenic protein-2 in rat vascular smooth muscle cells

A capillary electrophoresis immunoassay (CEIA) method based on enhanced chemiluminescence (CL) detection was developed and applied to arteriosclerosis pathology research in the medical field. The system of enzyme-horseradish peroxidase (HRP) catalyzing the luminol/H2O2/p-iodophenol reaction was adopted in this paper. HRP was detected with the detection limit (S/N = 3) of 4.4 pM (53 zmol), which represents one of the highest sensitivities of HRP reported yet. HRP was first linked to bone morphogenic protein-2 (BMP-2) in rat vascular smooth muscle (VSM) cells with noncompetitive format and analyzed by CE-CL. HRP-Ab(2)-mAb-BMP-2 complexes can be baseline separated from free HRP in 3 min. The detection limit (S/N = 3) of BMP-2 is 6.2 pM (75 zmol). This technique has been successfully applied to arteriosclerosis development mechanistic study by investigating the change of BMP-2 content in VSM cells, which were stimulated by angiotensin II for different times. The change trends of BMP-2 contents are well in accord with that of the commonly used pathology image analysis system. It proves that the CEIA-CL technique proposed could be developed into a sensitive and new method for clinical assay and pathology research.

2002 W.A.E. McBryde Award Lecture — Affinity recognition, capillary electrophoresis, and laser-induced fluorescence polarization for ultrasensitive bioanalysis

The combination of affinity recognition, capillary electrophoresis (CE), laser-induced fluorescence (LIF), and fluorescence polarization for the ultrasensitive determination of compounds of biological interest is described. Competitive immunoassays using CE–LIF eliminate the need for fluorescently labeling trace analytes of interest and are particularly useful for determination of small molecules, such as cyclosporine, gentamicin, vancomycin, and digoxin. Fluorescence polarization allows for differentiation of the antibody-bound from the unbound small molecules. Noncompetitive affinity CE–LIF assays are shown to be highly effective in the determination of biomarkers for DNA damage and HIV-1 infection. An antibody (or aptamer) is used as a fluorescent probe to bind with a target DNA adduct (or the reverse transcriptase of the HIV-1 virus), with the fluorescent reaction products being separated by CE and detected by LIF. Aptamers are attractive affinity probes for protein analysis because of high affinity, high specificity, and the potential for a wide range of target proteins. Fluorescence polarization provides unique information for studying molecular interactions. Innovative integrations of these technologies will have broad applications ranging from cancer research, to biomedical diagnosis, to pharmaceutical and environmental analyses.Key words: capillary electrophoresis, laser-induced fluorescence, fluorescence polarization, immunoassay, affinity probes, antibodies, aptamers, DNA damage, toxins, therapeutic drugs.

A2E-epoxides damage DNA in retinal pigment epithelial cells. Vitamin E and other antioxidants inhibit A2E-epoxide formation

The autofluorescent pigments that accumulate in retinal pigment epithelial cells with aging and in some retinal disorders have been implicated in the etiology of macular degeneration. The major constituent is the fluorophore A2E, a pyridinium bisretinoid. Light-exposed A2E-laden retinal pigment epithelium exhibits a propensity for apoptosis with light in the blue region of the spectrum being most damaging. Efforts to understand the events precipitating the death of the cells have revealed that during irradiation (430 nm), A2E self-generates singlet oxygen with the singlet oxygen in turn reacting with A2E to generate epoxides at carbon-carbon double bonds. Here we demonstrate that A2E-epoxides, independent of singlet oxygen, exhibit reactivity toward DNA with oxidative base changes being at least one of these lesions. Mass spectrometry revealed that the antioxidants vitamins E and C, butylated hydroxytoluene, resveratrol, a trolox analogue (PNU-83836-E), and bilberry extract reduce A2E-epoxidation, whereas single cell gel electrophoresis and cell viability studies revealed a corresponding reduction in the incidence of DNA damage and cell death. Vitamin E, a lipophilic antioxidant, produced a more pronounced decrease in A2E-epoxidation than vitamin C, and treatment with both vitamins simultaneously did not confer additional benefit. Studies in which singlet oxygen was generated by endoperoxide in the presence of A2E revealed that vitamin E, butylated hydroxytoluene, resveratrol, the trolox analogue, and bilberry reduced A2E-epoxidation by quenching singlet oxygen. Conversely, vitamin C and ginkgolide B were not efficient quenchers of singlet oxygen under these conditions.

