Bi-color detection of two target DNAs by non-radioactive in situ hybridization

Summary A non-radioactive in situ hybridization technique is described which allows the simultaneous detection of different DNA sequences. To demonstrate the feasibility of the proccdure, metaphases and interphase nuclei of a human-mouse somatic cell hybrid were simultaneously hybridized with mercurated total human DNA and a biotinylated mouse satellite DNA probe. After the hybridization, the probes were detected immunocytochemically using two different and independent affinity systems. By this approach we visualized the two DNA target sequences in metaphase chromosomes and in interphase nuclei with FITC and TRITC fluorescence, or blue (alkaline phosphatase) and brown (peroxidase) precipitated enzyme products. This method not only allows detection of intact chromosomes but also the visualization of rearrangements between parts of human and mouse chromosomes. Furthermore, the technique demonstrates the high topological resolution of nonradioactive in situ hybridizations.This investigation was supported in part by FUNGO, Foundation of Medical Scientific Research in The Netherlands (grant nr 13-54-21)     

Nonradioactive southwestern analysis using chemiluminescent detection.

Replacing radioactively labeled probes by nonradioactive ones and detection by chemiluminescence instead of colorimetry allows a nonhazardous handling and offers the possibility of easily reprobing filters in Southwestern analysis. Using the described procedure, we were able to determine the molecular weight of DNA-binding proteins and achieve a high signal-to-noise ratio.     

Determination of carbofuran by flow-injection with chemiluminescent detection.

It was found that carbofuran enhances the chemiluminescence reaction between sodium sulphite and Ce(4+) in sulphuric acid, and this formed the basis of a flow-injection system with chemiluminescence detection for determination of carbofuran. Under optimum conditions, the enhanced chemiluminescence intensity was linear, with the concentration of carbofuran in the range 8 x 10(-8)-1.0 x 10(-5) g[sol ]mL, with a detection limit of 2.84 x 10(-8) g[sol ]mL (3 s[sol ]k). The proposed method was applied to the analysis of carbofuran in cabbage, with satisfactory results. Copyright (c) 2005 John Wiley & Sons, Ltd.     

A two-step hybridization method for chemiluminescent detection of single copy genes.

We have developed a technique for the chemiluminescent detection of single copy genes that eliminates the high backgrounds and problems with probe labeling associated with existing methods. The procedure employs a primary hybridization of single-stranded probe DNA to immobilized target DNA, a secondary hybridization with a covalently cross-linked oligonucleotide-alkaline phosphatase conjugate, followed by incubation in the chemiluminescent substrate AMPPD and detection on x-ray film. The key to the success of this method is that the primary probe contains a region complementary to the target DNA as well as to the oligonucleotide sequence of the secondary probe-alkaline phosphatase conjugate. Here we report our results using the two-step hybridization procedure to detect single copy genes from genomic Southern blots.     

Bisulfite modification of immobilized DNAs for methylation detection

We have developed a novel method for detecting DNA methylation status of multiple samples, in which the DNA samples were firstly immobilized on the slide and treated with bisulfite directly on the chip. In this experiment, DNAs of pUC19 plasmid were restricted by the enzymes, and ligated with a linker bearing 5'-terminal acrylamide group at the sticky ends. Using universal acrylamide gel polymerization technique, a large amount of DNAs could be immobilized on the slide. The immobilized DNAs were converted by soaking the chip in bisulfite reaction mixtures for 16 h. The probes for detection of the methylation patterns of CpG sites hybridized with the converted DNAs on the microarray, and non-specifically bound probes were cleaned by electrophoresis. We have optimized the experimental conditions of both bisulfite treatment and electrophoresis to increase sensitivity and specificity. The results were further validated by bisulfite DNA sequencing. The experiments show that the method can simplify the experimental processes and increase the efficiency of the bisulfite treatment. This novel method could be used as a convenient tool to detect the methylation status of the multiple genes for a large amount of samples in the future.     

Derivatization of biomolecules for chemiluminescent detection in capillary electrophoresis

An overview is presented on the power and drawbacks of the relatively unfamiliar chemiluminescence-based detection technique applied in analysis by capillary electrophoresis, for determining chemically derivatized biomolecules. Examples of the most common systems are given for many series of biologically active compounds as well as for some pharmaceuticals. The most common chemiluminescent systems include the application of peroxyoxalate ester chemiluminescence, acridinium esters, luminol and derivatives, detection based on the tris(2,2'-bipyridine)ruthenium(III) system, the huge potentials offered by direct oxidations-though often with still unelucidated reaction mechanisms-and the powerful area of bioluminescence techniques, revealing as well the fast developing area of microchip-based analysis employing this specific luminescence principle.     

Photochemiluminescent detection of antiradical activity. VII. Comparison with a modified method of thermo-initiated free radical generation with chemiluminescent detection.

The method of photosensitized chemiluminescence (PCL) allows the quantification of water- and lipid-soluble antioxidants and activity of superoxide dismutase (SOD) in the same measuring system. However, it needs a special device, which we have described in a previous paper in this series. Another method suitable for the assay of water- and lipid-soluble antioxidants is the thermo-initiated decay of azo-compounds combined with the measurement of O2 consumption (Niki, 1985; Wayner et al., 1985). Its long duration and the complicated measuring procedure is not acceptable for routine medical applications. We show that a modification using CL detection of free radicals with luminol, has results comparable with PCL for the determination of non-enzymic water- and lipid-soluble antioxidants, SOD activity and oxidative modification of proteins. In contrast to PCL, it is possible to use any luminometer with a heatable measuring cell and to investigate coloured samples. While the new method has an overall higher sensitivity and is scalable to microtitre plates, PCL measurements can be made at different pH. The advantages and analytical information content of certain components of the integral antioxidative capacity of blood plasma are discussed in comparison with other methods.     

A sensitive CCD image system for detection of chemiluminescent reactions

A new ultra-sensitive light detection system is described for the detection of chemiluminescence reactions. The system consists of a CCD camera equipped with a two-stage image intensifier coupled to an image analysis system with real-time filtering capabilities. The sensitivity was determined with the enhanced chemiluminescence system using horseradish peroxidase as label. Additional possibilities for further increase in sensitivity and the potential use in immuoassays and other applications are discussed.     

Ultrasensitive chemiluminescent and colorigenic detection of DNA, RNA, and proteins in plant molecular biology.

Nonradioactive detection methods for DNA, RNA, and protein analysis have been the subject of research for several years. In this paper the application of the digoxigenin nucleic acid labeling system, in combination with the new alkaline phosphatase substrate 3-(2'-spiroadamantane)-4-methoxy-4-(3"-phosphoryloxy)-phenyl -1,2-dioxetane, to the special requirements of the analysis of transgenic plants is described. Earlier detection systems lacked the required ultrasensitive limits of detection necessary because of the large genomes found in plant cells. Routine detection of single-copy genes from transgenic plant species requires the detection of bands of picograms of specific DNA, which is easily achieved by employing the AMPPD substrate. Optimal conditions of genomic Southern analysis have been successfully adapted for Northern blotting techniques. Detection of foreign proteins in transgenic plants has proven difficult because of the very small amounts of detectable specific protein. Until now, utilization of biotinylated antibodies in combination with a streptavidin-alkaline phosphatase conjugate has been the most sensitive procedure. By introducing the AMPPD substrate, a further significant enhancement of sensitivity leading to detectable signals in the picogram range can be obtained.     

Sensitive chemiluminescent detection of digoxigenin-labeled nucleic acids: a fast and simple protocol and its applications.

A fast and simple protocol for the chemiluminescent detection of digoxigenin-labeled nucleic acids with anti-digoxigenin antibody Fab fragments coupled to alkaline phosphatase and 3-(4-methoxyspiro[1,2-dioxetane-3,2'-tricyclo-[3.3.1.1 (3,7)]decan]-4- yl)phenyl phosphate as substrate is described. The washing and blocking procedure was optimized to yield low background even on positively charged nylon membranes. The sensitivity of the system is equal or better than radioactive methods. Exposure to x-ray or Polaroid film for up to 30 minutes is sufficient for the detection of 70 femtograms of homologous DNA. Human single-copy genes are detected in Southern blots of as low as 0.3 microgram total placental DNA. Blots can be reprobed multiple times very easily. The advantages of the digoxigenin system are high sensitivity, absence of background and ease of reprobing and are illustrated by applications for single-copy gene detection in genomic blots of human DNA, Northern hybridizations to rare mRNA, detection of E. coli genes on blots of genomic digests after pulse field gel electrophoresis, as well as for nonradioactive DNA sequencing blots with digoxigenin-labeled primers.     

Nanopore sensor for fast label-free detection of short double-stranded DNAs

Functionalizing surface enhanced the molecular sensing ability of a fabricated nanopore by increasing the translocation duration time for a short double-stranded DNA. The surface of nanopore was derivatized with γ-aminopropyltriethoxysilane and the positively charged surface attracted DNA molecules when they were in the vicinity of nanopore. The translocation duration time of DNA increased due to the strong electrostatic interaction and it enabled us to detect a short double-stranded DNA (<1 kbp) that is under the size limit of a conventional solid state nanopore sensor. Both 539 and 910 bp double-stranded DNAs were analyzed with the surface functionalized nanopore and their translocation kinetics are presented in this work. The new feature of the surface modified nanopore that can detect short double-stranded DNA molecules could readily be applied for a rapid label-free diagnostic analysis in a Lab-On-a-Chip type DNA sensor.     

Conformations of satellite DNAs.

X-ray fiber diffraction studies of satellite DNAs from Gecarcinus lateralis, Drosophila virilis and Mus musculus, all of which have highly repetitious base sequences but with different degrees of sequence complexity, reveal only classical polynucleotide duplex structures in contrast to some highly repetitious synthetic DNAs.     

Channel-resolved multianalyte immunosensing system for flow-through chemiluminescent detection of alpha-fetoprotein and carcinoembryonic antigen

A novel flow-through immunosensing system for chemiluminescent (CL) multianalyte immunoassay was designed based on channel-resolved technique. Using alpha-fetoprotein (AFP) and carcinoembryonic antigen (CEA) as model analytes, two polyethersulfone membranes modified with the corresponding capture antibodies were set in two channels of a flow cell, and then two mixtures of the sample and corresponding alkaline phosphatase labeled antibodies were introduced into the channels for on-line incubation, respectively. Upon injection of CL substrate the catalyzed CL signals from the two channels were sequentially collected with the aid of an optical shutter for CL detection of two analytes. The antibodies immobilized membranes could be regenerated for reuse. Under optimal conditions AFP and CEA could be assayed in the ranges of 5.0-150 and 0.50-80 ng/ml with detection limits of 1.5 and 0.25 ng/ml, respectively. The assay results of clinical serum samples with the proposed system were in acceptable agreement with those with the reference method in single-analyte test mode. This novel immunosensing system based on the designed channel-resolved technique provided an automated, reusable, simple, sensitive and low-cost approach for multianalyte immunoassay without using of expensive array detector.