Ultrasensitive protein-DNA binding assays

Protein-DNA binding assays have been used in a variety of fields from fundamental studies regarding the binding process itself, to serving as probes for the detection, quantification and separation of target analytes. These assays have been used for the study of protein-DNA complex stoichiometry, the detection of DNA damage, and real-time separation of free and bound complexes by electrophoretic mobility. Synthetic DNA oligonucleotides, known as aptamers, have been increasingly used for affinity binding assays to proteins, as well as for separation studies and as biosensors. Recent advances have been made in protein-DNA binding assays using capillary electrophoresis, laser-induced fluorescence, fluorescence polarization, molecular beacons, and affinity chromatography.

Enhancement of immunocomplex detection and application to assays for DNA adduct of benzo[a]pyrene

The stability of antibody and formation of immunocomplexes are essential to high-sensitivity capillary electrophoresis immunoassays (CEIA). However, little attention has been paid to enhancing or maintaining immunocomplex formation and antibody stability to improve the performance of CEIA. We report here the use of nonspecific proteins, such as bovine serum albumin (BSA) and rabbit immunoglobulin (rIgG), to enhance immunocomplex formation and to stabilize antibodies and immunocomplexes for immunoassays. Complexes between DNA adducts of benzo[a]pyrenediol epoxide (BPDE) and their antibodies were examined using capillary electrophoresis with laser-induced fluorescence detection (CE-HF). A tetramethylrhodamine (TMR)-labeled single-stranded oligonucleotide (16-mer) containing a single BPDE adduct was used as a fluorescent probe to study its immunocomplexes with a monoclonal antibody (8E11). To examine the formation of larger complexes, a TMR-labeled secondary antibody (anti-mouse), a primary antibody (mouse monoclonal antibody 5D11), and BPDE adducts in cellular DNA were used. We demonstrate that the use of nonspecific proteins stabilized the antibody and greatly enhanced the formation and stability of the immunocomplexes, resulting in substantial improvements in the detection limit (10-fold) and the reproducibility of the analysis. Another advantageous consequence of the stabilization was a 150-fold reduction of the concentration of the antibody needed for the immunoassay, resulting in reduced background and cost. We successfully applied this technique to the determination of DNA adducts of BPDE using a competitive immunoassay. The results from both small complexes (between a primary antibody and an oligonucleotide) and larger complexes (among a secondary antibody, a primary antibody, and cellular DNA) indicate that the technique can be extended to other immunoassays. We suggest that nonspecific proteins may assist the formation and stabilization of antibody-antigen complexes by maintaining the correct conformation of the antibody and antigen for optimum binding.

Binding stoichiometry of DNA adducts with antibody studied by capillary electrophoresis and laser-induced fluorescence

Four oligonucleotides (fluorescently labeled and unlabeled 16- and 90-mer), each containing a single adduct of benzo[a]pyrene diol epoxide (BPDE), were synthesized and used to study the binding stoichiometry between the DNA adduct and its antibody. The free oligonucleotide and its complexes with mouse monoclonal antibody were separated using capillary electrophoresis and detected with laser-induced fluorescence (LIF). Two complexes, representing the 1:1 and 1:2 stoichiometry between the antibody and the DNA adduct, were clearly demonstrated. The stoichiometry depended upon the relative concentrations of the antibody and the DNA adducts. A new approach examining the binding of the antibody with a mixture of a tetramethylrhodamine (TMR)-labeled and unlabeled BPDE-16-mer revealed insights on ligand redistribution and exchange between the labeled and unlabeled BPDE-16-mer oligonucleotides in the complexes. The observation of this unique behavior has not been possible previously with other binding studies. A mixture of the antibody with the TMR-labeled BPDE- 16-mer and an unlabeled BPDE-90-mer further revealed the formation of three fluorescent complexes: antibody with one TMR-BPDE-16-mer molecule, antibody with two TMR-BPDE- 16-mer molecules, and antibody with one TMR-BPDE-16-mer and one BPDE-90-mer. The three complexes clearly demonstrated binding stoichiometry and ligand redistribution/exchange.